351
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Brueckner F, Cramer P. Structural basis of transcription inhibition by alpha-amanitin and implications for RNA polymerase II translocation. Nat Struct Mol Biol 2008; 15:811-8. [PMID: 18552824 DOI: 10.1038/nsmb.1458] [Citation(s) in RCA: 197] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2008] [Accepted: 06/05/2008] [Indexed: 12/28/2022]
Abstract
To study how RNA polymerase II translocates after nucleotide incorporation, we prepared elongation complex crystals in which pre- and post-translocation states interconvert. Crystal soaking with the inhibitor alpha-amanitin locked the elongation complex in a new state, which was refined at 3.4-A resolution and identified as a possible translocation intermediate. The DNA base entering the active site occupies a 'pretemplating' position above the central bridge helix, which is shifted and occludes the templating position. A leucine residue in the trigger loop forms a wedge at the shifted bridge helix, but moves by 13 A to close the active site during nucleotide incorporation. Our results support a Brownian ratchet mechanism that involves swinging of the trigger loop between open, wedged and closed positions, and suggest that alpha-amanitin impairs nucleotide incorporation and translocation by trapping the trigger loop and bridge helix.
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Affiliation(s)
- Florian Brueckner
- Gene Center and Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry and Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
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352
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Werner F. Structural evolution of multisubunit RNA polymerases. Trends Microbiol 2008; 16:247-50. [PMID: 18468900 DOI: 10.1016/j.tim.2008.03.008] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2008] [Revised: 03/05/2008] [Accepted: 03/05/2008] [Indexed: 11/29/2022]
Abstract
Evolutionarily related multisubunit RNA polymerases (RNAPs) facilitate gene transcription throughout the three domains of life. During the past seven years an increasing number of bacterial and eukaryotic RNAP structures have been solved; however, the archaeal enzyme remained elusive. Two reports from the Murakami and Cramer laboratories have now filled this gap in our knowledge and enable us to hypothesize about the evolution of the structure and function of RNAPs.
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Affiliation(s)
- Finn Werner
- Research Department of Structural and Molecular Biology, University College London, Gower Street, London, UK.
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353
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Early evolution of eukaryotic DNA-dependent RNA polymerases. Trends Genet 2008; 24:211-5. [PMID: 18384908 DOI: 10.1016/j.tig.2008.02.002] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2007] [Revised: 02/20/2008] [Accepted: 02/20/2008] [Indexed: 11/21/2022]
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354
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Characterization of the active site of yeast RNA polymerase II by DFT and ReaxFF calculations. Theor Chem Acc 2008. [DOI: 10.1007/s00214-008-0440-9] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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355
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May J, Fournier P, Patrick B, Perrin D. Synthesis, Characterisation, and In Vitro Evaluation of Pro2-Ile3-S-Deoxo-Amaninamide and Pro2-D-allo-Ile3-S-Deoxo-Amaninamide: Implications for Structure–Activity Relationships in Amanitin Conformation and Toxicity. Chemistry 2008; 14:3410-7. [DOI: 10.1002/chem.200701297] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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356
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Borukhov S, Nudler E. RNA polymerase: the vehicle of transcription. Trends Microbiol 2008; 16:126-34. [DOI: 10.1016/j.tim.2007.12.006] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2007] [Revised: 12/06/2007] [Accepted: 12/06/2007] [Indexed: 10/22/2022]
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357
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Kornberg R. The molecular basis of eukaryotic transcription (Nobel Lecture). Angew Chem Int Ed Engl 2008; 46:6956-65. [PMID: 17668892 DOI: 10.1002/anie.200701832] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Roger Kornberg
- Department of Structural Biology, Stanford University Medical School, 299 Campus Dr. West, Stanford CA, 94305-5126, USA.
