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Corrigendum: Parallel evolution of non-homologous isofunctional enzymes in methionine biosynthesis.

Nature chemical biology

Bastard K, Perret A, Mariage A, Bessonnet T, Pinet-Turpault A, Petit JL, Darii E, Bazire P, Vergne-Vaxelaire C, Brewee C, Debard A, Pellouin V, Besnard-Gonnet M, Artiguenave F, Médigue C, Vallenet D, Danchin A, Zaparucha A, Weissenbach J, Salanoubat M, de Berardinis V.
PMID: 28926556
Nat Chem Biol. 2017 Sep 19;13(10):1137. doi: 10.1038/nchembio1017-1137c.

No abstract available.

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Bastard K, Perret A, Mariage A, et al. Corrigendum: Parallel evolution of non-homologous isofunctional enzymes in methionine biosynthesis. Nat Chem Biol. 2017;13(10):1137doi: 10.1038/nchembio1017-1137c.
Bastard, K., Perret, A., Mariage, A., Bessonnet, T., Pinet-Turpault, A., Petit, J. L., Darii, E., Bazire, P., Vergne-Vaxelaire, C., Brewee, C., Debard, A., Pellouin, V., Besnard-Gonnet, M., Artiguenave, F., Médigue, C., Vallenet, D., Danchin, A., Zaparucha, A., Weissenbach, J., Salanoubat, M., & de Berardinis, V. (2017). Corrigendum: Parallel evolution of non-homologous isofunctional enzymes in methionine biosynthesis. Nature chemical biology, 13(10), 1137. https://doi.org/10.1038/nchembio1017-1137c
Bastard, Karine, et al. "Corrigendum: Parallel evolution of non-homologous isofunctional enzymes in methionine biosynthesis." Nature chemical biology vol. 13,10 (2017): 1137. doi: https://doi.org/10.1038/nchembio1017-1137c
Bastard K, Perret A, Mariage A, Bessonnet T, Pinet-Turpault A, Petit JL, Darii E, Bazire P, Vergne-Vaxelaire C, Brewee C, Debard A, Pellouin V, Besnard-Gonnet M, Artiguenave F, Médigue C, Vallenet D, Danchin A, Zaparucha A, Weissenbach J, Salanoubat M, de Berardinis V. Corrigendum: Parallel evolution of non-homologous isofunctional enzymes in methionine biosynthesis. Nat Chem Biol. 2017 Sep 19;13(10):1137. doi: 10.1038/nchembio1017-1137c. PMID: 28926556.
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Genome Sequence of the Obligate Gammaproteobacterial Methanotroph Methylomicrobium album Strain BG8.

Genome announcements

Kits KD, Kalyuzhnaya MG, Klotz MG, Jetten MS, Op den Camp HJ, Vuilleumier S, Bringel F, Dispirito AA, Murrell JC, Bruce D, Cheng JF, Copeland A, Goodwin L, Hauser L, Lajus A, Land ML, Lapidus A, Lucas S, Médigue C, Pitluck S, Woyke T, Zeytun A, Stein LY.
PMID: 23580712
Genome Announc. 2013 Apr 11;1(2):e0017013. doi: 10.1128/genomeA.00170-13.

The complete genome sequence of Methylomicrobium album strain BG8, a methane-oxidizing gammaproteobacterium isolated from freshwater, is reported. Aside from a conserved inventory of genes for growth on single-carbon compounds, M. album BG8 carries a range of gene inventories for...

