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

Publication Type:

Journal Article


Nucleic Acids Res, Volume 48, Issue 1, p.349-358 (2020)


<p>Modifications at the 5&#39;-end of RNAs play a pivotal role in determining their fate. In eukaryotes, the DXO/Rai1 family of enzymes removes numerous 5&#39;-end RNA modifications, thereby regulating RNA turnover. Mouse DXO catalyzes the elimination of incomplete 5&#39;-end caps (including pyrophosphate) and the non-canonical NAD+ cap on mRNAs, and possesses distributive 5&#39;-3&#39; exoribonuclease activity toward 5&#39;-monophosphate (5&#39;-PO4) RNA. Here, we demonstrate that DXO also catalyzes the hydrolysis of RNAs bearing a 5&#39;-hydroxyl group (5&#39;-OH RNA). The crystal structure of DXO in complex with a 5&#39;-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&#39;-OH RNA. Our nuclease assays confirm this prediction and demonstrate that this 5&#39;-hydroxyl dinucleotide hydrolase (HDH) activity for DXO is higher than the subsequent 5&#39;-3&#39; exoribonuclease activity for selected substrates. Fission yeast Rai1 also has HDH activity although it does not have 5&#39;-3&#39; exonuclease activity, and the Rat1-Rai1 complex can completely degrade 5&#39;-OH RNA. An Arabidopsis DXO1 variant is active toward 5&#39;-OH RNA but prefers 5&#39;-PO4 RNA. Collectively, these studies demonstrate the diverse activities of DXO/Rai1 and expands the collection of RNA substrates that can undergo 5&#39;-3&#39; mediated decay.</p>