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
Structural alignment of initiating bacterial RNAP (PDB 4G7O) and yeast RNAP II (PDB 4BBS) complexes shows that σ factors and TFIIB occupy homologous positions.9,17 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 BREup DNA anchor, which is missing in the structure.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f0001: Structural alignment of initiating bacterial RNAP (PDB 4G7O) and yeast RNAP II (PDB 4BBS) complexes shows that σ factors and TFIIB occupy homologous positions.9,17 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 BREup DNA anchor, which is missing in the structure.

Mentions: A structural comparison of bacterial RNAP and eukaryotic RNAP II initiating complexes is shown in Figure 1. σ factors include 4-HTH motifs, and TFIIB includes 2-HTH motifs within larger CLR/HTH domains. In Figure 1, HTH motifs are color-coded: H1 (yellow), H2 (red), and H3 (green) using brighter shades for σ than for TFIIB. Because the more C-terminal TFIIB CLR/HTH2 domain was missing from the original 4BBS structure, it was placed by modeling. The positioning is approximate, but the double-stranded (ds) BREup, to which TFIIB CLR/HTH2 binds, must be located near where CLR/HTH2 was placed. The two C-terminal σ and TFIIB HTH motifs appear to occupy homologous positions in the structures. The quality of the alignment can be judged from coincidence of homologous secondary structures in the overlay.Figure 1.


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

Burton SP, Burton ZF - Transcription (2014)

Structural alignment of initiating bacterial RNAP (PDB 4G7O) and yeast RNAP II (PDB 4BBS) complexes shows that σ factors and TFIIB occupy homologous positions.9,17 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 BREup DNA anchor, which is missing in the structure.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f0001: Structural alignment of initiating bacterial RNAP (PDB 4G7O) and yeast RNAP II (PDB 4BBS) complexes shows that σ factors and TFIIB occupy homologous positions.9,17 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 BREup DNA anchor, which is missing in the structure.
Mentions: A structural comparison of bacterial RNAP and eukaryotic RNAP II initiating complexes is shown in Figure 1. σ factors include 4-HTH motifs, and TFIIB includes 2-HTH motifs within larger CLR/HTH domains. In Figure 1, HTH motifs are color-coded: H1 (yellow), H2 (red), and H3 (green) using brighter shades for σ than for TFIIB. Because the more C-terminal TFIIB CLR/HTH2 domain was missing from the original 4BBS structure, it was placed by modeling. The positioning is approximate, but the double-stranded (ds) BREup, to which TFIIB CLR/HTH2 binds, must be located near where CLR/HTH2 was placed. The two C-terminal σ and TFIIB HTH motifs appear to occupy homologous positions in the structures. The quality of the alignment can be judged from coincidence of homologous secondary structures in the overlay.Figure 1.

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