201
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Temiakov D, Zenkin N, Vassylyeva MN, Perederina A, Tahirov TH, Kashkina E, Savkina M, Zorov S, Nikiforov V, Igarashi N, Matsugaki N, Wakatsuki S, Severinov K, Vassylyev DG. Structural basis of transcription inhibition by antibiotic streptolydigin. Mol Cell 2005; 19:655-66. [PMID: 16167380 DOI: 10.1016/j.molcel.2005.07.020] [Citation(s) in RCA: 124] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Streptolydigin (Stl) is a potent inhibitor of bacterial RNA polymerases (RNAPs). The 2.4 A resolution structure of the Thermus thermophilus RNAP-Stl complex showed that, in full agreement with the available genetic data, the inhibitor binding site is located 20 A away from the RNAP active site and encompasses the bridge helix and the trigger loop, two elements that are considered to be crucial for RNAP catalytic center function. Structure-based biochemical experiments revealed additional determinants of Stl binding and demonstrated that Stl does not affect NTP substrate binding, DNA translocation, and phosphodiester bond formation. The RNAP-Stl complex structure, its comparison with the closely related substrate bound eukaryotic transcription elongation complexes, and biochemical analysis suggest an inhibitory mechanism in which Stl stabilizes catalytically inactive (preinsertion) substrate bound transcription intermediate, thereby blocking structural isomerization of RNAP to an active configuration. The results provide a basis for a design of new antibiotics utilizing the Stl-like mechanism.
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Affiliation(s)
- Dmitry Temiakov
- Department of Cell Biology, School of Osteopathic Medicine, University of Medicine and Dentistry of New Jersey, Stratford, New Jersey 08084, USA
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202
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Tuske S, Sarafianos SG, Wang X, Hudson B, Sineva E, Mukhopadhyay J, Birktoft JJ, Leroy O, Ismail S, Clark AD, Dharia C, Napoli A, Laptenko O, Lee J, Borukhov S, Ebright RH, Arnold E. Inhibition of bacterial RNA polymerase by streptolydigin: stabilization of a straight-bridge-helix active-center conformation. Cell 2005; 122:541-52. [PMID: 16122422 PMCID: PMC2754413 DOI: 10.1016/j.cell.2005.07.017] [Citation(s) in RCA: 162] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2005] [Revised: 06/03/2005] [Accepted: 07/13/2005] [Indexed: 11/17/2022]
Abstract
We define the target, mechanism, and structural basis of inhibition of bacterial RNA polymerase (RNAP) by the tetramic acid antibiotic streptolydigin (Stl). Stl binds to a site adjacent to but not overlapping the RNAP active center and stabilizes an RNAP-active-center conformational state with a straight-bridge helix. The results provide direct support for the proposals that alternative straight-bridge-helix and bent-bridge-helix RNAP-active-center conformations exist and that cycling between straight-bridge-helix and bent-bridge-helix RNAP-active-center conformations is required for RNAP function. The results set bounds on models for RNAP function and suggest strategies for design of novel antibacterial agents.
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Affiliation(s)
- Steven Tuske
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway NJ 08854, USA
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway NJ 08854, USA
| | - Stefan G. Sarafianos
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway NJ 08854, USA
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway NJ 08854, USA
| | - Xinyue Wang
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway NJ 08854, USA
- Waksman Institute, Rutgers University, Piscataway NJ 08854, USA
- Howard Hughes Medical Institute, Piscataway NJ 08854, USA
| | - Brian Hudson
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway NJ 08854, USA
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway NJ 08854, USA
| | - Elena Sineva
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway NJ 08854, USA
- Waksman Institute, Rutgers University, Piscataway NJ 08854, USA
- Howard Hughes Medical Institute, Piscataway NJ 08854, USA
| | - Jayanta Mukhopadhyay
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway NJ 08854, USA
- Waksman Institute, Rutgers University, Piscataway NJ 08854, USA
- Howard Hughes Medical Institute, Piscataway NJ 08854, USA
| | - Jens J. Birktoft
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway NJ 08854, USA
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway NJ 08854, USA
| | - Olivier Leroy
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway NJ 08854, USA
- Waksman Institute, Rutgers University, Piscataway NJ 08854, USA
- Howard Hughes Medical Institute, Piscataway NJ 08854, USA
| | - Sajida Ismail
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway NJ 08854, USA
- Waksman Institute, Rutgers University, Piscataway NJ 08854, USA
- Howard Hughes Medical Institute, Piscataway NJ 08854, USA
| | - Arthur D. Clark
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway NJ 08854, USA
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway NJ 08854, USA
| | - Chhaya Dharia
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway NJ 08854, USA
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway NJ 08854, USA
| | - Andrew Napoli
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway NJ 08854, USA
- Waksman Institute, Rutgers University, Piscataway NJ 08854, USA
| | - Oleg Laptenko
- Department of Cell Biology, UMDNJ, Stratford NJ 08084, USA
| | - Jookyung Lee
- Department of Cell Biology, UMDNJ, Stratford NJ 08084, USA
| | | | - Richard H. Ebright
