Regulation and roles of phosphoenolpyruvate carboxykinase in plants

Phosphoenolpyruvate and Related Metabolic Pathways Contribute to the Regulation of Plant Growth and Development

Phosphoenolpyruvate (PEP) plays a key role in the development of plants and exists in a wide variety of species. Research on the metabolic activities of PEP in plants has received increasing attention. PEP regulates multiple processes in plant growth and development. This article provides a comprehensive summary of these pathways, including embryo formation, root development, synthesis of secondary metabolites, and the formation of lignification. We also summarize new findings, including PEP's role in nodule energy sensing and carbon allocation under the influence of ozone. This review displays the complex and differential regulatory pathways in plant growth and development and provides a reference for basic and applied research on PEP metabolism in plants.

Integrated omics analysis reveals the interactions among ROS metabolism and malate metabolism associated with chilling tolerance in peach fruit treated with hot air

Continuous supply of NADPH is necessary for the synthesis of ROS, which can be derived from the decarboxylation of malic acid, providing fuels for RbOHs to sustain ROS production. However, excessive accumulations of ROS lead to significant chilling injury (CI) in peaches during cold storage. Our previous studies indicated that hot air (HA) slows the CI progression in peaches by preventing malate degradation. In this study, we investigated the interactions among CI, ROS, and malate metabolism to elucidate the molecular mechanisms through which HA treatment alleviates CI in peaches. The results demonstrated that HA treatment inhibited both ROS accumulation and malate degradation. Transcriptomic and proteomic analyses revealed that HA impacts carbohydrate metabolism and ROS synthesis. Specifically, HA treatment down-regulated the expression of PpRbOHs, and increased the activities of SOD, CAT, APX, and GR. This resulted in reduced levels of H2O2 and O2- in peaches during low temperature storage. Regarding malate metabolism, HA treatment prevented the decrease in malic acid by enhancing the activities of PEPC and MDH while inhibiting NADP-ME activity. These findings were consistent with omics data, which showed that HA up-regulated the expression of PpPEPC and PpMDH, but down-regulated the expression of PpME. In summary, our results indicate that the increased resistance to CI in peaches treated with HA is linked to higher malate levels, which down-regulated the expression of PpRbOHs and inhibited ROS production, thereby reducing CI in peach fruit.

Comparative Physiological and Transcriptomics Profiling Provides Integrated Insight into Melatonin Mediated Salt and Copper Stress Tolerance in Selenicereus undatus L

Selenicereus undatus L., (pitaya) is an important tropical fruit crop, and faces significant challenges from soil salinity and heavy metal toxicity. This study explores the role of melatonin (M) in enhancing stress tolerance in pitaya against salinity (S) and copper (Cu) toxicity, both individually and in combination (SCu). SCu stress reduced plant biomass by ~54%, while melatonin application mitigated stress effects and increased plant growth by ~73.26% under SCuM compared to SCu treatment. Antioxidant activities were also modulated by stress. Transcriptomic analysis revealed 21 differentially expressed genes (DEGs) common across stress treatments and 13 DEGs specific to combined melatonin with stress treatments involved in stress signaling, secondary metabolite biosynthesis, and photosynthesis. A weighted gene co-expression network analysis (WGCNA) identified four gene modules (brown, dark green, dark grey, and grey) significantly associated with phenotypic traits. A protein-protein interaction (PPI) network analysis highlighted 14 hub genes per module, including GH3, JAZ, PAL, CCR, and POD, implicated in MAPK signaling, phenylpropanoid biosynthesis, and hormone signaling pathways. Integration of DESeq2 and WGCNA identified 12 key stress-responsive genes strongly correlated with phenotypic traits. This study provides insights into regulatory mechanisms underlying stress responses and highlights candidate genes for developing stress-resilient S. undatus through breeding programs.

The poetry of nitrogen and carbon metabolic shifts: The role of C/N in pitaya phase change

Pitaya, a desert plant, has an underexplored flowering mechanism due to a lack of functional validation assays. This study reveals that the transition from vegetative to generative growth in pitaya is regulated by significant metabolic shift, underscoring the importance of understanding and address the challenging issue pitaya's phase change. Lateral buds from 6-years-old 'Guanhuahong' pitaya (Hylocereus monacanthus) plants were collected on April 8th, 18th, and 28th 2023, representing early, middle, and late stages of phase transition, respectively. Results showed diminished nitrogen levels concurrent with increased carbon levels and carbon-to-nitrogen (C/N) ratios during pitaya phase transition. Transcriptomic analysis identified batches of differentially expressed genes (DEGs) involved in downregulating nitrogen metabolism and upregulating carbon metabolism. These batches of genes play a central role in the metabolic shifts that predominantly regulate the transition to the generative phase in pitaya. This study unveils the intricate regulatory network involving 6 sugar synthesis and transport, 11 photoperiod (e.g., PHY, CRY, PIF) and 6 vernalization (e.g., VIN3) pathways, alongside 11 structural flowering genes (FCA, FLK, LFY, AGL) out of a vast array of potential candidates in pitaya phase change. These findings provide insights into the metabolic pathways involved in pitaya's phase transition, offering a theoretical framework for managing flowering, guiding breeding strategies to optimize flowering timing and improve crop yields under varied nitrogen conditions.

Enhanced photorespiratory and TCA pathways by elevated CO2 to manage ammonium nutrition in tomato leaves

Plants grown under exclusive ammonium (NH4+) nutrition have high carbon (C) demand to sustain proper nitrogen (N) assimilation and energy required for plant growth, generally impaired when compared to nitrate (NO3-) nutrition. Thereby, the increment of the atmospheric carbon dioxide (CO2) concentration, in the context of climate change, will potentially allow plants to better face ammonium nutrition. In this work, tomato (Solanum lycopersicum L.) plants were grown under ammonium or nitrate nutrition in conditions of ambient (aCO2, 400 ppm) or elevated CO2 (eCO2, 800 ppm) atmosphere. Elevated CO2 increased photosynthesis rate and tomato shoot growth regardless of the N source. In the case of NH4+-fed leaves the positive effect of elevated CO2 occurred despite of the high tissue NH4+ accumulation. Under eCO2 ammonium nutrition triggered, among others, the modulation of genes related to C provision pathways (including carbonic anhydrase and glyoxylate cycle), antioxidant response and cell membranes protection. The enhanced photosynthate production at eCO2 facilitated C skeleton provision through the TCA cycle and anaplerotic pathways to promote amino acid synthesis. Moreover, photorespiratory activity was stimulated by eCO2 and contributed to yield serine as additional sink for NH4+ excess. Overall, these changes denote a connection between the respiratory and the photorespiratory pathways linked to ammonium nutrition. This metabolic strategy may allow crops to grow efficiently using ammonium as fertilizer in a future climate change scenario, while mitigating N losses.

The art of tartness: the genetics of organic acid content in fresh fruits

Organic acids are major determinants of fruit flavor and a primary focus of fruit crop breeding. The accumulation of organic acids is determined by their synthesis, degradation, and transport, all of which are manipulated by sophisticated genetic mechanisms. Constant exploration of the genetic basis of organic acid accumulation, especially through linkage analysis, association analysis, and evolutionary analysis, have identified numerous loci in recent decades. In this review, the genetic loci and genes responsible for malate and citrate contents in fruits are discussed from the genetic perspective. Technologies such as gene transformation and genome editing as well as efficient breeding using marker-assisted selection (MAS) and genomic selection (GS) are expected to break the bottleneck of traditional fruit crop breeding and promote fruit quality improvement.

