Role of TATA Binding Protein (TBP) in Yeast Ribosomal DNA Transcription by RNA Polymerase I: Defects in the Dual Functions of Transcription Factor UAF Cannot Be Suppressed by TBP

Siddiqi, Imran; Keener, John; Vu, Loan; Nomura, Masayasu

doi:10.1128/mcb.21.7.2292-2297.2001

Cited by 21 publications

(18 citation statements)

References 22 publications

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“…3). A significant increase in the TBP concentration in the absence of functional UAF enhances RPI transcription from the yeast core promoter in vitro, but in vivo, over-expression of TBP is unable to rescue the loss of UAF [103,104]. UAF subunits are not strictly required for yeast survival.…”

Section: Yeastmentioning

confidence: 94%

A housekeeper with power of attorney: the rRNA genes in ribosome biogenesis

Moss

Langlois

Gagnon-Kugler

et al. 2006

Cell. Mol. Life Sci.

270

262

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Ribosome biogenesis centres both physically and functionally on the activity of the ribosomal RNA (rRNA) genes. Ribosome assembly occurs co-transcriptionally on these genes, requires the coordinated expression and assembly of many hundreds of proteins and is finely tuned to cell and organism growth. This review presents contemporary understanding of the mode and the means of rRNA gene transcription and how growth factors, oncogenes and tumour suppressors regulate this transcription. It is argued that transcription elongation is a key mechanism regulating rRNA gene transcription. This unorthodox view provides a logical framework to explain the co-transcriptional phase of ribosome biogenesis.

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Section: Yeastmentioning

confidence: 94%

A housekeeper with power of attorney: the rRNA genes in ribosome biogenesis

Moss

Langlois

Gagnon-Kugler

et al. 2006

Cell. Mol. Life Sci.

270

262

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“…A basal level of initiation by yeast Pol I requires only Rrn3 and the heterotrimeric core factor (CF) in vitro (Bedwell et al, 2012;Keener et al, 1998;Pilsl et al, 2016). Full activity additionally depends on upstream activation factor (UAF), which binds the upstream promoter element (Hontz et al, 2008;Keys et al, 1996) and prevents rDNA transcription by Pol II (Hontz et al, 2008;Siddiqi et al, 2001aSiddiqi et al, , 2001bVu et al, 1999). The complete Pol I initiation system also comprises the TATA boxbinding protein (TBP) (Bedwell et al, 2012;Keener et al, 1998;Steffan et al, 1998).…”

Section: Introductionmentioning

confidence: 99%

Structural Basis of RNA Polymerase I Transcription Initiation

Engel

Gubbey

Neyer

et al. 2017

Cell

113

172

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Transcription initiation by RNA Polymerase I (Pol I) depends on the Core Factor (CF) complex to recognize the upstream promoter and assemble into a Pre-Initiation Complex (PIC). Here, we solve a structure of Saccharomyces cerevisiae Pol I-CF-DNA to 3.8 A ˚ resolution using single-particle cryo-electron microscopy. The structure reveals a bipartite architecture of Core Factor and its recognition of the promoter from À27 to À16. Core Factor's intrinsic mobility correlates well with different conformational states of the Pol I cleft, in addition to the stabilization of either Rrn7 N-terminal domain near Pol I wall or the tandem winged helix domain of A49 at a partially overlapping location. Comparison of the three states in this study with the Pol II system suggests that a ratchet motion of the Core Factor-DNA sub-complex at upstream facilitates promoter melting in an ATP-independent manner, distinct from a DNA translocase actively threading the downstream DNA in the Pol II PIC.

