1
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Wu FYH. Spectroscopic Studies of Metalloproteins and Metalloenzymes. J CHIN CHEM SOC-TAIP 2013. [DOI: 10.1002/jccs.198900078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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2
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Affiliation(s)
- Robert O J Weinzierl
- Department of Life Sciences, Division of Biomolecular Sciences, Imperial College London , Sir Alexander Fleming Building, Exhibition Road, London SW7 2AZ, United Kingdom
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3
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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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4
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5
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Abmayr SM, Workman JL. Transcription factors prominently in Lasker Award to Roeder. Cell 2003; 115:243-6. [PMID: 14636549 DOI: 10.1016/s0092-8674(03)00846-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Susan M Abmayr
- Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO 64110, USA
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6
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Yang Z, Hayes JJ. Xenopus transcription factor IIIA and the 5S nucleosome: development of a useful in vitro system. Biochem Cell Biol 2003; 81:177-84. [PMID: 12897852 DOI: 10.1139/o03-043] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
5S RNA genes in Xenopus are regulated during development via a complex interplay between assembly of repressive chromatin structures and productive transcription complexes. Interestingly, 5S genes have been found to harbor powerful nucleosome positioning elements and therefore have become an important model system for reconstitution of eukaryotic genes into nucleosomes in vitro. Moreover, the structure of the primary factor initiating transcription of 5S DNA, transcription factor IIIA, has been extensively characterized. This has allowed for numerous studies of the effect of nucleosome assembly and histone modifications on the DNA binding activity of a transcription factor in vitro. For example, linker histones bind 5S nucleosomes and repress TFIIIA binding in vitro in a similar manner to that observed in vivo. In addition, TFIIIA binding to nucleosomes assembled with 5S DNA is stimulated by acetylation or removal of the core histone tail domains. Here we review the development of the Xenopus 5S in vitro system and discuss recent results highlighting new aspects of transcription factor - nucleosome interactions,
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Affiliation(s)
- Zungyoon Yang
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, NY 14625, USA
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7
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Hirsch HA, Gu L, Henry RW. The retinoblastoma tumor suppressor protein targets distinct general transcription factors to regulate RNA polymerase III gene expression. Mol Cell Biol 2000; 20:9182-91. [PMID: 11094070 PMCID: PMC102176 DOI: 10.1128/mcb.20.24.9182-9191.2000] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The retinoblastoma protein (RB) represses RNA polymerase III transcription effectively both in vivo and in vitro. Here we demonstrate that the general transcription factors snRNA-activating protein complex (SNAP(c)) and TATA binding protein (TBP) are important for RB repression of human U6 snRNA gene transcription by RNA polymerase III. RB is associated with SNAP(c) as detected by both coimmunoprecipitation of endogenous RB with SNAP(c) and cofractionation of RB and SNAP(c) during chromatographic purification. RB also interacts with two SNAP(c) subunits, SNAP43 and SNAP50. TBP or a combination of TBP and SNAP(c) restores efficient U6 transcription from RB-treated extracts, indicating that TBP is also involved in RB regulation. In contrast, the TBP-containing complex TFIIIB restores adenovirus VAI but not human U6 transcription in RB-treated extracts, suggesting that TFIIIB is important for RB regulation of tRNA-like genes. These results suggest that different classes of RNA polymerase III-transcribed genes have distinct general transcription factor requirements for repression by RB.
