Reconstruction of the yeast protein-protein interaction network involved in nutrient sensing and global metabolic regulation

BMC Systems Biology

Volumn 4, Issue , 2010, Pages

  Nandy, Subir K ^a   Jouhten, Paula ^a   Nielsen, Jens ^a  

^a CHALMERS UNIVERSITY OF TECHNOLOGY   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

SACCHAROMYCES CEREVISIAE;

HOG1 PROTEIN, S CEREVISIAE; MITOGEN ACTIVATED PROTEIN KINASE; PHOSPHATIDYLINOSITOL 3 KINASE; PROTEIN SERINE THREONINE KINASE; SACCHAROMYCES CEREVISIAE PROTEIN; SNF1 RELATED PROTEIN KINASES; SNF1-RELATED PROTEIN KINASES; TOR1 PROTEIN, S CEREVISIAE; TRANSCRIPTION FACTOR;

ARTICLE; GENETICS; METABOLISM; METHODOLOGY; OPEN READING FRAME; PROTEIN ANALYSIS; SACCHAROMYCES CEREVISIAE; SIGNAL TRANSDUCTION; SYSTEMS BIOLOGY;

1-PHOSPHATIDYLINOSITOL 3-KINASE; MITOGEN-ACTIVATED PROTEIN KINASES; OPEN READING FRAMES; PROTEIN INTERACTION MAPPING; PROTEIN-SERINE-THREONINE KINASES; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; SIGNAL TRANSDUCTION; SYSTEMS BIOLOGY; TRANSCRIPTION FACTORS;

EID: 77954034972     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-4-68     Document Type: Article

References (45)