Metabolite Profiling of Hydroponic Lettuce Roots Affected by Nutrient Solution Flow: Insights from Comprehensive Analysis Using Widely Targeted Metabolomics and MALDI Mass Spectrometry Imaging Approaches

Root morphology, an important determinant of nutrient absorption and plant growth, can adapt to various growth environments to promote survival. Solution flow under hydroponic conditions provides a mechanical stimulus, triggering adaptive biological responses, including altered root morphology and enhanced root growth and surface area to facilitate nutrient absorption. To clarify these mechanisms, we applied untargeted metabolomics technology, detecting 1737 substances in lettuce root samples under different flow rates, including 17 common differential metabolites. The abscisic acid metabolic pathway product dihydrophaseic acid and the amino and nucleotide sugar metabolism factor N-acetyl-d-mannosamine suggest that nutrient solution flow rate affects root organic acid and sugar metabolism to regulate root growth. Spatial metabolomics analysis of the most stressed root bases revealed significantly enriched Kyoto Encyclopedia of Genes and Genomes pathways: "biosynthesis of cofactors" and "amino sugar and nucleotide sugar metabolism". Colocalization analysis of pathway metabolites revealed a flow-dependent spatial distribution, with higher flavin mononucleotide, adenosine-5'-diphosphate, hydrogenobyrinic acid, and D-glucosamine 6-phosphate under flow conditions, the latter two showing downstream-side enrichment. In contrast, phosphoenolpyruvate, 1-phospho-alpha-D-galacturonic acid, 3-hydroxyanthranilic acid, and N-acetyl-D-galactosamine were more abundant under no-flow conditions, with the latter two concentrated on the upstream side. As metabolite distribution is associated with function, observing their spatial distribution in the basal roots will provide a more comprehensive understanding of how metabolites influence plant morphology and response to environmental changes than what is currently available in the literature.

Transcriptome analysis of Reticulitermes flaviceps exposed to Mentha spicata essential oil and carvone indicates a potential neurotoxic mechanism of action characterized by intracellular calcium influx mediated by dopamine receptors

Reticulitermes flaviceps is an economically important pest in agriculture, forestry, and construction. Recent studies have shown an increase in research focusing on the anti-termite properties of plant essential oils, however, there remains a lack of information regarding the specific molecular mechanism involved. In this study, RNA-seq analysis was conducted on termites exposed to Mentha spicata essential oil (EO) and carvone, leading to the discovery of various genes that were expressed differentially under different treatment conditions. Numerous genes that exhibited a response to M. spicata EO and carvone found to be associated with stress-related pathways, such as drug metabolism cytochrome P450, glutathione metabolism, fatty acid metabolism, citric acid cycle, neuroactive ligand-receptor interaction, cell apoptosis, the AMPK signalling pathway, the mTOR signalling pathway, the longevity regulation pathway, ubiquitin-mediated protein hydrolysis, and the calcium signalling pathway. The up-regulation of genes (SPHK) associated with calcium channels, such as SPHK, indicates a potential mechanism of neurotoxicity, while the up-regulation of apoptosis-associated genes, including ACTB_G1, PYG, SQSTM1, RNF31, suggests a potential mechanism of cytotoxicity. The metabolism of M. spicata EO induces oxidative stress, elevates free Ca2+ levels in mitochondria, and initiates the generation of reactive oxygen species (ROS), ultimately resulting in programmed cell necrosis and apoptosis, as well as facilitating cellular autophagy. The monoterpenes exhibited neurotoxic and cytotoxic effects on R. flaviceps and could be exploited to advance termiticide development and eco-friendly termite control.

Mechanisms of harmful effects of Microcystis aeruginosa on a brackish water organism Moina mongolica based on physiological and transcriptomic responses

To investigate the detrimental impacts of cyanobacterial bloom, specifically Microcystis aeruginosa, on brackish water ecosystems, the study used Moina mongolica, a cladoceran species, as the test organism. In a chronic toxicology experiment, the survival and reproductive rates of M. mongolica were assessed under M. aeruginosa stress. It was observed that the survival rate of M. mongolica fed with M. aeruginosa significantly decreased with time and their reproduction rate dropped to zero, while the control group remained maintained stable and normal reproduction. To further explore the underlying molecular mechanisms of the effects of M. aeruginosa on M. mongolica, we conducted a transcriptomic analysis on newly hatched M. mongolica cultured under different food conditions for 24 h. The results revealed significant expression differences in 572 genes, with 233 genes significantly up-regulated and 339 genes significantly down-regulated. Functional analysis of these differentially expressed genes identified six categories of physiological functional changes, including nutrition and metabolism, oxidative phosphorylation, neuroimmunology, cuticle and molting, reproduction, and programmed cell death. Based on these findings, we outlined the basic mechanisms of microcystin toxicity. The discovery provides critical insights into the mechanisms of Microcystis toxicity on organisms and explores the response mechanisms of cladocerans under the stress of Microcystis.

Diurnal Rhythms in the Red Seaweed Gracilariopsis chorda are Characterized by Unique Regulatory Networks of Carbon Metabolism

Cellular and physiological cycles are driven by endogenous pacemakers, the diurnal and circadian rhythms. Key functions such as cell cycle progression and cellular metabolism are under rhythmic regulation, thereby maintaining physiological homeostasis. The photoreceptors phytochrome and cryptochrome, in response to light cues, are central input pathways for physiological cycles in most photosynthetic organisms. However, among Archaeplastida, red algae are the only taxa that lack phytochromes. Current knowledge about oscillatory rhythms is primarily derived from model species such as Arabidopsis thaliana and Chlamydomonas reinhardtii in the Viridiplantae, whereas little is known about these processes in other clades of the Archaeplastida, such as the red algae (Rhodophyta). We used genome-wide expression profiling of the red seaweed Gracilariopsis chorda and identified 3,098 rhythmic genes. Here, we characterized possible cryptochrome-based regulation and photosynthetic/cytosolic carbon metabolism in this species. We found a large family of cryptochrome genes in G. chorda that display rhythmic expression over the diurnal cycle and may compensate for the lack of phytochromes in this species. The input pathway gates regulatory networks of carbon metabolism which results in a compact and efficient energy metabolism during daylight hours. The system in G. chorda is distinct from energy metabolism in most plants, which activates in the dark. The green lineage, in particular, land plants, balance water loss and CO2 capture in terrestrial environments. In contrast, red seaweeds maintain a reduced set of photoreceptors and a compact cytosolic carbon metabolism to thrive in the harsh abiotic conditions typical of intertidal zones.

Mechanisms of metabolic adaptation in the duckweed Lemna gibba: an integrated metabolic, transcriptomic and flux analysis

BACKGROUND

Duckweeds are small, rapidly growing aquatic flowering plants. Due to their ability for biomass production at high rates they represent promising candidates for biofuel feedstocks. Duckweeds are also excellent model organisms because they can be maintained in well-defined liquid media, usually reproduce asexually, and because genomic resources are becoming increasingly available. To demonstrate the utility of duckweed for integrated metabolic studies, we examined the metabolic adaptation of growing Lemna gibba cultures to different nutritional conditions.

RESULTS

To establish a framework for quantitative metabolic research in duckweeds we derived a central carbon metabolism network model of Lemna gibba based on its draft genome. Lemna gibba fronds were grown with nitrate or glutamine as nitrogen source. The two conditions were compared by quantification of growth kinetics, metabolite levels, transcript abundance, as well as by 13C-metabolic flux analysis. While growing with glutamine, the fronds grew 1.4 times faster and accumulated more protein and less cell wall components compared to plants grown on nitrate. Characterization of photomixotrophic growth by 13C-metabolic flux analysis showed that, under both metabolic growth conditions, the Calvin-Benson-Bassham cycle and the oxidative pentose-phosphate pathway are highly active, creating a futile cycle with net ATP consumption. Depending on the nitrogen source, substantial reorganization of fluxes around the tricarboxylic acid cycle took place, leading to differential formation of the biosynthetic precursors of the Asp and Gln families of proteinogenic amino acids. Despite the substantial reorganization of fluxes around the tricarboxylic acid cycle, flux changes could largely not be associated with changes in transcripts.

CONCLUSIONS

Through integrated analysis of growth rate, biomass composition, metabolite levels, and metabolic flux, we show that Lemna gibba is an excellent system for quantitative metabolic studies in plants. Our study showed that Lemna gibba adjusts to different nitrogen sources by reorganizing central metabolism. The observed disconnect between gene expression regulation and metabolism underscores the importance of metabolic flux analysis as a tool in such studies.