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MESH Headings
- Adenoviruses, Human
- Autoradiography
- Cell Extracts
- Cell Nucleus/metabolism
- Chromatography
- Cloning, Molecular
- Electrophoresis, Polyacrylamide Gel
- HeLa Cells
- Humans
- Models, Genetic
- Precipitin Tests
- Promoter Regions, Genetic/genetics
- RNA Polymerase III/genetics
- RNA Polymerase III/metabolism
- RNA, Viral/genetics
- RNA, Viral/metabolism
- Recombinant Fusion Proteins/genetics
- Recombinant Fusion Proteins/metabolism
- Retinoblastoma Protein/genetics
- Retinoblastoma Protein/metabolism
- Ribonucleoprotein, U4-U6 Small Nuclear/genetics
- Ribonucleoprotein, U4-U6 Small Nuclear/metabolism
- TATA Box
- Transcription Factors/genetics
- Transcription Factors/metabolism
- Transcription, Genetic/genetics
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Affiliation(s)
- H A Hirsch
- Cell and Molecular Biology Program, Michigan State University, East Lansing, Michigan 48824, USA
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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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Pruzan R, Flint SJ. Transcription of adenovirus RNA polymerase III genes. Curr Top Microbiol Immunol 1995; 199 ( Pt 1):201-26. [PMID: 7555055 DOI: 10.1007/978-3-642-79496-4_11] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- R Pruzan
- Department of Molecular Biology, Princeton University, NJ 08544, USA
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10
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Moorefield B, Roeder R. Purification and characterization of human transcription factor IIIA. J Biol Chem 1994. [DOI: 10.1016/s0021-9258(17)31901-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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11
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Veldhoen N, You Q, Setzer DR, Romaniuk PJ. Contribution of individual base pairs to the interaction of TFIIIA with the Xenopus 5S RNA gene. Biochemistry 1994; 33:7568-75. [PMID: 8011622 DOI: 10.1021/bi00190a009] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The effects of a series of point mutations within the Xenopus borealis somatic-type 5S RNA gene on transcription factor IIIA (TFIIIA) binding affinity were quantified. These data define a critical sequence-dependent contact region within the classical box C promoter element from base pair 80 to 91. Substitution of GC base pairs at positions 81, 85, 86, 89, and 91 significantly reduce TFIIIA binding affinity. Base pairs located at other positions within the box C contact region provide a moderate contribution to TFIIIA-5S gene interaction. In contrast to the extensive set of sequence contacts within the box C element, TFIIIA interaction is localized primarily to two GC base pairs at positions 70 and 71 within the intermediate promoter element. A selected amplification and binding assay (SAAB) was performed with a synthetic internal control region (ICR) randomized from base pair 78 to 95 to identify box C promoter sequences bound with high affinity by TFIIIA. The wild-type 5S RNA gene sequence from 79 to 92 is strongly selected. These results are consistent with the critical role of the box C element in sequence-dependent promoter recognition by TFIIIA.
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Affiliation(s)
- N Veldhoen
- Department of Biochemistry and Microbiology, University of Victoria, British Columbia, Canada
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12
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13
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Nickol J, Rau DC. Zinc induces a bend within the transcription factor IIIA-binding region of the 5 S RNA gene. J Mol Biol 1992; 228:1115-23. [PMID: 1474581 DOI: 10.1016/0022-2836(92)90319-f] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Binding of Zn2+ to the 5 S RNA gene sequence of Xenopus borealis results in strong bending of the DNA, as inferred from transient electric birefringence data. The effect is specific for Zn2+; several other divalent ions are not able to induce a bend of a similar magnitude. Using five different fragments that span the binding sequence, we are able to estimate a bend magnitude of at least 55 degrees centered at base-pair +65 within the gene. This places the bend within the binding domain of the gene-regulatory protein transcription factor (TF) IIIA. Recent evidence has shown that the protein-DNA complex is also bent. Although our data do not allow us directly to link the two bends, our results suggest that TFIIIA could form a folded structure by stabilizing the same bent conformation that is induced by binding of Zn2+. The chemistry of Zn2+ binding to DNA, and the sequence around the bend center, suggest that the bend is most probably caused by joint co-ordination of Zn2+ to the N-7 groups of stacked purine residues.
