Thermodynamic analysis of the emergence of new regulatory properties in a phosphoribulokinase-glyceraldehyde 3-phosphate dehydrogenase complex

A Trajectory of Discovery: Metabolic Regulation by the Conditionally Disordered Chloroplast Protein, CP12

The chloroplast protein CP12, which is widespread in photosynthetic organisms, belongs to the intrinsically disordered proteins family. This small protein (80 amino acid residues long) presents a bias in its composition; it is enriched in charged amino acids, has a small number of hydrophobic residues, and has a high proportion of disorder-promoting residues. More precisely, CP12 is a conditionally disordered proteins (CDP) dependent upon the redox state of its four cysteine residues. During the day, reducing conditions prevail in the chloroplast, and CP12 is fully disordered. Under oxidizing conditions (night), its cysteine residues form two disulfide bridges that confer some stability to some structural elements. Like many CDPs, CP12 plays key roles, and its redox-dependent conditional disorder is important for the main function of CP12: the dark/light regulation of the Calvin-Benson-Bassham (CBB) cycle responsible for CO₂ assimilation. Oxidized CP12 binds to glyceraldehyde-3-phosphate dehydrogenase and phosphoribulokinase and thereby inhibits their activity. However, recent studies reveal that CP12 may have other functions beyond the CBB cycle regulation. In this review, we report the discovery of this protein, its features as a disordered protein, and the many functions this small protein can have.

Constructing de novo biosynthetic pathways for chemical synthesis inside living cells

Living organisms have evolved a vast array of catalytic functions that make them ideally suited for the production of medicinally and industrially relevant small-molecule targets. Indeed, native metabolic pathways in microbial hosts have long been exploited and optimized for the scalable production of both fine and commodity chemicals. Our increasing capacity for DNA sequencing and synthesis has revealed the molecular basis for the biosynthesis of a variety of complex and useful metabolites and allows the de novo construction of novel metabolic pathways for the production of new and exotic molecular targets in genetically tractable microbes. However, the development of commercially viable processes for these engineered pathways is currently limited by our ability to quickly identify or engineer enzymes with the correct reaction and substrate selectivity as well as the speed by which metabolic bottlenecks can be determined and corrected. Efforts to understand the relationship among sequence, structure, and function in the basic biochemical sciences can advance these goals for synthetic biology applications while also serving as an experimental platform for elucidating the in vivo specificity and function of enzymes and reconstituting complex biochemical traits for study in a living model organism. Furthermore, the continuing discovery of natural mechanisms for the regulation of metabolic pathways has revealed new principles for the design of high-flux pathways with minimized metabolic burden and has inspired the development of new tools and approaches to engineering synthetic pathways in microbial hosts for chemical production.

Pleiotropic modulation of carbon and nitrogen metabolism in Arabidopsis plants overexpressing the NAD kinase2 gene

Nicotinamide nucleotides (NAD and NADP) are important cofactors in many metabolic processes in living organisms. In this study, we analyzed transgenic Arabidopsis (Arabidopsis thaliana) plants that overexpress NAD kinase2 (NADK2), an enzyme that catalyzes the synthesis of NADP from NAD in chloroplasts, to investigate the impacts of altering NADP level on plant metabolism. Metabolite profiling revealed that NADP(H) concentrations were proportional to NADK activity in NADK2 overexpressors and in the nadk2 mutant. Several metabolites associated with the Calvin cycle were also higher in the overexpressors, accompanied by an increase in overall Rubisco activity. Furthermore, enhanced NADP(H) production due to NADK2 overexpression increased nitrogen assimilation. Glutamine and glutamate concentrations, as well as some other amino acids, were higher in the overexpressors. These results indicate that overexpression of NADK2 either directly or indirectly stimulates carbon and nitrogen assimilation in Arabidopsis under restricted conditions. Importantly, since neither up-regulation nor down-regulation of NADK2 activity affected the sum amount of NAD and NADP or the redox state, the absolute level of NADP and/or the NADP/NAD ratio likely plays a key role in regulating plant metabolism.