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Kits KD, Kalyuzhnaya MG, Klotz MG, et al. Genome Sequence of the Obligate Gammaproteobacterial Methanotroph Methylomicrobium album Strain BG8. Genome Announc. 2013;1(2):e0017013doi: 10.1128/genomeA.00170-13.
Kits, K. D., Kalyuzhnaya, M. G., Klotz, M. G., Jetten, M. S., Op den Camp, H. J., Vuilleumier, S., Bringel, F., Dispirito, A. A., Murrell, J. C., Bruce, D., Cheng, J. F., Copeland, A., Goodwin, L., Hauser, L., Lajus, A., Land, M. L., Lapidus, A., Lucas, S., Médigue, C., Pitluck, S., Woyke, T., Zeytun, A., & Stein, L. Y. (2013). Genome Sequence of the Obligate Gammaproteobacterial Methanotroph Methylomicrobium album Strain BG8. Genome announcements, 1(2), e0017013. https://doi.org/10.1128/genomeA.00170-13
Kits, K Dimitri, et al. "Genome Sequence of the Obligate Gammaproteobacterial Methanotroph Methylomicrobium album Strain BG8." Genome announcements vol. 1,2 (2013): e0017013. doi: https://doi.org/10.1128/genomeA.00170-13
Kits KD, Kalyuzhnaya MG, Klotz MG, Jetten MS, Op den Camp HJ, Vuilleumier S, Bringel F, Dispirito AA, Murrell JC, Bruce D, Cheng JF, Copeland A, Goodwin L, Hauser L, Lajus A, Land ML, Lapidus A, Lucas S, Médigue C, Pitluck S, Woyke T, Zeytun A, Stein LY. Genome Sequence of the Obligate Gammaproteobacterial Methanotroph Methylomicrobium album Strain BG8. Genome Announc. 2013 Apr 11;1(2):e0017013. doi: 10.1128/genomeA.00170-13. PMID: 23580712; PMCID: PMC3624686.
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Escherichia coli molecular genetic map (1000Kbp):update.

Molecular microbiology

Medigue C, Hénaut A, Danchin A.
PMID: 28776816
Mol Microbiol. 1990 Sep;4(9):1443-1454. doi: 10.1111/j.1365-2958.1990.tb02055.x.

The sequenced genes from Escherichia coli that are available in the EMBL library (release 21) have been localized on an updated and corrected version of the restriction map of the chromosome generated by kohara et al. (1987). One thousand...

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Medigue C, Hénaut A, Danchin A. Escherichia coli molecular genetic map (1000Kbp):update. Mol Microbiol. 1990;4(9):1443-1454doi: 10.1111/j.1365-2958.1990.tb02055.x.
Medigue, C., Hénaut, A., & Danchin, A. (1990). Escherichia coli molecular genetic map (1000Kbp):update. Molecular microbiology, 4(9), 1443-1454. https://doi.org/10.1111/j.1365-2958.1990.tb02055.x
Medigue, C, et al. "Escherichia coli molecular genetic map (1000Kbp):update." Molecular microbiology vol. 4,9 (1990): 1443-1454. doi: https://doi.org/10.1111/j.1365-2958.1990.tb02055.x
Medigue C, Hénaut A, Danchin A. Escherichia coli molecular genetic map (1000Kbp):update. Mol Microbiol. 1990 Sep;4(9):1443-1454. doi: 10.1111/j.1365-2958.1990.tb02055.x. PMID: 28776816.
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ProMetIS, deep phenotyping of mouse models by combined proteomics and metabolomics analysis.

Scientific data

Imbert A, Rompais M, Selloum M, Castelli F, Mouton-Barbosa E, Brandolini-Bunlon M, Chu-Van E, Joly C, Hirschler A, Roger P, Burger T, Leblanc S, Sorg T, Ouzia S, Vandenbrouck Y, Médigue C, Junot C, Ferro M, Pujos-Guillot E, de Peredo AG, Fenaille F, Carapito C, Herault Y, Thévenot EA.
PMID: 34862403
Sci Data. 2021 Dec 03;8(1):311. doi: 10.1038/s41597-021-01095-3.

Genes are pleiotropic and getting a better knowledge of their function requires a comprehensive characterization of their mutants. Here, we generated multi-level data combining phenomic, proteomic and metabolomic acquisitions from plasma and liver tissues of two C57BL/6 N mouse...