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Affiliation(s)
- J Nickol
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892
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14
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Lobo SM, Tanaka M, Sullivan ML, Hernandez N. A TBP complex essential for transcription from TATA-less but not TATA-containing RNA polymerase III promoters is part of the TFIIIB fraction. Cell 1992; 71:1029-40. [PMID: 1458534 DOI: 10.1016/0092-8674(92)90397-u] [Citation(s) in RCA: 152] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The TATA box-binding protein TBP directs transcription by all three eukaryotic RNA polymerases. In mammalian cells, TBP is found in at least three different complexes: SL1, D-TFIID, and B-TFIID. While SL1 and D-TFIID are involved in RNA polymerase I and II transcription, respectively, no unique function has been assigned to the B-TFIID complex. Here we show that the TFIIIB fraction required for RNA polymerase III transcription contains two separable components, one of which is a TBP-containing complex that may correspond to B-TFIID. For transcription of TATA-less RNA polymerase III genes such as the VAI, 5S, and 7SL genes, this complex cannot be replaced by either TBP alone or the D-TFIID complex. In contrast, TBP alone is active for basal transcription from the TATA-containing U6 promoter. This indicates different requirements for recruiting TBP to TATA-less and TATA-containing RNA polymerase III promoters.
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Affiliation(s)
- S M Lobo
- Cold Spring Harbor Laboratory, New York 11724
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15
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Lobe CG, Gruss P. From Drosophila to Mouse. Development 1992. [DOI: 10.1007/978-3-642-77043-2_27] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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16
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Chalker DL, Sandmeyer SB. Ty3 integrates within the region of RNA polymerase III transcription initiation. Genes Dev 1992; 6:117-28. [PMID: 1309715 DOI: 10.1101/gad.6.1.117] [Citation(s) in RCA: 173] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Over 190 independent insertions into target plasmids of the retrovirus-like element Ty3 were recovered and mapped. Ty3 was shown to insert upstream of tRNA, 5S, and U6 genes, all of which are transcribed by RNA polymerase III. Integration sites were within 1-4 nucleotides of the position of transcription initiation, even for one mutant gene where the polymerase III initiation site was shifted to a completely new context. Mutagenesis of a SUP2 tRNA gene target showed that integration required functional promoter elements but that it did not correlate in a simple way with target transcription. This is the first report directly linking a discrete genomic function with preferential insertion of a retrotransposon.
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Affiliation(s)
- D L Chalker
- Department of Microbiology and Molecular Genetics, University of California, Irvine 92717
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17
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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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18
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Lobo SM, Lister J, Sullivan ML, Hernandez N. The cloned RNA polymerase II transcription factor IID selects RNA polymerase III to transcribe the human U6 gene in vitro. Genes Dev 1991; 5:1477-89. [PMID: 1869050 DOI: 10.1101/gad.5.8.1477] [Citation(s) in RCA: 130] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Although the human U2 and U6 snRNA genes are transcribed by different RNA polymerases (i.e., RNA polymerases II and III, respectively), their promoters are very similar in structure. Both contain a proximal sequence element (PSE) and an octamer motif-containing enhancer, and these elements are interchangeable between the two promoters. The RNA polymerase III specificity of the U6 promoter is conferred by a single A/T-rich element located around position -25. Mutation of the A/T-rich region converts the U6 promoter into an RNA polymerase II promoter, whereas insertion of the A/T-rich region into the U2 promoter converts that promoter into an RNA polymerase III promoter. We show that this A/T-rich element can be replaced by a number of TATA boxes derived from mRNA promoters transcribed by RNA polymerase II with little effect on RNA polymerase III transcription. Furthermore, the cloned RNA polymerase II transcription factor TFIID both binds to the U6 A/T-rich region and directs accurate RNA polymerase III transcription in vitro. Mutations in the U6 A/T-rich region that convert the U6 promoter into an RNA polymerase II promoter also abolish TFIID binding. Together, these observations suggest that in the human snRNA promoters, unlike in mRNA promoters, binding of TFIID directs the assembly of RNA polymerase III transcription complexes, whereas the lack of TFIID binding results in the assembly of RNA polymerase II snRNA transcription complexes.
