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1. Alkanes increase the stability of early life membrane models under extreme pressure and temperature conditions

Author: Loreto Misuraca, Bruno Demé, Philippe Oger, and Judith Peters
Subjects: Chemistry, QD1-999
Abstract: Fatty acid membranes are implicated in several hypotheses about the origins of life, but whether their stability towards extremes of temperature, pressure, and ionic strength is sufficient to enable primitive biochemistry remains unclear. Here branched and linear alkanes are shown to stabilise a common model primordial membrane towards high temperatures and pressures
Published: 2021
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2. The Piezo-Hyperthermophilic Archaeon Thermococcus piezophilus Regulates Its Energy Efficiency System to Cope With Large Hydrostatic Pressure Variations

Author: Yann Moalic, Jordan Hartunians, Cécile Dalmasso, Damien Courtine, Myriam Georges, Philippe Oger, Zongze Shao, Mohamed Jebbar, and Karine Alain
Subjects: pressure, piezophile, thermococci, hydrothermal, transcriptomics, Microbiology, QR1-502
Abstract: Deep-sea ecosystems share a common physical parameter, namely high hydrostatic pressure (HHP). Some of the microorganisms isolated at great depths have a high physiological plasticity to face pressure variations. The adaptive strategies by which deep-sea microorganisms cope with HHP variations remain to be elucidated, especially considering the extent of their biotopes on Earth. Herein, we investigated the gene expression patterns of Thermococcus piezophilus, a piezohyperthermophilic archaeon isolated from the deepest hydrothermal vent known to date, under sub-optimal, optimal and supra-optimal pressures (0.1, 50, and 90 MPa, respectively). At stressful pressures [sub-optimal (0.1 MPa) and supra-optimal (90 MPa) conditions], no classical stress response was observed. Instead, we observed an unexpected transcriptional modulation of more than a hundred gene clusters, under the putative control of the master transcriptional regulator SurR, some of which are described as being involved in energy metabolism. This suggests a fine-tuning effect of HHP on the SurR regulon. Pressure could act on gene regulation, in addition to modulating their expression.
Published: 2021
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3. Acid Hydrolysis for the Extraction of Archaeal Core Lipids and HPLC-MS Analysis

Author: Maxime Tourte, Philippe Schaeffer, Vincent Grossi, and Philippe Oger
Subjects: Biology (General), QH301-705.5
Abstract: Lipid membranes are essential cellular elements as they provide cellular integrity and selective permeability under a broad range of environmental settings upon cell growth. In particular, Archaea are commonly recognized for their tolerance to extreme conditions, which is now widely accepted to stem from the unique structure of their lipids. While enhancing the stability of the archaeal cell membrane, the exceptional properties of archaeal lipids also hinder their extraction using regular procedures initially developed for bacterial and eukaryotic lipids. The protocol described here circumvents these issues by directly hydrolyzing the polar head group(s) of archaeal lipids and extracting the resulting core lipids. Although leading to a loss of information on the nature of polar heads, this procedure allows the quantitative extraction of core lipids for most types of archaeal cells in an efficient, reproducible, and rapid manner.
Published: 2021
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4. A Second T-Region of the Soybean-Supervirulent Chrysopine-Type Ti Plasmid pTiChry5, and Construction of a Fully Disarmed vir Helper Plasmid

Author: Karuppaiah Palanichelvam, Philippe Oger, Steven J. Clough, Chung Cha, Andrew F. Bent, and Stephen K. Farrand
Subjects: binary system, disarmed plasmid, Glycine max, T-DNA, Microbiology, QR1-502, Botany, QK1-989
Abstract: Agrobacterium tumefaciens Chry5, which is particularly virulent on soybeans, induces tumors that produce a family of Amadori-type opines that includes deoxyfructosyl glutamine (Dfg) and its lactone, chrysopine (Chy). Cosmid clones mapping to the right of the known oncogenic T-region of pTiChry5 conferred Amadori opine production on tumors induced by the nopaline strain C58. Sequence analysis of DNA held in common among these cosmids identified two 25-bp, direct repeats flanking an 8.5-kb segment of pTiChry5. These probable border sequences are closely related to those of other known T-regions and define a second T-region of pTiChry5, called T-right (TR), that confers production of the Amadori opines. The oncogenic T-left region (TL) was located precisely by identifying and sequencing the likely border repeats defining this segment. The two T-regions are separated by approximately 15 kb of plasmid DNA. Based on these results, we predicted that pKYRT1, a vir helper plasmid derived from pTiChry5, still contains all of TR and the leftmost 9 kb of TL. Consistent with this hypothesis, transgenic Arabidopsis thaliana plants selected for with a marker encoded by a binary plasmid following transformation with KYRT1 coinherited production of the Amadori opines at high frequency. All opine-positive transgenic plants also contained TR-DNA, while those plants that lacked TR-DNA failed to produce the opines. Moreover, A. thaliana infected with KYRT1 in which an nptII gene driven by the 35S promoter of Cauliflower mosaic virus was inserted directly into the vir helper plasmid yielded kanamycin-resistant transformants at a low but detectable frequency. These results demonstrate that pKYRT1 is not disarmed, and can transfer Ti plasmid DNA to plants. A new vir helper plasmid was constructed from pTiChry5 by two rounds of sacB-mediated selection for deletion events. This plasmid, called pKPSF2, lacks both of the known T-regions and their borders. pKPSF2 failed to transfer Ti plasmid DNA to plants, but mobilized the T-region of a binary plasmid at an efficiency indistinguishable from those of pKYRT1 and the nopaline-type vir helper plasmid pMP90.
Published: 2000
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5. Synthesis of Phospholipids Under Plausible Prebiotic Conditions and Analogies with Phospholipid Biochemistry for Origin of Life Studies

Author: Michele Fiore, Carolina Chieffo, Augustin Lopez, Dimitri Fayolle, Johal Ruiz, Laurent Soulère, Philippe Oger, Emiliano Altamura, Florence Popowycz, and René Buchet
Subjects: Evolution, Chemical, Space and Planetary Science, Cell Membrane, Origin of Life, Agricultural and Biological Sciences (miscellaneous), Phospholipids
Abstract: Phospholipids are essential components of biological membranes and are involved in cell signalization, in several enzymatic reactions, and in energy metabolism. In addition, phospholipids represent an evolutionary and non-negligible step in life emergence. Progress in the past decades has led to a deeper understanding of these unique hydrophobic molecules and their most pertinent functions in cell biology. Today, a growing interest in "prebiotic lipidomics" calls for a new assessment of these relevant biomolecules.
Published: 2022
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6. Biochemical and mutational studies of an endonuclease V from the hyperthermophilic crenarchaeon Sulfolobus islandicus REY15A

Author: Youcheng Yin, Jingru Shi, Likui Zhang, Qing Liu, Yong Gong, Philippe Oger, and Xipeng Liu
Subjects: Physiology, General Medicine, Applied Microbiology and Biotechnology, Biotechnology
Published: 2023
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7. High-Throughput Screening of Fosmid Libraries for Increased Identification of Novel N-Acyl Homoserine Lactone Degrading Enzymes

Author: Stephane Uroz and Philippe Oger
Published: 2022
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8. Metabarcoding of the Three Domains of Life in Aquatic Saline Ecosystems

Author: Delphine Melayah, Zélia Bontemps, Maxime Bruto, Agnès Nguyen, Philippe Oger, and Mylène Hugoni
Published: 2022
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9. Metabarcoding of the Three Domains of Life in Aquatic Saline Ecosystems

Author: Delphine, Melayah, Zélia, Bontemps, Maxime, Bruto, Agnès, Nguyen, Philippe, Oger, and Mylène, Hugoni
Subjects: Bacteria, High-Throughput Nucleotide Sequencing, Computational Biology, Biodiversity, Archaea, Ecosystem
Abstract: High-throughput amplicon sequencing, known as metabarcoding, is a powerful technique to decipher exhaustive microbial diversity considering specific gene markers. While most of the studies investigating ecosystem functioning through microbial diversity targeted only one domain of life, either bacteria, or archaea or microeukaryotes, the remaining challenge in microbial ecology is to uncover the integrated view of microbial diversity occurring in ecosystems. Indeed, interactions occurring between the different microbial counterparts are now recognized having a great impact on stability and resilience of ecosystems. Here, we summarize protocols describing sampling, molecular, and simultaneous metabarcoding of bacteria, archaea, and microeukaryotes, as well as a bioinformatic pipeline allowing the study of exhaustive microbial diversity in natural aquatic saline samples.
Published: 2022

10. High-Throughput Screening of Fosmid Libraries for Increased Identification of Novel N-Acyl Homoserine Lactone Degrading Enzymes

Author: Stephane, Uroz and Philippe, Oger
Abstract: Functional metagenomics is an essential and effective approach to recover new enzymes from the environment. In this chapter, we describe a procedure to construct metagenomic library to discover new N-acyl homoserine lactone (AHL) degrading enzymes based on a direct method or an indirect enrichment procedure. Applicable to any bacterial ecosystem, it enables rapid identification of functional enzymes effective to degrade AHLs.
Published: 2022

11. Biochemical characterization and mutational studies of endonuclease Q from the hyperthermophilic euryarchaeon Thermococcus gammatolerans

Author: Mai Wu, Guangyu Ma, Yushan Lin, Philippe Oger, Peng Cao, and Likui Zhang
Subjects: Cell Biology, Molecular Biology, Biochemistry
Published: 2023
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12. The mineral weathering ability of Collimonas pratensis PMB3(1) involves a Malleobactin‐mediated iron acquisition system

Author: Tiphaine Dhalleine, Stéphane Uroz, Marie-Pierre Turpault, Emmanuelle Morin, Philippe Oger, Laura Picard, Cédric Paris, Interactions Arbres-Microorganismes (IAM), Université de Lorraine (UL)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Unité de recherche Biogéochimie des Ecosystèmes Forestiers (BEF), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire d'Ingénierie des Biomolécules (LIBio), Université de Lorraine (UL), Plateau d’Analyse Structurale et Métabolomique (PASM), Microbiologie, adaptation et pathogénie (MAP), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Microbiology of Extreme Environments (M2E), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Ministère de l’Enseignement Supérieur, EC2CO program of the CNRS, ANR-11-LABX-0002,ARBRE,Recherches Avancées sur l'Arbre et les Ecosytèmes Forestiers(2011), Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon, and Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées de Lyon (INSA Lyon)
Subjects: Siderophore, Iron, [SDE.MCG]Environmental Sciences/Global Changes, Microorganism, Mutant, Siderophores, Mutagenesis (molecular biology technique), Weathering, Biology, Microbiology, 03 medical and health sciences, Oxalobacteraceae, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Chelation, Weather, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Minerals, 0303 health sciences, Strain (chemistry), 030306 microbiology, Hematite, Biochemistry, visual_art, visual_art.visual_art_medium, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: International audience; Mineral weathering by microorganisms is considered to occur through a succession of mechanisms based on acidification and chelation. While the role of acidification is established, the role of siderophores is difficult to disentangle from the effect of the acidification. We took advantage of the ability of strain Collimonas pratensis PMB3(1) to weather minerals but not to acidify depending on the carbon source to address the role of siderophores in mineral weathering. We identified a single non-ribosomal peptide synthetase responsible for siderophore biosynthesis in the PMB3(1) genome. By combining iron-chelating assays, targeted mutagenesis and chemical analyses (HPLC and LC-ESI-HRMS), we identified the siderophore produced as malleobactin X and how its production depends on the concentration of available iron. Comparison with the genome sequences of other collimonads evidenced that malleobactin production seems to be a relatively conserved functional trait, though some collimonads harbored other siderophore synthesis systems. We also revealed by comparing the wild-type strain and its mutant impaired in the production of malleobactin that the ability to produce this siderophore is essential to allow the dissolution of hematite under non-acidifying conditions. This study represents the first characterization of the siderophore produced by collimonads and its role in mineral weathering.
Published: 2021
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13. Characterization of a novel type III alcohol dehydrogenase from Thermococcus barophilus Ch5

