Endogenous protein phosphorylation in rat brain mitochondria: occurrence of a novel ATP-dependent form of the autophosphorylated enzyme succinyl-CoA synthetase

Mitochondrial phosphoproteomics of mammalian tissues

Mitochondria are essential for several biological processes including energy metabolism and cell survival. Accordingly, impaired mitochondrial function is involved in a wide range of human pathologies including diabetes, cancer, cardiovascular, and neurodegenerative diseases. Within the past decade a growing body of evidence indicates that reversible phosphorylation plays an important role in the regulation of a variety of mitochondrial processes as well as tissue-specific mitochondrial functions in mammals. The rapidly increasing number of mitochondrial phosphorylation sites and phosphoproteins identified is largely ascribed to recent advances in phosphoproteomic technologies such as fractionation, phosphopeptide enrichment, and high-sensitivity mass spectrometry. However, the functional importance and the specific kinases and phosphatases involved have yet to be determined for the majority of these mitochondrial phosphorylation sites. This review summarizes the progress in establishing the mammalian mitochondrial phosphoproteome and the technical challenges encountered while characterizing it, with a particular focus on large-scale phosphoproteomic studies of mitochondria from human skeletal muscle.

Succinyl-CoA synthetase is a phosphate target for the activation of mitochondrial metabolism

Succinyl-CoA synthetase (SCS) is the only mitochondrial enzyme capable of ATP production via substrate level phosphorylation in the absence of oxygen, but it also plays a key role in the citric acid cycle, ketone metabolism, and heme synthesis. Inorganic phosphate (P(i)) is a signaling molecule capable of activating oxidative phosphorylation at several sites, including NADH generation and as a substrate for ATP formation. In this study, it was shown that P(i) binds the porcine heart SCS alpha-subunit (SCSalpha) in a noncovalent manner and enhances its enzymatic activity, thereby providing a new target for P(i) activation in mitochondria. Coupling 32P labeling of intact mitochondria with SDS gel electrophoresis revealed that 32P labeling of SCSalpha was enhanced in substrate-depleted mitochondria. Using mitochondrial extracts and purified bacterial SCS (BSCS), we showed that this enhanced 32P labeling resulted from a simple binding of 32P, not covalent protein phosphorylation. The ability of SCSalpha to retain its 32P throughout the SDS denaturing gel process was unique over the entire mitochondrial proteome. In vitro studies also revealed a P(i)-induced activation of SCS activity by more than 2-fold when mitochondrial extracts and purified BSCS were incubated with millimolar concentrations of P(i). Since the level of 32P binding to SCSalpha was increased in substrate-depleted mitochondria, where the matrix P(i) concentration is increased, we conclude that SCS activation by P(i) binding represents another mitochondrial target for the P(i)-induced activation of oxidative phosphorylation and anaerobic ATP production in energy-limited mitochondria.

Mitochondrial modulation: reversible phosphorylation takes center stage?

In the past 1.5 billion years, mitochondria have evolved from oxygen-scavenging bacterial symbionts into primary control centers for energy production and cellular life-and-death processes in eukaryotes. This maturation of mitochondrial function has necessitated the coevolution of various mechanisms of communication with the rest of the cell. Emerging evidence indicates that reversible phosphorylation, the most prevalent form of cellular posttranslational modification, is an important and largely overlooked means of regulating mitochondrial functions. The steadily increasing number of reported mitochondrial kinases, phosphatases and phosphoproteins suggests that phosphorylation is likely to emerge as a common theme in the regulation of mitochondrial processes.

The phosphorylation of subunits of complex I from bovine heart mitochondria

In bovine heart mitochondria and in submitochondrial particles, membrane-associated proteins with apparent molecular masses of 18 and 10 kDa become strongly radiolabeled by [(32)P]ATP in a cAMP-dependent manner. The 18-kDa phosphorylated protein is subunit ESSS from complex I and not as previously reported the 18 k subunit (with the N-terminal sequence AQDQ). The phosphorylated residue in subunit ESSS is serine 20. In the 10 kDa band, the complex I subunit MWFE was phosphorylated on serine 55. In the presence of protein kinase A and cAMP, the same subunits of purified complex I were phosphorylated by [(32)P]ATP at the same sites. Subunits ESSS and MWFE both contribute to the membrane arm of complex I. Each has a single hydrophobic region probably folded into a membrane spanning alpha-helix. It is likely that the phosphorylation site of subunit ESSS lies in the mitochondrial matrix and that the site in subunit MWFE is in the intermembrane space. Subunit ESSS has no known role, but subunit MWFE is required for assembly into complex I of seven hydrophobic subunits encoded in the mitochondrial genome. The possible effects of phosphorylation of these subunits on the activity and/or the assembly of complex I remain to be explored.

