Maize Oxalyl-CoA Decarboxylase1 Degrades Oxalate and Affects the Seed Metabolome and Nutritional Quality

Sucrose-associated SnRK1a1-mediated phosphorylation of Opaque2 modulates endosperm filling in maize

During maize endosperm filling, sucrose not only serves as a source of carbon skeletons for storage-reserve synthesis but also acts as a stimulus to promote this process. However, the molecular mechanisms underlying sucrose and endosperm filling are poorly understood. In this study, we found that sucrose promotes the expression of endosperm-filling hub gene Opaque2 (O2), coordinating with storage-reserve accumulation. We showed that the protein kinase SnRK1a1 can attenuate O2-mediated transactivation, but sucrose can release this suppression. Biochemical assays revealed that SnRK1a1 phosphorylates O2 at serine 41 (S41), negatively affecting its protein stability and transactivation ability. We observed that mutation of SnRK1a1 results in larger seeds with increased kernel weight and storage reserves, while overexpression of SnRK1a1 causes the opposite effect. Overexpression of the native O2 (O2-OE), phospho-dead (O2-SA), and phospho-mimetic (O2-SD) variants all increased 100-kernel weight. Although O2-SA seeds exhibit smaller kernel size, they have higher accumulation of starch and proteins, resulting in larger vitreous endosperm and increased test weight. O2-SD seeds display larger kernel size but unchanged levels of storage reserves and test weight. O2-OE seeds show elevated kernel dimensions and nutrient storage, like a mixture of O2-SA and O2-SD seeds. Collectively, our study discovers a novel regulatory mechanism of maize endosperm filling. Identification of S41 as a SnRK1-mediated phosphorylation site in O2 offers a potential engineering target for enhancing storage-reserve accumulation and yield in maize.

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.

Rhubarb: A novel model plant to study the conundrum of calcium oxalate synthesis

The study investigated calcium oxalate (CaOx) crystal composition, accumulation, synthesis, and degradation in five rhubarb species from the North-Western Indian Himalayas. Techniques like optical and scanning electron microscopy (SEM), SEM-energy-dispersive X-ray spectroscopy (SEM-EDS), inductively coupled plasma-optical emission spectrometry (ICP-OES), X-ray diffraction spectroscopy (XRD), and real-time (qRT-PCR) expression analysis of strategic genes were used to understand the processes of oxalate synthesis and precipitation. Results showed crystals tend to accumulate around vascular bundles in all species, irrespective of size, indicating a consistent pattern. Crystal synthesis and accumulation were stress-driven, linked to substrate composition, and in planta soluble oxalate and calcium levels, paralleling oxalate precursors. Based on their availability, CaOx crystals precipitated heavy metals mostly associated with its weddellite form. Crystal content correlated positively with mRNA levels of calcium/oxalate/ascorbate-related and stress-responsive genes, and negatively with oxalate oxidation/decarboxylation genes. CaOx crystals were suggested as potential biominerals for addressing heavy metal stress in agriculture.

Disruption of the Arabidopsis Acyl-Activating Enzyme 3 Impairs Seed Coat Mucilage Accumulation and Seed Germination

The Acyl-activating enzyme (AAE) 3 gene encodes an oxalyl-CoA synthetase that catalyzes the conversion of oxalate to oxalyl-CoA as the first step in the CoA-dependent pathway of oxalate catabolism. Although the role of this enzyme in oxalate catabolism has been established, its biological roles in plant growth and development are less understood. As a step toward gaining a better understanding of these biological roles, we report here a characterization of the Arabidopsis thaliana aae3 (Ataae3) seed mucilage phenotype. Ruthidium red (RR) staining of Ataae3 and wild type (WT) seeds suggested that the observed reduction in Ataae3 germination may be attributable, at least in part, to a decrease in seed mucilage accumulation. Quantitative RT-PCR analysis revealed that the expression of selected mucilage regulatory transcription factors, as well as of biosynthetic and extrusion genes, was significantly down-regulated in the Ataae3 seeds. Mucilage accumulation in seeds from an engineered oxalate-accumulating Arabidopsis and Atoxc mutant, blocked in the second step of the CoA-dependent pathway of oxalate catabolism, were found to be similar to WT. These findings suggest that elevated tissue oxalate concentrations and loss of the oxalate catabolism pathway downstream of AAE3 were not responsible for the reduced Ataae3 seed germination and mucilage phenotypes. Overall, our findings unveil the presence of regulatory interplay between AAE3 and transcriptional control of mucilage gene expression.