Author: Philippe Oger, Yuting Li, Qing Liu, Leilei Wu, Likui Zhang, Donghao Jiang, Kunming Dong, Yangzhou University, Microbiologie, adaptation et pathogénie (MAP), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Microbiology of Extreme Environments (M2E), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Oger, Phil M., Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon, and Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées de Lyon (INSA Lyon)
Subjects: Protein Denaturation, Hot Temperature, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, Amino Acid Motifs, Alcohol, 02 engineering and technology, Biochemistry, Genes, Archaeal, Substrate Specificity, chemistry.chemical_compound, Structural Biology, Hyperthermophilic Archaea, Conserved Sequence, Phylogeny, Thermostability, chemistry.chemical_classification, 0303 health sciences, biology, Circular Dichroism, General Medicine, Hydrogen-Ion Concentration, 021001 nanoscience & nanotechnology, Aldehyde Oxidoreductases, Recombinant Proteins, Thermococcus, Thermococcus barophilus, 0210 nano-technology, Stereochemistry, Archaeal Proteins, Divalent, 03 medical and health sciences, Cations, Amino Acid Sequence, Molecular Biology, 030304 developmental biology, Alcohol dehydrogenase, Ethanol, Base Sequence, Sequence Homology, Amino Acid, Biochemical characteristics, Acetaldehyde, Substrate (chemistry), biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, [SDV.BIO] Life Sciences [q-bio]/Biotechnology, Kinetics, chemistry, Alcohols, Mutagenesis, Site-Directed, biology.protein, Thermococcales, [SDV.MP.BAC] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Sequence Alignment
Abstract: International audience; The genome of the hyperthermophilic and piezophilic euryarchaeaon Thermococcus barophilus Ch5 encodes three putative alcohol dehydrogenases (Tba ADHs). Herein, we characterized Tba ADH547 biochemically and probed its mechanism by mutational studies. Our data demonstrate that Tba ADH547 can oxidize ethanol and reduce acetaldehyde at high temperature with the same optimal temperature (75 o C) and exhibit similar thermostablilty for oxidization and reduction reactions. However, Tba ADH547 has different optimal pH for oxidation and reduction: 8.5 for oxidation and 7.0 for reduction. Tba ADH547 is dependent on a divalent ion for its oxidation activity, among which Mn 2+ is optimal. However, Tba ADH547 displays about 20% reduction activity without a divalent ion, and the maximal activity with Fe 2+. Furthermore, Tba ADH547 showcases a strong substrate preference for 1-butanol and 1-hexanol over ethanol and other alcohols. Similarly, Tba ADH547 prefers butylaldehyde to acetaldehyde as its reduction substrate. Mutational studies showed that the mutations of residues D195, H199, H262 and H234 to Ala result in the significant activity loss of Tba ADH547, suggesting that residues D195, H199, H262 and H234 are responsible for catalysis. Overall, Tba ADH547 is a thermoactive ADH with novel biochemical characteristics, thereby allowing this enzyme to be a potential biocatalyst.
Published: 2021
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14. Unravelling the Adaptation Mechanisms to High Pressure in Proteins

Author: Antonino Caliò, Cécile Dubois, Stéphane Fontanay, Michael Marek Koza, François Hoh, Christian Roumestand, Philippe Oger, Judith Peters, Oger, Phil M., Microbiology of Extreme Environments (M2E), Microbiologie, adaptation et pathogénie (MAP), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Centre de Biologie Structurale [Montpellier] (CBS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Institut Laue-Langevin (ILL), Laboratoire Interdisciplinaire de Physique [Saint Martin d’Hères] (LIPhy ), and Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)
Subjects: [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], [SDV.BBM.BS] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Acclimatization, Organic Chemistry, neutron scattering, General Medicine, origins of life, Adaptation, Physiological, Catalysis, Computer Science Applications, Inorganic Chemistry, protein dynamics, Hydrostatic Pressure, high pressure adaptation, Physical and Theoretical Chemistry, Molecular Biology, Spectroscopy
Abstract: International audience; Life is thought to have appeared in the depth of the sea under high hydrostatic pressure. Nowadays, it is known that the deep biosphere hosts a myriad of life forms thriving under high-pressure conditions. However, the evolutionary mechanisms leading to their adaptation are still not known. Here, we show the molecular bases of these mechanisms through a joint structural and dynamical study of two orthologous proteins. We observed that pressure adaptation involves the decoupling of protein–water dynamics and the elimination of cavities in the protein core. This is achieved by rearranging the charged residues on the protein surface and using bulkier hydrophobic residues in the core. These findings will be the starting point in the search for a complete genomic model explaining high-pressure adaptation.
Published: 2022
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15. Genomic and transcriptomic characterization of the Collimonas quorum sensing genes and regulon

Author: Stephane Uroz, Océane Geisler, Laure Fauchery, Raphaël Lami, Alice M S Rodrigues, Emmanuelle Morin, Johan H J Leveau, and Philippe Oger
Subjects: Ecology, Quorum Sensing, Genomics, Acyl-Butyrolactones, Transcriptome, Applied Microbiology and Biotechnology, Microbiology, Regulon
Abstract: Collimonads are well-adapted to nutrient-poor environments. They are known to hydrolyse chitin, produce antifungal metabolites, weather minerals, and are effective biocontrol agents protecting plants from fungal diseases. The production of N-acyl homoserine lactones (AHLs) was suggested to be a conserved trait of collimonads, but little is known about the genes that underlie this production or the genes that are controlled by AHLs. To improve our understanding of the role of AHLs in the ecology of collimonads, we carried out transcriptomic analyses, combined with chemical and functional assays, on strain Collimonas pratensis PMB3(1). The main AHLs produced by this strain were identified as 3-hydroxy-hexa- and octa-noyl-homoserine lactone. Genome analysis permitted to identify putative genes coding for the autoinducer synthase (colI) and cognate transcriptional regulator (colR). The ability to produce AHLs was lost in ΔcolI and ΔcolR mutants. Functional assays revealed that the two mutants metabolized glucose, formate, oxalate, and leucine better than the wild-type (WT) strain. Transcriptome sequencing analyses revealed an up-regulation of different metabolic pathways and of motility in the QS-mutants compared to the WT strain. Overall, our results provide insights into the role of the AHL-dependent regulation system of Collimonas in environment colonization, metabolism readjustment, and microbial interactions.
Published: 2022

16. Characterization and application of a family B DNA polymerase from the hyperthermophilic and radioresistant euryarchaeon Thermococcus gammatolerans

Author: Mai Wu, Philippe Oger, Donghao Jiang, Qi Gan, Zhihui Yang, Likui Zhang, Haoqiang Shi, Yangzhou University, Agricultural University of Hebei, Microbiologie, adaptation et pathogénie (MAP), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Microbiology of Extreme Environments (M2E), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon, and Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées de Lyon (INSA Lyon)
Subjects: Exonuclease, congenital, hereditary, and neonatal diseases and abnormalities, Chemical Phenomena, DNA polymerase, Archaeal Proteins, Gene Expression, DNA-Directed DNA Polymerase, 02 engineering and technology, DNA replication, Radiation Tolerance, Biochemistry, Substrate Specificity, law.invention, 03 medical and health sciences, chemistry.chemical_compound, Structural Biology, law, AP site, Cloning, Molecular, Molecular Biology, Magnesium ion, Polymerase, 030304 developmental biology, 0303 health sciences, biology, Temperature, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, General Medicine, 021001 nanoscience & nanotechnology, Archaea, Recombinant Proteins, Enzyme Activation, Thermococcus, chemistry, biology.protein, Recombinant DNA, Routine PCR, 0210 nano-technology, DNA, Protein Binding
Abstract: International audience; Thermococcus gammatolerans is anaerobic euryarchaeon which grows optimally at 88 °C and its genome encodes a family B DNA polymerase (Tga PolB). Herein, we cloned the gene of Tga PolB, expressed and purified the gene product, and characterized the enzyme biochemically. The recombinant Tga PolB can efficiently synthesize DNA at high temperature, and retain 93% activity after heated at 95 °C for 1.0 h, suggesting that the enzyme is thermostable. Furthermore, the optimal pH for the enzyme activity was measured to be 7.0–9.0. Tga PolB activity is dependent on a divalent cation, among which magnesium ion is optimal. NaCl at low concentration stimulates the enzyme activity but at high concentration inhibits enzyme activity. Interestingly, Tga PolB is able to efficiently bypass uracil in DNA, which is distinct from other archaeal family B DNA pols. By contrast, Tga PolB is halted by an AP site in DNA, as observed in other archaeal family B DNA polymerases. Furthermore, Tga PolB extends the mismatched ends with reduced efficiencies. The enzyme possesses 3′-5′ exonuclease activity and this activity is inhibited by dNTPs. The DNA binding assays showed that Tga PolB can efficiently bind to ssDNA and primed DNA, and have a marked preference for primed DNA. Last, Tga PolB can be used in routine PCR.
Published: 2020
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17. Unravelling the mechanisms of adaptation to high pressure in proteins

Author: Antonino Caliò, Michael Marek Koza, Stephane Fontanay, Philippe Oger, and Judith Peters
Abstract: Life is thought to have appeared in the depth of the sea, under high hydrostatic pressure. Nowadays, it is known that the deep biosphere hosts a myriad of life forms thriving under high pressure conditions. However, the evolutionary mechanisms leading to their adaptation are still not known. Here we show the molecular bases of these mechanisms through a neutron scattering study of two orthologous proteins. We observed that pressure adaptation involves the decoupling of protein-water dynamics and the elimination of cavities in the protein core. This is achieved by an enrichment of acidic residues on the protein surface and by the use of bulkier hydrophobic residues in the core. These findings will be the starting point in the search of a complete genomic model explaining high pressure adaptation.
Published: 2022
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18. High temperature molecular motions within a model protomembrane architecture

Author: Loreto Misuraca, Tatsuhito Matsuo, Aline Cisse, Josephine LoRicco, Antonio Caliò, Jean-Marc Zanotti, Bruno Demé, Philippe Oger, Judith Peters, Institut Laue-Langevin (ILL), Laboratoire Interdisciplinaire de Physique [Saint Martin d’Hères] (LIPhy ), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), National Institutes for Quantum and Radiological Science and Technology (QST), Microbiology of Extreme Environments (M2E), Microbiologie, adaptation et pathogénie (MAP), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Léon Brillouin (LLB - UMR 12), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), LLB - Matière molle et biophysique (MMB), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), This work was funded by the French National Research Agency program ANR 17-CE11-0012-01 to P. O. and J. P. L. M. was supported by a scholarship from the Institut Laue-Langevin (ILL) PhD program. The authors thank ILL for neutron beamtime on IN6-Sharp (DOI: 10.5291/ILL-DATA.CRG-2728)., and ANR-17-CE11-0012,ArchaeoMembranes,Des bicouches lipidiques stables au delà du point d'ébullition de l'eau(2017)
Subjects: [SDV.BBM.BP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, Motion, Hot Temperature, Lipid Bilayers, Temperature, General Physics and Astronomy, Artificial Cells, Physical and Theoretical Chemistry, Phospholipids
Abstract: Modern phospholipid membranes are known to be in a functional, physiological state, corresponding to the liquid crystalline phase, only under very precise external conditions. The phase is characterised by specific lipid motions, which seem mandatory to permit sufficient flexibility and stability for the membrane. It can be assumed that similar principles hold for proto-membranes at the origin of life although they were likely composed of simpler, single chain fatty acids and alcohols. In the present study we investigated molecular motions of four types of model membranes to shed light on the variations of dynamics and structure as a function of temperature as protocells might have existed close to hot vents. We find a clear hierarchy among the flexibilities of the samples, where some structural parameters seem to depend on the lipids used while others do not.
Published: 2022
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19. Membrane adaptation in the hyperthermophilic archaeon Pyrococcus furiosus relies upon a novel strategy involving glycerol monoalkyl glycerol tetraether lipids

