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

José Vicente Gomes-Filho (), Ruth Breuer, Hector Gabriel Morales-Filloy, Nadiia Pozhydaieva, Andreas Borst, Nicole Paczia, Jörg Soppa, Katharina Höfer, Andres Jäschke and Lennart Randau ()
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José Vicente Gomes-Filho: Philipps-Universität Marburg
Ruth Breuer: Philipps-Universität Marburg
Hector Gabriel Morales-Filloy: Heidelberg University
Nadiia Pozhydaieva: Max Planck Institute for Terrestrial Microbiology
Andreas Borst: Biocentre, Goethe-University
Nicole Paczia: Max Planck Institute for Terrestrial Microbiology
Jörg Soppa: Biocentre, Goethe-University
Katharina Höfer: Max Planck Institute for Terrestrial Microbiology
Andres Jäschke: Heidelberg University
Lennart Randau: Philipps-Universität Marburg

Nature Communications, 2023, vol. 14, issue 1, 1-12

Abstract: Abstract 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.

Date: 2023
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DOI: 10.1038/s41467-023-43377-x

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