A comparative study of short linear motif compositions of the influenza a virus ribonucleoproteins

PLoS ONE

Volumn 7, Issue 6, 2012, Pages

  Yang, Chu Wen ^a  

^a SOOCHOW UNIVERSITY   (Taiwan)

Author keywords

[No Author keywords available]

Indexed keywords

RIBONUCLEOPROTEIN; VIRUS PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; COMPARATIVE STUDY; CONTROLLED STUDY; INFLUENZA VIRUS A; NONHUMAN; PHYLOGENY; PROTEIN FUNCTION; PROTEIN INTERACTION; PROTEIN LOCALIZATION; PROTEOMICS; SEQUENCE ANALYSIS; SIGNAL TRANSDUCTION; VIRUS REPLICATION; VIRUS VIRULENCE; GENETICS; PROTEIN DATABASE; PROTEIN MOTIF;

AMINO ACID MOTIFS; DATABASES, PROTEIN; INFLUENZA A VIRUS; RIBONUCLEOPROTEINS; VIRAL PROTEINS;

EID: 84862025127     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0038637     Document Type: Article

References (60)

1. Diella F, Haslam N, Chica C, Budd A, Michael S, et al. (2008) Understanding eukaryotic linear motifs and their role in cell signaling and regulation. Front Biosci 13: 6580-6603.
2. Davey NE, Travé G, Gibson TJ, (2011) How viruses hijack cell regulation. Trends Biochem Sci 36: 159-169.
3. Dinkel H, Michael S, Weatheritt RJ, Davey NE, Van Roey K, et al. (2012) ELM-the database of eukaryotic linear motifs. Nucleic Acids Res 40: D242-D251.
4. Naffakh N, Tomoiu A, Rameix-Welti MA, van der Werf S, (2008) Host restriction of avian influenza viruses at the level of the ribonucleoproteins. Annu Rev Microbiol 62: 403-424.
5. Matrosovich M, Stech J, Klenk HD, (2009) Influenza receptors, polymerase and host range. Rev Sci Tech 28: 203-217.
6. Nistal-Villán E, García-Sastre, (2009) A New prospects for the rational design of antivirals. Nat Med 15: 1253-1254.
7. Zar JH, (2010) Biostatistical Analysis. Fifth Ed. Pearson Education, Inc.
8. Shannon CE, (1948) A mathematical theory of communication. Bell System Tech J 27: 379-423, 623-656.
9. Batista MV, Ferreira TA, Freitas AC, Balbino VQ, (2011) An entropy-based approach for the identification of phylogenetically informative genomic regions of Papillomavirus. Infect Genet Evol 11: 2026-2033.
10. Koo QY, Khan AM, Jung KO, Ramdas S, Miotto O, et al. (2009) Conservation and variability of West Nile virus proteins. PLoS One 4: e5352.
11. Li H, Hughes AL, Bano N, McArdle S, Livingston S, et al. (2011) Genetic diversity of near genome-wide hepatitis C virus sequences during chronic infection: evidence for protein structural conservation over time. PLoS One 6: e19562.
12. Chen GW, Chang SC, Mok CK, Lo YL, Kung YN, et al. (2006) Genomic signatures of human versus avian influenza A viruses. Emerg Infect Dis 12: 1353-1360.
13. Chen GW, Shih SR, (2009) Genomic signatures of influenza A pandemic (H1N1) 2009 virus. Emerg Infect Dis 15: 1897-1903.
14. Pan K, Deem MW, (2011) Quantifying selection and diversity in viruses by entropy methods, with application to the haemagglutinin of H3N2 influenza. J R Soc Interface 8: 1644-1653.
15. Abdel-Moneim AS, Shehab GM, Abu-Elsaad AA, (2011) Molecular evolution of the six internal genes of H5N1 equine influenza A virus. Arch Virol 156: 1257-1262.
16. Li J, Li Y, Hu Y, Chang G, Sun W, et al. (2011) PB1-mediated virulence attenuation of H5N1 influenza virus in mice is associated with PB2. J Gen Virol 92: 1435-1444.
17. Brown EG, Liu H, Kit LC, Baird S, Nesrallah M, (2001) Pattern of mutation in the genome of influenza A virus on adaptation to increased virulence in the mouse lung: identification of functional themes. Proc Natl Acad Sci U S A 98: 6883-6888.
18. Bussey KA, Desmet EA, Mattiacio JL, Hamilton A, Bradel-Tretheway B, et al. (2011) PA residues in the 2009 H1N1 pandemic influenza virus enhance avian influenza virus polymerase activity in mammalian cells. J Virol 85: 7020-7028.
