Two virulent sRNAs identified by genomic sequencing target the type III secretion system in rice bacterial blight pathogen

Abstract

BackgroundSmall non-coding RNA (sRNA) short sequences regulate various biological processes in all organisms, including bacteria that are animal or plant pathogens. Virulent or pathogenicity-associated sRNAs have been increasingly elucidated in animal pathogens but little is known about similar category of sRNAs in plant-pathogenic bacteria. This is particularly true regarding rice bacterial blight pathogen Xanthomonas oryzae pathovar oryzae (Xoo) as studies on the virulent role of Xoo sRNAs is very limited at present.ResultsThe number and genomic distribution of sRNAs in Xoo were determined by bioinformatics analysis based on high throughput sequencing (sRNA-Seq) of the bacterial cultures from virulence-inducing and standard growth media, respectively. A total of 601 sRNAs were identified in the Xoo genome and ten virulent sRNA candidates were screened out based on significant differences of their expression levels between the culture conditions. In addition, trans3287 and trans3288 were also selected as candidates due to high expression levels in both media. The differential expression of 12 sRNAs evidenced by the sRNA-Seq data was confirmed by a convincing quantitative method. Based on genetic analysis of Xoo ΔsRNA mutants generated by deletion of the 12 single sRNAs, trans217 and trans3287 were characterized as virulent sRNAs. They are essential not only for the formation of bacterial blight in a susceptible rice variety Nipponbare but also for the induction of hypersensitive response (HR) in nonhost plant tobacco. Xoo Δtrans217 and Δtrans3287 mutants fail to induce bacterial blight in Nipponbare and also fail to induce the HR in tobacco, whereas, genetic complementation restores both mutants to the wild type in the virulent performance and HR induction. Similar effects of gene knockout and complementation were found in the expression of hrpG and hrpX genes, which encode regulatory proteins of the type III secretion system. Consistently, secretion of a type III effector, PthXo1, is blocked in Δtrans217 or Δtrans3287 bacterial cultures but retrieved by genetic complementation to both mutants.ConclusionsThe genetic analysis characterizes trans217 and trans3287 as pathogenicity-associated sRNAs essential for the bacterial virulence on the susceptible rice variety and for the HR elicitation in the nonhost plant. The molecular evidence suggests that both virulent sRNAs regulate the bacterial virulence by targeting the type III secretion system.Electronic supplementary materialThe online version of this article (10.1186/s12870-018-1470-7) contains supplementary material, which is available to authorized users.

Genome‐wide screen and functional analysis in Xanthomonas reveal a large number of mRNA‐derived sRNAs, including the novel RsmA‐sequester RsmU

“…Work in the last decade has identified three virulence-related sRNAs amongst a number of other sRNAs in different Xanthomonas species (Jiang et al, 2010;Liang et al, 2011;Schmidtke et al, 2012Schmidtke et al, , 2013Hu et al, 2018). Nevertheless, the inventory of sRNAs in Xanthomonas is probably far from complete.…”

“…campestris (Xcc) is the causal agent of black rot disease of cruciferous crops (Mansfield et al ., 2012; Vicente and Holub, 2013) and is a member of a genus of phytopathogenic bacteria that infect many economically important crops causing severe disease and economic losses (Ryan et al ., 2011; An et al ., 2019). Work in the last decade has identified three virulence‐related sRNAs amongst a number of other sRNAs in different Xanthomonas species (Jiang et al ., 2010; Liang et al ., 2011; Schmidtke et al ., 2012, 2013; Hu et al ., 2018). Nevertheless, the inventory of sRNAs in Xanthomonas is probably far from complete.…”

Small RNAs as Fundamental Players in the Transference of Information During Bacterial Infectious Diseases

“…The Hfq chaperone mediates interactions between sRNAs and their targets helping to improve base-pair recognition (Massé et al, 2003;Lenz et al, 2004;Holmqvist and Vogel, 2018;Santiago-Frangos et al, 2019). This protein binds to the regulatory RNAs, helps to stabilize them, and leads the base pairing with the targets (Hu et al, 2018;Han et al, 2019). Hoekzema et al (2019) have suggested an additional mechanism, where the action of Hfq will unfold a hairpin in the targeted mRNA.…”

A key antisense sRNA modulates the oxidative stress response and virulence in Xanthomonas oryzae pv. oryzicola

“…oryzae ( Xoo ), which is closely related to Xoc , a recent study identified sRNAs trans217 and trans3287 as virulence-associated sRNAs that are required for pathogenicity in susceptible rice plants and for the elicitation of the hypersensitive response in nonhost plants. The authors suggested that these sRNAs directly regulate the T3SS in Xoo [ 18 ]. In a prior study [ 19 ], eight sRNAs were functionally characterized in Xoo ; among these, sRNA-Xoo1 was of special interest because it was conserved in other Xanthomonas spp., and its expression was Hfq-dependent.…”