Malate plays a crucial role in starch metabolism, ripening, and soluble solid content of tomato fruit and affects postharvest softening

Do storage reserves contribute to plant phenotypic plasticity?

The widespread colonization of diverse habitats by plants is attributed to their ability to adapt to changing environments through environmental phenotypic plasticity. This flexibility, particularly in carbon turnover, allows plants to adjust their physiology and development. Plants store carbon reserves as a metabolic strategy to overcome adversity, with a variety of isozymes evolving to enhance metabolic plasticity. Among these isoforms, some with entirely new functions have emerged, involved in novel metabolic pathways for carbon storage. Here, we discuss the role of these carbon stores, their impact on plant plasticity, methods by which such metabolic plasticity can be analyzed, and evolutionary aspects that have led to well-characterized as well as less well-known molecular mechanisms underlying carbon storage.

Chlorine Modulates Photosynthetic Efficiency, Chlorophyll Fluorescence in Tomato Leaves, and Carbohydrate Allocation in Developing Fruits

Chlorine (Cl) is an essential nutrient for higher plants, playing a critical role in their growth and development. However, excessive Cl application can be detrimental, leading to its limited use in controlled-environment agriculture. Recently, Cl has been recognized as a beneficial macronutrient, yet studies investigating its impact on plant growth and fruit quality remain scarce. In this study, we determined the optimal Cl concentration in nutrient solutions through a series of cultivation experiments. A comparative analysis of Cl treatments at 1, 2, and 3 mM revealed that 3 mM Cl- significantly enhanced chlorophyll content, biomass accumulation, and yield. Furthermore, we examined the effects of 3 mM Cl- (supplied as 1.5 mM CaCl2 and 3 mM KCl) on leaf photosynthesis, chlorophyll fluorescence, and fruit sugar metabolism. The results demonstrated that Cl- treatments enhanced the activity of Photosystem I (PS I) and Photosystem II (PS II), leading to a 25.53% and 28.37% increase in the net photosynthetic rate, respectively. Additionally, Cl- application resulted in a 12.3% to 16.5% increase in soluble sugar content in mature tomato fruits. During fruit development, Cl- treatments promoted the accumulation of glucose, fructose, and sucrose, thereby enhancing fruit sweetness and overall quality. The observed increase in glucose and fructose levels was attributed to the stimulation of invertase activity. Specifically, acidic invertase (AI) activity increased by 61.6% and 62.6% at the green ripening stage, while neutral invertase (NI) activity was elevated by 56.2% and 32.8% in the CaCl2 and KCl treatments, respectively, at fruit maturity. Furthermore, sucrose synthase (SS-I) activity was significantly upregulated by 1.5- and 1.4-fold at fruit maturity, while sucrose phosphate synthase (SPS) activity increased by 76.4% to 77.8% during the green ripening stage. These findings provide novel insights into the role of Cl- in tomato growth and metabolism, offering potential strategies for optimizing fertilization practices in protected horticulture.

A linker histone acts as a transcription factor to orchestrate malic acid accumulation in apple in response to sorbitol

High carbohydrate availability promotes malic acid accumulation in fleshy fruits, but the underlying mechanism is not known. Here, we show that antisense repression of ALDOSE-6-PHOSPHATE REDUCTASE in apple (Malus domestica) decreases the concentrations of sorbitol and malate and the transcript levels of several genes involved in vacuolar malate transport, including the aluminum-activated malate transporter (ALMT) gene MdALMT9 (Ma1), the P-ATPase gene MdPH5, the MYB transcription factor gene MdMYB73, and the cold-induced basic helix-loop-helix transcription factor gene MdCIbHLH1, in fruit and leaves. We identified a linker histone H1 variant, MdH1.1, which complements the Arabidopsis (Arabidopsis thaliana) H1 deficient mutant and functions as a transcription factor. MdH1.1 activates MdMYB73, MdCIbHLH1, and MdPH5 expression by directly binding to their promoters. MdMYB73, in return, binds to the promoter of MdH1.1 to enhance its transcription. This MdH1.1-MdMYB73 feedback loop responds to sorbitol, regulating Ma1 expression. Antisense suppression of either MdH1.1 or MdMYB73 expression significantly decreases whereas overexpression increases Ma1 expression and malate accumulation. These findings demonstrate that MdH1.1, in addition to being an architectural protein for chromatin structure, operates as a transcription factor orchestrating malic acid accumulation in response to sorbitol, revealing how sugar signaling modulates vacuolar malate transport via a linker histone in plants.

Sustained carbon import supports sugar accumulation and anthocyanin biosynthesis during fruit development and ripening in blueberry (Vaccinium ashei)

Fruit ripening is a highly coordinated process involving molecular and biochemical changes that collectively determine fruit quality. The underlying metabolic programs and their transitions leading to fruit ripening remain largely under-characterized in blueberry (Vaccinium sp.), which exhibits atypical climacteric behavior. In this study, we focused on sugar, acid and anthocyanin metabolism in two rabbiteye blueberry cultivars, Premier and Powderblue, during fruit development and ripening. Concentrations of the three major sugars, sucrose (Suc), glucose (Glc), and fructose (Fru) increased steadily during fruit development leading up to ripening, and increased dramatically by around 2-fold in 'Premier' and 2- to 3-fold in 'Powderblue' during the final stage of fruit ripening. Starch concentration was very low throughout fruit development in both cultivars indicating that it does not serve the role of a major transitory carbon (C) storage form in blueberry fruit. Together, these patterns indicate continued import of C, likely in the form of Suc, throughout blueberry fruit development. Concentrations of the predominant acids, malate and quinate, decreased during ripening, and may contribute to increased shikimate biosynthesis which, in-turn, allows for downstream phenylpropanoid metabolism leading to anthocyanin synthesis. Consistently, anthocyanin concentrations were highest in fully ripened blue fruit. Weighted gene co-expression network analysis (WGCNA) was performed using a 'Powderblue' fruit ripening transcriptome and targeted fruit metabolite concentration data. A 'dark turquoise' module positively correlated with sugars and anthocyanins, and negatively correlated with acids (malate, quinate), was identified. Gene Ontology (GO) enrichment analysis of this module identified transcripts related to sugar, acid, and phenylpropanoid metabolism pathways. Among these, increased transcript abundance of a VACUOLAR INVERTASE during ripening was consistent with sugar storage in the vacuole. In general, transcript abundance of the glycolysis pathway genes was upregulated during ripening. The transcript abundance of PHOSPHOENOLPYRUVATE (PEP) CARBOXYKINASE increased during fruit ripening and was negatively correlated with malate concentration, suggesting increased malate conversion to PEP, which supports anthocyanin production during fruit ripening. This was further supported by the co-upregulation of several anthocyanin biosynthesis-related genes. Together, this study provides insights into important metabolic programs, and their underlying gene expression patterns during fruit development and ripening in blueberry.

Combining transcriptomics and HPLC to uncover variations in quality formation between 'Benihoppe' and 'Fenyu No.1' strawberries

'Benihoppe' and 'Fenyu No.1' are representative varieties of red and pink strawberries in China, possess distinct hue and flavor profiles. This study analyzed the underlying biochemical and molecular differences of two varieties utilizing transcriptomics and high-performance liquid chromatography (HPLC). Ripening 'Benihoppe' fruits accumulated more sucrose and pelargonin-3-glucoside (P3G) with a little cyanidin and higher firmness. Whereas ripening 'Fenyu No.1' fruits contained more fructose, glucose, malic acid and ascorbic acid (AsA), but less P3G and citric acid. Moreover, genotype significantly influenced phenolic compounds contents in strawberries. Transcriptome analysis revealed that pectin degradation (PL, PG, PE), sucrose synthesis (CWINV, SUS, TPS) and citric acid metabolism (α-OGDH, ICDH, GAD, GS, GDH, PEPCK, AST) were weakened in 'Benihoppe' fruit. In contrast, the synthesis of sucrose (CWINH, SPS), citric acid (CS, PEPC), anthocyanin (F3H, F3'H, F3'5'H, DFR, UFGT and ANS), and citric acid transport (V-ATPase) was enhanced. In 'Fenyu No.1' fruit, the degradation of sucrose, citric acid, and pectin was enhanced, along with the synthesis of malic acid (ME) and ascorbic acid (PMM, MDHAR and GaLUR). However, anthocyanins synthesis, glucose metabolism (HK, G6PI, PFK, G6PDH, PGK, PGM, ENO, PK), fructose metabolism (FK), citric acid synthesis and transport, and AsA degradation (AO, APX) were relatively weak. RT-qPCR results corroborated the transcriptome data. In conclusion, this study revealed the distinctions and characteristics of strawberries with different fruit colors regarding texture, flavor and color formation processes. These findings offer valuable insights for regulating metabolic pathways and identifying key candidate genes to improve strawberry quality.

