Dynamic transcriptional and metabolic responses in yeast adapting to temperature stress.
Understanding the response processes in cellular systems to external perturbations is a central goal of large-scale molecular profiling experiments. We investigated the molecular response of yeast to increased and lowered temperatures relative to optimal reference conditions across two levels of molecular organization: the transcriptome using a whole yeast genome microarray and the metabolome applying the gas chromatography/mass spectrometry (GC/MS) technology with in vivo stable-isotope labeling for accurate relative quantification of a total of 50 different metabolites. The molecular adaptation of yeast to increased or lowered temperatures relative control conditions at both the metabolic and transcriptional level is dominated by temperature-inverted differential regulation patterns of transcriptional and metabolite responses and the temporal response observed to be biphasic. The set of previously described general environmental stress response (ESR) genes showed particularly strong temperature-inverted response patterns. Among the metabolites measured, trehalose was detected to respond strongest to the temperature stress and with temperature-inverted up- and downregulation relative to control, midtemperature conditions. Although associated with the same principal environmental parameter, the two different temperature regimes caused very distinct molecular response patterns at both the metabolite and the transcript level. While pairwise correlations between different transcripts and between different metabolites were found generally preserved under the various conditions, substantial differences were also observed indicative of changed underlying network architectures or modified regulatory relationships. Gene and associated gene functions were identified that are differentially regulated specifically under the gradual stress induction applied here compared to abrupt stress exposure investigated in previous studies, including genes of as of yet unidentified function and genes involved in protein synthesis and energy metabolism.
Strassburg
Katrin
K
Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany.
Walther
Dirk
D
Takahashi
Hiroki
H
Kanaya
Shigehiko
S
Kopka
Joachim
J
D000064:Acclimatization / Q000502:physiology*; D025341:Principal Component Analysis; D012441:Saccharomyces cerevisiae / Q000378:metabolism / Q000502:physiology*; D013312:Stress, Physiological; D013696:Temperature; D014158:Transcription, Genetic
Anal Biochem. 1992 Jul;204(1):118-23
1514678
Nat Biotechnol. 2000 Nov;18(11):1157-61
11062433
Methods Mol Biol. 2007;358:19-38
17035678
Nat Biotechnol. 2008 Oct;26(10):1155-60
18846089
Mol Cell. 2004 Mar 26;13(6):771-81
15053871
Biotechnol Bioeng. 2004 Mar 20;85(6):620-8
14966803
FEMS Yeast Res. 2008 Sep;8(6):829-38
18625028
Phytochemistry. 2007 Aug-Sep;68(16-18):2258-72
17475294
Trends Biotechnol. 2005 Jan;23(1):28-33
15629855
PLoS Comput Biol. 2009 Jan;5(1):e1000270
19180179
Genetics. 1986 May;113(1):35-43
3519363
J Biol Chem. 2002 Dec 20;277(51):50015-21
12379644
Mol Syst Biol. 2006;2:49
16969341
J Biochem. 2003 Sep;134(3):373-84
14561723
Yeast. 1997 Nov;13(14):1347-55
9392079
Mol Biol Cell. 2001 Feb;12(2):323-37
11179418
Science. 2007 Apr 27;316(5824):550-1
17463274
FEMS Microbiol Rev. 2000 Oct;24(4):469-86
10978547
Nature. 2004 Sep 16;431(7006):308-12
15372033
Bioinformatics. 2008 Mar 1;24(5):732-7
18204057
Mol Biol Cell. 2004 Dec;15(12):5492-502
15483057
Bioinformatics. 2005 Apr 15;21(8):1635-8
15613389
OMICS. 2010 Jun;14(3):261-74
20455750
Comp Funct Genomics. 2003;4(4):366-75
18629074
Genome Biol. 2003;4(10):R70
14519205
Mol Biol Cell. 2000 Dec;11(12):4241-57
11102521
Anal Biochem. 2005 Jan 15;336(2):164-71
15620880
Yeast. 1998 Jan 30;14(2):115-32
9483801