Structural basis for substrate binding and catalytic mechanism of a human RNA:m5C methyltransferase NSun6

Abstract

Abstract5-methylcytosine (m5C) modifications of RNA are ubiquitous in nature and play important roles in many biological processes such as protein translational regulation, RNA processing and stress response. Aberrant expressions of RNA:m5C methyltransferases are closely associated with various human diseases including cancers. However, no structural information for RNA-bound RNA:m5C methyltransferase was available until now, hindering elucidation of the catalytic mechanism behind RNA:m5C methylation. Here, we have solved the structures of NSun6, a human tRNA:m5C methyltransferase, in the apo form and in complex with a full-length tRNA substrate. These structures show a non-canonical conformation of the bound tRNA, rendering the base moiety of the target cytosine accessible to the enzyme for methylation. Further biochemical assays reveal the critical, but distinct, roles of two conserved cysteine residues for the RNA:m5C methylation. Collectively, for the first time, we have solved the complex structure of a RNA:m5C methyltransferase and addressed the catalytic mechanism of the RNA:m5C methyltransferase family, which may allow for structure-based drug design toward RNA:m5C methyltransferase–related diseases.

Clinicopathological signature and prognostic value of RNA:m5C methyltransferases in gliomas

“…The seven RNA:m 5 C methyltransferases were screened according to the method reported previously [11,17,18,20]. Furthermore, the RNA expression data of seven RNA:5-methylcytosine methyltransferases were extracted from the downloaded CGGA and TCGA datasets together with the clinical information.…”

“…This post-transcriptional modification of m 5 C has been detected in most RNA species, including messenger RNAs (mRNA), mitochondrial ribosomal RNAs (rRNAs), transfer RNAs (tRNAs), enhancer RNAs (eRNAs), cytoplasmic RNAs and non-coding RNAs [12][13][14][15]. m 5 C methylation of RNA is catalyzed by the NOL1/NOP2/sun domain RNA methyltransferase family and the DNA methyltransferase homologue TRDMT1 (formerly known as the DNA methyltransferase member DNMT2) in eukaryotes, but the function of the binding proteins and demethylases remains unclear, while there is evidence to suggest that YBX1 might be the binding protein for m 5 C [11,[15][16][17][18][19][20]. The cellular functions and modifications of these enzymes contribute to our understanding of the mechanism of m 5 C involvement in epigenetic inheritance related to various diseases, including tumors.…”

“…The NOL1/NOP2/sun domain RNA methyltransferase family consists of 7 members namely, NSUN1 (NOP2 nucleolar protein), NSUN2, NSUN3, NSUN4, NSUN5, NSUN6, and NSUN7. The biological function of these RNA:m 5 C methyltransferases and the modifications they induce have revealed their importance in several aspects of protein biosynthesis, cell proliferation and differentiation, as well as on mitochondrial and nuclear gene expression [18,20,21]. Moreover.…”

Translational Perspective on Epigenetics in Cardiovascular Disease

“…Finally, the role of RNA methylation provides another, largely unexplored, and potentially relevant layer of complexity to the function and significance of ncRNA. Verification of the presence and/or absence of methylation in the different RNA species, the enzymes involved, and the consequences for regulation of gene expression should further increase our understanding of their biological role (8,38). …”

m5C regulator-mediated methylation modification patterns and tumor microenvironment infiltration characterization in papillary thyroid carcinoma

“…Of them, m 5 C modi cation, a reversible RNA post-transcriptional modi cation, exerts an important part in the regulation of mRNA translation, export, alternative splicing (AS) and stabilization localization [14,15]. m 5 C in mRNAs has been extensively studied, and many articles reveal that m 5 C greatly affects mRNAs, tRNAs, and rRNAs [16].…”