Calcium Oxalate Crystals, the Plant 'Gemstones': Insights into Their Synthesis and Physiological Implications in Plants

From simple algal forms to the most advanced angiosperms, calcium oxalate (CaOx) crystals (CRs) occur in the majority of taxonomic groups of photosynthetic organisms. Various studies have demonstrated that this biomineralization is not a simple or random event but a genetically regulated coordination between calcium uptake, oxalate (OX) synthesis and, sometimes, environmental stresses. Certainly, the occurrence of CaOx CRs is old; however, questions related to their genesis, biosynthesis, significance and genetics exhibit robust evolution. Moreover, their speculated roles in bulk calcium regulation, heavy metal/OX detoxification, light reflectance and photosynthesis, and protection against grazing and herbivory, besides other characteristics, are gaining much interest. Thus, it is imperative to understand their synthesis and regulation in relation to the ascribed key functions to reconstruct future perspectives in harnessing their potential to achieve nutritious and pest-resistant crops amid anticipated global climatic perturbations. This review critically addresses the basic and evolving concepts of the origin (and recycling), synthesis, significance, regulation and fate vis-à-vis various functional aspects of CaOx CRs in plants (and soil). Overall, insights and conceptual future directions present them as potential biominerals to address future climate-driven issues.

Lemnaceae as Novel Crop Candidates for CO2 Sequestration and Additional Applications

Atmospheric carbon dioxide (CO2) is projected to be twice as high as the pre-industrial level by 2050. This review briefly highlights key responses of terrestrial plants to elevated CO2 and compares these with the responses of aquatic floating plants of the family Lemnaceae (duckweeds). Duckweeds are efficient at removing CO2 from the atmosphere, which we discuss in the context of their exceptionally high growth rates and capacity for starch storage in green tissue. In contrast to cultivation of terrestrial crops, duckweeds do not contribute to CO2 release from soils. We briefly review how this potential for contributions to stabilizing atmospheric CO2 levels is paired with multiple additional applications and services of duckweeds. These additional roles include wastewater phytoremediation, feedstock for biofuel production, and superior nutritional quality (for humans and livestock), while requiring minimal space and input of light and fertilizer. We, furthermore, elaborate on other environmental factors, such as nutrient availability, light supply, and the presence of a microbiome, that impact the response of duckweed to elevated CO2. Under a combination of elevated CO2 with low nutrient availability and moderate light supply, duckweeds' microbiome helps maintain CO2 sequestration and relative growth rate. When incident light intensity increases (in the presence of elevated CO2), the microbiome minimizes negative feedback on photosynthesis from increased sugar accumulation. In addition, duckweed shows a clear propensity for absorption of ammonium over nitrate, accepting ammonium from their endogenous N2-fixing Rhizobium symbionts, and production of large amounts of vegetative storage protein. Finally, cultivation of duckweed could be further optimized using hydroponic vertical farms where nutrients and water are recirculated, saving both resources, space, and energy to produce high-value products.

A Systemic Investigation of Genetic Architecture and Gene Resources Controlling Kernel Size-Related Traits in Maize

Grain yield is the most critical and complex quantitative trait in maize. Kernel length (KL), kernel width (KW), kernel thickness (KT) and hundred-kernel weight (HKW) associated with kernel size are essential components of yield-related traits in maize. With the extensive use of quantitative trait locus (QTL) mapping and genome-wide association study (GWAS) analyses, thousands of QTLs and quantitative trait nucleotides (QTNs) have been discovered for controlling these traits. However, only some of them have been cloned and successfully utilized in breeding programs. In this study, we exhaustively collected reported genes, QTLs and QTNs associated with the four traits, performed cluster identification of QTLs and QTNs, then combined QTL and QTN clusters to detect consensus hotspot regions. In total, 31 hotspots were identified for kernel size-related traits. Their candidate genes were predicted to be related to well-known pathways regulating the kernel developmental process. The identified hotspots can be further explored for fine mapping and candidate gene validation. Finally, we provided a strategy for high yield and quality maize. This study will not only facilitate causal genes cloning, but also guide the breeding practice for maize.

A conserved oxalyl-coenzyme A decarboxylase in oxalate catabolism

The ability to biosynthesize oxalic acid can provide beneficial functions to plants; however, uncontrolled or prolonged exposure to this strong organic acid results in multiple physiological problems. Such problems include a disruption of membrane integrity, mitochondrial function, metal chelation, and free radical formation. Recent work suggests that a CoA-dependent pathway of oxalate catabolism plays a critical role in regulating tissue oxalate concentrations in plants. Although this CoA-dependent pathway of oxalate catabolism is important, large gaps in our knowledge of the enzymes catalyzing each step remain. Evidence that an oxalyl-CoA decarboxylase (OXC) catalyzes the second step in this pathway, accelerating the conversion of oxalyl-CoA to formyl-CoA, has been reported. Induction studies revealed that OXC gene expression was upregulated in response to an exogenous oxalate supply. Phylogenetic analysis indicates that OXCs are conserved across plant species. Evolutionarily the plant OXCs can be separated into dicot and monocot classes. Multiple sequence alignments and molecular modeling suggest that OXCs have similar functionality with three conserved domains, the N-terminal PYR domain, the middle R domain, and the C-terminal PP domain. Further study of this CoA-dependent pathway of oxalate degradation would benefit efforts to develop new strategies to improve the nutrition quality of crops.