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Imbert A, Rompais M, Selloum M, et al. ProMetIS, deep phenotyping of mouse models by combined proteomics and metabolomics analysis. Sci Data. 2021;8(1):311doi: 10.1038/s41597-021-01095-3.
Imbert, A., Rompais, M., Selloum, M., Castelli, F., Mouton-Barbosa, E., Brandolini-Bunlon, M., Chu-Van, E., Joly, C., Hirschler, A., Roger, P., Burger, T., Leblanc, S., Sorg, T., Ouzia, S., Vandenbrouck, Y., Médigue, C., Junot, C., Ferro, M., Pujos-Guillot, E., de Peredo, A. G., Fenaille, F., Carapito, C., Herault, Y., & Thévenot, E. A. (2021). ProMetIS, deep phenotyping of mouse models by combined proteomics and metabolomics analysis. Scientific data, 8(1), 311. https://doi.org/10.1038/s41597-021-01095-3
Imbert, Alyssa, et al. "ProMetIS, deep phenotyping of mouse models by combined proteomics and metabolomics analysis." Scientific data vol. 8,1 (2021): 311. doi: https://doi.org/10.1038/s41597-021-01095-3
Imbert A, Rompais M, Selloum M, Castelli F, Mouton-Barbosa E, Brandolini-Bunlon M, Chu-Van E, Joly C, Hirschler A, Roger P, Burger T, Leblanc S, Sorg T, Ouzia S, Vandenbrouck Y, Médigue C, Junot C, Ferro M, Pujos-Guillot E, de Peredo AG, Fenaille F, Carapito C, Herault Y, Thévenot EA. ProMetIS, deep phenotyping of mouse models by combined proteomics and metabolomics analysis. Sci Data. 2021 Dec 03;8(1):311. doi: 10.1038/s41597-021-01095-3. PMID: 34862403.
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Genome Sequence of the Dichloromethane-Degrading Bacterium .

Genome announcements

Bringel F, Postema CP, Mangenot S, Bibi-Triki S, Chaignaud P, Farhan Ul Haque M, Gruffaz C, Hermon L, Louhichi Y, Maucourt B, Muller EEL, Nadalig T, Lajus A, Rouy Z, Médigue C, Barbe V, Janssen DB, Vuilleumier S.
PMID: 28751386
Genome Announc. 2017 Jul 27;5(30). doi: 10.1128/genomeA.00622-17.

The genome sequence of

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Bringel F, Postema CP, Mangenot S, et al. Genome Sequence of the Dichloromethane-Degrading Bacterium . Genome Announc. 2017;5(30)doi: 10.1128/genomeA.00622-17.
Bringel, F., Postema, C. P., Mangenot, S., Bibi-Triki, S., Chaignaud, P., Farhan Ul Haque, M., Gruffaz, C., Hermon, L., Louhichi, Y., Maucourt, B., Muller, E. E. L., Nadalig, T., Lajus, A., Rouy, Z., Médigue, C., Barbe, V., Janssen, D. B., & Vuilleumier, S. (2017). Genome Sequence of the Dichloromethane-Degrading Bacterium . Genome announcements, 5(30), . https://doi.org/10.1128/genomeA.00622-17
Bringel, Françoise, et al. "Genome Sequence of the Dichloromethane-Degrading Bacterium ." Genome announcements vol. 5,30 (2017). doi: https://doi.org/10.1128/genomeA.00622-17
Bringel F, Postema CP, Mangenot S, Bibi-Triki S, Chaignaud P, Farhan Ul Haque M, Gruffaz C, Hermon L, Louhichi Y, Maucourt B, Muller EEL, Nadalig T, Lajus A, Rouy Z, Médigue C, Barbe V, Janssen DB, Vuilleumier S. Genome Sequence of the Dichloromethane-Degrading Bacterium . Genome Announc. 2017 Jul 27;5(30). doi: 10.1128/genomeA.00622-17. PMID: 28751386; PMCID: PMC5532824.
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MicroScope: a platform for microbial genome annotation and comparative genomics.

Database : the journal of biological databases and curation

Vallenet D, Engelen S, Mornico D, Cruveiller S, Fleury L, Lajus A, Rouy Z, Roche D, Salvignol G, Scarpelli C, Médigue C.
PMID: 20157493
Database (Oxford). 2009;2009:bap021. doi: 10.1093/database/bap021. Epub 2009 Nov 25.

The initial outcome of genome sequencing is the creation of long text strings written in a four letter alphabet. The role of in silico sequence analysis is to assist biologists in the act of associating biological knowledge with these...

