A physical interaction network of dengue virus and human proteins

Molecular and Cellular Proteomics

Volumn 10, Issue 12, 2011, Pages

  Khadka, Sudip ^a   Vangeloff, Abbey D ^a   Zhang, Chaoying ^a   Siddavatam, Prasad ^b   Heaton, Nicholas S ^c   Wang, Ling ^a   Sengupta, Ranjan ^b   Sahasrabudhe, Sudhir ^d   Randall, Glenn ^c   Gribskov, Michael ^b   Kuhn, Richard J ^b   Perera, Rushika ^b   LaCount, Douglas J ^a  

^a PURDUE UNIVERSITY   (United States)

^b PURDUE UNIVERSITY   (United States)

^c UNIVERSITY OF CHICAGO   (United States)

^d Prolexys Pharmaceuticals   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CALRETICULIN; CELL PROTEIN; COMPLEMENT; DOUBLE STRANDED RNA; NONSTRUCTURAL PROTEIN 3; NONSTRUCTURAL PROTEIN 5; SMALL INTERFERING RNA; VIRUS PROTEIN; AUTOANTIGEN; DDX3X PROTEIN, HUMAN; DEAD BOX PROTEIN; ERC1 PROTEIN, HUMAN; GOLGIN SUBFAMILY A MEMBER 2; LUCIFERASE; MEMBRANE PROTEIN; NERVE PROTEIN; NS3 PROTEIN, FLAVIVIRUS; NUCLEAR PROTEIN; RNA HELICASE; SERINE PROTEINASE; SIGNAL TRANSDUCING ADAPTOR PROTEIN; TRIP11 PROTEIN, HUMAN; UBIQUITIN CONJUGATING ENZYME; UBIQUITIN CONJUGATING ENZYME UBC9; UBIQUITIN-CONJUGATING ENZYME UBC9; VIRUS DNA;

ARTICLE; CENTROSOME; CYTOSKELETON; DENGUE VIRUS; DNA BINDING; GENE INSERTION; HIGH THROUGHPUT SCREENING; MOLECULAR LIBRARY; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DOMAIN; PROTEIN EXPRESSION; PROTEIN FUNCTION; PROTEIN INTERACTION; PROTEIN LOCALIZATION; PROTEIN TARGETING; REPLICON; TWO HYBRID SYSTEM; VIRUS CELL INTERACTION; VIRUS GENE; VIRUS REPLICATION; BIOSYNTHESIS; DENGUE; GENE SILENCING; GENETICS; HOST PATHOGEN INTERACTION; HUMAN; METABOLISM; PHYSIOLOGY; PROTEIN PROTEIN INTERACTION; PROTEIN TRANSPORT; REPORTER GENE; RNA INTERFERENCE; TUMOR CELL LINE; VIROLOGY;

ADAPTOR PROTEINS, SIGNAL TRANSDUCING; AUTOANTIGENS; CALRETICULIN; CELL LINE, TUMOR; DEAD-BOX RNA HELICASES; DENGUE; DENGUE VIRUS; DNA, VIRAL; GENE KNOCKDOWN TECHNIQUES; GENES, REPORTER; HOST-PATHOGEN INTERACTIONS; HUMANS; LUCIFERASES; MEMBRANE PROTEINS; NERVE TISSUE PROTEINS; NUCLEAR PROTEINS; PROTEIN INTERACTION MAPS; PROTEIN TRANSPORT; RNA HELICASES; RNA INTERFERENCE; SERINE ENDOPEPTIDASES; TWO-HYBRID SYSTEM TECHNIQUES; UBIQUITIN-CONJUGATING ENZYMES; VIRAL NONSTRUCTURAL PROTEINS; VIRUS REPLICATION;

EID: 83055173247     PISSN: 15359476     EISSN: 15359484     Source Type: Journal    
DOI: 10.1074/mcp.M111.012187     Document Type: Article

References (132)

1. Llano, M., Saenz, D. T., Meehan, A., Wongthida, P., Peretz, M., Walker, W. H., Teo, W., and Poeschla, E. M. (2006) An essential role for LEDGF/p75 in HIV integration. Science 314, 461-464 (Pubitemid 44628966)
2. Maertens, G., Cherepanov, P., Pluymers, W., Busschots, K., De Clercq, E., Debyser, Z., and Engelborghs, Y. (2003) LEDGF/p75 is essential for nuclear and chromosomal targeting of HIV-1 integrase in human cells. J. Biol. Chem. 278, 33528-33539 (Pubitemid 37055807)
3. Galluzzi, L., Kepp, O., Morselli, E., Vitale, I., Senovilla, L., Pinti, M., Zitvogel, L., and Kroemer, G. (2010) Viral strategies for the evasion of immunogenic cell death. J. Intern Med. 267, 526-542
4. Chaurushiya, M. S., and Weitzman, M. D. (2009) Viral manipulation of DNA repair and cell cycle checkpoints. DNA Repair 8, 1166-1176
5. Skaug, B., and Chen, Z. J. (2010) Emerging role of ISG15 in antiviral immunity. Cell 143, 187-190
6. Brass, A. L., Dykxhoorn, D. M., Benita, Y., Yan, N., Engelman, A., Xavier, R. J., Lieberman, J., and Elledge, S. J. (2008) Identification of host proteins required for HIV infection through a functional genomic screen. Science 319, 921-926 (Pubitemid 351263756)
7. Brass, A. L., Huang, I. C., Benita, Y., John, S. P., Krishnan, M. N., Feeley, E. M., Ryan, B. J., Weyer, J. L., van der Weyden, L., Fikrig, E., Adams, D. J., Xavier, R. J., Farzan, M., and Elledge, S. J. (2009) The IFITM proteins mediate cellular resistance to influenza A H1N1 virus, West Nile virus, and dengue virus. Cell 139, 1243-1254
8. Bushman, F. D., Malani, N., Fernandes, J., D'Orso, I., Cagney, G., Diamond, T. L., Zhou, H., Hazuda, D. J., Espeseth, A. S., König, R., Bandyopadhyay, S., Ideker, T., Goff, S. P., Krogan, N. J., Frankel, A. D., Young, J. A., and Chanda, S. K. (2009) Host cell factors in HIV replication: meta-analysis of genome-wide studies. PLoS Pathog 5, e1000437
