Great strides have been made in understanding the evolution of gene regulation by focusing on the budding yeast. The budding yeast have similar lifestyles across a wide timespan of evolution and, like their cardinal member the model single-celled eukaryote, are relatively easy to culture in the lab. The phylum also has a long and growing list of members whose genomes have been fully sequenced. One important direction of study that took advantage of the status of budding yeast as a model phylum was the comparative study of gene expression data across species in response to a variety of stresses. A key result from those investigations was that there was a major shift in the set of genes activated under a broad set of stress conditions, termed the Environmental Stress Response, that coincided with an ancient interspecies hybridization, known as the yeast Whole Genome Hybridization (WGH), which doubled the number of chromosomes in an ancestor of S. cerevisiae. Although that result provided the field with a rich dataset and robust framework for identifying evolutionary shifts in gene programs, as well as some specific intriguing examples of shifts of entire programs of similarly regulated genes, The specific nature of the genetic rewirings that gave rose to these changes have yet to be illuminated.

We took advantage of unique tools for analyzing the PKA pathway, namely the ability to monitor pathway activity through nuclear localization of the transcription factor Msn2, as well as our ability to construct a mutant strain in which PKA could be inhibited directly to compare signaling and transcriptional responses in this pathway across two species that straddle the phylogenetic divide of the WGH, S. cerevisiae, and K. lactis.

In Chapter 2, by tracking nuclear localization of the stress responsive transcription factor Msn2 (or SC.Msn2) and its ortholog in K. lactis (KL.Msn2). We observed that, while S. cerevisiae senses a switch from glucose to sorbitol as a stress, K. lactis does not. We also saw that Nuclear localization of KL.Msn2 in S. cerevisiae was responsive to osmotic shock, but it was not responsive to PKA inhibition. Furthermore, replacing the nuclear localization sequence of KL.Msn2 with that of S. cerevisiae, resulted in responsiveness to PKA inhibition. By creating a K. lactis strain in which PKA could be directly inhibited we were able to see that PKA inhibition does cause KL.Msn2 nuclear localization in its native environment in a K. lactis cell. These results showed that nuclear localization of Msn2 in response to PKA inhibition is preserved in S. cerevisiae and K. lactis, but that the conditions that cause PKA inhibition between species are not preserved, and the specific link between PKA inhibition and Msn2 nuclear localization is altered between species.

In Chapter 3, by comparing the transcriptional profiles of S. cerevisiae strains in which PKA was inhibited, we identified substantial set of paralogs from the yeast WGH, termed ohnologs that were differentially expressed under PKA inhibition. We determined using similar data collected in K. lactis and with data from stress-based gene expression studies in multiple budding yeast species that a high-basal level with no regulation by PKA is likely to be the ancestral phenotype for most of these differentially expressed ohnologs. We then studied the emergence of their responsiveness to PKA inhibition by analyzing patterns of the appearance of Msn2/4 binding sites in the promoter sequences of a range of recently sequenced budding yeast species. These analyses revealed that regulation by PKA arose in some ohnolog pairs in one of the two parental lineages prior to the WGH, leading to differential expression afterwards. In other examples, regulation by PKA and differential expression appears to have arisen following the WGH. This result provides a clear illustration of the unique opportunities presented by a WGH event for generating functional divergence by bringing together two parental lineages with separately evolved regulation into one species. Importantly, it poses the idea that functional divergence of two paralogs can be facilitated through such regulatory divergence, which can persist even when functional differences are erased by gene conversion