Metabolic Pathways In Response Research Articles

Physiological and transcriptomic analysis reveals the toxicological mechanisms of polystyrene micro- and nano-plastics in Chlamydomonas reinhardtii

With the accumulation of plastic waste in the environment, the toxicity of micro- and nano-plastics (MNPs) to microalgae has attracted increasing attention. However, the underlying toxic mechanisms of MNPs remain to be elucidated. In this study, we synthesized micro- and nano-scale of polystyrene MNPs (PS MNPs) to investigate their toxicity and toxic mechanisms in Chlamydomonas reinhardtii. We found that PS MNPs significantly inhibit the production of photosynthetic pigments and increase soluble protein content. The detailed analysis of results shows that both materials affect photosynthetic efficiency by damaging the donor side, reaction center, and electron transfer of photosystem II. Moreover, compared to PS MPs, PS NPs have a greater negative impact on algal cells. Analyzing the transcriptome of cells suggests that the most sensitive metabolic pathways in response to PS MNPs involve oxidative phosphorylation, biosynthesis of secondary metabolites, and photosynthesis. Especially, genes related to photosynthesis and oxidative phosphorylation showed significant changes in expression after exposure to PS MNPs. This study provided molecular-level insights into the toxic mechanisms of PS MNPs on microalgae.

Transcriptomic responses to drought stress in the Patagonian southern beech Nothofagus alpina

BackgroundDeciphering the genetic architecture of drought tolerance could allow the candidate genes identification responding to water stress. In the Andean Patagonian forest, the genus Nothofagus represents an ecologically relevant species to be included in different genomic studies. These studies are scarce in South American ecosystems however represent an important source of genomic data in order to interpret future climate-change environment scenarios of these emblematic forests. Here, we achieved the assemblage of the transcriptome of N. alpina while searching for key genes of activated or suppressed metabolic pathways in response to drought stress.ResultsDe novo transcriptome assembly resulted in 104,030 transcripts. Following confirmation of drought conditions, based on reduction of leaf water potential and stomatal conductance, a differential gene expression analysis resulted in 2720 significantly expressed genes (1601 up-regulated and 1119 down-regulated). Enrichment analysis (over-representation analysis and gene set enrichment analysis) resulted in more than one hundred stress-responsive term ontologies (i.e. biological processes) and pathways. Terms such as response to abscisic acid and pathways such as plant hormone signal transduction or starch and sucrose metabolism were over-represented. Protein–protein interaction assessment resulted in networks with significantly expressed top common hub gene clusters (e.g. plant-type cell wall biogenesis among down-regulated or ABA-signalling among up-regulated). These networks evidenced important regulators at gene expression such as transcriptional factors.ConclusionsResponses of N. alpina seedlings to drought stress were evidenced by the activation of several genes linked to GO biological processes and KEGG pathways, which were mainly based on over-expression of specific protein kinases, phosphatases, synthases and transcription factors. This suggests an up-regulation of signalling pathways, triggered through plant hormones such as abscisic acid or auxin, which could counteract the osmotic stress created as a probable immediate response to drought. On the other hand, groups of carbon fixation genes related to the galactose metabolism, photosynthesis, secondary wall biogenesis, and fatty acid biosynthesis degradation were down-regulated under drought. Overall, our results provide new genomic data for understanding how non-model long-lived trees of Patagonian forests would acclimate to environmental changes.

Maize requires arogenate dehydratase 2 for resistance to Ustilago maydis and plant development.

Maize (Zea mays) smut is a common biotrophic fungal disease caused by Ustilago maydis and leads to low maize yield. Maize resistance to U. maydis is a quantitative trait. However, the molecular mechanism underlying the resistance of maize to U. maydis is poorly understood. Here, we reported that a maize mutant caused by a single gene mutation exhibited defects in both fungal resistance and plant development. maize mutant highly susceptible to U. maydis (mmsu) with a dwarf phenotype forms tumors in the ear. A map-based cloning and allelism test demonstrated that 1 gene encoding a putative arogenate dehydratase/prephenate dehydratase (ADT/PDT) is responsible for the phenotypes of the mmsu and was designated as ZmADT2. Combined transcriptomic and metabolomic analyses revealed that mmsu had substantial differences in multiple metabolic pathways in response to U. maydis infection compared with the wild type. Disruption of ZmADT2 caused damage to the chloroplast ultrastructure and function, metabolic flux redirection, and reduced the amounts of salicylic acid (SA) and lignin, leading to susceptibility to U. maydis and dwarf phenotype. These results suggested that ZmADT2 is required for maintaining metabolic flux, as well as resistance to U. maydis and plant development in maize. Meanwhile, our findings provided insights into the maize response mechanism to U. maydis infection.

