期刊
JOURNAL OF BIOLOGICAL CHEMISTRY
卷 294, 期 44, 页码 16465-16478出版社
AMER SOC BIOCHEMISTRY MOLECULAR BIOLOGY INC
DOI: 10.1074/jbc.RA119.010105
关键词
ribonuclease; endoribonuclease; RNA degradation; mRNA decay; RNA processing; RNA turnover; protein expression; RNA chaperone Hfq; RNase E; small guide RNA (sRNA)
资金
- Konkuk University
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.
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