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Affiliation(s)
- S M Lobo
- Cold Spring Harbor Laboratory, New York 11724
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19
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Shastry BS, Zhang ZG. Xenopus transcription factor IIIC (TFIIIC) specifically interacts with the "B" block region of the TFIIIA gene. Biochem Biophys Res Commun 1991; 175:1036-41. [PMID: 2025235 DOI: 10.1016/0006-291x(91)91669-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Transcription factors IIIC (TFIIIC), TFIIIB and RNA polymerase III are commonly required for class III gene transcription in vitro. To understand the diversity and specificity of Xenopus TFIIIC, we have further characterized this factor. Our analyses indicate that a partially purified TFIIIC fraction contains an activity which specifically recognizes the "B" block element of TFIIIA gene. Stable complex formation assays with HeLa cell extracts demonstrate that the TFIIIA gene can stably sequester TFIIIC. off
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Affiliation(s)
- B S Shastry
- Eye Research Institute of Oakland University, Rochester, MI 48309
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20
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Ozer J, Faber M, Chalkley R, Sealy L. Isolation and characterization of a cDNA clone for the CCAAT transcription factor EFIA reveals a novel structural motif. J Biol Chem 1990. [DOI: 10.1016/s0021-9258(18)45682-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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21
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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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22
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The identification of two antagonistic activities in a Xenopus oocyte extract that can modulate the in vitro transcription of RNA polymerase III genes. J Biol Chem 1990. [DOI: 10.1016/s0021-9258(19)38820-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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23
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Oei SL, Pieler T. A transcription stimulatory factor binds to the upstream region of Xenopus 5 S RNA and tRNA genes. J Biol Chem 1990. [DOI: 10.1016/s0021-9258(19)39139-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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24
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Kovelman R, Roeder RG. Sarkosyl defines three intermediate steps in transcription initiation by RNA polymerase III: application to stimulation of transcription by E1A. Genes Dev 1990; 4:646-58. [PMID: 1694510 DOI: 10.1101/gad.4.4.646] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We used Sarkosyl to analyze steps along the pathway of transcription initiation by RNA polymerase III. Sarkosyl (0.015%) inhibited transcription when present prior to incubation of RNA polymerase III, TFIIIB, and TFIIIC with the VAI gene, whereas it had no detectable effect on initiation or reinitiation of transcription when added subsequently. The formation of the corresponding 0.015% Sarkosyl-resistant complex required the presence of TFIIIC, TFIIIB, and RNA polymerase III but not nucleoside triphosphates. The addition of 0.05% Sarkosyl after this early step selectively inhibited a later step in the preinitiation pathway, allowing a single round of transcription after nucleoside triphosphate addition but blocking subsequent rounds of initiation. This step occurred prior to initiation because nucleoside triphosphates were not required for the formation of the corresponding 0.05% Sarkosyl-resistant complex. These observations provided a means to distinguish effects of regulatory factors on different steps in promoter activation and function. Using 0.05% Sarkosyl to limit reinitiation, we determined that the E1A-mediated stimulation of transcription by RNA polymerase III resulted from an increase in the number of active transcription complexes.
