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1. IFNγ causes mitochondrial dysfunction and oxidative stress in myositis

Author: Catalina Abad, Iago Pinal-Fernandez, Clement Guillou, Gwladys Bourdenet, Laurent Drouot, Pascal Cosette, Margherita Giannini, Lea Debrut, Laetitia Jean, Sophie Bernard, Damien Genty, Rachid Zoubairi, Isabelle Remy-Jouet, Bernard Geny, Christian Boitard, Andrew Mammen, Alain Meyer, and Olivier Boyer
Subjects: Science
Abstract: Abstract Idiopathic inflammatory myopathies (IIMs) are severe autoimmune diseases with poorly understood pathogenesis and unmet medical needs. Here, we examine the role of interferon γ (IFNγ) using NOD female mice deficient in the inducible T cell co-stimulator (Icos), which have previously been shown to develop spontaneous IFNγ-driven myositis mimicking human disease. Using muscle proteomic and spatial transcriptomic analyses we reveal profound myofiber metabolic dysregulation in these mice. In addition, we report muscle mitochondrial abnormalities and oxidative stress in diseased mice. Supporting a pathogenic role for oxidative stress, treatment with a reactive oxygen species (ROS) buffer compound alleviated myositis, preserved muscle mitochondrial ultrastructure and respiration, and reduced inflammation. Mitochondrial anomalies and oxidative stress were diminished following anti-IFNγ treatment. Further transcriptomic analysis in IIMs patients and human myoblast in vitro studies supported the link between IFNγ and mitochondrial dysfunction observed in mice. These results suggest that mitochondrial dysfunction, ROS and inflammation are interconnected in a self-maintenance loop, opening perspectives for mitochondria therapy and/or ROS targeting drugs in myositis.
Published: 2024
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2. Gingival proteomics reveals the role of TGF beta and YAP/TAZ signaling in Raine syndrome fibrosis

Author: Cláudio Rodrigues Rezende Costa, Rym Chalgoumi, Amina Baker, Clément Guillou, Paulo Marcio Yamaguti, Victor Simancas Escorcia, Lilia Abbad, Bruna Rabelo Amorin, Caroline Lourenço de Lima, Vidjea Cannaya, Mourad Benassarou, Ariane Berdal, Christos Chatziantoniou, Olivier Cases, Pascal Cosette, Renata Kozyraki, and Ana Carolina Acevedo
Subjects: FAM20C, FAM20A, Secretome, Proteome, Raine syndrome, TGF beta, Medicine, Science
Abstract: Abstract Raine syndrome (RNS) is a rare autosomal recessive osteosclerotic dysplasia. RNS is caused by loss-of-function disease-causative variants of the FAM20C gene that encodes a kinase that phosphorylates most of the secreted proteins found in the body fluids and extracellular matrix. The most common RNS clinical features are generalized osteosclerosis, facial dysmorphism, intracerebral calcifications and respiratory defects. In non-lethal RNS forms, oral traits include a well-studied hypoplastic amelogenesis imperfecta (AI) and a much less characterized gingival phenotype. We used immunomorphological, biochemical, and siRNA approaches to analyze gingival tissues and primary cultures of gingival fibroblasts of two unrelated, previously reported RNS patients. We showed that fibrosis, pathological gingival calcifications and increased expression of various profibrotic and pro-osteogenic proteins such as POSTN, SPARC and VIM were common findings. Proteomic analysis of differentially expressed proteins demonstrated that proteins involved in extracellular matrix (ECM) regulation and related to the TGFβ/SMAD signaling pathway were increased. Functional analyses confirmed the upregulation of TGFβ/SMAD signaling and subsequently uncovered the involvement of two closely related transcription cofactors important in fibrogenesis, Yes-associated protein (YAP) and transcriptional coactivator with PDZ-binding motif (TAZ). Knocking down of FAM20C confirmed the TGFβ-YAP/TAZ interplay indicating that a profibrotic loop enabled gingival fibrosis in RNS patients. In summary, our in vivo and in vitro data provide a detailed description of the RNS gingival phenotype. They show that gingival fibrosis and calcifications are associated with, and most likely caused by excessed ECM production and disorganization. They furthermore uncover the contribution of increased TGFβ–YAP/TAZ signaling in the pathogenesis of the gingival fibrosis.
Published: 2024
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3. BacA: a possible regulator that contributes to the biofilm formation of Pseudomonas aeruginosa

Author: Lisa Wallart, Mohamed Amine Ben Mlouka, Brahim Saffiedine, Laurent Coquet, Hung Le, Julie Hardouin, Thierry Jouenne, Gilles Phan, Marie-Christine Kiefer-Meyer, Eric Girard, Isabelle Broutin, and Pascal Cosette
Subjects: Pseudomonas aeruginosa, biofilm, rhamnolipids, proteome, crystallography, Psp system, Microbiology, QR1-502
Abstract: Previously, we pointed out in P. aeruginosa PAO1 biofilm cells the accumulation of a hypothetical protein named PA3731 and showed that the deletion of the corresponding gene impacted its biofilm formation capacity. PA3731 belongs to a cluster of 4 genes (pa3732 to pa3729) that we named bac for “Biofilm Associated Cluster.” The present study focuses on the PA14_16140 protein, i.e., the PA3732 (BacA) homolog in the PA14 strain. The role of BacA in rhamnolipid secretion, biofilm formation and virulence, was confirmed by phenotypic experiments with a bacA mutant. Additional investigations allow to advance that the bac system involves in fact 6 genes organized in operon, i.e., bacA to bacF. At a molecular level, quantitative proteomic studies revealed an accumulation of the BAC cognate partners by the bacA sessile mutant, suggesting a negative control of BacA toward the bac operon. Finally, a first crystallographic structure of BacA was obtained revealing a structure homologous to chaperones or/and regulatory proteins.
Published: 2024
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4. Validation in the ESPOIR cohort of vitamin K-dependent protein S (PROS) as a potential biomarker capable of predicting response to the methotrexate/etanercept combination

Author: Olivier Vittecoq, Clément Guillou, Julie Hardouin, Baptiste Gerard, Francis Berenbaum, Arnaud Constantin, Nathalie Rincheval, Bernard Combe, Thierry Lequerre, and Pascal Cosette
Subjects: PROS, CO7, Prediction, Rheumatoid arthritis, Etanercept, Adalimumab, Diseases of the musculoskeletal system, RC925-935
Abstract: Abstract Background To validate the ability of PROS (vitamin K-dependent protein S) and CO7 (complement component C7) to predict response to the methotrexate (MTX)/etanercept (ETA) combination in rheumatoid arthritis (RA) patients who received this therapeutic combination in a well-documented cohort. Method From the ESPOIR cohort, RA patients having received the MTX/ETA or MTX/adalimumab (ADA) combination as a first-line biologic treatment were included. Serum concentrations of PROS and CO7 were measured by ELISA prior to the initiation of ETA or ADA, at a time where the disease was active (DAS28 ESR > 3.2). The clinical efficacy (response/non-response) of both combinations has been evaluated after at least 6 months of treatment, according to the EULAR response criteria with some modifications. Results Thirty-two were treated by MTX/ETA; the numbers of responders and non-responders were 24 and 8, respectively. Thirty-three patients received the MTX/ADA combination; 27 and 5 patients were respectively responders and non-responders. While there were no differences for demographic, clinical, biological, and X-rays data, as well as for CO7, serum levels of PROS tended to be significantly higher in responders to the MTX/ETA combination (p = 0.08) while no difference was observed in the group receiving MTX/ADA. For PROS, the best concentration threshold to differentiate both groups was calculated at 40 μg/ml using ROC curve. The theranostic performances of PROS appeared better for the ETA/MTX combination. When considering the response to this combination, analysis of pooled data from ESPOIR and SATRAPE (initially used to validate PROS and CO7 as potential theranostic biomarkers) cohorts led to a higher theranostic value of PROS that became significant (p = 0.009). Conclusion PROS might be one candidate of a combination of biomarkers capable of predicting the response to MTX/ETA combination in RA patients refractory to MTX. Trial registration ClinicalTrials.gov identifiers: NCT03666091 and NCT00234234 .
Published: 2022
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5. Hepatoprotective Effect of Grape Seed and Skin Extract Against Lithium Exposure Examined by the Window of Proteomics

Author: Ali Mezni, Olfa Khazri, Frédérique Jarnier, Julie Hardouin, Ferid Limam, Thierry Jouenne, Ezzeddine Aouani, and Pascal Cosette
Subjects: Therapeutics. Pharmacology, RM1-950
Abstract: Context The liver is the organ by which the majority of substances are metabolized, including psychotropic drugs. Lithium (Li) used as drug for many neurological disorders such as bipolar disorders. Objective This study aims to assess lithium toxicity and to evaluate the hepatic-protective properties of a grape skin seed and extract (GSSE). Materials and methods Twenty-four male Wistar rats were exposed for 30 days to either various lithium concentrations, GSSE alone, or lithium supplemented with GSSE. The proteomic analysis revealed alterations of liver protein profiles after lithium treatments that were successfully identified by mass spectrometry. Results Lithium treatment induced an oxidative damage by the alteration of antioxidant enzymes activities such as superoxide dismutase, CAT, and Gpx. The regulated proteins are mainly involved in the respiratory electron transport chain, detoxification processes, ribosomal stress pathway, glycolysis, and cytoskeleton. Proteins were differentially expressed in a dose-dependent manner. Interestingly, GSSE reversed the situation and restored the level of liver proteins whose abundance was modified after lithium treatment, arguing for its protective activity. Conclusion Our data demonstrated the ability of proteomic analysis to underline the toxicity mechanisms of lithium in animal models. Based on these results, GSSE may be envisaged as a nutritional supplement to weaken the liver toxicity of lithium.
Published: 2022
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6. Variability of the response of human vaginal Lactobacillus crispatus to 17β-estradiol

Author: Maximilien Clabaut, Amine M. Boukerb, Amine Ben Mlouka, Amandine Suet, Ali Tahrioui, Julien Verdon, Magalie Barreau, Olivier Maillot, Agathe Le Tirant, Madina Karsybayeva, Coralie Kremser, Gérard Redziniak, Cécile Duclairoir-Poc, Chantal Pichon, Julie Hardouin, Pascal Cosette, Sylvie Chevalier, and Marc G. J. Feuilloley
Subjects: Medicine, Science
Abstract: Abstract We previously showed that the physiological concentration of 17β-estradiol in the vaginal environment is sufficient to affect the membrane dynamics and adhesion phenotype of the Lactobacillus crispatus strain CIP104459. However, L. crispatus is a heterogeneous species. Here, we investigated the effect of 17β-estradiol on the recently isolated L. crispatus vaginal strain V4, related to a cluster distant from CIP104459 and at the limit of being a different subspecies. Grown in the same medium, the two strains expressed a highly similar pool of proteins. However, in contrast to CIP104459, L. crispatus V4 showed high aggregation potential and 17β-estradiol promoted this phenotype. This effect was associated with large changes in cell-surface polarity and Lewis acid/base properties. In addition, we observed no effect on the membrane dynamics, contrary to CIP104459. These results can be explained by differences in the properties and organization of the S layer between the two strains. However, as for CIP104459, 17β-estradiol increased biosurfactant production of L. crispatus V4 and their adhesion to vaginal cells. This suggests that 17β-estradiol agonists would be valuable tools to favor a stable re-implantation of L. crispatus in the vaginal mucosa.
Published: 2021
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7. Phosphorylation of Extracellular Proteins in Acinetobacter baumannii in Sessile Mode of Growth

Author: Sébastien Massier, Brandon Robin, Marianne Mégroz, Amy Wright, Marina Harper, Brooke Hayes, Pascal Cosette, Isabelle Broutin, John D. Boyce, Emmanuelle Dé, and Julie Hardouin
Subjects: phosphorylation, Acinetobacter baumannii, biofilm, extracellular proteins, proteomics, Hcp, Microbiology, QR1-502
Abstract: Acinetobacter baumannii is a problematic nosocomial pathogen owing to its increasing resistance to antibiotics and its great ability to survive in the hospital environment, which is linked to its capacity to form biofilms. Structural and functional investigations of post-translational modifications, such as phosphorylations, may lead to identification of candidates for therapeutic targets against this pathogen. Here, we present the first S/T/Y phosphosecretome of two A. baumannii strains, the reference strain ATCC 17978 and the virulent multi-drug resistant strain AB0057, cultured in two modes of growth (planktonic and biofilm) using TiO2 chromatography followed by high resolution mass spectrometry. In ATCC 17978, we detected a total of 137 (97 phosphoproteins) and 52 (33 phosphoproteins) phosphosites in biofilm and planktonic modes of growth, respectively. Similarly, in AB0057, 155 (119 phosphoproteins) and 102 (74 phosphoproteins) phosphosites in biofilm and planktonic modes of growth were identified, respectively. Both strains in the biofilm mode of growth showed a higher number of phosphosites and phosphoproteins compared to planktonic growth. Several phosphorylated sites are localized in key regions of proteins involved in either drug resistance (β-lactamases), adhesion to host tissues (pilins), or protein secretion (Hcp). Site-directed mutagenesis of the Hcp protein, essential for type VI secretion system-mediated interbacterial competition, showed that four of the modified residues are essential for type VI secretion system activity.
Published: 2021
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8. Anti-Carbamylated Fibrinogen Antibodies Might Be Associated With a Specific Rheumatoid Phenotype and Include a Subset Recognizing In Vivo Epitopes of Its γ Chain One of Which Is Not Cross Reactive With Anti-Citrullinated Protein Antibodies

Author: Pauline Brevet, Claire Lattard, Clément Guillou, Pascal Rottenberg, Patrice Fardellone, Xavier Le-Loët, Thierry Lequerré, Pascal Cosette, Olivier Boyer, Manuel Fréret, and Olivier Vittecoq
Subjects: very early rheumatoid arthritis, anti-carbamylated protein antibodies (anti-CarP), fibrinogen, ACPA, prognosis, Immunologic diseases. Allergy, RC581-607
Abstract: To identify the targets recognized by anti-carbamylated protein antibodies (anti-CarP) in patients with early Rheumatoid Arthritis (RA), to study the cross-reactivity between anti-CarP and anti-citrullinated protein antibodies (ACPA) and to evaluate their prognostic value. 331 patients (184 RA and 147 other rheumatisms) from the Very Early Arthritis (VErA) French cohort were analyzed. We performed mass spectrometry analysis of RA sera displaying anti-CarP activity and epitope mapping of the carbamylated fibrinogen γ chain to identify immunodominant peptides. The specificity of these targets was studied using competition assays with the major antigens recognized by ACPA. The prognostic value of anti-carbamylated fibrinogen IgG antibodies (ACa-Fib IgG) was compared to that of anti-cyclic citrullinated peptide antibodies (anti-CCP) and anti-CarP using an in-house ELISA. Besides the α chain, the γ chain of fibrinogen, particularly one immunodominant epitope that has a specific reactivity, was identified as a circulating carbamylated target in sera. The prevalence of ACa-Fib was 37% at baseline and 10.9% for anti-CCP-negative RA. In anti-CCP-negative patients, ACa-Fib positivity was associated with a more inflammatory and erosive disease at baseline but not with rapid radiological progression, which remains strongly related to anti-CCP antibodies. Fibrinogen seems to be one of the antigens recognized in vivo by the anti-CarP response, particularly 2 epitopes of the γ chain, one of which is not cross reactive with ACPA. This specificity might be associated with a distinct clinical phenotype since ACa-Fib IgG were shown to be linked to systemic inflammation in very early RA but not to rapid radiological progression.
Published: 2021
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9. Pathogenesis of Enamel-Renal Syndrome Associated Gingival Fibromatosis: A Proteomic Approach

