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1. Identification of the optimal medical and surgical management for patients with perianal fistulising Crohn’s disease

Author: Mathilde Laland, Marie François, Ferdinando D'Amico, Camille Zallot, Charlène Brochard, Marie Dewitte, Laurent Siproudhis, Laurent Peyrin‐Biroulet, Guillaume Bouguen, CHU Pontchaillou [Rennes], Nutrition-Génétique et Exposition aux Risques Environnementaux (NGERE), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lorraine (UL), Humanitas University [Milan] (Hunimed), Centre Hospitalier Régional Universitaire de Nancy (CHRU Nancy), Centre d'Investigation Clinique [Rennes] (CIC), Université de Rennes (UR)-Hôpital Pontchaillou-Institut National de la Santé et de la Recherche Médicale (INSERM), Nutrition, Métabolismes et Cancer (NuMeCan), Université de Rennes (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Jonchère, Laurent
Subjects: [SDV] Life Sciences [q-bio], Crohn’s disease, medical and surgical management, [SDV]Life Sciences [q-bio], Gastroenterology, [SDV.MHEP.HEG]Life Sciences [q-bio]/Human health and pathology/Hépatology and Gastroenterology, perianal fistula, [SDV.MHEP.HEG] Life Sciences [q-bio]/Human health and pathology/Hépatology and Gastroenterology, combination therapy
Abstract: International audience; AIMS: The aims of our study were to assess the best medical and surgical approaches for Perianal Crohn’s Disease (PCD) in order to identify an optimal combined medical and surgical treatment. METHODS: Medical records of all patients with PCD treated with TNFα antagonists in two referral centers between 1998 and 2018 were reviewed. Predictors of long-term outcomes were identified using a Cox proportional hazard model. RESULTS: A total of 200 patients were included. Fifty-three patients (26.5%) were treated with adalimumab and 147 (73.5%) with infliximab. Combination of TNFα antagonist with an immunosuppressant and presence of proctitis were independently associated with fistula closure. Seton was placed in 127 patients (63.5%) before starting biological therapy. Eighty patients (40%) underwent additional perineal surgery. Prior PCD surgery, seton positioning, additional perineal surgery, and additional surgery within 52 weeks of anti-TNFα treatment were associated with an increased rate of fistula closure. Finally, medical combination therapy (anti-TNFα plus immunosuppressant) along with seton placement and additional surgery within one year was the best management for PCD patients (p=0,02). CONCLUSION: Combined medical and surgical management is required for the treatment of PCD patients. Medical combination therapy associated with seton placement and additional surgery within one year is the best management for PCD patients.
Published: 2023

2. The DendrisCHIP® Technology as a New, Rapid and Reliable Molecular Method for the Diagnosis of Osteoarticular Infections

Author: Elodie Bernard, Thomas Peyret, Mathilde Plinet, Yohan Contie, Thomas Cazaudarré, Yannick Rouquet, Matthieu Bernier, Stéphanie Pesant, Richard Fabre, Aurore Anton, Cathy Maugis-Rabusseau, Jean Marie François, Dendris SAS, Laboratoire CBM-Inovie, Institut de Mathématiques de Toulouse UMR5219 (IMT), Université Toulouse Capitole (UT Capitole), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université Toulouse - Jean Jaurès (UT2J), Université de Toulouse (UT)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Toulouse Biotechnology Institute (TBI), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), and Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: bone and joint infection, in vitro multiplex diagnostic, biochips, next-generation sequencing, microbial cultures, [SDV]Life Sciences [q-bio], Clinical Biochemistry
Abstract: International audience; Osteoarticular infections are major disabling diseases that can occur after orthopedic implant surgery in patients. The management of these infections is very complex and painful, requiring surgical intervention in combination with long-term antibiotic treatment. Therefore, early and accurate diagnosis of the causal pathogens is essential before formulating chemotherapeutic regimens. Although culture-based microbiology remains the most common diagnosis of osteoarticular infections, its regular failure to identify the causative pathogen as well as its long-term modus operandi motivates the development of rapid, accurate, and sufficiently comprehensive bacterial species-specific diagnostics that must be easy to use by routine clinical laboratories. Based on these criteria, we reported on the feasibility of our DendrisCHIP® technology using DendrisCHIP®OA as an innovative molecular diagnostic method to diagnose pathogen bacteria implicated in osteoarticular infections. This technology is based on the principle of microarrays in which the hybridization signals between oligoprobes and complementary labeled DNA fragments from isolates queries a database of hybridization signatures corresponding to a list of pre-established bacteria implicated in osteoarticular infections by a decision algorithm based on machine learning methods. In this way, this technology combines the advantages of a PCR-based method and next-generation sequencing (NGS) while reducing the limitations and constraints of the two latter technologies. On the one hand, DendrisCHIP®OA is more comprehensive than multiplex PCR tests as it is able to detect many more germs on a single sample. On the other hand, this method is not affected by the large number of nonclinically relevant bacteria or false positives that characterize NGS, as our DendrisCHIP®OA has been designed to date to target only a subset of 20 bacteria potentially responsible for osteoarticular infections. DendrisCHIP®OA has been compared with microbial culture on more than 300 isolates and a 40% discrepancy between the two methods was found, which could be due in part but not solely to the absence or poor identification of germs detected by microbial culture. We also demonstrated the reliability of our technology in correctly identifying bacteria in isolates by showing a convergence (i.e., same bacteria identified) with NGS superior to 55% while this convergence was only 32% between NGS and microbial culture data. Finally, we showed that our technology can provide a diagnostic result in less than one day (technically, 5 h), which is comparatively faster and less labor intensive than microbial cultures and NGS.
Published: 2022

3. Selection by UV Mutagenesis and Physiological Characterization of Mutant Strains of the Yeast Saprochaete suaveolens (Former Geotrichum fragrans) with Higher Capacity to Produce Flavor Compounds

Author: Alain Shum Cheong Sing, Melissa Tan, Héloïse Reiss, Thomas Petit, Yanis Caro, Jean-Marie François, Chimie et Biotechnologie des Produits Naturels (CHEMBIOPRO), Université de La Réunion (UR), Toulouse Biotechnology Institute (TBI), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Toulouse White Biotechnology (TWB), Region Reunion, and Europe for financial support
Subjects: Microbiology (medical), QH301-705.5, Saccharomyces cerevisiae, Mutant, yeast, volatile organic compounds (VOCs), UV, mutant, Plant Science, Article, Hydrolase, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Food science, Biology (General), Ecology, Evolution, Behavior and Systematics, Flavor, chemistry.chemical_classification, biology, Strain (chemistry), Chemistry, biology.organism_classification, Yeast, Amino acid, UVmutant, Enzyme
Abstract: Yeast volatile organic compounds (VOCs), i.e. low molecular weight organic acids, alcohols and esters, are considered as potential and sustainable sources of natural aromas that can replace commonly used artificial flavors in food and other industrial sectors. Although research generally focuses on the yeast Saccharomyces cerevisiae, other so-called unconventional yeasts (NCY) are beginning to attract the attention of researchers, particularly for their ability to produce alternative panels of VOCs. With this respect, a Saprochaete suaveolens strain isolated from dragon fruit in Reunion Island was shown to produce α-unsaturated esters from branched-chain amino acids (BCAAs) such as isobutyl, isoamyl or ethyl tiglate, which are rarely found in other yeasts strains. Given that β-oxidation allows the growth of S. suaveolens on BCAAs as sole carbon source, we developped a method based on UV mutagenesis to generate mutants that can no longer grow on BCAAs, while redirecting the carbon flow towards esterification of α-unsaturated esters. Among the 15,000 clones generated through UV irradiation, we identified nine clones unable to grow on BCAAs with one of them able to produce eight times more VOCs as compared to the wild-type strain. This higher production of α-unsaturated esters in this mutant strain coincided with an almost complete loss of enoyl-CoA hydratase activity of the β-oxidation pathways and with a twofold increase of acyl-CoA hydrolase with not significant changes in the enzymes of the Ehrlich pathway. Moreover, from our knowledge, it constituted the first example of VOCs enhancement in a microbial strain by UV mutagenesis.
Published: 2021

4. A Two-step Strategy for High-Value-Added Utilization of Rapeseed Meal by Concurrent Improvement of Phenolic Extraction and Protein Conversion for Microbial Iturin A Production

Author: Meng Wang, Chen Yang, Jean Marie François, Xia Wan, Qianchun Deng, Danyang Feng, Shiyu Deng, Shouwen Chen, Fenghong Huang, Wenchao Chen, Yangmin Gong, Chinese Academy of Agricultural Sciences (CAAS), Oil Crops Research Institute, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture-Chinese Academy of Agricultural Sciences (CAAS), Oil Crops and Lipids Process Technology National and Local Joint Engineering Laboratory, Hubei Key Laboratory of Lipid Chemistry and Nutrition, Toulouse Biotechnology Institute (TBI), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Hubei University, National Natural Science Foundation of China (NSFC)32001620, Natural Science Foundation of Hubei Province2019CFB378, Youth talent development program of Hubei province, Earmarked Fund for China Agriculture Research SystemCARS-12, and Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: 0106 biological sciences, Histology, Antioxidant, Rapeseed, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, Bacillus amyloliquefaciens, medicine.medical_treatment, Biomedical Engineering, Bioengineering, phenolic compounds, Bacterial growth, Raw material, protein residue, 01 natural sciences, 03 medical and health sciences, medicine, Food science, Original Research, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, Residue (complex analysis), biology, Chemistry, Extraction (chemistry), Bioengineering and Biotechnology, biology.organism_classification, fungal pretreatment, two-step strategy, rapeseed meal, Fermentation, microbial iturin A production, TP248.13-248.65, 010606 plant biology & botany, Biotechnology
Abstract: Rapeseed meal (RSM) is a major by-product of oil extraction from rapeseed, consists mainly of proteins and phenolic compounds. The use of RSM as protein feedstock for microbial fermentation is always hampered by phenolic compounds, which have antioxidant property with health-promoting benefits but inhibit bacterial growth. However, there is still not any good process that simultaneously improve extraction efficiency of phenolic compounds with conversion efficiency of protein residue into microbial production. Here we established a two-step strategy including fungal pretreatment followed by extraction of phenolic compounds. This could not only increase extraction efficiency and antioxidant property of phenolic compounds by about 2-fold, but also improve conversion efficiency of protein residue into iturin A production by Bacillus amyloliquefaciens CX-20 by about 33%. The antioxidant and antibacterial activities of phenolic extracts were influenced by both total phenolic content and profile, while microbial feedstock value of residue was greatly improved because protein content was increased by ∼5% and phenolic content was decreased by ∼60%. Moreover, this two-step process resulted in isolating more proteins from RSM, bringing iturin A production to 1.95 g/L. In conclusion, high-value-added and graded utilization of phenolic extract and protein residue from RSM with zero waste is realized by a two-step strategy, which combines both benefits of fungal pretreatment and phenolic extraction procedures.
Published: 2021

5. FLO11, a Developmental Gene Conferring Impressive Adaptive Plasticity to the Yeast Saccharomyces cerevisiae

Author: Clara Bouyx, Jean Marie François, Marion Schiavone, Toulouse Biotechnology Institute (TBI), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Lallemand SAS, Lallemand Inc. rue de Briquetiers, Blagnac, FranceSAIC2016/048SAIC/2018/010, Region Occitanie, Bd Marecal Juin, Toulouse, and France09003813
Subjects: Microbiology (medical), Saccharomyces cerevisiae, Biology, flocculins, Immunology and Allergy, Epigenetics, FLO11, Cell adhesion, Molecular Biology, Gene, Genetics, General Immunology and Microbiology, Biofilm, phenotypic variation, adhesins, biology.organism_classification, Yeast, Cell aggregation, Infectious Diseases, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Medicine, cell wall, adaptive plasticity, Adaptation
Abstract: The yeast Saccharomyces cerevisiae has a remarkable ability to adapt its lifestyle to fluctuating or hostile environmental conditions. This adaptation most often involves morphological changes such as pseudofilaments, biofilm formation, or cell aggregation in the form of flocs. A prerequisite for these phenotypic changes is the ability to self-adhere and to adhere to abiotic surfaces. This ability is conferred by specialized surface proteins called flocculins, which are encoded by the FLO genes family in this yeast species. This mini-review focuses on the flocculin encoded by FLO11, which differs significantly from other flocculins in domain sequence and mode of genetic and epigenetic regulation, giving it an impressive plasticity that enables yeast cells to swiftly adapt to hostile environments or into new ecological niches. Furthermore, the common features of Flo11p with those of adhesins from pathogenic yeasts make FLO11 a good model to study the molecular mechanism underlying cell adhesion and biofilm formation, which are part of the initial step leading to fungal infections.
Published: 2021

6. The dual role of amyloid-β-sheet sequences in the cell surface properties of FLO11-encoded flocculins in Saccharomyces cerevisiae

Author: Etienne Dague, Marie-Ange Teste, Jean Marie François, Clara Bouyx, Nathalie Sieczkowski, Anne Ortiz Julien, Marion Schiavone, Toulouse Biotechnology Institute (TBI), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Équipe Ingénierie pour les sciences du vivant (LAAS-ELIA), Laboratoire d'analyse et d'architecture des systèmes (LAAS), Université Toulouse Capitole (UT Capitole), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université Toulouse - Jean Jaurès (UT2J), Université de Toulouse (UT)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université Toulouse Capitole (UT Capitole), Université de Toulouse (UT), Lallemand SAS, Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse 1 Capitole (UT1), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse 1 Capitole (UT1), and Université Fédérale Toulouse Midi-Pyrénées
Subjects: Amyloid, QH301-705.5, Science, [PHYS.PHYS.PHYS-BIO-PH]Physics [physics]/Physics [physics]/Biological Physics [physics.bio-ph], Cell, Saccharomyces cerevisiae, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, [SDV.BC.IC]Life Sciences [q-bio]/Cellular Biology/Cell Behavior [q-bio.CB], medicine, amyloids, Biology (General), [PHYS.MECA.BIOM]Physics [physics]/Mechanics [physics]/Biomechanics [physics.med-ph], Candida albicans, Cell adhesion, [SDV.MP.MYC]Life Sciences [q-bio]/Microbiology and Parasitology/Mycology, 030304 developmental biology, 0303 health sciences, General Immunology and Microbiology, biology, 030306 microbiology, Chemistry, General Neuroscience, cell adhesion, General Medicine, FLO11, biology.organism_classification, Phenotype, Corpus albicans, Cell biology, Bacterial adhesin, cell surface, medicine.anatomical_structure, Medicine, AFM
Abstract: Fungal adhesins (Als) or flocculins are family of cell surface proteins that mediate adhesion to diverse biotic and abiotic surfaces. A striking characteristic of Als proteins originally identified in the pathogenic Candida albicans is to form functional amyloids that mediate cis-interaction leading to the formation of adhesin nanodomains and trans-interaction between amyloid sequences of opposing cells. In this report, we show that flocculins encoded by FLO11 in Saccharomyces cerevisiae behave like adhesins in C. albicans. To do so, we show that the formation of nanodomains under an external physical force requires a threshold number of amyloid-forming sequences in the Flo11 protein. Then, using a genome editing approach, we constructed strains expressing variants of the Flo11 protein under the endogenous FLO11 promoter, leading to the demonstration that the loss of amyloid-forming sequences strongly reduces cell-cell interaction but has no effect on either plastic adherence or invasive growth in agar, both phenotypes being dependent on the N- and C-terminal ends of Flo11p. Finally, we show that the location of Flo11 is not altered either by the absence of amyloid-forming sequences or by the removal of the N- or C-terminus of the protein.
Published: 2021

7. Evaluation of mixed-fermentation of Saccharomyces cerevisiae with Saprochaete suaveolens to produce natural fruity beer from industrial wort

Author: Laurent Robert, Jean-Marie François, Yanis Caro, Alain Shum-Cheong-Sing, Thomas Petit, Melissa Tan, Université de La Réunion (UR), Institut Universitaire de Technologie - Réunion (IUT Réunion), Soc Reunionnaise Brasserie SOREBRA, Toulouse Biotechnology Institute (TBI), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Regional Council of Reunion Island, and Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: Co-fermentation, Saccharomyces cerevisiae, education, 01 natural sciences, Natural aroma, Analytical Chemistry, 0404 agricultural biotechnology, Starter, [CHIM]Chemical Sciences, Food science, Saprochaete suaveolens, Non-conventional yeast, Aroma, biology, business.industry, Chemistry, 010401 analytical chemistry, food and beverages, Beer, 04 agricultural and veterinary sciences, General Medicine, biology.organism_classification, Geotrichum, 040401 food science, Yeast, 0104 chemical sciences, Flavoring Agents, Fruit, Fermentation, Odorants, Saccharomycetales, behavior and behavior mechanisms, Brewing, Composition (visual arts), business, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, Food Science
Abstract: International audience; Fruity beers can be promoted through production of flavoring compounds during fermentation by partial replacement of brewing yeast by non-conventional-yeasts with high aroma production abilities. We evaluated here the use of a wild Saprochaete suaveolens strain, producing atypical aroma compounds, to produce new natural fruity beer, while keeping classical production conditions used in brewing industry. S. suaveolens was inoculated as starter of culture during beer fermentation and the fermentation performance was evaluated through measurement of several physicochemical parameters. The aroma profile of the engineered beers was monitored using HS-SPME GC/MS. The results showed that high fruity aroma and low-ethanol content beers were obtained through single-fermentation using S. suaveolens. We also demonstrated that during mixed-fermentation, S. suaveolens maintained high metabolic activity and allowed production of beer enriched with fruity aroma. Production of high or low ethanol content fruity beer could be achieved by varying the composition of the starter of culture.
Published: 2021

8. Genome-wide screening of circadian and non-circadian impact of Neat1 genetic deletion

Author: Audrey Jacq, Séverine Guillen, Maria-Montserrat Bello-Goutierrez, Denis Becquet, Bénédicte Boyer, Anne-Marie François-Bellan, Jean-Louis Franc, Institut de neurophysiopathologie (INP), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), and Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)
Subjects: [SDV.NEU.NB]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Neurobiology, Biophysics, RNA-sequencing, Biology, Long non-coding RNA Neat1, Biochemistry, Genome, Transcriptome, 03 medical and health sciences, 0302 clinical medicine, Paraspeckles, Structural Biology, Circadian gene expression, Genetics, CRISPR, CRISPR/Cas9 edition, Circadian rhythm, ComputingMethodologies_COMPUTERGRAPHICS, 030304 developmental biology, 0303 health sciences, Cas9, RNA, 3. Good health, Computer Science Applications, Cell culture, 030220 oncology & carcinogenesis, 030217 neurology & neurosurgery, TP248.13-248.65, Research Article, Biotechnology
Abstract: Graphical abstract, Highlights • Neat1 deletion affects numerous circadian and non-circadian genes. • Neat1 deletion causes loss, modification or acquisition of gene circadian pattern. • Paraspeckles contribute significantly to the circadian transcriptome., The functions of the long non-coding RNA, Nuclear enriched abundant transcript 1 (Neat1), are poorly understood. Neat1 is required for the formation of paraspeckles, but its respective paraspeckle-dependent or independent functions are unknown. Several studies including ours reported that Neat1 is involved in the regulation of circadian rhythms. We characterized the impact of Neat1 genetic deletion in a rat pituitary cell line. The mRNAs whose circadian expression pattern or expression level is regulated by Neat1 were identified after high-throughput RNA sequencing of the circadian transcriptome of wild-type cells compared to cells in which Neat1 was deleted by CRISPR/Cas9. The numerous RNAs affected by Neat1 deletion were found to be circadian or non-circadian, targets or non-targets of paraspeckles, and to be associated with many key biological processes showing that Neat1, in interaction with the circadian system or independently, could play crucial roles in key physiological functions through diverse mechanisms.
Published: 2021

