Acylation of Proteins by Myristic Acid in Isolated Mitochondria

Post-translational palmitoylation of metabolic proteins

Numerous cellular proteins are post-translationally modified by addition of a lipid group to their structure, which dynamically influences the proteome by increasing hydrophobicity of proteins often impacting protein conformation, localization, stability, and binding affinity. These lipid modifications include myristoylation and palmitoylation. Palmitoylation involves a 16-carbon saturated fatty acyl chain being covalently linked to a cysteine thiol through a thioester bond. Palmitoylation is unique within this group of modifications, as the addition of the palmitoyl group is reversible and enzyme driven, rapidly affecting protein targeting, stability and subcellular trafficking. The palmitoylation reaction is catalyzed by a large family of Asp-His-His-Cys (DHHCs) motif-containing palmitoyl acyltransferases, while the reverse reaction is catalyzed by acyl-protein thioesterases (APTs), that remove the acyl chain. Palmitoyl-CoA serves an important dual purpose as it is not only a key metabolite fueling energy metabolism, but is also a substrate for this PTM. In this review, we discuss protein palmitoylation in regulating substrate metabolism, focusing on membrane transport proteins and kinases that participate in substrate uptake into the cell. We then explore the palmitoylation of mitochondrial proteins and the palmitoylation regulatory enzymes, a less explored field for potential lipid metabolic regulation.

Optical spectroscopy in turbid media using an integrating sphere: mitochondrial chromophore analysis during metabolic transitions

Recent evidence suggests that the activity of mitochondrial oxidative phosphorylation complexes (MOPCs) is modulated at multiple sites. Here, a method of optically monitoring electron distribution within and between MOPCs is described using a center-mounted sample in an integrating sphere (to minimize scattering effects) with a rapid-scanning spectrometer. The redox-sensitive MOPC absorbances (∼465-630 nm) were modeled using linear least squares analysis with individual chromophore spectra. Classical mitochondrial activity transitions (e.g., ADP-induced increase in oxygen consumption) were used to characterize this approach. Most notable in these studies was the observation that intermediates of the catalytic cycle of cytochrome oxidase are dynamically modulated with metabolic state. The MOPC redox state, along with measurements of oxygen consumption and mitochondrial membrane potential, was used to evaluate the conductances of different sections of the electron transport chain. This analysis then was applied to mitochondria isolated from rabbit hearts subjected to ischemia/reperfusion (I/R). Surprisingly, I/R resulted in an inhibition of all measured MOPC conductances, suggesting a coordinated down-regulation of mitochondrial activity with this well-established cardiac perturbation.

The mitochondrial proteome: a dynamic functional program in tissues and disease states

The nuclear DNA transcriptional programming of the mitochondria proteome varies dramatically between tissues depending on its functional requirements. This programming generally regulates all of the proteins associated with a metabolic or biosynthetic pathway associated with a given function, essentially regulating the maximum rate of the pathway while keeping the enzymes at the same molar ratio. This may permit the same regulatory mechanisms to function at low- and high-flux capacity situations. This alteration in total protein content results in rather dramatic changes in the mitochondria proteome between tissues. A tissues mitochondria proteome also changes with disease state, in Type 1 diabetes the liver mitochondrial proteome shifts to support ATP production, urea synthesis, and fatty acid oxidation. Acute flux regulation is modulated by numerous posttranslational events that also are highly variable between tissues. The most studied posttranslational modification is protein phosphorylation, which is found all of the complexes of oxidative phosphorylation and most of the major metabolic pathways. The functional significance of these modifications is currently a major area of research along with the kinase and phosphatase regulatory network. This near ubiquitous presence of protein phosphorylations, and other posttranslational events, in the matrix suggest that not all posttranslational events have functional significance. Screening methods are being introduced to detect the active or dynamic posttranslational sites to focus attention on sites that might provide insight into regulatory mechanisms.

