Characterization of the Small Untranslated RNA RyhB and Its Regulon inVibrio cholerae

Abstract

Numerous small untranslated RNAs (sRNAs) have been identified in Escherichia coli in recent years, and their roles are gradually being defined. However, few of these sRNAs appear to be conserved in Vibrio cholerae, and both identification and characterization of sRNAs in V. cholerae remain at a preliminary stage. We have characterized one of the few sRNAs conserved between E. coli and V. cholerae: RyhB. Sequence conservation is limited to the central region of the gene, and RyhB in V. cholerae is significantly larger than in E. coli. As in E. coli, V. cholerae RyhB is regulated by the iron-dependent repressor Fur, and it interacts with the RNAbinding protein Hfq. The regulons controlled by RyhB in V. cholerae and E. coli appear to differ, although some overlap is evident. Analysis of gene expression in V. cholerae in the absence of RyhB suggests that the role of this sRNA is not limited to control of iron utilization. Quantitation of RyhB expression in the suckling mouse intestine suggests that iron availability is not limiting in this environment, and RyhB is not required for colonization of this mammalian host by V. cholerae.In the past few years, it has become increasingly clear that small untranslated RNAs (sRNAs) regulate many diverse cellular processes. In Escherichia coli, sRNAs have already been shown to modulate sigma factor production, iron utilization, acid resistance, porin expression, and the response to oxidative stress, and functions still need to be defined for a majority of its more than 50 sRNAs (reviewed in reference 2). The modes of action of sRNAs have also been shown to be diverse. In general, sRNA-based regulation is thought to depend upon base pairing between short regions of complementary sequence in the sRNA and its target mRNA(s), although sRNAs that interact with proteins (e.g., CsrB and 6S RNA) have also been described (32,40). Pairing between an sRNA and an mRNA can promote or inhibit mRNA translation or increase or decrease mRNA stability, depending upon the RNAs involved (7,21,22,27). The location of the target sequence within an mRNA probably influences the events that follow binding to an sRNA; still, it is not fully understood how sRNA binding has such a range of consequences.Many of the sRNAs that interact with mRNAs also interact with the RNA-binding protein Hfq. Hfq has homology to eukaryotic Sm proteins and appears to function as an RNA chaperone (12,25,43). Hfq interacts with both sRNAs and mRNAs and can foster formation of sRNA:mRNA complexes. mRNAbinding sRNAs generally have reduced stability in strains lacking Hfq, and their regulatory roles are typically impaired in an hfq strain background (12,25,36). We recently reported that Vibrio cholerae lacking hfq is severely attenuated in its ability to colonize the small intestines of suckling mice and thus is largely avirulent in this commonly used model host for study of cholera pathogenesis (8). This finding suggested that one or more sRNAs might be critical for V. cholerae virulence. Lenz et al. subsequently identified fo...

Evolutionary patterns of Escherichia coli small RNAs and their regulatory interactions

“…However, the interaction between RyhB and sodB mRNA is mediated through other regions of the sRNAs in the two organisms (Davis et al 2005), suggesting that the different variants of Hfq might have different binding preferences, which might have supported the regulatory interactions for these sRNAs and, consequently, their maintenance inside the Enterobacteriales order.…”

The Small RNA RyhB Contributes to Siderophore Production and Virulence of Uropathogenic Escherichia coli

“…In V. cholerae, RyhB modulates the expression of several genes controlling motility, chemotaxis, and biofilm formation. However, a ⌬ryhB mutant is still able to infect mice (24,25). Production of capsular polysaccharide and iron acquisition systems, two factors required for survival within the human host, are regulated by RyhB in K. pneumoniae (26).…”

“…Thus, RyhB plays an essential role in bacteria that require adaptation to iron starvation. Moreover, this sRNA also contributes to many pathogenicity determinants, such as acid resistance in Shigella flexneri (21); eukaryotic cell invasion and cell-to-cell spread in Shigella dysenteriae (22,23); motility, chemotaxis, and biofilm formation in Vibrio cholerae (24,25); biosynthesis of capsular polysaccharide and iron acquisition in Klebsiella pneumoniae (26); and oxidative stress resistance, survival inside human macrophages, and iron acquisition in Salmonella enterica serovar Typhi (27).…”

Vibrio Iron Transport: Evolutionary Adaptation to Life in Multiple Environments

“…Analysis of the RyhB regulon in V. cholerae showed that RyhB influenced the synthesis of superoxide dismutase, TCA cycle enzymes, and proteins containing heme or iron-sulfur clusters (21,236). However, V. cholerae RyhB is considerably larger than its E. coli homolog (Ͼ200 nucleotides, compared to 90 for E. coli) and has a larger regulon, influencing the expression of genes involved in motility, chemotaxis, and biofilm formation.…”