251
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Knight JL, Mekler V, Mukhopadhyay J, Ebright RH, Levy RM. Distance-restrained docking of rifampicin and rifamycin SV to RNA polymerase using systematic FRET measurements: developing benchmarks of model quality and reliability. Biophys J 2004; 88:925-38. [PMID: 15542547 PMCID: PMC1305165 DOI: 10.1529/biophysj.104.050187] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
We are developing distance-restrained docking strategies for modeling macromolecular complexes that combine available high-resolution structures of the components and intercomponent distance restraints derived from systematic fluorescence resonance energy transfer (FRET) measurements. In this article, we consider the problem of docking small-molecule ligands within macromolecular complexes. Using simulated FRET data, we have generated a series of benchmarks that permit estimation of model accuracy based on the quantity and quality of FRET-derived distance restraints, including the number, random error, systematic error, distance distribution, and radial distribution of FRET-derived distance restraints. We find that expected model accuracy is 10 A or better for models based on: i), > or =20 restraints with up to 15% random error and no systematic error, or ii), > or =20 restraints with up to 15% random error, up to 10% systematic error, and a symmetric radial distribution of restraints. Model accuracies can be improved to 5 A or better by increasing the number of restraints to > or =40 and/or by optimizing the distance distribution of restraints. Using experimental FRET data, we have defined the positions of the binding sites within bacterial RNA polymerase of the small-molecule inhibitors rifampicin (Rif) and rifamycin SV (Rif SV). The inferred binding sites for Rif and Rif SV were located with accuracies of, respectively, 7 and 10 A relative to the crystallographically defined binding site for Rif. These accuracies agree with expectations from the benchmark simulations and suffice to indicate that the binding sites for Rif and Rif SV are located within the RNA polymerase active-center cleft, overlapping the binding site for the RNA-DNA hybrid.
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Affiliation(s)
- Jennifer L Knight
- Department of Chemistry and Chemical Biology and the BioMaPS Institute for Quantitative Biology, and Howard Hughes Medical Institute, Waksman Institute, Rutgers University, Piscataway, New Jersey 08854, USA
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252
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Malagon F, Tong AH, Shafer BK, Strathern JN. Genetic interactions of DST1 in Saccharomyces cerevisiae suggest a role of TFIIS in the initiation-elongation transition. Genetics 2004; 166:1215-27. [PMID: 15082542 PMCID: PMC1470799 DOI: 10.1534/genetics.166.3.1215] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
TFIIS promotes the intrinsic ability of RNA polymerase II to cleave the 3'-end of the newly synthesized RNA. This stimulatory activity of TFIIS, which is dependent upon Rpb9, facilitates the resumption of transcription elongation when the polymerase stalls or arrests. While TFIIS has a pronounced effect on transcription elongation in vitro, the deletion of DST1 has no major effect on cell viability. In this work we used a genetic approach to increase our knowledge of the role of TFIIS in vivo. We showed that: (1) dst1 and rpb9 mutants have a synthetic growth defective phenotype when combined with fyv4, gim5, htz1, yal011w, ybr231c, soh1, vps71, and vps72 mutants that is exacerbated during germination or at high salt concentrations; (2) TFIIS and Rpb9 are essential when the cells are challenged with microtubule-destabilizing drugs; (3) among the SDO (synthetic with Dst one), SOH1 shows the strongest genetic interaction with DST1; (4) the presence of multiple copies of TAF14, SUA7, GAL11, RTS1, and TYS1 alleviate the growth phenotype of dst1 soh1 mutants; and (5) SRB5 and SIN4 genetically interact with DST1. We propose that TFIIS is required under stress conditions and that TFIIS is important for the transition between initiation and elongation in vivo.
