1
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Zhang R, Zhang C, Lyu S, Wu H, Yuan M, Fang Z, Li F, Hou X. BcTFIIIA Negatively Regulates Turnip Mosaic Virus Infection through Interaction with Viral CP and VPg Proteins in Pak Choi (Brassica campestris ssp. chinensis). Genes (Basel) 2022; 13:genes13071209. [PMID: 35885992 PMCID: PMC9317785 DOI: 10.3390/genes13071209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 07/01/2022] [Accepted: 07/04/2022] [Indexed: 12/10/2022] Open
Abstract
TFIIIA is a zinc-finger transcription factor that is involved in post-transcriptional regulation during development. Here, the BcTFIIIA gene was isolated from pak choi. Sequence analysis showed that BcTFIIIA encodes 383 amino acids (aa) with an open reading frame (ORF) of 1152 base pairs (bp). We investigated the subcellular location of BcTFIIIA and found the localized protein in the nucleus. BcTFIIIA was suppressed when the pak choi was infected by the turnip mosaic virus (TuMV). The BcTFIIIA mRNA expression level in a resistant variety was higher than that in a sensitive variety, as determined by qRT-PCR analysis. Yeast two hybrid (Y2H) assay and bimolecular fluorescence complementation (BiFC) suggested that BcTFIIIA interacts with TuMV CP and VPg in vivo, respectively, and in vitro. A virus-induced gene silencing (VIGS) experiment showed that the silencing of BcTFIIIA gene expression in pak choi promoted the accumulation of TuMV. These results suggest that BcTFIIIA negatively regulates viral infection through the interaction with TuMV CP and VPg.
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Affiliation(s)
- Rujia Zhang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Ministry of Agriculture and Rural Affairs, Nanjing 210095, China; (R.Z.); (C.Z.); (S.L.); (H.W.); (M.Y.)
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crops, Nanjing Agricultural University, Nanjing 210095, China
| | - Changwei Zhang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Ministry of Agriculture and Rural Affairs, Nanjing 210095, China; (R.Z.); (C.Z.); (S.L.); (H.W.); (M.Y.)
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crops, Nanjing Agricultural University, Nanjing 210095, China
| | - Shanwu Lyu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Ministry of Agriculture and Rural Affairs, Nanjing 210095, China; (R.Z.); (C.Z.); (S.L.); (H.W.); (M.Y.)
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crops, Nanjing Agricultural University, Nanjing 210095, China
| | - Huiyuan Wu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Ministry of Agriculture and Rural Affairs, Nanjing 210095, China; (R.Z.); (C.Z.); (S.L.); (H.W.); (M.Y.)
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crops, Nanjing Agricultural University, Nanjing 210095, China
| | - Mengguo Yuan
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Ministry of Agriculture and Rural Affairs, Nanjing 210095, China; (R.Z.); (C.Z.); (S.L.); (H.W.); (M.Y.)
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crops, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhiyuan Fang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China;
| | - Fangfang Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China;
| | - Xilin Hou
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Ministry of Agriculture and Rural Affairs, Nanjing 210095, China; (R.Z.); (C.Z.); (S.L.); (H.W.); (M.Y.)
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crops, Nanjing Agricultural University, Nanjing 210095, China
- Correspondence:
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Enserink JM, Chymkowitch P. Cell Cycle-Dependent Transcription: The Cyclin Dependent Kinase Cdk1 Is a Direct Regulator of Basal Transcription Machineries. Int J Mol Sci 2022; 23:ijms23031293. [PMID: 35163213 PMCID: PMC8835803 DOI: 10.3390/ijms23031293] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/22/2022] [Accepted: 01/22/2022] [Indexed: 12/21/2022] Open
Abstract
The cyclin-dependent kinase Cdk1 is best known for its function as master regulator of the cell cycle. It phosphorylates several key proteins to control progression through the different phases of the cell cycle. However, studies conducted several decades ago with mammalian cells revealed that Cdk1 also directly regulates the basal transcription machinery, most notably RNA polymerase II. More recent studies in the budding yeast Saccharomyces cerevisiae have revisited this function of Cdk1 and also revealed that Cdk1 directly controls RNA polymerase III activity. These studies have also provided novel insight into the physiological relevance of this process. For instance, cell cycle-stage-dependent activity of these complexes may be important for meeting the increased demand for various proteins involved in housekeeping, metabolism, and protein synthesis. Recent work also indicates that direct regulation of the RNA polymerase II machinery promotes cell cycle entry. Here, we provide an overview of the regulation of basal transcription by Cdk1, and we hypothesize that the original function of the primordial cell-cycle CDK was to regulate RNAPII and that it later evolved into specialized kinases that govern various aspects of the transcription machinery and the cell cycle.
