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Your search keyword '"Philippe Oger"' showing total 4 results
Start Over Author "Philippe Oger" Journal international journal of biological macromolecules
4 results on '"Philippe Oger"'

1. 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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2. 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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3. 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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4. 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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