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Hoopes BC, Bowers GD, DiVisconte MJ. The two Saccharomyces cerevisiae SUA7 (TFIIB) transcripts differ at the 3'-end and respond differently to stress. Nucleic Acids Res 2000; 28:4435-43. [PMID: 11071930 PMCID: PMC113880 DOI: 10.1093/nar/28.22.4435] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Despite much information as to the structure and function of the general transcription factors, little is known about the regulation of their expression. Transcription of the Saccharomyces cerevisiae SUA7 (TFIIB) gene results in the formation of two discrete transcripts. It was originally reported that the two transcripts were derived from two promoters separated by approximately 80 bp. We have found that the two transcripts are instead derived from a common promoter and differ at the 3'-end by approximately 115 bp. The longer of the two transcripts has an unusually long 3'-untranslated region. We have analyzed the levels of these transcripts under different cell growth conditions and find that the relative amounts of the two transcripts vary. Approximately equal amounts of each transcript are observed during exponential growth, but stresses and growth limiting conditions lead to a decrease in the relative amount of the larger transcript. These results suggest that the expression of the SUA7 gene may be controlled by regulation of 3'-end formation or mRNA stability. One of the general transcription factors, then, may be subject to regulation by a general response of the mRNA processing machinery.
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Affiliation(s)
- B C Hoopes
- Department of Biology, Colgate University, 13 Oak Drive, Hamilton, NY 13346, USA.
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Wu WH, Pinto I, Chen BS, Hampsey M. Mutational analysis of yeast TFIIB. A functional relationship between Ssu72 and Sub1/Tsp1 defined by allele-specific interactions with TFIIB. Genetics 1999; 153:643-52. [PMID: 10511545 PMCID: PMC1460761 DOI: 10.1093/genetics/153.2.643] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
TFIIB is an essential component of the RNA polymerase II core transcriptional machinery. Previous studies have defined TFIIB domains required for interaction with other transcription factors and for basal transcription in vitro. In the study reported here we investigated the TFIIB structural requirements for transcription initiation in vivo. A library of sua7 mutations encoding altered forms of yeast TFIIB was generated by error-prone polymerase chain reaction and screened for conditional growth defects. Twenty-two single amino acid replacements in TFIIB were defined and characterized. These replacements are distributed throughout the protein and occur primarily at phylogenetically conserved positions. Most replacements have little or no effect on the steady-state protein levels, implying that each affects TFIIB function rather than synthesis or stability. In contrast to the initial sua7 mutants, all replacements, with one exception, have no effect on start site selection, indicating that specific TFIIB structural defects affect transcriptional accuracy. This collection of sua7 alleles, including the initial sua7 alleles, was used to investigate the allele specificity of interactions between ssu72 and sub1, both of which were initially identified as either suppressors (SUB1 2mu) or enhancers (sub1Delta, ssu72-1) of sua7 mutations. We show that the interactions of ssu72-1 and sub1Delta with sua7 are allele specific; that the allele specificities of ssu72 and sub1 overlap; and that each of the sua7 alleles that interacts with ssu72 and sub1 affects the accuracy of transcription start site selection. These results demonstrate functional interactions among TFIIB, Ssu72, and Sub1 and suggest that these interactions play a role in the mechanism of start site selection by RNA polymerase II.
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Affiliation(s)
- W H Wu
- Department of Biochemistry, Louisiana State University Medical Center, Shreveport, Louisiana 71130, USA
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Destruelle M, Menghini R, Frontali L, Bianchi MM. Regulation of the expression of the Kluyveromyces lactis PDC1 gene: carbon source-responsive elements and autoregulation. Yeast 1999; 15:361-70. [PMID: 10219994 DOI: 10.1002/(sici)1097-0061(19990330)15:5<361::aid-yea378>3.0.co;2-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
The yeast Kluyveromyces lactis has a single structural gene coding for pyruvate decarboxylase (KIPDC1). In order to study the regulation of the expression of KIPDC1, we have sequenced (EMBL Accession No. Y15435) its promoter and have fused the promoter to the reporter gene lacZ from E. coli. Transcription analysis in a Klpdc1 delta strain showed that KIPDC1 expression is subject to autoregulation. The PDC1 gene from Saccharomyces cerevisiae was able to complement the Rag- phenotype of the Klpdc1 delta mutant strain and it could also repress transcription of the KIPDC1-lacZ fusion on glucose. A deletion analysis of the promoter region was performed to study carbon source-dependent regulation and revealed that at least two cis-acting regions are necessary for full induction of gene expression on glucose. Other cis-elements mediate repression on ethanol.
