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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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2
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Acker J, Conesa C, Lefebvre O. Yeast RNA polymerase III transcription factors and effectors. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2012; 1829:283-95. [PMID: 23063749 DOI: 10.1016/j.bbagrm.2012.10.002] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Revised: 09/27/2012] [Accepted: 10/03/2012] [Indexed: 12/19/2022]
Abstract
Recent data indicate that the well-defined transcription machinery of RNA polymerase III (Pol III) is probably more complex than commonly thought. In this review, we describe the yeast basal transcription factors of Pol III and their involvements in the transcription cycle. We also present a list of proteins detected on genes transcribed by Pol III (class III genes) that might participate in the transcription process. Surprisingly, several of these proteins are involved in RNA polymerase II transcription. Defining the role of these potential new effectors in Pol III transcription in vivo will be the challenge of the next few years. This article is part of a Special Issue entitled: Transcription by Odd Pols.
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Affiliation(s)
- Joël Acker
- CEA, iBiTecS, Gif Sur Yvette, F-91191, France
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3
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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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Abstract
Transcriptional transactivators are important proteins which in addition to controlling the cell regulatory circuitries, can be manipulated for various biotechnological processes. The latter is of great interest for non-conventional yeasts used for industrial purposes. To facilitate the identification of these transactivators, we have reanalyzed the "Génolevures" data (FEBS Lett. 487 (2000); http://cbi.labri.u-bordeaux.fr/Genolevures/) for the presence of zinc finger (Zf) proteins. After analysis of 239 RST ("random sequence tag") sequences, we describe in this paper 161 homologs of the Saccharomyces cerevisiae Zf proteins present in one or several of 13 different hemiascomyceteous yeasts. These partial sequences have been evaluated on different criteria such as percentage of identity of the proteins, synteny, detailed analysis of the Zf motif and flanking regions, and iterative BLASTs. They can be used to fetch the corresponding gene.
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Affiliation(s)
- Francoise Bussereau
- Institut de Génétique et Microbiologie (CNRS UMR 8621), Bâtiment 400, Université Paris-Sud, 91405 Orsay Cedex, France
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5
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Schulman DB, Setzer DR. Functional analysis of the novel C-terminal domains of S pombe transcription factor IIIA. J Mol Biol 2003; 331:321-30. [PMID: 12888341 DOI: 10.1016/s0022-2836(03)00730-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Transcription factor IIIA from S.pombe exhibits a novel structural organization compared to its homologues in other species. TFIIIA from S.cerevisiae or vertebrates contains a total of nine C(2)H(2) zinc-finger domains and a non-zinc finger region at its C terminus. In addition, the S.cerevisiae protein possesses an 81-amino acid spacer between zinc fingers eight and nine. In contrast, the S.pombe TFIIIA sequence includes ten potential zinc finger motifs, with a 53-amino acid spacer between fingers nine and ten. Zinc finger nine of the S.pombe protein deviates from the consensus for a C(2)H(2) zinc finger, however, in that it does not include an appropriately positioned second Zn(2+)-coordinating histidine. We demonstrate here, through analysis of mutated forms of the protein, that the non-canonical ninth zinc finger is functional in both DNA binding and transcription. In addition, we have shown that the spacer preceding finger ten and finger ten itself are essential for the transcriptional function of S.pombe TFIIIA, but neither is required for wild-type 5S rRNA gene-binding activity.
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Affiliation(s)
- Deborah B Schulman
- Department of Molecular Biology and Microbiology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
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6
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Hanas JS, Hocker JR, Cheng YG, Lerner MR, Brackett DJ, Lightfoot SA, Hanas RJ, Madhusudhan KT, Moreland RJ. cDNA cloning, DNA binding, and evolution of mammalian transcription factor IIIA. Gene 2002; 282:43-52. [PMID: 11814676 DOI: 10.1016/s0378-1119(01)00796-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
cDNA for rat transcription factor IIIA (TFIIIA) was cloned by degenerate PCR and rapid amplification of cDNA ends. This cDNA coded for a protein with nine Cys(2)His(2) zinc fingers and a non-finger C-terminal tail; 63% amino acid (aa) sequence identity was observed with the Xenopus TFIIIA zinc finger region. Recombinant rat protein containing only the nine fingers afforded DNase I protection of the identical nucleotides protected by Xenopus laevis native TFIIIA on the Xenopus 5S RNA gene internal control region. A putative mouse TFIIIA clone was identified in an expressed sequence tag database by sequence similarity to rat TFIIIA. Recombinant nine-finger protein from this clone afforded DNase I protection of the Xenopus 5S rRNA gene like the native frog protein as did a recombinant nine-finger form of a putative human TFIIIA clone. These DNA binding results demonstrate that these clones code for the respective mammalian TFIIIAs. Rodent and human TFIIIAs share about 87% aa sequence identity in their zinc finger regions and have evolved to about the same extent as X. laevis and Xenopus borealis TFIIIAs. A monoclonal antibody against human p53 tumor suppressor bound to rat and mouse TFIIIA but not to human TFIIIA in Western blots. The N-terminal regions of rodent and human TFIIIA do not contain the oocyte-specific initiating Met and accompanying conserved residues found in fish and amphibian TFIIIAs. In their non-finger C-terminal tails, mammalian and amphibian TFIIIAs share a conserved transcription activation domain as well as conserved nuclear localization and nuclear export signals.
