Fast revelation of the motif mode for a yeast protein interaction network through intelligent agent-based distributed computing

Protein and Peptide Letters

Volumn 17, Issue 9, 2010, Pages 1091-1101

  Lee, Wei Po ^a   Tzou, Wen Shyong ^b,c  

^a NATIONAL SUN YAT SEN UNIVERSITY   (Taiwan)

^b Institute of Bioscience and Biotechnology   (Taiwan)

^c NATIONAL TAIWAN OCEAN UNIVERSITY   (Taiwan)

Author keywords

Adaptive computing; Evolutionary conservation; Gene ontology; Mobile agent; Motif mode; Protein protein interaction

Indexed keywords

PROTEIN;

ARTICLE; BIOLOGY; CHEMISTRY; GENETICS; METABOLISM; METHODOLOGY; PROTEIN ANALYSIS; PROTEIN MOTIF; THEORETICAL MODEL;

AMINO ACID MOTIFS; COMPUTATIONAL BIOLOGY; MODELS, THEORETICAL; PROTEIN INTERACTION MAPPING; PROTEINS;

EID: 78650133538     PISSN: 09298665     EISSN: None     Source Type: Journal    
DOI: 10.2174/092986610791760441     Document Type: Article

References (74)

1. Barabasi, A.L.; Oltvai, Z.N. Network biology: understanding the cell's functional organization. Nat. Rev. Genet., 2004, 90, 101-113. (Pubitemid 38160277)
2. Ciriello, G.; Guerr, C. A review on models and algorithms for motif discovery in protein-protein interaction networks. Brief Funct. Genomic. Proteomic., 2008, 7, 147-156. (Pubitemid 351728956)
3. Sharan, R.; Ulitsky, I.; Shamir, R. Network-based prediction of protein function. Mol. Syst. Biol., 2007, 3, 88.
4. Bork, P.; Jensen, L.J.; von Mering, C.; Ramani, A.K.; Lee, I.; Marcotte, E. M. Protein interaction networks from yeast to human. Curr. Opin. Struct. Biol., 2004, 14, 292-299. (Pubitemid 38749056)
5. Miller, J.P.; Lo, R.S.; Ben-Hur, A.; Desmarais, C.; Stagljar, I.; Noble, W.S.; Fields, S. Large-scale identification of yeast integral membrane protein interactions. Proc. Natl. Acad. Sci. U. S. A., 2005, 102, 12123-12128. (Pubitemid 41291139)
6. Schuldiner, M.; Collins, S.R.; Thompson, N.J.; Denic, V.; Bhamidipati, A.; Punna, T.; Ihmels, J.; Andrews, B.; Boone, C.; Greenblatt, J.F.; Weissman, J.S.; Krogan, N.J. Exploration of the function and organization of the yeast early secretory pathway through an epistatic miniarray profile. Cell, 2005, 123, 507-519. (Pubitemid 41546679)
7. Krogan, N.J.; Cagney, G.; Yu, H.; Zhong, G.; Guo, X.; Ignatchenko, A.; Li, J.; Pu, S.; Datta, N.; Tikuisis, A.P.; Punna, T.; Peregrin-Alvarez, J.M.; Shales, M.; Zhang, X.; Davey, M.; Robinson, M.D.; Paccanaro, A.; Bray, J.E.; Sheung, A.; Beattie, B.; Richards, D.P.; Canadien, V.; Lalev, A.; Mena, F.; Wong, P.; Starostine, A.; Canete, M.M.; Vlasblom, J.; Wu, S.; Orsi, C.; Collins, S.R.; Chandran, S.; Haw, R.; Rilstone, J. J.; Gandi, K.; Thompson, N.J.; Musso, G.; St Onge, P.; Ghanny, S.; Lam, M.H.; Butland, G.; Altaf-Ul, A.M.; Kanaya, S.; Shilatifard, A.; O'Shea, E.; Weissman, J.S.; Ingles, C. J.; Hughes, T.R.; Parkinson, J.; Gerstein, M.; Wodak, S.J.; Emili, A.; Greenblatt, J.F. Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature, 2006, 440, 637-643.
8. Shi, M.G.; Huang, D.S.; Li, X.L. A protein interaction network analysis for yeast integral membrane protein. Protein Pept. Lett., 2008, 15, 692-699.
9. Eom, Y.H.; Lee, S.; Jeong, H. Exploring local structural organization of metabolic networks using subgraph patterns. J. Theor. Biol., 2006, 241, 823-829. (Pubitemid 44080792)
