The shikimate pathway and aromatic amino Acid biosynthesis in plants

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.

Light emitting diodes improved the metabolism of rosmarinic acid and amino acids at the transcriptional level in two genotypes of Melissa officinalis L

In the present study, we used different LEDs to evaluate their effect on metabolic and transcriptional reprogramming of two genotypes (Ilam and Isfahan) of lemon balm grown under narrow-band LED lighting. Lemon balm plants were grown in four incubators equipped with artificial lighting and subjected to four LED lamps [White, Blue, Red, and mixed RB (Red+Blue) (70%:30%)] and in greenhouse conditions for 7weeks. The results showed significant increases in leaf number, pigment and soluble sugar contents, secondary metabolites, and calcium, magnesium, potassium and amino acid contents achieved in growth under mixed RB LEDs. As observed for the content of total phenolics, rosmarinic acid, and amino acids, the expression of genes involved in their production, including TAT , RAS , and DAHPS were also enhanced due to the mixed RB LED lighting. The best condition for both the plant growth and expression of genes was under the mixture of Red+Blue LED lamps. These observations indicate that the increase in secondary metabolites under mixed Red+Blue lights may be due to the increase in primary metabolites synthesis and the increased expression of genes that play an essential role in the production of secondary metabolites.

Effect of glycinebetaine on metabolite profiles of cold-stored strawberry revealed by 1H NMR-based metabolomics

Glycinebetaine (GB) has long been used as a preservative for refrigerated fruits, but the effect of GB on the global metabolites of cold-stored strawberries is still unclear. In this study, the effects of exogenous application of GB on quality-related metabolites of cold-stored strawberries were investigated by nuclear magnetic resonance (NMR)-based metabolomic analysis. The results showed that the application of GB (especially at the concentration of 10 mM) on cold-stored strawberries effectively stabilized the sugars (d-xylose and d-glucose) and amino acids (tyrosine, leucine, and tryptophan) content, and lowered the acid (acetic acid) content as well. Additionally, the GB content in strawberries also increased. This implies that the appropriate concentration of GB is a natural and safe treatment, which could maintain the quality of cold-stored strawberries by regulating levels of quality-related metabolites, and the ingestion of GB-preserved strawberries may serve as a source of methyl-donor supplementation in our daily diet.

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.

Molecular Traits Underlying the Growth Promotion and Metabolite Accumulation in Rheum palmatum Inoculated with Endophytic Trichoderma citrinoviride HT-1

Trichoderma spp. are an important plant-growth-promoting fungi. Trichoderma citrinoviride HT-1 was isolated from Rheum palmatum root, which has beneficial effects on growth and metabolite accumulation. However, the improvement mechanisms for growth and metabolite accumulation of T. citrinoviride HT-1 are unclear. In this study, RNA sequencing (RNA-seq) and high-performance liquid chromatography (HPLC) were used to measure the effect of different concentrations of conidial suspension of the HT-1 strain on the growth promotion and metabolite accumulation of R. palmatum seedlings. The results showed that the highest biomass and metabolites of R. palmatum seedlings were obtained through treatment with the HT-1 strain at a final spore concentration of 107 spores/mL. RNA sequencing indicated that 1662 genes were upregulated and 2155 genes were downregulated after inoculation with 107 spores/mL of the HT-1 strain. This strain induced significant upregulation of related genes in the phenylpropanoid biosynthesis pathway, plant hormone signal transduction pathway, biosynthesis of secondary metabolites pathway, and plant–pathogen interaction pathway in R. palmatum. The gene expression trends were revealed through quantitative real-time polymerase chain reaction (qRT-PCR) and were consistent with those determined by RNA-seq. Our results will help us to understand the growth-promoting mechanisms of the HT-1 strain on R. palmatum and provide a theoretical basis for the application of T. citrinoviride HT-1 as a biological fertilizer.

The genome of single-petal jasmine (Jasminum sambac) provides insights into heat stress tolerance and aroma compound biosynthesis

Jasmine [Jasminum sambac (L.) Aiton] is a commercially important cultivated plant species known for its fragrant flowers used in the perfume industry, medicine and cosmetics. In the present study, we obtained a draft genome for the J. sambac cultivar 'Danbanmoli' (JSDB, a single-petal phenotype). We showed that the final genome of J. sambac was 520.80 Mb in size (contig N50 = 145.43 kb; scaffold N50 = 145.53 kb) and comprised 35,363 genes. Our analyses revealed that the J. sambac genome has undergone only an ancient whole-genome duplication (WGD) event. We estimated that the lineage that has given rise to J. sambac diverged from the lineage leading to Osmanthus fragrans and Olea europaea approximately 31.1 million years ago (Mya). On the basis of a combination of genomic and transcriptomic analyses, we identified 92 transcription factors (TFs) and 206 genes related to heat stress response. Base on a combination of genomic, transcriptomic and metabolomic analyses, a range of aroma compounds and genes involved in the benzenoid/phenylpropanoid and terpenoid biosynthesis pathways were identified. In the newly assembled J. sambac genome, we identified a total of 122 MYB, 122 bHLH and 69 WRKY genes. Our assembled J. sambac JSDB genome provides fundamental knowledge to study the molecular mechanism of heat stress tolerance, and improve jasmine flowers and dissect its fragrance.

Exogenous aspartic acid alleviates salt stress-induced decline in growth by enhancing antioxidants and compatible solutes while reducing reactive oxygen species in wheat

Salinity is the primary environmental stress that adversely affects plants' growth and productivity in many areas of the world. Published research validated the role of aspartic acid in improving plant tolerance against salinity stress. Therefore, in the present work, factorial pot trials in a completely randomized design were conducted to examine the potential role of exogenous application of aspartic acid (Asp) in increasing the tolerance of wheat (Triticum aestivum L.) plants against salt stress. Wheat plants were sown with different levels of salinity (0, 30, or 60 mM NaCl) and treated with three levels of exogenous application of foliar spray of aspartic acid (Asp) (0, 0.4, 0.6, or 0.8 mM). Results of the study indicated that salinity stress decreased growth attributes like shoot length, leaf area, and shoot biomass along with photosynthesis pigments and endogenous indole acetic acid. NaCl stress reduced the total content of carbohydrates, flavonoid, beta carotene, lycopene, and free radical scavenging activity (DPPH%). However, Asp application enhanced photosynthetic pigments and endogenous indole acetic acid, consequently improving plant leaf area, leading to higher biomass dry weight either under salt-stressed or non-stressed plants. Exogenous application of Asp, up-regulate the antioxidant system viz. antioxidant enzymes (superoxide dismutase, peroxidase, catalase, and nitrate reductase), and non-enzymatic antioxidants (ascorbate, glutathione, total phenolic content, total flavonoid content, beta carotene, lycopene) contents resulted in declined in reactive oxygen species (ROS). The decreased ROS in Asp-treated plants resulted in reduced hydrogen peroxide, lipid peroxidation (MDA), and aldehyde under salt or non-salt stress conditions. Furthermore, Asp foliar application increased compatible solute accumulation (amino acids, proline, total soluble sugar, and total carbohydrates) and increased radical scavenging activity of DPPH and enzymatic ABTS. Results revealed that the quadratic regression model explained 100% of the shoot dry weight (SDW) yield variation. With an increase in Asp application level by 1.0 mM, the SDW was projected to upsurge through 956 mg/plant. In the quadratic curve model, if Asp is applied at a level of 0.95 mM, the SDW is probably 2.13 g plant^-1. This study concluded that the exogenous application of aspartic acid mitigated the adverse effect of salt stress damage on wheat plants and provided economic benefits.

