全部 标题 作者
关键词 摘要

OALib Journal期刊
ISSN: 2333-9721
费用:99美元

查看量下载量

相关文章

更多...
PLOS Biology  2010 

Complete Structural Model of Escherichia coli RNA Polymerase from a Hybrid Approach

DOI: 10.1371/journal.pbio.1000483

Full-Text   Cite this paper   Add to My Lib

Abstract:

The Escherichia coli transcription system is the best characterized from a biochemical and genetic point of view and has served as a model system. Nevertheless, a molecular understanding of the details of E. coli transcription and its regulation, and therefore its full exploitation as a model system, has been hampered by the absence of high-resolution structural information on E. coli RNA polymerase (RNAP). We use a combination of approaches, including high-resolution X-ray crystallography, ab initio structural prediction, homology modeling, and single-particle cryo-electron microscopy, to generate complete atomic models of E. coli core RNAP and an E. coli RNAP ternary elongation complex. The detailed and comprehensive structural descriptions can be used to help interpret previous biochemical and genetic data in a new light and provide a structural framework for designing experiments to understand the function of the E. coli lineage-specific insertions and their role in the E. coli transcription program.

References

[1]  Jokerst R. S, Weeks J. R, Zehring W. A, Greenleaf A. L (1989) Analysis of the gene encoding the largest subunit of RNA polymerase II in Drosophila. Mol Gen Genet 215: 266–275.
[2]  Sweetser D, Nonet M, Young R. A (1987) Prokaryotic and eukaryotic RNA polymerases have homologous core subunits. Proc Natl Acad Sci U S A 84: 1192–1196.
[3]  Lane W. J, Darst S. A (2009) Molecular evolution of multi-subunit RNA polymerases: sequence analysis. J Mol Biol 395: 671–685.
[4]  Iyer L. M, Koonin E. V, Aravind L (2004) Evolution of bacterial RNA polymerase: implications for large-scale bacterial phylogeny, domain accretion, and horizontal gene transfer. Gene 335: 73–88.
[5]  Zhang G, Campbell E. A, Minakhin L, Richter C, Severinov K, et al. (1999) Crystal structure of Thermus aquaticus core RNA polymerase at 3.3 ? resolution. Cell 98: 811–824.
[6]  Murakami K, Masuda S, Darst S. A (2002) Structural basis of transcription initiation: RNA polymerase holoenzyme at 4 ? resolution. Science 296: 1280–1284.
[7]  Vassylyev D. G, Sekine S, Laptenko O, Lee J, Vassylyeva M. N, et al. (2002) Crystal structure of a bacterial RNA polymerase holoenzyme at 2.6 ? resolution. Nature 417: 712–719.
[8]  Vassylyev D. G, Vassylyeva M. N, Perederina A, Tahirov T. H, Artsimovitch I (2007) Structural basis for transcription elongation by bacterial RNA polymerase. Nature 448: 157–162.
[9]  Iyer L. M, Koonin E. V, Aravind L (2003) Evolutionary connection between the catalytic subunits of DNA-dependent RNA polymerases and eukaryotic RNA-dependent RNA polymerases and the origin of RNA polymerases. BMC Struct Biol 3: 1–23.
[10]  Chlenov M, Masuda S, Murakami K. S, Nikiforov V, Darst S. A, et al. (2005) Structure and function of lineage-specific sequence insertions in the bacterial RNA polymerase b' subunit. J Mol Biol 353: 138–154.
[11]  Gross C. A, Chan C. L, Lonetto M. A (1996) A structure/function analysis of Escherichia coli RNA polymerase. Philos Trans R Soc London, B, Biol Sci 351: 475–482.
[12]  Mooney R. A, Artsimovitch I, Landick R (1998) Information processing by RNA polymerase: recognition of regulatory signals during RNA chain elongation. J Bacteriol 180: 3265–3275.