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Vallenet D, Engelen S, Mornico D, et al. MicroScope: a platform for microbial genome annotation and comparative genomics. Database (Oxford). 2009;2009:bap021doi: 10.1093/database/bap021.
Vallenet, D., Engelen, S., Mornico, D., Cruveiller, S., Fleury, L., Lajus, A., Rouy, Z., Roche, D., Salvignol, G., Scarpelli, C., & Médigue, C. (2009). MicroScope: a platform for microbial genome annotation and comparative genomics. Database : the journal of biological databases and curation, 2009bap021. https://doi.org/10.1093/database/bap021
Vallenet, D, et al. "MicroScope: a platform for microbial genome annotation and comparative genomics." Database : the journal of biological databases and curation vol. 2009 (2009): bap021. doi: https://doi.org/10.1093/database/bap021
Vallenet D, Engelen S, Mornico D, Cruveiller S, Fleury L, Lajus A, Rouy Z, Roche D, Salvignol G, Scarpelli C, Médigue C. MicroScope: a platform for microbial genome annotation and comparative genomics. Database (Oxford). 2009;2009:bap021. doi: 10.1093/database/bap021. Epub 2009 Nov 25. PMID: 20157493; PMCID: PMC2790312.
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Genome Sequence of the Sulfate-Reducing Bacterium Desulfotomaculum hydrothermale Lam5(T).

Genome announcements

Amin O, Fardeau ML, Valette O, Hirschler-Réa A, Barbe V, Médigue C, Vacherie B, Ollivier B, Bertin PN, Dolla A.
PMID: 23405336
Genome Announc. 2013 Jan;1(1). doi: 10.1128/genomeA.00114-12. Epub 2013 Jan 24.

Here, we report the draft genome sequence of Desulfotomaculum hydrothermale, a sulfate-reducing, spore-forming bacterium isolated from a Tunisian hot spring. The genome is composed of 2.7 Mb, with a G+C content of 49.48%, and it contains 2,643 protein-coding sequences.

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Amin O, Fardeau ML, Valette O, et al. Genome Sequence of the Sulfate-Reducing Bacterium Desulfotomaculum hydrothermale Lam5(T). Genome Announc. 2013;1(1)doi: 10.1128/genomeA.00114-12.
Amin, O., Fardeau, M. L., Valette, O., Hirschler-Réa, A., Barbe, V., Médigue, C., Vacherie, B., Ollivier, B., Bertin, P. N., & Dolla, A. (2013). Genome Sequence of the Sulfate-Reducing Bacterium Desulfotomaculum hydrothermale Lam5(T). Genome announcements, 1(1), . https://doi.org/10.1128/genomeA.00114-12
Amin, Oulfat, et al. "Genome Sequence of the Sulfate-Reducing Bacterium Desulfotomaculum hydrothermale Lam5(T)." Genome announcements vol. 1,1 (2013). doi: https://doi.org/10.1128/genomeA.00114-12
Amin O, Fardeau ML, Valette O, Hirschler-Réa A, Barbe V, Médigue C, Vacherie B, Ollivier B, Bertin PN, Dolla A. Genome Sequence of the Sulfate-Reducing Bacterium Desulfotomaculum hydrothermale Lam5(T). Genome Announc. 2013 Jan;1(1). doi: 10.1128/genomeA.00114-12. Epub 2013 Jan 24. PMID: 23405336; PMCID: PMC3569332.
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Comparative genomics of aeschynomene symbionts: insights into the ecological lifestyle of nod-independent photosynthetic bradyrhizobia.

Genes

Mornico D, Miché L, Béna G, Nouwen N, Verméglio A, Vallenet D, Smith AA, Giraud E, Médigue C, Moulin L.
PMID: 24704842
Genes (Basel). 2011 Dec 21;3(1):35-61. doi: 10.3390/genes3010035.

Tropical aquatic species of the legume genus Aeschynomene are stem- and root-nodulated by bradyrhizobia strains that exhibit atypical features such as photosynthetic capacities or the use of a nod gene-dependent (ND) or a nod gene-independent (NI) pathway to enter...

