RESUMEN
Phosphoenolpyruvate carboxylase (PEPC) is used in plant metabolism for fruit maturation or seed development as well as in the C4 and crassulacean acid metabolism (CAM) mechanisms in photosynthesis, where it is used for the capture of hydrated CO2 (bicarbonate). To find the yet unknown binding site of bicarbonate in this enzyme, we have first identified putative binding sites with nonequilibrium molecular dynamics simulations and then ranked these sites with alchemical free energy calculations with corrections of computational artifacts. Fourteen pockets where bicarbonate could bind were identified, with three having realistic binding free energies with differences with the experimental value below 1 kcal/mol. One of these pockets is found far from the active site at 14 Å and predicted to be an allosteric binding site. In the two other binding sites, bicarbonate is in direct interaction with the magnesium ion; neither sequence alignment nor the study of mutant K606N allowed to discriminate between these two pockets, and both are good candidates as the binding site of bicarbonate in phosphoenolpyruvate carboxylase.
Asunto(s)
Bicarbonatos , Simulación de Dinámica Molecular , Fosfoenolpiruvato Carboxilasa , Fosfoenolpiruvato Carboxilasa/metabolismo , Fosfoenolpiruvato Carboxilasa/química , Bicarbonatos/metabolismo , Sitios de Unión , Termodinámica , Conformación ProteicaRESUMEN
BACKGROUND AND AIMS: Phosphoenolpyruvate (PEP) carboxylase (PEPC) catalyses the irreversible carboxylation of PEP with bicarbonate to produce oxaloacetate. This reaction powers the carbon-concentrating mechanism (CCM) in plants that perform C4 photosynthesis. This CCM is generally driven by a single PEPC gene product that is highly expressed in the cytosol of mesophyll cells. We found two C4 grasses, Panicum miliaceum and Echinochloa colona, that each have two highly expressed PEPC genes. We characterized the kinetic properties of the two most abundant PEPCs in E. colona and P. miliaceum to better understand how the enzyme's amino acid structure influences its function. METHODS: Coding sequences of the two most abundant PEPC proteins in E. colona and P. miliaceum were synthesized by GenScript and were inserted into bacteria expression plasmids. Point mutations resulting in substitutions at conserved amino acid residues (e.g. N-terminal serine and residue 890) were created via site-directed PCR mutagenesis. The kinetic properties of semi-purified plant PEPCs from Escherichia coli were analysed using membrane-inlet mass spectrometry and a spectrophotometric enzyme-coupled reaction. KEY RESULTS: The two most abundant P. miliaceum PEPCs (PmPPC1 and PmPPC2) have similar sequence identities (>95 %), and as a result had similar kinetic properties. The two most abundant E. colona PEPCs (EcPPC1 and EcPPC2) had identities of ~78 % and had significantly different kinetic properties. The PmPPCs and EcPPCs had different responses to allosteric inhibitors and activators, and substitutions at the conserved N-terminal serine and residue 890 resulted in significantly altered responses to allosteric regulators. CONCLUSIONS: The two, significantly expressed C4Ppc genes in P. miliaceum were probably the result of genomes combining from two closely related C4Panicum species. We found natural variation in PEPC's sensitivity to allosteric inhibition that seems to bypass the conserved 890 residue, suggesting alternative evolutionary pathways for increased malate tolerance and other kinetic properties.
Asunto(s)
Fosfoenolpiruvato Carboxilasa , Poaceae , Secuencia de Aminoácidos , Poaceae/genética , Poaceae/metabolismo , Fosfoenolpiruvato Carboxilasa/genética , Fosfoenolpiruvato Carboxilasa/química , Fosfoenolpiruvato Carboxilasa/metabolismo , Evolución Biológica , Plantas/metabolismo , Serina/genética , CinéticaRESUMEN
Activation of phosphoenolpyruvate carboxylase (PEPC) enzymes by glucose 6-phosphate (G6P) and other phospho-sugars is of major physiological relevance. Previous kinetic, site-directed mutagenesis and crystallographic results are consistent with allosteric activation, but the existence of a G6P-allosteric site was questioned and competitive activation-in which G6P would bind to the active site eliciting the same positive homotropic effect as the substrate phosphoenolpyruvate (PEP)-was proposed. Here, we report the crystal structure of the PEPC-C4 isozyme from Zea mays with G6P well bound into the previously proposed allosteric site, unambiguously confirming its existence. To test its functionality, Asp239-which participates in a web of interactions of the protein with G6P-was changed to alanine. The D239A variant was not activated by G6P but, on the contrary, inhibited. Inhibition was also observed in the wild-type enzyme at concentrations of G6P higher than those producing activation, and probably arises from G6P binding to the active site in competition with PEP. The lower activity and cooperativity for the substrate PEP, lower activation by glycine and diminished response to malate of the D239A variant suggest that the heterotropic allosteric activation effects of free-PEP are also abolished in this variant. Together, our findings are consistent with both the existence of the G6P-allosteric site and its essentiality for the activation of PEPC enzymes by phosphorylated compounds. Furthermore, our findings suggest a central role of the G6P-allosteric site in the overall kinetics of these enzymes even in the absence of G6P or other phospho-sugars, because of its involvement in activation by free-PEP.