[13]  Darst S. A, Opalka N, Chacon P, Polyakov A, Richter C, et al. (2002) Conformational flexibility of bacterial RNA polymerase. Proc Natl Acad Sci U S A 99: 4296–4301.
[14]  Bose D, Pape T, Burrows P. C, Rappas M, Wigneshweraraj S, et al. (2008) Organization of an activator-bound RNA polymerase holoenzyme. Mol Cell 32: 337–346.
[15]  Hudson B, Quispe J, Lara-Gonzalez S, Kim Y, Berman H, et al. (2009) Three-dimensional EM structure of an intact activator-dependent transcription initiation complex. Proc Natl Acad Sci U S A 106: 19830–19835.
[16]  Kim D. E, Chivian D, Baker D (2004) Protein structure prediction and analysis using the Robetta server. Nucleic Acids Res 32: Suppl 2W526–W531.
[17]  Severinov K, Kashlev M, Severinova E, Bass I, McWilliams K, et al. (1994) A non-essential domain of E. coli RNA polymerase required for the action of the termination factor Alc. J Biol Chem 269: 14254–14259.
[18]  Artsimovitch I, Svetlov V, Murakami K. S, Landick R (2003) Co-overexpression of Escherichia coli RNA polymerase subunits allows isolation and analysis of mutant enzymes lacking lineage-specific sequence insertions. J Biol Chem 278: 12344–12355.
[19]  Lane W. J, Darst S. A (2009) Molecular evolution of multi-subunit RNA polymerases: structural analysis. J Mol Biol 395: 686–704.
[20]  Rayment I (1997) Reductive alkylation of lysine residues to alter crystallization properties of proteins. Methods Enzymol 276: 171–179.
[21]  Hendrickson W, Norton J. R, LeMaster D. M (1990) Selenomethionyl proteins produced for analysis by multiwavelength anomalous diffraction (MAD). EMBO J 9: 1665–1672.
[22]  Borukhov S, Severinov K, Kashlev M, Lebedev A, Bass I, et al. (1991) Mapping of trypsin cleavage and antibody-binding sites and delineation of a dispensable domain in the ? subunit of Escherichia coli RNA polymerase. J Biol Chem 266: 23921–23926.
[23]  Opalka N, Mooney R. A, Richter C, Severinov K, Landick R, et al. (1999) Direct localization of a b subunit domain on the three-dimensional structure of Escherichia coli RNA polymerase. Proc Natl Acad Sci USA 97: 617–622.
[24]  Basokur A. T (1998) Digital filter design using the hyperbolic tangent functions. J Balkan Geophys Soc 1: 14–18.
[25]  Hohn M, Tang G, Goodyear G, Baldwin P. R, Huang Z, et al. (2007) SPARX, a new environment for cryo-EM image processing. J Structural Biol 157: 47–55.
[26]  Kastner B, Fischer N, Golas M. M, Sander B, Dube P, et al. (2008) GraFix: sample preparation for single-particle electron cryomicroscopy. Nature Meth 5: 53–55.
[27]  Tan R. K-Z, Devkota B, Harvey S. C (2008) YUP.SCX: coaxing atomic models into medium resolution electron density maps. J Structural Biol 163: 163–174.
[28]  Korzheva N, Mustaev A, Kozlov M, Malhotra A, Nikiforov V, et al. (2000) A structural model of transcription elongation. Science 289: 619–625.
[29]  Zhang G, Darst S. A (1998) Structure of the Escherichia coli RNA polymerase a subunit amino-terminal domain. Science 281: 262–266.
[30]  Westblade L. F, Minakhin L, Kuznedelov K, Tackett A. J, Chang E, et al. (2008) Rapid isolation and identification of bacteriophage T4-encoded modifications of Escherichia coli RNA polymerase: a generic method to study bacteriophage/host interactions. J Proteome Res 7: 1244–1250.
[31]  Snyder L, Gold L, Kutter E (1976) A gene of bacteriophage T4 whose product prevents true late transcription on cytosine-containing T4 DNA. Proc Natl Acad Sci U S A 73: 3098–3102.
