A novel 5′-hydroxyl dinucleotide hydrolase activity for the DXO/Rai1 family of enzymes. Issue 1 (28th November 2019)

• Record Type: Journal Article
• Authors: Doamekpor, Selom K; Gozdek, Agnieszka; Kwasnik, Aleksandra; Kufel, Joanna; Tong, Liang
• Is Part Of: Nucleic acids research. Volume 48:Issue 1(2020)
• Page Start: 349
• Page End: 358
• Publication Date: 2019-11-28
• Subjects: Nucleic acids -- Periodicals; Molecular biology -- Periodicals; 572.805
• DOI: 10.1093/nar/gkz1107
• Languages: English
• ISSNs: 0305-1048

Abstract

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.