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Affiliation(s)
- M Destruelle
- Pasteur Institute, Cenci Bolognetti Foundation, Department of Cell and Developmental Biology, University of Rome La Sapienza, Rome, Italy
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Abstract
A yeast mutant was isolated encoding a single amino acid substitution [serine-53 --> proline (S53P)] in transcription factor TFIIB that impairs activation of the PHO5 gene in response to phosphate starvation. This effect is activation-specific because S53P did not affect the uninduced level of PHO5 expression, yet is not specific to PHO5 because Adr1-mediated activation of the ADH2 gene also was impaired by S53P. Pho4, the principal activator of PHO5, directly interacted with TFIIB in vitro, and this interaction was impaired by the S53P replacement. Furthermore, Pho4 induced a conformational change in TFIIB, detected by enhanced sensitivity to V8 protease. The S53P replacement also impaired activation of a lexA(op)-lacZ reporter by a LexA fusion protein to the activation domain of Adr1, thereby indicating that the transcriptional effect on ADH2 expression is specific to the activation function of Adr1. These results define an activation-specific role for TFIIB in vivo and suggest that certain activators induce a conformational change in TFIIB as part of their mechanism of transcriptional stimulation.
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Affiliation(s)
- W H Wu
- Department of Biochemistry, Division of Nucleic Acids Enzymology, University of Medicine and Dentistry of New Jersey-Robert Wood Johnson Medical School, 675 Hoes Lane, Piscataway, NJ 08854-5635, USA
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Prior C, Tizzani L, Fukuhara H, Wésolowski-Louvel M. RAG3 gene and transcriptional regulation of the pyruvate decarboxylase gene in Kluyveromyces lactis. Mol Microbiol 1996; 20:765-72. [PMID: 8793873 DOI: 10.1111/j.1365-2958.1996.tb02515.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The RAG3 gene has been cloned from a Kluyveromyces lactis genomic library by complementation of the rag3 mutation, which shows impaired fermentative growth on glucose in the presence of respiratory inhibitors. From the nucleotide sequence of the cloned DNA, which contained an open reading frame of 765 codons, the predicted protein is 49.5% identical to the Pdc2 protein of Saccharomyces cerevisiae, a regulator of pyruvate decarboxylase in this yeast. Measurement of the pyruvate decarboxylase activity in the original rag3-1 mutant and in the null mutant confirmed that the RAG3 gene is involved in pyruvate decarboxylase synthesis in K. lactis. The effect is exerted at the mRNA level of the pyruvate decarboxylase structural gene KIPDCA. Despite analogies between the RAG3 gene of K. lactis and the PDC2 gene of S. cerevisiae, these genes were unable to reciprocally complement.
