Dynamics of gene expression revealed by comparison of serial analysis of gene expression transcript profiles from yeast grown on two different carbon sources

Molecular Biology of the Cell

Volumn 10, Issue 6, 1999, Pages 1859-1872

  Kal, Arnoud J ^a,e   Van Zonneveld, Anton Jan ^a,f   Benes, Vladimir ^b   Van Den Berg, Marlene ^a   Koerkamp, Marian Groot ^a   Albermann, Kaj ^c   Strack, Normann ^c   Ruijter, Jan M ^a   Richter, Alexandra ^b   Dujon, Bernard ^d   Ansorge, Wilhelm ^b   Tabak, Henk F ^a  

^a UNIVERSITY OF AMSTERDAM   (Netherlands)

^b EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

^c MAX PLANCK INSTITUTE OF BIOCHEMISTRY   (Germany)

^d INSTITUT PASTEUR   (France)

^e IMPERIAL CANCER RESEARCH FUND   (United Kingdom)

^f CRUCELL HOLLAND BV   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

CARBON; MESSENGER RNA; TRANSCRIPTION FACTOR;

ARTICLE; FATTY ACID OXIDATION; GENE EXPRESSION REGULATION; GENE INDUCTION; NONHUMAN; OXIDATION REDUCTION REACTION; PRIORITY JOURNAL; PROTEIN EXPRESSION; RNA ANALYSIS; STATISTICAL ANALYSIS; STRAIN DIFFERENCE; YEAST;

EUKARYOTA; SALVIA;

EID: 0032979731     PISSN: 10591524     EISSN: None     Source Type: Journal    
DOI: 10.1091/mbc.10.6.1859     Document Type: Article

References (44)