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Affiliation(s)
- Jay S Hanas
- Department of Biochemistry and Molecular Biology, University of Oklahoma College of Medicine, Oklahoma City, OK 73104, USA.
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7
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Tsuji G, Kenmochi Y, Takano Y, Sweigard J, Farrall L, Furusawa I, Horino O, Kubo Y. Novel fungal transcriptional activators, Cmr1p of Colletotrichum lagenarium and pig1p of Magnaporthe grisea, contain Cys2His2 zinc finger and Zn(II)2Cys6 binuclear cluster DNA-binding motifs and regulate transcription of melanin biosynthesis genes in a developmentally specific manner. Mol Microbiol 2000; 38:940-54. [PMID: 11123670 DOI: 10.1046/j.1365-2958.2000.02181.x] [Citation(s) in RCA: 123] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Colletotrichum lagenarium and Magnaporthe grisea are plant pathogenic fungi that produce melanin during the appressorial differentiation stage of conidial germination and during the late stationary phase of mycelial growth. Here, we report the identification of genes for two unique transcription factors, CMR1 (Colletotrichum melanin regulation) and PIG1 (pigment of Magnaporthe), that are involved in melanin biosynthesis. Both Cmr1p and Pig1p contain two distinct DNA-binding motifs, a Cys2His2 zinc finger motif and a Zn(II)2Cys6 binuclear cluster motif. The presence of both these motifs in a single transcriptional regulatory protein is unique among known eukaryotic transcription factors. Deletion of CMR1 in C. lagenarium caused a defect in mycelial melanization, but not in appressorial melanization. Also, cmr1Delta mutants do not express the melanin biosynthetic structural genes SCD1 and THR1 during mycelial melanization, although the expression of these two genes was not affected during appressorial melanization.
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Affiliation(s)
- G Tsuji
- Laboratory of Plant Pathology, Faculty of Agriculture, Kyoto Prefectural University, Kyoto 606-8522, Japan
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8
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Moreland RJ, Dresser ME, Rodgers JS, Roe BA, Conaway JW, Conaway RC, Hanas JS. Identification of a transcription factor IIIA-interacting protein. Nucleic Acids Res 2000; 28:1986-93. [PMID: 10756201 PMCID: PMC103300 DOI: 10.1093/nar/28.9.1986] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Transcription factor IIIA (TFIIIA) activates 5S ribosomal RNA gene transcription in eukaryotes. The protein from vertebrates has nine contiguous Cys(2)His(2)zinc fingers which function in nucleic acid binding, and a C-terminal region involved in transcription activation. In order to identify protein partners for TFIIIA, yeast two-hybrid screens were performed using the C-terminal region of Xenopus TFIIIA as an attractor and a rat cDNA library as a source of potential partners. A cDNA clone was identified which produced a protein in yeast that interacted with Xenopus TFIIIA but not with yeast TFIIIA. This rat clone was sequenced and the primary structure of the human homolog (termed TFIIIA-intP for TFIIIA-interacting protein) was determined from expressed sequence tags. In vitro interaction of recombinant human TFIIIA-intP with recombinant Xenopus TFIIIA was demonstrated by immuno-precipitation of the complex using anti-TFIIIA-intP antibody. Interaction of rat TFIIIA with rat TFIIIA-intP was indicated by co-chromatography of the two proteins on DEAE-5PW following fractionation of a rat liver extract on cation, anion and gel filtration resins. In a HeLa cell nuclear extract, recombinant TFIIIA-intP was able to stimulate TFIIIA-dependent transcription of the Xenopus 5S ribosomal RNA gene but not TFIIIA-independent transcription of the human adenovirus VA RNA gene.