[32]  Snyder L, Jorissen L (1988) Escherichia coli mutations that prevent the action of the T4 unf/alc protein map in an RNA polymerase gene. Genetics 118: 173–180.
[33]  Nene V, Glass R (1984) Genetic studies on the b subunit of Escherichia coli RNA polyerase VI. A redundant region in the b polypeptide. Mol Gen Genet 196: 64–67.
[34]  Murakami K, Masuda S, Campbell E. A, Muzzin O, Darst S. A (2002) Structural basis of transcription initiation: an RNA polymerase holoenzyme/DNA complex. Science 296: 1285–1290.
[35]  Zakharova N, Bass I, Arsenieva E, Nikiforov V, Severinov K (1998) Mutations in and monoclonal antibody binding to evolutionary hypervariable region of E. coli RNA polymerase b' subunit inhibit transcript cleavage and transcript elongation. J Biol Chem 273: 19371–19374.
[36]  Luo J, Krakow J. S (1992) Characterization and epitope mapping of monoclonal antibodies directed against the beta' subunit of the Escherichia coli RNA polymerase. J Biol Chem 267: 18175–18181.
[37]  Weilbacher R. G, Hebron C, Feng G, Landick R (1994) Termination-altering amino acid substitutions in the beta' subunit of Escherichia coli RNA polymerase identify regions involved in RNA chain elongation. Genes & Development 8: 2913–2927.
[38]  Wang D, Bushnell D. A, Westover K. D, Kaplan C. D, Kornberg R. D (2006) Structural basis of transcription: role of the trigger loop in substrate specificity and catalysis. Cell 127: 941–954.
[39]  Vassylyev D. G, Vassylyeva M. N, Zhang J, Palangat M, Artsimovitch I, et al. (2007) Structural basis for substrate loading in bacterial RNA polymerase. Nature 448: 163–168.
[40]  Kaplan C. D, Larsson K-M, Kornberg R. D (2008) The RNA polymerase II trigger loop functions in substrate selection and is directly targeted by alpha-amanitin. Mol Cell 30: 547–556.
[41]  Kireeva M. L, Nedialkov Y. A, Cremona G. H, Purtov Y. A, Lubkowska L, et al. (2008) Transient reversal of RNA polymerase II active site closing controls fidelity of transcription elongation. Mol Cell 30: 557–566.
[42]  Bar-Nahum G, Epshtein V, Ruckenstein A. E, Rafikov R, Mustaev A, et al. (2005) A ratchet mechanism of transcription elongation and its control. Cell 120: 183–193.
[43]  Delgado M. A, Rintoul M. R, Farias R. N, Salomon R. A (2001) Escherichia coli RNA polymerase is the target of the cyclopeptide antibiotic microcin J25. J Bacteriol 183: 4543–4550.
[44]  Mukhopadhyay J, Sineva E, Knight J, Levy R. M, Ebright R. H (2004) Antibacterial peptide microcin J25 inhibits transcription by binding within and obstructing the RNA polymerase secondary channel. Mol Cell 14: 739–751.
[45]  Salomon R. A, Farias R. N (1992) Microcin-25, a novel antimicrobial peptide produced by Escherichia-coli. J Bacteriol 174: 7428–7435.
[46]  Yuzenkova J, Delgado M. A, Nechaev S, Savalia D, Epshtein V, et al. (2002) Mutations of bacterial RNA polymerase leading to resistance to microcin J25. J Biol Chem 277: 50867–50875.
[47]  Zillig W, Fujiki H, Blum W, Janekovi D, Schweig M, et al. (1975) In vivo and in vitro phosphorylation of DNA-dependent RNA polymerase of Escherichia coli by bacteriophage-T7-induced protein kinase. Proc Natl Acad Sci U S A 72: 2506–2510.
[48]  Severinova E, Severinov K (2006) Localization of the Escherichia coli RNA polymerase beta' subunit residue phosphorylated by bacteriophage T7 kinase Gp0.7. J Bacteriol 188: 3470–3476.
[49]  Severinov K, Mooney R, Darst S. A, Landick R (1997) Tethering of the large subunits of Escherichia coli RNA polymerase. J Biol Chem 272: 24137–24140.