Integrating multiple regulations on enzyme activity: the case of phosphoenolpyruvate carboxykinases

Data on protein post-translational modifications (PTMs) increased exponentially in the last years due to the refinement of mass spectrometry techniques and the development of databases to store and share datasets. Nevertheless, these data per se do not create comprehensive biochemical knowledge. Complementary studies on protein biochemistry are necessary to fully understand the function of these PTMs at the molecular level and beyond, for example, designing rational metabolic engineering strategies to improve crops. Phosphoenolpyruvate carboxykinases (PEPCKs) are critical enzymes for plant metabolism with diverse roles in plant development and growth. Multiple lines of evidence showed the complex regulation of PEPCKs, including PTMs. Herein, we present PEPCKs as an example of the integration of combined mechanisms modulating enzyme activity and metabolic pathways. PEPCK studies strongly advanced after the production of the recombinant enzyme and the establishment of standardized biochemical assays. Finally, we discuss emerging open questions for future research and the challenges in integrating all available data into functional biochemical models.

The ancient CgPEPCK-1, not CgPECK-2, evolved into a multifunctional molecule as an intracellular enzyme and extracellular PRR

Phosphoenolpyruvate carboxykinase (PEPCK) is a well-known lyase involved in gluconeogenesis, while their evolution and function differentiation have not been fully understood. In this study, by constructing a phylogenetic tree to examine PEPCKs throughout the evolution from poriferans to vertebrates, Mollusk was highlighted as the only phylum to exhibit two distinct lineages, Mollusca_PEPCK-1 and Mollusca_PEPCK-2. Further study of two representative members from Crassostrea gigas (CgPEPCK-1 and CgPEPCK-2) showed that they both shared conserved sequences and structural characteristics of the catalytic enzyme, while CgPEPCK-2 displayed a higher expression level than CgPEPCK-1 in all tested tissues, and CgPEPCK-1 was specifically implicated in the immune defense against LPS stimulation and Vibrio splendidus infection. Functional analysis revealed that CgPEPCK-2 had stronger enzymatic activity than CgPEPCK-1, while CgPEPCK-1 exhibited stronger binding activity with various PAMPs, and only the protein of CgPEPCK-1 increased significantly in hemolymph during immune stimulation. All results supported that distinct sequence and function differentiations of the PEPCK gene family should have occurred since Mollusk. The more advanced evolutionary branch Mollusca_PEPCK-2 should preserve its essential function as a catalytic enzyme to be more specialized and efficient, while the ancient branch Mollusca_PEPCK-1 probably contained some members, such as CgPEPCK-1, that should be integrated into the immune system as an extracellular immune recognition receptor.

Two phosphoenolpyruvate carboxykinases with differing biochemical properties in Chlamydomonas reinhardtii

Phosphoenolpyruvate carboxykinase (PEPCK) catalyses the reversible reaction of decarboxylation and phosphorylation of oxaloacetate (OAA) to generate phosphoenolpyruvate (PEP) and CO₂ playing mainly a gluconeogenic role in green algae. We found two PEPCK isoforms in Chlamydomonas reinhardtii and we cloned, purified and characterised both enzymes. ChlrePEPCK1 is more active as decarboxylase than ChlrePEPCK2. ChlrePEPCK1 is hexameric and its activity is affected by citrate, phenylalanine and malate, while ChlrePEPCK2 is monomeric and it is regulated by citrate, phenylalanine and glutamine. We postulate that the two PEPCK isoforms found originate from alternative splicing of the gene or regulated proteolysis of the enzyme. The presence of these two isoforms would be part of a mechanism to finely regulate the biological activity of PEPCKs.

Molecular and Physiological Responses of Citrus sinensis Leaves to Long-Term Low pH Revealed by RNA-Seq Integrated with Targeted Metabolomics

Low pH-induced alterations in gene expression profiles and organic acids (OA) and free amino acid (FAA) abundances were investigated in sweet orange [Citrus sinensis (L.) Osbeck cv. Xuegan] leaves. We identified 503 downregulated and 349 upregulated genes in low pH-treated leaves. Further analysis indicated that low pH impaired light reaction and carbon fixation in photosynthetic organisms, thereby lowering photosynthesis in leaves. Low pH reduced carbon and carbohydrate metabolisms, OA biosynthesis and ATP production in leaves. Low pH downregulated the biosynthesis of nitrogen compounds, proteins, and FAAs in leaves, which might be conducive to maintaining energy homeostasis during ATP deprivation. Low pH-treated leaves displayed some adaptive responses to phosphate starvation, including phosphate recycling, lipid remodeling, and phosphate transport, thus enhancing leaf acid-tolerance. Low pH upregulated the expression of some reactive oxygen species (ROS) and aldehyde detoxifying enzyme (peroxidase and superoxidase) genes and the concentrations of some antioxidants (L-tryptophan, L-proline, nicotinic acid, pantothenic acid, and pyroglutamic acid), but it impaired the pentose phosphate pathway and V_E and secondary metabolite biosynthesis and downregulated the expression of some ROS and aldehyde detoxifying enzyme (ascorbate peroxidase, aldo-keto reductase, and 2-alkenal reductase) genes and the concentrations of some antioxidants (pyridoxine and γ-aminobutyric acid), thus disturbing the balance between production and detoxification of ROS and aldehydes and causing oxidative damage to leaves.

Overexpression of ZmPCK2, a phosphoenolpyruvate carboxykinase gene from maize confers enhanced tolerance to water deficit stress in rice

Water deficit is one of the major abiotic stresses that limit plant growth and global crop yields. Phosphoenolpyruvate carboxykinase (PCK) plays important roles in regulating plant growth and development, but its role in water-deficit stress remains elusive. In this study, we found that overexpression of ZmPCK2 significantly enhanced the water-deficit tolerance of transgenic rice. The expression level of ZmPCK2 was strongly induced by PEG and ABA treatments. Overexpression of ZmPCK2 in rice increased stomatal closure and water saving by regulating malate metabolism under water-deficit conditions. Moreover, the expression of ZmPCK2 in rice up-regulated ABA biosynthesis and responsive genes under water-deficit stress, and ZmPCK2 transgenic rice showed hypersensitive to exogenous ABA at germination stage, suggesting that ZmPCK2 may be involved in ABA signalling pathway. Under water-deficit stress, the ZmPCK2 transgenic rice showed higher antioxidant enzyme activities and lower accumulation of reactive oxygen species (ROS) compared with non-transgenic (NT) plants, resulting in less oxidative damage. Taken together, we suggest that ZmPCK2 plays multiple roles in response to water-deficit stress by enhancing ABA signalling pathway, regulating malate metabolism, promoting stomatal closure and further activating the ROS-scavenging system.

Integrated Metabolomics and Transcriptomic Analysis of Hepatopancreas in Different Living Status Macrobrachium nipponense in Response to Hypoxia

As the basic element of aerobic animal life, oxygen participates in most physiological activities of animals. Hypoxia stress is often the subject of aquatic animal research. Macrobrachium nipponense, an economically important aquatic animal in southern China, has been affected by hypoxia for many years and this has resulted in a large amount of economic loss due to its sensitivity to hypoxia; Metabolism and transcriptome data were combined in the analysis of the hepatopancreas of M. nipponense in different physiological states under hypoxia; A total of 108, 86, and 48 differentially expressed metabolites (DEMs) were found in three different comparisons (survived, moribund, and dead shrimps), respectively. Thirty-two common DEMs were found by comparing the different physiological states of M. nipponense with the control group in response to hypoxia. Twelve hypoxia-related genes were identified by screening and analyzing common DEMs. GTP phosphoenolpyruvate carboxykinase (PEPCK) was the only differentially expressed gene that ranked highly in transcriptome analysis combined with metabolome analysis. PEPCK ranked highly both in transcriptome analysis and in combination with metabolism analysis; therefore, it was considered to have an important role in hypoxic response. This manuscript fills the one-sidedness of the gap in hypoxia transcriptome analysis and reversely deduces several new genes related to hypoxia from metabolites. This study contributes to the clarification of the molecular process associated with M. nipponense under hypoxic stress.

The effect of NH4+ on phosphoenolpyruvate carboxykinase gene expression, metabolic flux and citrate content of citrus juice sacs

Citrate is one of the most important metabolites determining the flavour of citrus fruit. It has been reported that nitrogen supply may have an impact on acid level of fruit. Here, the relationship between nitrogen metabolism and citrate catabolism was studied in pumelo juice sacs. Differences in metabolites, gene expression and flux distributions were analyzed in juice sacs incubated in medium with and without NH₄⁺. Compared with those incubated with NH₄⁺, juice sacs under nitrogen deficiency exhibited enhanced flux through phosphoenolpyruvate carboxykinase (PEPCK) and accelerated consumption of citrate, while the other two TCA cycle efflux points, through malic enzyme (ME) and glutamate dehydrogenase (GDH), were both repressed. Consistent with the estimated fluxes, the expression of PEPCK1 was upregulated under nitrogen deficiency, while that of GDH1, GDH2, NAD-ME1 and NADP-ME2 were all repressed. Thus, we propose that PEPCK1 contributes to citrate degradation under nitrogen limitation.

