Regulation of amino acid metabolic enzymes and transporters in plants

Ionic titanium is expected to improve the nutritional quality of Tartary buckwheat sprouts through flavonoids and amino acid metabolism

Tartary buckwheat sprouts are highly valued by consumers for their superior nutritional content. Ionic titanium (Ti) has been shown to enhance crop growth and improve nutritional quality. However, there is limited research on the impact of ionic Ti on the nutritional quality of Tartary buckwheat sprouts. This study cultivated Tartary buckwheat sprouts with ionic Ti and found that the high concentration of ionic Ti significantly increased the contents of chlorophyll a, chlorophyll b, and carotenoids (increased by 25.5%, 27.57%, and 15.11%, respectively). The lower concentration of ionic Ti has a higher accumulation of total flavonoids and total polyphenols. Metabolomics analysis by LC-MS revealed 589 differentially expressed metabolites and 54 significantly different metabolites, enriching 82 metabolic pathways, especially including amino acid biosynthesis and flavonoid biosynthesis. This study shows that ionic Ti can promote the growth of Tartary buckwheat sprouts, improve nutritional quality, and have huge development potential in food production.

RNA-seq reveals the gene expression in patterns in Populus × euramericana 'Neva' plantation under different precision water and fertilizer-intensive management

BACKGROUND

Populus spp. is a crucial fast-growing and productive tree species extensively cultivated in the mid-latitude plains of the world. However, the impact of intensive cultivation management on gene expression in plantation remains largely unexplored.

RESULTS

Precision water and fertilizer-intensive management substantially increased key enzyme activities of nitrogen transport, assimilation, and photosynthesis (1.12-2.63 times than CK) in Populus × euramericana 'Neva' plantation. Meanwhile, this management approach had a significant regulatory effect on the gene expression of poplar plantations. 1554 differential expression genes (DEGs)were identified in drip irrigation (ND) compared with conventional irrigation. Relative to ND, 2761-4116 DEGs, predominantly up-regulated, were identified under three drip fertilization combinations, among which 202 DEGs were mainly regulated by fertilization. Moreover, drip irrigation reduced the expression of cell wall synthesis-related genes to reduce unnecessary water transport. Precision drip and fertilizer-intensive management promotes the synergistic regulation of carbon and nitrogen metabolism and up-regulates the expression of major genes in nitrogen transport and assimilation processes (5 DEGs), photosynthesis (15 DEGs), and plant hormone signal transduction (11 DEGs). The incorporation of trace elements further enhanced the up-regulation of secondary metabolic process genes. In addition, the co-expression network identified nine hub genes regulated by precision water and fertilizer-intensive management, suggesting a pivotal role in regulating the growth of poplar.

CONCLUSION

Precision water and fertilizer-intensive management demonstrated the ability to regulate the expression of key genes and transcription factor genes involved in carbon and nitrogen metabolism pathways, plant hormone signal transduction, and enhance the activity of key enzymes involved in related processes. This regulation facilitated nitrogen absorption and utilization, and photosynthetic abilities such as light capture, light transport, and electron transport, which faintly synergistically regulate the growth of poplar plantations. These results provide a reference for proposing highly efficient precision intensive management to optimize the expression of target genes.

Lactiplantibacillus argentoratensis AGMB00912 alleviates salmonellosis and modulates gut microbiota in weaned piglets: a pilot study

This study aimed to evaluate the efficacy of Lactiplantibacillus argentoratensis AGMB00912 (LA) in reducing Salmonella Typhimurium infection in weaned piglets. The investigation focused on the influence of LA on the gut microbiota composition, growth performance, and Salmonella fecal shedding. The results indicated that LA supplementation significantly improved average daily gain and reduced the prevalence and severity of diarrhea. Fecal analysis revealed reduced Salmonella shedding in the LA-supplemented group. Furthermore, LA notably altered the composition of the gut microbiota, increasing the levels of beneficial Bacillus and decreasing those of harmful Proteobacteria and Spirochaetes. Histopathological examination showed less intestinal damage in LA-treated piglets than in the controls. The study also observed that LA affected metabolic functions related to carbohydrate, amino acid, and fatty acid metabolism, thereby enhancing gut health and resilience against infection. Short-chain fatty acid concentrations in the feces were higher in the LA group, suggesting improved gut microbial activity. LA supplementation enriched the population of beneficial bacteria, including Streptococcus, Clostridium, and Bifidobacterium, while reducing the number of harmful bacteria, such as Escherichia and Campylobacter. These findings indicate the potential of LA as a probiotic alternative for swine nutrition, offering protective effects to the gut microbiota against Salmonella infection.

Non-target metabolomics approach for the investigation of the hidden effects induced by atrazine and its degradation products on plant metabolism

Japanese radish (Raphanus sativus var. longipinnatus) plants grown under laboratory conditions were individually exposed to the same doses of atrazine (2-chloro-4-ethylamino-6-isopropylamino-1,3,5-triazine, ATR) or its main degradation products: either 2-amino-4-chloro-6-isopropylamino-1,3,5-triazine (DEA) or 2-amino-4-chloro-6-ethylamino-1,3,5-triazine (DIA) or desethyl-desisopropyl-atrazine (DEDIA) or 4-(ethylamino)-2-hydroxy-6-(isopropylamino)-1,3,5-triazine (HA), respectively. One week after treatment in plants exposed to ATR, DIA, and DEA, their concentrations were 7.8 μg/g, 9.7 μg/g, and 14.5 μg/g, respectively, while those treated with DEDIA and HA did not contain these compounds. These results were correlated with plant amino acid profile obtained by suspect screening analysis and metabolomic "fingerprint" based on non-target analysis, obtained by liquid chromatography coupled with QTRAP triple quadrupole mass spectrometer. In all cases, both ATR and its by-products were found to interfere with the plant's amino acid profile and modify its metabolic "fingerprint". Therefore, we proved that the non-target metabolomics approach is an effective tool for investigating the hidden effects of pesticides and their transformation products, which is particularly important as these compounds may reduce the quality of edible plants.

Selenium Nanomaterials Enhance Sheath Blight Resistance and Nutritional Quality of Rice: Mechanisms of Action and Human Health Benefit

In the current work, the foliar application of selenium nanomaterials (Se0 NMs) suppressed sheath blight in rice (Oryza sativa). The beneficial effects were nanoscale specific and concentration dependent. Specifically, foliar amendment of 5 mg/L Se0 NMs decreased the disease severity by 68.8% in Rhizoctonia solani-infected rice; this level of control was 1.57- and 2.20-fold greater than that of the Se ions with equivalent Se mass and a commercially available pesticide (Thifluzamide). Mechanistically, (1) the controlled release ability of Se0 NMs enabled a wider safe concentration range and greater bioavailability to Se0 NMs, and (2) transcriptomic and metabolomic analyses demonstrated that Se0 NMs simultaneously promoted the salicylic acid- and jasmonic-acid-dependent acquired disease resistance pathways, antioxidative system, and flavonoid biosynthesis. Additionally, Se0 NMs improved rice yield by 31.1%, increased the nutritional quality by 6.4-7.2%, enhanced organic Se content by 44.8%, and decreased arsenic and cadmium contents by 38.7 and 42.1%, respectively, in grains as compared with infected controls. Human simulated gastrointestinal tract model results showed that the application of Se0 NMs enhanced the bioaccessibility of Se in grains by 22.0% and decreased the bioaccessibility of As and Cd in grains by 20.3 and 13.4%, respectively. These findings demonstrate that Se0 NMs can serve as an effective and sustainable strategy to increase food quality and security.

Nematodes alter the taxonomic and functional profiles of benthic bacterial communities: A metatranscriptomic approach

Marine sediments cover 70% of the Earth's surface, and harbour diverse bacterial communities critical for marine biogeochemical processes, which affect climate change, biodiversity and ecosystem functioning. Nematodes, the most abundant and species-rich metazoan organisms in marine sediments, in turn, affect benthic bacterial communities and bacterial-mediated ecological processes, but the underlying mechanisms by which they affect biogeochemical cycles remain poorly understood. Here, we demonstrate using a metatranscriptomic approach that nematodes alter the taxonomic and functional profiles of benthic bacterial communities. We found particularly strong stimulation of nitrogen-fixing and methane-oxidizing bacteria in the presence of nematodes, as well as increased functional activity associated with methane metabolism and degradation of various carbon compounds. This study provides empirical evidence that the presence of nematodes results in taxonomic and functional shifts in active bacterial communities, indicating that nematodes may play an important role in benthic ecosystem processes.

