Decreased expression of cytosolic pyruvate kinase in potato tubers leads to a decline in pyruvate resulting in an in vivo repression of the alternative oxidase

Characterization of the pyruvate kinase gene family in soybean and identification of a putative salt responsive gene GmPK21

BACKGROUND

As a key regulatory enzyme in the glycolysis pathway, pyruvate kinase (PK) plays crucial roles in multiple physiological processes during plant growth and is also involved in the abiotic stress response. However, little information is known about PKs in soybean.

RESULTS

In this study, we identified 27 PK family genes against the genome of soybean cultivar Zhonghuang13. They were classified into 2 subfamilies including PKc and PKp. 22 segmental duplicated gene pairs and 1 tandem duplicated gene pair were identified and all of them experienced a strong purifying selective pressure during evolution. Furthermore, the abiotic stresses (especially salt stress) and hormone responsive cis-elements were present in the promoters of GmPK genes, suggesting their potential roles in abiotic stress tolerance. By performing the qRT-PCR, 6 GmPK genes that continuously respond to both NaCl and ABA were identified. Subsequently, GmPK21, which represented the most significant change under NaCl treatment was chosen for further study. Its encoded protein GmPK21 was localized in the cytoplasm and plasma membrane. The transgenic Arabidopsis overexpressing GmPK21 exhibited weakened salinity tolerance.

CONCLUSIONS

This study provides genomic information of soybean PK genes and a molecular basis for mining salt tolerance function of PKs in the future.

On the Significance of the ADNT1 Carrier in Arabidopsis thaliana under Waterlogging Conditions

Among the adenylate carriers identified in Arabidopsis thaliana, only the AMP/ATP transporter ADNT1 shows increased expression in roots under waterlogging stress conditions. Here, we investigated the impact of a reduced expression of ADNT1 in A. thaliana plants submitted to waterlogging conditions. For this purpose, an adnt1 T-DNA mutant and two ADNT1 antisense lines were evaluated. Following waterlogging, ADNT1 deficiency resulted in a reduced maximum quantum yield of PSII electron transport (significantly for adnt1 and antisense Line 10), indicating a higher impact caused by the stress in the mutants. In addition, ADNT1 deficient lines showed higher levels of AMP in roots under nonstress condition. This result indicates that the downregulation of ADNT1 impacts the levels of adenylates. ADNT1-deficient plants exhibited a differential expression pattern of hypoxia-related genes with an increase in non-fermenting-related-kinase 1 (SnRK1) expression and upregulation of adenylate kinase (ADK) under stress and non-stress conditions. Together, these results indicated that the lower expression of ADNT1 is associated with an early "hypoxic status" due to the perturbation of the adenylate pool caused by reduced AMP import by mitochondria. This perturbation, which is sensed by SnRK1, results in a metabolic reprogramming associated with early induction of the fermentative pathway in ADNT1 deficient plants.

Calcium lignosulfonate modulates physiological and biochemical responses to enhance shoot multiplication in Vanilla planifolia Andrews

Utilisation of calcium lignosulfonate (CaLS) in Vanilla planifolia has been reported to improve shoot multiplication. However, mechanisms responsible for such observation remain unknown. Here, we elucidated the underlying mechanisms of CaLS in promoting shoot multiplication of V. planifolia via comparative proteomics, biochemical assays, and nutrient analysis. The proteome profile of CaLS-treated plants showed enhancement of several important cellular metabolisms such as photosynthesis, protein synthesis, Krebs cycle, glycolysis, gluconeogenesis, and carbohydrate synthesis. Further biochemical analysis recorded that CaLS increased Rubisco activity, hexokinase activity, isocitrate dehydrogenase activity, total carbohydrate content, glutamate synthase activity and total protein content in plant shoot, suggesting the role of CaLS in enhancing shoot growth via upregulation of cellular metabolism. Subsequent nutrient analysis showed that CaLS treatment elevated the contents of several nutrient ions especially calcium and sodium ions. In addition, our study also revealed that CaLS successfully maintained the cellular homeostasis level through the regulation of signalling molecules such as reactive oxygen species and calcium ions. These results demonstrated that the CaLS treatment can enhance shoot multiplication in V. planifolia Andrews by stimulating nutrient uptake, inducing cell metabolism, and regulating cell homeostasis.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-023-01293-w.

Genome-Wide Analysis and Functional Characterization of Pyruvate Kinase (PK) Gene Family Modulating Rice Yield and Quality

Pyruvate kinase (PK) is one of the three rate-limiting enzymes of glycolysis, and it plays a pivotal role in energy metabolism. In this study, we have identified 10 PK genes from the rice genome. Initially, these genes were divided into two categories: cytoplasmic pyruvate kinase (PKc) and plastid pyruvate kinase (PKp). Then, an expression analysis revealed that OsPK1, OsPK3, OsPK4, OsPK6, and OsPK9 were highly expressed in grains. Moreover, PKs can form heteropolymers. In addition, it was found that ABA significantly regulates the expression of PK genes (OsPK1, OsPK4, OsPK9, and OsPK10) in rice. Intriguingly, all the genes were found to be substantially involved in the regulation of rice grain quality and yield. For example, the disruption of OsPK3, OsPK5, OsPK7, OsPK8, and OsPK10 and OsPK4, OsPK5, OsPK6, and OsPK10 decreased the 1000-grain weight and the seed setting rate, respectively. Further, the disruption of OsPK4, OsPK6, OsPK8, and OsPK10 through the CRISPR/Cas9 system showed an increase in the content of total starch and a decrease in protein content compared to the WT. Similarly, manipulations of the OsPK4, OsPK8, and OsPK10 genes increased the amylose content. Meanwhile, the grains of all CRISPR mutants and RNAi lines, except ospk6, showed a significant increase in the chalkiness rate compared to the wild type. Overall, this study characterizes the functions of all the genes of the PK gene family and shows their untapped potential to improve rice yield and quality traits.

Physiological and protein profiling analysis provides insight into the underlying molecular mechanism of potato tuber development regulated by jasmonic acid in vitro

BACKGROUND

Jasmonates (JAs) are one of important phytohormones regulating potato tuber development. It is a complex process and the underlying molecular mechanism regulating tuber development by JAs is still limited. This study attempted to illuminate it through the potential proteomic dynamics information about tuber development in vitro regulated by exogenous JA.

RESULTS

A combined analysis of physiological and iTRAQ (isobaric tags for relative and absolute quantification)-based proteomic approach was performed in tuber development in vitro under exogenous JA treatments (0, 0.5, 5 and 50 μΜ). Physiological results indicated that low JA concentration (especially 5 μM) promoted tuber development, whereas higher JA concentration (50 μM) showed inhibition effect. A total of 257 differentially expressed proteins (DEPs) were identified by iTRAQ, which provided a comprehensive overview on the functional protein profile changes of tuber development regulated by JA. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis indicated that low JA concentration (especially 5 μM) exhibited the promotion effects on tuber development in various cellular processes. Some cell wall polysaccharide synthesis and cytoskeleton formation-related proteins were up-regulated by JA to promote tuber cell expansion. Some primary carbon metabolism-related enzymes were up-regulated by JA to provide sufficient metabolism intermediates and energy for tuber development. And, a large number of protein biosynthesis, degradation and assembly-related were up-regulated by JA to promote tuber protein biosynthesis and maintain strict protein quality control during tuber development.

CONCLUSIONS

This study is the first to integrate physiological and proteomic data to provide useful information about the JA-signaling response mechanism of potato tuber development in vitro. The results revealed that the levels of a number of proteins involved in various cellular processes were regulated by JA during tuber development. The proposed hypothetical model would explain the interaction of these DEPs that associated with tuber development in vitro regulated by JA.