10. Wuchty, S.; Oltvai, Z.N.; Barabasi, A.L. Evolutionary conservation of motif constituents in the yeast protein interaction network. Nat. Genet., 2003, 35, 176-179. (Pubitemid 37187637)
11. Milo, R.; Shen-Orr, S.; Itzkovitz, S.; Kashtan, N.; Chklovskii, D.; Alon, U. Network motifs: simple building blocks of complex networks. Science, 2002, 298, 824-827. (Pubitemid 35231534)
12. Ashburner, M.; Ball, C.A.; Blake, J.A.; Botstein, D.; Butler, H.; Cherry, J.M.; Davis, A.P.; Dolinski, K.; Dwight, S.S.; Eppig, J.T.; Harris, M.A.; Hill, D.P.; Issel-Tarver, L.; Kasarskis, A.; Lewis, S.; Matese, J.C.; Richardson, J.E.; Ringwald, M.; Rubin, G.M.; Sherlock, G. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet., 2000, 25, 25-29. (Pubitemid 30257031)
13. Lee, W.P.; Jeng, B.C.; Pai, T.W.; Tsai, C.P.; Yu, C.Y.; Tzou, W.S. Differential evolutionary conservation of motif modes in the yeast protein interaction network. BMC Genomics, 2006, 7, 89.
14. Wernicke, S. Efficient detection of network motifs. IEEE/ACM Trans. Comput. Biol. Bioinform., 2006, 3, 347-359. (Pubitemid 44950084)
15. Bellifemine, F.; Caire, G.; Greenwood D. Developing Multi-Agent Systems with JADE; John Wiley &Sons, 2007.
16. Kuramochi, M.; Karypis, G. An efficient algorithm for discovering frequent subgraphs. IEEE Trans. on Knowledge and Data Engineering, 2004, 16, 1038-1051.
17. Messmer, B. T.; Bunke, H. Efficient subgraph isomorphism detection: a decomposition approach. IEEE Trans. Know. Data Eng., 2000, 12, 307-323.
18. Salwinski, L.; Miller, C.S.; Smith, A.J.; Pettit, F.K.; Bowie, J.U.; Eisenberg, D. The Database of Interacting Proteins: 2004 update. Nucleic Acids Res., 2004, 32, D449-D451. (Pubitemid 38081696)
19. Berglund, A.C.; Sjolund, E.; Ostlund, G.; Sonnhammer, E.L. In- Paranoid 6: eukaryotic ortholog clusters with inparalogs. Nucleic Acids Res., 2008, 36, D263-D266. (Pubitemid 351149733)
20. von Mering, C.; Krause, R.; Snel, B.; Cornell, M.; Oliver, SG.; Fields, S.; Bork P. Comparative assessment of large-scale data sets of protein-protein interactions. Nature, 2002, 417, 399-403. (Pubitemid 34563526)
21. Jeong, H.; Mason, S.P.; Barabasi, A.L.; Oltvai, Z.N. Lethality and centrality in protein networks. Nature, 2001, 411, 41-42. (Pubitemid 32428180)
22. Wagner, A.; Fell D.A. The small world inside large metabolic networks. Proc. Biol. Sci., 2001, 268, 1803-1810. (Pubitemid 32844028)
23. Przulj, N.; Corneil, D.G.; Jurisica, I. Modeling interactome: scalefree or geometric? Bioinformatics, 2004, 20, 3508-3515.
24. Ravasz, E.; Somera, A.L.; Mongru, D.A.; Oltvai, Z.N.; Barabasi, A.L. Hierarchical organization of modularity in metabolic networks. Science, 2002, 297, 1551-1555. (Pubitemid 34971002)
25. Ravasz, E.; Barabasi, A.L. Hierarchical organization in complex networks. Phys. Rev. E Stat. Nonlin. Soft Matter Phys., 2003, 67, 026112.
26. Dobrin, R.; Beg, Q.K.; Barabasi, A.L.; Oltvai, Z.N. Aggregation of topological motifs in the Escherichia coli transcriptional regulatory network. BMC Bioinformatics, 2004, 5, 10.
27. Vazquez, A.; Dobrin, R.; Sergi, D.; Eckmann, J.P.; Oltvai, Z.N.; Barabasi, A.L. The topological relationship between the large-scale attributes and local interaction patterns of complex networks. Proc. Natl. Acad. Sci., USA 2004, 101, 17940-17945. (Pubitemid 40054054)
28. Schwikowski, B.; Uetz, P.; Fields, S. A network of protein-protein interactions in yeast. Nat. Biotechnol., 2000, 18, 1257-1261.
