Structural insights into mechanisms of the small RNA methyltransferase HEN1

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Abstract
Some of the small RNAs involved in RNA silencing require addition on their 3′ terminal nucleotide of a 2′-O-methyl group in order for the precursor RNA to be processed correctly. This modification is performed by the HEN1 RNA methyltransferase, using AdoMet as a methyl donor. In this study, Ma and colleagues have solved the structure of a plant HEN1 in complex with an RNA duplex and the cofactor product, AdoHcy. The structure reveals how the enzyme recognizes the correct substrate and suggests a new mechanism for methylation. Some of the small RNAs involved in RNA silencing require the addition of a 2′-O-methyl group on the 3′ terminal nucleotide in order for the precursor RNA to be correctly processed. This modification is performed by the HEN1 RNA methyltransferase, the crystal structure of which — from Arabidopsis — is now solved. RNA silencing is a conserved regulatory mechanism in fungi, plants and animals that regulates gene expression and defence against viruses and transgenes1. Small silencing RNAs of ∼20–30 nucleotides and their associated effector proteins, the Argonaute family proteins, are the central components in RNA silencing2. A subset of small RNAs, such as microRNAs and small interfering RNAs (siRNAs) in plants, Piwi-interacting RNAs in animals and siRNAs in Drosophila, requires an additional crucial step for their maturation; that is, 2′-O-methylation on the 3′ terminal nucleotide3,4,5,6. A conserved S-adenosyl-l-methionine-dependent RNA methyltransferase, HUA ENHANCER 1 (HEN1), and its homologues are responsible for this specific modification3,4,5,7,8. Here we report the 3.1 Å crystal structure of full-length HEN1 from Arabidopsis in complex with a 22-nucleotide small RNA duplex and cofactor product S-adenosyl-l-homocysteine. Highly cooperative recognition of the small RNA substrate by multiple RNA binding domains and the methyltransferase domain in HEN1 measures the length of the RNA duplex and determines the substrate specificity. Metal ion coordination by both 2′ and 3′ hydroxyls on the 3′-terminal nucleotide and four invariant residues in the active site of the methyltransferase domain suggests a novel Mg2+-dependent 2′-O-methylation mechanism.