Regulation Of Nitrogen Metabolism Research Articles

Terrestrial dissolved organic matter inputs affect the nitrous oxide emission revealed by FT-ICR MS

Nitrous oxide (N2O) emission from lake systems could be affected via intrusion of terrestrial organic matter, causing impairment in biogeochemical cycling. The sources and mechanisms by which DOM (Dissolved organic matter) alters emissions of N2O are poorly understood. Here, we simulate different terrestrial DOM (anthropogenic sources, natural sources, and surface runoff) to assess the mechanisms affecting N2O emissions with variations of DOM. We used a combination of absorption spectroscopy, excitation-emission matrix fluorescence, and Fourier transform ion cyclotron resonance mass spectrometry to characterize DOM comprehensively. For the characterization of DOM, a combination of absorption spectroscopy, excitation-emission matrix fluorescence, and Fourier transform ion cyclotron resonance mass spectrometry was used. Microbial analysis was conducted to identify the potential microbial mechanisms. Different terrestrial DOM inputs primarily impact N2O emissions through the denitrification process (14.52 %, p < 0.05), with significant effects on the abundance of narG (12.97 %, p < 0.05) and nirK+S (10.13 %, p < 0.05). The biodegradable components in sediments directly promote N2O emissions, while in aquatic systems, the labile components (proteins, sugars, and lipids-like) were preferentially metabolized, producing reluctant derivatives. The biodegradable components (i.e., protein-like) from anthropogenic sources rapidly facilitate N2O production. Natural and surface runoff sources were the significant drivers for the continuous release and metabolism of DOM. N2O Loss emissions are negatively influenced by the regulation of carbon and nitrogen metabolism by nitrifiers and denitrifies in the sediment (p < 0.001). Metabolism of carbon and nitrogen regulated by nitrifier and denitrifies in the sediments negatively influences N2O flux (p < 0.001). N2O emissions were mainly influenced by bioavailability of inputs: DOM and varying terrestrial conditions. The results provide a theoretical base for the management of greenhouse gas emissions from lakes.

Molecular mechanisms of plant productivity enhancement by nano fertilizers for sustainable agriculture

Molecular mechanisms of plant productivity enhancement by nano fertilizers for sustainable agriculture

The impact of glutamine synthetase PbgsA on the growth, conidiation and mycophenolic acid production of Penicillium brevicompactum

Glutamine synthetase (GS) is a critical enzyme in nitrogen metabolism regulation and plays an essential role in the metabolic pathways involved in microbial growth and development. Penicillium brevicompactum, known for its rich repertoire of secondary metabolites, including mycophenolic acid (MPA), lacks research on the regulatory mechanisms of GS within this species. This study aimed to investigate the influence of GS on the growth, sporulation, and secondary metabolism of P. brevicompactum to elucidate the biological function of GS in this organism. We identified the glutamine synthetase gene (PbgsA) from P. brevicompactum and constructed PbgsA gene-overexpression and gene-silencing transformants. The impact of PbgsA on growth and sporulation was evaluated, revealing that PbgsA gene-overexpression transformants exhibited enhanced growth and significantly increased the expression levels of sporulation pathway genes (brlA, abaA, and wetA). Additionally, PbgsA gene-overexpression transformants produced higher MPA yields, with a maximum of 4.78 g/L, representing a 54.19 % increase compared to the wild type (WT). Conversely, PbgsA gene-silencing transformants showed reduced MPA production, with a minimum yield of 1.13 g/L, a 63.55 % decrease relative to the WT. Transcriptional analysis of the MPA biosynthetic gene cluster indicated that PbgsA exerted regulatory effects on certain biosynthetic pathway genes, such as mpaA and mpaB. This study demostrated the potential positive regulatory role of glutamine synthetase PbgsA in the growth, spore development, and secondary metabolism of P. brevicompactum, which provided a new strategy for genetic regulation in filamentous fungal.