Physiological and Transcriptomic Responses of Illicium difengpi to Drought Stress

Illicium difengpi Kib and Kim, an endangered plant unique to karst areas in China, has evolved an extremely high tolerance to arid environments. To elucidate the molecular mechanisms of the response to drought stress in I. difengpi, physiological index determination and transcriptome sequencing experiments were conducted in biennial seedlings grown under different soil moisture conditions (70~80%, 40~50% and 10~20%). With increasing drought stress, the leaf chlorophyll content decreased, while the proline (Pro), soluble sugar (SS) and malondialdehyde (MDA) contents increased; superoxide dismutase (SOD) and peroxidase (POD) activities also increased. Transcriptome sequencing and pairwise comparisons of the treatments revealed 2489, 4451 and 753 differentially expressed genes (DEGs) in CK70~80 vs. XP40~50, CK70~80 vs. XP10~20 and XP40~50 vs. XP10~20, respectively. These DEGs were divided into seven clusters according to their expression trends, and the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment results of different clusters indicated that genes in the hormone signal transduction and osmotic regulation pathways were greatly activated under mild drought stress. When drought stress increased, the DEGs related to membrane system and protein modification and folding were all upregulated; simultaneously, chitin catabolism- and glycolysis/gluconeogenesis-related genes were continuously upregulated throughout drought stress, while the genes involved in photosynthesis were downregulated. Here, 244 transcription factors derived from 10 families were also identified. These results lay a foundation for further research on the adaptation of I. difengpi to arid environments in karst areas and the establishment of a core regulatory relationship in its drought resistance mechanism.

Nitric oxide-mediated alternative pathway alleviates aluminum-induced programmed cell death in soybean root tips

Alternative pathway (AP) plays essential roles in plant adaptation to environmental stress. However, the exact role of AP in response to aluminum (Al) toxicity remains elusive. We here provide solid evidences that the activated AP capacity in root tips of soybean alleviated Al toxicity. Furthermore, inhibition of AP by pharmacological or transgenic approach aggravated Al-induced programmed cell death (PCD) occurrence mediated through reactive oxygen species (ROS)-dependent mitochondrial pathway. Our results also demonstrated that nitric oxide (NO) plays a negative role in PCD occurrence caused by Al in soybean root tips. Interestingly, the alleviating effect of NO on Al-induced PCD could be blocked by AP inhibition. Further investigation showed that NO mediates the induction of AP resulting from the upregulation of AOX expression and pyruvate content in Al-treated root tips of soybean. Taken together, our results clearly suggest that AP participates in the alleviation of Al toxicity and also plays a critical role in the alleviating effect of NO on Al-induced PCD occurrence, which will open up new avenues for the improvement of plant growth in acidic soils.

Dioscorea Alata Tuber Proteome Analysis Uncovers Differentially Regulated Growth-associated Pathways of Tuber Development

During its life cycle, the Dioscorea tuber undergoes multiple morphological and biochemical changes. To gain a better understanding of the metabolic changes associated with tuber growth, a stage-specific gel-free proteome analysis of four distinct morphological stages namely germinating tuber (S1), degrading tuber (S2), new tuber formation (S3) and tuber maturation (S4) was done and validated by principal component analysis. A comprehensive data set identifying 78.2% of the total 3,681 proteins was generated. PANTHER and KEGG MAPPER revealed both expected (carbohydrate metabolism and redox regulation) and novel biological processes (transcription factors and hormonal regulation) characteristic for each developmental stage. Higher abundance of the enzymes of ascorbate-glutathione cycle and carbohydrate metabolism was detected during tuber germination (S1) and tuber formation stages (S3) in comparison with the mature tuber. The presence of ethylene biosynthesis components during tuber formation hints toward its probable role in postharvest shelf life. The data set comprehensively describes the proteome of Dioscorea tuber and provides growth-specific markers for tuber germination (ascorbate peroxidase, monodehydroascorbate reductase, invertase) and tuber formation (sucrose synthase), which were validated by enzyme activity assays and Western blotting. The study provides information that may influence the direction of research for improving the productivity of this under-utilized and largely neglected crop.

Synergistic consortium of beneficial microorganisms in rice rhizosphere promotes host defense to blight-causing Xanthomonas oryzae pv. oryzae

Rice plants primed with beneficial microbes Bacillus amyloliquefaciens and Aspergillus spinulosporus with biocontrol potential against Xanthomonas oryzae pv. oryzae, provided protection from disease by reprogramming host defence response under pathogen challenge. Plant-beneficial microbe interactions taking place in the rhizosphere are widely used for growth promotion and mitigation of biotic stresses in plants. The present study aims to evaluate the defense network induced by beneficial microorganisms in the rice rhizosphere, and the three-way interaction involved upon inoculation with dreadful bacteria Xanthomonas oryzae pv. oryzae (Xoo). Differential expression of defense-related enzymes, proteins, and genes in rice variety Swarna primed with a microbial consortium of Bacillus amyloliquefaciens and Aspergillus spinulosporus were quantified in the presence and absence of Xoo. The time-based expression profile alterations in leaves under the five distinct treatments "(unprimed unchallenged, unprimed Xoo challenged, B. amyloliquefaciens primed and challenged, A. spinulosporus primed and challenged, B. amyloliquefaciens and A. spinulosporus consortium primed and challenged)" revealed differential early upregulation of SOD, PAL, PO, PPO activities and TPC content in beneficial microbes primed plants in comparison to unprimed challenged plants. The enhanced defense response in all the rice plants recruited with beneficial microbe was also reflected by reduced plant mortality and an increased plant dry biomass and chlorophyll content. Also, more than 550 protein spots were observed per gel by PD Quest software, a total of 55 differentially expressed protein spots were analysed used MALDI-TOF MS, out of which 48 spots were recognized with a significant score with direct or supporting roles in stress alleviation and disease resistance. qRT-PCR was carried out to compare the biochemical and proteomic data to mRNA levels. We conclude that protein biogenesis and alleviated resistance response may contribute to improved biotic stress adaptation. These results might accelerate the functional regulation of the Xoo-receptive proteins in the presence of beneficial rhizospheric microbes and their computation as promising molecular markers for superior disease management.

Review: Crucial role of inorganic pyrophosphate in integrating carbon metabolism from sucrose breakdown to starch synthesis in rice endosperm

The endosperm is a primary constituent of mature seeds in rice as well as in other cereal crops, serving as the major storage reserve of starch. Observations indicate that the central part of the endosperm is subject to hypoxic conditions, which require a switch of energy metabolism owing to limited mitochondrial respiration. Uniquely, this endosperm generates a large source of inorganic pyrophosphate (PPi) as a byproduct of the reaction of ADP glucose pyrophosphorylase in the cytosol. Recent results derived from examination of the mutants of cereal crops, especially rice, for PPi-utilizing enzymes clearly suggest an important role of PPi as an alternative energy currency for integrating carbon metabolism from sucrose breakdown to starch synthesis in the endosperm. Thus, the present review provides an outline of the interlaced PPi-dependent metabolic pathways, which are critical for starch synthesis in the endosperm in terms of energy metabolism, along with its application to enhance yield potential.

Mitochondria-Associated Pyruvate Kinase Complexes Regulate Grain Filling in Rice

Grain filling is a complex agronomic trait that directly determines grain weight and quality in rice (Oryza sativa). Nevertheless, key factors affecting grain filling remain poorly understood. Here, we identified a grain filling gene, OsPK3, encoding a pyruvate kinase (PK). The loss of function of OsPK3 caused reduced PK activity and Suc translocation defects from source to sink in rice, which led to compromised grain filling. OsPK3 was constitutively expressed but had relatively higher expression levels in leaf and developing caryopsis and specific expression signals in tissues involved in Suc transport and unloading, supporting its biological function in regulation of grain filling by affecting Suc translocation. Subcellular localization analysis of OsPK3 revealed its association with mitochondria, and OsPK3 physically interacted and formed heterodimers in vivo with two other PK isozymes, OsPK1 and OsPK4. Both OsPK1 and OsPK4 localized to the mitochondria and cytosol and were recruited to the mitochondria by OsPK3. Despite their high sequence similarity, OsPK1 and OsPK4 had distinct expression patterns. As observed for ospk3, disruption of OsPK1 caused pleiotropic defects, while OsPK4 loss of function led to severely chalky grains without other obvious defects. Collectively, we revealed that two mitochondria-associated pyruvate kinase complexes, OsPK3-OsPK1/OsPK4, are involved in regulation of grain filling by stage-specific fine-tuning of Suc translocation.

