Construction and application of a protein interaction map for white spot syndrome virus (WSSV)

Molecular and Cellular Proteomics

Volumn 13, Issue 1, 2014, Pages 269-282

  Sangsuriya, Pakkakul ^a,b   Huang, Jiun Yan ^c   Chu, Yu Fei ^c   Phiwsaiya, Kornsunee ^a,d   Leekitcharoenphon, Pimlapas ^a   Meemetta, Watcharachai ^a   Senapin, Saengchan ^a,d   Huang, Wei Pang ^c   Withyachumnarnkul, Boonsirm ^a,b,e   Flegel, Timothy W ^a,d,f   Lo, Chu Fang ^c,f  

^a MAHIDOL UNIVERSITY   (Thailand)

^b Mahidol University   (Thailand)

^c NATIONAL TAIWAN UNIVERSITY   (Taiwan)

^d NATIONAL SCIENCE AND TECHNOLOGY DEVELOPMENT AGENCY   (Thailand)

^e Shrimp Genetic Improvement Center   (Thailand)

^f NATIONAL CHENG KUNG UNIVERSITY   (Taiwan)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTION FACTOR GAL4; VIRUS PROTEIN;

ARTICLE; CHROMATIN IMMUNOPRECIPITATION; DNA BINDING; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; PROTEOMICS; RNA INTERFERENCE; TWO HYBRID SYSTEM; WHITE SPOT SYNDROME VIRUS;

ANIMALS; HOST-PATHOGEN INTERACTIONS; PENAEIDAE; PROTEIN INTERACTION MAPS; PROTEOMICS; TRANSCRIPTOME; VIRAL PROTEINS; WHITE SPOT SYNDROME VIRUS 1;

EID: 84891793954     PISSN: 15359476     EISSN: 15359484     Source Type: Journal    
DOI: 10.1074/mcp.M113.029199     Document Type: Article

References (77)

