Cell Type Specific Responses to Codon Usage Bias in Two Stem Cell Lineages

The redundancy inherent in the genetic code allows for multiple codons to encode for a single amino acid. These synonymous codons are used at different frequencies in the genome, with some being used more frequently than others. This phenomenon is known as codon bias. Although codon bias was not originally thought to affect gene expression, we now know that it impacts nearly every step of the central dogma. Previous work identified two Drosophila tissues that express genes enriched in rarely used codons: the larval brain and adult testes. Both tissues contain numerous stem cells which divide many times to produce specialized progeny. In my thesis work, I investigated codon bias regulation in these tissues at the cellular level. In the brain, I found that neural stem cells express very little protein from a rare-codon enriched reporter, while their progeny, the neurons, have high protein expression from the rare-codon enriched reporter. Next, through a targeted genetic screen, I identified a regulator of this response in neurons: the RNA binding protein Orb2. Orb2 stabilizes mRNA from the rare-codon-enriched reporter specifically in neurons, but not in neural progenitors. I then used RNA sequencing to identify mGluR as an endogenous rare codon-enriched gene that requires Orb2 for high mRNA expression and function in social activity. My work suggests that the convergence of rare codons and Orb2 regulation in an mRNA allows precise tuning of gene expression in neurons. Further work during my thesis revealed stage-specific regulation of codon usage during spermatogenesis, and pinpointed specific testis tRNA regulation that likely underlies tissue-specific codon regulation. My work has revealed that codon usage unlocks another layer of gene expression regulation, which is leveraged by the cell to direct temporal and spatial expression regulation during development and function of specialized cell types.