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway NJ 08854, USA
- Waksman Institute, Rutgers University, Piscataway NJ 08854, USA
- Howard Hughes Medical Institute, Piscataway NJ 08854, USA
| | - Eddy Arnold
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway NJ 08854, USA
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway NJ 08854, USA
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203
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Gong XQ, Zhang C, Feig M, Burton ZF. Dynamic error correction and regulation of downstream bubble opening by human RNA polymerase II. Mol Cell 2005; 18:461-70. [PMID: 15893729 DOI: 10.1016/j.molcel.2005.04.011] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2004] [Revised: 03/02/2005] [Accepted: 04/21/2005] [Indexed: 01/22/2023]
Abstract
The nucleotide triphosphate (NTP)-driven translocation hypothesis posits that NTP substrates bind to templated DNA sites prior to translocation into the active site. By using millisecond phase kinetics, we demonstrate this prediction in three different ways. First, we show that, in the presence of the translocation blocker alpha-amanitin, NTPs (but not deoxynucleotide triphosphate [dNTPs]) templated at downstream sites (i + 2 and i + 3) dislodge an active site (i + 1) NTP, which was otherwise fated to complete bond synthesis. Second, we show that NTPs templated at i + 2 and/or i + 3 downstream sites suppress misincorporation errors. Third, we show that NTPs templated at downstream sites stabilize the posttranslocated elongation complex at a stall position. Therefore, at least two NTP substrates pair to DNA templated sites downstream of the active site. These results demonstrate the mechanisms of NTP loading and transcriptional efficiency and fidelity for human RNA polymerase II and indicate regulation of downstream bubble opening by NTPs.
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Affiliation(s)
- Xue Q Gong
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, USA
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204
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Kulbachinskiy A, Feklistov A, Krasheninnikov I, Goldfarb A, Nikiforov V. Aptamers to Escherichia coli core RNA polymerase that sense its interaction with rifampicin, sigma-subunit and GreB. ACTA ACUST UNITED AC 2005; 271:4921-31. [PMID: 15606780 DOI: 10.1111/j.1432-1033.2004.04461.x] [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: 11/30/2022]
Abstract
Bacterial RNA polymerase (RNAP) is the central enzyme of gene expression that is responsible for the synthesis of all types of cellular RNAs. The process of transcription is accompanied by complex structural rearrangements of RNAP. Despite the recent progress in structural studies of RNAP, detailed mechanisms of conformational changes of RNAP that occur at different stages of transcription remain unknown. The goal of this work was to obtain novel ligands to RNAP which would target different epitopes of the enzyme and serve as specific probes to study the mechanism of transcription and conformational flexibility of RNAP. Using in vitro selection methods, we obtained 13 classes of ssDNA aptamers against Escherichia coli core RNAP. The minimal nucleic acid scaffold (an oligonucleotide construct imitating DNA and RNA in elongation complex), rifampicin and the sigma70-subunit inhibited binding of the aptamers to RNAP core but did not affect the dissociation rate of preformed RNAP-aptamer complexes. We argue that these ligands sterically block access of the aptamers to their binding sites within the main RNAP channel. In contrast, transcript cleavage factor GreB increased the rate of dissociation of preformed RNAP-aptamer complexes. This suggested that GreB that binds RNAP outside the main channel actively disrupts RNAP-aptamer complexes by inducing conformational changes in the channel. We propose that the aptamers obtained in this work will be useful for studying the interactions of RNAP with various ligands and regulatory factors and for investigating the conformational flexibility of the enzyme.
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205
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Arima Y, Nitta M, Kuninaka S, Zhang D, Fujiwara T, Taya Y, Nakao M, Saya H. Transcriptional Blockade Induces p53-dependent Apoptosis Associated with Translocation of p53 to Mitochondria. J Biol Chem 2005; 280:19166-76. [PMID: 15753095 DOI: 10.1074/jbc.m410691200] [Citation(s) in RCA: 117] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The tumor suppressor p53 functions as a transcriptional activator to induce cell cycle arrest and apoptosis in response to DNA damage. Although p53 was also shown to mediate apoptosis in a manner independent of its transactivation activity, the mechanism and conditions that trigger such cell death have remained largely unknown. We have now shown that inhibition of RNA polymerase II-mediated transcription by alpha-amanitin or RNA interference induced p53-dependent apoptosis. Inhibition of pol II-mediated transcription resulted in down-regulation of p21Cip1, which was caused by both transcriptional suppression and protein degradation, despite eliciting p53 accumulation, allowing the cells to progress into S phase and then to undergo apoptosis. This cell death did not require the transcription of p53 target genes and was preceded by translocation of the accumulated p53 to mitochondria. Our data thus suggested that blockade of pol II-mediated transcription induced p53 accumulation in mitochondria and was the critical factor for eliciting p53-dependent but transcription-independent apoptosis.