1. Lightner, D. V. (1996) A Handbook of Shrimp Pathology and Diagnostic Procedures for Diseases of Cultured Penaeid Shrimp. World Aquaculture Society, Baton Rouge, LA, U.S.A.
2. Leu, J. H., Yang, F., Zhang, X., Xu, X., Kou, G. H., and Lo, C. F. (2009) Whispovirus. Curr. Top. Microbiol. Immunol. 328, 197-227
3. Sánchez-Paz, A. (2010) White spot syndrome virus: an overview on an emergent concern. Vet. Res. 41, 43
4. Zhang, X., Huang, C., Tang, X., Zhuang, Y., and Hew, C. L. (2004) Identification of structural proteins from shrimp white spot syndrome virus (WSSV) by 2DE-MS. Proteins 55, 229-235
5. Witteveldt, J., Vermeesch, A. M., Langenhof, M., de Lang, A., Vlak, J. M., and van Hulten, M. C. W. (2005) Nucleocapsid protein VP15 is the basic DNA binding protein of white spot syndrome virus of shrimp. Arch. Virol. 150, 1121-1133
6. Xie, X., and Yang, F. (2006) White spot syndrome virus VP24 interacts with VP28 and is involved in virus infection. J. Gen. Virol. 87, 1903-1908
7. Chang, Y. S., Liu, W. J., Chou, T. L., Lee, Y. T., Lee, T. L., Huang, W. T., Kou, G. H., and Lo, C. F. (2008) Characterization of white spot syndrome virus envelope protein VP51A and its interaction with viral tegument protein VP26. J. Virol. 82, 12555-12564
8. Chen, J., Li, Z., and Hew, C. L. (2007) Characterization of a novel envelope protein WSV010 of shrimp white spot syndrome virus and its interaction with a major viral structural protein VP24. Virology 364, 208-213
9. Jie, Z., Xu, L., and Yang, F. (2008) The C-terminal region of envelope protein VP38 from white spot syndrome virus is indispensable for interaction with VP24. Arch. Virol. 153, 2103-2106
10. Wan, Q., Xu, L., and Yang, F. (2008) VP26 of white spot syndrome virus functions as a linker protein between the envelope and nucleocapsid of virions by binding with VP51. J. Virol. 82, 12598-12601
11. Liu, Q. H., Ma, C. Y., Chen, W. B., Zhang, X. L., Liang, Y., Dong, S. L., and Huang, J. (2009) White spot syndrome virus VP37 interacts with VP28 and VP26. Dis. Aquat. Organ. 85, 23-30
12. Zhou, Q., Xu, L., Li, H., Qi, Y. P., and Yang, F. (2009) Four major envelope proteins of white spot syndrome virus bind to form a complex. J. Virol. 83, 4709-4712
13. Lin, Y., Xu, L., and Yang, F. (2010) Tetramerization of white spot syndrome virus envelope protein VP33 and its interaction with VP24. Arch. Virol. 155, 833-838
14. Chang, Y. S., Liu, W. J., Lee, C. C., Chou, T. L., Lee, Y. T., Wu, T. S., Huang, J. Y., Huang, W. T., Lee, T. L., Kou, G. H., Wang, A. H., and Lo, C. F. (2010) A 3D model of the membrane protein complex formed by the white spot syndrome virus structural proteins. PLoS ONE 5, e10718
15. Li, Z., Xu, L., Li, F., Zhou, Q., and Yang, F. (2011) Analysis of white spot syndrome virus envelope protein complexome by two-dimensional blue native/SDS PAGE combined with mass spectrometry. Arch. Virol. 156, 1125-1135
16. Uetz, P., Giot, L., Cagney, G., Mansfield, T. A., Judson, R. S., Knight, J. R., Lockshon, D., Narayan, V., Srinivasan, M., Pochart, P., Qureshi-Emili, A., Li, Y., Godwin, B., Conover, D., Kalbfleisch, T., Vijayadamodar, G., Yang, M., Johnston, M., Fields, S., and Rothberg, J. M. (2000) A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 403, 623-627
17. Ito, T., Chiba, T., Ozawa, R., Yoshida, M., Hattori, M., and Sakaki, Y. (2001) A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc. Natl. Acad. Sci. U.S.A. 98, 4569-4574
18. Rain, J. C., Selig, L., De Reuse, H., Battaglia, V., Reverdy, C., Simon, S., Lenzen, G., Petel, F., Wojcik, J., Schächter, V., Chemama, Y., Labigne, A., and Legrain, P. (2001) The protein-protein interaction map of Helicobacter pylori. Nature 409, 211-215
