Chemostat-Based Micro-Array Analysis in Baker's Yeast

Advances in Microbial Physiology

Volumn 54, Issue , 2008, Pages

  Daran Lapujade, Pascale ^a   Daran, Jean Marc ^a   van Maris, Antonius J A ^a   de Winde, Johannes H ^a   Pronk, Jack T ^a  

^a DELFT UNIVERSITY OF TECHNOLOGY   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; TRANSCRIPTOME;

CELL FUNCTION; CHEMOSTAT; ENVIRONMENTAL STRESS; FUNGUS CULTURE; FUNGUS GROWTH; GENE FUNCTION; GROWTH RATE; HIGH THROUGHPUT SCREENING; METABOLOMICS; MICROARRAY ANALYSIS; NONHUMAN; NUCLEOTIDE SEQUENCE; PROTEIN FUNCTION; PROTEOMICS; REVIEW; SACCHAROMYCES CEREVISIAE; STEADY STATE; TRANSCRIPTION REGULATION;

SACCHAROMYCES CEREVISIAE;

EID: 53149102498     PISSN: 00652911     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S0065-2911(08)00004-0     Document Type: Review

References (174)

1. Abbott D.A., Knijnenburg T.A., de Poorter L.M.I., Reinders M.J.T., Pronk J.T., and van Maris A.J.A. Generic and specific transcriptional responses to different weak organic acids in anaerobic chemostat cultures of Saccharomyces cerevisiae. FEMS Yeast Res. 7 (2007) 819-833
2. Adams J., Paquin C., Oeller P.W., and Lee L.W. Physiological characterization of adaptive clones in evolving populations of the yeast, Saccharomyces cerevisiae. Genetics 110 (1985) 173-185
3. Aguilera J., Petit T., de Winde J.H., and Pronk J.T. Physiological and genome-wide transcriptional responses of Saccharomyces cerevisiae to high carbon dioxide concentrations. FEMS Yeast Res. 5 (2005) 579-593
4. Aguilera J., van Dijken J.P., de Winde J.H., and Pronk J.T. Carbonic anhydrase (Nce103p): an essential biosynthetic enzyme for growth of Saccharomyces cerevisiae at atmospheric carbon dioxide pressure. Biochem. J. 391 (2005) 311-316
5. Andreasen A.A., and Stier T.J.B. Anaerobic nutrition of Saccharomyces cerevisiae, I. Ergosterol requirement for growth in a defined medium. J. Cell. Comp. Physiol. 41 (1953) 23-36
6. Andreasen A.A., and Stier T.J.B. Anaerobic nutrition of Saccharomyces cerevisiae, II. Unsaturated fatty acid requirement for growth in a defined medium. J. Cell Comp. Physiol. 43 (1954) 271-281
7. Baganz F., Hayes A., Farquhar R., Butler P.R., Gardner D.C.J., and Oliver S.G. Quantitative analysis of yeast gene function using competition experiments in continuous culture. Yeast 14 (1998) 1417-1427
8. Baganz F., Hayes A., Marren D., Gardner D.C., and Oliver S.G. Suitability of replacement markers for functional analysis studies in Saccharomyces cerevisiae. Yeast 13 (1997) 1563-1573
9. Bailey J.E., Sburlati A., Hatzimanikatis V., Lee K., Renner W.A., and Tsai P.S. Inverse metabolic engineering: a strategy for directed genetic engineering of useful phenotypes. Biotechnol. Bioeng. 79 (2002) 568-579
10. Bakker B.M., Mensonides F.I.C., Teusink B., van Hoek P., Michels P.A.M., and Westerhoff H.V. Compartmentation protects trypanosomes from the dangerous design of glycolysis. Proc. Natl. Acad. Sci. U.S.A. 97 (2000) 2087-2092
11. Bammler T., Beyer R.P., Bhattacharya S., Boorman G.A., Boyles A., Bradford B.U., Bumgarner R.E., Bushel P.R., Chaturvedi K., Choi D., Cunningham M.L., Deng S., Dressman H.K., Fannin R.D., Farin F.M., Freedman J.H., Fry R.C., Harper A., Humble M.C., Hurban P., Kavanagh T.J., Kaufmann W.K., Kerr K.F., Jing L., Lapidus J.A., Lasarev M.R., Li J., Li Y.J., Lobenhofer E.K., Lu X., Malek R.L., Milton S., Nagalla S.R., O'malley J.P., Palmer V.S., Pattee P., Paules R.S., Perou C.M., Phillips K., Qin L.X., Qiu Y., Quigley S.D., Rodland M., Rusyn I., Samson L.D., Schwartz D.A., Shi Y., Shin J.L., Sieber S.O., Slifer S., Speer M.C., Spencer P.S., Sproles D.I., Swenberg J.A., Suk W.A., Sullivan R.C., Tian R., Tennant R.W., Todd S.A., Tucker C.J., Van Houten B., Weis B.K., Xuan S., and Zarbl H. Standardizing global gene expression analysis between laboratories and across platforms. Nat. Methods 2 (2005) 351-356
12. Barford J.P., and Hall R.J. An examination of the Crabtree effect in Saccharomyces cerevisiae: the role of respiratory adaptation. J. Gen. Microbiol. 114 (1979) 267-275
13. Barnett J.A., Payne R.W., and Yarrow D. Yeasts: Characteristics and Identification (1983), Cambridge University Press, Cambridge
14. Baugh L.R., Hill A.A., and Hunter C.P. Quantitative analysis of mRNA amplification by in vitro transcription. Nucleic Acids Res. 29 (2001) e29
15. Birrell G.W., Brown J.A., Wu H.I., Giaever G., Chu A.M., Davis R.W., and Brown J.M. Transcriptional response of Saccharomyces cerevisiae to DNA-damaging agents does not identify the genes that protect against these agents. Proc. Natl. Acad. Sci. U.S.A. 99 (2002) 8778-8783