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Affiliation(s)
- Yoshimi Arima
- Department of Tumor Genetics and Biology, Graduate School of Medical Sciences, Kumamoto University, Honjo, Kumamoto 860-8556, Japan
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206
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Pommier Y, Cherfils J. Interfacial inhibition of macromolecular interactions: nature's paradigm for drug discovery. Trends Pharmacol Sci 2005; 26:138-45. [PMID: 15749159 DOI: 10.1016/j.tips.2005.01.008] [Citation(s) in RCA: 130] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
One of nature's strategies for interfering with molecular interactions is to trap macromolecules in transition states with their partners in dead-end complexes that are unable to complete their biological function. This type of inhibition, which we refer to as "interfacial inhibition", is illustrated by two natural inhibitors, brefeldin A (BFA) and camptothecin (CPT), whose modes of action have been elucidated fully in structural studies. Interfacial inhibition occurs at the protein-protein interface in the case of BFA and at the protein-DNA interface in the case of CPT. In both systems, the drugs take advantage of transient structural and energetic conditions created by the macromolecular complex, which give rise to "hot-spots" for drug binding. In addition to these examples, several natural compounds such as forskolin, tubulin inhibitors and immunophilins target protein interfaces. We propose that interfacial inhibition is a paradigm for the discovery of drugs that interfere with macromolecular complexes.
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Affiliation(s)
- Yves Pommier
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-4255, USA.
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207
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Thiriet C, Hayes JJ. Replication-independent core histone dynamics at transcriptionally active loci in vivo. Genes Dev 2005; 19:677-82. [PMID: 15769942 PMCID: PMC1065721 DOI: 10.1101/gad.1265205] [Citation(s) in RCA: 114] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
We used a novel labeling technique in the naturally synchronous organism Physarum polycephalum to examine the fate of core histones in G2 phase. We find rapid exchange of H2A/H2B dimers with free pools that is greatly diminished by treatment of the cells with alpha-amanitin. This exchange is enhanced in pol II-coding sequences compared with extragenic regions or inactive loci. In contrast, H3/H4 tetramers exhibit far lower levels of exchange in the pol II-transcribed genes tested, suggesting that tetramer exchange occurs via a distinct mechanism. However, we find that transcribed regions of the ribosomal RNA gene loci exhibit rapid exchange of H3/H4 tetramers. Thus, our data show that the majority of the pol II transcription-dependent histone exchange is due to elongation in vivo rather than promoter remodeling or other pol II-dependent alterations in promoter structure and, in contrast to pol I, pol II transcription through nucleosomes in vivo causes facile exchange of both H2A/H2B dimers while allowing conservation of epigenetic "marks" and other post-translational modifications on H3 and H4.
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Affiliation(s)
- Christophe Thiriet
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York 14642, USA
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208
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Mukhopadhyay J, Sineva E, Knight J, Levy RL, Ebright RH. Antibacterial peptide microcin J25 inhibits transcription by binding within and obstructing the RNA polymerase secondary channel. Mol Cell 2005; 14:739-51. [PMID: 15200952 PMCID: PMC2754415 DOI: 10.1016/j.molcel.2004.06.010] [Citation(s) in RCA: 159] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2004] [Revised: 04/13/2004] [Accepted: 04/20/2004] [Indexed: 11/21/2022]
Abstract
The antibacterial peptide microcin J25 (MccJ25) inhibits transcription by bacterial RNA polymerase (RNAP). Biochemical results indicate that inhibition of transcription occurs at the level of NTP uptake or NTP binding by RNAP. Genetic results indicate that inhibition of transcription requires an extensive determinant, comprising more than 50 amino acid residues, within the RNAP secondary channel (also known as the "NTP-uptake channel" or "pore"). Biophysical results indicate that inhibition of transcription involves binding of MccJ25 within the RNAP secondary channel. Molecular modeling indicates that binding of MccJ25 within the RNAP secondary channel obstructs the RNAP secondary channel. We conclude that MccJ25 inhibits transcription by binding within and obstructing the RNAP secondary channel--acting essentially as a "cork in a bottle." Obstruction of the RNAP secondary channel represents an attractive target for drug discovery.
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Affiliation(s)
- Jayanta Mukhopadhyay
- Howard Hughes Medical Institute, Waksman Institute, and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway NJ 08854, USA
| | - Elena Sineva
- Howard Hughes Medical Institute, Waksman Institute, and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway NJ 08854, USA
| | - Jennifer Knight
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway NJ 08854, USA
| | - Ronald L. Levy
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway NJ 08854, USA
| | - Richard H. Ebright
- Howard Hughes Medical Institute, Waksman Institute, and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway NJ 08854, USA
- To whom correspondence should be addressed. Corresponding Author: Richard H. Ebright, Address: Waksman Institute, Rutgers University, Piscataway NJ 08854, USA, Telephone: (732) 445-5179, Telefax: (732) 445-5735,
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209
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Armache KJ, Mitterweger S, Meinhart A, Cramer P. Structures of Complete RNA Polymerase II and Its Subcomplex, Rpb4/7. J Biol Chem 2005; 280:7131-4. [PMID: 15591044 DOI: 10.1074/jbc.m413038200] [Citation(s) in RCA: 184] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We determined the x-ray structure of the RNA polymerase (Pol) II subcomplex Rpb4/7 at 2.3 A resolution, combined it with a previous structure of the 10-subunit polymerase core, and refined an atomic model of the complete 12-subunit Pol II at 3.8-A resolution. Comparison of the complete Pol II structure with structures of the Pol II core and free Rpb4/7 shows that the core-Rpb4/7 interaction goes along with formation of an alpha-helix in the linker region of the largest Pol II subunit and with folding of the conserved Rpb7 tip loop. Details of the core-Rpb4/7 interface explain facilitated Rpb4/7 dissociation in a temperature-sensitive Pol II mutant and specific assembly of Pol I with its Rpb4/7 counterpart, A43/14. The refined atomic model of Pol II serves as the new reference structure for analysis of the transcription mechanism and enables structure solution of complexes of the complete enzyme with additional factors and nucleic acids by molecular replacement.
