Speaker: Christopher Workman, DTU Bioengineering, Technical University of Denmark
Date: Thursday 6th June, 3.30 pm in the Small Lecture Theatre, Department of Statistics
Title: Does supply or demand drive codon optimization?
Abstract: Translation efficiency is partly determined by the law of mass action where higher tRNA concentrations are expected to result in more efficiently translated codons. Likely for this reason, cells have variable gene copy numbers of tRNA genes that result in different concentrations of charged tRNAs allowing some codons to be translated faster than others. This idea is well captured by the tRNA adaptation index (tAI) defined by dos Reis and colleagues in 2004, to estimate the translation efficiency of a transcript based on the tRNA gene copy numbers observed in the genome. The number of effective codons (Nc) (Wright 1990), which borrows from population genetics, estimates whether a transcript’s codons are constrained to use less than could be expected at random considering the degeneracy in the genetic code, was used to contrast with the tAI. Comparing the tAI with the Nc gives new perspectives on evolution of highly selective codon usage versus how well matched they are to tRNA pools. Studies in a broad selection of fungal genomes are used to illustrate these relationships and what they suggest about particular genes.