Genome-Wide Characterization of AspATs in Populus: Gene Expression Variation and Enzyme Activities in Response to Nitrogen Perturbations

Regulating Effect of Exogenous α-Ketoglutarate on Ammonium Assimilation in Poplar

Extensive industrial activities and anthropogenic agricultural practices have led to substantial ammonia release to the environment. Although croplands can act as ammonia sinks, reduced crop production under high concentrations of ammonium has been documented. Alpha-ketoglutarate (AKG) is a critical carbon source, displaying pleiotropic physiological functions. The objective of the present study is to disclose the potential of AKG to enhance ammonium assimilation in poplars. It showed that AKG application substantially boosted the height, biomass, and photosynthesis activity of poplars exposed to excessive ammonium. AKG also enhanced the activities of key enzymes involved in nitrogen assimilation: glutamine synthetase (GS) and glutamate synthase (GOGAT), elevating the content of amino acids, sucrose, and the tricarboxylic acid cycle (TCA) metabolites. Furthermore, AKG positively modulated key genes tied to glucose metabolism and ATP synthesis, while suppressing ATP-depleting genes. Correspondingly, both H+-ATPase activity and ATP content increased. These findings demonstrate that exogenously applying AKG improves poplar growth under a high level of ammonium treatment. AKG might function through sufficient carbon investment, which enhances the carbon-nitrogen balance and energy stability in poplars, promoting ammonium assimilation at high doses of ammonium. Our study provides novel insight into AKG's role in improving poplar growth in response to excess ammonia exposure.

CO2 enhances low-nitrogen adaption by promoting amino acid metabolism in Brassica napus

Increasing concentrations of atmospheric CO2 are driving climate change and negatively impacting the carbon-nitrogen (C/N) balance in crops, which in turn alters fertilizer use efficiency. In this study, Brassica napus was cultivated under different CO2 and NO3--N concentrations to study the impact of C/N ratio on plant growth. Elevated CO2 enhanced biomass and nitrogen assimilation efficiency under low NO3--N conditions, indicating an adaptation by Brassica napus. Transcriptome and metabolome analyses revealed that elevated CO2 promoted amino acid catabolism under low NO3--N conditions. This study provides new insights into how Brassica napus adapts to environmental change.

Expression levels of nitrogen assimilation-related genes, physiological responses, and morphological adaptations of three indica rice (Oryza sativa L. ssp. indica) genotypes subjected to nitrogen starvation conditions

Nitrogen (N) is an essential nutrient available to the plants in form of nitrate and ammonium. It is a macronutrient important for the plant growth and development, especially in cereal crops, which consume it for the production of amino acids, proteins/enzymes, nucleic acids, cell wall complexes, plant hormones, and vitamins. In rice production, 17 kg N uptake is required to produce 1 ton of rice. Considering this, many techniques have been developed to evaluate leaf greenness or SPAD value for assessing the amount of N application in the rice cultivar to maximize the grain yield. The aim of the present study was to investigate the morpho-physiological characteristics and relative expression level of N assimilation in three different rice genotypes (MT2, RD31, KDML105) under 1.00 × (full N), 0.50 × , 0.25 × (N depletion), and 0.00 × (N deficiency) at seedling stage and the morpho-physiological traits and the grain yield attributes under 1.00 × (full N) and 0.25 × (N depletion) were compared. Leaf chlorosis and growth inhibition in rice seedlings under N deficiency were evidently observed. Shoot height, number of leaves, shoot fresh weight, shoot dry weight, and root fresh weight in KDML105 under N deficiency were decreased by 27.65%, 42.11%, 65.44%, 47.90%, and 54.09% over the control (full N). Likewise, leaf greenness was lowest in KDML105 under N deficiency (78.57% reduction over the full N), leading to low photosynthetic abilities. In addition, expression of nitrogen assimilation-related genes, OsNR1, OsGln1;1, and OsGln2, in KDML105 under N depletion were increased within 3 h and then declined after the long incubation period, whereas those were unchanged in cvs. MT2 and RD31. Similarly, relative expression level of OsNADH-GOGAT, OsFd-GOGAT, and OsAspAt1 in KDML105 was peaked when subjected to 0.50 × N for 6 h and then declined after the long incubation period. Moreover, overall growth characters and physiological changes in cv. RD31 at vegetative stage under 0.25 × N were retained better than those in cvs. KDML105 and MT2, resulting in high yield at the harvesting process. In summary, N assimilated-related genes in rice seedlings under N depletion were rapidly regulated within 3-6 h, especially cv. KDML105 and MT2, then downregulated, resulting in physiological changes, growth inhibition, and yield reduction.

