Global Screening of Genes Essential for Growth in High-Pressure and Cold Environments: Searching for Basic Adaptive Strategies Using a Yeast Deletion Library

Abe, Fumiyoshi; Minegishi, Hiroaki

doi:10.1534/genetics.107.083063

Cited by 78 publications

(69 citation statements)

References 91 publications

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“…The reason for this growth phenotype of gtr and avl9⌬ mutants is not clear, but it could reflect defects in traffic due to reduced membrane fluidity under these conditions. Other mutations in nonessential genes that cause defective transport from the Golgi were also identified in the screen (3). Furthermore, at high pressure and cold temperature, the Tat2 permease is sorted to the vacuole even though TOR signaling seems unaffected (2), suggesting that the TORC1-regulated exocytic route is especially sensitive to conditions that reduce membrane fluidity.…”

Section: Discussionmentioning

confidence: 95%

A Chemical Genetic Screen for Modulators of Exocytic Transport Identifies Inhibitors of a Transport Mechanism Linked to GTR2 Function

Zhang¹,

Huang

Harsay³

2010

Eukaryot Cell

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Membrane and protein traffic to the cell surface is mediated by partially redundant pathways that are difficult to perturb in ways that yield a strong phenotype. Such robustness is expected in a fine-tuned process, regulated by environmental cues, that is required for controlled cell surface growth and cell proliferation. Synthetic genetic interaction screens are especially valuable for investigating complex processes involving partially redundant pathways or mechanisms. In a previous study, we used a triple-synthetic-lethal yeast mutant screen to identify a novel component of the late exocytic transport machinery, Avl9. In a chemicalgenetic version of the successful mutant screen, we have now identified small molecules that cause a rapid (within 15 min) accumulation of secretory cargo and abnormal Golgi compartment-like membranes at low concentration (<2 M), indicating that the compounds likely target the exocytic transport machinery at the Golgi. We screened for genes that, when overexpressed, suppress the drug effects, and found that the Ras-like small GTPase, Gtr2, but not its homolog and binding partner, Gtr1, efficiently suppresses the toxic effects of the compounds. Furthermore, assays for suppression of the secretory defect caused by the compounds suggest that Gtr proteins can regulate a pathway that is perturbed by the compounds. Because avl9⌬ and gtr mutants share some phenotypes, our results indicate that the small molecules identified by our chemical-genetic strategy are promising tools for understanding Avl9 function and the mechanisms that control late exocytic transport.

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Section: Discussionmentioning

confidence: 95%

A Chemical Genetic Screen for Modulators of Exocytic Transport Identifies Inhibitors of a Transport Mechanism Linked to GTR2 Function

Zhang¹,

Huang

Harsay³

2010

Eukaryot Cell

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“…Cold modifies enzyme kinetics (28, 58) and increases the molecular order of membrane lipids, i.e., rigidification (33), affecting the membrane environment and thus the activity of membrane-associated enzymes and transporters. Key processes such as plasma membrane ATPase activity (53), the higher proton motive force (39), and the transport of various amino acids (60) depend thus on temperature-instigated changes in membrane fluidity and become limiting factors for cell growth.In support of this view, previous reports have shown that tryptophan uptake is impaired after a downward shift in temperature (1) and that several cold-sensitive mutants are affected in tryptophan transport and biosynthesis (3,12,52). It has also been suggested that the sensitivity of tryptophan permeases to changes in membrane fluidity could determine or influence the growth temperature profile of tryptophan auxotroph strains of S. cerevisiae (1, 2).…”

mentioning

confidence: 78%

“…In support of this view, previous reports have shown that tryptophan uptake is impaired after a downward shift in temperature (1) and that several cold-sensitive mutants are affected in tryptophan transport and biosynthesis (3,12,52). It has also been suggested that the sensitivity of tryptophan permeases to changes in membrane fluidity could determine or influence the growth temperature profile of tryptophan auxotroph strains of S. cerevisiae (1, 2).…”

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confidence: 78%

Multicopy Suppression Screening of Saccharomyces cerevisiae Identifies the Ubiquitination Machinery as a Main Target for Improving Growth at Low Temperatures

Hernandez-Lopez

García-Marqués

Rández-Gil

et al. 2011

Appl Environ Microbiol

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A decrease in ambient temperature alters membrane functionality and impairs the proper interaction between the cell and its external milieu. Understanding how cells adapt membrane properties and modulate the activity of membrane-associated proteins is therefore of major interest from both the basic and the applied points of view. Here, we have isolated multicopy suppressors of the cold sensitivity phenotype of a trp1 strain of Saccharomyces cerevisiae. Three poorly characterized genes, namely, ALY2 encoding the endocytic adaptor, CAJ1 encoding the J protein, and UBP13 encoding the ubiquitin C-terminal hydrolase, were identified as mediating increased growth at 12°C of both Trp ؊ and Trp ؉ yeast strains. This effect was likely due to the downregulation of cold-instigated degradation of nutrient permeases, since it was missing from cells of the rsp5⌬ mutant strain, which contains a point mutation in the gene encoding ubiquitin ligase. Indeed, we found that 12°C treatments reduced the level of several membrane transporters, including Tat1p and Tat2p, two yeast tryptophan transporters, and Gap1, the general amino acid permease. We also found that the lack of Rsp5p increased the steady state level of Tat1p and Tat2p and that ALY2-engineered cells grown at 12°C had higher Tat2p and Gap1p abundance. Nevertheless, the high copy number of ALY2 or UBP13 improved cold growth even in the absence of Tat2p. Consistent with this, ALY2-and UBP13-engineered cells of the industrial QA23 strain grew faster and produced more CO 2 at 12°C than did the parental when maltose was used as the sole carbon source. Hence, the multicopy suppressors isolated in this work appear to contribute to the correct control of the cell surface protein repertoire and their engineering might have potential biotechnological applications.A major requirement for strain improvement involves stress tolerance and adaptability of cells to environmental stressors in industrial applications (22,47). For example, some industrial processes involving industrial strains of Saccharomyces cerevisiae, like brewing and some wine fermentations, take place at temperatures around 10 to 12°C, which is far below the optimal temperature for this organism (ϳ28°C). Growth at low temperature reduces the production by S. cerevisiae of higher alcohols and increases the amount of esters (10,20). The low fermentation temperature also has a prominent effect on primary flavors, which are retained to a greater degree. However, under these conditions, an extended lag phase before the onset of vigorous fermentation activity is observed, which reduces the cost-effectiveness and efficiency of production. In wine making, this lag phase also increases the risk of halted or sluggish fermentation (20). Hence, cold tolerance is an important biotechnological trait and there is an urgent need for strains able to ferment at low temperatures both quickly and in a reproducible way.Like other stressors, cold influences the structural and functional properties of cellular components negatively, both p...