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Affiliation(s)
- Francisco Malagon
- Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, USA
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253
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Zhang C, Burton ZF. Transcription factors IIF and IIS and nucleoside triphosphate substrates as dynamic probes of the human RNA polymerase II mechanism. J Mol Biol 2004; 342:1085-99. [PMID: 15351637 DOI: 10.1016/j.jmb.2004.07.070] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2004] [Revised: 07/20/2004] [Accepted: 07/21/2004] [Indexed: 11/28/2022]
Abstract
The mechanism for elongation catalyzed by human RNA polymerase II (RNAP II) has been analyzed using millisecond phase transient state kinetics. Here, we apply a running start, two-bond, double-quench protocol. Quenching the reaction with EDTA indicates NTP loading into the active site followed by rapid isomerization. HCl quenching defines the time of phosphodiester bond formation. Model-independent and global kinetic analyses were applied to simulate the RNAP II mechanism for forward elongation through the synthesis of two specific phosphodiester bonds, modeling rate data collected over a wide range of nucleoside triphosphate concentrations. We report adequate two-bond kinetic simulations for the reaction in the presence of TFIIF alone and in the presence of TFIIF+TFIIS, providing detailed insight into the RNAP II mechanism and into processive RNA synthesis. RNAP II extends an RNA chain through a substrate induced-fit mechanism, termed NTP-driven translocation. After rapid isomerization, chemistry is delayed. At a stall point induced by withholding the next templated NTP, RNAP II fractionates into at least two active and one paused conformation, revealed as different forward rates of elongation. In the presence of TFIIF alone or in the presence of TFIIF+TFIIS, rapid rates are very similar; although, with TFIIF alone the complex is more highly poised for forward synthesis. Based on steady-state analysis, TFIIF was thought to suppress transcriptional pausing, but this view is misleading. TFIIF supports elongation and suppresses pausing by stabilizing the post-translocated elongation complex. When TFIIS is present, RNA cleavage and transcriptional restart pathways are supported, but TFIIS has a role in suppression of transient pausing, which is the most important contribution of TFIIS to elongation from a stall position.
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Affiliation(s)
- Chunfen Zhang
- Department of Biochemistry and Molecular Biology, Michigan State University, E. Lansing, MI 48824-1319, USA
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254
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Lange U, Hausner W. Transcriptional fidelity and proofreading in Archaea and implications for the mechanism of TFS-induced RNA cleavage. Mol Microbiol 2004; 52:1133-43. [PMID: 15130130 DOI: 10.1111/j.1365-2958.2004.04039.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
We have addressed the question whether TFS, a protein that stimulates the intrinsic cleavage activity of the archaeal RNA polymerase, is able to improve the fidelity of transcription in Methanococcus. Using non-specific transcription experiments, we could demonstrate that misincorporation of non-templated nucleotides is reduced in the presence of TFS. A more detailed analysis revealed that elongation complexes containing a misincorporated nucleotide were arrested, but could be reactivated by TFS. RNase as well as exonuclease III footprinting experiments demonstrated that this arrest was not combined with extended backtracking. Analysis of paused elongation complexes demonstrated that TFS is able to induce a cleavage resynthesis cycle in such complexes, which resulted in the accumulation of dinucleotides corresponding to the last two nucleotides of the transcript. Further analysis of cleavage products revealed that, even under conditions that strongly promote misincorporation, still 50% of the released dinucleotides were correctly incorporated. Therefore, we assume that pausing of elongation complexes is an important determinant of TFS-induced RNA cleavage from the 3' end. As the incorporation rate of wrong nucleotides is about 700-fold reduced, it is possible that this delay also provides an appropriate time window for cleavage induction in order to maintain transcriptional fidelity by preventing misincorporation.
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Affiliation(s)
- Udo Lange
- Institut für Allgemeine Mikrobiologie, Christian-Albrechts-Universität, Am Botanischen Garten 1-9, 24118 Kiel, Germany
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255
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Abstract
New structural studies of RNA polymerase II (Pol II) complexes mark the beginning of a detailed mechanistic analysis of the eukaryotic mRNA transcription cycle. Crystallographic models of the complete Pol II, together with new biochemical and electron microscopic data, give insights into transcription initiation. The first X-ray analysis of a Pol II complex with a transcription factor, the elongation factor TFIIS, supports the idea that the polymerase has a 'tunable' active site that switches between mRNA synthesis and cleavage. The new studies also show that domains of transcription factors can enter polymerase openings, to modulate function during transcription.
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Affiliation(s)
- Patrick Cramer
- Institute of Biochemistry and Gene Center, University of Munich, Feodor-Lynen-Str. 25, 81377 Munich, Germany.