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358
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Epshtein V, Cardinale CJ, Ruckenstein AE, Borukhov S, Nudler E. An allosteric path to transcription termination. Mol Cell 2008; 28:991-1001. [PMID: 18158897 DOI: 10.1016/j.molcel.2007.10.011] [Citation(s) in RCA: 98] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2007] [Revised: 07/18/2007] [Accepted: 10/10/2007] [Indexed: 01/22/2023]
Abstract
Transcription termination signals in bacteria occur in RNA as a strong hairpin followed by a stretch of U residues at the 3' terminus. To release the transcript, RNA polymerase (RNAP) is thought to translocate forward without RNA synthesis. Here we provide genetic and biochemical evidence supporting an alternative model in which extensive conformational changes across the enzyme lead to termination without forward translocation. In this model, flexible parts of the RNA exit channel (zipper, flap, and zinc finger) assist the initial step of hairpin folding (nucleation). The hairpin then invades the RNAP main channel, causing RNA:DNA hybrid melting, structural changes of the catalytic site, and DNA-clamp opening induced by interaction with the G(trigger)-loop. Our results envision the elongation complex as a flexible structure, not a rigid body, and establish basic principles of the termination pathway that are likely to be universal in prokaryotic and eukaryotic systems.
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Affiliation(s)
- Vitaly Epshtein
- Department of Biochemistry, New York University School of Medicine, New York, NY 10016, USA
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359
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The X-ray crystal structure of RNA polymerase from Archaea. Nature 2008; 451:851-4. [PMID: 18235446 DOI: 10.1038/nature06530] [Citation(s) in RCA: 170] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2007] [Accepted: 12/06/2007] [Indexed: 11/09/2022]
Abstract
The transcription apparatus in Archaea can be described as a simplified version of its eukaryotic RNA polymerase (RNAP) II counterpart, comprising an RNAPII-like enzyme as well as two general transcription factors, the TATA-binding protein (TBP) and the eukaryotic TFIIB orthologue TFB. It has been widely understood that precise comparisons of cellular RNAP crystal structures could reveal structural elements common to all enzymes and that these insights would be useful in analysing components of each enzyme that enable it to perform domain-specific gene expression. However, the structure of archaeal RNAP has been limited to individual subunits. Here we report the first crystal structure of the archaeal RNAP from Sulfolobus solfataricus at 3.4 A resolution, completing the suite of multi-subunit RNAP structures from all three domains of life. We also report the high-resolution (at 1.76 A) crystal structure of the D/L subcomplex of archaeal RNAP and provide the first experimental evidence of any RNAP possessing an iron-sulphur (Fe-S) cluster, which may play a structural role in a key subunit of RNAP assembly. The striking structural similarity between archaeal RNAP and eukaryotic RNAPII highlights the simpler archaeal RNAP as an ideal model system for dissecting the molecular basis of eukaryotic transcription.
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360
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Vrentas CE, Gaal T, Berkmen MB, Rutherford ST, Haugen SP, Vassylyev DG, Ross W, Gourse RL. Still looking for the magic spot: the crystallographically defined binding site for ppGpp on RNA polymerase is unlikely to be responsible for rRNA transcription regulation. J Mol Biol 2008; 377:551-64. [PMID: 18272182 DOI: 10.1016/j.jmb.2008.01.042] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2007] [Revised: 01/15/2008] [Accepted: 01/16/2008] [Indexed: 10/22/2022]
Abstract
Identification of the RNA polymerase (RNAP) binding site for ppGpp, a central regulator of bacterial transcription, is crucial for understanding its mechanism of action. A recent high-resolution X-ray structure defined a ppGpp binding site on Thermus thermophilus RNAP. We report here effects of ppGpp on 10 mutant Escherichia coli RNAPs with substitutions for the analogous residues within 3-4 A of the ppGpp binding site in the T. thermophilus cocrystal. None of the substitutions in E. coli RNAP significantly weakened its responses to ppGpp. This result differs from the originally reported finding of a substitution in E. coli RNAP eliminating ppGpp function. The E. coli RNAPs used in that study likely lacked stoichiometric amounts of omega, an RNAP subunit required for responses of RNAP to ppGpp, in part explaining the discrepancy. Furthermore, we found that ppGpp did not inhibit transcription initiation by T. thermophilus RNAP in vitro or shorten the lifetimes of promoter complexes containing T. thermophilus RNAP, in contrast to the conclusion in the original report. Our results suggest that the ppGpp binding pocket identified in the cocrystal is not the one responsible for regulation of E. coli ribosomal RNA transcription initiation and highlight the importance of inclusion of omega in bacterial RNAP preparations.