Multi-Omics and Physiological Analysis Reveal Crosstalk Between Aphid Resistance and Nitrogen Fertilization in Wheat.

The availability of nitrogen (N) can dramatically influence crops resistance to herbivorous insects. However, the interaction between N fertilization and crop resistance to insects is not well understood. In this study, the effects of N fertilization on the grain aphid (Sitobion miscanthi) were investigated using three wheat (Triticum aestivum) cultivars with different aphid resistances. We measured aphid life cycle parameters, fecundity, survival rate, weight and feeding behavior, in conjunction with wheat metabolomics, transcriptomics and alien introgression analysis. Our results demonstrated that higher N application benefits aphid feeding across all three wheat cultivars. We also reveal that the highly resistant cultivar (ZM9) can only exert its resistance-advantage under low N fertilization, losing its advantage compared to moderately resistant cultivar YN19 and susceptible cultivar YN23 under higher N fertilization. The effects of N fertilization on wheat-aphid interactions were due to changes in the regulation of carbon and nitrogen metabolism. Integration of multi-omics highlighted specific aphid-induced differentially expressed genes (DEGs, e.g., TUB6, Tubulin 6; ENODL20, Early nodulin-like protein 20; ACT7 Actin 7; Prx47, Peroxidase 47) and significantly different metabolites (SDMs, e.g., crotonoside, guanine, 2'-O-methyladenosine, ferulic acid) in ZM9. Additionally, we report the unique SDMs-DEGs interactions, associated with introgression during wheat domestication, may help infer aphid resistance. In summary, this study provides new insights into the relationships between N fertilization practices, defense responses and integrated pest management for sustainable wheat production.

Regulation of MareA Gene on Monascus Growth and Metabolism Under Different Nitrogen Sources.

Monascus is a widely used natural microorganism in our country, which can produce useful secondary metabolites. Studies have shown that the nitrogen source directly affects the growth, reproduction, and secondary metabolites of Monascus. As a global transcriptional regulator of nitrogen metabolism, MareA gene is involved in the regulation of secondary metabolism. In this study, we found the MareA gene that is highly homologous to the AreA gene sequence, and used MareA to obtain ΔMareA and OE-MareA. Three strains were cultured with glutamine, urea, NaNO3, and (NH4)2SO4 nitrogen sources. The Monascus pigments and related genes were analyzed by solid-state fermentation under different nitrogen sources. The results showed that the pigment production of the ΔMareA decreased, but the OE-MareA did the opposite. The secondary metabolites of the three strains were analyzed by HPLC and expression level of pigment biosytnthesis gene was determined by RT-qPCR. The relative expression levels of four key Monascus pigment genes in ΔMareA were significantly upregulated in mppE gene, but downregulated in MpPKS5, mppG, and mppD genes. Monascus pigment genes were increased in OE-MareA. In terms of growth regulation, the expression of VosA and LaeA genes was significantly reduced in ΔMareA, while OE-MareA significantly promoted the expression of GprD genes. The pigment production and gene expression in ΔMareA were significantly lower than that of C100, while the opposite was true of OE-MareA when NaNO3 was added to the culture medium. In conclusion, MareA gene had different regulatory effects on Monascus growth and pigments metabolism under different nitrogen sources.

Nitrogen removal capability and mechanism of a novel low-temperature-tolerant simultaneous nitrification-denitrification bacterium Acinetobacter kyonggiensis AKD4.