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256
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Abstract
Nuclear export of mRNA is a central step in gene expression that shows extensive coupling to transcription and transcript processing. However, little is known about the fate of mRNA and its export under conditions that damage the DNA template and RNA itself. Here we report the discovery of four new factors required for mRNA export through a screen of all annotated nonessential Saccharomyces cerevisiae genes. Two of these factors, mRNA surveillance factor Rrp6 and DNA repair protein Lrp1, are nuclear exosome components that physically interact with one another. We find that Lrp1 mediates specific mRNA degradation upon DNA-damaging UV irradiation as well as general mRNA degradation. Lrp1 requires Rrp6 for genomic localization to genes encoding its mRNA targets, and Rrp6 genomic localization in turn correlates with transcription. Further, Rrp6 and Lrp1 are both required for repair of UV-induced DNA damage. These results demonstrate coupling of mRNA surveillance to mRNA export and suggest specificity of the RNA surveillance machinery for different transcript populations. Broadly, these findings link DNA and RNA surveillance to mRNA export.
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Affiliation(s)
- Haley Hieronymus
- Department of Systems Biology, Harvard Medical School and the Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA
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257
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Chen HT, Hahn S. Mapping the Location of TFIIB within the RNA Polymerase II Transcription Preinitiation Complex. Cell 2004; 119:169-80. [PMID: 15479635 DOI: 10.1016/j.cell.2004.09.028] [Citation(s) in RCA: 109] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2004] [Revised: 09/03/2004] [Accepted: 09/09/2004] [Indexed: 10/26/2022]
Abstract
Biochemical probes positioned on the surface of the general transcription factor TFIIB were used to probe the architecture of the RNA polymerase II (Pol II) transcription preinitiation complex (PIC). In PICs, the TFIIB linker and core domains are positioned over the central cleft and wall of Pol II. This positioning is not observed in the smaller Pol II-TFIIB complex. These results lead to a new model for the structure of the PIC, which agrees with most previously documented protein-DNA interactions within Pol II and archaea PICs. Specific interaction of the TFIIB core domain with Pol II positions and orients the promoter DNA over the Pol II central cleft, and TBP-DNA bending leads to bending of the promoter around the surface of Pol II. The TFIIF subunit Tfg1 was found in close proximity to the TFIIB B finger, linker, and core domains, suggesting that these two factors closely cooperate during initiation.
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Affiliation(s)
- Hung-Ta Chen
- Fred Hutchinson Cancer Research Center and Howard Hughes Medical Institute, 1100 Fairview Avenue North, Seattle, WA 98109 USA
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258
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Mei Kwei JS, Kuraoka I, Horibata K, Ubukata M, Kobatake E, Iwai S, Handa H, Tanaka K. Blockage of RNA polymerase II at a cyclobutane pyrimidine dimer and 6-4 photoproduct. Biochem Biophys Res Commun 2004; 320:1133-8. [PMID: 15249207 DOI: 10.1016/j.bbrc.2004.06.066] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2004] [Indexed: 11/29/2022]
Abstract
The blockage of transcription elongation by RNA polymerase II (pol II) at a DNA damage site on the transcribed strand triggers a transcription-coupled DNA repair (TCR), which rapidly removes DNA damage on the transcribed strand of the expressed gene and allows the resumption of transcription. To analyze the effect of UV-induced DNA damage on transcription elongation, an in vitro transcription elongation system using pol II and oligo(dC)-tailed templates containing a cyclobutane pyrimidine dimer (CPD) or 6-4 photoproduct (6-4PP) at a specific site was employed. The results showed that pol II incorporated nucleotides opposite the CPD and 6-4PP and then stalled. Pol II formed a stable ternary complex consisting of pol II, the DNA damage template, and the nascent transcript. Furthermore, atomic force microscopy imaging revealed that pol II stalled at the damaged region. These findings may provide the basis for analysis of the initiation step of TCR.
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Affiliation(s)
- Joan Seah Mei Kwei
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
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259
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Wery M, Shematorova E, Van Driessche B, Vandenhaute J, Thuriaux P, Van Mullem V. Members of the SAGA and Mediator complexes are partners of the transcription elongation factor TFIIS. EMBO J 2004; 23:4232-42. [PMID: 15359273 PMCID: PMC524382 DOI: 10.1038/sj.emboj.7600326] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2003] [Accepted: 06/21/2004] [Indexed: 11/09/2022] Open
Abstract
TFIIS, an elongation factor encoded by DST1 in Saccharomyces cerevisiae, stimulates transcript cleavage in arrested RNA polymerase II. Two components of the RNA polymerase II machinery, Med13 (Srb9) and Spt8, were isolated as two-hybrid partners of the conserved TFIIS N-terminal domain. They belong to the Cdk8 module of the Mediator and to a subform of the SAGA co-activator, respectively. Co-immunoprecipitation experiments showed that TFIIS can bind the Cdk8 module and SAGA in cell-free extracts. spt8Delta and dst1Delta mutants were sensitive to nucleotide-depleting drugs and epistatic to null mutants of the RNA polymerase II subunit Rpb9, suggesting that their elongation defects are mediated by Rpb9. rpb9Delta, spt8Delta and dst1Delta were lethal in cells lacking the Rpb4 subunit. The TFIIS N-terminal domain is also strictly required for viability in rpb4Delta, although it is not needed for binding to RNA polymerase II or for transcript cleavage. It is proposed that TFIIS and the Spt8-containing form of SAGA co-operate to rescue RNA polymerase II from unproductive elongation complexes, and that the Cdk8 module temporarily blocks transcription during transcript cleavage.
