Modeling binding of the conserved Csr/Rsm protein family across species of the γ-proteobacteria reveals niche-specific adaptation of the post-transcriptional regulon

Abstract

The {gamma}-proteobacteria are an exceptionally diverse bacterial class whose members thrive in environments from deep-sea vents to human intestinal tracts. Rapid gene expression responses mediated by global post-transcriptional regulatory networks like the Csr/Rsm system are critical for bacterial survival in dynamic niches. CsrA/RsmA functions as a global regulatory RNA-binding protein, directly controlling hundreds to thousands of mRNA targets simultaneously across the transcriptome to coordinate systems-level metabolic and behavioral responses. Despite conservation of the CsrA/RsmA regulatory protein across {gamma}-proteobacteria, the genes it regulates in different species remain poorly characterized. We extended a previously developed biophysical model of CsrA/RsmA-RNA binding from Escherichia coli and Pseudomonas aeruginosa to predict regulons across 16 diverse {gamma}-proteobacterial species. While CsrA/RsmA protein structure and RNA-binding motif recognition are highly conserved, predicted target regulons diverge dramatically across species. Pathway enrichment analysis demonstrated both conserved regulation of core metabolic processes and extensive species-specific regulation of niche-adapted functions including virulence, biocontrol, and environmental stress response. Only two gene groups were shared exclusively among non-pathogens, while pathogens showed no exclusively conserved targets, indicating extensive regulon rewiring. These findings demonstrate that post-transcriptional regulatory networks evolve primarily through mutations in RNA targets that create or eliminate regulatory binding sites, rapidly adapting target repertoires to ecological demands while the regulatory protein mechanism remains conserved. ImportanceThe CsrA/RsmA family represents one of the most influential global regulatory RNA-binding proteins in {gamma}-proteobacteria, directly binding and regulating hundreds of mRNA targets to orchestrate systems-scale control over metabolism, virulence, and environmental adaptation, yet how this conserved mechanism adapts across diverse niches remains unclear. By predicting CsrA/RsmA targets across 16 species, we demonstrate that regulatory evolution occurs primarily through changes in targeted genes rather than the regulatory protein itself. This conserved mechanism with flexible targets may represent an efficient evolutionary strategy for optimizing gene expression for specific lifestyles, highlighting the importance of studying regulation beyond model organisms.