DkWRKY interacts with pyruvate kinase gene DkPK1 and promotes natural deastringency in C-PCNA persimmon

PAs, also known as condensed tannins, cause the astringency sensation in the persimmon fruit. The astringency of Chinese pollination-constant non-astringent (C-PCNA) persimmon (Diospyros kaki Thunb.) can be naturally removed on the tree, but the regulatory mechanisms of deastringency remain to be elucidated. In our previous research, DkPK1 was shown to be involved in the natural loss of astringency of C-PCNA persimmon fruit. In the present study, yeast one-hybrid (Y1H) library screening using the DkPK1 promoter as baits identified two DkWRKY transcription factor genes (DkWRKY3 and -15). The transcript levels of both DkWRKY3 and -15 exhibited a positive correlation with the decrease in soluble proanthocyanidin (PA) content during the last developmental stage in C-PCNA persimmon. Multiple sequence analysis and subcellular localization confirmed that DkWRKY3 and -15 belonging to the group II and I families, respectively, were both located in the nucleus. Dual-luciferase and Y1H assays demonstrated that DkWRKY3 and -15 can transactivate the DkPK1 promoters. The combination of DkWRKY3 and -15 most likely produced an additive activation effect compared to a single activator on DkPK1, although the two transcriptional activators were not capable of interacting. Notably, DkWRKY3 and -15 showed ubiquitous expression in various organs and abundant upregulation in seeds. Furthermore, transient overexpression of both DkWRKY3 and -15 in persimmon leaves led to a significant decrease in the content of soluble PAs but a significant increase in the expression levels of the acetaldehyde metabolism-related DkPK, DkPDC and DkADH genes. Thus, we suggest that DkWRKY3 and -15 are the upstream regulators of DkPK1 and positively regulate the natural deastringency in C-PCNA persimmon.

The Lack of Mitochondrial Thioredoxin TRXo1 Affects In Vivo Alternative Oxidase Activity and Carbon Metabolism under Different Light Conditions

The alternative oxidase (AOX) constitutes a nonphosphorylating pathway of electron transport in the mitochondrial respiratory chain that provides flexibility to energy and carbon primary metabolism. Its activity is regulated in vitro by the mitochondrial thioredoxin (TRX) system which reduces conserved cysteines residues of AOX. However, in vivo evidence for redox regulation of the AOX activity is still scarce. In the present study, the redox state, protein levels and in vivo activity of the AOX in parallel to photosynthetic parameters were determined in Arabidopsis knockout mutants lacking mitochondrial trxo1 under moderate (ML) and high light (HL) conditions, known to induce in vivo AOX activity. In addition, 13C- and 14C-labeling experiments together with metabolite profiling were performed to better understand the metabolic coordination between energy and carbon metabolism in the trxo1 mutants. Our results show that the in vivo AOX activity is higher in the trxo1 mutants at ML while the AOX redox state is apparently unaltered. These results suggest that mitochondrial thiol redox systems are responsible for maintaining AOX in its reduced form rather than regulating its activity in vivo. Moreover, the negative regulation of the tricarboxylic acid cycle by the TRX system is coordinated with the increased input of electrons into the AOX pathway. Under HL conditions, while AOX and photosynthesis displayed similar patterns in the mutants, photorespiration is restricted at the level of glycine decarboxylation most likely as a consequence of redox imbalance.

Regulation of the Central Carbon Metabolism in Apple Fruit Exposed to Postharvest Low-Oxygen Stress

After harvest, fruit remain metabolically active and continue to ripen. The main goal of postharvest storage is to slow down the metabolic activity of the detached fruit. In many cases, this is accomplished by storing fruit at low temperature in combination with low oxygen (O2) and high carbon dioxide (CO2) partial pressures. However, altering the normal atmospheric conditions is not without any risk and can induce low-O2 stress. This review focuses on the central carbon metabolism of apple fruit during postharvest storage, both under normal O2 conditions and under low-O2 stress conditions. While the current review is focused on apple fruit, most research on the central carbon metabolism, low-O2 stress, and O2 sensing has been done on a range of different model plants (e.g., Arabidopsis, potato, rice, and maize) using various plant organs (e.g., seedlings, tubers, roots, and leaves). This review pulls together this information from the various sources into a coherent overview to facilitate the research on the central carbon metabolism in apple fruit exposed to postharvest low-O2 stress.

Mitochondrial alternative cyanide-resistant oxidase is involved in an increase of heat stress tolerance in spring wheat

The aim of this study was to determine the influence of different heat treatments on the alternative cyanide-resistant oxidase (AOX) capacity and establish a relation between the heat stress tolerance of spring wheat (Triticum aestivum L.), content of water-soluble carbohydrates in leaves and the alternative respiratory pathway (AP) capacity. We identified a positive relation between these studied parameters. Heat exposure at 39 °C for 24 h increased the heat stress tolerance of seedlings, content of water-soluble carbohydrates and AOX capacity, and the AOX capacity was also high after the subsequent influence of heat shock (50 °C for 3 h). The increased AOX capacity correlated with an increased level of water-soluble carbohydrates in leaves. The content of the AOX protein increased after heat exposure at 39 °C (for 3 h and 24 h) and after the subsequent influence of heat shock (50 °C for 1 and 3 h) at 39 °C for 24 h. We also detected that the content of AOX protein isoforms depends on the duration and intensity of heat treatment. It was concluded that AOX plays an important role in the acclimation of plants to high temperatures.

OsPKpα1 encodes a plastidic pyruvate kinase that affects starch biosynthesis in the rice endosperm

Pyruvate kinase (PK) is a key enzyme in glycolysis and carbon metabolism. Here, we isolated a rice (Oryza sativa) mutant, w59, with a white-core floury endosperm. Map-based cloning of w59 identified a mutation in OsPKpα1, which encodes a plastidic isoform of PK (PKp). OsPKpα1 localizes to the amyloplast stroma in the developing endosperm, and the mutation of OsPKpα1 in w59 decreases the plastidic PK activity, resulting in dramatic changes to the lipid biosynthesis in seeds. The w59 grains were also characterized by a marked decrease in starch content. Consistent with a decrease in number and size of the w59 amyloplasts, large empty spaces were observed in the central region of the w59 endosperm, at the early grain-filling stage. Moreover, a phylogenetic analysis revealed four potential rice isoforms of OsPKp. We validated the in vitro PK activity of these OsPKps through reconstituting active PKp complexes derived from inactive individual OsPKps, revealing the heteromeric structure of rice PKps, which was further confirmed using a protein-protein interaction analysis. These findings suggest a functional connection between lipid and starch synthesis in rice endosperm amyloplasts.

OsPK2 encodes a plastidic pyruvate kinase involved in rice endosperm starch synthesis, compound granule formation and grain filling

Starch is the main form of energy storage in higher plants. Although several enzymes and regulators of starch biosynthesis have been defined, the complete molecular machinery remains largely unknown. Screening for irregularities in endosperm formation in rice represents valuable prospect for studying starch synthesis pathway. Here, we identified a novel rice white-core endosperm and defective grain filling mutant, ospk2, which displays significantly lower grain weight, decreased starch content and alteration of starch physicochemical properties when compared to wild-type grains. The normal starch compound granules were drastically reduced and more single granules filled the endosperm cells of ospk2. Meanwhile, the germination rate of ospk2 seeds after 1-year storage was observably reduced compared with wild-type. Map-based cloning of OsPK2 indicated that it encodes a pyruvate kinase (PK, ATP: pyruvate 2-O-phosphotransferase, EC 2.7.1.40), which catalyses an irreversible step of glycolysis. OsPK2 has a constitutive expression in rice and its protein localizes in chloroplasts. Enzyme assay showed that the protein product from expressed OsPK2 and the crude protein extracted from tissues of wild-type exhibits strong PK activity; however, the mutant presented reduced protein activity. OsPK2 (PKpα1) and three other putative rice plastidic isozymes, PKpα2, PKpβ1 and PKpβ2, can interact to form heteromer. Moreover, the mutation leads to multiple metabolic disorders. Altogether, these results denote new insights into the role of OsPK2 in plant seed development, especially in starch synthesis, compound granules formation and grain filling, which would be useful for genetic improvement of high yield and rice grain quality.

