The Saccharomyces cerevisiae RNA polymerase III recruitment factor subunits Brf1 and Bdp1 impose a strict sequence preference for the downstream half of the TATA box

The Epstein-Barr virus-encoded small RNA (EBER) genes are transcribed by RNA polymerase III, but their transcription unit appears to contain both class II and class III promoter elements. One of these promoter element, a TATA-like box which we call the EBER TATA box, or ETAB, is located in a position typical for a class II TATA box but contains G/C residues in the normal T/A motif and a conserved thymidine doublet. Experiments using chloramphenicol acetyltransferase constructs and mutations in the TATA box of the adenovirus major late promoter showed that the ETAB promoter element does not substitute for a class II TATA box. However, when the ETAB promoter element sequence was changed to a class II TATA box consensus sequence, the EBER 2 gene was transcribed in vitro by both RNA polymerases II and III. From these results, we conclude that the ETAB promoter element is important for the exclusive transcription of the EBER 2 gene by RNA polymerase III.

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Rbs1 protein, an assembly factor of RNA polymerase III complex in the yeast Saccharomyces cerevisiae, induces a Gcn4 response and forms aggregates when overproduced

Gene ◽

10.1016/j.gene.2021.146034 ◽

2021 ◽

pp. 146034

Author(s):

Izabela Rudzińska ◽

Marta Płonka ◽

Alicja Armatowska ◽

Tomasz W. Turowski ◽

Magdalena Boguta

Keyword(s):

Saccharomyces Cerevisiae ◽

Rna Polymerase ◽

Rna Polymerase Iii ◽

Yeast Saccharomyces Cerevisiae ◽

Polymerase Iii ◽

Assembly Factor

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Distinct modes of TATA box utilization by the RNA polymerase III transcription machineries from budding yeast and higher plants

Gene ◽

10.1016/j.gene.2006.03.013 ◽

2006 ◽

Vol 379 ◽

pp. 12-25 ◽

Cited By ~ 12

Author(s):

Giorgio Dieci ◽

Yasushi Yukawa ◽

Mircko Alzapiedi ◽

Elisa Guffanti ◽

Roberto Ferrari ◽

...

Keyword(s):

Rna Polymerase ◽

Higher Plants ◽

Budding Yeast ◽

Rna Polymerase Iii ◽

Tata Box ◽

Polymerase Iii

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TATA-box DNA binding activity and subunit composition for RNA polymerase III transcription factor IIIB from Xenopus laevis.

Molecular and Cellular Biology ◽

10.1128/mcb.16.9.4639 ◽

1996 ◽

Vol 16 (9) ◽

pp. 4639-4647 ◽

Cited By ~ 8

Author(s):

S J McBryant ◽

E Meier ◽

A Leresche ◽

S J Sharp ◽

V J Wolf ◽

...

Keyword(s):

Dna Binding ◽

Rna Polymerase ◽

Transcriptional Activity ◽

Rna Polymerase Iii ◽

Sodium Dodecyl ◽

Binding Activity ◽

Tata Box ◽

Initiation Factor ◽

Dna Binding Activity ◽

Polymerase Iii

The RNA polymerase III transcription initiation factor TFIIIB contains the TATA-box-binding protein (TBP) and polymerase III-specific TBP-associated factors (TAFs). Previous studies have shown that DNA oligonucleotides containing the consensus TATA-box sequence inhibit polymerase III transcription, implying that the DNA binding domain of TBP is exposed in TFIIIB. We have investigated the TATA-box DNA binding activity of Xenopus TFIIIB, using transcription inhibition assays and a gel mobility shift assay. Gel shift competition assays with mutant and nonspecific DNAs demonstrate the specificity of the TFIIIB-TATA box DNA complex. The apparent dissociation constant for this protein-DNA interaction is approximately 0.4 nM, similar to the affinity of yeast TBP for the same sequence. TFIIIB transcriptional activity and TATA-box binding activity cofractionate during a series of four ion-exchange chromatographic steps, and reconstituted transcription reactions demonstrate that the TATA-box DNA-protein complex contains TFIIIB TAF activity. Polypeptides with apparent molecular masses of 75 and 92 kDa are associated with TBP in this complex. These polypeptides were renatured after elution from sodium dodecyl sulfate-gels and tested individually and in combination for TFIIIB TAF activity. Recombinant TBP along with protein fractions containing the 75- and 92-kDa polypeptides were sufficient to reconstitute TFIIIB transcriptional activity and DNA binding activity, suggesting that Xenopus TFIIIB is composed of TBP along with these polypeptides.