9. Hao, L., Sakurai, A., Watanabe, T., Sorensen, E., Nidom, C. A., Newton, M. A., Ahlquist, P., and Kawaoka, Y. (2008) Drosophila RNAi screen identifies host genes important for influenza virus replication. Nature 454, 890-893
10. Karlas, A., Machuy, N., Shin, Y., Pleissner, K. P., Artarini, A., Heuer, D., Becker, D., Khalil, H., Ogilvie, L. A., Hess, S., Mäurer, A. P., Muller, E., Wolff, T., Rudel, T., and Meyer, T. F. (2010) Genome-wide RNAi screen identifies human host factors crucial for influenza virus replication. Nature 463, 818-822
11. König, R., Stertz, S., Zhou, Y., Inoue, A., Hoffmann, H. H., Bhattacharyya, S., Alamares, J. G., Tscherne, D. M., Ortigoza, M. B., Liang, Y., Gao, Q., Andrews, S. E., Bandyopadhyay, S., De Jesus, P., Tu, B. P., Pache, L., Shih, C., Orth, A., Bonamy, G., Miraglia, L., Ideker, T., Garcia-Sastre, A., Young, J. A., Palese, P., Shaw, M. L., and Chanda, S. K. (2010) Human host factors required for influenza virus replication. Nature 463, 813-817
12. Känig, R., Zhou, Y., Elleder, D., Diamond, T. L., Bonamy, G. M., Irelan, J. T., Chiang, C. Y., Tu, B. P., De Jesus, P. D., Lilley, C. E., Seidel, S., Opaluch, A. M., Caldwell, J. S., Weitzman, M. D., Kuhen, K. L., Bandyopadhyay, S., Ideker, T., Orth, A. P., Miraglia, L. J., Bushman, F. D., Young, J. A., and Chanda, S. K. (2008) Global analysis of host-pathogen interactions that regulate early-stage HIV-1 replication. Cell 135, 49-60
13. Krishnan, M. N., Ng, A., Sukumaran, B., Gilfoy, F. D., Uchil, P. D., Sultana, H., Brass, A. L., Adametz, R., Tsui, M., Qian, F., Montgomery, R. R., Lev, S., Mason, P. W., Koski, R. A., Elledge, S. J., Xavier, R. J., Agaisse, H., and Fikrig, E. (2008) RNA interference screen for human genes associated with West Nile virus infection. Nature 455, 242-245
14. Li, Q., Brass, A. L., Ng, A., Hu, Z., Xavier, R. J., Liang, T. J., and Elledge, S. J. (2009) A genome-wide genetic screen for host factors required for hepatitis C virus propagation. Proc. Natl. Acad. Sci. U.S.A. 106, 16410-16415
15. Ng, T. I., Mo, H., Pilot-Matias, T., He, Y., Koev, G., Krishnan, P., Mondal, R., Pithawalla, R., He, W., Dekhtyar, T., Packer, J., Schurdak, M., and Molla, A. (2007) Identification of host genes involved in hepatitis C virus replication by small interfering RNA technology. Hepatology 45, 1413-1421 (Pubitemid 46918325)
16. Sessions, O. M., Barrows, N. J., Souza-Neto, J. A., Robinson, T. J., Hershey, C. L., Rodgers, M. A., Ramirez, J. L., Dimopoulos, G., Yang, P. L., Pearson, J. L., and Garcia-Blanco, M. A. (2009) Discovery of insect and human dengue virus host factors. Nature 458, 1047-1050
17. Shapira, S. D., Gat-Viks, I., Shum, B. O., Dricot, A., de Grace, M. M., Wu, L., Gupta, P. B., Hao, T., Silver, S. J., Root, D. E., Hill, D. E., Regev, A., and Hacohen, N. (2009) A physical and regulatory map of host-influenza interactions reveals pathways in H1N1 infection. Cell 139, 1255-1267
18. Tai, A. W., Benita, Y., Peng, L. F., Kim, S. S., Sakamoto, N., Xavier, R. J., and Chung, R. T. (2009) A functional genomic screen identifies cellular cofactors of hepatitis C virus replication. Cell Host Microbe 5, 298-307
19. Vaillancourt, F. H., Pilote, L., Cartier, M., Lippens, J., Liuzzi, M., Bethell, R. C., Cordingley, M. G., and Kukolj, G. (2009) Identification of a lipid kinase as a host factor involved in hepatitis C virus RNA replication. Virology 387, 5-10
20. Zhou, H., Xu, M., Huang, Q., Gates, A. T., Zhang, X. D., Castle, J. C., Stec, E., Ferrer, M., Strulovici, B., Hazuda, D. J., and Espeseth, A. S. (2008) Genome-scale RNAi screen for host factors required for HIV replication. Cell Host Microbe 4, 495-504
21. 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 (Pubitemid 47185953)
22. de Chassey, B., Navratil, V., Tafforeau, L., Hiet, M. S., Aublin-Gex, A., Agaugué, S., Meiffren, G., Pradezynski, F., Faria, B. F., Chantier, T., Le Breton, M., Pellet, J., Davoust, N., Mangeot, P. E., Chaboud, A., Penin, F., Jacob, Y., Vidalain, P. O., Vidal, M., André, P., Rabourdin-Combe, C., and Lotteau, V. (2008) Hepatitis C virus infection protein network. Mol. Syst. Biol. 4, 230
