Malate Dehydrogenase and NAD Malic Enzyme in the Oxidation of Malate by Sweet Potato Mitochondria

Over a range of concentrations from less than 0.1 mm to more than 70 mm, sweet potato root mitochondria display a bimodal substrate saturation isotherm for malate. The high affinity portion of the isotherm has an apparent Km for malate of 0.85 mm and fits a rectangular hyperbolic function. The low affinity portion of the isotherm is sigmoid in character and gives an apparent S(0.5) of 40.6 mm and a Hill number of 3.7.Extracts of sweet potato mitochondria contain both malate dehydrogenase and NAD malic enzyme. The malate dehydrogenase, assayed in the forward direction at pH 7.2, shows typical Michaelis-Menten kinetics with a Km for malate of 0.38 mm. The NAD malic enzyme shows pronounced sigmoidicity in response to malate with a Hill number of 3.5 and an S(0.5) of 41.6 mm.On the basis of the normal kinetics, the Km, and the fact that oxaloacetate production from malate by mitochondria appears most active at low malate concentrations, the high affinity portion of the malate isotherm with mitochondria is attributed to malate dehydrogenase. The low affinity portion of the malate isotherm with mitochondria is thought, on the basis of the similarity of S(0.5) values, the Hill numbers, and the greater production of pyruvate from malate at high malate concentrations, to represent the activity of the NAD malic enzyme.     

Trypsin-induced ATPase Activity in Potato Mitochondria

Potato mitochondria (Solanum tuberosum var. Russet Burbank), which readily phosphorylate ADP in oxidative phosphorylation, show low levels of ATPase activity which is stimulated neither by Mg²⁺, 2,4-dinitrophenol, incubation with respiratory substrates, nor disruption by sonication or treatment with Triton X-100, individually or in concert. Treatment of disrupted potato mitochondria with trypsin stimulates Mg²⁺-dependent, oligomycin-sensitive ATPase activity 10- to 15-fold, suggesting the presence of an ATPase inhibitor protein. Trypsin-induced ATPase activity was unaffected by uncoupler. Oligomycin-sensitive ATPase activity decreases as exposure to trypsin is increased. Incubation at alkaline pH or heating at 60 C for 2 minutes also activates ATPase of sonicated potato mitochondria. Disruption of cauliflower (Brassica oleracea), red sweet potato (Ipomoea batatas), and carrot (Daucus carota) mitochondria increases ATPase activity, which is further enhanced by treatment with trypsin. The significance of the tight association of the inhibitor protein and ATPase in potato mitochondria is not clear.     

Membrane-Associated NAD-Dependent Isocitrate Dehydrogenase in Potato Mitochondria

The oxidation isotherms for citrate and isocitrate by potato (Solanum tuberosum var. Russet Burbank) mitochondria in the presence of NAD differ markedly. Citrate oxidation shows positively cooperative kinetics with a sigmoid isotherm, whereas isocitrate oxidation shows Michaelis-Menten kinetics at concentrations up to 3 millimolar, and cooperative kinetics thereafter up to 30 millimolar. In the absence of exogenous NAD, the isocitrate isotherm is sigmoid throughout. The dual isotherm for isocitrate oxidation in the presence of exogenous NAD reflects the operation of two forms of isocitrate dehydrogenase, one in the matrix and one associated with the inner mitochondrial membrane. Whereas in intact mitochondria the activity of the membrane-bound enzyme is insensitive to rotenone, and to butylmalonate, an inhibitor of organic acid transport, isocitrate oxidation by the soluble matrix enzyme is inhibited by both. The membrane-bound isocitrate dehydrogenase does not operate through the NADH dehydrogenase on the outer face of the inner mitochondrial membrane, and is thus considered to face inward. The regulatory potential of isocitrate dehydrogenase in potato mitochondria may be realized by the apportionment of the enzyme between its soluble and bound forms.     

Cyanide-resistant Respiration of Sweet Potato Mitochondria

The oxidation of malate and succinate by sweet potato mitochondria (Ipomoea batatas [L.] Lam.) was blocked only partly by inhibitors of complexes III (2-heptyl-4-hydroxyquinoline-N-oxide) and IV (cyanide and azide). The respiration insensitive to inhibitors of complexes III and IV was inhibited by salicylhydroxamic acid. Essentially complete inhibition was obtained with inhibitors of complex I (rotenone, amytal, and thenoyltrifluoroacetone) and complex II (thenoyltrifluoroacetone). The observations indicated that electrons were transferred to the cyanide-resistant pathway from ubiquinone or from nonheme iron (iron-sulfur) proteins of complexes I and II before reaching the b cytochromes. In contrast, the oxidation of exogenous NADH did not involve the alternate pathway, as indicated by complete inhibition by inhibitors of complexes III and IV and the absence of an effect of inhibitors of complexes I and II. Hence, electrons from exogenous NADH appear to pass directly to complex III in sweet potato mitochondria.     

