Primary structure and analysis of the location of the regulatory disulfide bond of pea chloroplast NADP-malate dehydrogenase

Thioredoxin-h1 reduces and reactivates the oxidized cytosolic malate dehydrogenase dimer in higher plants

Cytosolic malate dehydrogenase (cytMDH) was captured by thioredoxin affinity chromatography as a possible target protein of cytosolic thioredoxin (Yamazaki, D., Motohashi, K., Kasama, T., Hara, Y., and Hisabori, T. (2004) Plant Cell Physiol. 45, 18-27). To further dissect this interaction, we aimed to determine whether cytMDH can interact with the cytosolic thioredoxin and whether its activity is redox-regulated. We obtained the active recombinant cytMDH that could be oxidized and rendered inactive. Inactivation was reversed by incubation with low concentrations of dithiothreitol in the presence of recombinant Arabidopsis thaliana thioredoxin-h1. Inactivation of cytMDH was found to result from formation of a homodimer. By cysteine mutant analysis and peptide mapping analysis, we were able to determine that the cytMDH homodimer occurs by formation of a disulfide bond via the Cys(330) residue. Moreover, we found this bond to be efficiently reduced by the reduced form of thioredoxin-h1. These results demonstrate that the oxidized form cytMDH dimer is a preferable target protein of the reduced form thioredoxin-h1 as suggested by thioredoxin affinity chromatography.

Thioredoxins: structure and function in plant cells

Thioredoxins are ubiquitous small-molecular-weight proteins (typically 100-120 amino-acid residues) containing an extremely reactive disulphide bridge with a highly conserved sequence -Cys-Gly(Ala/Pro)-Pro-Cys-. In bacteria and animal cells, thioredoxins participate in multiple reactions which require reduction of disulphide bonds on selected target proteins/ enzymes. There is now ample biochemical evidence that thioredoxins exert very specific functions in plants, the best documented being the redox regulation of chloroplast enzymes. Another area in which thioredoxins are believed to play a prominent role is in reserve protein mobilization during the process of germination. It has been discovered that thioredoxins constitute a large multigene family in plants with different-subcellular localizations, a unique feature in living cells so far. Evolutionary studies based on these molecules will be discussed, as well as the available biochemical and genetic evidence related to their functions in plant cells. Eukaryotic photosynthetic plant cells are also unique in that they possess two different reducing systems, one extrachloroplastic dependent on NADPH as an electron donor, and the other one chloroplastic, dependent on photoreduced ferredoxin. This review will examine in detail the latest progresses in the area of thioredoxin structural biology in plants, this protein being an excellent model for this purpose. The structural features of the reducing enzymes ferredoxin thioredoxin reductase and NADPH thioredoxin reductase will also be described. The properties of the target enzymes known so far in plants will be detailed with special emphasis on the structural features which make them redox regulatory. Based on sequence analysis, evidence will be presented that redox regulation of enzymes of the biosynthetic pathways first appeared in cyanobacteria possibly as a way to cope with the oxidants produced by oxygenic photosynthesis. It became more elaborate in the chloroplasts of higher plants where a co-ordinated functioning of the chloroplastic and extra chloroplastic metabolisms is required. CONTENTS Summary 543 I. Introduction 544 II. Thioredoxins from photosynthetic organisms as a structural model 545 III. Physiological functions 552 IV. The thioredoxin reduction systems 556 V. Structural aspects of target enzymes 558 VI. Concluding remarks 563 Acknowledgements 564 References 564.

Activation of partially folded mitochondrial malate dehydrogenase by thioredoxin

CD spectroscopy reveals that mitochondrial malate dehydrogenase in 3M guanidinium chloride shows little residual secondary structure. Refolding of the denatured protein by dilution with buffer of pH 7.5 does not restore the CD spectrum of the native enzyme. A partially folded intermediate, possessing 25% of the alpha-helix content of the native enzyme, is formed upon dilution. The partially folded intermediate binds the extrinsic probe 1-anilinonaphtalene-8-sulfonate, and the increase in fluorescence (tenfold) is accompanied by a blue shift in the band position of the emission spectrum. Partially folded malate dehydrogenase is devoid of catalytic activity. In vitro refolding of the denatured protein takes place in the presence of dithiotreitol and thioredoxin. In the presence of micromolar concentrations of thioredoxin, a recovery of approximately 70% of the catalytic activity was observed. Emission-anisotropy titrations of oxidized thioredoxin, tagged with a fluorescent probe, revealed that the oxidoreductase recognizes partially folded intermediates of malate dehydrogenase with a dissociation constant of 6 microM. Moreover, a covalently linked complex formed by thioredoxin and monomeric malate dehydrogenase was detected by SDS/PAGE. A general mechanism is postulated for the reactivation of denatured proteins by thioredoxin.

