Communicated by Dieter Söll, Yale University, New Haven, CT (received for review December 3, 2001)
The gene repertoires of M. kandleri and other archaeal methanogens. (A) Conserved and unique proteins in M. kandleri. (B) A Venn diagram of the shared and unique portions of the proteomes of archaeal methanogens. The number of COGs that are unique for the three methanogens is shown in parentheses in the central section. The number of COGs that include a given archaeal species and two or more bacteria, but no other archaea, is shown in brackets.
Genome trees of archaea. (A) Gene content tree. (B) Tree based on conserved gene pairs. Solid lines show terminal branches and internal branches with >90% bootstrap support, and dotted lines show internal branches with <90% support. The three methanogen species are highlighted by red, green, and blue. The bacterial species included as an outgroup are shown in magenta. Species abbreviations: Euryarchaeota: A. fulgidus (Arcfu), M. thermoautotrophicum (Metth), M. jannaschii (Metja), M. kandleri (Metka), Pyrococcus horikoshii (Pyrho), Pyrococcus abyssi (Pyrab), Thermoplasma volcanium (Thevo), Thermoplasma acidophilum (Theac), Halobacterium sp. (Halsp); Crenarchaeota: Aeropyrum pernix (Aper), Sulfolobus solfataricus (Sulso); bacteria: Thermotoga maritima (Thema), Deinococcus radiodurans (Deira), Escherichia coli (Escco).
The ML phylogenetic tree of archaea constructed by using concatenated alignments of ribosomal proteins. Thick solid lines indicate internal branches with Resampling of Estimated Log-Likelihoods bootstrap support >95%, thin solid lines indicate branches with 90–95% bootstrap support, and dotted lines indicate branches with <70% support. Distances are indicated in substitutions per site. Methanogens are highlighted. Species name abbreviations are as in Fig. 2.
Predicted functional systems and general metabolic pathways of M. kandleri compared with the counterparts in other archaeal methanogens. Specific enzymatic reactions predicted in a given species but not in the other two are color-coded blue (M. kandleri), green (M. thermoautotrophicus), and red (M. jannaschii). Gene identifiers are shown only for M. kandleri. The methanogenesis pathway is shown by magenta arrows. Reactions for which no candidate enzyme was confidently predicted are shown by dashed arrows. Final biosynthetic products are shown as follows: light blue for amino acids, dark yellow for nucleotides, brown for sugars, pink for cofactors. MF, methanofuran; FMF, formyl-methanofuran; H4MPT, tetrahydromethanopterin; CoM, coenzyme M.
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Slesarev et al. (2002) Proc. Natl. Acad. Sci. USA99 (7), 4644–4649. (10.1073/pnas.032671499) |
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