Evolutionarily Driven Domain Swap Alters Sigma Factor Dependence in Bacterial Signaling System

Functional diversity in bacteria is introduced by lineage specific expansion or horizontal gene transfer (HGT). Using modular bacterial signaling systems as a template, we experimentally validate domain swapping of modular proteins as an extension of the HGT model. We take a computational approach to explore the domain architecture of two-component systems (TCS) in select Pseudomonads. We find a transcriptional effector domain swap that reconstructed a duplicated sigma54-dependent TCS to a sigma70-dependent TCS. Through functional genomics approaches, we determine that the implicated TCSs are involved in consumption of short-chain carboxylic acids. We verify the relationship between the domain-swapped TCSs utilizing a mutational screen, in which we switch the specificity of the sigma70-dependent TCS output to the sigma54-dependent TCS input, and vice versa. Our findings suggest that this domain swap was maintained throughout α-, β-, γ- proteobacteria, thus domain swapping has potential to lead to fitness advantages and neofunctionalization.