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Mornico D, Miché L, Béna G, et al. Comparative genomics of aeschynomene symbionts: insights into the ecological lifestyle of nod-independent photosynthetic bradyrhizobia. Genes (Basel). 2011;3(1):35-61doi: 10.3390/genes3010035.
Mornico, D., Miché, L., Béna, G., Nouwen, N., Verméglio, A., Vallenet, D., Smith, A. A., Giraud, E., Médigue, C., & Moulin, L. (2011). Comparative genomics of aeschynomene symbionts: insights into the ecological lifestyle of nod-independent photosynthetic bradyrhizobia. Genes, 3(1), 35-61. https://doi.org/10.3390/genes3010035
Mornico, Damien, et al. "Comparative genomics of aeschynomene symbionts: insights into the ecological lifestyle of nod-independent photosynthetic bradyrhizobia." Genes vol. 3,1 (2011): 35-61. doi: https://doi.org/10.3390/genes3010035
Mornico D, Miché L, Béna G, Nouwen N, Verméglio A, Vallenet D, Smith AA, Giraud E, Médigue C, Moulin L. Comparative genomics of aeschynomene symbionts: insights into the ecological lifestyle of nod-independent photosynthetic bradyrhizobia. Genes (Basel). 2011 Dec 21;3(1):35-61. doi: 10.3390/genes3010035. PMID: 24704842; PMCID: PMC3899966.
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Draft Genome Sequence of Carnobacterium divergens V41, a Bacteriocin-Producing Strain.

Genome announcements

Remenant B, Borges F, Cailliez-Grimal C, Revol-Junelles AM, Marché L, Lajus A, Médigue C, Pilet MF, Prévost H, Zagorec M.
PMID: 27738030
Genome Announc. 2016 Oct 13;4(5). doi: 10.1128/genomeA.01109-16.

In this study, we present the draft genome sequence of Carnobacterium divergens V41. This strain was previously reported as producing divercin V41, a bacteriocin of interest for food biopreservation. Its genome revealed also the presence of a gene cluster...

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Remenant B, Borges F, Cailliez-Grimal C, et al. Draft Genome Sequence of Carnobacterium divergens V41, a Bacteriocin-Producing Strain. Genome Announc. 2016;4(5)doi: 10.1128/genomeA.01109-16.
Remenant, B., Borges, F., Cailliez-Grimal, C., Revol-Junelles, A. M., Marché, L., Lajus, A., Médigue, C., Pilet, M. F., Prévost, H., & Zagorec, M. (2016). Draft Genome Sequence of Carnobacterium divergens V41, a Bacteriocin-Producing Strain. Genome announcements, 4(5), . https://doi.org/10.1128/genomeA.01109-16
Remenant, Benoît, et al. "Draft Genome Sequence of Carnobacterium divergens V41, a Bacteriocin-Producing Strain." Genome announcements vol. 4,5 (2016). doi: https://doi.org/10.1128/genomeA.01109-16
Remenant B, Borges F, Cailliez-Grimal C, Revol-Junelles AM, Marché L, Lajus A, Médigue C, Pilet MF, Prévost H, Zagorec M. Draft Genome Sequence of Carnobacterium divergens V41, a Bacteriocin-Producing Strain. Genome Announc. 2016 Oct 13;4(5). doi: 10.1128/genomeA.01109-16. PMID: 27738030; PMCID: PMC5064103.
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Mutation Rate Inferred From Synonymous Substitutions in a Long-Term Evolution Experiment With Escherichia coli.

G3 (Bethesda, Md.)

Wielgoss S, Barrick JE, Tenaillon O, Cruveiller S, Chane-Woon-Ming B, Médigue C, Lenski RE, Schneider D.
PMID: 22207905
G3 (Bethesda). 2011 Aug 01;1(3):183-186. doi: 10.1534/g3.111.000406.

The quantification of spontaneous mutation rates is crucial for a mechanistic understanding of the evolutionary process. In bacteria, traditional estimates using experimental or comparative genetic methods are prone to statistical uncertainty and consequently estimates vary by over one order...