23. Ewing, R. M., Chu, P., Elisma, F., Li, H., Taylor, P., Climie, S., McBroom-Cerajewski, L., Robinson, M. D., O'Connor, L., Li, M., Taylor, R., Dharsee, M., Ho, Y., Heilbut, A., Moore, L., Zhang, S., Ornatsky, O., Bukhman, Y. V., Ethier, M., Sheng, Y., Vasilescu, J., Abu-Farha, M., Lambert, J. P., Duewel, H. S., Stewart, I. I., Kuehl, B., Hogue, K., Colwill, K., Gladwish, K., Muskat, B., Kinach, R., Adams, S. L., Moran, M. F., Morin, G. B., Topaloglou, T., and Figeys, D. (2007) Large-scale mapping of human protein-protein interactions by mass spectrometry. Mol. Syst. Biol. 3, 89
24. 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 (Pubitemid 41509356)
25. 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., Tokso ̈z, 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 (Pubitemid 41345212)
26. 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 (Pubitemid 43108191)
27. Behrends, C., Sowa, M. E., Gygi, S. P., and Harper, J. W. (2010) Network organization of the human autophagy system. Nature 466, 68-76
28. Sowa, M. E., Bennett, E. J., Gygi, S. P., and Harper, J. W. (2009) Defining the human deubiquitinating enzyme interaction landscape. Cell 138, 389-403
29. Mackenzie, J. S., Gubler, D. J., and Petersen, L. R. (2004) Emerging flaviviruses: the spread and resurgence of Japanese encephalitis, West Nile and dengue viruses. Nat. Med. 10, S98-109
30. Guha-Sapir, D., and Schimmer, B. (2005) Dengue fever: new paradigms for a changing epidemiology. Emerg Themes Epidemiol 2, 1
31. Martina, B. E., Koraka, P., and Osterhaus, A. D. (2009) Dengue virus pathogenesis: an integrated view. Clin. Microbiol Rev. 22, 564-581
32. Chen, Y., Maguire, T., Hileman, R. E., Fromm, J. R., Esko, J. D., Linhardt, R. J., and Marks, R. M. (1997) Dengue virus infectivity depends on envelope protein binding to target cell heparan sulfate. Nat. Med. 3, 866-871 (Pubitemid 27353446)
33. Miller, J. L., de Wet, B. J. M., Martinez-Pomares, L., Radcliffe, C. M., Dwek, R. A., Rudd, P. M., and Gordon, S. (2008) The mannose receptor mediates dengue virus infection of macrophages. PLoS Pathog 4, e17
34. Navarro-Sanchez, E., Altmeyer, R., Amara, A., Schwartz, O., Fieschi, F., Virelizier, J. L., Arenzana-Seisdedos, F., and Despres, P. (2003) Dendritic-cell-specific ICAM3-grabbing non-integrin is essential for the productive infection of human dendritic cells by mosquito-cell-derived dengue viruses. EMBO Rep 4, 723-728 (Pubitemid 36974759)
35. Porterfield, J. S. (1986) Antibody-dependent enhancement of viral infectivity. Adv. Virus Res. 31, 335-355
36. Tassaneetrithep, B., Burgess, T. H., Granelli-Piperno, A., Trumpfheller, C., Finke, J., Sun, W., Eller, M. A., Pattanapanyasat, K., Sarasombath, S., Birx, D. L., Steinman, R. M., Schlesinger, S., and Marovich, M. A. (2003) DC-SIGN (CD209) mediates dengue virus infection of human dendritic cells. J. Exp. Med. 197, 823-829 (Pubitemid 36437860)
37. Welsch, S., Miller, S., Romero-Brey, I., Merz, A., Bleck, C. K., Walther, P., Fuller, S. D., Antony, C., Krijnse-Locker, J., and Bartenschlager, R. (2009) Composition and three-dimensional architecture of the dengue virus replication and assembly sites. Cell Host Microbe 5, 365-375
38. Yu, I. M., Zhang, W., Holdaway, H. A., Li, L., Kostyuchenko, V. A., Chipman, P. R., Kuhn, R. J., Rossmann, M. G., and Chen, J. (2008) Structure of the immature dengue virus at low pH primes proteolytic maturation. Science 319, 1834-1837 (Pubitemid 351451592)
39. Li, L., Lok, S. M., Yu, I. M., Zhang, Y., Kuhn, R. J., Chen, J., and Rossmann, M. G. (2008) The flavivirus precursor membrane-envelope protein complex: structure and maturation. Science 319, 1830-1834 (Pubitemid 351451591)
40. Rothwell, C., Lebreton, A., Young Ng, C., Lim, J. Y., Liu, W., Vasudevan, S., Labow, M., Gu, F., and Gaither, L. A. (2009) Cholesterol biosynthesis modulation regulates dengue viral replication. Virology 389, 8-19
41. Ang, F., Wong, A. P., Ng, M. M., and Chu, J. J. (2010) Small interference RNA profiling reveals the essential role of human membrane trafficking genes in mediating the infectious entry of dengue virus. Virol J. 7, 24