Nitric Oxide Regulates Seedling Growth and Mitochondrial Responses in Aged Oat Seeds

Mitochondria are the source of reactive oxygen species (ROS) in plant cells and play a central role in the mitochondrial electron transport chain (ETC) and tricarboxylic acid cycle (TCA) cycles; however, ROS production and regulation for seed germination, seedling growth, as well as mitochondrial responses to abiotic stress, are not clear. This study was conducted to obtain basic information on seed germination, embryo mitochondrial antioxidant responses, and protein profile changes in artificial aging in oat seeds (Avena sativa L.) exposed to exogenous nitric oxide (NO) treatment. The results showed that the accumulation of H₂O₂ in mitochondria increased significantly in aged seeds. Artificial aging can lead to a loss of seed vigor, which was shown by a decline in seed germination and the extension of mean germination time (MGT). Seedling growth was also inhibited. Some enzymes, including catalase (CAT), glutathione reductase (GR), dehydroascorbate reductase (DHAR), and monodehydroascorbate reductase (MDHAR), maintained a lower level in the ascorbate-glutathione (AsA-GSH) scavenging system. Proteomic analysis revealed that the expression of some proteins related to the TCA cycle were down-regulated and several enzymes related to mitochondrial ETC were up-regulated. With the application of 0.05 mM NO in aged oat seeds, a protective effect was observed, demonstrated by an improvement in seed vigor and increased H₂O₂ scavenging ability in mitochondria. There were also higher activities of CAT, GR, MDHAR, and DHAR in the AsA-GSH scavenging system, enhanced TCA cycle-related enzymes (malate dehydrogenase, succinate-CoA ligase, fumarate hydratase), and activated alternative pathways, as the cytochrome pathway was inhibited. Therefore, our results indicated that seedling growth and seed germinability could retain a certain level in aged oat seeds, predominantly depending on the lower NO regulation of the TCA cycle and AsA-GSH. Thus, it could be concluded that the application of 0.05 mM NO in aged oat seeds improved seed vigor by enhancing the mitochondrial TCA cycle and activating alternative pathways for improvement.

An In Vivo Perspective of the Role(s) of the Alternative Oxidase Pathway

Despite intense research on the in vitro characterization of regulatory factors modulating the alternative oxidase (AOX) pathway, the regulation of its activity in vivo is still not fully understood. Advances concerning in vivo regulation of AOX based on the oxygen-isotope fractionation technique are reviewed, and regulatory factors that merit future research are highlighted. In addition, we review and discuss the main biological functions assigned to the plant AOX, and suggest future experiments involving in vivo activity measurements to test different hypothesized physiological roles.

Cytosolic glyceraldehyde-3-phosphate dehydrogenases play crucial roles in controlling cold-induced sweetening and apical dominance of potato (Solanum tuberosum L.) tubers

Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is an important enzyme that functions in producing energy and supplying intermediates for cellular metabolism. Recent researches indicate that GAPDHs have multiple functions beside glycolysis. However, little information is available for functions of GAPDHs in potato. Here, we identified 4 putative cytosolic GAPDH genes in potato genome and demonstrated that the StGAPC1, StGAPC2, and StGAPC3, which are constitutively expressed in potato tissues and cold inducible in tubers, encode active cytosolic GAPDHs. Cosuppression of these 3 GAPC genes resulted in low tuber GAPDH activity, consequently the accumulation of reducing sugars in cold stored tubers by altering the tuber metabolite pool sizes favoring the sucrose pathway. Furthermore, GAPCs-silenced tubers exhibited a loss of apical dominance dependent on cell death of tuber apical bud meristem (TAB-meristem). It was also confirmed that StGAPC1, StGAPC2, and StGAPC3 interacted with the autophagy-related protein 3 (ATG3), implying that the occurrence of cell death in TAB-meristem could be induced by ATG3 associated events. Collectively, the present research evidences first that the GAPC genes play crucial roles in diverse physiological and developmental processes in potato tubers.

Luxurious Nitrogen Fertilization of Two Sugar Cane Genotypes Contrasting for Lignin Composition Causes Changes in the Stem Proteome Related to Carbon, Nitrogen, and Oxidant Metabolism but Does Not Alter Lignin Content

Sugar cane is an important crop for sugar and biofuel production. Its lignocellulosic biomass represents a promising option as feedstock for second-generation ethanol production. Nitrogen fertilization can affect differently tissues and its biopolymers, including the cell-wall polysaccharides and lignin. Lignin content and composition are the most important factors associated with biomass recalcitrance to convert cell-wall polysaccharides into fermentable sugars. Thus it is important to understand the metabolic relationship between nitrogen fertilization and lignin in this feedstock. In this study, a large-scale proteomics approach based on GeLC-MS/MS was employed to identify and relatively quantify proteins differently accumulated in two contrasting genotypes for lignin composition after excessive nitrogen fertilization. From the ∼1000 nonredundant proteins identified, 28 and 177 were differentially accumulated in response to nitrogen from IACSP04-065 and IACSP04-627 lines, respectively. These proteins were associated with several functional categories, including carbon metabolism, amino acid metabolism, protein turnover, and oxidative stress. Although nitrogen fertilization has not changed lignin content, phenolic acids and lignin composition were changed in both species but not in the same way. Sucrose and reducing sugars increased in plants of the genotype IACSP04-065 receiving nitrogen.

Quantitative proteome-level analysis of paulownia witches' broom disease with methyl methane sulfonate assistance reveals diverse metabolic changes during the infection and recovery processes

Paulownia witches' broom (PaWB) disease caused by phytoplasma is a fatal disease that leads to considerable economic losses. Although there are a few reports describing studies of PaWB pathogenesis, the molecular mechanisms underlying phytoplasma pathogenicity in Paulownia trees remain uncharacterized. In this study, after building a transcriptome database containing 67,177 sequences, we used isobaric tags for relative and absolute quantification (iTRAQ) to quantify and analyze the proteome-level changes among healthy P. fortunei (PF), PaWB-infected P. fortunei (PFI), and PaWB-infected P. fortunei treated with 20 mg L^-1 or 60 mg L^-1 methyl methane sulfonate (MMS) (PFI-20 and PFI-60, respectively). A total of 2,358 proteins were identified. We investigated the proteins profiles in PF vs. PFI (infected process) and PFI-20 vs. PFI-60 (recovered process), and further found that many of the MMS-response proteins mapped to "photosynthesis" and "ribosome" pathways. Based on our comparison scheme, 36 PaWB-related proteins were revealed. Among them, 32 proteins were classified into three functional groups: (1) carbohydrate and energy metabolism, (2) protein synthesis and degradation, and (3) stress resistance. We then investigated the PaWB-related proteins involved in the infected and recovered processes, and discovered that carbohydrate and energy metabolism was inhibited, and protein synthesis and degradation decreased, as the plant responded to PaWB. Our observations may be useful for characterizing the proteome-level changes that occur at different stages of PaWB disease. The data generated in this study may serve as a valuable resource for elucidating the pathogenesis of PaWB disease during phytoplasma infection and recovery stages.

DkPK Genes Promote Natural Deastringency in C-PCNA Persimmon by Up-regulating DkPDC and DkADH Expression

The astringency of Chinese pollination-constant non-astringent (C-PCNA) persimmon (Diospyros kaki Thunb.) can be naturally removed on the tree. This process is controlled by a single locus and is dominant against other types of persimmons; therefore, this variant is an important candidate for commercial cultivation and the breeding of PCNA cultivars. In our previous study, six full-length coding sequences (CDS) for pyruvate kinase genes (DkPK1-6) were isolated, and DkPK1 is thought to be involved in the natural deastringency of C-PCNA persimmon fruit. Here, we characterize the eight other DkPK genes (DkPK7-14) from C-PCNA persimmon fruit based on transcriptome data. The transcript changes in DkPK7-14 genes and correlations with the proanthocyanidin (PA) content were investigated during different fruit development stages in C-PCNA, J-PCNA, and non-PCNA persimmon; DkPK7 and DkPK8 exhibited up-regulation patterns during the last developmental stage in C-PCNA persimmon that was negatively correlated with the decrease in soluble PAs. Phylogenetic analysis and subcellular localization analysis revealed that DkPK7 and DkPK8 are cytosolic proteins. Notably, DkPK7 and DkPK8 were ubiquitously expressed in various persimmon organs and abundantly up-regulated in seeds. Furthermore, transient over-expression of DkPK7 and DkPK8 in persimmon leaves led to a significant decrease in the content of soluble PAs but a significant increase in the expression levels of the pyruvate decarboxylase (DkPDC) and alcohol dehydrogenase genes (DkADH), which are closely related to acetaldehyde metabolism. The accumulated acetaldehyde that results from the up-regulation of the DkPDC and DkADH genes can combine with soluble PAs to form insoluble PAs, resulting in the removal of astringency from persimmon fruit. Thus, we suggest that both DkPK7 and DkPK8 are likely to be involved in natural deastringency via the up-regulation of DkPDC and DkADH expression during the last developmental stage in C-PCNA persimmon.

