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

Abstract

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...

Ribosome Biogenesis in the YeastSaccharomyces cerevisiae

“…Interestingly, only 2% of RNA polymerase I is competent for transcription in yeast whole-cell extracts, and the initiation-competent RNA polymerase I is tightly associated with Rrn3 (Milkereit and Tschochner 1998). Furthermore, yeast Rrn7 and its human ortholog, TAF1B, play the role of TFIIB, functionally conserved among RNA polymerases, in preinitiation complex formation (Knutson and Hahn 2011;Naidu et al 2011).…”

Structural insights into transcription initiation by yeast RNA polymerase I

“…UAF and TBP bind to the upstream promoter and have only a stimulatory effect in vitro (Keener et al , 1998), while CF, composed of Rrn7, Rrn6, and Rrn11, binds to the core promoter element (−38 to +5; Kulkens et al , 1991; Meier & Thoma, 2005) and is essential for the basal level of transcription (Keener et al , 1998). Rrn7 is a TFIIB‐like factor, has a similar domain structure as TFIIB and Brf1, comprising two central cyclin domains preceded by an N‐terminal Zn‐ribbon, B‐reader, and B‐linker, and had been predicted to be followed by a Pol I‐specific C‐terminal extension absent in TFIIB (Knutson & Hahn, 2011; Naidu et al , 2011). Rrn6 contains a β‐propeller followed by a helical domain, while Rrn11 comprises a central tetratricopeptide repeat (TPR) domain preceded by an N‐terminal extension (Knutson et al , 2014).…”

Mapping the Protein Interaction Network for TFIIB-Related Factor Brf1 in the RNA Polymerase III Preinitiation Complex

“…The C-terminal half of Brf1 (Brf1c) is Pol III specific and is not conserved among the members of the TFIIB family, which, in addition to Brf1 and TFIIB, also includes Rrn7 (TAF1B in humans) in the Pol I system (21)(22)(23)(24). Yeast Brf1c (aa 287 to 596) contains three homologous sequence blocks, I (aa 287 to 304), II (aa 461 to 515), and III (aa 570 to 596) (Fig.…”