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Affiliation(s)
- Catherine E Vrentas
- Department of Bacteriology, University of Wisconsin-Madison, 1550 Linden Drive, Madison, WI 53706, USA
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361
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Wittayanarakul K, Hannongbua S, Feig M. Accurate prediction of protonation state as a prerequisite for reliable MM-PB(GB)SA binding free energy calculations of HIV-1 protease inhibitors. J Comput Chem 2008; 29:673-85. [PMID: 17849388 DOI: 10.1002/jcc.20821] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Binding free energies were calculated for the inhibitors lopinavir, ritonavir, saquinavir, indinavir, amprenavir, and nelfinavir bound to HIV-1 protease. An MMPB/SA-type analysis was applied to conformational samples from 3 ns explicit solvent molecular dynamics simulations of the enzyme-inhibitor complexes. Binding affinities and the sampled conformations of the inhibitor and enzyme were compared between different HIV-1 protease protonation states to find the most likely protonation state of the enzyme in the complex with each of the inhibitors. The resulting set of protonation states leads to good agreement between calculated and experimental binding affinities. Results from the MMPB/SA analysis are compared with an explicit/implicit hybrid scheme and with MMGB/SA methods. It is found that the inclusion of explicit water molecules may offer a slight advantage in reproducing absolute binding free energies while the use of the Generalized Born approximation significantly affects the accuracy of the calculated binding affinities.
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362
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Gerber J, Reiter A, Steinbauer R, Jakob S, Kuhn CD, Cramer P, Griesenbeck J, Milkereit P, Tschochner H. Site specific phosphorylation of yeast RNA polymerase I. Nucleic Acids Res 2007; 36:793-802. [PMID: 18084032 PMCID: PMC2241885 DOI: 10.1093/nar/gkm1093] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
All nuclear RNA polymerases are phosphoprotein complexes. Yeast RNA polymerase I (Pol I) contains approximately 15 phosphate groups, distributed to 5 of the 14 subunits. Information about the function of the single phosphosites and their position in the primary, secondary and tertiary structure is lacking. We used a rapid and efficient way to purify yeast RNA Pol I to determine 13 phosphoserines and –threonines. Seven of these phosphoresidues could be located in the 3D-homology model for Pol I, five of them are more at the surface. The single phosphorylated residues were systematically mutated and the resulting strains and Pol I preparations were analyzed in cellular growth, Pol I composition, stability and genetic interaction with non-essential components of the transcription machinery. Surprisingly, all Pol I phosphorylations analyzed were found to be non-essential post-translational modifications. However, one mutation (subunit A190 S685D) led to higher growth rates in the presence of 6AU or under environmental stress conditions, and was synthetically lethal with a deletion of the Pol I subunit A12.2, suggesting a role in RNA cleavage/elongation or termination. Our results suggest that individual major or constitutively phosphorylated residues contribute to non-essential Pol I-functions.
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Affiliation(s)
- Jochen Gerber
- Institut für Biochemie, Mikrobiologie und Genetik, Universität Regensburg, Munich, Germany
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363
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Zamora-Sillero E, Shapovalov AV, Esteban FJ. Formation, control, and dynamics of N localized structures in the Peyrard-Bishop model. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2007; 76:066603. [PMID: 18233933 DOI: 10.1103/physreve.76.066603] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2007] [Indexed: 05/25/2023]
Abstract
We explore in detail the creation of stable localized structures in the form of localized energy distributions that arise from general initial conditions in the Peyrard-Bishop (PB) model. By means of a method based on the inverse scattering transform we study the solutions of PB model equations obtained in the form of planar waves whose amplitudes are described by the nonlinear Schrödinger equation (NLS). For localized initial conditions different from the pure N-soliton shape, we have obtained analytical results that predict and control the number, amplitude, and velocity of the NLS solitary waves. To verify the validity of these results we have carried out numerical simulations of the PB model with the use of realistic values of parameters and the initial conditions in the form of planar waves whose modulated amplitudes are given by the examples studied in the NLS. In the simulations we have found that N localized structures arise in agreement with the prediction of the analytical results obtained in the NLS.
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Affiliation(s)
- Elías Zamora-Sillero
- Departamento de Fisica Aplicada I, E.U.P. Universidad de Sevilla Virgen de Africa 7, 41011 Sevilla, Spain.
