Analysis of intraviral protein-protein interactions of the SARS coronavirus ORFeome

PLoS ONE

Volumn 2, Issue 5, 2007, Pages

  von Brunn, Albrecht ^a   Teepe, Carola ^a   Simpson, Jeremy C ^b   Pepperkok, Rainer ^b   Friedel, Caroline C ^a   Zimmer, Ralf ^a   Roberts, Rhonda ^c   Baric, Ralph ^c   Haas, Jürgen ^a  

^a UNIVERSITY OF MUNICH   (Germany)

^b EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

^c UNIVERSITY OF NORTH CAROLINA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

NONSTRUCTURAL PROTEIN 13; NONSTRUCTURAL PROTEIN 14; NONSTRUCTURAL PROTEIN 2; NONSTRUCTURAL PROTEIN 5; NONSTRUCTURAL PROTEIN 6; NONSTRUCTURAL PROTEIN 7; NONSTRUCTURAL PROTEIN 8; NONSTRUCTURAL PROTEIN 9; PROTEOME; STRUCTURAL PROTEIN; UNCLASSIFIED DRUG; VIRUS PROTEIN;

ARTICLE; CELLULAR DISTRIBUTION; CONTROLLED STUDY; GENETIC ANALYSIS; HUMAN; HUMAN CELL; IMMUNOFLUORESCENCE; IMMUNOPRECIPITATION; IN VITRO STUDY; MAMMAL CELL; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PATHOGENICITY; PROTEIN LOCALIZATION; PROTEIN PROTEIN INTERACTION; SARS CORONAVIRUS; VERO CELL; VIRUS CELL INTERACTION; VIRUS GENOME; VIRUS REPLICATION; AMINO ACID SEQUENCE; CHEMISTRY; FLUORESCENT ANTIBODY TECHNIQUE; GENOME; METABOLISM; MOLECULAR GENETICS;

MAMMALIA; SARS CORONAVIRUS;

AMINO ACID SEQUENCE; FLUORESCENT ANTIBODY TECHNIQUE; GENOME; MOLECULAR SEQUENCE DATA; OPEN READING FRAMES; SARS VIRUS; VIRAL PROTEINS;

EID: 35148862429     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0000459     Document Type: Article

References (48)