Physiological Ca2+ level and Ca2+-induced Permeability Transition Pore control protein phosphorylation in rat brain mitochondria

Phosphorylation of several low molecular mass proteins (3.5, 17, 23 and 29kDa) was observed in rat brain mitochondria (RBM) at ATP concentration close to that in the mitochondrial matrix. Furthermore, regulatory effects of Ca2+ on phosphorylation of these proteins were investigated. Protein phosphorylation was found to be modulated by Ca2+ in the physiological concentration range (10(-8) to 10(-6)M free Ca2+). Incorporation of 32P from [gamma-32P]ATP into the 17kDa protein was dramatically increased within the 10(-7) to 10(-6)M free Ca2+ range, whereas an opposite effect was observed for the 3.5kDa polypeptide. Strong de-phosphorylation of the 3.5kDa polypeptide and enhanced 32P-incorporation into the 17 and 23kDa proteins were found with supra-threshold Ca2+ loads and these effects were eliminated or reduced in the presence of cyclosporin A, an inhibitor of Permeability Transition Pore (PTP) opening. In the presence of calmidazolium (Cmz), a calmodulin antagonist, enhanced levels of phosphorylation of the 17 and 3.5kDa polypeptides were observed and the 17kDa protein phosphorylation was suppressed by H-8, a protein kinase A inhibitor. It is concluded that Ca2+ in physiological concentrations, as a second messenger, can control phosphorylation of the low molecular mass phospoproteins in RBM, in addition to well known regulation of some Krebs cycle dehydrogenases by Ca2+. The protein phosphorylation was strongly dependent on the Ca2+-induced PTP opening.

Purification of a serine and histidine phosphorylated mitochondrial nucleoside diphosphate kinase from Pisum sativum

For the first time, to our knowledge, a nucleoside diphosphate kinase (NDPK) has been purified from plant mitochondria (Pisum sativum L.). In intact pea leaf mitochondria, a 17.4-kDa soluble protein was phosphorylated in the presence of EDTA when [gamma-32P]ATP was used as the phosphate donor. Cell fractionation demonstrated that the 17.4-kDa protein is a true mitochondrial protein, and the lack of accessibility to EDTA of the matrix compartment in intact mitochondria suggested it may have an intermembrane space localization. The 17.4-kDa protein was purified from mitochondrial soluble proteins using ATP-agarose and anion exchange chromatography. Amino-acid sequencing of two peptides, resulting from a trypsin digestion, revealed high similarity with the conserved catalytic phosphohistidine site and with the C-terminal of NDPKs. Acid and alkali treatments of [32P]-labelled pea mitochondrial NDPK indicated the presence of acid-stable as well as alkali-stable phosphogroups. Thin-layer chromatography experiments revealed serine as the acid-stable phosphogroup. The alkali-stable labelling probably reflects phosphorylation of the conserved catalytic histidine residue. In phosphorylation experiments, the purified pea mitochondrial NDPK was labelled more heavily on serine than histidine residues. Furthermore, kinetic studies showed a faster phosphorylation rate for serine compared to histidine. Both ATP and GTP could be used as phosphate donor for histidine as well as serine labelling of the pea mitochondrial NDPK.

Genetic evidence for the expression of ATP- and GTP-specific succinyl-CoA synthetases in multicellular eucaryotes

Highly ATP- and GTP-specific isoforms of succinyl-CoA synthetase in pigeon incorporate the same alpha-subunit, but different beta-subunits (Johnson, J. D., Muhonen, W. W., and Lambeth, D. O. (1998) J. Biol. Chem. 273, 27573-27579). The sequences of the mature subunits were determined by methods based on reverse transcription-polymerase chain reaction. The 306-residue mature alpha-subunit in pigeon shows >88% identity to its homologues in pig and rat. The sequences of the mature ATP- and GTP-specific beta-subunits (A-beta and G-beta, respectively) in pigeon are 54% identical. These sequences were used to identify expressed sequence tags for human and mouse that were highly homologous to G-beta and A-beta, respectively. The sequences for mature A-beta and G-beta in mouse and human were completed and verified by polymerase chain reaction. The sequence of A-beta in pig was also obtained. The mammalian A-beta sequences show >89% identity to each other; the G-beta sequences are similarly related. However, pairwise comparisons of the A-beta and G-beta sequences revealed <53% identity. Alignment with two sequences of the beta-subunit in Caenorhabditis elegans suggests that the A-beta and G-beta genes arose by duplication early in the evolution of multicellular eucaryotes. The expression of A-beta is strong in numerous mouse and human tissues, which suggests that ATP-specific succinyl-CoA synthetase also plays an important role in species throughout the animal kingdom.