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Affiliation(s)
- Jorrit M. Enserink
- Section for Biochemistry and Molecular Biology, Faculty of Mathematics and Natural Sciences, University of Oslo, 0316 Oslo, Norway
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, 0379 Oslo, Norway
- Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, 0318 Oslo, Norway
- Correspondence: (J.M.E.); (P.C.)
| | - Pierre Chymkowitch
- Section for Biochemistry and Molecular Biology, Faculty of Mathematics and Natural Sciences, University of Oslo, 0316 Oslo, Norway
- Department of Microbiology, Oslo University Hospital, 0372 Oslo, Norway
- Correspondence: (J.M.E.); (P.C.)
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3
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Nguyen NTT, Saguez C, Conesa C, Lefebvre O, Acker J. Identification of proteins associated with RNA polymerase III using a modified tandem chromatin affinity purification. Gene 2015; 556:51-60. [DOI: 10.1016/j.gene.2014.07.070] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Revised: 07/25/2014] [Accepted: 07/29/2014] [Indexed: 01/12/2023]
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4
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Structure, function and regulation of Transcription Factor IIIA: From Xenopus to Arabidopsis. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2013; 1829:274-82. [DOI: 10.1016/j.bbagrm.2012.10.013] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Revised: 10/30/2012] [Accepted: 10/31/2012] [Indexed: 12/14/2022]
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5
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Acker J, Ozanne C, Kachouri-Lafond R, Gaillardin C, Neuvéglise C, Marck C. Dicistronic tRNA-5S rRNA genes in Yarrowia lipolytica: an alternative TFIIIA-independent way for expression of 5S rRNA genes. Nucleic Acids Res 2008; 36:5832-44. [PMID: 18790808 PMCID: PMC2566860 DOI: 10.1093/nar/gkn549] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
In eukaryotes, genes transcribed by RNA polymerase III (Pol III) carry their own internal promoters and as such, are transcribed as individual units. Indeed, a very few cases of dicistronic Pol III genes are yet known. In contrast to other hemiascomycetes, 5S rRNA genes of Yarrowia lipolytica are not embedded into the tandemly repeated rDNA units, but appear scattered throughout the genome. We report here an unprecedented genomic organization: 48 over the 108 copies of the 5S rRNA genes are located 3' of tRNA genes. We show that these peculiar tRNA-5S rRNA dicistronic genes are expressed in vitro and in vivo as Pol III transcriptional fusions without the need of the 5S rRNA gene-specific factor TFIIIA, the deletion of which displays a viable phenotype. We also report the existence of a novel putative non-coding Pol III RNA of unknown function about 70 nucleotide-long (RUF70), the 13 genes of which are devoid of internal Pol III promoters and located 3' of the 13 copies of the tDNA-Trp (CCA). All genes embedded in the various dicistronic genes, fused 5S rRNA genes, RUF70 genes and their leader tRNA genes appear to be efficiently transcribed and their products correctly processed in vivo.
