RESUMEN
Through current mass spectrometry methods and multiple RNA-Seq technologies, large metabolomics and transcriptomics datasets are readily obtainable, which provide a powerful and global perspective on metabolism. Indeed, one "omics" method is often not enough to draw strong conclusions about metabolism. Combining and interpreting multiple "omics" datasets remains a challenging task that requires careful statistical considerations and pre-planning. Here we describe a protocol for obtaining high-quality metabolomics and transcriptomics datasets in developing plant embryos followed by a robust approach to integration of the two. This protocol is readily adjustable and scalable to any other metabolically active organ or tissue.
Asunto(s)
Metabolómica , Plantas , Transcriptoma , Metabolómica/métodos , Plantas/genética , Plantas/metabolismo , Perfilación de la Expresión Génica/métodos , Espectrometría de Masas/métodos , Regulación de la Expresión Génica de las Plantas , MetabolomaRESUMEN
Pennycress (Thlaspi arvense L.), a member of the Brassicaceae family, produces seed oil high in erucic acid, suitable for biodiesel and aviation fuel. Although pennycress, a winter annual, could be grown as a dedicated bioenergy crop, an increase in its seed oil content is required to improve its economic competitiveness. The success of crop improvement relies upon finding the right combination of biomarkers and targets, and the best genetic engineering and/or breeding strategies. In this work, we combined biomass composition with metabolomic and transcriptomic studies of developing embryos from 22 pennycress natural variants to identify targets for oil improvement. The selected accession collection presented diverse levels of fatty acids at maturity ranging from 29% to 41%. Pearson correlation analyses, weighted gene co-expression network analysis and biomarker identifications were used as complementary approaches to detect associations between metabolite level or gene expression and oil content at maturity. The results indicated that improving seed oil content can lead to a concomitant increase in the proportion of erucic acid without affecting the weight of embryos. Processes, such as carbon partitioning towards the chloroplast, lipid metabolism, photosynthesis, and a tight control of nitrogen availability, were found to be key for oil improvement in pennycress. Besides identifying specific targets, our results also provide guidance regarding the best timing for their modification, early or middle maturation. Thus, this work lays out promising strategies, specific for pennycress, to accelerate the successful development of lines with increased seed oil content for biofuel applications.
Asunto(s)
Brassicaceae , Transcriptoma , Transcriptoma/genética , Ácidos Erucicos/metabolismo , Fitomejoramiento , Brassicaceae/genética , Brassicaceae/metabolismo , Aceites de Plantas/metabolismo , Semillas/genéticaRESUMEN
The Brassicaceae family comprises more than 3,700 species with a diversity of phenotypic characteristics, including seed oil content and composition. Recently, the global interest in Thlaspi arvense L. (pennycress) has grown as the seed oil composition makes it a suitable source for biodiesel and aviation fuel production. However, many wild traits of this species need to be domesticated to make pennycress ideal for cultivation. Molecular breeding and engineering efforts require the availability of an accurate genome sequence of the species. Here, we describe pennycress genome annotation improvements, using a combination of long- and short-read transcriptome data obtained from RNA derived from embryos of 22 accessions, in addition to public genome and gene expression information. Our analysis identified 27,213 protein-coding genes, as well as on average 6,188 biallelic SNPs. In addition, we used the identified SNPs to evaluate the population structure of our accessions. The data from this analysis support that the accession Ames 32872, originally from Armenia, is highly divergent from the other accessions, while the accessions originating from Canada and the United States cluster together. When we evaluated the likely signatures of natural selection from alternative SNPs, we found 7 candidate genes under likely recent positive selection. These genes are enriched with functions related to amino acid metabolism and lipid biosynthesis and highlight possible future targets for crop improvement efforts in pennycress.
