Regulation of coenzyme A levels by degradation: the 'Ins and Outs'

Abstract

Coenzyme A (CoA) is the predominant acyl carrier in mammalian cells and a cofactor that plays a key role in energy and lipid metabolism. CoA and its thioesters (acyl-CoAs) regulate a multitude of metabolic processes at different levels: as substrates, allosteric modulators, and via post-translational modification of histones and other non-histone proteins. Evidence is emerging that synthesis and degradation of CoA are regulated in a manner that enables metabolic flexibility in different subcellular compartments. Degradation of CoA occurs through distinct intra- and extracellular pathways that rely on the activity of specific hydrolases. The pantetheinase enzymes specifically hydrolyze pantetheine to cysteamine and pantothenate, the last step in the extracellular degradation pathway for CoA. This reaction releases pantothenate in the bloodstream, making this CoA precursor available for cellular uptake and de novo CoA synthesis. Intracellular degradation of CoA depends on specific mitochondrial and peroxisomal Nudix hydrolases. These enzymes are also active against a subset of acyl-CoAs and play a key role in the regulation of subcellular (acyl-)CoA pools and CoA-dependent metabolic reactions. The evidence currently available indicates that the extracellular and intracellular (acyl-)CoA degradation pathways are regulated in a coordinated and opposite manner by the nutritional state and maximize the changes in the total intracellular CoA levels that support the metabolic switch between fed and fasted states in organs like the liver. The objective of this review is to update the contribution of these pathways to the regulation of metabolism, physiology and pathology and to highlight the many questions that remain open.

Keywords: Coenzyme A; Metabolic regulation; Nudix hydrolase; Pantetheinases; Pantothenate/organelles.

Figure 1.. Extracellular and intracellular pathways for the degradation of CoA

Degradation of CoA inside and outside the cell occurs through a combination of specific and non-specific enzymes. In the extracellular space, CoA can be hydrolyzed to PPanSH by ENPP enzymes, with or without prior de-phosphorylation to dPCoA, a reaction likely catalyzed by AP. PPanSH can then be dephosphorylated to PanSH by AP or another promiscuous extracellular phosphatase, followed by the specific hydrolysis of PanSH to cysteamine and Pan catalyzed by VNN1–3. Intracellularly, NUDT7, NUDT8 and NUDT19 specifically hydrolyze CoA to PPanSH. These enzymes are also active against select acyl-CoAs. PPanSH could then be dephosphorylated to PanSH, as at least one enzyme, PANK4, is known to catalyze this reaction in vitro. Questions marks are used to specify that the actual identity of the proteins involved in a specific reaction remains unknown. Abbreviations are as follows: AP, alkaline phosphatase; CoA, coenzyme A; dPCoA, dephospho-CoA; ENPP, ectonucleotide pyrophosphatase/phosphodiesterase; LAP, lysosomal acid phosphatase; NUDT, nudix (nucleoside diphosphate linked moiety X)-type motif; Pan, pantothenate; PANK, pantothenate kinase; VNN, vanin.

Figure 2.. Schematic overview of the compartmentalization and interplay between the extracellular and intracellular pathways for (acyl-)CoA degradation and intracellular CoA synthesis