42. Heaton, N. S., Perera, R., Berger, K. L., Khadka, S., Lacount, D. J., Kuhn, R. J., and Randall, G. (2010) Dengue virus nonstructural protein 3 redistributes fatty acid synthase to sites of viral replication and increases cellular fatty acid synthesis. Proc. Natl. Acad. Sci. U.S.A. 107, 17345-17350
43. 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 (Pubitemid 41599828)
44. Guthrie, C., and Fink, G. R. (1981) Guide to yeast genetics and molecular biology, Academic Press, San Diego, CA
45. 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 (Pubitemid 30103994)
46. Ma, H., Kunes, S., Schatz, P. J., and Botstein, D. (1987) Plasmid construction by homologous recombination in yeast. Gene 58, 201-216 (Pubitemid 17164063)
47. James, P., Halladay, J., and Craig, E. A. (1996) Genomic libraries and a host strain designed for highly efficient two-hybrid selection in yeast. Genetics 144, 1425-1436
48. Vignali, M., McKinlay, A., LaCount, D. J., Chettier, R., Bell, R., Sahasrabudhe, S., Hughes, R. E., and Fields, S. (2008) Interaction of an atypical Plasmodium falciparum ETRAMP with human apolipoproteins. Malar J. 7, 211
49. Soellick, T. R., and Uhrig, J. F. (2001) Development of an optimized interaction-mating protocol for large-scale yeast two-hybrid analyses. Genome Biol. 2, RESEARCH0052
50. Brown, H. F., Wang, L., Khadka, S., Fields, S., and LaCount, D. J. (2011) A densely overlapping gene fragmentation approach improves yeast two-hybrid screens for Plasmodium falciparum proteins. Mol. Biochem. Parasitol 178, 56-59
51. Randall, G., Panis, M., Cooper, J. D., Tellinghuisen, T. L., Sukhodolets, K. E., Pfeffer, S., Landthaler, M., Landgraf, P., Kan, S., Lindenbach, B. D., Chien, M., Weir, D. B., Russo, J. J., Ju, J., Brownstein, M. J., Sheridan, R., Sander, C., Zavolan, M., Tuschl, T., and Rice, C. M. (2007) Cellular cofactors affecting hepatitis C virus infection and replication. Proc. Natl. Acad. Sci. U.S.A. 104, 12884-12889 (Pubitemid 47255249)
52. Abramoff, M. D., Magelhaes, P. J., and Ram, S. J. (2004) Image Processing with ImageJ. Biophotonics International 11, 36-42
53. Bolte, S., and Cordelieres, F. P. (2006) A guided tour into subcellular colocalization analysis in light microscopy. J. Microsc 224, 213-232 (Pubitemid 46010930)
54. Dyer, M. D., Murali, T. M., and Sobral, B. W. (2008) The landscape of human proteins interacting with viruses and other pathogens. PLoS Pathog 4, e32
55. Bader, G. D., Betel, D., and Hogue, C. W. (2003) BIND: the Biomolecular Interaction Network Database. Nucleic Acids Res. 31, 248-250 (Pubitemid 36150376)
56. Xenarios, I., Salwinski, L., Duan, X. J., Higney, P., Kim, S. M., and Eisenberg, D. (2002) DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions. Nucleic Acids Res. 30, 303-305 (Pubitemid 34679570)
57. Peri, S., Navarro, J. D., Amanchy, R., Kristiansen, T. Z., Jonnalagadda, C. K., Surendranath, V., Niranjan, V., Muthusamy, B., Gandhi, T. K., Gronborg, M., Ibarrola, N., Deshpande, N., Shanker, K., Shivashankar, H. N., Rashmi, B. P., Ramya, M. A., Zhao, Z., Chandrika, K. N., Padma, N., Harsha, H. C., Yatish, A. J., Kavitha, M. P., Menezes, M., Choudhury, D. R., Suresh, S., Ghosh, N., Saravana, R., Chandran, S., Krishna, S., Joy, M., Anand, S. K., Madavan, V., Joseph, A., Wong, G. W., Schiemann, W. P., Constantinescu, S. N., Huang, L., Khosravi-Far, R., Steen, H., Tewari, M., Ghaffari, S., Blobe, G. C., Dang, C. V., Garcia, J. G., Pevsner, J., Jensen, O. N., Roepstorff, P., Deshpande, K. S., Chinnaiyan, A. M., Hamosh, A., Chakravarti, A., and Pandey, A. (2003) Development of human protein reference database as an initial platform for approaching systems biology in humans. Genome Res. 13, 2363-2371 (Pubitemid 37266003)
58. Aranda, B., Achuthan, P., Alam-Faruque, Y., Armean, I., Bridge, A., Derow, C., Feuermann, M., Ghanbarian, A. T., Kerrien, S., Khadake, J., Kerssemakers, J., Leroy, C., Menden, M., Michaut, M., Montecchi-Palazzi, L., Neuhauser, S. N., Orchard, S., Perreau, V., Roechert, B., van Eijk, K., and Hermjakob, H. (2010) The IntAct molecular interaction database in 2010. Nucleic Acids Res. 38, D525-531
59. Hermjakob, H., Montecchi-Palazzi, L., Lewington, C., Mudali, S., Kerrien, S., Orchard, S., Vingron, M., Roechert, B., Roepstorff, P., Valencia, A., Margalit, H., Armstrong, J., Bairoch, A., Cesareni, G., Sherman, D., and Apweiler, R. (2004) IntAct: an open source molecular interaction database. Nucleic Acids Res. 32, D452-455 (Pubitemid 38081697)