Review: Nitrogen acquisition, assimilation, and seasonal cycling in perennial grasses

Perennial grasses seasonal nitrogen (N) cycle extends the residence and reuse time of N within the plant system, thereby enhancing N use efficiency. Currently, the mechanism of N metabolism has been extensively examined in model plants and annual grasses, and although perennial grasses exhibit similarities, they also possess distinct characteristics. Apart from assimilating and utilizing N throughout the growing season, perennial grasses also translocate N from aerial parts to perennial tissues, such as rhizomes, after autumn senescence. Subsequently, they remobilize the N from these perennial tissues to support new growth in the subsequent year, thereby ensuring their persistence. Previous studies indicate that the seasonal storage and remobilization of N in perennial grasses are not significantly associated with winter survival despite some amino acids and proteins associated with low temperature tolerance accumulating, but primarily with regrowth during the subsequent spring green-up stage. Further investigation can be conducted in perennial grasses to explore the correlation between stored N and dormant bud outgrowth in perennial tissues, such as rhizomes, during the spring green-up stage, building upon previous research on the relationship between N and axillary bud outgrowth in annual grasses. This exploration on seasonal N cycling in perennial grasses can offer valuable theoretical insights for new perennial grasses varieties with high N use efficiency through the application of gene editing and other advanced technologies.

Transcriptomic and Metabolomic Research on the Germination Process of Panax ginseng Overwintering Buds

Ginseng (Panax ginseng C. A. Meyer) is a perennial plant with a long dormancy period. While some researchers employ gibberellin and other substances to stimulate premature germination, this method is limited to laboratory settings and cannot be applied to the field cultivation of ginseng. The mechanism underlying the germination of ginseng overwintering buds remains largely unexplored. Understanding the internal changes during the dormancy release process in the overwintering buds would facilitate the discovery of potential genes, metabolites, or regulatory pathways associated with it. In this study, we approximately determined the onset of dormancy release through morphological observations and investigated the process of dormancy release in ginseng overwintering buds using transcriptomic and metabolomic approaches. Our analyses revealed that the germination process of ginseng overwintering buds is regulated by multiple plant hormones, each acting at different times. Among these, abscisic acid (ABA) and gibberellic acid (GA) serve as classical signaling molecules regulating the dormancy process, while other hormones may promote the subsequent growth of overwintering buds. Additionally, metabolic pathways associated with arginine may be involved in the dormancy release process. Polyamines synthesized downstream may promote the growth of overwintering buds after dormancy release and participate in subsequent reproductive growth. This study provides insights into the germination process of ginseng overwintering buds at the molecular level and serves as a reference for further exploration of the detailed mechanism underlying ginseng overwintering germination in the future.

UMAMIT44 is a key player in glutamate export from Arabidopsis chloroplasts

Selective partitioning of amino acids among organelles, cells, tissues, and organs is essential for cellular metabolism and plant growth. Nitrogen assimilation into glutamine and glutamate and de novo biosynthesis of most protein amino acids occur in chloroplasts; therefore, various transport mechanisms must exist to accommodate their directional efflux from the stroma to the cytosol and feed the amino acids into the extraplastidial metabolic and long-distance transport pathways. Yet, Arabidopsis (Arabidopsis thaliana) transporters functioning in plastidial export of amino acids remained undiscovered. Here, USUALLY MULTIPLE ACIDS MOVE IN AND OUT TRANSPORTER 44 (UMAMIT44) was identified and shown to function in glutamate export from Arabidopsis chloroplasts. UMAMIT44 controls glutamate homeostasis within and outside of chloroplasts and influences nitrogen partitioning from leaves to sinks. Glutamate imbalances in chloroplasts and leaves of umamit44 mutants impact cellular redox state, nitrogen and carbon metabolism, and amino acid (AA) and sucrose supply of growing sinks, leading to negative effects on plant growth. Nonetheless, the mutant lines adjust to some extent by upregulating alternative pathways for glutamate synthesis outside the plastids and by mitigating oxidative stress through the production of other amino acids and antioxidants. Overall, this study establishes that the role of UMAMIT44 in glutamate export from chloroplasts is vital for controlling nitrogen availability within source leaf cells and for sink nutrition, with an impact on growth and seed yield.

LC-QTOF/MS-based non-targeted metabolomics to explore the toxic effects of di(2-ethylhexyl) phthalate (DEHP) on Brassica chinensis L

Di(2-ethylhexyl) phthalate (DEHP) is a widely used plasticizer known to pose health risks to humans upon exposure. Recognizing the toxic nature of DEHP, our study aimed to elucidate the response mechanisms in Brassica chinensis L. (Shanghai Qing) when subjected to varying concentrations of DEHP (2 mg kg-1, 20 mg kg-1, and 50 mg kg-1), particularly under tissue stress. The findings underscored the substantial impact of DEHP treatment on the growth of Brassica chinensis L., with increased DEHP concentration leading to a notable decrease in chlorophyll levels and alterations in the content of antioxidant enzyme activities, particularly superoxide dismutase (SOD) and peroxidase (POD). Moreover, elevated DEHP concentrations correlated with increased malondialdehyde (MDA) levels. Our analysis detected a total of 507 metabolites in Brassica chinensis L., with 331 in shoots and 176 in roots, following DEHP exposure. There was a significant difference in the number of metabolites in shoots and roots, with 79 and 64 identified, respectively (VIP > 1, p < 0.05). Metabolic pathway enrichment in Brassica chinensis L. shoots revealed significant perturbations in valine, leucine, and isoleucine biosynthesis and degradation, aminoacyl-tRNA, and glucosinolate biosynthesis. In the roots of Brassica chinensis L., varying DEHP levels exerted a substantial impact on the biosynthesis of zeatin, ubiquinone terpenoids, propane, piperidine, and pyridine alkaloids, as well as glutathione metabolic pathways. Notably, DEHP's influence was more pronounced in the roots than in the shoots, with higher DEHP concentrations affecting a greater number of metabolic pathways. This experimental study provides valuable insights into the molecular mechanisms underlying DEHP-induced stress in Brassica chinensis L., with potential implications for human health and food safety.

Genome-wide identification and comparative analysis of the Amino Acid Transporter (AAT) gene family and their roles during Phaseolus vulgaris symbioses

Amino acid transporters (AATs) are essential integral membrane proteins that serve multiple roles, such as facilitating the transport of amino acids across cell membranes. They play a crucial role in the growth and development of plants. Phaseolus vulgaris, a significant legume crop, serves as a valuable model for studying root symbiosis. In this study, we have conducted an exploration of the AAT gene family in P. vulgaris. In this research, we identified 84 AAT genes within the P. vulgaris genome sequence and categorized them into 12 subfamilies based on their similarity and phylogenetic relationships with AATs found in Arabidopsis and rice. Interestingly, these AAT genes were not evenly distributed across the chromosomes of P. vulgaris . Instead, there was an unusual concentration of these genes located toward the outer edges of chromosomal arms. Upon conducting motif analysis and gene structural analysis, we observed a consistent presence of similar motifs and an intron-exon distribution pattern among the subfamilies. When we analyzed the expression profiles of PvAAT genes, we noted tissue-specific expression patterns. Furthermore, our investigation into AAT gene expression under rhizobial and mycorrhizal symbiotic conditions revealed that certain genes exhibited high levels of expression. Specifically, ATLa5 and LHT2 was notably upregulated under both symbiotic conditions. These findings point towards a potential role of AATs in the context of rhizobial and mycorrhizal symbiosis in P. vulgaris, in addition to their well-established regulatory functions.

Quality Evaluation of Asparagus officinalis by Profile of Amino Acids and Mineral Elements in Different Parts Combined with Chemometrics Methods

Asparagus officinalis has a homologous value in medicine and vegetables. Its immature stem, commonly called asparagus, is a central edible part. Asparagus skin and leaf also contain rich nutrients. However, these parts are often discarded. This study investigated amino acid and mineral elements in immature stem, skinless asparagus, asparagus skin, and leaf. Their quality was further evaluated by chemometrics methods such as principal component analysis and neural network analysis. The results showed amino acid content was high in immature stem and skinless asparagus and low in leaf, whereas the mineral elements were in four parts. Quality evaluation results showed four parts were divided into three grades. Immature stem and skinless asparagus were grouped into cluster 1 with the best quality as high-quality raw materials in food and health-care products. Meanwhile, three AA (Cys, His, Arg) and two mineral elements (Na, Cr) were identified as quality evaluation iconic substances.