Oxalate in Plants: Metabolism, Function, Regulation, and Application

Characterized by strong acidity, chelating ability, and reducing ability, oxalic acid, a low molecular weight dicarboxylic organic acid, plays important roles in the regulation of plant growth and development, the response to both biotic and abiotic stresses such as plant defense and heavy metals detoxification, and food quality. The metabolism of oxalic acid has been well-studied in microorganisms, fungi, and animals but remains less understood in plants. However, excessive accumulation of oxalic acid is detrimental to plants. Therefore, the level of oxalic acid has to be precisely controlled in plant tissues. In this review, we summarize the metabolism, function, and regulation of oxalic acid in plants, and we discuss solutions such as agricultural practices and plant biotechnology to manipulate oxalic acid metabolism to regulate plant responses to both external stimuli and internal developmental cues.

Ionomic Combined with Transcriptomic and Metabolomic Analyses to Explore the Mechanism Underlying the Effect of Melatonin in Relieving Nutrient Stress in Apple

Nutrient stress harms plant growth and yield. Melatonin is a biologically active, multifunctional hormone that relieves abiotic stress in plants. Although previous studies have shown that melatonin plays an important role in improving nutrient-use efficiency, the mechanism of its regulation of nutrient stress remains unclear. In this study, melatonin was applied to apple plants under nutrient stress, and morphological indices, physiological and biochemical indices, and stomatal morphology were evaluated. The response of apple plants to nutrient deficiency and the melatonin mechanism to alleviate nutrient stress were analyzed by combining ionome, transcriptome, and metabolome. The results showed that exogenous melatonin significantly alleviated the inhibitory effect of nutritional stress on the growth of apple plants by regulating stomatal morphology, improving antioxidant enzyme activity, promoting ion absorption, and utilizing and changing the absorption and distribution of minerals throughout the plant. The transcriptome results showed that melatonin alleviated nutrient stress and promoted nutrient absorption and utilization by regulating glutathione metabolism and upregulating some metal ion transport genes. The metabolome results indicated that levels of oxalic acid, L-ascorbic acid, anthocyanins (cyanidin-3-O-galactoside), lignans (lirioresinol A and syringaresinol), and melatonin significantly increased after exogenous melatonin was applied to plants under nutrient stress. These differentially expressed genes and the increase in beneficial metabolites may explain how melatonin alleviates nutrient stress in plants.

Riboflavin integrates cellular energetics and cell cycle to regulate maize seed development

Riboflavin is the precursor of essential cofactors for diverse metabolic processes. Unlike animals, plants can de novo produce riboflavin through an ancestrally conserved pathway, like bacteria and fungi. However, the mechanism by which riboflavin regulates seed development is poorly understood. Here, we report a novel maize (Zea mays L.) opaque mutant o18, which displays an increase in lysine accumulation, but impaired endosperm filling and embryo development. O18 encodes a rate-limiting bifunctional enzyme ZmRIBA1, targeted to plastid where to initiate riboflavin biosynthesis. Loss of function of O18 specifically disrupts respiratory complexes I and II, but also decreases SDH1 flavinylation, and in turn shifts the mitochondrial tricarboxylic acid (TCA) cycle to glycolysis. The deprivation of cellular energy leads to cell-cycle arrest at G1 and S phases in both mitosis and endoreduplication during endosperm development. The unexpected up-regulation of cell-cycle genes in o18 correlates with the increase of H3K4me3 levels, revealing a possible H3K4me-mediated epigenetic back-up mechanism for cell-cycle progression under unfavourable circumstances. Overexpression of O18 increases riboflavin production and confers osmotic tolerance. Altogether, our results substantiate a key role of riboflavin in coordinating cellular energy and cell cycle to modulate maize endosperm development.

A TetR family transcriptional regulator, SP_2854 can affect the butenyl-spinosyn biosynthesis by regulating glucose metabolism in Saccharopolyspora pogona

Background

Butenyl-spinosyn produced by Saccharopolyspora pogona exhibits strong insecticidal activity and a broad pesticidal spectrum. Currently, important functional genes involve in butenyl-spinosyn biosynthesis remain unknown, which leads to difficulty in efficiently understanding its regulatory mechanism, and improving its production by metabolic engineering.

Results

Here, we identified a TetR family transcriptional regulator, SP_2854, that can positively regulate butenyl-spinosyn biosynthesis and affect strain growth, glucose consumption, and mycelial morphology in S. pogona. Using targeted metabolomic analyses, we found that SP_2854 overexpression enhanced glucose metabolism, while SP_2854 deletion had the opposite effect. To decipher the overproduction mechanism in detail, comparative proteomic analysis was carried out in the SP-2854 overexpressing mutant and the original strain, and we found that SP_2854 overexpression promoted the expression of proteins involved in glucose metabolism.

Conclusion

Our findings suggest that SP_2854 can affect strain growth and development and butenyl-spinosyn biosynthesis in S. pogona by controlling glucose metabolism. The strategy reported here will be valuable in paving the way for genetic engineering of regulatory elements in actinomycetes to improve important natural products production.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12934-022-01808-2.

