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Talyzina A, Han Y, Banerjee C, Fishbain S, Reyes A, Vafabakhsh R, He Y. Structural basis of TFIIIC-dependent RNA polymerase III transcription initiation. Mol Cell 2023; 83:2641-2652.e7. [PMID: 37402369 PMCID: PMC10528418 DOI: 10.1016/j.molcel.2023.06.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 05/02/2023] [Accepted: 06/08/2023] [Indexed: 07/06/2023]
Abstract
RNA polymerase III (Pol III) is responsible for transcribing 5S ribosomal RNA (5S rRNA), tRNAs, and other short non-coding RNAs. Its recruitment to the 5S rRNA promoter requires transcription factors TFIIIA, TFIIIC, and TFIIIB. Here, we use cryoelectron microscopy (cryo-EM) to visualize the S. cerevisiae complex of TFIIIA and TFIIIC bound to the promoter. Gene-specific factor TFIIIA interacts with DNA and acts as an adaptor for TFIIIC-promoter interactions. We also visualize DNA binding of TFIIIB subunits, Brf1 and TBP (TATA-box binding protein), which results in the full-length 5S rRNA gene wrapping around the complex. Our smFRET study reveals that the DNA within the complex undergoes both sharp bending and partial dissociation on a slow timescale, consistent with the model predicted from our cryo-EM results. Our findings provide new insights into the transcription initiation complex assembly on the 5S rRNA promoter and allow us to directly compare Pol III and Pol II transcription adaptations.
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Affiliation(s)
- Anna Talyzina
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA; Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL, USA
| | - Yan Han
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Chiranjib Banerjee
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Susan Fishbain
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Alexis Reyes
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA; Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL, USA
| | - Reza Vafabakhsh
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA; Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL, USA
| | - Yuan He
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA; Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL, USA; Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA; Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Northwestern University, Chicago, IL, USA.
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2
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Talyzina A, Han Y, Banerjee C, Fishbain S, Reyes A, Vafabakhsh R, He Y. Structural basis of TFIIIC-dependent RNA Polymerase III transcription initiation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.16.540967. [PMID: 37292922 PMCID: PMC10245719 DOI: 10.1101/2023.05.16.540967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
RNA Polymerase III (Pol III) is responsible for transcribing 5S ribosomal RNA (5S rRNA), tRNAs, and other short non-coding RNAs. Its recruitment to the 5S rRNA promoter requires transcription factors TFIIIA, TFIIIC, and TFIIIB. Here we use cryo-electron microscopy to visualize the S. cerevisiae complex of TFIIIA and TFIIIC bound to the promoter. Brf1-TBP binding further stabilizes the DNA, resulting in the full-length 5S rRNA gene wrapping around the complex. Our smFRET study reveals that the DNA undergoes both sharp bending and partial dissociation on a slow timescale, consistent with the model predicted from our cryo-EM results. Our findings provide new insights into the mechanism of how the transcription initiation complex assembles on the 5S rRNA promoter, a crucial step in Pol III transcription regulation.
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Affiliation(s)
- Anna Talyzina
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, United States
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL, United States
| | - Yan Han
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, United States
| | - Chiranjib Banerjee
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, United States
| | - Susan Fishbain
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, United States
| | - Alexis Reyes
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, United States
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL, United States
| | - Reza Vafabakhsh
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, United States
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL, United States
| | - Yuan He
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, United States
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL, United States
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, United States
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Northwestern University, Chicago, IL, United States
- Lead contact
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3
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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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4
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Hydroxyl radical footprinting of protein-DNA complexes. Methods Mol Biol 2009. [PMID: 19378159 DOI: 10.1007/978-1-60327-015-1_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
This unit details the use of hydroxyl radicals to characterize protein-DNA interactions. This method may be used to assess the exact location of contacts between a protein and its cognate DNA and details of the complex structure. We describe several methods to prepare DNA templates for footprinting and ways to avoid many of the pitfalls associated with the use of hydroxyl radical footprinting. In addition, we describe in detail one example of the application of this technique.
