The zinc ribbon domains of the general transcription factors TFIIB and Brf: conserved functional surfaces but different roles in transcription initiation

Hahn, Steven; Roberts, Sadia

doi:10.1101/gad.14.6.719

Cited by 56 publications

(18 citation statements)

References 59 publications

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Section: Supporting Online Materialsmentioning

confidence: 99%

“…The TFIIB Zn ribbon is essential for recruitment of Pol II to the promoter (19,26,27). The Brf1 Zn ribbon is also involved in polymerase recruitment, though is not essential for this (24), and in promoter opening (27). TAF1B interacts with RRN3 and is, therefore, implicated in recruitment of initiation-competent Pol I (14, 28).…”

Section: Supporting Online Materialsmentioning

confidence: 99%

“…Such a postrecruitment role(s) could be intrinsic to the Zn ribbon, the connecting region, and the N-terminal cyclin-like fold domains of TAF1B. Alternatively, one or more of these domains could affect the positioning within Pol I of TAF1B domains essential for postrecruitment event(s), by analogy to TFIIB/TFIIB-like proteins (4,5,27). TAF1B has a role in Pol I recruitment as a component of the SL1 complex and, perhaps, directly through its interaction with RRN3, but our data imply that the Zn ribbon of TAF1B is not essential for recruitment.…”

Section: Supporting Online Materialsmentioning

confidence: 99%

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TAF1B Is a TFIIB-Like Component of the Basal Transcription Machinery for RNA Polymerase I

Naidu

Friedrich

Russell

et al. 2011

Science

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Transcription by eukaryotic RNA polymerases (Pols) II and III and archaeal Pol requires structurally-related general transcription factors TFIIB, Brf1 and TFB, respectively, which are essential for polymerase recruitment and initiation events. A TFIIB-like protein was not evident in the Pol I basal transcription machinery. We report that TAF1B, a subunit of Pol I basal transcription factor SL1, is structurally related to TFIIB/TFIIB-like proteins, through predicted Nterminal Zn-ribbon and cyclin-like fold domains. SL1, essential for Pol I recruitment to the ribosomal RNA gene promoter, also has an essential post-polymerase recruitment role, operating through TAF1B. Therefore, a TFIIB-related protein is implicated in pre-initiation complex assembly and post-polymerase recruitment events in Pol I transcription, underscoring the parallels between eukaryotic Pol I, II and III and archaeal transcription machineries.Transcription by the cellular RNA polymerases (Pols) requires general transcription factors (GTFs) for promoter recognition, pre-initiation complex (PIC) formation and initiation. Distinct Pols synthesize the major ribosomal RNAs (Pol I), the messenger RNAs (Pol II) and the small nuclear and transfer RNAs (Pol III) in eukaryotes, whereas a single Pol directs transcription in archaea(1). Basal transcription by Pols II and III and archaeal Pol requires the structurally-related GTFs TFIIB(2-5), Brf1(6, 7) and TFB(8, 9), respectively. In bacteria, sigma factor performs some TFIIB functions and shows topological similarities in association with its Pol(4, 5). TFIIB/TFIIB-like proteins interact with TBP, polymerase and DNA in the PIC and are pivotal in early transcription events, including polymerase recruitment to promoters and post-recruitment events leading to transcription start-site selection, initiation and promoter escape. Given the evolutionary conservation of TFIIB-like proteins and their essential roles in transcription by eukaryotic Pols II and III and archaeal Pol, the Pol I basal transcription machinery is predicted to include a TFIIB-like component.Pol I basal transcription factor SL1 is a complex of TBP and TBP-associated factors(10-12), essential for recruitment of Pol I to the human rDNA promoter(13-15). Using HHpred, a server for protein remote homologue detection and structure prediction(16), we discovered that the TAF1B (TBP-associated factor 1B/TAF I 63) subunit of human SL1 is structurally similar to TFIIB, having the signature N-terminal Zn-ribbon and core domain with two potential cyclin-like folds (Fig. 1, Fig. S1, Tables S1, S2). The structural similarity, conserved throughout TAF1B orthologues from human TAF1B to yeast Core Factor subunit Rrn7(17), extends to Brf1, Brf2 and TFB and to plant TFIIB-like proteins such as pBrp, which is important for Pol I transcription(18) (Fig. S2, Table S1). TAF1B orthologues contain a C-terminal domain ( Fig. S3) with no counterpart in TFIIB (Fig. 1, Fig. S1 Europe PMC Funders Author ManuscriptsEurope PMC Funders Author Manuscripts distinct fr...