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Affiliation(s)
- R Kovelman
- Laboratory of Biochemistry and Molecular Biology, Rockefeller University, New York, New York 10021-6399
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25
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Wolffe AP, Morse RH. The transcription complex of the Xenopus somatic 5 S RNA gene. A functional analysis of protein-DNA interactions outside of the internal control region. J Biol Chem 1990. [DOI: 10.1016/s0021-9258(19)39604-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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26
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27
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28
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Blanco J, Millstein L, Razik MA, Dilworth S, Cote C, Gottesfeld J. Two TFIIIA activities regulate expression of the Xenopus 5S RNA gene families. Genes Dev 1989; 3:1602-12. [PMID: 2575558 DOI: 10.1101/gad.3.10.1602] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Immunoblotting experiments with polyclonal and monoclonal anti-transcription factor IIIA (TFIIIA) antibodies reveal different electrophoretic forms of TFIIIA in extracts from immature and mature oocytes of Xenopus laevis. The well-characterized 39-kD TFIIIA species is present in approximately 10(12) copies per cell in stage I-III previtellogenic oocytes and declines in abundance by 10- to 20-fold during oogenesis. An immunologically related protein of apparent molecular mass of 42 kD is present at 2-4% of the level of 39-kD TFIIIA in immature oocytes, and the level of this protein increases dramatically during oogenesis. Both the 39- and 42-kD proteins are complexed with 5S RNA in 7S ribonucleoprotein (RNP) particles. High-level transcription of the oocyte-type 5S genes in vitro requires 39-kD immature oocyte TFIIIA, whereas both 39-kD TFIIIA and the mature oocyte TFIIIA species of 42 kD support somatic-type 5S transcription. TFIIIA of 42 kD does not support oocyte-type 5S transcription in a fractionated transcription system derived from mature oocytes. Both proteins, however, bind the oocyte-type and somatic-type genes with comparable affinities and exhibit similar DNase footprints on both genes. These results suggest a model for the developmental regulation of 5S RNA gene transcription where 42-kD TFIIIA serves as an activator of somatic-type 5S transcription and as a repressor of oocyte-type transcription during early embryogenesis.
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Affiliation(s)
- J Blanco
- Department of Molecular Biology, Research Institute of Scripps Clinic, La Jolla, California 92037
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29
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Xing YY, Worcel A. A 3' exonuclease activity degrades the pseudogene 5S RNA transcript and processes the major oocyte 5S RNA transcript in Xenopus oocytes. Genes Dev 1989; 3:1008-18. [PMID: 2777074 DOI: 10.1101/gad.3.7.1008] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Transcription of the major oocyte 5S RNA gene (o) and pseudogene (psi) of Xenopus laevis yields different RNAs with three different homologous systems: oocyte microinjection, whole oocyte extract, and fractionated TFIIIA + TFIIIB + TFIIIC components. Those peculiar results are caused by a 3' RNA exonuclease activity, which is inhibited in the oocyte extract, that rapidly degrades the pseudogene 5S RNA but does not degrade as readily the chimeric RNA transcripts generated by HindIII-truncated 5S RNA pseudogenes. The same, or a similar, RNase activity processes the 130- and the 142-base-long transcripts of the major oocyte 5S RNA gene into mature 120-base-long 5S RNA. We performed site-specific mutagenesis on the somatic 5S RNA gene and changed specific nucleotides on the somatic 5S RNA. These studies indicated that the structure that confers stability to the 5S RNA in vivo and in vitro is the 9-bp helix formed in 5S RNA, but not in psi 5S RNA, by the complementary 5' and 3' ends of the molecule.
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MESH Headings
- Animals
- Base Sequence
- Cloning, Molecular
- Exoribonucleases/metabolism
- Microinjections
- Molecular Sequence Data
- Nucleic Acid Conformation
- Nucleic Acid Hybridization
- Oocytes/metabolism
- Plasmids
- Pseudogenes
- RNA Processing, Post-Transcriptional
- RNA, Ribosomal/metabolism
- RNA, Ribosomal, 5S/genetics
- RNA, Ribosomal, 5S/metabolism
- Repetitive Sequences, Nucleic Acid
- Ribonucleases/antagonists & inhibitors
- Ribonucleases/metabolism
- Sequence Homology, Nucleic Acid
- Transcription, Genetic
- Xenopus laevis
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Affiliation(s)
- Y Y Xing
- Department of Biology, University of Rochester, New York 14627
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30
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Hayes J, Tullius TD, Wolffe AP. A Protein-Protein Interaction Is Essential for Stable Complex Formation on a 5 S RNA Gene. J Biol Chem 1989. [DOI: 10.1016/s0021-9258(18)83302-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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31
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Seifart KH, Wang L, Waldschmidt R, Jahn D, Wingender E. Purification of Human Transcription Factor IIIA and Its Interaction with a Chemically Synthesized Gene Encoding Human 5 S rRNA. J Biol Chem 1989. [DOI: 10.1016/s0021-9258(18)94243-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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32
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Iyer RK, Levinger LF. Visualization of RNA binding proteins by sequential gel shift and ultraviolet cross-linking. GENE ANALYSIS TECHNIQUES 1988; 5:125-9. [PMID: 2463962 DOI: 10.1016/0735-0651(88)90012-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
RNA binding proteins partially constitute the ribonucleoprotein or protein machinery for RNA processing (splicing, polyadenylation and 3' end formation), transport, and storage. We have devised a novel method for the detection of RNA binding proteins in vitro. The template for transcription is a cloned Drosophila melanogaster 5S rRNA gene. The method is a two-dimensional gel analysis involving: in vitro transcription of 32P-labeled 5S rRNA using a cellular S-100; resolution of labeled RNA protein complexes from unbound RNA on a first-dimension mobility shift gel; cross-linking of RNA to protein in gel by ultraviolet irradiation; degradation of the RNA by RNase A and T1; and analysis of 32P-protein patterns on a second-dimension discontinuous SDS gel by autoradiography. The pattern of proteins associated with 32P-5S rRNA is obtained by covalent transfer of 32P-nucleotides from RNA to the proteins with which the RNA was bound. This method could be useful in the analysis of RNA maturation and processing pathways.