Asunto(s)
Glucosa-6-Fosfato/química , Fosfoenolpiruvato Carboxilasa/química , Fosfoenolpiruvato/química , Proteínas de Plantas/química , Zea mays/enzimología , Regulación Alostérica , Dominio Catalítico , Glucosa-6-Fosfato/metabolismo , Cinética , Fosfoenolpiruvato/metabolismo , Fosfoenolpiruvato Carboxilasa/genética , Fosfoenolpiruvato Carboxilasa/metabolismo , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Zea mays/genéticaRESUMEN
Inorganic pyrophosphate (PPi) consists of two phosphate molecules and can act as an energy and phosphate donor in cellular reactions, similar to ATP. Several kinases use PPi as a substrate, and these kinases have recently been suggested to have evolved from ATP-dependent functional homologs, which have significant amino acid sequence similarity to PPi-utilizing enzymes. In contrast, phosphoenolpyruvate carboxykinase (PEPCK) can be divided into three types according to the phosphate donor (ATP, GTP, or PPi), and the amino acid sequence similarity of these PEPCKs is too low to confirm that they share a common ancestor. Here we solved the crystal structure of a PPi-PEPCK homolog from the bacterium Actinomyces israelii at 2.6 Å resolution and compared it with previously reported structures from ATP- and GTP-specific PEPCKs to assess the degrees of similarities and divergences among these PEPCKs. These comparisons revealed that they share a tertiary structure with significant value and that amino acid residues directly contributing to substrate recognition, except for those that recognize purine moieties, are conserved. Furthermore, the order of secondary structural elements between PPi-, ATP-, and GTP-specific PEPCKs was strictly conserved. The structure-based comparisons of the three PEPCK types provide key insights into the structural basis of PPi specificity and suggest that all of these PEPCKs are derived from a common ancestor.
Asunto(s)
Difosfatos/metabolismo , Fosfoenolpiruvato Carboxilasa/metabolismo , Difosfatos/química , Humanos , Modelos Moleculares , Fosfoenolpiruvato Carboxilasa/química , Conformación ProteicaRESUMEN
Phosphoenolpyruvate carboxylase (PEPC) is a tightly regulated cytosolic enzyme situated at a crucial branch point of central plant metabolism. The structure of AtPPC3, a C3 PEPC isozyme of the model plant Arabidopsis thaliana, in complex with the inhibitors aspartate and citrate was solved at 2.2-Å resolution. This represents the first PEPC structure with citrate bound. Aspartate and citrate binding sites are in close proximity (5.1-5.3â¯Å) and interactions between citrate and specific residues were identified. Citrate functions as a mixed (allosteric) inhibitor as it reduced AtPPC3's Vmax while increasing Km(PEP) values. The PEP saturation data gave an excellent fit to the mixed inhibition model, yielding Ki and Ki' (citrate) values of 9.3 and 42.5â¯mM, respectively. Citrate and aspartate inhibition of AtPPC3 was non-additive, likely due to their closely positioned binding sites, their similar negative charge, and type of binding residues. Fewer interactions and lower affinity for citrate support its observed weaker inhibition of AtPPC3 relative to aspartate. Citrate does not appear to induce further conformational change beyond aspartate owing to the similar structural mechanism of inhibition. AtPPC3 largely exhibits root-specific expression in Arabidopsis, where it is markedly upregulated during stresses such as excessive salinity or nutritional Pi deprivation that necessitate large increases in anaplerotic PEP carboxylation. The cytosolic citrate concentration of potato tubers suggests that AtPPC3's inhibition by citrate may be physiologically relevant. Our results provide novel insights into the structural basis of allosteric PEPC control and the kinetic effects brought about upon inhibitor binding.