SPECIFICITY AND FUNCTION OF GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE IN A FRESHWATER DIATOM, ASTERIONELLA FORMOSA (BACILLARIOPHYCEAE)(1)

The plastidic glyceraldehyde-3-phosphate dehydrogenase (GAPDH) catalyzes the only reductive step in the Calvin cycle and exists as different forms of which GapC1 enzyme is present in chromalveolates, such as diatoms. Biochemical studies on diatoms are still fragmentary, and, thus, in this report, GAPDH from the freshwater diatom Asterionella formosa Hassall has been purified and kinetically characterized. It is a homotetrameric enzyme with a molecular mass of ~150 ± 15 kDa. The enzyme showed Michaelis-Menten kinetics with respect to both cofactors, NADPH and NADH, with a 16-fold greater catalytic constant for NADPH. The Km for NADPH was 140 μM, the lowest affinity reported, while the catalytic constant, 815 s(-1) , is the highest reported. The Km for NADH was 93 μM, and the catalytic constant was 50 s(-1) , both are similar to reported values for other types of GAPDH. The GapC1 enzyme, like the Chlamydomonas reinhardtii A4 GAPDH, exhibits a cooperative behavior toward the substrate, 1,3-bisphosphoglyceric acid (BPGA), with both cofactors. Mass spectrometry analysis showed that when GapC1 enzyme was purified without reducing agents, it copurified with a small protein with a mass of 8.2 kDa. This protein was recognized by antibodies against CP12. When associated with this protein, GAPDH displayed a lag that disappeared upon incubation with reducing agent in the presence of either BPGA or NADPH as a consequence of dissociation of the GAPDH/CP12 complex. Thus, as in other species of algae and higher plants, regulation of GapC1 enzyme in A. formosa may occur through association-dissociation processes linked to dark-light transitions.

Thioredoxin-mediated reversible dissociation of a stromal multiprotein complex in response to changes in light availability

A Calvin cycle multiprotein complex including phosphoribulokinase (PRK), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), and a small protein, CP12, has previously been identified. In this article, we have studied this complex in leaves and have shown that dissociation and reassociation of the PRK/GAPDH/CP12 complex occurs in a time frame of minutes, allowing for rapid regulation of enzyme activity. Furthermore, we have shown that the extent of formation and dissociation of the PRK/GAPDH/CP12 complex correlates with the quantity of light. These data provide evidence linking the status of this complex with the rapid and subtle regulation of GAPDH and PRK activities in response to fluctuations in light availability. We have also demonstrated that dissociation of this complex depends on electron transport chain activity and that the major factor involved in the dissociation of the pea complex was thioredoxin f. We show here that both PRK and GAPDH are present in the reduced form in leaves in the dark, but are inactive, demonstrating the role of the PRK/GAPDH/CP12 complex in deactivating these enzymes in response to reductions in light intensity. Based on our data, we propose a model for thioredoxin f-mediated activation of PRK and GAPDH by two mechanisms: directly through reduction of disulfide bonds within these enzymes and indirectly by mediating the breakdown of the complex in response to changes in light intensity.

A model for carbohydrate metabolism in the diatom Phaeodactylum tricornutum deduced from comparative whole genome analysis

BACKGROUND

Diatoms are unicellular algae responsible for approximately 20% of global carbon fixation. Their evolution by secondary endocytobiosis resulted in a complex cellular structure and metabolism compared to algae with primary plastids.

METHODOLOGY/PRINCIPAL FINDINGS

The whole genome sequence of the diatom Phaeodactylum tricornutum has recently been completed. We identified and annotated genes for enzymes involved in carbohydrate pathways based on extensive EST support and comparison to the whole genome sequence of a second diatom, Thalassiosira pseudonana. Protein localization to mitochondria was predicted based on identified similarities to mitochondrial localization motifs in other eukaryotes, whereas protein localization to plastids was based on the presence of signal peptide motifs in combination with plastid localization motifs previously shown to be required in diatoms. We identified genes potentially involved in a C4-like photosynthesis in P. tricornutum and, on the basis of sequence-based putative localization of relevant proteins, discuss possible differences in carbon concentrating mechanisms and CO(2) fixation between the two diatoms. We also identified genes encoding enzymes involved in photorespiration with one interesting exception: glycerate kinase was not found in either P. tricornutum or T. pseudonana. Various Calvin cycle enzymes were found in up to five different isoforms, distributed between plastids, mitochondria and the cytosol. Diatoms store energy either as lipids or as chrysolaminaran (a beta-1,3-glucan) outside of the plastids. We identified various beta-glucanases and large membrane-bound glucan synthases. Interestingly most of the glucanases appear to contain C-terminal anchor domains that may attach the enzymes to membranes.

CONCLUSIONS/SIGNIFICANCE

Here we present a detailed synthesis of carbohydrate metabolism in diatoms based on the genome sequences of Thalassiosira pseudonana and Phaeodactylum tricornutum. This model provides novel insights into acquisition of dissolved inorganic carbon and primary metabolic pathways of carbon in two different diatoms, which is of significance for an improved understanding of global carbon cycles.