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Affiliation(s)
- R K Iyer
- School of Life and Health Sciences, University of Delaware, Newark 19716
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33
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Windsor WT, Lee TC, Daly TJ, Wu CW. Xenopus transcription factor IIIA binds to the flanking regions of the 5 S RNA gene intragenic control region in a unique and highly ordered state. J Biol Chem 1988. [DOI: 10.1016/s0021-9258(19)81510-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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34
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An N-terminally fused Xenopus transcription factor IIIA synthesized in Escherichia coli is biologically active. J Biol Chem 1988. [DOI: 10.1016/s0021-9258(19)81514-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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35
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Affiliation(s)
- W R Folk
- Department of Microbiology, University of Texas, Austin 78712
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36
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McConkey GA, Bogenhagen DF. TFIIIA binds with equal affinity to somatic and major oocyte 5S RNA genes. Genes Dev 1988; 2:205-14. [PMID: 3360323 DOI: 10.1101/gad.2.2.205] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Current models for the differential control of expression of Xenopus somatic and oocyte 5S RNA genes suggest that an impaired ability to bind TFIIIA contributes to the inactivation of oocyte 5S RNA genes in somatic cells. The somatic 5S RNA gene is transcribed more efficiently than the major oocyte 5S RNA gene in S-150 extracts of mature oocytes. However, this differential transcription efficiency is not determined simply by the relative affinity for binding of a positive transcription factor, TFIIIA. We have compared the abilities of somatic, major oocyte, and minor oocyte 5S RNA genes to bind TFIIIA using both a standard footprint competition assay and an indirect DNase protection assay. This indirect DNase protection assay permits the direct comparison of TFIIIA binding to two templates in one reaction. Both assay methods indicate that the major oocyte 5S RNA gene and the somatic 5S RNA gene bind TFIIIA with equal affinity. As a further control, we have confirmed earlier work indicating that the minor oocyte gene binds TFIIIA with a reduced affinity. Binding of TFIIIA to these three 5S RNA genes results in a different pattern of protection of each gene. We suggest that slight differences in the contacts between TFIIIA and the 5' border of the control region influence the ability of additional transcription factors to bind to the TFIIIA:5S DNA complex.