19. Giot, L., Bader, J. S., Brouwer, C., Chaudhuri, A., Kuang, B., Li, Y., Hao, Y. L., Ooi, C. E., Godwin, B., Vitols, E., Vijayadamodar, G., Pochart, P., Machineni, H., Welsh, M., Kong, Y., Zerhusen, B., Malcolm, R., Varrone, Z., Collis, A., Minto, M., Burgess, S., McDaniel, L., Stimpson, E., Spriggs, F., Williams, J., Neurath, K., Ioime, N., Agee, M., Voss, E., Furtak, K., Renzulli, R., Aanensen, N., Carrolla, S., Bickelhaupt, E., Lazovatsky, Y., DaSilva, A., Zhong, J., Stanyon, C. A., Finley, R. L., White, K. P., Braverman, M., Jarvie, T., Gold, S., Leach, M., Knight, J., Shimkets, R. A., McKenna, M. P., Chant, J., and Rothberg, J. M. (2003) A protein interaction map of Drosophila melanogaster. Science 302, 1727-1736
20. Li, S., Armstrong, C. M., Bertin, N., Ge, H., Milstein, S., Boxem, M., Vidalain, P.-O., Han, J.-D. J., Chesneau, A., Hao, T., Goldberg, D. S., Li, N., Martinez, M., Rual, J.-F., Lamesch, P., Xu, L., Tewari, M., Wong, S. L., Zhang, L. V., Berriz, G. F., Jacotot, L., Vaglio, P., Reboul, J., Hirozane-Kishikawa, T., Li, Q., Gabel, H. W., Elewa, A., Baumgartner, B., Rose, D. J., Yu, H., Bosak, S., Sequerra, R., Fraser, A., Mango, S. E., Saxton, W. M., Strome, S., van den Heuvel, S., Piano, F., Vandenhaute, J., Sardet, C., Gerstein, M., Doucette-Stamm, L., Gunsalus, K. C., Harper, J. W., Cusick, M. E., Roth, F. P., Hill, D. E., and Vidal, M. (2004) A map of the interactome network of the metazoan C. elegans. Science 303, 540-543
21. LaCount, D. J., Vignali, M., Chettier, R., Phansalkar, A., Bell, R., Hesselberth, J. R., Schoenfeld, L. W., Ota, I., Sahasrabudhe, S., Kurschner, C., Fields, S., and Hughes, R. E. (2005) A protein interaction network of the malaria parasite Plasmodium falciparum. Nature 438, 103-107
22. Rual, J. F., Venkatesan, K., Hao, T., Hirozane Kishikawa, T., Dricot, A., Li, N., Berriz, G. F., Gibbons, F. D., Dreze, M., Ayivi Guedehoussou, N., Klitgord, N., Simon, C., Boxem, M., Milstein, S., Rosenberg, J., Goldberg, D. S., Zhang, L. V., Wong, S. L., Franklin, G., Li, S., Albala, J. S., Lim, J., Fraughton, C., Llamosas, E., Cevik, S., Bex, C., Lamesch, P., Sikorski, R. S., Vandenhaute, J., Zoghbi, H. Y., Smolyar, A., Bosak, S., Sequerra, R., Doucette Stamm, L., Cusick, M. E., Hill, D. E., Roth, F. P., and Vidal, M. (2005) Towards a proteome-scale map of the human protein-protein interaction network. Nature 437, 1173-1178
23. Stelzl, U., Worm, U., Lalowski, M., Haenig, C., Brembeck, F. H., Goehler, H., Stroedicke, M., Zenkner, M., Schoenherr, A., Koeppen, S., Timm, J., Mintzlaff, S., Abraham, C., Bock, N., Kietzmann, S., Goedde, A., Toksöz, E., Droege, A., Krobitsch, S., Korn, B., Birchmeier, W., Lehrach, H., and Wanker, E. E. (2005) A human protein-protein interaction network: a resource for annotating the proteome. Cell 122, 957-968
24. Bartel, P. L., Roecklein, J. A., SenGupta, D., and Fields, S. (1996) A protein linkage map of Escherichia coli bacteriophage T7. Nat. Genet. 12, 72-77
25. McCraith, S., Holtzman, T., Moss, B., and Fields, S. (2000) Genome-wide analysis of vaccinia virus protein-protein interactions. Proc. Natl. Acad. Sci. U.S.A. 97, 4879-4884
26. Flajolet, M., Rotondo, G., Daviet, L., Bergametti, F., Inchauspé, G., Tiollais, P., Transy, C., and Legrain, P. (2000) A genomic approach of the hepatitis C virus generates a protein interaction map. Gene 242, 369-379
27. Uetz, P., Dong, Y. A., Zeretzke, C., Atzler, C., Baiker, A., Berger, B., Rajagopala, S. V., Roupelieva, M., Rose, D., Fossum, E., and Haas, J. (2006) Herpesviral protein networks and their interaction with the human proteome. Science 311, 239-242