Cotton cytosolic pyruvate kinase GhPK6 participates in fast fiber elongation regulation in a ROS-mediated manner

Cotton cytosolic pyruvate kinase GhPK6 is preferentially expressed in the late stage of fiber elongation process, transgenic experiments indicated that its expression level was negatively correlated to cell expansion rate. Pyruvate kinase (PK) plays vital regulatory roles in rapid cell growth in mammals. However, the function of PK in plant cell growth remains unclear. In allotetraploid upland cotton (Gossypium hirsutum L.), a total of 33 PK genes are encoded by the genome. Analysis of the transcriptome data indicated that only two cytosolic PK genes, GhPK6 and its duplicated gene GhPK26, are preferentially expressed in elongating cotton fiber cells. RT-qPCR and western blot analyses revealed that the expression of GhPK6 was negatively correlated with fiber elongation rate, which well explains the observed sharp increase of cytosolic PK activity at the end of fast fiber elongation process. Furthermore, virus-induced gene silencing of GhPK6 in cotton plants resulted in increased fiber cell elongation and reduced reactive oxygen species (ROS) accumulation. On the contrary, Arabidopsis plants ectopically expressing GhPK6 exhibited ROS-mediated growth inhibition, whereas the addition of ROS scavenging reagents could partly rescue this inhibition. These data collectively suggested that GhPK6 might play an important role in regulating cotton fiber elongation in a ROS-dependent inhibition manner.

Involvement of nitric oxide-mediated alternative pathway in tolerance of wheat to drought stress by optimizing photosynthesis

KEY MESSAGE

NO-mediated alternative pathway plays an important role in protecting wheat seedlings against drought stress through dissipating excessive reducing equivalents generated by photosynthesis. Alternative pathway (AP) has been proven to be involved in responses to various stresses. However, the mechanisms of AP in defense response to drought stress are still lacking. The aims of this work are to investigate the role of AP in drought tolerance and how AP is induced under drought stress using two wheat cultivars with different drought tolerance. Our results showed that Longchun22 cultivar is more tolerant to drought than 98SN146 cultivar. Seedlings exposed to drought led to a significant increase in AP, and it increased more in Longchun22. Furthermore, chlorophyll fluorescence parameters (Fv/Fm, ΦPSII, qP) decreased significantly in drought-treated seedlings, especially in 98SN146, indicating that photoinhibition occurred under drought stress. Pretreatment with SHAM, the malate-oxaloacetate shuttle activity and photosynthetic efficiency were further inhibited in drought-treated seedlings, resulting in more serious oxidative damage as indicated by higher levels of malondialdehyde and hydrogen peroxide. Moreover, NO modulated AP under drought stress by increasing AOX1a expression and pyruvate content. Taken together, these results indicate that NO-mediated AP is involved in optimizing photosynthesis under drought stress by avoiding the over-reduction of photosynthetic electron transport chain, thus reducing reactive oxygen species production and oxidative damage in wheat leaves.

Can stable isotope mass spectrometry replace ‎radiolabelled approaches in metabolic studies?

Metabolic pathways and the key regulatory points thereof can be deduced using isotopically labelled substrates. One prerequisite is the accurate measurement of the labeling pattern of targeted metabolites. The subsequent estimation of metabolic fluxes following incubation in radiolabelled substrates has been extensively used. Radiolabelling is a sensitive approach and allows determination of total label uptake since the total radiolabel content is easy to detect. However, the incubation of cells, tissues or the whole plant in a stable isotope enriched environment and the use of either mass spectrometry or nuclear magnetic resonance techniques to determine label incorporation within specific metabolites offers the possibility to readily obtain metabolic information with higher resolution. It additionally also offers an important complement to other post-genomic strategies such as metabolite profiling providing insights into the regulation of the metabolic network and thus allowing a more thorough description of plant cellular function. Thus, although safety concerns mean that stable isotope feeding is generally preferred, the techniques are in truth highly complementary and application of both approaches in tandem currently probably provides the best route towards a comprehensive understanding of plant cellular metabolism.

Both foliar and residual applications of herbicides that inhibit amino acid biosynthesis induce alternative respiration and aerobic fermentation in pea roots

The objective of this work was to ascertain whether there is a general pattern of carbon allocation and utilisation in plants following herbicide supply, independent of the site of application: sprayed on leaves or supplied to nutrient solution. The herbicides studied were the amino acid biosynthesis-inhibiting herbicides (ABIH): glyphosate, an inhibitor of aromatic amino acid biosynthesis, and imazamox, an inhibitor of branched-chain amino acid biosynthesis. All treated plants showed impaired carbon metabolism; carbohydrate accumulation was detected in both leaves and roots of the treated plants. The accumulation in roots was due to lack of use of available sugars as growth was arrested, which elicited soluble carbohydrate accumulation in the leaves due to a decrease in sink strength. Under aerobic conditions, ethanol fermentative metabolism was enhanced in roots of the treated plants. This fermentative response was not related to a change in total respiration rates or cytochrome respiratory capacity, but an increase in alternative oxidase capacity was detected. Pyruvate accumulation was detected after most of the herbicide treatments. These results demonstrate that both ABIH induce the less-efficient, ATP-producing pathways, namely fermentation and alternative respiration, by increasing the key metabolite, pyruvate. The plant response was similar not only for the two ABIH but also after foliar or residual application.

Isolation and Characterization of DkPK Genes Associated with Natural Deastringency in C-PCNA Persimmon

Chinese pollination-constant non-astringent (C-PCNA) persimmon (Diospyros kaki Thunb.) is considered to be an important germplasm resource for the breeding of PCNA cultivars, though its molecular mechanisms of astringency removal remain to be elucidated. Previously, we showed that the abundance of pyruvate kinase gene transcripts increased rapidly during astringency removal in C-PCNA persimmon fruit. Here, we report the full-length coding sequences of six novel DkPK genes from C-PCNA persimmon fruit isolated based on a complementary DNA (cDNA) library and transcriptome data. The expression patterns of these six DkPK genes and correlations with the soluble proanthocyanidin (PA) content were analyzed during various fruit development stages in different types of persimmon, with DkPK1 showing an expression pattern during the last stage in C-PCNA persimmon that was positively correlated with a decrease in soluble PAs. Phylogenetic analysis revealed that DkPK1 belongs to cytosolic-1 subgroup, and subcellular localization analysis confirmed that DkPK1 is located in the cytosol. Notably, tissue expression profiling revealed ubiquitous DkPK1 expression in different persimmon organs, with the highest expression in seeds. Furthermore, transient over-expression of DkPK1 in persimmon leaves resulted in a significant decrease in the content of soluble PAs but a significant increase in the transcript levels of pyruvate decarboxylase genes (DkPDC1, -3, -4, -5), which catalyze the conversion of pyruvate to acetaldehyde. Thus, we propose that an acetaldehyde-based coagulation effect reduces the content of soluble PAs. Taken together, our results suggest that DkPK1 might be involved in the natural removal of astringency at the last developmental stage in C-PCNA persimmon. This is the first report to identify several novel full-length DkPK genes as well as their potential roles in the natural loss of astringency in C-PCNA persimmon.

