Determination of sRNA expressions by RNA-seq in Yersinia pestis grown in vitro and during infection.

<h4>Background</h4>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 pathogen...

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Autores principales: Yanfeng Yan, Shanchun Su, Xiangrong Meng, Xiaolan Ji, Yi Qu, Zizhong Liu, Xiaoyi Wang, Yujun Cui, Zhongliang Deng, Dongsheng Zhou, Wencan Jiang, Ruifu Yang, Yanping Han
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Publicado: Public Library of Science (PLoS) 2013
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spelling oai:doaj.org-article:36540408a5fe4be2bc42be5d504633692021-11-18T08:55:43ZDetermination of sRNA expressions by RNA-seq in Yersinia pestis grown in vitro and during infection.1932-620310.1371/journal.pone.0074495https://doaj.org/article/36540408a5fe4be2bc42be5d504633692013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24040259/?tool=EBIhttps://doaj.org/toc/1932-6203<h4>Background</h4>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.<h4>Methodology and principal findings</h4>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.<h4>Conclusions and significance</h4>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.Yanfeng YanShanchun SuXiangrong MengXiaolan JiYi QuZizhong LiuXiaoyi WangYujun CuiZhongliang DengDongsheng ZhouWencan JiangRuifu YangYanping HanPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 8, Iss 9, p e74495 (2013)
institution DOAJ
collection DOAJ
language EN
topic Medicine
R
Science
Q
spellingShingle Medicine
R
Science
Q
Yanfeng Yan
Shanchun Su
Xiangrong Meng
Xiaolan Ji
Yi Qu
Zizhong Liu
Xiaoyi Wang
Yujun Cui
Zhongliang Deng
Dongsheng Zhou
Wencan Jiang
Ruifu Yang
Yanping Han
Determination of sRNA expressions by RNA-seq in Yersinia pestis grown in vitro and during infection.
description <h4>Background</h4>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.<h4>Methodology and principal findings</h4>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.<h4>Conclusions and significance</h4>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.
format article
author Yanfeng Yan
Shanchun Su
Xiangrong Meng
Xiaolan Ji
Yi Qu
Zizhong Liu
Xiaoyi Wang
Yujun Cui
Zhongliang Deng
Dongsheng Zhou
Wencan Jiang
Ruifu Yang
Yanping Han
author_facet Yanfeng Yan
Shanchun Su
Xiangrong Meng
Xiaolan Ji
Yi Qu
Zizhong Liu
Xiaoyi Wang
Yujun Cui
Zhongliang Deng
Dongsheng Zhou
Wencan Jiang
Ruifu Yang
Yanping Han
author_sort Yanfeng Yan
title Determination of sRNA expressions by RNA-seq in Yersinia pestis grown in vitro and during infection.
title_short Determination of sRNA expressions by RNA-seq in Yersinia pestis grown in vitro and during infection.
title_full Determination of sRNA expressions by RNA-seq in Yersinia pestis grown in vitro and during infection.
title_fullStr Determination of sRNA expressions by RNA-seq in Yersinia pestis grown in vitro and during infection.
title_full_unstemmed Determination of sRNA expressions by RNA-seq in Yersinia pestis grown in vitro and during infection.
title_sort determination of srna expressions by rna-seq in yersinia pestis grown in vitro and during infection.
publisher Public Library of Science (PLoS)
publishDate 2013
url https://doaj.org/article/36540408a5fe4be2bc42be5d50463369
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