Author: Victor Simancas Escorcia, Clément Guillou, Lilia Abbad, Louise Derrien, Claudio Rodrigues Rezende Costa, Vidjea Cannaya, Mourad Benassarou, Christos Chatziantoniou, Ariane Berdal, Ana Carolina Acevedo, Olivier Cases, Pascal Cosette, and Renata Kozyraki
Subjects: FAM20A, FAM20C, secretome analysis, enamel renal syndrome, gingival fibroblast, gingival fibromatosis, Diseases of the endocrine glands. Clinical endocrinology, RC648-665
Abstract: The enamel renal syndrome (ERS) is a rare disorder featured by amelogenesis imperfecta, gingival fibromatosis and nephrocalcinosis. ERS is caused by bi-allelic mutations in the secretory pathway pseudokinase FAM20A. How mutations in FAM20A may modify the gingival connective tissue homeostasis and cause fibromatosis is currently unknown. We here analyzed conditioned media of gingival fibroblasts (GFs) obtained from four unrelated ERS patients carrying distinct mutations and control subjects. Secretomic analysis identified 109 dysregulated proteins whose abundance had increased (69 proteins) or decreased (40 proteins) at least 1.5-fold compared to control GFs. Proteins over-represented were mainly involved in extracellular matrix organization, collagen fibril assembly, and biomineralization whereas those under-represented were extracellular matrix-associated proteins. More specifically, transforming growth factor-beta 2, a member of the TGFβ family involved in both mineralization and fibrosis was strongly increased in samples from GFs of ERS patients and so were various known targets of the TGFβ signaling pathway including Collagens, Matrix metallopeptidase 2 and Fibronectin. For the over-expressed proteins quantitative RT-PCR analysis showed increased transcript levels, suggesting increased synthesis and this was further confirmed at the tissue level. Additional immunohistochemical and western blot analyses showed activation and nuclear localization of the classical TGFβ effector phospho-Smad3 in both ERS gingival tissue and ERS GFs. Exposure of the mutant cells to TGFB1 further upregulated the expression of TGFβ targets suggesting that this pathway could be a central player in the pathogenesis of the ERS gingival fibromatosis.In conclusion our data strongly suggest that TGFβ -induced modifications of the extracellular matrix contribute to the pathogenesis of ERS. To our knowledge this is the first proteomic-based analysis of FAM20A-associated modifications.
Published: 2021
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10. Elicitation of Roots and AC-DC with PEP-13 Peptide Shows Differential Defense Responses in Multi-Omics

Author: Marie Chambard, Mohamed Amine Ben Mlouka, Lun Jing, Carole Plasson, Pascal Cosette, Jérôme Leprince, Marie-Laure Follet-Gueye, Azeddine Driouich, Eric Nguema-Ona, and Isabelle Boulogne
Subjects: root-associated cap-derived cells (root AC-DC), omics, PEP-13 elicitor, Glycine max, Cytology, QH573-671
Abstract: The root extracellular trap (RET) has emerged as a specialized compartment consisting of root AC-DC and mucilage. However, the RET’s contribution to plant defense is still poorly understood. While the roles of polysaccharides and glycoproteins secreted by root AC-DC have started to be elucidated, how the low-molecular-weight exudates of the RET contribute to root defense is poorly known. In order to better understand the RET and its defense response, the transcriptomes, proteomes and metabolomes of roots, root AC-DC and mucilage of soybean (Glycine max (L.) Merr, var. Castetis) upon elicitation with the peptide PEP-13 were investigated. This peptide is derived from the pathogenic oomycete Phytophthora sojae. In this study, the root and the RET responses to elicitation were dissected and sequenced using transcriptional, proteomic and metabolomic approaches. The major finding is increased synthesis and secretion of specialized metabolites upon induced defense activation following PEP-13 peptide elicitation. This study provides novel findings related to the pivotal role of the root extracellular trap in root defense.
Published: 2022
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11. Proteomic and transcriptomic study of brain microvessels in neonatal and adult mice.

Author: Baptiste Porte, Clémence Chatelain, Julie Hardouin, Céline Derambure, Yasmine Zerdoumi, Michèle Hauchecorne, Nicolas Dupré, Soumeya Bekri, Bruno Gonzalez, Stéphane Marret, Pascal Cosette, and Philippe Leroux
Subjects: Medicine, Science
Abstract: Infants born before 29 weeks gestation incur a major risk of preterm encephalopathy and subependymal/intracerebral/intraventricular haemorrhage. In mice, an ontogenic window of haemorrhage risk was recorded up to 5 days after birth in serpine1 knock-out animals. Using proteome and transcriptome approaches in mouse forebrain microvessels, we previously described the remodelling of extracellular matrix and integrins likely strengthening the vascular wall between postnatal day 5 (P5) and P10. Haemorrhage is the ultimate outcome of vessel damage (i.e., during ischaemia), although discreet vessel insults may be involved in the aetiology of preterm encephalopathy. In this study, we examined proteins identified by mass spectrometry and segregating in gene ontology pathways in forebrain microvessels in P5, P10, and adult wild type mice. In parallel, comparative transcript levels were obtained using RNA hybridization microarrays and enriched biological pathways were extracted from genes exhibiting at least a two-fold change in expression. Five major biological functions were observed in those genes detected both as proteins and mRNA expression undergoing at least a two-fold change in expression in one or more age comparisons: energy metabolism, protein metabolism, antioxidant function, ion exchanges, and transport. Adult microvessels exhibited the highest protein and mRNA expression levels for a majority of genes. Energy metabolism-enriched gene ontology pathways pointed to the preferential occurrence of glycolysis in P5 microvessels cells versus P10 and adult preparations enriched in aerobic oxidative enzymes. Age-dependent levels of RNA coding transport proteins at the plasma membrane and mitochondria strengthened our findings based on protein data. The data suggest that immature microvessels have fewer energy supply alternatives to glycolysis than mature structures. In the context of high energy demand, this constraint might account for vascular damage and maintenance of the high bleeding occurrence in specific areas in immature brain.
Published: 2017
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12. Foxg1-Cre Mediated Lrp2 Inactivation in the Developing Mouse Neural Retina, Ciliary and Retinal Pigment Epithelia Models Congenital High Myopia.

Author: Olivier Cases, Antoine Joseph, Antoine Obry, Mathieu D Santin, Sirine Ben-Yacoub, Michel Pâques, Sabine Amsellem-Levera, Ana Bribian, Manuel Simonutti, Sébastien Augustin, Thomas Debeir, José Alain Sahel, Annabel Christ, Fernando de Castro, Stéphane Lehéricy, Pascal Cosette, and Renata Kozyraki
Subjects: Medicine, Science
Abstract: Myopia is a common ocular disorder generally due to increased axial length of the eye-globe. Its extreme form high myopia (HM) is a multifactorial disease leading to retinal and scleral damage, visual impairment or loss and is an important health issue. Mutations in the endocytic receptor LRP2 gene result in Donnai-Barrow (DBS) and Stickler syndromes, both characterized by HM. To clearly establish the link between Lrp2 and congenital HM we inactivated Lrp2 in the mouse forebrain including the neural retina and the retinal and ciliary pigment epithelia. High resolution in vivo MRI imaging and ophthalmological analyses showed that the adult Lrp2-deficient eyes were 40% longer than the control ones mainly due to an excessive elongation of the vitreal chamber. They had an apparently normal intraocular pressure and developed chorioretinal atrophy and posterior scleral staphyloma features reminiscent of human myopic retinopathy. Immunomorphological and ultrastructural analyses showed that increased eye lengthening was first observed by post-natal day 5 (P5) and that it was accompanied by a rapid decrease of the bipolar, photoreceptor and retinal ganglion cells, and eventually the optic nerve axons. It was followed by scleral thinning and collagen fiber disorganization, essentially in the posterior pole. We conclude that the function of LRP2 in the ocular tissues is necessary for normal eye growth and that the Lrp2-deficient eyes provide a unique tool to further study human HM.
Published: 2015
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13. Escherichia coli response to uranyl exposure at low pH and associated protein regulations.

Author: Arbia Khemiri, Marie Carrière, Nicolas Bremond, Mohamed Amine Ben Mlouka, Laurent Coquet, Isabelle Llorens, Virginie Chapon, Thierry Jouenne, Pascal Cosette, and Catherine Berthomieu
Subjects: Medicine, Science
Abstract: Better understanding of uranyl toxicity in bacteria is necessary to optimize strains for bioremediation purposes or for using bacteria as biodetectors for bioavailable uranyl. In this study, after different steps of optimization, Escherichia coli cells were exposed to uranyl at low pH to minimize uranyl precipitation and to increase its bioavailability. Bacteria were adapted to mid acidic pH before exposure to 50 or 80 µM uranyl acetate for two hours at pH≈3. To evaluate the impact of uranium, growth in these conditions were compared and the same rates of cells survival were observed in control and uranyl exposed cultures. Additionally, this impact was analyzed by two-dimensional differential gel electrophoresis proteomics to discover protein actors specifically present or accumulated in contact with uranium.Exposure to uranium resulted in differential accumulation of proteins associated with oxidative stress and in the accumulation of the NADH/quinone oxidoreductase WrbA. This FMN dependent protein performs obligate two-electron reduction of quinones, and may be involved in cells response to oxidative stress. Interestingly, this WrbA protein presents similarities with the chromate reductase from E. coli, which was shown to reduce uranyl in vitro.
Published: 2014
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14. Identification of S100A9 as biomarker of responsiveness to the methotrexate/etanercept combination in rheumatoid arthritis using a proteomic approach.

Author: Antoine Obry, Thierry Lequerré, Julie Hardouin, Olivier Boyer, Patrice Fardellone, Peggy Philippe, Xavier Le Loët, Pascal Cosette, and Olivier Vittecoq
Subjects: Medicine, Science
Abstract: One way to optimize the drug prescription in rheumatoid arthritis (RA) is to identify predictive biomarkers of drug responsiveness. Here, we investigated the potential "theranostic" value of proteins of the S100 family by monitoring levels of both S100A8 and S100A9 in blood samples from RA patients.For proteomic analysis, peripheral blood mononuclear cells (PBMC) and serum samples were collected in patients prior to initiation of the methotrexate/etanercept (MTX/ETA) combination. Firstly, relative mass spectrometry (MS) quantification focusing on S100A8 and S100A9 proteins was carried out from PBMCs samples to identify potential biomarkers. The same approach was also performed from serum samples from responder (R) and non responder (NR) patients. Finally, to confirm these results, an absolute quantification of S100A8, S100A9 proteins and calprotectin (heterodimer of S100A8/S100A9) was carried out on the serum samples using ELISA.MS analyses revealed that both S100A8 and S100A9 proteins were significantly accumulated in PBMC from responders. In contrast to PBMC, only the S100A9 protein was significantly overexpressed in the serum of R patients. Absolute quantification by ELISA confirmed this result and pointed out a similar expression level of S100A8 protein and calprotectin in sera from both R and NR groups. Thus, the S100A9 protein revealed to be predictive of MTX/ETA responsiveness, contrarily to parameters of inflammation and auto-antibodies which did not allow significant discrimination.This is the first report of an overexpression of S100A9 protein in both PBMCs and serum of patients with subsequent response to the MTX/ETA combination. This protein thus represents an interesting biomarker candidate of therapeutic response in RA.
Published: 2014
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15. Identification of biofilm-associated cluster (bac) in Pseudomonas aeruginosa involved in biofilm formation and virulence.

Author: Camille Macé, Damien Seyer, Chanez Chemani, Pascal Cosette, Patrick Di-Martino, Benoit Guery, Alain Filloux, Marc Fontaine, Virginie Molle, Guy-Alain Junter, and Thierry Jouenne
Subjects: Medicine, Science
Abstract: Biofilms are prevalent in diseases caused by Pseudomonas aeruginosa, an opportunistic and nosocomial pathogen. By a proteomic approach, we previously identified a hypothetical protein of P. aeruginosa (coded by the gene pA3731) that was accumulated by biofilm cells. We report here that a Delta pA3731 mutant is highly biofilm-defective as compared with the wild-type strain. Using a mouse model of lung infection, we show that the mutation also induces a defect in bacterial growth during the acute phase of infection and an attenuation of the virulence. The pA3731 gene is found to control positively the ability to swarm and to produce extracellular rhamnolipids, and belongs to a cluster of 4 genes (pA3729-pA3732) not previously described in P. aeruginosa. Though the protein PA3731 has a predicted secondary structure similar to that of the Phage Shock Protein, some obvious differences are observed compared to already described psp systems, e.g., this unknown cluster is monocistronic and no homology is found between the other proteins constituting this locus and psp proteins. As E. coli PspA, the amount of the protein PA3731 is enlarged by an osmotic shock, however, not affected by a heat shock. We consequently named this locus bac for biofilm-associated cluster.
Published: 2008
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16. Purification and characterization of a novel high molecular weight alkaline protease produced by an endophytic Bacillus halotolerans strain CT2

Author: Dorra, Gharbi, Ines, Karkouch, Imen, Ben Slimene, Laurent, Coquet, Sana, Azaiez, Olfa, Tabbene, Pascal, Cosette, Thierry, Jouenne, and Ferid, Limam
Published: 2018
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17. Variability of the response of human vaginal Lactobacillus crispatus to 17β-estradiol

Author: Sylvie Chevalier, Maximilien Clabaut, Magalie Barreau, Gérard Redziniak, Madina Karsybayeva, Marc G. J. Feuilloley, Julie Hardouin, Agathe Le Tirant, Amine M. Boukerb, Cécile Duclairoir-Poc, Olivier Maillot, Amandine Suet, Amine Ben Mlouka, Julien Verdon, Pascal Cosette, Chantal Pichon, Coralie Kremser, Ali Tahrioui, Ecologie et biologie des interactions (EBI), Université de Poitiers-Centre National de la Recherche Scientifique (CNRS), Microbiologie de l'Eau (MDE), and Université de Poitiers-Centre National de la Recherche Scientifique (CNRS)-Université de Poitiers-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, Physiology, Science, [SDV]Life Sciences [q-bio], 030106 microbiology, Microbiology, Article, 03 medical and health sciences, Membrane dynamics, Humans, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], Lactobacillus crispatus, Multidisciplinary, Strain (chemistry), biology, Estradiol, Chemistry, Vaginal mucosa, Adhesion, biology.organism_classification, Phenotype, 030104 developmental biology, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Vagina, Medicine, Female, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, S-layer
Abstract: We previously showed that the physiological concentration of 17β-estradiol in the vaginal environment is sufficient to affect the membrane dynamics and adhesion phenotype of the Lactobacillus crispatus strain CIP104459. However, L. crispatus is a heterogeneous species. Here, we investigated the effect of 17β-estradiol on the recently isolated L. crispatus vaginal strain V4, related to a cluster distant from CIP104459 and at the limit of being a different subspecies. Grown in the same medium, the two strains expressed a highly similar pool of proteins. However, in contrast to CIP104459, L. crispatus V4 showed high aggregation potential and 17β-estradiol promoted this phenotype. This effect was associated with large changes in cell-surface polarity and Lewis acid/base properties. In addition, we observed no effect on the membrane dynamics, contrary to CIP104459. These results can be explained by differences in the properties and organization of the S layer between the two strains. However, as for CIP104459, 17β-estradiol increased biosurfactant production of L. crispatus V4 and their adhesion to vaginal cells. This suggests that 17β-estradiol agonists would be valuable tools to favor a stable re-implantation of L. crispatus in the vaginal mucosa.
Published: 2021
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18. Protective effect of grape seed and skin extract on cerebral ischemia in rat: implication of transition metals

Author: Safwen, Kadri, Selima, Smine, Mohamed, Elayed, Ferid, Limam, Pascal, Cosette, Mohamed, Amri, Ezzedine, Aouani, and Meherzia, Mokni
Published: 2015
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19. Phospho-secretome characterization of Acinetobacter baumannii in biofilm