Transcriptome Analysis and Metabolic Profiling Reveal the Key Regulatory Pathways in Drought Stress Responses and Recovery in Tomatoes

Drought stress is a major abiotic factor affecting tomato production and fruit quality. However, the genes and metabolites associated with tomato responses to water deficiency and rehydration are poorly characterized. To identify the functional genes and key metabolic pathways underlying tomato responses to drought stress and recovery, drought-susceptible and drought-tolerant inbred lines underwent transcriptomic and metabolomic analyses. A total of 332 drought-responsive and 491 rehydration-responsive core genes were robustly differentially expressed in both genotypes. The drought-responsive and rehydration-responsive genes were mainly related to photosynthesis-antenna proteins, nitrogen metabolism, plant-pathogen interactions, and the MAPK signaling pathway. Various transcription factors, including homeobox-leucine zipper protein ATHB-12, NAC transcription factor 29, and heat stress transcription factor A-6b-like, may be vital for tomato responses to water status. Moreover, 24,30-dihydroxy-12(13)-enolupinol, caffeoyl hawthorn acid, adenosine 5'-monophosphate, and guanosine were the key metabolites identified in both genotypes under drought and recovery conditions. The combined transcriptomic and metabolomic analysis highlighted the importance of 38 genes involved in metabolic pathways, the biosynthesis of secondary metabolites, the biosynthesis of amino acids, and ABC transporters for tomato responses to water stress. Our results provide valuable clues regarding the molecular basis of drought tolerance and rehydration. The data presented herein may be relevant for genetically improving tomatoes to enhance drought tolerance.

Key Role of Vegetation Cover in Alleviating Microplastic-Enhanced Carbon Emissions

Microplastics (MPs) are considered to influence fundamental biogeochemical processes, but the effects of plant residue-MP interactions on soil carbon turnover in urban greenspaces are virtually unknown. Here, an 84-day incubation experiment was constructed using four types of single-vegetation-covered soils (6 years), showing that polystyrene MP (PSMP) pollution caused an unexpectedly large increase in soil CO2 emissions. The additional CO2 originating from highly bioavailable active dissolved organic matter molecules (<380 °C, predominantly polysaccharides) was converted from persistent carbon (380-650 °C, predominantly aromatic compounds) rather than PSMP derivatives. However, the priming effect of PSMP derivatives was weakened in plant-driven soils (resistivity: shrub > tree > grass). This can be explained from two perspectives: (1) Plant residue-driven humification processes reduced the percentage of bioavailable active dissolved organic matter derived from the priming effects of PSMPs. (2) Plant residues accelerated bacterial community succession (dominated by plant residue types) but slowed fungal community demise (retained carbon turnover-related functional taxa), enabling specific enrichment of glycolysis, the citric acid cycle and the pentose phosphate pathway. These results provide a necessary theoretical basis to understand the role of plant residues in reducing PSMP harm at the ecological level and refresh knowledge about the importance of biodiversity for ecosystem stability.

Origin and Function of Amino Acids in Nectar and Nectaries of Pitcairnia Species with Particular Emphasis on Alanine and Glutamine

Floral nectar contains sugars and numerous other compounds, including amino acids, but little is known about their function and origin in nectar. Therefore, the amino acid, sugar, and inorganic ion concentrations, as well as the activity of alanine aminotransferase (AlaAT) and glutamine synthetase (GS) in nectar, nectaries, and leaves were analyzed in 30 Pitcairnia species. These data were compared with various floral traits, the pollinator type, and the phylogenetic relationships of the species to find possible causes for the high amino acid concentrations in the nectar of some species. The highest concentrations of amino acids (especially alanine) in nectar were found in species with reddish flowers. Furthermore, the concentration of amino acids in nectar and nectaries is determined through analyzing flower color/pollination type rather than phylogenetic relations. This study provides new insights into the origin of amino acids in nectar. The presence of almost all amino acids in nectar is mainly due to their transport in the phloem to the nectaries, with the exception of alanine, which is partially produced in nectaries. In addition, active regulatory mechanisms are required in nectaries that retain most of the amino acids and allow the selective secretion of specific amino acids, such as alanine.

Radiocarbon Flux Measurements Reveal Mechanistic Insight into Heat-Stress Induction of Nicotine Biosynthesis in Nicotiana attenuata

The effect of high-temperature (HT) stress on nicotine biosynthesis in Nicotiana attenuata was examined. Nicotine content was measured in mature leaves, young sink leaves, and in roots from well-watered plants grown at 25 °C as controls and from plants exposed to 38 °C and 43 °C temperatures applied for 24, 48, 72, and 96 h duration. At 38 °C, all leaf nicotine levels were significantly less than control plants for up to 72 h exposure but rose sharply thereafter to levels significantly greater than controls with 96 h exposure. In contrast, plants exposed to 43 °C never exhibited a reduction in leaf nicotine content and showed an increase in content with just 48 h exposure. Using radioactive 11CO2 and 13NO3-, we found that HT stress reduced both CO2 fixation and nitrate uptake. Furthermore, radiocarbon flux analysis revealed that 'new' carbon partitioning (as 11C) into the 11C-radiolabeled amino acid (AA) pool was significantly reduced with HT stress as were yields of [11C]-aspartic acid, an important AA in nicotine biosynthesis, and its beta-amido counterpart [11C]-asparagine. In contrast, [12C]-aspartic acid levels appeared unaffected at 38 °C but were elevated at 43 °C relative to controls. [12C]-Asparagine levels were noted to be elevated at both stress temperatures. Since HT reductions in carbon input and nitrogen uptake were noted to impede de novo AA biosynthesis, protein degradation at HT was examined as a source of AAs. Here, leaf total soluble protein (TSP) content was reduced 39% with long exposures to both stress temperatures. However, Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) which was 41% TSP appeared unaffected. Altogether, these results support the theory that plant proteins other than Rubisco degrade at elevated temperatures freeing up essential AAs in support of nicotine biosynthesis.

Jasmonates Coordinate Secondary with Primary Metabolism

Jasmonates (JAs), including jasmonic acid (JA), its precursor 12-oxo-phytodienoic acid (OPDA) and its derivatives jasmonoyl-isoleucine (JA-Ile), methyl jasmonate (MeJA), cis-jasmone (CJ) and other oxylipins, are important in the regulation of a range of ecological interactions of plants with their abiotic and particularly their biotic environments. Plant secondary/specialized metabolites play critical roles in implementing these ecological functions of JAs. Pathway and transcriptional regulation analyses have established a central role of JA-Ile-mediated core signaling in promoting the biosynthesis of a great diversity of secondary metabolites. Here, we summarized the advances in JAs-induced secondary metabolites, particularly in secondary metabolites induced by OPDA and volatile organic compounds (VOCs) induced by CJ through signaling independent of JA-Ile. The roles of JAs in integrating and coordinating the primary and secondary metabolism, thereby orchestrating plant growth-defense tradeoffs, were highlighted and discussed. Finally, we provided perspectives on the improvement of the adaptability and resilience of plants to changing environments and the production of valuable phytochemicals by exploiting JAs-regulated secondary metabolites.

Molecular Mechanisms of Pseudomonas-Assisted Plant Nitrogen Uptake: Opportunities for Modern Agriculture

Pseudomonas spp. make up 1.6% of the bacteria in the soil and are found throughout the world. More than 140 species of this genus have been identified, some beneficial to the plant. Several species in the family Pseudomonadaceae, including Azotobacter vinelandii AvOP, Pseudomonas stutzeri A1501, Pseudomonas stutzeri DSM4166, Pseudomonas szotifigens 6HT33bT, and Pseudomonas sp. strain K1 can fix nitrogen from the air. The genes required for these reactions are organized in a nitrogen fixation island, obtained via horizontal gene transfer from Klebsiella pneumoniae, Pseudomonas stutzeri, and Azotobacter vinelandii. Today, this island is conserved in Pseudomonas spp. from different geographical locations, which, in turn, have evolved to deal with different geo-climatic conditions. Here, we summarize the molecular mechanisms behind Pseudomonas-driven plant growth promotion, with particular focus on improving plant performance at limiting nitrogen (N) and improving plant N content. We describe Pseudomonas-plant interaction strategies in the soil, noting that the mechanisms of denitrification, ammonification, and secondary metabolite signaling are only marginally explored. Plant growth promotion is dependent on the abiotic conditions and differs at sufficient and deficient N. The molecular controls behind different plant responses are not fully elucidated. We suggest that superposition of transcriptome, proteome, and metabolome data and their integration with plant phenotype development through time will help fill these gaps. The aim of this review is to summarize the knowledge behind Pseudomonas-driven nitrogen fixation and to point to possible agricultural solutions. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

Insight into de-regulation of amino acid feedback inhibition: a focus on structure analysis method

Regulation of amino acid's biosynthetic pathway is of significant importance to maintain homeostasis and cell functions. Amino acids regulate their biosynthetic pathway by end-product feedback inhibition of enzymes catalyzing committed steps of a pathway. Discovery of new feedback resistant enzyme variants to enhance industrial production of amino acids is a key objective in industrial biotechnology. Deregulation of feedback inhibition has been achieved for various enzymes using in vitro and in silico mutagenesis techniques. As enzyme's function, its substrate binding capacity, catalysis activity, regulation and stability are dependent on its structural characteristics, here, we provide detailed structural analysis of all feedback sensitive enzyme targets in amino acid biosynthetic pathways. Current review summarizes information regarding structural characteristics of various enzyme targets and effect of mutations on their structures and functions especially in terms of deregulation of feedback inhibition. Furthermore, applicability of various experimental as well as computational mutagenesis techniques to accomplish feedback resistance has also been discussed in detail to have an insight into various aspects of research work reported in this particular field of study.