19. Chen GW, Shih SR, (2009) Genomic signatures of influenza A pandemic (H1N1) 2009 virus. Emerg Infect Dis 15: 1897-1903.
20. Finkelstein DB, Mukatira S, Mehta PK, Obenauer JC, Su X, et al. (2007) Persistent host markers in pandemic and H5N1 influenza viruses. J Virol 81: 10292-10299.
21. Foeglein Á, Loucaides EM, Mura M, Wise HM, Barclay WS, (2011) Influence of PB2 host-range determinants on the intranuclear mobility of the influenza A virus polymerase. J Gen Virol 92: 1650-1661.
22. Gabriel G, Dauber B, Wolff T, Planz O, Klenk HD, et al. (2005) The viral polymerase mediates adaptation of an avian influenza virus to a mammalian host. Proc Natl Acad Sci U S A 102: 18590-18595.
23. Li Z, Chen H, Jiao P, Deng G, Tian G, (2005) Molecular basis of replication of duck H5N1 influenza viruses in a mammalian mouse model. J Virol 79: 12058-12064.
24. Mok CK, Yen HL, Yu MY, Yuen KM, Sia SF, et al. (2011) Amino acid residues 253 and 591 of the PB2 protein of avian influenza virus A H9N2 contribute to mammalian pathogenesis. J Virol 85: 9641-9645.
25. Miotto O, Heiny AT, Albrecht R, García-Sastre A, Tan TW, et al. (2010) Complete-proteome mapping of human influenza A adaptive mutations: implications for human transmissibility of zoonotic strains. PLoS One 5: e9025.
26. Shinya K, Watanabe S, Ito T, Kasai N, Kawaoka Y, (2007) Adaptation of an H7N7 equine influenza A virus in mice. J Gen Virol 88: 547-553.
27. Song MS, Pascua PN, Lee JH, Baek YH, Lee OJ, et al. (2009) The polymerase acidic protein gene of influenza a virus contributes to pathogenicity in a mouse model. J Virol 83: 12325-12335.
28. Song MS, Pascua PN, Lee JH, Baek YH, Park KJ, et al. (2011) Virulence and genetic compatibility of polymerase reassortant viruses derived from the pandemic (H1N1) 2009 influenza virus and circulating influenza A viruses. J Virol 85: 6275-6286.
29. Tamuri AU, Dos Reis M, Hay AJ, Goldstein RA, (2009) Identifying changes in selective constraints: host shifts in influenza. PLoS Comput Biol 5: e1000564.
30. Yamada S, Hatta M, Staker BL, Watanabe S, Imai M, (2010) Biological and structural characterization of a host-adapting amino acid in influenza virus. PLoS Pathog 6: e1001034.
31. Yao Y, Mingay LJ, McCauley JW, Barclay WS, (2001) Sequences in influenza A virus PB2 protein that determine productive infection for an avian influenza virus in mouse and human cell lines. J Virol 75: 5410-5415.
32. Shapira SD, Gat-Viks I, Shum BO, Dricot A, de Grace MM, et al. (2009) A physical and regulatory map of host-influenza interactions reveals pathways in H1N1 infection. Cell 139: 1255-1267.
33. König R, Stertz S, Zhou Y, Inoue A, Hoffmann HH, et al. (2010) Human host factors required for influenza virus replication. Nature 463: 813-817.
34. Hutchinson EC, Orr OE, Man Liu S, Engelhardt OG, Fodor E, (2011) Characterization of the interaction between the influenza A virus polymerase subunit PB1 and the host nuclear import factor Ran-binding protein 5. J Gen Virol 92: 1859-1869.
35. Tarendeau F, Boudet J, Guilligay D, Mas PJ, Bougault CM, et al. (2007) Structure and nuclear import function of the C-terminal domain of influenza virus polymerase PB2 subunit. Nat Struct Mol Biol 14: 229-233.
36. Subbarao EK, London W, Murphy BR, (1993) A single amino acid in the PB2 gene of influenza A virus is a determinant of host range. J Virol 67: 1761-1764.
37. Massin P, van der Werf S, Naffakh N, (2001) Residue 627 of PB2 is a determinant of cold sensitivity in RNA replication of avian influenza viruses. J Virol 75: 5398-5404.
38. Hatta M, Hatta Y, Kim JH, Watanabe S, Shinya K, et al. (2007) Growth of H5N1 influenza A viruses in the upper respiratory tracts of mice. PLoS Pathog 3: 1374-1379.
39. Wang S, Liu Q, Pu J, Li Y, Keleta L, et al. (2008) Simplified recombinational approach for influenza A virus reverse genetics. J Virol Methods 151: 74-78.