Whole-genome resequencing identifies candidate genes and allelic variation in the MdNADP-ME promoter that regulate fruit malate and fructose contents in apple

Soluble sugar and organic acids are key determinants of fruit organoleptic quality and directly affect the commodity value and economic returns of fruit crops. We performed whole-genome sequencing of the apple varieties Gala and Xiahongrou, along with their F1 hybrids, to construct a high-density bin map. Our quantitative genetic analysis pinpointed 53 quantitative trait loci (QTLs) related to 11 sugar and acid traits. We identified a candidate gene, MdNADP-ME, responsible for malate degradation, in a stable QTL on linkage group 15. Sequence analysis revealed an A/C SNP in the promoter region (MEp-799) that influences binding of the MdMYB2 transcription factor, thereby affecting MdNADP-ME expression. In our study of various apple genotypes, this SNP has been demonstrated to be linked to malate and fructose levels. We also developed a dCAPS marker associated with fruit fructose content. These results substantiate the role of MdNADP-ME in maintaining the equilibrium between sugar and acid contents in apple fruits.

Carbon Dots-Mediated Photodynamic Treatment Reduces Postharvest Senescence and Decay of Grapes by Regulating the Antioxidant System

Grapes are susceptible to mold and decay during postharvest storage, and developing new technologies to extend their storage period has important application value. Photodynamic technology (PDT) in concurrence with carbon dots (CDs) proposes an innovative and eco-friendly preservation strategy. We examined the effects of carbon dots combined with photodynamic treatment on postharvest senescence and antioxidant system of table grape. The compounding of photodynamic technology with a 0.06 g L-1 CDs solution could possibly extend the postharvest storage period of grape berries. Through this strategy, we achieved a decreased rate of fruit rotting and weight loss alongside the delayed deterioration of fruit firmness, soluble solids, and titratable acid. As paired with photodynamic technology, CDs considerably decreased the postharvest storage loss of phenols, flavonoids, and reducing sugars as compared to the control group. Concurrently, it remarkably postponed the build-up of hydrogen peroxide (H2O2), superoxide anion (O2∙-), and malondialdehyde (MDA); elevated the levels of reduced ascorbic acid (AsA) and reduced glutathione (GSH); lowered the levels of dehydroascorbic acid (DHA) and oxidized glutathione (GSSG); raised the ratios of AsA/DHA and GSSH/GSSG; encouraged the activities of superoxide dismutase (SOD) and phenylalanine ammonia-lyase (PAL); and inhibited the activities of polyphenol oxidase (PPO) and lipoxygenase (LOX). Furthermore, it enhanced the iron reduction antioxidant capacity (FRAP) and DPPH radical scavenging capacity of grape berries. CDs combined with photodynamic treatment could efficiently lessen postharvest senescence and decay of grape berry while extending the storage time.

ZmPTOX1, a plastid terminal oxidase, contributes to redox homeostasis during seed development and germination

Maize plastid terminal oxidase1 (ZmPTOX1) plays a pivotal role in seed development by upholding redox balance within seed plastids. This study focuses on characterizing the white kernel mutant 3735 (wk3735) mutant, which yields pale-yellow seeds characterized by heightened protein but reduced carotenoid levels, along with delayed germination compared to wild-type (WT) seeds. We successfully cloned and identified the target gene ZmPTOX1, responsible for encoding maize PTOX-a versatile plastoquinol oxidase and redox sensor located in plastid membranes. While PTOX's established role involves regulating redox states and participating in carotenoid metabolism in Arabidopsis leaves and tomato fruits, our investigation marks the first exploration of its function in storage organs lacking a photosynthetic system. Through our research, we validated the existence of plastid-localized ZmPTOX1, existing as a homomultimer, and established its interaction with ferredoxin-NADP+ oxidoreductase 1 (ZmFNR1), a crucial component of the electron transport chain (ETC). This interaction contributes to the maintenance of redox equilibrium within plastids. Our findings indicate a propensity for excessive accumulation of reactive oxygen species (ROS) in wk3735 seeds. Beyond its known role in carotenoids' antioxidant properties, ZmPTOX1 also impacts ROS homeostasis owing to its oxidizing function. Altogether, our results underscore the critical involvement of ZmPTOX1 in governing seed development and germination by preserving redox balance within the seed plastids.

Harnessing the predicted maize pan-interactome for putative gene function prediction and prioritization of candidate genes for important traits

The recent assembly and annotation of the 26 maize nested association mapping population founder inbreds have enabled large-scale pan-genomic comparative studies. These studies have expanded our understanding of agronomically important traits by integrating pan-transcriptomic data with trait-specific gene candidates from previous association mapping results. In contrast to the availability of pan-transcriptomic data, obtaining reliable protein-protein interaction (PPI) data has remained a challenge due to its high cost and complexity. We generated predicted PPI networks for each of the 26 genomes using the established STRING database. The individual genome-interactomes were then integrated to generate core- and pan-interactomes. We deployed the PPI clustering algorithm ClusterONE to identify numerous PPI clusters that were functionally annotated using gene ontology (GO) functional enrichment, demonstrating a diverse range of enriched GO terms across different clusters. Additional cluster annotations were generated by integrating gene coexpression data and gene description annotations, providing additional useful information. We show that the functionally annotated PPI clusters establish a useful framework for protein function prediction and prioritization of candidate genes of interest. Our study not only provides a comprehensive resource of predicted PPI networks for 26 maize genomes but also offers annotated interactome clusters for predicting protein functions and prioritizing gene candidates. The source code for the Python implementation of the analysis workflow and a standalone web application for accessing the analysis results are available at https://github.com/eporetsky/PanPPI.

Genome-wide variants and optimal allelic combinations for citric acid in tomato

Citric acid (CA) plays a crucial role as a fruit flavor enhancer and serves as a mediator in multiple metabolic pathways in tomato fruit development. Understanding factors influencing CA metabolism is essential for enhancing fruit flavor and CA-mediated biological processes. The accumulation of CA, however, is influenced by a complex interplay of genetic and environmental factors, leading to challenges in accurately predicting and regulating its levels. In this study, we conducted a genome-wide association study (GWAS) on CA, employing six landmark models based on genome-wide variations including structural variants, insertions and deletions, and single nucleotide polymorphisms. The identification of 11 high-confidence candidate genes was further facilitated by leveraging linkage disequilibrium and causal variants associated with CA. The transcriptome data from candidate genes were examined, revealing higher correlations between the expression of certain candidate genes and changes in CA metabolism. Three CA-associated genes exerted a positive regulatory effect on CA accumulation, while the remaining genes exhibited negative impacts based on gene cluster and correlation analyses. The CA content of tomatoes is primarily influenced by improvement sweeps with minimal influence from domestication sweeps in the long-term breeding history, as evidenced by population differentiation and variants distribution. The presence of various causal variants within candidate genes is implicated in the heterogeneity of CA content observed among the tomato accessions. This observation suggests a potential correlation between the number of alternative alleles and CA content. This study offers significant function-based markers that can be utilized in marker-assisted breeding, thereby enhancing their value and applicability.