1. Ksiazek TG, Erdman D, Goldsmith CS, Zaki SR, Peret T, et al. (2003) A novel coronavirus associated with severe acute respiratory syndrome. N Engl J Med 348: 1953-1966.
2. Drosten C, Gunther S, Preiser W, van der WS, Brodt HR, et al. (2003) Identification of a novel coronavirus in patients with severe acute respiratory syndrome. N Engl J Med 348: 1967-1976.
3. Marra MA, Jones SJ, Astell CR, Holt RA, Brooks-Wilson A, et al. (2003) The Genome sequence of the SARS-associated coronavirus. Science 300: 1399-1404.
4. Rota PA, Oberste MS, Monroe SS, Nix WA, Campagnoli R, et al. (2003) Characterization of a novel coronavirus associated with severe acute respiratory syndrome. Science 300: 1394-1399.
5. Gorbalenya AE, Snijder EJ, Spaan WJ (2004) Severe acute respiratory syndrome coronavirus phylogeny: toward consensus. J Virol 78: 7863-7866.
6. Snijder EJ, Bredenbeck PJ, Dobbe JC, Thiel V, Ziebuhr J, et al. (2003) Unique and conserved features of genome and proteome of SARS-coronavirus, an early split-off from the coronavirus group 2 lineage. J Mol Biol 331: 991-1004.
7. Thiel V, Ivanov KA, Putics A, Hertzig T, Schelle B, et al. (2003) Mechanisms and enzymes involved in SARS coronavirus genome expression. J Gen Virol 84: 2305-2315.
8. Anand K, Ziebuhr J, Wadhwani P, Mesters JR, Hilgenfeld R (2003) Coronavirus main proteinase (3CLpro) structure: basis for design of anti-SARS drugs. Science 300: 1763-1767.
9. Bhardwaj K, Sun J, Holzenburg A, Guarino LA, Kan CC (2006) RNA recognition and cleavage by the SARS coronavirus endoribonuclease. J Mol Biol 361: 243-256.
10. Gorbalenya AE, Koonin EV, Donchenko AP, Blinov VM (1989) Coronavirus genome: prediction of putative functional domains in the non-structural polyprotein by comparative amino acid sequence analysis. Nucleic Acids Res 17: 4847-4861.
11. Harcourt BH, Jukneliene D, Kanjanahaluethai A, Bechill J, Severson KM, et al. (2004) Identification of severe acute respiratory syndrome coronavirus replicase products and characterization of papain-like protease activity. J Virol 78: 13600-13612.
12. Ivanov KA, Hertzig T, Rozanov M, Bayer S, Thiel V, et al. (2004) Major genetic marker of nidoviruses encodes a replicative endoribonuclease. Proc Natl Acad Sci U S A 101: 12694-12699.
13. Seybert A, Hegyi A, Siddell SG, Ziebuhr J (2000) The human coronavirus 229E superfamily 1 helicase has RNA and DNA duplex-unwinding activities with 5′- to-3′ polarity. RNA 6: 1056-1068.
14. Ziebuhr J, Snijder EJ, Gorbalenya AE (2000) Virus-encoded proteinases and proteolytic processing in the Nidovirales. J Gen Virol 81: 853-879.
15. Imbert I, Guillemot JC, Bourhis JM, Bussetta C, Coutard B, et al. (2006) A second, non-canonical RNA-dependent RNA polymerase in SARS coronavirus. EMBO J 25: 4933-4942.
16. Yount B, Roberts RS, Sims AC, Deming D, Frieman MB, et al. (2005) Severe acute respiratory syndrome coronavirus group-specific open reading frames encode nonessential functions for replication in cell cultures and mice. J Virol 79: 14909-14922.
17. Graham RL, Sims AC, Brockway SM, Baric RS, Denison MR (2005) The nsp2 replicase proteins of murine hepatitis virus and severe acute respiratory syndrome coronavirus are dispensable for viral replication. J Virol 79: 13399-13411.
18. Bost AG, Carnahan RH, Lu XT, Denison MR (2000) Four proteins processed from the replicase gene polyprotein of mouse hepatitis virus colocalize in the cell periphery and adjacent to sites of virion assembly. J Virol 74: 3379-3387.
19. Prentice E, McAuliffe J, Lu X, Subbarao K, Denison MR (2004) Identification and characterization of severe acute respiratory syndrome coronavirus replicase proteins. J Virol 78: 9977-9986.
20. Zhai Y, Sun F, Li X, Pang H, Xu X, et al. (2005) Insights into SARS-CoV transcription and replication from the structure of the nsp7-nsp8 hexadecamer. Nat Struct Mol Biol 12: 980-986.
21. He R, Leeson A, Ballantine M, Andonov A, Baker L, et al. (2004) Characterization of protein-protein interactions between the nucleocapsid protein and membrane protein of the SARS coronavirus. Virus Res 105: 121-125.
22. Ito N, Mossel EC, Narayanan K, Popov VL, Huang C, et al. (2005) Severe acute respiratory syndrome coronavirus 3a protein is a viral structural protein. J Virol 79: 3182-3186.
23. Shen S, Lin PS, Chao YC, Zhang A, Yang X, et al. (2005) The severe acute respiratory syndrome coronavirus 3a is a novel structural protein. Biochem Biophys Res Commun 330: 286-292.