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“…Since the yeast plasma membrane and cell wall composition are both affected by temperature (66,69), this response may reflect the need for continuous replacement of membrane and cell wall components. Intracellular membrane trafficking is also sensitive to temperature in mammalian cells (70)(71)(72), and in a genomewide screen for sensitivity to high pressure and low temperature, yeast mutants affected in membrane trafficking showed decreased fitness (73). A possible temperature-dependent alteration of the cell wall during DTC is further supported by the overrepresentation of target genes of the transcription factors Swi4 and Swi6, which are known to play an important role in the regulation of genes required for cell wall remodeling (69), among the DTCresponsive transcripts.…”

Section: Discussionmentioning

confidence: 99%

Physiological and Transcriptional Responses of Anaerobic Chemostat Cultures of Saccharomyces cerevisiae Subjected to Diurnal Temperature Cycles

Hebly

Ridder

Hulster

et al. 2014

Appl Environ Microbiol

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dDiurnal temperature cycling is an intrinsic characteristic of many exposed microbial ecosystems. However, its influence on yeast physiology and the yeast transcriptome has not been studied in detail. In this study, 24-h sinusoidal temperature cycles, oscillating between 12°C and 30°C, were imposed on anaerobic, glucose-limited chemostat cultures of Saccharomyces cerevisiae. After three diurnal temperature cycles (DTC), concentrations of glucose and extracellular metabolites as well as CO 2 production rates showed regular, reproducible circadian rhythms. DTC also led to waves of transcriptional activation and repression, which involved one-sixth of the yeast genome. A substantial fraction of these DTC-responsive genes appeared to respond primarily to changes in the glucose concentration. Elimination of known glucose-responsive genes revealed an overrepresentation of previously identified temperature-responsive genes as well as genes involved in the cell cycle and de novo purine biosynthesis. Indepth analysis demonstrated that DTC led to a partial synchronization of the cell cycle of the yeast populations in chemostat cultures, which was lost upon release from DTC. Comparison of DTC results with data from steady-state cultures showed that the 24-h DTC was sufficiently slow to allow S. cerevisiae chemostat cultures to acclimate their transcriptome and physiology at the DTC temperature maximum and to approach acclimation at the DTC temperature minimum. Furthermore, this comparison and literature data on growth rate-dependent cell cycle phase distribution indicated that cell cycle synchronization was most likely an effect of imposed fluctuations of the relative growth rate (/ max ) rather than a direct effect of temperature.T emperature directly influences the kinetics of all biochemical reactions and many cellular processes (1, 2). Within their temperature range for growth, many microorganisms adapt their metabolic networks and biomass composition to optimize their growth rate and viability in response to changing temperatures. Classical examples of temperature adaptation include modifications of membrane fluidity (3, 4) and the expression of heat shock proteins that assist in protein folding at high temperatures (5, 6).Laboratory studies on microbial temperature responses are based largely on two experimental systems. Acclimation, i.e., the result of complete physiological adaptation to a given temperature, has been studied both in batch cultures and in chemostats (7-9). In cold shock and heat shock experiments, the responses of microorganisms to sudden upshifts or downshifts in temperature are studied, typically over a time period ranging from a few minutes to a few hours (3, 10-13).In natural environments, microorganisms are subjected to several types of temperature dynamics. In exposed environments, one of the dominant aspects of temperature dynamics is related to circadian changes, with higher temperatures during the day and lower temperatures during the night. These 24-h temperature cycles, which are superimp...

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Global Screening of Genes Essential for Growth in High-Pressure and Cold Environments: Searching for Basic Adaptive Strategies Using a Yeast Deletion Library

Cited by 78 publications

References 91 publications

A Chemical Genetic Screen for Modulators of Exocytic Transport Identifies Inhibitors of a Transport Mechanism Linked to GTR2 Function

A Chemical Genetic Screen for Modulators of Exocytic Transport Identifies Inhibitors of a Transport Mechanism Linked to GTR2 Function

Multicopy Suppression Screening of Saccharomyces cerevisiae Identifies the Ubiquitination Machinery as a Main Target for Improving Growth at Low Temperatures

Physiological and Transcriptional Responses of Anaerobic Chemostat Cultures of Saccharomyces cerevisiae Subjected to Diurnal Temperature Cycles

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