9. Direct RNA-RNA interaction between Neat1 and RNA targets, as a mechanism for RNAs paraspeckle retention

Author: Anne-Marie François-Bellan, Audrey Jacq, Séverine Guillen, Maria-Montserrat Bello-Goutierrez, Denis Becquet, Jean-Louis Franc, Bénédicte Boyer, Institut de neurophysiopathologie (INP), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU), and Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)
Subjects: [SDV.NEU.NB]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Neurobiology, [SDV]Life Sciences [q-bio], Plasma protein binding, Biology, 03 medical and health sciences, 0302 clinical medicine, RNA targets, Paraspeckles, RNA- RNA interaction, Neat1, medicine, Animals, RNA Processing, Post-Transcriptional, Molecular Biology, Cells, Cultured, 030304 developmental biology, Cell Nucleus, 0303 health sciences, Messenger RNA, Mechanism (biology), Chemistry, RNA, RNA-Binding Proteins, Paraspeckle, Cell Biology, Cell cycle, Cell biology, Rats, medicine.anatomical_structure, 030220 oncology & carcinogenesis, Pituitary Gland, RNA splicing, RNA, Long Noncoding, psoralen, Nucleus, 030217 neurology & neurosurgery, Research Paper
Abstract: Paraspeckles are nuclear ribonucleic complex formed of a long non-coding RNA, nuclear-enriched abundant transcript one (Neat1) and associated RNA-binding proteins (RBP) whose cellular known functions are to sequester in the nucleus both proteins and RNAs. However, how RNAs are bound to paraspeckles is largely unknown. It is highly likely that binding of RNAs may occur via interactions with RBPs and accordingly, two structures present in the 3’UTR of some RNAs have been shown to allow their association to paraspeckles via protein binding. However, Neat1 could also be involved in the targeting of RNAs through direct RNA-RNA interactions. Using a RNA pull-down procedure adapted to select only RNAs engaged in direct RNA-RNA interactions and followed by RNA-seq we showed that in a rat pituitary cell line, GH4C1 cells, 1791 RNAs were associated with paraspeckles by direct interaction with Neat1. Neat1 was actually found able to bind more than 30% of the total transcripts targeted by the paraspeckles, we have identified in this cell line in a previous study. Furthermore, given the biological processes in which direct RNAs targets of Neat1 were involved as determined by gene ontology analysis, it was proposed that Neat1 played a major role in paraspeckle functions such as circadian rhythms, mRNA processing, RNA splicing and regulation of cell cycle. Finally, we provided evidence that direct RNA targets of Neat1 were preferentially bound to the 5’ end of Neat1 demonstrating that they are located in the shell region of paraspeckles.
Published: 2020

10. A Sequence determinant in 3’UTR of mRNAs for Nuclear Retention by Paraspeckles

Author: Manon Torres, Jean-Louis Franc, Audrey Jacq, Bénédicte Boyer, Séverine Guillen, Maria-Montserrat Bello-Goutierrez, Maya Belghazi, Anne-Marie François-Bellan, Claude Villard, Marie-Pierre Blanchard, Denis Becquet, Institut de neurophysiopathologie (INP), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), and Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)
Subjects: 0303 health sciences, Messenger RNA, Three prime untranslated region, Inverted repeat, [SDV]Life Sciences [q-bio], RNA, Paraspeckle, RNA-binding protein, Biology, Paraspeckles, Cell biology, 03 medical and health sciences, 0302 clinical medicine, 030217 neurology & neurosurgery, Nuclear localization sequence, 030304 developmental biology
Abstract: Paraspeckles are nuclear membraneless structures composed of a long non-coding RNA, Nuclear-Enriched-Abundant-Transcript-1 and RNA binding proteins, which associate numerous mRNAs. It is therefore believed that their cellular function is to sequester in the nucleus their associated proteins and/or target mRNAs. However, little is known about the molecular determinant in mRNA targets that allow their association to paraspeckles except that inverted repeats of Alu sequences (IRAlu) present in 3’UTR of mRNAs may allow this association. While in a previous study we established the list of paraspeckle target RNAs in a rat pituitary cell line, we didn’t find however, inverted repeated SINEs, the rat equivalent of primate IRAlus in 3’UTR of these RNAs. By developing a candidate gene strategy, we selected a paraspeckle target gene, namely calreticulin mRNA, and we searched for other potential RNA recruitment elements in its 3’UTR, since 3’UTRs usually contain the sequence recognition for nuclear localization. We found a 15-nucleotide sequence, present as a tandem repeat in 3’UTR of this mRNA, which is involved in the nuclear retention by paraspeckles. While being not overrepresented in the 3’UTR of the paraspeckle target RNAs, this recruitment element was present in near 30% of all 3’UTR mRNAs. In addition, since an oligonucleotide containing this sequence binds the paraspeckle protein component HNRNPK, it is proposed that HNRNPK may constitute a bridging protein between paraspeckles and target mRNAs.
Published: 2020

11. Termino-terminal Ureteral Laparoscopic Anastomosis in a Case of Deep Infiltrating Endometriosis

Author: Benjamín Bustos, Michel Canis, Raimundo Avilés, Pauline Chauvet, Nicolas Bourdel, Marie François, Service de Gynécologie [CHU Clermont-Ferrand], CHU Estaing [Clermont-Ferrand], CHU Clermont-Ferrand-CHU Clermont-Ferrand, Institut Pascal (IP), Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne (UCA)-Institut national polytechnique Clermont Auvergne (INP Clermont Auvergne), and Université Clermont Auvergne (UCA)-Université Clermont Auvergne (UCA)
Subjects: Adult, medicine.medical_specialty, Fistula, [SDV]Life Sciences [q-bio], Endometriosis, Hydronephrosis, Anastomosis, urologic and male genital diseases, 03 medical and health sciences, 0302 clinical medicine, Ureter, medicine, Humans, Ureteral Diseases, In patient, Laparoscopy, 030219 obstetrics & reproductive medicine, medicine.diagnostic_test, urogenital system, business.industry, Anastomosis, Surgical, Obstetrics and Gynecology, medicine.disease, female genital diseases and pregnancy complications, Deep infiltrating endometriosis, 3. Good health, Surgery, Stenosis, medicine.anatomical_structure, 030220 oncology & carcinogenesis, Female, business
Abstract: Study Objective Laparoscopic termino-terminal ureteral anastomosis has all the advantages of a minimally invasive approach in addition to the treatment of the pathologic condition [ 1 ]. Ureteral deep endometriosis can lead to severe consequences, such as hydroureteronephrosis and renal failure [ 2 , 3 ]. The main objective of this video is to present our surgical strategy and technique for cases of ureteral deep infiltrating endometriosis, which could help surgeons to understand and perform this surgery in a safe way in patients. Design Video demonstration of the technique. Setting French university tertiary-care hospital. Interventions This video presents a termino-terminal laparoscopic ureteral anastomosis and shows our team's strategy for surgical treatment in a 42-year-old woman with deep infiltrating ureteral left endometriosis, with consequent stenosis and left hydroureteronephrosis. A full resection of the endometriotic ureteral nodule was performed, followed by a termino-terminal anastomosis of the ureter. The use of intravenous indocyanine green to assess the postanastomotic ureteral perfusion and its risk of leakage or fistula are described in the video [ 2 , 3 , 4 , 5 ]. Conclusion Ureteral endometriosis can lead to severe consequences, and the surgical treatment can be difficult and, most times, incomplete. This video gives a detailed example of the strategy our team used to perform a termino-terminal ureteral laparoscopic anastomosis in a structured way.
Published: 2020

12. Polyunsaturated fatty acid metabolites: biosynthesis in Leishmania and role in parasite/host interaction

Author: Julien Pujo, Jean Marie François, Jessica Dalloux-Chioccioli, Pauline Le Faouder, Anne Abot, Lucie Paloque, Teresa Pérez-Berezo, Marie-Ange Teste, Gilles Dietrich, Malwina Mainka, Alexis Valentin, Nicolas Cenac, Justine Bertrand-Michel, Sandra Bourgeade-Delmas, Nils Helge Schebb, Céline Deraison, Corinne Rolland, Catherine Blanpied, Laboratoire de chimie de coordination (LCC), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut de Chimie de Toulouse (ICT-FR 2599), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Pharmacochimie et Biologie pour le Développement (PHARMA-DEV), Institut de Recherche pour le Développement (IRD)-Institut de Chimie de Toulouse (ICT-FR 2599), Université Fédérale Toulouse Midi-Pyrénées-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées, Institut de Recherche en Santé Digestive (IRSD ), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut des Maladies Métaboliques et Cardiovasculaires (I2MC), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM), Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés (LISBP), Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de la Recherche Agronomique (INRA), Faculty of Mathematics and Natural Sciences, Institut de Chimie de Toulouse (ICT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD)-Institut de Chimie de Toulouse (ICT), Université de Toulouse (UT), Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM), MetaToul Lipidomics, Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-MetaboHUB-MetaToul, MetaboHUB-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-MetaboHUB-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), University of Wuppertal, Region Midi-Pyrenees, ANR-11-INBS-0010,METABOHUB,Développement d'une infrastructure française distribuée pour la métabolomique dédiée à l'innovation(2011), European Project: 627487,EC:FP7:PEOPLE,FP7-PEOPLE-2013-IOF,EPIMACASE(2014), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut de Chimie de Toulouse (ICT-FR 2599), Université Fédérale Toulouse Midi-Pyrénées-Institut de Chimie du CNRS (INC)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut de Chimie du CNRS (INC)-Institut de Recherche pour le Développement (IRD), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Plateau MetaToul-LIPIDOMIQUE = MetaToul-Lipidomics, Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-MetaToul-MetaboHUB, Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Gulli, Marie-Hélène, Développement d'une infrastructure française distribuée pour la métabolomique dédiée à l'innovation - - METABOHUB2011 - ANR-11-INBS-0010 - INBS - VALID, THE ROLE OF ELASTASE/ELASTASE INHIBITOR IN DIALOG BETWEEN INTESTINAL EPITHELIAL CELLS AND MACROPHAGES IN INFLAMMATORY BOWEL DISEASES CONTEXT - EPIMACASE - - EC:FP7:PEOPLE2014-08-06 - 2016-08-05 - 627487 - VALID, Institut de Chimie de Toulouse (ICT-FR 2599), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-MetaboHUB-MetaToul, Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Ecole Nationale Vétérinaire de Toulouse (ENVT), and Institut National des Sciences Appliquées (INSA)-Université Fédérale Toulouse Midi-Pyrénées-Institut National des Sciences Appliquées (INSA)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)
Subjects: Male, 0301 basic medicine, Cytochrome P450, 030204 cardiovascular system & hematology, Biochemistry, Mice, chemistry.chemical_compound, 0302 clinical medicine, Endocrinology, Macrophage, Research Articles, Leishmania, chemistry.chemical_classification, biology, Chemistry, M2 Macrophage, 3. Good health, macrophages, Phenotype, Arachidonic acid, Docosahexaenoic acid, Fatty Acids, Unsaturated, ω-3, infection, Omega-3 fatty acids, Fatty acid metabolism, arachidonic acid, eicosanoids, omega-3, Infection, Polyunsaturated fatty acid, cytochrome P450, Macrophage polarization, CHO Cells, QD415-436, Biotechnologies, Host-Parasite Interactions, 03 medical and health sciences, Cricetulus, Animals, [CHIM.COOR]Chemical Sciences/Coordination chemistry, Macrophages, Cell Biology, [CHIM.COOR] Chemical Sciences/Coordination chemistry, biology.organism_classification, Mice, Inbred C57BL, 030104 developmental biology, Metabolism, biology.protein, Eicosanoids, metabolism
Abstract: International audience; Inside the human host, Leishmania infection starts with phagocytosis of infective promastigotes by macrophages. In order to survive, Leishmania has developed several strategies to manipulate macrophage functions. Among these strategies, Leishmania as a source of bioactive lipids has been poorly explored. Herein, we assessed the biosynthesis of polyunsaturated fatty acid metabolites by infective and noninfective stages of Leishmania and further explored the role of these metabolites in macrophage polarization. The concentration of docosahexaenoic acid metabolites, precursors of proresolving lipid mediators, was increased in the infective stage of the parasite compared with the noninfective stage, and cytochrome P450-like proteins were shown to be implicated in the biosynthesis of these metabolites. The treatment of macrophages with lipids extracted from the infective forms of the parasite led to M2 macrophage polarization and blocked the differentiation into the M1 phenotype induced by IFN-γ. In conclusion, Leishmania polyunsaturated fatty acid metabolites, produced by cytochrome P450-like protein activity, are implicated in parasite/host interactions by promoting the polarization of macrophages into a proresolving M2 phenotype.
Published: 2019

13. Integrated pH Measurement during Reaction Monitoring with Dual-Reception 1 H– 31 P NMR Spectroscopy

Author: Pierre Millard, Guy Lippens, Edern Cahoreau, Neil Cox, Jean-Luc Parrou, Rainer Kuemmerle, Jean-Marie François, Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés (LISBP), Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Synthèse, structure et fonction des biomolécules (SSFB), Université de Lille, Droit et Santé-Centre National de la Recherche Scientifique (CNRS), NMR facility from MetaToul (Toulouse metabolomics & fluxomics facilities, www.metatoul.fr), which is part of the French National Infrastructure for Metabolomics and Fluxomics MetaboHUB-AR- 11-INBS-0010 (www.metabohub.fr), and is supported by the Région Occitanie, the ERDF, the Toulouse Métropole and the French Minister of Education & Research, who are gratefully acknowledged., Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), MetaToul FluxoMet (TBI-MetaToul), MetaboHUB-MetaToul, MetaboHUB-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-MetaboHUB-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Toulouse Biotechnology Institute (TBI), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), and Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de la Recherche Agronomique (INRA)
Subjects: Imagination, Chemical substance, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, Chemistry, media_common.quotation_subject, 010401 analytical chemistry, Resonance, Ph measurement, 010402 general chemistry, 01 natural sciences, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], 0104 chemical sciences, Analytical Chemistry, Search engine, Molecule, 31p nmr spectroscopy, Sensitivity (control systems), Biological system, ComputingMilieux_MISCELLANEOUS, media_common
Abstract: International audience; Simultaneous detection of 1H and 31P NMR signals through a dual detection scheme with two receivers allows monitoring both the signals of a molecule and the pH of the solution through the resonance of the inorganic phosphate. We evaluate here the method in terms of sensitivity and ease of implementation, and show that the additional information obtained without any loss of information or increase in measuring time can be of practical importance in a number of biochemical systems
Published: 2019

14. Gene Expression Noise Produces Cell-to-Cell Heterogeneity in Eukaryotic Homologous Recombination Rate

Author: Jean-Pascal Capp, Jean-Marie François, Jian Liu, Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés (LISBP), Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), ANR-12-JSV6-0006, ANR-12-JSV6-0006,NOISYEAST,Expression génique aléatoire et variabilité phénotypique dans l'adaptation de la levure(2012), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), and Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de la Recherche Agronomique (INRA)
Subjects: 0301 basic medicine, rate of evolution, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, lcsh:QH426-470, DNA damage, stochastic gene expression, RAD52, Saccharomyces cerevisiae, Biotechnologies, yeast, brewer s, 03 medical and health sciences, 0302 clinical medicine, Single-cell analysis, Gene expression, Genetics, recombination, single-cell analysis, saccharomyces cerevisiae, Gene, Genetics (clinical), 030304 developmental biology, Original Research, 0303 health sciences, biology, Cell sorting, biology.organism_classification, Phenotype, Cell biology, lcsh:Genetics, recombinaison, 030104 developmental biology, 030220 oncology & carcinogenesis, Molecular Medicine, Homologous recombination, expression des gènes
Abstract: Variation in gene expression among genetically identical individual cells (called gene expression noise) directly contributes to phenotypic diversity. Whether such variation can impact genome stability and lead to variation in genotype remains poorly explored. We addressed this question by investigating whether noise in the expression of genes affecting homologous recombination (HR) activity either directly (RAD52) or indirectly (RAD27) confers cell-to-cell heterogeneity in HR rate inSaccharomyces cerevisiae. Using cell sorting to isolate subpopulations with various expression levels, we show that spontaneous HR rate is highly heterogeneous from cell-to-cell in clonal populations depending on the cellular amount of proteins affecting HR activity. Phleomycin-induced HR is even more heterogeneous, showing thatRAD27expression noise strongly affects the rate of recombination from cell-to-cell. Strong variations in HR rate between subpopulations are not correlated to strong changes in cell cycle stage. Moreover, this heterogeneity occurs even when simultaneously sorting cells at equal expression level of another gene involved in DNA damage response (BMH1) that is upregulated by DNA damage, showing that the initiating DNA damage is not responsible for the observed heterogeneity in HR rate. Thus gene expression noise seems mainly responsible for this phenomenon. Finally, HR rate non-linearly scales with Rad27 levels showing that total amount of HR cannot be explained solely by the time- or population-averaged Rad27 expression. Altogether, our data reveal interplay between heterogeneity at the gene expression and genetic levels in the production of phenotypic diversity with evolutionary consequences from microbial to cancer cell populations.
Published: 2019

15. Carbon sources and XlnR-dependent transcriptional landscape of CAZymes in the industrial fungus Talaromyces versatilis: when exception seems to be the rule