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364
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Nottebaum S, Tan L, Trzaska D, Carney HC, Weinzierl ROJ. The RNA polymerase factory: a robotic in vitro assembly platform for high-throughput production of recombinant protein complexes. Nucleic Acids Res 2007; 36:245-52. [PMID: 18025041 PMCID: PMC2248744 DOI: 10.1093/nar/gkm1044] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
The in-depth structure/function analysis of large protein complexes, such as RNA polymerases (RNAPs), requires an experimental platform capable of assembling variants of such enzymes in large numbers in a reproducible manner under defined in vitro conditions. Here we describe a streamlined and integrated protocol for assembling recombinant archaeal RNAPs in a high-throughput 96-well format. All aspects of the procedure including construction of redesigned expression plasmids, development of automated protein extraction/in vitro assembly methods and activity assays were specifically adapted for implementation on robotic platforms. The optimized strategy allows the parallel assembly and activity assay of 96 recombinant RNAPs (including wild-type and mutant variants) with little or no human intervention within 24 h. We demonstrate the high-throughput potential of this system by evaluating the side-chain requirements of a single amino acid position of the RNAP Bridge Helix using saturation mutagenesis.
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Affiliation(s)
- Sven Nottebaum
- Department of Life Sciences, Division of Cell- and Molecular Biology, Sir Alexander Fleming Building, Imperial College London, London SW7 2AZ, UK
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365
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Dimitri A, Goodenough AK, Guengerich FP, Broyde S, Scicchitano DA. Transcription processing at 1,N2-ethenoguanine by human RNA polymerase II and bacteriophage T7 RNA polymerase. J Mol Biol 2007; 375:353-66. [PMID: 18022639 DOI: 10.1016/j.jmb.2007.10.057] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2007] [Revised: 10/16/2007] [Accepted: 10/18/2007] [Indexed: 10/22/2022]
Abstract
The DNA lesion 1,N(2)-ethenoguanine (1,N(2)-epsilon G) is formed endogenously as a by-product of lipid peroxidation or by reaction with epoxides that result from the metabolism of the industrial pollutant vinyl chloride, a known human carcinogen. DNA replication past 1,N(2)-epsilon G and site-specific mutagenesis studies on mammalian cells have established the highly mutagenic and genotoxic properties of the damaged base. However, there is as yet no information on the processing of this lesion during transcription. Here, we report the results of transcription past a site-specifically modified 1,N(2)-epsilon G DNA template. This lesion contains an exocyclic ring obstructing the Watson-Crick hydrogen-bonding edge of guanine. Our results show that 1,N(2)-epsilon G acts as a partial block to the bacteriophage T7 RNA polymerase (RNAP), which allows nucleotide incorporation in the growing RNA with the selectivity A>G>(C=-1 deletion)>>U. In contrast, 1,N(2)-epsilon G poses an absolute block to human RNAP II elongation, and nucleotide incorporation opposite the lesion is not observed. Computer modeling studies show that the more open active site of T7 RNAP allows lesion bypass when the 1,N(2)-epsilon G adopts the syn-conformation. This orientation places the exocyclic ring in a collision-free empty pocket of the polymerase, and the observed base incorporation preferences are in agreement with hydrogen-bonding possibilities between the incoming nucleotides and the Hoogsteen edge of the lesion. On the other hand, in the more crowded active site of the human RNAP II, the modeling studies show that both syn- and anti-conformations of the 1,N(2)-epsilon G are sterically impermissible. Polymerase stalling is currently believed to trigger the transcription-coupled nucleotide excision repair machinery. Thus, our data suggest that this repair pathway is likely engaged in the clearance of the 1,N(2)-epsilon G from actively transcribed DNA.