Response mechanism of carbon metabolism of Pinus massoniana to gradient high temperature and drought stress

BackgroundThe carbon metabolism pathway is of paramount importance for the growth and development of plants, exerting a pivotal regulatory role in stress responses. The exacerbation of drought impacts on the plant carbon cycle due to global warming necessitates comprehensive investigation into the response mechanisms of Masson Pine (Pinus massoniana Lamb.), an exemplary pioneer drought-tolerant tree, thereby establishing a foundation for predicting future forest ecosystem responses to climate change.ResultsThe seedlings of Masson Pine were utilized as experimental materials in this study, and the transcriptome, metabolome, and photosynthesis were assessed under varying temperatures and drought intensities. The findings demonstrated that the impact of high temperature and drought on the photosynthetic rate and transpiration rate of Masson Pine seedlings was more pronounced compared to individual stressors. The analysis of transcriptome data revealed that the carbon metabolic pathways of Masson Pine seedlings were significantly influenced by high temperature and drought co-stress, with a particular impact on genes involved in starch and sucrose metabolism. The metabolome analysis revealed that only trehalose and Galactose 1-phosphate were specifically associated with the starch and sucrose metabolic pathways. Furthermore, the trehalose metabolic heat map was constructed by integrating metabolome and transcriptome data, revealing a significant increase in trehalose levels across all three comparison groups. Additionally, the PmTPS1, PmTPS5, and PmTPPD genes were identified as key regulatory genes governing trehalose accumulation.ConclusionsThe combined effects of high temperature and drought on photosynthetic rate, transpiration rate, transcriptome, and metabolome were more pronounced than those induced by either high temperature or drought alone. Starch and sucrose metabolism emerged as the pivotal carbon metabolic pathways in response to high temperature and drought stress in Masson pine. Trehalose along with PmTPS1, PmTPS5, and PmTPPD genes played crucial roles as metabolites and key regulators within the starch and sucrose metabolism.

Metabolic adaptations of Microbacterium sediminis YLB-01 in deep-sea high-pressure environments.

The deep-sea environment is an extremely difficult habitat for microorganisms to survive in due to its intense hydrostatic pressure. However, the mechanisms by which these organisms adapt to such extreme conditions remain poorly understood. In this study, we investigated the metabolic adaptations of Microbacterium sediminis YLB-01, a cold and stress-tolerant microorganism isolated from deep-sea sediments, in response to high-pressure conditions. YLB-01 cells were cultured at normal atmospheric pressure and 28 ℃ until they reached the stationary growth phase. Subsequently, the cells were exposed to either normal pressure or high pressure (30MPa) at 4 ℃ for 7days. Using NMR-based metabolomic and proteomic analyses of YLB-01 cells exposed to high-pressure conditions, we observed significant metabolic changes in several metabolic pathways, including amino acid, carbohydrate, and lipid metabolism. In particular, the high-pressure treatment stimulates cell division and triggers the accumulation of UDP-glucose, a critical factor in cell wall formation. This finding highlights the adaptive strategies used by YLB-01 cells to survive in the challenging high-pressure environments of the deep sea. Specifically, we discovered that YLB-01 cells regulate amino acid metabolism, promote carbohydrate metabolism, enhance cell wall synthesis, and improve cell membrane fluidity in response to high pressure. These adaptive mechanisms play essential roles in supporting the survival and growth of YLB-01 in high-pressure conditions. Our study offers valuable insights into the molecular mechanisms underlying the metabolic adaptation of deep-sea microorganisms to high-pressure environments. KEY POINTS: • NMR-based metabolomic and proteomic analyses were conducted on Microbacterium sediminis YLB-01 to investigate the significant alterations in several metabolic pathways in response to high-pressure treatment. • YLB-01 cells used adaptive strategies (such as regulated amino acid metabolism, promoted carbohydrate metabolism, enhanced cell wall synthesis, and improved cell membrane fluidity) to survive in the challenging high-pressure environment of the deep sea. • High-pressure treatment stimulated cell division and triggered the accumulation of UDP-glucose, a critical factor in cell wall formation, in Microbacterium sediminis YLB-01 cells.