1. Alber, T., and Kawasaki, G. (1982). Nucleotide sequence of the triose phosphate isomerase gene of Saccharomyces cerevisiae. J. Mol. Appl. Genet. 1, 419-434.
2. Albertini, M., Rehling, P., Erdmann, R., Girzalsky, W., Kiel, J.A.K.W., Veenhuis, M., and Kunau, W.H. (1997). Pex14p, a peroxisomal membrane protein binding both receptors of the two PTS-dependent import pathways. Cell 89, 83-92.
3. Altman, D.G. (1991). Practical Statistics for Medical Research, London: Chapman-Hall, 162-163.
4. Armitage, P., and Berry, G. (1987). Statistical Methods in Medical Research, Oxford: Blackwell Scientific Publications, 179-185.
5. Audic, S., and Claverie, J.M. (1997). The significance of digital gene expression profiles. Genome Res. 7, 986-995.
6. Cho, R.J., et al. (1998). A genome-wide transcriptional analysis of the mitotic cell cycle. Mol. Cell 2, 65-73.
7. De Duve, C. (1984). A Guided Tour of the Living Cell, New York: Scientific American Books, W.H. Freeman.
8. DeRisi, J.L., Iyer, V.R., and Brown, P.O. (1997). Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 278, 680-686.
9. de Vries, S., and Marres, C.A. (1987). The mitochondrial respiratory chain of yeast. Structure and biosynthesis and the role in cellular metabolism. Biochim. Biophys. Acta 895, 205-239.
10. Einerhand, A.W., Voorn-Brouwer, T.M., Erdmann, R., Kunau, W.H., and Tabak, H.F. (1991). Regulation of transcription of the gene coding for peroxisomal 3-oxoacyl-CoA thiolase of Saccharomyces cerevisiae. Eur. J. Biochem. 200, 113-122.
11. Elgersma, Y., Kwast, L., Klein, A., Voorn-Brouwer, T., van den Berg, M., Metzig, B., America, T., Tabak, H.F., and Distel, B. (1996). The SH3 domain of the Saccharomyces cerevisiae peroxisomal membrane protein Pex13p functions as a docking site for Pex5p, a mobile receptor for the import PTS1-containing proteins. J. Cell Biol. 135, 97-109.
12. Elgersma, Y., and Tabak, H.F. (1996). Proteins involved in peroxisome biogenesis and functioning. Biochim. Biophys. Acta 1286, 269-283.
13. Erdmann, R., and Blobel, G. (1995). Giant peroxisomes in oleic acid-induced Saccharomyces cerevisiae lacking the peroxisomal membrane protein Pmp27p. J. Cell Biol. 128, 509-523.
14. Erdmann, R., and Blobel, G. (1996). Identification of Pex13p a peroxisomal membrane receptor for the PTS1 recognition factor. J. Cell Biol. 135, 111-121.
15. Erfle, H., Ventzki, R., Voss, H., Rechmann, S., Benes, V., Stegemann, J., and Ansorge, W. (1997). Simultaneous loading of 200 sample lanes for DNA sequencing on vertical and horizontal, standard and ultrathin gels. Nucleic Acids Res. 25, 2229-2230.
16. Goffeau, A.E.A. (1997). The yeast genome directory. Nature 387S, 5-105.
17. Gould, S.J., Kalish, J.E., Morrell, J.C., Bjorkman, J., Urquhart, A.J., and Crane, D.I. (1996). Pex13p is an SH3 protein of the peroxisome membrane and a docking factor for the predominantly cytoplasmic PTS1 receptor. J. Cell Biol. 135, 85-95.
18. Gurvitz, A., Rottensteiner, H., Kilpelainen, S.H., Hartig, A., Hiltunen, J.K., Binder, M., Dawes, I.W., and 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.
19. Henke, B., Girzalsky, W., Berteaux-Lecellier, V., and Erdmann, R. (1998). IDP3 encodes a peroxisomal NADP-dependent isocitrate dehydrogenase required for the beta-oxidation of unsaturated fatty acids. J. Biol. Chem. 273, 3702-3711.
20. Holstege, F.C.P., Jennings, E.G., Wyrick, J.J., Lee, T.I., Hengarter, C.J., Green, M.R., Golub, T.R., Lander, E.S., and Young, R.A. (1998). Dissecting the regulatory circuitry of a eukaryotic genome. Cell 95, 717-728.
21. Jones, E.W. (1977). Proteinase mutants of Saccharomyces cerevisiae. Genetics 85, 23-33.
22. Kal, A.J. (1997). Transcriptional Regulation of Genes Encoding Peroxisomal Proteins in Saccharomyces cerevisiae, Ph.D. thesis, University of Amsterdam, Academic Medical Center.
23. Karpichev, I.V., Luo, Y., Marians, R.C., and Small, G.M. (1997). A complex containing two transcription factors regulates peroxisome proliferation and the coordinate induction of beta-oxidation enzymes in Saccharomyces cerevisiae. Mol. Cell. Biol. 17, 69-80.
24. Karpichev, I.V., and Small, G.M. (1998). Global regulatory functions of Oaflp and Pip2p (Oaf2p), transcription factors that regulate genes encoding peroxisomal proteins in Saccharomyces cerevisiae. Mol. Cell. Biol. 18, 6560-6570.
