Natural Selection for operons depends on genome size

Abstract

In prokaryotes, genome size is associated with metabolic versatility, regulatory complexity, effective population size and horizontal transfer rates. We therefore analyzed the co-variation of genome size and operon conservation to assess the evolutionary models of operon formation and maintenance. In agreement with previous results, intra-operonic pairs of essential and of highly expressed genes are more conserved. Interestingly, intra-operonic pairs of genes are also more conserved when they encode proteins at similar cell concentrations, suggesting a role of co-transcription in diminishing the cost of waste and shortfall in gene expression. Larger genomes have fewer and smaller operons that are also less conserved. Importantly, lower conservation in larger genomes was observed for all classes of operons in terms of gene expression, essentiality and balanced protein concentration. We reached very similar conclusions in independent analyses of three major bacterial clades (α- and β-Proteobacteria and Firmicutes). Operon conservation is inversely correlated to the abundance of transcription factors in the genome when controlled for genome size. This suggests a negative association between the complexity of genetic networks and operon conservation. These results show that genome size and/or its proxies are key determinants of the intensity of natural selection for operon organization. Our data fits better the evolutionary models based on the advantage of co-regulation than those based on genetic linkage or stochastic gene expression. We suggest that larger genomes with highly complex genetic networks and many transcription factors endure weaker selection for operons than smaller genomes with fewer alternative tools for genetic regulation.