Casein as protein and hydrolysate: Biostimulant or nitrogen source for Nicotiana tabacum plants grown in vitro?

In contrast to inorganic nitrogen (N) assimilation, the role of organic N forms, such as proteins and peptides, as sources of N and their impact on plant metabolism remains unclear. Simultaneously, organic biostimulants are used as priming agents to improve plant defense response. Here, we analysed the metabolic response of tobacco plants grown in vitro with casein hydrolysate or protein. As the sole source of N, casein hydrolysate enabled tobacco growth, while protein casein was used only to a limited extent. Free amino acids were detected in the roots of tobacco plants grown with protein casein but not in the plants grown with no source of N. Combining hydrolysate with inorganic N had beneficial effects on growth, root N uptake and protein content. The metabolism of casein-supplemented plants shifted to aromatic (Trp), branched-chain (Ile, Leu, Val) and basic (Arg, His, Lys) amino acids, suggesting their preferential uptake and/or alterations in their metabolic pathways. Complementarily, proteomic analysis of tobacco roots identified peptidase C1A and peptidase S10 families as potential key players in casein degradation and response to N starvation. Moreover, amidases were significantly upregulated, most likely for their role in ammonia release and impact on auxin synthesis. In phytohormonal analysis, both forms of casein influenced phenylacetic acid and cytokinin contents, suggesting a root system response to scarce N availability. In turn, metabolomics highlighted the stimulation of some plant defense mechanisms under such growth conditions, that is, the high concentrations of secondary metabolites (e.g., ferulic acid) and heat shock proteins.

The transcribed centromeric gene OsMRPL15 is essential for pollen development in rice

Centromeres consist of highly repetitive sequences that are challenging to map, clone, and sequence. Active genes exist in centromeric regions, but their biological functions are difficult to explore owing to extreme suppression of recombination in these regions. In this study, we used the CRISPR/Cas9 system to knock out the transcribed gene Mitochondrial Ribosomal Protein L15 (OsMRPL15), located in the centromeric region of rice (Oryza sativa) chromosome 8, resulting in gametophyte sterility. Osmrpl15 pollen was completely sterile, with abnormalities appearing at the tricellular stage including the absence of starch granules and disrupted mitochondrial structure. Loss of OsMRPL15 caused abnormal accumulation of mitoribosomal proteins and large subunit rRNA in pollen mitochondria. Moreover, the biosynthesis of several proteins in mitochondria was defective, and expression of mitochondrial genes was upregulated at the mRNA level. Osmrpl15 pollen contained smaller amounts of intermediates related to starch metabolism than wild-type pollen, while biosynthesis of several amino acids was upregulated, possibly to compensate for defective mitochondrial protein biosynthesis and initiate consumption of carbohydrates necessary for starch biosynthesis. These results provide further insight into how defects in mitoribosome development cause gametophyte male sterility.

Metabolic Reprogramming of Barley in Response to Foliar Application of Dichlorinated Functional Analogues of Salicylic Acid as Priming Agents and Inducers of Plant Defence

Designing innovative biological crop protection strategies to stimulate natural plant immunity is motivated by the growing need for eco-friendly alternatives to conventional biocidal agrochemicals. Salicylic acid (SA) and analogues are known chemical inducers of priming plant immunity against environmental stresses. The aim of the study was to study the metabolic reprogramming in barley plants following an application of three proposed dichlorinated inducers of acquired resistance. 3,5-Dichloroanthranilic acid, 2,6-dichloropyridine-4-carboxylic acid, and 3,5-dichlorosalicylic acid were applied to barley at the third leaf stage of development and harvested at 12, 24, and 36 h post-treatment. Metabolites were extracted using methanol for untargeted metabolomics analyses. Samples were analysed by ultra-high performance liquid chromatography coupled to high-definition mass spectrometry (UHPLC-HDMS). Chemometric methods and bioinformatics tools were used to mine and interpret the generated data. Alterations in the levels of both primary and secondary metabolites were observed. The accumulation of barley-specific metabolites, hordatines, and precursors was observed from 24 h post-treatment. The phenylpropanoid pathway, a marker of induced resistance, was identified among the key mechanisms activated by the treatment with the three inducers. No salicylic acid or SA derivatives were annotated as signatory biomarkers; instead, jasmonic acid precursors and derivatives were found as discriminatory metabolites across treatments. The study highlights differences and similarities in the metabolomes of barley after treatment with the three inducers and points to the triggering chemical changes associated with defence and resistance. This report is the first of its kind, and the knowledge acquired provides deeper insight into the role of dichlorinated small molecules as inducers of plant immunity and can be used in metabolomics-guided plant improvement programmes.

Ethylene treatment promotes umami taste-active amino acids accumulation of Torreya grandis nuts post-harvest by comparative chemical and transcript analyses

Amino acids play critical roles in physiological processes and also contribute significantly to fruit quality. In this study, the effect of exogenous ethylene on amino acids metabolism and related genes expression in Torreya grandis were investigated. The results revealed that ethylene treatment (3000 μL L^-1 for 24 h) significantly increased amino acids level. Umami amino acids were distinctly upregulated in ethylene-treated versus control nuts, with glutamic and aspartic acids to demonstrate 1.9-fold and 2.1-fold increase. Transcriptome analysis revealed that deferentially expressed genes were mainly enriched in alanine aspartate and glutamate metabolism. RT-qPCR confirmed that ethylene treatment up-regulated expression of their biosynthesis genes (TgGOGAT1, TgAATC1, TgAATC4) concurrent with suppression of their degradation enzymes (TgGS2, TgGAD1, TgGAD3, TgASNS1). Ethylene treatment appears to promote umami taste-active amino acids and improve T. grandis nut quality post-harvest.

Differences in phytohormone and flavonoid metabolism explain the sex differences in responses of Salix rehderiana to drought and nitrogen deposition

Due to global warming and the increase in nitrogen oxide emissions, plants experience drought and nitrogen (N) deposition. However, little is known about the acclimation to drought and N deposition of Salix species, which are dioecious woody plants. Here, an investigation into foliar N deposition combined with drought was conducted by assessing integrated phenotypes, phytohormones, transcriptomics, and metabolomics of male and female Salix rehderiana. The results indicated that there was greater transcriptional regulation in males than in females. Foliar N deposition induced an increase in foliar abscisic acid (ABA) levels in males, resulting in the inhibition of stomatal conductance, photosynthesis, carbon (C) and N accumulation, and growth, whereas more N was assimilated in females. Growth as well as C and N accumulation in drought-stressed S. rehderiana females increased after N deposition. Interestingly, drought decreased flavonoid biosynthesis whereas N deposition increased it in females. Both drought and N deposition increased flavonoid methylation in males and glycosylation in females. However, in drought-exposed S. rehderiana, N deposition increased the biosynthesis and glycosylation of flavonoids in females but decreased glycosylation in males. Therefore, foliar N deposition affects the growth and drought tolerance of S. rehderiana by altering the foliar ABA levels and the biosynthesis and modification of flavonoids. This work provides a basis for understanding how S. rehderiana may acclimate to N deposition and drought in the future.

Comprehensive analysis of physiological and metabolomic responses to drought reveals specific modulation of acquired tolerance mechanisms in rice

Mild stresses induce "acquired tolerance traits" (ATTs) that provide tolerance when stress becomes severe. Here, we identified the genetic variability in ATTs among a panel of rice germplasm accessions and demonstrated their relevance in protecting growth and productivity under water-limited conditions. Diverse approaches, including physiological screens, association mapping and metabolomics, were adopted and revealed 43 significant marker-trait associations. Nontargeted metabolomic profiling of contrasting genotypes revealed 26 "tolerance-related-induced" primary and secondary metabolites in the tolerant genotypes (AC-39000 and AC-39020) compared to the susceptible one (BPT-5204) under water-limited condition. Metabolites that help maintain cellular functions, especially Calvin cycle processes, significantly accumulated more in tolerant genotypes, which resulted in superior photosynthetic capacity and hence water use efficiency. Upregulation of the glutathione cycle intermediates explains the ROS homeostasis among the tolerant genotypes, maintaining spikelet fertility, and grain yield under stress. Bioinformatic dissection of a major effect quantitative trait locus on chromosome 8 revealed genes controlling metabolic pathways leading to the production of osmolites and antioxidants, such as GABA and raffinose. The study also led to the identification of specific trait donor genotypes that can be effectively used in translational crop improvement activities.