Involvement of two positively charged residues of Chlamydomonas reinhardtii glyceraldehyde-3-phosphate dehydrogenase in the assembly process of a bi-enzyme complex involved in CO2 assimilation

The glyceraldehyde-3-phosphate dehydrogenase (GAPDH) in the chloroplast of Chlamydomonas reinhardtii is part of a complex that also includes phosphoribulokinase (PRK) and CP12. We identified two residues of GAPDH involved in protein-protein interactions in this complex, by changing residues K128 and R197 into A or E. K128A/E mutants had a Km for NADH that was twice that of the wild type and a lower catalytic constant, whatever the cofactor. The kinetics of the mutant R197A were similar to those of the wild type, while the R197E mutant had a lower catalytic constant with NADPH. Only small structural changes near the mutation may have caused these differences, since circular dichroism and fluorescence spectra were similar to those of wild-type GAPDH. Molecular modelling of the mutants led to the same conclusion. All mutants, except R197E, reconstituted the GAPDH-CP12 subcomplex. Although the dissociation constants measured by surface plasmon resonance were 10-70-fold higher with the mutants than with wild-type GAPDH and CP12, they remained low. For the R197E mutation, we calculated a 4 kcal/mol destabilizing effect, which may correspond to the loss of the stabilizing effect of a salt bridge for the interaction between GAPDH and CP12. All the mutant GAPDH-CP12 subcomplexes failed to interact with PRK and to form the native complex. The absence of kinetic changes of all the mutant GAPDH-CP12 subcomplexes, compared to wild-type GAPDH-CP12, suggests that mutants do not undergo the conformation change essential for PRK binding.

Emergence of new regulatory mechanisms in the Benson-Calvin pathway via protein-protein interactions: a glyceraldehyde-3-phosphate dehydrogenase/CP12/phosphoribulokinase complex

Protein-protein interactions are involved in many metabolic pathways. This review will focus on the role of such associations in CO2 assimilation (Benson-Calvin cycle) and especially on the involvement of a GAPDH/CP12/PRK complex which has been identified in many photosynthetic organisms and may have an important role in the regulation of CO2 assimilation. The emergence of new kinetic and regulatory properties as a consequence of protein-protein interactions will be addressed as well as some of the questions raised by the existence of these supramolecular complexes such as composition, function, and assembly pathways. The presence and role of small intrinsically unstructured proteins like the 8.5 kDa protein CP12, involved in the regulation and/or assembly of these complexes will be discussed.

Metabolic channeling in plants

The organization of cooperating enzymes into macromolecular complexes is a central feature of cellular metabolism. A major advantage of such spatial organization is the transfer of biosynthetic intermediates between catalytic sites without diffusion into the bulk phase of the cell. This so-called "metabolic channeling" offers unique opportunities for enhancing and regulating cellular biochemistry. Studies in a number of plant primary and secondary metabolic systems continue to contribute to our understanding of the nature and importance of this phenomenon. This article reviews advances in four systems: the cysteine synthase complex, the Calvin cycle, cyanogenic glucoside biosynthesis, and the phenylpropanoid pathway. Each of these systems is providing new evidence for the importance of enzyme organization in cellular biochemistry as well as exclusive insights into the molecular basis of enzyme complex assembly. This review also explores current prospects for understanding metabolon structure, assembly, and biological function.

The small protein CP12: a protein linker for supramolecular complex assembly

CP12 is an 8.5-kDa nuclear-encoded chloroplast protein, isolated from higher plants. It forms part of a core complex of two dimers of phosphoribulokinase (PRK), two tetramers of glyceraldehyde 3-phosphate dehydrogenase (GAPDH), and CP12. The role of CP12 in this complex assembly has not been determined. To address this question, we cloned a cDNA encoding the mature CP12 from the green alga Chlamydomonas reinhardtii and expressed it in Escherichia coli. Sequence alignments show that it is very similar to other CP12s, with four conserved cysteine residues forming two disulfide bridges in the oxidized CP12. On the basis of reconstitution assays and surface plasmon resonance binding studies, we show that oxidized, but not reduced, CP12 acts as a linker in the assembly of the complex, and we propose a model in which CP12 associates with GAPDH, causing its conformation to change. This GAPDH/CP12 complex binds PRK to form a half-complex (one unit). This unit probably dimerizes due partially to interactions between the enzymes of each unit. Reduced CP12 being unable to reconstitute the complex, we studied the structures of oxidized and reduced CP12 by NMR and circular dichroism to determine whether reduction induced structural transitions. Oxidized CP12 is mainly composed of alpha helix and coil segments, and is extremely flexible, while reduced CP12 is mainly unstructured. Remarkably, CP12 has similar physicochemical properties to those of "intrinsically unstructured proteins" that are also involved in regulating macromolecular complexes, or in their assembly. CP12s are thus one of the few protein families of intrinsically unstructured proteins specific to plants.