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Affiliation(s)
- Maxime Wery
- Laboratoire de Génétique Moléculaire (URBM), Facultés Universitaires Notre-Dame de la Paix, Namur, Belgique
| | - Elena Shematorova
- Laboratoire de Physiogénomique, Service de Biochimie et Génétique Moléculaire, Gif-sur-Yvette Cedex, France
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Benoît Van Driessche
- Laboratoire de Génétique Moléculaire (URBM), Facultés Universitaires Notre-Dame de la Paix, Namur, Belgique
| | - Jean Vandenhaute
- Laboratoire de Génétique Moléculaire (URBM), Facultés Universitaires Notre-Dame de la Paix, Namur, Belgique
| | - Pierre Thuriaux
- Laboratoire de Physiogénomique, Service de Biochimie et Génétique Moléculaire, Gif-sur-Yvette Cedex, France
- Laboratoire de Physiogénomique, Service de Biochimie et Génétique Moléculaire, CEA-Saclay, Bât. 144, 91191 Gif-sur-Yvette Cedex, France. Tel.: +33 1 69 08 35 86; Fax: +33 1 69 08 47 12; E-mail:
| | - Vincent Van Mullem
- Laboratoire de Génétique Moléculaire (URBM), Facultés Universitaires Notre-Dame de la Paix, Namur, Belgique
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260
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Palangat M, Hittinger CT, Landick R. Downstream DNA selectively affects a paused conformation of human RNA polymerase II. J Mol Biol 2004; 341:429-42. [PMID: 15276834 DOI: 10.1016/j.jmb.2004.06.009] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2004] [Revised: 05/25/2004] [Accepted: 06/03/2004] [Indexed: 11/17/2022]
Abstract
Transcriptional pausing by human RNA polymerase II (RNAPII) in the HIV-1 LTR is caused principally by a weak RNA:DNA hybrid that allows rearrangement of reactive or catalytic groups in the enzyme's active site. This rearrangement creates a transiently paused state called the unactivated intermediate that can backtrack into a more long-lived paused species. We report that three different regions of the not-yet-transcribed DNA just downstream of the pause site affect the duration of the HIV-1 pause, and also can influence pause formation. Downstream DNA in at least one region, a T-tract from +5 to +8, increases pause duration by specifically affecting the unactivated intermediate, without corresponding effects on the active or backtracked states. We suggest this effect depends on RNAPII-modulated DNA plasticity and speculate it is mediated by the "trigger loop" thought to participate in RNAP's catalytic cycle. These findings provide a new framework for understanding downstream DNA effects on RNAP.
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Affiliation(s)
- Murali Palangat
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
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261
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Perederina A, Svetlov V, Vassylyeva MN, Tahirov TH, Yokoyama S, Artsimovitch I, Vassylyev DG. Regulation through the secondary channel--structural framework for ppGpp-DksA synergism during transcription. Cell 2004; 118:297-309. [PMID: 15294156 DOI: 10.1016/j.cell.2004.06.030] [Citation(s) in RCA: 272] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2004] [Revised: 06/02/2004] [Accepted: 06/04/2004] [Indexed: 10/26/2022]
Abstract
Bacterial transcription is regulated by the alarmone ppGpp, which binds near the catalytic site of RNA polymerase (RNAP) and modulates its activity. We show that the DksA protein is a crucial component of ppGpp-dependent regulation. The 2.0 A resolution structure of Escherichia coli DksA reveals a globular domain and a coiled coil with two highly conserved Asp residues at its tip that is reminiscent of the transcript cleavage factor GreA. This structural similarity suggests that DksA coiled coil protrudes into the RNAP secondary channel to coordinate a ppGpp bound Mg2+ ion with the Asp residues, thereby stabilizing the ppGpp-RNAP complex. Biochemical analysis demonstrates that DksA affects transcript elongation, albeit differently from GreA; augments ppGpp effects on initiation; and binds directly to RNAP, positioning the Asp residues near the active site. Substitution of these residues eliminates the synergy between DksA and ppGpp. Thus, the secondary channel emerges as a common regulatory entrance for transcription factors.
