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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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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 BREup 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.
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f0002: 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 BREup 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.

Mentions: In order to emphasize the similarities of bacterial σ factors and eukaryotic TFIIB, a simplified view was produced by removing RNAP and RNAP II from the image (Fig. 2). The quality of the alignment (and the alignment in Fig. 1) can be judged from the overlay of Mg and nucleic acids. The overlapping image of TFIIB CLR/HTH1 results from the overlay of two structures in creating the TFIIB model (PDBs 4BBS and 1AIS). Remarkably, σ CLR/HTH3.0-3.1 and TFIIB CLR/HTH1 occupy homologous positions, and σ CLR/HTH4.1-4.2 and TFIIB CLR/HTH2 also appear to occupy homologous positions. Again, the location of TFIIB CLR/HTH2 is not certain because it results from a model, not a structure, but the domain is placed with some confidence according to the expected location of ds BREup, which remains double-stranded during transcription bubble opening and to which CLR/HTH2 binds. Additionally, according to the model, TFIIB CLR/HTH2 appears to closely approach or interact with the N-terminal TFIIB Zn finger, providing a testable prediction of the model.Figure 2.


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

Burton SP, Burton ZF - Transcription (2014)

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

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

f0002: 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 BREup 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.
Mentions: In order to emphasize the similarities of bacterial σ factors and eukaryotic TFIIB, a simplified view was produced by removing RNAP and RNAP II from the image (Fig. 2). The quality of the alignment (and the alignment in Fig. 1) can be judged from the overlay of Mg and nucleic acids. The overlapping image of TFIIB CLR/HTH1 results from the overlay of two structures in creating the TFIIB model (PDBs 4BBS and 1AIS). Remarkably, σ CLR/HTH3.0-3.1 and TFIIB CLR/HTH1 occupy homologous positions, and σ CLR/HTH4.1-4.2 and TFIIB CLR/HTH2 also appear to occupy homologous positions. Again, the location of TFIIB CLR/HTH2 is not certain because it results from a model, not a structure, but the domain is placed with some confidence according to the expected location of ds BREup, which remains double-stranded during transcription bubble opening and to which CLR/HTH2 binds. Additionally, according to the model, TFIIB CLR/HTH2 appears to closely approach or interact with the N-terminal TFIIB Zn finger, providing a testable prediction of the model.Figure 2.

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