28. Calderwood, M. A., Venkatesan, K., Xing, L., Chase, M. R., Vazquez, A., Holthaus, A. M., Ewence, A. E., Li, N., Hirozane-Kishikawa, T., Hill, D. E., Vidal, M., Kieff, E., and Johannsen, E. (2007) Epstein-Barr virus and virus human protein interaction maps. Proc. Natl. Acad. Sci. U.S.A. 104, 7606-7611
29. Fossum, E., Friedel, C. C., Rajagopala, S. V., Titz, B., Baiker, A., Schmidt, T., Kraus, T., Stellberger, T., Rutenberg, C., Suthram, S., Bandyopadhyay, S., Rose, D., von Brunn, A., Uhlmann, M., Zeretzke, C., Dong, Y. A., Boulet, H., Koegl, M., Bailer, S. M., Koszinowski, U., Ideker, T., Uetz, P., Zimmer, R., and Haas, J. (2009) Evolutionarily conserved herpesviral protein interaction networks. PLoS Pathog. 5, e1000570
30. Wang, C. H., Lo, C. F., Leu, J. H., Chou, C. M., Yeh, P. Y., Chou, H. Y., Tung. M. C., Chang, C. F., Su, M. S., and Kou, G. H. (1995) Purification and genomic analysis of baculovirus associated with white spot syndrome (WSBV) of Penaeus monodon. Dis. Aquat. Organ. 23, 239-242
31. Lo, C. F., Hsu, H. C., Tsai, M. F., Ho, C. H., Peng, S. E., Kou, G. H., and Lightner, D. V. (1999) Specific genomic DNA fragment analysis of different geographical clinical samples of shrimp white spot syndrome virus. Dis. Aquat. Organ. 35, 175-185
32. Yang, F., He, J., Lin, X., Li, Q., Pan, D., Zhang, X., and Xu, X. (2001) Complete genome sequence of the shrimp white spot bacilliform virus. J. Virol. 75, 11811-11820
33. Hazbun, T. R., and Miller, J. P. (2005) Genome-wide analysis of proteinprotein interactions using a two-hybrid array. Chapter 37, in Protein- Protein Interactions, 2nd edition (eds. Golemis and Adams). Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, U.S.A.
34. Assenov, Y., Ramírez, F., Schelhorn, S. E., Lengauer, T., and Albrecht, M. (2008) Computing topological parameters of biological networks. Bioinformatics 24, 282-284
35. Leu, J. H., Kuo, Y. C., Kou, G. H., and Lo, C. F. (2008) Molecular cloning and characterization of an inhibitor of apoptosis protein (IAP) from the tiger shrimp, Penaeus monodon. Dev. Comp. Immunol. 32, 121-133
36. Elbashir, S. M., Lendeckel, W., and Tuschl, T. (2001) RNA interference is mediated by 21- and 22-nucleotide RNAs. Genes Dev. 15, 188-200
37. Senapin, S., Phiwsaiya, K., Anantasomboon, G., Sriphaijit, T., Browdy, C. L., and Flegel, T. W. (2010) Knocking down a Taura syndrome virus (TSV) binding protein Lamr is lethal for the whiteleg shrimp Penaeus vannamei. Fish Shellfish Immunol. 29, 422-429
38. Bell, T. A., and Lightner, D. V. (1988) A handbook of normal shrimp histology. World Aquaculture Society, Baton Rouge, LA, U.S.A.
39. Sambrook, J., and Russell, D. W. (2001) Molecular cloning: a laboratory manual. 3 ed. NY: Cold Spring Harbor
40. Shannon, P., Markiel, A., Ozier, O., Baliga, N. S., Wang, J. T., Ramage, D., Amin, N., Schwikowski, B., and Ideker, T. (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 13, 2498-2504
41. Cline, M. S., Smoot, M., Cerami, E., Kuchinsky, A., Landys, N., Workman, C., Christmas, R., Avila-Campilo, I., Creech, M., Gross, B., Hanspers, K., Isserlin, R., Kelley, R., Killcoyne, S., Lotia, S., Maere, S., Morris, J., Ono, K., Pavlovic, V., Pico, A. R., Vailaya, A., Wang, P. L., Adler, A., Conklin, B. R., Hood, L., Kuiper, M., Sander, C., Schmulevich, I., Schwikowski, B., Warner, G. J., Ideker, T., and Bader, G. D. (2007) Integration of biological networks and gene expression data using Cytoscape. Nat. Protoc. 2, 2366-2382
42. Jeong, H., Mason, S. P., Barabási, A. L., and Oltvai, Z. N. (2001) Lethality and centrality in protein networks. Nature 411, 41-42