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Affiliation(s)
- Anna Perederina
- Cellular Signaling Laboratory, Mikazuki-cho, Sayo, Hyogo 679-5148, Japan
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262
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Abstract
High-resolution crystal structures have highlighted functionally important regions in multisubunit RNA polymerases, including the secondary channel, or pore, which is postulated to allow the diffusion of small molecules both into and out of the active center of the enzyme. Recent work from several groups has illustrated how regulatory factors and small molecules can exploit the secondary channel to gain access to the active site and modify the transcription properties of RNA polymerase.
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Affiliation(s)
- Bryce E Nickels
- Department of Microbiology and Molecular Genetics, Harvard Medical School, 200 Longwood Avenue, Blg. D-1, Boston, MA 02115, USA
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263
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Mysiak ME, Holthuizen PE, van der Vliet PC. The adenovirus priming protein pTP contributes to the kinetics of initiation of DNA replication. Nucleic Acids Res 2004; 32:3913-20. [PMID: 15273278 PMCID: PMC506811 DOI: 10.1093/nar/gkh726] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Adenovirus (Ad) precursor terminal protein (pTP) in a complex with Ad DNA polymerase (pol) serves as a primer for Ad DNA replication. During initiation, pol covalently couples the first dCTP with Ser-580 of pTP. By using an in vitro reconstituted replication system comprised of purified proteins, we demonstrate that the conserved Asp-578 and Asp-582 residues of pTP, located close to Ser-580, are important for the initiation activity of the pTP/pol complex. In particular, the negative charge of Asp-578 is essential for this process. The introduced pTP mutations do not alter the binding capacity to DNA or polymerase, suggesting that the priming mechanism is affected. The Asp-578 or Asp-582 mutations increase the Km for dCTP incorporation, and higher dCTP concentrations or Mn2+ replacing Mg2+ partially relieve the initiation defect. Moreover, the kcat/Km values are reduced as a consequence of the pTP mutations. These observations demonstrate that pTP influences the catalytic activity of pol in initiation. Since both Asp residues are situated close to the pol active site during initiation, they may contribute to correct positioning of the OH group in Ser-580. Our results indicate that specific amino acids of the protein primer influence the ability of Ad5 DNA polymerase to initiate DNA replication.
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Affiliation(s)
- Monika E Mysiak
- Department of Physiological Chemistry, University Medical Centre Utrecht, Universiteitsweg 100, 3584 CG Utrecht, The Netherlands
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264
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Coulombe B, Jeronimo C, Langelier MF, Cojocaru M, Bergeron D. Interaction networks of the molecular machines that decode, replicate, and maintain the integrity of the human genome. Mol Cell Proteomics 2004; 3:851-6. [PMID: 15215308 PMCID: PMC4494826 DOI: 10.1074/mcp.r400009-mcp200] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The interaction of many proteins with genomic DNA is required for the expression, replication, and maintenance of the integrity of mammalian genomes. These proteins participate in processes as diverse as gene transcription and mRNA processing, as well as in DNA replication, recombination, and repair. This intricate system, where the various nuclear machineries interact with one another and bind to either common or distinct DNA regions to create an impressive network of protein-protein and protein-DNA interactions, is made even more complex by the need for a very stringent control in order to ensure normal cell growth and differentiation. A general methodology based on the in vivo pull-down of tagged components of nuclear machines and regulatory proteins was used to study genome-wide protein-protein and protein-DNA interactions in mammalian cells. In particular, this approach has been used in defining the interaction networks (or "interactome") formed by RNA polymerase II, a molecular machine that decodes the human genome. In addition, because this methodology allows for the purification of variant forms of tagged complexes having site-directed mutations in key elements, it can also be used for deciphering the relationship between the structure and the function of the molecular machines, such as RNA polymerase II, that by binding DNA play a central role in the pathway from the genome to the organism.