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Affiliation(s)
- R J Moreland
- Department of Biochemistry and Molecular Biology, University of Oklahoma College of Medicine, Oklahoma City, OK 73104, USA
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9
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Chédin S, Ferri ML, Peyroche G, Andrau JC, Jourdain S, Lefebvre O, Werner M, Carles C, Sentenac A. The yeast RNA polymerase III transcription machinery: a paradigm for eukaryotic gene activation. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 1999; 63:381-9. [PMID: 10384303 DOI: 10.1101/sqb.1998.63.381] [Citation(s) in RCA: 65] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- S Chédin
- Service de Biochimie et Génétique Moléculaire, CEA/Saclay, Gif-sur-Yvette, France
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10
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Dechampesme AM, Koroleva O, Leger-Silvestre I, Gas N, Camier S. Assembly of 5S ribosomal RNA is required at a specific step of the pre-rRNA processing pathway. J Cell Biol 1999; 145:1369-80. [PMID: 10385518 PMCID: PMC2133170 DOI: 10.1083/jcb.145.7.1369] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
A collection of yeast strains surviving with mutant 5S RNA has been constructed. The mutant strains presented alterations of the nucleolar structure, with less granular component, and a delocalization of the 25S rRNA throughout the nucleoplasm. The 5S RNA mutations affected helix I and resulted in decreased amounts of stable 5S RNA and of the ribosomal 60S subunits. The shortage of 60S subunits was due to a specific defect in the processing of the 27SB precursor RNA that gives rise to the mature 25S and 5.8S rRNA. The processing rate of the 27SB pre-rRNA was specifically delayed, whereas the 27SA and 20S pre-rRNA were processed at a normal rate. The defect was partially corrected by increasing the amount of mutant 5S RNA. We propose that the 5S RNA is recruited by the pre-60S particle and that its recruitment is necessary for the efficient processing of the 27SB RNA precursor. Such a mechanism could ensure that all newly formed mature 60S subunits contain stoichiometric amounts of the three rRNA components.
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MESH Headings
- Cell Nucleolus/genetics
- Cell Nucleolus/metabolism
- Cell Nucleus/genetics
- Cell Nucleus/metabolism
- Cytoplasm/genetics
- Cytoplasm/metabolism
- Fungal Proteins/genetics
- Fungal Proteins/metabolism
- Gene Expression
- Genes, Fungal
- Kinetics
- Molecular Weight
- Mutation
- Nucleic Acid Conformation
- RNA Precursors/chemistry
- RNA Precursors/genetics
- RNA Precursors/metabolism
- RNA Processing, Post-Transcriptional/genetics
- RNA, Fungal/chemistry
- RNA, Fungal/genetics
- RNA, Fungal/metabolism
- RNA, Ribosomal/chemistry
- RNA, Ribosomal/genetics
- RNA, Ribosomal/metabolism
- RNA, Ribosomal, 5S/chemistry
- RNA, Ribosomal, 5S/genetics
- RNA, Ribosomal, 5S/metabolism
- RNA-Binding Proteins/genetics
- RNA-Binding Proteins/metabolism
- Ribosomal Proteins/genetics
- Ribosomal Proteins/metabolism
- Ribosomes/chemistry
- Ribosomes/genetics
- Ribosomes/metabolism
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae/growth & development
- Saccharomyces cerevisiae/metabolism
- Saccharomyces cerevisiae Proteins
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Affiliation(s)
- A M Dechampesme
- Service de Biochimie et de Génétique Moléculaire, Commissariat á L'Energie Atomique (CEA)/Saclay, F-91191 Gif-sur-Yvette Cedex, France
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11
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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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12
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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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13
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Nouraini S, Hu J, McBroom LDB, Friesen JD. Mutations in an Abf1p binding site in the promoter of yeast RPO26 shift the transcription start sites and reduce the level of RPO26 mRNA. Yeast 1998. [DOI: 10.1002/(sici)1097-0061(199610)12:13<1339::aid-yea31>3.0.co;2-c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
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Hanas JS, Koelsch G, Moreland R, Wickham JQ. Differential requirements for basic amino acids in transcription factor IIIA-5S gene interaction. BIOCHIMICA ET BIOPHYSICA ACTA 1998; 1398:256-64. [PMID: 9655916 DOI: 10.1016/s0167-4781(98)00070-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Basic amino acids Arg, Lys, and His in the Cys2His2 zinc fingers of transcription factor IIIA (TFIIIA) potentially have important roles in factor binding to the extended internal control region (ICR) of the 5S ribosomal gene. Conserved and non-conserved basic residues in the N-terminal fingers I, II, III and the more C-terminal fingers V and IX were analyzed by site-directed mutagenesis and DNase I protection in order to assess their individual requirement in the DNA-binding mechanism. In the DNA recognition helix of finger II, the conserved Arg at position 62 (N-terminal side of the first zinc-coordinating histidine) was changed to a Leu or Gln. Both the R62L and R62Q mutations inhibited Xenopus TFIIIA-dependent DNase I footprinting along the entire 5S gene ICR. When His-58 (non-conserved basic residue with DNA-binding potential in the same helical region) was changed to a Gln, the mutated protein was able to protect the ICR from DNase I digestion. Therefore, Arg-62 is individually required for TFIIIA binding over the entire ICR whereas His-58 is not. Fingers V and IX have conserved Arg residues in positions identical to Arg-62 in finger II (Arg-154 in finger V and Arg-271 in finger IX). When these residues were changed to Leu and Ile respectively, TFIIIA-dependent DNase I protection was observed along the entire 5S gene ICR. These results indicate differing DNA-binding mechanisms by the N-terminal fingers versus the C-terminal fingers at the level of individual amino acid-nucleotide interactions. In the N-terminal finger I, the conserved Lys at position 11 outside the recognition helix and a conserved hydrophobic Trp at position 28 within the helix were changed to an Ala and Ser respectively. The K11A change inhibited TFIIIA-dependent DNase I protection to a much greater extent than the W28S change.
