Complete Genome Sequence of the Genetically Tractable Hydrogenotrophic Methanogen Methanococcus maripaludis

Journal Article · Thu Jan 01 00:00:00 EST 2004 · Journal of Bacteriology

DOI:https://doi.org/10.1128/JB.186.20.6956-6969.2004· OSTI ID:978722

Hendrickson, E L ^[1]; Kaul, R ^[1]; Zhou, Y ^[1]; Bovee, D ^[1]; Chapman, P ^[1]; Chung, J ^[1]; DeMarcario, E Conway ^[2]; Dodsworth, J A ^[1]; Gillett, W ^[1]; Graham, D E ^[3]; Hackett, M ^[1]; Haydock, A K ^[1]; Kang, A ^[1]; Land, Miriam L ^[4]; Levy, R ^[1]; Lie, T J ^[1]; Major, T A ^[5]; Moore, B C ^[1]; Porat, I ^[5]; Palmeriri, A ^[1] ; Rouse, G ^[1]; Saenphimmachak, C ^[1]; Soll, D ^[6]; Van Dien, S ^[7]; Wang, T ^[1]; Whitman, W B ^[5]; Xia, Q ^[1]; Zhang, Y ^[1]; Larimer, Frank W ^[4]; Olson, M V ^[1]; Leigh, J A ^[1]

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1. University of Washington
2. University at Albany (SUNY)
3. University of Texas
4. ORNL
5. University of Georgia, Athens, GA
6. Yale University
7. United Metabolics

The genome sequence of the genetically tractable, mesophilic, hydrogenotrophic methanogen Methanococcus maripaludis contains 1,722 protein-coding genes in a single circular chromosome of 1,661,137 bp. Of the protein-coding genes (open reading frames [ORFs]), 44% were assigned a function, 48% were conserved but had unknown or uncertain functions, and 7.5% (129 ORFs) were unique to M. maripaludis. Of the unique ORFs, 27 were confirmed to encode proteins by the mass spectrometric identification of unique peptides. Genes for most known functions and pathways were identified. For example, a full complement of hydrogenases and methanogenesis enzymes was identified, including eight selenocysteine-containing proteins, with each being paralogous to a cysteine-containing counterpart. At least 59 proteins were predicted to contain iron-sulfur centers, including ferredoxins, polyferredoxins, and subunits of enzymes with various redox functions. Unusual features included the absence of a Cdc6 homolog, implying a variation in replication initiation, and the presence of a bacterial-like RNase HI as well as an RNase HII typical of the Archaea. The presence of alanine dehydrogenase and alanine racemase, which are uniquely present among the Archaea, explained the ability of the organism to use L- and D-alanine as nitrogen sources. Features that contrasted with the related organism Methanocaldococcus jannaschii included the absence of inteins, even though close homologs of most intein-containing proteins were encoded. Although two-thirds of the ORFs had their highest Blastp hits in Methanocaldococcus jannaschii, lateral gene transfer or gene loss has apparently resulted in genes, which are often clustered, with top Blastp hits in more distantly related groups.

• Research Organization: Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
• Sponsoring Organization: USDOE Office of Science (SC)
• DOE Contract Number: DE-AC05-00OR22725
• OSTI ID: 978722
• Journal Information: Journal of Bacteriology, Vol. 186, Issue 20; ISSN 0021-9193
• Country of Publication: United States
• Language: English

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
99 GENERAL AND MISCELLANEOUS//MATHEMATICS, COMPUTING, AND INFORMATION SCIENCE
ALANINES
CHROMOSOMES
ENZYMES
GENES
HYDROGENASES
NITROGEN
OXIDOREDUCTASES
PEPTIDES
PROTEINS