Regulation of Protein Synthesis in Arabidopsis Thaliana through a Bioinformatic and Mathematical Lens

Organisms exist under constantly varying environmental and internal conditions, which necessitate the differential regulation of gene expression. To synthesize proteins, the ribosome translates the information encoded in the nucleotide sequence of an mRNA into the final, functional amino acid sequence. Knockouts of ribosomal proteins lead to lethality. One such protein is the ribosomal protein 6 of the small subunit (eS6/RPS6). We confirmed that the knockout of either one of two eS6 paralogs in Arabidopsis leads to stunted growth and chlorosis. Here, these phenotypes have been further characterized in seedlings by precisely quantifying the ribosome loading of mRNAs as well as by RNA-seq and proteomics. Loss of either RPS6 paralog causes widespread perturbations in chloroplast development, including in photosystem (PS)II and PSI, as well as ribosome biogenesis. Furthermore, we assess whether the phosphorylation status of eS6 plays a role in its regulation. Elimination of eS6 phosphorylation resulted in a mild phenotype with minor changes to the transcriptome, suggesting it is dispensable for most aspects of plant development. To more broadly understand the process of translation we developed a mathematical model that predicts the transcript population and the transcript’s association with ribosomes. Computational techniques have become a cornerstone of modern biology allowing for broad molecular characterization and subsequent development of formal explanations of biological phenomena. In this model we focus on the effect of transcript decapping on the mRNA population and its translational output. As expected, increased decapping reduces overall protein production, partly by reducing ribosomal load, but mainly by shifting the mRNA population from the translationally active, capped state to the inactive, decapped state. Additionally, in transcripts with low half-lives, we find that a significant proportion of the protein production occurs during cotranslational decay. Through these two projects we examine the ability of Arabidopsis to regulate its protein production.