16. Boer V.M., Daran J.M., Almering M.J.H., de Winde J.H., and Pronk J.T. Contribution of the Saccharomyces cerevisiae transcriptional regulator Leu3p to physiology and gene expression in nitrogen- and carbon-limited chemostat cultures. FEMS Yeast Res. 5 (2005) 885-897
17. Boer V.M., de Winde J.H., Pronk J.T., and Piper M.D.W. The genome-wide transcriptional responses of Saccharomyces cerevisiae grown on glucose in aerobic chemostat cultures limited for carbon, nitrogen, phosphorus or sulfur. J. Biol. Chem. 278 (2003) 3265-3274
18. Boer V.M., Tai S.L., Vuralhan Z., Arifin Y., Walsh M.C., Piper M.D.W., de Winde J.H., Pronk J.T., and Daran J.M. Transcriptional responses of Saccharomyces cerevisiae to preferred and nonpreferred nitrogen sources in glucose-limited chemostat cultures. FEMS Yeast Res. 7 (2007) 604-620
19. Bowtell D.D. Options available from start to finish for obtaining expression data by microarray. Nat. Genet. 21 (1999) 25-32
20. Brauer M.J., Saldanha A.J., Dolinski K., and Botstein D. Homeostatic adjustment and metabolic remodeling in glucose-limited yeast cultures. Mol. Biol. Cell 16 (2005) 2503-2517
21. Bro C., and Nielsen J. Impact of '-ome' analyses on inverse metabolic engineering. Metab. Eng. 6 (2004) 204-211
22. Bro C., Regenberg B., Lagniel G., Labarre J., Montero-Lomelí M., and Nielsen J. Transcriptional, proteomic, and metabolic responses to lithium in galactose-grown yeast cells. J. Biol. Chem. 278 (2003) 32141-32149
23. Bruckmann A., Steensma H.Y., de Mattos M.J.T., and van Heusden G.P.H. Regulation of transcription by Saccharomyces cerevisiae 14-3-3 proteins. Biochem. J. 382 (2004) 867-875
24. Butler P.R., Brown M., and Oliver S.G. Improvement of antibiotic titers from Streptomyces bacteria by interactive continuous selection. Biotechnol. Bioeng. 49 (1996) 185-196
25. Button D.K. Biochemical basis for whole-cell uptake kinetics: specific affinity, oligotrophic capacity, and the meaning of the michaelis constant. Appl. Environ. Microbiol. 57 (1991) 2033-2038
26. Cakar Z.P., Sauer U., and Bailey J.E. Metabolic engineering of yeast: the perils of auxotrophic hosts. Biotechnol. Lett. 21 (1999) 611-616
27. Cakar Z.P., Seker U.O.S., Tamerler C., Sonderegger M., and Sauer U. Evolutionary engineering of multiple-stress resistant Saccharomyces cerevisiae. FEMS Yeast Res. 5 (2005) 569-578
28. Castrillo J.O., and Oliver S.G. Yeast as a touchstone in post-genomic research: strategies for integrative analysis in functional genomics. J. Biochem. Mol. Biol. 37 (2004) 93-106
29. Castrillo J., Zeef L., Hoyle D., Zhang N., Hayes A., Gardner D., Cornell M., Petty J., Hakes L., Wardleworth L., Rash B., Brown M., Dunn W., Broadhurst D., O'Donoghue K., Hester S., Dunkley T., Hart S., Swainston N., Li P., Gaskell S., Paton N., Lilley K., Kell D., and Oliver S. Growth control of the eukaryote cell: a systems biology study in yeast. J. Biol. 6 (2007) 4
30. Causton H.C., Ren B., Koh S.S., Harbison C.T., Kanin E., Jennings E.G., Lee T.I., True H.L., Lander E.S., and Young R.A. Remodeling of yeast genome expression in response to environmental changes. Mol. Biol. Cell 12 (2001) 323-337
31. Chen G.A., Gharib T.G., Huang C.C., Taylor J.M.G., Misek D.E., Kardia S.L.R., Giordano T.J., Iannettoni M.D., Orringer M.B., Hanash S.M., and Beer D.G. Discordant protein and mRNA expression in lung adenocarcinomas. Mol. Cell Proteomics 1 (2002) 304-313
32. Cipollina C., van den Brink J., Daran-Lapujade P., Pronk J.T., Vai M., and de Winde J.H. Revisiting the role of yeast Sfp1 in ribosome biogenesis and cell size control: a chemostat study. Microbiology 154 (2008) 337-346
33. Cliften P., Sudarsanam P., Desikan A., Fulton L., Majors B., Waaterston R., Cohen B.A., and Johnston M. Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301 (2003) 71-76
34. Dalma-Weiszhausz D.D., Warrington J., Tanimoto E.Y., and Miyada C.G. The affymetrix GeneChip platform: an overview. Meth. Enzymol. 410 (2006) 3-28
35. Daran-Lapujade P., Jansen M.L.A., Daran J.M., van Gulik W., de Winde J.H., and Pronk J.T. Role of transcriptional regulation in controlling fluxes in central carbon metabolism of Saccharomyces cerevisiae, a chemostat culture study. J. Biol. Chem. 278 (2004) 3265-3274
36. Daran-Lapujade P., Rossell S., van Gulik W.M., Luttik M.A.H., de Groot M.J.L., Slijper M., Heck A.J.R., Daran J.M., de Winde J.H., Westerhoff H.V., Pronk J.T., and Bakker B.M. The fluxes through glycolytic enzymes in S. cerevisiae are predominantly regulated at post-transcriptional level. Proc. Natl. Acad. Sci. U.S.A. 104 (2007) 15753-15758
37. David L., Huber W., Granovskaia M., Toedling J., Palm C.J., Bofkin L., Jones T., Davis R.W., and Steinmetz L.M. A high-resolution map of transcription in the yeast genome. Proc. Natl. Acad. Sci. U.S.A. 103 (2006) 5320-5325
