title: Genomic insights into methanotrophy: the complete genome sequence of Methylococcus capsulatus (Bath).
abstract: Methanotrophs are ubiquitous bacteria that can use the greenhouse gas methane as a sole carbon and energy source for growth, thus playing major roles in global carbon cycles, and in particular, substantially reducing emissions of biologically generated methane to the atmosphere. Despite their importance, and in contrast to organisms that play roles in other major parts of the carbon cycle such as photosynthesis, no genome-level studies have been published on the biology of methanotrophs. We report the first complete genome sequence to our knowledge from an obligate methanotroph, Methylococcus capsulatus (Bath), obtained by the shotgun sequencing approach. Analysis revealed a 3.3-Mb genome highly specialized for a methanotrophic lifestyle, including redundant pathways predicted to be involved in methanotrophy and duplicated genes for essential enzymes such as the methane monooxygenases. We used phylogenomic analysis, gene order information, and comparative analysis with the partially sequenced methylotroph Methylobacterium extorquens to detect genes of unknown function likely to be involved in methanotrophy and methylotrophy. Genome analysis suggests the ability of M. capsulatus to scavenge copper (including a previously unreported nonribosomal peptide synthetase) and to use copper in regulation of methanotrophy, but the exact regulatory mechanisms remain unclear. One of the most surprising outcomes of the project is evidence suggesting the existence of previously unsuspected metabolic flexibility in M. capsulatus, including an ability to grow on sugars, oxidize chemolithotrophic hydrogen and sulfur, and live under reduced oxygen tension, all of which have implications for methanotroph ecology. The availability of the complete genome of M. capsulatus (Bath) deepens our understanding of methanotroph biology and its relationship to global carbon cycles. We have gained evidence for greater metabolic flexibility than was previously known, and for genetic components that may have biotechnological potential.
authors.affiliation: The Institute for Genomic Research, Rockville, Maryland, USA. nward@tigr.org
authors.forename: Naomi
authors.initials: N
authors.lastname: Ward
authors.forename: Øivind
authors.initials: Ø
authors.lastname: Larsen
authors.forename: James
authors.initials: J
authors.lastname: Sakwa
authors.forename: Live
authors.initials: L
authors.lastname: Bruseth
authors.forename: Hoda
authors.initials: H
authors.lastname: Khouri
authors.forename: A Scott
authors.initials: AS
authors.lastname: Durkin
authors.forename: George
authors.initials: G
authors.lastname: Dimitrov
authors.forename: Lingxia
authors.initials: L
authors.lastname: Jiang
authors.forename: David
authors.initials: D
authors.lastname: Scanlan
authors.forename: Katherine H
authors.initials: KH
authors.lastname: Kang
authors.forename: Matt
authors.initials: M
authors.lastname: Lewis
authors.forename: Karen E
authors.initials: KE
authors.lastname: Nelson
authors.forename: Barbara
authors.initials: B
authors.lastname: Methé
authors.forename: Martin
authors.initials: M
authors.lastname: Wu
authors.forename: John F
authors.initials: JF
authors.lastname: Heidelberg
authors.forename: Ian T
authors.initials: IT
authors.lastname: Paulsen
authors.forename: Derrick
authors.initials: D
authors.lastname: Fouts
authors.forename: Jacques
authors.initials: J
authors.lastname: Ravel
authors.forename: Hervé
authors.initials: H
authors.lastname: Tettelin
authors.forename: Qinghu
authors.initials: Q
authors.lastname: Ren
authors.forename: Tim
authors.initials: T
authors.lastname: Read
authors.forename: Robert T
authors.initials: RT
authors.lastname: DeBoy
authors.forename: Rekha
authors.initials: R
authors.lastname: Seshadri
authors.forename: Steven L
authors.initials: SL
authors.lastname: Salzberg
authors.forename: Harald B
authors.initials: HB
authors.lastname: Jensen
authors.forename: Nils Kåre
authors.initials: NK
authors.lastname: Birkeland
authors.forename: William C
authors.initials: WC
authors.lastname: Nelson
authors.forename: Robert J
authors.initials: RJ
authors.lastname: Dodson
authors.forename: Svenn H
authors.initials: SH
authors.lastname: Grindhaug
authors.forename: Ingeborg
authors.initials: I
authors.lastname: Holt
authors.forename: Ingvar
authors.initials: I
authors.lastname: Eidhammer
authors.forename: Inge
authors.initials: I
authors.lastname: Jonasen
authors.forename: Susan
authors.initials: S
authors.lastname: Vanaken
authors.forename: Terry
authors.initials: T
authors.lastname: Utterback
authors.forename: Tamara V
authors.initials: TV
authors.lastname: Feldblyum
authors.forename: Claire M
authors.initials: CM
authors.lastname: Fraser
authors.forename: Johan R
authors.initials: JR
authors.lastname: Lillehaug
authors.forename: Jonathan A
authors.initials: JA
authors.lastname: Eisen
mesh_terms: D001426:Bacterial Proteins / Q000737:chemistry; D002244:Carbon / Q000737:chemistry; D004579:Electron Transport; D005227:Fatty Acids / Q000737:chemistry; D015964:Gene Expression Regulation, Bacterial; D016678:Genome; D016680:Genome, Bacterial; D023281:Genomics / Q000379:methods; D008697:Methane / Q000737:chemistry / Q000378:metabolism*; D020619:Methylococcus capsulatus / Q000235:genetics*; D008954:Models, Biological; D008969:Molecular Sequence Data; D009584:Nitrogen / Q000737:chemistry; D010100:Oxygen / Q000737:chemistry / Q000378:metabolism; D010455:Peptides / Q000737:chemistry; D010802:Phylogeny; D017422:Sequence Analysis, DNA
chemical_list: D001426:Bacterial Proteins; D005227:Fatty Acids; D010455:Peptides; D002244:Carbon; D009584:Nitrogen; D008697:Methane; D010100:Oxygen