Characterization of the ATP- and GTP-specific succinyl-CoA synthetases in pigeon. The enzymes incorporate the same alpha-subunit

Two succinyl-CoA synthetases, one highly specific for GTP/GDP and the other for ATP/ADP, have been purified to homogeneity from pigeon liver and breast muscle. The two enzymes are differentially distributed in pigeon, with only the GTP-specific enzyme detected in liver and the ATP-specific enzyme in breast muscle. Based on assays in the direction of CoA formation, the ratios of GTP-specific to ATP-specific activities in kidney, brain, and heart are approximately 7, 1, and 0.1, respectively. Both enzymes have the characteristic alpha- and beta-subunits found in other succinyl-CoA synthetases. Studies of the alpha-subunit by electrophoresis, mass spectrometry, reversed-phase high performance liquid chromatography, and peptide mapping showed that it was the same in the two enzymes. Characterization of the beta-subunits by the same methods indicated that they were different, with the tryptic peptide maps providing evidence that the beta-subunits likely differ along their entire sequences. Because the two succinyl-CoA synthetases incorporate the same alpha-subunit, the determinants of nucleotide specificity must reside within the beta-subunit. Determination of the apparent Michaelis constants showed that the affinity of the GTP-specific enzyme for GDP is greater than that of the ATP-specific enzyme for ADP (7 versus 250 microM). Rather large differences in apparent Km values were also observed for succinate and phosphate.

Mitochondrial cytochrome c oxidase subunit IV is phosphorylated by an endogenous kinase

This study was undertaken to identify novel mitochondrial membrane proteins that are potential targets for phosphorylation. Mitochondrial membranes were incubated in the presence of [gamma-32P]ATP and the Triton X-114 extractable protein was subjected to ion-exchange and polyacrylamide gel chromatography to purify a major phosphorylated protein of approximately 17000 Da. The determined peptide sequence of the purified phosphoprotein corresponded to a segment of cytochrome c oxidase subunit IV, an inner membrane protein of 17160 Da. The identity of the phosphoprotein was confirmed by two-dimensional electrophoresis and Western blotting. The results identify mitochondrial cytochrome c oxidase subunit IV as a protein which is phosphorylated by an endogenous kinase.

ATP-citrate lyase is another enzyme the histidine phosphorylation of which is inhibited by vanadate

We have recently shown that phosphorylation of histidine residue of the alpha-subunit of the succinyl-CoA synthetase is inhibited by both vanadate and vanadyl. To assess the university of this inhibition, we have estimated the effect of vanadate on the phosphorylation of another enzyme ATP-citrate lyase, prepared from rat liver. This enzyme contains histidine as the only amino acid with an acid-labile (P-N) phosphate bond. The 67% inhibition of endogenous phosphorylation by 1 mM vanadate disappeared after cleavage of the acidic P-N bond of histidine with acidic sample solution. The remaining 33 per cent radioactivity was due to labelling of the acid-stable phosphoamino acids (P-serine and P-threonine), the phosphorylation of which was not affected by vanadate. The dose response curve for vanadate inhibition closely resembles that shown previously for inhibition of phosphorylation of histidine in the succinyl-CoA synthetase. The results suggest that the action of vanadate on histidinyl phosphorylation is a more general effect (like its influence on phosphorylation of the protein-bound tyrosine).

Inhibition of phosphorylation of the mitochondrial 34 kDa protein. A unique effect of vanadium ions?

We have shown previously that vanadate stimulates overall endogenous phosphorylation of proteins in subcellular particulate fractions. In brain mitochondria there is a single peptide band of Mr (approx.) 34 kDa, phosphorylation of which is inhibited rather than stimulated by both vanadate and vanadyl ions. Here, further characterization of this unique effect of vanadium ions is reported. Phosphorylation of the 34 kDa protein proceeds in the Triton X-100 extracts of mitochondria. The P-labeled 34 kDa band was recovered from TCA sediments of endogenously phosphorylated mitochondria. Acid lability of the phosphate linkage suggests a bond of P-N type. Phosphorylation of the 34 kDa protein is highly sensitive to Mg2+, while Mn2+ is a less potent activator. The results provide further evidence for existence of a protein occurring exclusively in mitochondria, the phosphorylation of which is selectively modified by both vanadate anion and vanadyl cation in a way differing from those hitherto described.