Author: Jean-Luc Parrou, Jean Marie François, Sébastien Déjean, Virginie Neugnot-Roux, Agustina Llanos, Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés (LISBP), Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de la Recherche Agronomique (INRA), Adisseo France SAS, Institut de Mathématiques de Toulouse UMR5219 (IMT), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse 1 Capitole (UT1)-Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Adisseo (Adisseo SAS, Antony, France), CIFRE (1558/2010), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse 1 Capitole (UT1), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Université Toulouse Capitole (UT Capitole), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université Toulouse - Jean Jaurès (UT2J), Université de Toulouse (UT)-Université Toulouse III - Paul Sabatier (UT3), and Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, Glucose repression, Glycosyl hydrolases, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, Transcription, Genetic, lcsh:QR1-502, 01 natural sciences, Applied Microbiology and Biotechnology, lcsh:Microbiology, Gene Expression Regulation, Fungal, Glycoside hydrolase, Biomass, Mycelium, Secretome, 2. Zero hunger, chemistry.chemical_classification, Genetics, 0303 health sciences, Talaromyces versatilis, Biomass deconstruction, CAZymes, Biotechnology, Filamentous fungi, Cellulose, Hemicellulose, Transcription factors, XlnR/XYR1, High-throughput qPCR, Bioengineering, Context (language use), Biotechnologies, Biology, Real-Time Polymerase Chain Reaction, Gene Expression Regulation, Enzymologic, Fungal Proteins, 03 medical and health sciences, Polysaccharides, 010608 biotechnology, Gene family, Gene, Transcription factor, Psychological repression, 030304 developmental biology, Research, Gene Expression Profiling, RT-qPCR, Carbon, Enzyme, Talaromyces, chemistry, Trans-Activators
Abstract: Background Research on filamentous fungi emphasized the remarkable redundancy in genes encoding hydrolytic enzymes, the similarities but also the large differences in their expression, especially through the role of the XlnR/XYR1 transcriptional activator. The purpose of this study was to evaluate the specificities of the industrial fungus Talaromyces versatilis, getting clues into the role of XlnR and the importance of glucose repression at the transcriptional level, to provide further levers for cocktail production. Results By studying a set of 62 redundant genes representative of several categories of enzymes, our results underlined the huge plasticity of transcriptional responses when changing nutritional status. As a general trend, the more heterogeneous the substrate, the more efficient to trigger activation. Genetic modifications of xlnR led to significant reorganisation of transcriptional patterns. Just a minimal set of genes actually fitted in a simplistic model of regulation by a transcriptional activator, and this under specific substrates. On the contrary, the diversity of xlnR+ versus ΔxlnR responses illustrated the existence of complex and unpredicted patterns of co-regulated genes that were highly dependent on the culture condition, even between genes that encode members of a functional category of enzymes. They notably revealed a dual, substrate-dependant repressor-activator role of XlnR, with counter-intuitive transcripts regulations that targeted specific genes. About glucose, it appeared as a formal repressive sugar as we observed a massive repression of most genes upon glucose addition to the mycelium grown on wheat straw. However, we also noticed a positive role of this sugar on the basal expression of a few genes, (notably those encoding cellulases), showing again the strong dependence of these regulatory mechanisms upon promoter and nutritional contexts. Conclusions The diversity of transcriptional patterns appeared to be the rule, while common and stable behaviour, both within gene families and with fungal literature, the exception. The setup of a new biotechnological process to reach optimized, if not customized expression patterns of enzymes, hence appeared tricky just relying on published data that can lead, in the best scenario, to approximate trends. We instead encourage preliminary experimental assays, carried out in the context of interest to reassess gene responses, as a mandatory step before thinking in (genetic) strategies for the improvement of enzyme production in fungi. Electronic supplementary material The online version of this article (10.1186/s12934-019-1062-8) contains supplementary material, which is available to authorized users.
Published: 2019

16. Rational engineering of a malate dehydrogenase for microbial production of 2,4-dihydroxybutyric acid via homoserine pathway

Author: Cláudio Remedios Frazão, Yoann Malbert, Christopher M. Topham, Jean Marie François, Thomas Walther, Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés (LISBP), Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Molecular Forces Consulting, Toulouse White Biotechnology (TWB), Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de la Recherche Agronomique (INRA), valorization service of the 'Toulouse Transfer Technology', ANR-14-CE06-0024,SYNPATHIC,Ingénierie robuste et évolution dirigée de voies metaboliques synthétiques par intégration de la microfluidique et de la génomique(2014), and Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, Models, Molecular, homosérine, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, Protein Conformation, Lactate dehydrogenase A, Homoserine, malate dehydrogenase, Dehydrogenase, Reductase, Biochemistry, Malate dehydrogenase, Substrate Specificity, 03 medical and health sciences, chemistry.chemical_compound, education, Butylene Glycols, Molecular Biology, chemistry.chemical_classification, education.field_of_study, Binding Sites, 030102 biochemistry & molecular biology, biology, Escherichia coli Proteins, Lactococcus lactis, Reproducibility of Results, protein engineering, Cell Biology, biology.organism_classification, ingénierie enzymatique, Turnover number, Biosynthetic Pathways, Alcohol Oxidoreductases, Butyrates, Kinetics, enzyme, 030104 developmental biology, Enzyme, chemistry, Metabolic Engineering, protéine, Mutagenesis, Site-Directed, synthetic biology, site-directed mutagenesis, escherichia coli, protein
Abstract: A synthetic pathway for the production of 2,4-dihydroxybutyric acid from homoserine, composed of two consecutive enzymatic reaction steps has been recently reported. An important step in this pathway consists in the reduction of 2-keto-4-hydroxybutyrate (OHB) into (L)-dihydroxybutyrate (DHB), by an enzyme with OHB reductase activity. In this study, we used a rational approach to engineer an OHB reductase by using the cytosolic (L)-malate dehydrogenase from Escherichia coli (Ec-Mdh) as the template enzyme. Structural analysis of (L)-malate dehydrogenase and (L)-lactate dehydrogenase enzymes acting on sterically cognate substrates revealed key residues in the substrate and co-substrate binding sites responsible for substrate discrimination. Accordingly, amino acid changes were introduced in a step-wise manner into these regions of the protein. This rational engineering led to the production of a Ec-Mdh-5E variant (I12V/R81A/M85E/G179D/D86S) with a turnover number (k cat ) on OHB that was increased by more than 2,000 fold (from 0.03 up to 65.0 s -1 ), which turned out to be 7 fold higher than that on its natural substrate oxaloacetate. Further kinetic analysis revealed the engineered enzyme to possess comparable catalytic efficiencies (k cat /K m ) between natural and synthetic OHB substrates (84 and 31 s -1 mM -1 , respectively). Shake-flask cultivation of an homoserine-overproducing E. coli strain expressing this improved OHB reductase together with a transaminase encoded by aspC able to convert homoserine to OHB resulted in 89 % increased DHB production as compared to our previous report using a E. coli host strain expressing an OHB reductase derived from the lactate dehydrogenase A of Lactococcus lactis
Published: 2018

17. Innovative DendrisChips® Technology for a Syndromic Approach of In Vitro Diagnosis: Application to the Respiratory Infectious Diseases

Author: Sylvain Messier, Philippe Besse, Tatiana Kempowsky, Alice Senescau, Jean Marie François, Richard Fabre, Elodie Bernard, Dendris SAS, Biopôle, Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés (LISBP), Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de la Recherche Agronomique (INRA), Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Region Midi Pyrenees [06001324, 07006292], ANR-10-BTBR-0004,IDEALG,Biotechnologies pour la valorisation des macroalgues(2010), Laboratoire Bio Pole, service pharmaceutique, Hospices Civils de Lyon (HCL)-Hôpital de la Croix-Rousse [CHU - HCL], Hospices Civils de Lyon (HCL), Institut de Mathématiques de Toulouse UMR5219 (IMT), Université Toulouse Capitole (UT Capitole), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université Toulouse - Jean Jaurès (UT2J), Université de Toulouse (UT)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Institut des Technologies Avancées en sciences du Vivant (ITAV), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse 1 Capitole (UT1), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, and Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, Microbiological culture, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, 030106 microbiology, Clinical Biochemistry, biochips, diagnostic, Biotechnologies, dendrimer, syndromic approach, law.invention, 03 medical and health sciences, 0302 clinical medicine, [MATH.MATH-ST]Mathematics [math]/Statistics [math.ST], law, Medicine, Multiplex, 030212 general & internal medicine, machine-learning methods, microbiologie, Biochip, Pathogen, ComputingMilieux_MISCELLANEOUS, Polymerase chain reaction, bactérie, lcsh:R5-920, biology, business.industry, in vitro diagnostic (IVD), Microbiology and Parasitology, DNA, biology.organism_classification, bacterium, Virology, In vitro, Microbiologie et Parasitologie, 3. Good health, PCR, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Infectious disease (medical specialty), puce à adn, business, lcsh:Medicine (General), Bacteria, pathogen, agent pathogène
Abstract: Clinical microbiology is experiencing the emergence of the syndromic approach of diagnosis. This paradigm shift will require innovative technologies to detect rapidly, and in a single sample, multiple pathogens associated with an infectious disease. Here, we report on a multiplex technology based on DNA-microarray that allows detecting and discriminating 11 bacteria implicated in respiratory tract infection. The process requires a PCR amplification of bacterial 16S rDNA, a 30 min hybridization step on species-specific oligoprobes covalently linked on dendrimers coated glass slides (DendriChips&reg, ) and a reading of the slides by a dedicated laser scanner. A diagnostic result is delivered in about 4 h as a predictive value of presence/absence of pathogens using a decision algorithm based on machine-learning method, which was constructed from hybridization profiles of known bacterial and clinical isolated samples and which can be regularly enriched with hybridization profiles from clinical samples. We demonstrated that our technology converged in more than 95% of cases with the microbiological culture for bacteria detection and identification.
Published: 2018

18. Deciphering the Origin, Evolution, and Physiological Function of the Subtelomeric Aryl-Alcohol Dehydrogenase Gene Family in the Yeast Saccharomyces cerevisiae

Author: Dong Dong Yang, Frank Rosenzweig, Gustavo M. de Billerbeck, Jean Marie François, Jin Jing Zhang, Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés (LISBP), Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de la Recherche Agronomique (INRA), School of Agriculture and Food Sciences, University of Queensland (UQ), School of Biology, Georgia Institute of Technology [Atlanta], Toulouse White Biotechnology (TWB), COST action FA0907 BIOFLAVOUR under the EU's Seventh Framework Programme for Research (FP7), Natural Science Foundation of China (NSFC 31301547), Ministry of Education (SRF for ROCS 2015), NASA NNX12AD87G, NIH R01HG003328, Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), University of Southern Queensland (USQ), and Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, expression génique, Evolution, 030106 microbiology, Saccharomyces cerevisiae, Ingénierie des aliments, Subtelomeric, Biology, yeast, brewer s, Applied Microbiology and Biotechnology, Genome, Lignin, Homology (biology), Evolution, Molecular, Fungal Proteins, 03 medical and health sciences, [SDV.IDA]Life Sciences [q-bio]/Food engineering, Gene family, Food engineering, saccharomyces cerevisiae, Aryl-alcohol dehydrogenases, AKR superfamily, Pseudogenization, Evolutionary and Genomic Microbiology, Gene, analyse phylogénique, Genetics, Whole genome sequencing, Ecology, séquence génomique, biology.organism_classification, Yeast, Open reading frame, Alcohol Oxidoreductases, 030104 developmental biology, Biochemistry, Multigene Family, gene expression, Pseudogenes, pseudogénisation, Food Science, Biotechnology
Abstract: Homology searches indicate that Saccharomyces cerevisiae strain BY4741 contains seven redundant genes that encode putative aryl-alcohol dehydrogenases (AAD). Yeast AAD genes are located in subtelomeric regions of different chromosomes, and their functional role(s) remain enigmatic. Here, we show that two of these genes, AAD4 and AAD14 , encode functional enzymes that reduce aliphatic and aryl-aldehydes concomitant with the oxidation of cofactor NADPH, and that Aad4p and Aad14p exhibit different substrate preference patterns. Other yeast AAD genes are undergoing pseudogenization. The 5′ sequence of AAD15 has been deleted from the genome. Repair of an AAD3 missense mutation at the catalytically essential Tyr 73 residue did not result in a functional enzyme. However, ancestral-state reconstruction by fusing Aad6 with Aad16 and by N-terminal repair of Aad10 restores NADPH-dependent aryl-alcohol dehydrogenase activities. Phylogenetic analysis indicates that AAD genes are narrowly distributed in wood-saprophyte fungi and in yeast that occupy lignocellulosic niches. Because yeast AAD genes exhibit activity on veratraldehyde, cinnamaldehyde, and vanillin, they could serve to detoxify aryl-aldehydes released during lignin degradation. However, none of these compounds induce yeast AAD gene expression, and Aad activities do not relieve aryl-aldehyde growth inhibition. Our data suggest an ancestral role for AAD genes in lignin degradation that is degenerating as a result of yeast's domestication and use in brewing, baking, and other industrial applications. IMPORTANCE Functional characterization of hypothetical genes remains one of the chief tasks of the postgenomic era. Although the first Saccharomyces cerevisiae genome sequence was published over 20 years ago, 22% of its estimated 6,603 open reading frames (ORFs) remain unverified. One outstanding example of this category of genes is the enigmatic seven-member AAD family. Here, we demonstrate that proteins encoded by two members of this family exhibit aliphatic and aryl-aldehyde reductase activity, and further that such activity can be recovered from pseudogenized AAD genes via ancestral-state reconstruction. The phylogeny of yeast AAD genes suggests that these proteins may have played an important ancestral role in detoxifying aromatic aldehydes in ligninolytic fungi. However, in yeast adapted to niches rich in sugars, AAD genes become subject to mutational erosion. Our findings shed new light on the selective pressures and molecular mechanisms by which genes undergo pseudogenization.
Published: 2018

19. Construction of a synthetic metabolic pathway for the production of 2,4-dihydroxybutyric acid from homoserine

Author: Clémentine Dressaire, Yoann Malbert, Jean Marie François, Florence Calvayrac, Thomas Walther, Hélène Cordier, Ceren Alkim, Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés (LISBP), Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Toulouse White Biotechnology (TWB), Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de la Recherche Agronomique (INRA), and Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, homosérine, voie métabolique, Lactate dehydrogenase A, Homoserine, Bioengineering, Reductase, Applied Microbiology and Biotechnology, Metabolic engineering, 03 medical and health sciences, chemistry.chemical_compound, ingénierie métabolique, [CHIM.GENI]Chemical Sciences/Chemical engineering, Bacterial Proteins, Escherichia coli, Génie chimique, education, Butylene Glycols, chemistry.chemical_classification, education.field_of_study, biology, Lactococcus lactis, Chimical engineering, metabolic pathway, biology.organism_classification, Amino acid, Metabolic pathway, Butyrates, 030104 developmental biology, Enzyme, chemistry, Biochemistry, metabolic engineering, Biotechnology
Abstract: 2,4-dihydroxybutyrate (DHB) is a precursor for the chemical synthesis of the methionine analogue 2-hydroxy-4-(methylthio)butyrate. Since no annotated metabolic pathway exists for its microbial production from sugar, we have conceived a two-step synthetic metabolic pathway which converts the natural amino acid homoserine to DHB. The pathway proceeds through the homoserine transaminase-catalyzed deamination of homoserine to obtain 2-oxo-4-hydroxybutyrate (OHB), and continues with the reduction of OHB to DHB, which is catalyzed by an OHB reductase enzyme. We identified homoserine transaminase and OHB reductase activity in several candidate enzymes which act on sterically cognate substrates, and improved OHB reductase activity of lactate dehydrogenase A of Lactococcus lactis by structure-based enzyme engineering. Fed-batch cultivation of a homoserine-overproducing Escherichia coli strain which expressed homoserine transaminase and OHB reductase enzymes resulted in the production of 5.3 g/L DHB at a yield of 0.1 g/g.
Published: 2018

20. Bimodality of gene expression from yeast promoter can be instigated by DNA context, inducing conditions and strain background

Author: Jean-Pascal Capp, Sevan Arabaciyan, Jian Liu, Jean Marie François, Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés (LISBP), Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de la Recherche Agronomique (INRA), Agence Nationale de la Recherche [ANR-12-JSV6-0006], Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), ANR-12-JSV6-0006,NOISYEAST,Expression génique aléatoire et variabilité phénotypique dans l'adaptation de la levure(2012), and Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, Transcriptional Activation, epistasis, Copper Sulfate, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, Transgene, Saccharomyces cerevisiae, Green Fluorescent Proteins, Context (language use), Biology, yeast, brewer s, Applied Microbiology and Biotechnology, Microbiology, fragment génomique, 03 medical and health sciences, Plasmid, Genes, Reporter, Gene Expression Regulation, Fungal, plasmid, Gene expression, cupric sulfate, saccharomyces cerevisiae, DNA, Fungal, Promoter Regions, Genetic, Strain (chemistry), promoteur, Gene Expression Profiling, promotor, Promoter, General Medicine, biology.organism_classification, Phenotype, CUP1, bimodalité, Recombinant Proteins, sulfate de cuivre, Cell biology, Artificial Gene Fusion, phenotypic heterogeneity, 030104 developmental biology, bimodal expression, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, plasmide, processus industriel, transgene expression, Plasmids, expression des gènes
Abstract: Bimodality in gene expression is thought to provide a high phenotypic heterogeneity that can be favourable for adaptation or unfavourable notably in industrial processes that require stable and homogeneous properties. Whether this property is produced or suppressed in different conditions has been understudied. Here we identified tens of Saccharomyces cerevisiae genomic fragments conferring bimodal yEGFP expression on centromeric plasmid and studied some of these promoters in different DNA contexts, inducing conditions or strain backgrounds. First, we observed that the bimodal behaviour identified on plasmid is generally suppressed at the genomic level. Second, an inducible promoter such as the copper-regulated CUP1 promoter can produce bimodal expression in a time- and dose-dependent fashion. For a given copper sulphate concentration, a constant proportion of the subpopulation is induced and only the induction level of this subpopulation changed with induction duration, while for a same induction time, higher copper sulphate concentrations induced more cells at higher levels. Third, we showed that bimodality conferred by the CUP1 promoter in expression profile is strain background dependent, revealing epistasis in the generation of bimodality. The influence of these parameters on bimodality has to be taken into account when considering transgene expression for industrial microbial productions.
Published: 2018

