Hydrolase Regulates NAD+ Metabolites and Modulates Cellular Redox

Although the classical redox functions of co-enzyme NAD⁺ are firmly established in metabolism, there are numerous enzymes that catalyze cleavage of NAD⁺ to yield free ADP-ribose (ADPr) or related metabolites, whose functions remain largely unknown. Here we show that the Nudix (nucleoside diphosphate linked to another moiety X) hydrolase Ysa1 from Saccharomyces cerevisiae is a major regulator of cellular ADPr and O-acetyl-ADP-ribose (OAADPr). OAADPr is the direct product of NAD⁺-dependent protein deacetylases (sirtuins) and is readily converted to ADPr. Ysa1 cleaves ADPr/OAADPr into ribose phosphate/acetyl-ribose phosphate and AMP. In cells lacking Ysa1 (Δysa1), ADPr and OAADPr levels increased ∼50%, with a corresponding decrease in AMP. Strikingly, Δysa1 cells display higher resistance to exogenous reactive oxygen species (ROS) and 40% lower basal levels of endogenous ROS, compared with wild type. The biochemical basis for these differences in ROS-related phenotypes was investigated, and the results provide evidence that increased ADPr/OAADPr levels protect cells via the following two pathways: (i) lower ROS production through inhibition of complex I of the mitochondrial electron transport chain, and (ii) generation of higher levels of NADPH to suppress ROS damage. The latter occurs through diverting glucose into the pentose phosphate pathway by ADPr inhibition of glyceraldehyde-3-phosphate dehydrogenase, a central enzyme of glycolysis.NAD⁺ is well known for its role as a hydride-transferring co-enzyme in many oxidation-reduction reactions of metabolism. However, NAD⁺ is also a substrate for NAD⁺ glycohydrolases, ADP-ribose transferases, poly(ADP-ribose) polymerases (PARPs),² cyclic ADP-ribose synthases (1, 2), and sirtuins (3, 4), all of which cleave the glycosidic bond of NAD⁺ to produce nicotinamide and an ADP-ribosyl product. Notably, sirtuins catalyze NAD⁺-dependent lysine deacetylation to generate nicotinamide, deacetylated lysine, and OAADPr (5, 6). OAADPr has been proposed to act as a second messenger, signaling to other processes that NAD⁺-dependent protein deacetylation has occurred (7–9). The biological functions and in vivo metabolism of OAADPr and free ADPr are largely unknown.Through a quantitative microinjection assay of starfish oocytes, both ADPr and OAADPr caused a delay/block in oocyte maturation, suggesting ADPr/OAADPr may have specific biological activity (10). In mammalian cells, intracellular ADPr/OAADPr can activate the TRPM2 (transient receptor melastatin-related ion channel 2) nonselective cationic channel (11–13). TRPM2 contains a conserved intracellular Nudix hydrolase domain (referred to as NudT9H) that directly binds ADPr/OAADPr, but it is incapable of cleaving the ligand because a major catalytic residue is missing (11, 14). Although still disputed, ADPr binding to NudT9H appears to be required for the well known oxidative stress activation of the channel (13, 15). Cell stress via puromycin treatment led to TRPM2-mediated cell death that was dependent on sirtuin deacetylases, presumably from the production of OAADPr (12).Increasing evidence suggests that free ADPr may function as a cellular signal. ADPr can be produced from the coordinate actions of PARPs and poly(ADP-ribose) glycohydrolase (PARG), which cleave ADPr polymers to free ADPr (16, 17). Under massive genotoxic stress, hyper-stimulation of the NAD⁺-dependent PARPs depletes cellular NAD⁺, which is linked to catastrophic ATP loss and cell death (18, 19). The mechanism by which PARP1 hyperactivity in the nucleus impairs ATP production in mitochondria is unclear. The fact that PARP1 and poly(ADP-ribose) are localized in the nucleus adds a perplexing aspect. However, recent data suggest that PARP1-induced loss of ATP requires PARG (20). Under conditions of PARP1 hyperactivation, it has been suggested that the PARG-dependent production of ADPr can exit the nucleus and interfere with ATP production in mitochondria (21, 22). Thus ADPr could be the molecular signal released from the nucleus of cells undergoing massive poly(ADP-ribosyl)ation and rapidly triggers mitochondrial dysfunction.In support for ADPr/OAADPr as potential signaling molecules, the existence of enzymes capable of metabolizing these compounds suggests that their cellular concentrations may be subject to tight regulation (23, 24). To understand the biological roles played by ADPr/OAADPr, it is essential to elucidate the degradation pathways that can modulate their levels. Previously we described the ability of several conserved members of the Nudix hydrolase family to hydrolyze in vitro the diphosphate linkage in ADPr/OAADPr, generating ribose phosphate or acetyl-ribose phosphate and AMP (10, 24). Here we examine the biochemical and cellular functions of the Nudix hydrolase Ysa1 (14) from Saccharomyces cerevisiae. We determined that Ysa1 is the major ADPr Nudix hydrolase and an important regulator of cellular ADPr/OAADPr levels. A Δysa1 strain displays increased resistance to both exogenously and endogenously generated ROS. Basal level of ROS decreased by 40% in the Ysa1 deletion strain. We provide biochemical evidence that increased ADPr/OAADPr levels protect cells via the following two pathways: (i) lower ROS production through the inhibition of complex I of the electron transport chain, and (ii) generation of higher NADPH levels to suppress ROS damage. The latter occurs by diverting glucose into the pentose phosphate pathway by ADPr inhibition of glycolysis.