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Affiliation(s)
- Karim-Jean Armache
- Gene Center, University of Munich (LMU), Department of Chemistry and Biochemistry, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
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210
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Ghosh M, Liu G, Randall G, Bevington J, Leffak M. Transcription factor binding and induced transcription alter chromosomal c-myc replicator activity. Mol Cell Biol 2005; 24:10193-207. [PMID: 15542830 PMCID: PMC529035 DOI: 10.1128/mcb.24.23.10193-10207.2004] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The observation that transcriptionally active genes generally replicate early in S phase and observations of the interaction between transcription factors and replication proteins support the thesis that promoter elements may have a role in DNA replication. To test the relationship between transcription and replication we constructed HeLa cell lines in which inducible green fluorescent protein (GFP)-encoding genes replaced the proximal approximately 820-bp promoter region of the c-myc gene. Without the presence of an inducer, basal expression occurred from the GFP gene in either orientation and origin activity was restored to the mutant c-myc replicator. In contrast, replication initiation was repressed upon induction of transcription. When basal or induced transcription complexes were slowed by the presence of alpha-amanitin, origin activity depended on the orientation of the transcription unit. To test mechanistically whether basal transcription or transcription factor binding was sufficient for replication rescue by the uninduced GFP genes, a GAL4p binding cassette was used to replace all regulatory sequences within approximately 1,400 bp 5' to the c-myc gene. In these cells, expression of a CREB-GAL4 fusion protein restored replication origin activity. These results suggest that transcription factor binding can enhance replication origin activity and that high levels of expression or the persistence of transcription complexes can repress it.
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Affiliation(s)
- M Ghosh
- Department of Biochemistry and Molecular Biology, Wright State University School of Medicine, 3640 Colonel Glenn Highway, Dayton, OH 45435, USA
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211
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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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212
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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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213
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Kuhlman P, Duff HL, Galant A. A fluorescence-based assay for multisubunit DNA-dependent RNA polymerases. Anal Biochem 2004; 324:183-90. [PMID: 14690681 DOI: 10.1016/j.ab.2003.08.038] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The properties of DNA-dependent RNA polymerases have been studied since the 1960s, but considerable interest in probing RNA polymerase structure/function relationships, the roles of different classes of RNA polymerases in cellular processes, and the feasibility of using RNA polymerases as drug targets still exists. Historically, RNA polymerase activity has been measured by the incorporation into RNA of radioisotopically labeled nucleotides. We report the development of an assay for RNA polymerase activity that uses the dye RiboGreen to detect transcripts by fluorescence and is thus free of the expense, short shelf life, and high handling costs of radioisotopes. The method is relatively quick and can be performed entirely in microplate format, allowing for the processing of dozens to hundreds of samples in parallel. It should thus be well-suited to use in drug screening and analysis of chromatographic fractions. As RiboGreen fluorescence is enhanced by binding to either RNA or DNA, template DNA must be removed by DNase digestion and ultrafiltration between the transcription and the detection phases of the assay procedure. Although RiboGreen fluorescence is sensitive to changes in solvent environment, solvent exchange in the ultrafiltration step allows comparison of transcription levels even under extremes of salt, pH, etc.
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Affiliation(s)
- Peter Kuhlman
- Department of Chemistry and Biochemistry, Denison University, Granville, OH 43023, USA.
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214
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Azubel M, Wolf SG, Sperling J, Sperling R. Three-Dimensional Structure of the Native Spliceosome by Cryo-Electron Microscopy. Mol Cell 2004; 15:833-9. [PMID: 15350226 DOI: 10.1016/j.molcel.2004.07.022] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2004] [Revised: 06/24/2004] [Accepted: 06/29/2004] [Indexed: 11/17/2022]
Abstract
Splicing of pre-mRNA occurs in a multicomponent macromolecular machine--the spliceosome. The spliceosome can be assembled in vitro by a stepwise assembly of a number of snRNPs and additional proteins on exogenously added pre-mRNA. In contrast, splicing in vivo occurs in preformed particles where endogenous pre-mRNAs are packaged with all five spliceosomal U snRNPs (penta-snRNP) together with other splicing factors. Here we present a three-dimensional image reconstruction by cryo-electron microscopy of native spliceosomes, derived from cell nuclei, at a resolution of 20 angstroms. The structure revealed an elongated globular particle made up of two distinct subunits connected to each other leaving a tunnel in between. We show here that the larger subunit is a suitable candidate to accommodate the penta-snRNP, and that the tunnel could accommodate the pre-mRNA component of the spliceosome. The features this structure reveals provide new insight into the global architecture of the native splicing machine.