Asunto(s)
Thlaspi , Biocombustibles , Aceites de Plantas/metabolismo , Semillas/genética , Thlaspi/genética , Thlaspi/metabolismo , TranscriptomaRESUMEN
Soybean oil is one of the most consumed vegetable oils worldwide. Genetic improvement of its concentration in seeds has been historically pursued due to its direct association with its market value. Engineering attempts aiming to increase soybean seed oil presented different degrees of success that varied with the genetic design and the specific variety considered. Understanding the embryo's responses to the genetic modifications introduced, is a critical step to successful approaches. In this work, the metabolic and transcriptional responses to AtWRI1 and AtDGAT1 expression in soybean seeds were evaluated. AtWRI1 is a master regulator of fatty acid (FA) biosynthesis, and AtDGAT1 encodes an enzyme catalysing the final and rate-limiting step of triacylglycerides biosynthesis. The events expressing these genes in the embryo did not show an increase in total FA content, but they responded with changes in the oil and carbohydrate composition. Transcriptomic studies revealed a down-regulation of genes putatively encoding for oil body packaging proteins, and a strong induction of genes annotated as lipases and FA biosynthesis inhibitors. Novel putative AtWRI1 targets, presenting an AW-box in the upstream region of the genes, were identified by comparison with an event that harbours only AtWRI1. Lastly, targeted metabolomics analysis showed that carbon from sugar phosphates could be used for FA competing pathways, such as starch and cell wall polysaccharides, contributing to the restriction in oil accumulation. These results allowed the identification of key cellular processes that need to be considered to break the embryo's natural restriction to uncontrolled seed lipid increase.
Asunto(s)
Regulación de la Expresión Génica de las Plantas , Glycine max , Metabolismo de los Hidratos de Carbono/genética , Desarrollo Embrionario , Regulación de la Expresión Génica de las Plantas/genética , Aceites de Plantas/metabolismo , Plantas Modificadas Genéticamente/genética , Semillas/genética , Semillas/metabolismo , Glycine max/genética , Glycine max/metabolismo , Factores de Transcripción/genéticaRESUMEN
KEY MESSAGE: NADP-ME2 from Arabidopsis thaliana exhibits a distinctive and complex regulation by fumarate, acting as an activator or an inhibitor according to substrate and effector concentrations. In this work, we used molecular modeling approach and site-directed mutagenesis to characterized the NADP-ME2 structural determinants necessary for allosteric regulation providing new insights for enzyme optimization. Structure-function studies contribute to deciphering how small modifications in the primary structure could introduce desirable characteristics into enzymes without affecting its overall functioning. Malic enzymes (ME) are ubiquitous and responsible for a wide variety of functions. The availability of a high number of ME crystal structures from different species facilitates comparisons between sequence and structure. Specifically, the structural determinants necessary for fumarate allosteric regulation of ME has been of particular interest. NADP-ME2 from Arabidopsis thaliana exhibits a distinctive and complex regulation by fumarate, acting as an activator or an inhibitor according to substrate and effector concentrations. However, the 3D structure for this enzyme is not yet reported. In this work, we characterized the NADP-ME2 allosteric site by structural modeling, molecular docking, normal mode analysis and mutagenesis. The regulatory site model and its docking analysis suggested that other C4 acids including malate, NADP-ME2 substrate, could also fit into fumarate's pocket. Besides, a non-conserved cluster of hydrophobic residues in the second sphere of the allosteric site was identified. The substitution of one of those residues, L62, by a less flexible residue as tryptophan, resulted in a complete loss of fumarate activation and a reduction of substrate affinities for the active site. In addition, normal mode analysis indicated that conformational changes leading to the activation could originate in the region surrounding L62, extending through the allosteric site till the active site. Finally, the results in this work contribute to the understanding of structural determinants necessary for allosteric regulation providing new insights for enzyme optimization.
