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.

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..

Figure 1.

Structural alignment of initiating bacterial RNAP (PDB 4G7O) and yeast RNAP II (PDB 4BBS) complexes shows that σ factors and TFIIB occupy homologous positions. HTH motifs are colored yellow (H1), red (H2) and green (H3). Brighter colors are used for σ and duller shades for TFIIB. TFIIB CLR/HTH₂ was placed by modeling, based on its predicted position bound to the ds BRE_up DNA anchor, which is missing in the structure.

Figure 2.

Relative positions of σ and TFIIB in initiating complexes. HTH motifs are colored yellow (H1), red (H2) and green (H3). Brighter colors are used for σ and duller shades for TFIIB. TFIIB CLR/HTH₂ was placed by modeling, based on its predicted position bound to the ds BRE_up DNA anchor. Placement of TFIIB CLR/HTH₂ indicates that the N-terminal Zn ribbon and the C-terminal CLR/HTH₂ are likely to interact. The quality of the alignment is indicated by the overlay of the Mg atoms and nucleic acids.

Figure 3.

Homologous binding of σ CLR/HTH_4.1-4.2 to the -35 region (PDB 1KU7) and archaeal TFB CLR/HTH₂ to BRE_up ds anchor DNA (PDB 1AIS). Anchor DNA-binding CLR/HTH domains are expected to remain in place as the bubble opens, but σ CLR/HTH_3.0-3.1 and TFB CLR/HTH₁ are expected to move in a downstream direction. In the overlay, note the structural homology of H1, T1, H2, T2 and H3 of σ and TFB. Colors are as shown in Figures 1–2.

Figure 4.

Sc TFIIB, Ms TFB and Tt σ factors are homologs. σ factors have 4-CLR/HTH motifs (regions 1.2, 2.1-2.4, 3.0-3.1 and 4.1-4.2). Grey shading indicates helical regions. Amino acids that are identical between either Sc TFIIB or Ms TFB and Tt σ are red; amino acids that are similar are in black bold type. Greatest similarity is within T1, H2, T2 and H3.

Figure 5.

(A) A model for σ and (B) a model for TFB/TFIIB in initial ds promoter recognition and in initiating RNAP and RNAP II complexes with an open bubble. σ and TFIIB are proposed to cluster CLR/HTH domains for initiation. Contact to ds anchor DNA maintains the position of the most C-terminal CLR/HTH domain (red). For bubble opening and initiation, more N-terminal CLR/HTH domains (blue) unpack in the downstream direction.

Figure 6.

A model for early evolution of promoters based on a 4-CLR/HTH PIF. A) a 4-CLR/HTH PIF for initiation on a bidirectional primordial promoter. B) a 4-CLR/HTH PIF for initiation on a unidirectional primordial promoter with an anchor DNA sequence. The C-terminal CLR/HTH domain is shaded red to indicate that it binds anchor DNA. Bacterial -35 and archaeal/eukaryotic BRE_up DNA elements are posited to be relics of primordial anchor DNA sequences. TATAAT (Pribnow box) and TATAAAAG boxes are posited to be derived from AT-rich primordial promoter sequences. CLR/HTH domains are posited to separate from the upstream anchor in the downstream direction as the bubble opens.

Figure 7.

A model for the genesis of life on earth focusing on multi-subunit RNAPs, GTFs and promoters. The red arrow indicates strong competition by eukaryotes suppressing mesophilic archaea. See the text for details.