21. RNA Pull-down Procedure to Identify RNA Targets of a Long Non-coding RNA

Author: Anne-Marie François-Bellan, Jean-Louis Franc, Marie-Pierre Blanchard, Mathias Moreno, Bénédicte Boyer, Séverine Guillen, Denis Becquet, Manon Torres, Centre de recherche en neurobiologie - neurophysiologie de Marseille (CRN2M), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut de neurophysiopathologie (INP), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU), This work was supported by Aix-Marseille University and CNRS and funded by a grant from Pfizer Laboratories, and Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)
Subjects: DNA and RNA shearing, RNA pull-down, network cross- linking, General Immunology and Microbiology, probe design, General Chemical Engineering, General Neuroscience, [SDV.NEU.NB]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Neurobiology, DNA and RNA shearing Date, Computational Biology, General Biochemistry, Genetics and Molecular Biology, Issue 134, Long non-coding RNA, lnc RNA, network cross-linking, Genetics, Humans, predicted RNA secondary structure, RNA, Long Noncoding, Cells, Cultured
Abstract: International audience; Long non-coding RNA (lncRNA), which are sequences of more than 200 nucleotides without a defined reading frame, belong to the regulatory non-coding RNA's family. Although their biological functions remain largely unknown, the number of these lncRNAs has steadily increased and it is now estimated that humans may have more than 10,000 such transcripts. Some of these are known to be involved in important regulatory pathways of gene expression which take place at the transcriptional level, but also at different steps of RNA co-and post-transcriptional maturation. In the latter cases, RNAs that are targeted by the lncRNA have to be identified. That's the reason why it is useful to develop a method enabling the identification of RNAs associated directly or indirectly with a lncRNA of interest. This protocol, which was inspired by previously published protocols allowing the isolation of a lncRNA together with its associated chromatin sequences, was adapted to permit the isolation of associated RNAs. We determined that two steps are critical for the efficiency of this protocol. The first is the design of specific anti-sense DNA oligonucleotide probes able to hybridize to the lncRNA of interest. To this end, the lncRNA secondary structure was predicted by bioinformatics and anti-sense oligonucleotide probes were designed with a strong affinity for regions that display a low probability of internal base pairing. The second crucial step of the procedure relies on the fixative conditions of the tissue or cultured cells that have to preserve the network between all molecular partners. Coupled with high throughput RNA sequencing, this RNA pull-down protocol can provide the whole RNA interactome of a lncRNA of interest.
Published: 2018

22. Engineering carbon-conserving synthetic pathways for assimilation and conversion of C5/C6 carbon sources into added value chemicals

Author: Cléa Lachaux, Ceren Alkim, Jean Marie François, Thomas Walther, Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés (LISBP), Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de la Recherche Agronomique (INRA), Toulouse White Biotechnology (TWB), Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Technische Universität Dresden (TUD), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), and Technische Universität Dresden = Dresden University of Technology (TU Dresden)
Subjects: 0106 biological sciences, 0303 health sciences, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, carbon, xylose, Bioengineering, Assimilation (biology), General Medicine, Pulp and paper industry, utilisation, 01 natural sciences, thermodynamic equilibrium, wood sugar, 03 medical and health sciences, équilibre thermodynamique, éthylène, 010608 biotechnology, biotechnologie blanche, Added value, Environmental science, carbone, glucose, Molecular Biology, 030304 developmental biology, Biotechnology
Abstract: Présenté au: 3. International Conference on Enzymology and Molecular BiologyDate: 05-06 Mars 2018 Lieu: Londres; The development of carbon efficient pathways for added value (bio)chemicals production is the essence of White Biotechnology. The limit of carbon conservation in all (bio)chemical syntheses is determined by the electron balance in substrate(s) and product(s). Natural pathways do not have often the stoichiometric capacity to produce a value-added compound at yields that correspond to the thermodynamic maximum. A good example of this lack of stoichiometric efficiency is the bioproduction of glycolic acid (GA), a two carbon compound of considerable industrial interest notably in cosmetics and biodegradable polymers. We addressed this objective by employing the following strategies. Firstly, we reconsider a new pathway for C5 assimilation that relies on the carbon-conserving aldolytic cleavage of X1P or R1P to yield the C2 compound glycolaldehyde and the C3 DHAP compound by expression of a ketohexo-1-kinase (Khk-C) and aldolase (Aldo-B). Glycoaldehyde is then either reduced into ethylene glycol or oxidized into glycolic acid usingh endogenous reductase/dehydrogenase. With this approach, EG and GA at yield close to maximal of 1 mol/mol sugar have been obtained. This synthetic pathway was then coimbined with the natural glyoxylate shunt, to yield a production of GA ∼30% from a xylose/glucose mixture (66%/33%) 30% higher than using the sole natural pathway. Yet, as this strategy does not avoid a loss of carbon at the level of pyruvate, we created a cycling route that overcome this loss and which allowed both hexoses and pentoses to be converted into glycolic acid at their highest theoretical yield
Published: 2018

23. Trehalose-6-phosphate promotes fermentation and glucose repression in Saccharomyces cerevisiae

Author: Rebeca L. Vicente, Sébastien Déjean, Jean-Luc Parrou, Lucie Spina, Jose P.L. Gómez, Jean Marie François, Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés (LISBP), Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Institut de Mathématiques de Toulouse UMR5219 (IMT), Université Toulouse Capitole (UT Capitole), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université Toulouse - Jean Jaurès (UT2J), Université de Toulouse (UT)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), ANR Blanc [07-2-200101], Region Midi Pyrenees (France), Toulouse Region Midi Pyrenees, Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de la Recherche Agronomique (INRA), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse 1 Capitole (UT1), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse 1 Capitole (UT1)-Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés ( LISBP ), Institut National de la Recherche Agronomique ( INRA ) -Institut National des Sciences Appliquées - Toulouse ( INSA Toulouse ), Institut National des Sciences Appliquées ( INSA ) -Institut National des Sciences Appliquées ( INSA ) -Centre National de la Recherche Scientifique ( CNRS ), Institut de Mathématiques de Toulouse UMR5219 ( IMT ), Université Toulouse 1 Capitole ( UT1 ) -Université Toulouse - Jean Jaurès ( UT2J ) -Université Toulouse III - Paul Sabatier ( UPS ), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-PRES Université de Toulouse-Institut National des Sciences Appliquées - Toulouse ( INSA Toulouse )
Subjects: 0301 basic medicine, trehalose 6-phosphate, Applied Microbiology, yeast, Applied Microbiology and Biotechnology, flux sensing, Glycolysis, Crabtree effect, lcsh:QH301-705.5, ComputingMilieux_MISCELLANEOUS, [SDV.MP.MYC]Life Sciences [q-bio]/Microbiology and Parasitology/Mycology, chemistry.chemical_classification, biology, quantitative analysis, Chemistry, filamentous fungi, glycolysis, Complementation, filamentous fungus, Biochemistry, analyse quantitative, TPS1, glucose repression, profil métabolique, Autre (Sciences du Vivant), Saccharomyces cerevisiae, Biochemistry, Genetics and Molecular Biology (miscellaneous), Microbiology, 03 medical and health sciences, Virology, capacité, Genetics, [ MATH.MATH-ST ] Mathematics [math]/Statistics [math.ST], mutant, Molecular Biology, levure, Sugar phosphates, Ethanol, Wild type, Cell Biology, biology.organism_classification, Yeast, champignon filamenteux, 030104 developmental biology, lcsh:Biology (General), Fermentation, Parasitology
Abstract: The yeast trehalose-6-phosphate synthase (Tps1) catalyzes the formation of trehalose-6-phosphate (T6P) in trehalose synthesis. Besides, Tps1 plays a key role in carbon and energy homeostasis in this microbial cell, as shown by the well documented loss of ATP and hyper accumulation of sugar phosphates in response to glucose addition in a mutant defective in this protein. The inability of a Saccharomyces cerevisiae tps1 mutant to cope with fermentable sugars is still a matter of debate. We reexamined this question through a quantitative analysis of the capability of TPS1 homologues from different origins to complement phenotypic defects of this mutant. Our results allowed to classify this complementation in three groups. A first group enclosed TPS1 of Klyveromyces lactis with that of S. cerevisiae as their expression in Sctps1 cells fully recovered wild type metabolic patterns and fermentation capacity in response to glucose. At the opposite was the group with TPS1 homologues from the bacteria Escherichia coli and Ralstonia solanacearum, the plant Arabidopsis thaliana and the insect Drosophila melanogaster whose metabolic profiles were comparable to those of a tps1 mutant, notably with almost no accumulation of T6P, strong impairment of ATP recovery and potent reduction of fermentation capacity, albeit these homologous genes were able to rescue growth of Sctps1 on glucose. In between was a group consisting of TPS1 homologues from other yeast species and filamentous fungi characterized by 5 to 10 times lower accumulation of T6P, a weaker recovery of ATP and a 3-times lower fermentation capacity than wild type. Finally, we found that glucose repression of gluconeogenic genes was strongly dependent on T6P. Altogether, our results suggest that the TPS protein is indispensable for growth on fermentable sugars, and points to a critical role of T6P as a sensing molecule that promotes sugar fermentation and glucose repression..
Published: 2018

24. A generic HTS assay for kinase screening: Validation for the isolation of an engineered malate kinase

Author: Isabelle André, Nelly Martineau, Audrey Baylac, Clément Auriol, Magali Remaud-Simeon, Jean-Marie François, Christopher M. Topham, Romain Irague, Thomas Walther, Toulouse White Biotechnology (TWB), Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés (LISBP), Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de la Recherche Agronomique (INRA), French National Research Agency (ANR programme d'Investissement d'Avenir, Project SYNTHACS) [ANR-10-BTBR-05-01], ANR-10-BTBR-0005,SYNTHACS,Biologie Synthétique pour la synthèse de molécules chimiques à haute valeur ajoutée à partir de ressources carbonées renouvelables(2010), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Andre, Isabelle, and Remaud Simeon, Magali
Subjects: 0301 basic medicine, Models, Molecular, enzymic activity, métabolisme du malate, Applied Microbiology, [SDV]Life Sciences [q-bio], Mutant, Malates, lcsh:Medicine, Protein Engineering, nicotinamide-adenine dinucleotide, 01 natural sciences, Biochemistry, nad, Substrate Specificity, Electricity, Catalytic Domain, Enzyme Inhibitors, lcsh:Science, Multidisciplinary, 010304 chemical physics, Kinase, Chemistry, Physics, activité enzymatique, Recombinant Proteins, Enzymes, Bioassays and Physiological Analysis, Physical Sciences, Engineering and Technology, Research Article, Biotechnology, Static Electricity, Library Screening, Research and Analysis Methods, Microbiology, Catalysis, 03 medical and health sciences, Industrial Microbiology, Electrostatics, 0103 physical sciences, Aspartate kinase, Enzyme kinetics, Aspartate Kinase, Kinase activity, Molecular Biology Techniques, Molecular Biology, Enzyme Assays, Gene Library, adénosine di phosphate, Molecular Biology Assays and Analysis Techniques, lcsh:R, Phosphotransferases, Substrate (chemistry), Biology and Life Sciences, Proteins, Genetic Variation, High-Throughput Screening Assays, Kinetics, 030104 developmental biology, adenosine pyrophosphate, Amino Acid Substitution, criblage, Enzymology, Biocatalysis, Mutagenesis, Site-Directed, lcsh:Q, NAD+ kinase, Directed Molecular Evolution, Biochemical Analysis, size grading, Pyruvate kinase, Cloning
Abstract: An end-point ADP/NAD(+) acid/alkali assay procedure, directly applicable to library screening of any type of ATP-utilising/ADP producing enzyme activity, was implemented. Typically, ADP production is coupled to NAD(+) co-enzyme formation by the conventional addition of pyruvate kinase and lactate dehydrogenase. Transformation of enzymatically generated NAD(+) into a photometrically active alkali derivative product is then achieved through the successive application of acidic/alkali treatment steps. The assay was successfully miniaturized to search for malate kinase activity in a structurally-guided library of LysC aspartate kinase variants comprising 6,700 clones. The screening procedure enabled the isolation of nine positive variants showing novel kinase activity on (L)-malate, the best mutant, LysC V115A: E119S:E434V exhibited strong substrate selectivity for (L)-malate compared to (L)-aspartate with a (k(cat)/K-m)(malate)/(k(cat)/K-m)(aspartate) ratio of 86. Double mutants V115A:E119S, V115A:E119C and E119S:E434V were constructed to further probe the origins of stabilising substrate binding energy gains for (L)-malate due to mutation. The introduction of less sterically hindering side-chains in engineered enzymes carrying E119S and V115A mutations increases the effective volume available for substrate binding in the catalytic pocket. Improved binding of the (L)-malate substrate may be assisted by less hindered movement of the Phe184 aromatic side-chain. Additional favourable long-range electostatic effects on binding arising from the E434V surface mutation are conditionally dependent upon the presence of the V115A mutation close to Phe184 in the active-site.
Published: 2018

25. Flavour production by Saprochaete and Geotrichum yeasts and their close relatives

Author: Carmen Nueno-Palop, Eric Grondin, Thomas Petit, Alain Shum Cheong Sing, Steve James, Jean Marie François, Laboratoire de Chimie des Substances Naturelles et des Sciences des Aliments (LCSNSA), Université de La Réunion (UR), Institute of Food Research [Norwich], Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés (LISBP), Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de la Recherche Agronomique (INRA), Démarche intégrée pour l'obtention d'aliments de qualité (UMR Qualisud), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Université de La Réunion (UR)-Université de Montpellier (UM)-Avignon Université (AU)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université Montpellier 1 (UM1), European Regional development Funds (ERDF), Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de La Réunion (UR)-Université de Montpellier (UM)-Avignon Université (AU)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université Montpellier 1 (UM1), Biotechnology and Biological Sciences Research Council (BBSRC), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université Montpellier 1 (UM1)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Avignon Université (AU)-Université de La Réunion (UR)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)
Subjects: 0301 basic medicine, Saprochaete, Ehyl tiglate, 030106 microbiology, Flavour, Geotrichum, yeast, Galactomyces, Analytical Chemistry, Dipodascus, 03 medical and health sciences, Unsaturated esters, Genus, [SDV.IDA]Life Sciences [q-bio]/Food engineering, Food science, biology, General Medicine, ethyl tiglate, teleomorphs, biology.organism_classification, Yeast, arôme, flavour, Flavoring Agents, Magnusiomyces, Biochemistry, Taste, Saccharomycetales, souche de levure, Food Science
Abstract: In this study, a total of 30 yeast strains belonging to the genera Dipodascus, Galactomyces, Geotrichum, Magnusiomyces and Saprochaete were investigated for volatile organic compound production using HS-SPME-GC/MS analysis. The resulting flavour profiles, including 36 esters and 6 alcohols compounds, were statistically evaluated by cluster and PCA analysis. Two main groups of strains were extracted from this analysis, namely a group with a low ability to produce flavour and a group producing mainly alcohols. Two other minor groups of strains including Saprochaete suaveolens, Geotrichum marinum and Saprochaete gigas were diverging significantly from the main groups precisely because they showed a good ability to produce a large diversity of esters. In particular, we found that the Saprochaete genus (and their closed relatives) was characterized by a high production of unsaturated esters arising from partial catabolism of branched chain amino-acids. These esters were produced by eight phylogenetically related strains of Saprochaete genus.
Published: 2017

26. A new function for the yeast trehalose-6P synthase (Tps1) protein, as key pro-survival factor during growth, chronological ageing, and apoptotic stress

Author: Marie-Ange Teste, Marjorie Petitjean, Jean Marie François, Isabelle Léger-Silvestre, Jean-Luc Parrou, Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés (LISBP), Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de la Recherche Agronomique (INRA), Laboratoire de biologie moléculaire eucaryote (LBME), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Centre de Biologie Intégrative (CBI), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Doctoral grant from the French Ministry of Education and Research., Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Centre de Biologie Intégrative (CBI), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3)
Subjects: 0301 basic medicine, Exonucleases, Aging, Programmed cell death, Saccharomyces cerevisiae Proteins, Saccharomyces cerevisiae, interaction génétique, résistance au stress, Apoptosis, yeast, 03 medical and health sciences, chemistry.chemical_compound, chronological life span, oxidative stress, NADH, NADPH Oxidoreductases, anti-apoptotic, tréhalose, [SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering, levure, Caspase, trehalose, apoptose, 030102 biochemistry & molecular biology, ATP synthase, biology, gene interaction, Hydrogen Peroxide, biology.organism_classification, Endonucleases, Trehalose, Yeast, Cell biology, ATP, 030104 developmental biology, acetic acid, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, chemistry, Biochemistry, Glucosyltransferases, Caspases, biology.protein, TPS1, Intracellular, Developmental Biology
Abstract: Looking back to our recent work that challenged the paradigm of trehalose in stress resistance in yeast, our objective was to revisit the role of this disaccharide in chronological life span (CLS), and in the control of apoptosis. Using a catalytically dead variant of the trehalose-6-phosphate synthase (Tps1) protein, (the first enzyme in the trehalose biosynthetic pathway), and by manipulating intracellular trehalose independently of this pathway, we demonstrated that trehalose has no role in CLS or in the inhibition of acetic acid or H 20 2-triggered cell death. We showed instead that, in the absence of any apoptotic stimulus, the Tps1 protein itself was necessary in preventing massive, spontaneous commitment of yeast cells to apoptosis during growth. Without Tps1p, the life span was shortened and cells were sensitized to acetic acid (AA) and H 20 2, whereas the overexpression of the inactive variant of Tps1p almost abolished AA-triggered apoptosis. Genetic interaction analysis of TPS1 and genes such as YCA1, NUC1 and AIF1 indicated that these key executioners of cell death partially relayed tps1Δ-triggered signaling. Our results suggested that the pro-survival role of Tps1p could be connected with its ability to preserve ATP levels in yeast cells.
Published: 2017

27. Paraspeckles as rhythmic nuclear mRNA anchorages responsible for circadian gene expression

Author: Mathias Moreno, Marie-Pierre Blanchard, Jean-Louis Franc, Manon Torres, Bénédicte Boyer, Denis Becquet, Anne-Marie François-Bellan, Séverine Guillen, Centre de recherche en neurobiologie - neurophysiologie de Marseille (CRN2M), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Structure et fonctionnement des systèmes hydriques continentaux (SISYPHE), Université Pierre et Marie Curie - Paris 6 (UPMC)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Mines Paris - PSL (École nationale supérieure des mines de Paris), Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), Université Pierre et Marie Curie - Paris 6 (UPMC)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-MINES ParisTech - École nationale supérieure des mines de Paris, and Université Pierre et Marie Curie - Paris 6 (UPMC)-École pratique des hautes études (EPHE)-MINES ParisTech - École nationale supérieure des mines de Paris-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, Regulation of gene expression, Genetics, Cell Nucleus, Extra View, [SDV.NEU.NB]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Neurobiology, Circadian clock, RNA, Paraspeckle, Cell Biology, Biology, Paraspeckles, Circadian Rhythm, 03 medical and health sciences, Cell nucleus, 030104 developmental biology, medicine.anatomical_structure, Gene Expression Regulation, Pituitary Gland, Gene expression, medicine, Animals, Circadian rhythm, RNA, Messenger, ComputingMilieux_MISCELLANEOUS
Abstract: Circadian clocks regulate rhythmic gene expression levels by means of mRNA oscillations that are mainly driven by post-transcriptional regulation. We identified a new post-transcriptional mechanism, which involves nuclear bodies called paraspeckles. Major components of paraspeckles including the long noncoding RNA Neat1, which is the structural component, and its major protein partners, as well as the number of paraspeckles, follow a circadian pattern in pituitary cells. Paraspeckles are known to retain within the nucleus RNAs containing inverted repeats of Alu sequences. We showed that a reporter gene in which these RNA duplex elements were inserted in the 3'-UTR region displayed a circadian expression. Moreover, circadian endogenous mRNA associated with paraspeckles lost their circadian pattern when paraspeckles were disrupted. This work not only highlights a new paraspeckle-based post-transcriptional mechanism involved in circadian gene expression but also provides the list of all mRNA associated with paraspeckles in the nucleus of pituitary cells.
Published: 2017