Phytotoxicity of microplastics to the floating plant Spirodela polyrhiza (L.): Plant functional traits and metabolomics

Freshwater ecosystems are gradually becoming sinks for terrestrial microplastics (MPs), posing a potential ecological risk. Although the effects of MPs on plankton and aquatic animals in freshwater ecosystems have been given increasing attention, the toxicity of MPs to the metabolism of aquatic plants remains unclear. Here, the model aquatic plant Spirodela polyrhiza (L.) Schleid. (S. polyrhiza) was exposed to polyvinyl chloride (PVC; 0, 10, 100 and 1000 mg/L) MPs, and changes in the plant functional traits and physiological metabolism were monitored. The results showed that the high dose of PVC MPs decreased the adventitious root elongation ratio by 41.68% and leaf multiplication ratio by 61.03% of S. polyrhiza, and resulted in the decrease in anthocyanin and nitrogen contents to 63.45% and 84.21% of the control group, respectively. Moreover, the widely targeted metabolomics analysis results showed 37 differential metabolites in the low-dose treatment and 119 differential metabolites in the high-dose treatment. PVC MPs interfered with organic matter accumulation by affecting carbon metabolism, nitrogen metabolism, amino acid metabolism and lipid metabolism, and S. polyrhiza resists PVC MP stress by regulating the synthesis and metabolism of secondary metabolites. PVC MPs had concentration-related toxicological effects on plant functional traits, inhibited plant growth and reproduction, affected plant nutrient metabolism, and exhibited profound effects on the nitrogen fate of aquatic plant habitats. Overall, we systematically summarized the metabolic response mechanisms of aquatic plants to PVC MP stress, providing a new perspective for studying the effects of MPs on plant trait function and ecological risks.

Methyl jasmonate redirects the dynamics of carbohydrates and amino acids toward the lignans accumulation in Linum album cells

Linum album accumulates lignans e.g., podophyllotoxin (PTOX) and 6-methoxy podophyllotoxin (6MPTOX). This study was aimed to figure out how different concentrations of MeJA (0, 50, 100, 150, and 200 μM) by affecting on free sugars and amino acids contents induce lignans accumulation in L. album cells. Results revealed that hydrogen peroxide (H₂O₂) content increased at 50μM, while it decreased at the high levels of MeJA (150 and 200 μM). Also, increasing trend of nitric oxide (NO) and lipid peroxidation levels peaked at 200 μM MeJA. An increased antioxidant enzymes activity was also observed in the treated cells. Moreover, an increase in rhamnose/xylose, glucose, and mannose was detected at 150 and 200 μM MeJA compared to the control. These compounds provide energy source and carbon skeleton for amino acids biosynthesis. Our results emphasized variations in amino acids levels in the presence of MeJA, where Phe level shifts along with synthesizing phenolics. Likewise, MeJA treatment switch on phenyl-ammonia lyase (PAL) and tyrosine-ammonia lyase (TAL) activities that regenerate phenolic compounds. Changes in phenolic acids (cinnamic, coumaric, caffeic, ferulic, and salicylic acid) and flavonoids (catechin, vitexin, myricetin, and kaempferol) were observed under MeJA treatment. Eventually, MeJA induced lignans production except for lariciresinol (LARI), so that the highest amounts of PTOX and 6MPTOX were analyzed at 50 μM, which were 4 and 5 time of control, respectively. Conclusively, it can be suggested that MeJA-induced oxidative status change redirects free sugars and amino acids toward the production of phenolic compounds especially lignans in L. album cells.

Integrating Metabolomics and Proteomics Technologies Provides Insights into the Flavor Precursor Changes at Different Maturity Stages of Arabica Coffee Cherries

The metabolic modulation of major flavor precursors during coffee cherry ripening is critical for the characteristic coffee flavor formation. However, the formation mechanism of flavor precursors during coffee cherry ripening remains unknown. In the present study, a colorimeter was employed to distinguish different maturity stages of coffee cherry based on the coffee cherry skin colors, and proteomics and metabolomics profiles were integrated to comprehensively investigate the flavor precursor dynamics involved in Arabica coffee cherry ripening. The data obtained in the present study provide an integral view of the critical pathways involved in flavor precursor changes during coffee cherry ripening. Moreover, the contributions of critical events in regulating the development of flavor precursors during the four ripening stages of coffee cherries, including the biosynthesis and metabolism pathways of organic acids, amino acids, flavonoids, and sugars, are discussed. Overall, a total of 456 difference express metabolites were selected, and they were identified as being concentrated in the four maturity stages of coffee cherries; furthermore, 76 crucial enzymes from the biosynthesis and metabolism of sugars, organic acids, amino acids, and flavonoids contributed to flavor precursor formation. Among these enzymes, 45 difference express proteins that could regulate 40 primary amino acids and organic acids flavor precursors were confirmed. This confirmation indicates that the metabolic pathways of amino acids and organic acids played a significant role in the flavor formation of Arabica coffee cherries during ripening. These results provide new insights into the protease modulation of flavor precursor changes in Arabica coffee cherry ripening.

The LHT Gene Family in Rice: Molecular Characterization, Transport Functions and Expression Analysis

Amino acid transporters (AATs) are integral membrane proteins and play important roles in plant growth and development as well as environmental responses. In contrast to the amino acid permease (AAP) subfamily, functional studies of the lysine and histidine transporter (LHT) subfamily have not been made in rice. In the current study, six LHT genes were found in the rice genome. To further investigate the functions of these genes, analyses were performed regarding gene and protein structures, chromosomal locations, evolutionary relationships, cis-acting elements of promoters, gene expression, and yeast complementation. We found that the six OsLHT genes are distributed on 4 out of the 12 chromosomes and that the six OsLHT genes were grouped into two clusters based on the phylogenetic analysis. Protein structure analyses showed that each OsLHT protein has 11 helical transmembrane domains. Yeast complementation assays showed that these OsLHT genes have conserved transport substrates within each cluster. The four members from cluster 1 showed broad amino acid selectivity, while OsLHT5 and OsLHT6 may transport other substrates besides amino acids. Additionally, quantitative real-time PCR analysis of the six OsLHT genes revealed that they have different expression patterns at different developmental stages and in different tissues. It also revealed that some OsLHT genes were responsive to PEG, NaCl and cold treatments, indicating their critical roles in abiotic stress response. Our results will be useful for further characterizing the crucial biological functions of rice LHT genes.

DROUGHT-INDUCED BRANCHED-CHAIN AMINO ACID AMINOTRANSFERASE enhances drought tolerance in rice

Plants accumulate several metabolites in response to drought stress, including branched-chain amino acids (BCAAs). However, the roles of BCAAs in plant drought responses and the underlying molecular mechanisms for BCAA accumulation remain elusive. Here, we demonstrate that rice (Oryza sativa) DROUGHT-INDUCED BRANCHED-CHAIN AMINO ACID AMINOTRANSFERASE (OsDIAT) mediates the accumulation of BCAAs in rice in response to drought stress. An in vitro enzyme activity assay indicated that OsDIAT is a branched-chain amino acid aminotransferase, and subcellular localization analysis revealed that OsDIAT localizes to the cytoplasm. The expression of OsDIAT was induced in plants upon exposure to abiotic stress. OsDIAT-overexpressing (OsDIATOX) plants were more tolerant to drought stress, whereas osdiat plants were more susceptible to drought stress compared with nontransgenic (NT) plants. Amino acid analysis revealed that BCAA levels were higher in OsDIATOX but lower in osdiat compared with in NT plants. Finally, the exogenous application of BCAAs improved plant tolerance to osmotic stress compared with that in control plants. Collectively, these findings suggest that OsDIAT mediates drought tolerance by promoting the accumulation of BCAAs.