38. de Groot M.J.L., Daran-Lapujade P., van Breukelen B., Knijnenburg T.H., Pronk J.T., Slijper M., and Heck A.J.R. Quantitative proteomics and transcriptomics of anaerobic and aerobic yeast cultures reveals post-transcriptional regulation of key cellular processes. Microbiology 153 (2007) 3864-3878
39. de Nicola R., Hazelwood L.A., Hulster E.A.F., Walsh M.C., Knijnenburg T.A., Reinders M.J.T., Walker G.M., Daran J.M., and Daran-Lapujade P. Physiological and transcriptional responses of Saccharomyces cerevisiae to zinc limitation in chemostat cultures. Appl. Environ. Microbiol. 73 (2007) 7680-7692
40. DeRisi J.L., Iyer V.R., and Brown P.O. Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 278 (1997) 680-686
41. Dickinson J.R., Salgado L.E., and Hewlins M.J. The catabolism of amino acids to long chain and complex alcohols in Saccharomyces cerevisiae. J. Biol. Chem. 278 (2003) 8028-8034
42. Diderich J.A., Schepper M.E., van Hoek P., Luttik M.A.H., van Dijken J.P., Pronk J.T., Klaasen P., Teixeira de Mattos J.M., van Dam K., and Kruckeberg A.L. Glucose uptake kinetics and transcription of HXT genes in chemostat cultures of Saccharomyces cerevisiae. J. Biol. Chem. 274 (1999) 15350-15359
43. Dykhuizen D.E., and Hartl D.L. Selection in chemostats. Microbiol. Rev. 47 (1983) 150-168
44. Ehrlich F. Uber die Bedingungen der Fuselolbildung and uber ihren Zusammenhang mit dem Eiweissaufbau der Hefe. Ber. Deut. Chem. Gesellsch. 40 (1907) 1027-1047
45. Ferea T.L., Botstein D., Brown P.O., and Rosenzweig R.F. Systematic changes in gene expression patterns following adaptive evolution in yeast. Proc. Natl. Acad. Sci. U.S.A. 96 (1999) 9721-9726
46. Flikweert M.T., de Swaaf M., van Dijken J.P., and Pronk J.T. Growth requirements of pyruvate-decarboxylase-negative Saccharomyces cerevisiae. FEMS Microbiol. Lett. 174 (1999) 73-79
47. Flikweert M.T., van der Zanden L., Janssen W.M.T.M., Steensma H.Y., van Dijken J.P., and Pronk J.T. Pyruvate decarboxylase: an indispensable enzyme for growth of Saccharomyces cerevisiae on glucose. Yeast 12 (1996) 247-257
48. Förster J., Famili I., Fu P., Palsson B.Ø., and Nielsen J. Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network. Genome Res. 13 (2003) 244-253
49. Friden P., and Schimmel P. LEU3 of Saccharomyces cerevisiae encodes a factor for control of RNA levels of a group of leucine-specific genes. Mol. Cell. Biol. 7 (1987) 2708-2717
50. Gancedo J.M. Yeast carbon catabolite repression. Microbiol. Mol. Biol. Rev. 62 (1998) 334-361
51. Gasch A.P., Spellman P.T., Kao C.M., Carmel-Harel O., Eisen M.B., Storz G., Botstein D., and Brown P.O. Genomic expression programs in the response of yeast cells to environmental changes. Mol. Biol. Cell 11 (2000) 4241-4257
52. Gasch A.P., and Werner-Washburne M. The genomics of yeast responses to environmental stress and starvation. Funct. Integr. Genomics 2 (2002) 181-192
53. Giaever G., Chu A.M., Ni L., Connelly C., Riles L., Véronneau S., Dow S., Lucau-Danila A., Anderson K., Andre B., Arkin A.P., Astromoff A., El Bakkoury M., Bangham R., Benito R., Brachat S., Campanaro S., Curtiss M., Davis K., Deutschbauer A., Entian K.D., Flaherty P., Foury F., Garfinkel D.J., Gerstein M., Gotte D., Güldener U., Hegemann J.H., Hempel S., Herman Z., Jaramillo D.F., Kelly D.E., Kelly S.L., Kötter P., LaBonte D., Lamb D.C., Lan N., Liang H., Liao H., Liu L., Luo C., Lussier M., Mao R., Menard P., Ooi S.L., Revuelta J.L., Roberts C.J., Rose M., Ross-Macdonald P., Scherens B., Schimmack G., Shafer B., Shoemaker D.D., Sookhai-Mahadeo S., Storms R.K., Strathern J.N., Valle G., Voet M., Volckaert G., Wang C.Y., Ward T.R., Wilhelmy J., Winzeler E.A., Yang Y., Yen G., Youngman E., Yu K., Bussey H., Boeke J.D., Snyder M., Philippsen P., Davis R.W., and Johnston M. Functional profiling of the Saccharomyces cerevisiae genome. Nature 418 (2002) 387-391
54. Goffeau A., Barrell B.G., Bussey H., Davis R.W., Dujon B., Feldmann H., Galibert F., Hoheisel J.D., Jacq C., Johnston M., Louis E.J., Mewes H.W., Murakami Y., Phillippsen P., Tettelin H., and Oliver S.G. Life with 6000 genes. Science 274 (1996) 563-567
55. Greenbaum D., Colangelo C., Williams K., and Gerstein M. Comparing protein abundance and mRNA expression levels on a genomic scale. Genome Biol. 4 (2003) 117.1-117.8
56. Gresham D., Ruderfer D.M., Pratt S.C., Schacherer J., Dunham M.J., Botstein D., and Kruglyak L. Genome-wide detection of polymorphisms at nucleotide resolution with a single DNA microarray. Science 311 (2006) 1932-1936
57. Gress T.M., Hoheisel J.D., Lennon G.G., Zehetner G., and Lehrach H. Hybridization fingerprinting of high-density cDNA-library arrays with cDNA pools derived from whole tissues. Mammalian Genome 3 (1992) 609-619