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5
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Yang Z, Zheng C, Thiriet C, Hayes JJ. The core histone N-terminal tail domains negatively regulate binding of transcription factor IIIA to a nucleosome containing a 5S RNA gene via a novel mechanism. Mol Cell Biol 2005; 25:241-9. [PMID: 15601846 PMCID: PMC538782 DOI: 10.1128/mcb.25.1.241-249.2005] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Reconstitution of a DNA fragment containing a 5S RNA gene from Xenopus borealis into a nucleosome greatly restricts binding of the primary 5S transcription factor, TFIIIA. Consistent with transcription experiments using reconstituted templates, removal of the histone tail domains stimulates TFIIIA binding to the 5S nucleosome greater than 100-fold. However, we show that tail removal increases the probability of 5S DNA unwrapping from the core histone surface by only approximately fivefold. Moreover, using site-specific histone-to-DNA cross-linking, we show that TFIIIA binding neither induces nor requires nucleosome movement. Binding studies with COOH-terminal deletion mutants of TFIIIA and 5S nucleosomes reconstituted with native and tailless core histones indicate that the core histone tail domains play a direct role in restricting the binding of TFIIIA. Deletion of only the COOH-terminal transcription activation domain dramatically stimulates TFIIIA binding to the native nucleosome, while further C-terminal deletions or removal of the tail domains does not lead to further increases in TFIIIA binding. We conclude that the unmodified core histone tail domains directly negatively influence TFIIIA binding to the nucleosome in a manner that requires the C-terminal transcription activation domain of TFIIIA. Our data suggest an additional mechanism by which the core histone tail domains regulate the binding of trans-acting factors in chromatin.
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Affiliation(s)
- Zungyoon Yang
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Box 712, Rochester, NY 14642, USA
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6
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Vitolo JM, Yang Z, Basavappa R, Hayes JJ. Structural features of transcription factor IIIA bound to a nucleosome in solution. Mol Cell Biol 2004; 24:697-707. [PMID: 14701742 PMCID: PMC343799 DOI: 10.1128/mcb.24.2.697-707.2004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Assembly of a DNA fragment containing a Xenopus borealis somatic-type 5S RNA gene into a nucleosome greatly restricts binding of the 5S gene-specific transcription factor IIIA (TFIIIA) to the 5S internal promoter. However, TFIIIA binds with high affinity to 5S nucleosomes lacking the N-terminal tail domains of the core histones or to nucleosomes in which these domains are hyperacetylated. The degree to which tail acetylation or removal improves TFIIIA binding cannot be simply explained by a commensurate change in the general accessibility of nucleosomal DNA. In order to investigate the molecular basis of how TFIIIA binds to the nucleosome and to ascertain if binding involves all nine zinc fingers and/or displacement of histone-DNA interactions, we examined the TFIIIA-nucleosome complex by hydroxyl radical footprinting and site-directed protein-DNA cross-linking. Our data reveal that the first six fingers of TFIIIA bind and displace approximately 20 bp of histone-DNA interactions at the periphery of the nucleosome, while binding of fingers 7 to 9 appears to overlap with histone-DNA interactions. Molecular modeling based on these results and the crystal structures of a nucleosome core and a TFIIIA-DNA cocomplex yields a precise picture of the ternary complex and a potentially important intermediate in the transition from naïve chromatin structure to productive polymerase III transcription complex.
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Affiliation(s)
- Joseph M Vitolo
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY 14625, USA
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7
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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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8
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Neely LS, Lee BM, Xu J, Wright PE, Gottesfeld JM. Identification of a minimal domain of 5 S ribosomal RNA sufficient for high affinity interactions with the RNA-specific zinc fingers of transcription factor IIIA. J Mol Biol 1999; 291:549-60. [PMID: 10448036 DOI: 10.1006/jmbi.1999.2985] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Transcription factor IIIA of Xenopuslaevis serves a dual function during oogenesis and early development: this zinc finger protein binds to the internal promoter element of the 5 S ribosomal RNA genes and acts as a positive transcription factor; additionally, the protein functions in 5 S RNA storage. The central four zinc fingers (zf4-7) of the nine-finger protein have been shown to bind 5 S rRNA with comparable or higher affinity than the full-length protein. The role of finger seven in binding affinity has been examined by deletion analysis. A zf4-6 protein binds 5 S RNA with about a sevenfold reduction in binding affinity, compared to zf4-7. The effect of non-specific competitor DNA on binding affinities of the zinc finger peptides was examined and found to have a significant effect on the measured affinities of these peptides for full-length and truncated versions of 5 S RNA. The interaction of zf4-6 with full-length 5 S RNA was far more sensitive to non-specific competitor concentration than was the zf4-7:5 S RNA interaction, suggesting that finger seven contributes to both affinity and specificity in this protein:RNA interaction. In order to map zinc finger binding sites on the 5 S RNA molecule, we generated truncated versions of the RNA and tested these molecules for their binding affinities with zf4-7 and zf4-6. Previous studies showed that a 75 nucleotide long RNA, comprising loop A, helix II, helix V, region E and helix IV, bound zf4-7 with high affinity. Selection and amplification binding assays (selex) have now been used to generate smaller high-affinity binding RNAs. We find that a 55 nucleotide long RNA, comprising loop A, helix V, region E and helix IV, but lacking helix II, retains high affinity for zf4-6. These data are consistent with the proposal that fingers 4-6 bind this central core of 5 S RNA and that finger seven binds the helix II region.