Exogenous application of Bradyrhizobium japonicum AC20 enhances soybean tolerance to atrazine via regulating rhizosphere soil microbial community and amino acid, carbohydrate metabolism related genes expression

Atrazine is used to control broad-leaved weeds in farmland and has negative impacts on soybean growth. Legume-rhizobium symbiosis plays an important role in regulating abiotic stress tolerance of plants, however, the mechanisms of rhizobia regulate the tolerance of soybean to atrazine based on the biochemical responses of the plant-soil system are limited. In this experiment, Glycine max (L.) Merr. Dongnong 252, planted in 20 mg kg^-1 of atrazine-contaminated soil, was inoculated with Bradyrhizobium japonicum AC20, and the plant growth, rhizosphere soil microbial diversity and the expression of the genes related to soybean carbon and nitrogen metabolism were assessed. The results indicated that strain AC20 inoculation alleviated atrazine-induced growth inhibition via increasing the contents of leghemoglobin and total nitrogen in soybean seedlings. The psbA gene expression level of the soybean seedlings that inoculated strain AC20 was 1.4 times than that of no rhizobium inoculating treatments. Moreover, the inoculated AC20 increased the abundance of Acidobacteria and Actinobacteria in soybean rhizosphere. Transcriptome analysis demonstrated that strain AC20 regulated the genes expression of amino acid metabolism and carbohydrate metabolism of soybean seedlings. Correlation analysis between 16S rRNA and transcriptome showed that strain AC20 reduced Planctomycetes abundance so as to down-regulated the expression of genes Glyma. 13G087800, Glyma. 12G005100 and Glyma.12G098900 involved in starch synthesis pathway of soybean leaves. These results provide available information for the rhizobia application to enhance the atrazine tolerate in soybean seedlings.

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.

New Insight into Aspartate Metabolic Pathways in Populus: Linking the Root Responsive Isoenzymes with Amino Acid Biosynthesis during Incompatible Interactions of Fusarium solani

Integrating amino acid metabolic pathways into plant defense and immune systems provides the building block for stress acclimation and host-pathogen interactions. Recent progress in L-aspartate (Asp) and its deployed metabolic pathways highlighted profound roles in plant growth and defense modulation. Nevertheless, much remains unknown concerning the multiple isoenzyme families involved in Asp metabolic pathways in Populus trichocarpa, a model tree species. Here, we present comprehensive features of 11 critical isoenzyme families, representing biological significance in plant development and stress adaptation. The in silico prediction of the molecular and genetic patterns, including phylogenies, genomic structures, and chromosomal distribution, identify 44 putative isoenzymes in the Populus genome. Inspection of the tissue-specific expression demonstrated that approximately 26 isogenes were expressed, predominantly in roots. Based on the transcriptomic atlas in time-course experiments, the dynamic changes of the genes transcript were explored in Populus roots challenged with soil-borne pathogenic Fusarium solani (Fs). Quantitative expression evaluation prompted 12 isoenzyme genes (PtGS2/6, PtGOGAT2/3, PtAspAT2/5/10, PtAS2, PtAspg2, PtAlaAT1, PtAK1, and PtAlaAT4) to show significant induction responding to the Fs infection. Using high-performance liquid chromatography (HPLC) and non-target metabolomics assay, the concurrent perturbation on levels of Asp-related metabolites led to findings of free amino acids and derivatives (e.g., Glutamate, Asp, Asparagine, Alanine, Proline, and α-/γ-aminobutyric acid), showing marked differences. The multi-omics integration of the responsive isoenzymes and differential amino acids examined facilitates Asp as a cross-talk mediator involved in metabolite biosynthesis and defense regulation. Our research provides theoretical clues for the in-depth unveiling of the defense mechanisms underlying the synergistic effect of fine-tuned Asp pathway enzymes and the linked metabolite flux in Populus.