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Affiliation(s)
- Maia Azubel
- Department of Genetics, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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215
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Iyer LM, Koonin EV, Aravind L. Evolution of bacterial RNA polymerase: implications for large-scale bacterial phylogeny, domain accretion, and horizontal gene transfer. Gene 2004; 335:73-88. [PMID: 15194191 DOI: 10.1016/j.gene.2004.03.017] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2003] [Revised: 02/12/2004] [Accepted: 03/05/2004] [Indexed: 10/26/2022]
Abstract
Comparative analysis of the domain architectures of the beta, beta', and sigma(70) subunits of bacterial DNA-dependent RNA polymerases (DdRp), combined with sequence-based phylogenetic analysis, revealed a fundamental split among bacteria. DNA-dependent RNA polymerase subunits of Group I, which includes Proteobacteria, Aquifex, Chlamydia, Spirochaetes, Cytophaga-Chlorobium, and Planctomycetes, are characterized by three distinct inserts, namely a Sandwich Barrel Hybrid Motif domain in the beta subunit, a beta-beta' module (BBM) 1 domain in the beta' subunit, and a distinct helical module in the sigma subunit. The DdRp subunits of remaining bacteria, which comprise Group II, lack these inserts, although some additional inserted domains are present in individual lineages. The separation of bacteria into Group I and Group II is generally compatible with the topologies of phylogenetic trees of the conserved regions of DdRp subunits and concatenated ribosomal proteins and might represent the primary bifurcation in bacterial evolution. A striking deviation from this evolutionary pattern is Aquifex whose DdRp subunits cluster within Group I, whereas phylogenetic analysis of ribosomal proteins identifies Aquifex as grouping with Thermotoga another bacterial hyperthemophile belonging to Group II. The inferred evolutionary scenario for the DdRp subunits includes domain accretion and rearrangement, with some likely horizontal transfer events. Although evolution of bacterial DdRp appeared to be generally dominated by vertical inheritance, horizontal transfer of complete genes for all or some of the subunits, resulting in displacement of the ancestral genes, might have played a role in several lineages, such as Aquifex, Thermotoga, and Fusobacterium.
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Affiliation(s)
- Lakshminarayan M Iyer
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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216
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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: 352] [Impact Index Per Article: 17.6] [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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217
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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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218
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Martin S, Pombo A. Transcription factories: quantitative studies of nanostructures in the mammalian nucleus. Chromosome Res 2004; 11:461-70. [PMID: 12971722 DOI: 10.1023/a:1024926710797] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Transcription by the three nuclear RNA polymerases is carried out in transcription factories. This conclusion has been drawn from estimates of the total number of nascent transcripts or active polymerase molecules and the number of transcription sites within a cell. Here we summarise the variety of methods used to determine these parameters, discuss their associated problems and outline future prospects.
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Affiliation(s)
- Sonya Martin
- MRC-Clinical Sciences Centre, Faculty of Medicine, Imperial College School of Science, Technology and Medicine, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
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219
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Rajjou L, Gallardo K, Debeaujon I, Vandekerckhove J, Job C, Job D. The effect of alpha-amanitin on the Arabidopsis seed proteome highlights the distinct roles of stored and neosynthesized mRNAs during germination. PLANT PHYSIOLOGY 2004; 134:1598-613. [PMID: 15047896 PMCID: PMC419834 DOI: 10.1104/pp.103.036293] [Citation(s) in RCA: 270] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2003] [Revised: 01/13/2004] [Accepted: 01/20/2004] [Indexed: 05/18/2023]
Abstract
To investigate the role of stored and neosynthesized mRNAs in seed germination, we examined the effect of alpha-amanitin, a transcriptional inhibitor targeting RNA polymerase II, on the germination of nondormant Arabidopsis seeds. We used transparent testa mutants, of which seed coat is highly permeable, to better ascertain that the drug can reach the embryo during seed imbibition. Even with the most permeable mutant (tt2-1), germination (radicle protrusion) occurred in the absence of transcription, while subsequent seedling growth was blocked. In contrast, germination was abolished in the presence of the translational inhibitor cycloheximide. Taken together, the results highlight the role of stored proteins and mRNAs for germination in Arabidopsis and show that in this species the potential for germination is largely programmed during the seed maturation process. The alpha-amanitin-resistant germination exhibited characteristic features. First, this germination was strongly slowed down, indicating that de novo transcription normally allows the synthesis of factor(s) activating the germination rate. Second, the sensitivity of germination to gibberellic acid was reduced 15-fold, confirming the role of this phytohormone in germination. Third, de novo synthesis of enzymes involved in reserve mobilization and resumption of metabolic activity was repressed, thus accounting for the failure in seedling establishment. Fourth, germinating seeds can recapitulate at least part of the seed maturation program, being capable of using mRNAs stored during development. Thus, commitment to germination and plant growth requires transcription of genes allowing the imbibed seed to discriminate between mRNAs to be utilized in germination and those to be destroyed.