28. Construction of a synthetic metabolic pathway for biosynthesis of the non-natural methionine precursor 2,4-dihydroxybutyric acid

Author: Isabelle André, Luce Lozano-Huguet, Christopher M. Topham, Audrey Baylac, Magali Remaud-Simeon, Nathalie Tarrat, Nelly Martineau, Clément Auriol, Hélène Cordier, Marc Maestracci, Marion Stodel, Romain Irague, Clémentine Dressaire, Jean Marie François, Thomas Walther, Yannick Malbert, Robert Huet, Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés (LISBP), Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de la Recherche Agronomique (INRA), Toulouse White Biotechnology (TWB), Surfaces, Interfaces et Nano-Objets (CEMES-SINanO), Centre d'élaboration de matériaux et d'études structurales (CEMES), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut de Chimie de Toulouse (ICT-FR 2599), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Adisseo France SAS, ANR-10-BTBR-05-01, Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie de Toulouse (ICT-FR 2599), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut de Chimie du CNRS (INC)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut de Chimie du CNRS (INC)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA), ANR-10-BTBR-0005,SYNTHACS,Biologie Synthétique pour la synthèse de molécules chimiques à haute valeur ajoutée à partir de ressources carbonées renouvelables(2010), Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut de Chimie de Toulouse (ICT), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), and Francois, Jean-Marie
Subjects: 0301 basic medicine, Models, Molecular, voie métabolique, General Physics and Astronomy, Reductase, synthon, chemistry.chemical_compound, Methionine, Malate Dehydrogenase, acide butyrique, Butylene Glycols, isobutyric acid, chemistry.chemical_classification, Multidisciplinary, Aldehyde Oxidoreductases, Butyrates, Process Engineering, Biochemistry, Metabolic Engineering, plasmide, Thermodynamics, Synthetic Biology, animal feeding, escherichia coli, Metabolic Networks and Pathways, aspartate kinase, aspartyl kinase, alimentation animale, Science, Biology, General Biochemistry, Genetics and Molecular Biology, Article, Metabolic engineering, 03 medical and health sciences, Biosynthesis, plasmid, Aspartate kinase, [SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering, Génie des procédés, malate, Phosphotransferases, Rational design, General Chemistry, metabolic pathway, Metabolic pathway, 030104 developmental biology, Enzyme, Glucose, chemistry, Mutagenesis, Site-Directed
Abstract: 2,4-Dihydroxybutyric acid (DHB) is a molecule with considerable potential as a versatile chemical synthon. Notably, it may serve as a precursor for chemical synthesis of the methionine analogue 2-hydroxy-4-(methylthio)butyrate, thus, targeting a considerable market in animal nutrition. However, no natural metabolic pathway exists for the biosynthesis of DHB. Here we have therefore conceived a three-step metabolic pathway for the synthesis of DHB starting from the natural metabolite malate. The pathway employs previously unreported malate kinase, malate semialdehyde dehydrogenase and malate semialdehyde reductase activities. The kinase and semialdehyde dehydrogenase activities were obtained by rational design based on structural and mechanistic knowledge of candidate enzymes acting on sterically cognate substrates. Malate semialdehyde reductase activity was identified from an initial screening of several natural enzymes, and was further improved by rational design. The pathway was expressed in a minimally engineered Escherichia coli strain and produces 1.8 g l−1 DHB with a molar yield of 0.15., 2,4-Dihydroxybutyric acid has potential to be a precursor to a range of industrially important products, however a natural metabolic pathway for its synthesis does not exist. Here the authors rationally design a synthetic pathway in E. coli by engineering enzymes from malate metabolism.
Published: 2017

29. Increased Ghrelin but Low Ghrelin-Reactive Immunoglobulins in a Rat Model of Methotrexate Chemotherapy-Induced Anorexia

Author: Akio Inui, Nicolas Lucas, Naouel Tennoune, Marie François, Aurore Cravezic, Moïse Coëffier, Kuniko Takagi, Stephanie Beutheu, Pierre Déchelotte, Romain Legrand, Christine Bole-Feysot, Sergueï O. Fetissov, Jean-Claude do Rego, Nutrition, inflammation et dysfonctionnement de l'axe intestin-cerveau (ADEN), Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institute for Research and Innovation in Biomedicine (IRIB), Normandie Université (NU)-Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), UNIROUEN - UFR Santé (UNIROUEN UFR Santé), Normandie Université (NU)-Normandie Université (NU), TargEDys Rouen, Service Commun d'Analyse Comportementale (SCAC), Normandie Université (NU)-Normandie Université (NU)-Institute for Research and Innovation in Biomedicine (IRIB), Normandie Université (NU)-Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), Service de nutrition [CHU Rouen], Normandie Université (NU)-Normandie Université (NU)-CHU Rouen, Normandie Université (NU), Kagoshima University Graduate School of Medical and Dental Sciences, Normandie Université (NU)-Normandie Université (NU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Normandie Université (NU)-Normandie Université (NU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Rouen Normandie (UNIROUEN), CHU Rouen, Normandie Université (NU)-Normandie Université (NU)-Université de Rouen Normandie (UNIROUEN), Department of Psychosomatic Internal Medicine, Kagoshima University, This work was supported from the EU INTERREG IVA 2 SeasProgram (7-003-FR_TC2N)., Duchange, Nathalie, Normandie Université (NU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-High-tech Research Infrastructures for Life Sciences (HeRacLeS), Normandie Université (NU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), and douville, sabine
Subjects: 0301 basic medicine, medicine.medical_specialty, [SDV.IMM] Life Sciences [q-bio]/Immunology, medicine.drug_class, autoantibodies, Endocrinology, Diabetes and Metabolism, media_common.quotation_subject, lcsh:TX341-641, Anorexia, Peptide hormone, chemotherapy, Anxiolytic, 03 medical and health sciences, Internal medicine, Orexigenic, intestinal inflammation, medicine, Nutrition, Original Research, media_common, Nutrition and Dietetics, Chemistry, Stomach, digestive, oral, and skin physiology, Appetite, 3. Good health, MESH: chemotherapy, intestina inflammation, anorexia, ghrelin, autoantibodies, [SDV.AEN] Life Sciences [q-bio]/Food and Nutrition, 030104 developmental biology, medicine.anatomical_structure, Endocrinology, anorexia, ghrelin, Anorectic, [SDV.IMM]Life Sciences [q-bio]/Immunology, Ghrelin, medicine.symptom, lcsh:Nutrition. Foods and food supply, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, hormones, hormone substitutes, and hormone antagonists, Food Science, medicine.drug
Abstract: International audience; Background and aims: Cancer chemotherapy is commonly accompanied by mucositis, anorexia, weight loss, and anxiety independently from cancer-induced anorexia–cachexia, further aggravating clinical outcome. Ghrelin is a peptide hormone produced in gastric mucosa that reaches the brain to stimulate appetite. In plasma, ghrelin is protected from degradation by ghrelin-reactive immunoglobulins (Ig). To analyze possible involvement of ghrelin in the chemotherapy-induced anorexia and anxiety, gastric ghrelin expression, plasma levels of ghrelin, and ghrelin-reactive IgG were studied in rats treated with methotrexate (MTX).Methods: Rats received MTX (2.5 mg/kg, subcutaneously) for three consecutive days and were killed 3 days later, at the peak of anorexia and weight loss. Control rats received phosphate-buffered saline. Preproghrelin mRNA expression in the stomach was analyzed by in situ hybridization. Plasma levels of ghrelin and ghrelin-reactive IgG were measured by immunoenzymatic assays and IgG affinity kinetics by surface plasmon resonance. Anxiety- and depression-like behaviors in MTX-treated anorectic and in control rats were evaluated in the elevated plus-maze and the forced-swim test, respectively.Results: In MTX-treated anorectic rats, the number of preproghrelin mRNA-producing cells was found increased (by 51.3%, p < 0.001) as well were plasma concentrations of both ghrelin and des-acyl-ghrelin (by 70.4%, p < 0.05 and 98.3%, p < 0.01, respectively). In contrast, plasma levels of total IgG reactive with ghrelin and des-acyl-ghrelin were drastically decreased (by 87.2 and 88.4%, respectively, both p < 0.001), and affinity kinetics of these IgG were characterized by increased small and big Kd, respectively. MTX-treated rats displayed increased anxiety- but not depression-like behavior.Conclusion: MTX-induced anorexia, weight loss, and anxiety are accompanied by increased ghrelin production and by a decrease of ghrelin-reactive IgG levels and affinity binding properties. Such changes of ghrelin-reactive IgG may underlie their decreased ghrelin-transporting capacities compromising ghrelin orexigenic and anxiolytic effects and contributing to chemotherapy-induced loss of appetite.
Published: 2016

30. Simultaneous production of glycolic acid via the glyoxylate shunt and the synthetic (D)-xylulose-1 phosphate pathway increases product yield

Author: Jean Marie François, Thomas Walther, Debora Trichez, Ceren Alkim, Lucie Spina, Yvan Cam, Toulouse White Biotechnology (TWB), Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés (LISBP), Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de la Recherche Agronomique (INRA), and Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, Chemistry, [SDV]Life Sciences [q-bio], Glyoxylate cycle, technology, industry, and agriculture, Bioengineering, General Medicine, 010501 environmental sciences, Phosphate, 01 natural sciences, chemistry.chemical_compound, 010608 biotechnology, Yield (chemistry), Organic chemistry, D-Xylulose, Molecular Biology, Glycolic acid, 0105 earth and related environmental sciences, Biotechnology
Abstract: Glycolic acid (GA) is an alpha-hydroxy acid with a wide range of chemical and pharmaceutical applications...
Published: 2016

31. Evidence for a Role for the Plasma Membrane in the Nanomechanical Properties of the Cell Wall as Revealed by an Atomic Force Microscopy Study of the Response of Saccharomyces cerevisiaeto Ethanol Stress

Author: Hélène Martin-Yken, Carolina Elsztein, Jean Marie François, Marion Schiavone, Marie-Ange Teste, Etienne Dague, Cécile Formosa-Dague, Marcos de Morais, Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés (LISBP), Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Équipe Ingénierie pour les sciences du vivant (LAAS-ELIA), Laboratoire d'analyse et d'architecture des systèmes (LAAS), Université Toulouse Capitole (UT Capitole), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université Toulouse - Jean Jaurès (UT2J), Université de Toulouse (UT)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université Toulouse Capitole (UT Capitole), Université de Toulouse (UT), Department of Genetics, Universidade Federal de Pernambuco [Recife] (UFPE), Region Midi Pyrenees [10051296], Direction Generale de l'Armement (DGA), CIFRE grant from ANRT, CAPES-FACEPE/PNPD program [681/2011, APQ-0201-2.02/10], Lallemand Inc., ANR-11-JSV5-0001,AFMYST,Etude Biophysique, biochimique et biomoléculaire de la paroi des levures.(2011), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse 1 Capitole (UT1), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse 1 Capitole (UT1), Université Fédérale Toulouse Midi-Pyrénées, Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de la Recherche Agronomique (INRA), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse 1 Capitole (UT1)-Université Toulouse - Jean Jaurès (UT2J)-Institut National Polytechnique (Toulouse) (Toulouse INP), and Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse 1 Capitole (UT1)-Université Toulouse - Jean Jaurès (UT2J)
Subjects: 0301 basic medicine, Physiology, Saccharomyces cerevisiae, Microscopy, Atomic Force, Applied Microbiology and Biotechnology, Cell membrane, Cell wall, 03 medical and health sciences, chemistry.chemical_compound, Cell Wall, medicine, Transcription factor, Ethanol, Ecology, biology, Cell Membrane, Wild type, biology.organism_classification, Yeast, 030104 developmental biology, Membrane, medicine.anatomical_structure, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Biochemistry, chemistry, Biophysics, Food Science, Biotechnology
Abstract: A wealth of biochemical and molecular data have been reported regarding ethanol toxicity in the yeast Saccharomyces cerevisiae . However, direct physical data on the effects of ethanol stress on yeast cells are almost nonexistent. This lack of information can now be addressed by using atomic force microscopy (AFM) technology. In this report, we show that the stiffness of glucose-grown yeast cells challenged with 9% (vol/vol) ethanol for 5 h was dramatically reduced, as shown by a 5-fold drop of Young's modulus. Quite unexpectedly, a mutant deficient in the Msn2/Msn4 transcription factor, which is known to mediate the ethanol stress response, exhibited a low level of stiffness similar to that of ethanol-treated wild-type cells. Reciprocally, the stiffness of yeast cells overexpressing MSN2 was about 35% higher than that of the wild type but was nevertheless reduced 3- to 4-fold upon exposure to ethanol. Based on these and other data presented herein, we postulated that the effect of ethanol on cell stiffness may not be mediated through Msn2/Msn4, even though this transcription factor appears to be a determinant in the nanomechanical properties of the cell wall. On the other hand, we found that as with ethanol, the treatment of yeast with the antifungal amphotericin B caused a significant reduction of cell wall stiffness. Since both this drug and ethanol are known to alter, albeit by different means, the fluidity and structure of the plasma membrane, these data led to the proposition that the cell membrane contributes to the biophysical properties of yeast cells. IMPORTANCE Ethanol is the main product of yeast fermentation but is also a toxic compound for this process. Understanding the mechanism of this toxicity is of great importance for industrial applications. While most research has focused on genomic studies of ethanol tolerance, we investigated the effects of ethanol at the biophysical level and found that ethanol causes a strong reduction of the cell wall rigidity (or stiffness). We ascribed this effect to the action of ethanol perturbing the cell membrane integrity and hence proposed that the cell membrane contributes to the cell wall nanomechanical properties.
Published: 2016

32. High-fat diet increases ghrelin-expressing cells in stomach, contributing to obesity

Author: Charlène Guérin, Nicolas Lucas, Sergueï O. Fetissov, Saïda Azhar, Moïse Coëffier, Tomas Hökfelt, Mohammed el Dhaybi, Swapnali Barde, Marie François, Romain Legrand, Pierre Déchelotte, Nutrition, inflammation et dysfonctionnement de l'axe intestin-cerveau (ADEN), Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institute for Research and Innovation in Biomedicine (IRIB), Normandie Université (NU)-Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), Karolinska Institutet [Stockholm], CHU Rouen, and Normandie Université (NU)
Subjects: Male, 0301 basic medicine, medicine.medical_specialty, Globulin, Endocrinology, Diabetes and Metabolism, 030209 endocrinology & metabolism, In situ hybridization, Diet, High-Fat, Immunoglobulin G, Mice, 03 medical and health sciences, 0302 clinical medicine, Orexigenic, Internal medicine, medicine, Animals, RNA, Messenger, Obesity, Autoantibodies, 2. Zero hunger, Nutrition and Dietetics, biology, Stomach, digestive, oral, and skin physiology, medicine.disease, Ghrelin, Mice, Inbred C57BL, Disease Models, Animal, 030104 developmental biology, Endocrinology, medicine.anatomical_structure, High-fat diet, Gastric Mucosa, biology.protein, Antibody, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, hormones, hormone substitutes, and hormone antagonists, medicine.drug
Abstract: International audience; ObjectivesMechanisms of high-fat diet (HFD)–induced obesity may involve ghrelin, an orexigenic and adipogenic hormone secreted by the stomach. Previous studies showed that obese subjects may display higher numbers of ghrelin-producing cells and increased affinity of plasma immunoglobulins (Ig) for ghrelin, protecting it from degradation. The aim of this study was to determine if a HFD in mice would increase the number of ghrelin-expressing cells and affinity of ghrelin-reactive IgG.MethodsObesity in mice was induced by consumption of a 13-wk HFD. The number of preproghrelin mRNA-expressing cells in the stomach was analyzed by in situ hybridization and compared with chow-fed, nonobese controls and with genetically obese ob/ob mice. Affinity of ghrelin-reactive IgG was analyzed using surface plasmon resonance. Plasma levels of ghrelin and des-acyl ghrelin were measured.ResultsHFD resulted in 30% of body fat content versus only 8% in controls (P < 0.001). The number of preproghrelin mRNA-producing cells was 15% (P < 0.05) higher in HFD-fed mice than in controls, contrasting with ob/ob mice, having a 41% (P < 0.001) decrease. Both models of obesity had normal plasma levels of ghrelin but a decrease of its des-acylated form. Ghrelin-reactive IgG affinity was found in the micromolar range with mean values of the dissociation equilibrium constant 1.5-fold (P < 0.05) lower in HFD-fed versus control mice.ConclusionResults from the present study showed that HFD in mice induces obesogenic changes, including increased numbers of ghrelin precursor-expressing cells and increased affinity of ghrelin-reactive IgG. Such changes may contribute to the mechanisms of HFD-induced obesity.
Published: 2016

33. Cell Surface Interference with Plasma Membrane and Transport Processes in Yeasts

Author: Jean Marie François, Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés (LISBP), Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de la Recherche Agronomique (INRA), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées, Institut National Polytechnique (Toulouse) (Toulouse INP), Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), and Université de Toulouse (UT)
Subjects: 0301 basic medicine, [SDV]Life Sciences [q-bio], 030106 microbiology, Cell, Saccharomyces cerevisiae, Transport, Cell surface, Cell membrane, Cell wall, 03 medical and health sciences, Yeasts, medicine, Membrane fluidity, Metal ions, biology, Membrane, biology.organism_classification, Transport protein, Membrane glycoproteins, medicine.anatomical_structure, Biochemistry, Biosorption, Biophysics, biology.protein, Porosity
Abstract: The wall of the yeast Saccharomyces cerevisiae is a shell of about 120 nm thick, made of two distinct layers, which surrounds the cell. The outer layer is constituted of highly glycosylated proteins and the inner layer is composed of beta-glucan and chitin. These two layers are interconnected through covalent linkages leading to a supramolecular architecture that is characterized by physical and chemical properties including rigidity, porosity and biosorption. The later property results from the presence of highly negative charged phosphate and carboxylic groups of the cell wall proteins, allowing the cell wall to act as an efficient barrier to metals ions, toxins and organic compounds. An intimate connection between cell wall and plasma membrane is indicated by the fact that changes in membrane fluidity results in change in cell wall nanomechanical properties. Finally, cell wall contributes to transport processes through the use of dedicated cell wall mannoproteins, as it is the case for Fit proteins implicated in the siderophore-iron bound transport and the Tir/Dan proteins family in the uptake of sterols.
Published: 2016