Understanding Maize Response to Nitrogen Limitation in Different Light Conditions for the Improvement of Photosynthesis

The photosynthetic capacity of leaves is determined by their content of nitrogen (N). Nitrogen involved in photosynthesis is divided between soluble proteins and thylakoid membrane proteins. In C4 plants, the photosynthetic apparatus is partitioned between two cell types: mesophyll cells and bundle sheath. The enzymes involved in the C4 carbon cycle and assimilation of nitrogen are localized in a cell-specific manner. Although intracellular distribution of enzymes of N and carbon assimilation is variable, little is known about the physiological consequences of this distribution caused by light changes. Light intensity and nitrogen concentration influence content of nitrates in leaves and can induce activity of the main enzymes involved in N metabolism, and changes that reduce the photosynthesis rate also reduce photosynthetic N use efficiency. In this review, we wish to highlight and discuss how/whether light intensity can improve photosynthesis in maize during nitrogen limitation. We described the general regulation of changes in the main photosynthetic and nitrogen metabolism enzymes, their quantity and localization, thylakoid protein abundance, intracellular transport of organic acids as well as specific features connected with C4 photosynthesis, and addressed the major open questions related to N metabolism and effects of light on photosynthesis in C4 plants.

Regional Heritability Mapping of Quantitative Trait Loci Controlling Traits Related to Growth and Productivity in Popcorn (Zea mays L.)

The method of regional heritability mapping (RHM) has become an important tool in the identification of quantitative trait loci (QTLs) controlling traits of interest in plants. Here, RHM was first applied in a breeding population of popcorn, to identify the QTLs and candidate genes involved in grain yield, plant height, kernel popping expansion, and first ear height, as well as determining the heritability of each significant genomic region. The study population consisted of 98 S1 families derived from the 9th recurrent selection cycle (C-9) of the open-pollinated variety UENF-14, which were genetically evaluated in two environments (ENV1 and ENV2). Seventeen and five genomic regions were mapped by the RHM method in ENV1 and ENV2, respectively. Subsequent genome-wide analysis based on the reference genome B73 revealed associations with forty-six candidate genes within these genomic regions, some of them are considered to be biologically important due to the proteins that they encode. The results obtained by the RHM method have the potential to contribute to knowledge on the genetic architecture of the growth and yield traits of popcorn, which might be used for marker-assisted selection in breeding programs.

Transcriptome analysis of hepatopancreas from different living states oriental river prawn (Macrobrachium nipponense) in response to hypoxia

As an important economical freshwater prawn, Macrobrachium nipponense has difficulty with adapting to hypoxia. In this study, comparative transcriptome analysis was used for the first time to explore the differences between different living states of Macrobrachium nipponense under hypoxia. A total of 94.22 Gb clean reads were obtained and assembled into 54,688 unigenes. A total of 224, 266, and 750 differently expressed genes were found in the comparison of the control and death groups, the control and moribund groups, and the control and survived groups, respectively. Three signal pathways closely related to hypoxia were found by enriching of the signal pathways in three comparison groups. In addition, much attention was focused on the differential genes in these pathways. Oxidative stress related genes, such as 70 kDa heat shock protein, phosphoenolpyruvate carboxykinase and cyclooxygenase were differentially expressed in different comparisons. After comparing with previous studies, cyclooxygenase was found to be an important hypoxia-related gene that is fully involved in the hypoxic response. Interestingly, two new genes with no Nr annotation were found in this manuscript. This manuscript will enrich our understanding of oxidative stress response to hypoxia and provide a theoretical basis for the subsequent solution of apoptosis caused by hypoxia.

Gluconeogenesis in Plants: A Key Interface between Organic Acid/Amino Acid/Lipid and Sugar Metabolism

Gluconeogenesis is a key interface between organic acid/amino acid/lipid and sugar metabolism. The aims of this article are four-fold. First, to provide a concise overview of plant gluconeogenesis. Second, to emphasise the widespread occurrence of gluconeogenesis and its utilisation in diverse processes. Third, to stress the importance of the vacuolar storage and release of Krebs cycle acids/nitrogenous compounds, and of the role of gluconeogenesis and malic enzyme in this process. Fourth, to outline the contribution of fine control of enzyme activity to the coordinate-regulation of gluconeogenesis and malate metabolism, and the importance of cytosolic pH in this.

Sucrose Metabolism and Transport in Grapevines, with Emphasis on Berries and Leaves, and Insights Gained from a Cross-Species Comparison

In grapevines, as in other plants, sucrose and its constituents glucose and fructose are fundamentally important and carry out a multitude of roles. The aims of this review are three-fold. First, to provide a summary of the metabolism and transport of sucrose in grapevines, together with new insights and interpretations. Second, to stress the importance of considering the compartmentation of metabolism. Third, to outline the key role of acid invertase in osmoregulation associated with sucrose metabolism and transport in plants.

Proteolytic cleavage of Arabidopsis thaliana phosphoenolpyruvate carboxykinase-1 modifies its allosteric regulation

Phosphoenolpyruvate carboxykinase (PEPCK) plays a crucial role in gluconeogenesis. In this work, we analyze the proteolysis of Arabidopsis thaliana PEPCK1 (AthPEPCK1) in germinating seedlings. We found that the amount of AthPEPCK1 protein peaks at 24-48 h post-imbibition. Concomitantly, we observed shorter versions of AthPEPCK1, putatively generated by metacaspase-9 (AthMC9). To study the impact of AthMC9 cleavage on the kinetic and regulatory properties of AthPEPCK1, we produced truncated mutants based on the reported AthMC9 cleavage sites. The Δ19 and Δ101 truncated mutants of AthPEPCK1 showed similar kinetic parameters and the same quaternary structure as the wild type. However, activation by malate and inhibition by glucose 6-phosphate were abolished in the Δ101 mutant. We propose that proteolysis of AthPEPCK1 in germinating seedlings operates as a mechanism to adapt the sensitivity to allosteric regulation during the sink-to-source transition.

Exploiting differences in the energy budget among C4 subtypes to improve crop productivity

C₄ crops of agricultural importance all belong to the NADP-malic enzyme (ME) subtype, and this subtype has been the template for C₄ introductions into C₃ crops, like rice, to improve their productivity. However, the ATP cost for the C₄ cycle in both NADP-ME and NAD-ME subtypes accounts for > 40% of the total ATP requirement for CO₂ assimilation. These high ATP costs, and the associated need for intense cyclic electron transport and low intrinsic quantum yield ΦCO2 , are major constraints in realizing strong improvements of canopy photosynthesis and crop productivity. Based on mathematical modelling, we propose a C₄ ideotype that utilizes low chloroplastic ATP requirements present in the nondomesticated phosphoenolpyruvate carboxykinase (PEP-CK) subtype. The ideotype is a mixed form of NAD(P)-ME and PEP-CK types, requires no cyclic electron transport under low irradiances, and its theoretical ΦCO2 is c. 25% higher than that of a C₄ crop type. Its cell-type-specific ATP and NADPH requirements can be fulfilled by local energy production. The ideotype is projected to have c. 10% yield advantage over NADP-ME-type crops and > 50% advantage over C₃ counterparts. The ideotype provides a unique (theoretical) case where ΦCO2 could be improved, thereby paving a new avenue for improving photosynthesis in both C₃ and C₄ crops.

Transcriptional response of Asarum heterotropoides Fr. Schmidt var. mandshuricum (Maxim.) Kitag. leaves grown under full and partial daylight conditions

BACKGROUND

Asarum heterotropides Fr. Schmidt var. mandshuricum (Maxim.) Kitag. is an important medicinal and industrial plant, which is used in the treatment of various diseases. The main bioactive ingredient is the volatile oil having more than 82 identified components of which methyleugenol, safrole, myristicin, and toluene account for about 70% of the total volume. As a sciophyte plant, the amount of light it absorbs through leaves is an important factor for growth and metabolism.