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Affiliation(s)
- J S Hanas
- Department of Biochemistry and Molecular Biology, University of Oklahoma College of Medicine, 940 Stanton Young Blvd., Oklahoma City, OK 73140, USA.
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15
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Nolte RT, Conlin RM, Harrison SC, Brown RS. Differing roles for zinc fingers in DNA recognition: structure of a six-finger transcription factor IIIA complex. Proc Natl Acad Sci U S A 1998; 95:2938-43. [PMID: 9501194 PMCID: PMC19673 DOI: 10.1073/pnas.95.6.2938] [Citation(s) in RCA: 191] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The crystal structure of the six NH2-terminal zinc fingers of Xenopus laevis transcription factor IIIA (TFIIIA) bound with 31 bp of the 5S rRNA gene promoter has been determined at 3.1 A resolution. Individual zinc fingers are positioned differently in the major groove and across the minor groove of DNA to span the entire length of the duplex. These results show how TFIIIA can recognize several separated DNA sequences by using fewer fingers than necessary for continuous winding in the major groove.
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Affiliation(s)
- R T Nolte
- Harvard Medical School, Boston, MA 02115, USA
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16
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Rowland O, Segall J. A hydrophobic segment within the 81-amino-acid domain of TFIIIA from Saccharomyces cerevisiae is essential for its transcription factor activity. Mol Cell Biol 1998; 18:420-32. [PMID: 9418889 PMCID: PMC115877 DOI: 10.1128/mcb.18.1.420] [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] [Received: 08/27/1997] [Accepted: 10/28/1997] [Indexed: 02/05/2023] Open
Abstract
Transcription factor IIIA (TFIIIA) binds to the internal control region of the 5S RNA gene as the first step in the in vitro assembly of a TFIIIB-TFIIIC-TFIIIA-DNA transcription complex. An 81-amino-acid domain that is present between zinc fingers 8 and 9 of TFIIIA from Saccharomyces cerevisiae is essential for the transcription factor activity of this protein (C. A. Milne and J. Segall, J. Biol. Chem. 268:11364-11371, 1993). We have monitored the effect of mutations within this domain on the ability of TFIIIA to support transcription of the 5S RNA gene in vitro and to maintain cell viability. TFIIIA with internal deletions that removed residues 282 to 315, 316 to 334, 328 to 341, or 342 to 351 of the 81-amino-acid domain retained activity, whereas TFIIIA with a deletion of the short leucine-rich segment 352NGLNLLLN359 at the carboxyl-terminal end of this domain was devoid of activity. Analysis of the effects of double and quadruple mutations in the region extending from residue 336 to 364 confirmed that hydrophobic residues in this portion of the 81-amino-acid domain, particularly L343, L347, L354, L356, L357, and L358, and to a lesser extent F336 and L337, contributed to the ability of TFIIIA to promote transcription. We propose that these hydrophobic residues play a role in mediating an interaction between TFIIIA and another component of the transcriptional machinery. We also found that TFIIIA remained active if either zinc finger 8 or zinc finger 9 was disrupted by mutation but that TFIIIA containing a disruption of both zinc finger 8 and zinc finger 9 was inactive.