60. Kerrien, S., Alam-Faruque, Y., Aranda, B., Bancarz, I., Bridge, A., Derow, C., Dimmer, E., Feuermann, M., Friedrichsen, A., Huntley, R., Kohler, C., Khadake, J., Leroy, C., Liban, A., Lieftink, C., Montecchi-Palazzi, L., Orchard, S., Risse, J., Robbe, K., Roechert, B., Thorneycroft, D., Zhang, Y., Apweiler, R., and Hermjakob, H. (2007) IntAct-open source resource for molecular interaction data. Nucleic Acids Res. 35, D561-565 (Pubitemid 46056270)
61. Chatr-aryamontri, A., Ceol, A., Palazzi, L. M., Nardelli, G., Schneider, M. V., Castagnoli, L., and Cesareni, G. (2007) MINT: the Molecular INTeraction database. Nucleic Acids Res. 35, D572-574 (Pubitemid 46056272)
62. Zanzoni, A., Montecchi-Palazzi, L., Quondam, M., Ausiello, G., Helmer-Citterich, M., and Cesareni, G. (2002) MINT: a Molecular INTeraction database. FEBS Lett. 513, 135-140 (Pubitemid 34242991)
63. Mewes, H. W., Amid, C., Arnold, R., Frishman, D., Güldener, U., Mannhaupt, G., Munsterkotter, M., Pagel, P., Strack, N., Stumpflen, V., Warfsmann, J., and Ruepp, A. (2004) MIPS: analysis and annotation of proteins from whole genomes. Nucleic Acids Res. 32, D41-44 (Pubitemid 38081600)
64. Matthews, L., Gopinath, G., Gillespie, M., Caudy, M., Croft, D., de Bono, B., Garapati, P., Hemish, J., Hermjakob, H., Jassal, B., Kanapin, A., Lewis, S., Mahajan, S., May, B., Schmidt, E., Vastrik, I., Wu, G., Birney, E., Stein, L., and D'Eustachio, P. (2009) Reactome knowledgebase of human biological pathways and processes. Nucleic Acids Res. 37, D619-622
65. Vastrik, I., D'Eustachio, P., Schmidt, E., Gopinath, G., Croft, D., de Bono, B., Gillespie, M., Jassal, B., Lewis, S., Matthews, L., Wu, G., Birney, E., and Stein, L. (2007) Reactome: a knowledge base of biologic pathways and processes. Genome Biol. 8, R39
66. Yu, J., and Finley, R. L., Jr. (2009) Combining multiple positive training sets to generate confidence scores for protein-protein interactions. Bioinformatics 25, 105-111
67. Batada, N. N., Reguly, T., Breitkreutz, A., Boucher, L., Breitkreutz, B.-J., Hurst, L. D., and Tyers, M. (2006) Stratus Not Altocumulus: A New View of the Yeast Protein Interaction Network. PLoS Biology 4, e317
68. Dennis, G., Jr., Sherman, B. T., Hosack, D. A., Yang, J., Gao, W., Lane, H. C., and Lempicki, R. A. (2003) DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biol. 4, P3
69. Huang, da, W., Sherman, B. T., Tan, Q., Kir, J., Liu, D., Bryant, D., Guo, Y., Stephens, R., Baseler, M. W., Lane, H. C., and Lempicki, R. A. (2007) DAVID Bioinformatics Resources: expanded annotation database and novel algorithms to better extract biology from large gene lists. Nucleic Acids Res. 35, W169-175
70. Maere, S., Heymans, K., and Kuiper, M. (2005) BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks. Bioinformatics 21, 3448-3449 (Pubitemid 41222459)
71. 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
72. 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 (Pubitemid 37428274)
73. Ozawa, T., Kaihara, A., Sato, M., Tachihara, K., and Umezawa, Y. (2001) Split luciferase as an optical probe for detecting protein-protein interactions in mammalian cells based on protein splicing. Anal Chem. 73, 2516-2521 (Pubitemid 32880651)
74. Paulmurugan, R., and Gambhir, S. S. (2007) Combinatorial library screening for developing an improved split-firefly luciferase fragment-assisted complementation system for studying protein-protein interactions. Anal Chem. 79, 2346-2353 (Pubitemid 46449015)
75. Pilot-Storck, F., Chopin, E., Rual, J. F., Baudot, A., Dobrokhotov, P., Robinson-Rechavi, M., Brun, C., Cusick, M. E., Hill, D. E., Schaeffer, L., Vidal, M., and Goillot, E. (2010) Interactome mapping of the phosphatidylinositol 3-kinase-mammalian target of rapamycin pathway identifies deformed epidermal autoregulatory factor-1 as a new glycogen synthase kinase-3 interactor. Mol. Cell Proteomics 9, 1578-1593