Metabolic profiling reveals ethylene mediated metabolic changes and a coordinated adaptive mechanism of 'Jonagold' apple to low oxygen stress

Apples are predominantly stored in controlled atmosphere (CA) storage to delay ripening and prolong their storage life. Profiling the dynamics of metabolic changes during ripening and CA storage is vital for understanding the governing molecular mechanism. In this study, the dynamics of the primary metabolism of 'Jonagold' apples during ripening in regular air (RA) storage and initiation of CA storage was profiled. 1-Methylcyclopropene (1-MCP) was exploited to block ethylene receptors and to get insight into ethylene mediated metabolic changes during ripening of the fruit and in response to hypoxic stress. Metabolic changes were quantified in glycolysis, the tricarboxylic acid (TCA) cycle, the Yang cycle and synthesis of the main amino acids branching from these metabolic pathways. Partial least square discriminant analysis of the metabolic profiles of 1-MCP treated and control apples revealed a metabolic divergence in ethylene, organic acid, sugar and amino acid metabolism. During RA storage at 18°C, most amino acids were higher in 1-MCP treated apples, whereas 1-aminocyclopropane-1-carboxylic acid (ACC) was higher in the control apples. The initial response of the fruit to CA initiation was accompanied by an increase of alanine, succinate and glutamate, but a decline in aspartate. Furthermore, alanine and succinate accumulated to higher levels in control apples than 1-MCP treated apples. The observed metabolic changes in these interlinked metabolites may indicate a coordinated adaptive strategy to maximize energy production.

Contributions of photosynthetic and non-photosynthetic cell types to leaf respiration in Vicia faba L. and their responses to growth temperature

In intact leaves, mitochondrial populations are highly heterogeneous among contrasting cell types; how such contrasting populations respond to sustained changes in the environment remains, however, unclear. Here, we examined respiratory rates, mitochondrial protein composition and response to growth temperature in photosynthetic (mesophyll) and non-photosynthetic (epidermal) cells from fully expanded leaves of warm-developed (WD) and cold-developed (CD) broad bean (Vicia faba L.). Rates of respiration were significantly higher in mesophyll cell protoplasts (MCPs) than epidermal cell protoplasts (ECPs), with both protoplast types exhibiting capacity for cytochrome and alternative oxidase activity. Compared with ECPs, MCPs contained greater relative quantities of porin, suggesting higher mitochondrial surface area in mesophyll cells. Nevertheless, the relative quantities of respiratory proteins (normalized to porin) were similar in MCPs and ECPs, suggesting that ECPs have lower numbers of mitochondria yet similar protein complement to MCP mitochondria (albeit with lower abundance serine hydroxymethyltransferase). Several mitochondrial proteins (both non-photorespiratory and photorespiratory) exhibited an increased abundance in response to cold in both protoplast types. Based on estimates of individual protoplast respiration rates, combined with leaf cell abundance data, epidermal cells make a small but significant (2%) contribution to overall leaf respiration which increases twofold in the cold. Taken together, our data highlight the heterogeneous nature of mitochondrial populations in leaves, both among contrasting cell types and in how those populations respond to growth temperature.

Roles of mitochondrial energy dissipation systems in plant development and acclimation to stress

BACKGROUND

Plants are sessile organisms that have the ability to integrate external cues into metabolic and developmental signals. The cues initiate specific signal cascades that can enhance the tolerance of plants to stress, and these mechanisms are crucial to the survival and fitness of plants. The adaption of plants to stresses is a complex process that involves decoding stress inputs as energy-deficiency signals. The process functions through vast metabolic and/or transcriptional reprogramming to re-establish the cellular energy balance. Members of the mitochondrial energy dissipation pathway (MEDP), alternative oxidases (AOXs) and uncoupling proteins (UCPs), act as energy mediators and might play crucial roles in the adaption of plants to stresses. However, their roles in plant growth and development have been relatively less explored.

SCOPE

This review summarizes current knowledge about the role of members of the MEDP in plant development as well as recent advances in identifying molecular components that regulate the expression of AOXs and UCPs. Highlighted in particular is a comparative analysis of the expression, regulation and stress responses between AOXs and UCPs when plants are exposed to stresses, and a possible signal cross-talk that orchestrates the MEDP, reactive oxygen species (ROS), calcium signalling and hormone signalling.

CONCLUSIONS

The MEDP might act as a cellular energy/metabolic mediator that integrates ROS signalling, energy signalling and hormone signalling with plant development and stress accumulation. However, the regulation of MEDP members is complex and occurs at transcriptional, translational, post-translational and metabolic levels. How this regulation is linked to actual fluxes through the AOX/UCP in vivo remains elusive.

Expression, purification and characterization of Solanum tuberosum recombinant cytosolic pyruvate kinase

The cDNA encoding for a Solanum tuberosum cytosolic pyruvate kinase 1 (PKc1) highly expressed in tuber tissue was cloned in the bacterial expression vector pProEX HTc. The construct carried a hexahistidine tag in N-terminal position to facilitate purification of the recombinant protein. Production of high levels of soluble recombinant PKc1 in Escherichia coli was only possible when using a co-expression strategy with the chaperones GroES-GroEL. Purification of the protein by Ni(2 +) chelation chromatography yielded a single protein with an apparent molecular mass of 58kDa and a specific activity of 34unitsmg(-1) protein. The recombinant enzyme had an optimum pH between 6 and 7. It was relatively heat stable as it retained 80% of its activity after 2min at 75°C. Hyperbolic saturation kinetics were observed with ADP and UDP whereas sigmoidal saturation was observed during analysis of phosphoenolpyruvate binding. Among possible effectors tested, aspartate and glutamate had no effect on enzyme activity, whereas α-ketoglutarate and citrate were the most potent inhibitors. When tested on phosphoenolpyruvate saturation kinetics, these latter compounds increased S0.5. These findings suggest that S. tuberosum PKc1 is subject to a strong control by respiratory metabolism exerted via citrate and other tricarboxylic acid cycle intermediates.

Metabolic control of redox and redox control of metabolism in plants

SIGNIFICANCE

Reduction-oxidation (Redox) status operates as a major integrator of subcellular and extracellular metabolism and is simultaneously itself regulated by metabolic processes. Redox status not only dominates cellular metabolism due to the prominence of NAD(H) and NADP(H) couples in myriad metabolic reactions but also acts as an effective signal that informs the cell of the prevailing environmental conditions. After relay of this information, the cell is able to appropriately respond via a range of mechanisms, including directly affecting cellular functioning and reprogramming nuclear gene expression.

RECENT ADVANCES

The facile accession of Arabidopsis knockout mutants alongside the adoption of broad-scale post-genomic approaches, which are able to provide transcriptomic-, proteomic-, and metabolomic-level information alongside traditional biochemical and emerging cell biological techniques, has dramatically advanced our understanding of redox status control. This review summarizes redox status control of metabolism and the metabolic control of redox status at both cellular and subcellular levels.

CRITICAL ISSUES

It is becoming apparent that plastid, mitochondria, and peroxisome functions influence a wide range of processes outside of the organelles themselves. While knowledge of the network of metabolic pathways and their intraorganellar redox status regulation has increased in the last years, little is known about the interorganellar redox signals coordinating these networks. A current challenge is, therefore, synthesizing our knowledge and planning experiments that tackle redox status regulation at both inter- and intracellular levels.

FUTURE DIRECTIONS

Emerging tools are enabling ever-increasing spatiotemporal resolution of metabolism and imaging of redox status components. Broader application of these tools will likely greatly enhance our understanding of the interplay of redox status and metabolism as well as elucidating and characterizing signaling features thereof. We propose that such information will enable us to dissect the regulatory hierarchies that mediate the strict coupling of metabolism and redox status which, ultimately, determine plant growth and development.

Identification and computational annotation of genes differentially expressed in pulp development of Cocos nucifera L. by suppression subtractive hybridization

BACKGROUND

Coconut (Cocos nucifera L.) is one of the world's most versatile, economically important tropical crops. Little is known about the physiological and molecular basis of coconut pulp (endosperm) development and only a few coconut genes and gene product sequences are available in public databases. This study identified genes that were differentially expressed during development of coconut pulp and functionally annotated these identified genes using bioinformatics analysis.

RESULTS

Pulp from three different coconut developmental stages was collected. Four suppression subtractive hybridization (SSH) libraries were constructed (forward and reverse libraries A and B between stages 1 and 2, and C and D between stages 2 and 3), and identified sequences were computationally annotated using Blast2GO software. A total of 1272 clones were obtained for analysis from four SSH libraries with 63% showing similarity to known proteins. Pairwise comparing of stage-specific gene ontology ids from libraries B-D, A-C, B-C and A-D showed that 32 genes were continuously upregulated and seven downregulated; 28 were transiently upregulated and 23 downregulated. KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis showed that 1-acyl-sn-glycerol-3-phosphate acyltransferase (LPAAT), phospholipase D, acetyl-CoA carboxylase carboxyltransferase beta subunit, 3-hydroxyisobutyryl-CoA hydrolase-like and pyruvate dehydrogenase E1 β subunit were associated with fatty acid biosynthesis or metabolism. Triose phosphate isomerase, cellulose synthase and glucan 1,3-β-glucosidase were related to carbohydrate metabolism, and phosphoenolpyruvate carboxylase was related to both fatty acid and carbohydrate metabolism. Of 737 unigenes, 103 encoded enzymes were involved in fatty acid and carbohydrate biosynthesis and metabolism, and a number of transcription factors and other interesting genes with stage-specific expression were confirmed by real-time PCR, with validation of the SSH results as high as 66.6%. Based on determination of coconut endosperm fatty acids content by gas chromatography-mass spectrometry, a number of candidate genes in fatty acid anabolism were selected for further study.