Author: Maxime Tourte, Vincent Grossi, Philippe Schaeffer, Philippe Oger, Microbiologie, adaptation et pathogénie (MAP), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Institut de Chimie de Strasbourg, Université de Strasbourg (UNISTRA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Géologie de Lyon - Terre, Planètes, Environnement (LGL-TPE), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut national des sciences de l'Univers (INSU - CNRS)-Université Jean Monnet - Saint-Étienne (UJM)-Centre National de la Recherche Scientifique (CNRS), ANR-17-CE11-0012,ArchaeoMembranes,Des bicouches lipidiques stables au delà du point d'ébullition de l'eau(2017), Microbiology of Extreme Environments (M2E), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), Laboratoire de Géologie de Lyon - Terre, Planètes, Environnement [Lyon] (LGL-TPE), Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-École normale supérieure - Lyon (ENS Lyon)
Subjects: Glycerol, Pyrococcus, H-shaped lipids, [SDV]Life Sciences [q-bio], chemistry.chemical_element, Microbiology, 03 medical and health sciences, chemistry.chemical_compound, Membrane Lipids, [CHIM.ANAL]Chemical Sciences/Analytical chemistry, tetraethers, Carbon source, Ecology, Evolution, Behavior and Systematics, extremophiles, 030304 developmental biology, 0303 health sciences, Archaeal membrane lipids, biology, 030306 microbiology, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, stress response, biology.organism_classification, Sulfur, Archaea, Carbon, Salinity, Pyrococcus furiosus, Membrane, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, chemistry, Biochemistry, Adaptation
Abstract: Microbes preserve membrane functionality under fluctuating environmental conditions by modulating their membrane lipid composition. Although several studies have documented membrane adaptations in Archaea, the influence of most biotic and abiotic factors on archaeal lipid compositions remains underexplored. Here, we studied the influence of temperature, pH, salinity, the presence/absence of elemental sulfur, the carbon source, and the genetic background on the core lipid composition of the hyperthermophilic neutrophilic marine archaeon Pyrococcus furiosus. Every growth parameter tested affected the core lipid composition to some extent, the carbon source and the genetic background having the greatest influence. Surprisingly, P. furiosus appeared to only marginally rely on the two major responses implemented by Archaea, i.e., the regulation of the ratio of diether to tetraether lipids and that of the number of cyclopentane rings in tetraethers. Instead, this species increased the ratio of glycerol monoalkyl glycerol tetraethers (GMGT, aka. H-shaped tetraethers) to glycerol dialkyl glycerol tetrathers (GDGT) in response to decreasing temperature and pH and increasing salinity, thus providing for the first time evidence of adaptive functions for GMGT. Besides P. furiosus, numerous other species synthesize significant proportions of GMGT, which suggests that this unprecedented adaptive strategy might be common in Archaea.Significance statementWe describe here the membrane adaptive strategies the hyperthermophilic, neutrophilic, and marine model archaeon Pyrococcus furiosus implements in response to one of the largest sets of environmental stressors tested to date, including temperature, pH, salinity, presence/absence of elemental sulfur, carbon source, and genetic background. In contrast to the other archaea investigated so far, which response mainly involves the modulation of their diether/tetraether ratio and/or of their average number of cyclopentane rings, P. furiosus regulates its monoalkyl (so called H-shaped) to dialkyl tetraether ratio. Our study thus provides for the first time evidence of adaptive functions of archaeal monoalkyl tetraethers towards low temperature and pH and high salinity.
Published: 2022
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20. Incorporation and localisation of alkanes in a protomembrane model by neutron diffraction

Author: Loreto Misuraca, Josephine LoRicco, Philippe Oger, Judith Peters, and Bruno Demé
Subjects: Biophysics, Cell Biology, Biochemistry
Published: 2023
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21. Biochemical characterization and mutational analysis of a mismatch glycosylase from the hyperthermophilic euryarchaeon Thermococcus barophilus Ch5

Author: Lei Wang, Tan Lin, Philippe Oger, Yong Gong, and Likui Zhang
Subjects: Thermococcus, DNA-(Apurinic or Apyrimidinic Site) Lyase, Cell Biology, Aeropyrum, Uracil, Molecular Biology, Biochemistry, Thymine
Abstract: Mismatch glycosylase (MIG) can excise thymine and uracil from mutagenic T:G and U:G mispairs, which arise from cytosine and 5-methylcytosine deamination, respectively. Here, we present evidence that a thermostable MIG from the hyperthermophilic euryarchaeon Thermococcus barophilus Ch5 (Tb-MIG) can remove thymine and uracil from T:G and U:G mispairs at high temperature, albeit at a low efficiency for U:G mispair. The enzyme displays maximum efficiency at 70
Published: 2021

22. Biology of Archaea, Volume 1 : Discovery, Evolution and Diversity of Archaea

Author: Béatrice Clouet-d'Orval, Bruno Franzetti, Philippe Oger, Béatrice Clouet-d'Orval, Bruno Franzetti, and Philippe Oger
Abstract: Archaea constitute a new branch of life alongside bacteria and eukaryotes. These microorganisms are unique in their cellular and molecular aspects. They have evolutionary links with the first eukaryotic cells and are now being used to elucidate fundamental biological questions. Champions of extremophilicity, archaea are helping to lift the veil on the limits of life on Earth. Biology of Archaea 1 explores the discovery and evolution of the field of archaea research. This book also looks at the evolutionary history of archaea and their integration into the tree of life, and examines this complex and extremely diverse world in terms of their ecological niches and their still largely unexplored virosphere.
Published: 2025

23. Biochemical characterization and mutational studies of the 8-oxoguanine DNA glycosylase from the hyperthermophilic and radioresistant archaeon Thermococcus gammatolerans

Author: Zhihui Yang, Yuting Li, Haoqiang Shi, Likui Zhang, Jianting Zheng, Dai Zhang, Philippe Oger, Yangzhou University, Peking University [Beijing], Agricultural University of Hebei, Microbiologie, adaptation et pathogénie (MAP), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Adaptation aux milieux extrêmes (AME), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon, and Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées de Lyon (INSA Lyon)
Subjects: Guanine, DNA Mutational Analysis, Mutant, Enzyme Activators, Cleavage (embryo), Applied Microbiology and Biotechnology, DNA Glycosylases, 03 medical and health sciences, chemistry.chemical_compound, Enzyme Stability, Enzyme Inhibitors, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, chemistry.chemical_classification, 0303 health sciences, biology, 030306 microbiology, Chemistry, Temperature, Thermococcus gammatolerans, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, General Medicine, Base excision repair, Hydrogen-Ion Concentration, biology.organism_classification, Thermococcus, Enzyme, Biochemistry, DNA glycosylase, Mutant Proteins, DNA, Biotechnology
Abstract: 8-oxoguanine (GO) is a major lesion found in DNA that arises from guanine oxidation. The hyperthermophilic and radioresistant euryarchaeon Thermococcus gammatolerans encodes an archaeal GO DNA glycosylase (Tg-AGOG). Here, we characterized biochemically Tg-AGOG and probed its GO removal mechanism by mutational studies. Tg-AGOG can remove GO from DNA at high temperature through a β-elimination reaction. The enzyme displays an optimal temperature, ca.85–95 °C, and an optimal pH, ca.7.0–8.5. In addition, Tg-AGOG activity is independent on a divalent metal ion. However, both Co2+ and Cu2+ inhibit its activity. The enzyme activity is also inhibited by NaCl. Furthermore, Tg-AGOG specifically cleaves GO-containing dsDNA in the order: GO:C, GO:T, GO:A, and GO:G. Moreover, the temperature dependence of cleavage rates of the enzyme was determined, and from this, the activation energy for GO removal from DNA was first estimated to be 16.9 ± 0.9 kcal/mol. In comparison with the wild-type Tg-AGOG, the R197A mutant has a reduced cleavage activity for GO-containing DNA, whereas both the P193A and F167A mutants exhibit similar cleavage activities for GO-containing DNA. While the mutations of P193 and F167 to Ala lead to increased binding, the mutation of R197 to Ala had no significant effect on binding. These observations suggest that residue R197 is involved in catalysis, and residues P193 and F167 are flexible for conformational change.
Published: 2019
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24. Biochemical characterization and mutational analysis of a novel flap endonuclease 1 from Thermococcus barophilus Ch5

Author: Tan Lin, Likui Zhang, Donghao Jiang, Leilei Wu, Kaige Chen, Li Li, Cuili Jin, Zheng Li, and Philippe Oger
Subjects: Thermococcus, Flap Endonucleases, Mutation, Humans, Cell Biology, Biochemistry
Abstract: Flap endonuclease 1 (FEN1) plays important roles in DNA replication, repair and recombination. Herein, we report biochemical characteristics and catalytic mechanism of a novel FEN1 from the hyperthermophilic euryarchaeon Thermococcus barophilus Ch5 (Tb-FEN1). As expected, the recombinant Tb-FEN1 can cleave 5'-flap DNA. However, the enzyme has no activity on cleaving pseudo Y DNA, which sharply contrasts with other archaeal and eukaryotic FEN1 homologs. Tb-FEN1 retains 24% relative activity after heating at 100 °C for 20 min, demonstrating that it is the most thermostable among all reported FEN1 proteins. The enzyme displays maximal activity in a wide range of pH from 7.0 to 9.5. The Tb-FEN1 activity is dependent on a divalent metal ion, among which Mg
Published: 2021

25. Straightforward Synthesis of Chiral Terpenoid Building Blocks by Ru-Catalyzed Enantioselective Hydrogenation

Author: Florence Popowycz, Philippe Oger, Laurent Soulère, Johal Ruiz, Institut de Chimie et Biochimie Moléculaires et Supramoléculaires (ICBMS), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut de Chimie du CNRS (INC)-École Supérieure Chimie Physique Électronique de Lyon-Centre National de la Recherche Scientifique (CNRS), Microbiologie, adaptation et pathogénie (MAP), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Microbiology of Extreme Environments (M2E), and Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL)
Subjects: Olefin fiber, 010405 organic chemistry, Chemistry, Terpenes, Monoterpene, Organic Chemistry, Enantioselective synthesis, Stereoisomerism, Alkenes, 010402 general chemistry, 01 natural sciences, Combinatorial chemistry, Moderate temperature, Terpenoid, Catalysis, 0104 chemical sciences, [CHIM.GENI]Chemical Sciences/Chemical engineering, Yield (chemistry), [CHIM.COOR]Chemical Sciences/Coordination chemistry, Hydrogenation, ComputingMilieux_MISCELLANEOUS
Abstract: Starting from commercially available (R)- and (S)-β-citronellol, two strategies were designed to synthesize all four stereoisomers of 2,6-dimethyloctane monoterpene chirons in four or five steps in 32-47% overall yield. The desired fragments were obtained by a key Ru-catalyzed asymmetric olefin hydrogenation step under moderate temperature (50 °C), pressure (4 bar), and low catalyst loadings (0.5 mol %) under optimized conditions. Screening of commercially available catalysts highlighted the key role of DM-SEGPHOS as an economically advantageous alternative to commonly used H8-BINAP for equal performances. These results open new possibilities for versatile and scalable syntheses of these useful building blocks.
Published: 2021
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26. Non-Polar Lipids as Regulators of Membrane Properties in Archaeal Lipid Bilayer Mimics

