UC San Diego

The control of gene expression is a highly complex process that is vital to an organism’s adaptation to fluctuating environments. The majority of a cell’s energy is directed towards protein synthesis, necessitating a tight regulation of the translation process. Past research has predominantly focused on the translational control of initiation, but there has been a growing appreciation for the complex interplay between both initiation and elongation rates. In this dissertation I use the budding-yeast Saccharomyces cerevisiae as a model organism to study the translational regulation of elongation. I attempt to determine the role of elongation during adaptative stress response and seek to quantify elongation rates across distinct conditions. In Chapter 2 we explore the regulation of translation during the stress response to glucose starvation. We use ribosomal profiling and in vivo luciferase reporter assays to demonstrate a slowdown of elongation rates during glucose starvation. Chapter 3 includes a discussion of the development of a luciferase reporter for quantification of elongation rates during translation. We quantify the impact of synonymous codon substitutions on the elongation rate of yeast-optimized yellow fluorescent protein (YFP) and provide further insight into the surveillance of translation and the roles of the proposed translation sensors Hel2 and Dhh1 in mediating ribosome pausing events. Chapter 4 investigates the effects of Dhh1 on the translational repression observed during glucose starvation. We identify a correlation between the shift in ribosome polarity we observe during glucose starvation and Dhh1 enrichment during glucose starvation previously published CLIP-seq dataset by (Cary et al., 2015) and detail the results of polysome profiling and luciferase reporter assays performed in a conditional Dhh1 knockdown.