Asunto(s)
Proteínas de Arabidopsis/metabolismo , Arabidopsis/enzimología , Ácido Cítrico/metabolismo , Fosfoenolpiruvato Carboxilasa/metabolismo , Regulación Alostérica , Arabidopsis/genética , Arabidopsis/metabolismo , Proteínas de Arabidopsis/química , Proteínas de Arabidopsis/genética , Ácido Aspártico/química , Ácido Aspártico/metabolismo , Sitios de Unión/genética , Ácido Cítrico/química , Cristalografía por Rayos X , Cinética , Modelos Moleculares , Fosfoenolpiruvato Carboxilasa/química , Fosfoenolpiruvato Carboxilasa/genética , Unión Proteica , Dominios ProteicosRESUMEN
The isozymes of photosynthetic phosphoenolpyruvate carboxylase from C4 plants (PEPC-C4) play a critical role in their atmospheric CO2 assimilation and productivity. They are allosterically activated by phosphorylated trioses or hexoses, such as d-glucose 6-phosphate, and inhibited by l-malate or l-aspartate. Additionally, PEPC-C4 isozymes from grasses are activated by glycine, serine, or alanine, but the allosteric site for these compounds remains unknown. Here, we report a new crystal structure of the isozyme from Zea mays (ZmPEPC-C4) with glycine bound at the monomer-monomer interfaces of the two dimers of the tetramer, making interactions with residues of both monomers. This binding site is close to, but different from, the one proposed to bind glucose 6-phosphate. Docking experiments indicated that d/l-serine or d/l-alanine could also bind to this site, which does not exist in the PEPC-C4 isozyme from the eudicot plant Flaveria, mainly because of a lysyl residue at the equivalent position of Ser-100 in ZmPEPC-C4 Accordingly, the ZmPEPC-C4 S100K mutant is not activated by glycine, serine, or alanine. Amino acid sequence alignments showed that PEPC-C4 isozymes from the monocot family Poaceae have either serine or glycine at this position, whereas those from Cyperaceae and eudicot families have lysine. The size and charge of the residue equivalent to Ser-100 are not only crucial for the activation of PEPC-C4 isozymes by neutral amino acids but also affect their affinity for the substrate phosphoenolpyruvate and their allosteric regulation by glucose 6-phosphate and malate, accounting for the reported kinetic differences between PEPC-C4 isozymes from monocot and eudicot plants.
Asunto(s)
Sitio Alostérico , Aminoácidos Neutros/metabolismo , Fosfoenolpiruvato Carboxilasa/química , Fosfoenolpiruvato Carboxilasa/metabolismo , Serina/metabolismo , Zea mays/enzimología , Isoenzimas/química , Isoenzimas/metabolismo , Cinética , Modelos Moleculares , Conformación Proteica , Especificidad por SustratoRESUMEN
Phosphoenolpyruvate carboxylase (PEPC) is a key enzyme in the C4 photosynthetic pathway of many of the world's worst weeds and a valuable target to develop C4 plant-selective herbicides. By virtual screening, analog synthesis, and in vitro validation, we identified pyrazolidine-3,5-diones as a new class of small molecules with inhibitory potential down to the submicromolar range against C4 PEPC and a selectivity factor of up to 16 over C3 PEPC. No other biological activity has yet been reported for the best compound, (3-bromophenyl)-4-(3-hydroxybenzylidene)-pyrazolidine-3,5-dione. A systematic variation in the substituents allowed the derivation of a qualitative structure-activity relationship. These findings make this compound class highly interesting for further investigations toward generating potent, C4 plant-selective herbicides with a low potential for unwanted effects.
