Figure 1

Orthologs of Rpb8 in archaea. (a) Multiple alignment of eukaryotic Rpb8 subunits and their archaeal orthologs (RpoG). The alignment was constructed using the combination of the results obtained with PROMALS [15] and MUSCLE [16], followed by manual correction on the basis of secondary structure prediction that was obtained using PSIPRED [17] and local alignments generated by PSI-BLAST. Sequences are denoted by their numeric Genbank Identifiers (GI numbers) and species names. The full species names are given in Figure 2. The positions of the first and the last residues of the aligned region in the corresponding protein are indicated for each sequence. The numbers within the alignment represent poorly conserved inserts that are not shown. The numbers of omitted amino acids for T. pendens and G. lamblia are indicated by reverse shading. Positions with identical amino acids in all aligned sequences are in bold face. The coloring is based on the consensus shown underneath the alignment; 'h' indicates hydrophobic residues (ACFILMVWYH), 'p' indicates polar residues (STEDKRNQH), 's' indicates small residues (AGCVDS). Secondary structure is shown for the crystal structure of human Rpb8 (pdb 2F3I); 'H' indicates α-helix and 'E' indicates extended conformation (β-strand). The PSIPRED secondary structure prediction is shown underneath the experimental secondary structure. The glycine doublet that is invariant in eukaryotic Rpb8 sequences is boxed. (b) Phylogenetic and genomic contexts of Rpb8/RpoG. The maximum likelihood phylogenetic tree of Rpb8/RpoG was constructed by local rearrangement of an original minimum evolution (Fitch) tree [18] using the MOLPHY program [19]. MOLPHY was also used to compute RELL bootstrap probabilities, which are indicated (as percentages) for selected major branches. Each terminal node of the tree is labeled by the full species name and the GI number. The genomic neighborhoods of the rpoG gene in Crenarchaeota and the "korarchaeal" genome are shown to the right of the respective branches of the tree. Orthologous genes are shown by arrows of the same color.