Author: Sébastien Massier, Brandon ROBIN, Pascal Cosette, Jouenne, T., Emmanuelle Dé, Julie Hardouin, Microbes, Intestin, Inflammation et Susceptibilité de l'Hôte (M2iSH), Institut National de la Recherche Agronomique (INRA)-Université d'Auvergne - Clermont-Ferrand I (UdA), Plate-forme de Protéomique PISSARO, 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)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut Fédératif de Recherches Multidisciplinaires sur les Peptides (IFRMP 23), CHU Rouen, Normandie Université (NU)-Normandie Université (NU)-Université Le Havre Normandie (ULH), Normandie Université (NU)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-CRLCC Henri Becquerel-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Polymères Biopolymères Surfaces (PBS), 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), Normandie Université (NU), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre de Recherche en Nutrition Humaine d'Auvergne (CRNH d'Auvergne)-Institut National de la Recherche Agronomique (INRA), 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), 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 National de la Santé et de la Recherche Médicale (INSERM)-Centre de Lutte Contre le Cancer Henri Becquerel Normandie Rouen (CLCC Henri Becquerel)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-CHU Rouen, Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS), 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), Institut de Chimie du CNRS (INC)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), 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)-Université Le Havre Normandie (ULH), Normandie Université (NU)-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)-Université Le Havre Normandie (ULH), Institut National de la Recherche Agronomique (INRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre de Recherche en Nutrition Humaine d'Auvergne (CRNH d'Auvergne), Normandie Université (NU)-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)-Normandie Université (NU)-Institute for Research and Innovation in Biomedicine (IRIB), 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)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Normandie Université (NU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre de Lutte Contre le Cancer Henri Becquerel Normandie Rouen (CLCC Henri Becquerel)-Centre National de la Recherche Scientifique (CNRS), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Institut Normand de Chimie Moléculaire Médicinale et Macromoléculaire (INC3M), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), 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)-Université de Caen Normandie (UNICAEN), and Normandie Université (NU)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)
Subjects: [SDV]Life Sciences [q-bio], ComputingMilieux_MISCELLANEOUS
Abstract: International audience
Published: 2019

20. Neuroprotective effect of grape seed extract on brain ischemia: a proteomic approach

Author: Salem Elkhaoui, Sami Zekri, Ferid Limam, Mohamed El Ayed, Meherzia Mokni, Pascal Cosette, Safwen Kadri, Ezzedine Aouani, Thierry Jouenne, Plate-forme de Protéomique PISSARO, 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)-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), Polymères Biopolymères Surfaces (PBS), 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), Institut de Chimie du CNRS (INC)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), 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)-Université Le Havre Normandie (ULH), Normandie Université (NU)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-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)-Université Le Havre Normandie (ULH), Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS), Faculté de Médecine de Tunis, Université de Tunis El Manar (UTM), Laboratoire des Substances Bioactives (Centre de Biotechnologie de Borj Cedria, Hammam-Lif) (LSBA), Centre de Biotechnologie de Borj Cédria (Hammam-Lif, Tunisie), Faculté des Sciences de Bizerte [Université de Carthage], and Université de Carthage - University of Carthage
Subjects: Male, Proteomics, 0301 basic medicine, food.ingredient, Ischemia, Down-Regulation, Hippocampal formation, Biology, Pharmacology, medicine.disease_cause, Biochemistry, Neuroprotection, Antioxidants, Brain Ischemia, Rats, Sprague-Dawley, Brain ischemia, 03 medical and health sciences, Cellular and Molecular Neuroscience, 0302 clinical medicine, food, medicine, Animals, ComputingMilieux_MISCELLANEOUS, Grape Seed Extract, Dentate gyrus, Brain, medicine.disease, 3. Good health, Oxidative Stress, Neuroprotective Agents, 030104 developmental biology, Reperfusion Injury, Grape seed extract, Proteome, Neurology (clinical), [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, 030217 neurology & neurosurgery, Oxidative stress
Abstract: Stroke is one of the leading causes of long-lasting disability in human and oxidative stress an important underlying cause. Molecular insights into pathophysiology of ischemic stroke are still obscure, and the present study investigated the protective effect of high dosage Grape Seed Extract (GSE 2.5 g/kg) on brain ischemia-reperfusion (I/R) injury using a proteomic approach. Ischemia was realized by occlusion of the common carotid arteries for 30 min followed by 1 h reperfusion on control or GSE pre-treated rats, and a label-free quantification followed by mass spectrometry analysis used to evaluate I/R induced alterations in protein abundance and metabolic pathways as well as the protection afforded by GSE. I/R-induced whole brain ionogram dyshomeostasis, ultrastructural alterations, as well as inflammation into hippocampal dentate gyrus area, which were evaluated using ICP-OES, transmission electron microscopy and immuno-histochemistry respectively. I/R altered the whole brain proteome abundance among which 108 proteins were significantly modified (35 up and 73 down-regulated proteins). Eighty-four proteins were protected upon GSE treatment among which 27 were up and 57 down-regulated proteins, suggesting a potent protective effect of GSE close to 78%of the disturbed proteome. Furthermore, GSE efficiently prevented the brain from I/R-induced ion dyshomeostasis, ultrastructural alterations, inflammatory biomarkers as CD56 or CD68 and calcium burst within the hippocampus. To conclude, a potent protective effect of GSE on brain ischemia is evidenced and clinical trials using high dosage GSE should be envisaged on people at high risk for stroke.
Published: 2019
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21. Utilization of Grape Seed Flour for Antimicrobial Lipopeptide Production by Bacillus amyloliquefaciens C5 Strain

Author: Siwar Soussi, Thierry Jouenne, Ferid Limam, Julie Hardouin, Dorra Gharbi, Olfa Tabbene, Pascal Cosette, Rym Essid, Salem Elkahoui, Laboratoire des Substances Bioactives (Centre de Biotechnologie de Borj Cedria, Hammam-Lif) (LSBA), Centre de Biotechnologie de Borj Cédria (Hammam-Lif, Tunisie), Polymères Biopolymères Surfaces (PBS), 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), Institut de Chimie du CNRS (INC)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), 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)-Université Le Havre Normandie (ULH), Normandie Université (NU)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-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)-Université Le Havre Normandie (ULH), and Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, Grape seed flour, Bacillus amyloliquefaciens, M9 mineral medium, [SDV]Life Sciences [q-bio], Flour, Bioengineering, Microbial Sensitivity Tests, Antimicrobial activity, 01 natural sciences, Applied Microbiology and Biotechnology, Biochemistry, Lipopeptide, Lipopeptides, Bacillomycin, chemistry.chemical_compound, Anti-Infective Agents, 010608 biotechnology, Vitis, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Food science, Molecular Biology, Strain (chemistry), biology, 010405 organic chemistry, General Medicine, biology.organism_classification, Antimicrobial, Thin-layer chromatography, 0104 chemical sciences, MALDI-TOF/MS, chemistry, Seeds, Antibacterial activity, Surfactin, Biotechnology
Abstract: International audience; An endophytic Bacillus amyloliquefaciens strain called C5, able to produce biosurfactant lipopeptides with a broad antibacterial activity spectrum, has been isolated from the roots of olive tree. Optimization of antibacterial activity was undertaken using grape seed flour (GSF) substrate at 0.02, 0.2, and 2% (w/v) in M9 medium. Strain C5 exhibited optimal growth and antimicrobial activity (MIC value of 60 μg/ml) when incubated in the presence of 0.2% GSF while lipopeptide production culminated at 2% GSF. Thin layer chromatography analysis of lipopeptide extract revealed the presence of at least three active spots at Rf 0.35, 0.59, and 0.72 at 0.2% GSF. Data were similar to those obtained in LB-rich medium. MALDI-TOF/MS analysis of lipopeptide extract obtained from 0.2% GSF substrate revealed the presence of surfactin and bacillomycin D. These results show that GSF could be used as a low-cost culture medium supplement for optimizing the production of biosurfactants by strain C5.
Published: 2019
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22. Predictors of treatment response in rheumatoid arthritis

Author: Pascal Cosette, Céline Derambure, Olivier Vittecoq, Thierry Lequerré, Pascal Rottenberg, CHU Bois-Guillaume, UNIROUEN - UFR Santé (UNIROUEN UFR Santé), Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU), Génomique et Médecine Personnalisée du Cancer et des Maladies Neuropsychiatriques (GPMCND), Normandie Université (NU)-Normandie Université (NU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Plate-forme de Protéomique PISSARO, 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)-Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), Service de rhumatologie [CHU Rouen], CHU Rouen, Normandie Université (NU)-Normandie Université (NU)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU), 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), Normandie Université (NU)-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)-Normandie Université (NU)-Institute for Research and Innovation in Biomedicine (IRIB), 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)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), and CCSD, Accord Elsevier
Subjects: Drug, Male, medicine.medical_specialty, Treatment response, [SDV.IMM] Life Sciences [q-bio]/Immunology, Proteome, media_common.quotation_subject, Risk Assessment, Severity of Illness Index, Arthritis, Rheumatoid, 03 medical and health sciences, 0302 clinical medicine, Rheumatology, Predictive Value of Tests, Rheumatoid Factor, Response prediction, medicine, Rheumatoid factor, Humans, 030212 general & internal medicine, Precision Medicine, Rheumatoid arthritis, Intensive care medicine, media_common, 030203 arthritis & rheumatology, [SDV.MHEP.RSOA] Life Sciences [q-bio]/Human health and pathology/Rhumatology and musculoskeletal system, Biological Products, business.industry, medicine.disease, Prognosis, Theranostics, 3. Good health, Review article, Clinical Practice, Treatment Outcome, [SDV.MHEP.RSOA]Life Sciences [q-bio]/Human health and pathology/Rhumatology and musculoskeletal system, Antirheumatic Agents, [SDV.IMM]Life Sciences [q-bio]/Immunology, Identification (biology), Drug Therapy, Combination, Female, Personalized medicine, Patient Safety, business, Transcriptome, Biomarkers
Abstract: International audience; The expanding array of drugs available for treating rheumatoid arthritis is creating challenges in drug selection for the individual patient. The identification of biomarkers that predict the treatment response prior to drug exposure is therefore a current priority. This new approach, known as theranostics, is a component of personalized medicine, which involves selecting the management strategies that are most effective for a given patient at a given point in time. Antibodies to citrullinated peptides, rheumatoid factor, and the interferon signature are the most robust and best validated biomarkers identified to date. Matrices containing clinical or laboratory parameters of diagnostic or prognostic relevance may help to select the best treatment for the individual patient. Furthermore, the development of large-scale approaches requiring no a priori knowledge, such as functional genomics and metabolomics, hold considerable promise, despite persistent difficulties in replicating findings. The complexity of the treatment response in a given patient and substantial variability across patients suggest that biomarkers may be more helpful in combination than singly. The objectives of this review article are to discuss the approaches used to identify theranostic biomarkers and to present an overview of currently available biomarkers and of their performance in everyday clinical practice. However, the range of biomarkers suitable for use in daily practice remains extremely narrow.
Published: 2019
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23. Brain proteomic modifications associated to protective effect of grape extract in a murine model of obesity

Author: Safwen Kadri, Ferid Limam, Selima Smine, Pascal Cosette, Thierry Jouenne, Manuel Fréret, Julie Hardouin, Ezzedine Aouani, Mohamed Amri, Antoine Obry, Polymères Biopolymères Surfaces (PBS), 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), Institut de Chimie du CNRS (INC)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), 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)-Université Le Havre Normandie (ULH), Normandie Université (NU)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-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)-Université Le Havre Normandie (ULH), Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS), Physiopathologie et biothérapies des maladies inflammatoires et autoimmunes, Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Faculté des Sciences Mathématiques, Physiques et Naturelles de Tunis (FST), Université de Tunis El Manar (UTM), Laboratoire des Substances Bioactives (Centre de Biotechnologie de Borj Cedria, Hammam-Lif) (LSBA), Centre de Biotechnologie de Borj Cédria (Hammam-Lif, Tunisie), Plate-forme de Protéomique PISSARO, Institute for Research and Innovation in Biomedicine (IRIB), 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), Normandie Université (NU)-Normandie Université (NU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Faculté des Sciences de Bizerte [Université de Carthage], Université de Carthage - University of Carthage, 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), and Normandie Université (NU)-Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)
Subjects: 0301 basic medicine, Proteomics, [SDV.NEU.NB]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Neurobiology, Biophysics, Pharmacology, Biology, medicine.disease_cause, Diet, High-Fat, Biochemistry, Antioxidants, Mass Spectrometry, Analytical Chemistry, 03 medical and health sciences, Mice, 0302 clinical medicine, Pharmacotherapy, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], medicine, Animals, Humans, Glycolysis, Calcium Signaling, Obesity, Molecular Biology, Calcium signaling, Grape Seed Extract, Brain, food and beverages, medicine.disease, 3. Good health, Rats, Oxidative Stress, 030104 developmental biology, Lipotoxicity, Gene Expression Regulation, Murine model, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, 030217 neurology & neurosurgery, Oxidative stress
Abstract: International audience; n recent years, the obesity epidemic has developed into a major health crisis worldwide. With current treatments limited to expensive, high-risk surgery and minimally efficacious pharmacotherapy, new therapeutic options are urgently needed to fight against this alarming trend. Though brain dysfunction has been studied linked to high fat diet (HFD) and grape seed and skin extract (GSSE) correction, the proteomic modifications linking the two effects on brain lipotoxicity are not well understood. To this end rats were exposed for 8 weeks to HFD treatment, to GSSE (500 mg/kg BW) and to binary mixture of HFD and GSSE to gain insight into the potential pathways altered with metabolic disease and the protection afforded by GSSE. Significant modifications of brain proteins were detected using mass spectrometry-based differential proteomics. These proteins were mainly related to oxidative stress, glycolysis and calcium signaling. Additionally, proteins involved in the cytoskeleton were also affected by HFD treatment. Interestingly, whether up- or down regulated protein abundances, GSSE corrected most of the disturbances of HFD treatment. These findings provide impetus for future therapeutic investigation on GSSE against other metabolic disorders.
Published: 2017
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24. Neuroprotective Activity of Grape Seed and Skin Extract Against Lithium Exposure Using Proteomic Research

Author: Olfa Khazri, Ferid Limam, Pascal Cosette, Abdelhafidh Khazri, Ezzeddine Aouani, Ali Mezni, Faculté des Sciences de Bizerte [Université de Carthage], Université de Carthage - University of Carthage, Laboratoire des Substances Bioactives (Centre de Biotechnologie de Borj Cedria, Hammam-Lif) (LSBA), Centre de Biotechnologie de Borj Cédria (Hammam-Lif, Tunisie), Plate-forme de Protéomique PISSARO, 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)-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), 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), and Normandie Université (NU)-Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)
Subjects: 0301 basic medicine, Male, Proteomics, food.ingredient, Proteome, [SDV.NEU.NB]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Neurobiology, Neuroscience (miscellaneous), Lithium, medicine.disease_cause, Neuroprotection, 03 medical and health sciences, Cellular and Molecular Neuroscience, 0302 clinical medicine, food, Phenols, Tandem Mass Spectrometry, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], medicine, Animals, Protein Interaction Maps, Rats, Wistar, Grape Seed Extract, Proteomic research, Chemistry, Brain, Wistar rats, Oxidative Stress, 030104 developmental biology, Neuroprotective Agents, Neurology, Biochemistry, GSSE, Grape seed extract, Phosphoprotein, Toxicity, Signal transduction, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, 030217 neurology & neurosurgery, Oxidative stress, Chromatography, Liquid
Abstract: International audience; Lithium (Li) has raised scientific concern because it represents a serious problem threatening human health. This study aimed firstly at analyzing and potentially quantifying the impact of Li and grape seed and skin extract (GSSE) separately and, secondly, describing the possible neuroprotective activity of GSSE against Li toxicity. To this end, rats were exposed for 30 days to different Li concentrations (0, 2, and 100 mg/kg bw), to GSSE (4000 mg/kg bw), and to binary mixture of Li and GSSE. Liquid chromatography (HPLC–MS/MS) analysis used for GSSE showed that 15 phenolic compounds are present in the extract. Significant modifications of proteins were detected in the brain using proteomics research after treatment. Proteins were successfully identified by a linear ion trap–Orbitrap mass spectrometer. These proteins can be roughly related to oxidative stress, glycolysis, signaling pathway, and inflammation. Additionally, proteins involved in cell junction such as myosin, spectrin, tubulin, ERM-binding phosphoprotein, and dynein were also affected by Li exposure. Dose response was detected for most expressed proteins after Li treatment. In contrast, GSSE induced the expression and/or the stabilization of some proteins changed after Li treatment in the brain showing its neuroprotective activity. These data demonstrate that proteomic analysis is a powerful tool to provide valuable insights into mechanisms of toxicity of Li in the nervous system of Wistar rats. To our knowledge, this is the first evidence of using GSSE as neuroprotective model against Li toxicity. These findings provide impetus for future investigation on GSSE against other toxic chemicals.
Published: 2017
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25. Glioprotective effect of Ulva rigida extract against UVB cellular damages