76. Boxem, M., Maliga, Z., Klitgord, N., Li, N., Lemmens, I., Mana, M., de Lichtervelde, L., Mul, J. D., van de Peut, D., Devos, M., Simonis, N., Yildirim, M. A., Cokol, M., Kao, H. L., de Smet, A. S., Wang, H., Schlaitz, A. L., Hao, T., Milstein, S., Fan, C., Tipsword, M., Drew, K., Galli, M., Rhrissorrakrai, K., Drechsel, D., Koller, D., Roth, F. P., Iakoucheva, L. M., Dunker, A. K., Bonneau, R., Gunsalus, K. C., Hill, D. E., Piano, F., Tavernier, J., van den Heuvel, S., Hyman, A. A., and Vidal, M. (2008) A protein domain-based interactome network for C. elegans early embryogenesis. Cell 134, 534-545
77. Braun, P., Tasan, M., Dreze, M., Barrios-Rodiles, M., Lemmens, I., Yu, H., Sahalie, J. M., Murray, R. R., Roncari, L., de Smet, A. S., Venkatesan, K., Rual, J. F., Vandenhaute, J., Cusick, M. E., Pawson, T., Hill, D. E., Tavernier, J., Wrana, J. L., Roth, F. P., and Vidal, M. (2009) An experimentally derived confidence score for binary protein-protein interactions. Nat. Methods 6, 91-97
78. Owsianka, A. M., and Patel, A. H. (1999) Hepatitis C virus core protein interacts with a human DEAD box protein DDX3. Virology 257, 330-340 (Pubitemid 29393401)
79. Doolittle, J. M., and Gomez, S. M. (2011) Mapping protein interactions between Dengue virus and its human and insect hosts. PLoS Negl Trop Dis 5, e954
80. Duan, X., Lu, X., Li, J., and Liu, Y. (2008) Novel binding between premembrane protein and vacuolar ATPase is required for efficient dengue virus secretion. Biochem. Biophys. Res. Commun. 373, 319-324
81. Johansson, M., Brooks, A. J., Jans, D. A., and Vasudevan, S. G. (2001) A small region of the dengue virus-encoded RNA-dependent RNA polymerase, NS5, confers interaction with both the nuclear transport receptor importin-beta and the viral helicase, NS3. J. Gen. Virol. 82, 735-745 (Pubitemid 32280030)
82. Bhuvanakantham, R., Li, J., Tan, T. T., and Ng, M. L. (2010) Human Sec3 protein is a novel transcriptional and translational repressor of flavivirus. Cell Microbiol 12, 453-472
83. Rawlinson, S. M., Pryor, M. J., Wright, P. J., and Jans, D. A. (2009) CRM1-mediated Nuclear Export of Dengue Virus RNA Polymerase NS5 Modulates Interleukin-8 Induction and Virus Production. J. Biol. Chem. 284, 15589-15597
84. Folly, B. B., Weffort-Santos, A. M., Fathman, C. G., and Soares, L. R. (2011) Dengue-2 structural proteins associate with human proteins to produce a coagulation and innate immune response biased interactome. BMC Infect Dis 11, 34
85. Ashour, J., Laurent-Rolle, M., Shi, P. Y., and Garcia-Sastre, A. (2009) NS5 of dengue virus mediates STAT2 binding and degradation. J. Virol. 83, 5408-5418
86. Mazzon, M., Jones, M., Davidson, A., Chain, B., and Jacobs, M. (2009) Dengue virus NS5 inhibits interferon-alpha signaling by blocking signal transducer and activator of transcription 2 phosphorylation. J. Infect Dis 200, 1261-1270
87. Anwar, A., Leong, K. M., Ng, M. L., Chu, J. J., and Garcia-Blanco, M. A. (2009) The polypyrimidine tract-binding protein is required for efficient dengue virus propagation and associates with the viral replication machinery. J. Biol. Chem. 284, 17021-17029
88. Chiu, M. W., Shih, H. M., Yang, T. H., and Yang, Y. L. (2007) The type 2 dengue virus envelope protein interacts with small ubiquitin-like modifier-1 (SUMO-1) conjugating enzyme 9 (Ubc9). J. Biomed Sci. 14, 429-444
89. De Nova-Ocampo, M., Villegas-Sepúlveda, N., and del Angel, R. M. (2002) Translation elongation factor-1alpha, La, and PTB interact with the 3′untranslated region of dengue 4 virus RNA. Virology 295, 337-347 (Pubitemid 34921320)
90. Jiang, L., Yao, H., Duan, X., Lu, X., and Liu, Y. (2009) Polypyrimidine tract-binding protein influences negative strand RNA synthesis of dengue virus. Biochem. Biophys. Res. Commun. 385, 187-192
91. Limjindaporn, T., Wongwiwat, W., Noisakran, S., Srisawat, C., Netsawang, J., Puttikhunt, C., Kasinrerk, W., Avirutnan, P., Thiemmeca, S., Sriburi, R., Sittisombut, N., Malasit, P., and Yenchitsomanus, P. T. (2009) Interaction of dengue virus envelope protein with endoplasmic reticulum-resident chaperones facilitates dengue virus production. Biochem. Biophys. Res. Commun. 379, 196-200
92. Agis-Juárez, R. A., Galvan, I., Medina, F., Daikoku, T., Padmanabhan, R., Ludert, J. E., and del Angel, R. M. (2009) Polypyrimidine tract-binding protein is relocated to the cytoplasm and is required during dengue virus infection in Vero cells. J. Gen. Virol. 90, 2893-2901
