Functional Genomics in Yeast

Living cells are complex biological systems with large networks of interactions between different macromolecules. A focus of systems biology is to study the dynamics of the living cells and their interactions through functional genomic approaches. High-throughput techniques and whole-genome screening experiments allow us to collect "big data" for various biochemical networks within the cell. The baker's yeast, Saccharomyces cerevisiae, is a single-cell eukaryotic model organism used for functional genomics approaches, the genome of which has considerable homology with the human genome. In this thesis, we used functional genomic approaches to study novel function(s) for genes and pathways affecting translation. The process of translation is an essential pathway that leads to the production of functional proteins for living cells. Dysregulation of this process and its associated pathways have been linked to many diseases, emphasizing the importance and need to investigate details of genes that influence this pathway. Much has been learned so far but there are still unknown regulations that require more examination. One of the main objectives of this thesis is to discover and study novel function of genes that affect the translation of structured mRNAs in yeast. We designed different constructs to evaluate the effect of nearly 5000 non-essential genes on the translation of reporter genes. Through whole-genome screening experiments and follow up assays we proposed the heretofore unknown involvement of five genes in the translation pathway. In the current thesis, YTA6, YPR096C, NAM7, PUS2, and RPL27B are proposed to be important for the translation of mRNAs with structured regions within their 5'-UTRs in yeast. In another study, we used translation in mitochondria as a strategy to investigate the ability of a specific 3'-UTR sequence to direct a reporter mRNA into yeast mitochondria. Lastly, using additional screenings we propose the involvement of dozens of more genes that seem to be important for the translation of structured mRNAs. Together, our findings contribute to a better understanding of the translation of structured mRNAs. They also indicate that our overall understanding of the regulations of translation may require additional studies in years to come.