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Affiliation(s)
- Loïc Rajjou
- Laboratoire Mixte Centre National de la Recherche Scientifique-Bayer CropScience, Bayer CropScience, F-69263 Lyon, France
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220
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Affiliation(s)
- Seth A Darst
- Rockefeller University, Box 224, 1230 York Avenue, New York, NY 10021, USA.
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221
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Abstract
Recent X-ray and cryo-electron microscopy studies have provided information about the basal eukaryotic transcription machinery and about Mediator, the complex involved in transcription regulation during initiation. On the basis of this structural information, a model describing the minimal transcription complex and its interaction with Mediator has been proposed. The model provides insight into the possible mechanisms of transcription initiation and regulation.
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Affiliation(s)
- Francisco J Asturias
- Department of Cell Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
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222
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Affiliation(s)
- Patrick Cramer
- Institute of Biochemistry and Gene Center, University of Munich, 81377 Munich, Germany
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223
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Abstract
Synthesis of eukaryotic mRNA by RNA polymerase II is an elaborate biochemical process that requires the concerted action of a large set of transcription factors. RNA polymerase II transcription proceeds through multiple stages designated preinitiation, initiation, and elongation. Historically, studies of the elongation stage of eukaryotic mRNA synthesis have lagged behind studies of the preinitiation and initiation stages; however, in recent years, efforts to elucidate the mechanisms governing elongation have led to the discovery of a diverse collection of transcription factors that directly regulate the activity of elongating RNA polymerase II. Moreover, these studies have revealed unanticipated roles for the RNA polymerase II elongation complex in such processes as DNA repair and recombination and the proper processing and nucleocytoplasmic transport of mRNA. Below we describe these recent advances, which highlight the important role of the RNA polymerase II elongation complex in regulation of eukaryotic gene expression.
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Affiliation(s)
- Ali Shilatifard
- Edward A. Doisey Department of Biochemistry, St. Louis University School of Medicine, St. Louis, Missouri 63104, USA.
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224
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Artsimovitch I, Chu C, Lynch AS, Landick R. A new class of bacterial RNA polymerase inhibitor affects nucleotide addition. Science 2003; 302:650-4. [PMID: 14576436 DOI: 10.1126/science.1087526] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
RNA polymerase (RNAP) is the central enzyme of gene expression. Despite availability of crystal structures, details of its nucleotide addition cycle remain obscure. We describe bacterial RNAP inhibitors (the CBR703 series) whose properties illuminate this mechanism. These compounds inhibit known catalytic activities of RNAP (nucleotide addition, pyrophosphorolysis, and Gre-stimulated transcript cleavage) but not translocation of RNA or DNA when translocation is uncoupled from catalysis. CBR703-resistance substitutions occur on an outside surface of RNAP opposite its internal active site. We propose that CBR703 compounds inhibit nucleotide addition allosterically by hindering movements of active site structures that are linked to the CBR703 binding site through a bridge helix.
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Affiliation(s)
- Irina Artsimovitch
- Department of Bacteriology, University of Wisconsin, Madison, WI 53706, USA
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225
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Kettenberger H, Armache KJ, Cramer P. Architecture of the RNA polymerase II-TFIIS complex and implications for mRNA cleavage. Cell 2003; 114:347-57. [PMID: 12914699 DOI: 10.1016/s0092-8674(03)00598-1] [Citation(s) in RCA: 272] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The transcription elongation factor TFIIS induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II. We have diffused TFIIS into Pol II crystals and derived a model of the Pol II-TFIIS complex from X-ray diffraction data to 3.8 A resolution. TFIIS extends from the polymerase surface via a pore to the internal active site, spanning a distance of 100 A. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active center. Our results support the idea that Pol II contains a single tunable active site for RNA polymerization and cleavage, in contrast to DNA polymerases with two separate active sites for DNA polymerization and cleavage.