Understory and canopy additions of nitrogen differentially affect carbon and nitrogen metabolism of Psychotria rubra in an evergreen broad-leaved forest

To assess the effects of nitrogen deposition on forest plants, researchers have conducted many nitrogen-addition experiments. Most of these experiments, however, failed to fully simulate atmospheric nitrogen deposition because they failed to assess interception of nitrogen deposition by the forest canopy. Here, we used transcriptomics, proteomics, and metabolomics to compare the effects of understory nitrogen addition (UAN), canopy nitrogen addition (CAN), and a control (no nitrogen addition) on carbon and nitrogen metabolism in leaves of Psychotria rubra, a dominant subtropical understory plant species in evergreen broad-leaved forests in South China. We first established a reference P. rubra transcriptome via RNA-seq and obtained a total of 93,986 unigenes from de novo assembly. Next, we quantitatively investigated the proteome and metabolome in leaves, and identified 4021 proteins and 562 metabolites. Under the CAN treatment and relative to the control, 36 genes were up-regulated and 23 were down-regulated, and we identified 46 up-regulated proteins and 49 down-regulated proteins. Under the UAN treatment and relative to the control, 1525 genes were up-regulated and 224 genes down-regulated, and we identified 35 up-regulated proteins and 71 down-regulated proteins. These differentially expressed genes and proteins were related to photosynthesis, amino acid metabolism, and flavonoid biosynthesis. Accordingly, 15 differentially accumulated metabolites in response to CAN and 20 in response to UAN were found; these differentially accumulated metabolites included 4 amino acids and 3 flavonoids. Taken together, our results show that the UAN treatment had a greater effect on photosynthesis, amino acid metabolism, and flavonoid biosynthesis than the CAN treatment. Most importantly, the results indicate that understory application of nitrogen in experiments may incorrectly estimate the effects of nitrogen deposition on nitrogen and carbon utilization by P. rubra and perhaps by other understory woody plants in the evergreen broad-leaved forests in South China as well.

Effects of simulated atmospheric nitrogen deposition on foliar chemistry and physiology of hybrid poplar seedlings

During recent decades, the southern and eastern regions of Asia have experienced high levels of atmospheric N deposition. Excess N deposition is predicted to influence tree growth and species composition in the regions, but visual or physiological assessments alone are not sufficient to determine the real effects of atmospheric N deposition. In this study, we simulated atmospheric wet deposition of inorganic N by spraying a NO₃^- solution (20 mmol⋅L^-1) or a mixture of NO₃^- (20 mmol⋅L^-1) plus NO₂^- (100 or 300 μmol⋅L^-1) on leaves of hybrid poplar (Populus alba × Populus berolinensis) seedlings and examined morphoanatomical traits and physiological processes. Leaves of seedlings sprayed with single or mixed N solutions developed marginal necrosis, curling, and small cracks on the adaxial surface. The silicon (Si)-rich crystals were larger (about 100% increase in crystal diameter compared to untreated seedlings) on the adaxial leaf surface, with a significant positive correlation between the atomic percentage of N and Si on the crystal areas of the surface. Leaves were sensitive to NO₂^- compared with NO₃^- even at a low concentration; water content, dry mass, and photochemical variables significantly declined and dark respiration increased only in leaves treated with mixed N form. Mixed N foliar applications significantly increased leaf concentrations of the free amino acids Glu, Gln, and Asn and organic acids oxaloacetic acid and citric acid. Besides, mixed N treatment stimulated leaf transamination, as indicated by significant increases in Ala and Asp concentrations and activities of glutamic oxalacetic transaminase and glutamic pyruvic transaminase. However, mixed N applications led to declines in leaf concentrations of putrescine (by 65%, p = 0.01) and spermine (by 53%, p = 0.01). A higher proportion of NO₂^- (300 μmol⋅L^-1) in mixed N solution was inhibitory to key N-metabolic enzymes and N translocation via the phloem. Our results showed that wet deposition of airborne N pollutants modified surface properties and induced additional detrimental effects related to N-compound foliar absorption. Furthermore, our findings indicate that detoxification of reactive N is apparently related to N assimilation and export from the treated leaves via the phloem.