CONCLUSION

Functional annotation of genes differentially expressed in coconut pulp development helped determine the molecular basis of coconut endosperm development. The SSH method identified genes related to fatty acids, carbohydrate and secondary metabolites. The results will be important for understanding gene functions and regulatory networks in coconut fruit.

The alternative respiratory pathway mediates carboxylate synthesis in white lupin cluster roots under phosphorus deprivation

Plant adaptations associated with a high efficiency of phosphorus (P) acquisition can be used to increase productivity and sustainability in a world with a growing population and decreasing rock phosphate reserves. White lupin (Lupinus albus) produces cluster roots that release carboxylates to efficiently mobilize P from P-sorbing soils. It has been hypothesized that an increase in the activity of the alternative oxidase (AOX) would allow for the mitochondrial oxidation of NAD(P)H produced during citrate synthesis in cluster roots at a developmental stage when there is a low demand for ATP. We used the oxygen-isotope fractionation technique to study the in vivo respiratory activities of the cytochrome oxidase pathway (COP) and the alternative oxidase pathway (AOP) in different root sections of white lupins grown hydroponically with and without P. In parallel, AOX protein levels and internal carboxylate concentrations were determined in cluster and non-cluster roots. Higher in vivo AOP activity was measured in cluster roots when malate and citrate concentrations were also high, thus confirming our hypothesis. AOX protein levels were not always correlated with in vivo AOP activity, suggesting post-translational regulation of AOX.

Optimization of photosynthesis by multiple metabolic pathways involving interorganelle interactions: resource sharing and ROS maintenance as the bases

The bioenergetic processes of photosynthesis and respiration are mutually beneficial. Their interaction extends to photorespiration, which is linked to optimize photosynthesis. The interplay of these three pathways is facilitated by two major phenomena: sharing of energy/metabolite resources and maintenance of optimal levels of reactive oxygen species (ROS). The resource sharing among different compartments of plant cells is based on the production/utilization of reducing equivalents (NADPH, NADH) and ATP as well as on the metabolite exchange. The responsibility of generating the cellular requirements of ATP and NAD(P)H is mostly by the chloroplasts and mitochondria. In turn, besides the chloroplasts, the mitochondria, cytosol and peroxisomes are common sinks for reduced equivalents. Transporters located in membranes ensure the coordinated movement of metabolites across the cellular compartments. The present review emphasizes the beneficial interactions among photosynthesis, dark respiration and photorespiration, in relation to metabolism of C, N and S. Since the bioenergetic reactions tend to generate ROS, the cells modulate chloroplast and mitochondrial reactions, so as to ensure that the ROS levels do not rise to toxic levels. The patterns of minimization of ROS production and scavenging of excess ROS in intracellular compartments are highlighted. Some of the emerging developments are pointed out, such as model plants, orientation/movement of organelles and metabolomics.

Evidence for extensive heterotrophic metabolism, antioxidant action, and associated regulatory events during winter hardening in Sitka spruce

BACKGROUND

Cold acclimation in woody perennials is a metabolically intensive process, but coincides with environmental conditions that are not conducive to the generation of energy through photosynthesis. While the negative effects of low temperatures on the photosynthetic apparatus during winter have been well studied, less is known about how this is reflected at the level of gene and metabolite expression, nor how the plant generates primary metabolites needed for adaptive processes during autumn.

RESULTS

The MapMan tool revealed enrichment of the expression of genes related to mitochondrial function, antioxidant and associated regulatory activity, while changes in metabolite levels over the time course were consistent with the gene expression patterns observed. Genes related to thylakoid function were down-regulated as expected, with the exception of plastid targeted specific antioxidant gene products such as thylakoid-bound ascorbate peroxidase, components of the reactive oxygen species scavenging cycle, and the plastid terminal oxidase. In contrast, the conventional and alternative mitochondrial electron transport chains, the tricarboxylic acid cycle, and redox-associated proteins providing reactive oxygen species scavenging generated by electron transport chains functioning at low temperatures were all active.

CONCLUSIONS

A regulatory mechanism linking thylakoid-bound ascorbate peroxidase action with "chloroplast dormancy" is proposed. Most importantly, the energy and substrates required for the substantial metabolic remodeling that is a hallmark of freezing acclimation could be provided by heterotrophic metabolism.

Modification of OsSUT1 gene expression modulates the salt response of rice Oryza sativa cv. Taipei 309

A metabolic depletion syndrome was discovered at early vegetative stages in roots of salt sensitive rice cultivars after prolonged exposure to 100mM NaCl. Metabolite profiling analyses demonstrate that this syndrome is part of the terminal stages of the rice salt response. The phenotype encompasses depletion of at least 30 primary metabolites including sucrose, glucose, fructose, glucose-6-P, fructose-6P, organic- and amino-acids. Based on these observations we reason that sucrose allocation to the root may modify the rice response to high salt. This hypothesis was tested using antisense lines of the salt responsive OsSUT1 gene in the salt sensitive Taipei 309 cultivar. Contrary to our expectations of a plant system impaired in one component of sucrose transport, we find improved gas exchange and photosynthetic performance as well as maintenance of sucrose levels in the root under high salinity. Two independent OsSUT1 lines with an antisense inhibition similar to the naturally occurring salt induced reduction of OsSUT1 gene expression showed these phenomena but not a more extreme antisense inhibition line. We investigated the metabolic depletion syndrome by metabolomic and physiological approaches and discuss our results with regard to the potential role of sucrose transporters and sucrose transport for rice salt acclimation.

Involvement of hydrogen peroxide, calcium, and ethylene in the induction of the alternative pathway in chilling-stressed Arabidopsis callus

The roles of ethylene, hydrogen peroxide (H(2)O(2)), and calcium in inducing the capacity of the alternative respiratory pathway (AP) under chilling temperature in Arabidopsis thaliana calli were investigated. Exposure of wild-type (WT) calli, but not the calli of ethylene-insensitive mutants, etr1-3 and ein2-1, to chilling led to a marked increase of the AP capacity and triggered a rapid ethylene emission and H(2)O(2) generation. Increasing ethylene emission by applying 1-aminocyclopropane-1-carboxylic (an ethylene precursor) markedly enhanced the AP capacity in WT calli, but not in etr1-3 and ein2-1 calli, whereas suppressing ethylene emission by applying aminooxyacetic acid (an ethylene biosynthesis inhibitor) abolished the chilling-induced AP capacity in WT calli. Furthermore, exogenous H(2)O(2) treatment increased the AP capacity in WT calli, but not in etr1-3 and ein2-1 calli, while both catalase (H(2)O(2) scavenger) and diphenylene iodonium (DPI, an inhibitor of NADPH oxidase) completely inhibited the chilling-induced H(2)O(2) generation and largely inhibited the chilling-induced AP capacity. Interestingly, the chilling-induced AP capacity was completely inhibited by DPI and EGTA (calcium chelator). Further investigation demonstrated that H(2)O(2) and calcium induced ethylene emission under chilling stress. Ethylene modulated the chilling-induced increase of pyruvate content and the expression of alternative oxidase genes (AOX1a and AOX1c). Taken together, these results indicate that H(2)O(2)-, calcium- and ethylene-dependent pathways are required for chilling-induced increase in AP capacity. However, only ethylene is indispensable for the activation of the AP capacity.