The Divalent Cation Pump and its Role in the Regulation of Malic Enzyme Activity in Purified Mitochondria from Potato Tuber

The control of the activity of the matrix-located malic enzyme(EC 1.1.1.39 [EC] ) by Mn²⁺ was investigated in Percoll-purified mitochondriafrom potato (Solarium tuberosum) tuber. Malic enzyme activitywas tightly controlled by the amount of Mn²⁺ available in thematrix space and could be stimulated by the addition of exogenousMn²⁺. A net uptake of Mn²⁺ into the matrix space of energizedmitochondria was measured. The uptake of Mn²⁺ was mediated bythe active cation pump present in the mitochondria. The activityof this cation pump was shown to be dependent on the membranepotential sustained by the activity of the respiratory chain.The uptake of Mn²⁺ was totally abolished in the presence ofan uncoupler and strongly depressed in the presence of rutheniumred, a specific inhibitor of the Ca²⁺-pump which is presentin animal mitochondria. Thus, the effect of Mn²⁺ on matrix-locatedMn²⁺-dependent malic enzyme was strongly influenced by the presenceof an uncoupler or of ruthenium red. In addition, this effectwas reduced in the presence of Ca²⁺. The possible physiologicalsignificance of the presence of this cation pump is discussedin relation to the presence of a matrix-located, NAD⁺-dependentmalic enzyme in plant mitochondria. (Received November 21, 1988; Accepted March 6, 1989)     

Effects of Ipomeamarone on Respiratory Enzyme System in Mitochondria

Ipomeamarone inhibited oxidation and phosphorylation in tightly coupled rat liver mitochondria. The inhibition of the oxygen uptake was higher when either β-hydroxybutyrate or α-ketoglutarate was supplied as the substrate than when succinate was used. In mitochondrial preparations which had been uncoupled, inhibitions of the electron transport chain from β-hydroxybutyrate to cytochrome c, and of the enzymes succinate cytochrome c oxidoreductase and β-hydroxybutyrate dehydrogenase were observed. Ipomeamarone inhibited also the ATP-inorganic phosphate exchange reaction, but did not act as an uncoupler; it repressed 2, 4-dinitropheaol-induced oxygen uptake.     

Activation Kinetics of NAD-Dependent Malic Enzyme of Cauliflower Bud Mitochondria

NAD-dependent malic enzyme (EC 1.1.1.39) was obtained from isolated mitochondria of cauliflower buds (Brassica oleracea L., var. botrytis). The NAD-linked activity is accompanied by a minor NADP-linked activity. Some contaminant NADP-malic enzyme from the supernatant and the plasma membrane is usually present in crude mitochondrial preparations. NAD-dependent malic enzyme has been purified 38-fold by ammonium sulfate fractionation and gel permeation chromatography, to a specific activity up to 2 micromoles per minute per milligram.     

丙酮酸对陈化马铃薯块茎切片线粒体抗氰呼吸的激活作用

用从陈化马铃薯切片纯化的线粒体进行实验发现：丙酮酸对总呼吸只有微弱的刺激作用,但可明显激活抗氰呼吸,并显著增强抗氰呼吸对总呼吸的贡献;丙酮酸对抗氰呼吸的激活作用可通过洗涤线粒体除去,重新加入丙酮酸又对抗氰呼吸产生激活作用;丙酮酸对抗氰呼吸的半最大激活浓度约为1．0mmol／L。上述结果表明丙酮酸对植物线粒体抗氰呼吸的激活作用可能具有普遍性。     

Malate Oxidation in Plant Mitochondria via Malic Enzyme and the Cyanide-insensitive Electron Transport Pathway