58. Griffin T.J., Gygi S.P., Ideker T., Rist B., Eng J., Hood L., and Aebersold R. Complementary profiling of gene expression at the transcriptome and proteome levels in Saccharomyces cerevisiae. Mol. Cell Proteomics 1 (2002) 323-333
59. Gu Z., Steinmetz L.M., Gu X., Scharfe C., Davis R.W., and Li W.H. Role of duplicate genes in genetic robustness against null mutations. Nature 421 (2003) 63-66
60. Gygi S.P., Rochon Y., Franza B.R., and Aebersold R. Correlation between protein and mRNA abundance in yeast. Mol. Cell. Biol. 19 (1999) 1720-1730
61. Harbison C.T., Gordon D.B., Lee T.I., Rinaldi N.J., Macisaac K.D., Danford T.W., Hannett N.M., Tagne J.B., Reynolds D.B., Yoo J., Jennings E.G., Zeitlinger J., Pokholok D.K., Kellis M., Rolfe P.A., Takusagawa K.T., Lander E.S., Gifford D.K., Fraenkel E., and Young R.A. Transcriptional regulatory code of a eukaryotic genome. Nature 431 (2004) 99-104
62. Harder W., Kuenen J.G., and Matin A. Microbial selection in continuous culture. J. Appl. Bacteriol. 43 (1977) 1-24
63. Hauser N.C., Vingron M., Scheideler M., Krems B., Hellmuth K., Entian K.D., and Hoheisel J.D. Transcriptional profiling on all open reading frames of Saccharomyces cerevisiae. Yeast 14 (1998) 1209-1221
64. Hayes A., Zhang N., Wu J., Butler P.R., Hauser N.C., Hoheisel J.D., Lim F.L., Sharrocks A.D., and Oliver S.G. Hybridization array technology coupled with chemostat culture: Tools to interrogate gene expression in Saccharomyces cerevisiae. Methods 26 (2002) 281-290
65. Hazelwood L.A., Tai S.L., Boer V.M., de Winde J.H., Pronk J.T., and Daran J.M. A new physiological role for Pdr12p in Saccharomyces cerevisiae: Export of aromatic and branched-chain organic acids produced in amino acid catabolism. FEMS Yeast Res. 6 (2006) 937-945
66. Hess D.C., Lu W.Y., Rabinowitz J.D., and Botstein D. Ammonium toxicity and potassium limitation in yeast. Plos. Biology 4 (2006) 2012-2023
67. Ho N.W.Y., Chen Z.D., and Brainard A.P. Genetically engineered Sacccharomyces yeast capable of effective cofermentation of glucose and xylose. Appl. Environ. Microbiol. 64 (1998) 1852-1859
68. Holstege F.C., Jennings E.G., Wyrick J.J., Lee T.I., Hengartner C.J., Green M.R., Golub T.R., Lander E.S., and Young R.A. Dissecting the regulatory circuitry of a eukaryotic genome. Cell 95 (1998) 717-728
69. Holyoak C.D., Bracey D., Piper P.W., Kuchler K., and Coote P.J. The Saccharomyces cerevisiae weak-acid-inducible ABC transporter Pdr12 transports fluorescein and preservative anions from the cytosol by an energy dependent mechanism. J. Bacteriol. 181 (1999) 4644-4652
70. Hoskisson P.A., and Hobbs G. Continuous culture-making a comeback?. Microbiology 151 (2005) 3153-3159
71. Ideker T., Thorsson V., Ranish J.A., Christmas R., Buhler J., Eng J.K., Bumgarner R., Goodlett D.R., Aebersold R., and Hood L. Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science 292 (2001) 929-934
72. Jansen M.L.A., Daran-Lapujade P., de Winde J.H., Piper M.D.W., and Pronk J.T. Prolonged maltose-limited cultivation of Saccharomyces cerevisiae selects for cells with improved maltose affinity and hypersensitivity. Appl. Environ. Microbiol. 70 (2004) 1956-1963
73. Jansen M.L.A., Diderich J.A., Mashego M.R., Hassane A., de Winde J.H., Daran-Lapujade P., and Pronk J.T. Prolonged selection in aerobic, glucose-limited chemostat cultures of Saccharomyces cerevisiae causes a partial loss of glycolytic capacity. Microbiology 151 (2005) 1657-1669
74. Järvinen A.K., Hautaniemi S., Edgren H., Auvinen P., Saarela J., Kallioniemi O.P., and Monni O. Are data from different gene expression microarray platforms comparable?. Genomics 83 (2004) 1164-1168
75. Jorgensen P., Rupes I., Sharom J.R., Schneper L., Broach J.R., and Tyers M. A dynamic transcriptional network communicates growth potential to ribosome synthesis and critical cell size. Genes Dev. 18 (2004) 2491-2505
76. Juneau K., Palm C., Miranda M., and Davis R.W. High-density yeast-tiling array reveals previously undiscovered introns and extensive regulation of meiotic splicing. Proc. Natl. Acad. Sci. U.S.A. 104 (2007) 1522-1527
77. Karhumaa K., Hähn-Hagerdal B., and Gorwa-Grauslund M.F. Investigation of limiting metabolic steps in the utilization of xylose by recombinant Saccharomyces cerevisiae using metabolic engineering. Yeast 22 (2005) 359-368
78. Kasemets K., Drews M., Nisamedtinov I., Adamberg K., and Paalme T. Modification of A-stat for the characterization of microorganisms. J. Microbiol. Methods 55 (2003) 187-200
79. Kellis M., Patterson N., Endrizzi M., Birren B., and Lander E.S. Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423 (2003) 241-254
80. Kirkpatrick C.R., and Schimmel P. Detection of leucine-independent DNA site occupancy of the yeast Leu3p transcriptional activator in vivo. Mol. Cell. Biol. 15 (1995) 4021-4030
