Fueling genome maintenance: On the versatile roles of NAD+ in preserving DNA integrity

Abstract

NAD⁺ is a versatile biomolecule acting as a master regulator and substrate in various cellular processes, including redox regulation, metabolism, and various signaling pathways. In this article, we concisely and critically review the role of NAD⁺ in mechanisms promoting genome maintenance. Numerous NAD⁺-dependent reactions are involved in the preservation of genome stability, the cellular DNA damage response, and other pathways regulating nucleic acid metabolism, such as gene expression and cell proliferation pathways. Of note, NAD⁺ serves as a substrate to ADP-ribosyltransferases, sirtuins, and potentially also eukaryotic DNA ligases, all of which regulate various aspects of DNA integrity, damage repair, and gene expression. Finally, we critically analyze recent developments in the field as well as discuss challenges associated with therapeutic actions intended to raise NAD⁺ levels.

Keywords: ARTs; DNA repair; NAD; PARPs; sirtuins.

Figure 1

Major DNA repair pathways. DNA repair occurs via different pathways involving multiple proteins, among them many are directly NAD⁺ dependent (shaded in orange). Repair of single-strand breaks (SSBs) through base excision repair (BER) involves NAD⁺-consuming PARP1 and PARP2. Double-strand breaks (DSBs) are repaired either through homologous recombination (HR) or nonhomologous end-joining (NHEJ) pathways, facilitated by multiple ARTDs and SIRTs. NAD⁺-dependent enzymes are also implicated in nucleotide excision repair (NER) as well as mismatch repair (MMR) pathways. A potential NAD⁺-dependent role of LIG IV is under discussion (see text for details). ARTD, diphtheria toxin–like ADP-ribosyltransferase; LIG IV, ligase IV; PARP, poly-ADP-ribose polymerase; SIRT, sirtuin.

Figure 2

NAD⁺biosynthesis and major cellular functions. Cellular NAD⁺ levels are maintained by biosynthesis from dietary precursors: amino acid tryptophan (Trp) and vitamin B3, which comprises nicotinic acid (NA), nicotinamide (NAM), and nicotinamide riboside (NR). Trp is converted to quinolinic acid (QA) in the kynurenine pathway and further by quinolinate phosphoribosyltransferase (QAPRT) into nicotinamide mononucleotide (NAMN). NAMN is also produced from NA in the Preiss–Handler pathway by nicotinic acid phosphoribosyltransferase (NAPRT). Both pathways are completed by the transformation of NAMN into nicotinic acid adenine dinucleotide (NAAD) by nicotinamide mononucleotide adenylyltransferases (NMNAT1, NMNAT2, and NMNAT3) and further into NAD⁺ by NAD⁺ synthetase (NADS). The salvage pathway recycles NAM produced by NAD⁺-consuming enzymes: sirtuins (SIRTs), ADP-ribosyltransferases (ARTDs), as well NAD⁺ glycohydrolases and cyclic ADP-ribose synthases. NAM is transformed by nicotinamide phosphoribosyltransferase (NAMPT) into nicotinamide mononucleotide (NMN), which is then turned into NAD⁺via NMNATs. This pathway can be also fueled by NR, derived from diet or from dephosphorylation of nicotinamide mononucleotide (NMN). NAD⁺ levels are balanced by subcellular compartmentalization of NAD⁺ synthesis and consumption. In the cytoplasm and mitochondria, NAD⁺ is utilized via multiple pathways in bioenergetics, maintenance of redox homeostasis, or cell signaling. Whereas the nuclear NAD⁺ pool contributes in addition to maintenance of genomic homeostasis mainly via the NAD⁺-dependent ARTDs and SIRTs (see text for details).

Figure 3

NAD⁺-consuming reactions in genome maintenance.A, diphtheria toxin-like ADP-ribosyltransferases (ARTDs) catalyze the cleavage of N-glycosidic bond and covalently attaches ADP ribose (ADPR) moiety to target molecules: protein, DNA, or RNA. ARTD family members perform a transfer of either single ADPR units (MARylation) or multiple ADPR units (PARylation), connected in a linear or branched manner. B, sirtuins (SIRTs) mediate a transfer of an acyl group from protein to NAD⁺-derived ADPR, producing O-acyl-ADPR and NAM. C, DNA ligase IV (LIG IV) potentially uses α-phosphate moiety of NAD⁺ to form a new phosphodiester bond in the process of DNA nick repair. For references, see text.