Asunto(s)
Herbicidas/química , Fosfoenolpiruvato Carboxilasa/antagonistas & inhibidores , Proteínas de Plantas/antagonistas & inhibidores , Pirazoles/química , Asteraceae/efectos de los fármacos , Asteraceae/enzimología , Asteraceae/crecimiento & desarrollo , Clonación Molecular , Diseño de Fármacos , Pruebas de Enzimas , Escherichia coli/genética , Escherichia coli/metabolismo , Expresión Génica , Herbicidas/síntesis química , Herbicidas/farmacología , Ensayos Analíticos de Alto Rendimiento , Isoenzimas/antagonistas & inhibidores , Isoenzimas/química , Isoenzimas/genética , Isoenzimas/metabolismo , Simulación del Acoplamiento Molecular , Fosfoenolpiruvato Carboxilasa/química , Fosfoenolpiruvato Carboxilasa/genética , Fosfoenolpiruvato Carboxilasa/metabolismo , Fotosíntesis/efectos de los fármacos , Proteínas de Plantas/química , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Malezas/efectos de los fármacos , Malezas/enzimología , Malezas/crecimiento & desarrollo , Pirazoles/síntesis química , Pirazoles/farmacología , Proteínas Recombinantes de Fusión/química , Proteínas Recombinantes de Fusión/genética , Proteínas Recombinantes de Fusión/metabolismo , Relación Estructura-Actividad , Interfaz Usuario-ComputadorRESUMEN
Phosphoenolpyruvate carboxylase (PEPC) is an important enzyme for CO2 fixation and primary metabolism in photosynthetic organisms including cyanobacteria. The kinetics and allosteric regulation of PEPCs have been studied in many organisms, but the biochemical properties of PEPC in the unicellular, non-nitrogen-fixing cyanobacterium Synechocystis sp. PCC 6803 have not been clarified. In this study, biochemical analysis revealed that the optimum pH and temperature of Synechocystis 6803 PEPC proteins were 7.3 and 30 °C, respectively. Synechocystis 6803 PEPC was found to be tolerant to allosteric inhibition by several metabolic effectors such as malate, aspartate, and fumarate compared with other cyanobacterial PEPCs. Comparative sequence and biochemical analysis showed that substitution of the glutamate residue at position 954 with lysine altered the enzyme so that it was inhibited by malate, aspartate, and fumarate. PEPC of the nitrogen-fixing cyanobacterium Anabaena sp. PCC 7120 was purified, and its activity was inhibited in the presence of malate. Substitution of the lysine at position 946 (equivalent to position 954 in Synechocystis 6803) with glutamate made Anabaena 7120 PEPC tolerant to malate. These results demonstrate that the allosteric regulation of PEPC in cyanobacteria is determined by a single amino acid residue, a characteristic that is conserved in different orders.
Asunto(s)
Anabaena/enzimología , Fosfoenolpiruvato Carboxilasa/antagonistas & inhibidores , Synechocystis/enzimología , Regulación Alostérica , Secuencia de Aminoácidos , Proteínas Bacterianas/antagonistas & inhibidores , Cinética , Fosfoenolpiruvato Carboxilasa/química , Fosfoenolpiruvato Carboxilasa/metabolismo , Análisis de Secuencia de ProteínaRESUMEN
Phosphoenolpyruvate carboxylase (PEPC) in Corynebacterium glutamicum ATCC13032, a glutamic-acid producing actinobacterium, is subject to feedback inhibition by metabolic intermediates such as aspartic acid and 2-oxoglutaric acid, which implies the importance of PEPC in replenishing oxaloacetic acid into the TCA cycle. Here, we investigated the effects of feedback-insensitive PEPC on glutamic acid production. A single amino-acid substitution in PEPC, D299N, was found to relieve the feedback control by aspartic acid, but not by 2-oxoglutaric acid. A simple mutant, strain R1, having the D299N substitution in PEPC was constructed from ATCC 13032 using the double-crossover chromosome replacement technique. Strain R1 produced glutamic acid at a concentration of 31.0 g/L from 100 g/L glucose in a jar fermentor culture under biotin-limited conditions, which was significantly higher than that of the parent, 26.0 g/L (1.19-fold), indicative of the positive effect of desensitized PEPC on glutamic acid production. Another mutant, strain DR1, having both desensitized PEPC and PYK-gene deleted mutations, was constructed in a similar manner using strain D1 with a PYK-gene deleted mutation as the parent. This mutation had been shown to enhance glutamic acid production in our previous study. Although marginal, strain D1 produced higher glutamic acid, 28.8 g/L, than ATCC13032 (1.11-fold). In contrast, glutamic acid production by strain DR-1 was elevated up to 36.9 g/L, which was 1.42-fold higher than ATCC13032 and significantly higher than the other three strains. The results showed a synergistic effect of these two mutations on glutamic acid production in C. glutamicum.