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Affiliation(s)
- G A McConkey
- Department of Pharmacological Sciences, State University of New York, Stony Brook 11794
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37
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Blair DG. Eukaryotic RNA polymerases. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. B, COMPARATIVE BIOCHEMISTRY 1988; 89:647-70. [PMID: 3288436 DOI: 10.1016/0305-0491(88)90306-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- D G Blair
- Department of Biochemistry, University of Saskatchewan, Saskatoon, Canada
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38
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Shang ZG, Windsor WT, Liao YD, Wu CW. Purification of Xenopus transcription factor IIIA and 5 S RNA from 7 S ribonucleoprotein particle by ammonium sulfate precipitation. Anal Biochem 1988; 168:156-63. [PMID: 2452584 DOI: 10.1016/0003-2697(88)90023-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
A simple and efficient method for purifying Xenopus transcription factor IIIA from the 7 S particle has been developed by taking advantage of the differential solubilities of the protein factor and 5 S RNA in ammonium sulfate solution. Conditions under which ammonium sulfate dissociates the 7 S particle and selectively precipitates factor IIIA while the 5 S RNA moiety remains in the supernatant were found. The method simultaneously purifies, in a nondestructive manner, both factor IIIA and 5 S RNA in high yield. Purification proceeds through several ammonium sulfate precipitations of the 7 S particle. Factor IIIA obtained by this method contains no detectable RNA and is highly active as judged by DNase I footprinting and in vitro transcription of the 5 S RNA gene, as well as reconstitution with 5 S RNA to form the 7 S particle. The molar extinction coefficients of factor IIIA at 205 and 280 nm were determined from the ultraviolet absorption spectra measured with the purified protein.
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Affiliation(s)
- Z G Shang
- Department of Pharmacological Sciences, School of Medicine, State University of New York, Stony Brook 11794
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39
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Chung J, Sussman DJ, Zeller R, Leder P. The c-myc gene encodes superimposed RNA polymerase II and III promoters. Cell 1987; 51:1001-8. [PMID: 3690658 DOI: 10.1016/0092-8674(87)90586-1] [Citation(s) in RCA: 93] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The first exon of the c-myc gene has unusual properties that suggest some further role in gene regulation. It encodes a large, evolutionarily conserved leader exon that is transcribed more frequently than the remaining exons of the c-myc gene. In what follows, we provide a possible explanation for these observations. We find that the major promoter of the c-myc gene is bifunctional; that is, it supports transcription by RNA polymerases II and III (pol II and III). Both enzymes initiate in vitro transcription from the major c-myc initiation site (P2), but pol III is completely blocked near the 3' end of the first exon while pol II, though partially blocked, transcribes through this region. These superimposed transcriptional activities suggest a potential regulatory mechanism by which one polymerase system could influence the activity of another.
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Affiliation(s)
- J Chung
- Department of Genetics, Harvard Medical School, Howard Hughes Medical Institute, Boston, Massachusetts 02115
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40
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Brow DA, Geiduschek EP. Modulation of yeast 5 S rRNA synthesis in vitro by ribosomal protein YL3. A possible regulatory loop. J Biol Chem 1987. [DOI: 10.1016/s0021-9258(18)47887-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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41
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Piper PW, Lockheart A, Bellatin J. The effects of protein synthesis inhibition, and of mutations rna1.1 and rna82.1, on the synthesis of small RNAs in yeast. FEBS Lett 1987; 214:143-8. [PMID: 3552724 DOI: 10.1016/0014-5793(87)80030-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Strains of Saccharomyces cerevisiae have been constructed that possess temperature-sensitive defects in tRNA precursor (pre-tRNA) splicing and which also lack the processing endonuclease that acts at the 3'-terminus of 5 S rRNA and 35 S rRNA precursors (pre-rRNAs). The unspliced pre-tRNAs accumulated by such strains at the nonpermissive temperature are identical in structure to those accumulated by pre-tRNA splicing-defective strains with a functional pre-5 S RNA processing enzyme. The pre-RNA processing activity is therefore not obligatorily involved in maturation of several yeast tRNAs. However, gels of the pulse-labelled RNAs of RNA82+ and rna82.1 strains provide evidence that this enzyme acts upon a few small unstable transcripts that are not 5 S RNA forms. The most prominent of these transcripts on gels was, in wild-type strains, an RNA 145 +/- 2 nucleotides in length.
