Remodeling of Yeast Genome Expression in Response to Environmental Changes

Causton, Helen C.; Ren, Bing; Koh, Sang Seok; Harbison, Christopher; Kanin, Elenita I.; Jennings, Ezra G.; Lee, Tong Ihn; True, Heather L.; Lander, Eric S.; Young, Richard A.

doi:10.1091/mbc.12.2.323

Cited by 1,210 publications

(1,367 citation statements)

References 65 publications

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“…When cells are exposed to such stresses, the cells immediately suspend both transportation of mRNAs to the specific compartments by loss of actin polarization and production of proteins by shutdown of translation initiation. During the shutdown, the intracellular profile of mRNAs is dramatically changed in response to the stress (Gancedo, 1998;Causton et al, 2001). The shutdown of translation at the initiation but not the elongation level would increase the proportion of mRNAs that are not protected by the ribosome.…”

Section: Discussionmentioning

confidence: 99%

Simultaneous yet Independent Regulation of Actin Cytoskeletal Organization and Translation Initiation by Glucose inSaccharomyces cerevisiae

Uesono

Ashe

Toh‐e

2004

MBoC

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Acute glucose deprivation rapidly but transiently depolarizes the actin cytoskeleton and inhibits translation initiation in Saccharomyces cerevisiae. Neither rapid actin depolarization nor translation inhibition upon glucose removal occurs in a reg1 disruptant, which is defective in glucose repression, or in the tpk1 w mutant, which has weak cAPK activity. In the absence of additional glucose, recovery of either actin polarization or translation initiation relies upon respiration, the Snf1p protein kinase, and the transcription factors Msn2p and Msn4p. The readdition of glucose to glucose-starved cells causes a rapid recovery of actin polarization as well as translation initiation without respiration. These results indicate that the simultaneous regulation of actin polarization and translation initiation is divided into three reactions: 1) rapid shutdown depending on Reg1p and cAPK after glucose removal, 2) slow adaptation depending on Snf1p and Msn2p/4p in the absence of glucose, and 3) rapid recovery upon readdition of glucose. On glucose removal, translation initiation is rapidly inhibited in a rom2 disruptant, which is defective in rapid actin depolarization, whereas rapid actin depolarization occurs in a pop2/caf1 disruptant, which is defective in rapid inhibition of translation initiation. Thus, translation initiation and actin polarization seem to be simultaneously but independently regulated by glucose deprivation. INTRODUCTIONThe actin cytoskeleton provides the structural basis for cell polarity in the yeast Saccharomyces cerevisiae and is organized primarily into two morphologically distinct structures: cortical patches and cables (Botstein et al., 1997). Cortical patches are discrete cytoskeletal bodies at the plasma membrane, whereas actin cables are long bundles of actin filaments that are oriented along the mother-bud axis. Both structures are polarized during the budding phase of the cell cycle. During early G1 phase, cortical patches and cables are randomly distributed. As a bud emerges, cortical patches cluster at the growing tip and cables extend from the mother cell into the bud. Near the end of bud growth, the patches and cables redistribute randomly, disrupting the asymmetric distribution of the actin cytoskeleton. At the end of mitosis, patches accumulate in and cables reorient toward the mother-bud neck in connection with cytokinesis and septum formation (Botstein et al., 1997).The actin cytoskeleton is also regulated in response to environmental stimuli. Mating pheromone causes polarization of the actin cytoskeleton toward the tip of the mating projection via the Cdc42p GTPase (Read et al., 1992;Leberer et al., 1997). In contrast, stresses such as osmotic shock, heat shock, and glucose starvation depolarize the actin cytoskeleton in budded cells as shown in Figure 1A (Novick et al., 1989;Chowdhury et al., 1992;Delley and Hall, 1999). In particular, the depolarization by heat or osmotic stress is known to be a rapid and transient reaction. A recent report has indicated that the rapid depol...

