Participation of two sRNA RyhB homologs from the fish pathogen Yersinia ruckeri in bacterial physiology

Small noncoding RNAs (sRNAs) are important regulators of gene expression and physiology in bacteria. RyhB is an iron-responsive sRNA well characterized in Escherichia coli and conserved in other Enterobacteriaceae. In this study, we identified and characterized two RyhB homologs (named RyhB-1 and RyhB-2) in the fish pathogen Yersinia ruckeri. We found that, as in other Enterobacteriaceae, both RyhB-1 and RyhB-2 are induced under iron starvation, repressed by the Fur regulator, and depend on Hfq for stability. Despite these similarities in expression, the mutant strains of Y. ruckeri lacking RyhB-1 (Delta ryhB-1) or RyhB-2 (Delta ryhB-2) exhibited differential phenotypes. In comparison with the wild type, the Delta ryhB-1 strain showed a hypermotile phenotype, reduced biofilm formation, increased replication rate, faster growth, and increased ATP levels in bacterial cultures. By contrast, in salmon cell cultures, the Delta ryhB-1 strain exhibited an increased survival. On the other hand, the Delta ryhB-2 strain was non-motile and showed augmented biofilm formation as compared to the wild type. The expression of a subset of RyhB conserved targets, selected from different bacterial species, was analyzed by quantitative RT-PCR in wild type, Delta ryhB-1, Delta ryhB-2, and Delta ryhB-1 Delta ryhB-2 strains cultured in iron-depleted media. RyhB-1 negatively affected the expression of most analyzed genes (sodB, acnA, sdhC, bfr, fliF, among others), whose functions are related to metabolism and motility, involving iron-containing proteins. Among the genes analyzed, only sdhC and bfr appeared as targets for RyhB-2. Taken together, these results indicate that Y. ruckeri RyhB homologs participate in the modulation of the bacterial physiology with non-redundant roles.

Automated summary

Small noncoding RNAs, such as RyhB, play vital roles in gene expression and physiology regulation in bacteria. In this study, two RyhB homologs, RyhB-1 and RyhB-2, were identified and characterized in the fish pathogen Yersinia ruckeri. Despite similar expression patterns under iron starvation, mutant strains lacking RyhB-1 or RyhB-2 exhibited distinct phenotypes, indicating non-redundant roles in modulating bacterial physiology.