Journal Article

The structure of the box C/D enzyme reveals regulation of RNA methylation

Rakwalska-Bange, Magdalena, Carlomagno, Teresa, Gabel, Frank, Simon, Bernd, Skjaerven, Lars, Lapinaite, Audrone

2013

Overview

Post-transcriptional modifications are essential to the cell life cycle, as they affect both pre-ribosomal RNA processing and ribosome assembly. The box C/D ribonucleoprotein enzyme that methylates ribosomal RNA at the 2′- O -ribose uses a multitude of guide RNAs as templates for the recognition of rRNA target sites. Two methylation guide sequences are combined on each guide RNA, the significance of which has remained unclear. Here we use a powerful combination of NMR spectroscopy and small-angle neutron scattering to solve the structure of the 390 kDa archaeal RNP enzyme bound to substrate RNA. We show that the two methylation guide sequences are located in different environments in the complex and that the methylation of physiological substrates targeted by the same guide RNA occurs sequentially. This structure provides a means for differential control of methylation levels at the two sites and at the same time offers an unexpected regulatory mechanism for rRNA folding. RNAs undergo many types of post-transcriptional modification, including methylation of ribosomal RNAs; here the structure of the archaeal box C/D ribonucleoprotein complex bound to substrate RNA is determined, showing that the two methylation guide sequences exist in different contexts and revealing sequential regulation of methylation at the two sites. Sequential methylation of the box C/D enzyme RNAs undergo many types of post-transcriptional modification. One of these is methylation of the 2′- O -ribose of rRNAs. The modifying enzyme, the box C/D ribonucleoprotein complex, identifies its targets using guide RNAs that recognize two methylation sites. Teresa Carlomagno and colleagues have solved the structure of the 390 kDa archaeal complex bound to substrate RNA. This work shows that the two methylation guide sequences exist in different contexts, a situation that facilitates sequential methylation at the two sites. The authors speculate that this regulated process may influence RNA folding as well.

• Publisher: Nature Publishing Group UK,Nature Publishing Group
• Subject: 631/337/1645/2570 / 631/535/878/1263 / Apoproteins / Apoproteins - chemistry / Apoproteins - metabolism / Archaeal Proteins / Archaeal Proteins - chemistry / Archaeal Proteins - metabolism / Asymmetry / Biocatalysis / Biochemistry, Molecular Biology / Chromosomal Proteins, Non-Histone / Chromosomal Proteins, Non-Histone - metabolism / Enzymes / Experiments / Humanities and Social Sciences / Life Sciences / Methylation / Microscopy / Models, Molecular / Molecular weight / multidisciplinary / Multiprotein Complexes / Multiprotein Complexes - chemistry / Multiprotein Complexes - metabolism / Nucleic Acid Conformation / Post-translational modification / Proteins / Pyrococcus furiosus / Pyrococcus furiosus - enzymology / Pyrococcus furiosus - genetics / Ribonucleoproteins, Small Nucleolar / Ribonucleoproteins, Small Nucleolar - chemistry / Ribonucleoproteins, Small Nucleolar - metabolism / RNA Folding / RNA Processing, Post-Transcriptional / RNA sequencing / RNA, Archaeal / RNA, Archaeal - chemistry / RNA, Archaeal - genetics / RNA, Archaeal - metabolism / RNA, Guide / RNA, Guide - chemistry / RNA, Guide - genetics / RNA, Guide - metabolism / RNA, Ribosomal / RNA, Ribosomal - chemistry / RNA, Ribosomal - metabolism / Science / Structural Biology