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Affiliation(s)
- Joël Acker
- Saclay Biology and Technologies Institute (iBiTec-S), CEA, 91191 Gif-sur-Yvette Cedex, France
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6
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Cloix C, Yukawa Y, Tutois S, Sugiura M, Tourmente S. In vitro analysis of the sequences required for transcription of the Arabidopsis thaliana 5S rRNA genes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2003; 35:251-261. [PMID: 12848829 DOI: 10.1046/j.1365-313x.2003.01793.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
In vivo, we have already shown that only two of the 5S rDNA array blocks of the Arabidopsis thaliana genome produce the mature 5S rRNAs. Deletions and point mutations were introduced in an Arabidopsis 5S rDNA-transcribed region and its 5'- and 3'-flanks in order to analyse their effects on transcription activity. In vitro transcription revealed different transcription control regions. One control region essential for transcription initiation was identified in the 5'-flanking sequence. The major sequence determinants were a TATA-like motif (-28 to -23), a GC dinucleotide (-12 to -11), a 3-bp AT-rich region (-4 to -2) and a C residue at -1. They are important for both accurate transcription initiation and transcription efficiency. Transcription level was regulated by polymerase III (Pol III) re-initiation rate as in tRNA genes in which TATA-like motif is involved. Active 5S rDNA transcription additionally required an intragenic promoter composed of an A-box, an Intermediate Element (IE) and a C-box. Double-stranded oligonucleotides corresponding to different fragments of the transcribed region, used as competitors, revealed the main importance of internal promoter elements. A stretch of four T is sufficient for transcription termination. Transcription of Arabidopsis 5S rDNA requires 30 bp of 5'-flanking region, a promoter internal to the transcribed region, and a stretch of T for transcription termination.
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Affiliation(s)
- Catherine Cloix
- U. M. R. 6547 BIOMOVE, Université Blaise Pascal, 24 Avenue des Landais, 63177 Aubière Cedex, France
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7
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Pizzi S, Dieci G, Frigeri P, Piccoli G, Stocchi V, Ottonello S. Domain organization and functional properties of yeast transcription factor IIIA species with different zinc stoichiometries. J Biol Chem 1999; 274:2539-48. [PMID: 9891026 DOI: 10.1074/jbc.274.4.2539] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Transcription factor IIIA (TFIIIA) binds to the 5 S rRNA gene through its zinc finger domain and directs the assembly of a multiprotein complex that promotes transcription initiation by RNA polymerase III. Limited proteolysis of TFIIIA forms with different zinc stoichiometries, in combination with DNA binding and in vitro transcription analyses, have been used herein to investigate the domain organization and zinc requirements of Saccharomyces cerevisiae TFIIIA. Species containing either nine, six, or three zinc equivalents were produced by reductive resaturation and controlled metal depletion of recombinant TFIIIA. Partial digestion of the metal-saturated, 9 Zn2+-liganded factor yields a stable intermediate comprising the eight N-terminal zinc fingers, and a less stable fragment corresponding to a C-terminal portion including the ninth finger. Proteolyzed TFIIIA has the same 5 S DNA binding ability of the intact protein yet no longer supports in vitro 5 S rRNA synthesis. Both the structural compactness and the 5 S DNA binding ability of the TFIIIA form only containing 3 zinc ions are severely compromised. In contrast, the 6 Zn2+-liganded species was found to be indistinguishable from metal-saturated TFIIIA. By demonstrating the existence of three classes of zinc-binding sites contributing differently to yeast TFIIIA structure and function, the present study provides new evidence for the remarkable flexibility built into this complex transcription factor.