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Affiliation(s)
- L S Neely
- Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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9
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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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10
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Nightingale KP, Wolffe AP. The interaction of TFIIIA with specific RNA-DNA heteroduplexes. J Biol Chem 1995; 270:22665-8. [PMID: 7559384 DOI: 10.1074/jbc.270.39.22665] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
We examine the association of transcription factor TFIIIA with RNA-DNA heteroduplexes containing sequences from the Xenopus borealis 5 S rRNA gene. Under conditions where TFIIIA selectively binds to 5 S rRNA or the internal control region of the 5 S rRNA gene, no specific association of TFIIIA with DNA-RNA heteroduplexes containing either strand of 5 S DNA could be detected. We discuss our results with respect to specific models of TFIIIA recognition of the internal control region and of DNA-RNA hybrids by zinc finger proteins.
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MESH Headings
- Animals
- Base Sequence
- DNA Primers
- DNA, Ribosomal/isolation & purification
- DNA, Ribosomal/metabolism
- DNA-Binding Proteins/isolation & purification
- DNA-Binding Proteins/metabolism
- Electrophoresis, Agar Gel
- Kinetics
- Molecular Sequence Data
- Nucleic Acid Heteroduplexes/isolation & purification
- Nucleic Acid Heteroduplexes/metabolism
- RNA, Antisense/isolation & purification
- RNA, Antisense/metabolism
- RNA, Ribosomal, 5S/genetics
- RNA, Ribosomal, 5S/isolation & purification
- RNA, Ribosomal, 5S/metabolism
- Transcription Factor TFIIIA
- Transcription Factors/isolation & purification
- Transcription Factors/metabolism
- Xenopus
- Zinc Fingers
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Affiliation(s)
- K P Nightingale
- Laboratory of Molecular Embryology, NICHD, National Institutes of Health, Bethesda, Maryland 20892-2710, USA
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11
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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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12
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Clemens KR, Wolf V, McBryant SJ, Zhang P, Liao X, Wright PE, Gottesfeld JM. Molecular basis for specific recognition of both RNA and DNA by a zinc finger protein. Science 1993; 260:530-3. [PMID: 8475383 DOI: 10.1126/science.8475383] [Citation(s) in RCA: 100] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Transcription factor IIIA (TFIIIA) from Xenopus oocytes binds both the internal control region of the 5S ribosomal RNA genes and the 5S RNA transcript itself. The nucleic acid binding domain of TFIIIA contains nine tandemly repeated zinc finger motifs. A series of precisely truncated forms of this protein have been constructed and assayed for 5S RNA and DNA binding. Different sets of zinc fingers were found to be responsible for high affinity interactions with RNA and with DNA. These results explain how a single protein can exhibit equal affinities for these two very different nucleic acids.