Asunto(s)
Corynebacterium glutamicum/metabolismo , Ácido Glutámico/biosíntesis , Fosfoenolpiruvato Carboxilasa/metabolismo , Ácido Aspártico/metabolismo , Ácido Aspártico/farmacología , Reactores Biológicos , Biotina/metabolismo , Ciclo del Ácido Cítrico , Corynebacterium glutamicum/enzimología , Retroalimentación Fisiológica , Glucosa/metabolismo , Ácido Glutámico/metabolismo , Ácidos Cetoglutáricos/metabolismo , Ácidos Cetoglutáricos/farmacología , Fosfoenolpiruvato Carboxilasa/química , Fosfoenolpiruvato Carboxilasa/genética , Piruvato Quinasa/deficiencia , Piruvato Quinasa/genéticaRESUMEN
Phosphoenolpyruvate carboxylase (PEPC) is a key enzyme of primary metabolism in bacteria, algae and vascular plants, and it undergoes allosteric regulation by various metabolic effectors. Rice (Oryza sativa) has five plant-type PEPCs, four cytosolic and one chloroplastic. We investigated their kinetic properties using recombinant proteins and found that, like most plant-type PEPCs, rice cytosolic isozymes were activated by glucose 6-phosphate and by alkaline pH. In contrast, no such activation was observed for the chloroplastic isozyme, Osppc4. In addition, Osppc4 showed low affinity for the substrate phosphoenolpyruvate (PEP) and very low sensitivities to allosteric inhibitors aspartate and glutamate. By comparing the isozyme amino acid sequences and three-dimensional structures simulated on the basis of the reported crystal structures, we identified two regions where Osppc4 has unique features that can be expected to affect its kinetic properties. One is the N-terminal extension; replacement of the extension of Osppc2a (cytosolic) with that from Osppc4 reduced the aspartate and glutamate sensitivities to about one-tenth of the wild-type values but left the PEP affinity unaffected. The other is the N-terminal loop, in which a conserved lysine at the N-terminal end is replaced with a glutamate-alanine pair in Osppc4. Replacement of the lysine of Osppc2a with glutamate-alanine lowered the PEP affinity to a quarter of the wild-type level (down to the Osppc4 level), without affecting inhibitor sensitivity. Both the N-terminal extension and the N-terminal loop are specific to plant-type PEPCs, suggesting that plant-type isozymes acquired these regions so that their activity could be regulated properly at the sites where they function.
Asunto(s)
Sitio Alostérico , Oryza/enzimología , Fosfoenolpiruvato Carboxilasa/química , Fosfoenolpiruvato Carboxilasa/metabolismo , Proteínas de Plantas/química , Proteínas de Plantas/metabolismo , Secuencia de Aminoácidos , Ácido Aspártico/metabolismo , Simulación por Computador , Retroalimentación Fisiológica , Cinética , Modelos Moleculares , Datos de Secuencia Molecular , Mutación/genética , Fosforilación , Fosfoserina/metabolismo , Proteínas de Plantas/genética , Proteínas Recombinantes/metabolismo , Alineación de Secuencia , Especificidad de la Especie , Transcripción GenéticaRESUMEN
Phosphoenolpyruvate carboxylase (PEPC) is a key enzyme of C4 photosynthesis. Besides, non-photosynthetic isoforms of PEPC are found in bacteria and all types of plants, although not in animals or fungi. A single residue in the allosteric feedback inhibitor site of PEPC was shown to adjust the affinity of the photosynthetic and non-photosynthetic isoforms for feedback inhibition by metabolites of the C4 pathway. Here, we applied computational screening and biochemical analyses to identify molecules that selectively inhibit C4 PEPC, but have no effect on the activity of non-photosynthetic PEPCs. We found two types of selective inhibitors, catechins and quinoxalines. Binding constants in the lower µM range and a strong preference for C4 PEPC qualify the quinoxaline compounds as potential selective herbicides to combat C4 weeds.
Asunto(s)
Productos Agrícolas , Inhibidores Enzimáticos/química , Inhibidores Enzimáticos/farmacología , Fosfoenolpiruvato Carboxilasa/antagonistas & inhibidores , Fotosíntesis/efectos de los fármacos , Malezas/efectos de los fármacos , Control de Malezas/métodos , Regulación Alostérica/efectos de los fármacos , Modelos Moleculares , Fosfoenolpiruvato Carboxilasa/química , Fosfoenolpiruvato Carboxilasa/metabolismo , Malezas/enzimología , Malezas/metabolismo , Conformación ProteicaRESUMEN
In order to mitigate CO2 accumulation and decrease the rate of global warming and climate change, we previously presented a strategy for the development of an efficient CO2 capture and utilization system. The system employs two recombinant enzymes, carbonic anhydrase and phosphoenolpyruvate carboxylase, which were originated from microalgae. Although utilization of this integrated system would require a large quantity of high quality PEPCase protein, such quantities could be produced by increasing the solubility of the Phaeodactylum tricornutum PEPCase 1 (PtPEPCase 1) protein in the Escherichia coli heterologous expression system. We first expressed the putative mitochondria targeting peptide- and chloroplast transit peptide-truncated proteins of PtPEPCase 1, mPtPEPCase 1 and cPtPEPCase 1, respectively, in E. coli. After affinity chromatography, the amount of purified PEPCase protein from 500mL of E. coli culture was greatest for cPtPEPCase 1 (1.99mg), followed by mPtPEPCase 1 (0.82mg) and PtPEPCase 1 (0.61mg). Furthermore, the enzymatic activity of mPtPEPCase 1 and cPtPEPCase 1 showed approximately 1.6-fold (32.19 units/mg) and 3-fold (59.48 units/mg) increases, respectively. Therefore, cPtPEPCase 1 purified using the E. coli heterogeneous expression system could be a strong candidate for a platform technology to capture CO2 and produce value-added four-carbon platform chemicals.