Cysteines of chloroplast NADP-malate dehydrogenase form mixed disulfides

Chloroplast NADP-malate dehydrogenase (NADP-MDH) from pea and from spinach was N-terminally truncated by limited proteolysis with Staphylococcus aureus protease V8. The resulting monomeric enzymes lacking, respectively, the 37 and 38 N-terminal amino acids were inactive. Reduction and addition of low concentrations of guanidine-HCl (50-100 mM) resulted in a highly active enzyme of 850 units per mg protein. Equilibration of the truncated enzyme with various glutathione (GSH) redox buffers and assaying its activity in the presence of guanidine-HCl was used to establish the existence of protein-GSH mixed disulfides. This finding was further confirmed using incorporation of radioactively labelled thiol. The possible function of such cysteine modifications under oxidative stress and their regeneration by the thioredoxin system in the light is discussed.

Mechanism of light modulation: identification of potential redox-sensitive cysteines distal to catalytic site in light-activated chloroplast enzymes

Light-dependent reduction of target disulfides on certain chloroplast enzymes results in a change in activity. We have modeled the tertiary structure of four of these enzymes, namely NADP-linked glyceraldehyde-3-P dehydrogenase, NADP-linked malate dehydrogenase, sedoheptulose bisphosphatase, and fructose bisphosphatase. Models are based on x-ray crystal structures from non-plant species. Each of these enzymes consists of two domains connected by a hinge. Modeling suggests that oxidation of two crucial cysteines to cystine would restrict motion around the hinge in the two dehydrogenases and influence the conformation of the active site. The cysteine residues in the two phosphatases are located in a region known to be sensitive to allosteric modifiers and to be involved in mediating structural changes in mammalian and microbial fructose bisphosphatases. Apparently, the same region is involved in covalent modification of phosphatase activity in the chloroplast.

Cloning, site-specific mutagenesis, expression and characterization of full-length chloroplast NADP-malate dehydrogenase from Pisum sativum

Chloroplast NADP-dependent malate dehydrogenase is regulated by a dithiol redox reaction. The assignment of the groups involved, requires the primary structure of the enzyme to be known. Using the polymerase chain reaction and the cDNA library of Pisum sativum, the sequence of the enzyme and its targeting signal was determined. The gene was cloned in Escherichia coli JM83 and expressed in E. coli JM83 and E. coli B at high yield. The determination of the physical properties of the gene product proves the recombinant protein to be indistinguishable from the enzyme purified from the plant. This holds true, in spite of the fact that the plant enzyme lacks 11 N-terminal residues. The lengths of the complete polypeptide chain of the recombinant enzyme and its transit peptide are 388 and 53 residues, respectively. The comparison of the sequences of the mature enzyme with those of known chloroplast NADP-MDH shows 83-95% identity, but with mitochondrial or bacterial MDH only approximately 20%. Reduction of the (inactive) oxidized enzyme with dithiothreitol allows mimicking of the in vivo activation. The reaction follows a consecutive second-order-kinetics mechanism. Guanidinium chloride (GdmCl) at concentrations below 0.4 M leads to a significant activation of the oxidized form of the enzyme. At [GdmCl] = 0.4-0.46 M, both oxidized and reduced NADP-MDH show highly cooperative changes in the hydrodynamic and spectral properties, indicating the synchronous breakdown of the quaternary, tertiary and secondary structures. Site-directed mutations C23A and C28A do not quench the regulatory properties of the enzyme; additional substitution of alanine for Cys206 and Cys376 renders the enzyme equally active in both the reduced and the oxidized state. Therefore, one can consider these residues, either alone or in combination with Cys23 and Cys28, as responsible for enzyme activation.

