The bacterial endoribonuclease RNase E can cleave RNA in the absence of the RNA chaperone Hfq

• Published in: The Journal of biological chemistry Vol. 294; no. 44; pp. 16465 - 16478
• Main Authors: Baek, Yu Mi, Jang, Kyoung-Jin, Lee, Hyobeen, Yoon, Soojin, Baek, Ahruem, Lee, Kangseok, Kim, Dong-Eun
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01.11.2019; American Society for Biochemistry and Molecular Biology
• Subjects: Binding Sites; endoribonuclease; Endoribonucleases - metabolism; Endoribonucleases - physiology; Enzymology; Escherichia coli - metabolism; Escherichia coli Proteins - metabolism; Escherichia coli Proteins - physiology; Host Factor 1 Protein - chemistry; Host Factor 1 Protein - metabolism; Host Factor 1 Protein - physiology; Molecular Chaperones - metabolism; mRNA decay; Nucleic Acid Conformation; protein expression; ribonuclease; Ribonuclease, Pancreatic; Ribonucleases - metabolism; RNA chaperone Hfq; RNA degradation; RNA processing; RNA Stability - physiology; RNA turnover; RNA, Bacterial - metabolism; RNA, Messenger - genetics; RNA, Small Untranslated - metabolism; RNase E; small guide RNA (sRNA); endoribonuclease; RNA turnover; RNase E; RNA degradation; RNA chaperone Hfq; RNA processing; protein expression; small guide RNA (sRNA); ribonuclease; mRNA decay
• ISSN: 0021-9258; 1083-351X
• DOI: 10.1074/jbc.RA119.010105

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.