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366
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Xiong Y, Burton ZF. A tunable ratchet driving human RNA polymerase II translocation adjusted by accurately templated nucleoside triphosphates loaded at downstream sites and by elongation factors. J Biol Chem 2007; 282:36582-92. [PMID: 17875640 DOI: 10.1074/jbc.m707014200] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
When nucleoside triphosphate (NTP) substrates and alpha-amanitin are added to a human RNA polymerase II elongation complex simultaneously, the reaction becomes stalled in the core of the bond synthesis mechanism. The mode of stalling is influenced by NTP substrates at the active site and at downstream sites and by transcription factor IIF (TFIIF) and TFIIS. NTP substrates templated at i+2, i+3, and i+4 downstream DNA sites can reverse the previously stable binding of an NTP loaded at the i+1 substrate site. Deoxy-(d)NTPs and NDPs (nucleoside diphosphates) do not substitute for NTPs at the i+2 and i+3 positions (considered together) or the i+4, i+5, and i+6 positions (considered together). The mode of stalling is altered by changing the number of downstream template sites that are accurately occupied by NTPs and by changing NTP concentration. In the presence of the translocation blocker alpha-amanitin, a steady state condition is established in which RNA polymerase II stably loads an NTP substrate at i+1 and forms a phosphodiester bond but cannot rapidly complete bond synthesis by releasing pyrophosphate. These observations support a role for incoming NTP substrates in stimulating translocation; results appear inconsistent with the secondary pore being the sole route of NTP entry for human RNA polymerase II, and results indicate mechanisms of dynamic error avoidance and error correction during rapid RNA synthesis.
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Affiliation(s)
- Yalin Xiong
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824-1319, USA
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367
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368
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Svetlov V, Belogurov GA, Shabrova E, Vassylyev DG, Artsimovitch I. Allosteric control of the RNA polymerase by the elongation factor RfaH. Nucleic Acids Res 2007; 35:5694-705. [PMID: 17711918 PMCID: PMC2034486 DOI: 10.1093/nar/gkm600] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Efficient transcription of long polycistronic operons in bacteria frequently relies on accessory proteins but their molecular mechanisms remain obscure. RfaH is a cellular elongation factor that acts as a polarity suppressor by increasing RNA polymerase (RNAP) processivity. In this work, we provide evidence that RfaH acts by reducing transcriptional pausing at certain positions rather than by accelerating RNAP at all sites. We show that ‘fast’ RNAP variants are characterized by pause-free RNA chain elongation and are resistant to RfaH action. Similarly, the wild-type RNAP is insensitive to RfaH in the absence of pauses. In contrast, those enzymes that may be prone to falling into a paused state are hypersensitive to RfaH. RfaH inhibits pyrophosphorolysis of the nascent RNA and reduces the apparent Michaelis–Menten constant for nucleotides, suggesting that it stabilizes the post-translocated, active RNAP state. Given that the RfaH-binding site is located 75 Å away from the RNAP catalytic center, these results strongly indicate that RfaH acts allosterically. We argue that despite the apparent differences in the nucleic acid targets, the time of recruitment and the binding sites on RNAP, unrelated antiterminators (such as RfaH and λQ) utilize common strategies during both recruitment and anti-pausing modification of the transcription complex.
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Affiliation(s)
- Vladimir Svetlov
- Department of Microbiology, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210 and Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, 720 20th Street South, Birmingham, AL 35294, USA
| | - Georgiy A. Belogurov
- Department of Microbiology, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210 and Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, 720 20th Street South, Birmingham, AL 35294, USA
| | - Elena Shabrova
- Department of Microbiology, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210 and Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, 720 20th Street South, Birmingham, AL 35294, USA
| | - Dmitry G. Vassylyev
- Department of Microbiology, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210 and Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, 720 20th Street South, Birmingham, AL 35294, USA
| | - Irina Artsimovitch
- Department of Microbiology, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210 and Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, 720 20th Street South, Birmingham, AL 35294, USA
- *To whom correspondence should be addressed. 614 292 6777614 292 8120
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369
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Affiliation(s)
- Roger D Kornberg
- Stanford University School of Medicine, Stanford, CA 94305-5400, USA.
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370
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371
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Toulokhonov I, Zhang J, Palangat M, Landick R. A Central Role of the RNA Polymerase Trigger Loop in Active-Site Rearrangement during Transcriptional Pausing. Mol Cell 2007; 27:406-19. [PMID: 17679091 DOI: 10.1016/j.molcel.2007.06.008] [Citation(s) in RCA: 171] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2007] [Revised: 05/10/2007] [Accepted: 06/06/2007] [Indexed: 11/15/2022]
Abstract
Transcriptional pausing by RNA polymerase is an underlying event in the regulation of transcript elongation, yet the physical changes in the transcribing complex that create the initially paused conformation remain poorly understood. We report that this nonbacktracked elemental pause results from an active-site rearrangement whose signature includes a trigger-loop conformation positioned near the RNA 3' nucleotide and a conformation of betaDloopII that allows fraying of the RNA 3' nucleotide away from the DNA template. During nucleotide addition, trigger-loop movements or folding appears to assist NTP-stimulated translocation and to be crucial for catalysis. At a pause, the trigger loop directly contributes to the paused conformation, apparently by restriction of its movement or folding, whereas a previously postulated unfolding of the bridge helix does not. This trigger-loop-centric model can explain many properties of transcriptional pausing.