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Affiliation(s)
- K R Clemens
- Department of Molecular Biology, Scripps Research Institute, La Jolla, CA 92037
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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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Makowski GS, Sunderman FW. The interactions of zinc, nickel, and cadmium with Xenopus transcription factor IIIA, assessed by equilibrium dialysis. J Inorg Biochem 1992; 48:107-19. [PMID: 1431887 DOI: 10.1016/0162-0134(92)80020-v] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Transcription factor IIIA (TFIIIA) was isolated from Xenopus ovary and treated with 1,10-phenanthroline to remove zinc. The interactions of apoTFIIIA with Zn2+, Ni2+, and Cd2+ were studied by equilibrium dialysis under anaerobic conditions (pH 7.0, 25 degrees C), using 65ZnCl2, 63NiCl2, and 109CdCl2 as the radioligands. The data for binding of Zn2+, Ni2+, and Cd2+ to apoTFIIIA were best-fitted by a model with two classes of binding sites. For Zn2+, the apparent dissociation constants (KdlZn and Kd2Zn) for the high- and low-affinity sites were 1.0 x 10(-8) and 2.6 x 10(-5) M; the apparent binding capacities of the two classes were 0.8 +/- 0.5 and 9.6 +/- 0.3 g-atoms of Zn/mol; the Hill coefficient was 1.18, consistent with positive cooperativity of Zn-binding sites. For Ni2+, the apparent KdlNi and Kd2Ni values were 2.3 x 10(-5) and 5.2 x 10(-4) M; the apparent binding capacities were 2.3 +/- 0.6 and 8.6 +/- 0.6 g-atoms of Ni/mol; the Hill coefficient was 1.20, consistent with positive cooperativity of Ni-binding sites. For Cd2+, the apparent KdlCd and Kd2Cd values were 2.8 x 10(-6) and 1.6 x 10(-4) M; the apparent binding capacities were 0.9 +/- 0.3 and 2.4 +/- 0.5 g-atoms of Cd/mol; the Hill coefficient was 0.53, consistent with negative cooperativity or heterogeneity of Cd-binding sites. This study has the following significance: First, it helps to resolve a controversy about the zinc content of purified TFIIIA. Second, it shows that the KdlZn of apoTFIIIA is less than the reported KdZn of thionein, consistent with the hypothesis that thionein modulates gene expression by competing with TFIIIA and other Zn-finger proteins for intracellular Zn2+ stores. Third, it confirms previous indirect evidence that the affinity of apoTFIIIA for Zn2+ is much greater than for Cd2+, and that the affinity for Cd2+ is greater than for Ni2+.
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Affiliation(s)
- G S Makowski
- Department of Laboratory Medicine, University of Connecticut Medical School, Farmington 06030
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15
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Abstract
The missing-nucleoside experiment, a recently developed approach for determining the positions along a DNA molecule that make energetically important contacts with protein, has been used to investigate the structure of the complex of transcription factor IIIA with a somatic 5 S RNA gene from Xenopus borealis. We detect three distinct regions of the 5 S promoter that are contacted by TFIIIA, corresponding to the A-box, intermediate element and C-box regions previously identified by mutagenesis experiments. The advantage of the missing-nucleoside experiment over mutagenesis is that additional information, directly related to the structure of the complex, is obtained. Of most importance is that contacts to each strand of DNA are determined independently, and can be assigned unambiguously as interactions with TFIIIA. Throughout the binding site the strongest contacts are made with the non-coding strand of the 5 S gene. The two groups of contacts at either end of the binding site (boxes A and C) are comprised of sets of approximately ten contiguous nucleosides for which the contacts are reflected, without stagger, from one strand to the other. In contrast, contacts in the center of the promoter (the intermediate element) are staggered about five base-pairs in the 5' direction with respect to each strand. These results, when analyzed in conjunction with the hydroxyl-radical footprint of the complex, support a model in which TFIIIA wraps around the DNA in the major groove of the helix for one turn at the two ends of the complex in boxes A and C, and lies on one side of the DNA helix in the center of the complex at the intermediate element.
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Affiliation(s)
- J J Hayes
- Laboratory of Molecular Embryology, National Institutes of Child Health and Human Development, Bethesda, MD 20892
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16
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17
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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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18
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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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19
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Abstract
Remarkable progress has been made in defining the functional significance of the protein-DNA interactions involved in transcription complex formation on yeast tRNA and 5S RNA genes. This new information leads to a re-evaluation of how the class III gene transcription machinery operates.
