Duck liver malic enzyme: sequence of a tryptic peptide containing the cysteine residue labeled by the substrate analog bromopyruvate

Peroxiredoxin 6 is the primary antioxidant enzyme for the maintenance of viability and DNA integrity in human spermatozoa

STUDY QUESTION

Are all components of the peroxiredoxins (PRDXs) system important to control the levels of reactive oxygen species (ROS) to maintain viability and DNA integrity in spermatozoa?

SUMMARY ANSWER

PRDX6 is the primary player of the PRDXs system for maintaining viability and DNA integrity in human spermatozoa.

WHAT IS KNOWN ALREADY

Mammalian spermatozoa are sensitive to high levels of ROS and PRDXs are antioxidant enzymes proven to control the levels of ROS generated during sperm capacitation to avoid oxidative damage in the spermatozoon. Low amounts of PRDXs are associated with male infertility. The absence of PRDX6 promotes sperm oxidative damage and infertility in mice.

STUDY DESIGN, SIZE, DURATION

Semen samples were obtained over a period of one year from a cohort of 20 healthy non-smoking volunteers aged 22-30 years old.

PARTICIPANTS/MATERIALS, SETTING, METHODS

Sperm from healthy donors was incubated for 2 h in the absence or presence of inhibitors for the 2-Cys PRDXs system (peroxidase, reactivation system and NADPH-enzymes suppliers) or the 1-Cys PRDX system (peroxidase and calcium independent-phospholipase A2 (Ca2+-iPLA2) activity). Sperm viability, DNA oxidation, ROS levels, mitochondrial membrane potential and 4-hydroxynonenal production were determined by flow cytometry.

MAIN RESULTS AND THE ROLE OF CHANCE

We observed a significant decrease in viable cells due to inhibitors of the 2-Cys PRDXs, PRDX6 Ca2+-iPLA2 activity or the PRDX reactivation system compared to controls (P ≤ 0.05). PRDX6 Ca2+-iPLA2 activity inhibition had the strongest detrimental effect on sperm viability and DNA oxidation compared to controls (P ≤ 0.05). The 2-Cys PRDXs did not compensate for the inhibition of PRDX6 peroxidase and Ca2+-iPLA2 activities.

LARGE SCALE DATA

Not applicable.

LIMITATIONS, REASONS FOR CAUTION

Players of the reactivation systems may differ among mammalian species.

WIDER IMPLICATIONS OF THE FINDINGS

The Ca2+-iPLA2 activity of PRDX6 is the most important and first line of defense against oxidative stress in human spermatozoa. Peroxynitrite is scavenged mainly by the PRDX6 peroxidase activity. These findings can help to design new diagnostic tools and therapies for male infertility.

STUDY FUNDING/COMPETING INTEREST(S)

This research was supported by The Canadian Institutes of Health Research (MOP 133661 to C.O.), and by RI MUHC-Desjardins Studentship in Child Health Research awarded to M.C.F. The authors have nothing to disclose.

Inhibition of energy-producing pathways of HepG2 cells by 3-bromopyruvate

3-BrPA (3-bromopyruvate) is an alkylating agent with anti-tumoral activity on hepatocellular carcinoma. This compound inhibits cellular ATP production owing to its action on glycolysis and oxidative phosphorylation; however, the specific metabolic steps and mechanisms of 3-BrPA action in human hepatocellular carcinomas, particularly its effects on mitochondrial energetics, are poorly understood. In the present study it was found that incubation of HepG2 cells with a low concentration of 3-BrPA for a short period (150 microM for 30 min) significantly affected both glycolysis and mitochondrial respiratory functions. The activity of mitochondrial hexokinase was not inhibited by 150 microM 3-BrPA, but this concentration caused more than 70% inhibition of GAPDH (glyceraldehyde-3-phosphate dehydrogenase) and 3-phosphoglycerate kinase activities. Additionally, 3-BrPA treatment significantly impaired lactate production by HepG2 cells, even when glucose was withdrawn from the incubation medium. Oxygen consumption of HepG2 cells supported by either pyruvate/malate or succinate was inhibited when cells were pre-incubated with 3-BrPA in glucose-free medium. On the other hand, when cells were pre-incubated in glucose-supplemented medium, oxygen consumption was affected only when succinate was used as the oxidizable substrate. An increase in oligomycin-independent respiration was observed in HepG2 cells treated with 3-BrPA only when incubated in glucose-supplemented medium, indicating that 3-BrPA induces mitochondrial proton leakage as well as blocking the electron transport system. The activity of succinate dehydrogenase was inhibited by 70% by 3-BrPA treatment. These results suggest that the combined action of 3-BrPA on succinate dehydrogenase and on glycolysis, inhibiting steps downstream of the phosphorylation of glucose, play an important role in HepG2 cell death.