Maize RNA 3'-terminal phosphate cyclase-like protein promotes 18S pre-rRNA cleavage and is important for kernel development

Plant ribosomes contain four specialized ribonucleic acids, the 5S, 5.8S, 18S, and 25S ribosomal RNAs (rRNAs). Maturation of the latter three rRNAs requires cooperative processing of a single transcript by several endonucleases and exonucleases at specific sites. In maize (Zea mays), the exact nucleases and components required for rRNA processing remain poorly understood. Here, we characterized a conserved RNA 3'-terminal phosphate cyclase (RCL)-like protein, RCL1, that functions in 18S rRNA maturation. RCL1 is highly expressed in the embryo and endosperm during early seed development. Loss of RCL1 function resulted in lethality due to aborted embryo cell differentiation. We also observed pleiotropic defects in the rcl1 endosperm, including abnormal basal transfer cell layer growth and aleurone cell identity, and reduced storage reserve accumulation. The rcl1 seeds had lower levels of mature 18S rRNA and the related precursors were altered in abundance compared with wild type. Analysis of transcript levels and protein accumulation in rcl1 revealed that the observed lower levels of zein and starch synthesis enzymes mainly resulted from effects at the transcriptional and translational levels, respectively. These results demonstrate that RCL1-mediated 18S pre-rRNA processing is essential for ribosome function and messenger RNA translation during maize seed development.

Paternal Zn-deficiency abolishes metabolic effects in offspring induced by diet type

Accumulating evidence implicates that offspring are susceptible to paternal alterations in numerous fetal disorders, such as growth and metabolic defects. However, less study has been conducted to define the relationship between paternal zinc deficiency (ZnD) and energy metabolism of offspring. In the present study, we used a paternal ZnD exposure (Zn at 0.3 μg/g) model to test energy metabolism of male and female offspring with the intervention of diet type (high-fat diet and low-fat diet). Our results demonstrated that paternal ZnD decreased body weight (BW) gain per week (P < 0.01) and ME intake per week (P < 0.05) at 11 weeks in male offspring with high-fat diet intervention but not in female offspring. Further, anabolism and catabolism of hepatic energy products also exhibited alterations. ZnD attenuated liver glucose but increased lipids content accompanied with elevated adiponectin and reduction in leptin level in serum, which exhibited lipid metabolic disturbance and smaller ratio of liver weight to BW in male but not female offspring. The qRT-PCR and liver energy metabolites analysis revealed that paternal ZnD mainly induced reduction in glucose tolerance and lowered glucose uptaking ability in male offspring and thereby alleviated glycolysis and the tricarboxylic acid cycle (TCA) cycle, which displayed a male gender-dependency. Therefore, we propose that paternal ZnD abolishes metabolic effects in male offspring induced by diet type intervention. Our findings reveal a novel link between paternal Zn-D and offspring energy metabolism.

The Peroxisomal-CoA Synthetase MoPcs60 Is Important for Fatty Acid Metabolism and Infectious Growth of the Rice Blast Fungus

Fatty acid metabolism is important for the maintenance of fatty acid homeostasis. Free fatty acids, which are toxic in excess, are activated by esterification with coenzyme A (CoA) and then subjected to β-oxidization. Fatty acid β-oxidation-related genes play critical roles in the development and virulence of several phytopathogens. In this study, we identified and characterized a peroxisomal-CoA synthetase in the rice blast fungus Magnaporthe oryzae, MoPCS60, which is a homolog of PCS60 in budding yeast. MoPCS60 was highly expressed during the conidial and early infectious stages and was induced under oleate treatment. Targeted deletion of MoPCS60 resulted in a significant reduction in growth rate when oleate and olive oil were used as the sole carbon sources. Compared with the wild-type strain Guy11, the ΔMopcs60 mutant exhibited fewer peroxisomes, more lipid droplets, and decreased pathogenicity. The distribution of MoPcs60 varied among developmental stages and was mainly localized to peroxisomes in the hyphae, conidia, and appressoria when treated with oleate. Our results suggest that MoPcs60 is a key peroxisomal-CoA synthetase involved in fatty acid β-oxidation and pathogenicity in rice blast fungi.

Integrated multi-omics analysis provides insights into genome evolution and phosphorus deficiency adaptation in pigeonpea (Cajanus cajan)

Pigeonpea (Cajanus cajan) is an important legume food crop and plays a crucial role in a secure food supply in many developing countries. Several previous studies have suggested that pigeonpea has great potential for phosphorus (P) deficiency tolerance, but little is known about the underlying mechanism. In this study, the physiological and molecular responses of pigeonpea roots to phosphate (Pi) starvation were investigated through integrating phenotypic, genomic, transcriptomic, metabolomic, and lipidomic analyses. The results showed that low-Pi treatment increased total root length, root surface area, and root acid phosphatase activity, and promoted the secretion of organic acids (e.g. citric acids, piscidic acids, and protocatechuic acids) and the degradation of phospholipids and other P-containing metabolites in the roots of pigeonpea. Consistent with the morphological, physiological, and biochemical changes, a large number of genes involved in these Pi-starvation responses were significantly upregulated in Pi-deficient pigeonpea roots. Among these Pi-starvation response genes upregulated by low-Pi treatment, four gene families were expanded through recent tandem duplication in the pigeonpea genome, namely phosphate transporter 1 (PHT1), phosphoethanolamine/phosphocholine phosphatase (PECP), fasciclin-like arabinogalactan protein (FLA), and glutamate decarboxylase (GAD). These gene families may be associated with Pi uptake from the soil, phospholipid recycling, root morphological remodeling, and regulation of organic acid exudation. Taken together, our results suggest that pigeonpea employs complex Pi-starvation responses to strengthen P acquisition and utilization during low-Pi stress. This study provides new insights into the genome evolution and P deficiency adaptation mechanism of pigeonpea.