40. Liu Q, Wang S, Ma G, Pu J, Forbes NE, et al. (2009) Improved and simplified recombineering approach for influenza virus reverse genetics. J Mol Genet Med 3: 225-231.
41. Dankar SK, Wang S, Ping J, Forbes NE, Keleta L, et al. (2011) Influenza A virus NS1 gene mutations F103L and M106I increase replication and virulence. Virol J 8: 13.
42. Forbes NE, Ping J, Dankar SK, Jia JJ, Selman M, et al. (2012) Multifunctional adaptive NS1 mutations are selected upon human influenza virus evolution in the mouse. PLoS One 7: e31839.
43. Hemerka JN, Wang D, Weng Y, Lu W, Kaushik RS, et al. (2009) Detection and characterization of influenza A virus PA-PB2 interaction through a bimolecular fluorescence complementation assay. J Virol 83: 3944-3955.
44. Suzuki T, Ainai A, Nagata N, Sata T, Sawa H, et al. (2011) A novel function of the N-terminal domain of PA in assembly of influenza A virus RNA polymerase. Biochem Biophys Res Commun 414: 719-726.
45. Deng Q, Wang D, Xiang X, Gao X, Hardwidge PR, et al. (2011) Application of a split luciferase complementation assay for the detection of viral protein-protein interactions. J Virol Methods 176: 108-111.
46. Foeglein Á, Loucaides EM, Mura M, Wise HM, Barclay WS, et al. (2011) Influence of PB2 host-range determinants on the intranuclear mobility of the influenza A virus polymerase. J Gen Virol 92: 1650-1661.
47. Tatham MH, Rodriguez MS, Xirodimas DP, Hay RT, (2009) Detection of protein SUMOylation in vivo. Nat Protoc 4: 1363-1371.
48. Sarge KD, Park-Sarge OK, (2009) Detection of proteins sumoylated in vivo and in vitro. Methods Mol Biol 590: 265-277.
49. Loregian A, Marsden HS, Palù G, (2002) Protein-protein interactions as targets for antiviral chemotherapy. Rev Med Virol 12: 239-262.
50. Geiss BJ, Stahla H, Hannah AM, Gari AM, Keenan SM, (2009) Focus on flaviviruses: current and future drug targets. Future Med Chem 1: 327-344.
51. Zhan P, Li W, Chen H, Liu X, (2010) Targeting protein-protein interactions: a promising avenue of anti-HIV drug discovery. Curr Med Chem 17: 3393-3409.
52. Elsawy KM, Twarock R, Verma CS, Caves LS, (2012) Peptide inhibitors of viral assembly: a novel route to broad-spectrum antivirals. J Chem Inf Model 52: 770-776.
53. Muratore G, Goracci L, Mercorelli B, Foeglein A, Digard P, et al. (2012) Small molecule inhibitors of influenza A and B viruses that act by disrupting subunit interactions of the viral polymerase. Proc Natl Acad Sci U S A 109: 6247-6252.
54. Mänz B, Götz V, Wunderlich K, Eisel J, Kirchmair J, et al. (2011) Disruption of the viral polymerase complex assembly as a novel approach to attenuate influenza A virus. J Biol Chem 286: 8414-8424.
55. Wunderlich K, Juozapaitis M, Ranadheera C, Kessler U, Martin A, et al. (2011) Identification of high-affinity PB1-derived peptides with enhanced affinity to the PA protein of influenza A virus polymerase. Antimicrob Agents Chemother 55: 696-702.
56. Wunderlich K, Mayer D, Ranadheera C, Holler AS, Mänz B, et al. (2009) Identification of a PA-binding peptide with inhibitory activity against influenza A and B virus replication. PLoS One 4: e7517.
57. Ghanem A, Mayer D, Chase G, Tegge W, Frank R, et al. (2007) Peptide-mediated interference with influenza A virus polymerase. J Virol 81: 7801-7804.
58. Wang NX, Lee HJ, Zheng JJ, (2008) Therapeutic use of PDZ protein-protein interaction antagonism. Drug News Perspect 21: 137-141.
59. Jiang S, Liao C, Bindu L, Yin B, Worthy KW, et al. (2009) Discovery of thioether-bridged cyclic pentapeptides binding to Grb2-SH2 domain with high affinity. Bioorg Med Chem Lett 19: 2693-2698.
60. Kadaveru K, Vyas J, Schiller MR, (2008) Viral infection and human disease-insights from minimotifs. Front Biosci 13: 6455-6471.