Mitochondrial tyrosine phosphoproteome: new insights from an up-to-date analysis

Mitochondrial Respiration-Dependent ANT2-UCP2 Interaction

Adenine nucleotide translocases (ANTs) and uncoupling proteins (UCPs) are known to facilitate proton leak across the inner mitochondrial membrane. However, it remains to be unravelled whether UCP2/3 contribute to significant amount of proton leak in vivo. Reports are indicative of UCP2 dependent proton-coupled efflux of C4 metabolites from the mitochondrial matrix. Previous studies have suggested that UCP2/3 knockdown (KD) contributes to increased ANT-dependent proton leak. Here we investigated the hypothesis that interaction exists between the UCP2 and ANT2 proteins, and that such interaction is regulated by the cellular metabolic demand. Protein-protein interaction was evaluated using reciprocal co-immunoprecipitation and in situ proximity ligation assay. KD of ANT2 and UCP2 was performed by siRNA in human embryonic kidney cells 293A (HEK293A) cells. Mitochondrial and cellular respiration was measured by high-resolution respirometry. ANT2-UCP2 interaction was demonstrated, and this was dependent on cellular metabolism. Inhibition of ATP synthase promoted ANT2-UCP2 interaction whereas high cellular respiration, induced by adding the mitochondrial uncoupler FCCP, prevented interaction. UCP2 KD contributed to increased carboxyatractyloside (CATR) sensitive proton leak, whereas ANT2 and UCP2 double KD reduced CATR sensitive proton leak, compared to UCP2 KD. Furthermore, proton leak was reduced in double KD compared to UCP2 KD. In conclusion, our results show that there is an interaction between ANT2-UCP2, which appears to be dynamically regulated by mitochondrial respiratory activity. This may have implications in the regulation of mitochondrial efficiency or cellular substrate utilization as increased activity of UCP2 may promote a switch from glucose to fatty acid metabolism.

Editorial of Special Issue "Protein Post-Translational Modifications in Signal Transduction and Diseases"

The making of a protein is based on the combination of 20 different monomers (22 considering selenocysteine and pyrrolysine, the latest present only in some archaea and bacteria) giving the possibility of building a variety of structures from the simplest to the most complex, rigid or highly dynamic, and suited to carry out a wide range of structural and functional roles [...].

Exogenous spermine preserves mitochondrial bioenergetics via regulating Src kinase signaling in the spinal cord

Regulation of mitochondrial metabolism is becoming an important target in inhibiting necrosis and apoptosis following secondary spinal cord injury, and physiological compounds that reduce mitochondrial dysfunction are regarded as efficient protective reagents following injury. It has been demonstrated that spermine, a polyamine composed of four primary amines, may be taken up by a mitochondria‑specific uniporter and may preserve mitochondrial bioenergetics, suggesting that it may be important in the pathophysiology of mitochondria. However, the protective mechanism has not yet been definitively clarified. In the present study, isolated spinal cord mitochondria were incubated with spermine to evaluate its physiological functions and Src kinase activities. The results revealed that spermine increased oxidative phosphorylation, attenuated mitochondrial swelling and maintained the membrane potential. An inhibitor of Src kinases, amino‑5-(4‑chlorophenyl)‑7‑(t‑butyl)pyrazolo[3,4‑d]pyrimidine (PP2), markedly reduced the effects of spermine. However, inhibition of tyrosine phosphatases by vanadate led to marginal increases in the effects of spermine. Therefore, the present study hypothesized that tyrosine phosphorylation sites are present in the subunits of respiratory chains and mitochondrial permeability transition pore proteins, which may be modified via phosphorylation and dephosphorylation. Furthermore, spermine may upregulate the phosphorylation of Src kinases, and PP2 and vanadate conversely regulate Src phosphorylation. The results of the present study suggest that spermine is a strategic regulator within mitochondria that may activate Src kinases in the spinal cord, and tyrosine phosphorylation signaling is a primary regulatory pathway of mitochondrial metabolism.

Human adenine nucleotide translocases physically and functionally interact with respirasomes

A network of interactions for human adenine nucleotide translocases, required for oxidative phosphorylation, is reported. Of particular interest is an evolutionarily conserved and functionally important association with respiratory supercomplexes, which is surprising because the respirasomes of yeast and mammals are different.

