DXO/Rai1 enzymes remove 5'-end FAD and dephospho-CoA caps on RNAs

Nucleic Acids Res. 2020 Jun 19;48(11):6136-6148. doi: 10.1093/nar/gkaa297.


In eukaryotes, the DXO/Rai1 enzymes can eliminate most of the incomplete and non-canonical NAD caps through their decapping, deNADding and pyrophosphohydrolase activities. Here, we report that these enzymes can also remove FAD and dephospho-CoA (dpCoA) non-canonical caps from RNA, and we have named these activities deFADding and deCoAping. The crystal structures of mammalian DXO with 3'-FADP or CoA and fission yeast Rai1 with 3'-FADP provide elegant insight to these activities. FAD and CoA are accommodated in the DXO/Rai1 active site by adopting folded conformations. The flavin of FAD and the pantetheine group of CoA contact the same region at the bottom of the active site tunnel, which undergoes conformational changes to accommodate the different cap moieties. We have developed FAD-capQ to detect and quantify FAD-capped RNAs and determined that FAD caps are present on short RNAs (with less than ∼200 nucleotides) in human cells and that these RNAs are stabilized in the absence of DXO.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Animals
  • Coenzyme A / metabolism*
  • Exoribonucleases / chemistry
  • Exoribonucleases / genetics
  • Exoribonucleases / metabolism*
  • Flavin-Adenine Dinucleotide / analysis
  • Flavin-Adenine Dinucleotide / metabolism*
  • HEK293 Cells
  • Humans
  • In Vitro Techniques
  • Kluyveromyces / enzymology*
  • Mice
  • Models, Molecular
  • NAD / metabolism
  • Nuclear Proteins / chemistry
  • Nuclear Proteins / genetics
  • Nuclear Proteins / metabolism*
  • RNA Caps / analysis
  • RNA Caps / metabolism*
  • RNA, Messenger / chemistry*
  • RNA, Messenger / metabolism*
  • Schizosaccharomyces pombe Proteins / metabolism*
  • Substrate Specificity
  • Transcription, Genetic


  • Nuclear Proteins
  • RNA Caps
  • RNA, Messenger
  • Schizosaccharomyces pombe Proteins
  • NAD
  • Flavin-Adenine Dinucleotide
  • dephosphocoenzyme A
  • Dxo protein, mouse
  • Exoribonucleases
  • Rai1 protein, S pombe
  • Coenzyme A