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The σ enigma: bacterial σ factors, archaeal TFB and eukaryotic TFIIB are homologs.

Burton SP, Burton ZF - Transcription (2014)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: a Department of Biochemistry and Molecular Biology ; Michigan State University ; E. Lansing , MI USA.

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.

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(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.
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f0005: (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.

Mentions: From structural and sequence similarities, a model for σ and TFB/TFIIB homology is proposed (Fig. 5). σ factor regions (extending from N→C 1, 2, 3 and 4) were defined historically based on homology among σ factors.21,22 The model in Figure 5 posits that σ homology regions 1-4 are each degenerated from one of 4-CLR/HTH domains, similar to the 2-CLR/HTH domains found in TFB/TFIIB. To distinguish C-terminal CLR/HTH domains from the more mobile N-terminal CLR/HTH domains, C-terminal CLR/HTH domains that bind anchor DNA sequences are colored red. σ CLR/HTH4.1-4.2 binds ds -35 anchor DNA, which remains double-stranded during bubble opening and initiation (Figure 3). σ CLR/HTH domains 1-3 are posited to spread from the ds anchor DNA sequence in the downstream direction as the bubble opens, as observed in Figures 1–2. Similarly, TFB/TFIIB has two CLR/HTH domains that are clustered for ds promoter recognition (Fig. 3). CLR/HTH2 remains bound to ds BREup anchor DNA, and CLR/HTH1 must spread from CLR/HTH2 and its bound ds DNA anchor in the downstream direction during bubble opening and initiation (Figs. 1–3). The -35 region and BREup DNA anchors, conserved in the three domains of life on earth, therefore, support the directionality of bubble opening and transcription. The initiating RNAP structure (Figs. 1–2) shows σ in its opened conformation. Currently, there is no RNAP-σ structure available that only contains ds promoter DNA.Figure 5.


The σ enigma: bacterial σ factors, archaeal TFB and eukaryotic TFIIB are homologs.

Burton SP, Burton ZF - Transcription (2014)

(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.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4581349&req=5

f0005: (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.
Mentions: From structural and sequence similarities, a model for σ and TFB/TFIIB homology is proposed (Fig. 5). σ factor regions (extending from N→C 1, 2, 3 and 4) were defined historically based on homology among σ factors.21,22 The model in Figure 5 posits that σ homology regions 1-4 are each degenerated from one of 4-CLR/HTH domains, similar to the 2-CLR/HTH domains found in TFB/TFIIB. To distinguish C-terminal CLR/HTH domains from the more mobile N-terminal CLR/HTH domains, C-terminal CLR/HTH domains that bind anchor DNA sequences are colored red. σ CLR/HTH4.1-4.2 binds ds -35 anchor DNA, which remains double-stranded during bubble opening and initiation (Figure 3). σ CLR/HTH domains 1-3 are posited to spread from the ds anchor DNA sequence in the downstream direction as the bubble opens, as observed in Figures 1–2. Similarly, TFB/TFIIB has two CLR/HTH domains that are clustered for ds promoter recognition (Fig. 3). CLR/HTH2 remains bound to ds BREup anchor DNA, and CLR/HTH1 must spread from CLR/HTH2 and its bound ds DNA anchor in the downstream direction during bubble opening and initiation (Figs. 1–3). The -35 region and BREup DNA anchors, conserved in the three domains of life on earth, therefore, support the directionality of bubble opening and transcription. The initiating RNAP structure (Figs. 1–2) shows σ in its opened conformation. Currently, there is no RNAP-σ structure available that only contains ds promoter DNA.Figure 5.

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: a Department of Biochemistry and Molecular Biology ; Michigan State University ; E. Lansing , MI USA.

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.

Show MeSH