The bacterial endoribonuclease RNase E can cleave RNA in the absence of the RNA chaperone Hfqopen access
- Authors
- Baek, Yu Mi; Jang, Kyoung-Jin; Lee,Hyobeen; Yoon, Soojin; Baek, Ahruem; Lee, Kangseok; Kim, Dong-Eun
- Issue Date
- Nov-2019
- Publisher
- American Society for Biochemistry and Molecular Biology Inc.
- Keywords
- ribonuclease; endoribonuclease; RNA degradation; mRNA decay; RNA processing; RNA turnover; small guide RNA (sRNA); RNase E; RNA chaperone Hfq; protein expression
- Citation
- Journal of Biological Chemistry, v.294, no.44, pp 16465 - 16478
- Pages
- 14
- Journal Title
- Journal of Biological Chemistry
- Volume
- 294
- Number
- 44
- Start Page
- 16465
- End Page
- 16478
- URI
- https://scholarworks.bwise.kr/cau/handle/2019.sw.cau/37103
- DOI
- 10.1074/jbc.RA119.010105
- ISSN
- 0021-9258
1083-351X
- Abstract
- RNase E is a component of the RNA degradosome complex and plays a key role in RNA degradation and maturation in Escherichia coli. RNase E-mediated target RNA degradation typically involves the RNA chaperone Hfq and requires small guide RNAs (sRNAs) acting as a seed by binding to short (7-12-bp) complementary regions in target RNA sequences. Here, using recombinantly expressed and purified proteins, site-directed mutagenesis, and RNA cleavage and protein cross-linking assays, we investigated Hfq-independent RNA decay by RNase E. Exploring its RNA substrate preferences in the absence of Hfq, we observed that RNase E preferentially cleaves AU-rich sites of single-stranded regions of RNA substrates that are annealed to an sRNA that contains a monophosphate at its 5-end. We further found that the quaternary structure of RNase E is also important for complete, Hfq-independent cleavage at sites both proximal and distal to the sRNA-binding site within target RNAs containing monophosphorylated 5-ends. Of note, genetic RNase E variants with unstable quaternary structure exhibited decreased catalytic activity. In summary, our results show that RNase E can degrade its target RNAs in the absence of the RNA chaperone Hfq. We conclude that RNase E-mediated, Hfq-independent RNA decay in E. coli requires a cognate sRNA sequence for annealing to the target RNA, a 5-monophosphate at the RNA 5-end, and a stable RNase E quaternary structure. © 2019 American Society for Biochemistry and Molecular Biology Inc.. All rights reserved.
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