Determination of sRNA Expressions by RNA-seq in Yersinia pestis Grown In Vitro and during Infection

• Published in: PloS one Vol. 8; no. 9; p. e74495
• Main Authors: Yan, Yanfeng, Su, Shanchun, Meng, Xiangrong, Ji, Xiaolan, Qu, Yi, Liu, Zizhong, Wang, Xiaoyi, Cui, Yujun, Deng, Zhongliang, Zhou, Dongsheng, Jiang, Wencan, Yang, Ruifu, Han, Yanping
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 11.09.2013; Public Library of Science (PLoS)
• Subjects: Animals; Antisense RNA; Bacteria; Base Sequence; Culture Media; Epidemiology; Female; Gene expression; Gene Expression Profiling; Gene Expression Regulation, Bacterial; Gene Library; Gene regulation; Gene sequencing; Genomes; Genomics; Health aspects; High-Throughput Nucleotide Sequencing; Host Factor 1 Protein - genetics; Host Factor 1 Protein - metabolism; Infection; Infections; Laboratories; Lung - metabolism; Lung - microbiology; Lung - pathology; Lungs; Mice; Mice, Inbred BALB C; Molecular Sequence Annotation; Molecular Sequence Data; Next-generation sequencing; Pathogenesis; Pathogens; Plague - microbiology; Post-transcription; Protein binding; Pseudotuberculosis; Quantitative analysis; Ribonucleic acid; RNA; RNA, Small Untranslated - classification; RNA, Small Untranslated - genetics; RNA, Small Untranslated - metabolism; RNA-binding protein; Sequence Homology, Nucleic Acid; Transcription (Genetics); Virulence; Yersinia pestis; Yersinia pestis - genetics; Yersinia pestis - isolation & purification; Yersinia pestis - metabolism; Yersinia pestis - pathogenicity; Yersinia pseudotuberculosis; Yersinia pseudotuberculosis - genetics; Beijing China; China
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0074495

Small non-coding RNAs (sRNAs) facilitate host-microbe interactions. They have a central function in the post-transcriptional regulation during pathogenic lifestyles. Hfq, an RNA-binding protein that many sRNAs act in conjunction with, is required for Y. pestis pathogenesis. However, information on how Yersinia pestis modulates the expression of sRNAs during infection is largely unknown. We used RNA-seq technology to identify the sRNA candidates expressed from Y. pestis grown in vitro and in the infected lungs of mice. A total of 104 sRNAs were found, including 26 previously annotated sRNAs, by searching against the Rfam database with 78 novel sRNA candidates. Approximately 89% (93/104) of these sRNAs from Y. pestis are shared with its ancestor Y. pseudotuberculosis. Ninety-seven percent of these sRNAs (101/104) are shared among more than 80 sequenced genomes of 135 Y. pestis strains. These 78 novel sRNAs include 62 intergenic and 16 antisense sRNAs. Fourteen sRNAs were selected for verification by independent Northern blot analysis. Results showed that nine selected sRNA transcripts were Hfq-dependent. Interestingly, three novel sRNAs were identified as new members of the transcription factor CRP regulon. Semi-quantitative analysis revealed that Y. pestis from the infected lungs induced the expressions of six sRNAs including RyhB1, RyhB2, CyaR/RyeE, 6S RNA, RybB and sR039 and repressed the expressions of four sRNAs, including CsrB, CsrC, 4.5S RNA and sR027. This study is the first attempt to subject RNA from Y. pestis-infected samples to direct high-throughput sequencing. Many novel sRNAs were identified and the expression patterns of relevant sRNAs in Y. pestis during in vitro growth and in vivo infection were revealed. The annotated sRNAs accounted for the most abundant sRNAs either expressed in bacteria grown in vitro or differentially expressed in the infected lungs. These findings suggested these sRNAs may have important functions in Y. pestis physiology or pathogenesis.