Physiological and Transcriptional Analysis Provides Insights into Tea Saponin Biosynthesis and Regulation in Response to SA in Camellia vietnamensis Huang

Camellia vietnamensis Huang is an important and famous woody oil crop with high economic value in China because of its high-quality, edible, and medicinal oil. As one of its major active components, tea saponin (triterpenoid saponin) has shown anticancer, antioxidant, bacteriostatic, and other pharmacological activities. In this study, C. vietnamensis was used as an experimental material to determine the tea saponin content and physiological activity indicators after salicylic acid (SA) treatment and to analyze the differential expression genes of key metabolic pathways in response to SA by combining transcriptome data. The results showed that SA treatment increased the content of tea saponin and total phenols in leaves; effectively promoted the activity of superoxide dismutase (SOD), peroxidase (POD), catalase (CAT), and ascorbate peroxidase (APX); and decreased the content of malondialdehyde (MDA). A total of 60,038 genes, including 5871 new genes, were obtained by the RNA-seq. There were 6609 significantly differential expression genes mainly enriched in pathways such as sesquiterpenoid and triterpenoid biosynthesis, terpenoid backbone biosynthesis, diterpenoid biosynthesis, and flavonoid biosynthesis. The SA-induced key structural genes (SQS, SQE, bAS, CYP450, and UGT) and transcription factors related to the tea saponin biosynthetic pathway were screened by weighted gene co-expression network analysis (WGCNA). The results of this study could provide a theoretical basis and a new technical method to improve the content of tea saponin, with its excellent anticancer activity, in C. vietnamensis.

Immune and metabolic perturbations in COVID-19-associated pulmonary mucormycosis: A transcriptome analysis of innate immune cells.

The mechanisms underlying COVID-19-associated pulmonary mucormycosis (CAPM) remain unclear. We use a transcriptomic analysis of the innate immune cells to investigate the host immune and metabolic response pathways in patients with CAPM. We enrolled subjects with CAPM (n = 5), pulmonary mucormycosis (PM) without COVID-19 (n = 5), COVID-19 (without mucormycosis, n = 5), healthy controls (n = 5) without comorbid illness and negative for SARS-CoV-2. Peripheral blood samples from cases were collected before initiating antifungal therapy, and neutrophils and monocytes were isolated. RNA sequencing was performed using Illumina HiSeqX from monocytes and neutrophils. Raw reads were aligned with HISAT-2 pipeline and DESeq2 was used for differential gene expression. Gene ontology (GO) and metabolic pathway analysis were performed using Shiny GO application and R packages (ggplot2, Pathview). The derangement of core immune and metabolic responses in CAPM patients was noted. Pattern recognition receptors, dectin-2, MCL, FcRγ receptors and CLEC-2, were upregulated, but signalling pathways such as JAK-STAT, IL-17 and CARD-9 were downregulated; mTOR and MAP-kinase signalling were elevated in monocytes from CAPM patients. The complement receptors, NETosis, and pro-inflammatory responses, such as S100A8/A9, lipocalin and MMP9, were elevated. The major metabolic pathways of glucose metabolism-glycolysis/gluconeogenesis, pentose phosphate pathway, HIF signalling and iron metabolism-ferroptosis were also upregulated in CAPM. We identified significant alterations in the metabolic pathways possibly leading to cellular iron overload and a hyperglycaemic state. Immune responses revealed altered recognition, signalling, effector functions and a pro-inflammatory state in monocytes and neutrophils from CAPM patients.

A pulse of simulated root exudation alters the composition and temporal dynamics of microbial metabolites in its immediate vicinity