34. The synthetic xylulose-1 phosphate pathway increases production of glycolic acid from xylose-rich sugar mixtures

Author: Jean Marie François, Thomas Walther, Lucie Spina, Ceren Alkim, Debora Trichez, Yvan Cam, Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés (LISBP), Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de la Recherche Agronomique (INRA), Toulouse White Biotechnology (TWB), Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Toulouse White Biotechnology (TWB) consortium (Project: PENTOSYS), CAPES foundation (Ministry of Education, Brazil), Institut National de la Recherche Agronomique-Region Midi-Pyrenees (INRA, France), Alkim, Ceren, Walther, Thomas, and Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, Stereochemistry, [SDV]Life Sciences [q-bio], Glyoxylate cycle, Management, Monitoring, Policy and Law, Xylose, Escherichia coli, Glycolic acid, Synthetic pathway, Glucose, Applied Microbiology and Biotechnology, Hydrolysate, 03 medical and health sciences, chemistry.chemical_compound, Sugar, Xylulose, Renewable Energy, Sustainability and the Environment, Research, Phosphate, 030104 developmental biology, General Energy, chemistry, Biochemistry, Yield (chemistry), Biotechnology
Abstract: Background: Glycolic acid (GA) is a two-carbon hydroxyacid with applications in the cosmetic, textile, and medical industry. Microbial GA production from all sugars can be achieved by engineering the natural glyoxylate shunt. The synthetic (D)-xylulose-1 phosphate (X1P) pathway provides a complementary route to produce GA from (D)-xylose. The simultaneous operation of the X1P and glyoxylate pathways increases the theoretical GA yield from xylose by 20 %, which may strongly improve GA production from hemicellulosic hydrolysates. Results: We herein describe the construction of an E. coli strain that produces GA via the glyoxylate pathway at a yield of 0.31, 0.29, and 0.37 g/g from glucose, xylose, or a mixture of glucose and xylose ( mass ratio: 33: 66 %), respectively. When the X1P pathway operates in addition to the glyoxylate pathway, the GA yields on the three substrates are, respectively, 0.39, 0.43, and 0.47 g/g. Upon constitutive expression of the sugar permease GalP, the GA yield of the strain which simultaneously operates the glyoxylate and X1P pathways further increases to 0.63 g/g when growing on the glucose/ xylose mixture. Under these conditions, the GA yield on the xylose fraction of the sugar mixture reaches 0.75 g/g, which is the highest yield reported to date. Conclusions: These results demonstrate that the synthetic X1P pathway has a very strong potential to improve GA production from xylose-rich hemicellulosic hydrolysates.
Published: 2016

35. Microbial production of propanol

Author: Jean Marie François, Thomas Walther, Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés (LISBP), Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Université Fédérale Toulouse Midi-Pyrénées, Université Toulouse III - Paul Sabatier (UT3), Institut National Polytechnique (Toulouse) (Toulouse INP), Toulouse White Biotechnology (TWB), Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de la Recherche Agronomique (INRA), ANR-10-BTBR-0005,SYNTHACS,Biologie Synthétique pour la synthèse de molécules chimiques à haute valeur ajoutée à partir de ressources carbonées renouvelables(2010), Agence Nationale de la Recherche (Investissements d'Avenir program) [ANR 10-BTBR-05 -01], Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), and Université de Toulouse (UT)
Subjects: 0301 basic medicine, Propanols, Microorganism, [SDV]Life Sciences [q-bio], Bioengineering, Isopropanol, 7. Clean energy, Applied Microbiology and Biotechnology, Chemical synthesis, Metabolic engineering, Propanol, 03 medical and health sciences, chemistry.chemical_compound, Biofuel, Yeasts, Organic chemistry, Synthetic biology, N-Propanol, Bacteria, integumentary system, Chemistry, n-propanol, 030104 developmental biology, Chemical engineering, 13. Climate action, Biofuels, Fermentation, Biotechnology, Renewable resource
Abstract: Both, n-propanol and isopropanol are industrially attractive value-added molecules that can be produced by microbes from renewable resources. The development of cost-effective fermentation processes may allow using these alcohols as a biofuel component, or as a precursor for the chemical synthesis of propylene. This review reports and discusses the recent progress which has been made in the biochemical production of propanol. Several synthetic propanol-producing pathways were developed that vary with respect to stoichiometry and metabolic entry point. These pathways were expressed in different host organisms and enabled propanol production from various renewable feedstocks. Furthermore, it was shown that the optimization of fermentation conditions greatly improved process performance, in particular, when continuous product removal prevented accumulation of toxic propanol levels. Although these advanced metabolic engineering and fermentation strategies have facilitated significant progress in the biochemical production of propanol, the currently achieved propanol yields and productivities appear to be insufficient to compete with chemical propanol synthesis. The development of biosynthetic pathways with improved propanol yields, the breeding or identification of microorganisms with higher propanol tolerance, and the engineering of propanol producer strains that efficiently utilize low-cost feedstocks are the major challenges on the way to industrially relevant microbial propanol production processes.
Published: 2016

36. Circadian RNA expression elicited by 3’-UTR IRAlu-paraspeckle associated elements

Author: Marie-Pierre Blanchard, Jean-Louis Franc, Séverine Guillen, Bénédicte Boyer, Anne-Marie François-Bellan, Mathias Moreno, Manon Torres, Denis Becquet, Centre de recherche en neurobiologie - neurophysiologie de Marseille (CRN2M), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), and Becquet, Denis
Subjects: 0301 basic medicine, Untranslated region, circadian rhythm, Intravital Microscopy, QH301-705.5, Science, [SDV.NEU.NB]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Neurobiology, Green Fluorescent Proteins, RNA-binding protein, Biology, General Biochemistry, Genetics and Molecular Biology, Cell Line, 03 medical and health sciences, Paraspeckles, Genes, Reporter, Gene expression, Animals, Biology (General), 3' Untranslated Regions, Genetics, Regulation of gene expression, Microscopy, Video, General Immunology and Microbiology, General Neuroscience, pituitary cells, Inverted Repeat Sequences, [SDV.NEU.NB] Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Neurobiology, RNA, Nuclear Proteins, RNA-Binding Proteins, Paraspeckle, General Medicine, circadian oscillators, Cell Biology, paraspeckle, Bacterial circadian rhythms, Cell biology, Rats, 030104 developmental biology, Gene Expression Regulation, Genes and Chromosomes, nuclear RNA retention, Medicine, RNA, Long Noncoding, Other, Research Article
Abstract: Paraspeckles are nuclear bodies form around the long non-coding RNA, Neat1, and RNA-binding proteins. While their role is not fully understood, they are believed to control gene expression at a post-transcriptional level by means of the nuclear retention of mRNA containing in their 3’-UTR inverted repeats of Alu sequences (IRAlu). In this study, we found that, in pituitary cells, all components of paraspeckles including four major proteins and Neat1 displayed a circadian expression pattern. Furthermore the insertion of IRAlu at the 3’-UTR of the EGFP cDNA led to a rhythmic circadian nuclear retention of the egfp mRNA that was lost when paraspeckles were disrupted whereas insertion of a single antisense Alu had only a weak effect. Using real-time video-microscopy, these IRAlu were further shown to drive a circadian expression of EGFP protein. This study shows that paraspeckles, thanks to their circadian expression, control circadian gene expression at a post-transcriptional level. DOI: http://dx.doi.org/10.7554/eLife.14837.001, eLife digest Many biological features of animals, including body temperature and hormone levels, follow daily rhythms that repeat every 24 hours. These so-called circadian rhythms are driven by an internal body clock and are essential for the organism to adapt to the daily cycle of light and dark. Circadian rhythms also take place inside individual cells – for example, the amount of a given protein in a cell often rises and falls over each 24-hour period. To generate these daily fluctuations, the processes used to make proteins based on the instructions encoded within a gene must be carefully controlled. Genes are first copied or ‘transcribed' into intermediate molecules called messenger RNAs (mRNAs). These mRNA molecules must then travel out of the cell’s nucleus before they can be de-coded to produce proteins. This means that daily fluctuations in mRNA and protein levels could occur because the rate at which the DNA is transcribed fluctuates or because controlling the steps that occur after transcription. However it is not clear how much these post-transcriptional steps contribute to circadian rhythms inside cells. Recently, structures called paraspeckles were seen inside the nucleus. These structures are made from a long RNA molecule that does not code for a protein, and a number of proteins that can bind mRNA molecules. Paraspeckles are thought to prevent certain mRNAs from leaving the nucleus and therefore stop them from being decoded to make proteins. Torres et al. have now investigated whether paraspeckles may play a role in circadian rhythms. Torres et al. looked at the long non-coding RNA and several proteins that are known to be components of paraspeckles in cells taken from the pituitary glands of rats using a variety of techniques. These cells were chosen because they were known to have a working circadian clock. The analysis showed that the levels of these components, as well as the number of paraspeckles within the nucleus, changed over the course of a daily cycle. Torres et al. then confirmed that mRNAs containing a sequence that is known to recruit mRNAs to paraspeckes (the IRAlu sequence) could be also retained in the nucleus or released with a circadian rhythm. This pattern was lost when the paraspeckles were disrupted. These findings suggest that daily fluctuations in protein levels can be post-transcriptionally controlled by paraspeckles rhythmically retaining mRNAs in the nucleus. Future studies could explore whether it may be possible to control circadian rhythms by targeting the paraspeckles, which could help to improve conditions where the internal body clock goes wrong. DOI: http://dx.doi.org/10.7554/eLife.14837.002
Published: 2016

37. Fuzzy logic selection as a new reliable tool to identify molecular grade signatures in breast cancer – the INNODIAG study

Author: Carine Valle, Tatiana Kempowsky-Hamon, Jean-Marie François, Gilles Favre, Delphine Labourdette, Sophie Lamarre, Magali Lacroix-Triki, Marie-Véronique Le Lann, Loubna Mhamdi, Lidwine Trouilh, Lyamine Hedjazi, Thomas Filleron, Florence Dalenc, Véronique Anton-Leberre, Laurence Roger, Équipe DIagnostic, Supervision et COnduite (LAAS-DISCO), Laboratoire d'analyse et d'architecture des systèmes (LAAS), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse 1 Capitole (UT1)-Université Toulouse - Jean Jaurès (UT2J)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse 1 Capitole (UT1)-Université Toulouse - Jean Jaurès (UT2J), Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés (LISBP), Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de la Recherche Agronomique (INRA), Institut Claudius Regaud, CRLCC Institut Claudius Regaud, Centre de Recherches en Cancérologie de Toulouse (CRCT), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Dendris SAS, Département d'oncologie médicale, Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse 1 Capitole (UT1), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse 1 Capitole (UT1), Université Fédérale Toulouse Midi-Pyrénées, Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), National Research Agency (Agence National pour la Recherche), 'BIOTECHNOLOGIES' program [ANR 2010 BIOT 004 06], 'pole de competitivite' Cancer-Bio-Sante from Midi Pyrenees, France, ANR, Laboratoire d'analyse et d'architecture des systèmes [Toulouse] ( LAAS ), Centre National de la Recherche Scientifique ( CNRS ) -Université Toulouse III - Paul Sabatier ( UPS ), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National des Sciences Appliquées - Toulouse ( INSA Toulouse ), Institut National des Sciences Appliquées ( INSA ) -Institut National des Sciences Appliquées ( INSA ) -Institut National Polytechnique [Toulouse] ( INP ), Institut des Maladies Métaboliques et Cardiovasculaires ( I2MC ), Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Hôpital de Rangueil, CHU Toulouse [Toulouse]-CHU Toulouse [Toulouse]-Université Toulouse III - Paul Sabatier ( UPS ), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Équipe DIagnostic, Supervision et COnduite ( LAAS-DISCO ), Institut National des Sciences Appliquées ( INSA ) -Institut National des Sciences Appliquées ( INSA ) -Institut National Polytechnique [Toulouse] ( INP ) -Centre National de la Recherche Scientifique ( CNRS ) -Université Toulouse III - Paul Sabatier ( UPS ), Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés ( LISBP ), Institut National de la Recherche Agronomique ( INRA ) -Institut National des Sciences Appliquées - Toulouse ( INSA Toulouse ), Institut National des Sciences Appliquées ( INSA ) -Institut National des Sciences Appliquées ( INSA ) -Centre National de la Recherche Scientifique ( CNRS ), Departement /u563 : Oncogenèse, Signalisation et Innovation thérapeutique, Centre de Physiopathologie Toulouse Purpan (ex IFR 30 et IFR 150), Université Toulouse III - Paul Sabatier ( UPS ), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-IFR30-IFR150-Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Université Toulouse III - Paul Sabatier ( UPS ), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-IFR30-IFR150-Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Institut Claudius Regaud, Department of Radiation Oncology and Medical Physics, Université Toulouse Capitole (UT Capitole), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université Toulouse - Jean Jaurès (UT2J), Université de Toulouse (UT)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université Toulouse Capitole (UT Capitole), Université de Toulouse (UT), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), and Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Oncology, [SDV]Life Sciences [q-bio], Bioinformatics, [ SDV.CAN ] Life Sciences [q-bio]/Cancer, Cohort Studies, Breast cancer, Databases, Genetic, Genetics(clinical), Precision Medicine, [ SDV.BIBS ] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Genetics (clinical), ComputingMilieux_MISCELLANEOUS, Oligonucleotide Array Sequence Analysis, Gene signatures, Prognosis, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], 3. Good health, Gene Expression Regulation, Neoplastic, Molecular grade, Female, DNA microarray, Algorithms, Research Article, medicine.medical_specialty, Decision Making, Breast Neoplasms, [SDV.CAN]Life Sciences [q-bio]/Cancer, Fuzzy logic, Sensitivity and Specificity, [ INFO.INFO-LG ] Computer Science [cs]/Machine Learning [cs.LG], Text mining, Internal medicine, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], medicine, Genetics, Humans, Neoplasm Invasiveness, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, [ INFO.INFO-AI ] Computer Science [cs]/Artificial Intelligence [cs.AI], business.industry, Gene Expression Profiling, Computational Biology, Reproducibility of Results, Gene signature, Precision medicine, medicine.disease, Gene expression profiling, Personalized medicine, Neoplasm Recurrence, Local, business
Abstract: Background Personalized medicine has become a priority in breast cancer patient management. In addition to the routinely used clinicopathological characteristics, clinicians will have to face an increasing amount of data derived from tumor molecular profiling. The aims of this study were to develop a new gene selection method based on a fuzzy logic selection and classification algorithm, and to validate the gene signatures obtained on breast cancer patient cohorts. Methods We analyzed data from four published gene expression datasets for breast carcinomas. We identified the best discriminating genes by comparing molecular expression profiles between histologic grade 1 and 3 tumors for each of the training datasets. The most pertinent probes were selected and used to define fuzzy molecular grade 1-like (good prognosis) and fuzzy molecular grade 3-like (poor prognosis) profiles. To evaluate the prognostic performance of the fuzzy grade signatures in breast cancer tumors, a Kaplan-Meier analysis was conducted to compare the relapse-free survival deduced from histologic grade and fuzzy molecular grade classification. Results We applied the fuzzy logic selection on breast cancer databases and obtained four new gene signatures. Analysis in the training public sets showed good performance of these gene signatures for grade (sensitivity from 90% to 95%, specificity 67% to 93%). To validate these gene signatures, we designed probes on custom microarrays and tested them on 150 invasive breast carcinomas. Good performance was obtained with an error rate of less than 10%. For one gene signature, among 74 histologic grade 3 and 18 grade 1 tumors, 88 cases (96%) were correctly assigned. Interestingly histologic grade 2 tumors (n = 58) were split in these two molecular grade categories. Conclusion We confirmed the use of fuzzy logic selection as a new tool to identify gene signatures with good reliability and increased classification power. This method based on artificial intelligence algorithms was successfully applied to breast cancers molecular grade classification allowing histologic grade 2 classification into grade 1 and grade 2 like to improve patients prognosis. It opens the way to further development for identification of new biomarker combinations in other applications such as prediction of treatment response. Electronic supplementary material The online version of this article (doi:10.1186/s12920-015-0077-1) contains supplementary material, which is available to authorized users.
Published: 2015

38. Combining atomic force microscopy and genetics to investigate the role of KNR4 inSaccharomyces Cerevisiae sensitivity to K9 killer toxin

Author: Ran Liu, Cécile Formosa-Dague, Adilia Dagkessamanskaia, Etienne Dague, Jean Marie François, Hélène Martin-Yken, Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés (LISBP), Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Équipe NanoBioSystèmes (LAAS-NBS), Laboratoire d'analyse et d'architecture des systèmes (LAAS), Université Toulouse Capitole (UT Capitole), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université Toulouse - Jean Jaurès (UT2J), Université de Toulouse (UT)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université Toulouse Capitole (UT Capitole), Université de Toulouse (UT), Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de la Recherche Agronomique (INRA), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse 1 Capitole (UT1)-Université Toulouse - Jean Jaurès (UT2J)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse 1 Capitole (UT1)-Université Toulouse - Jean Jaurès (UT2J), Yken, Helene, Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse 1 Capitole (UT1), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse 1 Capitole (UT1), and Université Fédérale Toulouse Midi-Pyrénées
Subjects: [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, MESH: K9 killer toxin, Saccharomyces cerevisiae, KNR4 gene deletion, Atomic Force Microscopy, Autre (Sciences du Vivant)
Abstract: International audience; K9 killer toxin is a small peptide secreted by the yeast Williopsis saturnus var: mrakii (previously known as Hansenula mrakii) with a strong cytocidal activity against sensitive yeast strains, including Saccharomyces cerevisiae. Treatment with this toxin results in the formation of pores at the surface of the cells, and more specifically at places where cell wall synthesis is the most active, namely at the tip of growing buds or mating projections. Yeast cells treated with K9 toxin then die by releasing cytoplasm and cellular materials from these pores. In the yeast S. cerevisiae, KNR4 protein localizes at the sites of polarized growth (bud tips, shmoo tips), which are also the sites where the toxin forms pores in the cell wall. Mutants defective in KNR4 gene are remarkably resistant to this toxin. In this study, we analyzed for the first time the biophysical effects of K9 on the yeast cell wall using Atomic Force Microscopy (AFM), a cutting edge technology that allows measuring the nanomechanical properties of living yeast cells, and their alterations by various drugs. To this end, we measured the effects of K9 toxin on the nanomechanical properties of the cell wall of S. cerevisiae wild-type cells and mutants deleted for KNR4 gene, at the short (2 h) and long term (20 h). Our results reveal an important cell wall remodeling occurring in wild- type cells already after 2 hours and only visible in knr4 mutant after 20 hours of treatment. Moreover, we investigated the role of Knr4 protein in the cells sensitivity towards the toxin. We were able to show that the presence of the N-terminal domain of Knr4 protein, which is required for its correct cellular localization at the bud tip during cell cycle, is essential for the toxin K9 wild-type sensitivity. In addition, a series of deletion mutants from the YKO collection in which the Knr4 cellular localization is also lost display a reduced sensitivity to the K9 toxin. Taken together, these results shed light on the importance of the proper localization of Knr4 protein at sites of intensive cell wall growth for the wild-type cells sensitivity to K9 killer toxin.
Published: 2015

