Establishing Yeast as a Model for Studying Horizontal Gene Transfer Dynamics in Eukaryotes

1. Unveil extrinsic and intrinsic factors underlying successful HGT in eukaryotes What makes certain lineages/species more prone to HGT than others is one of the most intriguing questions in the topic of eukaryotic HGT. For instance, the W/S clade exhibits unusually high HGT rates. However, in its sister lineage HGT is virtually absent. While ecology might have been crucial for the acquisition/maintenance of HGT-derived genes in the W/S clade, in distantly related yeasts that share the same ecology (Metschnikowia), HGT is virtually non-existent [10], indicating that intrinsic factors are involved. Clarifying this question can shed light onto the genetic predispositions of successful integration of foreign DNA in eukaryotes. Hence, we propose to perform comparative analyses between closely related lineages with disparate rates of HGT (W/S clade and sister lineage). From an applied point of view, it can elucidate conditions and features of eukaryotic cells that make them permeable to exogenous DNA; this can help to outline gene therapy strategies and design new approaches to circumvent issues associated with biotechnologically relevant genetically modified organisms (GMO). 2. Understand how distinct and recent selective pressures impact maintenance, evolutionary rates, and gene expression patterns of HGT-derived genes at the population level Studies on the dynamics of HGT in eukaryotes have been chiefly addressed at the species level. At the populational level, reports have been virtually limited to Saccharomyces cerevisiae in which specific HGT-derived regions were detected only in strains associated with anthropic environments. Some of these strains are phylogenetically distant, suggesting that gradual decay of previously acquired genes might happen at the population level in face of changing environmental conditions. In bacteria, for instance, HGT-derived genes are known to be more easily lost in face of selective pressures when compared to native core genes. In eukaryotes, these dynamics await population studies. Also, how expression of these genes is affected by fluctuating environmental conditions in the short-term when compared to native genes might shed light onto the ecological and adaptive importance of HGT. To shed light onto these questions we propose to perform in depth comparative omics analyses of a W/S-clade species that occupies two disparate ecological niches. 3. Uncover the early steps of successful exogenous DNA integration and selection in eukaryotes While the function and adaptive importance of several eukaryotic HGT events have been studied, more fundamental questions such as how exogenous DNA is taken up, integrated, and maintained remain unanswered. Also, the immediate fitness benefits (if any) of an HGT event are quite obscure. As most HGT events are significantly old, these questions are difficult to address. However, experimental evolution can be used to simulate an HGT event making it possible to control several factors and address, in real time, most of these questions. Fairly recent similar experiments have been conducted in bacteria [13]. Here we propose to simulate and follow the early steps of an HGT event by experimental evolution. Gathered evidence can contribute to the body of knowledge about the pre-requisites of exogenous DNA introduction into eukaryotic cells, which can be useful in the future for applications in biotechnology and medicine.