Author: Mohamed Amri, Olfa Masmoudi, Ines Bourguiba, Annick Schaumann, Amine Ben Mlouka, Julie Hardouin, Thierry Jouenne, Amel Zehlila, Pascal Cosette, Polymères Biopolymères Surfaces (PBS), 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), Institut de Chimie du CNRS (INC)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), 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)-Université Le Havre Normandie (ULH), Normandie Université (NU)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-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)-Université Le Havre Normandie (ULH), Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS), Neuroendocrinologie cellulaire et moléculaire, Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Plate-forme de Protéomique PISSARO, 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)-Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), Faculté des Sciences Mathématiques, Physiques et Naturelles de Tunis (FST), Université de Tunis El Manar (UTM), 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), and Normandie Université (NU)-Normandie Université (NU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, biology, Calmodulin, [SDV]Life Sciences [q-bio], Proteolytic enzymes, biology.organism_classification, Cellular viability, Ulva rigida, Lipid peroxidation, Superoxide dismutase, 03 medical and health sciences, chemistry.chemical_compound, 030104 developmental biology, 0302 clinical medicine, Biochemistry, Algae, chemistry, Catalase, biology.protein, Agronomy and Crop Science, 030217 neurology & neurosurgery, ComputingMilieux_MISCELLANEOUS
Abstract: Natural molecules from different origins exhibit high therapeutic potential. Among them, molecules from marine algae are of particular interest. In the present study, we investigated the preventive effect of a protein extract (PE) of Ulva rigida against UVB-induced cellular damages. We demonstrated that a treatment of cortical astrocytes with 50 μg of PE induced a strong glioprotective effect and suppressed harmful effects of UVB radiations, increasing in particular cellular viability. In additional assays, this extract promoted the activity of catalase and superoxide dismutase and inhibited the production of stress markers, such as H 2 O 2 or lipid peroxidation. As expected, proteolytic digestion or heating treatment of algal extract inhibited this preventive effect, arguing for the predominant role of the protein fraction. Thereafter, proteomic investigations allowed to identify several proteins from the extract, among which calmodulin revealed to represent an important contributor to the observed protective activities.
Published: 2017
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26. Impaired vitreous composition and retinal pigment epithelium function in the FoxG1::LRP2 myopic mice

Author: Pascal Cosette, Sébastien Augustin, Sirine Ben-Yacoub, Antoine Obry, Manuel Simonutti, Géraldine Toutirais, Renata Kozyraki, Olivier Cases, Antoine Joseph, Annabel Christ, HAL-UPMC, Gestionnaire, Institut de la Vision, Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Plate-forme de Protéomique PISSARO, 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)-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)-High-tech Research Infrastructures for Life Sciences (HeRacLeS), Normandie Université (NU)-Normandie Université (NU)-Institute for Research and Innovation in Biomedicine (IRIB), 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)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Physiopathologie et biothérapies des maladies inflammatoires et autoimmunes, Normandie Université (NU)-Normandie Université (NU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Microscopie Electronique [IBPS] (IBPS-ME), Institut de Biologie Paris Seine (IBPS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Max Delbrück Center for Molecular Medicine [Berlin] (MDC), Helmholtz-Gemeinschaft = Helmholtz Association, 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 National de la Santé et de la Recherche Médicale (INSERM)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Centre de Recherche des Cordeliers (CRC (UMR_S_1138 / U1138)), École pratique des hautes études (EPHE)-Université Paris Diderot - Paris 7 (UPD7)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU), Polymères Biopolymères Surfaces (PBS), 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), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Pierre et Marie Curie - Paris 6 (UPMC), Acides nucléiques : dynamique, ciblage, et fonctions biologiques - Régulation et dynamique des génomes (ANDCFB), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Max Delbrück Center for Molecular Medicine [Berlin], and Normandie Université (NU)-Normandie Université (NU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Rouen Normandie (UNIROUEN)
Subjects: 0301 basic medicine, genetic structures, Endocytic cycle, Mice, Transgenic, Nerve Tissue Proteins, Retinal Pigment Epithelium, Biology, Vitreous, Pathogenesis, Mice, 03 medical and health sciences, chemistry.chemical_compound, 0302 clinical medicine, low density lipoprotein receptor-related protein 2, lipoprotein receptor-related protein 2, High myopia, Myopia, medicine, [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, Animals, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, [SDV.MHEP.OS]Life Sciences [q-bio]/Human health and pathology/Sensory Organs, Molecular Biology, Retinal pigment epithelium, ADP-Ribosylation Factors, Retinal detachment, Forkhead Transcription Factors, Anatomy, medicine.disease, LRP2, eye diseases, Endocytosis, Cell biology, Vitreous Body, Low Density Lipoprotein Receptor-Related Protein-2, 030104 developmental biology, medicine.anatomical_structure, chemistry, [SDV.MHEP.OS] Life Sciences [q-bio]/Human health and pathology/Sensory Organs, Low-density lipoprotein, 030221 ophthalmology & optometry, Molecular Medicine, low density, sense organs, Homeostasis, Retinopathy
Abstract: International audience; High myopia (HM) is one of the main causes of visual impairment and blindness all over the world and an unsolved medical problem. Persons with HM are predisposed to other eye pathologies such as retinal detachment, myopic retinopathy or glaucomatous optic neuropathy, complications that may at least partly result from the extensive liquefaction of the myopic vitreous gel. To identify the involvement of the liquid vitreous in the pathogenesis of HM we here analyzed the vitreous of the recently described highly myopic low density lipoprotein receptor-related protein 2 (Lrp2)-deficient eyes. Whereas the gel-like fraction was not apparently modified, the volume of the liquid vitreous fraction (LVF) was much higher in the myopic eyes. Biochemical and proteome analysis of the LVF revealed several modifications including a marked decrease of potassium, sodium and chloride, of proteins involved in ocular tissue homeostasis and repair as well as of ADP-ribosylation factor 4 (ARF4), a protein possibly involved in LRP2 trafficking. A small number of proteins, mainly comprising known LRP2 ligands or proteins of the inflammatory response, were over expressed in the mutants. Moreover the morphology of the LRP2-deficient retinal pigment epithelium (RPE) cells was affected and the expression of ARF4 as well as of proteins involved in degradative endocytosis was strongly reduced. Our results support the idea that impairment of the RPE structure and most likely endocytic function may contribute to the vitreal modifications and pathogenesis of HM.
Published: 2017
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27. The aliphatic amidase AmiE is involved in regulation of Pseudomonas aeruginosa virulence

Author: Pascal Cosette, Alain Dufour, Alexandre Crépin, Sylvie Chevalier, Pierre Cornelis, Julie Hardouin, Thibaut Rosay, Julien Vieillard, Perrine Bortolotti, Thomas Clamens, Joerg Overhage, Benoit Guery, Fergal O'Gara, Takfarinas Kentache, Anke Neidig, Teddy Grandjean, Marc G. J. Feuilloley, Marlies J. Mooij, Emeline Bouffartigues, Mélanie Hillion, Olivier Lesouhaitier, Laboratoire de Microbiologie Signaux et Microenvironnement (LMSM), Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU), Laboratoire de Biotechnologie et Chimie Marines (LBCM), Université de Brest (UBO)-Université de Bretagne Sud (UBS)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Recherche translationelle relations hôte-pathogènes, Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille), Polymères Biopolymères Surfaces (PBS), 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), Institut de Chimie du CNRS (INC)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), 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)-Université Le Havre Normandie (ULH), Normandie Université (NU)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-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)-Université Le Havre Normandie (ULH), Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS), Université Lille 2 - Faculté de Médecine, Karlsruhe Institute of Technology (KIT), University College Cork (UCC), Chimie Organique et Bioorganique : Réactivité et Analyse (COBRA), Institut Normand de Chimie Moléculaire Médicinale et Macromoléculaire (INC3M), Normandie Université (NU)-Institut de Chimie du CNRS (INC)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie Organique Fine (IRCOF), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Plate-forme de Protéomique PISSARO, Institute for Research and Innovation in Biomedicine (IRIB), 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), Normandie Université (NU)-Normandie Université (NU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Biologie et physiologie des états septiques, IFR114-Université de Lille, Droit et Santé, This work was supported by grants from the Communauté d’Agglomération d’Evreux, the Conseil Général de l′Eure, European Union (FEDER), the French Association 'Vaincre la Mucoviscidose' and the Partenariats Hubert Curien (PHC Ulysses). Financial support by the BioInterfaces (BIF) Program of the Karlsruhe Institute of Technology (KIT) in the Helmholtz Association is gratefully acknowledged., We wish to thank Magalie Barreau and Olivier Maillot for technical assistance. T. Clamens and T. Rosay are recipients of a doctoral fellowship from the French Ministry of Research (MRE)., Vriendenkring VUB, Microbiology, Université de Bretagne Sud (UBS)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Institut Normand de Chimie Moléculaire Médicinale et Macromoléculaire (INC3M), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), 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)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Faculté de Médecine Henri Warembourg - Université de Lille, Institut de Chimie Organique Fine (IRCOF), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université de Rouen Normandie (UNIROUEN), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Institut Normand de Chimie Moléculaire Médicinale et Macromoléculaire (INC3M), Normandie Université (NU)-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)-Normandie Université (NU)-Institute for Research and Innovation in Biomedicine (IRIB), 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)-Université de Rouen Normandie (UNIROUEN), 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)-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)-Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), and Bazire, Alexis
Subjects: Male, 0301 basic medicine, Virulence regulation, MESH: Pseudomonas Infections/microbiology, Proteome, health care facilities, manpower, and services, MESH: Dictyostelium/microbiology, MESH: Virulence, medicine.disease_cause, MESH: Quorum Sensing, Pilus, chemistry.chemical_compound, MESH: Caenorhabditis elegans/microbiology, MESH: Amidohydrolases/metabolism, AmiE overproduction, Dictyostelium, MESH: Animals, Lung, health care economics and organizations, MESH: Pseudomonas aeruginosa/enzymology, Multidisciplinary, Virulence, Quorum Sensing, MESH: Proteome, Pseudomonas aeruginosa, Female, Life sciences, biology, MESH: Virulence Factors, Virulence Factors, 030106 microbiology, Homoserine, MESH: Biofilms, Biology, Microbiology, Article, Amidohydrolases, Amidase, 03 medical and health sciences, Pyocyanin, MESH: Mice, Inbred C57BL, ddc:570, Journal Article, medicine, Animals, Pseudomonas Infections, cardiovascular diseases, Caenorhabditis elegans, MESH: Lung/microbiology, MESH: Pseudomonas aeruginosa/pathogenicity, Biofilm, Bacteriology, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, MESH: Male, MESH: Pseudomonas Infections/enzymology, Mice, Inbred C57BL, Quorum sensing, chemistry, Biofilms, FOS: Biological sciences, Pseudomonas aeruginosa virulence, [SDV.MP.BAC] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, MESH: Female
Abstract: We have previously shown that the eukaryotic C-type natriuretic peptide hormone (CNP) regulates Pseudomonas aeruginosa virulence and biofilm formation after binding on the AmiC sensor, triggering the amiE transcription. Herein, the involvement of the aliphatic amidase AmiE in P. aeruginosa virulence regulation has been investigated. The proteome analysis of an AmiE over-producing strain (AmiE+) revealed an expression change for 138 proteins, including some that are involved in motility, synthesis of quorum sensing compounds and virulence regulation. We observed that the AmiE+ strain produced less biofilm compared to the wild type, and over-produced rhamnolipids. In the same line, AmiE is involved in P. aeruginosa motilities (swarming and twitching) and production of the quorum sensing molecules N-acyl homoserine lactones and Pseudomonas Quinolone Signal (PQS). We observed that AmiE overproduction reduced levels of HCN and pyocyanin causing a decreased virulence in different hosts (i.e. Dictyostelium discoideum and Caenorhabditis elegans). This phenotype was further confirmed in a mouse model of acute lung infection, in which AmiE overproduction resulted in an almost fully virulence decrease. Taken together, our data suggest that, in addition to its role in bacterial secondary metabolism, AmiE is involved in P. aeruginosa virulence regulation by modulating pilus synthesis and cell-to-cell communication.
Published: 2017
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28. Major remodeling of brain microvessels during neonatal period in the mouse: A proteomic and transcriptomic study

Author: Antoine Obry, Baptiste Porte, Thierry Lequerré, Soumeya Bekri, Yasmine Zerdoumi, Bruno J. Gonzalez, Céline Derambure, Philippe Leroux, Julie Hardouin, Pascal Cosette, Nicolas Dupré, Jean-Michel Flaman, Michèle Hauchecorne, Stéphane Marret, Endothélium microcirculatoire cérébral et lésions du système nerveux central au cours du développement (Néovasc), Université de Rouen Normandie (UNIROUEN), 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)-Institut National de la Santé et de la Recherche Médicale (INSERM), Génomique et Médecine Personnalisée du Cancer et des Maladies Neuropsychiatriques (GPMCND), Normandie Université (NU)-Normandie Université (NU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Polymères Biopolymères Surfaces (PBS), 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), Institut de Chimie du CNRS (INC)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), 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)-Université Le Havre Normandie (ULH), Normandie Université (NU)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-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)-Université Le Havre Normandie (ULH), Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS), Plate-forme de Protéomique PISSARO, 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), Génétique du cancer et des maladies neuropsychiatriques (GMFC), Service de rhumatologie [CHU Rouen], CHU Rouen, Normandie Université (NU)-Normandie Université (NU)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU), Physiopathologie et biothérapies des maladies inflammatoires et autoimmunes, Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU), Laboratoire de biochimie générale [Rouen], Normandie Université (NU)-Centre hospitalier universitaire de Rouen, Maladies neurodéveloppementales et neurovasculaires (NeuroDiderot (UMR_S_1141 / U1141)), Université Paris Diderot - Paris 7 (UPD7)-Institut National de la Santé et de la Recherche Médicale (INSERM), 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), Team 4 'NeoVasc' - INSERM U1245, Normandie Université (NU)-Normandie Université (NU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Rouen Normandie (UNIROUEN), Service de rhumatologie [Rouen], Normandie Université (NU)-Normandie Université (NU)-CHU Rouen, Institut de Physique du Globe de Paris (IPGP), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-IPG PARIS-Université Paris Diderot - Paris 7 (UPD7)-Université de La Réunion (UR)-Centre National de la Recherche Scientifique (CNRS), Schulich School of Music & CIRMMT, and McGill University
Subjects: Male, Proteomics, 0301 basic medicine, Proteases, Proteome, Microarray, [SDV]Life Sciences [q-bio], Vascular Remodeling, Bioinformatics, Transcriptome, Andrology, Extracellular matrix, Mice, 03 medical and health sciences, 0302 clinical medicine, Subependymal zone, Animals, Medicine, ComputingMilieux_MISCELLANEOUS, Cerebral Hemorrhage, business.industry, Glutamate receptor, Brain, Gene Expression Regulation, Developmental, Original Articles, medicine.disease, Mice, Inbred C57BL, 030104 developmental biology, Intraventricular hemorrhage, Neurology, Microvessels, Forebrain, Female, [SDV.NEU]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC], Neurology (clinical), Cardiology and Cardiovascular Medicine, business, 030217 neurology & neurosurgery
Abstract: Preterm infants born before 29 gestation weeks incur major risk of subependymal/intracerebral/intraventricular hemorrhage. In mice, neonate brain endothelial cells are more prone than adult cells to secrete proteases under glutamate challenge, and invalidation of the Serpine 1 gene is accompanied by high brain hemorrhage risk up to five days after birth. We hypothesized that the structural and functional states of microvessels might account for age-dependent vulnerability in mice up to five days after birth and might represent a pertinent paradigm to approach the hemorrhage risk window observed in extreme preterms. Mass spectrometry proteome analyses of forebrain microvessels at days 5, 10 and in adult mice revealed 899 proteins and 36 enriched pathways. Microarray transcriptomic study identified 5873 genes undergoing at least two-fold change between ages and 93 enriched pathways. Both approaches pointed towards extracellular matrix, cell adhesion and junction pathways, indicating delayed microvascular strengthening after P5. Furthermore, glutamate receptors, proteases and their inhibitors exhibited convergent evolutions towards excitatory aminoacid sensitivity and low proteolytic control likely accounting for vascular vulnerability in P5 mice. Thus, age vascular specificities must be considered in future therapeutic interventions in preterms. Data are available on ProteomeXchange (identifier PXD001718) and NCBI Gene-Expression-Omnibus repository (identification GSE67870).
Published: 2016
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29. Proteomics dedicated to biofilmology: What have we learned from a decade of research?