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Affiliation(s)
- O Rowland
- Department of Biochemistry, University of Toronto, Ontario, Canada
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17
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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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18
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Kehres DG, Subramanyan GS, Hung VS, Rogers GW, Setzer DR. Energetically unfavorable interactions among the zinc fingers of transcription factor IIIA when bound to the 5 S rRNA gene. J Biol Chem 1997; 272:20152-61. [PMID: 9242690 DOI: 10.1074/jbc.272.32.20152] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Xenopus transcription factor IIIA (TFIIIA) binds to over 50 base pairs in the internal control region of the 5 S rRNA gene, yet the binding energy for this interaction (DeltaG0 = -12.8 kcal/mol) is no greater than that exhibited by many proteins that occupy much smaller DNA targets. Despite considerable study, the distribution of the DNA binding energy among the various zinc fingers of TFIIIA remains poorly understood. By analyzing TFIIIA mutants with disruptions of individual zinc fingers, we have previously shown that each finger contributes favorably to binding (Del Rio, S., Menezes, S. R., and Setzer, D. R. (1993) J. Mol. Biol. 233, 567-579). Those results also suggested, however, that simultaneous binding by all nine zinc fingers of TFIIIA may involve a substantial energetic cost. Using complementary N- and C-terminal fragments and full-length proteins containing pairs of disrupted fingers, we now show that energetic interference indeed occurs between zinc fingers when TFIIIA binds to the 5 S rRNA gene and that the greatest interference occurs between fingers at opposite ends of the protein in the TFIIIA.5 S rRNA gene complex. Some, but not all, of the thermodynamically unfavorable strain in the TFIIIA.5 S rRNA gene complex may be derived from bending of the DNA that is necessary to accommodate simultaneous binding by all nine zinc fingers of TFIIIA. The energetics of DNA binding by TFIIIA thus emerges as a compromise between individual favorable contacts of importance along the length of the internal control region and long range strain or distortion in the protein, the 5 S rRNA gene, or both that is necessary to accommodate the various local interactions.
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Affiliation(s)
- D G Kehres
- Department of Molecular Biology and Microbiology, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106, USA
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19
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Oettel S, Härtel F, Kober I, Iben S, Seifart KH. Human transcription factors IIIC2 , IIIC1 and a novel component IIIC0 fulfil different aspects of DNA binding to various pol III genes. Nucleic Acids Res 1997; 25:2440-7. [PMID: 9171097 PMCID: PMC146769 DOI: 10.1093/nar/25.12.2440] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Human transcription factor IIIC2 interacts with the TFIIIA-5S DNA complex and forms a ternary TFIIIA/IIIC2-5S DNA complex. Formation of this complex does not preclude simultaneous binding of TFIIIC2to the B-box sequence of a second template. This suggests that the domain(s) or subunit(s) required for indirect recognition of the 5S promoter by TFIIIC2 are different from those necessary for direct binding of TFIIIC2 to B-box-containing pol III promoters. Whereas TFIIIC2 is only required for transcription of the 'classical' pol III genes, TFIIIC1 is generally required for transcription of all pol III genes, including that of the U6 gene. The activity of TFIIIC1 strongly enhances specific binding of basal pol III factors TFIIIA, TFIIIC2 and the PSE binding protein (PBP) to their cognate promoter elements and it acts independently of the corresponding termination regions. Moreover, we characterize an activity, TFIIIC0, purified from phosphocellulose fraction C, which shows strong DNase I protection of the termination region of several pol III genes and which is functionally and chromatographically distinct from TFIIIC1 and TFIIIC2.
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MESH Headings
- Animals
- Binding, Competitive
- Cell Line
- Cell Nucleus/metabolism
- Chromatography, Ion Exchange
- Cytoplasm/metabolism
- DNA Footprinting
- DNA Polymerase III/biosynthesis
- DNA Polymerase III/genetics
- DNA, Ribosomal/metabolism
- Deoxyribonuclease I
- Genes, Synthetic
- Humans
- Mice
- Promoter Regions, Genetic
- RNA, Ribosomal, 5S/biosynthesis
- RNA, Ribosomal, 5S/genetics
- Templates, Genetic
- Terminator Regions, Genetic
- Transcription Factor TFIIA
- Transcription Factors/isolation & purification
- Transcription Factors/metabolism
- Transcription Factors, TFIII
- Transcription, Genetic
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Affiliation(s)
- S Oettel
- Institut für Molekularbiologie und Tumorforschung, Philipps Universität Marburg, Lahnstrasse 3, D-35037 Marburg, Germany
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20
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Nouraini S, Hu J, McBroom LD, Friesen JD. Mutations in an Abf1p binding site in the promoter of yeast RPO26 shift the transcription start sites and reduce the level of RPO26 mRNA. Yeast 1996; 12:1339-50. [PMID: 8923739 DOI: 10.1002/(sici)1097-0061(199610)12:13%3c1339::aid-yea31%3e3.0.co;2-c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
A binding site for the transcription factor Abf1p was identified as an important promoter element of the gene that encodes Rpo26, a subunit common to all three yeast nuclear RNA polymerases (RNAP). Mutations in the Abf1p binding site were identified among a pool of rpo26 mutant alleles that confer synthetic lethality in combination with a temperature-sensitive mutation (rpo21-4) in the gene that encodes the largest subunit of RNAPII (Rpo21p). In the presence of the wild-type allele of RPO21 these rpo26 promoter mutations confer a cold-sensitive growth defect. Electrophoretic mobility-shift assays using purified Abf1p demonstrated that Abf1p binds to the RPO26 promoter and that the promoter mutations abolish this binding in vitro. Quantitation of the amount of RPO26 mRNA showed that mutations in the Abf1p binding site reduce the expression of RPO26 by approximately 60%. Mutations that affect Abf1p binding also result in a shift of the RPO26 transcriptional start sites to positions further upstream than normal. These results suggest that binding of the Abf1p transcription factor to the RPO26 promoter is important not only in establishing the level of transcription for this gene, but also in positioning the initiation sites of transcription.