Natural variations of OsAUX5, a target gene of OsWRKY78, control the neutral essential amino acid content in rice grains

Grain essential amino acid (EAA) levels contribute to rice nutritional quality. However, the molecular mechanisms underlying EAA accumulation and natural variation in rice grains remain unclear. Here we report the identification of a previously unrecognized auxin influx carrier subfamily gene, OsAUX5, which encodes an amino acid transporter that functions in uptake of multiple amino acids. We identified an elite haplotype of Pro::OsAUX5^Hap2 that enhances grain EAA accumulation without an apparent negative effect on agronomic traits. Natural variations of OsAUX5 occur in the cis elements of its promoter, which are differentially activated because of the different binding affinity between OsWRKY78 and the W-box, contributing to grain EAA variation among rice varieties. The two distinct haplotypes were shown to have originated from different Oryza rufipogon progenitors, which contributed to the divergence between japonica and indica. Introduction of the indica-type Pro::OsAUX5^Hap2 genotype into japonica could significantly increase EAA levels, indicating that indica-type Pro::OsAUX5^Hap2 can be utilized to increase grain EAAs of japonica varieties. Collectively, our study uncovers an WRKY78-OsAUX5-based regulatory mechanism controlling grain EAA accumulation and provides a potential target for breeding EAA-rich rice.

Key metabolites and mechanistic insights in forchlorfenuron controlling kiwifruit development

Forchlorfenuron (CPPU) is a plant growth regulator widely applied on kiwifruit to improve yield, however, there are rarely reports on its effects on the nutrients of kiwifruits. Based on UHPLC-Q-TOF-MS, the effects of CPPU on metabolism profile and nutrient substances of two kiwifruit varieties during development were investigated by non-targeted metabolomics. A total of 115 metabolites were identified, and 29 differential metabolites were confirmed and quantified using certified reference standards. Metabolic profile indicated that CPPU promoted kiwifruit development during the main expansion stages at the molecular level, and the effects varied slightly for different varieties. In the early and middle stages of kiwifruit development, the anthocyanin, flavone and flavonol biosynthesis were down-regulated in both varieties, and flavanols biosynthesis was down-regulated only in Hayward variety. Arginine biosynthesis was down-regulated at all stages till the harvest. Although the synthesis of these nutrient substances in kiwifruits was mostly down-regulated by CPPU, the negative effects became mild at harvest time, and positively, the significant increase of sucrose and decrease of organic acids at harvest time could help to improve the taste of kiwifruits.

Effects of Arbuscular Mycorrhizal Fungi on Alleviating Cadmium Stress in Medicago truncatula Gaertn

Heavy metal contamination is a global problem for ecosystems and human health. Remediation of contaminated soils has received much attention in the last decade. Aided mitigation of heavy metal phytotoxicity by arbuscular mycorrhizal fungi (AMF) is a cost-effective and environmentally friendly strategy. This study was carried out to investigate the mitigation effect of AMF inoculation on heavy metal toxicity in Medicago truncatula under soil cadmium stress. Therefore, a pot experiment was designed to evaluate the growth, chlorophyll fluorescence, Cd uptake and distribution, malondialdehyde (MDA) content, root soil physicochemical properties, and metabolite profile analysis of M. truncatula with/without AMF inoculation in Cd (20 mg/Kg)-contaminated soil. The results showed that inoculating AMF under Cd stress might enhance photosynthetic efficiency, increase plant biomass, decrease Cd and MDA content, and improve soil physicochemical properties in M. truncatula. Non-targeted metabolite analysis revealed that inoculation with AMF under Cd stress significantly upregulated the production of various amino acids in inter-root metabolism and increase organic acid and phytohormone synthesis. This study provides information on the physiological responses of mycorrhizal plants to heavy metal stress, which could help provide deeper insight into the mechanisms of heavy metal remediation by AMF.

Simulated Digestion and Fecal Fermentation Behaviors of Levan and Its Impacts on the Gut Microbiota

Levan is a microbial fructan widely explored in various fields owing to its excellent physical and biochemical properties. However, little is known about its digestion and fermentation characteristics in vitro. This study evaluated the potential prebiotic properties of levan obtained by enzymatic synthesis. Scanning electron microscopy, Fourier transform infrared spectroscopy, and nuclear magnetic resonance spectroscopy showed that the primary structures of levan remained stable after saliva-gastrointestinal digestion. The microtopography, molecular weight, and functional group of levan were seriously damaged during fecal fermentation. Moreover, the total short-chain fatty acid levels increased significantly, especially for propionic acid, butyric acid, and valeric acid. The 16S rDNA sequencing showed that levan mainly increased the abundance of Firmicutes; in genus levels, certain beneficial bacteria such as Megasphaera and Megamonas genera were remarkably promoted, and the proliferation of harmful genera was inhibited (such as Cedecea and Klebsiella). Overall, this study provided new insights into the potential probiotic mechanism of levan.

Overexpression of the FERONIA receptor kinase MdMRLK2 confers apple drought tolerance by regulating energy metabolism and free amino acids production

Drought is a major abiotic stress limiting the growth and production of apple trees worldwide. The receptor-like kinase FERONIA is involved in plant growth, development and stress responses; however, the function of FERONIA in apple under drought stress remains unclear. Here, the FERONIA receptor kinase gene MdMRLK2 from apple (Malus domestica) was shown to encode a plasma membrane-localized transmembrane protein and was significantly induced by abscisic acid and drought treatments. 35S::MdMRLK2 apple plants showed less photosystem damage and higher photosynthetic rates compared with wild-type (WT) plants, after withholding water for 7 days. 35S::MdMRLK2 apple plants also had enhanced energy levels, activated caspase activity and more free amino acids, than the WT, under drought conditions. By performing yeast two-hybrid screening, glyceraldehyde-3-phosphate dehydrogenase and MdCYS4, a member of cystatin, were identified as MdMRLK2 interaction partners. Moreover, under drought conditions, the 35S::MdMRLK2 apple plants were characterized by higher abscisic acid (ABA) content. Overall, these findings demonstrated that MdMRLK2 regulates apple drought tolerance, probably via regulating levels of energetic matters, free amino acids and ABA.

Spatial-temporal variations of proline and related amino acids reveal distinct nitrogenous utilization strategies in rice during detoxification of exogenous cyanide

Cyanide (CN^-) pollution in agricultural systems impairs amino acid metabolism in rice plants, hence decreasing their quality and yield. Meanwhile, little is known about the effects of CN^- assimilation on the innate pool of proline (Pro) and its synthesis-related amino acids (Pro-AAs) in rice plants. In this study, a hydroponic experiment was carried out to investigate the effect of exogenous KCN on indigenous levels of Pro-AAs, i.e., Pro, glutamate (Glu), arginine (Arg), and ornithine (Orn) in rice seedlings fertilized with either nitrate (NO₃^-) or ammonium (NH₄⁺) through the biochemical and RT-qPCR analysis. At the same KCN treatment concentration, the relative growth rate of NH₄⁺-fed rice seedlings was considerably higher than that of NO₃^--fed rice seedlings, but the residual concentration of CN^- in NH₄⁺-fed rice tissues was lower than that of NO₃^--fed rice tissues. Based on the UPLC and stoichiometry molar ratio calculations, it is evident that the Glu pathway contributed significantly to Pro synthesis in rice under KCN + NO₃^- treatments; whereas the Orn pathway governed the synthesis of Pro in rice under KCN + NH₄⁺ treatments. Moreover, transcriptional and bioinformatics analysis revealed that NH₄⁺ fertilization resulted in spatial-temporal differences in the genetic response in rice tissue during detoxification of CN^- compared with KCN + NO₃^- treatments. These findings suggested that the innate level of Pro serves as "a fishing float" to balance the flux between Pro and Pro-AAs in exogenous KCN-treated rice plants under different nitrogenous nutritional conditions.

Proteomic Analysis of Barley (Hordeum vulgare L.) Leaves in Response to Date Palm Waste Compost Application

Composts are an emerging biofertilizers used in agronomy that can improve crop performance, but much less is known regarding their modes of action. The current study aimed to investigate the differentially abundant proteins (DAPs) in barley leaves associated with growth promotion induced by application of date palm waste compost. Morphophysiological measurements revealed that compost induced a significant increase in plant height, chlorophyll content, gas exchange parameters and plant biomass. LC-MS/MS analyses indicate that compost induced global changes in the proteome of barley leaves. A total of 62 DAPs (26 upregulated and 36 downregulated) among a total of 2233 proteins were identified in response to compost application. The expression of DAPs was further validated based on qRT-PCR. Compost application showed altered abundance of several proteins related to abiotic stress, plant defense, redox homeostasis, transport, tricarboxylic acid cycle, carbohydrate, amino acid, energy and protein metabolism. Furthermore, proteins related to metabolic processes of phytohormone, DNA methylation and secondary metabolites were induced. These results indicate that barley responds to compost application by complex metabolism pathways and may result in a positive alteration in a physiological and metabolic barley plant state which consequently could lead to improved growth and stress adaptation observed in compost-treated plants.