Palmitoylation of ketogenic enzyme HMGCS2 enhances its interaction with PPARalpha and transcription at the Hmgcs2 PPRE

Excessive liver production of ketone bodies is one of many metabolic complications that can arise from diabetes, and in severe untreated cases, it can result in ketoacidosis, coma, and death. Mitochondrial HMG-CoA synthase (HMGCS2), the rate-limiting enzyme in ketogenesis, has been shown to interact with PPARalpha and act as a coactivator to up-regulate transcription from the PPRE of its own gene. Although protein palmitoylation is typically a cytosolic process that promotes membrane association, we recently identified 21 palmitoylated proteins in rat liver mitochondria, including HMGCS2. Herein, our data support a mechanism whereby palmitate is first added onto HMGCS2 active site Cys166 and then transacylated to Cys305. Palmitoylation promotes the HMGCS2/PPARalpha interaction, resulting in transcriptional activation from the Hmgcs2 PPRE. These results, together with the fact that 8 of the 21 palmitoylated mitochondrial proteins that we previously identified have nuclear receptor interacting motifs, demonstrate a novel--and perhaps ubiquitous--role for palmitoylation as a modulator of transcription.

Rapid and selective detection of fatty acylated proteins using omega-alkynyl-fatty acids and click chemistry

Progress in understanding the biology of protein fatty acylation has been impeded by the lack of rapid direct detection and identification methods. We first report that a synthetic omega-alkynyl-palmitate analog can be readily and specifically incorporated into GAPDH or mitochondrial 3-hydroxyl-3-methylglutaryl-CoA synthase in vitro and reacted with an azido-biotin probe or the fluorogenic probe 3-azido-7-hydroxycoumarin using click chemistry for rapid detection by Western blotting or flat bed fluorescence scanning. The acylated cysteine residues were confirmed by MS. Second, omega-alkynyl-palmitate is preferentially incorporated into transiently expressed H- or N-Ras proteins (but not nonpalmitoylated K-Ras), compared with omega-alkynyl-myristate or omega-alkynyl-stearate, via an alkali sensitive thioester bond. Third, omega-alkynyl-myristate is specifically incorporated into endogenous co- and posttranslationally myristoylated proteins. The competitive inhibitors 2-bromopalmitate and 2-hydroxymyristate prevented incorporation of omega-alkynyl-palmitate and omega-alkynyl-myristate into palmitoylated and myristoylated proteins, respectively. Labeling cells with omega-alkynyl-palmitate does not affect membrane association of N-Ras. Furthermore, the palmitoylation of endogenous proteins including H- and N-Ras could be easily detected using omega-alkynyl-palmitate as label in cultured HeLa, Jurkat, and COS-7 cells, and, promisingly, in mice. The omega-alkynyl-myristate and -palmitate analogs used with click chemistry and azido-probes will be invaluable to study protein acylation in vitro, in cells, and in vivo.

Domestication of the cardiac mitochondrion for energy conversion

The control of mitochondria energy conversion by cytosolic processes is reviewed. The nature of the cytosolic and mitochondrial potential energy homeostasis over wide ranges of energy utilization is reviewed and the consequences of this homeostasis in the control network are discussed. An analysis of the major candidate cytosolic signaling molecules ADP, Pi and Ca(2+) are reviewed based on the magnitude and source of the cytosolic concentration changes as well as the potential targets of action within the mitochondrial energy conversion system. Based on this analysis, Ca(2+) is the best candidate as a cytosolic signaling molecule for this process based on its ability to act as both a feedforward and feedback indicator of ATP hydrolysis and numerous targets within the matrix to provide a balanced activation of ATP production. These targets include numerous dehydrogenases and the F1-F0-ATPase. Pi is also a good candidate since it is an early signal of a mismatch between cytosolic ATP production and ATP synthesis in the presence of creatine kinase and has multiple targets within oxidative phosphorylation including NADH generation, electron flux in the cytochrome chain and a substrate for the F1-F0-ATPase. The mechanism of the coordinated activation of oxidative phosphorylation by these signaling molecules is discussed in light of the recent discoveries of extensive protein phosphorylation sites and other post-translational modifications. From this review it is clear that the control network associated with the maintenance of the cytosolic potential energy homeostasis is extremely complex with multiple pathways orchestrated to balance the sinks and sources in this system. New tools are needed to image and monitor metabolites within sub-cellular compartments to resolve many of these issues as well as the functional characterization of the numerous matrix post-translational events being discovered along with the enzymatic processes generating and removing these protein modifications.