The utility of metabolomics as a tool to inform maize biology

With the rise of high-throughput omics tools and the importance of maize and its products as food and bioethanol, maize metabolism has been extensively explored. Modern maize is still rich in genetic and phenotypic variation, yielding a wide range of structurally and functionally diverse metabolites. The maize metabolome is also incredibly dynamic in terms of topology and subcellular compartmentalization. In this review, we examine a broad range of studies that cover recent developments in maize metabolism. Particular attention is given to current methodologies and to the use of metabolomics as a tool to define biosynthetic pathways and address biological questions. We also touch upon the use of metabolomics to understand maize natural variation and evolution, with a special focus on research that has used metabolite-based genome-wide association studies (mGWASs).

Small kernel 501 (smk501) encodes the RUBylation activating enzyme E1 subunit ECR1 (E1 C-TERMINAL RELATED 1) and is essential for multiple aspects of cellular events during kernel development in maize

RUBylation plays essential roles in plant growth and development through regulating Cullin-RING ubiquitin E3 ligase (CRL) activities and the CRL-mediated protein degradations. However, the function of RUBylation in regulating kernel development remains unclear. Through genetic and molecular analyses of a small kernel 501 (smk501) mutant in maize (Zea mays), we cloned the smk501 gene, revealed its molecular function, and defined its roles in RUBylation pathway and seed development. Smk501 encodes a RUBylation activating enzyme E1 subunit ZmECR1 (E1 C-TERMINAL RELATED 1) protein. Destruction in RUBylation by smk501 mutation resulted in less embryo and endosperm cell number and smaller kernel size. The transcriptome and proteome profiling, hormone evaluation and cell proliferation observation revealed that disturbing ZmECR1 expression mainly affects pathways on hormone signal transduction, cell cycle progression and starch accumulation during kernel development. In addition, mutant in zmaxr1 (Auxin resistant 1), another RUB E1 subunit, also showed similar defects in kernel development. Double mutation of zmecr1 and zmaxr1 lead to empty pericarp kernel phenotype. RUBylation is a novel regulatory pathway affecting maize kernel development, majorly through its functions in modifying multiple cellular progresses.

Regulation of Oxalate Metabolism in Spinach Revealed by RNA-Seq-Based Transcriptomic Analysis

Although spinach (Spinacia oleracea L.) is considered to be one of the most nutrient-rich leafy vegetables, it is also a potent accumulator of anti-nutritional oxalate. Reducing oxalate content would increase the nutritional value of spinach by enhancing the dietary bioavailability of calcium and other minerals. This study aimed to investigate the proposed hypothesis that a complex network of genes associated with intrinsic metabolic and physiological processes regulates oxalate homeostasis in spinach. Transcriptomic (RNA-Seq) analysis of the leaf and root tissues of two spinach genotypes with contrasting oxalate phenotypes was performed under normal physiological conditions. A total of 2308 leaf- and 1686 root-specific differentially expressed genes (DEGs) were identified in the high-oxalate spinach genotype. Gene Ontology (GO) analysis of DEGs identified molecular functions associated with various enzymatic activities, while KEGG pathway analysis revealed enrichment of the metabolic and secondary metabolite pathways. The expression profiles of genes associated with distinct physiological processes suggested that the glyoxylate cycle, ascorbate degradation, and photorespiratory pathway may collectively regulate oxalate in spinach. The data support the idea that isocitrate lyase (ICL), ascorbate catabolism-related genes, and acyl-activating enzyme 3 (AAE3) all play roles in oxalate homeostasis in spinach. The findings from this study provide the foundation for novel insights into oxalate metabolism in spinach.

Biomass, chlorophyll fluorescence, and osmoregulation traits let differentiation of wild and cultivated Amaranthus under water stress

Amaranths are recognized by their high nutritive value and their natural tolerance to environmental stresses. In this study, physiological differences in response to water stress were compared between A. hybridus, a wild species considered as weed, and A. hypochondriacus, the most cultivated species for grain production, under the hypothesis that wild species have better adaptation to stress. In both species, photosynthetic parameters, pigments, and gene expression of selected genes were assessed. Biomass, effective quantum efficiency (Φ_PSII), photochemical quenching (q_P), and electron transport rate (ETR) values were reduced only in A. hybridus due to water deficit. Drought stress promoted proline accumulation by twice in A. hybridus but until three times in A. hypochondriacus. In both species, drought stress reduced net assimilation rate (A), transpiration rate (E), stomatal conductance (g_s), and the expression of phosphoenol pyruvate carboxylase (PEPC). While, maximum quantum efficiency (F_v/F_m), chlorophyll, betacyanins, and the expression of ribulose1-5, bisphosphate carboxylase/oxygenase large subunit (LSU) did not change when plants were subjected to water stress. Likewise, both species accumulated total phenolic compounds and Oxalyl-CoA gene was up-regulated in response to drought. Our results have shown that A. hypochondriacus, the cultivated species, exhibited better tolerance to drought than A. hybridus, the wild species, probably due to an unconsciously selected trait during the domestication process.