Identification of the succinate-CoA ligase protein gene family reveals that TaSUCL1-1 positively regulate cadmium resistance in wheat

The Succinate-CoA ligase (SUCL1) gene family is involved in energy metabolism, phytohormone signaling, and plant growth, development, and tolerance to stress. This is the first study to analyze the SUCL1 gene family in wheat (Triticum aestivum). 17 TaSUCL1 genes were identified in the complete genome sequence and classified into five subfamilies based on related genes found in three other species. The 17 TaSUCL1 genes were unevenly distributed across 11 chromosomes, and the collinearity of these genes was further investigated. Through using real-time qPCR (RT-qPCR) analysis, we identified the expression patterns of the TaSUCL1 genes under various tissues and different heavy metal stress conditions. The functions of selected TaSUCL1-1 gene were investigated by RNA interference (RNAi). This study provided a comprehensive analysis of the TaSUCL1 gene family. Within the TaSUCL1 genes, the exon-intron structure and motif composition exhibited significant similarity among members of the same evolutionary branch. Homology analysis and phylogenetic comparison of the SUCL1 genes in different plants offered valuable insights for studying the evolutionary characteristics of the SUCL1 genes. The expression levels of the TaSUCL1 genes in different tissues and under various metal stress conditions reveal its important role in plant growth and development. Gene function analysis demonstrated that TaSUCL1-1 silenced wheat plants exhibited a decrease in the total cadmium (Cd) concentrations and gene expression levels compared to the wild type (WT). Additionally, TaSUCL1-1 belonging to class c physically interacts with the β-amylase protein TaBMY1 as verified by yeast two-hybridization. This research provides a useful resource for further study of the function and molecular genetic mechanism of the SUCL1 gene family members.

Metabolomics to understand metabolic regulation underpinning fruit ripening, development, and quality

Classically fruit ripening and development was studied using genetic approaches, with understanding of metabolic changes that occurred in concert largely focused on a handful of metabolites including sugars, organic acids, cell wall components, and phytohormones. The advent and widespread application of metabolomics has, however, led to far greater understanding of metabolic components that play a crucial role not only in this process but also in influencing the organoleptic and nutritive properties of the fruits. Here we review how the study of natural variation, mutants, transgenics, and gene-edited fruits has led to a considerable increase in our understanding of these aspects. We focus on fleshy fruits such as tomato but also review berries, receptacle fruits, and stone-bearing fruits. Finally, we offer a perspective as to how comparative analyses and machine learning will likely further improve our comprehension of the functional importance of various metabolites in the future.

Introgression of a dominant phototropin1 mutant enhances carotenoids and boosts flavour-related volatiles in genome-edited tomato RIN mutants

The tomato (Solanum lycopersicum) ripening inhibitor (rin) mutation is known to completely repress fruit ripening. The heterozygous (RIN/rin) fruits have extended shelf life, ripen normally, but have inferior taste/flavour. To address this, we used genome editing to generate newer alleles of RIN (rinCR ) by targeting the K-domain. Unlike previously reported CRISPR alleles, the rinCR alleles displayed delayed onset of ripening, suggesting that the mutated K-domain represses the onset of ripening. The rinCR fruits had extended shelf life and accumulated carotenoids at an intermediate level between rin and progenitor line. Besides, the metabolites and hormonal levels in rinCR fruits were more akin to rin. To overcome the negative attributes of rin, we crossed the rinCR alleles with Nps1, a dominant-negative phototropin1 mutant, which enhances carotenoid levels in tomato fruits. The resulting Nps1/rinCR hybrids had extended shelf life and 4.4-7.1-fold higher carotenoid levels than the wild-type parent. The metabolome of Nps1/rinCR fruits revealed higher sucrose, malate, and volatiles associated with tomato taste and flavour. Notably, the boosted volatiles in Nps1/rinCR were only observed in fruits bearing the homozygous Nps1 mutation. The Nps1 introgression into tomato provides a promising strategy for developing cultivars with extended shelf life, improved taste, and flavour.

Coordinated Transcriptome and Metabolome Analyses of a Barley hvhggt Mutant Reveal a Critical Role of Tocotrienols in Endosperm Starch Accumulation

Tocotrienols and tocopherols (vitamin E) are potent antioxidants that are synthesized in green plants. Unlike ubiquitous tocopherols, tocotrienols predominantly accumulate in the endosperm of monocot grains, catalyzed by homogentiate geranylgeranyl transferase (HGGT). Previously, we generated a tocotrienol-deficient hvhggt mutant with shrunken barley grains. However, the relationship between tocotrienols and grain development remains unclear. Here, we found that the hvhggt lines displayed hollow endosperms with defective transfer cells and reduced aleurone layers. The carbohydrate and starch contents of the hvhggt endosperm decreased by approximately 20 and 23%, respectively. Weighted gene coexpression network analyses identified a critical gene module containing HvHGGT, which was strongly associated with the hvhggt mutation and enriched with gene functions in starch and sucrose metabolism. Metabolome measurements revealed an elevated soluble sugar content in the hvhggt endosperm, which was significantly associated with the identified gene modules. The hvhggt endosperm had significantly higher NAD(H) and NADP(H) contents and lower levels of ADPGlc (regulated by redox balance) than the wild-type, consistent with the absence of tocotrienols. Interestingly, exogenous α-tocotrienol spraying on developing hvhggt spikes partially rescued starch accumulation and endosperm defects. Our study supports a potential novel function of tocotrienols in grain starch accumulation and endosperm development in monocot crops.

Optimization of apple fruit flavor by MdVHP1-2 via modulation of soluble sugar and organic acid accumulation

For fleshy fruits, the content and ratio of organic acids and soluble sugars are key factors for their flavor. Therefore, a better understanding of soluble sugar and organic acid accumulation in vacuoles is essential to the improvement of fruit quality. Vacuolar-type inorganic pyrophosphatase (V-PPase) has been found in various plants with crucial functions based on the hydrolysis of PPi. However, the effects of V-PPase on the soluble sugar and organic acid accumulation in apple fruit remain unclear. In this study, MdVHP1-2, a V-PPase protein in the vacuolar membrane, was identified. The results showed a positive correlation between the expression of MdVHP1-2 and the sugar/acid ratio during ripening of apple fruits. A series of transgenic analyses showed that overexpression of MdVHP1-2 significantly elevated the contents of soluble sugars and organic acids as well as the sugar/acid ratio in apple fruits and calli. Additionally, transient interference induced by MdVHP1-2 expression inhibited the accumulation of soluble sugars and organic acids in apple fruits. In summary, this study provides insight into the mechanisms by which MdVHP1-2 modulates fruit flavor through mediation of soluble sugar and organic acid accumulation, thereby facilitating improvement of the overall quality of apple and other fruits.

Dynamic shifts in primary metabolism across fruit development stages in Capsicum chinense (cv. Habanero)

The development of fleshy fruits involves changes in size and mass, followed by cell differentiation, which is associated with anatomical and histological changes. Parallel to these changes, metabolic alterations lead to the production of osmolytes and energy that modify cell turgor pressure, thereby promoting cell expansion and fruit growth. Detailed information is known about these processes in climacteric fruits (e.g. tomato); however, the regulation of metabolism and its association with anatomical changes in non-climacteric fruit development are poorly understood. In this study, we used detailed anatomical and histological analyses to define three developmental phases of chili pepper (Capsicum chinense cv. Habanero): cell division, cell expansion, and ripening. We showed that each was marked by distinct metabolic profiles, underpinning the switches in energy metabolism to support cellular processes. Interestingly, mitochondrial activity was high in the early stages of development and declined over time, with a modest increase in O2 consumption by pericarp tissues at the beginning of the ripening stage. This respiratory-like burst was associated with the degradation of starch and malate, which are the sources of energy and carbon required for other processes associated with fruit maturation.

Interactions with microbial consortia have variable effects in organic carbon and production of exometabolites among genotypes of Populus trichocarpa

Poplar is a short-rotation woody crop frequently studied for its significance as a sustainable bioenergy source. The successful establishment of a poplar plantation partially depends on its rhizosphere-a dynamic zone governed by complex interactions between plant roots and a plethora of commensal, mutualistic, symbiotic, or pathogenic microbes that shape plant fitness. In an exploratory endeavor, we investigated the effects of a consortium consisting of ectomycorrhizal fungi and a beneficial Pseudomonas sp. strain GM41 on plant growth (including height, stem girth, leaf, and root growth) and as well as growth rate over time, across four Populus trichocarpa genotypes. Additionally, we compared the level of total organic carbon and plant exometabolite profiles across different poplar genotypes in the presence of the microbial consortium. These data revealed no significant difference in plant growth parameters between the treatments and the control across four different poplar genotypes at 7 weeks post-inoculation. However, total organic carbon and exometabolite profiles were significantly different between the genotypes and the treatments. These findings suggest that this microbial consortium has the potential to trigger early signaling responses in poplar, influencing its metabolism in ways crucial for later developmental processes and stress tolerance.