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Affiliation(s)
- A P Wolffe
- Laboratory of Molecular Embryology, NICHD, National Institutes of Health, Bethesda, Maryland 20891
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20
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Abstract
The DNA double helix exhibits local sequence-dependent polymorphism at the level of the single base pair and dinucleotide step. Curvature of the DNA molecule occurs in DNA regions with a specific type of nucleotide sequence periodicities. Negative supercoiling induces in vitro local nucleotide sequence-dependent DNA structures such as cruciforms, left-handed DNA, multistranded structures, etc. Techniques based on chemical probes have been proposed that make it possible to study DNA local structures in cells. Recent results suggest that the local DNA structures observed in vitro exist in the cell, but their occurrence and structural details are dependent on the DNA superhelical density in the cell and can be related to some cellular processes.
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Affiliation(s)
- E Palecek
- Max-Planck Institut für Biophysikalische Chemie, Göttingen, BRD
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21
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Shastry BS. Xenopus transcription factor IIIA (XTFIIIA): after a decade of research. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 1991; 56:135-44. [PMID: 1947129 DOI: 10.1016/0079-6107(91)90017-m] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Xenopus transcription factor IIIA (XTFIIIA) is the first eukaryotic transcription factor purified to homogeneity and is specifically required for the 5S RNA gene transcription. It contains two structural domains and nine zinc finger motifs through which it recognizes the promoter region of the 5S RNA gene. It also binds to 5S RNA and serves to store 5S RNA in the form of 7S ribonucleoprotein particles in oocytes. Additionally, it forms a metastable complex with 5S DNA and promotes the formation of stable and competent transcription complexes. Its expression is developmentally controlled at the level of transcription and translation. Moreover, it participates in the assembly of active chromatin templates and at least, in part, is responsible for the developmental regulation of two kinds of 5S RNA genes in Xenopus.
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Affiliation(s)
- B S Shastry
- Eye Research Institute of Oakland University, Rochester, MI 48309
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Han M, Cyran F, Fisher M, Kim S, Ginsburg A. Xenopus transcription factor IIIA. Evidence for heterogeneity of Zn2+ binding affinities and specific labeling of cysteine 287. J Biol Chem 1990. [DOI: 10.1016/s0021-9258(18)77418-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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Abstract
The biosynthesis of proteins and nucleic acids in eukaryotes requires the participation of numerous small RNAs, many of which are products of RNA polymerase III transcription. How cells are able to coordinate the synthesis of these RNAs during growth and replication has been the subject of recent exciting and thought-provoking studies. We review the progress in this area, and focus upon shared properties between transcription systems having different functions.
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Affiliation(s)
- J M Palmer
- Department of Biochemistry, University of Missouri, Columbia 65211
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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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25
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Purification and characterization of Saccharomyces cerevisiae transcription factor TFIIIC. Polypeptide composition defined with polyclonal antibodies. J Biol Chem 1990. [DOI: 10.1016/s0021-9258(19)34089-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Klein-Hitpass L, Tsai SY, Weigel NL, Allan GF, Riley D, Rodriguez R, Schrader WT, Tsai MJ, O'Malley BW. The progesterone receptor stimulates cell-free transcription by enhancing the formation of a stable preinitiation complex. Cell 1990; 60:247-57. [PMID: 2153462 DOI: 10.1016/0092-8674(90)90740-6] [Citation(s) in RCA: 180] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Highly purified chicken progesterone receptor (cPR) is shown to stimulate RNA synthesis directly in an in vitro transcription assay. Stimulation of transcription by cPR requires the presence of progesterone response elements (PREs) in the template and can be specifically inhibited by addition of competitor oligonucleotides containing PREs. Binding of receptor to two PREs is cooperative and leads to synergistic (27-fold) stimulation of transcription. A purified fusion protein containing the DNA binding domain of cPR linked to yeast ubiquitin was produced in E. coli and also functions in the transcription assay. Using this in vitro transcription system, we demonstrate that hormone-free cPR activated by salt treatment induces transcription of a test gene in a hormone-independent manner. Finally, we present evidence that the progesterone receptor acts by facilitating the formation of a stable preinitiation complex at the target gene promoter and thus augments the initiation of transcription by RNA polymerase II.
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Affiliation(s)
- L Klein-Hitpass
- Department of Cell Biology, Baylor College of Medicine, Houston, Texas 77030
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