A low-temperature-tolerant simultaneous nitrification-denitrification bacterial strain of Acinetobacter kyonggiensis (AKD4) was identified. It showed high efficiency in total nitrogen (TN) removal (92.45% at 10°C and 87.51% at 30°C), indicating its excellent low-temperature tolerance. Transcriptomic analysis revealed possible metabolic mechanisms under low-temperature stress. Genes involved in cell growth, including ATP synthase (atpADGH), amino acid (glyA, dctA, and ilvE), and TCA cycle metabolism (gltA, fumC, and mdh) were remarkably upregulated from 1.05-3.44-fold at 10°C, suggesting that their actions enhance survivability at low temperatures. The expression levels of genes associated with nitrogen assimilation (glnAE, gltBD, and gdhA), nitrogen metabolism regulation (ntrC, glnB, and glnD), and denitrification processes (napA) were increased from 1.01-4.38-fold at 10°C, which might have contributed to the bacterium's highly efficient nitrogen removal performance at low temperatures. Overall, this study offers valuable insights into transcriptome, and enhances the comprehension of the low-temperature-tolerant mechanism of simultaneous nitrification and denitrification processes.

Effect of the PotN Protein on Activities of the GlnR and PotA Proteins in the Cells of Lentilactobacillus hilgardii

Bacterial PII-like proteins are global regulators of nitrogen and energy metabolism, which respond to nutrient availability by binding their partner proteins, thus modulating their activity. The PotN protein from Lentilactobacillus hilgardii, a member of the new family of PII-like proteins, is capable of competitive binding of ATP and ADP, thus regulating metabolism in response to the cell energy status. Thus, under ADP excess, PotN binds this nucleotide and interacts mostly with the PotA subunit of the polyamine АВС transporter, suppressing its ATPase activity. PotN also dissociates from the transcription factor GlnR, restoring its ability to bind DNA and modulate expression of the genes of the GlnR regulon. On the contrary, in the ATP state PotN dissociates from PotA and binds to the GlnR factor.

Core microbes in Cordyceps militaris sclerotia and their nitrogen metabolism-related ecological functions.

The model Cordyceps species Cordyceps militaris is rich in therapeutic compounds. It has recently been demonstrated that symbiotic microbes in sclerotia affect Cordyceps' growth, development, and secondary metabolite production. In this study, core microbes were identified based on C. militaris sclerotia samples obtained from the same site over 5 years. Additionally, bacterial strains isolated from C. militaris sclerotia were found to affect metabolite production and nitrogen utilization, based on functional tests. Moreover, based on the bacterial nitrogen metabolism capacity in the sclerotia and its influence on C. militaris metabolite production, we deduced that bacteria in the sclerotia can indirectly affect C. militaris metabolite production by regulating nitrogen metabolism. This is the first report on how bacteria in the sclerotia affect C. militaris metabolite production from the perspective of the nitrogen cycle. The results increase our understanding of microbial functions in C. militaris sclerotia.

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

Populus spp. is a crucial fast-growing and productive tree species extensively cultivated in the mid-latitude plains of the world. However, the impact of intensive cultivation management on gene expression in plantation remains largely unexplored. Precision water and fertilizer-intensive management substantially increased key enzyme activities of nitrogen transport, assimilation, and photosynthesis (1.12-2.63 times than CK) in Populus × euramericana 'Neva' plantation. Meanwhile, this management approach had a significant regulatory effect on the gene expression of poplar plantations. 1554 differential expression genes (DEGs)were identified in drip irrigation (ND) compared with conventional irrigation. Relative to ND, 2761-4116 DEGs, predominantly up-regulated, were identified under three drip fertilization combinations, among which 202 DEGs were mainly regulated by fertilization. Moreover, drip irrigation reduced the expression of cell wall synthesis-related genes to reduce unnecessary water transport. Precision drip and fertilizer-intensive management promotes the synergistic regulation of carbon and nitrogen metabolism and up-regulates the expression of major genes in nitrogen transport and assimilation processes (5 DEGs), photosynthesis (15 DEGs), and plant hormone signal transduction (11 DEGs). The incorporation of trace elements further enhanced the up-regulation of secondary metabolic process genes. In addition, the co-expression network identified nine hub genes regulated by precision water and fertilizer-intensive management, suggesting a pivotal role in regulating the growth of poplar. Precision water and fertilizer-intensive management demonstrated the ability to regulate the expression of key genes and transcription factor genes involved in carbon and nitrogen metabolism pathways, plant hormone signal transduction, and enhance the activity of key enzymes involved in related processes. This regulation facilitated nitrogen absorption and utilization, and photosynthetic abilities such as light capture, light transport, and electron transport, which faintly synergistically regulate the growth of poplar plantations. These results provide a reference for proposing highly efficient precision intensive management to optimize the expression of target genes.