43. Vallabhajosyula, R. R., Chakravarti, D., Lutfeali, S., Ray, A., and Raval, A. (2009) Identifying hubs in protein interaction networks. PLoS ONE 4, e5344
44. Barabási, A. L., and Albert, R. (1999) Emergence of scaling in random networks. Science 286, 509-512
45. Barabási, A. L., and Oltvai, Z. N. (2004) Network biology: understanding the cell's functional organization. Nat. Rev. Genet. 5, 101-113
46. Wang, H. C., Wang, H. C., Kou, G. H., Lo, C. F., and Huang, W. P. (2007) Identification of icp11, the most highly expressed gene of shrimp white spot syndrome virus (WSSV). Dis. Aquat. Organ. 74, 179-189
47. Wang, H. C., Wang, H. C., Ko, T. P., Lee, Y. M., Leu, J. H., Ho, C. H., Huang, W. P., Lo, C. F., and Wang, A. H. (2008) White spot syndrome virus protein ICP11: a histone-binding DNA mimic that disrupts nucleosome assembly. Proc. Natl. Acad. Sci. U.S.A. 105, 20758-20763
48. Li, F., Li, M., Ke, W., Ji, Y., Bian, X., and Yan, X. (2009) Identification of the immediate-early genes of white spot syndrome virus. Virology 385, 267-274
49. Iuchi, S. (2001) Three classes of C2H2 zinc finger proteins. Cell. Mol. Life Sci. 58, 625-635
50. Lee, J. H., Vittone, V., Diefenbach, E., Cunningham, A. L., and Diefenbach, R. J. (2008) Identification of structural protein-protein interactions of herpes simplex virus type 1. Virology 378, 347-354
51. To, A., Bai, Y., Shen, A., Gong, H., Umamoto, S., Lu, S., and Liu, F. (2011) Yeast two hybrid analyses reveal novel binary interactions between human cytomegalovirus-encoded virion proteins. PLoS ONE 6, e17796
52. Parrish, J. R., Gulyas, K. D., and Finley, R. L. (2006) Yeast two-hybrid contributions to interactome mapping. Curr. Opin. Biotechnol. 17, 387-393
53. Stanyon, C. A., Liu, G., Mangiola, B. A., Patel, N., Giot, L., Kuang, B., Zhang, H., Zhong, J., and Finley, R. L. (2004) A Drosophila proteininteraction map centered on cell-cycle regulators. Genome Biol. 5, R96
54. Formstecher, E., Aresta, S., Collura, V., Hamburger, A., Meil, A., Trehin, A., Reverdy, C., Betin, V., Maire, S., Brun, C., Jacq, B., Arpin, M., Bellaiche, Y., Bellusci, S., Benaroch, P., Bornens, M., Chanet, R., Chavrier, P., Delattre, O., Doye, V., Fehon, R., Faye, G., Galli, T., Girault, J.-A., Goud, B., de Gunzburg, J., Johannes, L., Junier, M.-P., Mirouse, V., Mukherjee, A., Papadopoulo, D., Perez, F., Plessis, A., Rossé, C., Saule, S., Stoppa- Lyonnet, D., Vincent, A., White, M., Legrain, P., Wojcik, J., Camonis, J., and Daviet, L. (2005) Protein interaction mapping: a Drosophila case study. Genome Res. 15, 376-384
55. Rozen, R., Sathish, N., Li, Y., and Yuan, Y. (2008) Virion-wide protein interactions of Kaposi's sarcoma-associated herpesvirus. J. Virol. 82, 4742-4750
56. Huang, C., Zhang, X., Lin, Q., Xu, X., Hu, Z., and Hew, C. L. (2002) Proteomic analysis of shrimp white spot syndrome viral proteins and characterization of a novel envelope protein VP466. Mol. Cell. Proteomics 1, 223-231
57. Tsai, J. M., Wang, H. C., Leu, J. H., Hsiao, H. H., Wang, A. H., Kou, G. H., and Lo, C. F. (2004) Genomic and proteomic analysis of thirty-nine structural proteins of shrimp white spot syndrome virus. J. Virol. 78, 11360-11370
58. Lan, Y., Xu, X., Yang, F., and Zhang, X. (2006) Transcriptional profile of shrimp white spot syndrome virus (WSSV) genes with DNA microarray. Arch. Virol. 151, 1723-1733
59. Kim, P. M., Sboner, A., Xia, Y., and Gerstein, M. (2008) The role of disorder in interaction networks: a structural analysis. Mol. Syst. Biol. 4, 179
