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Journal of Bacteriology, October 2004, p. 6956-6969, Vol. 186, No. 20
0021-9193/04/$08.00+0     DOI: 10.1128/JB.186.20.6956-6969.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.

Complete Genome Sequence of the Genetically Tractable Hydrogenotrophic Methanogen Methanococcus maripaludis{dagger}

E. L. Hendrickson,1 R. Kaul,2,3 Y. Zhou,3 D. Bovee,3 P. Chapman,3 J. Chung,3 E. Conway de Macario,4 J. A. Dodsworth,1 W. Gillett,3 D. E. Graham,5 M. Hackett,6 A. K. Haydock,1 A. Kang,3 M. L. Land,7 R. Levy,3 T. J. Lie,1 T. A. Major,8 B. C. Moore,1 I. Porat,8 A. Palmeiri,3 G. Rouse,3 C. Saenphimmachak,3 D. Söll,9 S. Van Dien,10 T. Wang,1,6 W. B. Whitman,8 Q. Xia,1,6 Y. Zhang,1,6 F. W. Larimer,7 M. V. Olson,2,3,11 and J. A. Leigh1*

Department of Medicine, Division of Medical Genetics,2 Departments of Microbiology,1 Chemical Engineering,6 Genome Sciences, University of Washington,11 University of Washington Genome Center,3 United Metabolics, Seattle, Washington,10 Wadsworth Center, New York State Department of Health, Division of Molecular Medicine, The University at Albany (SUNY), Albany, New York,4 Department of Chemistry and Biochemistry, The University of Texas at Austin, Austin, Texas,5 Genome Analysis and Systems Modeling, Oak Ridge National Laboratory, Oak Ridge, Tennessee,7 Department of Microbiology, University of Georgia, Athens, Georgia,8 Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut9

Received 12 May 2004/ Accepted 13 July 2004

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.

* Corresponding author. Mailing address: University of Washington, Microbiology, Box 357242, Seattle, WA 98195-7242. Phone: (206) 685-1390. Fax: (206) 543-8297. E-mail: leighj{at}u.washington.edu.

{dagger} Supplemental material for this article may be found at http://jb.asm.org/.

Journal of Bacteriology, October 2004, p. 6956-6969, Vol. 186, No. 20
0021-9193/04/$08.00+0     DOI: 10.1128/JB.186.20.6956-6969.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.



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