Impact of the Deletion of Genes of the Nitrogen Metabolism on Triacylglycerol, Cardiolipin and Actinorhodin Biosynthesis in Streptomyces coelicolor.

Since nitrogen limitation is known to be an important trigger of triacylglycerol (TAG) accumulation in most microorganisms, we first assessed the global lipid content of 21 strains derived from Streptomyces coelicolor M145 deleted for genes involved in nitrogen metabolism. Seven of these strains deleted for genes encoding proteins involved in polyamine (GlnA2/SCO2241, GlnA3/SCO6962, GlnA4/SCO1613), or protein (Pup/SCO1646) degradation, in the regulation of nitrogen metabolism (GlnE/SCO2234 and GlnK/SCO5584), or the global regulator DasR/SCO5231 that controls negatively the degradation of N-acetylglucosamine, a constituent of peptidoglycan, had a higher TAG content than the original strain, whereas five of these strains (except the glnA2 and pup mutants) had a lower cardiolipin (CL) content. The production of the blue polyketide actinorhodin (ACT) was totally abolished in the dasR mutant in both Pi conditions, whereas the deletion of pup, glnA2, glnA3, and glnA4 was correlated with a significant increase in total ACT production, but mainly in Pi limitation. Unexpectedly, ACT production was strongly reduced in the glnA3 mutant in Pi proficiency. Altogether, our data suggest that high TAG and ACT biosynthesis and low CL biosynthesis might all contribute to the lowering of oxidative stress resulting from nitrogen limitation or from other causes.

Elucidating biogeochemical characterization of nitrogen in the vadose zone integrating geochemistry, microorganism, and numerical simulation

A thorough comprehension of nitrogen biogeochemical processes in the vadose zone is crucial for the effective prevention and remediation of soil-groundwater system contamination. Despite the growing research on this subject, the full scope of nitrogen biogeochemical characterization in different geological environments remains poorly understood. This study addresses this knowledge gap by integrating geochemical, microbiological and numerical simulation approaches to gain a deeper insight into nitrogen biogeochemistry in agriculture. Our findings indicate the biogeochemical behavior of nitrogen in the vadose zone is mediated by microorganisms, driven by hydraulics, influenced by geological conditions and environmental factors. Along the groundwater flow, NH4+-N was found to be heavily accumulated in the topsoil of 0–40 cm, while NO3−-N was transported and driven by hydrodynamics from both vertical and horizontal directions. Microbial diversity, species composition and functional microorganisms were significantly influenced by soil depth, rather than geomorphological types. Oxidation-reduction potential (ORP), total organic carbon (TOC), soil moisture (MOI), bicarbonate (HCO3−), and ferrous (Fe2+) were identified as the principal environmental factors that regulate nitrogen metabolism and the dominant biochemical processes, encompassing nitrogen fixation, nitrification, and denitrification. Driven by hydrodynamics, NH4+-N, NO2−-N and NO3−-N tend to form distinct biochemical reaction zones in the vertical vadose zone. These areas are dynamic and subject to geomorphologies. It should be noted that NO3−-N can migrate towards groundwater from the clayey sand in the Alluvial Plain, which presents a potential risk of groundwater contamination. The fissure structure of loess may serve as the major transport pathway for groundwater nitrogen contamination in the Loess Tableland. This finding highlights the importance of integrating microbiology, geochemistry and hydraulics to elucidate the biogeochemical processes of nitrogen in the vadose zone with a dynamic mindset.