Author: Nicholas J. Brooks, Marta Salvador-Castell, Judith Peters, Roland Winter, Philippe Oger, Microbiologie, adaptation et pathogénie (MAP), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Microbiology of Extreme Environments (M2E), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Imperial College London, Technische Universität Dortmund [Dortmund] (TU), Laboratoire Interdisciplinaire de Physique [Saint Martin d’Hères] (LIPhy ), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), Engineering & Physical Science Research Council (EPSRC), Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon, and Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées de Lyon (INSA Lyon)
Subjects: 0301 basic medicine, Hydrostatic pressure, Lipid Bilayers, 02 engineering and technology, Cell membrane, chemistry.chemical_compound, Squalane, Membrane fluidity, polyisoprenoids, Biology (General), Lipid bilayer, Spectroscopy, ComputingMilieux_MISCELLANEOUS, Liposome, Temperature, General Medicine, 021001 nanoscience & nanotechnology, Computer Science Applications, [SDV.BBM.BP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, Chemistry, Membrane, medicine.anatomical_structure, lipids (amino acids, peptides, and proteins), fluorescence, 0210 nano-technology, Laurdan, Squalene, QH301-705.5, Membrane Fluidity, 0699 Other Biological Sciences, Catalysis, Article, Inorganic Chemistry, 03 medical and health sciences, 0399 Other Chemical Sciences, medicine, squalane, archaea, cell membrane, permeability, Physical and Theoretical Chemistry, Molecular Biology, QD1-999, 0604 Genetics, Chemical Physics, Organic Chemistry, Cell Membrane, Archaea, 030104 developmental biology, chemistry, Liposomes, Biophysics
Abstract: The modification of archaeal lipid bilayer properties by the insertion of apolar molecules in the lipid bilayer midplane has been proposed to support cell membrane adaptation to extreme environmental conditions of temperature and hydrostatic pressure. In this work, we characterize the insertion effects of the apolar polyisoprenoid squalane on the permeability and fluidity of archaeal model membrane bilayers, composed of lipid analogues. We have monitored large molecule and proton permeability and Laurdan generalized polarization from lipid vesicles as a function of temperature and hydrostatic pressure. Even at low concentration, squalane (1 mol%) is able to enhance solute permeation by increasing membrane fluidity, but at the same time, to decrease proton permeability of the lipid bilayer. The squalane physicochemical impact on membrane properties are congruent with a possible role of apolar intercalants on the adaptation of Archaea to extreme conditions. In addition, such intercalant might be used to cheaply create or modify chemically resistant liposomes (archeaosomes) for drug delivery.
Published: 2021
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27. Acid Hydrolysis for the Extraction of Archaeal Core Lipids and HPLC-MS Analysis

Author: Vincent Grossi, Philippe Schaeffer, Philippe Oger, Maxime Tourte, Microbiologie, adaptation et pathogénie (MAP), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Microbiology of Extreme Environments (M2E), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Institut de Chimie de Strasbourg, Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), Laboratoire de Géologie de Lyon - Terre, Planètes, Environnement [Lyon] (LGL-TPE), Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-École normale supérieure - Lyon (ENS Lyon), Université de Strasbourg (UNISTRA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Géologie de Lyon - Terre, Planètes, Environnement (LGL-TPE), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut national des sciences de l'Univers (INSU - CNRS)-Université Jean Monnet - Saint-Étienne (UJM)-Centre National de la Recherche Scientifique (CNRS), and ANR-17-CE11-0012,ArchaeoMembranes,Des bicouches lipidiques stables au delà du point d'ébullition de l'eau(2017)
Subjects: Strategy and Management, [SDE.MCG]Environmental Sciences/Global Changes, Industrial and Manufacturing Engineering, Cell membrane, Cell wall, 03 medical and health sciences, [SDU.STU.GC]Sciences of the Universe [physics]/Earth Sciences/Geochemistry, medicine, Methods Article, Extremophile, Semipermeable membrane, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, biology, 030306 microbiology, Mechanical Engineering, Extraction (chemistry), Metals and Alloys, biology.organism_classification, Membrane, medicine.anatomical_structure, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Biochemistry, lipids (amino acids, peptides, and proteins), Acid hydrolysis, Archaea
Abstract: Lipid membranes are essential cellular elements as they provide cellular integrity and selective permeability under a broad range of environmental settings upon cell growth. In particular, Archaea are commonly recognized for their tolerance to extreme conditions, which is now widely accepted to stem from the unique structure of their lipids. While enhancing the stability of the archaeal cell membrane, the exceptional properties of archaeal lipids also hinder their extraction using regular procedures initially developed for bacterial and eukaryotic lipids. The protocol described here circumvents these issues by directly hydrolyzing the polar head group(s) of archaeal lipids and extracting the resulting core lipids. Although leading to a loss of information on the nature of polar heads, this procedure allows the quantitative extraction of core lipids for most types of archaeal cells in an efficient, reproducible, and rapid manner.
Published: 2021
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28. Biochemical characterization and mutational studies of a novel 3-methlyadenine DNA glycosylase II from the hyperthermophilic Thermococcus gammatolerans

Author: Philippe Oger, Likui Zhang, Kunming Dong, Yong Gong, Donghao Jiang, Yangzhou University, Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Microbiologie, adaptation et pathogénie (MAP), Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon, Microbiology of Extreme Environments (M2E), Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université Claude Bernard Lyon 1 (UCBL), and Oger, Phil M.
Subjects: DNA, Bacterial, Hot Temperature, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, DNA Repair, Biochemistry, base excision repair, Divalent, law.invention, DNA Glycosylases, Substrate Specificity, 03 medical and health sciences, chemistry.chemical_compound, 0302 clinical medicine, Bacterial Proteins, law, [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Amino Acid Sequence, Molecular Biology, 030304 developmental biology, chemistry.chemical_classification, 0303 health sciences, Hypoxanthine, biology, alkylated DNA, Adenine, DNA glycosylase, Thermococcus gammatolerans, deaminated DNA, Cell Biology, Base excision repair, Hydrogen-Ion Concentration, biology.organism_classification, [SDV.BIO] Life Sciences [q-bio]/Biotechnology, Thermococcus, Kinetics, Enzyme, chemistry, 030220 oncology & carcinogenesis, Mutation, Recombinant DNA, Sequence Alignment, DNA, DNA Damage
Abstract: International audience; The hyperthermophilic and radioresistant euryarchaeon Thermococcus gammatolerans encodes a putative 3-methlyadenine DNA glycosylase II (Tg-AlkA). Herein, we report biochemical characterization and catalytic mechanism of Tg-AlkA. The recombinant Tg-AlkA can excise hypoxanthine (Hx) and 1-methlyadenine (1-meA) from dsDNA with varied efficiencies at high temperature. Notably, Tg-AlkA is a bi-functional glycosylase, which is sharply distinct from all the reported AlkAs. Biochemical data show that the optimal temperature and pH of Tg-AlkA for removing Hx from dsDNA are ca.70°C and ca.7.0-8.0, respectively. Furthermore, the Tg-AlkA activity is independent of a divalent metal ion, and Mg 2+ stimulates the Tg-AlkA activity whereas other divalent ions inhibit the enzyme activity with varied degrees. Mutational studies show that the Tg-AlkA W204A and D223A mutants abolish completely the excision activity, thereby suggesting that residues W204 and D223 are involved in catalysis. Surprisingly, the mutations of W204, D223, Y139 and W256 to alanine in Tg-AlkA lead to the increased affinity for binding DNA substrate with varied degrees, suggesting that these residues are flexible for conformational change of the enzyme. Therefore, Tg-AlkA is a novel AlkA that can remove Hx and 1-meA from dsDNA, thus providing insights into repair of deaminated and alkylated bases in DNA from hyperthermophilic Thermococcus.
Published: 2021

29. Identification of a novel bifunctional uracil DNA glycosylase from Thermococcus barophilus Ch5

Author: Philippe Oger, Yong Gong, Qi Gan, Likui Zhang, Donghao Jiang, Haoqiang Shi, Li Miao, Yangzhou University, Institute of High Energy Physics, Chinese Academy of Sciences [Changchun Branch] (CAS), Microbiologie, adaptation et pathogénie (MAP), Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon, Microbiology of Extreme Environments (M2E), Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), and Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL)
Subjects: DNA Repair, Deamination, Applied Microbiology and Biotechnology, 03 medical and health sciences, chemistry.chemical_compound, AP site, Uracil, Uracil-DNA Glycosidase, Hyperthermophilic Archaea, Phylogeny, 030304 developmental biology, 0303 health sciences, biology, 030302 biochemistry & molecular biology, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, General Medicine, Base excision repair, biology.organism_classification, Bifunctional glycosylase, Thermococcus, Thermococcus barophilus, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, chemistry, Biochemistry, DNA glycosylase, Uracil-DNA glycosylase, Uracil DNA glycosylase, Cytosine, Biotechnology
Abstract: Genomes of hyperthermophiles are facing a severe challenge due to increased deamination rates of cytosine induced by high temperature, which could be counteracted by base excision repair mediated by uracil DNA glycosylase (UDG) or other repair pathways. Our previous work has shown that the two UDGs (Tba UDG247 and Tba UDG194) encoded by the genome of the hyperthermophilic euryarchaeon Thermococcus barophilus Ch5 can remove uracil from DNA at high temperature. Herein, we provide evidence that Tba UDG247 is a novel bifunctional glycosylase which can excise uracil from DNA and further cleave the phosphodiester bo nd of the generated apurinic/apyrimidinic (AP) site, which has never been described to date. In addition to cleaving uracil-containing DNA, Tba UDG247 can also cleave AP-containing ssDNA although at lower efficiency, thereby suggesting that the enzyme might be involved in repair of AP site in DNA. Kinetic analyses showed that Tba UDG247 displays a faster rate for uracil excision than for AP cleavage, thus suggesting that cleaving AP site by the enzyme is a rate-limiting step for its bifunctionality. Phylogenetic analysis showed that Tba UDG247 is clustered on a separate branch distant from all the reported UDGs. Overall, we designated Tba UDG247 as the prototype of a novel family of bifunctional UDGs. KEY POINTS: We first reported a novel DNA glycosylase with bifunctionality. Tba UDG247 possesses an AP lyase activity.
Published: 2021
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30. Identification of a novel type of glucose dehydrogenase involved in the mineral weathering ability of Collimonas pratensis strain PMB3(1)