93. Stoermer, K. A., and Morrison, T. E. (2011) Complement and viral pathogenesis. Virology 411, 362-373
94. Avirutnan, P., Punyadee, N., Noisakran, S., Komoltri, C., Thiemmeca, S., Auethavornanan, K., Jairungsri, A., Kanlaya, R., Tangthawornchaikul, N., Puttikhunt, C., Pattanakitsakul, S. N., Yenchitsomanus, P. T., Mongkolsapaya, J., Kasinrerk, W., Sittisombut, N., Husmann, M., Blettner, M., Vasanawathana, S., Bhakdi, S., and Malasit, P. (2006) Vascular leakage in severe dengue virus infections: a potential role for the nonstructural viral protein NS1 and complement. J. Infect Dis 193, 1078-1088
95. Nascimento, E. J., Silva, A. M., Cordeiro, M. T., Brito, C. A., Gil, L. H., Braga-Neto, U., and Marques, E. T. (2009) Alternative complement pathway deregulation is correlated with dengue severity. PLoS One 4, e6782
96. Harries, P. A., Schoelz, J. E., and Nelson, R. S. (2010) Intracellular transport of viruses and their components: utilizing the cytoskeleton and membrane highways. Mol. Plant Microbe Interact 23, 1381-1393
97. Hsieh, M. J., White, P. J., and Pouton, C. W. (2010) Interaction of viruses with host cell molecular motors. Curr. Opin. Biotechnol 21, 633-639
98. Lyman, M. G., and Enquist, L. W. (2009) Herpesvirus interactions with the host cytoskeleton. J. Virol. 83, 2058-2066
99. Ward, B. M. (2011) The taking of the cytoskeleton one two three: how viruses utilize the cytoskeleton during egress. Virology 411, 244-250
100. Wileman, T. (2007) Aggresomes and pericentriolar sites of virus assembly: cellular defense or viral design? Annu Rev. Microbiol. 61, 149-167
101. Martin-Serrano, J., and Marsh, M. (2007) ALIX catches HIV. Cell Host Microbe 1, 5-7 (Pubitemid 46508687)
102. Kapoor, M., Zhang, L., Ramachandra, M., Kusukawa, J., Ebner, K. E., and Padmanabhan, R. (1995) Association between NS3 and NS5 proteins of dengue virus type 2 in the putative RNA replicase is linked to differential phosphorylation of NS5. J. Biol. Chem. 270, 19100-19106
103. Chua, J. J., Ng, M. M., and Chow, V. T. (2004) The non-structural 3 (NS3) protein of dengue virus type 2 interacts with human nuclear receptor binding protein and is associated with alterations in membrane structure. Virus Res. 102, 151-163 (Pubitemid 38490331)
104. Miller, S., Kastner, S., Krijnse-Locker, J., Bühler, S., and Bartenschlager, R. (2007) The non-structural protein 4A of dengue virus is an integral membrane protein inducing membrane alterations in a 2K-regulated manner. J. Biol. Chem. 282, 8873-8882 (Pubitemid 47093477)
105. Miller, S., Sparacio, S., and Bartenschlager, R. (2006) Subcellular localization and membrane topology of the Dengue virus type 2 Non-structural protein 4B. J. Biol. Chem. 281, 8854-8863 (Pubitemid 43847992)
106. 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
107. Kumar, D., Nath, L., Kamal, M. A., Varshney, A., Jain, A., Singh, S., and Rao, K. V. (2010) Genome-wide analysis of the host intracellular network that regulates survival of Mycobacterium tuberculosis. Cell 140, 731-743
108. Ahlquist, P. (2006) Parallels among positive-strand RNA viruses, reverse-transcribing viruses and double-stranded RNA viruses. Nat. Rev. Microbiol 4, 371-382
109. Gold, L. I., Eggleton, P., Sweetwyne, M. T., Van Duyn, L. B., Greives, M. R., Naylor, S. M., Michalak, M., and Murphy-Ullrich, J. E. (2010) Calreticulin: non-endoplasmic reticulum functions in physiology and disease. FASEB J. 24, 665-683
110. Michalak, M., Corbett, E. F., Mesaeli, N., Nakamura, K., and Opas, M. (1999) Calreticulin: one protein, one gene, many functions. Biochem. J. 344 Pt 2, 281-292 (Pubitemid 30011581)
111. Afshar, N., Black, B. E., and Paschal, B. M. (2005) Retrotranslocation of the chaperone calreticulin from the endoplasmic reticulum lumen to the cytosol. Mol. Cell Biol. 25, 8844-8853 (Pubitemid 41429076)
112. Burns, K., Duggan, B., Atkinson, E. A., Famulski, K. S., Nemer, M., Bleackley, R. C., and Michalak, M. (1994) Modulation of gene expression by calreticulin binding to the glucocorticoid receptor. Nature 367, 476-480 (Pubitemid 24046052)
