Cold Adaptation in Budding Yeast

Schade, Babette; Jansen, Gregor; Whiteway, Malcolm; Entian, Karl Dieter; Thomas, David Y.

doi:10.1091/mbc.e04-03-0167

Cited by 159 publications

(246 citation statements)

References 77 publications

Supporting

Mentioning

196

Contrasting

Unclassified

Order By: Relevance

“…A similar number of 2,592 (709) genes were cold responsive. Although under heat conditions most changes occurred early and appeared to be transient, cold adaptation showed a second phase of transcriptional responses consistent with previous reports (Schade et al, 2004).…”

Section: Transcript-level Changes In Response To Changing Temperaturessupporting

confidence: 91%

“…When exposed to increased or lowered temperatures, also microbial organisms such as yeast have evolved mechanisms enabling them to adapt immediately after temperature alterations. With the advent of whole genome microarray technology, the study of system-wide responses to environmental perturbations at the transcriptional level has become the main focus of stressresponse molecular biology including the response of yeast to temperature shock (Becerra et al, 2003;Causton et al, 2001;Gasch et al, 2000;Sahara et al, 2002;Sakaki et al, 2003;Schade et al, 2004). Although many genes were observed to alter their expression levels specifically to temperature stress conditions, a subset of genes and their associated transcripts were also found to be induced or repressed upon exposure to a wide range of other environmental perturbations (Causton et al, 2001;Gasch et al, 2000), suggesting the existence of specific and general stress-response mechanisms.…”

mentioning

confidence: 99%

See 1 more Smart Citation

Dynamic Transcriptional and Metabolic Responses in Yeast Adapting to Temperature Stress

Strassburg

Walther

Takahashi

et al. 2010

OMICS: A Journal of Integrative Biology

View full text Add to dashboard Cite

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.

show abstract

Section: Transcript-level Changes In Response To Changing Temperaturessupporting

confidence: 91%

mentioning

confidence: 99%

Dynamic Transcriptional and Metabolic Responses in Yeast Adapting to Temperature Stress

Strassburg

Walther

Takahashi

et al. 2010

OMICS: A Journal of Integrative Biology

View full text Add to dashboard Cite

show abstract

“…These functionally conserved proteins prevent protein aggregation and facilitate protein degradation or refolding (Schade et al, 2004). Among those, that were up-regulated, we found Tmelhsp30, Tmelhsp9 and Tmelhspa12a, while Tmelhsp90 and its co-chaperonines were down-regulated.…”

Section: Environmental Stress-responsive Genes Are Present In the Trumentioning

confidence: 79%

“…A number of HSPs are also induced when yeast cells are cultured at 4 °C for several months (Homma et al, 2003), suggesting that the induction of various HSPs might be needed to adjust and live at 4 °C. Schade et al (2004) found HSP genes expressed in late cold response (later than 12 h after exposure to low temperatures). Studies on adaptation to cold in batch cultures of S. cerevisiae revealed up-regulation of HSP26 and HSP42 at low temperatures ( Schade et al, 2004), while they were down-regulated in chemostat cultures (Tai et al, 2007).…”

Section: Environmental Stress-responsive Genes Are Present In the Trumentioning

confidence: 96%

“…Schade et al (2004) found HSP genes expressed in late cold response (later than 12 h after exposure to low temperatures). Studies on adaptation to cold in batch cultures of S. cerevisiae revealed up-regulation of HSP26 and HSP42 at low temperatures ( Schade et al, 2004), while they were down-regulated in chemostat cultures (Tai et al, 2007). Interestingly, the highest fold in qRT-PCR was found for the Tmelhsp9_1 gene (fold = 104,459), which belongs to the HSP9/12 family.…”

Section: Environmental Stress-responsive Genes Are Present In the Trumentioning

confidence: 96%

See 1 more Smart Citation

The Perigord black truffle responds to cold temperature with an extensive reprogramming of its transcriptional activity

Zampieri

Balestrini

Kohler

et al. 2011

Fungal Genetics and Biology

View full text Add to dashboard Cite

The Tuber melanosporum genome has been analysed with the aim of identifying and characterizing the genes involved in the environmental stress response. A whole genome array (7496 genes/probe) was used to verify the fungal transcriptional profiling upon a cold temperature period (7 days at 4 °C). A total of 423 genes resulted to be differentially expressed in a significant manner (>2.5-fold; p-value < 0.05) in the mycelia exposed to cold, compared to the control ones: 187 of these genes were up-regulated, while 236 were down-regulated. Sixty-six and fifty-one percent, respectively, of the up-or down-regulated transcripts had no KOG classification and were clustered as unclassified proteins, which was the most abundant category in the both up-and down-regulated genes. A gene subset, containing a range of biological functions, was chosen to validate the microarray experiment through quantitative real time PCR (qRT-PCR). The analysis confirmed the array data for 16 out of 22 of the considered genes, confirming that a cold temperature period influences the truffle global gene expression. The expressed genes, which mostly resulted to be genes for heat shock proteins (HSPs) and genes involved in cell wall and lipid metabolism, could be involved in mechanisms, which are responsible for fungal adaptation. Since truffle ascomata develop during the winter period, we hypothesize that these differentially expressed genes may help the truffle to adapt to low temperatures and/or perceive environmental signals that regulate the fructification.

show abstract

Gene expression profiles of vitrified in vivo derived 8‐cell stage mouse embryos detected by high density oligonucleotide microarrays

Mamo

Bodó

Kobolák

et al. 2006

Molecular Reproduction Devel

View full text Add to dashboard Cite

Very little is known about the effect of vitrification on gene functions after warming. The goals of our study were to compare the gene expression patterns, and identify those most affected. For this, 8-cell stage embryos were collected from ICR mice and vitrified with solid surface vitrification technique, while maintaining equal numbers of embryos as control. Total RNAs were extracted and two rounds of amplification were employed. Finally three micrograms of contrasting RNA samples were hybridized on the Agilent Mouse 22 K oligonucleotide slides and the results were analyzed with subsequent verification by independent real-time PCR analyses. The two rounds of amplification with 5 ng tRNA input have yielded 15-16 microg of cRNA. The analyses of repeated hybridizations showed 20,183 genes/ESTs as common signatures, and unsupervised analysis identified 628 differentially expressed (P < 0.01) genes. However, with at least 1.5-fold change considerations, 183 genes were differentially expressed (P < 0.01) out of which 107 were upregulated. The independent analysis with real-time PCR and unamplified samples fully confirmed the results of microarray, indicating the linearity of amplification. Furthermore, this novel gene expression study for vitrified embryos identified many new candidate genes with overrepresentation in some important biological processes. Thus, it is possible to conclude that the expression pattern reflected a broad spectrum of consequences of vitrification on embryos, with most effects on metabolism, regulatory role and stress response genes and allowed the identification of new candidate marker genes for cryosurvival.

show abstract

Cold Adaptation in Budding Yeast

Cited by 159 publications

References 77 publications

Dynamic Transcriptional and Metabolic Responses in Yeast Adapting to Temperature Stress

Dynamic Transcriptional and Metabolic Responses in Yeast Adapting to Temperature Stress

The Perigord black truffle responds to cold temperature with an extensive reprogramming of its transcriptional activity

Gene expression profiles of vitrified in vivo derived 8‐cell stage mouse embryos detected by high density oligonucleotide microarrays

Contact Info

Product

Resources

About