Effects of N-terminal truncations upon chloroplast NADP-malate dehydrogenases from pea and spinach

Using the purification procedure of Fickenscher and Scheibe (Biochim. Biophys. Acta 749 (1983), 249-254) and a modification of the method, we produced a series of NADP-MDH forms from spinach and pea-leaf extracts that were characterized by a stepwise shortening of the N-terminal sequences. Limited proteolysis of the enzymes resulted in the generation of even shorter forms. Immunoprecipitation of the NADP-MDH from crude extracts revealed that the sequences of the intact enzymes from pea, spinach and maize started at a position (Ser) identical with that established for the Sorghum enzyme (Crétin, C., et al. (1990) Eur. J. Biochem. 192, 299-303). Spinach NADP-MDH isolated by conventional methods was shown to represent the intact form. Thus, the kinetic, regulatory and structural properties of the various truncated forms could be compared with those of an intact form. Removal of 5 or 11 amino acids, as occurred during isolation of the pea NADP-MDH, was without any significant effect. The enzymes were all dimeric and still exhibited the characteristic redox-regulatory properties. However, removal of 31 and 37 amino acids using aminopeptidase K resulted in the formation of active monomers characterized by only slightly lowered affinities towards the substrates, a shift of their pH optimum from 8 to 7, the loss of oxaloacetate inhibition and an increased maximal velocity. Although these forms lacked most or all of the N-terminal extra-peptide, including the 2 cysteines involved in redox-modification, they were still sensitive to the redox-potential. However, the low concentration of thiol required for immediate and complete restoration of any lost activity (40 mM beta-mercaptoethanol) suggested that this reaction might not be relevant for redox-regulation in vivo.

A thioredoxin-independent fully active NADP-malate dehydrogenase obtained by site-directed mutagenesis

A triple cysteine mutant of sorghum leaf NADP-malate dehydrogenase has been constructed by site-directed mutagenesis, combining the previously obtained mutation of the two N-terminal cysteines with the mutation of the most internal of the two C-terminal cysteines. The construct, over-expressed in E. coli, yielded an always active, dithiol-insensitive enzyme. It can be concluded that the dithiol activation of the unmodified enzyme involves a maximum of two different disulfides per subunit, and that none of the mutated cysteines is implicated in catalysis.

Molecular cloning and expression of chloroplast NADP-malate dehydrogenase during Crassulacean acid metabolism induction by salt stress

A full-length cDNA clone for NADP(+)-dependent malate dehydrogenase (NADP-MDH; EC 1.1.1.82) from the facultative CAM plant,Mesembryanthemum crystallinum has been isolated and characterized. NADP-MDH is responsible for the reduction of oxaloacetate to malate in the chloroplasts of higher plants. The cDNA clone is 1747 bp in size and contains a single open reading frame encoding a 441 amino acid long precursor polypeptide with a predicted molecular weight of 47 949. The predicted, mature NADP-MDH polypeptide sequence fromM. crystallinum shares 82.7% to 84% amino acid identity with other known higher plant sequences. Genomic Southern blot analysis ofM. crystallinum DNA indicates that MDH is encoded by a small gene family. Steady-state transcript levels for chloroplast NADP-MDH decrease transiently in the leaves after salt stress and then increase to levels greater than two-fold higher than in unstressed plants. Transcript levels in roots are extremely low and are unaffected by salt-stress treatment. In vitro transcription run-on experiments using isolated nuclei from leaf tissue confirm that the accumulation of NADP-MDH transcripts is, at least in part, the result of increased transcription of this gene during salt stress. The salt-stress-induced expression pattern of this enzyme suggests that it may participate in the CO2 fixation pathway during CAM.

Conformational flexibility of the regulatory site of phosphoribulokinase as demonstrated with bifunctional reagents

Phosphoribulokinase (PRK) is one of several chloroplastic enzymes whose activity is regulated by thiol-disulfide exchange via thioredoxin. Activation entails reduction of an active-site disulfide bond between Cys16 and Cys55. Bifunctional cross-linking reagents have been used to approximate the interresidue distance between Cys16 and Cys55, an issue which impinges on the relative conformational states of the activated and deactivated forms of the enzyme. Spinach PRK is rapidly inactivated by stoichiometric levels of 4,4'-difluoro-3,3'-dinitrodiphenyl sulfone (FNPS) or 1,5-difluoro-2,4-dinitrobenzene (DFNB), which span 9 and 3.5 A, respectively. ATP, but not ribulose 5-phosphate, retards the rate of inactivation, suggesting that modification has occurred at the nucleotide binding domain of the active site. Sulfhydryl modification is indicated by partial reversibility of inactivation as effected by exogenous thiols. Tryptic mapping by reverse-phase chromatography of [14C]carboxymethylated enzyme, subsequent to its reaction with either FNPS or DFNB, demonstrates modification of Cys16 and Cys55 by both reagents, and formation of only one major chromophoric peptide in each case. On the basis of the sequence analysis of the purified chromophoric peptides, Cys16 and Cys55 are cross-linked by both FNPS and DFNB. Thus, the intrasubunit distance between the beta-sulfhydryls of Cys16 and Cys55 is dynamic rather than static. Diminished conformational flexibility upon oxidation of the regulatory sulfhydryls to a disulfide may be partially responsible for the concomitant loss of enzymatic activity.

