title: The σ enigma: bacterial σ factors, archaeal TFB and eukaryotic TFIIB are homologs.
abstract: 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.
authors.affiliation: a Department of Biochemistry and Molecular Biology ; Michigan State University ; E. Lansing , MI USA.
authors.forename: Samuel P
authors.initials: SP
authors.lastname: Burton
authors.forename: Zachary F
authors.initials: ZF
authors.lastname: Burton
mesh_terms: D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D001105:Archaea / Q000378:metabolism*; D019843:Archaeal Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D001419:Bacteria / Q000378:metabolism*; D001426:Bacterial Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D001665:Binding Sites; D004247:DNA / Q000737:chemistry / Q000378:metabolism; D030562:Databases, Protein; D056890:Eukaryota / Q000378:metabolism*; D019143:Evolution, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D011401:Promoter Regions, Genetic; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D016415:Sequence Alignment; D012808:Sigma Factor / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D035581:Transcription Factor TFIIB / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*
chemical_list: D019843:Archaeal Proteins; D001426:Bacterial Proteins; D012808:Sigma Factor; D035581:Transcription Factor TFIIB; C106466:transcription factor B, Archaea; D004247:DNA
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.