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.