A novel strategy involved in [corrected] anti-oxidative defense: the conversion of NADH into NADPH by a metabolic network

The reduced nicotinamide adenine dinucleotide phosphate (NADPH) is pivotal to the cellular anti-oxidative defence strategies in most organisms. Although its production mediated by different enzyme systems has been relatively well-studied, metabolic networks dedicated to the biogenesis of NADPH have not been fully characterized. In this report, a metabolic pathway that promotes the conversion of reduced nicotinamide adenine dinucleotide (NADH), a pro-oxidant into NADPH has been uncovered in Pseudomonas fluorescens exposed to oxidative stress. Enzymes such as pyruvate carboxylase (PC), malic enzyme (ME), malate dehydrogenase (MDH), malate synthase (MS), and isocitrate lyase (ICL) that are involved in disparate metabolic modules, converged to create a metabolic network aimed at the transformation of NADH into NADPH. The downregulation of phosphoenol carboxykinase (PEPCK) and the upregulation of pyruvate kinase (PK) ensured that this metabolic cycle fixed NADH into NADPH to combat the oxidative stress triggered by the menadione insult. This is the first demonstration of a metabolic network invoked to generate NADPH from NADH, a process that may be very effective in combating oxidative stress as the increase of an anti-oxidant is coupled to the decrease of a pro-oxidant.

Structure and function of malic enzymes, a new class of oxidative decarboxylases

Malic enzyme is a tetrameric protein with double dimer structure in which the dimer interface is more intimately contacted than the tetramer interface. Each monomeric unit of the enzyme is composed of four structural domains, which show a different folding topology from those of the other oxidative decarboxylases. The active center is located at the interface between domains B and C. For human mitochondrial malic enzyme, there is an exo nucleotide-binding site for the inhibitor ATP and an allosteric site for the activator fumarate, located at the tetramer and dimer interfaces, respectively. Crystal structures of the enzyme in various complexed forms indicate that the enzyme may exist in equilibrium among two open and two closed forms. Interconversion among these forms involves rigid-body movements of the four structural domains. Substrate binding at the active site shifts the open form to the closed form that represents an active site closure. Fumarate binding at the allosteric site induces the interconversion between forms I and II, which is mediated by the movements of domains A and D. Structures of malic enzyme from different sources are compared with an emphasis on the differences and their implications to structure-function relationships. The binding modes of the substrate, product, cofactors, and transition-state analogue at the active site, as well as ATP and fumarate at the exo site and allosteric site, respectively, provide a clear account for the catalytic mechanism, nucleotide specificities, allosteric regulation, and functional roles of the quaternary structure. The proposed catalytic mechanism involves tyrosine-112 and lysine-183 as the general acid and base, respectively. In addition, a divalent metal ion (Mn(2+) or Mg(2+)) is essential in helping the catalysis. Binding of the metal ion also plays an important role in stabilizing the quaternary structural integrity of the enzyme.

