Evolution of the B-Block Binding Subunit of TFIIIC That Binds to the Internal Promoter for RNA Polymerase III
Figure 4
Comparison of the primary structures of the archaeal B-block binding proteins with the regions conserved in the eukaryotic B-block binding subunits. Each of the scientific names is followed by the GI number, aa sequence, and aa positions. The B-block_TFIIIC regions in the archaeal proteins are colored in blue (see Table 2). Green arrows indicate common residues both in Archaea and eukaryotic conserved regions. Green dotted arrows mean no conservation between the two alignments just above and just below the arrows. (a) Clustal Omega alignment of archaeal proteins defined or annotated as B-block binding subunits in the NCBI protein database. Amino acid residues of the N-terminal and C-terminal ends which were not conserved in the nine protein sequences were cropped in this alignment. (b) Clustal Omega alignments of the archaeal sequences with each of regions I, II, III, and IV in the eukaryotic B-block binding subunits. Regions II and III of the A. thaliana and D. melanogaster proteins (GI: 15218016 and GI: 20129503) were used for comparison with archaeal proteins. This is because these sequences are used in the previous alignments of regions II and III (Figure 3 in [10]) and were detected in DELTA-BLAST searches using the M. conradii sequence as a query in this study (Figure 2). These two proteins could precisely link the previous regions II and III alignments to the present alignment with the archaeal sequence. The alignments of regions II and III are shown in a combined form via the M. conradii sequence for clarity. Amino acid residues shown in magenta were conserved also in the alignments of Figures and in [10]. For comparison of the archaeal sequences with region IV, the C-terminal regions of the fungal proteins which were detected at significant -values in Figure 2 were aligned with their related archaeal sequences. Just below the alignment, the C-terminal regions of several eukaryotic B-block binding subunits (region IV) were aligned (see also Figure 3D in [10]). To examine whether the archaeal proteins are related to region I, the N-terminal regions of the eukaryotic B-block binding subunits which were simultaneously detected with the authentic B-block_TFIIIC regions were visually searched for from the results of DELTA-BLAST. Clustal Omega was then performed. -values of the matches to the N-terminal regions in DELTA-BLAST were higher than threshold (shown in parentheses next to the aa positions of the Clustal alignments). An alignment of the N-terminal regions of several eukaryotic B-block binding subunits (region I) is shown at the bottom of the Figure (see also Figure 3A in [10]).