Silybin protected from avermectin-induced carp (Cyprinus carpio) nephrotoxicity by regulating PPAR-γ-involved inflammation, oxidative stress, ferroptosis and autophagy

Avermectin, a widely used deworming drug, poses a significant threat to fisheries. Silybin is recognized for its antioxidant and anti-inflammatory properties. The kidney, being crucial for fish survival, plays a vital role in maintaining ion balance, nitrogen metabolism, and hormone regulation. While residual avermectin in water could pose a risk to carp (Cyprinus carpio), it remains unclear whether silybin can alleviate the renal tissue toxicity induced by avermectin in this species. In current study, we developed a model of long-term exposure of carp to avermectin to investigate the potential protective effect of silybin against avermectin-induced nephrotoxicity. The results indicated that avermectin induced renal inflammation, oxidative stress, ferroptosis, and autophagy in carp. Silybin suppressed the mRNA transcript levels of pro-inflammatory factors, increased catalase (CAT) activity, reduced glutathione (GSH) activity, diminished reactive oxygen species (ROS) accumulation in renal tissues, and promoted the activation of the Nrf2-Keap1 signaling pathway. Furthermore, the transcript levels of ferroptosis-associated proteins, including gpx4 and slc7a11, were significantly reduced, while those of cox2, ftl, and ncoa4 were elevated. The transcript levels of autophagy-related genes, including p62 and atg5, were also regulated. Network pharmacological analysis revealed that silybin inhibited ROS accumulation and mitigated avermectin-induced renal inflammation, oxidative stress, ferroptosis, and autophagy in carp through the involvement of PPAR-γ. Silybin exerted its anti-inflammatory effect through the NF-κB pathway and antioxidant effect through the Nrf2-Keap1 pathway, induced renal cell iron efflux through the SLC7A11/GSH/GPX4, and suppressed autophagy initiation via the PI3K/AKT pathway. This study provides evidence of the protective effect of silybin against avermectin-induced nephrotoxicity in carp, highlighting its potential as a therapeutic agent to alleviate the adverse effects of avermectin exposure in fish.

Atmospheric NO2 enhances tolerance to low temperature by promoting nitrogen and carbon metabolism in tobacco

With abnormal global climate change and the frequent occurrence of extreme weather, low-temperature stress poses an increasingly serious threat to the diversity of plants. Low temperatures accompanied by limitations in nitrogen cause a series of morphological, physiological, and molecular changes in plants. Nitrogen dioxide (NO2) is a gas that is considered to be a toxic air pollutant. However, NO2 in the atmosphere can be absorbed by plants and participate in nitrogen metabolism. In this study, tobacco (Nicotiana tabacum L.) seedlings were fumigated with a concentration of 4 µL·L−1 NO2 at 4 ℃ for 10 days. NO2 promoted the glutamine synthetase-glutamate synthase (GS/GOGAT) pathway in the leaves at low temperatures, which transforms more organic nitrogen that can be directly utilized by the plants, and improves the skeleton for carbon metabolism. Moreover, gamma-aminobutyric acid (GABA) was generated through the ornithine and glutamate pathways, and the biosynthesis of proline was also enhanced after treatment with NO2. Together, these compounds regulate the osmotic balance of tobacco leaf cells under low-temperature stress. NO2 activated the ascorbate-glutathione (AsA-GSH) cycle in the leaves under low-temperature stress, and this antioxidant enzyme system synergistically removed the intracellular free radicals that result from reactive oxygen species. Additionally, NO2 significantly increased the content of nitric oxide (NO) in the leaves under low-temperature stress and enhanced the opening of stomata, thus, improving photosynthesis in the leaves. The biosynthesis of chlorophyll in the leaves was inhibited by low-temperature stress, but NO2 promotes the biosynthesis of chlorophyll directly or through the nitric acid signaling pathway and improves the ability of plants to capture light energy. NO2 also alleviates the photoinhibition induced by cold stress by regulating photosynthetic electron transfer and absorbing more energy for the assimilation of photosynthetic carbon. This improves the photochemical efficiency of tobacco leaves. In conclusion, NO2 enhanced the tolerance of tobacco seedlings to low temperature by regulating nitrogen metabolism, the osmotic balance, antioxidant system, and photosynthesis.