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Wielgoss S, Barrick JE, Tenaillon O, et al. Mutation Rate Inferred From Synonymous Substitutions in a Long-Term Evolution Experiment With Escherichia coli. G3 (Bethesda). 2011;1(3):183-186doi: 10.1534/g3.111.000406.
Wielgoss, S., Barrick, J. E., Tenaillon, O., Cruveiller, S., Chane-Woon-Ming, B., Médigue, C., Lenski, R. E., & Schneider, D. (2011). Mutation Rate Inferred From Synonymous Substitutions in a Long-Term Evolution Experiment With Escherichia coli. G3 (Bethesda, Md.), 1(3), 183-186. https://doi.org/10.1534/g3.111.000406
Wielgoss, Sébastien, et al. "Mutation Rate Inferred From Synonymous Substitutions in a Long-Term Evolution Experiment With Escherichia coli." G3 (Bethesda, Md.) vol. 1,3 (2011): 183-186. doi: https://doi.org/10.1534/g3.111.000406
Wielgoss S, Barrick JE, Tenaillon O, Cruveiller S, Chane-Woon-Ming B, Médigue C, Lenski RE, Schneider D. Mutation Rate Inferred From Synonymous Substitutions in a Long-Term Evolution Experiment With Escherichia coli. G3 (Bethesda). 2011 Aug 01;1(3):183-186. doi: 10.1534/g3.111.000406. PMID: 22207905; PMCID: PMC3246271.
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The Odyssey of the Ancestral Escherich Strain through Culture Collections: an Example of Allopatric Diversification.

mSphere

Desroches M, Royer G, Roche D, Mercier-Darty M, Vallenet D, Médigue C, Bastard K, Rodriguez C, Clermont O, Denamur E, Decousser JW.
PMID: 29404421
mSphere. 2018 Jan 31;3(1). doi: 10.1128/mSphere.00553-17. eCollection 2018.

More than a century ago, Theodor Escherich isolated the bacterium that was to become

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Desroches M, Royer G, Roche D, et al. The Odyssey of the Ancestral Escherich Strain through Culture Collections: an Example of Allopatric Diversification. mSphere. 2018;3(1)doi: 10.1128/mSphere.00553-17.
Desroches, M., Royer, G., Roche, D., Mercier-Darty, M., Vallenet, D., Médigue, C., Bastard, K., Rodriguez, C., Clermont, O., Denamur, E., & Decousser, J. W. (2018). The Odyssey of the Ancestral Escherich Strain through Culture Collections: an Example of Allopatric Diversification. mSphere, 3(1), . https://doi.org/10.1128/mSphere.00553-17
Desroches, M, et al. "The Odyssey of the Ancestral Escherich Strain through Culture Collections: an Example of Allopatric Diversification." mSphere vol. 3,1 (2018). doi: https://doi.org/10.1128/mSphere.00553-17
Desroches M, Royer G, Roche D, Mercier-Darty M, Vallenet D, Médigue C, Bastard K, Rodriguez C, Clermont O, Denamur E, Decousser JW. The Odyssey of the Ancestral Escherich Strain through Culture Collections: an Example of Allopatric Diversification. mSphere. 2018 Jan 31;3(1). doi: 10.1128/mSphere.00553-17. eCollection 2018. PMID: 29404421; PMCID: PMC5793043.
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[No title available]

Frontiers in microbiology

Dias GM, Bidault A, Le Chevalier P, Choquet G, Der Sarkissian C, Orlando L, Medigue C, Barbe V, Mangenot S, Thompson CC, Thompson FL, Jacq A, Pichereau V, Paillard C.
PMID: 29515533
Front Microbiol. 2018 Feb 19;9:227. doi: 10.3389/fmicb.2018.00227. eCollection 2018.

The Brown Ring Disease (BRD) caused high mortality rates since 1986 in the Manila clam

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Dias GM, Bidault A, Le Chevalier P, et al. . Front Microbiol. 2018;9:227doi: 10.3389/fmicb.2018.00227.
Dias, G. M., Bidault, A., Le Chevalier, P., Choquet, G., Der Sarkissian, C., Orlando, L., Medigue, C., Barbe, V., Mangenot, S., Thompson, C. C., Thompson, F. L., Jacq, A., Pichereau, V., & Paillard, C. (2018). . Frontiers in microbiology, 9227. https://doi.org/10.3389/fmicb.2018.00227
Dias, Graciela M, et al. "." Frontiers in microbiology vol. 9 (2018): 227. doi: https://doi.org/10.3389/fmicb.2018.00227
Dias GM, Bidault A, Le Chevalier P, Choquet G, Der Sarkissian C, Orlando L, Medigue C, Barbe V, Mangenot S, Thompson CC, Thompson FL, Jacq A, Pichereau V, Paillard C. . Front Microbiol. 2018 Feb 19;9:227. doi: 10.3389/fmicb.2018.00227. eCollection 2018. PMID: 29515533; PMCID: PMC5825899.
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