Asunto(s)
Diatomeas/enzimología , Fosfoenolpiruvato Carboxilasa/metabolismo , Secuencia de Aminoácidos , Biocatálisis , Ciclo del Carbono , Dióxido de Carbono/metabolismo , Diatomeas/genética , Escherichia coli/genética , Escherichia coli/metabolismo , Concentración de Iones de Hidrógeno , Cinética , Datos de Secuencia Molecular , Mutagénesis , Fosfoenolpiruvato Carboxilasa/química , Fosfoenolpiruvato Carboxilasa/genética , Ingeniería de Proteínas , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Solubilidad , TemperaturaRESUMEN
In subfamily Suaedoideae, four independent gains of C4 photosynthesis are proposed, which includes two parallel origins of Kranz anatomy (sections Salsina and Schoberia) and two independent origins of single-cell C4 anatomy (Bienertia and Suaeda aralocaspica). Additional phylogenetic support for this hypothesis was generated from sequence data of the C-terminal portion of the phosphoenolpyruvate carboxylase (PEPC) gene used in C4 photosynthesis (ppc-1) in combination with previous sequence data. ppc-1 sequence was generated for 20 species in Suaedoideae and two outgroup Salsola species that included all types of C4 anatomies as well as two types of C3 anatomies. A branch-site test for positively selected codons was performed using the software package PAML. From labelling of the four branches where C4 is hypothesized to have developed (foreground branches), residue 733 (maize numbering) was identified to be under positive selection with a posterior probability >0.99 and residue 868 at the >0.95 interval using Bayes empirical Bayes (BEB). When labelling all the branches within C4 clades, the branch-site test identified 13 codons to be under selection with a posterior probability >0.95 by BEB; this is discussed considering current information on functional residues. The signature C4 substitution of an alanine for a serine at position 780 in the C-terminal end (which is considered a major determinant of affinity for PEP) was only found in four of the C4 species sampled, while eight of the C4 species and all the C3 species have an alanine residue; indicating that this substitution is not a requirement for C4 function.
Asunto(s)
Chenopodiaceae/enzimología , Fosfoenolpiruvato Carboxilasa/genética , Fotosíntesis , Secuencia de Bases , Chenopodiaceae/genética , Modelos Estadísticos , Modelos Estructurales , Datos de Secuencia Molecular , Fosfoenolpiruvato Carboxilasa/química , Fosfoenolpiruvato Carboxilasa/metabolismo , Filogenia , Hojas de la Planta/enzimología , Hojas de la Planta/genética , Proteínas de Plantas/química , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Selección Genética , Análisis de Secuencia de ADNAsunto(s)
Flaveria/enzimología , Fosfoenolpiruvato Carboxilasa/química , Fosfoenolpiruvato Carboxilasa/metabolismo , Proteínas de Plantas/química , Proteínas de Plantas/metabolismo , Plantas/enzimología , Dominio Catalítico , Cristalización , Flaveria/química , Flaveria/genética , Regulación Enzimológica de la Expresión Génica , Modelos Moleculares , Fosfoenolpiruvato Carboxilasa/genética , Proteínas de Plantas/genética , Plantas/química , Plantas/genéticaRESUMEN
Metabolic flux analysis (MFA) is a powerful approach for quantifying plant central carbon metabolism based upon a combination of extracellular flux measurements and intracellular isotope labeling measurements. In this chapter, we present the method of isotopically nonstationary (13)C MFA (INST-MFA), which is applicable to autotrophic systems that are at metabolic steady state but are sampled during the transient period prior to achieving isotopic steady state following the introduction of (13)CO2. We describe protocols for performing the necessary isotope labeling experiments, sample collection and quenching, nonaqueous fractionation and extraction of intracellular metabolites, and mass spectrometry (MS) analysis of metabolite labeling. We also outline the steps required to perform computational flux estimation using INST-MFA. By combining several recently developed experimental and computational techniques, INST-MFA provides an important new platform for mapping carbon fluxes that is especially applicable to autotrophic organisms, which are not amenable to steady-state (13)C MFA experiments.
