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

• Published in: Nature communications 2023-11, Vol.14 (1), p.7597-7597, Article 7597
• Main Authors: Gomes-Filho, José Vicente, Breuer, Ruth, Morales-Filloy, Hector Gabriel, Pozhydaieva, Nadiia, Borst, Andreas, Paczia, Nicole, Soppa, Jörg, Höfer, Katharina, Jäschke, Andres, Randau, Lennart
• Format: Article
• Language: English
• Subjects: 38/77; 45; 45/22; 45/71; 45/88; 45/90; 45/91; 631/326/26/2523; 631/326/26/2527; 631/337/1645/2570; Adenosine diphosphate; Archaea; Bacteria; Biodegradation; Enzymes; Exonuclease; Gene deletion; Gram-positive bacteria; High temperature; Humanities and Social Sciences; Mesophilic archaea; multidisciplinary; NAD; Nicotinamide; Proteins; Ribonucleic acid; Ribose; RNA; RNA polymerase; Science; Science (multidisciplinary); Thermal degradation
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-023-43377-x

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.