CoA released in the bloodstream from digested food, cell damage or exocytosis (globally referred to as ‘Recycled cellular content’) is degraded to PanSH by the combined activity of promiscuous phosphatases and pyrophosphatases. PanSH is then specifically hydrolyzed to Pan and cysteamine by the action of the VNN enzymes (VNN1 and 3 in mice and VNN1–3 in humans). Pan is taken up in each cell from the bloodstream through SMVT and used to synthesize CoA. Mouse PANK2 resides in the cytosol, while human PANK2 resides in the mitochondrial intermembrane space. In spite of the different subcellular localization of the PANK1–3 isoforms, Pan is likely released into the cytosol. The localization of COASY, the last enzyme in the CoA biosynthetic pathway, is still debated; thus, the subcellular compartment where CoA is synthesized is presently unclear. Major subcellular pools of CoA and acyl-CoAs exist in the cytosol, mitochondria and peroxisomes. The pools of free CoA in the mitochondria and peroxisomes are in part created by the existence of dedicated transporters that can exchange CoA for another adenine-containing substrate, including 3’,5’-ADP. Unlike human SLC25A42 and SLC25A17, the activity of SLC25A16 has not been reconstituted in vitro and this putative CoA transporter is in parenthesis. Peroxisomes can also directly import a variety of acyl-CoAs through the ABCD1–3 transporters. Intracellular reactions that hydrolyze (acyl-)CoA are currently known to occur in the lysosomes, peroxisomes, and mitochondria. In the lysosomes, CoA can be dephosphorylated to dPCoA, likely by the action of LAP. Long-chain acyl-CoAs could be first hydrolyzed to CoA plus a non-esterified fatty acid by the lysosomal enzyme PPT, followed by dephosphorylation of CoA by LAP. Export of lysosomal dPCoA to the cytosol is expected to require a transporter, but none is currently known. Overall, the presence of CoA metabolites inside the lysosomes could be the result of intracellular scavenging processes, such as autophagy, which can recycle metabolites for a cell-autonomous use or export them in the extracellular milieu by fusion with the plasma membrane. Peroxisomes and mitochondria contain the (acyl-)CoA-degrading enzymes NUDT7, NUDT19 and NUDT8, which hydrolyze CoA and acyl-CoAs to PPanSH or its acylated derivative (acyl-PPanSH), respectively, and 3’,5-ADP. Acyl-PPanSH produced in the peroxisomes could be hydrolyzed to PPanSH by acyl-CoA thioesterases, possibly ACOT3 and ACOT8, and released in the cytosol. Cytosolic PPanSH could directly re-enter the CoA biosynthetic pathway downstream of the regulated step catalyzed by the PANKs; alternatively, PPanSH could be dephosphorylated to PanSH by an intracellular phosphatase. An inactive human PANK isoform, PANK4, has been shown to possess this activity in vitro. With respect to (acyl-)CoA degradation in the mitochondria, it remains to be confirmed whether NUDT8 and COASY co-localize to the matrix, where PPanSH produced by degradation could be recycled to CoA. Furthermore, the ability of mitochondrial ACOTs to hydrolyze acyl-PPanSH to PanSH remains untested. Dotted lines indicate unresolved issues, such as the ability of PPanSH to diffuse across membranes and the enzymatic activities of mitochondrial ACOTs, which have not been experimentally confirmed. Questions marks are used to specify that the actual identity of the proteins involved in a specific reaction or process remains unknown. Abbreviations are as follows: ABCD, ATP-binding cassette subfamily D; ACOT, acyl-CoA thioesterase; AP, alkaline phosphatase; BPNT1, bisphosphate 3’-nucleotidase 1; cyt, cytosol; CoA, coenzyme A; COASY, coenzyme A synthase; dPCoA, dephospho-CoA; ENPP, ectonucleotide pyrophosphatase/phosphodiesterase; IMS, mitochondrial intermembrane space; LAP, lysosomal acid phosphatase; NUDT, nudix (nucleoside diphosphate linked moiety X)-type motif; OMM, mitochondrial outer membrane space; Pan, pantothenate; PANK, pantothenate kinase; PanSH, pantetheine; PPanSH, phosphopantetheine; PPCDC, phosphopantothenoylcysteine decarboxylase; PPCS, phosphopantothenoylcysteine synthetase; PPT, palmitoyl-protein thioesterase; SLC, solute carrier; SMVT, sodium-dependent multivitamin transporter; VNN, vanin.

Figure 3.. Regulation of extracellular and intracellular degradation pathways for CoA in the fed and fasted states

In the fed state, food-derived CoA is likely the main source of Pan, which is released in the bloodstream by the action of the extracellular degradation pathway in the intestine. The concentration of Pan in the blood is also regulated by urinary excretion. In the liver, feeding after a fast stimulates the intracellular degradation pathway to achieve a net decrease in total intracellular CoA levels, mainly driven by a decline in the concentration of free CoA. In the fasted state, systemic VNN1 levels raise considerably in the blood and this enzyme could be involved in the recycling of Pan released from damaged cells or exocytosis. Another source of Pan is the microbiota. The contribution of recycled cellular content and microbiota to the circulating levels of Pan is currently unknown (dotted lines). Supported by decreased urinary excretion, Pan levels in the blood increase in the fasted state, making more substrate available for the increase in CoA synthesis observed in the liver. Concurrently, hepatic NUDT7 expression decreases. While NUDT8 levels remain unchanged with fasting and feeding, other mechanisms (allosteric and/or post-translational regulation) could modulate the activity of this mitochondrial enzyme, which would be expected to be higher in the fed state compared to the fasted state.