29. Hong, E.L.; Balakrishnan, R.; Dong, Q.; Christie, K.R.; Park, J.; Binkley, G.; Costanzo, M.C.; Dwight, S.S.; Engel, S.R.; Fisk, D.G.; Hirschman, J.E.; Hitz, B.C.; Krieger, C.J.; Livstone, M.S.; Miyasato, S.R.; Nash, R.S.; Oughtred, R.; Skrzypek, M.S.; Weng, S.; Wong, E.D.; Zhu, K.K.; Dolinski, K.; Botstein, D.; Cherry, J.M. Gene Ontology annotations at SGD: new data sources and annotation methods. Nucleic Acids Res., 2008, 36, D577-D581. (Pubitemid 351149788)
30. Santamaria, P.G.; Finley, D.; Ballesta, J.P.; Remacha, M. Rpn6p, a proteasome subunit from Saccharomyces cerevisiae, is essential for the assembly and activity of the 26 S proteasome. J. Biol. Chem., 2003, 278, 6687-6695. (Pubitemid 36800655)
31. Saito, A.; Watanabe, T.K.; Shimada, Y.; Fujiwara, T.; Slaughter, C.A.; DeMartino, G.N.; Tanahashi, N.; Tanaka, K. cDNA cloning and functional analysis of p44.5 and p55, two regulatory subunits of the 26S proteasome. Gene, 1997, 203, 241-250. (Pubitemid 27522136)
32. Glickman, M.H.; Rubin, D.M.; Fried, V.A.; Finley, D. The regulatory particle of the Saccharomyces cerevisiae proteasome. Mol. Cell. Biol., 1998, 18, 3149-3162. (Pubitemid 28240488)
33. Takeuchi, J.; Toh-e, A. Genetic dissection of the yeast 26S proteasome: cell cycle defects caused by the Deltarpn9 mutation. Biochimie, 2001, 83, 333-340. (Pubitemid 32293654)
34. Chernova, T.A.; Allen, K.D.; Wesoloski, L.M.; Shanks, J.R.; Chernoff, Y.O.; Wilkinson, K.D. Pleiotropic effects of Ubp6 loss on drug sensitivities and yeast prion are due to depletion of the free ubiquitin pool. J. Biol. Chem., 2003, 278, 52102-52115. (Pubitemid 38035796)
35. Guterman, A.; Glickman, M.H. Complementary roles for Rpn11 and Ubp6 in deubiquitination and proteolysis by the proteasome. J. Biol. Chem., 2004, 279, 1729-1738. (Pubitemid 38084440)
36. Groll, M.; Heinemeyer, W.; Jager, S.; Ullrich, T.; Bochtler, M.; Wolf, D.H.; Huber, R. The catalytic sites of 20S proteasomes and their role in subunit maturation: a mutational and crystallographic study. Proc. Natl. Acad. Sci. USA, 1999, 96, 10976-10983. (Pubitemid 29487315)
37. Russell, S.J.; Steger, K.A.; Johnston, S.A. Subcellular localization, stoichiometry, and protein levels of 26 S proteasome subunits in yeast. J. Biol. Chem., 1999, 274, 21943-21952.
38. Takeuchi, J.; Toh-e, A. Genetic evidence for interaction between components of the yeast 26S proteasome: combination of a mutation in RPN12 (a lid component gene) with mutations in RPT1 (an ATPase gene) causes synthetic lethality. Mol. Gen. Genet., 1999, 262, 145-153. (Pubitemid 29423912)
39. Tone, Y.; Tanahashi, N.; Tanaka, K.; Fujimuro, M.; Yokosawa, H.; Toh-e, A. Nob1p, a new essential protein, associates with the 26S proteasome of growing saccharomyces cerevisiae cells. Gene, 2000, 243, 37-45. (Pubitemid 30079703)
40. Glickman, M.H.; Rubin, D.M.; Fu, H.; Larsen, CN.; Coux, O.; Wefes, I.; Pfeifer, G.; Cjeka, Z.; Vierstra, R.; Baumeister, W.; Fried, V.; Finley, D. Functional analysis of the proteasome regulatory particle. Mol. Biol. Rep., 1999, 26, 21-28. (Pubitemid 29223246)
41. Rubin, D.M.; Glickman, M.H.; Larsen, C.N.; Dhruvakumar, S.; Finley, D. Active site mutants in the six regulatory particle ATPases reveal multiple roles for ATP in the proteasome. EMBO J., 1998, 17, 4909-4919. (Pubitemid 28408458)
42. Strunnikov, A.V.; Hogan, E.; Koshland, D. SMC2, a Saccharomyces cerevisiae gene essential for chromosome segregation and condensation, defines a subgroup within the SMC family. Genes Dev., 1995, 9, 587-599.