Starch deficiency in tomato causes transcriptional reprogramming that modulates fruit development, metabolism, and stress responses

Tomato (Solanum lycopersicum) fruit store carbon as starch during early development and mobilize it at the onset of ripening. Starch accumulation has been suggested to buffer fluctuations in carbon supply to the fruit under abiotic stress, and contribute to sugar levels in ripe fruit. However, the role of starch accumulation and metabolism during fruit development is still unclear. Here we show that the tomato mutant adpressa (adp) harbors a mutation in a gene encoding the small subunit of ADP-glucose pyrophosphorylase that abolishes starch synthesis. The disruption of starch biosynthesis causes major transcriptional and metabolic remodeling in adp fruit but only minor effects on fruit size and ripening. Changes in gene expression and metabolite profiles indicate that the lack of carbon flow into starch increases levels of soluble sugars during fruit growth, triggers a readjustment of central carbohydrate and lipid metabolism, and activates growth and stress protection pathways. Accordingly, adp fruits are remarkably resistant to blossom-end rot, a common physiological disorder induced by environmental stress. Our results provide insights into the effects of perturbations of carbohydrate metabolism on tomato fruit development, with potential implications for the enhancement of protective mechanisms against abiotic stress in fleshy fruit.

How metabolism and development are intertwined in space and time

Developmental transitions, occurring throughout the life cycle of plants, require precise regulation of metabolic processes to generate the energy and resources necessary for the committed growth processes. In parallel, the establishment of new cells, tissues, and even organs, alongside their differentiation provoke profound changes in metabolism. It is increasingly being recognized that there is a certain degree of feedback regulation between the components and products of metabolic pathways and developmental regulators. The generation of large-scale metabolomics datasets during developmental transitions, in combination with molecular genetic approaches has helped to further our knowledge on the functional importance of metabolic regulation of development. In this perspective article, we provide insights into studies that elucidate interactions between metabolism and development at the temporal and spatial scales. We additionally discuss how this influences cell growth-related processes. We also highlight how metabolic intermediates function as signaling molecules to direct plant development in response to changing internal and external conditions.

Multi-omics quantitative data of tomato fruit unveils regulation modes of least variable metabolites

BACKGROUND

The composition of ripe fruits depends on various metabolites which content evolves greatly throughout fruit development and may be influenced by the environment. The corresponding metabolism regulations have been widely described in tomato during fruit growth and ripening. However, the regulation of other metabolites that do not show large changes in content have scarcely been studied.

RESULTS

We analysed the metabolites of tomato fruits collected on different trusses during fruit development, using complementary analytical strategies. We identified the 22 least variable metabolites, based on their coefficients of variation. We first verified that they had a limited functional link with the least variable proteins and transcripts. We then posited that metabolite contents could be stabilized through complex regulations and combined their data with the quantitative proteome or transcriptome data, using sparse partial-least-square analyses. This showed shared regulations between several metabolites, which interestingly remained linked to early fruit development. We also examined regulations in specific metabolites using correlations with individual proteins and transcripts, which revealed that a stable metabolite does not always correlate with proteins and transcripts of its known related pathways.

CONCLUSIONS

The regulation of the least variable metabolites was then interpreted regarding their roles as hubs in metabolic pathways or as signalling molecules.

NADP-Dependent Malic Enzyme Genes in Sweet Pepper Fruits: Involvement in Ripening and Modulation by Nitric Oxide (NO)

NADPH is an indispensable cofactor in a wide range of physiological processes that is generated by a family of NADPH dehydrogenases, of which the NADP-dependent malic enzyme (NADP-ME) is a member. Pepper (Capsicum annuum L.) fruit is a horticultural product consumed worldwide that has great nutritional and economic relevance. Besides the phenotypical changes that pepper fruit undergoes during ripening, there are many associated modifications at transcriptomic, proteome, biochemical and metabolic levels. Nitric oxide (NO) is a recognized signal molecule with regulatory functions in diverse plant processes. To our knowledge, there is very scarce information about the number of genes encoding for NADP-ME in pepper plants and their expression during the ripening of sweet pepper fruit. Using a data mining approach to evaluate the pepper plant genome and fruit transcriptome (RNA-seq), five NADP-ME genes were identified, and four of them, namely CaNADP-ME2 to CaNADP-ME5, were expressed in fruit. The time course expression analysis of these genes during different fruit ripening stages, including green immature (G), breaking point (BP) and red ripe (R), showed that they were differentially modulated. Thus, while CaNADP-ME3 and CaNADP-ME5 were upregulated, CaNADP-ME2 and CaNADP-ME4 were downregulated. Exogenous NO treatment of fruit triggered the downregulation of CaNADP-ME4. We obtained a 50-75% ammonium-sulfate-enriched protein fraction containing CaNADP-ME enzyme activity, and this was assayed via non-denaturing polyacrylamide gel electrophoresis (PAGE). The results allow us to identify four isozymes designated from CaNADP-ME I to CaNADP-ME IV. Taken together, the data provide new pieces of information on the CaNADP-ME system with the identification of five CaNADP-ME genes and how the four genes expressed in pepper fruits are modulated during ripening and exogenous NO gas treatment.

Cell-type-specific metabolism in plants

Every plant organ contains tens of different cell types, each with a specialized function. These functions are intrinsically associated with specific metabolic flux distributions that permit the synthesis of the ATP, reducing equivalents and biosynthetic precursors demanded by the cell. Investigating such cell-type-specific metabolism is complicated by the mosaic of different cells within each tissue combined with the relative scarcity of certain types. However, techniques for the isolation of specific cells, their analysis in situ by microscopy, or modeling of their function in silico have permitted insight into cell-type-specific metabolism. In this review we present some of the methods used in the analysis of cell-type-specific metabolism before describing what we know about metabolism in several cell types that have been studied in depth; (i) leaf source and sink cells; (ii) glandular trichomes that are capable of rapid synthesis of specialized metabolites; (iii) guard cells that must accumulate large quantities of the osmolytes needed for stomatal opening; (iv) cells of seeds involved in storage of reserves; and (v) the mesophyll and bundle sheath cells of C4 plants that participate in a CO₂ concentrating cycle. Metabolism is discussed in terms of its principal features, connection to cell function and what factors affect the flux distribution. Demand for precursors and energy, availability of substrates and suppression of deleterious processes are identified as key factors in shaping cell-type-specific metabolism.

PANTOTHENATE KINASE4, LOSS OF GDU2, and TRANSPOSON PROTEIN1 affect the canalization of tomato fruit metabolism

Most studies investigating quantitative traits focus on mean levels per genotype rather than the variation between different individuals of one genotype or the variation elicited by different environments. Consequently, the genes that govern this effect are not well understood. The concept, named canalization, which describes a lack of variation, is well known in the context of developmental processes but is poorly studied for quantitative traits such as metabolism. In this study, we selected 8 putative candidate genes from previously identified canalized metabolic quantitative trait loci and created genome-edited tomato (Solanum lycopersicum) mutants of these genes for experimental validation. Most lines showed wild-type morphology, except for an ARF-like protein mutant showing aberrant phenotypes in the form of scarred fruit cuticles. In greenhouse trials with different irrigation conditions, whole-plant traits showed a general increase of their level toward the more optimal irrigation conditions, whereas most metabolic traits showed an increase toward the other end of the gradient. Mutants of a PANTOTHENATE KINASE 4, the AIRP ubiquitin gene LOSS OF GDU2, and TRANSPOSON PROTEIN 1 grown under these conditions showed an overall improved plant performance. Additional effects, on both target and other metabolites in tomato fruits, regarding the mean level at specific conditions and, ergo, the cross-environment coefficient of variation, were observed. However, variation between individuals remained unaffected. In conclusion, this study supports the idea of distinct sets of genes regulating different types of variation.