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Affiliation(s)
- S Nouraini
- Department of Genetics, Hospital for Sick Children, Toronto, Canada
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21
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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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22
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Abstract
Transcription factor IIIA is a very extensively studied eukaryotic gene specific factor. It is a special member of the zinc finger family of nucleic acid binding proteins with multiple functions. Its N-terminal polypeptide (280 amino acid residue containing peptide; finger containing region) carries out sequence specific DNA and RNA binding and the C-terminal peptide (65 amino acid residue containing peptide; non-finger region) is involved in the transactivation process possibly by interacting with other general factors. It is a unique factor in the sense that it binds to two structurally different nucleic acids, DNA and RNA. It accomplishes this function through its zinc fingers, which are arranged into a cluster of nine motifs. Over the past three years there has been considerable interest in determining the structural features of zinc fingers, identifying the fingers that preferentially recognize DNA and RNA, defining the role of metal binding ligands and the linker region in promotor recognition and the role of C-terminal amino acid sequence in the gene activation. This article briefly reviews our current knowledge on this special protein in these areas.
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Affiliation(s)
- B S Shastry
- Eye Research Institute, Oakland University, Rochester, MI 48309-4401, USA
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23
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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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24
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Johnson ES, Ma PC, Ota IM, Varshavsky A. A proteolytic pathway that recognizes ubiquitin as a degradation signal. J Biol Chem 1995; 270:17442-56. [PMID: 7615550 DOI: 10.1074/jbc.270.29.17442] [Citation(s) in RCA: 640] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Previous work has shown that a fusion protein bearing a "nonremovable" N-terminal ubiquitin (Ub) moiety is short-lived in vivo, the fusion's Ub functioning as a degradation signal. The proteolytic system involved, termed the UFD pathway (Ub fusion degradation), was dissected in the yeast Saccharomyces cerevisiae by analyzing mutations that perturb the pathway. Two of the five genes thus identified, UFD1 and UFD5, function at post-ubiquitination steps in the UFD pathway. UFD3 plays a role in controlling the concentration of Ub in a cell: ufd3 mutants have greatly reduced levels of free Ub, and the degradation of Ub fusions in these mutants can be restored by overexpressing Ub. UFD2 and UFD4 appear to influence the formation and topology of a multi-Ub chain linked to the fusion's Ub moiety. UFD1, UFD2, and UFD4 encode previously undescribed proteins of 40, 110, and 170 kDa, respectively. The sequence of the last approximately 280 residues of Ufd4p is similar to that of E6AP, a human protein that binds to both the E6 protein of oncogenic papilloma viruses and the tumor suppressor protein p53, whose Ub-dependent degradation involves E6AP. UFD5 is identical to the previously identified SON1, isolated as an extragenic suppressor of sec63 alleles that impair the transport of proteins into the nucleus. UFD5 is essential for activity of both the UFD and N-end rule pathways (the latter system degrades proteins that bear certain N-terminal residues). We also show that a Lys --> Arg conversion at either position 29 or position 48 in the fusion's Ub moiety greatly reduces ubiquitination and degradation of Ub fusions to beta-galactosidase. By contrast, the ubiquitination and degradation of Ub fusions to dihydrofolate reductase are inhibited by the UbR29 but not by the UbR48 moiety. ufd4 mutants are unable to ubiquitinate the fusion's Ub moiety at Lys29, whereas ufd2 mutants are impaired in the ubiquitination at Lys48. These and related findings suggest that Ub-Ub isopeptide bonds in substrate-linked multi-Ub chains involve not only the previously identified Lys48 but also Lys29 of Ub, and that structurally different multi-Ub chains have distinct functions in Ub-dependent protein degradation.
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Affiliation(s)
- E S Johnson
- Division of Biology, California Institute of Technology, Pasadena 91125, USA
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25
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Drew PD, Nagle JW, Canning RD, Ozato K, Biddison WE, Becker KG. Cloning and expression analysis of a human cDNA homologous to Xenopus TFIIIA. Gene 1995; 159:215-8. [PMID: 7622052 DOI: 10.1016/0378-1119(95)00145-v] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
We report here the nucleotide sequence of a clone, C2H2-34.10, isolated from a human brain cDNA library using degenerate oligodeoxyribonucleotide hybridization. C2H2-34.10 has extensive homology to the Xenopus laevis 5S DNA/RNA-binding protein, TFIIIA. The deduced amino acid (aa) sequence of the human clone gives a protein of 363 aa with identity to TFIIIA from both X. laevis (57%) and Rana pipiens (59%). This human clone contains nine C2H2-type zinc fingers like frog TFIIIA. Northern blot analysis indicates that the C2H2-34.10 RNA is expressed in human ovary, as well as human neuronal cell lines.