Multi-omics analysis reveals the molecular changes accompanying heavy-grazing-induced dwarfing of Stipa grandis

Heavy grazing significantly reduces Stipa grandis growth. To enhance our understanding of plant responses to heavy grazing, we conducted transcriptomic, proteomic, and metabolic analyses of the leaves of non-grazed plants (NG) and heavy-grazing-induced dwarf plants (HG) of S. grandis. A total of 101 metabolites, 167 proteins, and 1,268 genes differed in abundance between the HG and NG groups. Analysis of Kyoto Encyclopedia of Genes and Genomes pathways among differentially accumulated metabolites (DAMs) revealed that the most enriched pathways were flavone and flavonol biosynthesis, tryptophan metabolism, and phenylpropanoid biosynthesis. An integrative analysis of differentially expressed genes (DEGs) and proteins, and DAMs in these three pathways was performed. Heavy-grazing-induced dwarfism decreased the accumulation of DAMs enriched in phenylpropanoid biosynthesis, among which four DAMs were associated with lignin biosynthesis. In contrast, all DAMs enriched in flavone and flavonol biosynthesis and tryptophan metabolism showed increased accumulation in HG compared with NG plants. Among the DAMs enriched in tryptophan metabolism, three were involved in tryptophan-dependent IAA biosynthesis. Some of the DEGs and proteins enriched in these pathways showed different expression trends. The results indicated that these pathways play important roles in the regulation of growth and grazing-associated stress adaptions of S. grandis. This study enriches the knowledge of the mechanism of heavy-grazing-induced growth inhibition of S. grandis and provides valuable information for restoration of the productivity in degraded grassland.

Bacillus H47 triggers Olea europaea metabolism activating DOXP and shikimate pathways simultaneously and modifying leaf extracts’ antihypertensive activity

Improvement of plant adaptation by beneficial bacteria (PGPB) may be achieved by triggering multiple pathways to overcome the environmental stress on plant’s growth cycle, activating plant’s metabolism. The present work reports the differential ability of three Bacillus strains to trigger olive tree metabolism, among which, only H47 was outstanding increasing iridoid and flavonol concentration. One-year old olive seedlings grown open air, under harsh conditions of water shortage in saline soils, were root-inoculated with three Bacillus PGPB strains throughout a 12-month period after which, photosynthesis was determined; photosynthetic pigments and bioactive secondary metabolites (iridoids and flavonols) were analyzed, and a study of gene expression of both pathways involved was undertaken to unravel molecular targets involved in the activation. All three strains increased plant fitness based on photosynthetic values, increasing energy dissipation capacity to lower oxidative stress; only H47 increased CO2 fixation and transpiration. Bacillus H47 was found to trigger synthases in the DOXP pathway (up to 5-fold in DOXP-synthase, 3.5-fold in Iridoid synthase, and 2-fold in secologanin synthase) associated to a concomitant increase in iridoids (up to 5-fold in oleuropein and 2-fold in its precursor secologanin). However, despite the 2-fold increases detected in the two predominant flavonols, gene expression was not enhanced, suggesting involvement of a pulse activation model proposed for innate immunity. Furthermore, the activity of leaf extracts to inhibit Angiotensin Converting Enzyme was evaluated, to explore further uses of plant debris with higher added value. Despite the increases in iridoids, leaf extracts from H47 did not increase ACE inhibition, and still, increased antihypertensive potential in oil obtained with this strain is to be explored, as leaves are the source for these metabolites which further translocate to fruits. In summary, Bacillus H47 is an effective strain to increase plant adaptation to dry and saline environments, activates photosynthesis and secondary metabolism in olive tree.

Quercetin: Its Antioxidant Mechanism, Antibacterial Properties and Potential Application in Prevention and Control of Toxipathy

Quercetin, as a flavonol compound found in plants, has a variety of biological activities. It is widely present in nature and the human diet, with powerful oxidative properties and biological activities. In this review, the antioxidant mechanism and broad-spectrum antibacterial properties of quercetin are revealed; the intervention effects of quercetin on pesticide poisoning and the pathway of action are investigated; the toxic effects of main mycotoxins on the collection and the detoxification process of quercetin are summarized; whether it is able to reduce the toxicity of mycotoxins is proved; and the harmful effects of heavy metal poisoning on the collection, the prevention, and control of quercetin are evaluated. This review is expected to enrich the understanding of the properties of quercetin and promote its better application in clinical practice.

MYC transcription factors coordinate tryptophan-dependent defence responses and compromise seed yield in Arabidopsis

Robust plant immunity negatively affects other fitness traits, including growth and seed production. Jasmonate (JA) confers broad-spectrum protection against plant consumers by stimulating the degradation of JASMONATE ZIM-DOMAIN (JAZ) proteins, which in turn relieves repression on transcription factors (TFs) coincident with reduced growth and fecundity. The molecular mechanisms underlying JA-mediated decreases in fitness remain largely unknown. To assess the contribution of MYC TFs to growth and reproductive fitness at high levels of defence, we mutated three MYC genes in a JAZ-deficient mutant (jazD) of Arabidopsis thaliana that exhibits strong defence and low seed yield. Genetic epistasis analysis showed that de-repression of MYC TFs in jazD not only conferred strong resistance to insect herbivory but also reduced shoot and root growth, fruit size and seed yield. We also provided evidence that the JAZ-MYC module coordinates the supply of tryptophan with the production of indole glucosinolates and the proliferation of endoplasmic reticulum bodies that metabolise glucosinolates through the action of β-glucosidases. Our results establish MYCs as major regulators of growth- and reproductive-defence trade-offs and further indicate that these factors coordinate tryptophan availability with the production of amino acid-derived defence compounds.

Regulation Mechanism of Plant Pigments Biosynthesis: Anthocyanins, Carotenoids, and Betalains

Anthocyanins, carotenoids, and betalains are known as the three major pigments in the plant kingdom. Anthocyanins are flavonoids derived from the phenylpropanoid pathway. They undergo acylation and glycosylation in the cytoplasm to produce anthocyanin derivatives and deposits in the cytoplasm. Anthocyanin biosynthesis is regulated by the MBW (comprised by R2R3-MYB, basic helix-loop-helix (bHLH) and WD40) complex. Carotenoids are fat-soluble terpenoids whose synthetic genes also are regulated by the MBW complex. As precursors for the synthesis of hormones and nutrients, carotenoids are not only synthesized in plants, but also synthesized in some fungi and bacteria, and play an important role in photosynthesis. Betalains are special water-soluble pigments that exist only in Caryophyllaceae plants. Compared to anthocyanins and carotenoids, the synthesis and regulation mechanism of betalains is simpler, starting from tyrosine, and is only regulated by MYB (myeloblastosis). Recently, a considerable amount of novel information has been gathered on the regulation of plant pigment biosynthesis, specifically with respect to aspects. In this review, we summarize the knowledge and current gaps in our understanding with a view of highlighting opportunities for the development of pigment-rich plants.

Carbon and nitrogen metabolic regulation in freshwater plant Ottelia alismoides in response to carbon limitation: A metabolite perspective

Carbon and nitrogen metabolism are basic, but pivotal metabolic pathways in plants and are tightly coupled. Maintaining the balance of carbon and nitrogen metabolism is critical for plant survival. Comprehensively revealing the metabolic balance of carbon-nitrogen interactions is important and helpful for understanding the adaptation of freshwater plants to CO₂ limited aqueous environment. A comprehensive metabolomics analysis combined with physiological measurement was performed in the freshwater plant Ottelia alismoides acclimated to high and low CO₂, respectively, for a better understanding of how the carbon and nitrogen metabolic adjustment in freshwater plants respond to carbon limitation. The present results showed that low CO₂ acclimated O. alismoides exhibited significant diurnal titratable acidity and malate fluctuations, as well as an opposite diel pattern of starch change and high enzymatic activities required for crassulacean acid metabolism (CAM) photosynthesis, which indicates that CAM was induced under low CO₂. Moreover, the metabolomic analysis showed that most intermediates of glycolysis, pentose phosphate pathway (PPP) and tricarboxylic acid (TCA) cycle, were increased under low CO₂, indicative of active respiration in low-CO₂-treated O. alismoides. Meanwhile, the majority of amino acids involved in pathways of glutamate and arginine metabolism, aspartate metabolism, and the branched-chain amino acids (BCAAs) metabolism were significantly increased under low CO₂. Notably, γ-aminobutyric acid (GABA) level was significantly higher in low CO₂ conditions, indicating a typical response with GABA shunt compensated for energy deprivation at low CO₂. Taken together, we conclude that in low-CO₂-stressed O. alismoides, CAM photosynthesis was induced, leading to higher carbon and nitrogen as well as energy requirements. Correspondingly, the respiration was greatly fueled via numerous starch degradation to ensure CO₂ fixation in dark, while accompanied by linked promoted N metabolism, presumably to produce energy and alternative carbon sources and nitrogenous substances for supporting the operation of CAM and enhancing tolerance for carbon limitation. This study not only helps to elucidate the regulating interaction between C and N metabolism to adapt to different CO₂ but also provides novel insights into the effects of CO₂ variation on the metabolic profiling of O. alismoides.