Asunto(s)
Análisis de Flujos Metabólicos , Plantas/metabolismo , Dióxido de Carbono/metabolismo , Isótopos de Carbono , Pruebas de Enzimas , Marcaje Isotópico , Cinética , Fosfoenolpiruvato Carboxilasa/química , Fotosíntesis , Hojas de la Planta/química , Hojas de la Planta/metabolismo , Proteínas de Plantas/química , Plantas/química , Semillas/metabolismo , Almidón/química , Almidón/aislamiento & purificación , Almidón/metabolismo , Fosfatos de Azúcar/química , Fosfatos de Azúcar/metabolismo , Espectrometría de Masas en Tándem , Transaminasas/químicaRESUMEN
Accumulating evidence indicates important functions for phosphoenolpyruvate (PEP) carboxylase (PEPC) in inorganic phosphate (Pi)-starved plants. This includes controlling the production of organic acid anions (malate, citrate) that are excreted in copious amounts by proteoid roots of nonmycorrhizal species such as harsh hakea (Hakea prostrata). This, in turn, enhances the bioavailability of mineral-bound Pi by solubilizing Al(3+), Fe(3+), and Ca(2+) phosphates in the rhizosphere. Harsh hakea thrives in the nutrient-impoverished, ancient soils of southwestern Australia. Proteoid roots from Pi-starved harsh hakea were analyzed over 20 d of development to correlate changes in malate and citrate exudation with PEPC activity, posttranslational modifications (inhibitory monoubiquitination versus activatory phosphorylation), and kinetic/allosteric properties. Immature proteoid roots contained an equivalent ratio of monoubiquitinated 110-kD and phosphorylated 107-kD PEPC polypeptides (p110 and p107, respectively). PEPC purification, immunoblotting, and mass spectrometry indicated that p110 and p107 are subunits of a 430-kD heterotetramer and that they both originate from the same plant-type PEPC gene. Incubation with a deubiquitinating enzyme converted the p110:p107 PEPC heterotetramer of immature proteoid roots into a p107 homotetramer while significantly increasing the enzyme's activity under suboptimal but physiologically relevant assay conditions. Proteoid root maturation was paralleled by PEPC activation (e.g. reduced Km [PEP] coupled with elevated I50 [malate and Asp] values) via in vivo deubiquitination of p110 to p107, and subsequent phosphorylation of the deubiquitinated subunits. This novel mechanism of posttranslational control is hypothesized to contribute to the massive synthesis and excretion of organic acid anions that dominates the carbon metabolism of the mature proteoid roots.
Asunto(s)
Fosfatos/deficiencia , Fosfoenolpiruvato Carboxilasa/metabolismo , Raíces de Plantas/enzimología , Raíces de Plantas/crecimiento & desarrollo , Proteaceae/enzimología , Proteaceae/crecimiento & desarrollo , Ubiquitinación , Ácidos Carboxílicos/metabolismo , Cinética , Fosfatos/farmacología , Fosfoenolpiruvato Carboxilasa/química , Fosfoenolpiruvato Carboxilasa/aislamiento & purificación , Fosforilación/efectos de los fármacos , Hojas de la Planta/efectos de los fármacos , Hojas de la Planta/metabolismo , Raíces de Plantas/efectos de los fármacos , Proteaceae/efectos de los fármacos , Proteína Fosfatasa 2/metabolismo , Subunidades de Proteína/metabolismo , Espectrometría de Masa por Láser de Matriz Asistida de Ionización Desorción , Factores de Tiempo , Ubiquitinación/efectos de los fármacosRESUMEN
The C4-photosynthetic carbon cycle is an elaborated addition to the classical C3-photosynthetic pathway, which improves solar conversion efficiency. The key enzyme in this pathway, phosphoenolpyruvate carboxylase, has evolved from an ancestral non-photosynthetic C3 phosphoenolpyruvate carboxylase. During evolution, C4 phosphoenolpyruvate carboxylase has increased its kinetic efficiency and reduced its sensitivity towards the feedback inhibitors malate and aspartate. An open question is the molecular basis of the shift in inhibitor tolerance. Here we show that a single-point mutation is sufficient to account for the drastic differences between the inhibitor tolerances of C3 and C4 phosphoenolpyruvate carboxylases. We solved high-resolution X-ray crystal structures of a C3 phosphoenolpyruvate carboxylase and a closely related C4 phosphoenolpyruvate carboxylase. The comparison of both structures revealed that Arg884 supports tight inhibitor binding in the C3-type enzyme. In the C4 phosphoenolpyruvate carboxylase isoform, this arginine is replaced by glycine. The substitution reduces inhibitor affinity and enables the enzyme to participate in the C4 photosynthesis pathway.