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Inactivation of the protein phosphatase 2A regulatory subunit A results in morphological and transcriptional defects in Saccharomyces cerevisiae

Molecular and Cellular Biology ◽

10.1128/mcb.12.11.4946-4959.1992 ◽

1992 ◽

Vol 12 (11) ◽

pp. 4946-4959

Author(s):

W van Zyl ◽

W Huang ◽

A A Sneddon ◽

M Stark ◽

S Camier ◽

...

Keyword(s):

Saccharomyces Cerevisiae ◽

Rna Polymerase ◽

Protein Phosphatase ◽

Protein Phosphatase 2A ◽

Rna Polymerase Iii ◽

Regulatory Subunit ◽

Predicted Amino Acid Sequence ◽

Major Protein ◽

Polymerase Iii ◽

Phosphatase 2A

We have determined that TPD3, a gene previously identified in a screen for mutants defective in tRNA biosynthesis, most likely encodes the A regulatory subunit of the major protein phosphatase 2A species in the yeast Saccharomyces cerevisiae. The predicted amino acid sequence of the product of TPD3 is highly homologous to the sequence of the mammalian A subunit of protein phosphatase 2A. In addition, antibodies raised against Tpd3p specifically precipitate a significant fraction of the protein phosphatase 2A activity in the cell, and extracts of tpd3 strains yield a different chromatographic profile of protein phosphatase 2A than do extracts of isogenic TPD3 strains. tpd3 deletion strains generally grow poorly and have at least two distinct phenotypes. At reduced temperatures, tpd3 strains appear to be defective in cytokinesis, since most cells become multibudded and multinucleate following a shift to 13 degrees C. This is similar to the phenotype obtained by overexpression of the protein phosphatase 2A catalytic subunit or by loss of CDC55, a gene that encodes a protein with homology to a second regulatory subunit of protein phosphatase 2A. At elevated temperatures, tpd3 strains are defective in transcription by RNA polymerase III. Consistent with this in vivo phenotype, extracts of tpd3 strains fail to support in vitro transcription of tRNA genes, a defect that can be reversed by addition of either purified RNA polymerase III or TFIIIB. These results reinforce the notion that protein phosphatase 2A affects a variety of biological processes in the cell and provide an initial identification of critical substrates for this phosphatase.

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Inactivation of the protein phosphatase 2A regulatory subunit A results in morphological and transcriptional defects in Saccharomyces cerevisiae.

Molecular and Cellular Biology ◽

10.1128/mcb.12.11.4946 ◽

1992 ◽

Vol 12 (11) ◽

pp. 4946-4959 ◽

Cited By ~ 94

Author(s):

W van Zyl ◽

W Huang ◽

A A Sneddon ◽

M Stark ◽

S Camier ◽

...

Keyword(s):

Saccharomyces Cerevisiae ◽

Rna Polymerase ◽

Protein Phosphatase ◽

Protein Phosphatase 2A ◽

Rna Polymerase Iii ◽

Regulatory Subunit ◽

Predicted Amino Acid Sequence ◽

Major Protein ◽

Polymerase Iii ◽

Phosphatase 2A

We have determined that TPD3, a gene previously identified in a screen for mutants defective in tRNA biosynthesis, most likely encodes the A regulatory subunit of the major protein phosphatase 2A species in the yeast Saccharomyces cerevisiae. The predicted amino acid sequence of the product of TPD3 is highly homologous to the sequence of the mammalian A subunit of protein phosphatase 2A. In addition, antibodies raised against Tpd3p specifically precipitate a significant fraction of the protein phosphatase 2A activity in the cell, and extracts of tpd3 strains yield a different chromatographic profile of protein phosphatase 2A than do extracts of isogenic TPD3 strains. tpd3 deletion strains generally grow poorly and have at least two distinct phenotypes. At reduced temperatures, tpd3 strains appear to be defective in cytokinesis, since most cells become multibudded and multinucleate following a shift to 13 degrees C. This is similar to the phenotype obtained by overexpression of the protein phosphatase 2A catalytic subunit or by loss of CDC55, a gene that encodes a protein with homology to a second regulatory subunit of protein phosphatase 2A. At elevated temperatures, tpd3 strains are defective in transcription by RNA polymerase III. Consistent with this in vivo phenotype, extracts of tpd3 strains fail to support in vitro transcription of tRNA genes, a defect that can be reversed by addition of either purified RNA polymerase III or TFIIIB. These results reinforce the notion that protein phosphatase 2A affects a variety of biological processes in the cell and provide an initial identification of critical substrates for this phosphatase.

