Quantitative proteomic analysis reveals environmental interaction and epistasis in the responses to complex stimuli in Saccharomyces cerevisiae.

摘要

The genotype of a cell and its interactions with the environment determine the cell's biochemical state. Although, the cellular responses to a single stimulus have been extensively studied, the response to concurrent stimuli is important and often neglected. There is need for a unifying conceptual framework to model the effects of multiple environmental stimuli applied concurrently. To build such a concept, we hypothesized that, as an abstraction, environmental stimuli can be treated as analogous to genetic elements. This would allow modeling of the effects of multiple stimuli using the concepts and tools developed for studying gene interactions. We defined an environmental interaction as the interaction between different environmental stimuli that affect the same observable characteristic or trait. Similar to the statistical definition of genetic epistasis, environmental epistasis is an environmental interaction in which the effects of the individual stimuli are not independent of each other. We devised a methodology using dominance in environmental interactions to identify proteins and pathways important for responding to a stimulus. We tested our hypothesis using quantitative proteomic analysis of cellular response of yeast S. cerevisiae to concurrent environmental stimuli.