Author: Marie-Pierre Turpault, Stéphane Uroz, Laura Picard, Philippe Oger, Interactions Arbres-Microorganismes (IAM), Université de Lorraine (UL)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Unité de recherche Biogéochimie des Ecosystèmes Forestiers (BEF), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Microbiologie, adaptation et pathogénie (MAP), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Microbiology of Extreme Environments (M2E), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), French Ministere de l'Enseignement Superieur, de la Recherche et de l'Innovation, EC2CO program, ANR-11-LABX-0002,ARBRE,Recherches Avancées sur l'Arbre et les Ecosytèmes Forestiers(2011), Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon, and Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées de Lyon (INSA Lyon)
Subjects: 0301 basic medicine, 030106 microbiology, Mutant, Biology, Applied Microbiology and Biotechnology, Microbiology, 03 medical and health sciences, chemistry.chemical_compound, Pyrroloquinoline quinone, Glucose/Methanol/Choline oxidoreductase, Glucose dehydrogenase, Oxidoreductase, Oxalobacteraceae, mineral weathering, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Weather, chemistry.chemical_classification, Minerals, Ecology, Collimonas, Glucose 1-Dehydrogenase, PQQ-independent glucose dehydrogenase, biology.organism_classification, Complementation, biotite, 030104 developmental biology, Collimonas pratensis PMB3(1), chemistry, Biochemistry, [SDE]Environmental Sciences, Gluconic acid, Bacteria
Abstract: The exact molecular mechanisms as well as the genes involved in the mineral weathering (MW) process by bacteria remain poorly characterized. To date, a single type of glucose dehydrogenase (GDH) depending on a particular co-factor named pyrroloquinoline quinone (PQQ) is known. These enzymes allow the production of gluconic acid through the oxidation of glucose. However, it remains to be determined how bacteria missing PQQ-dependent GDH and/or the related pqq biogenesis genes weather minerals. In this study, we considered the very effective mineral weathering bacterial strain PMB3(1) of Collimonas pratensis. Genome analysis revealed that it does not possess the PQQ based system. The use of random mutagenesis, gene complementation and functional assays allowed us to identify mutants impacted in their ability to weather mineral. Among them, three mutants were strongly altered on their acidification and biotite weathering abilities (58 to 75% of reduction compared to WT) and did not produce gluconic acid. The characterization of the genomic regions allowed noticeably to the identification of a Glucose/Methanol/Choline oxidoreductase. This region appeared very conserved among collimonads and related genera. This study represents the first demonstration of the implication of a PQQ-independent GDH in the mineral weathering process and explains how Collimonas weather minerals.
Published: 2020
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31. Draft Genome Sequence of Collimonas pratensis Strain PMB3(1), an Effective Mineral-Weathering and Chitin-Hydrolyzing Bacterial Strain

Author: Philippe Oger, Marie-Pierre Turpault, Laura Picard, Stéphane Uroz, Interactions Arbres-Microorganismes (IAM), Université de Lorraine (UL)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Unité de recherche Biogéochimie des Ecosystèmes Forestiers (BEF), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Microbiologie, adaptation et pathogénie (MAP), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), and Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, 0301 basic medicine, Antifungal, medicine.drug_class, [SDV]Life Sciences [q-bio], Collimonas pratensis, Mycorrhizosphere, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, chemistry.chemical_compound, Immunology and Microbiology (miscellaneous), Chitin, Botany, Genetics, medicine, Molecular Biology, Whole genome sequencing, biology, Strain (chemistry), Genome Sequences, food and beverages, biology.organism_classification, Bacterial strain, 030104 developmental biology, chemistry, Scleroderma citrinum
Abstract: We announce the draft genome sequence of Collimonas pratensis PMB3(1), isolated from the Scleroderma citrinum mycorrhizosphere. In addition to its mineral-weathering effectiveness and antifungal activity, this strain is characterized by genomic features that give it great potential as a biocontrol and plant growth-promoting agent in nutrient-poor soils.
Published: 2020
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32. 700 MPa sample stick for studying liquid samples or solid-gas reactions down to 1.8 K and up to 550 K

Author: Y. Memphis, Bruno Demé, J. Maurice, Claude Payre, Jean-Paul Gonzales, Eddy Lelièvre-Berna, Julien Gonthier, S. Vial, Philippe Oger, Judith Peters, Institut Laue-Langevin (ILL), Laboratoire de Géologie de Lyon - Terre, Planètes, Environnement (LGL-TPE), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut national des sciences de l'Univers (INSU - CNRS)-Université Jean Monnet - Saint-Étienne (UJM)-Centre National de la Recherche Scientifique (CNRS), Microbiologie, adaptation et pathogénie (MAP), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Adaptation aux milieux extrêmes (AME), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Laboratoire Interdisciplinaire de Physique [Saint Martin d’Hères] (LIPhy), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), and Université Grenoble Alpes (UGA)
Subjects: Nuclear and High Energy Physics, Solid gas, Materials science, Nuclear Energy and Engineering, [PHYS.PHYS.PHYS-BIO-PH]Physics [physics]/Physics [physics]/Biological Physics [physics.bio-ph], Sample (material), Analytical chemistry, 02 engineering and technology, 010402 general chemistry, 021001 nanoscience & nanotechnology, 0210 nano-technology, 01 natural sciences, 0104 chemical sciences
Abstract: International audience
Published: 2017
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33. Characterization of a Family IV uracil DNA glycosylase from the hyperthermophilic euryarchaeon Thermococcus barophilus Ch5

Author: Haoqiang Shi, Likui Zhang, Liping Ran, Qi Gan, Zhihui Yang, Mengfan He, Philippe Oger, Yangzhou University, Microbiologie, adaptation et pathogénie (MAP), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Microbiology of Extreme Environments (M2E), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Agricultural University of Hebei, Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon, and Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées de Lyon (INSA Lyon)
Subjects: Stereochemistry, Archaeal Proteins, 02 engineering and technology, Sodium Chloride, Biochemistry, Substrate Specificity, 03 medical and health sciences, chemistry.chemical_compound, Structural Biology, Enzyme Stability, Amino Acid Sequence, DNA Cleavage, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], Uracil-DNA Glycosidase, Molecular Biology, 030304 developmental biology, Ions, chemistry.chemical_classification, 0303 health sciences, biology, Temperature, Uracil, DNA, Salt Tolerance, General Medicine, Hydrogen-Ion Concentration, 021001 nanoscience & nanotechnology, biology.organism_classification, Enzyme assay, Thermococcus, Kinetics, Thermococcus barophilus, Enzyme, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, chemistry, Metals, DNA glycosylase, Uracil-DNA glycosylase, biology.protein, 0210 nano-technology
Abstract: International audience; The hyperthermophilic euryarchaeon Thermococcus barophilus Ch5 encodes two uracil DNA glycosylases (UDGs): Tba UDG247 and Tba UDG194. Herein, we characterized biochemically Tba UDG194. Compared with Tba UDG247, Tba UDG194 exhibits different biochemical characteristics. At >85 °C, >90 cleavage percentage was observed, suggesting that Tba UDG194 can remove uracil from DNA at physiological temperature of its host. Thus, the enzyme is the most thermophilic glycosylase among all the reported UDGs. Furthermore, the optimal pH of the enzyme activity was estimated to be 10, which is higher than that of Tba UDG247. Similar to Tba UDG247, Tba UDG194 activity is independent on a divalent metal ion. Mn2+, Zn2+ and Cu2+ display inhibitory effect on the enzyme activity at varied degreed whereas Mg2+ and Ca2+ have no detectable effect on the enzyme activity. In addition, Tba UDG194 is a salt-tolerant enzyme that retains compromised activity at 600 mM NaCl. Furthermore, Tba UDG 194 displays the following substrate preference: U ≈ U/G > U/T > U/A > U/C. The Arrhenius activation energy was estimated to be 20.1 ± 3.4 kcal/mol, theoretically representing the energy barrier for uracil removal from DNA by Tba UDG194. Overall, our observations suggest that Tba UDG194 might be involved in removal of uracil in DNA in Thermococcus cells.
Published: 2020
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34. An alternative pathway for repair of deaminated bases in DNA triggered by archaeal NucS endonuclease

Author: Zhihui Yang, Yuxiao Wang, Likui Zhang, Haoqiang Shi, Jianting Zheng, Qi Gan, Mai Wu, Philippe Oger, Yangzhou University, Agricultural University of Hebei, Microbiologie, adaptation et pathogénie (MAP), Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon, Microbiology of Extreme Environments (M2E), Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), and Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université Claude Bernard Lyon 1 (UCBL)
Subjects: DNA repair, Archaeal Proteins, Deamination, Biochemistry, 03 medical and health sciences, chemistry.chemical_compound, Endonuclease, 0302 clinical medicine, fluids and secretions, DNA Breaks, Double-Stranded, Cloning, Molecular, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], Molecular Biology, 030304 developmental biology, 0303 health sciences, biology, Single-Strand Specific DNA and RNA Endonucleases, Thermococcus gammatolerans, Uracil, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Cell Biology, biology.organism_classification, Thermococcus, DNA Repair Enzymes, DNA, Archaeal, chemistry, 030220 oncology & carcinogenesis, Phosphodiester bond, biology.protein, DNA mismatch repair, DNA, DNA Damage
Abstract: International audience; Recent studies show that NucS endonucleases participate in mismatch repair in several archaea and bacteria. However, the function of archaeal NucS endonucleases has not been completely clarified. Here, we describe a NucS endonuclease from the hyperthermophilic and radioresistant archaeon Thermococcus gammatolerans (Tga NucS) that can cleave uracil (U)-and hypoxanthine (I)-containing dsDNA at 80°C. Biochemical evidence shows that the cleavage sites of the enzyme are at the second phosphodiester on the 5′-site of U or I, and at the third phosphodiester on the 5′-site of the opposite base of U or I, creating a double strand break with a 4-nt 5′-overhang.The ends of the cleaved product of Tga NucS are ligatable, possessing 5′-phosphate and 3′-hydroxyl termini, which can be utilized by DNA repair proteins or enzymes. Tga NucS displays a preference for U/G-and I/T-containing dsDNA over other pairs with U or I, suggesting that the enzyme is responsible for repair of U and I in DNA that arise from deamination. Biochemical characterization of cleaving U-and I-containing DNA by Tga NucS was also investigated. The DNA-binding results show that the enzyme exhibits a higher affinity for normal, U-and I-containing dsDNA than for normal, U-and I-containing ssDNA. Therefore, we present an alternative pathway for repair of deaminated bases in DNA triggered by archaeal NucS endonuclease in hyperthermophilic archaea.
Published: 2020
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35. Structural Characterization of an Archaeal Lipid Bilayer as a Function of Hydration and Temperature

Author: Marta Salvador-Castell, Bruno Demé, Philippe Oger, Judith Peters
Published: 2020
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36. High-pressure Adaptation of Extremophiles and Biotechnological Applications

Author: Philippe Oger, Judith Peters, Marta Salvador-Castell, Oger, Phil M., Microbiologie, adaptation et pathogénie (MAP), Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon, Microbiology of Extreme Environments (M2E), Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Laboratoire Interdisciplinaire de Physique [Saint Martin d’Hères] (LIPhy ), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), and Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Université Claude Bernard Lyon 1 (UCBL)
Subjects: [PHYS.PHYS.PHYS-BIO-PH] Physics [physics]/Physics [physics]/Biological Physics [physics.bio-ph], [PHYS.PHYS.PHYS-BIO-PH]Physics [physics]/Physics [physics]/Biological Physics [physics.bio-ph], adaptation, Biology, piezophile, On cells, high pressure, stress, 13. Climate action, High pressure, Extremophile, deep biosphere, Biochemical engineering, Adaptation, Organism
Abstract: International audience; (about 150 words) During the last decades, high pressure has been an important physical parameter not only to study biomolecules, but also for its biotechnological applications. High pressure affects organism's ability to survive by altering most of cell's macromolecules. These effects can be used, for example, to inactivate microorganisms, enhance enzymatic reactions or to modulate cell activities. Moreover, some organisms are capable to growth under high pressures thanks to their adaptation at all cellular levels. Such adaptation confers a wide range of potentially interesting macromolecules still to be discovered. In this chapter, we firstly present the different effects of pressure on cells and the diverse strategies used to cope against this harsh environment. Secondly, we explored the pressure biotechnological applications on pressure-sensitive and adapted-pressure organisms.
Published: 2020