39. Remodeling of glial coverage of glutamatergic synapses in the rat nucleus tractus solitarii after ozone inhalation

Author: Jean-Pierre Kessler, Caroline Strube, Virginie Penalba, Olivier Bosler, Keodavanh Chounlamountry, Bénédicte Boyer, Anne-Marie François-Bellan, Centre de recherche en neurobiologie - neurophysiologie de Marseille (CRN2M), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut de neurophysiopathologie (INP), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS), Laboratoire de neurophysiologie cellulaire (LNPC), Université de la Méditerranée - Aix-Marseille 2-Centre National de la Recherche Scientifique (CNRS), and Dumonceaud, Corinne
Subjects: Male, [SDV]Life Sciences [q-bio], [SDV.NEU.NB]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Neurobiology, air pollution, Biochemistry, 0302 clinical medicine, central nervous system CNS, glutamine synthase, O 3, ComputingMilieux_MISCELLANEOUS, 0303 health sciences, Air Pollutants, Neuronal Plasticity, Glial fibrillary acidic protein, biology, GFAP, medicine.anatomical_structure, Excitatory Amino Acid Transporter 2, [SDV.NEU]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC], Astrocyte, NTS, brain, Central nervous system, Glutamic Acid, Nerve Tissue Proteins, S100 Calcium Binding Protein beta Subunit, glutamate transporter 1, 03 medical and health sciences, Cellular and Molecular Neuroscience, Glutamatergic, Glutamate-Ammonia Ligase, Administration, Inhalation, Glial Fibrillary Acidic Protein, medicine, Solitary Nucleus, Animals, Rats, Wistar, nucleus tractus solitarii, 030304 developmental biology, Lung, business.industry, [SDV.NEU.NB] Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Neurobiology, astrocytes, Vagus nerve, Rats, Cytoskeletal Proteins, ozone, nervous system, Synapses, biology.protein, GLT1, business, Neuroscience, Nucleus, 030217 neurology & neurosurgery, Biomarkers, Respiratory tract
Abstract: International audience; Besides the well-described inflammatory and dysfunction effects on the respiratory tract, accumulating evidence indicates that ozone (O3 ) exposure also affects central nervous system functions. However, the mechanisms through which O3 exerts toxic effects on the brain remain poorly understood. We previously showed that O3 exposure caused a neuronal activation in regions of the rat nucleus tractus solitarii (NTS) overlapping terminal fields of vagal lung afferents. Knowing that O3 exposure can impact astrocytic protein expression, we decided to investigate whether it may induce astroglial cellular alterations in the NTS. Using electron microscopy and immunoblot techniques, we showed that in O3 -exposed animals, the astrocytic coverage of NTS glutamatergic synapses was 19% increased while the astrocyte volume fraction and membrane density were not modified. Moreover, the expression of glial fibrillary acidic protein and S100β, which are known to be increased in reactive astroglia, did not change. These results indicate that O3 inhalation induces a glial plasticity that is restricted to the peri-synaptic coverage without overall astroglial activation. Taken together, these findings, along with our previous observations, support the conclusion that O3 -induced pulmonary inflammation results in a specific activation of vagal lung afferents rather than non-specific overall brain alterations mediated by blood-borne agents. Exposure to ozone, a major atmospheric pollutant, induces an increase in the glial coverage of neurons that is restricted to peri-synaptic compartments. This observation does not support the view that the ozone-induced neuronal disorders are related to non-specific overall brain alterations. It rather argues for a specific activation of the vagus nerve in response to pulmonary inflammation.
Published: 2015

40. Structural plasticity of the circadian timing system. An overview from flies to mammals

Author: Anne-Marie François-Bellan, Jean-Louis Franc, Olivier Bosler, Clémence Girardet, Denis Becquet, Centre de recherche en neurobiologie - neurophysiologie de Marseille (CRN2M), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), and Dumonceaud, Corinne
Subjects: Neuronal Plasticity, Endocrine and Autonomic Systems, Suprachiasmatic nucleus, Circadian clock, Vertebrate, Biology, Adaptation, Physiological, Paraspeckles, Circadian Rhythm, biology.animal, Circadian Clocks, Neuroplasticity, Animals, Humans, Master clock, Suprachiasmatic Nucleus, Circadian rhythm, sense organs, Adaptation, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], skin and connective tissue diseases, Neuroscience, [SDV.BBM.BC] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM]
Abstract: International audience; The circadian timing system orchestrates daily variations in physiology and behavior through coordination of multioscillatory cell networks that are highly plastic in responding to environmental changes. Over the last decade, it has become clear that this plasticity involves structural changes and that the changes may be observed not only in central brain regions where the master clock cells reside but also in clock-controlled structures. This review considers experimental data in invertebrate and vertebrate model systems, mainly flies and mammals, illustrating various forms of structural circadian plasticity from cellular to circuit-based levels. It highlights the importance of these plastic events in the functional adaptation of the clock to the changing environment.
Published: 2015

41. Ghrelin-reactive immunoglobulins and anxiety, depression and stress-induced cortisol response in adolescents. The TRAILS study

Author: Marie François, Johanna M. Schaefer, Pierre Déchelotte, Sergueï O. Fetissov, Frank C. Verhulst, Christine Bole-Feysot, Nutrition, inflammation et dysfonctionnement de l'axe intestin-cerveau (ADEN), Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institute for Research and Innovation in Biomedicine (IRIB), Normandie Université (NU)-Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), UNIROUEN - UFR Santé (UNIROUEN UFR Santé), Normandie Université (NU)-Normandie Université (NU), Department of Child and Adolescent Psychiatry & Psychology, Erasmus Medical Center, Rotterdam, The Netherlands., Service de nutrition [CHU Rouen], CHU Rouen, Normandie Université (NU)-Normandie Université (NU)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU), and Child and Adolescent Psychiatry / Psychology
Subjects: Male, Cortisol secretion, medicine.medical_specialty, Adolescent, Hydrocortisone, Population, Immunoglobulins, Anxiety, medicine.disease_cause, Sex Factors, SDG 3 - Good Health and Well-being, Internal medicine, Orexigenic, Influenza, Human, Influenza A virus, medicine, Humans, Simplexvirus, Saliva, education, Biological Psychiatry, ComputingMilieux_MISCELLANEOUS, Pharmacology, education.field_of_study, biology, Depression, digestive, oral, and skin physiology, Autoantibody, Ghrelin, 3. Good health, Endocrinology, Immunology, biology.protein, Female, medicine.symptom, Antibody, Psychology, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, Stress, Psychological, hormones, hormone substitutes, and hormone antagonists, medicine.drug
Abstract: Background: Ghrelin, a hunger hormone, has been implicated in the regulation of stress-response, anxiety and depression. Ghrelin-reactive immunoglobulins (Ig) were recently identified in healthy and obese humans showing abilities to increase ghrelin's stability and orexigenic effects. Here we studied if ghrelin-reactive Ig are associated with anxiety and depression and with the stress-induced cortisol response in a general population of adolescents. Furthermore, to test the possible infectious origin of ghrelin-reactive Ig, their levels were compared with serum IgG against common viruses. Methods: We measured ghrelin-reactive IgM, IgG and IgA in serum samples of 1199 adolescents from the Dutch TRAILS study and tested their associations with 1) anxiety and depression symptoms assessed with the Youth Self-Report, 2) stress-induced salivary cortisol levels and 3) IgG against human herpesvirus 1, 2, 4 and 6 and Influenza A and B viruses. Results: Ghrelin-reactive IgM and IgG correlated positively with levels of antibodies against Influenza A virus. Ghrelin-reactive IgM correlated negatively with antibodies against Influenza B virus. Ghrelin-reactive IgM correlated positively with anxiety scores in girls and ghrelin-reactive IgG correlated with stress-induced cortisol secretion, but these associations were weak and not significant after correction for multiple testing. Conclusion: These data indicate that production of ghrelin-reactive autoantibodies could be influenced by viral infections. Serum levels of ghrelin-reactive autoantibodies probably do not play a role in regulating anxiety, depression and the stress-response in adolescents from the general population. (C) 2015 Elsevier Inc. All rights reserved.
Published: 2015

42. Natural Yeast Promoter Variants Reveal Epistasis in the Generation of Transcriptional-Mediated Noise and Its Potential Benefit in Stressful Conditions

Author: Jean-Pascal Capp, Jean-Marie François, Hélène Martin-Yken, Sylvie Dequin, Frederic Bigey, Jian Liu, Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés (LISBP), Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Sciences Pour l'Oenologie (SPO), Institut National de la Recherche Agronomique (INRA)-Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Institut de Recherche pour le Développement (IRD [Nouvelle-Calédonie])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université Montpellier 1 (UM1)-Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA), Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de la Recherche Agronomique (INRA), Université Montpellier 1 (UM1)-Institut de Recherche pour le Développement (IRD [Nouvelle-Calédonie])-Institut National de la Recherche Agronomique (INRA)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Capp, Jean-Pascal, Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), and Université Montpellier 1 (UM1)-Institut National de la Recherche Agronomique (INRA)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)
Subjects: [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Transcription, Genetic, stochastic gene expression, stress resistance and tolerance, [SDV]Life Sciences [q-bio], Saccharomyces cerevisiae, variabilité phénotypique, résistance au stress, 03 medical and health sciences, souche industrielle, Stress, Physiological, Gene Expression Regulation, Fungal, industrial wine yeast, Genetic variation, Gene expression, Genetics, saccharomyces cerevisiae, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Promoter Regions, Genetic, expression du génome, Gene, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, 0303 health sciences, Vegetal Biology, biology, 030302 biochemistry & molecular biology, Genetic Variation, Epistasis, Genetic, Promoter, biology.organism_classification, Phenotype, Agricultural sciences, Noise, protéine, copper, phenotypic variability and heterogeneity, Epistasis, Genome, Fungal, tolérance au stress, Biologie végétale, Sciences agricoles, Research Article
Abstract: International audience; The increase in phenotypic variability through gene expression noise is proposed to be an evolutionary strategy in selective environments. Differences in promoter-mediated noise between Saccharomyces cerevisiae strains could have been selected for thanks to the benefit conferred by gene expression heterogeneity in the stressful conditions, for instance, those experienced by industrial strains. Here, we used a genome-wide approach to identify promoters conferring high noise levels in the industrial wine strain EC1118. Many promoters of genes related to environmental factors were identified, some of them containing genetic variations compared with their counterpart in the laboratory strain S288c. Each variant of eight promoters has been fused to yeast-Enhanced Green Fluorescent Protein and integrated in the genome of both strains. Some industrial variants conferred higher expression associated, as expected, with lower noise, but other variants either increased or decreased expression without modifying variability, so that they might exhibit different levels of transcriptional-mediated noise at equal mean. At different induction conditions giving similar expression for both variants of the CUP1 promoter, we indeed observed higher noise with the industrial variant. Nevertheless, this difference was only observed in the industrial strain, revealing epistasis in the generation of promoter-mediated noise. Moreover, the increased expression variability conferred by this natural yeast promoter variant provided a clear benefit in the face of an environmental stress. Thus, modulation of gene expression noise by a combination of promoter modifications and trans-influences might be a possible adaptation mechanism in yeast.
Published: 2015

43. Effect of the cultivation mode on red pigments production from [i]Monascus ruber[/i]

Author: Jean Marie François, Hassan Hajjaj, G. Goma, Laboratoire de Biotechnologie Végétale et Biologie Moléculaire, Faculté des Sciences, Université de Moulay Ismail (UMI), Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés (LISBP), Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de la Recherche Agronomique (INRA), Université Moulay Ismail (UMI), Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), and Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, Monascus ruber, [SDV]Life Sciences [q-bio], chemistry.chemical_element, 01 natural sciences, Industrial and Manufacturing Engineering, 03 medical and health sciences, chemistry.chemical_compound, Pigment, 010608 biotechnology, Botany, Food science, Mycotoxin, fermentation, 030304 developmental biology, 0303 health sciences, biology, Citrinin and red pigments, Monascus, biology.organism_classification, Nitrogen, Filamentous fungus, Citrinin, chemistry, visual_art, visual_art.visual_art_medium, Fermentation, Food Science
Abstract: Summary In submerged cultures performed in chemically defined fermentation medium containing glucose and glutamate, the growth and production of water-soluble red pigments and citrinin by the filamentous fungus Monascus ruber were studied under various carbon/nitrogen (C/N) ratios. The specific production of the red pigments was optimal at a glucose/glutamate ratio of about 10 and then steadily decreased at higher C/N ratio. In contrast, the production of the mycotoxin increased with increased C/N with an optimum in the range of 30–45. In a fed-batch mode, it was also found that the production of pigments was not favoured in fed-batch mode by feeding the medium with glucose while keeping the C/N ratio lower than 10. This low production likely resulted from concurrent high accumulation of L-malic acid that was reported to inhibit this production. In contrast, this mode of cultivation was rather favourable for the production of the mycotoxin.
Published: 2015

44. Yeast tolerance to various stresses relies on the Trehalose-6P Synthase (Tps1) protein, not on trehalose

Author: Jean-Marie François, Marie-Ange Teste, Marjorie Petitjean, Jean-Luc Parrou, Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés (LISBP), Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Fondazione Edmund Mach. San Michele All'adige, ITA., Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de la Recherche Agronomique (INRA), Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés ( LISBP ), Institut National de la Recherche Agronomique ( INRA ) -Institut National des Sciences Appliquées - Toulouse ( INSA Toulouse ), Institut National des Sciences Appliquées ( INSA ) -Institut National des Sciences Appliquées ( INSA ) -Centre National de la Recherche Scientifique ( CNRS ), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées, and Grant 10051296 from Region Midi Pyrénées, a CNRS PEP2I grant, and a doctoral grant from the French Ministry of Education and Research
Subjects: RT-qPCR-reference genes, [SDV]Life Sciences [q-bio], Saccharomyces cerevisiae, Mutant, heat shock protein (hsp), Biochemistry, chemistry.chemical_compound, atp, desiccation, oxidative stress, saccharomyces cerevisiae, Molecular Biology, ComputingMilieux_MISCELLANEOUS, chemistry.chemical_classification, biology, ATP synthase, [ SDV ] Life Sciences [q-bio], heat shock factor protein 1 (hsf1), heat shock, viability, RT-qPCR, Trehalose, Cell Biology, biology.organism_classification, Yeast, Normalization, Enzyme, Metabolism, chemistry, biology.protein, Desiccation, Adenosine triphosphate
Abstract: Background: Decades of observations strengthened the idea that trehalose is a chemical chaperone. Results: A catalytically inactive variant of the trehalose-6P synthase (Tps1) maintains cell survival and energy homeostasis under stress exposure. Conclusion: The Tps1 protein itself, not trehalose, is crucial for cell integrity. Significance: This work provides unbiased evidence for an alternative function of Tps1, a new moonlighting protein. Trehalose is a stable disaccharide commonly found in nature, from bacteria to fungi and plants. For the model yeast Saccharomyces cerevisiae, claims that trehalose is a stress protectant were based indirectly either on correlation between accumulation of trehalose and high resistance to various stresses or on stress hypersensitivity of mutants deleted for TPS1, which encodes the first enzyme in trehalose biosynthetic pathway. Our goal was to investigate more directly which one, between trehalose and/or the Tps1 protein, may serve yeast cells to withstand exposure to stress. By employing an original strategy that combined the use of mutant strains expressing catalytically inactive variants of Tps1, with MAL(+) yeast strains able to accumulate trehalose from an exogenous supply, we bring for the first time unbiased proof that trehalose does not protect yeast cells from dying and that the stress-protecting role of trehalose in this eukaryotic model was largely overestimated. Conversely, we identified the Tps1 protein as a key player for yeast survival in response to temperature, oxidative, and desiccation stress. We also showed by robust RT-quantitative PCR and genetic interaction analysis that the role of Tps1 in thermotolerance is not dependent upon Hsf1-dependent transcription activity. Finally, our results revealed that the Tps1 protein is essential to maintain ATP levels during heat shock. Altogether, these findings supported the idea that Tps1 is endowed with a regulatory function in energy homeostasis, which is essential to withstand adverse conditions and maintain cellular integrity.
Published: 2015

45. Tracking the best reference genes for RT-qPCR data normalization in filamentous fungi

Author: Jean-Luc Parrou, Jean Marie François, Agustina Llanos, Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés (LISBP), Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de la Recherche Agronomique (INRA), Adisseo France SAS, CINABio-Adisseo (Adisseo SAS, Antony, France), CIFRE [1558/2010], Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), and Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Normalization (statistics), Candidate gene, Filamentous fungi, Talaromyces, RNA-seq, RT-qPCR, Reference genes, Normalization, Gene expression, In silico, [SDV]Life Sciences [q-bio], Computational biology, Biology, Real-Time Polymerase Chain Reaction, Database normalization, 03 medical and health sciences, Gene Expression Regulation, Plant, Genetics, Gene, Phylogeny, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, 030306 microbiology, Gene Expression Profiling, Fungi, Reference Standards, Molecular biology, Gene expression profiling, RNA, DNA microarray, Research Article, Biotechnology
Abstract: Background A critical step in the RT-qPCR workflow for studying gene expression is data normalization, one of the strategies being the use of reference genes. This study aimed to identify and validate a selection of reference genes for relative quantification in Talaromyces versatilis, a relevant industrial filamentous fungus. Beyond T. versatilis, this study also aimed to propose reference genes that are applicable more widely for RT-qPCR data normalization in filamentous fungi. Results A selection of stable, potential reference genes was carried out in silico from RNA-seq based transcriptomic data obtained from T. versatilis. A dozen functionally unrelated candidate genes were analysed by RT-qPCR assays over more than 30 relevant culture conditions. By using geNorm, we showed that most of these candidate genes had stable transcript levels in most of the conditions, from growth environments to conidial germination. The overall robustness of these genes was explored further by showing that any combination of 3 of them led to minimal normalization bias. To extend the relevance of the study beyond T. versatilis, we challenged their stability together with sixteen other classically used genes such as β-tubulin or actin, in a representative sample of about 100 RNA-seq datasets. These datasets were obtained from 18 phylogenetically distant filamentous fungi exposed to prevalent experimental conditions. Although this wide analysis demonstrated that each of the chosen genes exhibited sporadic up- or down-regulation, their hierarchical clustering allowed the identification of a promising group of 6 genes, which presented weak expression changes and no tendency to up- or down-regulation over the whole set of conditions. This group included ubcB, sac7, fis1 and sarA genes, as well as TFC1 and UBC6 that were previously validated for their use in S. cerevisiae. Conclusions We propose a set of 6 genes that can be used as reference genes in RT-qPCR data normalization in any field of fungal biology. However, we recommend that the uniform transcription of these genes is tested by systematic experimental validation and to use the geometric averaging of at least 3 of the best ones. This will minimize the bias in normalization and will support trustworthy biological conclusions. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1224-y) contains supplementary material, which is available to authorized users.
Published: 2015