Insight into the effect of low temperature treatment on trichome density and related differentially expressed genes in Chinese cabbage

Trichome is important for help plant resist adversity and external damage. However, it often affects the appearance and taste of vegetables. In the present study, the trichome density of leaves from two Chinese cabbage cultivars with and without trichomes treated at low temperature are analyzed by biological microscope, and the differentially expressed genes related to trichomes formation were screened through transcriptome sequencing. The results showed that the number of leaves trichomes was reduced by 34.7% at low temperature compared with room temperature. A total of 661 differentially expression genes effecting trichomes formation were identified at the CT vs C, LCT vs LC, CT vs LCT. Several differentially expression genes from every comparison group were enriched in plant hormone signal transduction and amino acid biosynthesis pathway. Combined with the central genes obtained by WGCNA analysis, five candidate genes Bra029778, Bra026393, Bra030270, Bra037264 and Bra009655 were screened. qRT-PCR analysis verified that the gene expression differences were in line with the trend of transcriptome data. This study not only found possible new key genes and laid a foundation for revealing the molecular mechanism regulating the formation of trichome in Chinese cabbage, but also provided a new way to study plant surface trichomes.

Unraveling metabolic patterns and molecular mechanisms underlying storability in sugar beet

BACKGROUND

Sugar beet is an important crop for sugar production. Sugar beet roots are stored up to several weeks post-harvest waiting for processing in the sugar factories. During this time, sucrose loss and invert sugar accumulation decreases the final yield and processing quality. To improve storability, more information about post-harvest metabolism is required. We investigated primary and secondary metabolites of six sugar beet varieties during storage. Based on their variety-specific sucrose loss, three storage classes representing well, moderate, and bad storability were compared. Furthermore, metabolic data were visualized together with transcriptome data to identify potential mechanisms involved in the storage process.

RESULTS

We found that sugar beet varieties that performed well during storage have higher pools of 15 free amino acids which were already observable at harvest. This storage class-specific feature is visible at harvest as well as after 13 weeks of storage. The profile of most of the detected organic acids and semi-polar metabolites changed during storage. Only pyroglutamic acid and two semi-polar metabolites, including ferulic acid, show higher levels in well storable varieties before and/or after 13 weeks of storage. The combinatorial OMICs approach revealed that well storable varieties had increased downregulation of genes involved in amino acid degradation before and after 13 weeks of storage. Furthermore, we found that most of the differentially genes involved in protein degradation were downregulated in well storable varieties at both timepoints, before and after 13 weeks of storage.

CONCLUSIONS

Our results indicate that increased levels of 15 free amino acids, pyroglutamic acid and two semi-polar compounds, including ferulic acid, were associated with a better storability of sugar beet taproots. Predictive metabolic patterns were already apparent at harvest. With respect to elongated storage, we highlighted the role of free amino acids in the taproot. Using complementary transcriptomic data, we could identify potential underlying mechanisms of sugar beet storability. These include the downregulation of genes for amino acid degradation and metabolism as well as a suppressed proteolysis in the well storable varieties.

Transcriptome Analysis Reveals Critical Genes and Pathways in Carbon Metabolism and Ribosome Biogenesis in Poplar Fertilized with Glutamine

Exogenous Gln as a single N source has been shown to exert similar roles to the inorganic N in poplar 'Nanlin895' in terms of growth performance, yet the underlying molecular mechanism remains unclear. Herein, transcriptome analyses of both shoots (L) and roots (R) of poplar 'Nanlin895' fertilized with Gln (G) or the inorganic N (control, C) were performed. Compared with the control, 3109 differentially expressed genes (DEGs) and 5071 DEGs were detected in the GL and GR libraries, respectively. In the shoots, Gln treatment resulted in downregulation of a large number of ribosomal genes but significant induction of many starch and sucrose metabolism genes, demonstrating that poplars tend to distribute more energy to sugar metabolism rather than ribosome biosynthesis when fertilized with Gln-N. By contrast, in the roots, most of the DEGs were annotated to carbon metabolism, glycolysis/gluconeogenesis and phenylpropanoid biosynthesis, suggesting that apart from N metabolism, exogenous Gln has an important role in regulating the redistribution of carbon resources and secondary metabolites. Therefore, it can be proposed that the promotion impact of Gln on poplar growth and photosynthesis may result from the improvement of both carbon and N allocation, accompanied by an efficient energy switch for growth and stress responses.

Bruceine D may affect the phenylpropanoid biosynthesis by acting on ADTs thus inhibiting Bidens pilosa L. seed germination

Bruceine D is a natural quassinoid, which was successfully isolated in our research group from the residue of Brucea javanica (L.) seeds. Our previous research showed that Bruceine D prevented Bidens pilosa L. seed germination by suppressing the activity of key enzymes and the expression levels of key genes involved in the phenylpropanoid biosynthesis pathway. In this study, integrated analyses of non-targeted metabolomic and transcriptomic were performed. A total of 356 different accumulated metabolites (DAMs) were identified, and KEGG pathway analyses revealed that most of these DAMs were involved in phenylpropanoid biosynthesis. The decreased expression of ADTs and content of L-phenylalanine implicates that Bruceine D may suppress the downstream phenylpropanoid biosynthesis pathway by disrupting primary metabolism, that is, the phenylalanine biosynthesis pathway, thus inhibiting the final products, resulting in the interruption of B. pilosa seed germination. These results suggest that Bruceine D may inhibit the B. pilosa seed germination by suppressing phenylpropanoid biosynthesis through acting on ADTs.

Regulation of Drought and Salt Tolerance by OsSKL2 and OsASR1 in Rice

Abiotic stresses such as salinity and drought greatly impact the growth and production of crops worldwide. Here, a shikimate kinase-like 2 (SKL2) gene was cloned from rice and characterized for its regulatory function in salinity and drought tolerance. OsSKL2 was localized in the chloroplast, and its transcripts were significantly induced by drought and salinity stress as well as H₂O₂ and abscisic acid (ABA) treatment. Meanwhile, overexpression of OsSKL2 in rice increased tolerance to salinity, drought and oxidative stress by increasing antioxidant enzyme activity, and reducing levels of H₂O₂, malondialdehyde, and relative electrolyte leakage. In contrast, RNAi-induced suppression of OsSKL2 increased sensitivity to stress treatment. Interestingly, overexpression of OsSKL2 also increased sensitivity to exogenous ABA, with an increase in reactive oxygen species (ROS) accumulation. Moreover, OsSKL2 was found to physically interact with OsASR1, a well-known chaperone-like protein, which also exhibited positive roles in salt and drought tolerance. A reduction in ROS production was also observed in leaves of Nicotiana benthamiana showing transient co-expression of OsSKL2 with OsASR1. Taken together, these findings suggest that OsSKL2 together with OsASR1 act as important regulatory factors that confer salt and drought tolerance in rice via ROS scavenging.