Regulation of nitrogen metabolism by COE2 under low sulfur stress in Arabidopsis

The interplay between nitrogen and sulfur assimilation synergistically supports and sustains plant growth and development, operating in tandem to ensure coordinated and optimal outcomes. Previously, we characterized Arabidopsis CHLOROPHYLL A/B-BINDING (CAB) overexpression 2 (COE2) mutant, which has a mutation in the NITRIC OXIDE-ASSOCIATED (NOA1) gene and exhibits deficiency in root growth under low nitrogen (LN) stress. This study found that the growth suppression in roots and shoots in coe2 correlates with decreased sensitivity to low sulfur stress treatment compared to the wild-type. Therefore, we examined the regulatory role of COE2 in nitrogen and sulfur interaction by assessing the expression of nitrogen metabolism-related genes in coe2 seedlings under low sulfur stress. Despite the notable upregulation of nitrate reductase genes (NIA1 and NIA2), there was a considerable reduction in nitrogen uptake and utilization, resulting in a substantial growth penalty. Moreover, the elevated expression of miR396 perhaps complemented growth stunting by selectively targeting and curtailing the expression levels of GROWTH REGULATING FACTOR 2 (GRF2), GRF4, and GRF9. This study underscores the vital role of COE2-mediated nitrogen signaling in facilitating seedling growth under sulfur deficiency stress.

Orphan response regulator NnaR is critical for nitrate and nitrite assimilation in Mycobacterium abscessus.

Mycobacterium abscessus (Mab) is an opportunistic pathogen afflicting individuals with underlying lung disease such as Cystic Fibrosis (CF) or immunodeficiencies. Current treatment strategies for Mab infections are limited by its inherent antibiotic resistance and limited drug access to Mab in its in vivo niches resulting in poor cure rates of 30-50%. Mab's ability to survive within macrophages, granulomas and the mucus laden airways of the CF lung requires adaptation via transcriptional remodeling to counteract stresses like hypoxia, increased levels of nitrate, nitrite, and reactive nitrogen intermediates. Mycobacterium tuberculosis (Mtb) is known to coordinate hypoxic adaptation via induction of respiratory nitrate assimilation through the nitrate reductase narGHJI. Mab, on the other hand, does not encode a respiratory nitrate reductase. In addition, our recent study of the transcriptional responses of Mab to hypoxia revealed marked down-regulation of a locus containing putative nitrate assimilation genes, including the orphan response regulator nnaR (nitrate/nitrite assimilation regulator). These putative nitrate assimilation genes, narK3 (nitrate/nitrite transporter), nirBD (nitrite reductase), nnaR, and sirB (ferrochelatase) are arranged contiguously while nasN (assimilatory nitrate reductase identified in this work) is encoded in a different locus. Absence of a respiratory nitrate reductase in Mab and down-regulation of nitrogen metabolism genes in hypoxia suggest interplay between hypoxia adaptation and nitrate assimilation are distinct from what was previously documented in Mtb. The mechanisms used by Mab to fine-tune the transcriptional regulation of nitrogen metabolism in the context of stresses e.g. hypoxia, particularly the role of NnaR, remain poorly understood. To evaluate the role of NnaR in nitrate metabolism we constructed a Mab nnaR knockout strain (MabΔnnaR ) and complement (MabΔnnaR+C ) to investigate transcriptional regulation and phenotypes. qRT-PCR revealed NnaR is necessary for regulating nitrate and nitrite reductases along with a putative nitrate transporter. Loss of NnaR compromised the ability of Mab to assimilate nitrate or nitrite as sole nitrogen sources highlighting its necessity. This work provides the first insights into the role of Mab NnaR setting a foundation for future work investigating NnaR's contribution to pathogenesis.