An Arabidopsis Oxalyl-CoA Decarboxylase, AtOXC, Is Important for Oxalate Catabolism in Plants

Considering the widespread occurrence of oxalate in nature and its broad impact on a host of organisms, it is surprising that so little is known about the turnover of this important acid. In plants, oxalate oxidase is the most well-studied enzyme capable of degrading oxalate, but not all plants possess this activity. Recently, acyl-activating enzyme 3 (AAE3), encoding an oxalyl-CoA synthetase, was identified in Arabidopsis. This enzyme has been proposed to catalyze the first step in an alternative pathway of oxalate degradation. Since this initial discovery, this enzyme and proposed pathway have been found to be important to other plants and yeast as well. In this study, we identify, in Arabidopsis, an oxalyl-CoA decarboxylase (AtOXC) that is capable of catalyzing the second step in this proposed pathway of oxalate catabolism. This enzyme breaks down oxalyl-CoA, the product of AtAAE3, into formyl-CoA and CO₂. AtOXC:GFP localization suggested that this enzyme functions within the cytosol of the cell. An Atoxc knock-down mutant showed a reduction in the ability to degrade oxalate into CO₂. This reduction in AtOXC activity resulted in an increase in the accumulation of oxalate and the enzyme substrate, oxalyl-CoA. Size exclusion studies suggest that the enzyme functions as a dimer. Computer modeling of the AtOXC enzyme structure identified amino acids of predicted importance in co-factor binding and catalysis. Overall, these results suggest that AtOXC catalyzes the second step in this alternative pathway of oxalate catabolism.

Genome-wide association study identified candidate genes for seed size and seed composition improvement in M. truncatula

Grain legumes are highly valuable plant species, as they produce seeds with high protein content. Increasing seed protein production and improving seed nutritional quality represent an agronomical challenge in order to promote plant protein consumption of a growing population. In this study, we used the genetic diversity, naturally present in Medicago truncatula, a model plant for legumes, to identify genes/loci regulating seed traits. Indeed, using sequencing data of 162 accessions from the Medicago HAPMAP collection, we performed genome-wide association study for 32 seed traits related to seed size and seed composition such as seed protein content/concentration, sulfur content/concentration. Using different GWAS and postGWAS methods, we identified 79 quantitative trait nucleotides (QTNs) as regulating seed size, 41 QTNs for seed composition related to nitrogen (i.e. storage protein) and sulfur (i.e. sulfur-containing amino acid) concentrations/contents. Furthermore, a strong positive correlation between seed size and protein content was revealed within the selected Medicago HAPMAP collection. In addition, several QTNs showed highly significant associations in different seed phenotypes for further functional validation studies, including one near an RNA-Binding Domain protein, which represents a valuable candidate as central regulator determining both seed size and composition. Finally, our findings in M. truncatula represent valuable resources to be exploitable in many legume crop species such as pea, common bean, and soybean due to its high synteny, which enable rapid transfer of these results into breeding programs and eventually help the improvement of legume grain production.

Maize kernel development

Maize (Zea mays) is a leading cereal crop in the world. The maize kernel is the storage organ and the harvest portion of this crop and is closely related to its yield and quality. The development of maize kernel is initiated by the double fertilization event, leading to the formation of a diploid embryo and a triploid endosperm. The embryo and endosperm are then undergone independent developmental programs, resulting in a mature maize kernel which is comprised of a persistent endosperm, a large embryo, and a maternal pericarp. Due to the well-characterized morphogenesis and powerful genetics, maize kernel has long been an excellent model for the study of cereal kernel development. In recent years, with the release of the maize reference genome and the development of new genomic technologies, there has been an explosive expansion of new knowledge for maize kernel development. In this review, we overviewed recent progress in the study of maize kernel development, with an emphasis on genetic mapping of kernel traits, transcriptome analysis during kernel development, functional gene cloning of kernel mutants, and genetic engineering of kernel traits.

Cytosolic malate dehydrogenase 4 modulates cellular energetics and storage reserve accumulation in maize endosperm

Cytosolic malate dehydrogenase (MDH) is a key enzyme that regulates the interconversion between malate and oxaloacetate (OAA). However, its role in modulating storage compound accumulation in maize endosperm is largely unknown. Here, we characterized a novel naturally occurring maize mdh4-1 mutant, which produces small, opaque kernels and exhibits reduced starch but enhanced lysine content. Map-based cloning, functional complementation and allelism analyses identified ZmMdh4 as the causal gene. Enzymatic assays demonstrated that ZmMDH4 predominantly catalyses the conversion from OAA to malate. In comparison, the activity of the mutant enzyme, which lacks one glutamic acid (Glu), was completed abolished, demonstrating that the Glu residue was essential for ZmMDH4 function. Knocking down ZmMdh4 in vivo led to a substantial metabolic shift towards glycolysis and a dramatic disruption in the activity of the mitochondrial complex I, which was correlated with transcriptomic alterations. Taken together, these results demonstrate that ZmMdh4 regulates the balance between mitochondrial respiration and glycolysis, ATP production and endosperm development, through a yet unknown feedback regulatory mechanism in mitochondria.