Proteomic and metabolic disturbances in lignin-modified Brachypodium distachyon

Lignin biosynthesis begins with the deamination of phenylalanine and tyrosine (Tyr) as a key branch point between primary and secondary metabolism in land plants. Here, we used a systems biology approach to investigate the global metabolic responses to lignin pathway perturbations in the model grass Brachypodium distachyon. We identified the lignin biosynthetic protein families and found that ammonia-lyases (ALs) are among the most abundant proteins in lignifying tissues in grasses. Integrated metabolomic and proteomic data support a link between lignin biosynthesis and primary metabolism mediated by the ammonia released from ALs that is recycled for the synthesis of amino acids via glutamine. RNA interference knockdown of lignin genes confirmed that the route of the canonical pathway using shikimate ester intermediates is not essential for lignin formation in Brachypodium, and there is an alternative pathway from Tyr via sinapic acid for the synthesis of syringyl lignin involving yet uncharacterized enzymatic steps. Our findings support a model in which plant ALs play a central role in coordinating the allocation of carbon for lignin synthesis and the nitrogen available for plant growth. Collectively, these data also emphasize the value of integrative multiomic analyses to advance our understanding of plant metabolism.

A Metabolomic Approach to Assess the Toxicity of the Olive Tree Endophyte Bacillus sp. PTA13 Lipopeptides to the Aquatic Macrophyte Lemna minor L

Pesticides represent a major human input into the ecosystem, posing a serious risk to non-target organisms. Therefore, there is pressure toward the reduction in their use and the discovery of alternative sources of bioactivity. Endophytic microorganisms represent a source of bioactivity, whose potential for plant protection has been recently established. In this context, an olive tree endophytic Bacillus sp. was isolated, exhibiting superior antifungal activity, mainly attributed to its major surfactin, iturin, and fengycin and the minor gageotetrin and bacilotetrin groups of lipopeptides (LP). Based on the potential of LP and the lack of information on their toxicity to aquatic organisms, we have investigated the toxicity of an LP extract to the model macrophyte Lemna minor L. The extract exhibited low phytotoxicity (EC₅₀ = 419 μg·mL^-1), and for the investigation of its effect on the plant, GC/EI/MS metabolomics was applied following exposure to sub-lethal doses (EC₂₅ and EC₅₀). Results revealed a general disturbance of plants' biosynthetic capacity in response to LP treatments, with substantial effect on the amino acid pool and the defense mechanism regulated by jasmonate. There are no previous reports on the phytotoxicity of LP to L. minor, with evidence supporting their improved toxicological profile and potential in plant protection.

Biosynthetic mechanisms of isoflavone accumulation affected by different growth patterns in Astragalus mongholicus products

BACKGROUND

At present, Astragalus mongholicus products on the market represent two growth patterns: imitative wild A. mongholicus (WAM) and cultivated A. mongholicus (CAM). The 6-year-old WAM (A6) and 2-year-old CAM (B2) products are often sold as commodities. This study aimed to explore the effects of the abovementioned growth patterns on the biosynthetic mechanisms of isoflavone accumulation in A. mongholicus products.

RESULTS

In this paper, the content of calycosin-7-O-β-D-glucoside in 6-year-old WAM (A6) was significantly higher than that in 2-year-old CAM (B2) based on high-performance liquid chromatography. Tissue anatomy indicated that A6 has developed phloem fibers, thickened secondary walls, and a more well-developed vascular system than B2. Thirteen differentially accumulated metabolites were found in A6 and B2 by UHPLC-ESI-Q-TOF-MS/MS, of which isoflavones were highly and significantly enriched in A6. By combining transcriptomics and metabolomics analysis, we found that the metabolomics profile was the same as the transcriptomics profile in both A6 and B2. In total, 11 novel isoflavone-related genes were isolated using BLAST and functional annotation through RNA-Seq and Iso-Seq. The results of integrated analysis, Short Time-series Expression Miner analysis, and Pearson correlation analysis showed that the regulation of four key enzymes, cinnamate 4-hydroxylase, 6-deoxychalcone synthase, chalcone reductase, and chalcone isomerase, led to the high accumulation of isoflavones in A6. In addition, AmUFGT (c778119) and AmUCGT (c303354) were predicted to be 7-O-glycosyltransferases by phylogenetic analysis; these genes catalyze formononetin and calycosin, respectively.

CONCLUSIONS

The findings of this work will clarify the differences in the biosynthetic mechanism of isoflavone accumulation between A6 and B2, which will guide the cultivation of A. mongholicus.

The roles of epigenetic modifications in the regulation of auxin biosynthesis

Auxin is one of the most important plant growth regulators of plant morphogenesis and response to environmental stimuli. Although the biosynthesis pathway of auxin has been elucidated, the mechanisms regulating auxin biosynthesis remain poorly understood. The transcription of auxin biosynthetic genes is precisely regulated by complex signaling pathways. When the genes are expressed, epigenetic modifications guide mRNA synthesis and therefore determine protein production. Recent studies have shown that different epigenetic factors affect the transcription of auxin biosynthetic genes. In this review, we focus our attention on the molecular mechanisms through which epigenetic modifications regulate auxin biosynthesis.

Hairy roots: An untapped potential for production of plant products

While plants are an abundant source of valuable natural products, it is often challenging to produce those products for commercial application. Often organic synthesis is too expensive for a viable commercial product and the biosynthetic pathways are often so complex that transferring them to a microorganism is not trivial or feasible. For plants not suited to agricultural production of natural products, hairy root cultures offer an attractive option for a production platform which offers genetic and biochemical stability, fast growth, and a hormone free culture media. Advances in metabolic engineering and synthetic biology tools to engineer hairy roots along with bioreactor technology is to a point where commercial application of the technology will soon be realized. We discuss different applications of hairy roots. We also use a case study of the advancements in understanding of the terpenoid indole alkaloid pathway in Catharanthus roseus hairy roots to illustrate the advancements and challenges in pathway discovery and in pathway engineering.

Comparative Proteomics Study on the Postharvest Senescence of Volvariella volvacea

Volvariella volvacea is difficult to store after harvest, which restricts the production and circulation of V. volvacea fruiting bodies. Low-temperature storage is the traditional storage method used for most edible fungi. However, V. volvacea undergoes autolysis at low temperatures. When fruiting bodies are stored at 15 °C (suitable temperature), V. volvacea achieves the best fresh-keeping effect. However, the molecular mechanism underlying the postharvest senescence of V. volvacea remains unclear. Based on this information, we stored V. volvacea fruiting bodies at 15 °C after harvest and then analyzed the texture and phenotype combined with the results of previous physiological research. Four time points (0, 24, 60, and 96 h) were selected for the comparative proteomics study of V. volvacea during storage at 15 °C. A variety of proteins showed differential expressions in postharvest V. volvacea at 15 °C. Further comparison of the gene ontology (GO) enrichment analysis and KEGG pathways performed at different sampling points revealed proteins that were significantly enriched at several time points. At the same time, we also analyzed differentially expressed proteins (DEPs) related to the RNA transport, fatty acid biosynthesis and metabolism, and amino acid biosynthesis and metabolism pathways, and discussed the molecular functions of the PAB1, RPG1, ACC1, ADH3, ADH2, ALD5, and SDH2 proteins in postharvest V. volvacea senescence. Our results showed that many biological processes of the postharvest senescence of V. volvacea changed. Most importantly, we found that most RNA transport-related proteins were down-regulated, which may lead to a decrease in related gene regulation. Our results also showed that the expression of other important proteins, such as the fatty acid metabolism related proteins increased; and changes in fatty acid composition affected the cell membrane, which may accelerate the ripening and perception of V. volvacea fruiting bodies. Therefore, our research provides a reference for further studies on the aging mechanism of V. volvacea.

The Kelch-F-box protein SMALL AND GLOSSY LEAVES 1 (SAGL1) negatively influences salicylic acid biosynthesis in Arabidopsis thaliana by promoting the turn-over of transcription factor SYSTEMIC ACQUIRED RESISTANCE DEFICIENT 1 (SARD1)

Salicylic acid (SA) is a key phytohormone regulating plant immunity. Although the transcriptional regulation of SA biosynthesis has been well-studied, its post-translational regulation is largely unknown. We report that a Kelch repeats-containing F-box (KFB) protein, SMALL AND GLOSSY LEAVES 1 (SAGL1), negatively influences SA biosynthesis in Arabidopsis thaliana by mediating the proteolytic turnover of SYSTEMIC ACQUIRED RESISTANCE DEFICIENT 1 (SARD1), a master transcription factor that directly drives SA biosynthesis during immunity. Loss of SAGL1 resulted in characteristic growth inhibition. Combining metabolomic, transcriptional and phenotypic analyses, we found that SAGL1 represses SA biosynthesis and SA-mediated immune activation. Genetic crosses to mutants that are deficient in SA biosynthesis blocked the SA overaccumulation in sagl1 and rescued its growth. Biochemical and proteomic analysis identified that SAGL1 interacts with SARD1 and promotes the degradation of SARD1 in a proteasome-dependent manner. These results unravelled a critical role of KFB protein SAGL1 in maintaining SA homeostasis via controlling SARD1 stability.

