Identification of NAD-RNA species and ADPR-RNA decapping in Archaea

NAD is a coenzyme central to metabolism that also serves as a 5 '-terminal cap for bacterial and eukaryotic transcripts. Thermal degradation of NAD can generate nicotinamide and ADP-ribose (ADPR). Here, we use LC-MS/MS and NAD captureSeq to detect and identify NAD-RNAs in the thermophilic model archaeon Sulfolobus acidocaldarius and in the halophilic mesophile Haloferax volcanii. None of the four Nudix proteins of S. acidocaldarius catalyze NAD-RNA decapping in vitro, but one of the proteins (Saci_NudT5) promotes ADPR-RNA decapping. NAD-RNAs are converted into ADPR-RNAs, which we detect in S. acidocaldarius total RNA. Deletion of the gene encoding the 5 '-3 ' exonuclease Saci-aCPSF2 leads to a 4.5-fold increase in NAD-RNA levels. We propose that the incorporation of NAD into RNA acts as a degradation marker for Saci-aCPSF2. In contrast, ADPR-RNA is processed by Saci_NudT5 into 5 '-p-RNAs, providing another layer of regulation for RNA turnover in archaeal cells. NAD serves as a 5 '-terminal cap for bacterial and eukaryotic transcripts, and can be degraded at high temperatures to generate ADP-ribose (ADPR). Here, Gomes-Filho et al. identify NAD-RNAs in thermophilic and mesophilic archaea and provide insights into NAD- and ADPR-mediated turnover of RNAs in these organisms.