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Affiliation(s)
- Hubert Kettenberger
- Institute of Biochemistry, Gene Center, University of Munich, Feodor-Lynen-Str. 25, 81377 Munich, Germany
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226
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Seshadri V, McArthur AG, Sogin ML, Adam RD. Giardia lamblia RNA polymerase II: amanitin-resistant transcription. J Biol Chem 2003; 278:27804-10. [PMID: 12734189 DOI: 10.1074/jbc.m303316200] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Giardia lamblia is an early branching eukaryote, and although distinctly eukaryotic in its cell and molecular biology, transcription and translation in G. lamblia demonstrate important differences from these processes in higher eukaryotes. The cyclic octapeptide amanitin is a relatively selective inhibitor of eukaryotic RNA polymerase II (RNAP II) and is commonly used to study RNAP II transcription. Therefore, we measured the sensitivity of G. lamblia RNAP II transcription to alpha-amanitin and found that unlike most other eukaryotes, RNAP II transcription in Giardia is resistant to 1 mg/ml amanitin. In contrast, 50 microg/ml amanitin inhibits 85% of RNAP III transcription activity using leucyl-tRNA as a template. To better understand transcription in G. lamblia, we identified 10 of the 12 known eukaryotic rpb subunits, including all 10 subunits that are required for viability in Saccharomyces cerevisiae. The amanitin motif (amanitin binding site) of Rpb1 from G. lamblia has amino acid substitutions at six highly conserved sites that have been associated with amanitin resistance in other organisms. These observations of amanitin resistance of Giardia RNA polymerase II support previous proposals of the mechanism of amanitin resistance in other organisms and provide a molecular framework for the development of novel drugs with selective activity against G. lamblia.
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Affiliation(s)
- Vishwas Seshadri
- Department of Microbiology, University of Arizona College of Medicine, Tucson, Arizona 85724-5049, USA
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227
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Abstract
PURPOSE OF REVIEW Structural biology is one of the most informative disciplines available to biochemical research. It unites technologies that can reveal high-resolution (often atomic) details of the inner workings of biochemical systems. These insights are crucial for an understanding of basic life processes, such as the reaction mechanism of a drug-converting enzyme, signal transduction from one protein to another, activation of a metabolic pathway by a gene effector, action modes of drugs, or the consequences of a mutation on the function of an enzyme. Structural biology is also vital for characterizing the molecular basis of many diseases and often provides a starting platform for the development of specifically tuned therapies, for example by designing drugs that bind to particular targets in order to affect their functionality. An overview of the main techniques as well as some selected case studies are presented. RECENT FINDINGS Recent advances in the three major structure determination techniques (X-ray crystallography, nuclear magnetic resonance spectroscopy, and electron microscopy) have made it possible to obtain three-dimensional structural information on larger systems, at higher resolution and with much less effort than in the past. Because these techniques often provide complementary information, combining them is particularly powerful for gaining comprehensive insights into complex systems, as illustrated by the recent structure determinations of the low-density lipoprotein receptor and the ribosome. SUMMARY Structural biology is no longer exclusive to a few dedicated specialists. Many of its techniques are now easily accessible and can be used as tools in general life science research.
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Affiliation(s)
- Mischa Machius
- Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, USA.
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228
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Santangelo TJ, Mooney RA, Landick R, Roberts JW. RNA polymerase mutations that impair conversion to a termination-resistant complex by Q antiterminator proteins. Genes Dev 2003; 17:1281-92. [PMID: 12756229 PMCID: PMC196057 DOI: 10.1101/gad.1082103] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2003] [Accepted: 03/24/2003] [Indexed: 11/24/2022]
Abstract
Bacteriophage lambda Q-protein stably binds and modifies RNA polymerase (RNAP) to a termination-resistant form. We describe amino acid substitutions in RNAP that disrupt Q-mediated antitermination in vivo and in vitro. The positions of these substitutions in the modeled RNAP/DNA/RNA ternary elongation complex, and their biochemical properties, suggest that they do not define a binding site for Q in RNAP, but instead act by impairing interactions among core RNAP subunits and nucleic acids that are essential for Q modification. A specific conjecture is that Q modification stabilizes interactions of RNAP with the DNA/RNA hybrid and optimizes alignment of the nucleic acids in the catalytic site. Such changes would inhibit the activity of the RNA hairpin of an intrinsic terminator to disrupt the 5'-terminal bases of the hybrid and remove the RNA 3' terminus from the active site.
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Affiliation(s)
- Thomas J Santangelo
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
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229
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Abstract
The elongation of transcripts by RNA polymerase II (RNAPII) is subject to regulation and requires the services of a host of accessory proteins. Although the biochemical mechanisms underlying elongation and its regulation remain obscure, recent progress sets the stage for rapid advancement in our understanding of this phase of transcription. High-resolution crystal structures will allow focused analyses of RNAPII in all its functional states. Several recent studies suggest specific roles for the C-terminal heptad repeats of the largest subunit of RNAPII in elongation. Proteomic approaches are being used to identify new transcription-elongation factors and to define interactions between elongation factors and RNAPII. Finally, a combination of genetic analysis and the localization of factors on transcribed chromatin is being used to confirm a role for factors in elongation.
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Affiliation(s)
- Grant A Hartzog
- Department of MCD Biology, University of California, Santa Cruz, California 95064, USA.