Protein phosphorylation in isolated mitochondria and the effects of protein kinase C

When isolated intact rat liver mitochondria are incubated with [gamma-32P]ATP the major phosphorylated proteins are those of 47 and 36 kDa. Phosphorylation of the 47 kDa protein, but not of the 36 kDa protein, is inhibited by carboxyatractyloside, an inhibitor of mitochondrial ATP uptake, while phosphorylation of the 36 kDa protein is inhibited by various uncouplers and an inhibitor of mitochondrial respiration. Addition of purified protein kinase C to the isolated mitochondria leads to the phosphorylation of 69, 37 and 17 kDa proteins. As with other substrates for protein kinase C, phosphorylation of these proteins is dependent on Ca2+ and markedly stimulated by various tumor promoters.

The subcellular distribution of a membrane-bound calmodulin-stimulated protein kinase

Incubation of subcellular fractions isolated from rat cerebral cortex with [gamma-32P]ATP results in the phosphorylation of a number of proteins including two with apparent molecular weights of approximately 50,000 and 60,000 daltons. These phosphoproteins were shown to be the autophosphorylated subunits of a calmodulin-stimulated protein kinase by a number of physicochemical criteria, including their mobility on non-equilibrium pH gradient electrophoresis, their phosphopeptide profiles and phosphorylation characteristics. When a crude membrane fraction obtained following osmotic lysis of a P2 fraction was labeled and subsequently fractionated on sucrose density gradients, approximately 80% of the autophosphorylated kinase was associated with fractions enriched in synaptic plasma membranes. Other substrates of calmodulin kinase(s) were similarly distributed. Detergent extraction of synaptic plasma membranes to produce synaptic junctions and post-synaptic densities indicated that the majority of the autophosphorylated kinase was solubilized, apparently as a holoenzyme. The major post synaptic density protein (mPSDp) was not readily extracted by detergents and was largely unlabeled under the conditions used for phosphorylation, and yet this protein is structurally closely related to the kinase subunit. It is possible that this lack of labeling is due to the mPSDp being attached to the PSD in a different way or being present there in a different isoenzymic form from that of the readily autophosphorylated enzyme subunit. Thus, the data suggest that, in vitro at least, a number of pools of calmodulin kinase exist in neuronal membranes.

Depolarisation-dependent protein phosphorylation in rat cortical synaptosomes: factors determining the magnitude of the response

The sequence of molecular events linking depolarisation-dependent calcium influx to the release of neurotransmitters from nerve terminals is unknown; however, calcium-stimulated protein phosphorylation may play a role. In this study the incorporation of phosphate into proteins was investigated using an intact postmitochondrial pellet isolated from rat cerebral cortex. The rate and relative incorporation of label into individual phosphoproteins depended on the prelabelling time and buffer concentrations of calcium and phosphate. After prelabelling for 45 min, depolarisation caused a greater than 20% increase in the labelling of 10 phosphoproteins, and this initial increase was maximal with 41 mM K+ for 5 s, or 30 microM veratridine for 15 s, in the presence of 1 mM calcium. Both agents also led to an initial dephosphorylation of four phosphoproteins. Depolarisation for 5 min led to a significant decrease in the labelling of all phosphoproteins. All of the depolarisation-stimulated changes in protein phosphorylation were calcium-dependent. The depolarisation conditions found to optimally alter the phosphorylation of synaptosomal proteins find many parallels in studies on calcium uptake and neurotransmitter release. However, the uniform responses of such a large number of phosphoproteins to the multitude of depolarisation conditions studied suggest that the changes could equally well relate to recovery events such as biosynthesis of neurotransmitters and regulation of intraterminal metabolic activity.

The effect of dichloroacetate on the phosphorylation of mitochondria proteins

Succinyl-CoA synthetase and the alpha-subunit of pyruvate dehydrogenase are phosphorylated after incubation of mitochondria from brain, heart, and liver with [gamma-32P]ATP. Dichloroacetate, a known specific inhibitor for pyruvate dehydrogenase kinase, inhibits not only the phosphate incorporation into the alpha-subunit of pyruvate dehydrogenase but also the autophosphorylation of succinyl-CoA synthetase. AMP also inhibits the phosphorylation of both proteins. Phosphorylation of the alpha-subunit of pyruvate dehydrogenase in liver mitochondria is significantly lower than in mitochondria from other tissues.