Structural comparisons of initiating RNA polymerase complexes and structure-based amino acid sequence alignments of general transcription initiation factors (eukaryotic TFIIB, archaeal TFB and bacterial σ factors) show that these proteins are homologs. TFIIB and TFB each have two-five-helix cyclin-like repeats (CLRs) that include a C-terminal helix-turn-helix (HTH) motif (CLR/HTH domains). Four homologous HTH motifs are present in bacterial σ factors that are relics of CLR/HTH domains. Sequence similarities clarify models for σ factor and TFB/TFIIB evolution and function and suggest models for promoter evolution. Commitment to alternate modes for transcription initiation appears to be a major driver of the divergence of bacteria and archaea.
Keywords: BRE, TFB/TFIIB recognition element; CLR/HTH, cyclin-like repeat/helix-turn-helix domain; DDRP, DNA-dependent RNA polymerase; DPBB, double psi beta barrel; GTF, general transcription factor; LECA, last eukaryotic common ancestor; LUCA, last universal common ancestor; Ms, Methanocaldococcus sp. FS406-22,; PIF, primordial initiation factor; RDRP, RNA-dependent RNA polymerase; RNAP, RNA polymerase; Sc, Saccharomyces cerevisiae; TFB, transcription factor B; TFIIB, transcription factor for RNAP II; factor B, Tt, Thermus thermophilus..