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230
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Iyer LM, Koonin EV, Aravind L. Evolutionary connection between the catalytic subunits of DNA-dependent RNA polymerases and eukaryotic RNA-dependent RNA polymerases and the origin of RNA polymerases. BMC STRUCTURAL BIOLOGY 2003; 3:1. [PMID: 12553882 PMCID: PMC151600 DOI: 10.1186/1472-6807-3-1] [Citation(s) in RCA: 160] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2003] [Accepted: 01/28/2003] [Indexed: 12/02/2022]
Abstract
BACKGROUND The eukaryotic RNA-dependent RNA polymerase (RDRP) is involved in the amplification of regulatory microRNAs during post-transcriptional gene silencing. This enzyme is highly conserved in most eukaryotes but is missing in archaea and bacteria. No evolutionary relationship between RDRP and other polymerases has been reported so far, hence the origin of this eukaryote-specific polymerase remains a mystery. RESULTS Using extensive sequence profile searches, we identified bacteriophage homologs of the eukaryotic RDRP. The comparison of the eukaryotic RDRP and their homologs from bacteriophages led to the delineation of the conserved portion of these enzymes, which is predicted to harbor the catalytic site. Further, detailed sequence comparison, aided by examination of the crystal structure of the DNA-dependent RNA polymerase (DDRP), showed that the RDRP and the beta' subunit of DDRP (and its orthologs in archaea and eukaryotes) contain a conserved double-psi beta-barrel (DPBB) domain. This DPBB domain contains the signature motif DbDGD (b is a bulky residue), which is conserved in all RDRPs and DDRPs and contributes to catalysis via a coordinated divalent cation. Apart from the DPBB domain, no similarity was detected between RDRP and DDRP, which leaves open two scenarios for the origin of RDRP: i) RDRP evolved at the onset of the evolution of eukaryotes via a duplication of the DDRP beta' subunit followed by dramatic divergence that obliterated the sequence similarity outside the core catalytic domain and ii) the primordial RDRP, which consisted primarily of the DPBB domain, evolved from a common ancestor with the DDRP at a very early stage of evolution, during the RNA world era. The latter hypothesis implies that RDRP had been subsequently eliminated from cellular life forms and might have been reintroduced into the eukaryotic genomes through a bacteriophage. Sequence and structure analysis of the DDRP led to further insights into the evolution of RNA polymerases. In addition to the beta' subunit, beta subunit of DDRP also contains a DPBB domain, which is, however, distorted by large inserts and does not harbor a counterpart of the DbDGD motif. The DPBB domains of the two DDRP subunits together form the catalytic cleft, with the domain from the beta' subunit supplying the metal-coordinating DbDGD motif and the one from the beta subunit providing two lysine residues involved in catalysis. Given that the two DPBB domains of DDRP contribute completely different sets of active residues to the catalytic center, it is hypothesized that the ultimate ancestor of RNA polymerases functioned as a homodimer of a generic, RNA-binding DPBB domain. This ancestral protein probably did not have catalytic activity and served as a cofactor for a ribozyme RNA polymerase. Subsequent evolution of DDRP and RDRP involved accretion of distinct sets of additional domains. In the DDRPs, these included a RNA-binding Zn-ribbon, an AT-hook-like module and a sandwich-barrel hybrid motif (SBHM) domain. Further, lineage-specific accretion of SBHM domains and other, DDRP-specific domains is observed in bacterial DDRPs. In contrast, the orthologs of the beta' subunit in archaea and eukaryotes contains a four-stranded alpha + beta domain that is shared with the alpha-subunit of bacterial DDRP, eukaryotic DDRP subunit RBP11, translation factor eIF1 and type II topoisomerases. The additional domains of the RDRPs remain to be characterized. CONCLUSIONS Eukaryotic RNA-dependent RNA polymerases share the catalytic double-psi beta-barrel domain, containing a signature metal-coordinating motif, with the universally conserved beta' subunit of DNA-dependent RNA polymerases. Beyond this core catalytic domain, the two classes of RNA polymerases do not have common domains, suggesting early divergence from a common ancestor, with subsequent independent domain accretion. The beta-subunit of DDRP contains another, highly diverged DPBB domain. The presence of two distinct DPBB domains in two subunits of DDRP is compatible with the hypothesis that the ith the hypothesis that the ultimate ancestor of RNA polymerases was a RNA-binding DPBB domain that had no catalytic activity but rather functioned as a homodimeric cofactor for a ribozyme polymerase.
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Affiliation(s)
- Lakshminarayan M Iyer
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - L Aravind
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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231
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Epshtein V, Mustaev A, Markovtsov V, Bereshchenko O, Nikiforov V, Goldfarb A. Swing-gate model of nucleotide entry into the RNA polymerase active center. Mol Cell 2002; 10:623-34. [PMID: 12408829 DOI: 10.1016/s1097-2765(02)00640-8] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Each elementary step of transcription involves translocation of the 3' terminus of RNA in the RNA polymerase active center, followed by the entry of a nucleoside triphosphate. The structural basis of these transitions was studied using RNA-protein crosslinks. The contacts were mapped and projected onto the crystal structure, in which the "F bridge" helix in the beta' subunit is either bent or relaxed. Bending/relaxation of the F bridge correlates with lateral movements of the RNA 3' terminus. The bent conformation is sterically incompatable with the occupancy of the nucleotide site, suggesting that the switch regulates both the entry of substrates and the translocation of the transcript. The switch occurs as part of a cooperative transition of a larger structural domain that consists of the F helix and the supporting G loop.
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