Exogenous γ-aminobutyric acid (GABA) alleviates nitrogen deficiency by mediating nitrate uptake and assimilation in Andrographis paniculata seedlings

γ-Aminobutyric acid (GABA) plays significant metabolic and signaling roles in plant stress responses. Recent studies have proposed that GABA alleviates plant nitrogen (N) deficient stress; however, the mechanism by which GABA mediates plant N deficiency adaptation remains not yet well understood. Herein we found in a medicinal plant Andrographis paniculata that 5 mmol L^-1 exogenous GABA promoted plant growth under N deficient (1 mmol L^-1 NO₃^-) condition, with remarkably increments in total N and NO₃^- concentrations in plants. GABA increased N assimilation and protein synthesis by up-regulating the activities and expression of N metabolic enzymes. GABA also increased the accumulation of α-ketoglutarate and malate, which could facilitate the assimilation of NO₃^-. Inhibition of NR by Na₂WO₄ counteracted the promoting effects of GABA on plant growth, and the effects of GABA were not affected by L-DABA and 3-MP, the inhibitors of GABA transaminase (GABA-T) and glutamate decarboxylase (GAD), respectively. These results suggested that the nutritional role of GABA was excluded in promoting plant growth under low N condition. The results of ¹⁵N isotopic tracing and NRTs transcription indicated that exogenous GABA could up-regulate NRT2.4 and NRT3.2 to increase plant NO₃^- uptake under N deficient condition. Interestingly, primidone, an inhibitor of GABA receptor, impeded the effects of GABA on plant growth and N accumulation. Thus, our results revealed that exogenous GABA acted as a signal to up-regulate NRTs via its receptor to increase NO₃^- uptake, and subsequently promoted NO₃^- assimilation to alleviate N deficiency in A. paniculata.

Multiple-model GWAS identifies optimal allelic combinations of quantitative trait loci for malic acid in tomato

Malic acid (MA) is an important flavor acid in fruits and acts as a mediator in a series of metabolic pathways. It is important to understand the factors affecting MA metabolism for fruit flavor improvement and to understand MA-mediated biological processes. However, the metabolic accumulation of MA is controlled by complex heredity and environmental factors, making it difficult to predict and regulate the metabolism of MA. In this study, we carried out a genome-wide association study (GWAS) on MA using eight milestone models with two-environment repeats. A series of associated SNP variations were identified from the GWAS, and 15 high-confidence annotated genes were further predicted based on linkage disequilibrium and lead SNPs. The transcriptome data of candidate genes were explored within different tomato organs as well as various fruit tissues, and suggested specific expression patterns in fruit pericarp. Based on the genetic parameters of population differentiation and SNP distribution, tomato MA content has been more influenced by domestication sweeps and less affected by improvement sweeps in the long-term history of tomato breeding. In addition, genotype × environment interaction might contribute to the difference in domestication phenotypic data under different environments. This study provides new genetic insights into how tomato changed its MA content during breeding and makes available function-based markers for breeding by marker-assisted selection.

Ethylene inhibits malate accumulation in apple by transcriptional repression of aluminum-activated malate transporter 9 via the WRKY31-ERF72 network

Malic acid accumulation in the vacuole largely determines acidity and perception of sweetness of apple. It has long been observed that reduction in malate level is associated with increase in ethylene production during the ripening process of climacteric fruits, but the molecular mechanism linking ethylene to malate reduction is unclear. Here, we show that ethylene-modulated WRKY transcription factor 31 (WRKY31)-Ethylene Response Factor 72 (ERF72)-ALUMINUM ACTIVATED MALATE TRANSPORTER 9 (Ma1) network regulates malate accumulation in apple fruit. ERF72 binds to the promoter of ALMT9, a key tonoplast transporter for malate accumulation of apple, transcriptionally repressing ALMT9 expression in response to ethylene. WRKY31 interacts with ERF72, suppressing its transcriptional inhibition activity on ALMT9. In addition, WRKY31 directly binds to the promoters of ERF72 and ALMT9, transcriptionally repressing and activating ERF72 and ALMT9, respectively. The expression of WRKY31 decreases in response to ethylene, lowering the transcription of ALMT9 directly and via its interactions with ERF72. These findings reveal that the regulatory complex WRKY31 forms with ERF72 responds to ethylene, linking the ethylene signal to ALMT9 expression in reducing malate transport into the vacuole during fruit ripening.

Biotechnological approaches for controlling postharvest fruit softening

Fruit softening is the major factor determining the postharvest life of fruit, affecting bruise and damage susceptibility, pathogen colonisation, and consumer satisfaction, all of which contribute to product losses in the supply chain and consumers' homes. Ripening-related changes to the cell wall, cuticle and soluble sugars largely determine softening, and some are amenable to biotechnological intervention, for example, by manipulation of the expression of genes encoding cell wall-modifying proteins or wax and cutin synthases. In this review, we discuss work exploring the role of genes involved in cell wall and cuticle properties, and recent developments in the silencing of multiple genes by targeting single transcription factors. Identification of transcription factors that control the expression of suites of genes encoding cell wall-modifying proteins provides exciting targets for biotechnology.

Transcriptome and Metabolome Analyses Reveals the Pathway and Metabolites of Grain Quality Under Phytochrome B in Rice (Oryza sativa L.)

BACKGROUND

Grain size and chalkiness is a critical agronomic trait affecting rice yield and quality. The application of transcriptomics to rice has widened the understanding of complex molecular responsive mechanisms, differential gene expression, and regulatory pathways under varying conditions. Similarly, metabolomics has also contributed drastically for rice trait improvements. As master regulators of plant growth and development, phys influence seed germination, vegetative growth, photoperiodic flowering, shade avoidance responses. OsPHYB can regulate a variety of plant growth and development processes, but little is known about the roles of rice gene OsPHYB in modulating grain development.

RESULTS

In this study, rice phytochrome B (OsPHYB) was edited using CRISPR/Cas9 technology. We found that OsPHYB knockout increased rice grain size and chalkiness, and increased the contents of amylose, free fatty acids and soluble sugar, while the gel consistency and contents of proteins were reduced in mutant grains. Furthermore, OsPHYB is involved in the regulation of grain size and chalk formation by controlling cell division and complex starch grain morphology. Transcriptomic analysis revealed that loss of OsPHYB function affects multiple metabolic pathways, especially enhancement of glycolysis, fatty acid, oxidative phosphorylation, and antioxidant pathways, as well as differential expression of starch and phytohormone pathways. An analysis of grain metabolites showed an increase in the free fatty acids and lysophosphatidylcholine, whereas the amounts of sugars, alcohols, amino acids and derivatives, organic acids, phenolic acids, alkaloids, nucleotides and derivatives, and flavonoids decreased, which were significantly associated with grain size and chalk formation.

CONCLUSIONS

Our study reveals that, OsPHYB plays an important regulatory role in the growth and development of rice grains, especially grain size and chalkiness. Furthermore, OsPHYB regulates grain size and chalkiness formation by affecting gene metabolism interaction network. Thus, this study not only revealed that OsPHYB plays a vital role in regulating grain size and chalkiness of rice but reveal new functions and highlighted the importance and value of OsPHYB in rice grain development and provide a new strategy for yield and quality improvement in rice breeding.

Physiological and Transcriptomic Analyses Reveal the Effects of Elevated Root-Zone CO2 on the Metabolism of Sugars and Starch in the Roots of Oriental Melon Seedlings

Root-zone CO2 is a major factor that affects crop growth, development, nutrient uptake, and metabolism. Oriental melon is affected by root-zone gases during growth, the microstructure, sugar and starch contents, enzymatic activities related to sugar and starch metabolism, and gene expression in the roots of oriental melon seedlings were investigated under three root-zone CO2 concentrations (CK: 0.2%, T1: 0.4%, T2: 1.1%). Elevated root-zone CO2 altered the cellular microstructure, accelerated the accumulation and release of starch grains, disrupted organelle formation, and accelerated root senescence. The sugar and starch contents and metabolic activity in the roots increased within a short duration following treatment. Compared to the control, 232 and 1492 differentially expressed genes (DEGs) were identified on the 6th day of treatment in T1 and T2 plants, respectively. The DEGs were enriched in three metabolic pathways. The majority of genes related to sucrose and starch hydrolysis were upregulated, while the genes related to sucrose metabolism were downregulated. The study revealed that oriental melon seedlings adapt to elevated root-zone CO2 stress by adjusting sugar and starch metabolism at the transcriptome level and provides new insights into the molecular mechanism underlying the response to elevated root-zone CO2 stress.