Modulation, via protein-protein interactions, of glyceraldehyde-3-phosphate dehydrogenase activity through redox phosphoribulokinase regulation

The activity of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) embedded in the phosphoribulokinase (PRK).GAPDH.CP12 complex was increased 2-3-fold by reducing agents. This occurred by interaction with PRK as the cysteinyl sulfhydryls (4 SH/subunit) of GAPDH within the complex were unchanged whatever the redox state of the complex. But isolated GAPDH was not activated. Alkylation plus mass spectrometry also showed that PRK had one disulfide bridge and three SH groups per monomer in the active oxidized complex. Reduction disrupted this disulfide bridge to give 2 more SH groups and a much more active enzyme. We assessed the kinetics and dynamics of the interactions between PRK and GAPDH/CP12 using biosensors to measure complex formation in real time. The apparent equilibrium binding constant for GAPDH/CP12 and PRK was 14 +/- 1.6 nm for oxidized PRK and 62 +/- 10 nm for reduced PRK. These interactions were neither pH- nor temperature-dependent. Thus, the dynamics of PRK.GAPDH.CP12 complex formation and GAPDH activity are modulated by the redox state of PRK.

Molecular and biochemical characterization of hexokinase from Trypanosoma cruzi

The Trypanosoma cruzi hexokinase gene has been cloned, sequenced, and expressed as an active enzyme in Escherichia coli. Sequence analysis revealed 67% identity with its counterpart in Trypanosoma brucei but low similarity with all other available hexokinase sequences including those of human. It contains an N-terminal peroxisome-targeting signal (PTS-2) and has a calculated basic isoelectric point (pI = 9.67), a feature often associated with glycosomal proteins. The polypeptide has a predicted mass of approximately 50 kDa similar to that of many non-vertebrate hexokinases and the vertebrate hexokinase isoenzyme IV. The natural enzyme was purified to homogeneity from T. cruzi epimastigotes and appeared to exist in several aggregation states, an apparent tetramer being the predominant form. Its kinetic properties were compared with those of the purified recombinant protein. Higher K(m) values for glucose and ATP were found for the (His)(6)-tag-containing recombinant hexokinase. However, removal of the tag produced an enzyme displaying similar values as the natural enzyme (K(m) for glucose = 43 and 60 microM for the natural and the recombinant protein, respectively). None of these enzymes presented activity with fructose. As reported previously for hexokinases from several trypanosomatids, no inhibition was exerted by glucose 6-phosphate (G6-P). In contrast, a mixed-type inhibition was observed with inorganic pyrophosphate (PPi, K(i) = 0.5mM).

Characterization of native and recombinant A4 glyceraldehyde 3-phosphate dehydrogenase. Kinetic evidence for confromation changes upon association with the small protein CP12

A4 glyceraldehyde 3-phosphate dehydrogenase (GAPDH) was purified from the green alga Chlamydomonas reinhardtii and was also overexpressed in Escherichia coli. Both purified A4 tetramers of recombinant and native GAPDH were characterized for the first time. The pH optimum for both native and recombinant enzymes was close to 7.8. The pKs of the residues involved in catalysis indicate that a cysteine and a histidine may take part in catalysis by chloroplast GAPDH, as is the case for glycolytic GAPDH. Native and recombinant GAPDH show Michaelis-Menten kinetics with respect to their cofactors, NADH and NADPH, with greater specificity for NADPH. The kinetic parameters are similar to those of the heterotetrameric A2B2 spinach chloroplast GAPDH. Native C. reinhardtii and recombinant GAPDHs exhibit a cooperative behavior towards the substrate 1,3-bisphosphoglycerate (BPGA). This positive cooperativity is specific to the C. reinhardtii enzyme, as higher plant A2B2 GAPDHs show Michaelis-Menten kinetics. Native GAPDH has twofold lower catalytic constant and K0.5 for BPGA than recombinant GAPDH. Mass spectrometry analysis of native GAPDH shows that it is a complex of GAPDH and the small protein CP12. In vitro reconstitution assays indicate that the kinetic differences are the result conformation changes of GAPDH upon association with CP12.