Non-radioactive detection of palmitoylated mitochondrial proteins using an azido-palmitate analogue

While palmitoylation is typically thought of as a cytosolic process resulting in membrane attachment of the palmitoylated proteins, numerous mitochondrial proteins have been shown to be palmitoylated following in vitro labeling of mitochondria with radioactive or bioorthogonal analogues of fatty acids. The fatty acylation of two liver mitochondrial enzymes, methylmalonyl semialdehyde dehydrogenase and carbamoyl phosphate synthetase 1, has been studied in great detail. In both cases palmitoylation of an active site cysteine residue occurred spontaneously and resulted in inhibition of enzymatic activity, thus, suggesting that palmitoylation may be a direct means to regulate the activity of metabolic enzymes within the mitochondria. The progress of investigators working on protein fatty acylation has long been impeded by the long exposure time required to detect the incorporation of [(3)H]-fatty acids into protein by fluorography (often 1-3 months or more). Significant reduction in exposure times has been achieved by the use of [(125)I]-iodofatty acids but these analogues are also hazardous and not commercially available. Herein, we describe a sensitive chemical labeling method for the detection of palmitoylated mitochondrial proteins. The method uses azido-fatty acid analogues that can be attached to proteins and reacted with tagged phosphines via a modified Staudinger ligation. Recently, we used this labeling method, combined with mass spectrometry analysis of the labeled proteins, to identify 21 palmitoylated proteins from rat liver mitochondria.

Identification of palmitoylated mitochondrial proteins using a bio-orthogonal azido-palmitate analogue

Increased levels of circulating saturated free fatty acids, such as palmitate, have been implicated in the etiology of type II diabetes and cancer. In addition to being a constituent of glycerolipids and a source of energy, palmitate also covalently attaches to numerous cellular proteins via a process named palmitoylation. Recognized for its roles in membrane tethering, cellular signaling, and protein trafficking, palmitoylation is also emerging as a potential regulator of metabolism. Indeed, we showed previously that the acylation of two mitochondrial proteins at their active site cysteine residues result in their inhibition. Herein, we sought to identify other palmitoylated proteins in mitochondria using a nonradioactive bio-orthogonal azido-palmitate analog that can be selectively derivatized with various tagged triarylphosphines. Our results show that, like palmitate, incorporation of azido-palmitate occurred on mitochondrial proteins via thioester bonds at sites that could be competed out by palmitoyl-CoA. Using this method, we identified 21 putative palmitoylated proteins in the rat liver mitochondrial matrix, a compartment not recognized for its content in palmitoylated proteins, and confirmed the palmitoylation of newly identified mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase. We postulate that covalent modification and perhaps inhibition of various mitochondrial enzymes by palmitoyl-CoA could lead to the metabolic impairments found in obesity-related diseases.