An Arabidopsis GCMS chemical ionization technique to quantify adaptive responses in central metabolism

We present a methodology to survey central metabolism in 13CO2-labeled Arabidopsis (Arabidopsis thaliana) rosettes by ammonia positive chemical ionization-gas chromatography-mass spectrometry. This technique preserves the molecular ion cluster of methyloxime/trimethylsilyl-derivatized analytes up to 1 kDa, providing unambiguous nominal mass assignment of >200 central metabolites and 13C incorporation rates into a subset of 111 from the tricarboxylic acid (TCA) cycle, photorespiratory pathway, amino acid metabolism, shikimate pathway, and lipid and sugar metabolism. In short-term labeling assays, we observed plateau labeling of ∼35% for intermediates of the photorespiratory cycle except for glyoxylate, which reached only ∼4% labeling and was also present at molar concentrations several fold lower than other photorespiratory intermediates. This suggests photorespiratory flux may involve alternate intermediate pools besides the generally accepted route through glyoxylate. Untargeted scans showed that in illuminated leaves, noncyclic TCA cycle flux and citrate export to the cytosol revert to a cyclic flux mode following methyl jasmonate (MJ) treatment. MJ also caused a block in the photorespiratory transamination of glyoxylate to glycine. Salicylic acid treatment induced the opposite effects in both cases, indicating the antagonistic relationship of these defense signaling hormones is preserved at the metabolome level. We provide complete chemical ionization spectra for 203 Arabidopsis metabolites from central metabolism, which uniformly feature the unfragmented pseudomolecular ion as the base peak. This unbiased, soft ionization technique is a powerful screening tool to identify adaptive metabolic trends in photosynthetic tissue and represents an important advance in methodology to measure plant metabolic flux.

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.

CRISPR/Cas9 disruption of UGT71L1 in poplar connects salicinoid and salicylic acid metabolism and alters growth and morphology

Salicinoids are salicyl alcohol-containing phenolic glycosides with strong antiherbivore effects found only in poplars and willows. Their biosynthesis is poorly understood, but recently a UDP-dependent glycosyltransferase, UGT71L1, was shown to be required for salicinoid biosynthesis in poplar tissue cultures. UGT71L1 specifically glycosylates salicyl benzoate, a proposed salicinoid intermediate. Here, we analyzed transgenic CRISPR/Cas9-generated UGT71L1 knockout plants. Metabolomic analyses revealed substantial reductions in the major salicinoids, confirming the central role of the enzyme in salicinoid biosynthesis. Correspondingly, UGT71L1 knockouts were preferred to wild-type by white-marked tussock moth (Orgyia leucostigma) larvae in bioassays. Greenhouse-grown knockout plants showed substantial growth alterations, with decreased internode length and smaller serrated leaves. Reinserting a functional UGT71L1 gene in a transgenic rescue experiment demonstrated that these effects were due only to the loss of UGT71L1. The knockouts contained elevated salicylate (SA) and jasmonate (JA) concentrations, and also had enhanced expression of SA- and JA-related genes. SA is predicted to be released by UGT71L1 disruption, if salicyl salicylate is a pathway intermediate and UGT71L1 substrate. This idea was supported by showing that salicyl salicylate can be glucosylated by recombinant UGT71L1, providing a potential link of salicinoid metabolism to SA and growth impacts. Connecting this pathway with growth could imply that salicinoids are under additional evolutionary constraints beyond selective pressure by herbivores.

Exogenous stimulation-induced biosynthesis of volatile compounds: Aroma formation of oolong tea at postharvest stage

Volatile organic compounds (VOCs) are produced by plants responding to biotic and abiotic stresses. According to their biosynthetic sources, induced VOCs are divided into three major classes: terpenoids, phenylpropanoid/benzenoid, and fatty acid derivatives. These compounds with specific aroma characteristics importantly contribute to the aroma quality of oolong tea. Shaking and rocking is the crucial procedure for the aroma formation of oolong tea by exerting mechanical damage to fresh tea leaves. Abundant studies have been carried out to investigate the formation mechanisms of VOCs during oolong tea processing in recent years. This review systematically introduces the biosynthesis of VOCs in plants, and the volatile changes due to biotic and abiotic stresses are summarized and expatiated, using oolong tea as an example.

Rethinking the Intrinsic Sensitivity of Fungi to Glyphosate

The 5-enolpyruvylshikimate 3-phosphate synthase (EPSPS) is the central enzyme of the shikimate pathway to synthesize the three aromatic amino acids in fungi, plants, and prokaryotes. This enzyme is the target of the herbicide glyphosate. In most plants and prokaryotes, the EPSPS protein is constituted by a single domain family, the EPSP synthase (PF00275) domain, whereas in fungi, the protein is formed by a multi-domain structure from combinations of 22 EPSPS-associated domains. The most common multi-domain EPSPS structure in fungi involves five EPSPS-associated domains of the shikimate pathway. In this article, we analyze 390 EPSPS proteins of fungi to determine the extent of the EPSPS-associated domains. Based on the current classification of the EPSPS protein, most fungal species are intrinsically sensitive to glyphosate. However, complex domain architectures may have multiple responses to the herbicide. Further empirical studies are needed to determine the effect of glyphosate on fungi, taking into account the diversity of multi-domain architectures of the EPSPS. This research opens the door to novel biotechnological applications for microbial degradation of glyphosate.

Metagenomic assembled genomes unravel purple non‑sulfur bacteria (PNSB) involved in integrating C, N, P biotransformation

Purple non‑sulfur bacteria (PNSB) based bioprocess has been developed to remove carbon, nitrogen and phosphorus from wastewater. However, the interactions of various bioconversion of carbon (C), nitrogen (N) and phosphorus (P) are not completely clear. In this study, a genome-centric metagenomic approach was employed to delineate the shift in microbial community structures and functional genes under light and dark conditions. Seven and 22 metagenomic assembled genomes (MAGs) were recovered from samples in light and dark conditions, accounting for a substantial portion of microbes. Under light, Rhodopseudomonas palustris promoted complex metabolic processes and interactions for C, N and P conversions. Burkholderia contaminans was discovered as new potential organisms for simultaneous C, N and P removal. Metagenomics analysis confirmed genes involved in the synthesis of glycogen, poly-β-hydroxybutyrate, poly-P, amino acids and carotenoids in R. palustris. The substrate transformation mechanisms and potential pathways were proposed according to the detected metabolites. Our findings provided insights into a new biological system with simultaneous C, N and P bioconversions, and improved the understanding of interactions among the key populations.

The Ethylene Response Factor ERF5 Regulates Anthocyanin Biosynthesis in 'Zijin' Mulberry Fruits by Interacting with MYBA and F3H Genes

Ethylene promotes ripening in fruits as well as the biosynthesis of anthocyanins in plants. However, the question of which ethylene response factors (ERFs) interact with the genes along the anthocyanin biosynthesis pathway is yet to be answered. Herein, we conduct an integrated analysis of transcriptomes and metabolome on fruits of two mulberry genotypes ('Zijin', ZJ, and 'Dashi', DS, with high and low anthocyanin abundance, respectively) at different post-flowering stages. In total, 1035 upregulated genes were identified in ZJ and DS, including MYBA in the MBW complex and anthocyanin related genes such as F3H. A KEGG analysis suggested that flavonoid biosynthesis and plant hormone signaling transduction pathways were significantly enriched in the upregulated gene list. In particular, among 103 ERF genes, the expression of ERF5 showed the most positive correlation with the anthocyanin change pattern across both genotypes and in the post-flowering stages, with a Pearson correlation coefficient (PCC) of 0.93. Electrophoresis mobility shift assay (EMSA) and luciferase assay suggested that ERF5 binds to the promoter regions of MYBA and F3H and transcriptionally activates their gene expression. We elucidated a potential mechanism by which ethylene enhances anthocyanin accumulation in mulberry fruits and highlighted the importance of the ERF5 gene in controlling the anthocyanin content in mulberry species. This knowledge could be used for engineering purposes in future mulberry breeding programs.