Malate oxidation in plant mitochondria proceeds through the activities of two enzymes: a malate dehydrogenase and a NAD⁺-dependent malic enzyme. In cauliflower, mitochondria malate oxidation via malate dehydrogenase is rotenone- and cyanide-sensitive. Addition of exogenous NAD⁺ stimulates the oxidation of malate via malic enzyme and generates an electron flux that is both rotenone- and cyanide-insensitive. The same effects of exogenous NAD⁺ are also observed with highly cyanide-sensitive mitochondria from white potato tubers or with mitochondria from spinach leaves. Both enzymes are located in the matrix, but some experimental data also suggest that part of malate dehydrogenase activity is also present outside the matrix compartment (adsorbed cytosolic malate dehydrogenase?). It is concluded that malic enzyme and a specific pool of NAD⁺/NADH are connected to the cyanide-insensitive alternative pathway by a specific rotenone-insensitive NADH dehydrogenase located on the inner face of the inner membrane. Similarly, malate dehydrogenase and another specific pool of NAD⁺/NADH are connected to the cyanide- (and antimycin-) sensitive pathway by a rotenone-sensitive NADH dehydrogenase located on the inner face of the inner membrane. A general scheme of electron transport in plant mitochondria for the oxidation of malate and NADH can be given, assuming that different pools of ubiquinone act as a branch point between various dehydrogenases, the cyanide-sensitive cytochrome pathway and the cyanide-insensitive alternative pathway.     

A Human Dynamin-related Protein Controls the Distribution of Mitochondria

Mitochondria exist as a dynamic tubular network with projections that move, break, and reseal in response to local environmental changes. We present evidence that a human dynamin-related protein (Drp1) is specifically required to establish this morphology. Drp1 is a GTPase with a domain structure similar to that of other dynamin family members. To identify the function of Drp1, we transiently transfected cells with mutant Drp1. A mutation in the GTPase domain caused profound alterations in mitochondrial morphology. The tubular projections normally present in wild-type cells were retracted into large perinuclear aggregates in cells expressing mutant Drp1. The morphology of other organelles was unaffected by mutant Drp1. There was also no effect of mutant Drp1 on the transport functions of the secretory and endocytic pathways. By EM, the mitochondrial aggregates found in cells that were transfected with mutant Drp1 appear as clusters of tubules rather than a large mass of coalescing membrane. We propose that Drp1 is important for distributing mitochondrial tubules throughout the cell. The function of this new dynamin-related protein in organelle morphology represents a novel role for a member of the dynamin family of proteins.     

Phosphoproteins and Protein Kinase Activities Intrinsic to Inner Membranes of Potato Tuber Mitochondria

Inside-out submitochondrial particles (IO-SMP) were isolatedand purified from potato (Solanum tuberosum L. cv.) tubers.When these IO-SMP were incubated with [ ³²P]ATP more then 20proteins became labelled as a result of phosphorylation. The³²P incorporation was stimulated by the oxidising reagent ferricyanide.Except for a 17 kDa protein which was phosphorylated only inthe absence of divalent cations, the protein phosphorylationrequired Mg²⁺. The time for half-maximum ³²P incorporation was4 mm for the 22 kDa phospho-F₁ -subunit and 2 min for the 28kDa phospho-F₀ b-subunit of the proton-ATPase. The K_m for ATPfor the detected phosphoproteins was between 65 µM and110 µM. The pH optimum for protein phosphorylation ininner membranes was between pH 6 and 8, and for the F₁ -subunitand the F₀ b-subunit the pH optima were 6.5–8 and pH 8,respectively. A 37 kDa phosphoprotein was phosphorylated ona histidine residue while the remainder of the inner membraneproteins were phosphorylated on serine or threonine residues.Two autophosphorylated putative kinases were identified: oneat 16.5 kDa required divalent cations for autophosphorylation,while another at 30 kDa did not. A 110 kDa protein was labelledonly with [-³²P] suggesting adenylylation. ³ Present address; Novartis Seeds AB, Box 302, S-261 23 Landskrona,Sweden.     

NAD Malic Enzyme and the Control of Carbohydrate Metabolism in Potato Tubers

Potato (Solanum tuberosum) plants were transformed with a cDNA encoding the 59-kD subunit of the potato tuber NAD-dependent malic enzyme (NADME) in the antisense orientation. Measurements of the maximum catalytic activity of NADME in tubers revealed a range of reductions in the activity of this enzyme down to 40% of wild-type activity. There were no detrimental effects on plant growth or tuber yield. Biochemical analyses of developing tubers indicated that a reduction in NADME activity had no detectable effects on flux through the tricarboxylic acid cycle. However, there was an effect on glycolytic metabolism with significant increases in the concentration of 3-phosphoglycerate and phosphoenolpyruvate. These results suggest that alterations in the levels of intermediates toward the end of the glycolytic pathway may allow respiratory flux to continue at wild-type rates despite the reduction in NADME. There was also a statistically significant negative correlation between NADME activity and tuber starch content, with tubers containing reduced NADME having an increased starch content. The effect on plastid metabolism may result from the observed glycolytic perturbations.     

