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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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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.
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f0004: 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.

Mentions: Based on structural homology, protein sequence alignments of Saccharomyces cerevisiae (Sc) TFIIB, Methanocaldococcus sp. FS406-22 (Ms) TFB and Thermus thermophilus (Tt) σ factor were generated (Fig. 4). Remarkably, with structure as a guide, a reasonable σ to TFB and σ to TFIIB homology model was constructed. Similarities between the Tt σ factor and Ms/Sc TFB/TFIIB are most notable in T1, H2, T2 and H3. Because of sequence identity and similarity, when aligning according to turns and helices, bacterial σ factors are concluded to be homologs of archaeal/eukaryotic TFB/TFIIB. To reinforce this conclusion, multiple archaeal TFB and bacterial σ factor sequences are aligned in Figures S1-S4. Consistent with structural alignments (Figs. 1–3), multiple sequence alignments of bacterial σ CLR/HTH3.0-3.1 and CLR/HTH4.1-4.2 show remarkable in-phase similarity to archaeal TFB, particularly across T1, H2, T2 and H3 (Figs. S3-S4). Consistent with the homology model, within σ CLR/HTH4.1-4.2 H2, some alternate σ factors show significantly higher identity and similarity to TFB CLR/HTH2 compared to the Tt σ factor used in the original alignment (Fig. 4; Fig. S4). Despite the ancient time of divergence for σ factors and TFB/TFIIB, alignments of linear sequence are convincing (Fig. 4; Figs. S1–S4), and structural comparisons are compelling (Figs. 1–3) for homology among these GTFs.Figure 4.


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

Burton SP, Burton ZF - Transcription (2014)

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

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

f0004: 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.
Mentions: Based on structural homology, protein sequence alignments of Saccharomyces cerevisiae (Sc) TFIIB, Methanocaldococcus sp. FS406-22 (Ms) TFB and Thermus thermophilus (Tt) σ factor were generated (Fig. 4). Remarkably, with structure as a guide, a reasonable σ to TFB and σ to TFIIB homology model was constructed. Similarities between the Tt σ factor and Ms/Sc TFB/TFIIB are most notable in T1, H2, T2 and H3. Because of sequence identity and similarity, when aligning according to turns and helices, bacterial σ factors are concluded to be homologs of archaeal/eukaryotic TFB/TFIIB. To reinforce this conclusion, multiple archaeal TFB and bacterial σ factor sequences are aligned in Figures S1-S4. Consistent with structural alignments (Figs. 1–3), multiple sequence alignments of bacterial σ CLR/HTH3.0-3.1 and CLR/HTH4.1-4.2 show remarkable in-phase similarity to archaeal TFB, particularly across T1, H2, T2 and H3 (Figs. S3-S4). Consistent with the homology model, within σ CLR/HTH4.1-4.2 H2, some alternate σ factors show significantly higher identity and similarity to TFB CLR/HTH2 compared to the Tt σ factor used in the original alignment (Fig. 4; Fig. S4). Despite the ancient time of divergence for σ factors and TFB/TFIIB, alignments of linear sequence are convincing (Fig. 4; Figs. S1–S4), and structural comparisons are compelling (Figs. 1–3) for homology among these GTFs.Figure 4.

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