43. Haeusler, R.A.; Pratt-Hyatt, M.; Good, P.D.; Gipson, T.A.; Engelke, D.R. Clustering of yeast tRNA genes is mediated by specific association of condensin with tRNA gene transcription complexes. Genes Dev., 2008, 22, 2204-2214.
44. Michaelis, C.; Ciosk, R.; Nasmyth, K. Cohesins: chromosomal proteins that prevent premature separation of sister chromatids. Cell, 1997, 91, 35-45. (Pubitemid 27431311)
45. Klein, F.; Mahr, P.; Galova, M.; Buonomo, S.B.; Michaelis, C.; Nairz, K.; Nasmyth, K. A central role for cohesins in sister chromatid cohesion, formation of axial elements, and recombination during yeast meiosis. Cell, 1999, 98, 91-103. (Pubitemid 29331199)
46. Jones, S.; Sgouros, J. The cohesin complex: sequence homologies, interaction networks and shared motifs. Genome Biol., 2001, 2, RESEARCH0009.
47. Kanemaki, M.; Kurokawa, Y.; Matsu-ura, T.; Makino, Y.; Masani, A.; Okazaki, K.; Morishita, T.; Tamura, T.A. TIP49b, a new RuvBlike DNA helicase, is included in a complex together with another RuvB-like DNA helicase, TIP49a. J. Biol. Chem., 1999, 274, 22437-22444.
48. Jonsson, Z.O.; Dhar, S.K.; Narlikar, G.J.; Auty, R.; Wagle, N.; Pellman, D.; Pratt, R.E.; Kingston, R.; Dutta, A. Rvb1p and Rvb2p are essential components of a chromatin remodeling complex that regulates transcription of over 5% of yeast genes. J. Biol. Chem., 2001, 276, 16279-16288.
49. Jonsson, Z.O.; Jha, S.; Wohlschlegel, J.A.; Dutta, A. Rvb1p/Rvb2p recruit Arp5p and assemble a functional Ino80 chromatin remodeling complex. Mol. Cell., 2004, 16, 465-477. (Pubitemid 39504799)
50. Marsischky, G.T.; Filosi, N.; Kane, M.F.; Kolodner, R. Redundancy of Saccharomyces cerevisiae MSH3 and MSH6 in MSH2- dependent mismatch repair. Genes Dev., 1996, 10, 407-420. (Pubitemid 26085996)
51. Bowers, J.; Sokolsky, T.; Quach, T.; Alani, E. A mutation in the MSH6 subunit of the Saccharomyces cerevisiae MSH2-MSH6 complex disrupts mismatch recognition. J. Biol. Chem., 1999, 274, 16115-16125.
52. Vanacova, S.; Wolf, J.; Martin, G.; Blank, D.; Dettwiler, S.; Friedlein, A.; Langen, H.; Keith, G.; Keller, W. A new yeast poly(A) polymerase complex involved in RNA quality control. PLoS Biol., 2005, 3, e189.
53. LaCava, J.; Houseley, J.; Saveanu, C.; Petfalski, E.; Thompson, E.; Jacquier, A. and Tollervey, D. RNA degradation by the exosome is promoted by a nuclear polyadenylation complex. Cell, 2005, 121, 713-724. (Pubitemid 40797594)
54. Tsurimoto, T. PCNA binding proteins. Front. Biosci., 1999, 4, D849-D858.
55. Liu, Y.; Flanagan, J.J.; Barlowe, C. Sec22p export from the endoplasmic reticulum is independent of SNARE pairing. J. Biol. Chem., 2004, 279, 27225-27232. (Pubitemid 38812560)
56. Liu, Y.; Barlowe, C. Analysis of Sec22p in endoplasmic reticulum/ Golgi transport reveals cellular redundancy in SNARE protein function. Mol. Biol. Cell, 2002, 13, 3314-3324. (Pubitemid 35034265)
57. Ram, R.J.; Li, B.; Kaiser, C.A. Identification of Sec36p, Sec37p, and Sec38p: components of yeast complex that contains Sec34p and Sec35p. Mol. Biol. Cell, 2002, 13, 1484-1500. (Pubitemid 34522633)
58. Loh, E.; Hong, W. The binary interacting network of the conserved oligomeric Golgi tethering complex. J. Biol. Chem., 2004, 279, 24640-24648. (Pubitemid 38725331)
