Fig. 3: C-terminal lobe-specific signatures of TBP and their interaction with TFIIB homologs.

a The spatio-temporal context is confined to archaea and eukaryotes (temporal) and the C-terminal TBP-lobes (spatial). The conserved residues are mapped on to TBP–TFIIB complex structure (bottom right; PDB identifier: 1c9b). The most prominent conserved glutamate residues at C.L3.2 and C.L3.4 that mediate interactions with TFIIB are highlighted in a box. b TFB in archaea and its eukaryotic ortholog TFIIB have conserved Arg and Thr that interact, respectively, with conserved glutamate residues at C.L3.2 and C.L3.4 of TBP C-terminal lobes. c Orthogonal TBP–TFIIB system in dsDNA viruses. The Venn diagram depicts the shared presence of TBP and TFIIB homologs in viral genomes. A large number of viral genomes contain both TBP and TFIIB homologs more often than expected by chance (Fisher’s exact test). The residues at C.L.3.2 of viral TBPs C-terminal lobe and equivalent residues in the viral TFIIB orthologs of the Arg residue in eukaryotic TFIIBs that interact with C.L.3.2 TBP residue are shown to co-evolve (see “Methods” section). d Eukaryotic paralogs of TFIIB, i.e. Brf1/2 (Pol III system) contain a conserved Arg that could interact with Glu (C.L3.2) of TBP, which is also observed in co-complex structures (PDB identifier: 6f40 and 4roc, respectively). Human TAF1B or yeast Rrn7p (Pol I system) and its homologs do not possess the critical Arg that could interact with Glu of C.L3.2.