Fitness Effects of Changing Codon Bias of two genes – mauA and mtdA in Methylobacterium extorquens AM1

Abstract

Organisms have a codon bias i.e. they use certain codons more frequently than others that code for the same amino acid. Studies have shown that changing the codon bias of a gene can have a negative impact on fitness due to decreased mRNA and protein levels. Mechanisms like tRNA-codon imbalance, ribosome pausing and altered mRNA secondary structure have been proposed to explain the fitness effects of altering codon usage. We are studying the fitness effects of changing the codon bias of two genes, mauA and mtdA in Methylobacterium extorquens. Changing the codon bias of fae, another gene in M. extorquens has a negative impact on fitness. By comparing the trends in fitness effects across genes from the same pathway, we may unearth the mechanistic basis of this effect. We generated codon usage variants of mauA and mtdA and quantified their growth rates. Preliminary analysis shows that fitness effects in mauA strains are similar to those of fae. While those seen in mtdA codon usage variants appear to depend on the carbon substrate available, though this may be an artefact of the FLAG tag introduced into the sequence. Also, a previous study in the lab evolved the codon altered fae strains and sequenced them. Here we analyse this sequence data to identify background mutations that could contribute to increasing fitness. Our preliminary data supports the hypothesis that fitness effects of synonymous mutations are context dependent.