A novel 5′-hydroxyl dinucleotide hydrolase activity for the DXO/Rai1 family of enzymes

Journal Article · Thu Nov 28 00:00:00 EST 2019 · Nucleic Acids Research

DOI:https://doi.org/10.1093/nar/gkz1107· OSTI ID:1576024

Doamekpor, Selom K. ^[1]; Gozdek, Agnieszka ^[2]; Kwasnik, Aleksandra ^[2]; Kufel, Joanna  ^[2]; Tong, Liang  ^[1]

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1. Department of Biological Sciences, Columbia University, New York, NY 10027, USA
2. Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland

Abstract Modifications at the 5′-end of RNAs play a pivotal role in determining their fate. In eukaryotes, the DXO/Rai1 family of enzymes removes numerous 5′-end RNA modifications, thereby regulating RNA turnover. Mouse DXO catalyzes the elimination of incomplete 5′-end caps (including pyrophosphate) and the non-canonical NAD+ cap on mRNAs, and possesses distributive 5′-3′ exoribonuclease activity toward 5′-monophosphate (5′-PO4) RNA. Here, we demonstrate that DXO also catalyzes the hydrolysis of RNAs bearing a 5′-hydroxyl group (5′-OH RNA). The crystal structure of DXO in complex with a 5′-OH RNA substrate mimic at 2.0 Å resolution provides elegant insight into the molecular mechanism of this activity. More importantly, the structure predicts that DXO first removes a dinucleotide from 5′-OH RNA. Our nuclease assays confirm this prediction and demonstrate that this 5′-hydroxyl dinucleotide hydrolase (HDH) activity for DXO is higher than the subsequent 5′-3′ exoribonuclease activity for selected substrates. Fission yeast Rai1 also has HDH activity although it does not have 5′-3′ exonuclease activity, and the Rat1-Rai1 complex can completely degrade 5′-OH RNA. An Arabidopsis DXO1 variant is active toward 5′-OH RNA but prefers 5′-PO4 RNA. Collectively, these studies demonstrate the diverse activities of DXO/Rai1 and expands the collection of RNA substrates that can undergo 5′-3′ mediated decay.

• Research Organization: Argonne National Laboratory (ANL), Argonne, IL (United States)
• Sponsoring Organization: USDOE Office of Science (SC); National Institutes of Health (NIH); National Science Centre
• Grant/Contract Number: AC02-06CH11357; R35GM118093; S10OD012018; UMO-2014/15/B/NZ2/02302; P41 GM103403
• OSTI ID: 1576024
• Alternate ID(s): OSTI ID: 1591903
• Journal Information: Nucleic Acids Research, Journal Name: Nucleic Acids Research Vol. 48 Journal Issue: 1; ISSN 0305-1048
• Publisher: Oxford University Press
• Country of Publication: United Kingdom
• Language: English

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
nucleic acid enzymes