Kinetics and control of oxidative phosphorylation in rat liver mitochondria after dexamethasone treatment

The present investigation was undertaken in order to evaluate the contributions of ATP synthesis and proton leak reactions to the rate of active respiration of liver mitochondria, which is altered following dexamethasone treatment (1.5 mg/kg per day for 5 days). We applied top-down metabolic control analysis and its extension, elasticity analysis, to gain insight into the mechanisms of glucocorticoid regulation of mitochondrial bioenergetics. Liver mitochondria were isolated from dexamethasone-treated, pair-fed and control rats when in a fed or overnight fasted state. Injection of dexamethasone for 5 days resulted in an increase in the fraction of the proton cycle of phosphorylating liver mitochondria, which was associated with a decrease in the efficiency of the mitochondrial oxidative phosphorylation process in liver. This increase in proton leak activity occurred with little change in the mitochondrial membrane potential, despite a significant decrease in the rate of oxidative phosphorylation. Regulation analysis indicates that mitochondrial membrane potential homoeostasis is achieved by equal inhibition of the mitochondrial substrate oxidation and phosphorylation reactions in rats given dexamethasone. Our results also suggest that active liver mitochondria from dexamethasone-treated rats are capable of maintaining phosphorylation flux for cellular purposes, despite an increase in the energetic cost of mitochondrial ATP production due to increased basal proton permeability of the inner membrane. They also provide a complete description of the effects of dexamethasone treatment on liver mitochondrial bioenergetics.

Characterization and function of mitochondrial nitric-oxide synthase

The mitochondrial production of nitric oxide is catalyzed by a nitric-oxide synthase. This enzyme has the same cofactor and substrate requirements as other constitutive nitric-oxide synthases. Its occurrence was demonstrated in various mitochondrial preparations (intact, purified mitochondria, permeabilized mitochondria, mitoplasts, submitochondrial particles) from different organs (liver, heart) and species (rat, pig). Endogenous nitric oxide reversibly inhibits oxygen consumption and ATP synthesis by competitive inhibition of cytochrome oxidase. The increased K(m) of cytochrome oxidase for oxygen and the steady-state reduction of the electron chain carriers provided experimental evidence for the direct interaction of this oxidase with endogenous nitric oxide. The increase in hydrogen peroxide production by nitric oxide-producing mitochondria not accompanied by the full reduction of the respiratory chain components indicated that cytochrome c oxidase utilizes nitric oxide as an alternative substrate. Finally, effectors or modulators of cytochrome oxidase (the irreversible step in oxidative phosphorylation) had been proposed during the last 40 years. Nitric oxide is the first molecule that fulfills this role (it is a competitive inhibitor, produced at a fair rate near the target site) extending the oxygen gradient to tissues.

Role of palmitoylation/depalmitoylation reactions in G-protein-coupled receptor function

G-protein-coupled receptors (GPCRs) constitute one of the largest protein families in the human genome. They are subject to numerous post-translational modifications, including palmitoylation. This review highlights the dynamic nature of palmitoylation and its role in GPCR expression and function. The palmitoylation of other proteins involved in GPCR signaling, such as G-proteins, regulators of G-protein signaling, and G-protein-coupled receptor kinases, is also discussed.

Biochemistry of mitochondrial nitric-oxide synthase

We reported that the generation of nitric oxide by mitochondria is catalyzed by a constitutive, mitochondrial nitric-oxide synthase (mtNOS). Given that this production may establish the basis for a novel regulatory pathway of energy metabolism, oxygen consumption, and oxygen free radical production, it becomes imperative to identify unequivocally and characterize this enzyme to provide a basis for its regulation. The mitochondrial localization of mtNOS was supported by following the hepatic distribution of mtNOS, immunoblotting submitochondrial fractions, and immunohistochemistry of liver tissues. mtNOS was identified as brain NOS alpha by various methods (mass spectrometry of proteolytic fragments, amino acid analysis, molecular weight, pI, and analysis of PCR fragments), excluding the occurrence of a novel isoform or other splice variants. Distribution of mtNOS transcript indicated its occurrence in liver, brain, heart, muscle, kidney, lung, testis, and spleen. In contrast to brain NOS, mtNOS has two post-translational modifications: acylation with myristic acid and phosphorylation at the C terminus. The former modification is a reversible and post-translational process, which may serve for subcellular targeting or membrane anchoring. The latter modification could be linked to enzymatic regulation. These results are discussed in terms of the role that nitric oxide may have in cellular bioenergetics.

