The Exploration of Novel Regulatory Relationships Drives Haloarchaeal Operon-Like Structural Dynamics over Short Evolutionary Distances

Operons are a dominant feature of bacterial and archaeal genome organization. Numerous investigations have related aspects of operon structure to operon function, making operons exemplars for studies aimed at deciphering Nature’s design principles for genomic organization at a local scale. We consider this understanding to be both fundamentally important and ultimately useful in the de novo design of increasingly complex synthetic circuits. Here we analyze the evolution of the genomic context of operon-like structures in a set of 76 sequenced and annotated species of halophilic archaea. The phylogenetic depth and breadth of this dataset allows insight into changes in operon-like structures over shorter evolutionary time scales than have been studied in previous cross-species analysis of operon evolution. Our analysis, implemented in the updated software package JContextExplorer finds that operon-like context as measured by changes in structure frequently differs from a sequence divergence model of whole-species phylogeny and that changes seem to be dominated by the exploration of novel regulatory relationships.