Host infection selects for sRNA variants that drive bacterial social cheating

Abstract

Single-nucleotide mutations in regulatory small RNAs (sRNAs) represent a largely unexplored route to social cheating during bacterial infection. Here we show that arcZ, encoding a conserved Hfq-dependent sRNA in the plant pathogen Dickeya solani, undergoes recurrent single-nucleotide mutations during potato tuber infection. Five distinct arcZ alleles define a graded series of ArcZ functional impairment in which antifungal and protease activities are progressively reduced while virulence is compromised only in a subset of alleles. All five variants gain a fitness advantage exclusively during co-infection with wild-type arcZ1 cells. This advantage is strongest when variants are rare and declines as cheater frequency increases, ultimately correlating with reduced total bacterial productivity, the canonical signature of social cheating and a tragedy of the commons. No fitness benefit is detected in vitro. Transcriptomic profiling of five arcZ variants identifies a conserved core of 186 downregulated genes enriched in secreted and diffusible functions. Systematic genetic dissection, supported by quantitative proteomics, establishes BudAB-dependent acetoin production as the dominant cooperative public good exploited during infection. Wild-type arcZ1cells divert pyruvate flux toward acetoin via the BudAB pathway, maintaining a less acidic tissue environment that sustains disease progression; arcZ variants, which repress this pathway, exploit the resulting pH buffering without contributing to it. These results establish pleiotropic regulatory sRNAs as a previously unrecognized class of mutational targets for the emergence of social cheaters during host infection. StatementBacterial populations are not genetically uniform: variants that exploit the cooperative activities of their neighbors, social cheaters, can emerge rapidly within infected tissue and undermine collective bacterial productivity. We show that single-nucleotide mutations in the sRNA ArcZ of Dickeya solani are recurrently selected during potato infection, generating cheater variants that cease contributing to a shared metabolic benefit. Wild-type cells divert pyruvate toward acetoin, buffering tissue pH and sustaining disease; mutant variants exploit this pH maintenance without producing acetoin themselves. Because a single arcZ mutation simultaneously represses a conserved set of 186 genes, including genes involved in secreted and diffusible functions, regulatory sRNA genes represent a previously unrecognized and unusually efficient mutational target for the evolution of social cheating during infection.