共查询到20条相似文献,搜索用时 31 毫秒
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Shafagh A Waters Sean P McAteer Grzegorz Kudla Ignatius Pang Nandan P Deshpande Timothy G Amos Kai Wen Leong Marc R Wilkins Richard Strugnell David L Gally David Tollervey Jai J Tree 《The EMBO journal》2017,36(3):374-387
RNA sequencing studies have identified hundreds of non‐coding RNAs in bacteria, including regulatory small RNA (sRNA). However, our understanding of sRNA function has lagged behind their identification due to a lack of tools for the high‐throughput analysis of RNA–RNA interactions in bacteria. Here we demonstrate that in vivo sRNA–mRNA duplexes can be recovered using UV‐crosslinking, ligation and sequencing of hybrids (CLASH). Many sRNAs recruit the endoribonuclease, RNase E, to facilitate processing of mRNAs. We were able to recover base‐paired sRNA–mRNA duplexes in association with RNase E, allowing proximity‐dependent ligation and sequencing of cognate sRNA–mRNA pairs as chimeric reads. We verified that this approach captures bona fide sRNA–mRNA interactions. Clustering analyses identified novel sRNA seed regions and sets of potentially co‐regulated target mRNAs. We identified multiple mRNA targets for the pathotype‐specific sRNA Esr41, which was shown to regulate colicin sensitivity and iron transport in E. coli. Numerous sRNA interactions were also identified with non‐coding RNAs, including sRNAs and tRNAs, demonstrating the high complexity of the sRNA interactome. 相似文献
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Yongjian Zhang Xiangyu Wu Lixing Yuan 《The Plant journal : for cell and molecular biology》2020,102(4):823-837
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Benjamin Diel Magali Dequivre Florence Wisniewski-Dyé Ludovic Vial Florence Hommais 《Environmental microbiology》2019,21(8):3063-3075
Plasmids are mobile DNAs that can adjust host cell functions for their own amplification and dissemination. We identified Quorum sensing flagella small RNA regulator (QfsR), a small RNA, transcribed from the virulence tumour-inducing (Ti) plasmid in the phytopathogen Agrobacterium fabrum. QfsR is widely conserved throughout RepABC plasmids carried by Rhizobiaceae. Target prediction, expression analysis and site-direct mutagenesis experiments showed that QfsR directly pairs within polycistronic mRNAs transcribed from chromosome (genes involved in flagella apparatus) and Ti plasmid (genes involved in conjugative transfer). QfsR leads to a coordinated expression of whole polycistronic mRNA molecules. Whereas a lack of QfsR represses motility, its overproduction increases the quorum sensing signal accumulation and the Ti plasmid conjugative transfer. Based on these observations, we propose QfsR as a hub connecting regulatory networks of motility and plasmid conjugative transfer. To our knowledge, QfsR is the first example of a plasmid-encoded sRNA that controls chromosomal polycistronic gene expression. 相似文献
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The Restorer‐of‐fertility‐like 2 pentatricopeptide repeat protein and RNase P are required for the processing of mitochondrial orf291 RNA in Arabidopsis
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Sota Fujii Takamasa Suzuki Philippe Giegé Tetsuya Higashiyama Nobuya Koizuka Toshiharu Shikanai 《The Plant journal : for cell and molecular biology》2016,86(6):504-513
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