Members of the adenine nucleotide translocase (ANT) family exchange ADP for ATP across the mitochondrial inner membrane, an activity that is essential for oxidative phosphorylation (OXPHOS). Mutations in or dysregulation of ANTs is associated with progressive external ophthalmoplegia, cardiomyopathy, nonsyndromic intellectual disability, apoptosis, and the Warburg effect. Binding partners of human ANTs have not been systematically identified. The absence of such information has prevented a detailed molecular understanding of the assorted ANT-associated diseases, including insight into their disparate phenotypic manifestations. To fill this void, in this study, we define the interactomes of two human ANT isoforms. Analogous to its yeast counterpart, human ANTs associate with heterologous partner proteins, including the respiratory supercomplex (RSC) and other solute carriers. The evolutionarily conserved ANT–RSC association is particularly noteworthy because the composition, and thereby organization, of RSCs in yeast and human is different. Surprisingly, absence of the major ANT isoform only modestly impairs OXPHOS in HEK293 cells, indicating that the low levels of other isoforms provide functional redundancy. In contrast, pharmacological inhibition of OXPHOS expression and function inhibits ANT-dependent ADP/ATP exchange. Thus ANTs and the OXPHOS machinery physically interact and functionally cooperate to enhance ANT transport capacity and mitochondrial respiration.

Subcellular Partitioning of Protein Tyrosine Phosphatase 1B to the Endoplasmic Reticulum and Mitochondria Depends Sensitively on the Composition of Its Tail Anchor

The canonical protein tyrosine phosphatase PTP1B is an important regulator of diverse cellular signaling networks. PTP1B has long been thought to exert its influence solely from its perch on the endoplasmic reticulum (ER); however, an additional subpopulation of PTP1B has recently been detected in mitochondria extracted from rat brain tissue. Here, we show that PTP1B’s mitochondrial localization is general (observed across diverse mammalian cell lines) and sensitively dependent on the transmembrane domain length, C-terminal charge and hydropathy of its short (≤35 amino acid) tail anchor. Our electron microscopy of specific DAB precipitation revealed that PTP1B localizes via its tail anchor to the outer mitochondrial membrane (OMM), with fluorescence lifetime imaging microscopy establishing that this OMM pool contributes to the previously reported cytoplasmic interaction of PTP1B with endocytosed epidermal growth factor receptor. We additionally examined the mechanism of PTP1B’s insertion into the ER membrane through heterologous expression of PTP1B’s tail anchor in wild-type yeast and yeast mutants of major conserved ER insertion pathways: In none of these yeast strains was ER targeting significantly impeded, providing in vivo support for the hypothesis of spontaneous membrane insertion (as previously demonstrated in vitro). Further functional elucidation of the newly recognized mitochondrial pool of PTP1B will likely be important for understanding its complex roles in cellular responses to external stimuli, cell proliferation and diseased states.

The life of plant mitochondrial complex I

The mitochondrial NADH dehydrogenase complex (complex I) of the respiratory chain has several remarkable features in plants: (i) particularly many of its subunits are encoded by the mitochondrial genome, (ii) its mitochondrial transcripts undergo extensive maturation processes (e.g. RNA editing, trans-splicing), (iii) its assembly follows unique routes, (iv) it includes an additional functional domain which contains carbonic anhydrases and (v) it is, indirectly, involved in photosynthesis. Comprising about 50 distinct protein subunits, complex I of plants is very large. However, an even larger number of proteins are required to synthesize these subunits and assemble the enzyme complex. This review aims to follow the complete "life cycle" of plant complex I from various molecular perspectives. We provide arguments that complex I represents an ideal model system for studying the interplay of respiration and photosynthesis, the cooperation of mitochondria and the nucleus during organelle biogenesis and the evolution of the mitochondrial oxidative phosphorylation system.

Myotonic dystrophy protein kinase (DMPK) prevents ROS-induced cell death by assembling a hexokinase II-Src complex on the mitochondrial surface

The biological functions of myotonic dystrophy protein kinase (DMPK), a serine/threonine kinase whose gene mutations cause myotonic dystrophy type 1 (DM1), remain poorly understood. Several DMPK isoforms exist, and the long ones (DMPK-A/B/C/D) are associated with the mitochondria, where they exert unknown activities. We have studied the isoform A of DMPK, which we have found to be prevalently associated to the outer mitochondrial membrane. The kinase activity of mitochondrial DMPK protects cells from oxidative stress and from the ensuing opening of the mitochondrial permeability transition pore (PTP), which would otherwise irreversibly commit cells to death. We observe that DMPK (i) increases the mitochondrial localization of hexokinase II (HK II), (ii) forms a multimeric complex with HK II and with the active form of the tyrosine kinase Src, binding its SH3 domain and (iii) it is tyrosine-phosphorylated by Src. Both interaction among these proteins and tyrosine phosphorylation of DMPK are increased under oxidative stress, and Src inhibition selectively enhances death in DMPK-expressing cells after HK II detachment from the mitochondria. Down-modulation of DMPK abolishes the appearance of muscle markers in in vitro myogenesis, which is rescued by oxidant scavenging. Our data indicate that, together with HK II and Src, mitochondrial DMPK is part of a multimolecular complex endowed with antioxidant and pro-survival properties that could be relevant during the function and differentiation of muscle fibers.