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Affiliation(s)
- Benoit Coulombe
- Laboratory of Gene Transcription, Institut de Recherches Cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, Québec, Canada H2W 1R7.
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265
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Hahn S. Structure and mechanism of the RNA polymerase II transcription machinery. Nat Struct Mol Biol 2004; 11:394-403. [PMID: 15114340 PMCID: PMC1189732 DOI: 10.1038/nsmb763] [Citation(s) in RCA: 354] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2003] [Accepted: 03/22/2004] [Indexed: 11/09/2022]
Abstract
Advances in structure determination of the bacterial and eukaryotic transcription machinery have led to a marked increase in the understanding of the mechanism of transcription. Models for the specific assembly of the RNA polymerase II transcription machinery at a promoter, conformational changes that occur during initiation of transcription, and the mechanism of initiation are discussed in light of recent developments.
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Affiliation(s)
- Steven Hahn
- Fred Hutchinson Cancer Research Center and Howard Hughes Medical Institute, 1100 Fairview Ave N., A1-162, Seattle, Washington 98109, USA.
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266
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da Costa e Silva O, Lorbiecke R, Garg P, Müller L, Wassmann M, Lauert P, Scanlon M, Hsia AP, Schnable PS, Krupinska K, Wienand U. The Etched1 gene of Zea mays (L.) encodes a zinc ribbon protein that belongs to the transcriptionally active chromosome (TAC) of plastids and is similar to the transcription factor TFIIS. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2004; 38:923-39. [PMID: 15165185 DOI: 10.1111/j.1365-313x.2004.02094.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Etched1 (et1) is a pleiotropic, recessive mutation of maize that causes fissured and cracked mature kernels and virescent seedlings. Microscopic examinations of the et1 phenotype revealed an aberrant plastid development in mutant kernels and mutant leaves. Here, we report on the cloning of the et1 gene by transposon tagging, the localization of the gene product in chloroplasts, and its putative function in the plastid transcriptional apparatus. Several alleles of Mutator (Mu)-induced et1 mutants, the et1-reference (et1-R) mutant, and Et1 wild-type were cloned and analyzed at the molecular level. Northern analyses with wild-type plants revealed that Et1 transcripts are present in kernels, leaves, and other types of tissue, and no Et1 expression could be detected in the et1 mutants analyzed. The ET1 protein is imported by chloroplasts and has been immunologically detected in transcriptionally active chromosome (TAC) fractions derived from chloroplasts. Accordingly, the relative transcriptional activity of TAC fractions was significantly reduced in chloroplasts of et1-R plants. ET1 is the first zinc ribbon (ZR) protein shown to be targeted to plastids. With regard to its localization and its striking structural similarity to the eukaryotic transcription elongation factor TFIIS, it is feasible that ET1 functions in plastid transcription elongation by reactivation of arrested RNA polymerases.
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Affiliation(s)
- Oswaldo da Costa e Silva
- Institut für Allgemeine Botanik und Botanischer Garten, Universität Hamburg, Ohnhorststr. 18, D-22 609 Hamburg, Germany
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267
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Gong XQ, Nedialkov YA, Burton ZF. Alpha-amanitin blocks translocation by human RNA polymerase II. J Biol Chem 2004; 279:27422-7. [PMID: 15096519 DOI: 10.1074/jbc.m402163200] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Our laboratory has developed methods for transient state kinetic analysis of human RNA polymerase II elongation. In these studies, multiple conformations of the RNA polymerase II elongation complex were revealed by their distinct elongation potential and differing dependence on nucleoside triphosphate substrate. Among these are conformations that appear to correspond to different translocation states of the DNA template and RNA-DNA hybrid. Using alpha-amanitin as a dynamic probe of the RNA polymerase II mechanism, we show that the most highly poised conformation of the elongation complex, which we interpreted previously as the posttranslocated state, is selectively resistant to inhibition with alpha-amanitin. Because initially resistant elongation complexes form only a single phosphodiester bond before being rendered inactive in the following bond addition cycle, alpha-amanitin inhibits elongation at each translocation step.
