Limits...
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.

Show MeSH
Homologous binding of σ CLR/HTH4.1-4.2 to the -35 region (PDB 1KU7) and archaeal TFB CLR/HTH2 to BREup ds anchor DNA (PDB 1AIS).26,33 Anchor DNA-binding CLR/HTH domains are expected to remain in place as the bubble opens, but σ CLR/HTH3.0-3.1 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.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4581349&req=5

f0003: Homologous binding of σ CLR/HTH4.1-4.2 to the -35 region (PDB 1KU7) and archaeal TFB CLR/HTH2 to BREup ds anchor DNA (PDB 1AIS).26,33 Anchor DNA-binding CLR/HTH domains are expected to remain in place as the bubble opens, but σ CLR/HTH3.0-3.1 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.

Mentions: To further the argument for homology of σ factors and TFB/TFIIB, a structural comparison of ds DNA promoter binding is shown (Fig. 3). Bacterial -35 promoter regions and archaeal/eukaryotic BREup are considered here to be “anchor” DNA sequences. Binding of C-terminal CLR/HTH domains to ds upstream anchor DNA is posited to allow directional downstream promoter opening by more mobile N-terminal CLR/HTH domains, a concept in promoter evolution and GTF structure and function discussed in further detail below. In Figure 3, a structure of bacterial σ CLR/HTH4.1-4.2 bound to ds -35 region promoter DNA is aligned with archaeal CLR/HTH2 in a co-crystal of ds BRE and TATAAAAG box DNA with GTFs TFB and TBP. Despite distortion of ds DNA by TBP binding in the minor groove, the overlay of σ CLR/HTH4.1-4.2 and TFB CLR/HTH2 is surprisingly precise and supports the structural homology of σ CLR/HTH4.1-4.2 and TFB CLR/HTH2. From this comparison, furthermore, bacterial -35 regions and archaeal/eukaryotic BREup DNA anchor sequences appear to serve a similar anchoring function in the evolution of promoters. Very interestingly, TFIIB CLR/HTH1 and CLR/HTH2 bound to ds BREdown and BREup are clustered on either side of the TBP “stirrup” (Fig. 3), but spread apart in the structural model for initiation (Figs. 1–2). As BREdown becomes single-stranded, CLR/HTH1 must move in the downstream direction for transcription initiation, but CLR/HTH2 is expected to remain in place, bound to the ds BREup anchor. A similar model for spreading of CLR/HTH domains from the ds -35 anchor DNA during bubble opening is considered likely for bacterial σ factors (see below).Figure 3.


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

Burton SP, Burton ZF - Transcription (2014)

Homologous binding of σ CLR/HTH4.1-4.2 to the -35 region (PDB 1KU7) and archaeal TFB CLR/HTH2 to BREup ds anchor DNA (PDB 1AIS).26,33 Anchor DNA-binding CLR/HTH domains are expected to remain in place as the bubble opens, but σ CLR/HTH3.0-3.1 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.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f0003: Homologous binding of σ CLR/HTH4.1-4.2 to the -35 region (PDB 1KU7) and archaeal TFB CLR/HTH2 to BREup ds anchor DNA (PDB 1AIS).26,33 Anchor DNA-binding CLR/HTH domains are expected to remain in place as the bubble opens, but σ CLR/HTH3.0-3.1 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.
Mentions: To further the argument for homology of σ factors and TFB/TFIIB, a structural comparison of ds DNA promoter binding is shown (Fig. 3). Bacterial -35 promoter regions and archaeal/eukaryotic BREup are considered here to be “anchor” DNA sequences. Binding of C-terminal CLR/HTH domains to ds upstream anchor DNA is posited to allow directional downstream promoter opening by more mobile N-terminal CLR/HTH domains, a concept in promoter evolution and GTF structure and function discussed in further detail below. In Figure 3, a structure of bacterial σ CLR/HTH4.1-4.2 bound to ds -35 region promoter DNA is aligned with archaeal CLR/HTH2 in a co-crystal of ds BRE and TATAAAAG box DNA with GTFs TFB and TBP. Despite distortion of ds DNA by TBP binding in the minor groove, the overlay of σ CLR/HTH4.1-4.2 and TFB CLR/HTH2 is surprisingly precise and supports the structural homology of σ CLR/HTH4.1-4.2 and TFB CLR/HTH2. From this comparison, furthermore, bacterial -35 regions and archaeal/eukaryotic BREup DNA anchor sequences appear to serve a similar anchoring function in the evolution of promoters. Very interestingly, TFIIB CLR/HTH1 and CLR/HTH2 bound to ds BREdown and BREup are clustered on either side of the TBP “stirrup” (Fig. 3), but spread apart in the structural model for initiation (Figs. 1–2). As BREdown becomes single-stranded, CLR/HTH1 must move in the downstream direction for transcription initiation, but CLR/HTH2 is expected to remain in place, bound to the ds BREup anchor. A similar model for spreading of CLR/HTH domains from the ds -35 anchor DNA during bubble opening is considered likely for bacterial σ factors (see below).Figure 3.

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