Abstract
Using global approaches and high-throughput technologies in virology brings a new vision of the infections physiology and allows the identification of cellular factors, mandatory for viral life cycle, that could be targeted by original therapeutic agents. It opens perspectives for the treatment of viral infections by acting on cellular pathways that the virus must use for its own replication. Combining these new molecules with classical antiviral drugs and immunomodulators diversifies and enlarges the antiviral arsenal and contributes to fight drug resistance.
Our laboratory and others are constructing virus–human interactomes to propose a comprehensive analysis of viral infection at the cellular level. Studying these infection maps, where the viral infection can be visualized as perturbation of the human protein–protein interaction network, and identifying the biological functions that are impaired by these perturbations may lead to discovery of new therapeutic targets. These virus–human interaction maps are constructed in a stringent yeast two-hybrid system by screening human cDNA libraries with viral proteins as bait and integrating interactions mined from literature and public databases.
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References
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.
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 USA 104, 7606–7611.
Konig, 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.
de Chassey, B., Navratil, V., Tafforeau, L., Hiet, M. S., Aublin-Gex, A., Agaugue, 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., Andre, P., Rabourdin-Combe, C., and Lotteau, V. (2008) Hepatitis C virus infection protein network, Mol Syst Biol 4, 230.
Zhang, L., Villa, N. Y., Rahman, M. M., Smallwood, S., Shattuck, D., Neff, C., Dufford, M., Lanchbury, J. S., Labaer, J., and McFadden, G. (2009) Analysis of vaccinia virus-host protein-protein interactions: validations of yeast two-hybrid screenings, J Proteome Res 8, 4311–4318.
Bailer, S. M., and Haas, J. (2009) Connecting viral with cellular interactomes, Curr Opin Microbiol 12, 453–459.
Fields, S., and Song, O. (1989) A novel genetic system to detect protein-protein interactions, Nature 340, 245–246.
Fromont-Racine, M., Rain, J. C., and Legrain, P. (1997) Toward a functional analysis of the yeast genome through exhaustive two- hybrid screens, Nat Genet 16, 277–282.
Navratil, V., de Chassey, B., Meyniel, L., Delmotte, S., Gautier, C., Andre, P., Lotteau, V., and Rabourdin-Combe, C. (2009) VirHostNet: a knowledge base for the management and the analysis of proteome-wide virus-host interaction networks, Nucleic Acids Res 37, D661–D668.
Louvet, O., Doignon, F., and Crouzet, M. (1997) Stable DNA-binding yeast vector allowing high-bait expression for use in the two-hybrid system, Biotechniques 23, 816–818, 820.
Gholami, A., Kassis, R., Real, E., Delmas, O., Guadagnini, S., Larrous, F., Obach, D., Prevost, M. C., Jacob, Y., and Bourhy, H. (2008) Mitochondrial dysfunction in lyssavirus-induced apoptosis, J Virol 82, 4774–4784.
Li, L., Elledge, S. J., Peterson, C. A., Bales, E. S., and Legerski, R. J. (1994) Specific association between the human DNA repair proteins XPA and ERCC1, Proc Natl Acad Sci USA 91, 5012–5016.
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.
Harper, J. W., Adami, G. R., Wei, N., Keyomarsi, K., and Elledge, S. J. (1993) The p21 Cdk-interacting protein Cip1 is a potent inhibitor of G1 cyclin-dependent kinases, Cell 75, 805–816.
Petermann, R., Mossier, B. M., Aryee, D. N., and Kovar, H. (1998) A recombination based method to rapidly assess specificity of two-hybrid clones in yeast, Nucleic Acids Res 26, 2252–2253.