81. Klevecz R.R., and Murray D.B. Genome wide oscillations in expression-wavelet analysis of time series data from yeast expression arrays uncovers the dynamic architecture of phenotype. Mol. Biol. Rep. 28 (2001) 73-82
82. Knijnenburg T.A., de Winde J.H., Daran J.M., Daran-Lapujade P., Pronk J.T., Reinders M.J.T., and Wessels L.F.A. Exploiting combinatorial cultivation conditions to infer transcriptional regulation. BMC Genomics 8 (2007) 25
83. Koerkamp M.G., Rep M., Bussemaker H.J., Hardy G.P.M.A., Mul A., Piekarska K., Szigyarto C.A., de Mattos J.M.T., and Tabak H.F. Dissection of transient oxidative stress response in Saccharomyces cerevisiae by using DNA microarrays. Mol. Biol. Cell 13 (2002) 2783-2794
84. Kolkman A., Daran-Lapujade P., Fullaondo A., Olsthoorn M.M.A., Pronk J.T., Slijper M., and Heck A.J.R. Proteome analysis of yeast response to various nutrient limitations. Mol. Syst. Biol. 2 (2006) 2006
85. Kraakman L.S., Griffioen G., Zerp S., Groeneveld P., Thevelein J.M., Mager W.H., and Planta R.J. Growth-related expression of ribosomal protein genes in Saccharomyces cerevisiae. Mol. Syst. Biol. 239 (1993) 196-204
86. Kresnowati M.T.A.P., van Winden W.A., Almering M.J.H., ten Pierick A., Ras C., Knijnenburg T.A., Daran-Lapujade P., Pronk J.T., Heijnen J.J., and Daran J.M. When transcriptome meets metabolome: fast cellular responses of yeast to sudden relief of glucose limitation. Mol. Syst. Biol. 2 (2006) 49
87. Kroczek R.A. Southern and Northern analysis. J. Chromatogr. B, Biomed. Appl. 618 (1993) 133-145
88. Kuenen J.G., Beudeker R.F., Shively J.M., and Codd G.A. Microbiology of thiobacilli and other sulfur-oxidizing autotrophs, mixotrophs and heterotrophs. Philos. Trans. R. Soc. Lond., B, Biol. Sci. 298 (1982) 473-497
89. Kurowski W.M., and Pirt S.J. Growth dynamics of Agrobacterium tumefaciens in chemostat cultures limited by carbon source and mineral nutrients. Arch. Microbiol. 104 (1975) 197-199
90. Kuyper M., Hartog M.M.P., Toirkens M.J., Almering M.J.H., Winkler A.A., van Dijken J.P., and Pronk J.T. Metabolic engineering of a xylose-isomerase-expressing Saccharomyces cerevisiae strain for rapid anaerobic xylose fermentation. FEMS Yeast Res. 5 (2005) 399-409
91. Kuyper M., Toirkens M.J., Diderich J.A., Winkler A.A., van Dijken J.P., and Pronk J.T. Evolutionary engineering of mixed-sugar utilization by a xylose-fermenting Saccharomyces cerevisiae strain. FEMS Yeast Res. 5 (2005) 925-934
92. Lange H.C., and Heijnen J.J. Statistical reconciliation of the elemental and molecular biomass composition of Saccharomyces cerevisiae. Biotechnol. Bioeng. 75 (2001) 334-344
93. Larsson C., von Stockar U., Marison I., and Gustafsson L. Growth and metabolism of Saccharomyces cerevisiae in chemostat cultures under carbon-, nitrogen-, or carbon- and nitrogen-limiting conditions. J. Bacteriol. 175 (1993) 4809-4816
94. Lashkari D.A., DeRisi J.L., McCusker J.H., Namath A.F., Gentile C., Hwang S.Y., Brown P.O., and Davis R.W. Yeast microarrays for genome wide parallel genetic and gene expression analysis. Proc. Natl. Acad. Sci. U.S.A. 94 (1997) 13057-13062
95. Lee T.I., Rinaldi N.J., Robert F., Odom D.T., Bar-Joseph Z., Gerber G.K., Hannett N.M., Harbison C.T., Thompson C.M., Simon I., Zeitlinger J., Jennings E.G., Murray H.L., Gordon D.B., Ren B., Wyrick J.J., Tagne J.B., Volkert T.L., Fraenkel E., Gifford D.K., and Young R.A. Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298 (2002) 799-804
96. Li C.M., and Klevecz R.R. A rapid genome-scale response of the transcriptional oscillator to perturbation reveals a period-doubling path to phenotypic change. Proc. Natl. Acad. Sci. U.S.A. 103 (2006) 16254-16259
97. Magasanik B., and Kaiser C.A. Nitrogen regulation in Saccharomyces cerevisiae. Gene 290 (2002) 1-18
98. Mager W.H., and Planta R.J. Coordinate expression of ribosomal protein genes in yeast as a function of cellular growth rate. Mol. Cell. Biochem. 104 (1991) 181-187
99. Mashego M.R., Jansen M.L., Vinke J.L., van Gulik W.M., and Heijnen J.J. Changes in the metabolome of Saccharomyces cerevisiae associated with evolution in aerobic glucose-limited chemostats. FEMS Yeast Res. 5 (2005) 419-430
100. Mashego M.R., van Gulik W.M., Vinke J.L., and Heijnen J.J. Critical evaluation of sampling techniques for residual glucose determination in carbon-limited chemostat culture of Saccharomyces cerevisiae. Biotechnol. Bioeng. 83 (2003) 395-399
101. Monod J. Recherche sur la croissance des cultures bactériennes (1942), Hermann et Cie, Paris
102. Monod J. The Growth of Bacterial Cultures. Annu. Rev. Microbiol. 3 (1949) 371-394