24. Huang C, Ito N, Tseng CT, Makino S (2006) Severe acute respiratory syndrome coronavirus 7a accessory protein is a viral structural protein. J Virol 80: 7287-7294.
25. Fang X, Ye L, Timani KA, Li S, Zen Y, et al. (2005) Peptide domain involved in the interaction between membrane protein and nucleocapsid protein of SARS-associated coronavirus. J Biochem Mol Biol 38: 381-385.
26. Uetz P, Dong YA, Zeretzke C, Atzler C, Baiker A, et al. (2006) Herpesviral protein networks and their interaction with the human proteome. Science 311: 239-242.
27. Rual JF, Venkatesan K, Hao T, Hirozane-Kishikawa T, Dricot A, et al. (2005) Towards a proteome-scale map of the human protein-protein interaction network. Nature 437: 1173-1178.
28. Stelzl U, Worm U, Lalowski M, Haenig C, Brembeck FH, et al. (2005) A human protein-protein interaction network: a resource for annotating the proteome. Cell 122: 957-968.
29. Lehner B, Fraser AG (2004) A first-draft human protein-interaction map. Genome Biol 5: R63.
30. Simpson JC, Wellenreuther R, Poustka A, Pepperkok R, Wiemann S (2000) Systematic subcellular localization of novel proteins identified by large-scale cDNA sequencing. EMBO Rep 1: 287-292.
31. Bartlam M, Yang H, Rao Z (2005) Structural insights into SARS coronavirus proteins. Curr Opin Struct Biol 15: 664-672.
32. Flajolet M, Rotondo G, Daviet L, Bergametti F, Inchauspe G, et al. (2000) A genomic approach of the hepatitis C virus generates a protein interaction map. Gene 242: 369-379.
33. Choi IR, Stenger DC, French R (2000) Multiple interactions among proteins encoded by the mite-transmitted wheat streak mosaic tritimovirus. Virology 267: 185-198.
34. Guo D, Rajamaki ML, Saarma M, Valkonen JP (2001) Towards a protein interaction map of potyviruses: protein interaction matrixes of two potyviruses based on the yeast two-hybrid system 2. J Gen Virol 82: 935-939.
35. Cuconati A, Xiang W, Lahser F, Pfister T, Wimmer E (1998) A protein linkage map of the P2 nonstructural proteins of poliovirus 3. J Virol 72: 1297-1307.
36. Sutton G, Fry E, Carter L, Sainsbury S, Walter T, et al. (2004) The nsp9 replicase protein of SARS-coronavirus, structure and functional insights. Structure 12: 341-353.
37. Brockway SM, Clay CT, Lu XT, Denison MR (2003) Characterization of the expression, intracellular localization, and replication complex association of the putative mouse hepatitis virus RNA-dependent RNA polymerase. J Virol 77: 10515-10527.
38. Huang C, Narayanan K, Ito N, Peters CJ, Makino S (2006) Severe acute respiratory syndrome coronavirus 3a protein is released in membranous structures from 3a protein-expressing cells and infected cells. J Virol 80: 210-217.
39. Meier C, Aricescu AR, Assenberg R, Aplin RT, Gilbert RJ, et al. (2006) The crystal structure of ORF-9b, a lipid binding protein from the SARS coronavirus. Structure 14: 1157-1165.
40. Tan YJ, Lim SG, Hong W (2006) Understanding the accessory viral proteins unique to the severe acute respiratory syndrome (SARS) coronavirus. Antiviral Res 72: 78-88.
41. Yuan X, Li J, Shan Y, Yang Z, Zhao Z, et al. (2005) Subcellular localization and membrane association of SARS-CoV 3a protein. Virus Res 109: 191-202.
42. Yuan X, Shan Y, Zhao Z, Chen J, Cong Y (2005) G0/G1 arrest and apoptosis induced by SARS-CoV 3b protein in transfected cells. Virol J 2: 66.
43. Chan WS, Wu C, Chow SC, Cheung T, To KF, et al. (2005) Coronaviral hypothetical and structural proteins were found in the intestinal surface enterocytes and pneumocytes of severe acute respiratory syndrome (SARS). Mod Pathol 18: 1432-1439.
44. Chow SC, Ho CY, Tam TT, Wu C, Cheung T, et al. (2006) Specific epitopes of the structural and hypothetical proteins elicit variable humoral responses in SARS patients. J Clin Pathol 59: 468-476.
45. Xenarios I, Rice DW, Salwinski L, Baron MK, Marcotte EM, et al. (2000) DIP: the database of interacting proteins. Nucleic Acids Res 28: 289-291.
46. Peri S, Navarro JD, Amanchy R, Kristiansen TZ, Jonnalagadda CK, et al. (2003) Development of human protein reference database as an initial platform for approaching systems biology in humans. Genome Res 13: 2363-2371.
47. Erdös P, Renyi A (1959) On random graphs. Publicationes Mathematicae 6: 290-297.
48. Maslov S, Sneppen K (2002) Specificity and stability in topology of protein networks. Science 296: 910-913.