1. Landry CR, Oh J, Hartl DL, Cavalieri D. Genome-wide scan reveals that genetic variation for transcriptional plasticity in yeast is biased towards multi-copy and dispensable genes. Gene 2006, 366:343-351. 10.1016/j.gene.2005.10.042, 16427747.
2. Feder ME, Mitchell-Olds T. Evolutionary and ecological functional genomics. Nature Rev Genetics 2003, 4:651-657.
3. Polge C, Thomas M. SNF1/AMPK/SnRK1 kinases, global regulators at the heart of energy control?. TRENDS in Plant Sc 2006, 12:20-28.
4. Usaite R, Jewett MC, Oliveira AP, Yates JR, Olsson L, Nielsen J. Reconstruction of the yeast Snf1 kinase regulatory network reveals its role as a global energy regulator. Mol Sys Biol 2009, 5:319-330.
5. Levine AJ, Hu W, Feng Z, Gil G. Reconstructing signal transduction pathways: Challenges and Oppurtunities. Annals New York Acad Sci 2007, 1115:32-50.
6. Fazio A, Jewett MC, Daran-Lapujade P, Mustacchi R, Usaite R, Pronk JT, Workman CT, Nielsen J. Transcription factor control of growth rate dependent genes in Saccharomyces cerevisiae: A three factor design. BMC Genomics 2008, 9:341. 10.1186/1471-2164-9-341, 2500033, 18638364.
7. Nicklas B, Ferndahl C, Mostad P, Wilks MDB, Chang C, Showe L, Gustafsson L, Larsson C, Bill RM. Transcriptome analysis of a respiratory Saccharomyces cerevisiae strain suggests the expression of its phenotype is glucose insensitive and predominantly controlled by Hap4, Cat8 and Mig1. BMC Genomics 2008, 9:365. 10.1186/1471-2164-9-365, 2536679, 18671860.
8. Lage R, Dieguez C, Vidal-Puig A, Lopez M. AMPK: a metabolic gauge regulating whole-body energy homeostasis. Cell 2008, 14:539-549.
9. Yang Q, Inoki K, Kim E, Guan K-L. TSC1/TSC2 and Rheb have different effects on TORC1 and TORC2 activity. PNAS 2006, 103:6811-6816. 10.1073/pnas.0602282103, 1458976, 16627617.
10. Fabrizio P, Longo VD. Chronological aging-induced apoptosis in yeast. Biochimica et Biophysica Acta 2008, 1783:1280-1285. 2536486, 18445486.
11. Ciesla M, Towpik J, Graczyk D, Oficjalska-Pham D, Harismendy O, Suleau A, Balicki K, Conesa C, Lefebvre O, Boguta M. Maf1 Is Involved in Coupling Carbon Metabolism to RNA Polymerase III Transcription. Molecular and Cellular Biol 2007, 27:7693-7702.
12. Nordlander B, Krantz M, Hohmann S. Hog1-mediated metabolic adjustments following hyperosmotic shock in the yeast Saccharomyces cerevisiae. Topics in Current Genet 2008, 20:141-158.
13. Vincent O, Townley R, Kuchin S, Carlson M. Subcellular localization of the Snf1 kinase is regulated by specific β subunits and a novel glucose signaling mechanism. Genes and Dev 2001, 15:1104-1114. 10.1101/gad.879301, 312685, 11331606.
14. Schneper L, Duvel K, Broach JR. Sense and sensibility: nutritional response and signal integration in yeast. Curr Opin Microbiol 2004, 7:624-630. 10.1016/j.mib.2004.10.002, 15556035.
15. Capaldi AP, Kaplan T, Liu Y, Habib N, Regev A, Friedman N, O'Shea EK. Structure and function of a transcriptional network activated by the MAPK Hog1. Nat Genet 2008, 40:1300-1306. 10.1038/ng.235, 2825711, 18931682.
16. Enjalbert B, Smith DA, Cornell MJ, Alam I, Nicholls S, Brown AJP, Quinn J. Role of the Hog1 Stress-activated Protein Kinase in the Global Transcriptional Response to Stress in the Fungal Pathogen Candida albicans. Molecular Biol Cell 2006, 17:1018-1032.
17. Lin N, Wu BL, Jansen R, Gerstein M, Zhao HY. Information assessment on predicting protein-protein interactions. BMC Bioinformatics 2004, 5:154. 10.1186/1471-2105-5-154, 529436, 15491499.
18. Cao JP, MA YC, Li YX, Shi TL. The application of the computational methods in protein-protein interaction study. Chinese Bulletin of Life Sci 2005, 17:82-87.
19. Uetz P, Giot L, Cagney G, Mansfield TA, Judson RS, Knight JR, 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, Rothberg JM. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 2000, 403:623-631. 10.1038/35001009, 10688190.
20. Ito T, Chiba T, Ozawa R, Yoshida M, Hattori M, Sakaki Y. A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc Natl acad Sci 2001, 98:4569-4574. 10.1073/pnas.061034498, 31875, 11283351.
21. Wang J, Li C, Wang E, Wang X. Uncovering the rules for protein-protein interactions from genomic data. Proc Natl Acad Sci 2009, 106:3752-3757. 10.1073/pnas.0806427106, 2656152, 19237561.
22. Beltrao P, Serrano L. Specificity and Evolvability in Eukaryotic Protein Interaction Networks. PLOS Comput Biol 2007, 3:e25. 10.1371/journal.pcbi.0030025, 1797819,1797819, 17305419.
23. Bader S, Kuhner S, Gavin AC. Interaction networks for system biology. FEBS Lett 2008, 582:1220-1224. 10.1016/j.febslet.2008.02.015, 18282471.
24. Wang B, Chen P, Huang DS, Li JJ, Lok TM, Lyu MR. Predicting protein interaction sites from residue spatial sequence profile and evlution rate. FEBS Lett 2006, 580:380-384. 10.1016/j.febslet.2005.11.081, 16376878.
25. Kie C, Beltrao P, Serrano L. Analyzing protein interaction networks using structural information. Annual Rev Biochem 2008, 77:415-441.