Pea-Tea Intercropping Improves Tea Quality through Regulating Amino Acid Metabolism and Flavonoid Biosynthesis

Pea-tea intercropping is an excellent cultivation method that can improve tea quality. However, the underlying mechanism is still unclear. The present study was aimed at elucidating the mechanism of the effect of pea-tea intercropping on tea quality through a high-throughput method. Transcriptome and metabolome analyses were conducted to identify the changes in gene expression and metabolites changes intercropping, respectively. In addition, the amino acids and catechins were detected using the LC-MS method and quantified absolutely. The results showed that total polyphenols and catechins decreased but amino acids increased in pea intercropped tea shoots. Correspondingly, genes related to amino acid metabolism and flavonoid biosynthesis were differentially expressed. For amino acid metabolism, 11 differentially expressed genes were identified, including 5 upregulated and 6 downregulated genes. Meanwhile, three genes involved in carbohydrate transport and metabolism were upregulated in pea intercropped tea plants. These genes were also involved in amino acid metabolism. For flavonoid biosynthesis, two downregulated genes were identified, which were the flavonol synthase and anthocyanidin synthase genes and followed a similar pattern to changes in catechins and polyphenols. These advances have opened new horizons for understanding the biochemical mechanisms of amino acids and flavonoids in improving tea quality in the pea-tea intercropping cultivation model.

Genome-wide association studies of five free amino acid levels in rice

Rice (Oryza sativa L.) is one of the important staple foods for human consumption and livestock use. As a complex quality trait, free amino acid (FAA) content in rice is of nutritional importance. To dissect the genetic mechanism of FAA level, five amino acids' (Val, Leu, Ile, Arg, and Trp) content and 4,325,832 high-quality SNPs of 448 rice accessions were used to conduct genome-wide association studies (GWAS) with nine different methods. Of these methods, one single-locus method (GEMMA), seven multi-locus methods (mrMLM, pLARmEB, FASTmrEMMA, pKWmEB, FASTmrMLM, ISIS EM-BLASSO, and FarmCPU), and the recent released 3VmrMLM were adopted for methodological comparison of quantitative trait nucleotide (QTN) detection and identification of stable quantitative trait nucleotide loci (QTLs). As a result, 987 QTNs were identified by eight multi-locus GWAS methods; FASTmrEMMA detected the most QTNs (245), followed by 3VmrMLM (160), and GEMMA detected the least QTNs (0). Among 88 stable QTLs identified by the above methods, 3VmrMLM has some advantages, such as the most common QTNs, the highest LOD score, and the highest proportion of all detected stable QTLs. Around these stable QTLs, candidate genes were found in the GO classification to be involved in the primary metabolic process, biosynthetic process, and catalytic activity, and shown in KEGG analysis to have participated in metabolic pathways, biosynthesis of amino acids, and tryptophan metabolism. Natural variations of candidate genes resulting in the content alteration of five FAAs were identified in this association panel. In addition, 95 QTN-by-environment interactions (QEIs) of five FAA levels were detected by 3VmrMLM only. GO classification showed that the candidate genes got involved in the primary metabolic process, transport, and catalytic activity. Candidate genes of QEIs played important roles in valine, leucine, and isoleucine degradation (QEI_09_03978551 and candidate gene LOC_Os09g07830 in the Leu dataset), tryptophan metabolism (QEI_01_00617184 and candidate gene LOC_Os01g02020 in the Trp dataset), and glutathione metabolism (QEI_12_09153839 and candidate gene LOC_Os12g16200 in the Arg dataset) pathways through KEGG analysis. As an alternative of the multi-locus GWAS method, these findings suggested that the application of 3VmrMLM may provide new insights into better understanding FAA accumulation and facilitate the molecular breeding of rice with high FAA level.

Endophytic nitrogen-fixing bacteria DX120E inoculation altered the carbon and nitrogen metabolism in sugarcane

Endophytic nitrogen-fixing bacteria are versatile and widely distributed in plants. Numerous strains of endophytic nitrogen-fixing bacteria are used as biofertilizers to minimize the utilization of chemical fertilizers, improve nutrient use efficiency, increase crop productivity, and reduce environmental pollution. However, the mechanism underlying the interaction between nitrogen-fixing bacteria and plants is still unclear. So, the present study was planned to assess the effects of endophytic nitrogen-fixing bacteria on sugarcane by analyzing the changes in physiological and biochemical activities. In the current study, Klebsiella variicola DX120E, an endophytic nitrogen-fixing bacterium, was inoculated on sugarcane varieties B8 and ROC22 to evaluate the effects on nitrogen and carbon metabolism-related enzymatic activity and biomass. Results showed that DX120E inoculation improved the enzymatic activities related to gluconeogenesis and nitrogen metabolism increased the sugarcane plant’s height, cane juice Brix, biomass, chlorophyll, and soluble sugar content in sugarcane. Metabolomics analysis revealed that the metabolome modules were highly enriched in carbon and nitrogen metabolic pathways of strain-affected sugarcane than uninoculated control. The identified carbohydrates were associated with the glycolysis or gluconeogenesis and tricarboxylic acid (TCA) cycle in plants. Metabolomic profiling in the present investigation showed that carbohydrate metabolism is coordinated with nitrogen metabolism to provide carbon skeletons and energy to amino acid synthesis, and amino acid degradation results in several metabolites used by the citric acid cycle as an energy source. Moreover, differentially expressed metabolites of non-proteinogenic amino acids have a further complementary role to the action of endophytic nitrogen-fixing bacteria. Meanwhile, a significant difference in metabolites and metabolic pathways present in stems and leaves of B8 and ROC22 varieties was found. This study discovered the potential benefits of DX120E in sugarcane and suggested candidate regulatory elements to enhance interactions between nitrogen-fixing microbes and sugarcane.

The Effect of Short-Term Temperature Pretreatments on Sugars, Organic Acids, and Amino Acids Metabolism in Valencia Orange Fruit

Temperature pretreatment is one of the most important factors which significantly affects the postharvest quality of citrus fruit. In this study, late-ripening Valencia orange (citrus sinensis) fruits were used to investigate the effect of short-term treatment at low (6°C), room (20°C), and high (40°C) temperatures on fruit quality. Our results revealed that both low and room-temperature treatments maintained the content of sugars and organic acids, whereas high-temperature treatments elevated the accumulation of sugars but decreased the content of citric acid. In fruit peel (flavedo and albedo), the accumulation of sugars and organic acids responding to temperatures was diverse and mostly different from that in the pulp. Meanwhile, GABA and several amino acids were upregulated under short-term high-temperature treatment but downregulated in response to low-temperature treatment in both peel and pulp. Furthermore, PCA and correlation analysis revealed that the short-term temperature treatments changed the metabolic flow, and GABA was positively correlated with sugars and organic acids. Our study analyzed the metabolic changes of fruit peel and pulp in response to short-term temperature treatments and revealed that GABA may act as a signaling molecular involved in temperature-controlled quality changes.

Metabolome genome-wide association study provides biochemical and genetic insights into natural variation of primary metabolites in sesame

Plants' primary metabolites are of great importance from the survival and nutritional perspectives. However, the genetic bases underlying the profiles of primary metabolites in oilseed crops remain largely unclear. As one of the main oilseed crops, sesame (Sesamum indicum L.) is a potential model plant for investigating oil metabolism in plants. Therefore, the objective of this study is to disclose the genetic variants associated with variation in the content of primary metabolites in sesame. We performed a comprehensive metabolomics analysis of primary metabolites in 412 diverse sesame accessions using gas chromatography-mass spectrometry and identified a total of 45 metabolites, including fatty acids, monoacylglycerols (MAGs), and amino acids. Genome-wide association study unveiled 433 significant single-nucleotide polymorphism loci associated with variation in primary metabolite contents in sesame. By integrating diverse genomic analyses, we identified 10 key candidate causative genes of variation in MAG, fatty acid, asparagine, and sucrose contents. Among them, SiDSEL was significantly associated with multiple traits. SiCAC3 and SiKASI were strongly associated with variation in oleic acid and linoleic acid contents. Overexpression of SiCAC3, SiKASI, SiLTPI.25, and SiLTPI.26 in transgenic Arabidopsis and Saccharomyces cerevisiae revealed that SiCAC3 is a potential target gene for improvement of unsaturated fatty acid levels in crops. Furthermore, we found that it may be possible to breed several quality traits in sesame simultaneously. Our results provide valuable genetic resources for improving sesame seed quality and our understanding of oilseed crops' primary metabolism.