Root exudation increases the concentration of readily available carbon (C) compounds in its immediate environment. This creates ‘hotspots’ of microbial activity characterized by accelerated soil organic matter turnover with direct implications for nutrient availability for plants. However, our knowledge of the microbial metabolic processes occurring in the immediate vicinity of roots during and after a root exudation event is still limited.Using reverse microdialysis, we simulated root exudation by releasing a13C-labelled mix of low-molecular-weight organic C compounds at mm-sized locations in undisturbed soil. Combined with stable isotope tracing, we investigated the fine-scale temporal and spatial response of microbial metabolism, soil chemistry, and traced microbial respiration and uptake of exuded compounds.Our results show that a 9-h simulated root exudation pulse leads to i) a large local respiration event and ii) alteration of the temporal dynamics of soil metabolites over the following 12 day at the exudation spot. Notably, we observed a threefold increase in ammonium concentrations at 12 h and increased nitrate concentrations five days after the pulse. Moreover, various short-chain fatty acids (acetate, propionate, formate) increased over the following days, indicating altered microbial metabolic pathways and activity. Phospholipid and neutral lipid fatty acids (PLFAs, NLFAs) of all major microbial groups were significantly 13C-enriched within a 5 mm radius around the microdialysis probes, but not beyond. The highest relative 13C enrichment was observed in fungal NLFAs, indicating that a significant proportion of the exuded compounds had been incorporated into fungal storage compounds.Our findings indicate that the punctual release of low-molecular-weight organic C compounds into intact soil significantly changes microbial metabolism and activity in its immediate surroundings, enhancing mineralization of native organic nitrogen. This highlights the versatility of microbial metabolic pathways in response to rapidly changing C availability and their effectiveness in increasing nutrient availability near plant roots.

Salinity alleviates arsenicstress-induced oxidative damage via antioxidative defense and metabolic adjustment in the root of the halophyte Salvadora persica.

Arsenic tolerance in the halophyte Salvadora persica is achieved by enhancing antioxidative defense and modulations of various groups of metabolites like amino acids, organic acids, sugars, sugar alcohols, and phytohormones. Salvadora persica is a facultative halophyte that thrives under high saline and arid regions of the world. In present study, we examine root metabolic responses of S. persica exposed to individual effects of high salinity (750mM NaCl), arsenic (600µM As), and combined treatment of salinity and arsenic (250mM NaCl + 600µM As) to decipher its As and salinity resistance mechanism. Our results demonstrated that NaCl supplementation reduced the levels of reactive oxygen species (ROS) under As stress. The increased activities of antioxidant enzymes like superoxide dismutase (SOD), catalase (CAT), glutathione peroxidase (GPX), and glutathione reductase (GR) maintained appropriate levels of ROS [superoxide (O2•-) and hydrogen peroxide (H2O2)] under salinity and/or As stress. The metabolites like sugars, amino acids, polyphenols, and organic acids exhibited higher accumulations when salt was supplied with As. Furthermore, comparatively higher accumulations of glycine, glutamate, and cystine under combined stress of salt and As may indicate its role in glutathione and phytochelatins (PCs) synthesis in root. The levels of phytohormones such as salicylate, jasmonate, abscisic acid, and auxins were significantly increased under high As with and without salinity stress. The amino acid metabolism, glutathione metabolism, carbohydrate metabolism, tricarboxylic acid cycle (TCA cycle), phenylpropanoid biosynthesis, and phenylalanine metabolism are the most significantly altered metabolic pathways in response to NaCl and/or As stress. Our study decoded the important metabolites and metabolic pathways involved in As and/or salinity tolerance in root of the halophyte S. persica providing clues for development of salinity and As resistance crops.

Unraveling the carbohydrate metabolic characteristics of Leuconostoc mesenteroides J18 through metabolite and transcriptome analyses

The metabolic characteristics of Leuconostoc mesenteroides subsp. mesenteroides J18, which is mainly responsible for kimchi fermentation, on various carbon sources were investigated through carbon utilization, metabolite, and transcriptome analyses at different culture conditions (10 and 30 °C with/without 2.5% NaCl). The metabolic features of strain J18 were relatively similar across the four culture conditions. However, the metabolic characteristics of strain J18 showed significant variations depending on the carbon source. These distinct metabolic traits of strain J18 on various carbon sources were validated through transcriptomic analyses and the reconstruction of metabolic pathways. The transcriptional expression of the metabolic pathways in response to each carbon source consistently correlated with the production profiles of metabolites, including ethanol, acetoin, diacetyl, and riboflavin, in each carbon source. Our findings suggests that the abundance of Leu. mesenteroides during fermentation and the taste and flavor of fermented food products can be controlled by altering the carbon sources.