RESULTS

We grew Asarum plants under full, 50, 28, and 12% sunlight conditions to investigate the effect of different light irradiances on the four major volatile oil components. We employed de novo transcriptome sequencing to understand the transcriptional behavior of Asarum leaves regarding the biosynthetic pathways of the four volatile oil components, photosynthesis and biomass accumulation, and hormone signaling. Our results demonstrated that the increasing light conditions promoted higher percent of the four components. Under full sunlight conditions, cinnamyl alcohol dehydrogenase and cytochrome p450719As were upregulated and led the increased methyleugenol, safrole, and myristicin. The transcriptomic data also showed that Asarum leaves, under full sunlight conditions, adjust their photosynthesis-antenna proteins as a photoprotective response with the help of carotenoids. Plant hormone-signaling related genes were also differentially expressed between full sunlight and low light conditions.

CONCLUSIONS

High light induces accumulation of major bioactive ingredients A. heterotropides volatile oil and this is ascribed to upregulation of key genes such as cinnamyl alcohol dehydrogenase and cytochrome p450719As. The transcriptome data presented here lays the foundation of further understanding of light responses in sciophytes and provides guidance for increasing bioactive molecules in Asarum.

Biochemical characterization of phosphoenolpyruvate carboxykinases from Arabidopsis thaliana

ATP-dependent phosphoenolpyruvate carboxykinases (PEPCKs, EC 4.1.1.49) from C4 and CAM plants have been widely studied due to their crucial role in photosynthetic CO2 fixation. However, our knowledge on the structural, kinetic and regulatory properties of the enzymes from C3 species is still limited. In this work, we report the recombinant production and biochemical characterization of two PEPCKs identified in Arabidopsis thaliana: AthPEPCK1 and AthPEPCK2. We found that both enzymes exhibited high affinity for oxaloacetate and ATP, reinforcing their role as decarboxylases. We employed a high-throughput screening for putative allosteric regulators using differential scanning fluorometry and confirmed their effect on enzyme activity by performing enzyme kinetics. AthPEPCK1 and AthPEPCK2 are allosterically modulated by key intermediates of plant metabolism, namely succinate, fumarate, citrate and α-ketoglutarate. Interestingly, malate activated and glucose 6-phosphate inhibited AthPEPCK1 but had no effect on AthPEPCK2. Overall, our results demonstrate that the enzymes involved in the critical metabolic node constituted by phosphoenolpyruvate are targets of fine allosteric regulation.

Effects of calcium treatment on malate metabolism and γ-aminobutyric acid (GABA) pathway in postharvest apple fruit

Calcium treatment effects on malate metabolism and the GABA pathway in 'Cripps Pink' apple fruit during storage were investigated. Postharvest apple fruit treated with 1% and 4% calcium chloride solutions were stored at 25 ± 1 °C. The 4% calcium treatment suppressed declines in titratable acidity and malate content and increased succinate and oxalate concentrations. Calcium treatment also reduced the respiration rate and decreased ethylene production peak during storage. Moreover, 4% calcium treatment significantly enhanced cyNAD-MDH and PEPC activities and upregulated MdMDH1, MdMDH2, MdPEPC1 and MdPEPC2 expression while inhibiting cyNADP-ME and PEPCK activities and downregulating MdME1, MdME4 and MdPEPCK2 expression. Surprisingly, calcium treatment changed the content of some free amino acids (GABA, proline, alanine, aspartic acid and glutamate), two of which (glutamate and GABA) are primary metabolites of the GABA pathway. Furthermore, calcium application enhanced GABA pathway activity by increasing MdGAD1, MdGAD2, MdGABA-T1/2 and MdSSADH transcript levels.

Regulation and Evolution of C4 Photosynthesis

C₄ photosynthesis evolved multiple times independently from ancestral C₃ photosynthesis in a broad range of flowering land plant families and in both monocots and dicots. The evolution of C₄ photosynthesis entails the recruitment of enzyme activities that are not involved in photosynthetic carbon fixation in C₃ plants to photosynthesis. This requires a different regulation of gene expression as well as a different regulation of enzyme activities in comparison to the C₃ context. Further, C₄ photosynthesis relies on a distinct leaf anatomy that differs from that of C₃, requiring a differential regulation of leaf development in C₄. We summarize recent progress in the understanding of C₄-specific features in evolution and metabolic regulation in the context of C₄ photosynthesis.

Transcriptional and Biochemical Characterization of Cytosolic Pyruvate Kinases in Arabidopsis thaliana

Glycolysis is a central catabolic pathway in every living organism with an essential role in carbohydrate breakdown and ATP synthesis, thereby providing pyruvate to the tricarboxylic acid cycle (TCA cycle). The cytosolic pyruvate kinase (cPK) represents a key glycolytic enzyme by catalyzing phosphate transfer from phosphoenolpyruvate (PEP) to ADP for the synthesis of ATP. Besides its important functions in cellular energy homeostasis, the activity of cytosolic pyruvate kinase underlies tight regulation, for instance by allosteric effectors, that impact stability of its quaternary structure. We determined five cytosol-localized pyruvate kinases, out of the fourteen putative pyruvate kinase genes encoded by the Arabidopsis thaliana genome, by investigation of phylogeny and localization of yellow fluorescent protein (YFP) fusion proteins. Analysis of promoter β-glucuronidase (GUS) reporter lines revealed an isoform-specific expression pattern for the five enzymes, subject to plant tissue and developmental stage. Investigation of the heterologously expressed and purified cytosolic pyruvate kinases revealed that these enzymes are differentially regulated by metabolites, such as citrate, fructose-1,6-bisphosphate (FBP) and ATP. In addition, measured in vitro enzyme activities suggest that pyruvate kinase subunit complexes consisting of cPK2/3 and cPK4/5 isoforms, respectively, bear regulatory properties. In summary, our study indicates that the five identified cytosolic pyruvate kinase isoforms adjust the carbohydrate flux through the glycolytic pathway in Arabidopsis thaliana, by distinct regulatory qualities, such as individual expression pattern as well as dissimilar responsiveness to allosteric effectors and enzyme subgroup association.

Stone Fruits: Growth and Nitrogen and Organic Acid Metabolism in the Fruits and Seeds-A Review

Stone fruits of the Rosaceae family consist of several distinct parts, and these include the flesh, woody endocarp, and seed. To understand the metabolism of these fruits, it is necessary to have knowledge of both their structure and growth characteristics. The nitrogen metabolism of the different tissues of stone fruits is interlinked. For example, there is an import and storage of nitrogenous compounds in the endocarp that are then exported to the seed. Moreover, there are links between the metabolism of nitrogen and that of malic/citric acids. In this article, the structure and growth characteristics, together with the import/export, contents, metabolism, and functions of nitrogenous compounds and organic acids in the different parts of stone fruits and their seeds are reviewed.

Analysis of the Barley Malt Rootlet Proteome

Barley seeds are one of the main ingredients of the malting industry for brewing beer. The barley rootlets that are separated from the kilned seeds at the end of the malting process and used as animal feed are one of the byproducts of this industry. In this study, the proteome of rootlets derived from two stages of the malting process, germination and kilning, from a popular malting barley variety were analyzed. A label-free shotgun proteomics strategy was used to identify more than 800 proteins from the barley rootlets. A high coverage and high confidence Gene Ontology annotations of the barley genome was used to facilitate the functional annotation of the proteins that were identified in the rootlets. An analysis of these proteins using Kellogg Encyclopedia of Genes and Genomes (KEGG) and Plant Reactome databases indicated the enrichment of pathways associated with phytohormones, protein biosynthesis, secondary metabolism, and antioxidants. Increased levels of jasmonic acid and auxin in the rootlets further supported the in silico analysis. As a rich source of proteins and amino acids use of these by-products of the malting industry for animal feed is validated. This study also indicates rootlets as a potential source of naturally occurring phenylpropanoids and antioxidants that can be further exploited in the development of functional foods.