Author: Thierry Jouenne, Arbia Khemiri, Pascal Cosette, Polymères Biopolymères Surfaces (PBS), 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), Institut de Chimie du CNRS (INC)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), 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)-Université Le Havre Normandie (ULH), Normandie Université (NU)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-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)-Université Le Havre Normandie (ULH), Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS), Plate-forme de Protéomique PISSARO, Institute for Research and Innovation in Biomedicine (IRIB), Université de Rouen Normandie (UNIROUEN), 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), and Normandie Université (NU)-Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)
Subjects: Proteomics, 0301 basic medicine, Microbiology (medical), Proteome, [SDV]Life Sciences [q-bio], 030106 microbiology, Immunology, General Medicine, Computational biology, Biology, Bioinformatics, 03 medical and health sciences, Gene Expression Regulation, Biofilms, Humans, Immunology and Allergy, ComputingMilieux_MISCELLANEOUS, Signal Transduction, Microbial Biofilms
Abstract: Advances in proteomics techniques over the past decade, closely integrated with genomic and physicochemical approach, have played a great role in developing knowledge of the biofilm lifestyle of bacteria. Despite bacterial proteome versatility, many studies have demonstrated the ability of proteomics approaches to elucidating the biofilm phenotype. Though these investigations have been largely used for biofilm studies in the last decades, they represent, however, a very low percentage of proteomics works performed up to now. Such approaches have offered new targets for combating microbial biofilms by providing a comprehensive quantitative and qualitative overview of their protein cell content. Herein, we summarized the state of the art in knowledge about biofilm physiology after one decade of proteomic analysis. In a second part, we highlighted missing research tracks for the next decade, emphasizing the emergence of posttranslational modifications in proteomic studies stemming from recent advances in mass spectrometry-based proteomics.
Published: 2016
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30. Characterization of endophytic Bacillus strains from tomato plants (Lycopersicon esculentum) displaying antifungal activity against Botrytis cinerea Pers

Author: Rania Belaid, Christophe Rihouey, Ines Karkouch, Thierry Jouenne, Imen Ben Slimene, Marwa Bejaoui, Sana Azaeiz, Pascal Cosette, Ferid Limam, Asma Kefi, Polymères Biopolymères Surfaces (PBS), 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), Institut de Chimie du CNRS (INC)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), 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)-Université Le Havre Normandie (ULH), Normandie Université (NU)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-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)-Université Le Havre Normandie (ULH), Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS), Plate-forme de Protéomique PISSARO, Institute for Research and Innovation in Biomedicine (IRIB), Université de Rouen Normandie (UNIROUEN), 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)-Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), Laboratoire des Substances Bioactives (Centre de Biotechnologie de Borj Cedria, Hammam-Lif) (LSBA), and Centre de Biotechnologie de Borj Cédria (Hammam-Lif, Tunisie)
Subjects: Spectrometry, Mass, Electrospray Ionization, Antifungal Agents, food.ingredient, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, Physiology, Bacillus, Microbial Sensitivity Tests, Fungus, DNA, Ribosomal, Plant Roots, Applied Microbiology and Biotechnology, Lycopersicon, Microbiology, Lipopeptides, chemistry.chemical_compound, food, Solanum lycopersicum, Antibiosis, Botany, Endophytes, Pest Control, Biological, Mycelium, ComputingMilieux_MISCELLANEOUS, Plant Diseases, Botrytis cinerea, Botrytis, Base Sequence, Plant Stems, biology, fungi, food and beverages, General Medicine, biology.organism_classification, Plant Leaves, Biological Control Agents, chemistry, Peptides, Surfactin, Antagonism, Antimicrobial Cationic Peptides, Biotechnology
Abstract: Eighty endophytic bacteria were isolated from healthy tissues of roots, stems, leaves and fruits of tomato plants (Lycopersicon esculentum). Four strains, named BL1, BT5, BR8 and BF11 were selected for their antagonism against Botrytis cinerea, a phytopathogenic fungus responsible of gray mold in several important crops, with growth inhibitory activity ranging from 27 to 53%. Morphological, biochemical, and molecular parameters as 16S rDNA sequencing demonstrated that the selected bacterial strains were related to Bacillus species which are known to produce and secrete a lot of lipopeptides with strong inhibitory effect against pathogen mycelial growth. Electrospray mass spectrometry analysis showed that these strains produced heterogeneous mixture of antibiotics belonging to fengycin and surfactin for BL1 and BT5, to iturin and surfactin for BR8, to bacillomycin D, fengycin and surfactin for BF11. Furthermore, these bacteria exhibited biocontrol potential by reducing the disease severity when tested on detached leaflets. Based on their antifungal activity against Botrytis cinerea, these strains could be used for biological control of plant diseases.
Published: 2015
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31. Characterization of new outer membrane proteins of Pseudomonas aeruginosa using a combinatorial peptide ligand library

Author: Emmanuelle Dé, Pascal Cosette, Thierry Jouenne, Julie Hardouin, Arbia Khemiri, Philippe Chan Tchi Song, Mohamed Amine Ben Mlouka, Damien Seyer, Equipe de recherche sur les relations matrice extracellulaire-cellules (ERRMECe), Fédération INSTITUT DES MATÉRIAUX DE CERGY-PONTOISE (I-MAT), Université de Cergy Pontoise (UCP), Université Paris-Seine-Université Paris-Seine-Université de Cergy Pontoise (UCP), Université Paris-Seine-Université Paris-Seine, Polymères Biopolymères Surfaces (PBS), 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), Institut de Chimie du CNRS (INC)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), 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)-Université Le Havre Normandie (ULH), Normandie Université (NU)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-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)-Université Le Havre Normandie (ULH), Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS), Plate-forme de Protéomique PISSARO, Institute for Research and Innovation in Biomedicine (IRIB), Université de Rouen Normandie (UNIROUEN), 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), and Normandie Université (NU)-Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)
Subjects: Two-dimensional gel electrophoresis, biology, Chemistry, Pseudomonas aeruginosa, [SDV]Life Sciences [q-bio], Albumin, Shotgun, biology.organism_classification, medicine.disease_cause, Biochemistry, Blood proteins, Molecular biology, Analytical Chemistry, Membrane protein, Peptide Library, medicine, Electrophoresis, Gel, Two-Dimensional, Bacterial outer membrane, Bacteria, ComputingMilieux_MISCELLANEOUS, Bacterial Outer Membrane Proteins
Abstract: Most often, the use of ProteoMiner beads has been restricted to human serum proteins for the normalization of major proteins, such as albumin. However, there are other situations of interest in which the presence of major proteins would quench the signals of low abundance polypeptides. We propose the use of these beads for investigating the envelope of the gram-negative bacterium Pseudomonas aeruginosa. Initially, we performed comparative 2D electrophoresis to qualitatively evaluate the incidence of the normalization stage. This demonstrated a significant reduction of the major membrane proteins. Thereafter, using shotgun analysis, the same protein extract was targeted by using combinatorial peptide ligand library capture. This treatment yielded 154 additional outer membrane proteins (OMPs) uncovered by the study of the crude sample.
Published: 2015
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32. Characterization of N-terminal protein modifications in Pseudomonas aeruginosa PA14

Author: Pascal Cosette, Julie Hardouin, Tassadit Ouidir, Frédérique Jarnier, Thierry Jouenne, Plate-forme de Protéomique PISSARO, Institute for Research and Innovation in Biomedicine (IRIB), Université de Rouen Normandie (UNIROUEN), 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)-Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), Polymères Biopolymères Surfaces (PBS), 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), Institut de Chimie du CNRS (INC)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), 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)-Université Le Havre Normandie (ULH), Normandie Université (NU)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-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)-Université Le Havre Normandie (ULH), and Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Proteomics, Proteome, Molecular Sequence Data, Amino-Acid N-Acetyltransferase, Biophysics, Peptide, Cleavage (embryo), medicine.disease_cause, Biochemistry, 03 medical and health sciences, chemistry.chemical_compound, Methionine, Bacterial Proteins, medicine, [CHIM]Chemical Sciences, Amino Acid Sequence, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, chemistry.chemical_classification, 0303 health sciences, biology, Pseudomonas aeruginosa, 030302 biochemistry & molecular biology, Acetylation, biology.organism_classification, Bacterial Processes, Peptide Fragments, chemistry, Protein Processing, Post-Translational, Bacteria
Abstract: Even though protein initiator methionine excision (NME) and N-terminal acetylation (NTA) have been relatively well investigated in eukaryotic proteomes, few studies were dedicated to these modifications in bacteria up to now. In this work, we investigated, for the first time, the N-terminal proteome of the bacterium Pseudomonas aeruginosa PA14 by studying the NME and NTA processes using proteomic approaches. For NME, most of proteins had their initiator Met cleaved (63%) and the nature of the penultimate residue seems to be essential for this cleavage. Concerning NTA, two methods were applied (protein fractionation and peptide enrichment). This allowed us to identify 117 Nα-acetylated proteins, among them 113 have not yet been described as modified in bacteria. Most often, the non-acetylated form was over-represented compared to the acetylated form, arguing that this latter was a minor part of the total abundance of a given protein. Furthermore, some proteins with acetylated initiator methionine were observed. The present work significantly enlarges the number of N-terminally modified proteins in bacteria and confirms that these modifications are a general and fundamental process, not only restricted to eukaryotes. Biological significance Protein modifications in prokaryotes have been detected more recently than in eukaryotes. Methionine cleavage and N-terminal acetylation are two common protein N-terminal modifications. Despite their importance in bacterial processes, they are less investigated. The characterization of N-terminal acetylation in bacteria is a challenge because no antibody exists and it is a less frequent modification than in eukaryotes. We used proteomic approaches (enrichment, fractionation, nanoLC–MS/MS, and bioinformatic analyses) to investigate the N-terminal methionine excision and to profile the N-terminal acetylome of P. aeruginosa strain PA14. From our results, around 60% of the proteins had their iMet cleaved. In total, 117 proteins were identified constituting the largest dataset in prokaryotes. Among them, proteins kept their initiator methionine and were acetylated. These results may facilitate the design of experiments to better understand the role of acetylation at the protein N-terminus of P. aeruginosa PA14.
Published: 2015
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33. Growth Retardation, Reduced Invasiveness, and Impaired Colistin-Mediated Cell Death Associated with Colistin Resistance Development in Acinetobacter baumannii

Author: Athanassios Tsakris, Spyros Pournaras, Emmanuelle Dé, Yassine Nait Chabane, Julie Hardouin, Aggeliki Poulou, Ioulia Kristo, Konstantina Dafopoulou, Pascal Cosette, Demosthenes Makris, Department of Microbiology, University of Thessaly [Volos] (UTH), Serres General Hospital, Intensive Care Unit, University of Thessaly [Volos] (UTH)-University Hospital of Larisa, Polymères Biopolymères Surfaces (PBS), 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), Institut de Chimie du CNRS (INC)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), 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)-Université Le Havre Normandie (ULH), Normandie Université (NU)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-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)-Université Le Havre Normandie (ULH), Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS), Plate-forme de Protéomique PISSARO, Institute for Research and Innovation in Biomedicine (IRIB), Université de Rouen Normandie (UNIROUEN), 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)-Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), National and Kapodistrian University of Athens (NKUA), Institut Normand de Chimie Moléculaire Médicinale et Macromoléculaire (INC3M), and Normandie Université (NU)
Subjects: Acinetobacter baumannii, medicine.drug_class, [SDV]Life Sciences [q-bio], Antibiotics, Microbial Sensitivity Tests, Drug resistance, medicine.disease_cause, Microbiology, Superoxide dismutase, Bacterial Proteins, Mechanisms of Resistance, Drug Resistance, Bacterial, Operon, medicine, Humans, [CHIM]Chemical Sciences, Pharmacology (medical), ComputingMilieux_MISCELLANEOUS, Aged, Antibacterial agent, Aconitate Hydratase, Pharmacology, Microbial Viability, biology, Colistin, Superoxide Dismutase, Pseudomonas aeruginosa, Gene Expression Regulation, Bacterial, Peroxiredoxins, biochemical phenomena, metabolism, and nutrition, Middle Aged, equipment and supplies, Catalase, biology.organism_classification, Anti-Bacterial Agents, Clone Cells, Infectious Diseases, biology.protein, Neisseriaceae, Acinetobacter Infections, medicine.drug
Abstract: Two colistin-susceptible/colistin-resistant (Col s /Col r ) pairs of Acinetobacter baumannii strains assigned to international clone 2, which is prevalent worldwide, were sequentially recovered from two patients after prolonged colistin administration. Compared with the respective Col s isolates (Ab248 and Ab299, both having a colistin MIC of 0.5 μg/ml), both Col r isolates (Ab249 and Ab347, with colistin MICs of 128 and 32 μg/ml, respectively) significantly overexpressed pmrCAB genes, had single-amino-acid shifts in the PmrB protein, and exhibited significantly slower growth. The Col r isolate Ab347, tested by proteomic analysis in comparison with its Col s counterpart Ab299, underexpressed the proteins CsuA/B and C from the csu operon (which is necessary for biofilm formation). This isolate also underexpressed aconitase B and different enzymes involved in the oxidative stress response (KatE catalase, superoxide dismutase, and alkyl hydroperoxide reductase), suggesting a reduced response to reactive oxygen species (ROS) and, consequently, impaired colistin-mediated cell death through hydroxyl radical production. Col s isolates that were indistinguishable by macrorestriction analysis from Ab299 caused six sequential bloodstream infections, and isolates indistinguishable from Ab248 caused severe soft tissue infection, while Col r isolates indistinguishable from Ab347 and Ab249 were mainly colonizers. In particular, a Col s isolate identical to Ab299 was still invading the bloodstream 90 days after the colonization of this patient by Col r isolates. These observations indicate considerably lower invasiveness of A. baumannii clinical isolates following the development of colistin resistance.
Published: 2014
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34. Design and Synthesis of Epicocconone Analogues with Improved Fluorescence Properties

