Specific Codons Control Cellular Resources and Fitness

Abstract

ABSTRACTAs biotechnology research progresses from simply overexpressing proteins to creating intricate metabolic pathways, gene circuits, and complex phenotypes, harmonizing gene fitness in the context of a host organism has become essential. A significant amount of recent work has focused on decoupling gene expression from host resources to improve the outcome of synthetic biology and metabolic engineering efforts. While insightful, few of these studies have investigated the mechanistic underpinnings of resource allocation during translation elongation. There is a degeneracy in codons – but they are not equivalent. While there is an understanding that codon use is unequal in native genes, there is less knowledge of how this usage bias modulates the supply and demand of protein translation resources. Here we investigate how the partitioning of microbial translational resources, specifically through allocation of tRNA by incorporating dissimilar codon usage bias, can drastically alter expression of proteins and reduce the burden on the host resources. By isolating individual codons experimentally, we find heterologous gene expression can trans-regulate fitness of the host and other heterologous genes. Interestingly, specific codons drive profitable or catastrophic phenotypic outcomes. We correlate codon usage patterns with genetic fitness and empirically derive a novel coding scheme for multi-gene expression called Codon Harmony Index (CHI, χ). CHI enables the design of harmonious multi-gene expression systems while avoiding catastrophic cellular burden.