103. Monod J. La technique de culture continue theorie et applications. Annales de l'Institut Pasteur 79 (1950) 390-410
104. Murata Y., Homma T., Kitagawa E., Momose Y., Sato M.S., Odani M., Shimizu H., Hasegawa-Mizusawa M., Matsumoto R., Mizukami S., Fujita K., Parveen M., Komatsu Y., and Iwahashi H. Genome-wide expression analysis of yeast response during exposure to 4 degrees C. Extremophiles 10 (2006) 117-128
105. Negre N., Lavrov S., Hennetin J., Bellis M., and Cavalli G. Mapping the distribution of chromatin proteins by ChIP on chip. Meth. Enzymol. 410 (2006) 316-341
106. Nielsen J., and Olsson L. An expanded role for microbial physiology in metabolic engineering and functional genomics: moving towards sytems biology. FEMS Yeast Res. 2 (2002) 175-181
107. Noorman H.J., Baksteen J., Heijnen J.J., and Luyben K.C.A.M. The bioreactor overflow device: an undesired selective separator in continuous cultures. J. Gen. Microbiol. 137 (1991) 2171-2177
108. Novick A. Bacteria with high levels of specific enzymes. In: Zarrow M.X. (Ed). Growth in living systems - Proceedings of the Purdue Growth Symposium (1961), Basic Books, NY 93-106
109. Novick A., and Szilard L. Description of the chemostat. Science 112 (1950) 715-716
110. Novick A., and Szilard L. Experiments with the chemostat on spontaneous mutations of bacteria. Proc. Natl. Acad. Sci. U.S.A. 36 (1950) 708-719
111. Paalme T., Elken R., Kahru A., Vanatalu K., and Vilu R. The growth rate control in Escherichia coli at near to maximum growth rates: the A-stat approach. Antonie van Leeuwenhoek 71 (1997) 217-230
112. Peña-Castillo L., and Hughes T.R. Why are there still over 1000 uncharacterized yeast genes?. Genetics 176 (2007) 7-14
113. Petersson A., Almeida J.R.M., Modig T., Karhumaa K., Hähn-Hagerdal B., Gorwa-Grauslund M.F., and Lidén G. A 5-hydroxymethyl furfural reducing enzyme encoded by the Saccharomyces cerevisiae ADH6 gene conveys HMF tolerance. Yeast 23 (2006) 455-464
114. Piper M.D.W., Daran-Lapujade P., Bro C., Regenberg B., Knudsen S., Nielsen J., and Pronk J.T. Reproducibility of oligonucleotide microarray transcriptome analyses: an interlaboratory comparison using chemostat cultures of Saccharomyces cerevsiae. J. Biol. Chem. 277 (2002) 37001-37008
115. Pirt S.J. Maintenance energy: a general model for energy-limited and energy-sufficient growth. Arch. Microbiol. 133 (1982) 300-302
116. Planta R.J., and Mager W.H. The list of cytoplasmic ribosomal proteins of Saccharomyces cerevisiae. Yeast 14 (1998) 471-477
117. Postma E., Kuiper A., Tomasouw W.F., Scheffers W.A., and van Dijken J.P. Competition for glucose between the yeasts Saccharomyces cerevisiae and Candida utilis. Appl. Environ. Microbiol. 55 (1989) 3214-3220
118. Postma E., Verduyn C., Scheffers W.A., and van Dijken J.P. Enzymic analysis of the crabtree effect in glucose-limited chemostat cultures of Saccharomyces cerevisiae. Appl. Environ. Microbiol. 55 (1989) 468-477
119. Pratt J.M., Petty J., Riba-Garcia I., Robertson D.H.L., Gaskell S.J., Oliver S.G., and Beynon R.J. Dynamics of protein turnover, a missing dimension in proteomics. Mol. Cell Proteomics 1 (2002) 579-591
120. Pronk J.T. Auxotrophic yeast strains in fundamental and applied research. Appl. Environ. Microbiol. 68 (2002) 2095-2100
121. Raghevendran V., Patil K.R., Olsson L., and Nielsen J. Hap4 is not essential for activation of respiration at low specific growth rates in Saccharomyces cerevisiae. J. Biol. Chem. 281 (2006) 12308-12314
122. Regenberg B., Grotkjaer T., Winther O., Fausbøll A., Bro C., Åkesson M., Hansen L.K., Brunak S., and Nielsen J. Growth-rate regulated genes on chromosomes and around replication origins in Saccharomyces cerevisiae. Genome Biol. 7 (2006) R107
123. Rieger M., Käppeli O., and Fiechter A. The role of limited respiration in the incomplete oxidation of glucose by Saccharomyces cerevisiae. J. Gen. Microbiol. 129 (1983) 653-661
124. Ronen M., and Botstein D. Transcriptional response of steady-state yeast cultures to transient perturbations in carbon source. Proc. Natl. Acad. Sci. U.S.A. 103 (2006) 389-394
125. Rossell S., van der Weijden C.C., Kruckeberg A.L., Bakker B.M., and Westerhoff H.V. Hierarchical and metabolic regulation of glucose influx in starved Saccharomyces cerevisiae. FEMS Yeast Res. 5 (2005) 611-619
126. Rossell S., van der Weijden C.C., Lindenbergh A., van Tuijl A., Francke C., Bakker B.M., and Westerhoff H.V. Unraveling the complexity of flux regulation: a new method demonstrated for nutrient starvation in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. U.S.A. 103 (2006) 2166-2171
127. Rouwenhorst R.J., van der Baan A.A., Scheffers W.A., and van Dijken J.P. Production and localization of beta-fructosidase in asynchronous and synchronous chemostat cultures of yeasts. Appl. Environ. Microbiol. 57 (1991) 557-562