Author: Peter Karuso, Xavier Franck, Bertrand Naudin, Philippe A. Peixoto, Malcolm S. Ball, Thibault Alle, Pascal Cosette, Agathe Boulangé, Chimie Organique et Bioorganique : Réactivité et Analyse (COBRA), Institut Normand de Chimie Moléculaire Médicinale et Macromoléculaire (INC3M), Institut de Chimie du CNRS (INC)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), 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)-Université Le Havre Normandie (ULH), Normandie Université (NU)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Institut de Chimie du CNRS (INC)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie Organique Fine (IRCOF), Université de Rouen Normandie (UNIROUEN), and Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Fluorophore, Epicocconone, Chemistry Techniques, Synthetic, [CHIM.THER]Chemical Sciences/Medicinal Chemistry, Ring (chemistry), Biochemistry, Catalysis, symbols.namesake, chemistry.chemical_compound, Colloid and Surface Chemistry, Drug Stability, [CHIM.ANAL]Chemical Sciences/Analytical chemistry, Stokes shift, Organic chemistry, Benzopyrans, Furans, ComputingMilieux_MISCELLANEOUS, Fluorescent Dyes, Detection limit, Natural product, Chemistry, [CHIM.ORGA]Chemical Sciences/Organic chemistry, Total synthesis, General Chemistry, [CHIM.CATA]Chemical Sciences/Catalysis, Ketones, Combinatorial chemistry, Fluorescence, [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, Spectrometry, Fluorescence, Cyclization, Drug Design, symbols, Thermodynamics, [CHIM.CHEM]Chemical Sciences/Cheminformatics
Abstract: Epicocconone is a natural latent fluorophore that is widely used in biotechnology because of its large Stokes shift and lack of fluorescence in its unconjugated state. However, the low photostability and quantum yields of epicocconone have limited its wider use, and in the absence of a total synthesis, this limitation has been a long-standing problem. Here we report a general strategy for the synthesis of epicocconone analogues that relies on a 2-iodoxybenzoic acid-mediated dearomatization and on the replacement of the triene tail of the natural product by an aromatic ring. This design element is general and the synthesis is straightforward, providing ready access to libraries of polyfunctional fluorophores with long Stokes shifts based on the epicocconone core. Our structural modifications resulted in analogues with increased photostability and quantum yields compared with the natural product. Staining proteomic gels with these new analogues showed significant lowering of the detection limit and a 30% increase in the number of low-abundance proteins detected. These epiccoconone analogues will substantially improve the discovery rate of biomarker needles in the proteomic haystack.
Published: 2014
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35. N-glycosidase treatment with 18O labeling and de novo sequencing argues for flagellin FliC glycopolymorphism in Pseudomonas aeruginosa

Author: Arbia Khemiri, Bertrand Naudin, Pascal Cosette, Philippe Chan Tchi Song, Thierry Jouenne, Xavier Franck, Chimie Organique et Bioorganique : Réactivité et Analyse (COBRA), Institut Normand de Chimie Moléculaire Médicinale et Macromoléculaire (INC3M), Institut de Chimie du CNRS (INC)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), 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)-Université Le Havre Normandie (ULH), Normandie Université (NU)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Institut de Chimie du CNRS (INC)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie Organique Fine (IRCOF), Université de Rouen Normandie (UNIROUEN), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Polymères Biopolymères Surfaces (PBS), 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)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), Normandie Université (NU)-Université Le Havre Normandie (ULH), and Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS)
Subjects: PNGase F, Glycosylation, Molecular Sequence Data, Biochemistry, Analytical Chemistry, 03 medical and health sciences, chemistry.chemical_compound, Oxygen Radioisotopes, Tandem Mass Spectrometry, Consensus sequence, Peptide-N4-(N-acetyl-beta-glucosaminyl) Asparagine Amidase, Amino Acid Sequence, Deamidation, Glycoproteins, 030304 developmental biology, chemistry.chemical_classification, 0303 health sciences, Polymorphism, Genetic, biology, Chemistry, [CHIM.ORGA]Chemical Sciences/Organic chemistry, 030302 biochemistry & molecular biology, Pseudomonas, biology.organism_classification, Peptide Fragments, Biotinylation, Pseudomonas aeruginosa, biology.protein, Glycoprotein, Flagellin
Abstract: International audience; In prokaryote organisms, N-glycosylation of proteins is often correlated to cell-cell recognition and extracellular events. Those glycoproteins are potential targets for infection control. To date, many surface-glycosylated proteins from bacterial pathogens have been described. However, N-linked Pseudomonas surface-associated glycoproteins remain underexplored. We report a combined enrichment and labeling strategy to identify major glycoproteins on the outside of microorganisms. More precisely, bacteria were exposed to a mix of biotinylated lectins able to bind with glycoproteins. The latter were then recovered by avidin beads, digested with trypsin, and submitted to mass spectrometry. The targeted mixture of glycoproteins was additionally deglycosylated in the presence of H2(18)O to incorporate (18)O during PNGase F treatment and were also analyzed using mass spectrometry. This approach allowed us to identify a few tens of potential N-glycoproteins, among which flagellin FliC was the most abundant. To detect the possible sites of FliC modifications, a de novo sequencing step was also performed to discriminate between spontaneous deamidation and N-glycan loss. This approach led to the proposal of three potential N-glycosylated sites on the primary sequence of FliC: N26, N69, and N439, with two of these three asparagines belonging to an N-X-(S/T) consensus sequence. These observations suggest that flagellin FliC is a heterogeneous protein mixture containing both O- and N-glycoforms.
Published: 2013
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36. VBNC Legionella pneumophila cells are still able to produce virulence proteins

Author: Christian Lacombe, Jacques Frère, Laurent Coquet, Thierry Jouenne, Mohamad Koubar, Laëtitia Alleron, Arbia Khemiri, Pascal Cosette, Laboratoire de Chimie et Microbiologie de l'Eau (LCME), Centre National de la Recherche Scientifique (CNRS)-Université de Poitiers-Institut de Chimie du CNRS (INC), Polymères, biopolymères, membranes (PBM), Centre National de la Recherche Scientifique (CNRS)-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)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU), Polymères Biopolymères Surfaces (PBS), 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), Institut de Chimie du CNRS (INC)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), 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)-Université Le Havre Normandie (ULH), Normandie Université (NU)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-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)-Université Le Havre Normandie (ULH), Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS), Microbiologie de l'Eau (MDE), Ecologie et biologie des interactions (EBI), and Université de Poitiers-Centre National de la Recherche Scientifique (CNRS)-Université de Poitiers-Centre National de la Recherche Scientifique (CNRS)
Subjects: Environmental Engineering, Proteome, Virulence Factors, Protein subunit, Hypothetical protein, Virulence, Legionella pneumophila, Microbiology, 03 medical and health sciences, Bacterial Proteins, Ribosomal protein, Waste Management and Disposal, 030304 developmental biology, Water Science and Technology, Civil and Structural Engineering, Infectivity, 0303 health sciences, Microbial Viability, biology, 030306 microbiology, Ecological Modeling, Cell Membrane, Chloramines, Esterases, biology.organism_classification, Pollution, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Biochemistry, Protein Biosynthesis, Bacterial outer membrane, Bacteria
Abstract: International audience; Legionella pneumophila is the agent responsible for legionellosis. Numerous bacteria, including L. pneumophila, can enter into a viable but not culturable (VBNC) state under unfavorable environmental conditions. In this state, cells are unable to form colonies on standard medium but are still alive. Here we show that VBNC L. pneumophila cells, obtained by monochloramine treatment, were still able to synthesize proteins, some of which are involved in virulence. Protein synthesis was measured using (35)S-labeling and the proteomes of VBNC and culturable cells then compared. This analysis allowed the identification of nine proteins that were accumulated in the VBNC state. Among them, four were involved in virulence, i.e., the macrophage infectivity potentiator protein, the hypothetical protein lpl2247, the ClpP protease proteolytic subunit and the 27 kDa outer membrane protein. Others, i.e., the enoyl reductase, the electron transfer flavoprotein (alpha and beta subunits), the 50S ribosomal proteins (L1 and L25) are involved in metabolic and energy production pathways. However, resuscitation experiments performed with Acanthamoeba castellanii failed, suggesting that the accumulation of virulence factors by VBNC cells is not sufficient to maintain their virulence.
Published: 2013
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37. Antioxidative and DNA Protective Effects of Bacillomycin D-Like Lipopeptides Produced by B38 Strain

Author: Maria Luisa Mangoni, Imen Ben Slimene, Pascal Cosette, Olfa Tabbene, Ferid Limam, Salem Elkahoui, Dorra Gharbi, Mohamed Najib Alfeddy, Thierry Jouenne, Plate-forme de Protéomique PISSARO, Institute for Research and Innovation in Biomedicine (IRIB), Université de Rouen Normandie (UNIROUEN), 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)-Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), Department of Biochemical Sciences 'Rossi Fanelli', Institut Pasteur, Fondation Cenci Bolognetti - Istituto Pasteur Italia, Fondazione Cenci Bolognetti, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Università degli Studi di Roma 'La Sapienza' = Sapienza University [Rome], Polymères Biopolymères Surfaces (PBS), 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), Institut de Chimie du CNRS (INC)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), 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)-Université Le Havre Normandie (ULH), Normandie Université (NU)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-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)-Université Le Havre Normandie (ULH), Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS), Laboratoire des Substances Bioactives (Centre de Biotechnologie de Borj Cedria, Hammam-Lif) (LSBA), and Centre de Biotechnologie de Borj Cédria (Hammam-Lif, Tunisie)
Subjects: 0106 biological sciences, Antioxidant, Stereochemistry, medicine.medical_treatment, Iron, [SDV]Life Sciences [q-bio], Bioengineering, Free radicals, 01 natural sciences, Applied Microbiology and Biotechnology, Biochemistry, Lipopeptide, Lipid peroxidation, 03 medical and health sciences, chemistry.chemical_compound, Bacillomycin, Lipopeptides, 010608 biotechnology, Antioxidant compounds, medicine, Antifungal activity, Reactive oxygen species, Molecular Biology, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, chemistry.chemical_classification, 0303 health sciences, Superoxide, General Medicine, DNA, Free Radical Scavengers, 3. Good health, Amino acid, Culture Media, Oxidative Stress, chemistry, Hydroxyl radical, Lipid Peroxidation, Peptides, Biotechnology, Antimicrobial Cationic Peptides, DNA Damage
Abstract: In the present study, we evaluated the antioxidant and the scavenging ability of C14, C15 and C16 bacillomycin D-like lipopeptides produced by B38 strain. They all displayed strong reducing power activity, hydroxyl and superoxide anion radicals scavenging activities and inhibition of lipid peroxidation. In addition, they were found to protect plasmid DNA damage from hydroxyl radical oxidation. Data suggested that their antioxidant potency can be attributed to the hydrophobic and aromatic side-chain groups of their amino acids as well as to the aliphatic chain of their beta amino fatty acids. Note that the hydrocarbon chain length did not interfere with the antioxidant power. Overall, such bacillomycin D lipopeptides which exhibit antioxidant and radical scavenging activities may be useful for cosmetic, therapeutic or pharmaceutical purposes in order to delay or prevent oxidative deterioration of manufactured products.
Published: 2012
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38. Combined Proteomic and Molecular Approaches for Cloning and Characterization of Copper–Zinc Superoxide dismutase (Cu, Zn-SOD2) from Garlic (Allium sativum)

Author: M. Nejib Marzouki, Pascal Cosette, Aymen Ezzine, Imen Hadji Sfaxi, Laurent Coquet, Thierry Jouenne, Institut National des Sciences Appliquées et de Technologie - Carthage (INSAT Carthage), Polymères, biopolymères, membranes (PBM), Centre National de la Recherche Scientifique (CNRS)-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)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU), Plate-forme de Protéomique PISSARO, Institute for Research and Innovation in Biomedicine (IRIB), Université de Rouen Normandie (UNIROUEN), 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)-Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), Polymères Biopolymères Surfaces (PBS), 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), Institut de Chimie du CNRS (INC)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), 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)-Université Le Havre Normandie (ULH), Normandie Université (NU)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-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)-Université Le Havre Normandie (ULH), Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS), Laboratory of Protein Engineering and Bioactive Molecules (LIP-MB), National Institute of Applied Sciences and Technology, and Université de Carthage - University of Carthage
Subjects: Cell Extracts, Models, Molecular, Proteomics, 0106 biological sciences, [SDV]Life Sciences [q-bio], Sus scrofa, Melanoma, Experimental, Polymerase Chain Reaction, 01 natural sciences, Applied Microbiology and Biotechnology, Biochemistry, Mass Spectrometry, Mice, Protein Isoforms, Electrophoresis, Gel, Two-Dimensional, Cloning, Molecular, Peptide sequence, ComputingMilieux_MISCELLANEOUS, Gel electrophoresis, 0303 health sciences, Nucleic acid sequence, Biotechnology, Sequence analysis, Molecular Sequence Data, Bioengineering, Sequence alignment, Biology, Superoxide dismutase, 03 medical and health sciences, Complementary DNA, Animals, Amino Acid Sequence, Garlic, Molecular Biology, 030304 developmental biology, Base Sequence, Superoxide Dismutase, Endothelial Cells, Sequence Analysis, DNA, Molecular biology, Open reading frame, Cytoprotection, Doxorubicin, Drug Resistance, Neoplasm, biology.protein, Peptides, Sequence Alignment, Chromatography, Liquid, 010606 plant biology & botany
Abstract: Superoxide dismutases (SODs; EC 1.15.1.1) are key enzymes in the cells protection against oxidant agents. Thus, SODs play a major role in the protection of aerobic organisms against oxygen-mediated damages. Three SOD isoforms were previously identified by zymogram staining from Allium sativum bulbs. The purified Cu, Zn-SOD2 shows an antagonist effect to an anticancer drug and alleviate cytotoxicity inside tumor cells lines B16F0 (mouse melanoma cells) and PAE (porcine aortic endothelial cells). To extend the characterization of Allium SODs and their corresponding genes, a proteomic approach was applied involving two-dimensional gel electrophoresis and LC-MS/MS analyses. From peptide sequence data obtained by mass spectrometry and sequences homologies, primers were defined and a cDNA fragment of 456 bp was amplified by RT-PCR. The cDNA nucleotide sequence analysis revealed an open reading frame coding for 152 residues. The deduced amino acid sequence showed high identity (82-87%) with sequences of Cu, Zn-SODs from other plant species. Molecular analysis was achieved by a protein 3D structural model.
Published: 2012
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39. Membrane proteomes of Pseudomonas aeruginosa and Acinetobacter baumannii

