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PLoS ONE 4, 5 (2009) e5584
Methylobacterium genome sequences: a reference blueprint to investigate microbial metabolism of C1 compounds from natural and industrial sources.
Stéphane Vuilleumier 1, 2, 3, Ludmila Chistoserdova, Ming-Chun Lee 4, 5, 6, Françoise Bringel 3, Aurélie Lajus 7, 8, Yang Zhou 9, 10, 11, Benjamin Gourion, Valérie Barbe 7, 8, 12, Jean Chang 13, 14, 15, Stéphane Cruveiller 7, 8, 12, Carole Dossat 12, Will Gillett, Christelle Gruffaz 3, Eric Haugen, Edith Hourcade, Ruth Levy 16, 17, 18, Sophie Mangenot 3, 12, 19, Emilie Muller 20, 21, 22, Thierry Nadalig 3, 23, Marco Pagni, Christian Penny, Rémi Peyraud, David G Robinson 24, 25, 26, David Roche 27, 28, 29, Zoé Rouy 7, 8, 12, Channakhone Saenampechek, Grégory Salvignol, David Vallenet 8, 12, 30, Zaining Wu 31, 32, Christopher J Marx, Julia A Vorholt, Maynard V Olson, Rajinder Kaul 33, 34, 35, Jean Weissenbach 7, 8, 12, Claudine Médigue 7, 8, 12, Mary E Lidstrom
(2009)

BACKGROUND: Methylotrophy describes the ability of organisms to grow on reduced organic compounds without carbon-carbon bonds. The genomes of two pink-pigmented facultative methylotrophic bacteria of the Alpha-proteobacterial genus Methylobacterium, the reference species Methylobacterium extorquens strain AM1 and the dichloromethane-degrading strain DM4, were compared. METHODOLOGY/PRINCIPAL FINDINGS: The 6.88 Mb genome of strain AM1 comprises a 5.51 Mb chromosome, a 1.26 Mb megaplasmid and three plasmids, while the 6.12 Mb genome of strain DM4 features a 5.94 Mb chromosome and two plasmids. The chromosomes are highly syntenic and share a large majority of genes, while plasmids are mostly strain-specific, with the exception of a 130 kb region of the strain AM1 megaplasmid which is syntenic to a chromosomal region of strain DM4. Both genomes contain large sets of insertion elements, many of them strain-specific, suggesting an important potential for genomic plasticity. Most of the genomic determinants associated with methylotrophy are nearly identical, with two exceptions that illustrate the metabolic and genomic versatility of Methylobacterium. A 126 kb dichloromethane utilization (dcm) gene cluster is essential for the ability of strain DM4 to use DCM as the sole carbon and energy source for growth and is unique to strain DM4. The methylamine utilization (mau) gene cluster is only found in strain AM1, indicating that strain DM4 employs an alternative system for growth with methylamine. The dcm and mau clusters represent two of the chromosomal genomic islands (AM1: 28; DM4: 17) that were defined. The mau cluster is flanked by mobile elements, but the dcm cluster disrupts a gene annotated as chelatase and for which we propose the name "island integration determinant" (iid). CONCLUSION/SIGNIFICANCE: These two genome sequences provide a platform for intra- and interspecies genomic comparisons in the genus Methylobacterium, and for investigations of the adaptive mechanisms which allow bacterial lineages to acquire methylotrophic lifestyles.
1:  Centre of Ecology, Evolution and Biogeochemistry (CEEB)
EAWAG
2:  EPFL Institut de Génie de l'environnement EPFL (EPFL)
Université de Lausanne
3:  Génétique moléculaire, génomique, microbiologie (GMGM)
CNRS : UMR7156 – Université Louis Pasteur - Strasbourg I
4:  EWHA Womans University (EWHA)
EWHA
5:  Laboratoire d'automatique et de génie des procédés (LAGP)
Université Claude Bernard - Lyon I
6:  Department of Geographical and Earth Sciences
University of Glasgow
7:  Structure et évolution des génomes (SEG)
CNRS : UMR8030 – CNS – Université d'Evry-Val d'Essonne
8:  Génomique métabolique (UMR 8030)
CNRS : UMR8030 – CEA : DSV/IG – Université d'Evry-Val d'Essonne
9:  Cold and Arid Regions Environmental and Engineering Research Institute
Cold and Arid Regions Environmental and Engineering Research Institute
10:  Department of Ecology and Evolutionary Biology
University of Kansas
11:  Ningbo Institute of Technology (NIT)
Zhejiang University
12:  Genoscope-Centre national de séquençage (GENOSCOPE)
CEA : DSV/IG
13:  Institute of Hydrobiology - Chinese Academy of Sciences
Marine and Estuarine Fisheries (Ministry of Agriculture)
14:  State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology
Chinese Academy of Sciences
15:  Institute of Applied Mechanics
National Taiwan University
16:  Département de Mécanique des fluides et énergétique (ONERA - MFE)
ONERA
17:  Bureau d'économie théorique et appliquée (BETA)
CNRS : UMR7522 – Université Louis Pasteur - Strasbourg I
18:  Neuro-anatomie fonctionnelle du comportement et de ses troubles
INSERM : U610 – IFR70 – Université Pierre et Marie Curie (UPMC) - Paris VI
19:  Centre National de Séquençage
Université d'Evry-Val d'Essonne
20:  Laboratoire Hétéroéléments et Coordination (DCPH)
CNRS : UMR7653 – Polytechnique - X
21:  Laboratoire Ecologie Fonctionnelle et Environnement (EcoLab)
PRES Université de Toulouse – Institut National Polytechnique de Toulouse - INPT – Université Paul Sabatier (UPS) - Toulouse III – Observatoire Midi-Pyrénées – CNRS : UMR5245
22:  Kirchhoff Institut für Physik
Universität Heidelberg
23:  IFREMER (IFREMER)
Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)
24:  University of Ulster
University of Ulster
25:  The Institute of Hydrology
The Institute of Hydrology
26:  Microbiologie cellulaire et moléculaire et pathogénicité (MCMP)
CNRS : UMR5234 – Université Victor Segalen - Bordeaux II
27:  Laboratoire des Sciences du Climat et de l'Environnement [Gif-sur-Yvette] (LSCE - UMR 8212)
CNRS : UMR8212 – CEA : DSM/LSCE – Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)
28:  Institut Pierre-Simon-Laplace (IPSL)
CNRS : FR636 – Institut de recherche pour le développement [IRD] – CEA – CNES – INSU – Université Pierre et Marie Curie (UPMC) - Paris VI – Université de Versailles Saint-Quentin-en-Yvelines (UVSQ) – École normale supérieure [ENS] - Paris
29:  Department of Paleoclimatology and Geomorphology - Faculty of Earth and Life Sciences
Vrije Universiteit Amsterdam
30:  Institut de biologie et chimie des protéines [Lyon] (IBCP)
CNRS : UMR5086 – Université Claude Bernard - Lyon I
31:  Laboratoire d'Electronique et des Technologies de l'Information (LETI)
CEA : DRT/LETI
32:  State Key Joint Laboratory of Environmental Simulation and Pollution Control
College of Environmental Sciences and Engineering
33:  Institut fur Theorie der Kondensierten Materie
Universität Karlsruhe
34:  Department of Physics
Duke University
35:  Duke Physics
Duke University
Life Sciences/Biochemistry, Molecular Biology