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“…In human cells, this complex is called SL1 and contains TBP and the TAF 1 s TAF 1 110, TAF 1 63, TAF I 48, and TAF I 41. The TAF 1 equivalents in fission and budding yeast are called Rrn6, Rrn7, and Rrn11, respectively, and are found with TBP in a complex called core factor (1,2). The minor subunits of SL1 have no equivalents in yeast.…”

mentioning

confidence: 99%

Rrn7 Protein, an RNA Polymerase I Transcription Factor, Is Required for RNA Polymerase II-dependent Transcription Directed by Core Promoters with a HomolD Box Sequence

Rojas

Moreira-Ramos

Zock-Emmenthal

et al. 2011

Journal of Biological Chemistry

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The region in promoters that specifies the transcription machinery is called the core promoter, displaying core promoter elements (CPE) necessary for establishment of a preinitiation complex and the initiation of transcription. A classical CPE is the TATA box. In fission yeast, Schizosaccharomyces pombe, a new CPE, called HomolD box, was discovered. Collectively, 141 ribosomal protein genes encoding the full set of 79 different ribosomal proteins and more than 60 other housekeeping genes display a HomolD box in the core promoter. Here, we show that transcription directed by the HomolD box requires the RNA polymerase II machinery, including the general transcription factors. Most intriguingly, however, we identify, by DNA affinity purification, Rrn7 as the protein binding to the HomolD box. Rrn7 is an evolutionary conserved member of the RNA polymerase I machinery involved in transcription initiation of core ribosomal DNA promoters. ChIP shows that Rrn7 cross-links to a ribosomal protein gene promoter containing the HomolD box but not to a promoter containing a TATA box. Taken together, our results suggest that Rrn7 is an excellent candidate to be involved in the coordination of ribosomal DNA and ribosomal gene transcription during ribosome synthesis and, therefore, offer a new perspective to study conservation and evolvability of regulatory networks in eukaryotes.Ribosome biogenesis in eukaryotes is a highly coordinated process involving three different RNA polymerases. RNA polymerase III (RNAPIII) 3 synthesizes the small 5 S RNA. RNAPI synthesizes the large rRNA precursor. Transcription at ribosomal RNA core promoters is initiated by the TATA binding protein (TBP) and TBP-associated factors (TAF 1 s) forming a preinitiation complex (PIC). In human cells, this complex is called SL1 and contains TBP and the TAF 1 s TAF 1 110, TAF 1 63, TAF I 48, and TAF I 41. The TAF 1 equivalents in fission and budding yeast are called Rrn6, Rrn7, and Rrn11, respectively, and are found with TBP in a complex called core factor (1, 2). The minor subunits of SL1 have no equivalents in yeast. RNAPII, finally, transcribes the ribosomal protein-encoding genes (3). RNAPII-dependent transcription also requires a PIC. In a TATA box containing core promoters, the first step in the formation of the PIC is the binding of TBP to the TATA box. TBP binds to the TATA box complexed with TFIID (TAF 11 s) followed by the other GTFs TFIIB, TFIIF, TFIIE, and TFIIH, respectively, to complete PIC formation for the recruitment of pol II (4 -6). However, it is also discussed that a preassembled holoenzyme including pol II, TBP, and the GTFs are targeted with the help of the mediator complex onto the DNA in the core promoter region for PIC formation (7,8).The 141 ribosomal protein genes of fission yeast encoding the full set of 79 ribosomal proteins are TATA-less promoters. Instead, they all contain the highly conserved sequence CAGT-CACA or its inverted form, TGTGACTG, within 100 bp upstream of the ATG start codon. This sequence was termed the HomolD bo...

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Role of TATA Binding Protein (TBP) in Yeast Ribosomal DNA Transcription by RNA Polymerase I: Defects in the Dual Functions of Transcription Factor UAF Cannot Be Suppressed by TBP

Cited by 21 publications

References 22 publications

A housekeeper with power of attorney: the rRNA genes in ribosome biogenesis

A housekeeper with power of attorney: the rRNA genes in ribosome biogenesis

Structural Basis of RNA Polymerase I Transcription Initiation

Rrn7 Protein, an RNA Polymerase I Transcription Factor, Is Required for RNA Polymerase II-dependent Transcription Directed by Core Promoters with a HomolD Box Sequence

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