Transcriptomic and Widely Targeted Metabolomic Approach Identified Diverse Group of Bioactive Compounds, Antiradical Activities, and Their Associated Genes in Six Sugarcane Varieties

Sugarcane is cultivated mainly for its high sucrose content but it can also produce many metabolites with promising antioxidant potential. However, very few studies have been reported on the biosynthesis of metabolites in sugarcane to date. In this study, we have identified a wide range of amino acids and organic acids in the rind of six sugarcane varieties by the LC-MS/MS method. A total number of 72 amino acids and 55 organic acid compounds were characterized; among these, 100 were reported for the first time. Moreover, 13 amino acids and seven organic acids were abundantly distributed in all varieties tested and considered major amino acids and organic acids in sugarcane. The variety Taitang134 (F134) showed the highest content of total amino acids, whereas the varieties ROC16 and Yuetang93/159 (YT93/159) had maximum content of organic acids. The amino acids of the rind extract presented higher antioxidant capacity than the organic acids of the rind extract. In addition, the transcriptomic and metabolic integrated analysis highlighted some candidate genes associated with amino acid biosynthesis in sugarcane. We selected a transcription factor gene, MYB(t), and over-expressed it in Arabidopsis. The transgenic plants showed a higher accumulation of amino acids with higher antiradical activity compared with the wild-type Arabidopsis plants. Thus, we characterize a wide range of amino acids and organic acids and their antiradical activities in different sugarcane varieties and present candidate genes that can be potentially valuable for the genetic improvement of metabolites in sugarcane bagasse

Genome-Wide Association Study With Growth-Related Traits and Secondary Metabolite Contents in Red- and White-Heart Chinese Fir

Chinese fir [Cunninghamia lanceolata (Lamb.) Hook] is an important evergreen coniferous tree species that is widely distributed in many southern provinces of China and has important economic value. The Chinese fir accounts for 1/4 and 1/3 of the total artificial forest area and stock volume, respectively. Red-heart Chinese fir is popular in the market because of its high density and red heartwood. The long-growth cycle hindered the breeding process of Chinese fir, while molecular marker-assisted breeding could accelerate it. However, Chinese fir, a perennial conifer species, has a large genome, which has not yet been published. In this study, the growth-related traits and secondary metabolite contents of red- and white-heart Chinese fir were measured and found to be different between them. There are extremely significant differences among growth-related traits (p < 0.001), but secondary metabolite contents have different correlations due to differences in chemical structure. Moreover, genotype effect analysis of the substantially correlated single nucleotide polymorphisms (SNPs) revealed that most of the loci related to each growth-related traits were different from each other, indicating a type specificity of the genes regulated different growth-related traits. Furthermore, among the loci related to secondary metabolite contents, nine loci associated with multiple metabolite phenotypes such as Marker21022_4, Marker21022_172, Marker24559_31, Marker27425_37, Marker20748_85, Marker18841_115, Marker18841_198, Marker65846_146, and Marker21486_163, suggesting the presence of pleiotropic genes. This study identified the potential SNP markers associated with secondary metabolites in Chinese fir, thus setting the basis for molecular marker-assisted selection.

Combining analyses of metabolite profiles and phosphorus fractions to explore high phosphorus utilization efficiency in maize

Phosphorus (P) limitation is a significant factor restricting crop production in agricultural systems, and enhancing the internal P utilization efficiency (PUE) of crops plays an important role in ensuring sustainable P use in agriculture. To better understand how P is remobilized to affect crop growth, we first screened P-efficient (B73 and GEMS50) and P-inefficient (Liao5114) maize genotypes at the same shoot P content, and then analyzed P pools and performed non-targeted metabolomic analyses to explore changes in cellular P fractions and metabolites in maize genotypes with contrasting PUE. We show that lipid P and nucleic acid P concentrations were significantly lower in lower leaves of P-efficient genotypes, and these P pools were remobilized to a major extent in P-efficient genotypes. Broad metabolic alterations were evident in leaves of P-efficient maize genotypes, particularly affecting products of phospholipid turnover and phosphorylated compounds, and the shikimate biosynthesis pathway. Taken together, our results suggest that P-efficient genotypes have a high capacity to remobilize lipid P and nucleic acid P and promote the shikimate pathway towards efficient P utilization in maize.

Virtual screening of natural products against 5-enolpyruvylshikimate-3-phosphate synthase using the Anagreen herbicide-like natural compound library

The shikimate pathway enzyme 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) catalyzes a reaction involved in the production of amino acids essential for plant growth and survival. EPSPS is the main target of glyphosate, a broad-spectrum herbicide that acts as a competitive inhibitor concerning phosphoenolpyruvate (PEP), which is the natural substrate of EPSPS. In the present study, we introduce a natural compound library, named Anagreen, which is a compendium of herbicide-like compounds obtained from different natural product databases. Herein, we combined the structure- and ligand-based virtual screening strategies to explore Anagreen against EPSPS using the structure of glyphosate complexed with a T102I/P106S mutant of EPSPS from Eleusine indica (EiEPSPS) as a starting point. First, ligand-based pharmacophore screening was performed to select compounds with a similar pharmacophore to glyphosate. Then, structure-based pharmacophore modeling was applied to build a model which represents the molecular features of glyphosate. Then, consensus docking was performed to rank the best poses of the natural compounds against the PEP binding site, and then molecular dynamics simulations were performed to analyze the stability of EPSPS complexed with the selected ligands. Finally, we have investigated the binding affinity of the complexes using free energy calculations. The selected hit compound, namely AG332841, showed a stable conformation and binding affinity to the EPSPS structure and showed no structural similarity to the already known weed EPSPS inhibitors. Our computational study aims to clarify the inhibition of the mutant EiEPSPS, which is resistant to glyphosate, and identify new potential herbicides from natural products.

An Antifungal Role of Hydrogen Sulfide on Botryosphaeria Dothidea and Amino Acid Metabolism Involved in Disease Resistance Induced in Postharvest Kiwifruit

Botryosphaeria dothidea is a major pathogen responsible for postharvest kiwifruit soft rot. This study aimed to determine the influence of hydrogen sulfide (H₂S) on postharvest resistance to kiwifruit soft rot and the antifungal role of H₂S against B. dothidea. The results indicated that H₂S (20 μl L^-1) restricted the lesion area following inoculation with B. dothidea. H₂S enhanced the production of shikimic acid, tyrosine, tryptophan, and phenylalanine while also increasing the total phenols, flavonoids, and lignin. H₂S upregulated the expression of AcDHQS, AcSDH, AcSK, AcPAL, AcCAD, and AcCHS. Additionally, sodium hydrosulfide (NaHS)-released H₂S inhibited mycelial growth. NaHS concentrations of 20 and 40 mmol L^-1 significantly decreased the mycelial weight and malondialdehyde content (MDA) content while increasing cell membrane conductivity and membrane leakage. The results indicate that H₂S induces resistance in kiwifruit via a microbicidal role and amino acid metabolism involved in postharvest kiwifruit disease resistance.

Point mutations that boost aromatic amino acid production and CO2 assimilation in plants

Aromatic compounds having unusual stability provide high-value chemicals and considerable promise for carbon storage. Terrestrial plants can convert atmospheric CO₂ into diverse and abundant aromatic compounds. However, it is unclear how plants control the shikimate pathway that connects the photosynthetic carbon fixation with the biosynthesis of aromatic amino acids, the major precursors of plant aromatic natural products. This study identified suppressor of tyra2 (sota) mutations that deregulate the first step in the plant shikimate pathway by alleviating multiple effector-mediated feedback regulation in Arabidopsis thaliana. The sota mutant plants showed hyperaccumulation of aromatic amino acids accompanied by up to a 30% increase in net CO₂ assimilation. The identified mutations can be used to enhance plant-based, sustainable conversion of atmospheric CO₂ to high-energy and high-value aromatic compounds.