Titanium dioxide nanoparticles alleviates polystyrene nanoplastics induced growth inhibition by modulating carbon and nitrogen metabolism via melatonin signaling in maize.

Nanoplastics, are emerging pollutants, present a potential hazard to food security and human health. Titanium dioxide nanoparticles (Nano-TiO2), serving as nano-fertilizer in agriculture, may be important in alleviating polystyrene nanoplastics (PSNPs) toxicity. Here, we performed transcriptomic, metabolomic and physiological analyzes to identify the role of Nano-TiO2 in regulating the metabolic processes in PSNPs-stressed maize seedlings (Zea mays L.). The growth inhibition by PSNPs stress was partially relieved by Nano-TiO2. Furthermore, when considering the outcomes obtained from RNA-seq, enzyme activity, and metabolite content analyses, it becomes evident that Nano-TiO2 significantly enhance carbon and nitrogen metabolism levels in plants. In comparison to plants that were not subjected to Nano-TiO2, plants exposed to Nano-TiO2 exhibited enhanced capabilities in maintaining higher rates of photosynthesis, sucrose synthesis, nitrogen assimilation, and protein synthesis under stressful conditions. Meanwhile, Nano-TiO2 alleviated the oxidative damage by modulating the antioxidant systems. Interestingly, we also found that Nano-TiO2 significantly enhanced the endogenous melatonin levels in maize seedlings. P-chlorophenylalanine (p-CPA, a melatonin synthesis inhibitor) declined Nano-TiO2-induced PSNPs tolerance. Taken together, our data show that melatonin is involved in Nano-TiO2-induced growth promotion in maize through the regulation of carbon and nitrogen metabolism.

Proteomic and metabolomic insights into seed germination of Ferula assa-foetida

Cold stratification is known to affect the speed of seed germination; however, its regulation at the molecular level in Ferula assa-foetida remains ambiguous. Here, we used cold stratification (4 °C in the dark) to induce germination in F. assa-foetida and adopted a proteomic and metabolomic approach to understand the molecular mechanism of germination. Compared to the control, we identified 209 non-redundant proteins and 96 metabolites in germinated F. assa-foetida seed. Results highlight the common and unique regulatory mechanisms like signaling cascade, reactivation of energy metabolism, activation of ROS scavenging system, DNA repair, gene expression cascade, cytoskeleton, and cell wall modulation in F. assa-foetida germination. A protein-protein interaction network identifies 18 hub protein species central to the interactome and could be a key player in F. assa-foetida germination. Further, the predominant metabolic pathways like glucosinolate biosynthesis, arginine and proline metabolism, cysteine and methionine metabolism, aminoacyl-tRNA biosynthesis, and carotenoid biosynthesis in germinating seed may indicate the regulation of carbon and nitrogen metabolism is prime essential to maintain the physiology of germinating seedlings. The findings of this study provide a better understanding of cold stratification-induced seed germination, which might be utilized for genetic modification and traditional breeding of Ferula assa-foetida. SignificanceSeed germination is the fundamental checkpoint for plant growth and development, which has ecological significance. Ferula assa-foetida L., commonly known as “asafoetida,” is a medicinal and food crop with huge therapeutic potential. To date, our understanding of F. assa-foetida seed germination is rudimentary. Therefore, studying the molecular mechanism that governs dormancy decay and the onset of germination in F. assa-foetida is essential for understanding the basic principle of seed germination, which could offer to improve genetic modification and traditional breeding.

Glutamine as sole nitrogen source prevents induction of nitrate transporter gene NRT2.4 and affects amino acid metabolism in Arabidopsis.