Asunto(s)
Aminoácidos/metabolismo , Proteínas de Arabidopsis/química , Proteínas de Arabidopsis/metabolismo , Arabidopsis/enzimología , Malato-Deshidrogenasa (NADP+)/química , Malato-Deshidrogenasa (NADP+)/metabolismo , Transducción de Señal , Sitio Alostérico , Fluorescencia , Cinética , Simulación del Acoplamiento Molecular , Proteínas Mutantes/metabolismo , Mutación/genéticaRESUMEN
La fibrosis pulmonar a causa del metotrexato es un efecto adverso infrecuente, observado principalmente en los pacientes con artritis reumatoide, aunque también se vio, de manera escasa, en el tratamiento de la psoriasis. Se presenta el caso de un paciente con psoriasis que desarrolló fibrosis pulmonar por metotrexato.
Pulmonary fibrosis due to methotrexate is an infrequent adverse event, observed mainly in patients with rheumatoid arthritis, although it has also been poorly described in the treatment of psoriasis. We present the case of a patient with psoriasis who developed pulmonary fibrosis due to methotrexate.
Asunto(s)
Humanos , Masculino , Anciano , Psoriasis/tratamiento farmacológico , Fibrosis Pulmonar/inducido químicamente , Metotrexato/efectos adversos , Fármacos Dermatológicos/efectos adversos , Fototerapia , Fibrosis Pulmonar/diagnóstico por imagen , Tomografía Computarizada por Rayos X , Interleucina-17/uso terapéutico , Adalimumab/uso terapéutico , Inhibidores de Interleucina/uso terapéutico , Antiinflamatorios/uso terapéuticoRESUMEN
Because dams block migratory routes of potamodromous fish to their spawning areas, and energy generation changes natural flow seasonality, it is necessary to identify spawning areas and their conditions. This information will help in management decisions in the Magdalena River basin regarding the future hydropower development. We identified which characteristics of the tributaries to the Magdalena River are important for determining potamodromous fish spawning grounds, and we estimated the percentage of future loss of spawning areas because of dam development. Ichthyoplankton density is directly related to the floodplain area, and inversely related with channel slope. Low channel slopes offer adult fish a longer distance for their upstream migration and a longer time for embryo development during their drift downstream from the spawning areas to nursery habitats (floodplain lakes). These features could increase the migration distance of the adults, the time for initial embryo development, and, because of its relationship with nursery habitats access, the offspring survival. The potential loss of the actual spawning grounds in the river network was estimated to be nearly 70% because of new dams. Our findings will help to reduce conflicts between hydropower and ecological interests.(AU)
La construcción de hidroeléctricas puede afectar la reproducción de los peces migratorios potamódromos, ya sea porque las represas bloquean las rutas migratorias a sus áreas de desove, o porque la generación de energía cambia la estacionalidad del flujo natural. Esto hace necesario generar información sobre las áreas de desove y sus características, que permitan tomar decisiones de manejo, teniendo en cuenta el desarrollo hidroeléctrico propuesto a futuro en la cuenca del río Magdalena. Identificamos qué características de algunos afluentes del río Magdalena son importantes para los desoves y estimamos el porcentaje de pérdida futura de áreas de desoves debido al desarrollo hidroeléctrico. La densidad del ictioplancton se relacionó directamente con el área de la llanura aluvial e inversamente con la pendiente del canal. Estas características aumentan la distancia de migración de los adultos maduros, el tiempo para el desarrollo inicial del embrión y la supervivencia de la descendencia debido a la proximidad y/o conectividad con los hábitats de cría. La pérdida potencial de las zonas de desove en la red fluvial se estimó en casi el 70% debido a las nuevas presas. Nuestros hallazgos ayudarán a tomar decisiones sostenibles para reducir los conflictos entre intereses de desarrollo hidroeléctrico y ecológicos.(AU)
Asunto(s)
Animales , Migración Animal , Energía Hidroeléctrica , Peces/embriología , Desarrollo EmbrionarioRESUMEN
Soybean seed composition has a profound impact on its market value and commercial use as an important commodity. Increases in oil and protein content have been historically pursued by breeders and genetic engineers; consequently, rapid methods for their quantification are well established. The interest in complete carbohydrate profiles in mature seeds, on the other hand, has recently increased due to numerous attempts to redirect carbohydrates into oil and protein or to offer specialty seed with a specific sugar profile to meet animal nutritional requirements. In this work, a sequential protocol for quantifying reserve and structural carbohydrates in soybean seed was developed and validated. Through this procedure, the concentrations of soluble sugars, sugar alcohols, starch, hemicellulose, and crystalline cellulose can be determined in successive steps from the same starting material using colorimetric assays, LC-MS/MS, and GC-MS. The entire workflow was evaluated using internal standards to estimate the recovery efficiency. Finally, it was successfully applied to eight soybean genotypes harvested from two locations, and the resulting correlations of carbohydrate and oil or protein are presented. This methodology has the potential not only to guide soybean cultivar optimization processes but also to be expanded to other crops with only slight modifications.
