Abstract
Proteins interact with each other for performing essential functions of an organism. They change partners to get involved in various processes at different times or locations. Studying variations of protein interactions within a specific process would help better understand the dynamic features of the protein interactions and their functions. We studied the protein interaction network of Saccharomyces cerevisiae (yeast) during the brewing of Japanese sake. In this process, yeast cells are exposed to several stresses. Analysis of protein interaction networks of yeast during this process helps to understand how protein interactions of yeast change during the sake brewing process. We used gene expression profiles of yeast cells for this purpose. Results of our experiments revealed some characteristics and behaviors of yeast hubs and non-hubs and their dynamical changes during the brewing process. We found that just a small portion of the proteins (12.8 to 21.6%) is responsible for the functional changes of the proteins in the sake brewing process. The changes in the number of edges and hubs of the yeast protein interaction networks increase in the first stages of the process and it then decreases at the final stages.
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Breitkreutz, B.J., C. Stark, and M. Tyers. 2003. The GRID: the General Repository for Interaction Datasets. Genome Biol. 4, R23.
Butland, G., J.M. Peregrín-Alvarez, J. Li, W. Yang, X. Yang, V. Canadien, A. Starostine, and et al. 2005. Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 433, 531–537.
Cho, K.H. and O. Wolkenhauer. 2005. System Biology: Discovering the dynamic behavior of biochemical networks. BioSyst. Rev. 1, 9–17.
Chu S., J. DeRisi, M. Eisen, J. Mulholland, D. Botstein, P.O. Brown, and I. Herskowitz. 1998. The transcriptional program of sporulation in budding yeast. Science 282, 699–705.
Ekman, D., S. Light, A. Björklund, and A. Elofsson. 2006. What properties characterize the hub proteins of the protein-protein interaction network of Saccharomyces cerevisiae? Genome Biol. 7, R45.
Gasch, A.P., P.T. Spellman, C.M. Kao, O. Carmel-Harel, M.B. Eisen, G. Storz, D. Botstein, and P.O. Brown. 2000. Genomic expression programs in the response of Yeast ells to environmental changes. Mol. Biol. Cell 11, 4241–4257.
Gavin, A.C., P. Aloy, P. Grandi, R. Krause, M. Boesche, M. Marzioch, C. Rau, and et al. 2006. Proteome survey reveals modularity of the yeast cell machinery. Nature 440, 631–636.
Giot, L., J.S. Bader, C. Brouwer, A. Chaudhuri, B. Kuang, Y. Li, Y.L. Hao, and et al. 2003. A protein interaction map of Drosophila melanogaster. Science 302, 1727–1736.
Goffeau, A., B.G. Barrell, H. Bussey, R.W. Davis, B. Dujon, H. Feldmann, F. Galibert, and et al. 1996. Life with 6000 genes. Science 274, 563–567.
Hazbun, T.R. and S. Fields. 2001. Networking proteins in yeast. Proc. Natl. Acad. Sci. USA 98, 4277–4278.
Hermjakob, H., L. Montecchi-Palazzi, C. Lewington, S. Mudali, S. Kerrien, S. Orchard, M. Vingron, and et al. 2004. IntAct: an open source molecular interaction database. Nucleic Acids Res. 1, D452–455.
Ho, Y., A. Gruhler, A. Heilbut, G.D. Bader, L. Moore, S.L. Adams, A. Millar, and et al. 2002. Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415, 180–183.
Ito, T., T. Chiba, R. Ozawa, M. Yoshida, M. Hattori, and Y. Sakaki. 2001. A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc. Natl. Acad. Sci. USA 98, 4569–4574.
Jeong, H., S.P. Mason, A.L. Barabási, and Z.N. Oltvai. 2001. Lethality and centrality in protein networks. Nature 411, 41–42.
Komurov, K. and M. White. 2007. Revealing static and dynamic modular architecture of the eukaryotic protein interaction network. Mol. Syst. Biol. 3, 110.
Krogan, N.J., G. Cagney, H. Yu, G. Zhong, X. Guo, A. Ignatchenko, J. Li, and et al. 2006. Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature 440, 637–643.
Li, S., C.M. Armstrong, N. Bertin, H. Ge, S. Milstein, M. Boxem, P.O. Vidalain, and et al. 2004. A map of the interactome network of the metazoan C. elegans. Science 303, 540–543.
Li, F.T. and X. Jia. 2006. Dynamical analysis of protein regulatory network in budding yeast nucleus. Chin. Phys. Lett. 23, 2307–2310.
Maslov, S. and K. Sneppen. 2002. Specificity and stability in topology of proteins networks. Science 296, 910–913.
Mirzarezaee, M., B.N. Araabi, and M. Sadeghi. 2010. Features analysis for identification of date and party hubs in protein interaction network of Saccharomyces cerevisiae. BMC Syst. Biol. 4, 172.
Platzer, A., P. Perco, A. Lukas, and B. Mayer. 2007. Characterization of protein-interaction networks in tumors. BMC Bioinformatics 8, 224.
Roberts, C.J., B. Nelson, M.J. Marton, R. Stoughton, M.R. Meyer, H.A. Bennett, Y.D. He, and et al. 2000. Signaling and circuitry of multiple MAPK pathways revealed by a matrix of global gene expression profiles. Science 287, 873–880.
Rual, J.F., K. Venkatesan, T. Hao, T. Hirozane-Kishikawa, A. Dricot, N. Li, G.F. Berriz, and et al. 2005. Towards a proteome-scale map of the human protein-protein interaction network. Nature 437, 1173–1178.
Salwinski, L., C.S. Miller, A.J. Smith, F.K. Pettit, J.U. Bowie, and D. Eisenberg. 2004. The database of interacting proteins, Nucleic Acids Res. 32, D449–451.
Schwikowski, B., P. Uetz, and S. Fields. 2000. A network of protein-protein interactions in yeast, Nature Biotech. 18, 1257–1261.
Spellman, P.T., G. Sherlock, M.Q. Zhang, V.R. Iyer, K. Anders, M.B. Eisen, P.O. Brown, D. Botstein, and B. Futcher. 1998. Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol. Biol. Cell 9, 3273–3297.
Stelzl, U., U. Worm, M. Lalowski, C. Haenig, F.H. Brembeck, H. Goehler, M. Stroedicke, and et al. 2005. A human protein-protein interaction network: a resource for annotating the proteome. Cell 122, 957–968.
Travers, K.J., C.K. Patil, L. Wodicka, C. Haenig, F. Brembeck, H. Goehler, M. Stroedicke, and et al. 2000. Functional and genomic analyses reveal an essential coordination between the unfolded protein response and ER-associated degradation. Cell 101, 249–258.
Uetz, P., L. Giot, G. Cagney, T.A. Mansfield, R.S. Judson, J.R. Knight, D. Lockshon, and et al. 2000. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 403, 623–627.
Vázqueza, A., A. Flammini, A. Maritan, and A. Vespignani, 2003. Modeling of protein interaction networks. ComPlexUs 1, 38–44.
Wu, H., X. Zheng, Y. Araki, H. Sahara, H. Takagi, and H. Shimoi. 2006. Global gene expression analysis of yeast cells during sake brewing. Appl. Environ. Microbiol. 72, 7353–7358.
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Mirzarezaee, M., Sadeghi, M. & Araabi, B.N. Dynamical analysis of yeast protein interaction network during the sake brewing process. J Microbiol. 49, 965–973 (2011). https://doi.org/10.1007/s12275-011-1194-y
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DOI: https://doi.org/10.1007/s12275-011-1194-y