Plants assimilate inorganic nitrogen (N) to glutamine. Glutamine is the most abundant amino acid in most plant species, the N-supplying precursor of all N-containing compounds in the cell and the first organic nitrogen molecule formed from inorganic nitrogen taken up by the roots. In addition to its role in plant nutrition, glutamine most likely also has a function as a signaling molecule in the regulation of nitrogen metabolism. We investigated whether glutamine influences the high-affinity transporter system for nitrate uptake. Therefore, we analyzed the expression of the nitrate transporter NRT2.4, which is inducible by N deficiency, in Arabidopsis thaliana grown under different nitrogen starvation scenarios, comparing nitrate or glutamine as the sole nitrogen source. Using the reporter line ProNRT2.4:GFP and two independent knockout lines, nrt2.4-1 and nrt2.4-2, we analyzed gene expression and amino acid profiles. We showed that the regulation of NRT2.4 expression depends on available nitrogen in general, for example on glutamine as a nitrogen source, and not specifically on nitrate. In contrast to high nitrate concentrations, amino acid profiles changed to an accumulation of amino acids containing more than one nitrogen during growth in high glutamine concentrations, indicating a switch to nitrogen storage metabolism. Furthermore, we demonstrated that the nrt2.4-2 line shows unexpected effects on NRT2.5 gene expression and the amino acids profile in shoots under high glutamine supply conditions compared to Arabidopsis wild type and nrt2.4-1, suggesting non-NRT2.4-related metabolic consequences in this knockout line.

Plant Growth-Promoting Rhizobacteria Are Key to Promoting the Growth and Furanocoumarin Synthesis of Angelica dahurica var. formosana under Low-Nitrogen Conditions.

Microbiomes are the most important members involved in the regulation of soil nitrogen metabolism. Beneficial interactions between plants and microbiomes contribute to improving the nitrogen utilization efficiency. In this study, we investigated the Apiaceae medicinal plant Angelica dahurica var. formosana. We found that under a low-nitrogen treatment, the abundance of carbon metabolites in the rhizosphere secretions of A. dahurica var. formosana significantly increased, thereby promoting the ratio of C to N in rhizosphere and nonrhizosphere soils, increasing carbon sequestration, and shaping the microbial community composition, thus promoting a higher yield and furanocoumarin synthesis. Confirmation through the construction of a synthetic microbial community and feedback experiments indicated that beneficial plant growth-promoting rhizobacteria play a crucial role in improving nitrogen utilization efficiency and selectively regulating the synthesis of target furanocoumarins under low nitrogen conditions. These findings may contribute additional theoretical evidence for understanding the mechanisms of interaction between medicinal plants and rhizosphere microorganisms.

Protein NirP1 regulates nitrite reductase and nitrite excretion in cyanobacteria

When the supply of inorganic carbon is limiting, photosynthetic cyanobacteria excrete nitrite, a toxic intermediate in the ammonia assimilation pathway from nitrate. It has been hypothesized that the excreted nitrite represents excess nitrogen that cannot be further assimilated due to the missing carbon, but the underlying molecular mechanisms are unclear. Here, we identified a protein that interacts with nitrite reductase, regulates nitrogen metabolism and promotes nitrite excretion. The protein, which we named NirP1, is encoded by an unannotated gene that is upregulated under low carbon conditions and controlled by transcription factor NtcA, a central regulator of nitrogen homeostasis. Ectopic overexpression of nirP1 in Synechocystis sp. PCC 6803 resulted in a chlorotic phenotype, delayed growth, severe changes in amino acid pools, and nitrite excretion. Coimmunoprecipitation experiments indicated that NirP1 interacts with nitrite reductase, a central enzyme in the assimilation of ammonia from nitrate/nitrite. Our results reveal that NirP1 is widely conserved in cyanobacteria and plays a crucial role in the coordination of C/N primary metabolism by targeting nitrite reductase.