tRNA m1G9 modification depends on substrate-specific RNA conformational changes induced by the methyltransferase Trm10

• Type of Material: Article
• Authors: Sarah Strassler, Emory University; Isobel E. Bowles, Ohio State University, Columbus; Aiswarya Krishnamohan, Ohio State University, Columbus; Hyejeong Kim, Ohio State University, Columbus; Catherine B. Edgington, Ohio State University, Columbus; Emily G. Kuiper, Emory University; Clio J. Hancock, Emory University; Lindsay R. Comstock, Wake Forest University; Jane E. Jackman, Ohio State University, Columbus; Graeme Conn, Emory University
• Language: English
• Date: 2023-11-08
• Publisher: American Society for Biochemistry and Molecular Biology
• Publication Version: Final Published Version
• Copyright Statement: © 2023 The Authors
• License: Creative Commons Attribution 4.0 International
• Final Published Version (URL): https://doi.org/10.1016/j.jbc.2023.105443
• Title of Journal or Parent Work: Journal of Biological Chemistry
• Volume: 299
• Issue: 12
• Start Page: 105443
• Grant/Funding Information: This research was supported by the National Institute of General Medical Sciences award R01 GM130135 (to J. E. J. and G. L. C.), the NSF GRFP award 1937971 (to S. E. S.), and the OSU Center for RNA Biology Graduate Fellowship (to I. E. B.). Research reported in this publication was also supported by the Office of the Director, NIH, under award number S10 OD023582.
• Keywords: RNA methylation; SPOUT methyltransferase; SHAPE RNA structure probing; substrate recognition; transfer RNA (tRNA); RNA structure
• Research Categories: Biology, Molecular; Biology, Neuroscience

Abstract

The methyltransferase Trm10 modifies a subset of tRNAs on the base N1 position of the ninth nucleotide in the tRNA core. Trm10 is conserved throughout Eukarya and Archaea, and mutations in the human gene (TRMT10A) have been linked to neurological disorders such as microcephaly and intellectual disability, as well as defects in glucose metabolism. Of the 26 tRNAs in yeast with guanosine at position 9, only 13 are substrates for Trm10. However, no common sequence or other posttranscriptional modifications have been identified among these substrates, suggesting the presence of some other tRNA feature(s) that allow Trm10 to distinguish substrate from nonsubstrate tRNAs. Here, we show that substrate recognition by Saccharomyces cerevisiae Trm10 is dependent on both intrinsic tRNA flexibility and the ability of the enzyme to induce specific tRNA conformational changes upon binding. Using the sensitive RNA structure-probing method SHAPE, conformational changes upon binding to Trm10 in tRNA substrates, but not nonsubstrates, were identified and mapped onto a model of Trm10-bound tRNA. These changes may play an important role in substrate recognition by allowing Trm10 to gain access to the target nucleotide. Our results highlight a novel mechanism of substrate recognition by a conserved tRNA modifying enzyme. Further, these studies reveal a strategy for substrate recognition that may be broadly employed by tRNA-modifying enzymes which must distinguish between structurally similar tRNA species.