Functional Characterization of a Drought-Responsive Invertase Inhibitor from Maize (Zea mays L.)

Invertases (INVs) play essential roles in plant growth in response to environmental cues. Previous work showed that plant invertases can be post-translationally regulated by small protein inhibitors (INVINHs). Here, this study characterizes a proteinaceous inhibitor of INVs in maize (Zm-INVINH4). A functional analysis of the recombinant Zm-INVINH4 protein revealed that it inhibited both cell wall and vacuolar invertase activities from maize leaves. A Zm-INVINH4::green fluorescent protein fusion experiment indicated that this protein localized in the apoplast. Transcript analysis showed that Zm-INVINH4 is specifically expressed in maize sink tissues, such as the base part of the leaves and young kernels. Moreover, drought stress perturbation significantly induced Zm-INVINH4 expression, which was accompanied with a decrease of cell wall invertase (CWI) activities and an increase of sucrose accumulation in both base parts of the leaves 2 to 7 days after pollinated kernels. In summary, the results support the hypothesis that INV-related sink growth in response to drought treatment is (partially) caused by a silencing of INV activity via drought-induced induction of Zm-INVINH4 protein.

Functional Characterization of Invertase Inhibitors PtC/VIF1 and 2 Revealed Their Involvements in the Defense Response to Fungal Pathogen in Populus trichocarpa

In higher plants, cell wall invertase (CWI) and vacuolar invertase (VI) were considered to be essential coordinators in carbohydrate partitioning, sink strength determination, and stress responses. An increasing body of evidence revealed that the tight regulation of CWI and VI substantially depends on the post-translational mechanisms, which were mediated by small proteinaceous inhibitors (C/VIFs, Inhibitor of β-Fructosidases). As yet, the extensive survey of the molecular basis and biochemical property of C/VIFs remains largely unknown in black cottonwood (Populus trichocarpa Torr. & A. Gray), a model species of woody plants. In the present work, we have initiated a systematic review of the genomic structures, phylogenies, cis-regulatory elements, and conserved motifs as well as the tissue-specific expression, resulting in the identification of 39 genes encoding C/VIF in poplar genome. We characterized two putative invertase inhibitors PtC/VIF1 and 2, showing predominant transcript levels in the roots and highly divergent responses to the selected stress cues including fusarium wilt, drought, ABA, wound, and senescence. In silico prediction of the signal peptide hinted us that they both likely had the apoplastic targets. Based on the experimental visualization via the transient and stable transformation assays, we confirmed that PtC/VIF1 and 2 indeed secreted to the extracellular compartments. Further validation of their recombinant enzymes revealed that they displayed the potent inhibitory affinities on the extracted CWI, supporting the patterns that act as the typical apoplastic invertase inhibitors. To our knowledge, it is the first report on molecular characterization of the functional C/VIF proteins in poplar. Our results indicate that PtC/VIF1 and 2 may exert essential roles in defense- and stress-related responses. Moreover, novel findings of the up- and downregulated C/VIF genes and functional enzyme activities enable us to further unravel the molecular mechanisms in the promotion of woody plant performance and adapted-biotic stress, underlying the homeostatic control of sugar in the apoplast.