Molecular mechanism for the regulation of human mitochondrial NAD(P)+-dependent malic enzyme by ATP and fumarate

The regulation of human mitochondrial NAD(P)+-dependent malic enzyme (m-NAD-ME) by ATP and fumarate may be crucial for the metabolism of glutamine for energy production in rapidly proliferating tissues and tumors. Here we report the crystal structure at 2.2 A resolution of m-NAD-ME in complex with ATP, Mn2+, tartronate, and fumarate. Our structural, kinetic, and mutagenesis studies reveal unexpectedly that ATP is an active-site inhibitor of the enzyme, despite the presence of an exo binding site. The structure also reveals the allosteric binding site for fumarate in the dimer interface. Mutations in this binding site abolished the activating effects of fumarate. Comparison to the structure in the absence of fumarate indicates a possible molecular mechanism for the allosteric function of this compound.

Structural studies of the pigeon cytosolic NADP(+)-dependent malic enzyme

Malic enzymes are widely distributed in nature, and have important biological functions. They catalyze the oxidative decarboxylation of malate to produce pyruvate and CO(2) in the presence of divalent cations (Mg(2+), Mn(2+)). Most malic enzymes have a clear selectivity for the dinucleotide cofactor, being able to use either NAD(+) or NADP(+), but not both. Structural studies of the human mitochondrial NAD(+)-dependent malic enzyme established that malic enzymes belong to a new class of oxidative decarboxylases. Here we report the crystal structure of the pigeon cytosolic NADP(+)-dependent malic enzyme, in a closed form, in a quaternary complex with NADP(+), Mn(2+), and oxalate. This represents the first structural information on an NADP(+)-dependent malic enzyme. Despite the sequence conservation, there are large differences in several regions of the pigeon enzyme structure compared to the human enzyme. One region of such differences is at the binding site for the 2'-phosphate group of the NADP(+) cofactor, which helps define the cofactor selectivity of the enzymes. Specifically, the structural information suggests Lys362 may have an important role in the NADP(+) selectivity of the pigeon enzyme, confirming our earlier kinetic observations on the K362A mutant. Our structural studies also revealed differences in the organization of the tetramer between the pigeon and the human enzymes, although the pigeon enzyme still obeys 222 symmetry.

Mapping the active site topography of the NAD-malic enzyme via alanine-scanning site-directed mutagenesis

The NAD-malic enzyme cDNA has been subcloned into the pQE expression vector, expressed with a six-His tag, and purified. The His-tagged enzyme is purified by a combination of Ni-NTA and orange A agarose column chromatography with a yield of 45% and an estimated purity of >90%. The tag and linker have no effect on the kinetic parameters of the enzyme compared to the wild-type enzyme. Alanine-scanning site-directed mutagenesis has been carried out on all of the conserved neutral acid residues of the NAD-malic enzyme from Ascaris suum. Data obtained confirm the predicted role of D178 and D295 in metal ion binding, the likely role of D294, D361, and E440 in the NAD binding site, and the role of E58 and D272 in malate binding. Decreases in V/E(t) by 10(4)-fold and in V/K(malate)E(t) by 10(7)-fold, when D295 is changed to alanine, suggest that it is a likely candidate for the general base that accepts a proton from the malate hydroxyl in the oxidation step.

Swine cytosolic malic enzyme: cDNA cloning, sequencing, and localization

A highly significant genetic association has been found between some alleles of the swine Major Histocompatibility Complex SLA (Swine Leukocyte Antigen genetic complex) and the cytosolic malic enzymatic activity level in muscles. The aim of this study was to find out whether this genetic association was due to a close linkage of the SLA region and the gene coding for the enzyme. Since no swine cytosolic malic enzyme sequence (ME1) was available, we isolated several overlapping fragments that spanned the almost entire malic enzyme transcript both by screening of a swine cDNA library and by RT-PCR. The results indicated the existence of two transcripts of 2. 0 and 3.1 kb, which probably correspond to two alternative forms of one gene. The sequence of the transcript was highly similar to the other published mammalian cytosolic NADP+-dependent malic enzyme cDNA, especially within the four functional domains. Two major bands at 3.7 and 2.4 kb were detected on Northern blots containing the RNA from 25 tissues from fetuses and adult pigs. A high expression level was found in the adrenal gland, muscle, liver, and peripheral nerves. The analysis of malic enzyme RFLPs in five SLA informative families revealed an independent segregation of the ME1 gene from the SLA region. In situ hybridization results localized the cytosolic malic enzyme on the swine Chromosome (Chr) 1p1.2, except that the association between SLA and the malic enzyme activity level was due to a physical genetic linkage. Thus, the mechanisms underlying this association remain to be elucidated.