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Affiliation(s)
- P D Drew
- Neuroimmunology Branch-Molecular Immunology Section, National Institute of Neurological Diseases and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
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26
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Proctor RH, Hohn TM, McCormick SP, Desjardins AE. Tri6 encodes an unusual zinc finger protein involved in regulation of trichothecene biosynthesis in Fusarium sporotrichioides. Appl Environ Microbiol 1995; 61:1923-30. [PMID: 7646028 PMCID: PMC167455 DOI: 10.1128/aem.61.5.1923-1930.1995] [Citation(s) in RCA: 168] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
In Fusarium sporotrichioides, several genes required for biosynthesis of the trichothecene mycotoxin T-2 toxin are closely linked. Further characterization of this gene cluster has revealed a gene, Tri6, that specifies a 217-amino-acid protein with regions similar to Cys2His2 zinc finger proteins. Temporal expression of Tri6 is similar to that of trichothecene biosynthetic pathway genes. Analysis of Tri6 transcripts indicated that transcription is initiated in two regions and that within each region there may be at least four initiation sites. Disruption of Tri6 resulted in a mutant that did not produce trichothecenes but that did accumulate low levels of the trichothecene precursor trichodiene. The Tri6 mutant was unable to convert six trichothecene biosynthetic intermediates to T-2 toxin, and transcription of two biosynthetic genes, Tri4 and Tri5, was greatly reduced in the mutant relative to the wild type. In addition, the product of Tri6 functioned as a transcriptional activator in Saccharomyces cerevisiae when fused to the DNA binding region of GAL4. These results indicate that Tri6 encodes a protein involved in the transcriptional regulation of trichothecene biosynthetic genes in F. sporotrichioides.
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Affiliation(s)
- R H Proctor
- Mycotoxin Research Unit, National Center for Agricultural Utilization Research, USDA Agricultural Research Service, Peoria, Illinois 61604-3902, USA
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27
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Shpakovski GV. The fission yeast Schizosaccharomyces pombe rpb6 gene encodes the common phosphorylated subunit of RNA polymerase and complements a mutation in the corresponding gene of Saccharomyces cerevisiae. Gene X 1994; 147:63-9. [PMID: 8088549 DOI: 10.1016/0378-1119(94)90039-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
A single-copy gene, homologous to the RPB6 gene from Saccharomyces cerevisiae, encoding a small phosphorylated subunit common to all three forms of nuclear DNA-dependent RNA polymerase was isolated from the fission yeast Schizosaccharomyces pombe. Its cDNA copy consists of an open reading frame of 142 codons and encodes an acidic protein (predicted pI 4.1) with a M(r) of 15,730. The genomic copy of Sz. pombe rpb6 contains an intron (219 nucleotides) located at codon 92, a position which does not correspond to the single intron of the S. cerevisiae gene. The sequencing of both genomic and cDNA copies of rpb6 allowed us to determine the probable positions of the start and stop of rpb6 transcription and to identify a putative TATA box. The primary structures of the Sz. pombe and S. cerevisiae Rpb6 proteins have 60.7% identity, with the same general organization: a highly acidic N-terminal region followed by a short basic region and a C terminus featuring a putative heptad Leu repeat. The C-terminal half of the sequence is particularly well conserved and, therefore, probably contains the most important functional domain. Moreover, a heterospecific complementation test showed that rpb6 from Sz. pombe fully complements a complete deletion of its S. cerevisiae homologue.