Targeted approaches to improve tomato fruit taste

Tomato (Solanum lycopersicum) is the most valuable fruit and horticultural crop species worldwide. Compared with the fruits of their progenitors, those of modern tomato cultivars are, however, often described as having unsatisfactory taste or lacking flavor. The flavor of a tomato fruit arises from a complex mix of tastes and volatile metabolites, including sugars, acids, amino acids, and various volatiles. However, considerable differences in fruit flavor occur among tomato varieties, resulting in mixed consumer experiences. While tomato breeding has traditionally been driven by the desire for continual increases in yield and the introduction of traits that provide a long shelf-life, consumers are prepared to pay a reasonable premium for taste. Therefore, it is necessary to characterize preferences of tomato flavor and to define its underlying genetic basis. Here, we review recent conceptual and technological advances that have rendered this more feasible, including multi-omics-based QTL and association analyses, along with the use of trained testing panels, and machine learning approaches. This review proposes how the comprehensive datasets compiled to date could allow a precise rational design of tomato germplasm resources with improved organoleptic quality for the future.

A comparative transcriptomics and eQTL approach identifies SlWD40 as a tomato fruit ripening regulator

Although multiple vital genes with strong effects on the tomato (Solanum lycopersicum) ripening process have been identified via the positional cloning of ripening mutants and cloning of ripening-related transcription factors (TFs), recent studies suggest that it is unlikely that we have fully characterized the gene regulatory networks underpinning this process. Here, combining comparative transcriptomics and expression QTLs, we identified 16 candidate genes involved in tomato fruit ripening and validated them through virus-induced gene silencing analysis. To further confirm the accuracy of the approach, one potential ripening regulator, SlWD40 (WD-40 repeats), was chosen for in-depth analysis. Co-expression network analysis indicated that master regulators such as RIN (ripening inhibitor) and NOR (nonripening) as well as vital TFs including FUL1 (FRUITFUL1), SlNAC4 (NAM, ATAF1,2, and CUC2 4), and AP2a (Activating enhancer binding Protein 2 alpha) strongly co-expressed with SlWD40. Furthermore, SlWD40 overexpression and RNAi lines exhibited substantially accelerated and delayed ripening phenotypes compared with the wild type, respectively. Moreover, transcriptome analysis of these transgenics revealed that expression patterns of ethylene biosynthesis genes, phytoene synthase, pectate lyase, and branched chain amino transferase 2, in SlWD40-RNAi lines were similar to those of rin and nor fruits, which further demonstrated that SlWD40 may act as an important ripening regulator in conjunction with RIN and NOR. These results are discussed in the context of current models of ripening and in terms of the use of comparative genomics and transcriptomics as an effective route for isolating causal genes underlying differences in genotypes.

Reduced auxin signalling through the cyclophilin gene DIAGEOTROPICA impacts tomato fruit development and metabolism during ripening

Auxin is an important hormone playing crucial roles during fruit growth and ripening; however, the metabolic impact of changes in auxin signalling during tomato (Solanum lycopersicum L.) ripening remains unclear. Here, we investigated the significance of changes in auxin signalling during different stages of fruit development by analysing changes in tomato fruit quality and primary metabolism using mutants with either lower or higher auxin sensitivity [diageotropica (dgt) and entire mutants, respectively]. Altered auxin sensitivity modifies metabolism, through direct impacts on fruit respiration and fruit growth. We verified that the dgt mutant plants exhibit reductions in fruit set, total fruit dry weight, fruit size, number of seeds per fruit, and fresh weight loss during post-harvest. Sugar accumulation was associated with delayed fruit ripening in dgt, probably connected with reduced ethylene levels and respiration, coupled with a lower rate of starch degradation. In contrast, despite exhibiting parthenocarpy, increased auxin perception (entire) did not alter fruit ripening, leading to only minor changes in primary metabolism. By performing a comprehensive analysis, our results connect auxin signalling and metabolic changes during tomato fruit development, indicating that reduced auxin signalling led to extensive changes in sugar concentration and starch metabolism during tomato fruit ripening.

Atlas of phenotypic, genotypic and geographical diversity present in the European traditional tomato

The Mediterranean basin countries are considered secondary centres of tomato diversification. However, information on phenotypic and allelic variation of local tomato materials is still limited. Here we report on the evaluation of the largest traditional tomato collection, which includes 1499 accessions from Southern Europe. Analyses of 70 traits revealed a broad range of phenotypic variability with different distributions among countries, with the culinary end use within each country being the main driver of tomato diversification. Furthermore, eight main tomato types (phenoclusters) were defined by integrating phenotypic data, country of origin, and end use. Genome-wide association study (GWAS) meta-analyses identified associations in 211 loci, 159 of which were novel. The multidimensional integration of phenoclusters and the GWAS meta-analysis identified the molecular signatures for each traditional tomato type and indicated that signatures originated from differential combinations of loci, which in some cases converged in the same tomato phenotype. Our results provide a roadmap for studying and exploiting this untapped tomato diversity.

Comparative study on the influence of silicon and selenium to mitigate arsenic induced stress by modulating TCA cycle, GABA, and polyamine synthesis in rice seedlings

Arsenic contamination of groundwater is a major concern for its usage in crop irrigation in many regions of the world. Arsenic is absorbed by rice plants mainly from arsenic contaminated water during irrigation. It hampers growth and agricultural productivity. The aim of the study was to mitigate the toxic effects of arsenate (As-V) [25 μM, 50 μM, and 75 μM] by silicon (Si) [2 mM] and selenium (Se) [5 μM] amendments on the activity of the TCA cycle, synthesis of γ-aminobutyric acid (GABA) and polyamines (PAs) in rice (Oryza sativa L. cv. MTU-1010) seedlings and to identify which chemical was more potential to combat this threat. As(V) application decreased the activities of tested respiratory enzymes and increased the levels of organic acids (OAs) in the test seedlings. Application of Si with As(V) and Se with As(V) increased the activities of respiratory enzymes and the levels of OAs. The effects were more pronounced during Si amendments. The activities of GABA synthesizing enzymes along with accumulation of GABA were increased under As(V) stress. During joint application of Si with As(V) and Se with As(V) the activity and the level of said parameters were decreased that indicating defensive role of these chemicals to resist As(V) toxicity in rice and Si amendments showed greater potential to reduce As(V) induced damages in the test seedlings. PAs trigger tolerance mechanism against As(V) in plants. PAs such as putrescine, spermidine and spermine were synthesized more during Si and Se amendments in As(V) contaminated rice seedlings to combat the toxic effects of As(V). Si amendments substantially modulated the toxic effects caused by As(V) over Se amendments in the As(V) challenged test seedlings. Thus, in future application of Si enriched fertilizer will be beneficial to grow rice plants with normal vigor in arsenic contaminated soil.

The metabolic changes that effect fruit quality during tomato fruit ripening

As the most valuable organ of tomato plants, fruit has attracted considerable attention which most focus on its quality formation during the ripening process. A considerable amount of research has reported that fruit quality is affected by metabolic shifts which are under the coordinated regulation of both structural genes and transcriptional regulators. In recent years, with the development of the next generation sequencing, molecular and genetic analysis methods, lots of genes which are involved in the chlorophyll, carotenoid, cell wall, central and secondary metabolism have been identified and confirmed to regulate pigment contents, fruit softening and other aspects of fruit flavor quality. Here, both research concerning the dissection of fruit quality related metabolic changes, the transcriptional and post-translational regulation of these metabolic pathways are reviewed. Furthermore, a weighted gene correlation network analysis of representative genes of fruit quality has been carried out and the potential of the combined application of the gene correlation network analysis, fine-mapping strategies and next generation sequencing to identify novel candidate genes determinants of fruit quality is discussed.

Long-read transcriptome sequencing provides insight into lignan biosynthesis during fruit development in Schisandra chinensis

BACKGROUND

Schisandra chinensis, an ancient member of the most basal angiosperm lineage which is known as the ANITA, is a fruit-bearing vine with the pharmacological effects of a multidrug system, such as antioxidant, anti-inflammatory, cardioprotective, neuroprotective, anti-osteoporosis effects. Its major bioactive compound is represented by lignans such as schisandrin. Molecular characterization of lignan biosynthesis in S. chinensis is of great importance for improving the production of this class of active compound. However, the biosynthetic mechanism of schisandrin remains largely unknown.