128. Rudra D., Zhao Y., and Warner J.R. Central role of Ifh1p-Fhl1p interaction in the synthesis of yeast ribosomal proteins. EMBO J. 24 (2005) 533-542
129. Sahara T., Goda T., and Ohgiya S. Comprehensive expression analysis of time-dependent genetic responses in yeast cells to low temperature. J. Biol. Chem. 277 (2002) 50015-50021
130. Saldanha A.J., Brauer M.J., and Botstein D. Nutritional homeostasis in batch and steady-state cultures of yeast. Mol. Biol. Cell 15 (2004) 4089-4104
131. Salusjarvi L., Pitkänen J.P., Aristidou A., Ruohonen L., and Penttila M. Transcription analysis of recombinant Saccharomyces cerevisiae reveals novel responses to xylose. Appl. Biochem. Biotechnol. 128 (2006) 237-261
132. Sauer U. Evolutionary engineering of industrially important microbial phenotypes. Adv. Biochem. Eng. Biotechnol. 73 (2001) 130-169
133. Schade B., Jansen G., Whiteway M., Entian K.D., and Thomas D.Y. Cold adaptation in budding yeast. Mol. Biol. Cell 15 (2004) 5492-5502
134. Sherman F. Getting started with yeast. Meth. Enzymol. 194 (1991) 3-21
135. Shoemaker D.D., Lashkari D.A., Morris D., Mittmann M., and Davis R.W. Quantitative phenotypic analysis of yeast deletion mutants using a highly parallel molecular bar-coding strategy. Nat. Genet. 14 (1996) 450-456
136. Smith J.J., Ramsey S.A., Marelli M., Marzolf B., Hwang D., Saleem R.A., Rachubinski R.A., and Aitchison J.D. Transcriptional responses to fatty acid are coordinated by combinatorial control. Mol. Syst. Biol. 3 (2007) 115
137. Sonderegger M., and Sauer U. Evolutionary engineering of Saccharomyces cerevisiae for anaerobic growth on xylose. Appl. Environ. Microbiol. 69 (2003) 1990-1998
138. Stouthamer A.H. A theoretical study on the amount of ATP required for synthesis of microbial cell material. Antonie van Leeuwenhoek 39 (1973) 545-565
139. Stückrath I., Lange H.C., Kötter P., van Gulik W.M., Entian K.D., and Heijnen J.J. Characterization of null mutants of the glyoxylate cycle and gluconeogenic enzymes in S. cerevisiae through metabolic network modeling verified by chemostat cultivation. Biotechnol. Bioeng. 77 (2002) 61-72
140. Tai S.L., Boer V.M., Daran-Lapujade P., Walsh M.C., de Winde J.H., Daran J.M., and Pronk J.T. Two-dimensional transcriptome analysis in chemostat cultures: combinatorial effects of oxygen availability and macronutrient limitation in Saccharomyces cerevisiae. J. Biol. Chem. 280 (2005) 437-447
141. Tai S.L., Daran-Lapujade P., Luttik M.A.H., Walsh M.C., Diderich J.A., Krijger G.C., van Gulik W.M., Pronk J.T., and Daran J.M. Control of the glycolytic flux in Saccharomyces cerevisiae grown at low temperature: a multi-level analysis in anaerobic chemostat cultures. J. Biol. Chem. 282 (2007) 10243-10251
142. Tai S.L., Daran-Lapujade P., Walsh M.C., Pronk J.T., Daran J.M., Pronk J.T., and Daran J.M. Acclimation of Saccharomyces cerevisiae to low temperature: a chemostat-based transcriptome analysis. Mol. Biol. Cell 18 (2007) 5100-5112
143. Tai S.L., Snoek I., Luttik M.A.H., Almering M.J.H., Walsh M.C., Pronk J.T., and Daran J.M. Correlation between transcript profiles and fitness of deletion mutants in anaerobic chemostat cultures of Saccharomyces cerevisiae. Microbiology 153 (2007) 877-886
144. Tan P.K., Downey T.J., Spitznagel Jr. E.L., Xu P., Fu D., Dimitrov D.S., Lempicki R.A., Raaka B.M., and Cam M.C. Evaluation of gene expression measurements from commercial microarray platforms. Nucleic Acids Res. 31 (2003) 5676-5684
145. ter Kuile B.H., and Westerhoff H.V. Transcriptome meets metabolome: hierarchical and metabolic regulation of the glycolytic pathway. FEBS Lett. 500 (2001) 169-171
146. ter Linde J.J.M., and Steensma H.Y. A microarray-assisted screen for potential Hap1 and Rox1 target genes in Saccharomyces cerevisiae. Yeast 19 (2002) 825-840
147. ter Linde J.J.M., Liang H., Davis R.W., Steensma H.Y., van Dijken J.P., and Pronk J.T. Genome-wide transcriptional analysis of aerobic and anaerobic chemostat cultures of Saccharomyces cerevisiae. J. Bacteriol. 181 (1999) 7409-7413
148. ter Schure E.G., Sillje H.H., Vermeulen E.E., Kalhorn J.W., Verkleij A.J., Boonstra J., and Verrips C.T. Repression of nitrogen catabolic genes by ammonia and glutamine in nitrogen-limited continuous cultures of Saccharomyces cerevisiae. Microbiology 144 (1998) 1451-1462
149. Theobald U., Mailinger W., Baltes M., Rizzi M., and Reuss M. In vivo analysis of metabolic dynamics in Saccharomyces cerevisiae: I. experimental observations. Biotechnol. Bioeng. 55 (1997) 305-316
150. Ulbricht R.J., Northup S.J., and Thomas J.A. A review of 5-hydroxymethylfurfural (HMF) in parenteral solutions. Fundam. Appl.
