The Journal of Microbiology

, Volume 49, Issue 6, pp 965–973 | Cite as

Dynamical analysis of yeast protein interaction network during the sake brewing process

Articles
  • 106 Downloads

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.

Keywords

protein interaction network dynamical analysis sake brewing hubs Saccharomyces cerevisiae 

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

Supplementary material

12275_2011_1194_MOESM1_ESM.pdf (1.7 mb)
Supplementary material, approximately 1.71 MB.

References

  1. Breitkreutz, B.J., C. Stark, and M. Tyers. 2003. The GRID: the General Repository for Interaction Datasets. Genome Biol. 4, R23.PubMedCrossRefGoogle Scholar
  2. 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.PubMedCrossRefGoogle Scholar
  3. Cho, K.H. and O. Wolkenhauer. 2005. System Biology: Discovering the dynamic behavior of biochemical networks. BioSyst. Rev. 1, 9–17.Google Scholar
  4. 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.PubMedCrossRefGoogle Scholar
  5. 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.PubMedCrossRefGoogle Scholar
  6. 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.PubMedGoogle Scholar
  7. 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.PubMedCrossRefGoogle Scholar
  8. 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.PubMedCrossRefGoogle Scholar
  9. 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.CrossRefGoogle Scholar
  10. Hazbun, T.R. and S. Fields. 2001. Networking proteins in yeast. Proc. Natl. Acad. Sci. USA 98, 4277–4278.PubMedCrossRefGoogle Scholar
  11. 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.CrossRefGoogle Scholar
  12. 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.PubMedCrossRefGoogle Scholar
  13. 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.PubMedCrossRefGoogle Scholar
  14. Jeong, H., S.P. Mason, A.L. Barabási, and Z.N. Oltvai. 2001. Lethality and centrality in protein networks. Nature 411, 41–42.PubMedCrossRefGoogle Scholar
  15. Komurov, K. and M. White. 2007. Revealing static and dynamic modular architecture of the eukaryotic protein interaction network. Mol. Syst. Biol. 3, 110.PubMedCrossRefGoogle Scholar
  16. 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.PubMedCrossRefGoogle Scholar
  17. 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.PubMedCrossRefGoogle Scholar
  18. Li, F.T. and X. Jia. 2006. Dynamical analysis of protein regulatory network in budding yeast nucleus. Chin. Phys. Lett. 23, 2307–2310.CrossRefGoogle Scholar
  19. Maslov, S. and K. Sneppen. 2002. Specificity and stability in topology of proteins networks. Science 296, 910–913.PubMedCrossRefGoogle Scholar
  20. 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.PubMedCrossRefGoogle Scholar
  21. Platzer, A., P. Perco, A. Lukas, and B. Mayer. 2007. Characterization of protein-interaction networks in tumors. BMC Bioinformatics 8, 224.PubMedCrossRefGoogle Scholar
  22. 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.PubMedCrossRefGoogle Scholar
  23. 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.PubMedCrossRefGoogle Scholar
  24. 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.PubMedCrossRefGoogle Scholar
  25. Schwikowski, B., P. Uetz, and S. Fields. 2000. A network of protein-protein interactions in yeast, Nature Biotech. 18, 1257–1261.CrossRefGoogle Scholar
  26. 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.PubMedGoogle Scholar
  27. 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.PubMedCrossRefGoogle Scholar
  28. 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.PubMedCrossRefGoogle Scholar
  29. 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.PubMedCrossRefGoogle Scholar
  30. Vázqueza, A., A. Flammini, A. Maritan, and A. Vespignani, 2003. Modeling of protein interaction networks. ComPlexUs 1, 38–44.CrossRefGoogle Scholar
  31. 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.PubMedCrossRefGoogle Scholar

Copyright information

© The Microbiological Society of Korea and Springer-Verlag Berlin Heidelberg  2011

Authors and Affiliations

  1. 1.Department of Computer EngineeringIslamic Azad University, Science and Research BranchTehranIran
  2. 2.National Institute of Genetic Engineering and Biotechnology (NIGEB)TehranIran
  3. 3.School of Computer SciencesInstitute for Research in Fundamental Sciences, IPMTehranIran
  4. 4.Control and Intelligent Processing Center of Excellence, School of Electrical and Computer EngineeringUniversity of TehranTehranIran
  5. 5.School of Cognitive SciencesInstitute for Research in Fundamental Sciences, IPMTehranIran

Personalised recommendations