Author: Annick Schaumann, Stéphane Alexandre, Laurent Coquet, Thierry Jouenne, Bertrand Naudin, Christophe Rihouey, Axel Siroy, Emmanuelle Dé, A.C. Duncan, Guy-Alain Junter, Pascal Cosette, 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), Polymères Biopolymères Surfaces (PBS), 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), Institut de Chimie du CNRS (INC)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), 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)-Université Le Havre Normandie (ULH), Normandie Université (NU)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-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)-Université Le Havre Normandie (ULH), Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS), CEA Le Ripault (CEA Le Ripault), Direction des Applications Militaires (DAM), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), International Livestock Research Institute [CGIAR, Ethiopie] (ILRI), Consultative Group on International Agricultural Research [CGIAR] (CGIAR), Université de Rouen Normandie (UNIROUEN), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Institut Normand de Chimie Moléculaire Médicinale et Macromoléculaire (INC3M), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), 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)-Université de Caen Normandie (UNICAEN), and Normandie Université (NU)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Acinetobacter baumannii, Proteomics, Proteome, Virulence, medicine.disease_cause, Microbiology, 03 medical and health sciences, Antibiotic resistance, Bacterial Proteins, [CHIM.ANAL]Chemical Sciences/Analytical chemistry, medicine, Humans, Pseudomonas Infections, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, biology, 030306 microbiology, Pseudomonas aeruginosa, Chemistry, Membrane Proteins, General Medicine, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Membrane protein, Efflux, Bacterial outer membrane, Acinetobacter Infections
Abstract: Acinetobacter baumannii and Pseudomonas aeruginosa are known for their intrinsic resistance to antibiotics. Between mechanisms involved in this resistance, diminished expression of outer membrane proteins and up-regulation of efflux pumps play an important role. The characterization of membrane proteins is consequently necessary because of their importance in the antibiotic resistance but also in virulence. This review presents proteomic investigations aiming to describe the protein content of the membranes of these two bacterial species.
Published: 2011
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40. Triggering of the Antibacterial Activity of Bacillus subtilis B38 Strain against Methicillin-Resistant Staphylococcus aureus

Author: Maria Luisa Mangoni, Olfa Tabbene, Pascal Cosette, Najib Elfeddy, Ines Karkouch, Thierry Jouenne, Imen Ben Slimene, Ferid Limam, Plate-forme de Protéomique PISSARO, Institute for Research and Innovation in Biomedicine (IRIB), Université de Rouen Normandie (UNIROUEN), 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)-Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), Polymères Biopolymères Surfaces (PBS), 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), Institut de Chimie du CNRS (INC)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), 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)-Université Le Havre Normandie (ULH), Normandie Université (NU)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-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)-Université Le Havre Normandie (ULH), Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS), Laboratoire des Substances Bioactives (Centre de Biotechnologie de Borj Cedria, Hammam-Lif) (LSBA), and Centre de Biotechnologie de Borj Cédria (Hammam-Lif, Tunisie)
Subjects: Methicillin-Resistant Staphylococcus aureus, Hot Temperature, [SDV]Life Sciences [q-bio], Bioengineering, Microbial Sensitivity Tests, Bacillus subtilis, medicine.disease_cause, Applied Microbiology and Biotechnology, Biochemistry, Microbiology, 03 medical and health sciences, antibacterial activity, Bacterial Proteins, Antibiosis, medicine, induction, Molecular Biology, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Antibacterial agent, 0303 health sciences, biology, Strain (chemistry), 030306 microbiology, Chemistry, General Medicine, autoinducing compound, bacillus subtilis, mrsa, biology.organism_classification, Bacillales, Methicillin-resistant Staphylococcus aureus, Coculture Techniques, Anti-Bacterial Agents, Culture Media, Staphylococcus aureus, Electrophoresis, Polyacrylamide Gel, Antibacterial activity, Bacteria, Biotechnology
Abstract: When cultured in minimal growth medium, the B38 strain of Bacillus subtilis did not exhibit any antibacterial activity against methicillin-resistant Staphylococcus aureus (MRSA) clinical isolate. Coculturing B38 strain with viable MRSA cells weakly increased antibacterial activity production (20 AU/ml). Addition of dead MRSA cells in a B38 culture, increased by 8-fold the B. subtilis strain antibacterial activity reaching 160 AU/ml against MRSA strain. This antibacterial activity recovered from cell-free supernatants was stimulated by an autoinducing compound which is sensitive to the action of proteinase K suggesting a proteinaceous nature. This compound was heat-stable till 80 °C and showed a molecular mass around 20 kDa as determined by SDS-PAGE. These results suggest that the production of antibacterial compounds by B38 strain is dependent on the amount of the autoinducing compound.
Published: 2011
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41. Biofilm-induced modifications in the proteome of Pseudomonas aeruginosa planktonic cells

Author: David Vaudry, Thierry Jouenne, Anthony Collet, Guy-Alain Junter, Philippe Chan Tchi Song, Pascal Cosette, Hubert Vaudry, Yohan Nigaud, Plate-forme de Protéomique PISSARO, Institute for Research and Innovation in Biomedicine (IRIB), Université de Rouen Normandie (UNIROUEN), 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)-Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), Polymères Biopolymères Surfaces (PBS), 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), Institut de Chimie du CNRS (INC)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), 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)-Université Le Havre Normandie (ULH), Normandie Université (NU)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-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)-Université Le Havre Normandie (ULH), Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS), Différenciation et communication neuronale et neuroendocrine (DC2N), Normandie Université (NU)-Normandie Université (NU)-Institut National de la Santé et de la Recherche Médicale (INSERM), and Neuroendocrinologie cellulaire et moléculaire
Subjects: Proteome, [SDV]Life Sciences [q-bio], Biophysics, Gene Expression, Biology, Reductase, medicine.disease_cause, Biochemistry, Analytical Chemistry, Microbiology, 03 medical and health sciences, Bioreactors, 4-Butyrolactone, Bacterial Proteins, Gene expression, medicine, Homoserine, Molecular Biology, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, 030306 microbiology, Pseudomonas aeruginosa, fungi, Biofilm, Quorum Sensing, Plankton, Quorum sensing, Alcohol Oxidoreductases, Oxidative Stress, Biofilms, 3-Oxoacyl-(Acyl-Carrier-Protein) Reductase, Autoinducer
Abstract: While recent studies focused on Quorum Sensing (QS) role in the cell-to-cell communication in free or biofilm cultures, no work has been devoted up to now to investigate the communication between sessile and planktonic bacteria. In this aim, we elaborated an original two-chambered bioreactor and used a proteomic approach to study the alterations induced by Pseudomonas aeruginosa biofilm cells on protein expression in planktonic counterparts (named SIPs for Surface-Influenced Planktonics). Proteomic analyses revealed the existence of 31 proteins whose amount varied in SIPs, among which five corresponded to hypothetic proteins and two (the Fur and BCP proteins) are involved in bacterial response to oxidative stress. An increase in the concentration of C(4)-HSL (rhlR-rhlI-dependent QS) and 3-oxo-C(12)-HSL (lasR-lasI-dependent QS) autoinducer molecules was shown in the planktonic compartment. Interestingly, among proteins that were accumulated by SIPs was 3-oxoacyl-[acyl-carrier-protein] reductase, a protein involved in the production of the autoinducer 3-oxo-C(12)-HSL. These results demonstrate that planktonic organisms are able to detect the presence of a biofilm in their close environment and to modify their gene expression in consequence.
Published: 2010
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42. A new antibacterial and antioxidant S07-2 compound produced by Bacillus subtilis B38

Author: Ferid Limam, Thierry Jouenne, Maria Luisa Mangoni, Salem Elkahoui, Olfa Tabbene, Pascal Cosette, Ines Karkouch, Plate-forme de Protéomique PISSARO, Institute for Research and Innovation in Biomedicine (IRIB), Université de Rouen Normandie (UNIROUEN), 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)-Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), Polymères Biopolymères Surfaces (PBS), 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), Institut de Chimie du CNRS (INC)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), 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)-Université Le Havre Normandie (ULH), Normandie Université (NU)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-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)-Université Le Havre Normandie (ULH), Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS), Laboratoire des Substances Bioactives (Centre de Biotechnologie de Borj Cedria, Hammam-Lif) (LSBA), and Centre de Biotechnologie de Borj Cédria (Hammam-Lif, Tunisie)
Subjects: Preservative, Erythrocytes, Hot Temperature, antioxidant, [SDV]Life Sciences [q-bio], Bacillus subtilis, Microbial Sensitivity Tests, Microbiology, Enterococcus faecalis, Antioxidants, cyclic peptide, 03 medical and health sciences, Inhibitory Concentration 50, Drug Stability, bacillus subtilis, PEG ratio, Genetics, Humans, Molecular Biology, ComputingMilieux_MISCELLANEOUS, Chromatography, High Pressure Liquid, 030304 developmental biology, Chelating Agents, chemistry.chemical_classification, 0303 health sciences, Chromatography, Microbial Viability, biology, 030306 microbiology, Hydrogen-Ion Concentration, biology.organism_classification, Chromatography, Ion Exchange, Bacillales, Listeria monocytogenes, Cyclic peptide, Anti-Bacterial Agents, Molecular Weight, antibacterial, Biochemistry, chemistry, Salmonella enteritidis, Antibacterial activity, Bacteria, Peptide Hydrolases
Abstract: An antibacterial compound, S07-2, was purified to homogeneity by hydrophobic interaction, anion exchange, C18 reverse-phase and HS PEG HPLC. The molecular mass of S07-2 was 905.6 Da as determined by MS. The S07-2 compound was resistant to high temperatures (up to 100 degrees C) and could withstand a wide range of pH from 3 to 10. In addition, its antibacterial activity was preserved after treatment with proteases. Biochemical characterization revealed its cyclic peptide structure. This compound showed a bactericidal effect against important food-spoilage bacteria and food-borne pathogens including Listeria monocytogenes and Enterococcus faecalis with lethal concentration values of 62.5 microg mL(-1) and against Salmonella enteritidis at a concentration of 31.25 microg mL(-1). However, no cytotoxic effect against human erythrocytes was recorded. Furthermore, the S07-2 compound displayed a remarkable Fe(2+)-chelating activity (EC(50)=9.76 microg mL(-1)) and 1-diphenyl-2-picrylhydrazyl-scavenging capacity (IC(50)=65 microg mL(-1)). All these chemical and biological features make S07-2 a useful compound in the food industry as a natural preservative.
Published: 2010
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43. Proteomic analysis of Staphylococcus aureus biofilms grown in vitro on mechanical heart valve leaflets

Author: Thierry Jouenne, Guy-Alain Junter, Jean-François Lemeland, Pascal Cosette, Laetitia Benard, Pierre-Yves Litzler, Service de chirurgie cadiovasculaire et thoracique [Rouen], Hôpital Charles Nicolle [Rouen]-CHU Rouen, Normandie Université (NU)-Normandie Université (NU)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU), Plate-forme de Protéomique PISSARO, Institute for Research and Innovation in Biomedicine (IRIB), Université de Rouen Normandie (UNIROUEN), 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)-Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), Polymères Biopolymères Surfaces (PBS), 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), Institut de Chimie du CNRS (INC)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), 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)-Université Le Havre Normandie (ULH), Normandie Université (NU)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-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)-Université Le Havre Normandie (ULH), and Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Staphylococcus aureus, Prosthesis-Related Infections, Proteome, [SDV]Life Sciences [q-bio], Cell, Biomedical Engineering, medicine.disease_cause, Mechanical heart-valve, Microbiology, Biomaterials, 03 medical and health sciences, Bacterial Proteins, medicine, Humans, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, Leaflet (botany), biology, 030306 microbiology, Metals and Alloys, Biofilm, biology.organism_classification, Heart Valves, In vitro, medicine.anatomical_structure, Biofilms, Heart Valve Prosthesis, Ceramics and Composites, Bacteria
Abstract: The in vitro colonization of three commercial heart valve leaflets by Staphylococcus aureus was investigated. The leaflets, made of pyrolytic carbon alloyed with or without silicon, displayed similar surface properties (wettability, roughness) and were readily colonized by S. aureus that formed patchy biofilms on the three supports. A proteomic approach was used to assess the physiological status of biofilm populations by comparing their protein maps to those of bacteria cultured as free cells in the presence or absence of biofilm substratum. Principal component analysis (PCA) revealed, for each tested leaflet, statistical relationships between the protein maps of the biofilm and free-floating microbial populations. A spot-by-spot comparison of protein levels on two-dimensional electropherograms showed that many proteins were accumulated or underproduced by microbial populations grown in the presence of a leaflet compared with protein levels in control free populations. The number of accumulated proteins was noticeably higher than that of underproduced polypeptides. This protein overproduction was emphasized in biofilm populations. Several proteins, some of which were identified, were differentially produced by both surface-associated planktonic and biofilm-grown cell populations compared with control free-cell ones cultured in the absence of leaflet, whatever the leaflet tested. The potential of this proteomic approach for fighting against microbial adhesion and biofilm formation is discussed.
Published: 2009
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44. Outer-membrane proteomic maps and surface-exposed proteins of Legionella pneumophila using cellular fractionation and fluorescent labelling

Author: Pascal Cosette, Arbia Khemiri, Hubert Vaudry, Thierry Jouenne, David Vaudry, P. Chan Tchi Song, A. Galland, Sciences et Méthodes Séparatives (SMS), Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU), Différenciation et communication neuronale et neuroendocrine (DC2N), Normandie Université (NU)-Normandie Université (NU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Neuroendocrinologie cellulaire et moléculaire, Institut Fédératif de Recherches Multidisciplinaires sur les Peptides (IFRMP 23), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre de Lutte Contre le Cancer Henri Becquerel Normandie Rouen (CLCC Henri Becquerel)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU)-Université Le Havre Normandie (ULH), Normandie Université (NU)-CHU Rouen, Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS), Polymères Biopolymères Surfaces (PBS), 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), Institut de Chimie du CNRS (INC)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), 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)-Université Le Havre Normandie (ULH), Normandie Université (NU)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), and Normandie Université (NU)-Université Le Havre Normandie (ULH)
Subjects: Proteomics, Surface Properties, Legionella, [SDV]Life Sciences [q-bio], Cell Fractionation, Peptide Mapping, Sensitivity and Specificity, Biochemistry, Legionella pneumophila, Analytical Chemistry, 03 medical and health sciences, Membranome, Electrophoresis, Gel, Two-Dimensional, ComputingMilieux_MISCELLANEOUS, Fluorescent Dyes, 030304 developmental biology, Gel electrophoresis, 0303 health sciences, Staining and Labeling, biology, 030306 microbiology, Chemistry, Reproducibility of Results, biology.organism_classification, Cell fractionation, Bacterial outer membrane, Bacteria, Bacterial Outer Membrane Proteins
Abstract: Bacterial surface-associated proteins play crucial roles in host-pathogen interactions and pathogenesis. The identification of these proteins represents an important goal of bacterial proteomics for vaccine development, but also for environmental concerns such as microbial biosensing. Here, we developed such an approach for Legionella pneumophila, a bacterium that causes severe pneumonia. We propose a complementary strategy consisting of (1) a fluorescent labelling of surface-exposed proteins in parallel with (2) a fractionation of the outer-membrane protein extract. These two distinct protein populations were subsequently separated using two-dimensional gel electrophoresis and characterised by mass spectrometry. Within these populations, we found proteins which were expected for the compartments studied, but also a great number of proteins never experimentally described, and also a non-negligible fraction of proteins never described in these fractions. These data provided new routes of inspection for transport and host recognition for Legionella pneumophila. In addition, these results on the membranome and surfaceome show that Legionella in the stationary phase of growth possesses the major determinants to infect host cells.
Published: 2008
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45. Identification of Biofilm-Associated Cluster (bac) in Pseudomonas aeruginosa Involved in Biofilm Formation and Virulence