37. Induction of non-lamellar phases in archaeal lipids at high temperature and high hydrostatic pressure by apolar polyisoprenoids

Author: Judith Peters, Philippe Oger, Marta Salvador-Castell, Nicholas J. Brooks, Microbiologie, adaptation et pathogénie (MAP), Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon, Microbiology of Extreme Environments (M2E), Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Adaptation aux milieux extrêmes (AME), Department of Chemistry [Imperial College London], Imperial College London, Institut Laue-Langevin (ILL), ILL, Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), and Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL)
Subjects: Squalene, Hot Temperature, Hydrostatic pressure, Lipid Bilayers, Biophysics, 02 engineering and technology, Biochemistry, Cell membrane, 03 medical and health sciences, chemistry.chemical_compound, Membrane Lipids, Squalane, medicine, Hydrostatic Pressure, Lamellar structure, Lipid bilayer, 030304 developmental biology, 0303 health sciences, Cell Biology, 021001 nanoscience & nanotechnology, Archaea, [SDV.BBM.BP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, Membrane, medicine.anatomical_structure, chemistry, Cytoplasm, Membrane curvature, lipids (amino acids, peptides, and proteins), 0210 nano-technology
Abstract: International audience; It is now well established that cell membranes are much more than a barrier that separate the cytoplasm from the outside world. Regarding membrane's lipids and their self-assembling, the system is highly complex, for example, the cell membrane needs to adopt different curvatures to be functional. This is possible thanks to the presence of non-lamellar-forming lipids, which tend to curve the membrane. Here, we present the effect of squalane, an apolar isoprenoid molecule, on an archaea-like lipid membrane. The presence of this molecule provokes negative membrane curvature and forces lipids to self-assemble under inverted cubic and inverted hexagonal phases. Such non-lamellar phases are highly stable under a broad range of external extreme conditions, e.g. temperatures and high hydrostatic pressures, confirming that such apolar lipids could be included in the architecture of membranes arising from cells living under extreme environments.
Published: 2019
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38. Biochemical characterization of a thermostable DNA ligase from the hyperthermophilic euryarchaeon Thermococcus barophilus Ch5

Author: Hongxun Chen, Zhihui Yang, Yanchao Huang, Mianwen Rui, Haoqiang Shi, Likui Zhang, Qi Gan, Chuandeng Tu, Philippe Oger, Yangzhou University, Agricultural University of Hebei, Microbiologie, adaptation et pathogénie (MAP), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Adaptation aux milieux extrêmes (AME), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon, and Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées de Lyon (INSA Lyon)
Subjects: Hot Temperature, DNA Ligases, Archaeal Proteins, Applied Microbiology and Biotechnology, Substrate Specificity, law.invention, 03 medical and health sciences, chemistry.chemical_compound, law, Enzyme Stability, Ligase activity, Cloning, Molecular, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, chemistry.chemical_classification, 0303 health sciences, DNA ligase, biology, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], 030306 microbiology, DNA replication, DNA, General Medicine, Hydrogen-Ion Concentration, biology.organism_classification, Enzyme assay, Thermococcus, Thermococcus barophilus, chemistry, Biochemistry, Recombinant DNA, biology.protein, Biotechnology
Abstract: DNA ligases are essential enzymes for DNA replication, repair, and recombination processes by catalyzing a nick-joining reaction in double-stranded DNA. The genome of the hyperthermophilic euryarchaeon Thermococcus barophilus Ch5 encodes a putative ATP-dependent DNA ligase (Tba ligase). Herein, we characterized the biochemical properties of the recombinant Tba ligase. The enzyme displays an optimal nick-joining activity at 65–70 °C and retains its DNA ligation activity even after heated at 100 °C for 2 h, suggesting the enzyme is a thermostable DNA ligase. The enzyme joins DNA over a wide pH spectrum ranging from 5.0–10.0, and its optimal pH is 6.0–9.0. Tba ligase activity is dependent on a divalent metal ion: Mn2+, Mg2+, or Ca2+ is an optimal ion for the enzyme activity. The enzyme activity is inhibited by NaCl with high concentrations. Tba ligase is ATP-dependent and can also use UTP as a weak cofactor; however, the enzyme with high concentrations could function without an additional nucleotide cofactor. Mass spectrometric result shows that the residue K250 of Tba ligase is AMPylated, suggesting that the enzyme is bound to AMP. The substitution of K250 of Tba ligase with Ala abolishes the enzyme activity. In addition, the mismatches at the first position 3′ to the nick suppress Tba ligase activity more than those at the first position 5′ to the nick. The enzyme also discriminates more effectively mismatches at 3′ to the nick than those at 5′ to the nick in a ligation cycling reaction, suggesting that the enzyme might have potential application in single nucleotide polymorphism.
Published: 2019
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39. Biochemical characterization and mutational studies of a thermostable uracil DNA glycosylase from the hyperthermophilic euryarchaeon Thermococcus barophilus Ch5

Author: Hongxun Chen, Likui Zhang, Haiyue Hou, Yinuo Xu, Qi Gan, Haoqiang Shi, Yuqi Wu, Zhihui Yang, Donghao Jiang, Li Miao, Youcheng Yin, Philippe Oger, Yangzhou University, Agricultural University of Hebei, Microbiologie, adaptation et pathogénie (MAP), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Microbiology of Extreme Environments (M2E), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon, and Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées de Lyon (INSA Lyon)
Subjects: Models, Molecular, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, Chemical Phenomena, Molecular Conformation, 02 engineering and technology, Biochemistry, law.invention, Substrate Specificity, 03 medical and health sciences, chemistry.chemical_compound, Structure-Activity Relationship, Structural Biology, law, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Amino Acid Sequence, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], Uracil-DNA Glycosidase, Molecular Biology, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, chemistry.chemical_classification, 0303 health sciences, biology, Chemistry, Uracil, General Medicine, Base excision repair, 021001 nanoscience & nanotechnology, biology.organism_classification, Recombinant Proteins, Thermococcus, Thermococcus barophilus, Kinetics, Enzyme, DNA glycosylase, Uracil-DNA glycosylase, Mutation, Recombinant DNA, Thermodynamics, 0210 nano-technology, DNA
Abstract: Uracil DNA glycosylases (UDGs) play an important role in removing uracil from DNA to initiate DNA base excision repair. Here, we characterized biochemically a thermostable UDG from the hyperthermophilic euryarchaeon Thermococcus barophilus Ch5 (Tba UDG), and probed its mechanism by mutational analysis. The recombinant Tba UDG cleaves exclusively uracil-containing ssDNA and dsDNA at 65°C. The enzyme displays an optimal cleavage activity at 70-75°C. Tba UDG cleaves DNA over a wide pH spectrum ranging from 4.0 to 11.0 with an optimal pH of 7.0-9.0. In addition, Tba UDG activity is independent on a divalent metal ion; however, both Zn2+ and Cu2+ completely inhibit the enzyme activity. Tba UDG activity is also inhibited by high NaCl concentration. Tba UDG removes uracil from DNA with the following preference: U≈U/G>U/T≈U/C>U/A. Kinetic results showed that Tba UDG cleaves uracil-containing ssDNA and dsDNA at a similar rate. The mutational studies showed that the E118A, N159A and H216A mutants completely abolish cleavage activity and retain compromised binding activity while the Y127A mutant displays similar cleavage and binding activities with the wild-type protein, suggesting that residues E118, N159 and H216 are essential for uracil removal and necessary for uracil recognition.
Published: 2019
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40. Alkanes increase the stability of early life membrane models under extreme pressure and temperature conditions

Author: Judith Peters, Loreto Misuraca, Philippe Oger, Bruno Demé, Institut Laue-Langevin (ILL), ILL, Microbiology of Extreme Environments (M2E), Microbiologie, adaptation et pathogénie (MAP), Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon, Laboratoire Interdisciplinaire de Physique [Saint Martin d’Hères] (LIPhy ), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), and Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Chemistry, Bilayer, Vesicle, 02 engineering and technology, General Chemistry, 010402 general chemistry, 021001 nanoscience & nanotechnology, 01 natural sciences, Biochemistry, 0104 chemical sciences, [SDV.BBM.BP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, Membrane, Order (biology), 13. Climate action, Abiogenesis, Chemical physics, Ionic strength, Materials Chemistry, Environmental Chemistry, Extremophile, Molecule, 0210 nano-technology, QD1-999, [PHYS.COND.CM-SCM]Physics [physics]/Condensed Matter [cond-mat]/Soft Condensed Matter [cond-mat.soft]
Abstract: Terrestrial life appeared on our planet within a time window of [4.4–3.5] billion years ago. During that time, it is suggested that the first proto-cellular forms developed in the surrounding of deep-sea hydrothermal vents, oceanic crust fractures that are still present nowadays. However, these environments are characterized by extreme temperature and pressure conditions that question the early membrane compartment’s capability to endure a stable structural state. Recent studies proposed an adaptive strategy employed by present-day extremophiles: the use of apolar molecules as structural membrane components in order to tune the bilayer dynamic response when needed. Here we extend this hypothesis on early life protomembrane models, using linear and branched alkanes as apolar stabilizing molecules of prebiotic relevance. The structural ordering and chain dynamics of these systems have been investigated as a function of temperature and pressure. We found that both types of alkanes studied, even the simplest linear ones, impact highly the multilamellar vesicle ordering and chain dynamics. Our data show that alkane-enriched membranes have a lower multilamellar vesicle swelling induced by the temperature increase and are significantly less affected by pressure variation as compared to alkane-free samples, suggesting a possible survival strategy for the first living forms. Fatty acid membranes are implicated in several hypotheses about the origins of life, but whether their stability towards extremes of temperature, pressure, and ionic strength is sufficient to enable primitive biochemistry remains unclear. Here branched and linear alkanes are shown to stabilise a common model primordial membrane towards high temperatures and pressures
Published: 2021
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41. Novel Intact Polar and Core Lipid Compositions in the Pyrococcus Model Species, P. furiosus and P. yayanosii, Reveal the Largest Lipid Diversity Amongst Thermococcales

