Expression and functional profiling reveal distinct gene classes involved in fatty acid metabolism

Molecular Systems Biology

Volumn 2, Issue , 2006, Pages

  Smith, Jennifer J ^a   Sydorskyy, Yaroslav ^a   Marelli, Marcello ^a   Hwang, Daehee ^a   Bolouri, Hamid ^a   Rachubinski, Richard A ^b   Aitchison, John D ^a,b  

^a INSTITUTE FOR SYSTEMS BIOLOGY   (United States)

^b UNIVERSITY OF ALBERTA   (Canada)

Author keywords

Data integration; Fatty acid metabolism; Fitness data set; Myristate; Peroxisome biogenesis

Indexed keywords

FATTY ACID; MYRISTIC ACID; OLEIC ACID;

ARTICLE; CELL STRUCTURE; DATA ANALYSIS; FATTY ACID METABOLISM; GENE EXPRESSION PROFILING; GENE FUNCTION; GENE IDENTIFICATION; GENETIC ANALYSIS; GENOME ANALYSIS; METABOLIC REGULATION; NONHUMAN; PEROXISOME; PRIORITY JOURNAL; SACCHAROMYCES; STRUCTURE ANALYSIS; TRANSCRIPTION REGULATION;

FATTY ACIDS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, FUNGAL; GENES, FUNGAL; LIPID METABOLISM; MYRISTIC ACID; OLEIC ACID; TRANSCRIPTION, GENETIC; YEASTS;

EID: 33745437465     PISSN: 17444292     EISSN: 17444292     Source Type: Journal    
DOI: 10.1038/msb4100051     Document Type: Article

References (26)