26. Li JJ, Huang DS, Wang B, Chen P. Identifying protein-protein interfacial residues in heterocomplexes using residue conservation scores. Int J Biol Macromol 2006, 38:241-247. 10.1016/j.ijbiomac.2006.02.024, 16600360.
27. Herrgård MJ, Swainston N, Dobson P, Dunn WB, Arga KY, Arvas M, Bluthgen N, Borger S, Costenoble R, Heinemann M, Hucka M, Novere NL, Li P, Liebermeister W, Mo ML, Oliveira AP, Petranovic D, Pettifer S, Simeonidis E, Smallbone K, Spasic I, Weichart D, Brent R, Broomhead DS, Westerhoff HV, Kirdar B, Penttila M, Klipp E, Palsson BO, Sauer U, Oliver SG, Mendes P, Nielsen J, Kell DB. A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology. Nature Biotechnol 2008, 26:1155-1160.
28. Monteiro PT, Mendes ND, Teixeira MC, d'Orey S, Tenreiro S, Mira NP, Pais H, Francisco AP, Carvalho AM, Lourenco AB, Sa-Correia I, Oliveira AL, Freitas AT. YEASTRACT-DISCOVERER: new tools to improve the analysis of transcriptional regulatory associations in Saccharomyces cerevisiae. Nucl Acids Res 2008, 36:D132-D136. 10.1093/nar/gkm976, 2238916, 18032429.
29. Ptacek J, Devgan G, Michaud G, Zhu H, Zhu X, Fasolo J, Guo H, Jona G, Breitkreutz A, Sopko R, McCartney RR, Schmidt MC, Rachidi N, Lee S-J, Mah AS, Meng L, Stark MJR, Stern DF, Virgilio CD, Tyers M, Andrews B, Gerstein M, Schweitzer B, Predki PF, Snyder M. Global analysis of protein phosphorylation in yeast. Nature 2005, 438:679-684. 10.1038/nature04187, 16319894.
30. Yu H, Braun P, Yildirim MA, Lemmens I, Venkatesan K, Sahalie J, Hirozane-Kishikawa T, Gebreab F, Li N, Simonis N, Hao T, Rual JF, Dricot A, Vazquez A, Murray RR, Simon C, Tardivo L, Tam S, Svrzikapa N, Fan C, Smet de A-S, Motyl A, Hudson ME, Park J, Xin X, Cusick ME, Moore T, Boone C, Snyder M, Roth FP, Barabasi A-L, Tavernier J, Hill DE, Vidal M. High-quality binary protein interaction map of the yeast interactome network. Science 2008, 322:104-110. 10.1126/science.1158684, 2746753, 18719252.
31. Collins SR, Kemmeren P, Zhao X-C, Greenblatt JF, Spencer F, Holstege FCP, Weissman JS, Krogan NJ. Toward a comprehensive atlas of the physical interactome of Saccharomyces cerevisiae. Mol Cell Proteomics 2007, 6:439-450.
32. Reguly T, Breitkreutz A, Boucher L, Breitkreutz BJ, Hon GC, Myers CL, Parsons A, Friesen H, Oughtred R, Tong A, Stark C, Ho Y, Botstein D, Andrews B, Boone C, Troyanskya OG, Idekar T, Dolinski K, Batada NN, Tyers M. Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae. J Biol 2006, 5:11. 10.1186/jbiol36, 1561585, 16762047.
33. Castrillo JI, Zeef LA, Hoyle DC, Zhang N, Hayes A, Gardner DCJ, Cornell MJ, Petty J, Hakes L, Wardleworth L, Rash B, Brown M, Dunn WB, Broadhurst D, O'Donoghue K, Hester SS, Dunkley TPJ, Hart SR, Swainston N, Li P, Gaskell SJ, Paton NW, Lilley KS, Kell DB, Oliver SG. Growth control of the eukaryote cell: a systems biology study in yeast. J Biol 2007, 6:4. 10.1186/jbiol54, 2373899, 17439666.
34. Brauer MJ, Huttenhower C, Airoldi EM, Rosenstein R, Matese JC, Gresham D, Boer VM, Troyanskaya OG, Botstein D. Coordination of Growth Rate, Cell Cycle, Stress Response, and Metabolic Activity in Yeast. Mol Biol Cell 2008, 19:352-367. 10.1091/mbc.E07-08-0779, 2174172, 17959824.
35. Stark C, Breitkreutz BJ, Reguly T, Boucher L, Breitkreutz A, Tyers M. BioGRID: a general repository for interaction datasets. Nucleic Acids Res 2006, 34:D535-D539. 10.1093/nar/gkj109, 1347471, 16381927.
36. Patil KR, Nielsen J. Uncovering transcriptional regulation of metabolism by using metabolic network topology. PNAS 2005, 22:2685-2689.
37. Ideker T, Thorsson V, Ranish JA, Christmas R, Buhlar J, Eng JK, Burngarner R, Goodlett DR, Aebersold R, Hood L. Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science 2001, 292:929-934. 10.1126/science.292.5518.929, 11340206.
38. R: A language and environment for statistical computing. , http://www.R-project.org
39. Bolstad BM, Irizarry RA, Åstrand M, Speed TP. A comparison of Normalization Methods for High Density Oligonucleotides Array Data Based on Bias and Variance. Bioinformatics 2003, 19:185-193. 10.1093/bioinformatics/19.2.185, 12538238.
40. Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, Scherf U, Speed TP. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 2003, 4:249-264. 10.1093/biostatistics/4.2.249, 12925520.
41. Gautier L, Cope L, Bolstad BM, Irizarry RA. affy---analysis of Affymetrix GeneChip data at the probe level. Bioinformatics 2004, 20:307-315. 10.1093/bioinformatics/btg405, 14960456.
42. Smyth GK. Limma: linear models for microarray data. Bioinformatics and Computational Biology Solutions using R and Bioconductor 2005, 397-420. Springer, New York, Gentleman R, Carey V, Dudoit S, Irizarry R, Huber W.
43. Wettenhall JM, Simpson KM, Satterley K, Smyth GK. affylmGUI: a graphical user interface for linear modeling of single channel microarray data. 2006, 22:897-899.
44. Schäfer J, Strimmer K. An empirical Bayes approach to inferring large-scale gene association networks. Bioinformatics 2004, 21:754-764. 10.1093/bioinformatics/bti062, 15479708.
45. Smyth GK. Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Statistical Appl Genetics and Molecular Biol 2004, 3:3.