Genomic insights into methanotrophy: the complete genome sequence of Methylococcus capsulatus (Bath).

Naomi Ward,Hoda Khouri,Ingvar Eidhammer,Terry Utterback,Rekha Seshadri,A Scott Durkin,Matt Lewis,Hervé Tettelin,Lingxia Jiang,Nils Kåre Birkeland,James Sakwa,Ingeborg Holt,George Dimitrov,Inge Jonasen,Jacques Ravel,Martin Wu,Øivind Larsen,Qinghu Ren,Harald B Jensen ,Claire M Fraser ,William Nelson ,Ian T Paulsen ,Timothy D Read ,Susan E Vanaken ,Steven L Salzberg ,Robert J Dodson ,Robert T Deboy ,Live J Bruseth ,Johan R Lillehaug ,David J Scanlan ,Barbara A Methé ,Karen E Nelson ,John F Heidelberg ,Svenn Helge Grindhaug ,Derrick E Fouts ,Katherine H Kang ,Tamara Feldblyum ,Jonathan A Eisen

doi:10.1371/journal.pbio.0020303

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.

Highlights

Methanotrophic bacteria such as Methylococcus capsulatus are responsible for the oxidation of biologically generated methane (Soehngen 1906), and they are of great environmental importance in reducing the amount of this greenhouse gas released to the Earth’s atmosphere
Of the 89 genes putatively involved in methylotrophy in M. extorquens, we found orthologs of 69, mostly in the categories of energy and carbon metabolism; the remaining 20 genes found in M. extorquens but not M. capsulatus (Bath) are involved in the metabolism of other C1 compounds not used by M. capsulatus
Our analysis of the M. capsulatus (Bath) genome has illuminated the genomic basis for the highly specialized methanotrophic lifestyle, including redundant pathways involved in methanotrophy and duplicated genes for essential enzymes such as the methane monooxygenase (MMO)

Summary

Introduction

Methanotrophic bacteria such as Methylococcus capsulatus are responsible for the oxidation of biologically generated methane (Soehngen 1906), and they are of great environmental importance in reducing the amount of this greenhouse gas released to the Earth’s atmosphere. There is one candidate flavodoxin present (MCA1697) in the M. capsulatus (Bath) genome; two ferredoxins (MCA0238 and MCA0232) physically located within a cluster of genes encoding proteins involved in nitrogen fixation (see Nitrogen Metabolism section above) more likely serve in this capacity In aerobes, these carriers are usually reduced by NADH/NADPH, reverse electron transport could be involved in this organism. Further support for anaerobiosis is provided by a putative large c-type cytochrome (MCA2189) that contains 17 heme groups and is located adjacent to several hypothetical proteins, including an oxidoreductase and an alkaline phosphatase important to the central metabolism of phosphorous compounds This cytochrome has significant matches only to high molecularweight cytochromes in the metal-ion reducers Shewanella oneidensis, Desulfovibrio vulgaris, and Geobacter sulfurreducens, suggesting that M. capsulatus may have the ability to undergo metabolism at a lower redox potential than previously known. Three hypothetical proteins were identified in these clusters, suggesting a role in C1 metabolism

Conclusions

Materials and Methods