113. Coppolino, M., Leung-Hagesteijn, C., Dedhar, S., and Wilkins, J. (1995) Inducible interaction of integrin alpha 2 beta 1 with calreticulin. Dependence on the activation state of the integrin. J. Biol. Chem. 270, 23132-23138
114. Coppolino, M. G., Woodside, M. J., Demaurex, N., Grinstein, S., St-Arnaud, R., and Dedhar, S. (1997) Calreticulin is essential for integrin-mediated calcium signalling and cell adhesion. Nature 386, 843-847 (Pubitemid 27181259)
115. Alefantis, T., Flaig, K. E., Wigdahl, B., and Jain, P. (2007) Interaction of HTLV-1 Tax protein with calreticulin: implications for Tax nuclear export and secretion. Biomed Pharmacother 61, 194-200 (Pubitemid 46705478)
116. Braakman, I., and van Anken, E. (2000) Folding of viral envelope glycoproteins in the endoplasmic reticulum. Traffic 1, 533-539
117. Nakhasi, H. L., Ramanujam, M., Atreya, C. D., Hobman, T. C., Lee, N., Esmaili, A., and Duncan, R. C. (2001) Rubella virus glycoprotein interaction with the endoplasmic reticulum calreticulin and calnexin. Arch Virol. 146, 1-14 (Pubitemid 32200751)
118. Otteken, A., and Moss, B. (1996) Calreticulin interacts with newly synthesized human immunodeficiency virus type 1 envelope glycoprotein, suggesting a chaperone function similar to that of calnexin. J. Biol. Chem. 271, 97-103 (Pubitemid 26026563)
119. Chen, M. H., and Frey, T. K. (1999) Mutagenic analysis of the 3′ cis-acting elements of the rubella virus genome. J. Virol. 73, 3386-3403
120. Singh, N. K., Atreya, C. D., and Nakhasi, H. L. (1994) Identification of calreticulin as a rubella virus RNA binding protein. Proc. Natl. Acad. Sci. U.S.A. 91, 12770-12774
121. Obeid, M., Tesniere, A., Ghiringhelli, F., Fimia, G. M., Apetoh, L., Perfettini, J. L., Castedo, M., Mignot, G., Panaretakis, T., Casares, N., Métivier, D., Larochette, N., van Endert, P., Ciccosanti, F., Piacentini, M., Zitvogel, L., and Kroemer, G. (2007) Calreticulin exposure dictates the immunogenicity of cancer cell death. Nat. Med. 13, 54-61 (Pubitemid 46067386)
122. Kepp, O., Senovilla, L., Galluzzi, L., Panaretakis, T., Tesniere, A., Schlemmer, F., Madeo, F., Zitvogel, L., and Kroemer, G. (2009) Viral subversion of immunogenic cell death. Cell Cycle 8, 860-869
123. Yocupicio-Monroy, M., Padmanabhan, R., Medina, F., and del Angel, R. M. (2007) Mosquito La protein binds to the 3′ untranslated region of the positive and negative polarity dengue virus RNAs and relocates to the cytoplasm of infected cells. Virology 357, 29-40 (Pubitemid 44822599)
124. Monier, S., Jollivet, F., Janoueix-Lerosey, I., Johannes, L., and Goud, B. (2002) Characterization of novel Rab6-interacting proteins involved in endosome-to-TGN transport. Traffic 3, 289-297 (Pubitemid 34303261)
125. Infante, C., Ramos-Morales, F., Fedriani, C., Bornens, M., and Rios, R.
126. Pernet-Gallay, K., Antony, C., Johannes, L., Bornens, M., Goud, B., and Rios, R. M. (2002) The overexpression of GMAP-210 blocks anterograde and retrograde transport between the ER and the Golgi apparatus. Traffic 3, 822-832 (Pubitemid 35277008)
127. Nakamura, N., Rabouille, C., Watson, R., Nilsson, T., Hui, N., Slusarewicz, P., Kreis, T. E., and Warren, G. (1995) Characterization of a cis-Golgi matrix protein, GM130. J. Cell Biol. 131, 1715-1726 (Pubitemid 26007969)
128. Navratil, V., de Chassey, B., Combe, C. R., and Lotteau, V. (2011) When the human viral infectome and diseasome networks collide: towards a systems biology platform for the aetiology of human diseases. BMC Syst Biol. 5, 13
129. Green, P. Cross-Match program (part of Phrap package from Phil Green's documentation, www.phrap.org)
130. Ducut Sigala, J. L., Bottero, V., Young, D. B., Shevchenko, A., Mercurio, F., and Verma, I. M. (2004) Activation of transcription factor NF-kappaB requires ELKS, an IkappaB kinase regulatory subunit. Science 304, 1963-1967 (Pubitemid 38822188)
131. Wu, Z. H., Shi, Y., Tibbetts, R. S., and Miyamoto, S. (2006) Molecular linkage between the kinase ATM and NF-kappaB signaling in response to genotoxic stimuli. Science 311, 1141-1146
132. Wu, Z. H., Wong, E. T., Shi, Y., Niu, J., Chen, Z., Miyamoto, S., and Tergaonkar, V. (2010) ATM- and NEMO-dependent ELKS ubiquitination coordinates TAK1-mediated IKK activation in response to genotoxic stress. Mol Cell 40, 75-86