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372
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Vassylyev DG, Vassylyeva MN, Zhang J, Palangat M, Artsimovitch I, Landick R. Structural basis for substrate loading in bacterial RNA polymerase. Nature 2007; 448:163-8. [PMID: 17581591 DOI: 10.1038/nature05931] [Citation(s) in RCA: 294] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2007] [Accepted: 05/11/2007] [Indexed: 01/22/2023]
Abstract
The mechanism of substrate loading in multisubunit RNA polymerase is crucial for understanding the general principles of transcription yet remains hotly debated. Here we report the 3.0-A resolution structures of the Thermus thermophilus elongation complex (EC) with a non-hydrolysable substrate analogue, adenosine-5'-[(alpha,beta)-methyleno]-triphosphate (AMPcPP), and with AMPcPP plus the inhibitor streptolydigin. In the EC/AMPcPP structure, the substrate binds to the active ('insertion') site closed through refolding of the trigger loop (TL) into two alpha-helices. In contrast, the EC/AMPcPP/streptolydigin structure reveals an inactive ('preinsertion') substrate configuration stabilized by streptolydigin-induced displacement of the TL. Our structural and biochemical data suggest that refolding of the TL is vital for catalysis and have three main implications. First, despite differences in the details, the two-step preinsertion/insertion mechanism of substrate loading may be universal for all RNA polymerases. Second, freezing of the preinsertion state is an attractive target for the design of novel antibiotics. Last, the TL emerges as a prominent target whose refolding can be modulated by regulatory factors.
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Affiliation(s)
- Dmitry G Vassylyev
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Schools of Medicine and Dentistry, 402B Kaul Genetics Building, 720 20th Street South, Birmingham, Alabama 35294, USA.
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373
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Vassylyev DG, Vassylyeva MN, Perederina A, Tahirov TH, Artsimovitch I. Structural basis for transcription elongation by bacterial RNA polymerase. Nature 2007; 448:157-62. [PMID: 17581590 DOI: 10.1038/nature05932] [Citation(s) in RCA: 345] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2007] [Accepted: 05/11/2007] [Indexed: 11/08/2022]
Abstract
The RNA polymerase elongation complex (EC) is both highly stable and processive, rapidly extending RNA chains for thousands of nucleotides. Understanding the mechanisms of elongation and its regulation requires detailed information about the structural organization of the EC. Here we report the 2.5-A resolution structure of the Thermus thermophilus EC; the structure reveals the post-translocated intermediate with the DNA template in the active site available for pairing with the substrate. DNA strand separation occurs one position downstream of the active site, implying that only one substrate at a time can specifically bind to the EC. The upstream edge of the RNA/DNA hybrid stacks on the beta'-subunit 'lid' loop, whereas the first displaced RNA base is trapped within a protein pocket, suggesting a mechanism for RNA displacement. The RNA is threaded through the RNA exit channel, where it adopts a conformation mimicking that of a single strand within a double helix, providing insight into a mechanism for hairpin-dependent pausing and termination.
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Affiliation(s)
- Dmitry G Vassylyev
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Schools of Medicine and Dentistry, 402B Kaul Genetics Building, 720 20th Street South, Birmingham, Alabama 35294, USA.
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374
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Alic N, Ayoub N, Landrieux E, Favry E, Baudouin-Cornu P, Riva M, Carles C. Selectivity and proofreading both contribute significantly to the fidelity of RNA polymerase III transcription. Proc Natl Acad Sci U S A 2007; 104:10400-5. [PMID: 17553959 PMCID: PMC1965525 DOI: 10.1073/pnas.0704116104] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We examine here the mechanisms ensuring the fidelity of RNA synthesis by RNA polymerase III (Pol III). Misincorporation could only be observed by using variants of Pol III deficient in the intrinsic RNA cleavage activity. Determination of relative rates of the reactions producing correct and erroneous transcripts at a specific position on a tRNA gene, combined with computational methods, demonstrated that Pol III has a highly efficient proofreading activity increasing its transcriptional fidelity by a factor of 10(3) over the error rate determined solely by selectivity (1.8 x 10(-4)). We show that Pol III slows down synthesis past a misincorporation to achieve efficient proofreading. We discuss our findings in the context of transcriptional fidelity studies performed on RNA Pols, proposing that the fidelity of transcription is more crucial for Pol III than Pol II.
