Model-driven analysis of experimentally determined growth phenotypes for 465 yeast gene deletion mutants under 16 different conditions

Abstract

BACKGROUND: Understanding the response of complex biochemical networks to genetic perturbations and environmental variability is a fundamental challenge in biology. Integration of high-throughput experimental assays and genome-scale computational methods is likely to produce insight otherwise unreachable, but specific examples of such integration have only begun to be explored. RESULTS: In this study, we measured growth phenotypes of 465 Saccharomyces cerevisiae gene deletion mutants under 16 metabolically relevant conditions and integrated them with the corresponding flux balance model predictions. We first used discordance between experimental results and model predictions to guide a stage of experimental refinement, which resulted in a significant improvement in the quality of the experimental data. Next, we used discordance still present in the refined experimental data to assess the reliability of yeast metabolism models under different conditions. In addition to estimating predictive capacity based on growth phenotypes, we sought to explain these discordances by examining predicted flux distributions visualized through a new, freely available platform. This analysis led to insight into the glycerol utilization pathway and the potential effects of metabolic shortcuts on model results. Finally, we used model predictions and experimental data to discriminate between alternative raffinose catabolism routes. CONCLUSIONS: Our study demonstrates how a new level of integration between high throughput measurements and flux balance model predictions can improve understanding of both experimental and computational results. The added value of a joint analysis is a more reliable platform for specific testing of biological hypotheses, such as the catabolic routes of different carbon sources.AMD is supported by a Genome Scholar and Faculty Transition award (K22 HG002908) from the NIH/NHGRI. DS acknowledges support by the US Department of Energy, the National Institute of Health and the NASA Astrobiology Institute. The authors would also like to thank Zhenjun Hu for help with flux visualization in VisANT and Dan Fraenkel for comments on the manuscript. It is with sadness that we report the premature passing of our co-author Kaisheen Wong, who participated enthusiastically and productively in this project as a high school student. (AMD; K22 HG002908 - Genome Scholar and Faculty Transition award; NIH/NHGRI; US Department of Energy; National Institute of Health; NASA Astrobiology Institute)Published versio