On Aromaticity of the Aromatic α-Amino Acids and Tuning of the NICS Indices to Find the Aromaticity Order

The NICS aromaticity indices of the rings in flexible phenylalanine (Phe), tryptophan (Trp), tyrosine (Tyr), and histidine (His) chiral molecules were analyzed. These molecules have several dozens of conformers, and their rings are slightly non-planar. Therefore, the population-averaged NICS_pav index was defined, and the NICS scans had to be performed with respect to planes found by the least-squares routine. A rule differentiating an obverse and a reverse ring face in aromatic amino acids was formulated. The NICS scan minima corresponding to the obverse and reverse face were unequal, which prompted us to use the term ring face aromaticity/ring face tropicity. It appeared that for Phe, Trp, Tyr, and His, the reverse face has always had higher ring face aromaticity/ring face tropicity than the obverse one. Despite the NICS modifications, uncertainty about the amino acid aromaticity order remained. This motivated us to use the integral INICS index newly proposed by Stanger as well. Then, the following sequence was obtained: Trp(phenyl) > Phe > Trp(pyrrole) > His > Tyr. The juxtaposition of the INICS indices of amino acids with that of some model rings revealed a fair transferability of the values. Finally, analysis of the substituent effect on INICS demonstrated that the aromaticity of Tyr is the lowest due to the strength of the OH group π-electron-donating effect able to perturb enough the ring charge distribution and its magnetic aromaticity. The NICS calculations were executed using the ARONICS program written within the project.

Natural variance at the interface of plant primary and specialized metabolism

Plants produce a large number of diverse metabolites when they grow and develop as well as when they respond to the changing external environment. These are an important source of human nutrition and medicine. In this review we emphasized the major issues of the primary-specialized metabolic interface in plant metabolism, described the metabolic flow from primary to specialized metabolism, and the conservation and diversity of primary and specialized metabolites. At the same time, we summarized the regulatory mechanisms underpinning the dynamic balance primary and specialized metabolism based on multi-omics integration analysis, as well as the natural variation of primary and specialized metabolic pathways and genes during the plant evolution. Moreover, the discovery and optimization of the synthesis and regulation elements of various primary to specialized metabolic flows provide the possibility for precise modification and personalized customization of metabolic pathways, which will greatly promote the development of synthetic biology.

3-Deoxy-D-arabino-heptulosonate 7-phosphate synthase as the gatekeeper of plant aromatic natural product biosynthesis

The shikimate pathway connects the central carbon metabolism with the biosynthesis of aromatic amino acids-l-tyrosine, l-phenylalanine, and l-tryptophan-which play indispensable roles as precursors of numerous aromatic phytochemicals. Despite the importance of the shikimate pathway-derived products for both plant physiology and human society, the regulatory mechanism of the shikimate pathway remains elusive. This review summarizes the recent progress and current understanding on the plant 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase (DAHP synthase or DHS) enzymes that catalyze the committed reaction of the shikimate pathway. We particularly focus on how the DHS activity is regulated in plants in comparison to those of microbes and discuss potential roles of DHS as the critical gatekeeper for the production of plant aromatic compounds.

Integrate Small RNA and Degradome Sequencing to Reveal Drought Memory Response in Wheat (Triticum aestivum L.)

Drought has gradually become one of the most severe abiotic stresses on plants. Plants that experience stress training can exhibit enhanced stress tolerance. According to MicroRNA (miRNA) sequencing data, this study identified 195 candidate drought memory-related miRNAs in wheat, and targets of 64 (32.8%) candidate miRNAs were validated by degradome sequencing. Several drought memory-related miRNAs such as tae-miR9676-5p, tae-MIR9676-p3_1ss21GA, tae-miR171a, tae-miR531_L-2, tae-miR408_L-1, PC-3p-5049_3565, tae-miR396c-5p, tae-miR9778, tae-miR164a-5p, and tae-miR9662a-3p were validated as having a strong response to drought memory by regulating the expression of their target genes. In addition, overexpression of drought memory-related miRNA, tae-miR531_L-2, can remarkably improve the drought tolerance of transgenic Arabidopsisthaliana. Drought memory can regulate plant cellular signal transduction, plant biosynthetic processes, and other biological processes to cope with drought via transcriptional memory. In addition, drought memory-related miRNAs can promote starch and sucrose catabolism and soluble sugar accumulation and regulate proline homeostasis to improve plant drought resistance. Our results could contribute to an understanding of drought memory in wheat seedlings and may provide a new strategy for drought-resistant breeding.

Duodenal Metabolic Profile Changes in Heat-Stressed Broilers

Simple Summary

Heat stress (HS) represents an environmental and socio-economic burden to the poultry industry worldwide. However, the underpinning mechanisms for HS responses are still not well defined. Here, we used a high-throughput analysis to determine the metabolite profiles in acute and chronic heat-stressed broilers in comparison with thermoneutral and pair-fed birds. The results showed that HS altered several duodenal metabolites in a duration-dependent manner and identified potential metabolite signatures.

Abstract

Heat stress (HS) is devastating to poultry production sustainability worldwide. In addition to its adverse effects on growth, welfare, meat quality, and mortality, HS alters the gut integrity, leading to dysbiosis and leaky gut syndrome; however, the underlying mechanisms are not fully defined. Here, we used a high-throughput mass spectrometric metabolomics approach to probe the metabolite profile in the duodenum of modern broilers exposed to acute (AHS, 2 h) or chronic cyclic (CHS, 8 h/day for 2 weeks) HS in comparison with thermoneutral (TN) and pair-fed birds. Ultra high performance liquid chromatography coupled with high resolution mass spectrometry (UHPLC–HRMS) identified a total of 178 known metabolites. The trajectory analysis of the principal component analysis (PCA) score plots (both 2D and 3D maps) showed clear separation between TN and each treated group, indicating a unique duodenal metabolite profile in HS birds. Within the HS groups, partial least squares discriminant analysis (PLS-DA) displayed different clusters when comparing metabolite profiles from AHS and CHS birds, suggesting that the metabolite signatures were also dependent on HS duration. To gain biologically related molecule networks, the above identified duodenal metabolites were mapped into the Ingenuity Pathway Analysis (IPA) knowledge-base and analyzed to outline the most enriched biological functions. Several common and specific top canonical pathways were generated. Specifically, the adenosine nucleotide degradation and dopamine degradation pathways were specific for the AHS group; however, the UDP-D-xylose and UDP-D-glucuronate biosynthesis pathways were generated only for the CHS group. The top diseases enriched by the IPA core analysis for the DA metabolites, including cancer, organismal (GI) injury, hematological, cardiovascular, developmental, hereditary, and neurological disorders, were group-specific. The top altered molecular and cellular functions were amino acid metabolism, molecular transport, small molecule biochemistry, protein synthesis, cell death and survival, and DNA damage and repair. The IPA-causal network predicted that the upstream regulators (carnitine palmitoyltransferase 1B, CPT1B; histone deacetylase 11, HDAC11; carbonic anhydrase 9, CA9; interleukin 37, IL37; glycine N-methyl transferase, GNMT; GATA4) and the downstream mediators (mitogen-activated protein kinases, MAPKs; superoxide dismutase, SOD) were altered in the HS groups. Taken together, these data showed that, independently of feed intake depression, HS induced significant changes in the duodenal metabolite profile in a duration-dependent manner and identified a potential duodenal signature for HS.