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Affiliation(s)
- Xue Q Gong
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824-1319, USA
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268
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StrÄter N, Maier T, Skerra A, Schürrle K, Schepers U. Biochemie und Molekularbiologie 2003. NACHRICHTEN AUS DER CHEMIE 2004. [PMCID: PMC7168105 DOI: 10.1002/nadc.20040520309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | | | - Arne Skerra
- Lehrstuhl für Biologische Chemie Technische Universität München
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Brochier C, Forterre P, Gribaldo S. Archaeal phylogeny based on proteins of the transcription and translation machineries: tackling the Methanopyrus kandleri paradox. Genome Biol 2004; 5:R17. [PMID: 15003120 PMCID: PMC395767 DOI: 10.1186/gb-2004-5-3-r17] [Citation(s) in RCA: 98] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2003] [Revised: 01/05/2004] [Accepted: 01/21/2004] [Indexed: 11/25/2022] Open
Abstract
This article presents a phylogenetic analysis of the Archea based on sets of transcription and translation proteins. The phylogenies shed light on the evolutionary position of Methanopyrus kandleri. Background Phylogenetic analysis of the Archaea has been mainly established by 16S rRNA sequence comparison. With the accumulation of completely sequenced genomes, it is now possible to test alternative approaches by using large sequence datasets. We analyzed archaeal phylogeny using two concatenated datasets consisting of 14 proteins involved in transcription and 53 ribosomal proteins (3,275 and 6,377 positions, respectively). Results Important relationships were confirmed, notably the dichotomy of the archaeal domain as represented by the Crenarchaeota and Euryarchaeota, the sister grouping of Sulfolobales and Aeropyrum pernix, and the monophyly of a large group comprising Thermoplasmatales, Archaeoglobus fulgidus, Methanosarcinales and Halobacteriales, with the latter two orders forming a robust cluster. The main difference concerned the position of Methanopyrus kandleri, which grouped with Methanococcales and Methanobacteriales in the translation tree, whereas it emerged at the base of the euryarchaeotes in the transcription tree. The incongruent placement of M. kandleri is likely to be the result of a reconstruction artifact due to the high evolutionary rates displayed by the components of its transcription apparatus. Conclusions We show that two informational systems, transcription and translation, provide a largely congruent signal for archaeal phylogeny. In particular, our analyses support the appearance of methanogenesis after the divergence of the Thermococcales and a late emergence of aerobic respiration from within methanogenic ancestors. We discuss the possible link between the evolutionary acceleration of the transcription machinery in M. kandleri and several unique features of this archaeon, in particular the absence of the elongation transcription factor TFS.
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Affiliation(s)
- Céline Brochier
- Equipe Phylogénomique, Université Aix-Marseille I, Centre Saint-Charles, 13331 Marseille Cedex 3, France.
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270
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Affiliation(s)
- Patrick Cramer
- Institute of Biochemistry and Gene Center, University of Munich, 81377 Munich, Germany
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271
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Sosunova E, Sosunov V, Kozlov M, Nikiforov V, Goldfarb A, Mustaev A. Donation of catalytic residues to RNA polymerase active center by transcription factor Gre. Proc Natl Acad Sci U S A 2003; 100:15469-74. [PMID: 14668436 PMCID: PMC307591 DOI: 10.1073/pnas.2536698100] [Citation(s) in RCA: 102] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2003] [Indexed: 11/18/2022] Open
Abstract
During transcription elongation, RNA polymerase (RNAP) occasionally loses its grip on the growing RNA end and backtracks on the DNA template. Prokaryotic Gre factors rescue the backtracked ternary elongating complex through stimulation of an intrinsic endonuclease activity, which removes the disengaged 3' RNA segment. By using RNA-protein crosslinking in defined ternary elongating complexes, site-directed mutagenesis, discriminative biochemical assays, and docking of the two protein structures, we show that Gre acts by providing two carboxylate residues for coordination of catalytic Mg2+ ion in the RNAP active center. A similar mechanism is suggested for the functionally analogous eukaryotic SII factor. The results expand the general two-metal model of RNAP catalytic mechanism whereby one of the Mg2+ ions is permanently retained, whereas the other is recruited ad hoc by an auxiliary factor.