1. Begley TJ, Rosenbach AS, Ideker T, Samson LD (2004) Hot spots for modulating toxicity identified by genomic phenotyping and localization mapping. Mol Cell 16: 117-125
2. Birrell GW, Brown JA, Wu HI, Giaever G, Chu AM, Davis RW, Brown JM (2002) Transcriptional response of Saccharomyces cerevisiae to DNA-damaging agents does not identify the genes that protect against these agents. Proc Natl Acad Sci USA 99: 8778-8783
3. Bowman AW, Azzalini A (1997) Applied Smoothing Techniques for Data Analysis. Oxford University Press: Oxford
4. Fagarasanu M, Fagarasanu A, Tam YY, Aitchison JD, Rachubinski RA (2005) Inp1p is a peroxisomal membrane protein required for peroxisome inheritance in Saccharomyces cerevisiae. J Cell Biol 169: 765-775
5. Forster J, Famili I, Fu P, Palsson BO, Nielsen J (2003) Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network. Genome Res 13: 244-253
6. Giaever G, Chu AM, Ni L, Connelly C, Riles L, Veronneau S, Dow S, Lucau-Danila A, Anderson K, Andre B, Arkin AP, Astromoff A, El-Bakkoury M, Bangham R, Benito R, Brachat S, Campanaro S, Curtiss M, Davis K, Deutschbauer A, Entian KD, Flaherty P, Foury F, Garfinkel DJ, Gerstein M, Gotte D, Guldener U, Hegemann JH, Hempel S, Herman Z, Jaramillo DF, Kelly DE, Kelly SL, Kotter P, LaBonte D, Lamb DC, Lan N, Liang H, Liao H, Liu L, Luo C, Lussier M, Mao R, Menard P, Ooi SL, Revuelta JL, Roberts CJ, Rose M, Ross-Macdonald P, Scherens B, Schimmack G, Shafer B, Shoemaker DD, Sookhai-Mahadeo S, Storms RK, Strathern JN, Valle G, Voet M, Volckaert G, Wang CY, Ward TR, Wilhelmy J, Winzeler EA, Yang Y, Yen G, Youngman E, Yu K, Bussey H, Boeke JD, Snyder M, Philippsen P, Davis RW, Johnston M (2002) Functional profiling of the Saccharomyces cerevisiae genome. Nature 418: 387-391
7. Gimeno CJ, Ljungdahl PO, Styles CA, Fink GR (1992) Unipolar cell divisions in the yeast S. cerevisiae lead to filamentous growth: regulation by starvation and RAS. Cell 68: 1077-1090
8. Gurvitz A, Rottensteiner H, Kilpelainen SH, Hartig A, Hiltunen JK, Binder M, Dawes IW, Hamilton B (1997) The Saccharomyces cerevisiae peroxisomal 2,4-dienoyl-CoA reductase is encoded by the oleate-inducible gene SPS19. J Biol Chem 272: 22140-22147
9. Harbison CT, Gordon DB, Lee TI, Rinaldi NJ, Macisaac KD, Danford TW, Hannett NM, Tagne JB, Reynolds DB, Yoo J, Jennings EG, Zeitlinger J, Pokholok DK, Kellis M, Rolfe PA, Takusagawa KT, Lander ES, Gifford DK, Fraenkel E, Young RA (2004) Transcriptional regulatory code of a eukaryotic genome. Nature 431: 99-104
10. Hedges L, Olkin I (1985) Statistical Method for Meta-analysis. San Diego, CA: Academic Press
11. Hiltunen JK, Mursula AM, Rottensteiner H, Wierenga RK, Kastaniotis AJ, Gurvitz A (2003) The biochemistry of peroxisomal beta-oxidation in the yeast Saccharomyces cerevisiae. FEMS Microbiol Rev 27: 35-64
12. Hoepfner D, van den Berg M, Philippsen P, Tabak HF, Hettema EH (2001) A role for Vpslp, actin, and the Myo2p motor in peroxisome abundance and inheritance in Saccharomyces cerevisiae. J Cell Biol 155: 979-990
13. Huh WK, Falvo JV, Gerke LC, Carroll AS, Howson RW, Weissman JS, O'Shea EK (2003) Global analysis of protein localization in budding yeast. Nature 425: 686-691
14. Igamberdiev AU, Lea PJ (2002) The role of peroxisomes in the integration of metabolism and evolutionary diversity of photosynthetic organisms. Phytochemistry 60: 651-674
15. Kiel JA, Emmrich K, Meyer HE, Kunau WH (2005) Ubiquitination of the peroxisomal targeting signal type 1 receptor, Pex5p, suggests the presence of a quality control mechanism during peroxisomal matrix protein import. J Biol Chem 280: 1921-1930
16. Koerkamp MG, Rep M, Bussemaker HJ, Hardy GP, Mul A, Piekarska K, Szigyarto CA, De Mattos JM, Tabak HF (2002) Dissection of transient oxidative stress response in Saccharomyces cerevisiae by using DNA microarrays. Mol Biol Cell 13: 2783-2794
17. Kragt A, Voorn-Brouwer T, van den Berg M, Distel B (2005) The Saccharomyces cerevisiae peroxisomal import receptor Pex5p is monoubiquitinated in wild type cells. J Biol Chem 280: 7867-7874
18. Marelli M, Smith JJ, Jung S, Yi E, Nesvizhskii AI, Christmas RH, Saleem RA, Tam YY, Fagarasanu A, Goodlett DR, Aebersold R, Rachubinski RA, Aitchison JD (2004) Quantitative mass spectrometry reveals a role for the GTPase Rho1p in actin organization on the peroxisome membrane. J Cell Biol 167: 1099-1112
19. Prinz S, Avila-Campillo I, Aldridge C, Srinivasan A, Dimitrov K, Siegel AF, Galitski T (2004) Control of yeast filamentous-form growth by modules in an integrated molecular network. Genome Res 14: 380-390
20. Purdue PE, Lazarow PB (2001) Pex18p is constitutively degraded during peroxisome biogenesis. J Biol Chem 276: 47684-47689
21. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13: 2498-2504
22. Smith JJ, Marelli M, Christmas RH, Vizeacoumar FJ, Dilworth DJ, Ideker T, Galitski T, Dimitrov K, Rachubinski RA, Aitchison JD (2002) Transcriptome profiling to identify genes involved in peroxisome assembly and function. J Cell Biol 158: 259-271
23. Tabak HF, Murk JL, Braakman I, Geuze HJ (2003) Peroxisomes start their life in the endoplasmic reticulum. Traffic 4: 512-518
24. Titorenko VI, Eitzen GA, Rachubinski RA (1996) Mutations in the PAYS gene of the yeast Yarrowia lipolytica cause the accumulation of multiple subpopulations of peroxisomes. J Biol Chem 271: 20307-20314
25. Titorenko VI, Rachubinski RA (2001) The life cycle of the peroxisome. Nat Rev Mol Cell Biol 2: 357-368
26. Titorenko VI, Rachubinski RA (2004) The peroxisome: orchestrating important developmental decisions from inside the cell. J Cell Biol 164: 641-645