25. Kunau, W.H., Buhne, S., de la Garza, M., Kionka, C., Mateblowski, M., Schultz-Borchard, U., and Thieringer, R. (1988). Comparative enzymology of beta-oxidation. Biochem. Soc. Trans. 16, 418-420.
26. Larsson, C., Påhlman, I.-L., Ansell, R., Rigoulet, M., Adler, L., and Gustafsson, L. (1998). The importance of the glycerol 3-phosphate shuttle during aerobic growth of Saccharomyces cerevisiae. Yeast 14, 347-357.
27. Luo, Y., Karpichev, I.V., Kohanski, R., and Small, G.M. (1996). Purification, identification, and properties of a Saccharomyces cerevisiae oleate-activated upstream activating sequence-binding protein that is involved in the activation of. POX1, J. Biol. Chem. 271, 12068-12075.
28. Madden, S.L., Galella, E.A., Zhu, J.S., Bertelsen, A.H., and Beaudry, G.A. (1997). SAGE transcript profiles for p53-dependent growth regulation. Oncogene 15, 1079-1085.
29. Mager, W.H., Planta, R.J., Ballesta, J.-P.G., Lee, J.C., Mizuta, K., Suzuki, K., Warner, J.R., and Woolford, J. (1997). A new nomenclature for the cytoplasmic ribosomal proteins of Saccharomyces cerevisiae. Nucleic Acids Res. 25, 4872-4875.
30. Mewes, H.W., Albermann, K., Heumann, K., Liebl, S., and Pfeiffer, F. (1997). MIPS - a database for protein sequences, homology data and yeast genome information. Nucleic Acids Res. 25, 28-30.
31. Passreiter, M., Anton, M., Lay, D., Frank, R., Harter, C., Wieland, F.T., Gorgas, K., and Just, W.W. (1998). Peroxisome biogenesis -involvement of Arf and coatomer. J. Cell Biol. 141, 373-383.
32. Ronnow, B., and Kielland-Brandt, M.C. (1993). GUT2, a gene for mitochondrial glycerol 3-phosphate dehydrogenase of Saccharomyces cerevisiae. Yeast 9, 1121-1130.
33. Rottensteiner, H., Kal, A.J., Filipits, M., Binder, M., Hamilton, B., Tabak, H.F., and Ruis, H. (1996). Pip2p: a transcriptional regulator of peroxisome proliferation in the yeast Saccharomyces cerevisiae. EMBO J. 15, 2924-2934.
34. Rottensteiner, H., Kal, A.J., Hamilton, B., Ruis, H., and Tabak, H.F. (1997). A heterodimer of the Zn(2)Cys(6) transcription factors Pip2p and Oaf1p controls induction of genes encoding peroxisomal proteins in Saccharcmyces cerevisiae. Eur. J. Biochem. 247, 776-783.
35. Tabak, H.F., Elgersma, Y., Hettema, E., Franse, M.M., Voorn-Brouwer, T., and Distel, B. (1995). Transport of proteins and metabolites across the impermeable membrane of peroxisomes. Cold Spring Harb. Symp. Quant. Biol. 60, 649-655.
36. van Roermund, C.W., Elgersma, Y., Singh, N., Wanders, R.J., and Tabak, H.F. (1995). The membrane of peroxisomes in Saccharomyces cerevisiae is impermeable to NAD(H) and acetyl-CoA under in vivo conditions. EMBO J. 14, 3480-3486.
37. van Roermund, C.W.T., Hettema, E.H., Kal, A.J., van den Berg, M., Tabak, H.F., and Wanders, R.J.A. (1998). Peroxisomal beta-oxidation of polyunsaturated fatty acids in Saccharomyces cerevisiae: isocitrate dehydrogenase provides NADPH for reduction of double bonds at even positions. EMBO J. 17, 677-687.
38. Veenhuis, M., Mateblowski, M., Kunau, W.H., and Harder, W. (1987). Proliferation of microbodies in Saccharomyces cerevisiae. Yeast 3, 77-84.
39. Velculescu, V.E., Zhang, L., Vogelstein, B., and Kinzler, K.W. (1995). Serial analysis of gene expression. Science 270, 484-487.
40. Velculescu, V.E., Zhang, L., Zhou, W., Vogelstein, J., Basrai, M.A., Bassett, D.E., Jr., Hieter, P., Vogelstein, B., and Kinzler, K.W. (1997). Characterization of the yeast transcriptome. Cell 88, 243-251.
41. Wiemann, S., Stegemann, J., Grothues, D., Bosch, A., Estivill, X., Schwager, C., Zimmermann, J., Voss, H., and Ansorge, W. (1995). Simultaneous on-line DNA sequencing on both strands with two fluorescent dyes. Anal. Biochem. 224, 117-121.
42. Williamson, V.M., Bennetzen, J., Young, E.T., Nasmyth, K., and Hall, B.D. (1980). Isolation of the structural gene for alcohol dehydrogenase by genetic complementation in yeast. Nature 283, 214-216.
43. Wodicka, L., Dong, H.L., Mittmann, M., Ho, M.H., and Lockhart, D.J. (1997). Genome-wide expression monitoring in Saccharomyces cerevisiae. Nat. Biotech. 15, 1359-1367.
44. Zhang, L., Zhou, W., Velculescu, V.E., Kern, S.E., Hruban, R.H., Hamilton, S.R., Vogelstein, B., and Kinzler, K.W. (1997). Gene expression profiles in normal and cancer cells. Science 276, 1268-1272.