Changes in the microsomal proteome of tomato fruit during ripening

The variations in the membrane proteome of tomato fruit pericarp during ripening have been investigated by mass spectrometry-based label-free proteomics. Mature green (MG30) and red ripe (R45) stages were chosen because they are pivotal in the ripening process: MG30 corresponds to the end of cellular expansion, when fruit growth has stopped and fruit starts ripening, whereas R45 corresponds to the mature fruit. Protein patterns were markedly different: among the 1315 proteins identified with at least two unique peptides, 145 significantly varied in abundance in the process of fruit ripening. The subcellular and biochemical fractionation resulted in GO term enrichment for organelle proteins in our dataset, and allowed the detection of low-abundance proteins that were not detected in previous proteomic studies on tomato fruits. Functional annotation showed that the largest proportion of identified proteins were involved in cell wall metabolism, vesicle-mediated transport, hormone biosynthesis, secondary metabolism, lipid metabolism, protein synthesis and degradation, carbohydrate metabolic processes, signalling and response to stress.

Characterization of a high-growth-rate mutant strain of Pyropia yezoensis using physiology measurement and transcriptome analysis

A mutant strain of Pyropia yezoensis, strain E, was isolated from the free-living conchocelis of a pure strain (NA) treated with ethyl methane sulfonate. The incremental quantities of young strain E blades were higher than those of NA after 14 d of cultivation, indicating that young blades of mutant strain E released more archeospores. The mean length and weight of large E blades were both over three times greater than those of NA after 4 weeks of cultivation. The photosynthetic parameters (Fv/Fm, Y[I], Y[II], and O₂ evolution rate) and pigment contents (including phycoerythrin and phycocyanin) of strain E blades were higher than those of NA (P < 0.05). The cellular respiratory rate of strain E blades was lower than that of NA (P < 0.05). In order to investigate the causes of changes in strain E blades, total RNA in strain E and NA blades were sequenced using the Illumina Hiseq platform. Compared with NA, 1,549 unigenes were selected in strain E including 657 up-regulated and 892 down-regulated genes. According to the physiology measurement and differentially expressed genes analysis, cell respiration in strain E might decrease, whereas anabolic-like photosynthesis and protein biosynthesis might increase compared with NA. This means substance accumulation might be greater than decomposition in strain E. This might explain why strain E blades showed improved growth compared with NA. In addition, several genes related to stress resistance were up-regulated in strain E indicating that strain E might have a higher stress resistance. The sequencing dataset may be conducive to Pyropia yezoensis molecular breeding research.

WRINKLED1 transcription factor orchestrates the regulation of carbon partitioning for C18:1 (oleic acid) accumulation in Siberian apricot kernel

WRINKLED1 (WRI1), an APETALA2 (AP2)-type transcription factor, has been shown to be required for the regulation of carbon partitioning into fatty acid (FA) synthesis in plant seeds. To our knowledge, the regulatory network of WRI1 remains unknown in Prunus sibirica kernel (PSK), a novel woody biodiesel feedstock in China. In this study, based on the transcriptional data from developing oilseeds of multiple plant species, we identified 161 WRI1-coexpressed genes using weighted gene co-expression network analysis (WGCNA). The major portion of WRI1-coexpressed genes was characterized to be involved in carbon partitioning and FA biosynthesis. Additionally, we detected the temporal patterns for oil content and FA compositions in developing PSK from two different germplasms (AS-85 and AS-86). The major differences between the two germplasms are higher contents of oil and C18:1 in AS-85 than in AS-86 at a mature stage. Thus, AS-85 and AS-86 are desirable materials to explore the molecular and metabolic mechanisms of oil accumulation in Siberian apricot. Expression analysis in developing PSK of AS-85 and AS-86 indicated that the expression level of P. sibirica WRI1 (PsWRI1) was closely correlated to accumulative rate of oil. Also, the comparison of expression profiles in developing PSK of AS-85 and AS-86 displayed that the pPK, E1-α, E2, TAL, BC, MCMT, BS, SAD and FAD2 have a high correlation with PsWRI1. Transient expression showed that Pro_SAD- and Pro_BS-driving GUS expression showed no substantial difference between AS-85 and AS-86, while the expression level of Pro_PEPCK-AS-85 driving GUS was significantly higher than that of Pro_PEPCK-AS-86 driving GUS. Additionally, transient co-transformation with PsWRI1 revealed that Pro_SAD, Pro_PEPCK and Pro_BS activity could be specifically up-regulated by PsWRI1. This regulatory mechanism of PsWRI1 may create a steep concentration difference, thereby facilitating carbon flux into C18:1 accumulation in developing PSK. Overall, all our findings imply a versatile mechanism of WRI1 to optimize carbon allocation for oil accumulation, which can provide reference for researching the woody biodiesel plants.

Analysis of the distribution of assimilation products and the characteristics of transcriptomes in rice by submergence during the ripening stage

Background

Research on the submergence stress of rice has concentrated on the quiescence strategy to survive in long-term flooding conditions based on Submergence-1A (SUB1A). In the case of the ripening period, it is important that submergence stress can affect the quality as well as the survival of rice. Therefore, it is essential to understand the changes in the distribution of assimilation products in grain and ripening characteristics in submergence stress conditions. However, such studies have been insufficient at the physiological and molecular biological levels.

Results

We confirmed that the distribution rate of assimilation products in grain was decreased by submergence treatment. These results were caused by an increase in the distribution rate of assimilation products to the stem according to escape strategy. To understand this phenomenon at the molecular level, we analyzed the relative expression levels of genes related to sucrose metabolism, and found that the sucrose phosphate synthase gene (OsSPS), which induces the accumulation of sucrose in tissues, was decreased in the seeds and leaves, but not in the stems. Furthermore, the sucrose transporter gene (OsSUT) related to sucrose transport decreased in the seeds and leaves, but increased in stems. We also analyzed the biological metabolic processes related to starch and sucrose synthesis, carbon fixation, and glycolysis using the KEGG mapper with selected differentially expressed genes (DEGs) in seeds, stems, and leaves caused by submergence treatment. We found that the expression of genes for each step related to starch and D-glucose synthesis was down-regulated in the seeds and leaves but up-regulated in the stem.

Conclusion

The results of this study provide basic data for the development of varieties and corresponding technologies adapted to submergence conditions, through understanding the action network of the elements that change in the submergence condition, as well as information regarding useful DEGs.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-5320-7) contains supplementary material, which is available to authorized users.

Gluconeogenesis and nitrogen metabolism in maize

Two pathways can be used by gluconeogenesis in plants: one employs phosphoenolpyruvate carboxykinase (PEPCK) and the other pyruvate orthophosphate dikinase (PPDK). The occurrence-location of these enzymes was determined in developing kernels of maize. PPDK was much more abundant than PEPCK in extracts of whole kernels. However, their location within the kernel was different. PPDK was particularly abundant in the peripheral endosperm (in which alanine is abundant), whereas PEPCK was localised in the pedicel and basal endosperm transfer cells (where asparagine is metabolised). The abundance of these enzymes was also determined in maize roots where there was a massive increase in abundance of PEPCK and a small increase in abundance of PPDK when they were fed ammonium; PEPCK was located in the pericycle and various cell types associated with the vasculature. On the other hand, there was a large increase in abundance of PPDK in roots subjected to anoxia (which induces an accumulation of alanine), whereas the abundance of PEPCK was decreased. These results show: firstly, that gluconeogenesis can potentially occur in many different tissues of maize. Secondly, within one organ PPDK can be abundant in some tissues and PEPCK in others. Thirdly, the abundance of PPDK and PEPCK is often associated with the metabolism of certain nitrogenous compounds and can be dramatically altered by factors related to nitrogen metabolism. In maize roots and developing kernels PPDK was associated with alanine metabolism. By contrast, the presence of PEPCK in maize roots and kernels was associated with either ammonium or asparagine metabolism. We propose that gluconeogenesis is often a component of a widespread mechanism that is used in coordinating the import/mobilisation of nitrogenous compounds with their utilisation. Further, potentially component of this mechanism may have provided building blocks that were used in the evolution of processes such as C₄ photosynthesis, Crassulacean acid metabolism, stomatal metabolism and the biochemical pH stat.