Wild Soybean Oxalyl-CoA Synthetase Degrades Oxalate and Affects the Tolerance to Cadmium and Aluminum Stresses

Acyl activating enzyme 3 (AAE3) was identified as being involved in the acetylation pathway of oxalate degradation, which regulates the responses to biotic and abiotic stresses in various higher plants. Here, we investigated the role of Glycine sojaAAE3 (GsAAE3) in Cadmium (Cd) and Aluminum (Al) tolerances. The recombinant GsAAE3 protein showed high activity toward oxalate, with a Km of 105.10 ± 12.30 μM and Vmax of 12.64 ± 0.34 μmol min-1 mg-1 protein, suggesting that it functions as an oxalyl-CoA synthetase. The expression of a GsAAE3-green fluorescent protein (GFP) fusion protein in tobacco leaves did not reveal a specific subcellular localization pattern of GsAAE3. An analysis of the GsAAE3 expression pattern revealed an increase in GsAAE3 expression in response to Cd and Al stresses, and it is mainly expressed in root tips. Furthermore, oxalate accumulation induced by Cd and Al contributes to the inhibition of root growth in wild soybean. Importantly, GsAAE3 overexpression increases Cd and Al tolerances in A. thaliana and soybean hairy roots, which is associated with a decrease in oxalate accumulation. Taken together, our data provide evidence that the GsAAE3-encoded protein plays an important role in coping with Cd and Al stresses.

New insights into the functions of carbon-calcium inclusions in plants

Carbon-calcium inclusions (CCaI) either as calcium oxalate crystals (CaOx) or amorphous calcium carbonate cystoliths are spread among most photosynthetic organisms. They represent dynamic structures with a significant construction cost and their appearance during evolution indicates an ancient origin. Both types of inclusions share some similar functional characteristics providing adaptive advantages such as the regulation of Ca levels, and the release of CO₂ and water molecules upon decomposition. The latter seems to be essential under drought conditions and explains the intense occurrence of these structures in plants thriving in dry climates. It seems, however, that for plants CaOx may represent a more prevalent storage system compared with CaCO₃ due to the multifunctionality of oxalate. This compound participates in a number of important soil biogeochemical processes, creates endosymbiosis with beneficial bacteria and provides tolerance against a combination of abiotic (nutrient deprivation, metal toxicity) and biotic (pathogens, herbivores) stress factors. We suggest a re-evaluation of the roles of these fascinating plant structures under a new and holistic approach that could enhance our understanding of carbon sequestration at the whole plant level and provide future perspectives.

Carotenoids modulate kernel texture in maize by influencing amyloplast envelope integrity

The mechanism that creates vitreous endosperm in the mature maize kernel is poorly understood. We identified Vitreous endosperm 1 (Ven1) as a major QTL influencing this process. Ven1 encodes β-carotene hydroxylase 3, an enzyme that modulates carotenoid composition in the amyloplast envelope. The A619 inbred contains a nonfunctional Ven1 allele, leading to a decrease in polar and an increase in non-polar carotenoids in the amyloplast. Coincidently, the stability of amyloplast membranes is increased during kernel desiccation. The lipid composition in endosperm cells in A619 is altered, giving rise to a persistent amyloplast envelope. These changes impede the gathering of protein bodies and prevent them from interacting with starch grains, creating air spaces that cause an opaque kernel phenotype. Genetic modifiers were identified that alter the effect of Ven1^A619, while maintaining a high β-carotene level. These studies provide insight for breeding vitreous kernel varieties and high vitamin A content in maize.

Very little is known about how vitreous endosperm in the mature maize kernel is created. Here, via map-based cloning, the authors find that mutation of a β-carotene hydroxylase 3 encoding gene Ven1 affects carotenoids and lipids composition, which consequently influences amyloplast envelope integrity.

Loss of Function of an RNA Polymerase III Subunit Leads to Impaired Maize Kernel Development

Kernel size is an important factor determining grain yield. Although a number of genes affecting kernel development in maize (Zea mays) have been identified by analyzing kernel mutants, most of the corresponding mutants cannot be used in maize breeding programs due to low germination or incomplete seed development. Here, we characterized small kernel7, a recessive small-kernel mutant with a mutation in the gene encoding the second-largest subunit of RNA polymerase III (RNAPΙΙΙ; NRPC2). A frame shift in ZmNRPC2 leads to a premature stop codon, resulting in significantly reduced levels of transfer RNAs and 5S ribosomal RNA, which are transcribed by RNAPΙΙΙ. Loss-of-function nrpc2 mutants created by CRISPR/CAS9 showed significantly reduced kernel size due to altered endosperm cell size and number. ZmNRPC2 affects RNAPIII activity and the expression of genes involved in cell proliferation and endoreduplication to control kernel development via physically interacting with RNAPIII subunits RPC53 and AC40, transcription factor class C1 and Floury3. Notably, unlike the semidominant negative mutant floury3, which has defects in starchy endosperm, small kernel7 only affects kernel size but not the composition of kernel storage proteins. Our findings provide novel insights into the molecular network underlying maize kernel size, which could facilitate the genetic improvement of maize in the future.