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Affiliation(s)
- C Prior
- Institut Curie, Section de Biologie, Centre Universitaire Orsay, France
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Sun ZW, Hampsey M. Synthetic enhancement of a TFIIB defect by a mutation in SSU72, an essential yeast gene encoding a novel protein that affects transcription start site selection in vivo. Mol Cell Biol 1996; 16:1557-66. [PMID: 8657130 PMCID: PMC231141 DOI: 10.1128/mcb.16.4.1557] [Citation(s) in RCA: 82] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
An ssu72 mutant of Saccharomyces cerevisiae was identified as an enhancer of a TFIIB defect (sua7-1) that confers both a cold-sensitive growth defect and a downstream shift in transcription start site selection. The ssu72-1 allele did not affect cold sensitivity but, in combination with sua7-1, created a heat-sensitive phenotype. Moreover, start site selection at the ADH1 gene was dramatically shifted further downstream of the normal sites. Both of these effects could be rescued by either SUA7 or SSU72, thereby defining a functional relationship between the two genes. SSU72 is a single-copy, essential gene encoding a novel protein of 206 amino acids. The ssu72-1 allele is the result of a 30-bp duplication creating a sequence encoding a Cys-X2-Cys-X6-Cys-X2-Cys zinc binding motif near the N terminus of Ssu72p. Mutational analysis demonstrated that the N terminus of Ssu72p is essential for function and that cysteine residues in both the normal and mutant proteins are critical. We discuss the possibility that the potential zinc binding motif of Ssu72 facilitates assembly of the transcription preinitiation complex and that this effect is important for accurate start site selection in vivo.
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Affiliation(s)
- Z W Sun
- Department of Biochemistry and Molecular Biology, Louisiana State University Medical Center, Shreveport, 71130, USA
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Khoo B, Brophy B, Jackson SP. Conserved functional domains of the RNA polymerase III general transcription factor BRF. Genes Dev 1994; 8:2879-90. [PMID: 7995525 DOI: 10.1101/gad.8.23.2879] [Citation(s) in RCA: 115] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
In Saccharomyces cerevisiae, two components of the RNA polymerase III (Pol III) general transcription factor TFIIIB are the TATA-binding protein (TBP) and the B-related factor (BRF), so called because its amino-terminal half is homologous to the Pol II transcription factor IIB (TFIIB). We have cloned BRF genes from the yeasts Kluyveromyces lactis and Candida albicans. Despite the large evolutionary distance between these species and S. cerevisiae, the BRF proteins are conserved highly. Although the homology is most pronounced in the amino-terminal half, conserved regions also exist in the carboxy-terminal half that is unique to BRF. By assaying for interactions between BRF and other Pol III transcription factors, we show that it is able to bind to the 135-kD subunit of TFIIIC and also to TBP. Surprisingly, in addition to binding the TFIIB-homologous amino-terminal portion of BRF, TBP also interacts strongly with the carboxy-terminal half. Deleting two conserved regions in the BRF carboxy-terminal region abrogates this interaction. Furthermore, TBP mutations that selectively inhibit Pol III transcription in vivo impair interactions between TBP and the BRF carboxy-terminal domain. Finally, we demonstrate that BRF but not TFIIB binds the Pol III subunit C34 and we define a region of C34 necessary for this interaction. These observations provide insights into the roles performed by BRF in Pol III transcription complex assembly.
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Affiliation(s)
- B Khoo
- Wellcome/CRC Institute, Cambridge University, UK
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Pinto I, Wu WH, Na JG, Hampsey M. Characterization of sua7 mutations defines a domain of TFIIB involved in transcription start site selection in yeast. J Biol Chem 1994. [DOI: 10.1016/s0021-9258(18)43851-3] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Affiliation(s)
- P E Sudbery
- Department of Molecular Biology, University of Sheffield, U.K
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Mulder W, Scholten IH, Nagelkerken B, Grivell LA. Isolation and characterisation of the linked genes, FPS1 and QCR8, coding for farnesyl-diphosphate synthase and the 11 kDa subunit VIII of the mitochondrial bc1-complex in the yeast Kluyveromyces lactis. BIOCHIMICA ET BIOPHYSICA ACTA 1994; 1219:713-8. [PMID: 7948032 DOI: 10.1016/0167-4781(94)90234-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The KlQCR8 gene of the yeast Kluyveromyces lactis encoding subunit VIII of the mitochondrial bc1 complex is 70.2% identical to its counterpart in Saccharomyces cerevisiae (ScQCR8). As in S. cerevisiae, chromosomal linkage between the K. lactis QCR8 and FPS1 genes is conserved, the two genes being separated by only 292 bp. Disruption of the KlQCR8 gene results in a respiratory-deficient phenotype. Compared with S. cerevisiae, expression of the KlQCR8 gene in glucose-grown cells is relatively high, yet is significantly induced when the cells are grown on non-fermentable carbon sources. The QCR8 promoters regions of the two yeasts lack overall DNA sequence similarity, but share DNA-binding sites for the transcription factors ABF1, CPF1 and HAP2/3/4. Deletion from the KlQCR8 promoter of a 93 bp region containing these sites significantly lowers mRNA levels during growth on either glucose or ethanol/glycerol, with a consequent reduction of growth rate on ethanol/glycerol.