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Affiliation(s)
- S Pizzi
- Institute of Biochemical Sciences, University of Parma, I-43100 Parma, Italy
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8
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Bumbulis MJ, Wroblewski G, McKean D, Setzer DR. Genetic analysis of Xenopus transcription factor IIIA. J Mol Biol 1998; 284:1307-22. [PMID: 9878352 DOI: 10.1006/jmbi.1998.2285] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We describe a method for the genetic analysis of the DNA-binding properties of Xenopus transcription factor IIIA (TFIIIA). In this approach, a transcriptional activator with the DNA-binding specificity of Xenopus TFIIIA is expressed in yeast cells, where it specifically activates expression of a beta-galactosidase reporter gene containing one or more Xenopus 5 S rRNA genes that function as upstream activator sequences. This transcription-promoting activity was used as the basis for a genetic assay of Xenopus TFIIIA's DNA-binding function in yeast, an assay that we show can be calibrated quantitatively to allow the affinity of the Xenopus TFIIIA-5 S rRNA gene interaction to be deduced from measurements of beta-galactosidase activity. We have combined this genetic assay with a simple and efficient method of mutagenesis that makes use of error-prone PCR and homologous recombination to generate and screen large numbers of TFIIIA mutants for those with altered 5 S rRNA gene-binding affinity. Over 30 such mutants have been identified and partially characterized. The mutants we have obtained provide strong support for the application to intact TFIIIA of recent structural models of the N-terminal zinc fingers of the protein bound to fragments of the 5 S rRNA gene. Other mutants permit identification of important residues in more C-terminal zinc fingers of TFIIIA for which high-resolution structural information is not currently available. Finally, our results have interesting implications with respect to the mechanism of activation of transcription by RNA polymerase II in yeast.
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Affiliation(s)
- M J Bumbulis
- Department of Molecular Biology and Microbiology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
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9
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Ogilvie MK, Hanas JS. Molecular biology of vertebrate transcription factor IIIA: cloning and characterization of TFIIIA from channel catfish oocytes. Gene 1997; 203:103-12. [PMID: 9426240 DOI: 10.1016/s0378-1119(97)00499-x] [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: 02/05/2023]
Abstract
TFIIIA regulates 5S rRNA synthesis and is the prototype of the Cys2His2 superfamily of zinc finger proteins. Because the TFIIIA aa sequence is highly diverged, elucidating species variation in this factor will yield insights into how zinc fingers bind DNA and how this protein regulates RNAPIII transcription. This study reports the identification, cloning and functional divergence of oocyte TFIIIA from the channel catfish. Catfish oocyte TFIIIA was identified by its association with 5S rRNA in immature ovarian tissue, its molecular weight, and by peptide sequence similarities with Xenopus TFIIIA. The cDNA for this factor was cloned by degenerate PCR and found to code for nine Cys2His2 zinc fingers and a C-terminal tail; only about 40% aa sequence identity was observed with Xenopus TFIIIA. The N-terminal region of catfish TFIIIA contains the oocyte-specific initiating Met amino acid and accompanying conserved residues found in amphibian TFIIIAs but not found in yeast or human TFIIIAs. Catfish TFIIIA lacks the conserved transcription activation domain in its C-terminal tail found in amphibian and human TFIIIA. Catfish TFIIIA was able to bind the catfish and Xenopus 5S RNA genes but did not efficiently promote 5S gene transcription in a rodent RNAPIII transcription system, as did Xenopus TFIIIA. Amino acid conservation in catfish, amphibian, and human TFIIIA zinc fingers allows deduction of possible finger recognition helix alignments along the conserved 5S gene ICRs. For the three N-terminal fingers, this leads to deduction of a compact polypeptide structure with conserved basic residues contacting conserved G nts in the 5S gene C box.
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Affiliation(s)
- M K Ogilvie
- University of Oklahoma College of Medicine, Department of Biochemistry and Molecular Biology, Oklahoma City 73104, USA
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10
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Wyszko E, Barciszewska M. Purification and characterization of transcription factor IIIA from higher plants. EUROPEAN JOURNAL OF BIOCHEMISTRY 1997; 249:107-12. [PMID: 9363760 DOI: 10.1111/j.1432-1033.1997.t01-2-00107.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Transcription factor IIIA (TF IIIA) binds and specifically activates transcription of eukaryotic 5S rRNA genes. It also forms a 7S ribonucleoprotein complex with mature 5S rRNA. Here, we describe the purification and properties of pTF IIIA from higher plants. The purified protein from tulip (Tulipa whittalii) has a molecular mass of about 40 kDa and also binds 5S rRNA and 5S rRNA genes. pTF IIIA also facilitates the transcription of a 5S rRNA gene in a HeLa cell extract.