59. Stearns, T.; Willingham, M.C.; Botstein, D.; Kahn, R.A. ADPribosylation factor is functionally and physically associated with the Golgi complex. Proc. Natl. Acad. Sci. USA, 1990, 87, 1238-1242.
60. Sewell, J.L.; Kahn, R.A. Sequences of the bovine and yeast ADPribosylation factor and comparison to other GTP-binding proteins. Proc. Natl. Acad. Sci. USA, 1988, 85, 4620-4624.
61. Stearns, T.; Kahn, R.A.; Botstein, D.; Hoyt, M.A. ADP ribosylation factor is an essential protein in Saccharomyces cerevisiae and is encoded by two genes. Mol. Cell. Biol., 1990, 10, 6690-6699. (Pubitemid 120004614)
62. Giraudo, C.G.; Maccioni, H.J. Endoplasmic reticulum export of glycosyltransferases depends on interaction of a cytoplasmic dibasic motif with Sar1. Mol. Cell. Biol., 2003, 14, 3753-3766. (Pubitemid 37151624)
63. Barlowe, C.; d'Enfert, C.; Schekman, R. Purification and characterization of SAR1p, a small GTP-binding protein required for transport vesicle formation from the endoplasmic reticulum. J. Biol. Chem., 1993, 268, 873-879. (Pubitemid 23019716)
64. Cosson, P.; Demolliere, C.; Hennecke, S.; Duden R.; Letourneur, F. Delta- and zeta-COP, two coatomer subunits homologous to clathrin-associated proteins, are involved in ER retrieval. EMBO J., 1996, 15, 1792-1798. (Pubitemid 26119215)
65. Stevens, S.W.; Abelson, J. Purification of the yeast U4/U6.U5 small nuclear ribonucleoprotein particle and identification of its proteins. Proc. Natl. Acad. Sci., USA, 1999, 96, 7226-7231. (Pubitemid 29299643)
66. Gottschalk, A.; Neubauer, G.; Banroques, J.; Mann, M.; Luhrmann, R.; Fabrizio, P. Identification by mass spectrometry and functional analysis of novel proteins of the yeast [U4/U6.U5] tri-snRNP. EMBO J., 1999, 18, 4535-4548. (Pubitemid 29391263)
67. Stevens, S.W.; Barta, I.; Ge, H.Y.; Moore, R.E.; Young, MK.; Lee, T.D.; Abelson, J. Biochemical and genetic analyses of the U5, U6, and U4/U6 x U5 small nuclear ribonucleoproteins from Saccharomyces cerevisiae. RNA, 2001, 7, 1543-1553. (Pubitemid 33078930)
68. Stevens, S.W.; Ryan, D.E.; Ge, H.Y.; Moore, R.E.; Young, M.K.; Lee, T.D.; Abelson, J. Composition and functional characterization of the yeast spliceosomal penta-snRNP. Mol. Cell., 2002, 9, 31-44. (Pubitemid 34127769)
69. Beggs, J.D. Lsm proteins and RNA processing. Biochem. Soc. Trans., 2005, 33, 433-438. (Pubitemid 40873859)
70. He, W.; Parker, R. Functions of Lsm proteins in mRNA degradation and splicing. Curr. Opin. Cell. Biol., 2000, 12, 346-350. (Pubitemid 30265065)
71. Coller, J.M.; Tucker, M.; Sheth, U.; Valencia-Sanchez, M.A.; Parker, R. The DEAD box helicase, Dhh1p, functions in mRNA decapping and interacts with both the decapping and deadenylase complexes. RNA, 2001, 7, 1717-1727. (Pubitemid 34042287)
72. Tseng-Rogenski, S.S.; Chong, J.L.; Thomas, C.B.; Enomoto, S.; Berman, J.; Chang, T.H. Functional conservation of Dhh1p, a cytoplasmic DExD/H-box protein present in large complexes. Nucleic Acids Res., 2003, 31, 4995-5002. (Pubitemid 37441866)
73. Bergkessel, M.; Reese, J.C. An essential role for the Saccharomyces cerevisiae DEAD-box helicase DHH1 in G1/S DNA-damage checkpoint recovery. Genetics, 2004, 167, 21-33. (Pubitemid 38736367)
74. Finn, R.D.; Tate, J.; Mistry, J.; Coggill, P.C.; Sammut, S.J.; Hotz, H.R.; Ceric, G.; Forslund, K.; Eddy, S.R.; Sonnhammer, E.L.; Bateman, A. The Pfam protein families database. Nucleic Acids Res., 2008, 36, D281-D288. (Pubitemid 351149737)