The hidden code in the coding sequence: how embedded features impact protein function

The redundancy in the genetic code, with 61 codons encoding only 20 amino acids, means that multiple coding-sequences can encode the same protein and not all mutations result in altered amino acid sequences. While these “synonymous” mutations have long been overlooked, emerging evidence shows that this redundancy carries hidden regulatory information that can influence ribosome speed and, in turn, protein expression and function. Understanding this “hidden-layer” of regulation is critical for identifying disease-associated synonymous mutations and for improving mRNA therapeutic design. For example, current mRNA therapies utilise optimal codons, as these are most efficiently translated by ribosomes, but my data suggests non-optimal codons impart important regulatory information that controls co-translational processes. Here, reporter assays, advanced microscopy and transcriptome-wide approaches will be used to investigate how codon optimality shapes protein function. Novel assays to quantify co-translational complex assembly will reveal critical sequence elements and regulatory factors. Live-cell imaging will demonstrate how mRNAs that encode interacting proteins find each other within the cell, and the consequence of specific synonymous mutations on protein function will be investigated. Finally, how ribosome speed influences the fate of nascent proteins will be examined, using direct RNA-sequencing to understand how RNA modifications regulate this process.