Regulation of mitochondrial carbamoyl-phosphate synthetase 1 activity by active site fatty acylation

In addition to its role in reversible membrane localization of signal-transducing proteins, protein fatty acylation could play a role in the regulation of mitochondrial metabolism. Previous studies have shown that several acylated proteins exist in mitochondria isolated from COS-7 cells and rat liver. Here, a prominent fatty-acylated 165-kDa protein from rat liver mitochondria was identified as carbamoyl-phosphate synthetase 1 (CPS 1). Covalently attached palmitate was linked to CPS 1 via a thioester bond resulting in an inhibition of CPS 1 activity at physiological concentrations of palmitoyl-CoA. This inhibition corresponds to irreversible inactivation of CPS 1 and occurred in a time- and concentration-dependent manner. Fatty acylation of CPS 1 was prevented by preincubation with N-ethylmaleimide and 5'-p-fluorosulfonylbenzoyladenosine, an ATP analog that reacts with CPS 1 active site cysteine residues. Our results suggest that fatty acylation of CPS 1 is specific for long-chain fatty acyl-CoA and very likely occurs on at least one of the essential cysteine residues inhibiting the catalytic activity of CPS 1. Inhibition of CPS 1 by long-chain fatty acyl-CoAs could reduce amino acid degradation and urea secretion, thereby contributing to nitrogen sparing during starvation.

Acylation stabilizes a protease-resistant conformation of protoporphyrinogen oxidase, the molecular target of diphenyl ether-type herbicides

Protein acylation is an important way in which a number of proteins with a variety of functions are modified. The physiological role of the acylation of cellular proteins is still poorly understood. Covalent binding of fatty acids to nonintegral membrane proteins is thought to produce transient or permanent enhancement of the association of the polypeptide chains with biological membranes. In this paper, we investigate the functional role for the palmitoylation of an atypical membrane-bound protein, yeast protoporphyrinogen oxidase, which is the molecular target of diphenyl ether-type herbicides. Palmitoylation stabilizes an active heat- and protease-resistant conformation of the protein. Palmitoylation of protoporphyrinogen oxidase has been demonstrated to occur in vivo both in yeast cells and in a heterologous bacterial expression system, where it may be inhibited by cerulenin leading to the accumulation of degradation products of the protein. The thiol ester linking palmitoleic acid to the polypeptide chain was shown to be sensitive to hydrolysis by hydroxylamine and also by the widely used serine-protease inhibitor phenylmethylsulfonyl fluoride.

Effect of fatty acids on energy coupling processes in mitochondria

Long-chain fatty acids are natural uncouplers of oxidative phosphorylation in mitochondria. The protonophoric mechanism of this action is due to transbilayer movement of undissociated fatty acid in one direction and the passage of its anion in the opposite direction. The transfer of the dissociated form of fatty acid can be, at least in some kinds of mitochondrion, facilitated by adenine nucleotide translocase. Apart from dissipating the electrochemical proton gradient, long-chain fatty acids decrease the activity of the respiratory chain by mechanism(s) not fully understood. In intact cells and tissues fatty acids operate mostly as excellent respiratory substrates, providing electrons to the respiratory chain. This function masks their potential uncoupling effect which becomes apparent only under special physiological or pathological conditions characterized by unusual fatty acid accumulation. Short- and medium-chain fatty acids do not have protonophoric properties. Nevertheless, they contribute to energy dissipation because of slow intramitochondrial hydrolysis of their activation products, acyl-AMP and acyl-CoA. Long-chain fatty acids increase permeability of mitochondrial membranes to alkali metal cations. This is due to their ionophoric mechanism of action. Regulatory function of fatty acids with respect to specific cation channels has been postulated for the plasma membrane of muscle cells, but not demonstrated in mitochondria. Under cold stress, cold acclimation and arousal from hibernation the uncoupling effect of fatty acids may contribute to increased thermogenesis, especially in the muscle tissue. In brown adipose tissue, the special thermogenic organ of mammals, long-chain fatty acids promote operation of the unique natural uncoupling protein, thermogenin. As anionic amphiphiles, long-chain fatty acids increase the negative surface charge of biomembranes, thus interfering in their enzymic and transporting functions.