Downregulation of OsPK1, a cytosolic pyruvate kinase, by T-DNA insertion causes dwarfism and panicle enclosure in rice

Pyruvate kinase (PK) catalyzes the final step of glycolysis. There are few reports on the role of PK in rice. Here, we identified a novel rice dwarf mutant, designated as ospk1, showing dwarfism, panicle enclosure, reduced seed set, and outgrowth of axillary buds from culm nodes. Sequence analyses of 5'-RACE indicated that a single T-DNA was inserted in the transcriptional regulatory region of OsPK1 in ospk1. Quantitative RT-PCR result showed that OsPK1 expression was decreased by approximately 90% in ospk1 compared with that in WT. Enzyme assay and transient expression in protoplasts indicated that OsPK1 encodes a cytosolic PK (PK(c)). Complementation with OsPK1 demonstrated that OsPK1 is responsible for the phenotype of ospk1. Quantitative RT-PCR and GUS staining analyses exhibited that OsPK1 was expressed mainly in leaf mesophyll cells, phloem companion cells in stems, and cortical parenchyma cells in roots. The transcriptions of four other putative enzymes involved in the glycolysis/gluconeogenesis pathway were altered in ospk1. The amount of pyruvate is decreased in ospk1. We propose that OsPK1 plays an important role through affecting the glycolytic pathway. The contents of glucose and fructose were markedly accumulated in flag leaf blade and panicle of ospk1. The sucrose level in panicle of ospk1 was decreased by approximately 84%. These findings indicated that both monosaccharide metabolism and sugar transport are altered due to the decreased expression of OsPK1. Together, these results provide new insights into the role of PK(c) in plant morphological development, especially plant height.

Unraveling the role of fermentation in the mode of action of acetolactate synthase inhibitors by metabolic profiling

Herbicides that inhibit branched chain amino acid biosynthesis induce aerobic fermentation. The role of fermentation in the mode of action of these herbicides is not known, nor is the importance of this physiological response in the growth inhibition and the lethality caused by them. Metabolic profiling was used to compare the effects of the herbicide imazethapyr (IM) on pea plants with two other treatments that also induce fermentation: hypoxia and the exogenous supply pyruvate for seven days. While hypoxic roots did not show internal anoxia, feeding pyruvate or applying IM to the roots led to internal anoxia, probably related to the respiratory burst detected. The three treatments induced ethanol fermentation, but fermentation induced following herbicide treatment was earlier than that following pyruvate supply and was not associated with a decrease in the energy status. No striking changes were detected in the metabolic profiling of hypoxic roots, indicating that metabolism was only slightly impaired. Feeding pyruvate resulted in marked succinate accumulation and a general amino acid accumulation. IM-treated roots showed a general accumulation of glycolytic metabolites upstream of pyruvate, a decrease in some TCA intermediates and an increase in the free amino acid pool sizes. All treatments caused GABA and putrescine accumulation. Our results indicate that IM supply impairs carbon/nitrogen metabolism and this impaired metabolism is likely to be related to the growth arrest detected. As growth is arrested, carbohydrates and glycolytic intermediates accumulate and energy becomes more available.

Regulation of respiration in plants: a role for alternative metabolic pathways

Respiratory metabolism includes the reactions of glycolysis, the tricarboxylic acid cycle and the mitochondrial electron transport chain, but is also directly linked with many other metabolic pathways such as protein and lipid biosynthesis and photosynthesis via photorespiration. Furthermore, any change in respiratory activity can impact the redox status of the cell and the production of reactive oxygen species. In this review, it is discussed how respiration is regulated and what alternative pathways are known that increase the metabolic flexibility of this vital metabolic process. By looking at the adaptive responses of respiration to hypoxia or changes in the oxygen availability of a cell, the integration of regulatory responses of various pathways is illustrated.

Combined noninvasive imaging and modeling approaches reveal metabolic compartmentation in the barley endosperm

The starchy endosperm of cereals is a priori taken as a metabolically uniform tissue. By applying a noninvasive assay based on (13)C/(1)H-magnetic resonance imaging (MRI) to barley (Hordeum vulgare) grains, we uncovered metabolic compartmentation in the endosperm. (13)C-Suc feeding during grain filling showed that the primary site of Ala synthesis was the central region of the endosperm, the part of the caryopsis experiencing the highest level of hypoxia. Region-specific metabolism in the endosperm was characterized by flux balance analysis (FBA) and metabolite profiling. FBA predicts that in the central region of the endosperm, the tricarboxylic acid cycle shifts to a noncyclic mode, accompanied by elevated glycolytic flux and the accumulation of Ala. The metabolic compartmentation within the endosperm is advantageous for the grain's carbon and energy economy, with a prominent role being played by Ala aminotransferase. An investigation of caryopses with a genetically perturbed tissue pattern demonstrated that Ala accumulation is a consequence of oxygen status, rather than being either tissue specific or dependent on the supply of Suc. Hence the (13)C-Ala gradient can be used as an in vivo marker for hypoxia. The combination of MRI and metabolic modeling offers opportunities for the noninvasive analysis of metabolic compartmentation in plants.

Integrative response of plant mitochondrial electron transport chain to nitrogen source

Nitrogen (N) availability is widely known as a determinant of plant growth and respiration rate. However, less attention has been paid to the effect of the type of N source (nitrate, nitrite or ammonium) on the respiratory system. This review summarizes the latest findings on this topic, with an emphasis on the effect of ammonium and nitric oxide (NO) on the respiratory system, and the physiological role of alternative oxidase (AOX). First, concentrated ammonium has been found to increase plant respiration rate (ammonium-dependent respiratory increase, ARI). We will introduce two hypotheses to explain ARI, futile ammonium cycling and excess reducing equivalents, and verify the validity of each hypothesis. We suggest that these two hypotheses are not necessarily mutually exclusive. Second, gene expression of AOX is suppressed when N is predominately available as nitrate instead of ammonium. We will discuss possible signaling pathways leading to this expression pattern. Third, while AOX expression is induced by NO, AOX activity itself is insensitive to NO. In contrast, activity of cytochrome c oxidase (COX) is sensitive to NO. We outline the NO production pathway, focusing on nitrite-dependent NO production, and discuss the physiological significance of the fact that AOX activity is insensitive to NO. Finally, this review aims to build an integrated scheme of the respiratory response to the type of N source, considering leaves in high light conditions or hypoxic roots.

The use of natural genetic diversity in the understanding of metabolic organization and regulation

The study of metabolic regulation has traditionally focused on analysis of specific enzymes, emphasizing kinetic properties, and the influence of protein interactions and post-translational modifications. More recently, reverse genetic approaches permit researchers to directly determine the effects of a deficiency or a surplus of a given enzyme on the biochemistry and physiology of a plant. Furthermore, in many model species, gene expression atlases that give important spatial information concerning the quantitative expression level of metabolism-associated genes are being produced. In parallel, "top-down" approaches to understand metabolic regulation have recently been instigated whereby broad genetic diversity is screened for metabolic traits and the genetic basis of this diversity is defined thereafter. In this article we will review recent examples of this latter approach both in the model species Arabidopsis thaliana and the crop species tomato (Solanum lycopersicum). In addition to highlighting examples in which this genetic diversity approach has proven promising, we will discuss the challenges associated with this approach and provide a perspective for its future utility.

A seed high-lysine trait is negatively associated with the TCA cycle and slows down Arabidopsis seed germination

• Lysine is a nutritionally important essential amino acid, but significant elevation of its levels in Arabidopsis seeds, by enhancing its synthesis and blocking its catabolism, causes a retardation of germination. Here, we hypothesized that this negative effect is associated with changes in primary metabolism and gene expression programs that are essential for early germination. • Seeds at different stages of germination sensu stricto of the seed-high-lysine genotype were subjected to detailed analysis of primary metabolism, using GC-MS, as well as microarray analysis and two-dimensional, isoelectric focusing, sodium dodecylsulfate polyacrylamide gel electrophoresis, to detect storage protein mobilization. • Our results exposed a major negative effect of the seed-specific increased lysine synthesis and knockout of its catabolism on the levels of a number of TCA cycle metabolites. This metabolic alteration also influences significantly the transcriptome, primarily attenuating the boost of specific transcriptional programs that are essential for seedling establishment, such as the onset of photosynthesis, as well as the turnover of specific transcriptional programs associated with seed embryonic traits. • Our results indicate that catabolism of the aspartic acid family of amino acids is an important contributor to the energy status of plants, and hence to the onset of autotrophic growth-associated processes during germination.