Author: Anaïs Cario, Vanessa Kuentz, Maxime Tourte, Philippe Schaeffer, Vincent Grossi, Philippe Oger, Microbiologie, adaptation et pathogénie (MAP), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Microbiology of Extreme Environments (M2E), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Institut de Chimie de Strasbourg, Université de Strasbourg (UNISTRA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Géologie de Lyon - Terre, Planètes, Environnement (LGL-TPE), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut national des sciences de l'Univers (INSU - CNRS)-Université Jean Monnet - Saint-Étienne (UJM)-Centre National de la Recherche Scientifique (CNRS), ANR-17-CE11-0012,ArchaeoMembranes,Des bicouches lipidiques stables au delà du point d'ébullition de l'eau(2017), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), Laboratoire de Géologie de Lyon - Terre, Planètes, Environnement [Lyon] (LGL-TPE), Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-École normale supérieure - Lyon (ENS Lyon)
Subjects: Pyrococcus, lcsh:QR1-502, P yayanosii, [SDV.BC.BC]Life Sciences [q-bio]/Cellular Biology/Subcellular Processes [q-bio.SC], Glycerophospholipids, Biochemistry, lcsh:Microbiology, 03 medical and health sciences, chemistry.chemical_compound, P furiosus, tetraethers, Glycerol, P. furiosus, Molecular Biology, phospholipids, 030304 developmental biology, glycerophospholipids, 0303 health sciences, core lipids, biology, 030306 microbiology, Chemistry, P. yayanosii, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Lipidome, biology.organism_classification, Thermococcales, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, archaeal membrane lipids, Pyrococcus furiosus, Polar, Archaea
Abstract: Elucidating the lipidome of Archaea is essential to understand their tolerance to extreme environmental conditions. Previous characterizations of the lipid composition of Pyrococcus species, a model genus of hyperthermophilic archaea belonging to the Thermococcales order, led to conflicting results, which hindered the comprehension of their membrane structure and the putative adaptive role of their lipids. In an effort to clarify the lipid composition data of the Pyrococcus genus, we thoroughly investigated the distribution of both the core lipids (CL) and intact polar lipids (IPL) of the model Pyrococcus furiosus and, for the first time, of Pyrococcus yayanosii, the sole obligate piezophilic hyperthermophilic archaeon known to date. We showed a low diversity of IPL in the lipid extract of P. furiosus, which nonetheless allowed the first report of phosphatidyl inositol-based glycerol mono- and trialkyl glycerol tetraethers. With up to 13 different CL structures identified, the acid methanolysis of Pyrococcus furiosus revealed an unprecedented CL diversity and showed strong discrepancies with the IPL compositions reported here and in previous studies. By contrast, P. yayanosii displayed fewer CL structures but a much wider variety of polar heads. Our results showed severe inconsistencies between IPL and CL relative abundances. Such differences highlight the diversity and complexity of the Pyrococcus plasma membrane composition and demonstrate that a large part of its lipids remains uncharacterized. Reassessing the lipid composition of model archaea should lead to a better understanding of the structural diversity of their lipidome and of their physiological and adaptive functions.
Published: 2020
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42. The first study on the impact of osmolytes in whole cells of high temperature-adapted microorganisms

Author: Marta Salvador-Castell, Maksym Golub, Philippe Oger, Judith Peters, Jacques Ollivier, Nicolas Martinez, Microbiologie, adaptation et pathogénie (MAP), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Microbiology of Extreme Environments (M2E), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Institut Laue-Langevin (ILL), ILL, Laboratoire Interdisciplinaire de Physique [Saint Martin d’Hères] (LIPhy), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon, and Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées de Lyon (INSA Lyon)
Subjects: Hot Temperature, Diffusion, Hydrostatic pressure, Context (language use), 02 engineering and technology, Cell Enlargement, Glyceric Acids, 010402 general chemistry, 01 natural sciences, Heating, Molecular dynamics, Bacterial Proteins, Osmotic Pressure, Piezophile, Osmotic pressure, biology, Chemistry, Water, General Chemistry, 021001 nanoscience & nanotechnology, Condensed Matter Physics, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 0104 chemical sciences, Thermococcus, [SDV.BBM.BP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, Thermococcus barophilus, Osmolyte, Biophysics, 0210 nano-technology, Mannose
Abstract: International audience; The hyperthermophilic piezophile Thermococcus barophilus displays a strong stress response characterized by the accumulation of the organic osmolyte mannosylglycerate during growth under sub-optimal pressure conditions (0.1 MPa). Taking advantage of this known effect, the impact of osmolytes in piezophiles in an otherwise identical cellular context was investigated, by comparing T. barophilus cells grown under low or optimal pressures (40 MPa). Using neutron scattering techniques, we studied the molecular dynamics of live cells of T. barophilus at different pressures and temperatures. We show that in presence of osmolytes, cells present a higher diffusion coefficient of hydration water and an increase of bulk water motions at high temperature. In absence of osmolytes, the T. barophilus cellular dynamics is more responsive to high temperature and high hydrostatic pressure. These results give therefore clear evidences for a protecting effect of osmolytes on proteins.
Published: 2019
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43. In Search for the Membrane Regulators of Archaea

Author: Marta Salvador-Castell, Philippe Oger, Maxime Tourte, Microbiologie, adaptation et pathogénie (MAP), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Microbiology of Extreme Environments (M2E), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon, and Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées de Lyon (INSA Lyon)
Subjects: 0301 basic medicine, Polyterpenes, archaea, Lipid composition, 030106 microbiology, Regulator, Review, adaptation, Catalysis, lcsh:Chemistry, Inorganic Chemistry, 03 medical and health sciences, Membrane Lipids, neutron diffraction, polyterpenes, polyisoprenoids, polyprenols, diphytanyl phospholipids, Physical and Theoretical Chemistry, ether lipids, lcsh:QH301-705.5, Molecular Biology, Gene, Spectroscopy, quinones, biology, Chemistry, Organic Chemistry, Cell Membrane, carotenoids, General Medicine, membrane organization, biology.organism_classification, Adaptation, Physiological, Hopanoids, Computer Science Applications, [SDV.BBM.BP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, 030104 developmental biology, Membrane, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, lcsh:Biology (General), lcsh:QD1-999, Biochemistry, phase transition, lipids (amino acids, peptides, and proteins), membrane modulators, Bacteria, Archaea
Abstract: International audience; Archaea, the most extremophilic domain of life, contain ether and branched lipids which provide extraordinary bilayer properties. We determined the structural characteristics of diether archaeal-like phospholipids as functions of hydration and temperature by neutron diffraction. Hydration and temperature are both crucial parameters for the self-assembly and physicochemical properties of lipid bilayers. In this study, we detected non-lamellar phases of archaeal-like lipids at low hydration levels, and lamellar phases at levels of 90% relative humidity or more exclusively. Moreover, at 90% relative humidity, a phase transition between two lamellar phases was discernible. At full hydration, lamellar phases were present up to 70ᵒC and no phase transition was observed within the temperature range studied (from 25 °C to 70 °C). In addition, we determined the neutron scattering length density and the bilayer's structural parameters from different hydration and temperature conditions. At the highest levels of hydration, the system exhibited rearrangements on its corresponding hydrophobic region. Furthermore, the water uptake of the lipids examined was remarkably high. We discuss the effect of ether linkages and branched lipids on the exceptional characteristics of archaeal phospholipids.
Published: 2019
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44. Biochemical characterization of a thermostable endonuclease V from the hyperthermophilic euryarchaeon Thermococcus barophilus Ch5

Author: Xinyuan Zhu, Yuxiao Wang, Likui Zhang, Philippe Oger, Haoqiang Shi, Zhihui Yang, Yuting Li, Yangzhou University, Microbiologie, adaptation et pathogénie (MAP), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), University of Bath [Bath], Lab-STICC_UBO_MOM_DIM, Laboratoire des sciences et techniques de l'information, de la communication et de la connaissance (Lab-STICC), Université européenne de Bretagne - European University of Brittany (UEB)-École Nationale d'Ingénieurs de Brest (ENIB)-Université de Bretagne Sud (UBS)-Université de Brest (UBO)-Télécom Bretagne-Institut Brestois du Numérique et des Mathématiques (IBNM), Université de Brest (UBO)-École Nationale Supérieure de Techniques Avancées Bretagne (ENSTA Bretagne)-Institut Mines-Télécom [Paris] (IMT)-Centre National de la Recherche Scientifique (CNRS)-Université européenne de Bretagne - European University of Brittany (UEB)-École Nationale d'Ingénieurs de Brest (ENIB)-Université de Bretagne Sud (UBS)-Université de Brest (UBO)-Télécom Bretagne-Institut Brestois du Numérique et des Mathématiques (IBNM), Université de Brest (UBO)-École Nationale Supérieure de Techniques Avancées Bretagne (ENSTA Bretagne)-Institut Mines-Télécom [Paris] (IMT)-Centre National de la Recherche Scientifique (CNRS), Johns Hopkins University (JHU), Istituto Nazionale di Fisica Nucleare, Sezione di Milano (INFN), Istituto Nazionale di Fisica Nucleare (INFN), Laboratoire de Géologie de Lyon - Terre, Planètes, Environnement [Lyon] (LGL-TPE), Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-École normale supérieure - Lyon (ENS Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Adaptation aux milieux extrêmes (AME), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Laboratoire national des champs magnétiques intenses - Toulouse (LNCMI-T), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])
Subjects: 0301 basic medicine, DNA Repair, DNA repair, [SDV]Life Sciences [q-bio], Gene Expression, Biochemistry, Substrate Specificity, 03 medical and health sciences, Endonuclease, chemistry.chemical_compound, Deoxyribonuclease (Pyrimidine Dimer), Structural Biology, Enzyme Stability, Amino Acid Sequence, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], DNA Cleavage, Molecular Biology, ComputingMilieux_MISCELLANEOUS, Thermostability, chemistry.chemical_classification, Ions, biology, Temperature, General Medicine, Hydrogen-Ion Concentration, biology.organism_classification, Enzyme assay, Recombinant Proteins, Enzyme Activation, Thermococcus, Thermococcus barophilus, Kinetics, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, 030104 developmental biology, Enzyme, chemistry, Metals, biology.protein, DNA, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract: International audience; Endonuclease V (Endo V) is an important enzyme for repairing deoxyinosine in DNA. While bacterial and eukaryotic endo Vs have been well studied, knowledge of archaeal endo Vs is limited. Here, we first presented biochemical characterization of a thermostable endonuclease V from the hyperthermophilic euryarchaeon Thermococcus barophilus Ch5 (Tba endo V). The recombinant enzyme possessed optimal endonuclease activity for cleaving deoxyinosine-containing DNA at 70–90 °C. Furthermore, Tba endo V can withstand 100 °C for 120 min without significant loss of its activity, suggesting the enzyme is thermostable. Tba endo V exhibited varying cleavage efficiencies at various pH levels from 6.0 to 11.0, among which an optimal pH for the enzyme was 8.0–9.0. In addition, a divalent metal ion was required for the enzyme to cleave DNA. Mn2+ and Mg2+ were optimal ions for the enzyme's activity whereas Ca2+, Zn2+ and Co2+ inhibited the enzyme activity. Moreover, the enzyme activity was suppressed by high NaCl concentration. Tba endo V bound to all DNA substrates; however, the enzyme exhibited a higher affinity for binding to deoxyinosine-containing DNA than normal DNA. Our work provides valuable information for revealing the role of Tba endo V in the base excision repair pathway for deoxyinosine repair in Thermococcus.
Published: 2018
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45. Probing the Structure and Dynamics of Cells, Cell Components and Endogenous Nanoparticles Under Extreme Conditions with Neutrons