Artemisinin counteracts Edwardsiella tarda-induced liver inflammation and metabolic changes in juvenile fat greenling Hexagrammos otakii

Emerging evidence suggests that artemisinin (ART) can modulate pathogen-induced immune responses and metabolic dysregulation. However, whether this modulation is associated with metabolic pathways related to oxidative stress and inflammation remains unclear. The aim of this study was to investigate the antioxidant and anti-inflammatory effects on the ART-fed juvenile fat greenling Hexagrammos otakii and the associated metabolic pathways in response to ART administration using an integrated biochemical and metabolomic approach. Biochemical analysis and histological examination showed that ART significantly increased body weight gain and improved tissue structure. ART effectively attenuated reactive oxygen species (ROS), malondialdehyde (MDA) and inflammatory responses (NFκB, TNF-α, IL-6, and MCP-1) in the Edwardsiella tarda-induced H. otakii model. Liver metabolomics analysis revealed that twenty-nine metabolites were up-regulated and twenty-one metabolites were down-regulated after ART administration compared to those in pathogen-induced fish. Pathway analysis indicated that ART alleviated the E. tarda-induced inflammation and oxidative stress through two major pathways, namely lipid metabolism and amino acid metabolism. Taken together, ART showed great potential as a natural feed additive against pathogen-induced oxidative stress and inflammation.

Cross-Species Metabolomic Analyses inthe Brassicaceae Reveals Common Responses to Ultraviolet-B Exposure.

Exposure to UV-B radiation, an intrinsic component of solar light, is detrimental to all living organisms as chromophore units of DNA, RNA and proteins readily absorb high-energy photons. Indirect damage to the same molecules and lipids is mediated by elevated reactive oxygen species (ROS) levels, a side effect of exposure to UV-B stress. To protect themselves from UV-B radiation, plants produce phytochemical sunscreens, among which flavonoids have shown to be particularly effective. The core aglycone of flavonoid molecules is subjected to chemical decoration, such as glycosylation and acylation, further improving sunscreen properties. In particular, acylation, which adds a phenolic ring to flavonoid molecules, enhances the spectral absorption of UV-A and UV-B rays, providing to this class of compounds exceptional shielding power. In this study, we comprehensively analyzed the responses to UV-B radiation in four Brassicaceae species, including Arabidopsis thaliana, Brassica napus, Brassica oleracea, and Brassica rapa. Our study revealed a complete reprogramming of the central metabolic pathway in response to UV-B radiation characterized by increased production of functional precursors of specialized metabolites with UV-B shielding properties, indicating a targeted effort of plant metabolism to provide increased protection. The analysis of specialized metabolites and transcripts revealed the activation of the phenylpropanoid-acetate pathway, leading to the production of specific classes of flavonoids and a cross-species increase in phenylacylated-flavonoid glucosides with synapoyl glycoside decorations. Interestingly, our analysis also revealed that acyltransferase genes of the class of serine carboxypeptidase-like (SCPLs) proteins are costitutively expressed, but downregulated in response to UV-B radiation, possibly independently of the ELONGATED HYPOCOTYL 5 (HY5) signaling pathway.

Metabolic Pathway Modeling in Muscle of Male Marathon Mice (DUhTP) and Controls (DUC)-A Possible Role of Lactate Dehydrogenase in Metabolic Flexibility.

In contracting muscles, carbohydrates and fatty acids serve as energy substrates; the predominant utilization depends on the workload. Here, we investigated the contribution of non-mitochondrial and mitochondrial metabolic pathways in response to repeated training in a polygenic, paternally selected marathon mouse model (DUhTP), characterized by exceptional running performance and an unselected control (DUC), with both lines descended from the same genetic background. Both lines underwent three weeks of high-speed treadmill training or were sedentary. Both lines' muscles and plasma were analyzed. Muscle RNA was sequenced, and KEGG pathway analysis was performed. Analyses of muscle revealed no significant selection-related differences in muscle structure. However, in response to physical exercise, glucose and fatty acid oxidation were stimulated, lactate dehydrogenase activity was reduced, and lactate formation was inhibited in the marathon mice compared with trained control mice. The lack of lactate formation in response to exercise appears to be associated with increased lipid mobilization from peripheral adipose tissue in DUhTP mice, suggesting a specific benefit of lactate avoidance. Thus, results from the analysis of muscle metabolism in born marathon mice, shaped by 35 years (140 generations) of phenotype selection for superior running performance, suggest increased metabolic flexibility in male marathon mice toward lipid catabolism regulated by lactate dehydrogenase.