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42
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Bertling W, Dingermann T, Kaiserwerth M. Comparative study of 5′ flanking sequences of eukaryotic genes: possible functional implications. Int J Biol Macromol 1987. [DOI: 10.1016/0141-8130(87)90028-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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43
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Pieler T, Hamm J, Roeder RG. The 5S gene internal control region is composed of three distinct sequence elements, organized as two functional domains with variable spacing. Cell 1987; 48:91-100. [PMID: 3791417 DOI: 10.1016/0092-8674(87)90359-x] [Citation(s) in RCA: 156] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Systematic oligonucleotide-directed mutagenesis within the internal control region of the Xenopus laevis somatic 5S RNA gene identifies three distinct sequence elements that regulate transcription activity: box A, containing the common, conserved class III promoter domain, and two 5S-gene-specific segments, termed intermediate element and box C. Analysis of the individual steps in the formation of the stable initiation complex reveals that the two 5S-gene-specific elements are the main determinants for the stable binding of TFIIIA. In contrast, TFIIIC binding appears to be dependent on interactions with TFIIIA and on direct DNA interactions in box A as well as probably in box C. Alterations of the spacing between the two major promoter domains of from -3 to +10 nucleotides are tolerated, although they reduce transcription activity and were found to prevent the formation of a stable initiation complex.
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44
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Lofquist A, Sharp S. The 5'-flanking sequences of Drosophila melanogaster tRNA5Asn genes differentially arrest RNA polymerase III. J Biol Chem 1986. [DOI: 10.1016/s0021-9258(18)66913-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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45
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Abstract
Replication of the Xenopus laevis 5S RNA gene in vitro is unimpeded by the presence of a complete transcription complex assembled on the internal control region of the gene. The transcription complex is disrupted by passage of the replication fork, specific transcription factors are displaced, and the daughter 5S RNA genes are inactivated. We have been unable to demonstrate that any "memory" of the preexisting transcription complex is transmitted to the daughter DNA duplexes following replication.
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46
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Selker EU, Morzycka-Wroblewska E, Stevens JN, Metzenberg RL. An upstream signal is required for in vitro transcription of Neurospora 5S RNA genes. MOLECULAR & GENERAL GENETICS : MGG 1986; 205:189-92. [PMID: 3025558 DOI: 10.1007/bf02428052] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The DNA sequences upstream of the 5S RNA genes in Neurospora crassa are largely different from one another, but share a short consensus sequence located in the segment 29 to 26 nucleotides preceding the transcribed region. Differences among flanking sequences do not appear to affect transcription. Deletion analysis indicates, however, that a DNA segment including the conserved "TATA box" is required for in vitro transcription of Neurospora 5S RNA genes.
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47
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48
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Hazuda DJ, Wu CW. DNA-activated ATPase activity associated with Xenopus transcription factor A. J Biol Chem 1986. [DOI: 10.1016/s0021-9258(18)67224-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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49
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Bieker JJ, Roeder RG. Characterization of the nucleotide requirement for elimination of the rate-limiting step in 5 S RNA gene transcription. J Biol Chem 1986. [DOI: 10.1016/s0021-9258(18)67576-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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50
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Yeast class III gene transcription factors and homologous RNA polymerase III form ternary transcription complexes stable to disruption by N-lauroyl-sarcosine (sarcosyl). Arch Biochem Biophys 1986; 246:783-800. [PMID: 2423033 DOI: 10.1016/0003-9861(86)90335-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Yeast Class III gene transcription factors and RNA polymerase III were used to form ternary transcription complexes on a tRNASer gene in vitro under UTP-limiting transcription conditions. These ternary transcription complexes were composed of template DNA, proteins, and RNA. We have shown that the RNAs contained in these complexes represented specifically initiated nascent pre-tRNASer transcripts. These nascent RNAs could be very efficiently elongated to full-length pre-tRNASer molecules, even in the presence of the ionic detergent sarcosyl. Partial purification (greater than 100-fold) of these sarcosyl-resistant ternary transcription complexes could be achieved in a single step via sucrose gradient sedimentation. Comparable sarcosyl-resistant ternary transcription complexes could not be formed using purified yeast RNA polymerase III as the only protein component of the complex.
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