60. Stein, A., Pache, R. A., Bernadò, P., Pons, M., and Aloy, P. (2009) Dynamic interactions of proteins in complex networks: a more structured view. FEBS J. 276, 5390-5405
61. Tyagi, M., Shoemaker, B. A., Bryant, S. H., and Panchenko, A. R. (2009) Exploring functional roles of multibinding protein interfaces. Protein Sci. 18, 1674-1683
62. Tsai, C. J., Ma, B., and Nussinov, R. (2009) Protein-protein interaction networks: how can a hub protein bind so many different partners? Trends Biochem. Sci. 34, 594-600
63. Dyson, H. J. (2011) Expanding the proteome: disordered and alternatively folded proteins. Q. Rev. Biophys. 44, 467-518
64. Dunker, A. K., Cortese, M. S., Romero, P., Iakoucheva, L. M., and Uversky, V. N. (2005) Flexible nets. The roles of intrinsic disorder in protein interaction networks. FEBS J. 272, 5129-5148
65. Dosztányi, Z., Chen, J., Dunker, A. K., Simon, I., and Tompa, P. (2006) Disorder and sequence repeats in hub proteins and their implications for network evolution. J. Proteome. Res. 5, 2985-2995
66. Haynes, C., Oldfield, C. J., Ji, F., Klitgord, N., Cusick, M. E., Radivojac, P., Uversky, V. N., Vidal, M., and Iakoucheva, L. M. (2006) Intrinsic disorder is a common feature of hub proteins from four eukaryotic interactomes. PLoS Comput. Biol. 2, e100
67. Robalino, J., Bartlett, T., Shepard, E., Prior, S., Jaramillo, G., Scura, E., Chapman, R. W., Gross, P. S., Browdy, C. L., and Warr, G. W. (2005) Double-stranded RNA induces sequence-specific antiviral silencing in addition to nonspecific immunity in a marine shrimp: convergence of RNA interference and innate immunity in the invertebrate antiviral response? J. Virol. 79, 13561-13571
68. Westenberg, M., Heinhuis, B., Zuidema, D., and Vlak, J. M. (2005) siRNA injection induces sequence-independent protection in Penaeus monodon against white spot syndrome virus. Virus Res. 114, 133-139
69. Wu, Y., Lü, L., Weng, S. P., Chan, S. M., and He, J. G. (2007) Inhibition of white spot syndrome virus in Litopenaeus vannamei shrimp by sequence- specific siRNA. Aquaculture 271, 21-30
70. Kim, C. S., Kosuke, Z., Nam, Y. K., Kim, S. K., and Kim, K. H. (2007) Protection of shrimp (Penaeus chinensis) against white spot syndrome virus (WSSV) challenge by double-stranded RNA. Fish Shellfish Immunol. 23, 242-246
71. Attasart, P., Kaewkhaw, R., Chimwai, C., Kongphom, U., Namramoon, O., and Panyim, S. (2009) Inhibition of white spot syndrome virus replication in Penaeus monodon by combined silencing of viral rr2 and shrimp PmRab7. Virus Res. 145, 127-133
72. Sanjuktha, M., Stalin Raj, V., Aravindan, K., Alavandi, S. V., Poornima, M., and Santiago, T. C. (2012) Comparative efficacy of double-stranded RNAs targeting WSSV structural and nonstructural genes in controlling viral multiplication in Penaeus monodon. Arch. Virol. 157, 993-998
73. Wang, A., Johnston, S. C., Chou, J., and Dean, D. (2010) A systemic network for Chlamydia pneumoniae entry into human cells. J. Bacteriol. 192, 2809-2815
74. Yu, H., Kim, P. M., Sprecher, E., Trifonov, V., and Gerstein, M. (2007) The importance of bottlenecks in protein networks: correlation with gene essentiality and expression dynamics. PLoS Comput. Biol. 3, e59
75. Zeng, J., Zhang, J., Tanaka, T., and Rabbitts, T. H. (2013) Single domain antibody fragments as drug surrogates targeting protein-protein interactions inside cells. Antibodies 2, 306-320
76. Metallo, S. (2010) Intrinsically disordered proteins are potential drug targets. Curr. Opin. Chem. Biol. 14, 481-488
77. Ge, H., Walhout, A. J., and Vidal, M. (2003) Integrating 'omic' information: a bridge between genomics and systems biology. Trends Genet. 19, 551-560