Identification and characterization of small RNAs inYersinia pestis

Abstract

Yersinia pestis, the etiologic agent of plague, is closely related to Yersinia pseudotuberculosis evolutionarily but has a very different mode of infection. The RNA-binding regulatory protein, Hfq, mediates regulation by small RNAs (sRNAs) and is required for virulence of both Y. pestis and Y. pseudotuberculosis. Moreover, Hfq is required for growth of Y. pestis, but not Y. pseudotuberculosis, at 37°C. Together, these observations suggest that sRNAs play important roles in the virulence and survival of Y. pestis, and that regulation by sRNAs may account for some of the differences between Y. pestis and Y. pseudotuberculosis. We have used a deep sequencing approach to identify 31 sRNAs in Y. pestis. The majority of these sRNAs are not conserved outside the Yersiniae. Expression of the sRNAs was confirmed by Northern analysis and we developed deep sequencing approaches to map 5ʹ and 3ʹ ends of many sRNAs simultaneously. Expression of the majority of the sRNAs we identified is dependent upon Hfq. We also observed temperature-dependent effects on the expression of many sRNAs, and differences in expression patterns between Y. pestis and Y. pseudotuberculosis. Thus, our data suggest that regulation by sRNAs plays an important role in the lifestyle switch from flea to mammalian host, and that regulation by sRNAs may contribute to the phenotypic differences between Y. pestis and Y. pseudotuberculosis.

Genome-Wide Analysis of Small RNAs Expressed by Yersinia pestis Identifies a Regulator of the Yop-Ysc Type III Secretion System

“…While there exists some overlap in the sRNA sets discovered in each of these studies, there are a large number of potential sRNAs that are unique to each study. Recently, Beauregard et al identified 15 previously unannotated sRNAs in the KIM6ϩ strain of Y. pestis (33). This group also identified several previously annotated sRNAs and multiple Ysrs described in our previous study; we subsequently detected in Y. pestis CO92 the expression of 2 Ysrs found in the KIM6ϩ strain (Ysr164 and Ysr172).…”

“…This group also identified several previously annotated sRNAs and multiple Ysrs described in our previous study; we subsequently detected in Y. pestis CO92 the expression of 2 Ysrs found in the KIM6ϩ strain (Ysr164 and Ysr172). A second report identified 104 sRNAs in Y. pestis strain 201 from both in vitro-and in vivo-derived samples, and 56 of these were not identified by our previous study or by the study of Beauregard et al (33). In the current study, only one of the sRNAs identified (Ysr222 or sR049) was also detected by Yan et al (35).…”

“…These data build upon our previous study as well as those from several other groups that have identified sRNAs in Yersinia (31,(33)(34)(35). While there exists some overlap in the sRNA sets discovered in each of these studies, there are a large number of potential sRNAs that are unique to each study.…”

“…Recently, several studies have catalogued multiple cohorts of sRNAs expressed by Y. pestis and Y. pseudotuberculosis under various conditions (30,31,(33)(34)(35), but a specific sRNA that contributes to the regulation of the T3SS in Y. pestis has not been identified. Here we present evidence for the posttranscriptional regulation of the synthesis of the T3SS effector protein YopJ by the Yersinia-specific sRNA Ysr141, as well as describe the identification of 63 additional putative sRNAs expressed by Y. pestis.…”

Reannotation of Yersinia pestis Strain 91001 Based on Omics Data

“…The expression profile data were obtained from microarray hybridization experiments, 32 and the sRNA data were obtained from RNA-seq results. 18 In addition, data from related literatures, including MS data from the KIM, CO92, and PestoidesF strains, and sRNA data from the 91001 and KIM strains, 33,34 were collected manually.…”