46. Optimization of ethylene glycol production from (D)-xylose via a synthetic pathway implemented in Escherichia coli

Author: Ceren Alkim, Clément Auriol, Philippe Besse, Lucie Spina, Amélie Vax, Jean Marie François, Yvan Cam, Francois Bartolo, Debora Trichez, Thomas Walther, Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés (LISBP), Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Toulouse White Biotechnology (TWB), Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de la Recherche Agronomique (INRA), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées, Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA), Toulouse White Biotechnology (TWB) consortium (Project: PENTOSYS), CAPES foundation (Ministry of Education, Brazil), Institut National de la Recherche Agronomique-Region Midi-Pyrenees (INRA, France), Alkim, Ceren, Cam, Yvan, Walther, Thomas, Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Université de Toulouse (UT), and Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)
Subjects: Xylose isomerase, [SDV]Life Sciences [q-bio], Bioengineering, Glycolaldehyde Dehydrogenase, Xylose, Biology, 7. Clean energy, Applied Microbiology and Biotechnology, Metabolic engineering, 03 medical and health sciences, chemistry.chemical_compound, Bioreactors, ingénierie métabolique, Xylose metabolism, [SDV.IDA]Life Sciences [q-bio]/Food engineering, Escherichia coli, [SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering, Ethylene glycol, 030304 developmental biology, 0303 health sciences, Glycolaldehyde, 030306 microbiology, Research, Synthetic metabolic pathway, éthylène glycol, Aldolase A, chemistry, Biochemistry, biology.protein, Metabolic Networks and Pathways, Biotechnology
Abstract: Background Ethylene glycol (EG) is a bulk chemical that is mainly used as an anti-freezing agent and a raw material in the synthesis of plastics. Production of commercial EG currently exclusively relies on chemical synthesis using fossil resources. Biochemical production of ethylene glycol from renewable resources may be more sustainable. Results Herein, a synthetic pathway is described that produces EG in Escherichia coli through the action of (d)-xylose isomerase, (d)-xylulose-1-kinase, (d)-xylulose-1-phosphate aldolase, and glycolaldehyde reductase. These reactions were successively catalyzed by the endogenous xylose isomerase (XylA), the heterologously expressed human hexokinase (Khk-C) and aldolase (Aldo-B), and an endogenous glycolaldehyde reductase activity, respectively, which we showed to be encoded by yqhD. The production strain was optimized by deleting the genes encoding for (d)-xylulose-5 kinase (xylB) and glycolaldehyde dehydrogenase (aldA), and by overexpressing the candidate glycolaldehyde reductases YqhD, GldA, and FucO. The strain overproducing FucO was the best EG producer reaching a molar yield of 0.94 in shake flasks, and accumulating 20 g/L EG with a molar yield and productivity of 0.91 and 0.37 g/(L.h), respectively, in a controlled bioreactor under aerobic conditions. Conclusions We have demonstrated the feasibility to produce EG from (d)-xylose via a synthetic pathway in E. coli at approximately 90 % of the theoretical yield. Electronic supplementary material The online version of this article (doi:10.1186/s12934-015-0312-7) contains supplementary material, which is available to authorized users.
Published: 2015

47. Mapping land use competition in the rural–urban fringe and future perspectives on land policies: A case study of Meknès (Morocco)

Author: Jean-Pierre Chéry, Elodie Valette, Marie François, Marta Debolini, Environnement Méditerranéen et Modélisation des Agro-Hydrosystèmes (EMMAH), Avignon Université (AU)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Territoires, Environnement, Télédétection et Information Spatiale (UMR TETIS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-AgroParisTech-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA), Innovation et Développement dans l'Agriculture et l'Alimentation (UMR Innovation), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), ANR-2010-STRA-007,Végé-Culture,Mesure des performances de systèmes complexes à base de plantes à multiplication végétative en zone tropicale humide, Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-AgroParisTech-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), and This work was supported by the French National Research Agency (DAUME ANR-2010-STRA-007-01) and by the 2011-2012 Research Award sponsored by the Global Fund for Environment and Conflict Resolution assigned to Marta Debolini through the CICR - Center for Environmental Conflict Resolution of the Columbia University (NY)
Subjects: [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Rural–urban fringe, Geography, Planning and Development, Land management, [SDV.SA.AGRO]Life Sciences [q-bio]/Agricultural sciences/Agronomy, Spatial multi-criteria analysis, Management, Monitoring, Policy and Law, Vulnerability to urbanization Land use planning Peri-urban areas Spatial multi-criteria analysis GIS-MCDA Spatial explicit indicators, Peri-urban areas, Competition (economics), [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Agricultural land, Urbanization, Agricultural productivity, Nature and Landscape Conservation, Land use, business.industry, Environmental resource management, Forestry, Land-use planning, [SDV.SA.AEP]Life Sciences [q-bio]/Agricultural sciences/Agriculture, economy and politics, [SHS.GEO]Humanities and Social Sciences/Geography, 15. Life on land, Land use planning, [SDE.ES]Environmental Sciences/Environmental and Society, E11 - Économie et politique foncières, Geography, GIS-MCDA, Spatial explicit indicators, Vulnerability to urbanization, business
Abstract: International audience; The geographical and socio-economic characteristics of peri-urban areas make them particularly vulnerable to land use competition. They are transitional zones, in continuous transformation, where various economic activities attempt to co-exist in equilibrium. Peri-urban agriculture plays a key role in this dynamic, functioning in a complex system that includes a large and diverse set of stakeholders which act to provide environmental and economic services to cities. The work described in this paper was undertaken to develop a methodology to map land use competition in terms of vulnerability to urbanization of agricultural lands, based on explicit spatial indicators set up in a GIS-based multi-criteria analysis (hereafter GIS-MCDA). The applied indicators are generated from an analysis of existing drivers of land use competition within the peri-urban area of Meknes (Morocco). This area is particularly interesting because of its agricultural characteristics, and because of recent changes in the dynamics of land use and tenure. This case study indicates a high risk of land competition in 37% of the area examined, and a very high risk in 16% of the area. The highest risk areas are located in the southern part of the peri-urban region, which is also considered the most valuable in terms of agricultural production. The map we have developed can be considered a preliminary tool for improving new planning strategies to manage land resource competition in rural–urban fringe zones. The approach presented is particularly useful as a simplified methodology to obtain spatialized indicators for the drivers of land use competition when data are limited, as often found in developing countries.
Published: 2015

48. A comparative study on the potential of epiphytic yeasts isolated from tropical fruits to produce flavoring compounds

Author: Alain Shum Cheong Sing, Yanis Caro, Eric Grondin, Thomas Petit, Carmen Nueno-Palop, Jean Marie François, Ando Lalaniaina Randrianierenana, Marson Raherimandimby, Steve James, Laboratoire de Chimie des Substances Naturelles et des Sciences des Aliments (LCSNSA), Université de La Réunion (UR), Université d'Antananarivo, Institute of Food Research [Norwich], Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés (LISBP), Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de la Recherche Agronomique (INRA), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées, Institut National Polytechnique (Toulouse) (Toulouse INP), Institut National de la Recherche Agronomique (INRA), Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Region Reunion and Europe, Biotechnology and Biological Sciences Research Council (BBSRC), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), and Université de Toulouse (UT)
Subjects: Sequence analysis, principal component analysis, Microorganism, Biology, yeast, flavors, Microbiology, DNA, Ribosomal, Rhodotorula mucilaginosa, Yeasts, Botany, Madagascar, Cluster Analysis, [CHIM]Chemical Sciences, Flavor, biodiversity, 2. Zero hunger, Tropical Climate, Volatile Organic Compounds, General Medicine, Candida pararugosa, Yeast, Flavoring Agents, Fruit, Food Microbiology, Epiphyte, Gas chromatography, Reunion, Food Science, biotechnology
Abstract: International audience; In recent years, there has been an increasing interest in identifying and characterizing the yeast flora associated with diverse types of habitat because of the many potential desirable technological properties of these microorganisms, especially in food applications. In this study, a total of 101 yeast strains were isolated from the skins of tropical fruits collected in several locations in the South West Indian Ocean. Sequence analysis of the D1/D2 domains of the large subunit (LSU) ribosomal RNA gene identified 26 different species. Among them, two species isolated from the skins of Cape gooseberry and cocoa beans appeared to represent putative new yeast species, as their LSU D1/D2 sequence was only 97.1% and 97.4% identical to that of the yeasts Rhodotorula mucilaginosa and Candida pararugosa, respectively. A total of 52 Volatile Organic Compounds (VOCs) were detected by Head Space Solid Phase Micro Extraction coupled to Gas Chromatography and Mass Spectroscopy (HS–SPME–GC/MS) from the 26 yeast species cultivated on a glucose rich medium. Among these VOCs, 6 uncommon compounds were identified, namely ethyl but-2-enoate, ethyl 2-methylbut-2-enoate (ethyl tiglate), ethyl 3-methylbut-2-enoate, 2-methylpropyl 2-methylbut-2-enoate, butyl 2-methylbut-2-enoate and 3-methylbutyl 2-methylbut-2-enoate, making them possible yeast species-specific markers. In addition, statistical methods such as Principal Component Analysis allowed to associate each yeast species with a specific flavor profile. Among them, Saprochaete suaveolens (syn: Geotrichum fragrans) turned to be the best producer of flavor compounds, with a total of 32 out of the 52 identified VOCs in its flavor profile.
Published: 2015

49. Bacterial ClpB heat-shock protein, an antigen-mimetic of the anorexigenic peptide α-MSH, at the origin of eating disorders

Author: Naouel Tennoune, Martine Pestel-Caron, Jonathan Breton, Christine Bole-Feysot, Marie François, Kuniko Takagi, Pierre Déchelotte, Anu Järv, J-C Do Rego, Wassila Ouelaa, Sergueï O. Fetissov, Romain Legrand, Philippe Chan, Y. Chabane, Kirsti Akkermann, David Vaudry, Nicolas Lucas, Ibtissem Ghouzali, Emmanuelle Dé, Jaanus Harro, Institute for Research and Innovation in Biomedicine (IRIB), Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut de biologie et chimie des protéines [Lyon] (IBCP), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Institut Pascal (IP), SIGMA Clermont (SIGMA Clermont)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS), University of Tartu, Nutrition, inflammation et dysfonctionnement de l'axe intestin-cerveau (ADEN), Normandie Université (NU)-Normandie Université (NU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Plateforme de génomique [SFR Necker], Structure Fédérative de Recherche Necker (SFR Necker - UMS 3633 / US24), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Groupe de Recherche sur l'Adaptation Microbienne (GRAM 2.0), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU), Différenciation et communication neuronale et neuroendocrine (DC2N), Institut Normand de Chimie Moléculaire Médicinale et Macromoléculaire (INC3M), Normandie Université (NU)-Normandie Université (NU)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), Normandie Université (NU)-Université Le Havre Normandie (ULH), Normandie Université (NU)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Institut national des sciences appliquées Rouen Normandie (INSA Rouen Normandie), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Polymères Biopolymères Surfaces (PBS), Normandie Université (NU)-Normandie Université (NU)-Institut national des sciences appliquées Rouen Normandie (INSA Rouen Normandie), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Institut Normand de Chimie Moléculaire Médicinale et Macromoléculaire (INC3M), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), Normandie Université (NU)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Normandie Université (NU)-Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), SIGMA Clermont (SIGMA Clermont)-Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Descartes - Paris 5 (UPD5)-Centre National de la Recherche Scientifique (CNRS)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Descartes - Paris 5 (UPD5)-Centre National de la Recherche Scientifique (CNRS), Normandie Université (NU)-Normandie Université (NU)-Université de Caen Normandie (UNICAEN), Institut de Chimie du CNRS (INC)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Université Le Havre Normandie (ULH), Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS)-Université de Caen Normandie (UNICAEN), Institut national des sciences appliquées Rouen Normandie (INSA Rouen Normandie), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut de Chimie du CNRS (INC)-Institut Normand de Chimie Moléculaire Médicinale et Macromoléculaire (INC3M), Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS), Institut Pascal - Clermont Auvergne (IP), Sigma CLERMONT (Sigma CLERMONT)-Université Clermont Auvergne (UCA)-Centre National de la Recherche Scientifique (CNRS), Graduate School of Engineering, Yokohama National University, Centre National de la Recherche Scientifique (CNRS)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Assistance publique - Hôpitaux de Paris (AP-HP) (APHP), Centre National de la Recherche Scientifique (CNRS)-Normandie Université (NU), Normandie Université (NU)-Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences appliquées Rouen Normandie (INSA Rouen Normandie), Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA), Pathology Department, and Ippokration Hospital
Subjects: Adult, Male, medicine.medical_specialty, Adolescent, [SDV]Life Sciences [q-bio], Immunoblotting, medicine.disease_cause, Feeding and Eating Disorders, Mice, Young Adult, Cellular and Molecular Neuroscience, Antigen, Internal medicine, Heat shock protein, Escherichia coli, medicine, Animals, Humans, [CHIM]Chemical Sciences, Heat-Shock Proteins, Biological Psychiatry, ComputingMilieux_MISCELLANEOUS, Autoantibodies, 2. Zero hunger, biology, Escherichia coli Proteins, Autoantibody, Endopeptidase Clp, 3. Good health, Mice, Inbred C57BL, Melanocortin 4 receptor, Disease Models, Animal, Psychiatry and Mental health, Endocrinology, alpha-MSH, Immunology, biology.protein, Original Article, Electrophoresis, Polyacrylamide Gel, Female, Antibody, CLPB, hormones, hormone substitutes, and hormone antagonists, Hormone
Abstract: The molecular mechanisms at the origin of eating disorders (EDs), including anorexia nervosa (AN), bulimia and binge-eating disorder (BED), are currently unknown. Previous data indicated that immunoglobulins (Igs) or autoantibodies (auto-Abs) reactive with α-melanocyte-stimulating hormone (α-MSH) are involved in regulation of feeding and emotion; however, the origin of such auto-Abs is unknown. Here, using proteomics, we identified ClpB heat-shock disaggregation chaperone protein of commensal gut bacteria Escherichia coli as a conformational antigen mimetic of α-MSH. We show that ClpB-immunized mice produce anti-ClpB IgG crossreactive with α-MSH, influencing food intake, body weight, anxiety and melanocortin receptor 4 signaling. Furthermore, chronic intragastric delivery of E. coli in mice decreased food intake and stimulated formation of ClpB- and α-MSH-reactive antibodies, while ClpB-deficient E. coli did not affect food intake or antibody levels. Finally, we show that plasma levels of anti-ClpB IgG crossreactive with α-MSH are increased in patients with AN, bulimia and BED, and that the ED Inventory-2 scores in ED patients correlate with anti-ClpB IgG and IgM, which is similar to our previous findings for α-MSH auto-Abs. In conclusion, this work shows that the bacterial ClpB protein, which is present in several commensal and pathogenic microorganisms, can be responsible for the production of auto-Abs crossreactive with α-MSH, associated with altered feeding and emotion in humans with ED. Our data suggest that ClpB-expressing gut microorganisms might be involved in the etiology of EDs.
Published: 2014

50. A combined chemical and enzymatic method to determine quantitatively the polysaccharide components in the cell wall of yeasts

Author: Hélène Martin-Yken, Etienne Dague, Cécile Formosa, Amélie Vax, Marion Schiavone, Jean Marie François, Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés (LISBP), Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de la Recherche Agronomique (INRA), Lallemand S.A.S., Laboratoire d'analyse et d'architecture des systèmes (LAAS), Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse 1 Capitole (UT1), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées, Équipe NanoBioSystèmes (LAAS-NBS), Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse 1 Capitole (UT1), Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Université Toulouse Capitole (UT Capitole), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université Toulouse - Jean Jaurès (UT2J), Université de Toulouse (UT)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT), and Université de Toulouse (UT)-Université Toulouse Capitole (UT Capitole)
Subjects: [SDV]Life Sciences [q-bio], 6)-glucan, Antifungal drug, 3)-glucan, macromolecular substances, Polysaccharide, chitin, Applied Microbiology and Biotechnology, Microbiology, glucanases, Cell wall, SACCHAROMYCES-CEREVISIAE, chemistry.chemical_compound, Chitin, Stress, Physiological, Yeasts, Enzymatic hydrolysis, [SDV.IDA]Life Sciences [q-bio]/Food engineering, BIOSYNTHESIS, [SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering, Glucans, ALKALI-SOLUBLE GLUCAN, chemistry.chemical_classification, CANDIDA-ALBICANS, FUNGAL, ARCHITECTURE, biology, MEMBRANE-PROTEIN, Hydrolysis, Aspergillus niger, Reproducibility of Results, Fungal Polysaccharides, (1, General Medicine, biology.organism_classification, Yeast, INTEGRITY, carbohydrates (lipids), chemistry, Biochemistry, chitinase, Mutation, Chitinase, BETA-GLUCANS, biology.protein, cell wall
Abstract: International audience; A reliable method to determine cell wall polysaccharides composition in yeast is presented, which combines acid and enzymatic hydrolysis. Sulphuric acid treatment is used to determine mannans, whereas specific hydrolytic enzymes are employed in a two sequential steps to quantify chitin and the proportion of -(1,3) and -(1,6)-glucan in the total -glucan of the cell wall. In the first step, chitin and -(1,3)-glucan were hydrolysed into their corresponding monomers N-acetylglucosamine and glucose, respectively, by the combined action of a chitinase from Streptomyces griseus and a pure preparation of endo/exo--(1,3)-glucanase from Trichoderma species. This step was followed by addition of recombinant endo--(1,6)-glucanase from Trichoderma harzianum with -glucosidase from Aspergillus niger to hydrolyse the remaining -glucan. This latter component corresponded to a highly branched -(1,6)-glucan that contained about 75-80% of linear -(1,6)-glucose linked units as deduced from periodate oxidation. We validated this novel method by showing that the content of -(1,3), -(1,6)-glucan or chitin was dramatically decreased in yeast mutants defective in the biosynthesis of these cell wall components. Moreover, we found that heat shock at 42 degrees C in Saccharomyces cerevisiae and treatment of this yeast species and Candida albicans with the antifungal drug caspofungin resulted in 2- to 3-fold increase of chitin and in a reduction of -(1,3)-glucan accompanied by an increase of -(1,6)-glucan, whereas ethanol stress had apparently no effect on yeast cell wall composition.
Published: 2014

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