The regulation of zein biosynthesis in maize endosperm

We review the current knowledge regarding the regulation of zein storage proteins biosynthesis and protein body formation, which are crucial processes for the successful accumulation of nutrients in maize kernels. Storage proteins in the seeds of crops in the grass family (Poaceae) are a major source of dietary protein for humans. In maize (Zea mays), proteins are the second largest nutrient component in the kernels, accounting for ~ 10% of the kernel weight. Over half of the storage proteins in maize kernels are zeins, which lack two essential amino acids, lysine and tryptophan. This deficiency limits the use of maize proteins in the food and feed industries. Zeins are encoded by a large super-gene family. During endosperm development, zeins accumulate in protein bodies, which are derived from the rough endoplasmic reticulum. In recent years, our knowledge of the pathways of zein biosynthesis and their deposition within the endosperm has been greatly expanded. In this review, we summarize the current understanding of zeins, including the genes encoding these proteins, their expression patterns and transcriptional regulation, the process of protein body formation, and other biological processes affecting zein accumulation.

An update on the maize zein-gene family in the post-genomics era

Maize (Zea mays) is a cereal crop of global food importance. However, the deficiency of essential amino acids, more importantly lysine, methionine and tryptophan, in the major seed storage zein proteins makes corn nutritionally of low value for human consumption. The idea of improving maize nutritional value prompted the search for maize natural mutants harboring low zein contents and higher amount of lysine. These studies resulted in the identification of more than dozens of maize opaque mutants in the previous few decades,o2mutant being the most extensively studied one. However, the high lysine contents but soft kernel texture and chalky endosperm halted the widespread application and commercial success of maize opaque mutants, which ultimately paved the way for the development of Quality Protein Maize (QPM) by modifying the soft endosperm ofo2 mutant into lysine-rich hard endosperm. The previous few decades have witnessed a marked progress in maize zein research. It includes elucidation of molecular mechanism underlying the role of different zein genes in seed endosperm development by cloning different components of zein family, exploring the general organization, function and evolution of zein family members within maize species and among other cereals, and elucidating the cis- and trans-regulatory elements modulating the regulation of different molecular players of maize seed endosperm development. The current advances in high quality reference genomes of maize lines B73 and Mo17 plus the completion of ongoing pan genome sequencing projects of more maize lines with NGS technologies are expected to revolutionize maize zein gene research in near future. This review highlights the recent advances in QPM development and its practical application in the post genomic era, genomic and physical composition and evolution of zein family, and expression, regulation and downstream role of zein genes in endosperm development. Moreover, recent genomic tools and methods developed for functional validation of maize zein genes are also discussed.

Graphical abstract

EMB-7L is required for embryogenesis and plant development in maize involved in RNA splicing of multiple chloroplast genes

Embryo and endosperm originate from the double fertilization, but they have different developmental fates and biological functions. We identified a previously undescribed maize seed mutant, wherein the embryo appears to be more severely affected than the endosperm (embryo-specific, emb). In the W22 background, the emb embryo arrests at the transition stage whereas its endosperm appears nearly normal in size. At maturity, the embryo in W22-emb is apparently small or even invisible. In contrast, the emb endosperm develops into a relative normal size. We cloned the mutant gene on the Chromosome 7L and designated it emb-7L. This gene is generally expressed, but it has a relatively higher expression level in leaves. Emb-7L encodes a chloroplast-localized P-type pentatricopeptide repeat (PPR) protein, consistent with the severe chloroplast deficiency in emb-7L albino seedling leaves. Full transcriptome analysis of the leaves of WT and emb-7L seedlings reveals that transcription of chloroplast protein-encoding genes are dramatically variable with pre-mRNA intron splicing apparently affected in a tissue-dependent pattern and the chloroplast structure and activity were dramatically affected including chloroplast membrane and photosynthesis machinery component and synthesis of metabolic products (e.g., fatty acids, amino acids, starch).

Manipulation of oxalate metabolism in plants for improving food quality and productivity

Oxalic acid is a naturally occurring metabolite in plants and a common constituent of all plant-derived human diets. Oxalic acid has diverse unrelated roles in plant metabolism, including pH regulation in association with nitrogen metabolism, metal ion homeostasis and calcium storage. In plants, oxalic acid is also a pathogenesis factor and is secreted by various fungi during host infection. Unlike those of plants, fungi and bacteria, the human genome does not contain any oxalate-degrading genes, and therefore, the consumption of large amounts of plant-derived oxalate is considered detrimental to human health. In this review, we discuss recent biotechnological approaches that have been used to reduce the oxalate content of plant tissues.