[50]  Doublie S (1997) Preparation of selenomethionyl proteins for phase determination. Methods Enzymol 276: 523–530.
[51]  Otwinowski Z, Minor W (1997) Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol 276: 307–326.
[52]  Sheldrick G. M (2008) A short history of SHELX. Acta Crystallogr A 64: 112–122.
[53]  de La Fortelle E, Irwin J. J, Bricogne G (1997) SHARP: a maximum-likelihood heavy-atom parameter refinement and phasing program for the MIR and MAD methods. In: Bourne P, Watenpaugh K, editors. Crystallographic computing. Boston: Kluwer Academic Publishers. pp. 1–9.
[54]  Langer G, Cohen S. X, Lamzin V. S, Perrakis A (2008) Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7. Nature Protocols 3: 1171–1179.
[55]  Emsley P, Cowtan K (2004) Coot: model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr 60: 2126–2132.
[56]  Murshudov G. N, Vagin A. A, Dodson E. J (1997) Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr D Biol Crystallogr D53: 240–255.
[57]  Nechaev S, Kamali-Moghaddam M, Andre E, Leonetti J-P, Geiduschek E. P (2004) The bacteriophage T4 late-transcription coactivator gp33 binds the flap domain of Escherichia coli RNA polymerase. Proc Natl Acad Sci U S A 101: 17365–17370.
[58]  Campbell E. A, Darst S. A (2000) The anti-s factor SpoIIAB forms a 2:1 complex with sF, contacting multiple conserved regions of the s factor. J Mol Biol 300: 17–28.
[59]  Sali A, Potterton L, Yuan F, van-Vlijmen H, Karplus M (1995) Evaluation of comparative protein modeling by MODELLER. Proteins 23: 318–326.
[60]  Opalka N, Chlenov M, Chacon P, Rice W. J, Wriggers W, et al. (2003) Structure and function of the transcription elongation factor GreB bound to bacterial RNA polymerase. Cell 114: 335–345.
[61]  Ludtke S. J, Baldwin P. R, Chiu W (1999) EMAN: semi-automated software for high resolution single particle reconstructions. J Structural Biol 128: 82–97.
[62]  Craighead J. L, Chang W. H, Asturias F. J (2002) Structure of yeast RNA polymerase II in solution: implications for enzyme regulation and interaction with promoter DNA. Structure (Camb) 10: 1117–1125.
[63]  Frank J, Radermacher M, Penczek P, Zhu J, Li Y, et al. (1996) SPIDER and WEB: processing and visualization of images in 3D electron microscopy and related fields. J Struct Biol 116: 190–199.
[64]  Penczek P, Grassucci R. A, Frank J (1994) The ribosome at improved resolution: new techniques for merging and orientation refinement in 3D cryo-electron microscopy of biological particles. Ultramicroscopy 53: 251–270.
[65]  Edgar R. C (2004) MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformat 5: 113.
[66]  Pei J, Sadreyev R, Grishin N. V (2003) PCMA: fast and accurate multiple sequence alignment based on profile consistency. Bioinformatics 19: 427–428.
[67]  Saxton W. O, Baumeister W (1982) The correlation averaging of a regularly arranged bacterial-cell envelope protein. J Microsc 127: 127–138.
[68]  Harauz G, van Heel M (1986) Exact filters for general geometry three-dimensional reconstruction. Optik 73: 146–156.
[69]  Baker N. A, Sept D, Joseph S, Holst M. J, McCammon J. A (2001) Electrostatics of nanosystems: application to microtubules and the ribosome. Proc Natl Acad Sci U S A 98: 10037–10041.
[70]  Caffrey D. R, Dana P. H, Mathur V, Ocano M, Hong E-J, et al. (2007) PFAAT version 2.0: a tool for editing, annotating, and analyzing multiple sequence alignments. BMC Bioinformat 8: 381.

Full-Text

Contact Us

service@oalib.com

QQ:3279437679

WhatsApp +8615387084133