Involvement of Phe19 in the Mn(2+)-L-malate binding and the subunit interactions of pigeon liver malic enzyme

A triple mutant, F19S/N250S/L353Q, of pigeon liver malic enzyme was found to have no detectable enzymatic activity [Chou, W.-Y., Huang, S.-M., & Chang, G.-G. (1994) Arch. Biochem. Biophys. 310, 158-166]. In the present study, point mutants at these positions (F19S, N250S, and L353Q) were prepared by site-directed mutagenesis. Both N250S and L353Q have kinetic properties similar to those of the wild-type. On the other hand, the K(m)(app) values for both Mn2+ and L-malate of F19S were increased by approximately 10-fold, while the kcat value was decreased by 5-fold, which results in a decrease of the apparent catalytic efficiency (kcat/K(mNADP)K(mMal)K(mMn) by approximately 300-fold. These results clearly indicate that the F19S mutation is mainly responsible for the undetectable enzyme activity of the triple mutant. Three more Phe19 mutants (F19Y, F19G, and F19A) were then prepared. There is a direct correlation between the size of the substitutes and the affinities for Mn2+ and L-malate. The kinetic parameters for F19Y were similar to those for wild-type. Both F19A and F19G reveal a 5-fold decrease of kcat values. Two K(dMn) values for the high- and low-affinity sites, respectively, were detectable for the wild-type. On the contrary, only one K(dMn) value was detected for the F19 mutants, which was increased in the order of F19G > F19A > F19S > F19Y, with F19G being the most affected mutant. The K(mMal) values of F19G and F19A were increased 100- and 6-fold, respectively. The catalytic efficiency (kcat/K(mNADP)K(dMal)K(dMn)) of F19G was decreased to only 0.01% of that of the wild-type. The above results clearly indicate that the hydrophobic aromatic ring at position 19 plays a critical role in L-malate and Mn2+ binding. Furthermore, all mutants that have a small residue at position 19 exist as monomers. Therefore, Phe19 may locate in or near the regions for Mn(2+)-L-malate binding as well as for the subunit contact. These results are compatible with the asymmetric model for the quaternary structure of malic enzyme we proposed previously [Chang, G.-G., Huang, T.-M., Huang, S.-M., & Chou, W.-Y. (1994) Eur. J. Biochem. 225, 1021-1027]. The possible roles of the N-terminus of malic enzyme were also addressed.

Primary structure of the hydrogenosomal malic enzyme of Trichomonas vaginalis and its relationship to homologous enzymes

The complete nucleotide sequence has been established for two genes (maeA and maeB) coding for different subunits of the hydrogenosomal malic enzyme [malate dehydrogenase (decarboxylating) EC 1.1.1.39] of Trichomonas vaginalis. Two further genes (maeC and maeD) of this enzyme have been partially sequenced. The complete open reading frames code for polypeptides of 567 amino acids in length. These two open reading frames are similar with less than 12 percent pairwise nucleotide differences and less than 9 percent pairwise amino acid differences. The open reading frames of the two partially sequenced genes correspond to the amino-terminal part of the polypeptides coded and are similar to the corresponding parts of the completely sequenced ones. The deduced translation products of the two complete genes differ in their calculated pI values by 1.5 pH unit. The genes code for polypeptides which contain 12 or 11 amino-terminal amino-acyl residues not present in the proteins isolated from the cell. Other hydrogenosomal enzymes also have similar amino-terminal extensions which probably play a role in organellar targeting and translocation of the newly synthesized polypeptides. A comparison of 19 related enzymes from bacteria and eukaryotes with the maeA product revealed 34-45 percent amino acid identity. Phylogenetic reconstruction based on nonconservative amino acid differences with maximum parsimony (phylogenetic analysis using parsimony, PAUP) and distance based (neighbor-joining, NJ) methods showed that the T. vaginalis enzyme is the most divergent of all eukaryotic malic enzymes, indicating its long independent evolutionary history.

