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Journal of Bacteriology, January 2006, p. 642-658, Vol. 188, No. 2
0021-9193/06/$08.00+0     doi:10.1128/JB.188.2.642-658.2006
Copyright © 2006, American Society for Microbiology. All Rights Reserved.

The Genome Sequence of Methanosphaera stadtmanae Reveals Why This Human Intestinal Archaeon Is Restricted to Methanol and H₂ for Methane Formation and ATP Synthesis

Wolfgang F. Fricke,^1, Henning Seedorf,^2, Anke Henne,^1, Markus Krüer,² Heiko Liesegang,¹ Reiner Hedderich,³ Gerhard Gottschalk,^1* and Rudolf K. Thauer²

Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg August University, 37077 Göttingen, Germany,¹ Department of Biochemistry,² Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany³

Received 23 August 2005/ Accepted 20 October 2005

Methanosphaera stadtmanae has the most restricted energy metabolism of all methanogenic archaea. This human intestinal inhabitant can generate methane only by reduction of methanol with H₂ and is dependent on acetate as a carbon source. We report here the genome sequence of M. stadtmanae, which was found to be composed of 1,767,403 bp with an average G+C content of 28% and to harbor only 1,534 protein-encoding sequences (CDS). The genome lacks 37 CDS present in the genomes of all other methanogens. Among these are the CDS for synthesis of molybdopterin and for synthesis of the carbon monoxide dehydrogenase/acetyl-coenzyme A synthase complex, which explains why M. stadtmanae cannot reduce CO₂ to methane or oxidize methanol to CO₂ and why this archaeon is dependent on acetate for biosynthesis of cell components. Four sets of mtaABC genes coding for methanol:coenzyme M methyltransferases were found in the genome of M. stadtmanae. These genes exhibit homology to mta genes previously identified in Methanosarcina species. The M. stadtmanae genome also contains at least 323 CDS not present in the genomes of all other archaea. Seventy-three of these CDS exhibit high levels of homology to CDS in genomes of bacteria and eukaryotes. These 73 CDS include 12 CDS which are unusually long (>2,400 bp) with conspicuous repetitive sequence elements, 13 CDS which exhibit sequence similarity on the protein level to CDS encoding enzymes involved in the biosynthesis of cell surface antigens in bacteria, and 5 CDS which exhibit sequence similarity to the subunits of bacterial type I and III restriction-modification systems.

Dedicated to Terry Miller.

W.F.F. and H.S. contributed equally to this work.

Present address: Qiagen AG, Hilden, Germany.

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