Limited proteolysis of NADP-malate dehydrogenase from pea chloroplast by aminopeptidase K yields monomers. Evidence of proteolytic degradation of NADP-malate dehydrogenase during purification from pea

NADP-malate dehydrogenase (L-malate: NADP oxidoreductase, EC 1.1.1.82) from leaves of Pisum sativum has been purified to homogeneity, as judged by polyacrylamide gel electrophoresis. In the crude leaf extract and in the absence of protease inhibitors in the isolation medium, the N-terminus of NADP-MDH was found to be highly susceptible to proteolysis. Evidence of proteolysis during purification includes observations of reduced subunit size on SDS-PAGE and reduced specific activity. Experiments were carried out to investigate the function of the N-terminal amino acid sequence extension of NADP-MDH. Limited proteolysis of highly active (600 units/mg protein) NADP-MDH using aminopeptidase K yielded catalytically active monomers of 34.7 kDa. The results support the conclusions that the N-terminal region is located at the surface of the protein, and that for maintenance of the native NADP-MDH dimer an N-terminal amino acid sequence is important.

Construction of a stable dimer of Bacillus stearothermophilus lactate dehydrogenase

A molecular graphics analysis of the features which prevent cytosolic malate dehydrogenase dimers from forming tetramers was evaluated by its success in predicting the synthesis of a version of the LDH framework which is a stable dimer. Surface residues responsible for malate dehydrogenases being dimers were revealed by superimposing the structures of two dimers of pig cytosolic malate dehydrogenase on one homologous tetramer of L-lactate dehydrogenase from Bacillus stearothermophilus. Four regions were identified as composing the P-axis dimer-dimer interface. Two regions of the dimer were surface loops that collided when built as a tetramer: a large loop (residues 203-207, KNOBI) and a small loop (residues 264-269, KNOBII), and these were candidates to explain the dimeric character of malate dehydrogenase. The analysis was tested by constructing a synthetic B. stearothermophilus lactate dehydrogenase (KNOBI) containing the large malate dehydrogenase loop (residues 203-207 being AYIKLQAKE, and extra four amino acids). The new construct was thermotolerant (90 degrees C) and enzymically active with kcat and KM (pyruvate) values similar to those of the wild-type enzyme. However, whereas the allosteric activator fructose 1,6-bisphosphate decreased KM 100 times for wild type, it had no influence on KNOBI. The molecular volumes of 1-120 microM concentrations of the construct were measured by time-resolved decay of tryptophan fluorescence anisotropy and by gel filtration. Both methods showed the molecular weight of wild type increased from dimer to tetramer with Kd about 20 microM dimer. KNOBI remained a dimer under these conditions.(ABSTRACT TRUNCATED AT 250 WORDS)

A prediction of the three-dimensional structure of maize NADP(+)-dependent malate dehydrogenase which explains aspects of light-dependent regulation unique to plant enzymes

A model has been built for the plant NADP-malate dehydrogenase from Zea mays, a key enzyme in photosynthesis, which undergoes light-dependent regulation. The model was based on sequence and presumed structural homology to the known three-dimensional structure of mammalian porcine cytosolic NAD-malate dehydrogenase. A cystine-loop present in an extended C-terminal region of plant NADP-malate dehydrogenases was modelled using molecular mechanics and computer graphical methods, based on the assumption that a disulphide bridge exists in the inactive form of the enzyme between Cys351 and Cys363. The predicted conformation of the intact C-terminal cystine-loop suggests that the extended polypeptide will bind in the active centre and inhibit enzyme activity. Another ionizable cysteine residue in the active site is predicted to control the charge of the catalytic His215 and might be responsible for the uniquely tight binding of the positively charged nicotinamide ring of NADP+ in this and other C4 and C3 plant NADP-malate dehydrogenases.