Impact of Foliar Application of Amino Acids on Essential Oil Content, Odor Profile, and Flavonoid Content of Different Mint Varieties in Field Conditions

Mint is an industrial plant that is a good source of essential oil and many phenolic compounds that have several positive benefits to human health and can be used to prevent the development of many diseases. The aim of this research was to investigate the possibility of increasing essential oil and flavonoid content, changing the chemical composition of these compounds in different mint cultivars under foliar application with precursors (phenylalanine, tryptophan, and tyrosine) at two concentrations, 100 and 200 mg L^-1, to enable the possibilities for wider use of these plants when they are grown in field conditions. Spraying with phenylalanine at 100 mg L^-1 concentration increased essential oil content in Mentha piperita 'Granada' plants by 0.53 percentage units. Foliar application with tyrosine solutions at 100 mg L^-1 concentration most effectively influenced the essential oil odor profile Mentha spicata 'Crispa'. The highest number of total flavonoids was in Mentha piperita 'Swiss' sprayed with tyrosine at 100 mg L^-1 concentration. The flavonoid content depended on the mint cultivar, amino acids, and their concentration. The results showed that the effect of amino acid solutions on different secondary metabolites' quantitative and qualitative composition differed depending on the mint cultivar; therefore, amino acids and their concentrations must be selected based on the cultivar they are targeting.

Using transcriptomic and metabolomic data to investigate the molecular mechanisms that determine protein and oil contents during seed development in soybean

Soybean [Glycine max (L.) Merri.] is one of the most valuable global crops. And vegetable soybean, as a special type of soybean, provides rich nutrition in people's life. In order to investigate the gene expression networks and molecular regulatory mechanisms that regulate soybean seed oil and protein contents during seed development, we performed transcriptomic and metabolomic analyses of soybean seeds during development in two soybean varieties that differ in protein and oil contents. We identified a total of 41,036 genes and 392 metabolites, of which 12,712 DEGs and 315 DAMs were identified. Analysis of KEGG enrichment demonstrated that DEGs were primarily enriched in phenylpropanoid biosynthesis, glycerolipid metabolism, carbon metabolism, plant hormone signal transduction, linoleic acid metabolism, and the biosynthesis of amino acids and secondary metabolites. K-means analysis divided the DEGs into 12 distinct clusters. We identified candidate gene sets that regulate the biosynthesis of protein and oil in soybean seeds, and present potential regulatory patterns that high seed-protein varieties may be more sensitive to desiccation, show earlier photomorphogenesis and delayed leaf senescence, and thus accumulate higher protein contents than high-oil varieties.

Comprehensive genomic characterization of cotton cationic amino acid transporter genes reveals that GhCAT10D regulates salt tolerance

BACKGROUND

The cationic amino acid transporters (CAT) play indispensable roles in maintaining metabolic functions, such as synthesis of proteins and nitric oxide (NO), biosynthesis of polyamine, and flow of amino acids, by mediating the bidirectional transport of cationic amino acids in plant cells.

RESULTS

In this study, we performed a genome-wide and comprehensive study of 79 CAT genes in four species of cotton. Localization of genes revealed that CAT genes reside on the plasma membrane. Seventy-nine CAT genes were grouped into 7 subfamilies by phylogenetic analysis. Structure analysis of genes showed that CAT genes from the same subgroup have similar genetic structure and exon number. RNA-seq and real-time PCR indicated that the expression of most GhCAT genes were induced by salt, drought, cold and heat stresses. Cis-elements analysis of GhCAT promoters showed that the GhCAT genes promoters mainly contained plant hormones responsive elements and abiotic stress elements, which indicated that GhCAT genes may play key roles in response to abiotic stress. Moreover, we also conducted gene interaction network of the GhCAT proteins. Silencing GhCAT10D expression decreased the resistance of cotton to salt stress because of a decrease in the accumulation of NO and proline.

CONCLUSION

Our results indicated that CAT genes might be related with salt tolerance in cotton and lay a foundation for further study on the regulation mechanism of CAT genes in cationic amino acids transporting and distribution responsing to abiotic stress.

Differentially reset transcriptomes and genome bias response orchestrate wheat response to phosphate deficiency

Phosphorus (P) is an essential macronutrient for all organisms. Phosphate (Pi) deficiency reduces grain yield and quality in wheat. Understanding how wheat responds to Pi deficiency at the global transcriptional level remains limited. We revisited the available RNA-seq transcriptome from Pi-starved wheat roots and shoots subjected to Pi starvation. Genome-wide transcriptome resetting was observed under Pi starvation, with a total of 917 and 2338 genes being differentially expressed in roots and shoots, respectively. Chromosomal distribution analysis of the gene triplets and differentially expressed genes (DEGs) revealed that the D genome displayed genome induction bias and, specifically, the chromosome 2D might be a key contributor to Pi-limiting triggered gene expression response. Alterations in multiple metabolic pathways pertaining to secondary metabolites, transcription factors and Pi uptake-related genes were evidenced. This study provides genomic insight and the dynamic landscape of the transcriptional changes contributing to the hexaploid wheat during Pi starvation. The outcomes of this study and the follow-up experiments have the potential to assist the development of Pi-efficient wheat cultivars.

Water retention and metabolic changes improve desiccation tolerance in Barbacenia graminifolia (Velloziaceae)

Barbacenia graminifolia is a Velloziaceae species endemic to the campos rupestres in Serra do Cipó, Minas Gerais state (Brazil). This biome is characterised by high irradiance and limited water conditions. Unlike other resurrection plants, B. graminifolia can maintain a high hydric status (>80%) after 28 days of water suppression before desiccation. We investigated the physiological and metabolic mechanisms associated with structural changes that allow B. graminifolia to maintain hydration under a prolonged water deficit and to recover after desiccation. After 30 days of water deficit, desiccated plants exhibited chlorophyll degradation, a 178.4% and 193.7% increase in total carotenoids and MDA, respectively, and twice the CAT and APX activity compared to hydrated plants. The metabolite profile showed increased amino acids, carbohydrates, saturated fatty acids and benzoic acids during dehydration, while trichloroacetic acid cycle acids were higher in hydrated and rehydrated plants. Anatomical and ultrastructural data corroborated the physiological and metabolic changes and revealed the presence of mucilaginous cells with high water retention capacity. Our data indicated that combined strategies of assimilatory metabolism shutdown, accumulation of compatible solutes and antioxidant compounds, increase in hydrophilic molecules, changes in the composition of membrane lipids and remodelling of cell organelles conditioned the efficiency of B. graminifolia in delaying water loss, tolerating further desiccation and quickly recovering after rehydration. These attributes evidence that this species is well adapted to cope with adverse environmental conditions, mainly directing the metabolism to an efficient antioxidant response and improving its capacity to retain water during the dry season.

Integrated metabolomic and transcriptomic analyses of two peanut (Arachis hypogaea L.) cultivars differing in amino acid metabolism of the seeds

Peanut is an important economic crop worldwide. The content of amino acids, especially essential amino acids, is an important nutritional quality trait of peanut seeds. However, the regulation of amino acid metabolism in peanut seeds is poorly understood. Here, two peanut cultivars, Zhonghuahei 1 and Zhongkaihua 151, with high and low free amino acids in mature seeds, respectively, were selected to investigate the regulatory mechanisms of amino acids during seed development. Zhonghuahei 1 is composed of significantly higher arginine (Arg), asparagine (Asn), and glutamate (Glu) contents than Zhongkaihua 151. However, the metabolomic analyses indicated that the contents of most amino acids were significantly lower in Zhonghuahei 1 at the early developmental stage, while they were reverse at the middle and late stages. Transcriptomic analyses also revealed that the differentially expressed genes between the two cultivars during different stages were enriched in multiple pathways associated with amino acid metabolism. Among them, the Arg biosynthesis pathway showed different regulatory profiles between the two cultivars according to the temporal analysis of gene expression patterns. Subsequent gene co-expression network analysis showed that the gene module darkorange was significantly correlated with Arg content, with an enriched Arg biosynthesis pathway. Accordingly, a gene regulatory network for Arg biosynthesis and metabolism, including key genes (ALDH, ASS1, OTC, and GAD) and transcription factors (GATA, HEX, and ATF), was constructed. These findings provide insights into the regulatory network of amino acid metabolism in peanuts and provide candidate genes that can be applied to facilitate peanut breeding with desirable seeds.

News about amino acid metabolism in plant-microbe interactions

Plants constantly come into contact with a diverse mix of pathogenic and beneficial microbes. The ability to distinguish between them and to respond appropriately is essential for plant health. Here we review recent progress in understanding the role of amino acid sensing, signaling, transport, and metabolism during plant-microbe interactions. Biochemical pathways converting individual amino acids into active compounds have recently been elucidated, and comprehensive large-scale approaches have brought amino acid sensors and transporters into focus. These findings show that plant central amino acid metabolism is closely interwoven with stress signaling and defense responses at various levels. The individual biochemical mechanisms and the interconnections between the different processes are just beginning to emerge and might serve as a foundation for new plant protection strategies.