Adaptive Mutations that Prevent Crosstalk Enable the Expansion of Paralogous Signaling Protein Families

Abstract

Orthologous proteins often harbor numerous substitutions, but whether these differences result from neutral or adaptive processes is usually unclear. To tackle this challenge, we examined the divergent evolution of a model bacterial signaling pathway comprising the kinase PhoR and its cognate substrate PhoB. We show that the specificity-determining residues of these proteins are typically under purifying selection but have, in α-proteobacteria, undergone a burst of diversification followed by extended stasis. By reversing mutations that accumulated in an α-proteobacterial PhoR, we demonstrate that these substitutions were adaptive, enabling PhoR to avoid crosstalk with a paralogous pathway that arose specifically in α-proteobacteria. Our findings demonstrate that duplication and the subsequent need to avoid crosstalk strongly influence signaling protein evolution. These results provide a concrete example of how system-wide insulation can be achieved postduplication through a surprisingly limited number of mutations. Our work may help explain the apparent ease with which paralogous protein families expanded in all organisms.

Navigating cancer network attractors for tumor-specific therapy

“…Notably, direct mutagenesis of these determinants of specificity has been used to rewire the entire histidine kinase signaling system in bacteria in a predictive manner 54 . Recent follow-up work indicates that mutations in determinants of specificity prevent cross-talk and allow protein family expansions 55 , in a process similar to the one powered by negative selection over Src homology 3 (SH3) protein domains that show similar specificity 56 . We propose that similar studies in human signaling networks, coupled with mapping of cancer mutations on these determinants of specificity, would shed new light on whether signaling rewiring is a general principle of oncogenesis and tumor progression, knowledge of which would in turn be critical as molecular therapies target proteins and their networks and not genes.…”

Determinants of specificity in two-component signal transduction

“…Consistently, an examination of the specificity residues in two-component proteins from an individual organism typically reveals significant differences in almost all possible pairwise comparisons of kinases or regulators [37]. In rare cases, the specificity residues of some two-component proteins are similar, indicating potentially advantageous cross-regulation [41].…”

“…The answer appears, in many cases, to be gene duplication events and the birth of new pathways [3,37]. Phylogenetic analyses indicate that, for most species, the majority of new twocomponent pathways emerge through gene duplication [38,39].…”

“…This intermolecular coevolution enables the insulation of the two new pathways while maintaining phosphotransfer within each system. Evidence for this model comes from the inspection of specificity residues in two-component signaling proteins derived from a relatively recent gene duplication [37]. For instance, while there is a single copy of EnvZ-OmpR in γ-proteobacteria, there are two copies in most α-proteobacteria (Fig.…”

“…The insulation of recently duplicated pathways may also require changes in other existing twocomponent pathways [37]. For instance, in α-proteobacteria a duplication of the NtrB-NtrC system produced the NtrY-NtrX system, and the specificity residues of NtrY-NtrX subsequently diverged from those of NtrB-NtrC to yield two insulated pathways.…”