Genome-Wide Association Studies to Identify Loci and Candidate Genes Controlling Kernel Weight and Length in a Historical United States Wheat Population

Although kernel weight (KW) is a major component of grain yield, its contribution to yield genetic gain during breeding history has been minimal. This highlights an untapped potential for further increases in yield via improving KW. We investigated variation and genetics of KW and kernel length (KL) via genome-wide association studies (GWAS) using a historical and contemporary soft red winter wheat population representing 200 years of selection and breeding history in the United States. The observed changes of KW and KL over time did not show any conclusive trend. The population showed a structure, which was mainly explained by the time and location of germplasm development. Cluster sharing by germplasm from more than one breeding population was suggestive of episodes of germplasm exchange. Using 2 years of field-based phenotyping, we detected 26 quantitative trait loci (QTL) for KW and 27 QTL for KL with -log₁₀(p) > 3.5. The search for candidate genes near the QTL on the wheat genome version IWGSCv1.0 has resulted in over 500 genes. The predicted functions of several of these genes are related to kernel development, photosynthesis, sucrose and starch synthesis, and assimilate remobilization and transport. We also evaluated the effect of allelic polymorphism of genes previously reported for KW and KL by using Kompetitive Allele Specific PCR (KASP) markers. Only TaGW2 showed significant association with KW. Two genes, i.e., TaSus2-2B and TaGS-D1 showed significant association with KL. Further physiological studies are needed to decipher the involvement of these genes in KW and KL development.

Shade compromises the photosynthetic efficiency of NADP-ME less than that of PEP-CK and NAD-ME C4 grasses

The high energy cost and apparently low plasticity of C4 photosynthesis compared with C3 photosynthesis may limit the productivity and distribution of C4 plants in low light (LL) environments. C4 photosynthesis evolved numerous times, but it remains unclear how different biochemical subtypes perform under LL. We grew eight C4 grasses belonging to three biochemical subtypes [NADP-malic enzyme (NADP-ME), NAD-malic enzyme (NAD-ME), and phosphoenolpyruvate carboxykinase (PEP-CK)] under shade (16% sunlight) or control (full sunlight) conditions and measured their photosynthetic characteristics at both low and high light. We show for the first time that LL (during measurement or growth) compromised the CO2-concentrating mechanism (CCM) to a greater extent in NAD-ME than in PEP-CK or NADP-ME C4 grasses by virtue of a greater increase in carbon isotope discrimination (∆P) and bundle sheath CO2 leakiness (ϕ), and a greater reduction in photosynthetic quantum yield (Φmax). These responses were partly explained by changes in the ratios of phosphoenolpyruvate carboxylase (PEPC)/initial Rubisco activity and dark respiration/photosynthesis (Rd/A). Shade induced a greater photosynthetic acclimation in NAD-ME than in NADP-ME and PEP-CK species due to a greater Rubisco deactivation. Shade also reduced plant dry mass to a greater extent in NAD-ME and PEP-CK relative to NADP-ME grasses. In conclusion, LL compromised the co-ordination of the C4 and C3 cycles and, hence, the efficiency of the CCM to a greater extent in NAD-ME than in PEP-CK species, while CCM efficiency was less impacted by LL in NADP-ME species. Consequently, NADP-ME species are more efficient at LL, which could explain their agronomic and ecological dominance relative to other C4 grasses.

A GTP-dependent Phosphoenolpyruvate Carboxykinase from Crassostrea gigas Involved in Immune Recognition

Phosphoenolpyruvate carboxykinase (PEPCK) is well known as a key enzyme involved in the metabolic pathway of gluconeogenesis in organisms, but the information about its involvement in immune response is still very limited. In the present study, a novel PEPCK homolog named CgPEPCK was identified from oyster Crassostrea gigas. The deduced amino acid sequence of CgPEPCK shared 52%-74% similarities with those from other known PEPCKs. There were one conserved guanosine triphosphate (GTP) binding site, one substrate binding site, one metal binding site and one active site in CgPEPCK. The mRNA transcripts of CgPEPCK were constitutively expressed in all the tested tissues including hemolymph, mantle, gill, muscle, gonad and hepatopancreas. CgPEPCK proteins were mainly distributed in adductor muscle, gonad, gill and mantle, and rarely detected in hepatopancreas by using immunohistochemical analysis. After the stimulations with lipopolysaccharide (LPS), peptidoglycan (PGN), Vibrio splendidus and V. anguillarum, CgPEPCK transcripts in hemocytes were significantly up-regulated and peaked at 6 h (LPS, 9.62-fold, p < 0.01), 9 h (PGN, 4.25-fold, p < 0.01), 12 h (V. splendidus, 5.72-fold, p < 0.01), 3 h (V. anguillarum, 2.87-fold, p < 0.01), respectively. The recombinant CgPEPCK protein (rCgPEPCK) exhibited Mn²⁺/Mg²⁺ dependent GTP binding activity, and the activities to bind LPS and PGN, but not β-1,3-glucan (GLU), lipoteichoic acid (LTA), mannan (MAN) nor polyinosinic-polycytidylic (Poly I: C). It could also bind Escherichia coli, Staphylococcus aureus, Micrococcus luteus and significantly inhibit their growth. All these results collectively suggested that CgPEPCK could not only exert GTP binding activity involved in gluconeogenesis, but also mediate the bacteria recognition and clearance in immune response of oysters.

Short-term thermal photosynthetic responses of C4 grasses are independent of the biochemical subtype

C4 photosynthesis evolved independently many times, resulting in multiple biochemical pathways; however, little is known about how these different pathways respond to temperature. We investigated the photosynthetic responses of eight C4 grasses belonging to three biochemical subtypes (NADP-ME, PEP-CK, and NAD-ME) to four leaf temperatures (18, 25, 32, and 40 °C). We also explored whether the biochemical subtype influences the thermal responses of (i) in vitro PEPC (Vpmax) and Rubisco (Vcmax) maximal activities, (ii) initial slope (IS) and CO2-saturated rate (CSR) derived from the A-Ci curves, and (iii) CO2 leakage out of the bundle sheath estimated from carbon isotope discrimination. We focussed on leakiness and the two carboxylases because they determine the coordination of the CO2-concentrating mechanism and are important for parameterizing the semi-mechanistic C4 photosynthesis model. We found that the thermal responses of Vpmax and Vcmax, IS, CSR, and leakiness varied among the C4 species independently of the biochemical subtype. No correlation was observed between Vpmax and IS or between Vcmax and CSR; while the ratios Vpmax/Vcmax and IS/CSR did not correlate with leakiness among the C4 grasses. Determining mesophyll and bundle sheath conductances in diverse C4 grasses is required to further elucidate how C4 photosynthesis responds to temperature.

Phylogenic and phosphorylation regulation difference of phosphoenolpyruvate carboxykinase of C3 and C4 plants

In C4 plants, phosphoenolpyruvate carboxykinase (PEPCK) plays a key role in the C4 cycle. PEPCK is also involved in gluconeogenesis and is conserved in both lower and higher organisms, including in animals and plants. A phylogenic tree constructed from PEPCK sequences from bacteria to higher plants indicates that the C4 Poaceae PEPCKs are conserved and have diverged from the PEPCKs of C3 plants. The maximum enzymatic activities of wild-type and phosphorylation mimic PEPCK proteins indicate that there is a significant difference between C3 and C4 plant PEPCKs. The conserved PEPCK phosphorylation sites are regulated differently in C3 and C4 plants. These results suggest that the functions of PEPCK have been conserved, but that sequences have diverged and regulation of PEPCK is important in C4 plants, but not in herbaceous and, in particular, woody C3 plants.

Geochemically distinct carbon isotope distributions in Allochromatium vinosum DSM 180T grown photoautotrophically and photoheterotrophically

Anoxygenic, photosynthetic bacteria are common at redox boundaries. They are of interest in microbial ecology and geosciences through their role in linking the carbon, sulfur, and iron cycles, yet much remains unknown about how their flexible carbon metabolism-permitting either autotrophic or heterotrophic growth-is recorded in the bulk sedimentary and lipid biomarker records. Here, we investigated patterns of carbon isotope fractionation in a model photosynthetic sulfur-oxidizing bacterium, Allochromatium vinosum DSM180^T . In one treatment, A. vinosum was grown with CO₂ as the sole carbon source, while in a second treatment, it was grown on acetate. Different intracellular isotope patterns were observed for fatty acids, phytol, individual amino acids, intact proteins, and total RNA between the two experiments. Photoautotrophic CO₂ fixation yielded typical isotopic ordering for the lipid biomarkers: δ¹³ C values of phytol > n-alkyl lipids. In contrast, growth on acetate greatly suppressed intracellular isotopic heterogeneity across all molecular classes, except for a marked ¹³ C-depletion in phytol. This caused isotopic "inversion" in the lipids (δ¹³ C values of phytol < n-alkyl lipids). The finding suggests that inverse δ¹³ C patterns of n-alkanes and pristane/phytane in the geologic record may be at least in part a signal for photoheterotrophy. In both experimental scenarios, the relative isotope distributions could be predicted from an isotope flux-balance model, demonstrating that microbial carbon metabolisms can be interrogated by combining compound-specific stable isotope analysis with metabolic modeling. Isotopic differences among molecular classes may be a means of fingerprinting microbial carbon metabolism, both in the modern environment and the geologic record.

