Inhomogeneous exclusion processes and the efficiency of translation

Motivated by recent experiments on an antibiotic resistance gene, we investigate genetic interactions between synonymous mutations in the framework of exclusion models of translation. We show  that the range of possible interactions is markedly different depending on whether translation efficiency is assumed to  be proportional to ribosome current or ribosome speed. In the first case every mutational effect has a definite sign that  is independent of genetic background, whereas in the second case the effect-sign can vary depending on the presence of other  mutations. The latter result is demonstrated using configurations of multiple translational bottlenecks induced by slow codons.