INTERMEDIATE CLEAVAGE PEPTIDASE55 Modifies Enzyme Amino Termini and Alters Protein Stability in Arabidopsis Mitochondria

Precursor proteins containing mitochondrial peptide signals are cleaved after import by a mitochondrial processing peptidase. In yeast (Saccharomyces cerevisiae) and human (Homo sapiens), INTERMEDIATE CLEAVAGE PEPTIDASE55 (ICP55) plays a role in stabilizing mitochondrial proteins by the removal of single amino acids from mitochondrial processing peptidase-processed proteins. We have investigated the role of a metallopeptidase (At1g09300) from Arabidopsis (Arabidopsis thaliana) that has sequence similarity to yeast ICP55. We identified this protein in mitochondria by mass spectrometry and have studied its function in a transfer DNA insertion line (icp55). Monitoring of amino-terminal peptides showed that Arabidopsis ICP55 was responsible for the removal of single amino acids, and its action explained the −3 arginine processing motif of a number of mitochondrial proteins. ICP55 also removed single amino acids from mitochondrial proteins known to be cleaved at nonconserved arginine sites, a subset of mitochondrial proteins specific to plants. Faster mitochondrial protein degradation rates not only for ICP55 cleaved protein but also for some non-ICP55 cleaved proteins were observed in Arabidopsis mitochondrial samples isolated from icp55 than from the wild type, indicating that a complicated protease degradation network has been affected. The lower protein stability of isolated mitochondria and the lack of processing of target proteins in icp55 were complemented by transformation with the full-length ICP55. Analysis of in vitro degradation rates and protein turnover rates in vivo of specific proteins indicated that serine hydroxymethyltransferase was affected in icp55. The maturation of serine hydroxymethyltransferase by ICP55 is unusual, as it involves breaking an amino-terminal diserine that is not known as an ICP55 substrate in other organisms and that is typically considered a sequence that stabilizes rather than destabilizes a protein.Plant mitochondria provide energy production through respiration. Most mitochondrial proteins responsible for the machinery of respiration and metabolism are synthesized in the cytosol and imported into mitochondria. After import, N-terminal presequences containing targeting signals are cleaved from many proteins by the mitochondrial processing peptidase (MPP; Sjoling and Glaser, 1998; Zhang and Glaser, 2002), and the mitochondrial presequences themselves are then degraded by presequence peptidases (Ståhl et al., 2002; Moberg et al., 2003; Bhushan et al., 2005) and oligopeptidase (Kmiec et al., 2013). The specificity of the MPP cutting sites has been analyzed by comparison of the experimentally determined N-terminal sequences of mature proteins with the amino acid sequences of the precursor proteins. From this analysis, the most frequently observed MPP cleavage sites are referred to as −2 from an Arg (the −2R cleavage group) and −3 from an Arg (the −3R cleavage group) within the presequence (Zhang et al., 2001; Huang et al., 2009). However, despite the clear presence of both groups in experimental data, the −3R motif did not fit the high-resolution structure of MPP, which revealed −2R as the only probable cleavage site (Taylor et al., 2001). In yeast (Saccharomyces cerevisiae), there are also a group of mitochondrial proteins with a −10R motif that are now known to be first cleaved by MPP and then by OCTAPEPTIDYL AMINOPEPTIDASE1 (Oct1; Isaya et al., 1991; Vögtle et al., 2011). In plants, a group of mitochondrial proteins with nonconserved Arg cleavage sites has been reported (Huang et al., 2009). For many years, it has remained unclear why mitochondrial proteins from plants and yeast differed in the cleavage motif and what other proteases might be involved in these processes in plants.The identification of INTERMEDIATE CLEAVAGE PEPTIDASE55 (P40005.1) in yeast mitochondria solved the long-standing problem of apparent −2R and −3R cleavage sites by MPP (Vögtle et al., 2009). In yeast, ICP55 removes one residue from the mature protein after cleavage by MPP, leading to the Arg residue in the presequence being −3 from the position of the final N terminus of the mature protein. Therefore, the −3R group of proteins undergo a two-step cleavage, first by MPP and then a single amino acid removal by ICP55. In yeast, ICP55 cleaves exclusively after a Tyr, Leu, or Phe, leaving the first residue of the mature protein to typically be Ser, Ala, or Thr (Vögtle et al., 2009). Our analysis of plant mitochondrial presequence cleavage motifs indicated that the major −3R group (55%–58%) in Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa; Huang et al., 2009) had a very similar motif to that cleaved by ICP55 in yeast (Vögtle et al., 2009). ICP55 belongs to the M24 metallopeptidase peptidase family and is critical for mitochondrial protein stability in yeast (Vögtle et al., 2009). The stability, abundance, and turnover of mitochondrial proteins in yeast are also determined by other mitochondrial proteases (Brandner et al., 2005). Plant mitochondria also contain many other proteases, such as filamentation temperature sensitive H protein, long undivided filaments protein, caseinolytic protease, and degradation of periplasmic protein classes (Gibala et al., 2009; Rigas et al., 2009; Kmiec et al., 2012; Kwasniak et al., 2012; Solheim et al., 2012). Metallopeptidase and other protease classes could be part of a complex network controlling protein stability and, thus, the rate of protein turnover in plant mitochondria (van Wijk, 2015).We have compiled lists of Arabidopsis mitochondrial proteins using organelle isolation, fractionation, and proteomic analysis (Heazlewood et al., 2004; Taylor et al., 2011). Our in-depth analysis of mitochondrial matrix proteins has identified a protein with unknown function encoded by the gene At1g09300. This protein has some similarity to yeast ICP55 ({"type":"entrez-protein","attrs":{"text":"P40051.1","term_id":"731481","term_text":"P40051.1"}}P40051.1) and has been suggested to be an ICP55-like protein in plants based on sequence comparisons (Kwasniak et al., 2012). In this study, we have examined the role of this ICP55-like protein (At1g09300) in the cleavage of plant mitochondrial proteins using peptide mass spectrometry (MS) to compare the wild type with a transfer DNA (T-DNA) insertion line, icp55. The plant mitochondrial ICP55-like protein is not only responsible for −3R group protein cleavage, as observed in yeast, but also the cleavage of non-R group proteins that are only found in plant mitochondria, to our knowledge. The lack of ICP55 alters mitochondrial protein stability, as indicated by an analysis of protein degradation rates in isolated mitochondria. We also show that serine hydromethyltransferase (SHMT) is processed by ICP55, a degradation product of SHMT is stabilized in vitro in the absence of ICP55, and SHMT turns over more rapidly in vivo in icp55. The maturation of SHMT by cleavage of a diserine represents a new substrate class for ICP55 and appears to destabilize rather than stabilize this enzyme.     

