The complete genome sequence of the thermophilic archaeon Methanobacterium thermoautotrophicum ΔH has been determined using a whole-genome shotgun sequencing approach. The genome is 1,751,377 base pairs long and contains 1,855 open reading frames (ORFs), of which 844 (46%) have been assigned putative functions based on their similarity to database sequences. Additionally, 514 (28%) of the ORFs are related to sequences with unknown functions, and 496 (27%) have little or no homology to public databases. Comparisons with archaeal, bacterial, and eucaryal databases show that 1,013 of the putative gene products (54%) are most similar to sequences from other archaeal organisms. Comparisons with the genome of Methanococcus jannaschii reveal extensive divergence between the two methanogens, with only 352 (19%) of M. thermoautotrophicum ORFs encoding sequences that are >50% identical to M. jannaschii polypeptides. When compared to sequences from eucaryal and bacterial domains, 786 (42%) are more similar to bacterial sequences and 241 (13%) to eucaryal sequences. The bacterial domain-like gene products include those involved in cofactor and small molecule biosynthesis, intermediary metabolism, transport, nitrogen fixation, regulatory functions, and environmental interactions. Most proteins involved in DNA metabolism, transcription, and translation are more similar to eucaryal sequences. The genome has features typical of bacteria, including genes encoding polypeptides related to eucaryal proteins. There are 24 polypeptides that could form two-component sensor kinase-response regulator systems and homologs of the bacterial Hsp70-response proteins DnaK and DnaJ, which are absent in M. jannaschii. DNA replication initiation and chromosome packaging in M. thermoautotrophicum are predicted to have eucaryal features, based on the presence of two Cdc6 homologs and three histones, although the presence of an ftsZ gene indicates a bacterial type of cell division initiation. The DNA polymerases include an X-family repair type and an unusual archaeal B type formed by two separate polypeptides. The DNA-dependent RNA polymerase (RNAP) subunits A', A", B', B" and H are encoded in a typical archaeal RNAP operon, although a second A' subunit-encoding gene is present at a remote location. There are two rRNA operons, and 39 tRNA genes are dispersed around the genome, although most occur in clusters. Three of the tRNA genes have introns, including the tRNApro (GGG) gene, which contains aThe complete genome sequence of the thermophilic archaeon Methanobacterium thermoautotrophicum ΔH has been determined using a whole-genome shotgun sequencing approach. The genome is 1,751,377 base pairs long and contains 1,855 open reading frames (ORFs), of which 844 (46%) have been assigned putative functions based on their similarity to database sequences. Additionally, 514 (28%) of the ORFs are related to sequences with unknown functions, and 496 (27%) have little or no homology to public databases. Comparisons with archaeal, bacterial, and eucaryal databases show that 1,013 of the putative gene products (54%) are most similar to sequences from other archaeal organisms. Comparisons with the genome of Methanococcus jannaschii reveal extensive divergence between the two methanogens, with only 352 (19%) of M. thermoautotrophicum ORFs encoding sequences that are >50% identical to M. jannaschii polypeptides. When compared to sequences from eucaryal and bacterial domains, 786 (42%) are more similar to bacterial sequences and 241 (13%) to eucaryal sequences. The bacterial domain-like gene products include those involved in cofactor and small molecule biosynthesis, intermediary metabolism, transport, nitrogen fixation, regulatory functions, and environmental interactions. Most proteins involved in DNA metabolism, transcription, and translation are more similar to eucaryal sequences. The genome has features typical of bacteria, including genes encoding polypeptides related to eucaryal proteins. There are 24 polypeptides that could form two-component sensor kinase-response regulator systems and homologs of the bacterial Hsp70-response proteins DnaK and DnaJ, which are absent in M. jannaschii. DNA replication initiation and chromosome packaging in M. thermoautotrophicum are predicted to have eucaryal features, based on the presence of two Cdc6 homologs and three histones, although the presence of an ftsZ gene indicates a bacterial type of cell division initiation. The DNA polymerases include an X-family repair type and an unusual archaeal B type formed by two separate polypeptides. The DNA-dependent RNA polymerase (RNAP) subunits A', A", B', B" and H are encoded in a typical archaeal RNAP operon, although a second A' subunit-encoding gene is present at a remote location. There are two rRNA operons, and 39 tRNA genes are dispersed around the genome, although most occur in clusters. Three of the tRNA genes have introns, including the tRNApro (GGG) gene, which contains a