Tryptophan Levels as a Marker of Auxins and Nitric Oxide Signaling

The aromatic amino acid tryptophan is the main precursor for indole-3-acetic acid (IAA), which involves various parallel routes in plants, with indole-3-acetaldoxime (IAOx) being one of the most common intermediates. Auxin signaling is well known to interact with free radical nitric oxide (NO) to perform a more complex effect, including the regulation of root organogenesis and nitrogen nutrition. To fathom the link between IAA and NO, we use a metabolomic approach to analyze the contents of low-molecular-mass molecules in cultured cells of Arabidopsis thaliana after the application of S-nitrosoglutathione (GSNO), an NO donor or IAOx. We separated the crude extracts of the plant cells through ion-exchange columns, and subsequent fractions were analyzed by gas chromatography-mass spectrometry (GC-MS), thus identifying 26 compounds. A principal component analysis (PCA) was performed on N-metabolism-related compounds, as classified by the Kyoto Encyclopedia of Genes and Genomes (KEGG). The differences observed between controls and treatments are mainly explained by the differences in Trp contents, which are much higher in controls. Thus, the Trp is a shared response in both auxin- and NO-mediated signaling, evidencing some common signaling mechanism to both GSNO and IAOx. The differences in the low-molecular-mass-identified compounds between GSNO- and IAOx-treated cells are mainly explained by their concentrations in benzenepropanoic acid, which is highly associated with IAA levels, and salicylic acid, which is related to glutathione. These results show that the contents in Trp can be a marker for the study of auxin and NO signaling.

Deciphering the Potential Role of Symbiotic Plant Microbiome and Amino Acid Application on Growth Performance of Chickpea Under Field Conditions

The unprecedented rise in the human population has increased pressure on agriculture production. To enhance the production of crops, farmers mainly rely on the use of chemical fertilizers and pesticides, which have, undoubtedly, increased the production rate but at the cost of losing sustainability of the environment in the form of genetic erosion of indigenous varieties of crops and loss of fertile land. Therefore, farming practices need to upgrade toward the use of biological agents to maintain the sustainability of agriculture and the environment. In this context, using microbial inoculants and amino acids may present a more effective, safer, economical, and sustainable alternative means of realizing higher productivity of crops. Therefore, field experiments were performed on chickpea for two succeeding years using Rhizobium and L-methionine (at three levels, i.e., 5, 10, and 15 mg L-1) separately and in combinations. The results show that the application of Rhizobium and all the three levels of L-methionine increased the growth and yield of chickpea. There was a higher response to a lower dose of L-methionine, i.e., 5 mg L-1. It has been found that maximum grain yield (39.96 and 34.5% in the first and second years, respectively) of chickpea was obtained with the combined use of Rhizobium and L-methionine (5 mg L-1). This treatment was also the most effective in enhancing nodule number (91.6 and 58.19%), leghemoglobin (161.1 and 131.3%), and protein content (45.2 and 45%) of plants in both years. Likewise, photosynthetic pigments and seed chemical composition were significantly improved by Rhizobium inoculation. However, these effects were prominent when Rhizobium inoculation was accompanied by L-methionine. In conclusion, utilizing the potential of combined use of L-methionine and microbial inoculant could be a better approach for developing sustainable agriculture production.

Enantioselective Response of Wheat Seedlings to Imazethapyr: From the Perspective of Fe and the Secondary Metabolite DIMBOA

The responses of trace elements and secondary metabolites to stress can reflect plant adaptation to the environment. If and how the imperative trace element Fe and the defensive secondary metabolite 2,4-dihydroxy-7-methoxy-2H-1,4-benzoxazine-3(4H)-one (DIMBOA) mediate the toxicity of chiral herbicides to nontarget plants remains inconclusive. We found that the herbicidal-active imazethapyr enantiomer [(R)-IM] stimulated heme oxygenase-1 activity, triggered the release of the catalytic product Fe²⁺, increased reactive oxygen species production, decreased the DIMBOA content, and increased the DIMBOA-Fe content. XAFS analyses and in vitro Fenton assays demonstrated that DIMBOA could relieve phytotoxicity by chelating excessive Fe³⁺ to restore Fe homeostasis. The free radical scavenging ability of the chelate of DIMBOA and Fe was also involved. This work refines the dual role of DIMBOA and Fe in mediating the enantioselective phytotoxicity of chiral herbicides, which provides a new direction for improving the herbicide resistance of crops.

Aerobic composting of chicken manure with penicillin G: Community classification and quorum sensing mediating its contribution to humification

Chicken manure containing antibiotics is a hazardous biological waste. The purpose of our study was to investigate how different concentrations of penicillin G alter the bacterial community to affect humification during aerobic composting of chicken manure. The effect of quorum sensing on the bacterial community was also evaluated. Penicillin G mainly affects low fold changes (within 4) for low-abundance (within 200) microbial genera. We found that the bacterial community cooperated to regulate humus and humic acid synthesis. The microbial genera that make up the bacterial community are different, but each bacterial community may have the same ecological function. Quorum sensing affects humic acid synthesis by regulating carbohydrate metabolism and amino acid metabolism in bacterial communities through mechanisms such as the pentose phosphate pathway and the shikimate pathway. This work presents an understanding of the impact of quorum sensing on the collaboration between bacterial communities during composting.

Leaf uptake of atmospheric monocyclic aromatic hydrocarbons depends on plant species and compounds

Large amounts of monocyclic aromatic hydrocarbons (MAHs) are emitted into the atmosphere, but it is unclear which compounds among MAHs are effectively removed by the above-ground parts of plants. Although fumigation experiments of MAHs at unrealistically high concentrations (~ppmv) have been conducted, experiments with ambient concentrations have scarcely been conducted. In the present study, MAHs, including benzene, toluene, phenol, benzaldehyde, and benzyl alcohol, with concentrations ranging from several to several tens ppbv, were individually fumigated to four plant species, and the uptake was monitored using proton-transfer-reaction mass spectrometry and gas chromatography-mass spectrometry. No detectable uptake was observed for benzene and toluene, but phenol, benzaldehyde, and benzyl alcohol were significantly taken up by the plants. The uptake rate normalized to fumigated concentration varied from 3 to 50 mmol m^-2s^-1 during the light period, depending on light intensity and compounds. The difference in uptake capability may be attributed not only to different metabolic activities but also to different values of Henry's law constant, which regulates the partitioning of these compounds into the liquid phase in leaves. The uptake of phenol, benzaldehyde, and benzyl alcohol was affected by stomatal conductance, suggesting that stomatal opening is the main factor regulating the uptake of the three MAHs. This is the first observation that anisole is emitted when phenol is fumigated to Spathiphyllum clevelandii, suggesting that phenol is methylated to anisole within plant leaves. Anisole is more volatile than phenol, meaning that methylation enhances the emission of xenobiotics into the atmosphere by converting them to more volatile compounds. This conversion ratio decreased with an increase in phenol concentration (from 1.3 to 143 ppbv). Considering low reaction rate coefficient of anisole with OH radicals and low conversion ratio from phenol to anisole, it is concluded that plants act to effectively remove oxygenated MAHs from the atmosphere.

Intramolecular carbon isotope signals reflect metabolite allocation in plants

Stable isotopes at natural abundance are key tools to study physiological processes occurring outside the temporal scope of manipulation and monitoring experiments. Whole-molecule carbon isotope ratios (13C/12C) enable assessments of plant carbon uptake yet conceal information about carbon allocation. Here, we identify an intramolecular 13C/12C signal at tree-ring glucose C-5 and C-6 and develop experimentally testable theories on its origin. More specifically, we assess the potential of processes within C3 metabolism for signal introduction based (inter alia) on constraints on signal propagation posed by metabolic networks. We propose that the intramolecular signal reports carbon allocation into major metabolic pathways in actively photosynthesizing leaf cells including the anaplerotic, shikimate, and non-mevalonate pathway. We support our theoretical framework by linking it to previously reported whole-molecule 13C/12C increases in cellulose of ozone-treated Betula pendula and a highly significant relationship between the intramolecular signal and tropospheric ozone concentration. Our theory postulates a pronounced preference for leaf cytosolic triose-phosphate isomerase to catalyse the forward reaction in vivo (dihydroxyacetone phosphate to glyceraldehyde 3-phosphate). In conclusion, intramolecular 13C/12C analysis resolves information about carbon uptake and allocation enabling more comprehensive assessments of carbon metabolism than whole-molecule 13C/12C analysis.