Author: Alain Filloux, Camille Macé, Damien Seyer, Thierry Jouenne, Patrick Di-Martino, Virginie Molle, Chanez Chemani, Benoit Guery, Marc Fontaine, Guy-Alain Junter, Pascal Cosette, Polymères Biopolymères Surfaces (PBS), 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), Institut de Chimie du CNRS (INC)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), 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)-Université Le Havre Normandie (ULH), Normandie Université (NU)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-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)-Université Le Havre Normandie (ULH), Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS), Equipe de recherche sur les relations matrice extracellulaire-cellules (ERRMECe), Fédération INSTITUT DES MATÉRIAUX DE CERGY-PONTOISE (I-MAT), Université de Cergy Pontoise (UCP), Université Paris-Seine-Université Paris-Seine-Université de Cergy Pontoise (UCP), Université Paris-Seine-Université Paris-Seine, Université Lille 2 - Faculté de Médecine, Biologie et physiologie des états septiques, IFR114-Université de Lille, Droit et Santé, MRC Centre for Molecular Microbiology and Infection [Imperial College, London] (CMBI), Imperial College London, Université de Rouen Normandie (UNIROUEN), Normandie Université (NU), Institut de biologie et chimie des protéines [Lyon] (IBCP), Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon, The French Cystic Fibrosis Foundation (VLM), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Institut Normand de Chimie Moléculaire Médicinale et Macromoléculaire (INC3M), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), 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)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Faculté de Médecine Henri Warembourg - Université de Lille, Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), and MOLLE, Virginie
Subjects: Male, Mutant, Outer membrane proteins, medicine.disease_cause, Bacterial Adhesion, Infectious Diseases/Bacterial Infections, Mice, Biochemistry/Protein Chemistry, Opportunistic infections, Phage shock, 0303 health sciences, Mice, Inbred BALB C, Multidisciplinary, Virulence, Microbiology/Immunity to Infections, Multidisciplinary Sciences, Multigene Family, Pseudomonas aeruginosa, Medicine, Science & Technology - Other Topics, Biological Assay, Microbiology/Cellular Microbiology and Pathogenesis, Research Article, Surface Properties, General Science & Technology, Science, Hypothetical protein, Molecular Sequence Data, Locus (genetics), Biology, Microbiology, 03 medical and health sciences, Bacterial Proteins, Osmotic Pressure, Cell Line, Tumor, MD Multidisciplinary, medicine, Animals, Humans, Pseudomonas Infections, Amino Acid Sequence, Mutant strains, Vascular permeability, Gene, DNA sequence analysis, 030304 developmental biology, Science & Technology, 030306 microbiology, Biofilm, Computational Biology, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Kinetics, Bacterial biofilms, Protein structure prediction, Genes, Bacterial, Biofilms, Mutation, Glycolipids, [SDV.MP.BAC] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Heat-Shock Response
Abstract: International audience; Biofilms are prevalent in diseases caused by Pseudomonas aeruginosa, an opportunistic and nosocomial pathogen. By a proteomic approach, we previously identified a hypothetical protein of P. aeruginosa (coded by the gene pA3731) that was accumulated by biofilm cells. We report here that a DpA3731 mutant is highly biofilm-defective as compared with the wild-type strain. Using a mouse model of lung infection, we show that the mutation also induces a defect in bacterial growth during the acute phase of infection and an attenuation of the virulence. The pA3731 gene is found to control positively the ability to swarm and to produce extracellular rhamnolipids, and belongs to a cluster of 4 genes (pA3729-pA3732) not previously described in P. aeruginosa. Though the protein PA3731 has a predicted secondary structure similar to that of the Phage Shock Protein, some obvious differences are observed compared to already described psp systems, e.g., this unknown cluster is monocistronic and no homology is found between the other proteins constituting this locus and psp proteins. As E. coli PspA, the amount of the protein PA3731 is enlarged by an osmotic shock, however, not affected by a heat shock. We consequently named this locus bac for biofilm-associated cluster.
Published: 2008
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46. Identification of Proteins Regulated by PACAP in PC12 Cells by 2D Gel Electrophoresis Coupled to Mass Spectrometry

Author: Jérôme Leprince, Alexis Lebon, Laurent Coquet, Thierry Jouenne, Alain Fournier, Damien Seyer, Bruno J. Gonzalez, Pascal Cosette, David Vaudry, Hubert Vaudry, Philippe Chan, Plate-Forme de Recherche en Imagerie Cellulaire de Haute-Normandie (PRIMACEN), Université de Rouen Normandie (UNIROUEN), 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), Equipe de recherche sur les relations matrice extracellulaire-cellules (ERRMECe), Fédération INSTITUT DES MATÉRIAUX DE CERGY-PONTOISE (I-MAT), Université de Cergy Pontoise (UCP), Université Paris-Seine-Université Paris-Seine-Université de Cergy Pontoise (UCP), Université Paris-Seine-Université Paris-Seine, Polymères Biopolymères Surfaces (PBS), 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), Institut de Chimie du CNRS (INC)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), 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)-Université Le Havre Normandie (ULH), Normandie Université (NU)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-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)-Université Le Havre Normandie (ULH), Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS), Polymères, biopolymères, membranes (PBM), Centre National de la Recherche Scientifique (CNRS)-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)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU), Neuroendocrinologie cellulaire et moléculaire, Normandie Université (NU)-Normandie Université (NU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Différenciation et communication neuronale et neuroendocrine (DC2N), Montreal Heart Institute (MONTREAL HEART INSTITUTE), Endothélium microcirculatoire cérébral et lésions du système nerveux central au cours du développement (Néovasc), and Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de la Santé et de la Recherche Médicale (INSERM)
Subjects: Neurite, MESH: Rats, Protein subunit, [SDV.NEU.NB]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Neurobiology, Protein Array Analysis, PC12 cell line, [CHIM.THER]Chemical Sciences/Medicinal Chemistry, Proteomics, PC12 Cells, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, chemistry.chemical_compound, 0302 clinical medicine, History and Philosophy of Science, Hsp27, [SDV.BC.IC]Life Sciences [q-bio]/Cellular Biology/Cell Behavior [q-bio.CB], Animals, MESH: PC12 Cells, Electrophoresis, Gel, Two-Dimensional, MESH: Animals, MESH: Proteins, 030304 developmental biology, Gel electrophoresis, 0303 health sciences, Two-dimensional gel electrophoresis, biology, MESH: Protein Array Analysis, General Neuroscience, MESH: Pituitary Adenylate Cyclase-Activating Polypeptide, Proteins, MESH: Electrophoresis, Gel, Two-Dimensional, Molecular biology, Rats, Cell biology, Tubulin, chemistry, MESH: Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, biology.protein, [SDV.SP.PHARMA]Life Sciences [q-bio]/Pharmaceutical sciences/Pharmacology, Pituitary Adenylate Cyclase-Activating Polypeptide, 030217 neurology & neurosurgery
Abstract: International audience; The rat pheochromocytoma PC12 cell line has been widely used as a model to study neuronal differentiation. In particular, after serum depletion, PC12 cells stop to proliferate and undergo apoptosis. Under such conditions, treatment with pituitary adenylate cyclase-activating polypeptide (PACAP) promotes cell survival and induces neurite outgrowth. The identification of the proteins regulated by PACAP in PC12 cells under apoptotic conditions should provide valuable information concerning the mechanisms controlling neuronal cell survival and differentiation. To this aim, PC12 cells cultured in serum-free medium were treated with PACAP (10(-7) M), proteins were extracted, separated by two-dimensional gel electrophoresis (2-DE), and identified by MALDI-ToF mass spectrometry. The comparison between 16 2-DE maps led to the characterization of 110 proteins regulated by PACAP among which 22 have been identified by automatic query of the Mascot, Aldente, and Profound servers with the ProGeR-CDD database. Seventy-six percent of these proteins, including the p17 subunit of caspase-3, the heat shock protein hsp60, and the GTPase ran were found to be repressed whereas the others notably hsp27, tubulin beta-5, and calmodulin were overexpressed. Investigation of the putative functions indicated that some of the proteins regulated by PACAP and identified in the present article could control cell survival or differentiation.
Published: 2006
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47. Proteomic comparison of outer membrane protein patterns of sessile and planktonic Pseudomonas aeruginosa cells

Author: Damien Seyer, Christof Lenz, Hubert Vaudry, Emmanuelle Dé, Pascal Cosette, Laurent Coquet, Thierry Jouenne, Axel Siroy, Equipe de recherche sur les relations matrice extracellulaire-cellules (ERRMECe), Fédération INSTITUT DES MATÉRIAUX DE CERGY-PONTOISE (I-MAT), Université de Cergy Pontoise (UCP), Université Paris-Seine-Université Paris-Seine-Université de Cergy Pontoise (UCP), Université Paris-Seine-Université Paris-Seine, Polymères Biopolymères Surfaces (PBS), 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), Institut de Chimie du CNRS (INC)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), 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)-Université Le Havre Normandie (ULH), Normandie Université (NU)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-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)-Université Le Havre Normandie (ULH), Normandie Université (NU)-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), Neuroendocrinologie cellulaire et moléculaire, Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut Fédératif de Recherches Multidisciplinaires sur les Peptides (IFRMP 23), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre de Lutte Contre le Cancer Henri Becquerel Normandie Rouen (CLCC Henri Becquerel)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU)-Université Le Havre Normandie (ULH), and Normandie Université (NU)-CHU Rouen
Subjects: 0303 health sciences, 030306 microbiology, Pseudomonas aeruginosa, [SDV]Life Sciences [q-bio], Biofilm, Biology, medicine.disease_cause, Mass spectrometry, Applied Microbiology and Biotechnology, Phenotype, Microbiology, 03 medical and health sciences, Electrophoresis, medicine, Scanning densitometry, Bacterial outer membrane, Waste Management and Disposal, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology
Abstract: We have compared the outer membrane protein (OMP) pattern of sessile Pseudomonas aeruginosa cells with that of its stationary-phase free-floating counterparts. Two-dimensional electrophoretic gels were compared using computing scanning densitometry. The level of 103 OMPs (i.e. about 50% of the spots that fulfilled our statistical selection threshold) was significantly and reproducibly different in biofilm organisms as compared with their planktonic counterparts. Some OMPs that specifically either accumulated or decreased were identified by mass spectrometry and the role of these proteins in the biofilm phenotype is discussed.
Published: 2005
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48. Proteomics of Biofilm Bacteria

Author: Pascal Cosette, Sébastien Vilain, Guy-Alain Junter, Thierry Jouenne, Polymères Biopolymères Surfaces (PBS), 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), Institut de Chimie du CNRS (INC)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), 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)-Université Le Havre Normandie (ULH), Normandie Université (NU)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-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)-Université Le Havre Normandie (ULH), Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS), Biotechnologie des protéines recombinantes à visée santé, Université de Bordeaux (UB)-Institut Polytechnique de Bordeaux, Plate-forme de Protéomique PISSARO, Institute for Research and Innovation in Biomedicine (IRIB), Université de Rouen Normandie (UNIROUEN), 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), and Normandie Université (NU)-Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)
Subjects: 0303 health sciences, biology, 030306 microbiology, Chemistry, [SDV]Life Sciences [q-bio], Biofilm, biology.organism_classification, Proteomics, Biochemistry, Microbiology, 03 medical and health sciences, Molecular Biology, Bacteria, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology
Abstract: International audience
Published: 2004
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49. Comparative proteomic analysis of planktonic and immobilized Pseudomonas aeruginosa cells: a multivariate statistical approach

Author: Sébastien Vilain, Guy-Alain Junter, Thierry Jouenne, Marie Hubert, Pascal Cosette, Catherine Lange, Biotechnologie des protéines recombinantes à visée santé, Université de Bordeaux (UB)-Institut Polytechnique de Bordeaux, Plate-forme de Protéomique PISSARO, Institute for Research and Innovation in Biomedicine (IRIB), Université de Rouen Normandie (UNIROUEN), 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)-Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), Chimie Organique et Bioorganique : Réactivité et Analyse (COBRA), Institut Normand de Chimie Moléculaire Médicinale et Macromoléculaire (INC3M), Institut de Chimie du CNRS (INC)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), 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)-Université Le Havre Normandie (ULH), Normandie Université (NU)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Institut de Chimie du CNRS (INC)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie Organique Fine (IRCOF), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Spectrométrie de Masse Bio-organique [Rouen], Normandie Université (NU)-Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS), Polymères Biopolymères Surfaces (PBS), 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)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), Normandie Université (NU)-Université Le Havre Normandie (ULH), and Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Proteomics, Proteome, [SDV]Life Sciences [q-bio], Biophysics, medicine.disease_cause, Biochemistry, Matrix (chemical analysis), 03 medical and health sciences, Bacterial Proteins, medicine, Electrophoresis, Gel, Two-Dimensional, Molecular Biology, Incubation, Cells, Cultured, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, Chromatography, biology, 030306 microbiology, Pseudomonas aeruginosa, Biofilm, Cell Biology, Plankton, biology.organism_classification, Electrophoresis, Cell culture, Biofilms, Principal component analysis, Bacteria
Abstract: The protein maps of Pseudomonas aeruginosa cells from two natural (attached) and one artificial (gel-entrapped) immobilized-cell (IC) systems, together with their free (suspended) counterparts, were compared after incubation for 18 or 48 h in a minimal salt medium. Principal component analysis (PCA) was used to interpret the variations in protein spot densities that were observed on electropherogram obtained by two-dimensional electrophoresis (2-DE). PCA of the 2-DE data, a matrix of 933 rows (observations, i.e., spot density values) and 12 columns (variables, i.e., incubation conditions), in which observations were standardized horizontally, extracted four principal components (PCs) accounting for 78.75% of the variability in the protein expression profiles. PC1 opposed the two modes of growth (planktonic and immobilized) while PC2 discriminated between the incubation times of free cell cultures. The incubation conditions of ICs, including the immobilization procedure (entrapment vs attachment) and the nature of the biofilm substratum, were fairly separated in PC3 × PC4. The dependence of the protein patterns on the cell immobilization process was further illustrated by the identification of a number of peptides whose amount remained unchanged or was altered in ICs compared to free bacteria. These results reinforce the topical assertion that bacteria in the immobilized state display a specific physiological behavior but also question the existence of a unique IC phenotype.
Published: 2004
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50. Biofilm Proteome: Homogeneity or Versatility?

Author: Jean-Paul Dupont, Thierry Jouenne, Pascal Cosette, Sébastien Vilain, Guy-Alain Junter, Irène Zimmerlin, Biotechnologie des protéines recombinantes à visée santé, Université de Bordeaux (UB)-Institut Polytechnique de Bordeaux, Plate-forme de Protéomique PISSARO, Institute for Research and Innovation in Biomedicine (IRIB), Université de Rouen Normandie (UNIROUEN), 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)-Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), Morphodynamique Continentale et Côtière (M2C), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS), Polymères Biopolymères Surfaces (PBS), 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), Institut de Chimie du CNRS (INC)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), 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)-Université Le Havre Normandie (ULH), Normandie Université (NU)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), and Normandie Université (NU)-Université Le Havre Normandie (ULH)
Subjects: Surface Properties, proteome, [SDV]Life Sciences [q-bio], Biology, medicine.disease_cause, Biochemistry, biofilm, Microbiology, 03 medical and health sciences, Bacterial Proteins, medicine, Cell Adhesion, Electrophoresis, Gel, Two-Dimensional, Cell adhesion, 030304 developmental biology, Gel electrophoresis, 0303 health sciences, 030306 microbiology, Pseudomonas aeruginosa, Biofilm, General Chemistry, biochemical phenomena, metabolism, and nutrition, Antimicrobial, biology.organism_classification, Plankton, Phenotype, multivariate analysis, P. aeruginosa, Biofilms, Proteome, Microscopy, Electron, Scanning, Gels, Bacteria
Abstract: International audience; The problems associated with biofilm infections in humans result from the distinct characteristics of biofilms, in particular their high level of resistance to antibiotics. One of the hypotheses that have been advanced to explain this resistance to antimicrobials is the phenotypic differentiation of biofilm cells. Although many studies on biofilms have highlighted physiological alterations following the attachment of bacteria to a surface, no studies have explicitly demonstrated a “biofilm” physiology. To contribute to this topical debate, we used principal component analysis to interpret spot quantity variations observed on electropherograms obtained by two-dimensional gel electrophoresis of crude protein extracts from planktonic and sessile Pseudomonas aeruginosa cells. These analyses showed that the proteome of attached P. aeruginosa cells differs from that of their planktonic counterparts. Furthermore, we found that the proteome of sessile P. aeruginosa is strongly dependent on the nature of the biofilm substratum.
Published: 2004
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