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Affiliation(s)
- W Mulder
- Section for Molecular Biology, Biocentrum Amsterdam, The Netherlands
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Mulder W, Winkler AA, Scholten IH, Zonneveld BJ, de Winde JH, Yde Steensma H, Grivell LA. Centromere promoter factors (CPF1) of the yeasts Saccharomyces cerevisiae and Kluyveromyces lactis are functionally exchangeable, despite low overall homology. Curr Genet 1994; 26:198-207. [PMID: 7859301 DOI: 10.1007/bf00309548] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The KlCPF1 gene, coding for the centromere and promoter factor CPF1 from Kluyveromyces lactis, has been cloned by functional complementation of the methionine auxotrophic phenotype of a Saccharomyces cerevisiae mutant lacking ScCPF1. The amino-acid sequences of both CPF1 proteins show a relatively-low overall identity (31%), but a highly-homologous C-terminal domain (86%). This region constitutes the DNA-binding domain with basic-helix-loop-helix and leucine-zipper motifs, features common to the myc-related transcription factor family. The N-terminal two-thirds of the CPF1 proteins show no significant similarity, although the presence of acidic regions is a shared feature. In KlCPF1, the acidic region is a prominent stretch of approximately 40 consecutive aspartate and glutamate residues, suggesting that this part might be involved in transcriptional activation. In-vitro mobility-shift experiments were used to establish that both CPF1 proteins bind to the consensus binding site RTCACRTG (CDEI element). In contrast to S. cerevisiae, CPF1 gene-disruption is lethal in K. lactis. The homologous CPF1 genes were transformed to both S. cerevisiae and K. lactis cpf1-null strains. Indistinguishable phenotypes were observed, indicating that, not withstanding the long nonconserved N-terminal region, the proteins are sufficiently homologous to overcome the phenotypes associated with cpf1 gene-disruption.
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Affiliation(s)
- W Mulder
- Section for Molecular Biology, Biocentrum Amsterdam, The Netherlands
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Gibson TJ, Thompson JD, Blocker A, Kouzarides T. Evidence for a protein domain superfamily shared by the cyclins, TFIIB and RB/p107. Nucleic Acids Res 1994; 22:946-52. [PMID: 8152925 PMCID: PMC307913 DOI: 10.1093/nar/22.6.946] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Cyclins, TFIIB and RB play major roles in cell cycle and/or gene regulation. Earlier work has suggested common ancestry for the TFIIB repeats and RB pocket B which share 20% sequence identity. We now report that database searches with profiles based on a multiple alignment of cyclin core regions (the 'cyclin box') detect the TFIIB repeats with equivalent scores to divergent cyclins. Several features of the sequences support the notion of common ancestry: e.g. cyclins A/B, C and D share approximately 20-30% identity but each have approximately 15-20% identity with vertebrate TFIIB, showing that conserved cyclin features underlie the match. These results suggest the presence of a domain superfamily, which we term the TR domain, in nuclear regulatory proteins belonging to the TFIIB, cyclin and RB families, that has been duplicated many times during eukaryotic evolution. The TR domain appears to function in protein-protein interactions.
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Affiliation(s)
- T J Gibson
- European Molecular Biology Laboratory, Heidelberg, Germany
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