Mitochondrial c-Src regulates cell survival through phosphorylation of respiratory chain components

Mitochondrial protein tyrosine phosphorylation is an important mechanism for the modulation of mitochondrial functions. In the present study, we have identified novel substrates of c-Src in mitochondria and investigated their function in the regulation of oxidative phosphorylation. The Src family kinase inhibitor PP2 {amino-5-(4-chlorophenyl)-7-(t-butyl) pyrazolo [3,4d] pyrimidine} exhibits significant reduction of respiration. Similar results were obtained from cells expressing kinase-dead c-Src, which harbours a mitochondrial-targeting sequence. Phosphorylation-site analysis selects c-Src targets, including NDUFV2 (NADH dehydrogenase [ubiquinone] flavoprotein 2) at Tyr(193) of respiratory complex I and SDHA (succinate dehydrogenase A) at Tyr(215) of complex II. The phosphorylation of these sites by c-Src is supported by an in vivo assay using cells expressing their phosphorylation-defective mutants. Comparison of cells expressing wild-type proteins and their mutants reveals that NDUFV2 phosphorylation is required for NADH dehydrogenase activity, affecting respiration activity and cellular ATP content. SDHA phosphorylation shows no effect on enzyme activity, but perturbed electron transfer, which induces reactive oxygen species. Loss of viability is observed in T98G cells and the primary neurons expressing these mutants. These results suggest that mitochondrial c-Src regulates the oxidative phosphorylation system by phosphorylating respiratory components and that c-Src activity is essential for cell viability.

Src kinases are important regulators of mitochondrial functions

Mitochondria produce the most part of the energy used by the cells. This energetic production occurs through the oxidative phosphorylation (OXPHOS) process. Mitochondrial functions such as OXPHOS need to be tightly regulated to respect the needs of cells. Phosphorylation of mitochondrial proteins now appears as a major regulation pathway of mitochondrial functions. Several kinases and phosphatases are specifically targeted to mitochondria where they modulate mitochondrial functions. However, we still poorly understand the extent of tyrosine phosphorylation events on mitochondrial metabolism. Among the tyrosine-kinases observed in mitochondria, Src kinases emerge as key players. In the past years, several mitochondrial proteins were shown to be substrates of Src kinases. Notably, these kinases can impact greatly OXPHOS and apoptosis. Important regulators of Src kinases activity are also observed in mitochondria. The aim of this review is to summarize the recent findings on how overall mitochondrial tyrosine phosphorylation events and more specifically Src kinases can influence mitochondrial functions. The different mechanisms of Src kinases regulation and translocation into mitochondria will be also discussed. This article is part of a Directed Issue entitled: Bioenergetic dysfunction, adaptation and therapy.

Novel tyrosine phosphorylation sites in rat skeletal muscle revealed by phosphopeptide enrichment and HPLC-ESI-MS/MS

Tyrosine phosphorylation plays a fundamental role in many cellular processes including differentiation, growth and insulin signaling. In insulin resistant muscle, aberrant tyrosine phosphorylation of several proteins has been detected. However, due to the low abundance of tyrosine phosphorylation (<1% of total protein phosphorylation), only a few tyrosine phosphorylation sites have been identified in mammalian skeletal muscle to date. Here, we used immunoprecipitation of phosphotyrosine peptides prior to HPLC-ESI-MS/MS analysis to improve the discovery of tyrosine phosphorylation in relatively small skeletal muscle biopsies from rats. This resulted in the identification of 87 distinctly localized tyrosine phosphorylation sites in 46 muscle proteins. Among them, 31 appear to be novel. The tyrosine phosphorylated proteins included major enzymes in the glycolytic pathway and glycogen metabolism, sarcomeric proteins, and proteins involved in Ca(2+) homeostasis and phosphocreatine resynthesis. Among proteins regulated by insulin, we found tyrosine phosphorylation sites in glycogen synthase, and two of its inhibitors, GSK-3α and DYRK1A. Moreover, tyrosine phosphorylation sites were identified in several MAP kinases and a protein tyrosine phosphatase, SHPTP2. These results provide the largest catalogue of mammalian skeletal muscle tyrosine phosphorylation sites to date and provide novel targets for the investigation of human skeletal muscle phosphoproteins in various disease states.