title: Determination of sRNA expressions by RNA-seq in Yersinia pestis grown in vitro and during infection.
abstract: BACKGROUND
  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.
  
  
  RESULTS
  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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China.
authors.forename: Yanfeng
authors.initials: Y
authors.lastname: Yan
authors.forename: Shanchun
authors.initials: S
authors.lastname: Su
authors.forename: Xiangrong
authors.initials: X
authors.lastname: Meng
authors.forename: Xiaolan
authors.initials: X
authors.lastname: Ji
authors.forename: Yi
authors.initials: Y
authors.lastname: Qu
authors.forename: Zizhong
authors.initials: Z
authors.lastname: Liu
authors.forename: Xiaoyi
authors.initials: X
authors.lastname: Wang
authors.forename: Yujun
authors.initials: Y
authors.lastname: Cui
authors.forename: Zhongliang
authors.initials: Z
authors.lastname: Deng
authors.forename: Dongsheng
authors.initials: D
authors.lastname: Zhou
authors.forename: Wencan
authors.initials: W
authors.lastname: Jiang
authors.forename: Ruifu
authors.initials: R
authors.lastname: Yang
authors.forename: Yanping
authors.initials: Y
authors.lastname: Han
mesh_terms: D000818:Animals; D001483:Base Sequence; D003470:Culture Media; D005260:Female; D020869:Gene Expression Profiling; D015964:Gene Expression Regulation, Bacterial; D015723:Gene Library; D059014:High-Throughput Nucleotide Sequencing; D035001:Host Factor 1 Protein / Q000235:genetics* / Q000378:metabolism; D008168:Lung / Q000378:metabolism / Q000382:microbiology* / Q000473:pathology; D051379:Mice; D008807:Mice, Inbred BALB C; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D010930:Plague / Q000382:microbiology; D058727:RNA, Small Untranslated / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D012689:Sequence Homology, Nucleic Acid; D014774:Virulence; D015010:Yersinia pestis / Q000235:genetics* / Q000302:isolation & purification / Q000378:metabolism / Q000472:pathogenicity; D015011:Yersinia pseudotuberculosis / Q000235:genetics
chemical_list: D003470:Culture Media; D035001:Host Factor 1 Protein; D058727:RNA, Small Untranslated
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