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Affiliation(s)
- Ekaterina Sosunova
- Public Health Research Institute, 225 Warren Street, Newark, NJ 07103, USA
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272
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Laptenko O, Lee J, Lomakin I, Borukhov S. Transcript cleavage factors GreA and GreB act as transient catalytic components of RNA polymerase. EMBO J 2003; 22:6322-34. [PMID: 14633991 PMCID: PMC291851 DOI: 10.1093/emboj/cdg610] [Citation(s) in RCA: 160] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2003] [Revised: 10/06/2003] [Accepted: 10/14/2003] [Indexed: 11/13/2022] Open
Abstract
Prokaryotic transcription elongation factors GreA and GreB stimulate intrinsic nucleolytic activity of RNA polymerase (RNAP). The proposed biological role of Gre-induced RNA hydrolysis includes transcription proofreading, suppression of transcriptional pausing and arrest, and facilitation of RNAP transition from transcription initiation to transcription elongation. Using an array of biochemical and molecular genetic methods, we mapped the interaction interface between Gre and RNAP and identified the key residues in Gre responsible for induction of nucleolytic activity in RNAP. We propose a structural model in which the C-terminal globular domain of Gre binds near the opening of the RNAP secondary channel, the N-terminal coiled-coil domain (NTD) protrudes inside the RNAP channel, and the tip of the NTD is brought to the immediate vicinity of RNAP catalytic center. Two conserved acidic residues D41 and E44 located at the tip of the NTD assist RNAP by coordinating the Mg2+ ion and water molecule required for catalysis of RNA hydrolysis. If so, Gre would be the first transcription factor known to directly participate in the catalytic act of RNAP.
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Affiliation(s)
- Oleg Laptenko
- Department of Microbiology and Immunology, SUNY Health Science Center at Brooklyn, 450 Clarkson Avenue, BSB 3-27, Brooklyn, NY 11203, USA
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273
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Zhang C, Yan H, Burton ZF. Combinatorial control of human RNA polymerase II (RNAP II) pausing and transcript cleavage by transcription factor IIF, hepatitis delta antigen, and stimulatory factor II. J Biol Chem 2003; 278:50101-11. [PMID: 14506279 DOI: 10.1074/jbc.m307590200] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
When RNA polymerase II (RNAP II) is forced to stall, elongation complexes (ECs) are observed to leave the active pathway and enter a paused state. Initially, ECs equilibrate between active and paused conformations, but with stalls of a long duration, ECs backtrack and become sensitive to transcript cleavage, which is stimulated by the EC rescue factor stimulatory factor II (TFIIS/SII). In this work, the rates for equilibration between the active and pausing pathways were estimated in the absence of an elongation factor, in the presence of hepatitis delta antigen (HDAg), and in the presence of transcription factor IIF (TFIIF), with or without addition of SII. Rates of equilibration between the active and paused states are not very different in the presence or absence of elongation factors HDAg and TFIIF. SII facilitates escape from stalled ECs by stimulating RNAP II backtracking and transcript cleavage and by increasing rates into and out of the paused EC. TFIIF and SII cooperate to merge the pausing and active pathways, a combinatorial effect not observed with HDAg and SII. In the presence of HDAg and SII, pausing is observed without stimulation of transcript cleavage, indicating that the EC can pause without backtracking beyond the pre-translocated state.
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Affiliation(s)
- Chunfen Zhang
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824-1319, USA
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274
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Conaway RC, Kong SE, Conaway JW. TFIIS and GreB: two like-minded transcription elongation factors with sticky fingers. Cell 2003; 114:272-4. [PMID: 12914690 DOI: 10.1016/s0092-8674(03)00607-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Ronald C Conaway
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
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275
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Opalka N, Chlenov M, Chacon P, Rice WJ, Wriggers W, Darst SA. Structure and function of the transcription elongation factor GreB bound to bacterial RNA polymerase. Cell 2003; 114:335-45. [PMID: 12914698 DOI: 10.1016/s0092-8674(03)00600-7] [Citation(s) in RCA: 177] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Bacterial GreA and GreB promote transcription elongation by stimulating an endogenous, endonucleolytic transcript cleavage activity of the RNA polymerase. The structure of Escherichia coli core RNA polymerase bound to GreB was determined by cryo-electron microscopy and image processing of helical crystals to a nominal resolution of 15 A, allowing fitting of high-resolution RNA polymerase and GreB structures. In the resulting model, the GreB N-terminal coiled-coil domain extends 45 A through a channel directly to the RNA polymerase active site. The model leads to detailed insights into the mechanism of Gre factor activity that explains a wide range of experimental observations and points to a key role for conserved acidic residues at the tip of the Gre factor coiled coil in modifying the RNA polymerase active site to catalyze the cleavage reaction. Mutational studies confirm that these positions are critical for Gre factor function.
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Affiliation(s)
- Natacha Opalka
- The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
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