Structure of the L Protein of Vesicular Stomatitis Virus from Electron Cryomicroscopy

Overview

Journal Cell

Publisher Cell Press

Specialty Cell Biology

Date 2015 Jul 7

PMID 26144317

Citations 161

Authors

Bo Liang

Zongli Li

Simon Jenni

Amal A Rahmeh

Benjamin M Morin

Timothy Grant

Nikolaus Grigorieff

Stephen C Harrison

Sean P J Whelan

Affiliations

Soon will be listed here.

Abstract

The large (L) proteins of non-segmented, negative-strand RNA viruses, a group that includes Ebola and rabies viruses, catalyze RNA-dependent RNA polymerization with viral ribonucleoprotein as template, a non-canonical sequence of capping and methylation reactions, and polyadenylation of viral messages. We have determined by electron cryomicroscopy the structure of the vesicular stomatitis virus (VSV) L protein. The density map, at a resolution of 3.8 Å, has led to an atomic model for nearly all of the 2109-residue polypeptide chain, which comprises three enzymatic domains (RNA-dependent RNA polymerase [RdRp], polyribonucleotidyl transferase [PRNTase], and methyltransferase) and two structural domains. The RdRp resembles the corresponding enzymatic regions of dsRNA virus polymerases and influenza virus polymerase. A loop from the PRNTase (capping) domain projects into the catalytic site of the RdRp, where it appears to have the role of a priming loop and to couple product elongation to large-scale conformational changes in L.

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References

Chen V, Arendall 3rd W, Headd J, Keedy D, Immormino R, Kapral G . MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr D Biol Crystallogr. 2010; 66(Pt 1):12-21. PMC: 2803126. DOI: 10.1107/S0907444909042073. View

Rahmeh A, Li J, Kranzusch P, Whelan S . Ribose 2'-O methylation of the vesicular stomatitis virus mRNA cap precedes and facilitates subsequent guanine-N-7 methylation by the large polymerase protein. J Virol. 2009; 83(21):11043-50. PMC: 2772757. DOI: 10.1128/JVI.01426-09. View

Emsley P, Lohkamp B, Scott W, Cowtan K . Features and development of Coot. Acta Crystallogr D Biol Crystallogr. 2010; 66(Pt 4):486-501. PMC: 2852313. DOI: 10.1107/S0907444910007493. View

Rahmeh A, Schenk A, Danek E, Kranzusch P, Liang B, Walz T . Molecular architecture of the vesicular stomatitis virus RNA polymerase. Proc Natl Acad Sci U S A. 2010; 107(46):20075-80. PMC: 2993402. DOI: 10.1073/pnas.1013559107. View

Grigorieff N, Harrison S . Near-atomic resolution reconstructions of icosahedral viruses from electron cryo-microscopy. Curr Opin Struct Biol. 2011; 21(2):265-73. PMC: 3088881. DOI: 10.1016/j.sbi.2011.01.008. View

Tekes G, Rahmeh A, Whelan S . A freeze frame view of vesicular stomatitis virus transcription defines a minimal length of RNA for 5' processing. PLoS Pathog. 2011; 7(6):e1002073. PMC: 3107219. DOI: 10.1371/journal.ppat.1002073. View

Morin B, Rahmeh A, Whelan S . Mechanism of RNA synthesis initiation by the vesicular stomatitis virus polymerase. EMBO J. 2012; 31(5):1320-9. PMC: 3297992. DOI: 10.1038/emboj.2011.483. View

Rahmeh A, Morin B, Schenk A, Liang B, Heinrich B, Brusic V . Critical phosphoprotein elements that regulate polymerase architecture and function in vesicular stomatitis virus. Proc Natl Acad Sci U S A. 2012; 109(36):14628-33. PMC: 3437890. DOI: 10.1073/pnas.1209147109. View

Lyumkis D, Brilot A, Theobald D, Grigorieff N . Likelihood-based classification of cryo-EM images using FREALIGN. J Struct Biol. 2013; 183(3):377-388. PMC: 3824613. DOI: 10.1016/j.jsb.2013.07.005. View

10.

Morin B, Whelan S . Sensitivity of the polymerase of vesicular stomatitis virus to 2' substitutions in the template and nucleotide triphosphate during initiation and elongation. J Biol Chem. 2014; 289(14):9961-9. PMC: 3975040. DOI: 10.1074/jbc.M113.542761. View

11.

Krumm S, Yan D, Hovingh E, Evers T, Enkirch T, Reddy G . An orally available, small-molecule polymerase inhibitor shows efficacy against a lethal morbillivirus infection in a large animal model. Sci Transl Med. 2014; 6(232):232ra52. PMC: 4080709. DOI: 10.1126/scitranslmed.3008517. View

12.

Pflug A, Guilligay D, Reich S, Cusack S . Structure of influenza A polymerase bound to the viral RNA promoter. Nature. 2014; 516(7531):355-60. DOI: 10.1038/nature14008. View

13.

Reich S, Guilligay D, Pflug A, Malet H, Berger I, Crepin T . Structural insight into cap-snatching and RNA synthesis by influenza polymerase. Nature. 2014; 516(7531):361-6. DOI: 10.1038/nature14009. View

14.

Barr J, Wertz G . Polymerase slippage at vesicular stomatitis virus gene junctions to generate poly(A) is regulated by the upstream 3'-AUAC-5' tetranucleotide: implications for the mechanism of transcription termination. J Virol. 2001; 75(15):6901-13. PMC: 114418. DOI: 10.1128/JVI.75.15.6901-6913.2001. View

15.

Egloff M, Benarroch D, Selisko B, Romette J, Canard B . An RNA cap (nucleoside-2'-O-)-methyltransferase in the flavivirus RNA polymerase NS5: crystal structure and functional characterization. EMBO J. 2002; 21(11):2757-68. PMC: 125380. DOI: 10.1093/emboj/21.11.2757. View

16.

Whelan S, Wertz G . Transcription and replication initiate at separate sites on the vesicular stomatitis virus genome. Proc Natl Acad Sci U S A. 2002; 99(14):9178-83. PMC: 123114. DOI: 10.1073/pnas.152155599. View

17.

Tao Y, Farsetta D, Nibert M, Harrison S . RNA synthesis in a cage--structural studies of reovirus polymerase lambda3. Cell. 2002; 111(5):733-45. DOI: 10.1016/s0092-8674(02)01110-8. View

18.

Mindell J, Grigorieff N . Accurate determination of local defocus and specimen tilt in electron microscopy. J Struct Biol. 2003; 142(3):334-47. DOI: 10.1016/s1047-8477(03)00069-8. View

19.

Rosenthal P, Henderson R . Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy. J Mol Biol. 2003; 333(4):721-45. DOI: 10.1016/j.jmb.2003.07.013. View

20.

Baltimore D, Huang A, Stampfer M . Ribonucleic acid synthesis of vesicular stomatitis virus, II. An RNA polymerase in the virion. Proc Natl Acad Sci U S A. 1970; 66(2):572-6. PMC: 283083. DOI: 10.1073/pnas.66.2.572. View