RESULTS

To understand the potential key catalytic steps and their regulation of schisandrin biosynthesis, we generated genome-wide transcriptome data from three different tissues of S. chinensis cultivar Cheongsoon, including leaf, root, and fruit, via long- and short-read sequencing technologies. A total of 132,856 assembled transcripts were generated with an average length of 1.9 kb and high assembly completeness. Overall, our data presented effective, accurate gene annotation in the prediction of functional pathways. In particular, the annotation revealed the abundance of transcripts related to phenylpropanoid biosynthesis. Remarkably, transcriptome profiling during fruit development of S. chinensis cultivar Cheongsoon revealed that the phenylpropanoid biosynthetic pathway, specific to coniferyl alcohol biosynthesis, showed a tendency to be upregulated at the postfruit development stage. Further the analysis also revealed that the pathway forms a transcriptional network with fruit ripening-related genes, especially the ABA signaling-related pathway. Finally, candidate unigenes homologous to isoeugenol synthase 1 (IGS1) and dirigent-like protein (DIR), which are subsequently activated by phenylpropanoid biosynthesis and thus catalyze key upstream steps in schisandrin biosynthesis, were identified. Their expression was increased at the postfruit development stage, suggesting that they may be involved in the regulation of schisandrin biosynthesis in S. chinensis.

CONCLUSIONS

Our results provide new insights into the production and accumulation of schisandrin in S. chinensis berries and will be utilized as a valuable transcriptomic resource for improving the schisandrin content.

Malate metabolism mediated by the cytoplasmic malate dehydrogenase gene MdcyMDH affects sucrose synthesis in apple fruit

The types and proportions of soluble sugar and organic acid in fruit significantly affect flavor quality. However, there are few reports on the crosstalk regulation between metabolism of organic acid and sugar in fruit. Here, we found that the overexpression of cytoplasmic malate dehydrogenase genes (MdcyMDHs) not only increased the malate content but also increased the sucrose concentration in transgenic apple calli and mature fruit. Enzyme activity assays indicated that the overexpression of MdcyMDH1 and MdcyMDH5 enhanced sucrose phosphate synthase (SPS) activity in transgenic materials. RNA-seq and expression analysis showed that the expression levels of SPS genes were up-regulated in MdcyMDH1-overexpressed apple fruit and MdcyMDH5-overexpressed apple calli. Further study showed that the inhibition of MdSPSB2 or MdSPSC2 expression in MdcyMDH1 transgenic fruit could reduce or eliminate, respectively, the positive effect of MdcyMDH1 on sucrose accumulation. Moreover, some starch cleavage-related genes (MdBAM6.1/6.2, MdBMY8.1/8.2, MdISA1) and the key gluconeogenesis-related phosphoenolpyruvate carboxykinase MdPEPCK1 gene were significantly up-regulated in the transcriptome differentially expressed genes of mature fruit overexpressing MdcyMDH1. These results indicate that alteration of malate metabolism mediated by MdcyMDH might regulate the expression of MdSPSs and SPS activity via affecting starch metabolism or gluconeogenesis, and thus accelerate sucrose synthesis and accumulation in fruit.

Comparative genomic analysis of the tricarboxylic acid cycle members in four Solanaceae vegetable crops and expression pattern analysis in Solanum tuberosum

Background

The tricarboxylic acid (TCA) cycle is crucial for energy supply in animal, plant, and microbial cells. It is not only the main pathway of carbohydrate catabolism but also the final pathway of lipid and protein catabolism. Some TCA genes have been found to play important roles in the growth and development of tomato and potato, but no comprehensive study of TCA cycle genes in Solanaceae crops has been reported.

Results

In this study, we analyzed TCA cycle genes in four important Solanaceae vegetable crops (potato (Solanum tuberosum), tomato (Solanum lycopersicum), eggplant (Solanum melongena), and pepper (Capsicum annuum)) based on comparative genomics. The four Solanaceae crops had a total of 180 TCA cycle genes: 43 in potato, 44 in tomato, 40 in eggplant, and 53 in pepper. Phylogenetic analysis, collinearity analysis, and tissue expression patterns revealed the conservation of and differences in TCA cycle genes between the four Solanaceae crops and found that there were unique subgroup members in Solanaceae crops that were independent of Arabidopsis genes. The expression analysis of potato TCA cycle genes showed that (1) they were widely expressed in various tissues, and some transcripts like Soltu.DM.01G003320.1(SCoAL) and Soltu.DM.04G021520.1 (SDH) mainly accumulate in vegetative organs, and some transcripts such as Soltu.DM.12G005620.3 (SDH) and Soltu.DM.02G007400.4 (MDH) are preferentially expressed in reproductive organs; (2) several transcripts can be significantly induced by hormones, such as Soltu.DM.08G023870.2 (IDH) and Soltu.DM.06G029290.1 (SDH) under ABA treatment, and Soltu.DM.07G021850.2 (CSY) and Soltu.DM.09G026740.1 (MDH) under BAP treatment, and Soltu.DM.02G000940.1 (IDH) and Soltu.DM.01G031350.4 (MDH) under GA treatment; (3) Soltu.DM.11G024650.1 (SDH) can be upregulated by the three disease resistance inducers including Phytophthora infestans, acibenzolar-S-methyl (BTH), and DL-β-amino-n-butyric acid (BABA); and (4) the levels of Soltu.DM.01G045790.1 (MDH), Soltu.DM.01G028520.3 (CSY), and Soltu.DM.12G028700.1 (CSY) can be activated by both NaCl and mannitol. The subcellular localization results of three potato citrate synthases showed that Soltu.DM.01G028520.3 was localized in mitochondria, while Soltu.DM.12G028700.1 and Soltu.DM.07G021850.1 were localized in the cytoplasm.

Conclusions

This study provides a scientific foundation for the comprehensive understanding and functional studies of TCA cycle genes in Solanaceae crops and reveals their potential roles in potato growth, development, and stress response.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-08109-9.

Mechanisms and regulation of organic acid accumulation in plant vacuoles

In fleshy fruits, organic acids are the main source of fruit acidity and play an important role in regulating osmotic pressure, pH homeostasis, stress resistance, and fruit quality. The transport of organic acids from the cytosol to the vacuole and their storage are complex processes. A large number of transporters carry organic acids from the cytosol to the vacuole with the assistance of various proton pumps and enzymes. However, much remains to be explored regarding the vacuolar transport mechanism of organic acids as well as the substances involved and their association. In this review, recent advances in the vacuolar transport mechanism of organic acids in plants are summarized from the perspectives of transporters, channels, proton pumps, and upstream regulators to better understand the complex regulatory networks involved in fruit acid formation.

A genome-wide association study reveals that the 2-oxoglutarate/malate translocator mediates seed vigor in rice

Seed vigor is an important trait for the direct seeding of rice (Oryza sativa L.). In this study, we examined the genetic architecture of variation in the germination rate using a diverse panel of rice accessions. Four quantitative trait loci for germination rate were identified using a genome-wide association study during early germination. One candidate gene, encoding the 2-oxoglutarate/malate translocator (OsOMT), was validated for qGR11. Disruption of this gene (Osomt mutants) reduced seed vigor, including seed germination and seedling growth, in rice. Functional analysis revealed that OsOMT influences seed vigor mainly by modulating amino acid levels and glycolysis and tricarboxylic acid cycle processes. The levels of most amino acids, including the Glu family (Glu, Pro, Arg, and GABA), Asp family (Asp, Thr, Lys, Ile, and Met), Ser family (Ser, Gly, and Cys), and others (His, Ala, Leu, and Val), were significantly reduced in the mature grains and the early germinating seeds of Osomt mutants compared to wild type (WT). The glucose and soluble sugar contents, as well as adenosine triphosphate levels, were significantly decreased in germinating seeds of Osomt mutants compared to WT. These results provide important insights into the role of OsOMT in seed vigor in rice.

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.

