All organisms must be able to sense and respond to their environment and defend themselves against environmental stress. We previously used DNA microarrays to examine the yeast response to environmental stresses and identified a large gene expression program, called the environmental stress response (ESR), that is activated by many types of stress. The ESR consists of ~1000 gene expression changes and includes ~600 repressed genes and ~350 induced genes.We are combining functional genomics and computational biology with traditional techniques in genetics, biochemistry, and molecular biology to understand the role, regulation, and evolution of the ESR.

The ESR is triggered by diverse types of stress, however the regulation of this program is condition-specific and governed by many different transcription factors, RNA binding proteins, and upstream signaling pathways depending on the conditions. We are taking an integrated approach to elucidate the signal transduction network that governs this response. In addition to learning how the ESR is coordinated, we are using this system to decipher rules of signal transduction and transcriptional regulation in this model eukaryote.

We are also exploring the evolution of gene expression regulation, signal transduction, and environmental interactions. Using comparative genomic approaches, we are examining the variation in stress-triggered gene expression changes within and between species in the Ascomycete clade. This information, coupled with genomic comparisons of the more than 20 fungal genomes currently available, is being used to develop models for the evolution of gene expression patterns and environmental responses.