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Section: Supporting Online Materialsmentioning

confidence: 99%

Section: Supporting Online Materialsmentioning

confidence: 99%

Section: Supporting Online Materialsmentioning

confidence: 99%

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TAF1B Is a TFIIB-Like Component of the Basal Transcription Machinery for RNA Polymerase I

Naidu

Friedrich

Russell

et al. 2011

Science

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“…A characteristic feature of the Ph1601p structure is that the C-terminal domain folds in the zinc ribbon domain. To date, the structures of several distinct zinc ribbon domains have been determined mainly by NMR ( − ). This fold consists of a rubredoxin knuckle containing the first CXXC motif followed by a β-strand of variable length connected to an antiparallel strand by a flexible loop.…”

Section: Discussionmentioning

confidence: 99%

“…Despite the structural similarity of the zinc ribbon domain, proteins containing this mini domain have very diverse amino acid sequence and function. Examples include the RNA polymerase II initiation factor TFIIB ( , ), elongation factors TFIIS (), and eukaryotic translational initiation factor 2γ ( , ). The only conserved sequence features of this fold appear to be the CXXC (H) and CXXC motifs.…”

Section: Discussionmentioning

confidence: 99%

Crystal Structure of a Ribonuclease P Protein Ph1601p from Pyrococcus horikoshii OT3: An Archaeal Homologue of Human Nuclear Ribonuclease P Protein Rpp21^,

et al. 2005

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Ribonuclease P (RNase P) is a ribonucleoprotein complex involved in the removal of 5' leader sequences from tRNA precursors (pre-tRNA). The human protein Rpp21 is essential for human RNase P activity in tRNA processing in vitro. The crystal structure of Ph1601p from the hyperthermophilic archaeon Pyrococcus horikoshii OT3, the archaeal homologue of Rpp21, was determined using the multiple anomalous dispersion (MAD) method with the aid of anomalous scattering in zinc and selenium at 1.6 A resolution. Ph1601p comprises an N-terminal domain (residues 1-55), a central linker domain (residues 56-79), and a C-terminal domain (residues 80-120), forming an L-shaped structure. The N-terminal domain consists of two long alpha-helices, while the central and C-terminal domains fold in a zinc ribbon domain. The electrostatic potential representation indicates the presence of positively charged clusters along the L arms, suggesting a possible role in RNA binding. A single zinc ion binds the well-ordered binding site that consists of four Cys residues (Cys68, Cys71, Cys97, and Cys100) and appears to stabilize the relative positions of the N- and C-domains. Mutations of Cys68 and Cys71 or Cys97 and Cys100 to Ser destabilize the protein structure, which results in inactivation of the RNase P activity. In addition, site-directed mutagenesis suggests that Lys69 at the central loop and Arg86 and Arg105 at the zinc ribbon domain are strongly involved in the functional activity, while Arg22, Tyr44, Arg65, and Arg84 play a modest role in the activity.

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C2H2 proteins: Evolutionary aspects of domain architecture and diversification

Bonchuk,

Georgiev

2024

BioEssays

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The largest group of transcription factors in higher eukaryotes are C2H2 proteins, which contain C2H2‐type zinc finger domains that specifically bind to DNA. Few well‐studied C2H2 proteins, however, demonstrate their key role in the control of gene expression and chromosome architecture. Here we review the features of the domain architecture of C2H2 proteins and the likely origin of C2H2 zinc fingers. A comprehensive investigation of proteomes for the presence of proteins with multiple clustered C2H2 domains has revealed a key difference between groups of organisms. Unlike plants, transcription factors in metazoans contain clusters of C2H2 domains typically separated by a linker with the TGEKP consensus sequence. The average size of C2H2 clusters varies substantially, even between genomes of higher metazoans, and with a tendency to increase in combination with SCAN, and especially KRAB domains, reflecting the increasing complexity of gene regulatory networks.

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The zinc ribbon domains of the general transcription factors TFIIB and Brf: conserved functional surfaces but different roles in transcription initiation

Cited by 56 publications

References 59 publications

TAF1B Is a TFIIB-Like Component of the Basal Transcription Machinery for RNA Polymerase I

TAF1B Is a TFIIB-Like Component of the Basal Transcription Machinery for RNA Polymerase I

Crystal Structure of a Ribonuclease P Protein Ph1601p from Pyrococcus horikoshii OT3: An Archaeal Homologue of Human Nuclear Ribonuclease P Protein Rpp21^,

C2H2 proteins: Evolutionary aspects of domain architecture and diversification

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The zinc ribbon domains of the general transcription factors TFIIB and Brf: conserved functional surfaces but different roles in transcription initiation

Cited by 56 publications

References 59 publications

TAF1B Is a TFIIB-Like Component of the Basal Transcription Machinery for RNA Polymerase I

TAF1B Is a TFIIB-Like Component of the Basal Transcription Machinery for RNA Polymerase I

Crystal Structure of a Ribonuclease P Protein Ph1601p from Pyrococcus horikoshii OT3: An Archaeal Homologue of Human Nuclear Ribonuclease P Protein Rpp21,

C2H2 proteins: Evolutionary aspects of domain architecture and diversification

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Crystal Structure of a Ribonuclease P Protein Ph1601p from Pyrococcus horikoshii OT3: An Archaeal Homologue of Human Nuclear Ribonuclease P Protein Rpp21^,