Characterization of recombinant and endogenous ADP-ribosylation factors synthesized in Sf9 insect cells

ADP-ribosylation factors (ARFs) are a family of highly conserved, 20-kDa guanine nucleotide-binding proteins that participate in protein trafficking and enhance cholera toxin-catalyzed ADP-ribosylation. ARF 2 from bovine retinal cDNA was expressed in Sf9 insect cells using recombinant baculovirus and compared to the major insect cell ARF (Sf9 ARF) and to recombinant ARF 2 expressed in Escherichia coli (E. coli rARF 2). The 150000g supernatant and particulate fractions of freeze-thawed, recombinant ARF 2 baculovirus-infected cells contained immunoreactive proteins of 20 and 21 kDa at significantly higher levels than were found in uninfected cells. Infected Sf9 cells incorporated [3H]myristate only into the 20-kDa protein. Sf9 cell recombinant ARF 2 (Sf9 rARF 2) and Sf9 ARF were separated by isoelectric focusing or ion-exchange chromatography and identified by microsequencing of HPLC-purified tryptic peptides. Sf9 ARF displayed considerable sequence identity to mammalian class I ARFs. Both Sf9 ARF and Sf9 rARF 2 stimulated in a GTP-dependent manner cholera toxin-catalyzed ADP-ribosylation. The Ka for GTP of Sf9 ARF was, however, significantly lower than that of Sf9 rARF 2 or E. coli rARF 2. Myristoylation did not significantly affect the ability of ARF 2 to enhance cholera toxin-catalyzed ADP-ribosylation or the Ka for GTP. Despite the sequence identities and the fact that both were synthesized in insect cells, the endogenous Sf9 ARF was functionally different from Sf9 rARF 2.

Development of hydrophobicity parameters to analyze proteins which bear post- or cotranslational modifications

We have determined hydrophobicity parameters for the side chains of 22 common post- or cotranslationally modified amino acyl residues and for the standard unmodified amino acids as well. This "comprehensive" parameter set is the first such reported. Parameters determined for the side chains of the standard 20 amino acids correlate well with those of widely accepted sets. Our parameters have also been evaluated by hydrophobicity profiles and by transverse hydrophobic moment calculations on cytosolic, secreted, and membranous model proteins, with favorable results. Many of the hydrophobicity parameters for the post- or cotranslationally modified derivatives are of remarkable magnitude, especially those for oligosaccharide-bound Asn and fatty-acylated Cys or amino terminus. Thus, the comprehensive parameter set determined here greatly extends our ability to analyze homology, membrane directedness, and folding potential of proteins.

Synthesis of myristoyl-carba(dethia)-coenzyme A and S-(3-oxohexadecyl)-coenzyme A, two potent inhibitors of myristoyl-CoA:protein N-myristoyltransferase

1. Two non-hydrolysable analogues of myristoyl-coenzyme A were synthesised and spectroscopically characterized. Myristoyl-carba(dethia)coenzyme A was prepared in a multistep synthesis starting from tridecyl vinyl ketone. S-(3-Oxohexadecyl)-coenzyme A was synthesised from 3-oxohexadecyl chloride by direct condensation with coenzyme A. 2. Both analogues were strong competitive inhibitors of N-myristoyltransferase from yeast. Ki values of 0.3 and 0.25 microM were determined for myristoyl-carba(dethia)-coenzyme A and S-(3-oxohexadecyl)-coenzyme A, respectively.