Comprehensive Expression Analysis of Time-dependent Genetic Responses in Yeast Cells to Low Temperature

Abstract

We performed genome-wide expression analysis to determine genetic responses in Saccharomyces cerevisiae to a low temperature environment using a cDNA microarray. Approximately 25% of the genes in the yeast genome were found to be involved in the response of yeast to low temperature. This finding of a large number of genes being involved in the response to low temperature enabled us to give a functional interpretation to the genetic responses to the stimulus. Functional and clustering analyses of temporal changes in gene expression revealed that global states of the expressions of up-regulated genes could be characterized as having three phases (the early, middle, and late phases). In each phase, genes related to rRNA synthesis, ribosomal proteins, or several stress responses are time-dependently up-regulated, respectively. Through these phases, yeast cells may improve reduced efficiency of translation and enhance cell protection mechanisms to survive under a low temperature condition. Furthermore, these time-dependent regulations of these genes would be controlled by the cAMP-protein kinase A pathway. The results of our study provide a global description of transcriptional response for adaptation to low temperature in yeast cells.Low temperatures are known to have several effects on biochemical and physiological properties in various cells (e.g. low efficiency of protein translation, low fluidity of cellular membrane, stabilization of double helix or secondary structure of DNA or RNA molecule, slow folding of protein, and decrease of enzymatic activities) (1-3). Most organisms would have developed adaptive mechanisms to cope with these phenomena. The mechanisms underlying low temperature-dependent gene expression and responses to low temperature have been studied in few organisms (4 -6).In prokaryotes, especially Escherichia coli, when cells grown at 37°C are exposed to a low temperature, such as 15°C, a set of proteins called cold shock proteins are transiently induced (7). CspA has been identified as a major cold shock protein (8) and has been suggested to act as an RNA chaperone to increase efficiency of translation under a low temperature condition (9). It has been reported that Bacillus and Synechococcus species increase synthesis and stability of desaturases, which catalyze unsaturation of fatty acids in the membrane phopholipids under a low temperature condition (4, 10). Induction of desaturases by low temperature has also been found in eukaryotic species, such as plants (5, 6), protozoan (12), dimorphic fungus (13), fish (14), and yeast (15). These findings suggest that cellular responses to low temperature, such as improvement of reduced translation and decreased membrane fluidity, and their mechanisms are common in various organisms.In yeast, Saccharomyces cerevisiae, several cold-inducible genes have been identified. NSR1, one of the cold-inducible genes, encodes a nucleolin-like protein related to rRNA processing and ribosomal biosynthesis (16 -18). TIP1 (temperatureinducible protein) and the other m...

Carbohydrate utilization and the lager yeast transcriptome during brewery fermentation

“…Technology is now available to determine the genome-wide transcriptional response of yeast to environmental changes and has been used to elucidate the transcriptional response to a number of brewery-relevant parameters, including, for example, availability of oxygen and anaerobiosis (Aguilera et al, 2005;Lai et al, 2005), ageing (Fabrizio et al, 2005;Laun et al, 2005), dehydration and hydration (Singh et al, 2005), ethanol toxicity (Alexandre et al, 2001;Caba et al, 2005;Fujita et al, 2006;van Voorst et al, 2006), glucose repression and diauxic shift (DeRisi et al, 1997;Griffin et al, 2002), nutrient limitation (Causton et al, 2001;Gasch et al, 2000), osmotic stress (Gasch et al, 2000), oxidative stress (Causton et al, 2001;Gasch et al, 2000;Koerkamp et al, 2002), pH (Causton et al, 2001), salt stress (Caba et al, 2005), sugar stress (Ando et al, 2006;Erasmus et al, 2003) and temperature change (Causton et al, 2001;Gasch et al, 2000;Homma et al, 2003;Sahara et al, 2002). However, very few studies have utilized production strains of yeast or have involved incubation in brewery wort (Smart, 2007).…”

The Donor Subsite of Trehalose-6-phosphate Synthase

“…Even in so-called "normal" organisms, trehalose synthesis is elevated under stress conditions (most recently reviewed in Ref. 1), including dehydration, stationary phase culture, salt-stress (5), heat-shock (2), high pressure (6), extreme cold (7), exposure to oxygen radicals (8,9), and anoxia (10).…”

Cryoprotection with L‐ and meso‐Trehalose: Stereochemical Implications

“…This preconditioning induces a systemic adaptive response and stimulates the production of a large assortment of proteins, including trehalose synthetase (Tps1, Tps2) and several temperature shock proteins, followed by the accumulation of intracellular trehalose. [22] It should be mentioned that the additional stabilization does not involve uptake of exogenous trehalose, as the cell survival rates were unaffected by the presence or absence of extracellular sugar during the precooling stage, prior to freezing (see Supporting Information).…”