Pellet, J., Tafforeau, L., Lucas-Hourani, M., Navratil, V., Meyniel, L., Achaz, G., Guironnet-Paquet, A., Aublin-Gex, A., Caignard, G., Cassonnet, P., Chaboud, A., Chantier, T., Deloire, A., Demeret, C., Le Breton, M., Neveu, G., Jacotot, L., Vaglio, P., Delmotte, S., Gautier, C., Combet, C., Deleage, G., Favre, M., Tangy, F., Jacob, Y., Andre, P., Lotteau, V., Rabourdin-Combe, C., and Vidalain, P. O. (2010) ViralORFeome: an integrated database to generate a versatile collection of viral ORFs, Nucleic Acids Res 38, D371–D378.
Li, S., Armstrong, C. M., Bertin, N., Ge, H., Milstein, S., Boxem, M., Vidalain, P. O., Han, J. D., 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.
Pellet, J., Meyniel, L., Vidalain, P. O., de Chassey, B., Tafforeau, L., Lotteau, V., Rabourdin-Combe, C., and Navratil, V. (2009) pISTil: a pipeline for yeast two-hybrid Interaction Sequence Tags identification and analysis, BMC research notes 2, 220.
Orchard, S., Salwinski, L., Kerrien, S., Montecchi-Palazzi, L., Oesterheld, M., Stumpflen, V., Ceol, A., Chatr-aryamontri, A., Armstrong, J., Woollard, P., Salama, J. J., Moore, S., Wojcik, J., Bader, G. D., Vidal, M., Cusick, M. E., Gerstein, M., Gavin, A. C., Superti-Furga, G., Greenblatt, J., Bader, J., Uetz, P., Tyers, M., Legrain, P., Fields, S., Mulder, N., Gilson, M., Niepmann, M., Burgoon, L., De Las Rivas, J., Prieto, C., Perreau, V. M., Hogue, C., Mewes, H. W., Apweiler, R., Xenarios, I., Eisenberg, D., Cesareni, G., and Hermjakob, H. (2007) The minimum information required for reporting a molecular interaction experiment (MIMIx), Nat Biotechnol 25, 894–898.
Staden, R., Beal, K. F., and Bonfield, J. K. (2000) The Staden package, 1998, Methods Mol Biol 132, 115–130.
Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D. J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Res 25, 3389–3402.
Ruohonen, L., Aalto, M. K., and Keranen, S. (1995) Modifications to the ADH1 promoter of Saccharomyces cerevisiae for efficient production of heterologous proteins, J Biotechnol 39, 193–203.
Hartley, J. L., Temple, G. F., and Brasch, M. A. (2000) DNA cloning using in vitro site-specific recombination, Genome Res 10, 1788–1795.
Walhout, A. J., Temple, G. F., Brasch, M. A., Hartley, J. L., Lorson, M. A., van den Heuvel, S., and Vidal, M. (2000) GATEWAY recombinational cloning: application to the cloning of large numbers of open reading frames or ORFeomes, Methods Enzymol 328, 575–592.
Tornow, J., and Santangelo, G. M. (1990) Efficient expression of the Saccharomyces cerevisiae glycolytic gene ADH1 is dependent upon a cis-acting regulatory element (UASRPG) found initially in genes encoding ribosomal proteins, Gene 90, 79–85.
Fields, S., and Sternglanz, R. (1994) The two-hybrid system: an assay for protein-protein interactions, Trends Genet 10, 286–292.
Durfee, T., Becherer, K., Chen, P. L., Yeh, S. H., Yang, Y., Kilburn, A. E., Lee, W. H., and Elledge, S. J. (1993) The retinoblastoma protein associates with the protein phosphatase type 1 catalytic subunit, Genes Dev 7, 555–569.
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.
Vidalain, P. O., Boxem, M., Ge, H., Li, S., and Vidal, M. (2004) Increasing specificity in high-throughput yeast two-hybrid experiments, Methods 32, 363–370.
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Tafforeau, L., Rabourdin-Combe, C., Lotteau, V. (2012). Virus–Human Cell Interactomes. In: Suter, B., Wanker, E. (eds) Two Hybrid Technologies. Methods in Molecular Biology, vol 812. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-61779-455-1_6
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DOI: https://doi.org/10.1007/978-1-61779-455-1_6
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