Two mitochondrial phosphatases, PP2c63 and Sal2, are required for posttranslational regulation of the TCA cycle in Arabidopsis

Protein phosphorylation is a well-established post-translational mechanism that regulates protein functions and metabolic pathways. It is known that several plant mitochondrial proteins are phosphorylated in a reversible manner. However, the identities of the protein kinases/phosphatases involved in this mechanism and their roles in the regulation of the tricarboxylic acid (TCA) cycle remain unclear. In this study, we isolated and characterized plants lacking two mitochondrially targeted phosphatases (Sal2 and PP2c63) along with pyruvate dehydrogenase kinase (PDK). Protein-protein interaction analysis, quantitative phosphoproteomics, and enzymatic analyses revealed that PDK specifically regulates pyruvate dehydrogenase complex (PDC), while PP2c63 nonspecifically regulates PDC. When recombinant PP2c63 and Sal2 proteins were added to mitochondria isolated from mutant plants, protein-protein interaction and enzymatic analyses showed that PP2c63 directly phosphorylates and modulates the activity of PDC, while Sal2 only indirectly affects TCA cycle enzymes. Characterization of steady-state metabolite levels and fluxes in the mutant lines further revealed that these phosphatases regulate flux through the TCA cycle, and that altered metabolism in the sal2 pp2c63 double mutant compromises plant growth. These results are discussed in the context of current models of the control of respiration in plants.

The NAC transcription factor FaRIF controls fruit ripening in strawberry

In contrast to climacteric fruits such as tomato, the knowledge on key regulatory genes controlling the ripening of strawberry, a nonclimacteric fruit, is still limited. NAC transcription factors (TFs) mediate different developmental processes in plants. Here, we identified and characterized Ripening Inducing Factor (FaRIF), a NAC TF that is highly expressed and induced in strawberry receptacles during ripening. Functional analyses based on stable transgenic lines aimed at silencing FaRIF by RNA interference, either from a constitutive promoter or the ripe receptacle-specific EXP2 promoter, as well as overexpression lines showed that FaRIF controls critical ripening-related processes such as fruit softening and pigment and sugar accumulation. Physiological, metabolome, and transcriptome analyses of receptacles of FaRIF-silenced and overexpression lines point to FaRIF as a key regulator of strawberry fruit ripening from early developmental stages, controlling abscisic acid biosynthesis and signaling, cell-wall degradation, and modification, the phenylpropanoid pathway, volatiles production, and the balance of the aerobic/anaerobic metabolism. FaRIF is therefore a target to be modified/edited to control the quality of strawberry fruits.

Effects of Trichoderma harzianum on Photosynthetic Characteristics and Fruit Quality of Tomato Plants

The beneficial role of fungi from the Trichoderma genus and its secondary metabolites in promoting plant growth, uptake and use efficiency of macronutrients and oligo/micro-nutrients, activation of plant secondary metabolism and plant protection from diseases makes it interesting for application in environmentally friendly agriculture. However, the literature data on the effect of Trichoderma inoculation on tomato fruit quality is scarce. Commercially used tomato cultivars were chosen in combination with indigenous Trichodrema species previously characterized on molecular and biochemical level, to investigate the effect of Trichoderma on photosynthetic characteristics and fruit quality of plants grown in organic system of production. Examined cultivars differed in the majority of examined parameters. Response of cultivar Gružanski zlatni to Trichoderma application was more significant. As a consequence of increased epidermal flavonols and decreased chlorophyll, the nitrogen balance index in leaves has decreased, indicating a shift from primary to secondary metabolism. The quality of its fruit was altered in the sense of increased total flavonoids content, decreased starch, increased Bioaccumulation Index (BI) for Fe and Cr, and decreased BI for heavy metals Ni and Pb. Higher expression of swolenin gene in tomato roots of more responsive tomato cultivar indicates better root colonization, which correlates with observed positive effects of Trichodrema.

Molecular and Hormonal Mechanisms Regulating Fleshy Fruit Ripening

This article focuses on the molecular and hormonal mechanisms underlying the control of fleshy fruit ripening and quality. Recent research on tomato shows that ethylene, acting through transcription factors, is responsible for the initiation of tomato ripening. Several other hormones, including abscisic acid (ABA), jasmonic acid (JA) and brassinosteroids (BR), promote ripening by upregulating ethylene biosynthesis genes in different fruits. Changes to histone marks and DNA methylation are associated with the activation of ripening genes and are necessary for ripening initiation. Light, detected by different photoreceptors and operating through ELONGATED HYPOCOTYL 5(HY5), also modulates ripening. Re-evaluation of the roles of 'master regulators' indicates that MADS-RIN, NAC-NOR, Nor-like1 and other MADS and NAC genes, together with ethylene, promote the full expression of genes required for further ethylene synthesis and change in colour, flavour, texture and progression of ripening. Several different types of non-coding RNAs are involved in regulating expression of ripening genes, but further clarification of their diverse mechanisms of action is required. We discuss a model that integrates the main hormonal and genetic regulatory interactions governing the ripening of tomato fruit and consider variations in ripening regulatory circuits that operate in other fruits.

Comparative transcriptome analysis reveals key genes potentially related to organic acid and sugar accumulation in loquat

Organic acids and sugars are the primary components that determine the quality and flavor of loquat fruits. In the present study, major organic acids, sugar content, enzyme activities, and the expression of related genes were analyzed during fruit development in two loquat cultivars, ’JieFangZhong’ (JFZ) and ’BaiLi’ (BL). Our results showed that the sugar content increased during fruit development in the two cultivars; however, the organic acid content dramatically decreased in the later stages of fruit development. The differences in organic acid and sugar content between the two cultivars primarily occured in the late stage of fruit development and the related enzymes showed dynamic changes in activies during development. Phosphoenolpyruvate carboxylase (PEPC) and mNAD malic dehydrogenase (mNAD-MDH) showed higher activities in JFZ at 95 days after flowering (DAF) than in BL. However, NADP-dependent malic enzyme (NADP-ME) activity was the lowest at 95 DAF in both JFZ and BL with BL showing higher activity compared with JFZ. At 125 DAF, the activity of fructokinase (FRK) was significantly higher in JFZ than in BL. The activity of sucrose synthase (SUSY) in the sucrose cleavage direction (SS-C) was low at early stages of fruit development and increased at 125 DAF. SS-C activity was higher in JFZ than in BL. vAI and sucrose phosphate synthase (SPS) activities were similar in the two both cultivars and increased with fruit development. RNA-sequencing was performed to determine the candidate genes for organic acid and sugar metabolism. Our results showed that the differentially expressed genes (DEGs) with the greated fold changes in the later stages of fruit development between the two cultivars were phosphoenolpyruvate carboxylase 2 (PEPC2), mNAD-malate dehydrogenase (mNAD-MDH), cytosolic NADP-ME (cyNADP-ME2), aluminum-activated malate transporter (ALMT9), subunit A of vacuolar H⁺-ATPase (VHA-A), vacuolar H⁺-PPase (VHP1), NAD-sorbitol dehydrogenase (NAD-SDH), fructokinase (FK), sucrose synthase in sucrose cleavage (SS-C), sucrose-phosphate synthase 1 (SPS1), neutral invertase (NI), and vacuolar acid invertase (vAI). The expression of 12 key DEGs was validated by quantitative reverese transcription PCR (RT-qPCR). Our findings will help understand the molecular mechanism of organic acid and sugar formation in loquat, which will aid in breeding high-quality loquat cultivars.

Carbon Dioxide Pretreatment and Cold Storage Synergistically Delay Tomato Ripening through Transcriptional Change in Ethylene-Related Genes and Respiration-Related Metabolism

The effects of CO₂ pretreatment before cold storage on tomato quality were investigated using physicochemical and transcriptome changes. Harvested tomatoes were treated with 30% or 60% CO₂ for 3 h before storage at 4 °C for 14 d (cold storage), followed by transfer to 20 °C for 8 d (ambient conditions). The CO₂-treated fruits were firmer with a better appearance than untreated fruits, even after being transferred from 4 °C storage to 20 °C for 8 d. CO₂ pretreatment coupled with cold storage synergistically delayed tomato ripening by reducing respiration and lowering lycopene production. The tomatoes treated with 30% and 60% CO₂ had fewer pits than untreated fruits after cold storage, even after being transferred to ambient conditions. Moreover, the 60% CO₂ treatment significantly suppressed the decay rate. Transcriptome and metabolome functional enrichment analyses commonly showed the involvement of CO₂-responsive genes or metabolites in sucrose and starch metabolism, as well as biosynthesis of secondary metabolites—in particular, glycolysis reduction. The most frequently detected domain was the ethylene-responsive factor. These results indicate that altered ethylene biosynthesis and ethylene signaling, via ethylene-responsive transcription factors and respiration-related pathways, appear to control CO₂-induced fruit quality.