Asunto(s)
Carbohidratos/análisis , Glycine max/química , Aceites de Plantas/análisis , Semillas/química , Proteínas de Soja/análisis , Flujo de Trabajo , Cromatografía Liquida , Espectrometría de Masas en TándemRESUMEN
In acidic soils, aluminum (Al) toxicity is a significant limitation to crop production worldwide. Given its Al-binding capacity, malate allows internal as well as external detoxification strategies to cope with Al stress, but little is known about the metabolic processes involved in this response. Here, we analyzed the relevance of NADP-dependent malic enzyme (NADP-ME), which catalyzes the oxidative decarboxylation of malate, in Al tolerance. Plants lacking NADP-ME1 (nadp-me1) display reduced inhibition of root elongation along Al treatment compared with the wild type (wt). Moreover, wt roots exposed to Al show a drastic decrease in NADP-ME1 transcript levels. Although malate levels in seedlings and root exudates are similar in nadp-me1 and wt, a significant increase in intracellular malate is observed in roots of nadp-me1 after long exposure to Al. The nadp-me1 plants also show a lower H2 O2 content in root apices treated with Al and no inhibition of root elongation when exposed to glutamate, an amino acid implicated in Al signaling. Proteomic studies showed several differentially expressed proteins involved in signal transduction, primary metabolism and protection against biotic and other abiotic stimuli and redox processes in nadp-me1, which may participate directly or indirectly in Al tolerance. The results indicate that NADP-ME1 is involved in adjusting the malate levels in the root apex, and its loss results in an increased content of this organic acid. Furthermore, the results suggest that NADP-ME1 affects signaling processes, such as the generation of reactive oxygen species and those that involve glutamate, which could lead to inhibition of root growth.
Asunto(s)
Aluminio/toxicidad , Proteínas de Arabidopsis/metabolismo , Arabidopsis/enzimología , Malato-Deshidrogenasa (NADP+)/metabolismo , Malatos/metabolismo , Arabidopsis/genética , Arabidopsis/fisiología , Proteínas de Arabidopsis/genética , Mutación con Pérdida de Función , Malato-Deshidrogenasa (NADP+)/genética , Raíces de Plantas/enzimología , Raíces de Plantas/genética , Raíces de Plantas/fisiología , Proteómica , Estrés FisiológicoRESUMEN
Arabidopsis thaliana possesses three cytosolic (NADP-ME1-3) and one plastidic (NADP-ME4) NADP-dependent malic enzymes. NADP-ME2 and -ME4 show constitutive expression, in contrast to NADP-ME1 and -ME3, which are restricted to particular tissues. Here, we show that NADP-ME1 transcript and protein were almost undetectable during normal vegetative growth, but gradually increased and reached levels higher than those of the other isoforms in the latest stages of seed development. Accordingly, in knockout nadp-me1 mature seeds the total NADP-ME activity was significantly lower than in wild type mature seeds. The phenotypic analysis of nadp-me1 plants indicated alterations of seed viability and germination. Besides, the treatment with abscisic acid (ABA), NaCl and mannitol specifically induced the accumulation of NADP-ME1 in seedlings. In line with this, nadp-me1 plants show a weaker response of primary and lateral root length and stomatal opening to the presence of ABA. The results suggest that NADP-ME1 plays a specialized role, linked to ABA signaling during the seed development as well as in the response to water deficit stress.
