Extracting Biological Insight from Complex Genome-Scale Data: Connecting Growth Control and Stress Response in Yeast

David Botstein
Department of Molecular Biology, Princeton University

(April 11, 2011 2:30 PM - 3:30 PM)

Extracting Biological Insight from Complex Genome-Scale Data: Connecting Growth Control and Stress Response in Yeast

Abstract

The maintenance of cellular homeostasis in the face of rapidly changing environmental conditions has been the focus of our research for the past five years. Specifically, we have studied the relationship between the growth rate, which we can control directly by setting the dilution rate in chemostats, and the initiation of cell division cycle, response to environmental stress, and metabolism. We have exploited high-throughput methods, some of our own devising, to follow gene expression, metabolite levels, and relative fitness of mutants on a comprehensive scale in order to obtain a view of the integration of these functions at the system level. The results of these studies, which have involved collaborations with many other laboratories in the Lewis-Sigler Institute, include the following: 1) Expression of a substantial fraction (ca. 1/4) of the yeast genes is strongly correlated with the growth rate regardless of the limiting nutrient. Some genes are expressed more as growth rate increases (positive slope) and others are expressed more as the growth rate decreases (negative slope). These slopes are related to the periodic expression of the same genes in the metabolic cycle, which we have shown, by counting individual mRNAs by fluorescence in situ hybridization (FISH), is an intrinsic feature of yeast cell metabolism. 2) The levels of intracellular metabolites, in contrast, depend strongly on the limiting nutrient and relatively little on the growth rate. Only two (glutathione and trehalose) show strong negative slopes and a handful (e.g. ribose phosphate and fructose bis-phosphate) show strong positive slopes. 3) Starvation for phosphorus, sulfur or nitrogen ("natural nutrients") results in cell-cycle arrest, long-term (weeks) survival and sparing of residual glucose. Starvation, in auxotrophs, for leucine, uracil or histidine, in contrast, fail to arrest the cell cycle promptly, die much more rapidly and waste residual glucose. The glucose wasting is reminiscent of the Warburg effect seen in tumor cells. 4) Mutants that suppress starvation lethality and glucose wasting appear in genes already implicated in nutrient sensing. Genome-scale assessment of fitness during starvation provides a quantitative assessment of the contribution of each of the non-essential yeast genes to nutrient sensing and/or starvation survival. It seems to us that much of what has been described as "stress response" would better be described as the consequence of slowing growth. The metabolic cycle, which separates oxidative and fermentative metabolism, appears to play a central role in growth-rate regulation. We are testing models in which metabolite levels, position in the metabolic cycle, external nutrient sensing as well as cell size are used to gate entry into the S-phase of the cell division cycle.