Asunto(s)
Sustitución de Aminoácidos/genética , Flaveria/enzimología , Fosfoenolpiruvato Carboxilasa/genética , Fosfoenolpiruvato Carboxilasa/metabolismo , Fotosíntesis , Secuencia de Aminoácidos , Sitios de Unión , Cristalografía por Rayos X , Inhibidores Enzimáticos/farmacología , Retroalimentación Fisiológica/efectos de los fármacos , Flaveria/efectos de los fármacos , Concentración 50 Inhibidora , Cinética , Modelos Moleculares , Datos de Secuencia Molecular , Mutagénesis/efectos de los fármacos , Mutagénesis/genética , Proteínas Mutantes/química , Proteínas Mutantes/metabolismo , Fosfoenolpiruvato Carboxilasa/antagonistas & inhibidores , Fosfoenolpiruvato Carboxilasa/química , Fotosíntesis/efectos de los fármacos , Electricidad Estática , Especificidad por Sustrato/efectos de los fármacos , Zea mays/enzimologíaRESUMEN
CO(2)-consuming reactions, in particular carboxylations, play important roles in technical processes and in nature. Their kinetic behavior and the reaction mechanisms of carboxylating enzymes are difficult to study because CO(2) is inconvenient to handle as a gas, exists in equilibrium with bicarbonate in aqueous solution, and typically yields products that show no significant spectroscopic differences from the reactants in the UV/Vis range. Here we demonstrate the utility of 3-nitrophenylacetic acid and related compounds (caged CO(2)) in conjunction with infrared spectroscopy as widely applicable tools for the investigation of such reactions, permitting convenient measurement of the kinetics of CO(2) consumption. The use of isotopically labeled caged CO(2) provides a tool for the assignment of infrared absorption bands, thus aiding insight into reaction intermediates and mechanisms.
Asunto(s)
Dióxido de Carbono/química , Ácido Acético/química , Aminas/química , Dominio Catalítico , Cinética , Nitrobencenos/química , Fosfoenolpiruvato Carboxilasa/química , Fosfoenolpiruvato Carboxilasa/genética , Fosfoenolpiruvato Carboxilasa/metabolismo , Fotólisis , Proteínas Recombinantes/biosíntesis , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Ribulosa-Bifosfato Carboxilasa/química , Ribulosa-Bifosfato Carboxilasa/metabolismo , Espectrofotometría Infrarroja , Spinacia oleracea/enzimología , Rayos Ultravioleta , Agua/químicaRESUMEN
Phosphoenolpyruvate carboxylase is an ubiquitous cytosolic enzyme that catalyzes the ß-carboxylation of phosphoenolpyruvate (PEP) and is encoded by multigene family in plants. It plays an important role in carbon economy of plants by assimilating CO2 into organic acids for subsequent C4 or CAM photosynthesis or to perform several anaplerotic roles in non-photosynthetic tissues. In this study, a cDNA clone encoding for PEPC polypeptide possessing signature motifs characteristic to ZmC4PEPC was isolated from Pennisetum glaucum (PgPEPC). Deduced amino acid sequence revealed its predicted secondary structure consisting of forty alpha helices and eight beta strands is well conserved among other PEPC homologs irrespective of variation in their primary amino acid sequences. Predicted PgPEPC quartenary structure is a tetramer consisting of a dimer of dimers,which is globally akin to maize PEPC crystal structure with respect to major chain folding wherein catalytically important amino acid residues of active site geometry are conserved. Recombinant PgPEPC protein expressed in E. coli and purified to homogeneity, possessed in vitro ß-carboxylation activity that is determined using a coupled reaction converting PEP into malate. Tetramer is the most active form, however, it exists in various oligomeric forms depending upon the protein concentration, pH, ionic strength of the media and presence of its substrate or effecters. Recombinant PgPEPC protein confers enhanced growth advantage to E. coli under harsh growth conditions in comparison to their respective controls; suggesting that PgPEPC plays a significant role in stress adaptation.