Substrate-dependent effects of quaternary structure on RNase E activity
- Christopher J. Moore1,5,
- Hayoung Go1,2,5,
- Eunkyoung Shin2,5,
- Hye-Jeong Ha2,
- Saemee Song2,3,
- Nam-Chul Ha3,
- Yong-Hak Kim4,
- Stanley N. Cohen1,5 and
- Kangseok Lee2,5
- 1Department of Genetics, Stanford University, Stanford, California 94305, USA;
- 2Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea;
- 3Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Republic of Korea;
- 4Department of Microbiology, Catholic University of Daegu School of Medicine, Daegu 42472, Republic of Korea
- Corresponding authors: sncohen{at}stanford.edu, kangseok{at}cau.ac.kr
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↵5 These authors contributed equally to this work.
Abstract
RNase E is an essential, multifunctional ribonuclease encoded in E. coli by the rne gene. Structural analysis indicates that the ribonucleolytic activity of this enzyme is conferred by rne-encoded polypeptide chains that (1) dimerize to form a catalytic site at the protein-protein interface, and (2) multimerize further to generate a tetrameric quaternary structure consisting of two dimerized Rne-peptide chains. We identify here a mutation in the Rne protein's catalytic region (E429G), as well as a bacterial cell wall peptidoglycan hydrolase (Amidase C [AmiC]), that selectively affect the specific activity of the RNase E enzyme on long RNA substrates, but not on short synthetic oligonucleotides, by enhancing enzyme multimerization. Unlike the increase in specific activity that accompanies concentration-induced multimerization, enhanced multimerization associated with either the E429G mutation or interaction of the Rne protein with AmiC is independent of the substrate's 5′ terminus phosphorylation state. Our findings reveal a previously unsuspected substrate length-dependent regulatory role for RNase E quaternary structure and identify cis-acting and trans-acting factors that mediate such regulation.
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Footnotes
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Supplemental material is available for this article.
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Article published online ahead of print. Article and publication date are online at http://www.genesdev.org/cgi/doi/10.1101/gad.335828.119.
- Received December 5, 2019.
- Accepted December 15, 2020.
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