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MESH Headings
- DNA, Plant/genetics
- DNA, Plant/metabolism
- DNA, Ribosomal/genetics
- DNA, Ribosomal/metabolism
- DNA-Binding Proteins/isolation & purification
- DNA-Binding Proteins/metabolism
- Genes, Plant
- HeLa Cells
- Humans
- Molecular Weight
- Plant Proteins/isolation & purification
- Plant Proteins/metabolism
- Plants/genetics
- Plants/metabolism
- RNA, Plant/genetics
- RNA, Plant/metabolism
- RNA, Ribosomal, 5S/genetics
- RNA, Ribosomal, 5S/metabolism
- Ribonucleoproteins/metabolism
- Transcription Factor TFIIIA
- Transcription Factors/isolation & purification
- Transcription Factors/metabolism
- Transcription, Genetic
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Affiliation(s)
- E Wyszko
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego, Poznań
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11
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Rowland O, Segall J. Interaction of wild-type and truncated forms of transcription factor IIIA from Saccharomyces cerevisiae with the 5 S RNA gene. J Biol Chem 1996; 271:12103-10. [PMID: 8662611 DOI: 10.1074/jbc.271.20.12103] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Transcription factor (TF) IIIA, which contains nine zinc finger motifs, binds to the internal control region of the 5S RNA gene as the first step in the assembly of a multifactor complex that promotes accurate initiation of transcription by RNA polymerase III. We have monitored the interaction of wild-type and truncated forms of yeast TFIIIA with the 5 S RNA gene. The DNase I footprints obtained with full-length TFIIIA and a polypeptide containing the amino-terminal five zinc fingers (TF5) were indistinguishable, extending from nucleotides +64 to +99 of the 5 S RNA gene. This suggests that fingers 6 through 9 of yeast TFIIIA are not in tight association with DNA. The DNase I footprint obtained with a polypeptide containing the amino-terminal four zinc fingers (TF4) was 14 base pairs shorter than that of TF5, extending from nucleotides +78 to +99 on the nontranscribed strand and from nucleotides +79 to +98 on the transcribed strand of the 5 S RNA gene. Protection provided by a polypeptide containing the first three zinc fingers (TF3) was similar to that provided by TF4, with the exception that protection on the nontranscribed strand ended at nucleotide +80, rather than nucleotide +78. Methylation protection analysis indicated that finger 5 makes major groove contacts with guanines +73 and +74. The amino-terminal four zinc fingers make contacts that span the internal control region, which extends from nucleotides +81 to +94 of the 5 S RNA gene, with finger 4 appearing to contact guanine +82. Measurements of the apparent Kd values of the TFIIIA.DNA complexes indicated that the amino-terminal three zinc fingers of TFIIIA have a binding energy that is similar to that of the full-length protein.
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Affiliation(s)
- O Rowland
- Department of Biochemistry, University of Toronto, Ontario, Canada
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12
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Huet J, Manaud N, Dieci G, Peyroche G, Conesa C, Lefebvre O, Ruet A, Riva M, Sentenac A. RNA polymerase III and class III transcription factors from Saccharomyces cerevisiae. Methods Enzymol 1996; 273:249-67. [PMID: 8791617 DOI: 10.1016/s0076-6879(96)73024-0] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- J Huet
- Service de Biochimie et de Génétique Moléculaire, Commissariat á l'Energie Atomique, Gif sur Yvette, France
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13
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Lefebvre O, Rüth J, Sentenac A. A mutation in the largest subunit of yeast TFIIIC affects tRNA and 5 S RNA synthesis. Identification of two classes of suppressors. J Biol Chem 1994. [DOI: 10.1016/s0021-9258(17)31663-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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14
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Abstract
Xenopus transcription factor, termed TFIIIA, is the first eukaryotic transcription factor purified to homogeneity and one of the most extensively characterized polymerase III gene factors at the levels both of the protein and its gene. It is an abundant protein in oocytes and is specifically required for the 5S RNA gene transcription. It promotes the formation of a stable transcription complex by first binding to the internal control region of the 5S RNA gene through its zinc finger motifs. It contains two structural domains and associates with 5S RNA to form 7S ribonucleoprotein particles in oocytes. Its expression is developmentally controlled at the level of transcription and translation. It participates in the assembly of active chromatin templates and, at least in part, is responsible for the differential expression of two kinds of 5S RNA genes in Xenopus.