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Affiliation(s)
- G V Shpakovski
- Laboratory of Molecular Biology, National Institute of Mental Health, Bethesda, MD 20892
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28
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Wolffe AP. The role of transcription factors, chromatin structure and DNA replication in 5 S RNA gene regulation. J Cell Sci 1994; 107 ( Pt 8):2055-63. [PMID: 7983167 DOI: 10.1242/jcs.107.8.2055] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Differential expression of the oocyte and somatic 5 S RNA genes during Xenopus development can be explained by changes in transcription factor and histone interactions with the two types of gene. Both factors and histones bind 5 S RNA genes with specificity. Protein-protein interactions determine the stability of potentially transcriptionally active or repressed nucleoprotein complexes. A decline in transcription factor abundance, differential binding of transcription factors to oocyte and somatic 5 S genes, and increased competition with the histones for association with DNA during early embryogenesis, can account for the developmental decision to selectively repress the oocyte genes, while retaining the somatic genes in the transcriptionally active state. The 5 S ribosomal genes of Xenopus are perhaps the simplest eukaryotic genes to show regulated expression during development. A large multigene family (oocyte 5 S DNA) is transcriptionally active in oocytes but is repressed in somatic cells, whereas a small multigene family (somatic 5 S DNA) is active in both cell types. A potential molecular mechanism to explain the developmental switch that turns off oocyte 5 S DNA transcription has been experimentally reconstructed in vitro and more recently tested in vivo. Central to this mechanism is the specific association of both transcription factors and histones with 5 S RNA genes. How the interplay of histones and transcription factors is thought to affect transcription, and how their respective contributions might change during development from an oocyte, to an embryo and eventually to a somatic cell is the focus of this review.
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Affiliation(s)
- A P Wolffe
- Laboratory of Molecular Embryology, National Institute of Child Health and Human Development, NIH, Bethesda, MD 20892
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29
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Casalone E, Colella CM, Daly S, Fontana S, Torricelli I, Polsinelli M. Cloning and characterization of a sulphite-resistance gene of Saccharomyces cerevisiae. Yeast 1994; 10:1101-10. [PMID: 7992510 DOI: 10.1002/yea.320100812] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
In this paper we describe the cloning and sequencing of the gene (SUL1) responsible for sulphite resistance in a Saccharomyces cerevisiae mutant (Casalone et al., 1992). The deduced amino acid sequence predicted that the gene codes for a zinc-finger protein with five fingers. Comparison of wild-type and mutant gene sequences demonstrated that the mutation event was a transversion from C to G; as a consequence of the mutation a histidine substituted an aspartic acid, affecting directly the fourth finger structure. The SUL1 gene sequence corresponds to that of FZF1 gene (Breitwieser et al., 1993) to which no function was attributed.
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Affiliation(s)
- E Casalone
- Department of Animal Biology and Genetics, University of Florence, Italy
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30
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Affiliation(s)
- N A Woychik
- Roche Institute of Molecular Biology, Nutley, NJ 07110
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31
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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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32
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Abstract
Over ten years ago transcription factor IIIA (TFIIIA) was identified as the only protein that binds specifically to both RNA and DNA. Although many details of its biochemical and biological activities have since been discovered, the complicated, multifunctional nature of this protein is still not fully understood. This article reviews interesting and perhaps important developments in the TFIIIA story.
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Affiliation(s)
- T Pieler
- Max-Planck-Institut für Molekulare Genetik, Berlin, Germany
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33
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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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34
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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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35
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36
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Gaskins CJ, Smith JF, Ogilvie MK, Hanas JS. Comparison of the sequence and structure of transcription factor IIIA from Bufo americanus and Rana pipiens. Gene 1992; 120:197-206. [PMID: 1398134 DOI: 10.1016/0378-1119(92)90094-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Amino acid (aa) sequences of transcription factor IIIA (TFIIIA) from the toad, Bufo americanus, and the grass frog, Rana pipiens, were determined by cDNA cloning and DNA sequencing. The 3'-untranslated regions of the cDNAs reveal that the TFIIIA gene polyadenylation signal is ATTAAA, rather than the conventional AATAAA. The B. americanus and R. pipiens proteins share about 60% aa sequence homology with each other and with Xenopus laevis TFIIIA. Although these results indicate that TFIIIA has more sequence variation than other DNA-binding proteins, a number of conserved features are evident and of likely functional significance. These include potential guanine nucleotide-binding sites at arginines in zinc fingers (ZnF) II, V, and IX, acidic residues between metal-coordinating cysteines, and a basic region in the C-terminal tail possibly involved in transcription promotion. Sequence similarity also exists in an aa stretch bridging the ninth ZnF and C-terminal tail of both TFIIIA and the 5S RNA-binding protein, p43. DNase I protection analyses demonstrate that B. americanus and R. pipiens TFIIIA interact with the internal control region (ICR) of the Xenopus borealis 5S RNA-encoding gene (5S) in different manners: the B. americanus interaction is similar to X. laevis TFIIIA, protecting the entire 5S gene ICR (nt +96 to +43) from DNase I digestion, whereas the R. pipiens TFIIIA strongly protects the ICR from nt +96 up to +78 and less strongly from +78 to +43. Possibly accounting for the binding differences observed, R. pipiens and R. catesbeiana oocyte 5S RNAs (and by inference 5S genes) were found to contain a G or U at nt position 50 while B. americanus, X. laevis, and other eukaryotic 5S RNAs have an A in the analogous position (nt 53 in generalized eukaryotic structure).
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Affiliation(s)
- C J Gaskins
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City 73190
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37
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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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