RESUMEN
NAD(P)-malic enzyme (NAD(P)-ME) catalyzes the reversible oxidative decarboxylation of malate to pyruvate, CO2 , and NAD(P)H and is present as a multigene family in Arabidopsis thaliana. The carboxylation reaction catalyzed by purified recombinant Arabidopsis NADP-ME proteins is faster than those reported for other animal or plant isoforms. In contrast, no carboxylation activity could be detected in vitro for the NAD-dependent counterparts. In order to further investigate their putative carboxylating role in vivo, Arabidopsis NAD(P)-ME isoforms, as well as the NADP-ME2del2 (with a decreased ability to carboxylate pyruvate) and NADP-ME2R115A (lacking fumarate activation) versions, were functionally expressed in the cytosol of pyruvate carboxylase-negative (Pyc- ) Saccharomyces cerevisiae strains. The heterologous expression of NADP-ME1, NADP-ME2 (and its mutant proteins), and NADP-ME3 restored the growth of Pyc- S. cerevisiae on glucose, and this capacity was dependent on the availability of CO2 . On the other hand, NADP-ME4, NAD-ME1, and NAD-ME2 could not rescue the Pyc- strains from C4 auxotrophy. NADP-ME carboxylation activity could be measured in leaf crude extracts of knockout and overexpressing Arabidopsis lines with modified levels of NADP-ME, where this activity was correlated with the amount of NADP-ME2 transcript. These results indicate that specific A. thaliana NADP-ME isoforms are able to play an anaplerotic role in vivo and provide a basis for the study on the carboxylating activity of NADP-ME, which may contribute to the synthesis of C4 compounds and redox shuttling in plant cells.
Asunto(s)
Proteínas de Arabidopsis/genética , Arabidopsis/enzimología , Malato-Deshidrogenasa (NADP+)/genética , Malatos/metabolismo , NADP/metabolismo , NAD/metabolismo , Ácido Pirúvico/metabolismo , Saccharomyces cerevisiae/enzimología , Arabidopsis/genética , Proteínas de Arabidopsis/metabolismo , Dióxido de Carbono/metabolismo , Clonación Molecular , Expresión Génica , Prueba de Complementación Genética , Ingeniería Genética , Glucosa/metabolismo , Isoenzimas/genética , Isoenzimas/metabolismo , Malato-Deshidrogenasa (NADP+)/metabolismo , Hojas de la Planta/enzimología , Hojas de la Planta/genética , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Saccharomyces cerevisiae/genética , Transformación Genética , TransgenesRESUMEN
Dermatofibrosarcoma protuberans (DFSP) is a malignant fibrohistiocytic tumor that appears exclusively on the skin. It is a low-grade malignant soft tissue tumor of subcutaneous tissues that has a propensity for local recurrence but seldom metastasizes. It may rarely occur on the head and neck accounting for less than one percent of total head and neck malignancies. We present a man with a giant DFSP on the face. Oncological, functional, and aesthetic aspects are set forth.
RESUMEN
Malic enzymes (ME) catalyze the decarboxylation of malate generating pyruvate, CO2 and NADH or NADPH. In some organisms it has been established that ME is involved in lipids biosynthesis supplying carbon skeletons and reducing power. In this work we studied the MEs of soybean and castor, metabolically different oilseeds. The comparison of enzymatic activities, transcript profiles and organic acid contents suggest different metabolic strategies operating in soybean embryo and castor endosperm in order to generate precursors for lipid biosynthesis. In castor, the malate accumulation pattern agrees with a central role of this metabolite in the provision of carbon to plastids, where the biosynthesis of fatty acids occurs. In this regard, the genome of castor possesses a single gene encoding a putative plastidic NADP-ME, whose expression level is high when lipid deposition is active. On the other hand, NAD-ME showed an important contribution to the maturation of soybean embryos, perhaps driving the carbon relocation from mitochondria to plastids to support the fatty acids synthesis in the last stages of seed filling. These findings provide new insights into intermediary metabolism in oilseeds and provide new biotechnological targets to improve oil yields.
