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

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 canmore » undergo 5′-3′ mediated decay.« less

Authors:
 [1];  [2];  [2]; ORCiD logo [2]; ORCiD logo [1]
  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
Publication Date:
Sponsoring Org.:
USDOE
OSTI Identifier:
1576024
Grant/Contract Number:  
AC02-06CH11357
Resource Type:
Published Article
Journal Name:
Nucleic Acids Research
Additional Journal Information:
Journal Name: Nucleic Acids Research; Journal ID: ISSN 0305-1048
Publisher:
Oxford University Press
Country of Publication:
United Kingdom
Language:
English

Citation Formats

Doamekpor, Selom K., Gozdek, Agnieszka, Kwasnik, Aleksandra, Kufel, Joanna, and Tong, Liang. A novel 5′-hydroxyl dinucleotide hydrolase activity for the DXO/Rai1 family of enzymes. United Kingdom: N. p., 2019. Web. doi:10.1093/nar/gkz1107.
Doamekpor, Selom K., Gozdek, Agnieszka, Kwasnik, Aleksandra, Kufel, Joanna, & Tong, Liang. A novel 5′-hydroxyl dinucleotide hydrolase activity for the DXO/Rai1 family of enzymes. United Kingdom. doi:10.1093/nar/gkz1107.
Doamekpor, Selom K., Gozdek, Agnieszka, Kwasnik, Aleksandra, Kufel, Joanna, and Tong, Liang. Thu . "A novel 5′-hydroxyl dinucleotide hydrolase activity for the DXO/Rai1 family of enzymes". United Kingdom. doi:10.1093/nar/gkz1107.
@article{osti_1576024,
title = {A novel 5′-hydroxyl dinucleotide hydrolase activity for the DXO/Rai1 family of enzymes},
author = {Doamekpor, Selom K. and Gozdek, Agnieszka and Kwasnik, Aleksandra and Kufel, Joanna and Tong, Liang},
abstractNote = {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.},
doi = {10.1093/nar/gkz1107},
journal = {Nucleic Acids Research},
number = ,
volume = ,
place = {United Kingdom},
year = {2019},
month = {11}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
DOI: 10.1093/nar/gkz1107

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