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Affiliation(s)
- B S Shastry
- Eye Research Institute, Oakland University, Rochester, Michigan 48309
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15
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Poon D, Knittle R, Sabelko K, Yamamoto T, Horikoshi M, Roeder R, Weil P. Genetic and biochemical analyses of yeast TATA-binding protein mutants. J Biol Chem 1993. [DOI: 10.1016/s0021-9258(18)53495-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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16
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Willis IM. RNA polymerase III. Genes, factors and transcriptional specificity. EUROPEAN JOURNAL OF BIOCHEMISTRY 1993; 212:1-11. [PMID: 8444147 DOI: 10.1111/j.1432-1033.1993.tb17626.x] [Citation(s) in RCA: 188] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Recent studies on RNA polymerase III (pol III) gene transcription have provided a new awareness of the molecular complexity of this process. Fortunately, while the number of transcription components has been increasing, fundamental similarities have emerged regarding the function of eukaryotic promoter elements and the factors that bind them to form preinitiation complexes. Among these, the ability of transcription factor IIIB (TFIIIB) and pol III to transcribe the Saccharomyces cerevisiae U6 gene suggests that the concept of a minimal pol II promoter comprising a TATA box and an initiator region has a parallel in the pol III system. Furthermore, for each of the three classes of eukaryotic RNA polymerase, the assembly of transcription preinitiation complexes and, to some extent, the nature of these complexes appears to be more similar than was previously anticipated. This work highlights the novel functions and transcriptional properties of newly identified pol III genes, discusses the diversity of pol III promoter structures and presents the notion that the exclusive use of extragenic promoters by some pol III genes (so-called type-3 genes) may have evolved since the divergence of yeast and higher eukaryotes. Additionally, recent progress is reviewed on the identification and cloning of subunits for TFIIIC and TFIIIB. Particular emphasis is given to two components of TFIIIB, the TATA-binding protein and a protein with TFIIB homology (PCF4), since the properties of these molecules suggest a model whereby the polymerase specificity of transcription complexes is determined.
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Affiliation(s)
- I M Willis
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461
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17
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Braun BR, Bartholomew B, Kassavetis GA, Geiduschek EP. Topography of transcription factor complexes on the Saccharomyces cerevisiae 5 S RNA gene. J Mol Biol 1992; 228:1063-77. [PMID: 1474578 DOI: 10.1016/0022-2836(92)90315-b] [Citation(s) in RCA: 81] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Locations of component proteins of yeast RNA polymerase III transcription factors (TFIII) A, C and B on a 5 S rRNA gene have been determined by site-specific DNA-protein photo-crosslinking. Comparison with a previously analyzed tRNA gene shows that similar nucleoprotein structures assemble on these two genes despite their differently located internal promoter elements. A principal signature of this homology is the placement of the 95 kDA subunit of TFIIIC, which associates with the box A promoter element of the tRNA gene. On the 5 S rRNA gene, the 95 kDa subunit occupies the same space in the absence of a box A sequence, and despite the presence of a box A-like sequence 30 base-pairs further downstream. A 90 kDa component that was not previously recognized as an integral part of TFIIIC has been specifically located at the 3' end of the 5 S rRNA gene.