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A Novel Upstream RNA Polymerase III Promoter Element Becomes Essential When the Chromatin Structure of the Yeast U6 RNA Gene Is Altered

Molecular and Cellular Biology ◽

10.1128/mcb.21.19.6429-6439.2001 ◽

2001 ◽

Vol 21 (19) ◽

pp. 6429-6439 ◽

Cited By ~ 23

Author(s):

Michael P. Martin ◽

Valerie L. Gerlach ◽

David A. Brow

Keyword(s):

Rna Polymerase ◽

Rna Polymerase Iii ◽

Point Mutations ◽

Tata Box ◽

Initiation Factor ◽

Base Pairs ◽

Polymerase Iii ◽

U6 Rna

ABSTRACT The Saccharomyces cerevisiae U6 RNA gene,SNR6, possesses upstream sequences that allow productive binding in vitro of the RNA polymerase III (Pol III) transcription initiation factor IIIB (TFIIIB) in the absence of TFIIIC or other assembly factors. TFIIIC-independent transcription ofSNR6 in vitro is highly sensitive to point mutations in a consensus TATA box at position −30. In contrast, the TATA box is dispensable for SNR6 transcription in vivo, apparently because TFIIIC bound to the intragenic A block and downstream B block can recruit TFIIIB via protein-protein interactions. A mutant allele ofSNR6 with decreased spacing between the A and B blocks,snr6-Δ42, exhibits increased dependence on the upstream sequences in vivo. Unexpectedly, we find that in vivo expression of snr6-Δ42 is much more sensitive to mutations in a (dT-dA)7 tract between the TATA box and transcription start site than to mutations in the TATA box itself. Inversion of single base pairs in the center of the dT-dA tract nearly abolishes transcription of snr6-Δ42, yet inversion of all 7 base pairs has little effect on expression, indicating that the dA-dT tract is relatively orientation independent. Although it is within the TFIIIB footprint, point mutations in the dT-dA tract do not inhibit TFIIIB binding or TFIIIC-independent transcription ofSNR6 in vitro. In the absence of the chromatin architectural protein Nhp6, dT-dA tract mutations are lethal even when A-to-B block spacing is wild type. We conclude that the (dT-dA)7 tract and Nhp6 cooperate to direct productive transcription complex assembly on SNR6 in vivo.

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Differential Utilization of TATA Box-binding Protein (TBP) and TBP-related Factor 1 (TRF1) at Different Classes of RNA Polymerase III Promoters

Journal of Biological Chemistry ◽

10.1074/jbc.c113.503094 ◽

2013 ◽

Vol 288 (38) ◽

pp. 27564-27570 ◽

Cited By ~ 8

Author(s):

Neha Verma ◽

Ko-Hsuan Hung ◽

Jin Joo Kang ◽

Nermeen H. Barakat ◽

William E. Stumph

Keyword(s):

Rna Polymerase ◽

Binding Protein ◽

Rna Polymerase Iii ◽

Tata Box ◽

Related Factor ◽

U6 Snrna ◽

Polymerase Iii ◽

Tata Box Binding Protein ◽

In Cells

In the fruit fly Drosophila melanogaster, RNA polymerase III transcription was found to be dependent not upon the canonical TATA box-binding protein (TBP) but instead upon the TBP-related factor 1 (TRF1) (Takada, S., Lis, J. T., Zhou, S., and Tjian, R. (2000) Cell 101, 459–469). Here we confirm that transcription of fly tRNA genes requires TRF1. However, we unexpectedly find that U6 snRNA gene promoters are occupied primarily by TBP in cells and that knockdown of TBP, but not TRF1, inhibits U6 transcription in cells. Moreover, U6 transcription in vitro effectively utilizes TBP, whereas TBP cannot substitute for TRF1 to promote tRNA transcription in vitro. Thus, in fruit flies, different classes of RNA polymerase III promoters differentially utilize TBP and TRF1 for the initiation of transcription.

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