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Affiliation(s)
- Nazif Alic
- Commissariat à l'Énergie Atomique, Institut de Biologie et de Technologies de Saclay, F-91191 Gif sur Yvette Cedex, France
| | - Nayla Ayoub
- Commissariat à l'Énergie Atomique, Institut de Biologie et de Technologies de Saclay, F-91191 Gif sur Yvette Cedex, France
| | - Emilie Landrieux
- Commissariat à l'Énergie Atomique, Institut de Biologie et de Technologies de Saclay, F-91191 Gif sur Yvette Cedex, France
| | - Emmanuel Favry
- Commissariat à l'Énergie Atomique, Institut de Biologie et de Technologies de Saclay, F-91191 Gif sur Yvette Cedex, France
| | - Peggy Baudouin-Cornu
- Commissariat à l'Énergie Atomique, Institut de Biologie et de Technologies de Saclay, F-91191 Gif sur Yvette Cedex, France
| | - Michel Riva
- Commissariat à l'Énergie Atomique, Institut de Biologie et de Technologies de Saclay, F-91191 Gif sur Yvette Cedex, France
- To whom correspondence should be addressed. E-mail:
| | - Christophe Carles
- Commissariat à l'Énergie Atomique, Institut de Biologie et de Technologies de Saclay, F-91191 Gif sur Yvette Cedex, France
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375
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Kashkina E, Anikin M, Brueckner F, Lehmann E, Kochetkov SN, McAllister WT, Cramer P, Temiakov D. Multisubunit RNA polymerases melt only a single DNA base pair downstream of the active site. J Biol Chem 2007; 282:21578-82. [PMID: 17526498 DOI: 10.1074/jbc.c700098200] [Citation(s) in RCA: 18] [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
To extend the nascent transcript, RNA polymerases must melt the DNA duplex downstream from the active site to expose the next acceptor base for substrate binding and incorporation. A number of mechanisms have been proposed to account for the manner in which the correct substrate is selected, and these differ in their predictions as to how far the downstream DNA is melted. Using fluorescence quenching experiments, we provide evidence that cellular RNA polymerases from bacteria and yeast melt only one DNA base pair downstream from the active site. These data argue against a model in which multiple NTPs are lined up downstream of the active site.
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Affiliation(s)
- Ekaterina Kashkina
- Department of Cell Biology, University of Medicine and Dentistry of New Jersey, School of Osteopathic Medicine, Stratford, NJ 08084, USA
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376
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Brueckner F, Cramer P. DNA photodamage recognition by RNA polymerase II. FEBS Lett 2007; 581:2757-60. [PMID: 17521634 DOI: 10.1016/j.febslet.2007.05.014] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2007] [Accepted: 05/06/2007] [Indexed: 01/22/2023]
Abstract
During gene transcription, RNA polymerase (Pol) II encounters obstacles, including lesions in the DNA template. Here, we review a recent structure-function analysis of Pol II transcribing DNA with a bulky photo-lesion in the template strand. The study provided the molecular basis for recognition of a damaged DNA by Pol II, which is the first step in transcription-coupled DNA repair (TCR). The results have general implications for damage recognition and the TCR mechanism.
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Affiliation(s)
- Florian Brueckner
- Gene Center Munich, Department of Chemistry and Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, D-81377 Munich, Germany
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377
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Abstract
The 2006 Nobel Prize in Chemistry has been awarded to Roger Kornberg for elucidating the molecular basis of eukaryotic transcription. The prize caps a decades-long quest to unlock one of the central mysteries of molecular biology-how RNA transcripts are assembled.
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Affiliation(s)
- Robert Landick
- Department of Bacteriology, 420 Henry Mall, University of Wisconsin-Madison, Madison, WI 53706, USA.
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