Author: Judith Peters, Ruth Prassl, Philippe Oger, Institut de biologie structurale (IBS - UMR 5075 ), Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), Microbiologie, adaptation et pathogénie (MAP), Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon, Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Oger, Phil M., Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), and Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Physics, Flexibility (engineering), 0303 health sciences, [PHYS.PHYS.PHYS-BIO-PH] Physics [physics]/Physics [physics]/Biological Physics [physics.bio-ph], [PHYS.PHYS.PHYS-BIO-PH]Physics [physics]/Physics [physics]/Biological Physics [physics.bio-ph], Hydrostatic pressure, Nanoparticle, Neutron scattering, 010402 general chemistry, 01 natural sciences, 0104 chemical sciences, 03 medical and health sciences, Molecular dynamics, Atomic nucleus, Particle, Neutron, Biological system, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology
Abstract: Biological cells are fascinating systems of inconceivable complexity, which fulfil various functions. Among others, cells are able to execute motions, to produce heat, to breathe, to subsist, to grow wand proliferate and to die. Science aims at deciphering the different functionalities and activities of, and inside, the cells and how their different components participate to them. The methods employed are also versatile, as optical approaches by microscopies, modelling and simulations, spectroscopies, thermodynamic measurements and much more, each procuring some pieces of the puzzle. Although the different investigations are laborious and time consuming, research is the only way to disentangle the world at the microscopic level surrounding us. In the present study, we cite a few examples of studies on whole cells and cell components by different neutron scattering techniques to illustrate the modern possibilities. As neutrons are not charged, they have interactions directly with the atomic nuclei and give access to structural as well as dynamical information through coherent and incoherent neutron scattering. These techniques can be applied to the same samples and under identical experimental conditions so that we can gain knowledge on the correlations between structural and dynamical functions. Here, we present applications of neutron experiments to decipher the behaviour of complex biological samples, which study was not possible by other probes. The first example focuses on the molecular basis of the adaptation of cells living under extreme conditions, such as Archaea from the deep sea hydrothermal vents which experience both high temperature and high pressure stresses. Molecular dynamics seems to play a key role for adaptation as it is increased for the proteome of cells from such environment, in contrast to common expectation. In the second example, we exposed endogenous nanoparticles, low density lipoproteins, to high hydrostatic pressure, to shed light on the flexibility and stability of such particles under extreme conditions. Here we found that the native particle was surprisingly resistant to pressure application, concerning both dynamics and structure, while a modified form thereof was not.
Published: 2018

46. Complete Genome Sequences of 11 Type Species from the Thermococcus Genus of Hyperthermophilic and Piezophilic Archaea

Author: Philippe Oger
Subjects: 0301 basic medicine, Genetics, biology, Strain (biology), Thermococcus barossii, biology.organism_classification, Genome, 03 medical and health sciences, Type species, 030104 developmental biology, Type (biology), Genus, Thermococcus, Molecular Biology, Archaea
Abstract: We report here the genome sequences of the type strains of the species Thermococcus barossii , T. celer , T. chitonophagus , T. gorgonarius , T. pacificus , T. peptonophilus , T. profundus , T. radiotolerans , T. siculi , and T. thioreducens , as well as the prototype of a possible type strain of a novel Thermococcus species, strain P6.
Published: 2018
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47. Genome expression of Thermococcus barophilus and Thermococcus kodakarensis in response to different hydrostatic pressure conditions

Author: Grégoire Michoud, Viggó Þór Marteinsson, Pauline Vannier, Mohamed Jebbar, Philippe Oger, MATIS - Prokaria, Laboratoire de microbiologie des environnements extrêmophiles (LM2E), Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Microbiologie, adaptation et pathogénie (MAP), Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon, and Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Université Claude Bernard Lyon 1 (UCBL)
Subjects: DNA Replication, Carbohydrate transport, Hydrostatic pressure, [SDV.BID]Life Sciences [q-bio]/Biodiversity, Biology, 7. Clean energy, Microbiology, Genome, Archaeal, Stress, Physiological, Hydrostatic Pressure, Amino Acids, Molecular Biology, Gene, ComputingMilieux_MISCELLANEOUS, chemistry.chemical_classification, Gene Expression Profiling, Nucleotide transport, General Medicine, biology.organism_classification, Amino acid, Thermococcus kodakarensis, Thermococcus, Thermococcus barophilus, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, chemistry, Biochemistry, Coenzyme transport
Abstract: Transcriptomes were analyzed for two related hyperthermophilic archaeal species, the piezophilic Thermococcus barophilus strain MP and piezosensitive Thermococcus kodakarensis strain KOD1 subjected to high hydrostatic pressures. A total of 378 genes were differentially expressed in T. barophilus cells grown at 0.1, 40 and 70 MPa, whereas 141 genes were differentially regulated in T. kodakarensis cells grown at 0.1 and 25 MPa. In T. barophilus cells grown under stress conditions (0.1 and 70 MPa), 178 upregulated genes were distributed among three clusters of orthologous groups (COG): energy production and conversion (C), inorganic ion transport and metabolism (P) and carbohydrate transport and metabolism (G), whereas 156 downregulated genes were distributed among: amino acid transport and metabolism (E), replication, recombination and repair (L) and nucleotide transport and metabolism (F). The expression of 141 genes was regulated in T. kodakarensis cells grown under stress conditions (25 MPa); 71 downregulated genes belong to three COG: energy production and conversion (C), amino acid transport and metabolism (E) and transcription (K), whereas 70 upregulated genes are associated with replication, recombination and repair (L), coenzyme transport (H) and defense mechanisms (V).
Published: 2015
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48. Methanogenic microbial community of the Eastern Paris Basin: Potential for energy production from organic-rich shales

Author: Philippe Oger, Gilles Dromart, Charlotte Périot, Margaux Meslé, Laboratoire de Géologie de Lyon - Terre, Planètes, Environnement [Lyon] (LGL-TPE), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Géologie de Lyon - Terre, Planètes, Environnement (LGL-TPE), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Institut national des sciences de l'Univers (INSU - CNRS)-Université Jean Monnet - Saint-Étienne (UJM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: chemistry.chemical_classification, animal structures, Methanogenesis, Ecology, Stratigraphy, Microorganism, [SDU.STU]Sciences of the Universe [physics]/Earth Sciences, Geology, Structural basin, Spatial distribution, Methane, chemistry.chemical_compound, Fuel Technology, chemistry, Microbial population biology, 13. Climate action, Environmental chemistry, Economic Geology, Organic matter, Microcosm, ComputingMilieux_MISCELLANEOUS
Abstract: Shallow, thermally immature organic-rich shales represent considerable resources in the Paris Basin (France). We investigated the presence of methanogenic consortia (i.e., syntrophic bacteria and methanogens) in the Lower Toarcian Paper Shales formation, to link geochemical and lithological properties of the rocks to the spatial distribution of microbial communities. The presence of methanogenic microbial populations, demonstrated via their growth in enrichment cultures, occurs throughout most of the rock layers, and may be explained by the transport of organics and microorganisms within the formation. The enriched consortia were able to utilize the organic matter of the rock as sole carbon source in microcosm, indicating a strong potential of these microbial communities for methanogenesis in situ.
Published: 2015
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49. Microbial diversity and adaptation to high hydrostatic pressure in deep-sea hydrothermal vents prokaryotes

Author: Eric Girard, Mohamed Jebbar, Bruno Franzetti, Philippe Oger, Laboratoire de microbiologie des environnements extrêmophiles (LM2E), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS), Institut de biologie structurale (IBS - UMR 5075 ), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Laboratoire de Biologie Moléculaire de la Cellule (LBMC), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Géologie de Lyon - Terre, Planètes, Environnement (LGL-TPE), Université de Lyon-Université de Lyon-Institut national des sciences de l'Univers (INSU - CNRS)-Université Jean Monnet - Saint-Étienne (UJM)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-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)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon, Laboratoire de Géologie de Lyon - Terre, Planètes, Environnement [Lyon] (LGL-TPE), Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-École normale supérieure - Lyon (ENS Lyon)
Subjects: Bacteria, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], biology, Ecology, Thermophile, Hydrostatic pressure, Biodiversity, General Medicine, biology.organism_classification, Adaptation, Physiological, Archaea, Microbiology, Deep sea, Thermococcales, Hydrothermal Vents, Microbial ecology, Piezophile, Hydrostatic Pressure, Molecular Medicine, Hydrothermal vent
Abstract: International audience; Prokaryotes inhabiting in the deep sea vent ecosystem will thus experience harsh conditions of temperature, pH, salinity or high hydrostatic pressure (HHP) stress. Among the fifty-two piezophilic and piezotolerant prokaryotes isolated so far from different deep-sea environments, only fifteen (four Bacteria and eleven Archaea) that are true hyper/thermophiles and piezophiles have been isolated from deep-sea hydrothermal vents; these belong mainly to the Thermococcales order. Different strategies are used by microorganisms to thrive in deep-sea hydrothermal vents in which "extreme" physico-chemical conditions prevail and where non-adapted organisms cannot live, or even survive. HHP is known to impact the structure of several cellular components and functions, such as membrane fluidity, protein activity and structure. Physically the impact of pressure resembles a lowering of temperature, since it reinforces the structure of certain molecules, such as membrane lipids, and an increase in temperature, since it will also destabilize other structures, such as proteins. However, universal molecular signatures of HHP adaptation are not yet known and are still to be deciphered.
Published: 2015
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50. The Effect of Crowding on Protein Stability, Rigidity, and High Pressure Sensitivity in Whole Cells

Author: Philippe Oger, Maksym Golub, Grégoire Michoud, Judith Peters, Jacques Ollivier, Nicolas Martinez, Mohamed Jebbar, Institut Laue-Langevin (ILL), Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Laboratoire de microbiologie des environnements extrêmophiles (LM2E), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Géologie de Lyon - Terre, Planètes, Environnement (LGL-TPE), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut national des sciences de l'Univers (INSU - CNRS)-Université Jean Monnet - Saint-Étienne (UJM)-Centre National de la Recherche Scientifique (CNRS), Microbiologie, adaptation et pathogénie (MAP), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Adaptation aux milieux extrêmes (AME), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), ILL, Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Laboratoire de Géologie de Lyon - Terre, Planètes, Environnement [Lyon] (LGL-TPE), Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-École normale supérieure - Lyon (ENS Lyon), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), and Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL)
Subjects: 0301 basic medicine, Cell type, Lysis, [SDV]Life Sciences [q-bio], Hydrostatic pressure, 010402 general chemistry, 01 natural sciences, 03 medical and health sciences, Bacterial Proteins, Electrochemistry, Hydrostatic Pressure, General Materials Science, Spectroscopy, biology, Chemistry, Protein Stability, Water, Surfaces and Interfaces, Condensed Matter Physics, biology.organism_classification, Crowding, 0104 chemical sciences, Thermococcales, 030104 developmental biology, Membrane, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Osmolyte, Proteome, Biophysics, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract: International audience; In live cells, high concentrations up to 300-400 mg/mL, as in Eschericia coli (Ellis, R J. Curr. Opin. Struct. Biol. 2001, 11, 114) are achieved which have effects on their proper functioning. However, in many experiments only individual parts of the cells as proteins or membranes are studied in order to get insight into these specific components and to avoid the high complexity of whole cells, neglecting by the way the influence of crowding. In the present study, we investigated cells of the order of Thermococcales, which are known to live under extreme conditions, in their intact form and after cell lysis to extract the effect of crowding on the molecular dynamics of the proteome and of water molecules. We found that some parameters characterizing the dynamics within the cells seem to be intrinsic to the cell type, as flexibility typical for the proteome, others are more specific to the cellular environment, as bulk water's residence time and some fractions of particles participating to the different motions, which make the lysed cells' dynamics similar to the one of another Thermococcale adapted to live under high hydrostatic pressure. In contrast to studies on the impact of crowding on pure proteins we show here that the release of crowding constraints on proteins leads to an increase in the rigidity and a decrease in the high pressure sensitivity. In a way similar to high pressure adaptation in piezophiles, the hydration water layer is decreased for the lysed cells, demonstrating a first link between protein adaptation and the impact of crowding or osmolytes on proteins.
Published: 2018
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