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Section: Discussionmentioning

confidence: 99%

Simultaneous yet Independent Regulation of Actin Cytoskeletal Organization and Translation Initiation by Glucose inSaccharomyces cerevisiae

Uesono

Ashe

Toh‐e

2004

MBoC

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“…Thus, the identification of all genes and proteins regulated by H 2 O 2 is an important step toward treatments that might confer tolerance to multiple, but interrelated, stresses. In addition to induction/repression of antioxidant defense genes, ROS are known to similarly affect expression of a variety of other genes involved in different signaling pathways in microbes (28), yeast (45), plants (46), and animals (19).…”

Section: Ros and Gene Expressionmentioning

confidence: 99%

Oxidative stress: molecular perception and transduction of signals triggering antioxidant gene defenses

2005

Braz J Med Biol Res

963

470

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Molecular oxygen (O 2 ) is the premier biological electron acceptor that serves vital roles in fundamental cellular functions. However, with the beneficial properties of O 2 comes the inadvertent formation of reactive oxygen species (ROS) such as superoxide (O 2 •-), hydrogen peroxide, and hydroxyl radical (OH • ). If unabated, ROS pose a serious threat to or cause the death of aerobic cells. To minimize the damaging effects of ROS, aerobic organisms evolved non-enzymatic and enzymatic antioxidant defenses. The latter include catalases, peroxidases, superoxide dismutases, and glutathione S-transferases (GST). Cellular ROS-sensing mechanisms are not well understood, but a number of transcription factors that regulate the expression of antioxidant genes are well characterized in prokaryotes and in yeast. In higher eukaryotes, oxidative stress responses are more complex and modulated by several regulators. In mammalian systems, two classes of transcription factors, nuclear factor κB and activator protein-1, are involved in the oxidative stress response. Antioxidant-specific gene induction, involved in xenobiotic metabolism, is mediated by the "antioxidant responsive element" (ARE) commonly found in the promoter region of such genes. ARE is present in mammalian GST, metallothioneine-I and MnSod genes, but has not been found in plant Gst genes. However, ARE is present in the promoter region of the three maize catalase (Cat) genes. In plants, ROS have been implicated in the damaging effects of various environmental stress conditions. Many plant defense genes are activated in response to these conditions, including the three maize Cat and some of the superoxide dismutase (Sod) genes. Correspondence

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“…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).…”

Section: B R Gibson Et Almentioning

confidence: 99%

Carbohydrate utilization and the lager yeast transcriptome during brewery fermentation

Gibson

Boulton

Box

et al. 2008

Yeast

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The fermentable carbohydrate composition of wort and the manner in which it is utilized by yeast during brewery fermentation have a direct influence on fermentation efficiency and quality of the final product. In this study the response of a brewing yeast strain to changes in wort fermentable carbohydrate concentration and composition during full-scale (3275 hl) brewery fermentation was investigated by measuring transcriptome changes with the aid of oligonucleotide-based DNA arrays. Up to 74% of the detectable genes showed a significant (p ≤ 0.01) differential expression pattern during fermentation and the majority of these genes showed transient or prolonged peaks in expression following the exhaustion of the monosaccharides from the wort. Transcriptional activity of many genes was consistent with their known responses to glucose de/repression under laboratory conditions, despite the presence of di-and trisaccharide sugars in the wort. In a number of cases the transcriptional response of genes was not consistent with their known responses to glucose, suggesting a degree of complexity during brewery fermentation which cannot be replicated in small-scale wort fermentations or in laboratory experiments involving defined media.

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Remodeling of Yeast Genome Expression in Response to Environmental Changes

Cited by 1,210 publications

References 65 publications

Simultaneous yet Independent Regulation of Actin Cytoskeletal Organization and Translation Initiation by Glucose inSaccharomyces cerevisiae

Simultaneous yet Independent Regulation of Actin Cytoskeletal Organization and Translation Initiation by Glucose inSaccharomyces cerevisiae

Oxidative stress: molecular perception and transduction of signals triggering antioxidant gene defenses

Carbohydrate utilization and the lager yeast transcriptome during brewery fermentation

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