Respiratory Chain Complexes in Dynamic Mitochondria Display a Patchy Distribution in Life Cells

Background

Mitochondria, the main suppliers of cellular energy, are dynamic organelles that fuse and divide frequently. Constraining these processes impairs mitochondrial is closely linked to certain neurodegenerative diseases. It is proposed that functional mitochondrial dynamics allows the exchange of compounds thereby providing a rescue mechanism.

Methodology/Principal Findings

The question discussed in this paper is whether fusion and fission of mitochondria in different cell lines result in re-localization of respiratory chain (RC) complexes and of the ATP synthase. This was addressed by fusing cells containing mitochondria with respiratory complexes labelled with different fluorescent proteins and resolving their time dependent re-localization in living cells. We found a complete reshuffling of RC complexes throughout the entire chondriome in single HeLa cells within 2–3 h by organelle fusion and fission. Polykaryons of fused cells completely re-mixed their RC complexes in 10–24 h in a progressive way. In contrast to the recently described homogeneous mixing of matrix-targeted proteins or outer membrane proteins, the distribution of RC complexes and ATP synthase in fused hybrid mitochondria, however, was not homogeneous but patterned. Thus, complete equilibration of respiratory chain complexes as integral inner mitochondrial membrane complexes is a slow process compared with matrix proteins probably limited by complete fusion. In co-expressing cells, complex II is more homogenously distributed than complex I and V, resp. Indeed, this result argues for higher mobility and less integration in supercomplexes.

Conclusion/Significance

Our results clearly demonstrate that mitochondrial fusion and fission dynamics favours the re-mixing of all RC complexes within the chondriome. This permanent mixing avoids a static situation with a fixed composition of RC complexes per mitochondrion.