Histone Acetylation Modifications Affect Tissue-Dependent Expression of Poplar Homologs of C4 Photosynthetic Enzyme Genes

Histone modifications play important roles in regulating the expression of C₄ photosynthetic genes. Given that all enzymes required for the C₄ photosynthesis pathway are present in C₃ plants, it has been hypothesized that this expression regulatory mechanism has been conserved. However, the relationship between histone modification and the expression of homologs of C₄ photosynthetic enzyme genes has not been well determined in C₃ plants. In the present study, we cloned nine hybrid poplar (Populus simonii × Populus nigra) homologs of maize (Zea mays) C₄ photosynthetic enzyme genes, carbonic anhydrase (CA), pyruvate orthophosphate dikinase (PPDK), phosphoenolpyruvate carboxykinase (PCK), and phosphoenolpyruvate carboxylase (PEPC), and investigated the correlation between the expression levels of these genes and the levels of promoter histone acetylation modifications in four vegetative tissues. We found that poplar homologs of C₄ homologous genes had tissue-dependent expression patterns that were mostly well-correlated with the level of histone acetylation modification (H3K9ac and H4K5ac) determined by chromatin immunoprecipitation assays. Treatment with the histone deacetylase inhibitor trichostatin A further confirmed the role of histone acetylation in the regulation of the nine target genes. Collectively, these results suggest that both H3K9ac and H4K5ac positively regulate the tissue-dependent expression pattern of the PsnCAs, PsnPPDKs, PsnPCKs, and PsnPEPCs genes and that this regulatory mechanism seems to be conserved among the C₃ and C₄ species. Our findings provide new insight that will aid efforts to modify the expression pattern of these homologs of C₄ genes to engineer C₄ plants from C₃ plants.

Transcriptional Profiling and Identification of Heat-Responsive Genes in Perennial Ryegrass by RNA-Sequencing

Perennial ryegrass (Lolium perenne) is one of the most widely used forage and turf grasses in the world due to its desirable agronomic qualities. However, as a cool-season perennial grass species, high temperature is a major factor limiting its performance in warmer and transition regions. In this study, a de novo transcriptome was generated using a cDNA library constructed from perennial ryegrass leaves subjected to short-term heat stress treatment. Then the expression profiling and identification of perennial ryegrass heat response genes by digital gene expression analyses was performed. The goal of this work was to produce expression profiles of high temperature stress responsive genes in perennial ryegrass leaves and further identify the potentially important candidate genes with altered levels of transcript, such as those genes involved in transcriptional regulation, antioxidant responses, plant hormones and signal transduction, and cellular metabolism. The de novo assembly of perennial ryegrass transcriptome in this study obtained more total and annotated unigenes compared to previously published ones. Many DEGs identified were genes that are known to respond to heat stress in plants, including HSFs, HSPs, and antioxidant related genes. In the meanwhile, we also identified four gene candidates mainly involved in C₄ carbon fixation, and one TOR gene. Their exact roles in plant heat stress response need to dissect further. This study would be important by providing the gene resources for improving heat stress tolerance in both perennial ryegrass and other cool-season perennial grass plants.

Phosphorylation of phosphoenolpyruvate carboxykinase (PEPCK) and phosphoenolpyruvate carboxylase (PEPC) in the flesh of fruits

This study determined whether phosphoenolpyruvate carboxykinase (PEPCK) and phosphoenolpyruvate carboxylase (PEPC) are phosphorylated in the flesh of a range of fruits. This was done by incubating fruit flesh with ³²P[P] (where ³²P[P] = ³²PO₄^3-), then PEPCK and PEPC were immunoprecipitated from extracts using specific antisera. The incorporation of ³²P[P] into these enzymes was then determined by autoradiography of SDS-PAGE gels. Both enzymes were subject to phosphorylation in vivo in the flesh of grape, tomato, cherry and plum. PEPCK was also subject to phosphorylation in vivo in developing grape seeds. Proteolytic cleavage of PEPCK showed that it was phosphorylated at a site(s) located on its N-terminal extension. Potentially phosphorylation of these enzymes could contribute to the coordinate regulation of their activities in the flesh of fruits and in developing seeds.

Phosphoenolpyruvate carboxykinase, pyruvate orthophosphate dikinase and isocitrate lyase in both tomato fruits and leaves, and in the flesh of peach and some other fruits

In this study the occurrence of a number of enzymes involved in gluconeogenesis was investigated in both tomato fruits and leaves during their development and senescence and in some other fruits. The enzymes studied were phosphoenolpyruvate carboxykinase (PEPCK), pyruvate orthophosphate dikinase (PPDK) and glyoxysomal isocitrate lyase (ICL). PPDK was detected in the ripe flesh of tomato, and much smaller amounts were detected in the flesh of both peach and pepper, whereas it was not detected (not present or at very low abundance) in the other fruits which were investigated (apricot, aubergine, blackberry, blueberry, cherry, grape, plum, raspberry and red current). By contrast PEPCK was present in the flesh of all the fruits investigated. Very small amounts of ICL were detected in ripe tomato flesh. PEPCK was present in the skin, flesh, locular gel and columella of tomato fruit, and in these its abundance increased greatly during ripening. PPDK showed a similar distribution, however, its abundance did not increase during ripening. PEPCK was not detected in tomato leaves at any stage of their development or senescence. The content of PPDK g(-1) fresh weight (FW) increased in tomato leaves as they matured, however, it declined during their senescence. In tomato leaves the content of ICL g(-1) FW increased until the mid-stage of development, then decreased as the leaf matured, and then increased during the latter stages of senescence. In the flesh of tomato fruits the contents of PPDK and PEPCK g(-1) FW decreased during senescence. The results suggest that in fruits other than tomato the bulk of any gluconeogenic flux proceeds via PEPCK, whereas in tomato both PEPCK and PPDK could potentially be utilised. Further, the results indicate that the conversion of pyruvate/acetyl-CoA to malate by the glyoxylate cycle, for which ICL is necessary, is not a major pathway utilised by gluconeogenesis in fruits under normal conditions of growth. Finally, the results contribute to our understanding of the role of several enzymes in the senescence of both leaves and fruits.

The contribution of stored malate and citrate to the substrate requirements of metabolism of ripening peach (Prunus persica L. Batsch) flesh is negligible. Implications for the occurrence of phosphoenolpyruvate carboxykinase and gluconeogenesis

The first aim of this study was to determine the contribution of stored malate and citrate to the substrate requirements of metabolism in the ripening flesh of the peach (Prunus persica L. Batsch) cultivar Adriatica. In the flesh, stored malate accumulated before ripening could contribute little or nothing to the net substrate requirements of metabolism. This was because there was synthesis and not dissimilation of malate throughout ripening. Stored citrate could potentially contribute a very small amount (about 5.8%) of the substrate required by metabolism when the whole ripening period was considered, and a maximum of about 7.5% over the latter part of ripening. The second aim of this study was to investigate why phosphoenolpyruvate carboxykinase (PEPCK) an enzyme utilised in gluconeogenesis from malate and citrate is present in peach flesh. The occurrence and localisation of enzymes utilised in the metabolism of malate, citrate and amino acids were determined in peach flesh throughout its development. Phosphoenolpyruvate carboxylase (essential for the synthesis of malate and citrate) was present in the same cells and at the same time as PEPCK and NADP-malic enzyme (both utilised in the dissimilation of malate and citrate). A hypothesis is presented to explain the presence of these enzymes and to account for the likely occurrence of gluconeogenesis.