Asunto(s)
Glycine max/enzimología , Malato Deshidrogenasa/metabolismo , Proteínas de Plantas/metabolismo , Ricinus communis/enzimología , Semillas/enzimología , Carbono/metabolismo , Ricinus communis/crecimiento & desarrollo , Metabolismo de los Lípidos , Plastidios/metabolismo , Semillas/crecimiento & desarrollo , Glycine max/crecimiento & desarrolloRESUMEN
Arabidopsis thaliana has four NADP-dependent malic enzymes (NADP-ME 1-4) for reversible malate decarboxylation, with NADP-ME2 being the only cytosolic isoform ubiquitously expressed and responsible for most of the total activity. In this work, we further investigated its physiological function by characterizing Arabidopsis plants over-expressing NADP-ME2 constitutively. In comparison to wild type, these plants exhibited reduced rosette and root sizes, delayed flowering time and increased sensitivity to mannitol and polyethylene glycol. The increased NADP-ME2 activity led to a decreased expression of other ME and malate dehydrogenase isoforms and generated a redox imbalance with opposite characteristics depending on the time point of the day analyzed. The over-expressing plants also presented a higher content of C4 organic acids and sugars under normal growth conditions. However, the accumulation of these metabolites in the over-expressing plants was substantially less pronounced after osmotic stress exposure compared to wild type. Also, a lower level of several amino acids and osmoprotector compounds was observed in transgenic plants. Thus, the gain of NADP-ME2 expression has profound consequences in the modulation of primary metabolism in A. thaliana, which reflect the relevance of this enzyme and its substrates and products in plant homeostasis.
Asunto(s)
Proteínas de Arabidopsis/genética , Arabidopsis/fisiología , Regulación de la Expresión Génica de las Plantas , Malato-Deshidrogenasa (NADP+)/genética , Arabidopsis/enzimología , Arabidopsis/genética , Arabidopsis/crecimiento & desarrollo , Proteínas de Arabidopsis/metabolismo , Ritmo Circadiano , Regulación Enzimológica de la Expresión Génica , Malato-Deshidrogenasa (NADP+)/metabolismo , Plantas Modificadas Genéticamente/genética , Plantas Modificadas Genéticamente/crecimiento & desarrollo , Plantas Modificadas Genéticamente/fisiología , Estrés FisiológicoRESUMEN
Drought stress conditions modify source-sink relations, thereby influencing plant growth, adaptive responses, and consequently crop yield. Invertases are key metabolic enzymes regulating sink activity through the hydrolytic cleavage of sucrose into hexose monomers, thus playing a crucial role in plant growth and development. However, the physiological role of invertases during adaptation to abiotic stress conditions is not yet fully understood. Here it is shown that plant adaptation to drought stress can be markedly improved in tomato (Solanum lycopersicum L.) by overexpression of the cell wall invertase (cwInv) gene CIN1 from Chenopodium rubrum. CIN1 overexpression limited stomatal conductance under normal watering regimes, leading to reduced water consumption during the drought period, while photosynthetic activity was maintained. This caused a strong increase in water use efficiency (up to 50%), markedly improving water stress adaptation through an efficient physiological strategy of dehydration avoidance. Drought stress strongly reduced cwInv activity and induced its proteinaceous inhibitor in the leaves of the wild-type plants. However, the CIN1-overexpressing plants registered 3- to 6-fold higher cwInv activity in all analysed conditions. Surprisingly, the enhanced invertase activity did not result in increased hexose concentrations due to the activation of the metabolic carbohydrate fluxes, as reflected by the maintenance of the activity of key enzymes of primary metabolism and increased levels of sugar-phosphate intermediates under water deprivation. The induced sink metabolism in the leaves explained the maintenance of photosynthetic activity, delayed senescence, and increased source activity under drought stress. Moreover, CIN1 plants also presented a better control of production of reactive oxygen species and sustained membrane protection. Those metabolic changes conferred by CIN1 overexpression were accompanied by increases in the concentrations of the senescence-delaying hormone trans-zeatin and decreases in the senescence-inducing ethylene precursor 1-aminocyclopropane-1-carboxylic acid (ACC) in the leaves. Thus, cwInv critically functions at the integration point of metabolic, hormonal, and stress signals, providing a novel strategy to overcome drought-induced limitations to crop yield, without negatively affecting plant fitness under optimal growth conditions.