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MESH Headings
- Base Sequence
- DNA Probes/radiation effects
- DNA, Ribosomal/genetics
- DNA, Ribosomal/metabolism
- Genes, Fungal/genetics
- Genes, Fungal/radiation effects
- Molecular Sequence Data
- RNA Polymerase III/metabolism
- RNA Polymerase III/radiation effects
- RNA, Ribosomal, 5S/genetics
- RNA, Transfer, Tyr/genetics
- RNA, Transfer, Tyr/radiation effects
- Saccharomyces cerevisiae/genetics
- Transcription Factor TFIIIA
- Transcription Factor TFIIIB
- Transcription Factors/metabolism
- Transcription Factors/radiation effects
- Transcription Factors, TFIII
- Ultraviolet Rays
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Affiliation(s)
- B R Braun
- Department of Biology, University of California, San Diego, La Jolla 92093-0634
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18
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Mazabraud A, Wegnez M, Denis H. Origin of several abundant proteins of amphibian oocytes. J Mol Evol 1992. [DOI: 10.1007/bf00160215] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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19
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Archambault J, Milne C, Schappert K, Baum B, Friesen J, Segall J. The deduced sequence of the transcription factor TFIIIA from Saccharomyces cerevisiae reveals extensive divergence from Xenopus TFIIIA. J Biol Chem 1992. [DOI: 10.1016/s0021-9258(19)50728-1] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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20
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Hanas JS, Gaskins CJ, Smith JF, Ogilvie MK. Structure, function, evolution of transcription factor IIIA. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1992; 43:205-39. [PMID: 1410446 DOI: 10.1016/s0079-6603(08)61048-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- J S Hanas
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City 73190
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21
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Shastry BS, Greenstein D. The assembly of functional preinitiation complexes and transcription of 5S RNA-encoding genes containing point mutations. Gene 1991; 107:269-78. [PMID: 1748297 DOI: 10.1016/0378-1119(91)90327-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The transcription of several Syrian hamster 5S RNA-encoding genes (5S genes) containing single and multiple point mutations in and around the intragenic control region has been analyzed in a HeLa cell-free system. Although most genes with point mutations displayed normal levels of transcription, several exhibited a three- to fivefold reduction in transcription. These mutations interfere with the interaction between the 5S genes and the soluble factors. The above studies help to establish the importance of specific nucleotides within the 5S gene for productive interactions of individual transcription factors in vitro.
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Affiliation(s)
- B S Shastry
- Eye Research Institute of Oakland University, Rochester, MI 48309
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22
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Affiliation(s)
- J L Woolford
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213
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23
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Shastry BS. Xenopus transcription factor IIIA (XTFIIIA): after a decade of research. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 1991; 56:135-44. [PMID: 1947129 DOI: 10.1016/0079-6107(91)90017-m] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Xenopus transcription factor IIIA (XTFIIIA) is the first eukaryotic transcription factor purified to homogeneity and is specifically required for the 5S RNA gene transcription. It contains two structural domains and nine zinc finger motifs through which it recognizes the promoter region of the 5S RNA gene. It also binds to 5S RNA and serves to store 5S RNA in the form of 7S ribonucleoprotein particles in oocytes. Additionally, it forms a metastable complex with 5S DNA and promotes the formation of stable and competent transcription complexes. Its expression is developmentally controlled at the level of transcription and translation. Moreover, it participates in the assembly of active chromatin templates and at least, in part, is responsible for the developmental regulation of two kinds of 5S RNA genes in Xenopus.
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Affiliation(s)
- B S Shastry
- Eye Research Institute of Oakland University, Rochester, MI 48309
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Waldschmidt R, Jahn D, Teichmann M, Jahn M, Meissner W, Seifart KH. Physical and immunological characterization of human transcription factor IIIA. EUROPEAN JOURNAL OF BIOCHEMISTRY 1990; 194:167-76. [PMID: 2253613 DOI: 10.1111/j.1432-1033.1990.tb19441.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Human transcription factor IIIA (htFIIIA), specifically required for transcription of the gene for 5S ribosomal RNA has been characterized with respect to some of its physical, immunological and functional properties. TFIIIA from HeLa cells, which selectively binds 5S RNA, is a monomer of approximately 35 kDa with a Stokes' radius of approximately 2.65 nm and a sedimentation coefficient of approximately 2.8 S. These values indicate that the human protein is of rather globular shape and hence diverges not only in molecular mass but also in most of the molecular properties from its highly asymmetric counterpart in Xenopus laevis oocytes. By raising specific polyclonal antibodies against hTFIIIA it was shown in Western immunoblots that there was no cross-reaction between anti-hTFIIIA antibodies and the amphibian protein. Conversely, monoclonal antibodies against three domains of X. laevis TFIIIA antibodies and the amphibian protein. Conversely, monoclonal antibodies against three domains of X. laevis TFIIIA did not cross-react with the human transcription factor. The polyclonal antisera raised against hTFIIIA specifically neutralized binding of the human transcription factor to 5S DNA and abolished in vitro transcription of 5S RNA but these antibodies were unable to inhibit 5S RNA synthesis in cellular extracts from Xenopus, Drosophila or yeast cells. Finally, the species variation of TFIIIA could be substantiated by electrophoretic mobility shift assays revealing preferential binding of hTFIIIA to the homologous 5S RNA gene.