151. Usaite R., Patil K.R., Grotkjaer T., Nielsen J., and Regenberg B. Global transcriptional and physiological responses of Saccharomyces cerevisiae to ammonium, L-alanine, or L-glutamine limitation. Appl. Environ. Microbiol. 72 (2006) 6194-6203
152. van de Peppel J., Kemmeren P., van Bakel H., Radonjić M., van Leenen D., and Holstege F.C.P. Monitoring global messenger RNA changes in externally controlled microarray experiments. EMBO Rep. 4 (2003) 387-393
153. van Dijken J.P., Bauer J., Brambilla L., Duboc P., François J.M., Gancedo C., Giuseppin M.L.F., Heijnen J.J., Hoare M., Lange H.C., Madden E.A., Niederberger P., Nielsen J., Parrou J.L., Petit T., Porro D., Reuss M., van Riel N., Rizzi M., Steensma H.Y., Verrips C.T., Vindeløv J., and Pronk J.T. An interlaboratory comparison of physiological and genetic properties of four Saccharomyces cerevisiae strains. Enzyme Microb. Technol. 26 (2000) 706-714
154. van Dijken J.P., Weusthuis R.A., and Pronk J.T. Kinetics of growth and sugar consumption in yeasts. Antonie van Leeuwenhoek 63 (1993) 343-352
155. van Kleeff B.H.A., Kuenen J.G., and Heijnen J.J. Heat flux measurements for the fast monitoring of dynamic responses to glucose additions by yeasts that were subjected to different feeding regimes in continuous culture. Biotechnol. Prog. 12 (1996) 510-518
156. 2-independent, glucose-tolerant and pyruvate-hyperproducing yeast. Appl. Environ. Microbiol. 70 (2004) 159-166
157. van Maris A.J.A., Konings W.N., van Dijken J.P., and Pronk J.T. Microbial export of lactic and 3-hydroxypropanoic acid: implications for industrial fermentation processes. Metab. Eng. 6 (2004) 245-255
158. van Maris A.J.A., Winkler A.A., Kuyper M., de Laat W.T.A.M., van Dijken J.P.., and Pronk J.T. Development of efficient xylose fermentation in Saccharomyces cerevisiae: xylose isomerase as a key component. Adv. Biochem. Eng. Biotechnol. 108 (2007) 179-204
159. van Verseveld H.W., Chesbro W.R., Braster M., and Stouthamer A.H. Eubacteria have 3 growth modes keyed to nutrient flow-Consequences for the concept of maintenance and maximal growth yield. Arch. Microbiol. 137 (1984) 176-184
160. Velculescu V.E., Zhang L., Vogelstein B., and Kinzler K.W. Serial analysis of gene expression. Science 270 (1995) 484-487
161. Visser W., Scheffers W.A., Batenburg-van der Vegte W.H., and van Dijken J.P. Oxygen requirements of yeasts. Appl. Environ. Microbiol. 56 (1990) 3785-3792
162. Vodovotz Y., Clermont G., Hunt C.A., Lefering R., Bartels J., Seydel R., Hotchkiss J., Ta'asan S., Neugebauer E., and An G. Evidence-based modeling of critical illness: an initial consensus from the Society for Complexity in Acute Illness. J. Crit. Care 22 (2007) 77-84
163. von Meyenburg K.H. Energetics of the budding cycle of Saccharomyces cerevisiae during glucose limited aerobic growth. Archiv für Mikrobiologie 66 (1969) 289-303
164. Vuralhan Z., Luttik M.A.H., Tai S.L., Boer V.M., Morais M.A., Schipper D., Almering M.J.H., Kötter P., Dickinson J.R., Daran J.M., and Pronk J.T. Physiological characterization of the ARO10-dependent, broad-substrate-specificity 2-oxo acid decarboxylase activity of Saccharomyces cerevisiae. Appl. Environ. Microbiol. 71 (2005) 3276-3284
165. Vuralhan Z., Morais M.A., Tai S.L., Piper M.D., and Pronk J.T. Identification and characterization of phenylpyruvate decarboxylase genes in Saccharomyces cerevisiae. Appl. Environ. Microbiol. 69 (2003) 4534-4541
166. Wade P.A., and Jaehning J.A. Transcriptional corepression in vitro: a Mot1p-associated form of TATA-binding protein is required for repression by Leu3p. Mol. Cell. Biol. 16 (1996) 1641-1648
167. Wahlbom C.F., Otero R.R.C., van Zyl W.H., Hähn-Hagerdal B., and Jonsson L.J. Molecular analysis of a Saccharomyces cerevisiae mutant with improved ability to utilize xylose shows enhanced expression of proteins involved in transport, initial xylose metabolism, and the pentose phosphate pathway. Appl. Environ. Microbiol. 69 (2003) 740-746
168. Watson J.D., and Crick F.H.C. Molecular structure of nucleic acids. Nature 171 (1953) 737-738
169. Weusthuis R.A., Pronk J.T., Vandenbroek P.J.A., and Vandijken J.P. Chemostat cultivation as a tool for studies on sugar-transport in yeasts. Microbiol. Rev. 58 (1994) 616-630
170. Winzeler E.A., Shoemaker D.D., Astromoff A., Liang H., Anderson K., Andre B., Bangham R., Benito R., Boeke J.D., Bussey H., Chu A.M., Connelly C., Davis K., Dietrich F., Whelen Dow S., El Bakkoury M., Foury F., Friend S.H., Gentalen E., Giaever G., Hegemann J.H., Jones T., Laub M., Liao H., Liebundguth N., Lockhart D.J., Lucau-Danila A., Lussier M., M'Rabet N., Menard P., Mittman M., Pai C., Rebischung C., Revuelta J.L., Riles L., Roberts C.J., Ross-MacDonald P., Scherens B., Snyder M., Sookhai-Mahadeo S., Storms R.K., Vorst O., Voet M., Volckaert G., Ward T.R., Wysocki R., Yen G.S., Yu K., Zimmermann K., Philippsen P., Johnston M., and Davis R.W. Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science 285 (1999) 901-906
171. Wittmann C., Hans M., van Winden W.A., Ras C., and Heijnen J.J. Dynamics of intracellular metabolites of glycolysis and TCA cycle during cell-cycle-related oscillation in Saccharomyces cerevisiae. Biotechnol. Bioeng. 89 (2005) 839-847
172. Wolber P.K., Collins P.J., Lucas A.B., De Witte A., and Shannon K.W. The Agilent in situ-synthesized microarray platform. Meth. Enzymol. 410 (2006) 28-57
173. Wu J., Zhang N.S., Hayes A., Panoutsopoulou K., and Oliver S.G. Global analysis of nutrient control of gene expression in Saccharomyces cerevisiae during growth and starvation. Proc. Natl. Acad. Sci. U.S.A. 101 (2004) 3148-3153
174. Zhang Z., Hesselberth J.R., and Fields S. Genome-wide identification of spliced introns using a tiling microarray. Genome Res. 17 (2007) 503-509