Asunto(s)
Pared Celular/enzimología , Chenopodium/genética , Sequías , Expresión Génica Ectópica , Regulación de la Expresión Génica de las Plantas , Proteínas de Plantas/genética , Solanum lycopersicum/fisiología , beta-Fructofuranosidasa/genética , Chenopodium/metabolismo , Solanum lycopersicum/enzimología , Solanum lycopersicum/genética , Fotosíntesis , Hojas de la Planta/metabolismo , Proteínas de Plantas/metabolismo , Plantas Modificadas Genéticamente/genética , Plantas Modificadas Genéticamente/metabolismo , beta-Fructofuranosidasa/metabolismoRESUMEN
Arabidopsis thaliana is a plant species that accumulates high levels of organic acids and uses them as carbon, energy and reducing power sources. Among the enzymes that metabolize these compounds, one of the most important ones is malic enzyme (ME). A. thaliana contains four malic enzymes (NADP-ME 1-4) to catalyze the reversible oxidative decarboxylation of malate in the presence of NADP. NADP-ME2 is the only one located in the cell cytosol of all Arabidopsis organs providing most of the total NADP-ME activity. In the present work, the regulation of this key enzyme by fumarate was investigated by kinetic assays, structural analysis and a site-directed mutagenesis approach. The final effect of this metabolite on NADP-ME2 forward activity not only depends on fumarate and substrate concentrations but also on the pH of the reaction medium. Fumarate produced an increase in NADP-ME2 activity by binding to an allosteric site. However at higher concentrations, fumarate caused a competitive inhibition, excluding the substrate malate from binding to the active site. The characterization of ME2-R115A mutant, which is not activated by fumarate, confirms this hypothesis. In addition, the reverse reaction (reductive carboxylation of pyruvate) is also modulated by fumarate, but in a different way. The results indicate pH-dependence of the fumarate modulation with opposite behavior on the two activities analyzed. Thereby, the coordinated action of fumarate over the direct and reverse reactions would allow a precise and specific modulation of the metabolic flux through this enzyme, leading to the synthesis or degradation of C(4) compounds under certain conditions. Thus, the physiological context might be exerting an accurate control of ME activity in planta, through changes in metabolite and substrate concentrations and cytosolic pH.
Asunto(s)
Arabidopsis/enzimología , Ácidos Carboxílicos/metabolismo , Fumaratos/farmacología , Malato Deshidrogenasa/metabolismo , Regulación Alostérica/efectos de los fármacos , Sitio Alostérico , Sustitución de Aminoácidos , Arabidopsis/efectos de los fármacos , Arabidopsis/genética , Proteínas de Arabidopsis/efectos de los fármacos , Proteínas de Arabidopsis/genética , Proteínas de Arabidopsis/metabolismo , Citosol/enzimología , Activación Enzimática/efectos de los fármacos , Concentración de Iones de Hidrógeno , Cinética , Malato Deshidrogenasa/efectos de los fármacos , Malato Deshidrogenasa/genética , Malatos/metabolismo , Mutagénesis Sitio-Dirigida , NADP/metabolismo , Estructura Terciaria de Proteína , Proteínas Recombinantes de FusiónRESUMEN
The Arabidopsis thaliana genome contains four genes encoding NADP-malic enzymes (NADP-ME1-4). Two isoenzymes, NADP-ME2 and NADP-ME3, which are shown to be located in the cytosol, share a remarkably high degree of identity (90%). However, they display different expression patterns and show distinct kinetic properties, especially with regard to their regulation by effectors, in both the forward (malate oxidative decarboxylation) and reverse (pyruvate reductive carboxylation) reactions. In order to identify the domains in the primary structure that could be responsible for the regulatory differences, four chimeras between these isoenzymes were constructed and analysed. All chimeric versions exhibited the same native structures as the parental proteins. Analysis of the chimeras constructed indicated that the region from amino acid residue 303 to the C-terminal end of NADP-ME2 is critical for fumarate activation. However, the region flanked by amino acid residues 303 and 500 of NADP-ME3 is involved in the pH-dependent inhibition by high malate concentration. Furthermore, the N-terminal region of NADP-ME2 is necessary for the activation by succinate of the reverse reaction. Overall, the results show that NADP-ME2 and NADP-ME3 are able to distinguish and interact differently with similar C(4) acids as a result of minimal structural differences. Therefore, although the active sites of NADP-ME2 and NADP-ME3 are highly conserved, both isoenzymes acquire different allosteric sites, leading to the creation of proteins with unique regulatory mechanisms, probably best suited to the specific organ and developmental pattern of expression of each isoenzyme.