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Affiliation(s)
- R Waldschmidt
- Institut für Molekularbiologie und Tumorforschung, Marburg/Lahnberge, Federal Republic of Germany
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26
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Zhang ZG, Shastry BS. Specific interaction of a partially purified Xenopus transcription factor IIIC (TFIIIC) with frog tRNA gene. Biochem Biophys Res Commun 1990; 172:692-7. [PMID: 2241962 DOI: 10.1016/0006-291x(90)90729-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Transcription factor IIIC (TFIIIC) from Xenopus has been partially purified and characterized. Footprinting analyses indicate that a partially purified TFIIIC fraction contains an activity which specifically recognizes the "B" block element of tRNA gene. In addition, two other regions located downstream from the "B" block sequence are also protected. Protection experiments on 5S genes by DNAase I with either TFIIIC alone or TFIIIA and TFIIIC produced a minimal change in the cleavage pattern implying that TFIIIC does not intimately associate with DNA. The implications of these findings in relation to the class III gene transcription are discussed.
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Affiliation(s)
- Z G Zhang
- Eye Research Institute of Oakland University, Rochester, Michigan 48309
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27
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Purification and characterization of Saccharomyces cerevisiae transcription factor TFIIIC. Polypeptide composition defined with polyclonal antibodies. J Biol Chem 1990. [DOI: 10.1016/s0021-9258(19)34089-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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28
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Kassavetis GA, Braun BR, Nguyen LH, Geiduschek EP. S. cerevisiae TFIIIB is the transcription initiation factor proper of RNA polymerase III, while TFIIIA and TFIIIC are assembly factors. Cell 1990; 60:235-45. [PMID: 2404611 DOI: 10.1016/0092-8674(90)90739-2] [Citation(s) in RCA: 428] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The S. cerevisiae RNA polymerase III (pol III) transcription factor TFIIIB binds to DNA upstream of the transcription start site of the SUP4 tRNA(Tyr) gene in a TFIIIC-dependent reaction and to the major 5S rRNA gene in a reaction requiring TFIIIC and TFIIIA. It is shown here that TFIIIB alone correctly positions pol III for repeated cycles of transcription on both genes, with the same efficiency as fully assembled transcription complexes. Thus, TFIIIB is the sole transcription initiation factor of S. cerevisiae pol III; TFIIIC and TFIIIA are assembly factors for TFIIIB. The TFIIIB-dependent binding of pol III to the SUP4 tRNA and 5S rRNA genes has been analyzed in binary (protein and DNA only) and precisely arrested ternary (protein, DNA, and RNA) transcription complexes. Pol III unwinds at least 14 bp of DNA at the SUP4 transcription start in a temperature-dependent process. The unwound DNA segment moves downstream with nascent RNA as a transcription bubble of approximately the same size.
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Affiliation(s)
- G A Kassavetis
- Department of Biology, University of California, San Diego, La Jolla 92093
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29
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Transcription of the 5 S rRNA gene of Saccharomyces cerevisiae requires a promoter element at +1 and a 14-base pair internal control region. J Biol Chem 1989. [DOI: 10.1016/s0021-9258(19)47218-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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