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

5 years ago

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