Cloning, sequencing and functional expression of a cDNA encoding a NADP-dependent malic enzyme from human liver

This work reports the structure of a cDNA (ME) encoding a human malic enzyme (ME) (malate NADP oxidoreductase, EC 1.1.1.40) elucidated by joining several overlapping fragments amplified by PCR from human hepatic cDNA or from cDNA libraries. The full-length cDNA has an open reading frame (ORF) of 1719 bp that encodes a 572-amino-acid protein of 64 113 Da, similar to the native monomeric, cytosolic, NADP-dependent ME isolated from human liver. The comparison of the structure of this cDNA with that of the human mitochondrial NAD(P)-dependent ME (EC 1.1.1.39) shows a homology of 63%, suggesting that these two forms originated from the same gene. The expression of the cDNA in Escherichia coli as a translational fusion (glutathione S-transferase::ME) protein yielded a product of the predicted mass. The recombinant protein shows NADP-dependent malate oxidoreductase activity and is virtually inactive with NAD. It also shows other distinct features of the native cytosolic NADP-dependent ME, like Mn2+ dependence, similar substrate (Km = 117 microM) and cofactor affinity (Km = 2 microM) constants, and a lack of allosteric regulation. In human proliferative cells, the NADP-dependent ME activity is poorly expressed and barely inducible by thyroid hormones.

Purification, cDNA cloning and heterologous expression of the human mitochondrial NADP(+)-dependent malic enzyme

Mitochondrial NADP(+)-dependent malic enzyme (ME; EC 1.1.1.39) has been purified to homogeneity and characterized kinetically from bovine heart. Partial amino acid sequence information allowed amplification of a specific bovine cDNA, which was used to isolate a full-length human cDNA of this isoform of ME. The cDNA is 1930 bp long and codes for a protein of 604 amino acids. Comparison of the amino acid sequence of this isoform with published sequences of other human ME isoforms shows stretches of homology interrupted by larger regions with significant differences. The human protein has been expressed in Escherichia coli, and the recombinant human protein has the same kinetic properties as the corresponding protein purified from bovine heart. Northern blot analysis showed a strong tissue-specific transcription with a predominantly high expression-rate in organs with a low division-rate.

Redox regulation of maize NADP-malic enzyme by thiol-disulfide interchange: effect of reduced thioredoxin on activity

Incubation of C4 NADP-malic enzyme from maize leaves with the oxidant o-iodosobenzoate leads to the reversible and complete inactivation of the enzyme. The time-course of inactivation is biphasic with the rate depending on the o-iodosobenzoate concentration. The inactivation is partially prevented by L-malate, NADP and Mg2+ alone, while NADP plus Mg2+ afford total protection. The complete reversal of the inactivation by the reductive agents dithiothreitol and 2-mercaptoethanol suggests that the modification of the enzyme by o-iodosobenzoate occurs concomitant with the oxidation of one or more pairs of sulfhydryl groups to the disulfide state, producing a conformationally altered form of the protein or directly modifying the active site. Titration of free thiol groups before and after inactivation of maize malic enzyme by o-iodosobenzoate shows a decrease in the accessible groups from 7 to 5, suggesting inactivation is accompanied by oxidation of two vicinal thiols. The oxidized form of the enzyme is rapidly reactivated by incubation with chemical and photochemically reduced thioredoxin in vitro, while the 'dark' activity of the enzyme is enhanced to the level of the 'light' activity by dithiothreitol. This evidence suggests that a reversible reduction and oxidation of disulfide bonds may take place during the regulation of the enzyme, indicating that the redox state of the disulfide bonds of C4 NADP-malic enzyme from maize leaves is important for the expression of maximal catalytic activity.

