4 years ago

New molecular insights into an archaeal RNase J reveal a conserved processive exoribonucleolysis mechanism of the RNase J family

New molecular insights into an archaeal RNase J reveal a conserved processive exoribonucleolysis mechanism of the RNase J family
Xiuzhu Dong, Defeng Li, Na Feng, Xin Zheng, Jie Li
RNase J, a prokaryotic 5′-3′ exo/endoribonuclease, contributes to mRNA decay, rRNA maturation, and post-transcriptional regulation. Yet the processive-exoribonucleolysis mechanism remains obscure. Here, we solved the first RNA-free and RNA-bound structures of an archaeal RNase J, and through intensive biochemical studies provided detailed mechanistic insights into the catalysis and processivity. Distinct dimerization/tetramerization patterns were observed for archaeal and bacterial RNase Js, and unique archaeal Loops I and II were found involved in RNA interaction. A hydrogen-bond-network was identified for the first time that assists catalysis by facilitating efficient proton transfer in the catalytic center. A conserved 5′-monophosphate-binding pocket that coordinates the RNA 5′-end ensures the 5′-monophosphate preferential exoribonucleolysis. To achieve exoribonucleolytic processivity, the 5′-monophosphate-binding pocket and nucleotide +4 binding site anchor RNA within the catalytic track; the 5′-capping residue Leu37 of the sandwich pocket coupled with the 5′-monophosphate-binding pocket are dedicated to translocating and controlling the RNA orientation for each exoribonucleolytic cycle. The processive-exoribonucleolysis mechanism was verified as conserved in bacterial RNase J and also exposes striking parallels with the non-homologous eukaryotic 5′-3′ exoribonuclease, Xrn1. The findings in this work shed light on not only the molecular mechanism of the RNase J family, but also the evolutionary convergence of divergent exoribonucleases. This article is protected by copyright. All rights reserved. This work, through studies on an archaeal RNase J in parallel with a bacterial homolog, reports new insights into the catalysis and exoribonucleolytic processivity of the RNase J family. A hydrogen-bond-network assisting the two-zinc-ion catalysis was identified for the first time. Two major sites anchor RNA, and Leu37, coupled with the 5′-monophosphate-binding pocket, translocate RNA. Interestingly, the disclosed mechanisms of RNase J expose parallels with the non-homologous Xrn1, sustaining the evolutionary principle of ‘different enzymes, but conserved strategy'.

Publisher URL: http://onlinelibrary.wiley.com/resolve/doi

DOI: 10.1111/mmi.13769

You might also like
Discover & Discuss Important Research

Keeping up-to-date with research can feel impossible, with papers being published faster than you'll ever be able to read them. That's where Researcher comes in: we're simplifying discovery and making important discussions happen. With over 19,000 sources, including peer-reviewed journals, preprints, blogs, universities, podcasts and Live events across 10 research areas, you'll never miss what's important to you. It's like social media, but better. Oh, and we should mention - it's free.

  • Download from Google Play
  • Download from App Store
  • Download from AppInChina

Researcher displays publicly available abstracts and doesn’t host any full article content. If the content is open access, we will direct clicks from the abstracts to the publisher website and display the PDF copy on our platform. Clicks to view the full text will be directed to the publisher website, where only users with subscriptions or access through their institution are able to view the full article.