ArticleBMC bioinformatics2006
Use of physiological constraints to identify quantitative design principles for gene expression in yeast adaptation to heat shock.
Article in BMC bioinformatics, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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10 citing papers in PubMed.
- Regulation of the Na+/K+-ATPase Ena1 Expression by Calcineurin/Crz1 under High pH Stress: A Quantitative Study.PloS one · 2016Article
- Canonical modeling of the multi-scale regulation of the heat stress response in yeast.Metabolites · 2012Article
- Modelling the regulation of thermal adaptation in Candida albicans, a major fungal pathogen of humans.PloS one · 2012Article
- Article
- Genome-wide analysis of yeast stress survival and tolerance acquisition to analyze the central trade-off between growth rate and cellular robustness.Molecular biology of the cell · 2011Article
- Steady-state global optimization of metabolic non-linear dynamic models through recasting into power-law canonical models.BMC systems biology · 2011Article
- Analysis of operating principles with S-system models.Mathematical biosciences · 2011Article
- Minimization of biosynthetic costs in adaptive gene expression responses of yeast to environmental changes.PLoS computational biology · 2010Article
- Identifying quantitative operation principles in metabolic pathways: a systematic method for searching feasible enzyme activity patterns leading to cellular adaptive responses.BMC bioinformatics · 2009Article
- Coordination of the dynamics of yeast sphingolipid metabolism during the diauxic shift.Theoretical biology & medical modelling · 2007Article
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3 authors.
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Abstract
backgroundUnderstanding the relationship between gene expression changes, enzyme activity shifts, and the corresponding physiological adaptive response of organisms to environmental cues is crucial in explaining how cells cope with stress. For example, adaptation of yeast to heat shock involves a characteristic profile of changes to the expression levels of genes coding for enzymes of the glycolytic pathway and some of its branches. The experimental determination of changes in gene expression profiles provides a descriptive picture of the adaptive response to stress. However, it does not explain why a particular profile is selected for any given response.
resultsWe used mathematical models and analysis of in silico gene expression profiles (GEPs) to understand how changes in gene expression correlate to an efficient response of yeast cells to heat shock. An exhaustive set of GEPs, matched with the corresponding set of enzyme activities, was simulated and analyzed. The effectiveness of each profile in the response to heat shock was evaluated according to relevant physiological and functional criteria. The small subset of GEPs that lead to effective physiological responses after heat shock was identified as the result of the tuning of several evolutionary criteria. The experimentally observed transcriptional changes in response to heat shock belong to this set and can be explained by quantitative design principles at the physiological level that ultimately constrain changes in gene expression.
conclusionOur theoretical approach suggests a method for understanding the combined effect of changes in the expression of multiple genes on the activity of metabolic pathways, and consequently on the adaptation of cellular metabolism to heat shock. This method identifies quantitative design principles that facilitate understating the response of the cell to stress.
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