Asunto(s)
Proteínas de Arabidopsis/química , Proteínas de Arabidopsis/metabolismo , Arabidopsis/enzimología , Malato-Deshidrogenasa (NADP+)/química , Malato-Deshidrogenasa (NADP+)/metabolismo , Regulación Alostérica , Sitio Alostérico/genética , Secuencia de Aminoácidos , Arabidopsis/genética , Proteínas de Arabidopsis/genética , Secuencia de Bases , Dominio Catalítico/genética , Coenzima A/farmacología , Citosol/enzimología , Cartilla de ADN/genética , Activación Enzimática/efectos de los fármacos , Fumaratos/farmacología , Genes de Plantas , Proteínas Fluorescentes Verdes/química , Proteínas Fluorescentes Verdes/genética , Proteínas Fluorescentes Verdes/metabolismo , Concentración de Iones de Hidrógeno , Isoenzimas/química , Isoenzimas/genética , Isoenzimas/metabolismo , Cinética , Malato Deshidrogenasa , Malato-Deshidrogenasa (NADP+)/genética , Datos de Secuencia Molecular , Estructura Terciaria de Proteína , Proteínas Recombinantes de Fusión/química , Proteínas Recombinantes de Fusión/genética , Proteínas Recombinantes de Fusión/metabolismo , Homología de Secuencia de AminoácidoRESUMEN
The Arabidopsis thaliana genome contains four NADP-malic enzymes genes (NADP-ME1-4). NADP-ME4 is localized to plastids whereas the other isoforms are cytosolic. NADP-ME2 and 4 are constitutively expressed, while NADP-ME1 is restricted to secondary roots and NADP-ME3 to trichomes and pollen. Although the four isoforms share remarkably high degree of identity (75-90%), recombinant NADP-ME1 through 4 show distinct kinetic properties, both in the forward (malate oxidative decarboxylation) and reverse (pyruvate reductive carboxylation) reactions. The four isoforms behave differently in terms of reversibility, with NADP-ME2 presenting the highest reverse catalytic efficiency. When analyzing the activity of each isoform in the presence of metabolic effectors, NADP-ME2 was the most highly regulated isoform, especially in its activation by certain effectors. Several metabolites modulate both the forward and reverse reactions, exhibiting dual effects in some cases. Therefore, pyruvate reductive carboxylation may be relevant in vivo, especially in some cellular compartments and conditions. In order to identify residues or segments of the NADP-ME primary structure that could be involved in the differences among the isoforms, NADP-ME2 mutants and deletions were analysed. The results obtained show that Arg115 is involved in fumarate activation, while the amino-terminal part is critical for aspartate and CoA activation, as well as for the reverse reaction. As a whole, these studies show that minimal changes in the primary structure are responsible for the different kinetic behaviour of each AtNADP-ME isoform. In this way, the co-expression of some isoforms in the same cellular compartment would not imply redundancy but represents specificity of function.