Using periodate-oxidized nucleotide as affinity label for the nucleotide site of proteins

The active site of pigeon liver malic enzyme was labeled with a fluorescent affinity label, the periodate-oxidized aminopyridine adenine dinucleotide phosphate. The modified enzyme was subjected to proteolytic digestion with trypsin. The resulted peptides were then separated with reversed-phase high-performance liquid chromatography on Waters muBondapak C18 column. Two pure fluorescent peptides were obtained after three runs of the chromatography. The peptides were then subjected to automatic Edman degradation on a Beckman peptide sequencer and subsequently separated and identified with phenylthiohydantoin C18 column. No sequence was obtained. The possible reasons for the failure in sequencing the periodate-oxidized nucleotides labeled active site peptide and some possible pitfalls in using these reagents were discussed.

Essential sulfhydryl group of malic enzyme from Escherichia coli

The activity of malic enzyme from Escherichia coli was unaffected by the monovalent cations Na+ or Li+ at 10 mM. At 100 mM, Li+ or Na+ inhibited the enzyme activity by 88% and 83%, respectively. However, the enzyme activity was stimulated by 40-80-fold with 10 mM K+, Rb+, Cs+, or NH4+. Less stimulation was observed with 100 mM of these stimulating cations. The stimulatory effect was lost after the enzyme was dialyzed against Tris-Cl buffer, but was regained after incubating the dialyzed enzyme with dithiothreitol. The regenerated enzyme was inactivated by 5,5'-dithiobis(2-nitrobenzoic acid). The resulting inactive thionitrobenzoyl enzyme could be regenerated to the active thiol-enzyme by dithiothreitol or converted to the inactive thiocyanoylated enzyme by KCN. The thiocyanoylated enzyme was insensitive to K+ stimulation, which suggested the essentiality of the sulfhydryl groups of the E. coli malic enzyme.

Duck liver 'malic' enzyme. Expression in Escherichia coli and characterization of the wild-type enzyme and site-directed mutants

A cDNA for duck liver 'malic' enzyme (EC 1.1.1.40) was subcloned into pUC-8, and the active enzyme was expressed in Escherichia coli TG-2 cells as a fusion protein including a 15-residue N-terminal leader from beta-galactosidase coded by the lacZ' gene. C99S and R70Q mutants of the enzyme were generated by the M13 mismatch technique. The recombinant enzymes were purified to near homogeneity by a simple two-step procedure and characterized relative to the enzyme isolated from duck liver. The natural duck enzyme has a subunit molecular mass of approx. 65 kDa, and the following kinetic parameters for oxidative decarboxylation of L-malate at pH 7.0: Km NADP+ (4.6 microM); Km L-malate (73 microM); kcat (160 s-1); Ka (2.4 microM) and Ka' (270 microM), dissociation constants of Mn2+ at 'tight' (activating) and 'weak' metal sites; and substrate inhibition (51% of kcat. at 8 mM-L-malate). Properties of the E. coli-derived recombinant wild-type enzyme are indistinguishable from those of the natural duck enzyme. Kinetic parameters of the R70Q mutant are relatively unaltered, indicating that Arg-70 is not required for the reaction. The C99S mutant has unchanged Km for NADP+ and parameters for the 'weak' sites (i.e. inhibition by L-malate, Ka'); however, kcat. decreased 3-fold and Km for L-malate and Ka each increased 4-fold, resulting in a catalytic efficiency [kcat./(Km NADP+ x Km L-malate x Ka)] equal to 3.7% of the natural duck enzyme. These results suggest that the positioning of Cys-99 in the sequence is important for proper binding of L-malate and bivalent metal ions.