Treatment of Macrophages with Gram-Negative and -Positive Bacterial Secretomes Induce Distinct Metabolic Signatures

Infectious diseases represent major health and economic challenges globally. Emergence of multiple drug-resistant bacteria in the community and hospital has become a worldwide concern that requires novel approaches for rapid diagnosis and treatment. Metabolomics approach is a powerful tool providing important chemical information about the cellular phenotype of living systems, and the changes in their metabolic pathways in response to various perturbations. Metabolomics has become an important tool to study host-pathogen interactions and to discover potential novel therapeutic targets. In this study, untargeted LC-MS metabolic profiling was applied to differentiate between the impact of the secretome of the Gram-positive S. aureus SH1000 and Gram-negative P. aeruginosa PAO1 bacterial pathogens on THP-1 macrophages. The results showed that S. aureus and P. aeruginosa secretome affected alanine, aspartate and glutamate metabolism; sphingolipid metabolism; glycine and serine metabolism; GL metabolism; and tryptophan metabolism with different trends in THP-1 macrophages. However, the impact of both bacterial secretome on arginine and proline metabolism was similar. These data could contribute to a better understanding of pathogenesis and resistance of these bacteria and could pave the way for developing new therapeutics that selectively targeting Gram-positive or Gram-negative bacteria.

Secondary metabolites responses of plants exposed to ozone: an update.

Tropospheric ozone (O3) is a secondary pollutant that causes oxidative stress in plants due to the generation of excess reactive oxygen species (ROS). Phenylpropanoid metabolism is induced as a usual response to stress in plants, and induction of key enzyme activities and accumulation of secondary metabolites occur, upon O3 exposure to provide resistance or tolerance. The phenylpropanoid, isoprenoid, and alkaloid pathways are the major secondary metabolic pathways from which plant defense metabolites emerge. Chronic exposure to O3 significantly accelerates the direction of carbon flows toward secondary metabolic pathways, resulting in a resource shift in favor of the synthesis of secondary products. Furthermore, since different cellular compartments have different levels of ROS sensitivity and metabolite sets, intracellular compartmentation of secondary antioxidative metabolites may play a role in O3-induced ROS detoxification. Plants' responses to resource partitioning often result in a trade-off between growth and defense under O3 stress. These metabolic adjustments help the plants to cope with the stress as well as for achieving new homeostasis. In this review, we discuss secondary metabolic pathways in response to O3 in plant species including crops, trees, and medicinal plants; and how the presence of this stressor affects their role as ROS scavengers and structural defense. Furthermore, we discussed how O3 affects key physiological traits in plants, foliar chemistry, and volatile emission, which affects plant-plant competition (allelopathy), and plant-insect interactions, along with an emphasis on soil dynamics, which affect the composition of soil communities via changing root exudation, litter decomposition, and other related processes.

Root and Leaf Anatomy, Ion Accumulation, and Transcriptome Pattern under Salt Stress Conditions in Contrasting Genotypes of Sorghum bicolor.

Roots from salt-susceptible ICSR-56 (SS) sorghum plants display metaxylem elements with thin cell walls and large diameter. On the other hand, roots with thick, lignified cell walls in the hypodermis and endodermis were noticed in salt-tolerant CSV-15 (ST) sorghum plants. The secondary wall thickness and number of lignified cells in the hypodermis have increased with the treatment of sodium chloride stress to the plants (STN). Lignin distribution in the secondary cell wall of sclerenchymatous cells beneath the lower epidermis was higher in ST leaves compared to the SS genotype. Casparian thickenings with homogenous lignin distribution were observed in STN roots, but inhomogeneous distribution was evident in SS seedlings treated with sodium chloride (SSN). Higher accumulation of K+ and lower Na+ levels were noticed in ST compared to the SS genotype. To identify the differentially expressed genes among SS and ST genotypes, transcriptomic analysis was carried out. Both the genotypes were exposed to 200 mM sodium chloride stress for 24 h and used for analysis. We obtained 70 and 162 differentially expressed genes (DEGs) exclusive to SS and SSN and 112 and 26 DEGs exclusive to ST and STN, respectively. Kyoto Encyclopaedia of Genes and Genomes (KEGG) and Gene Ontology (GO) enrichment analysis unlocked the changes in metabolic pathways in response to salt stress. qRT-PCR was performed to validate 20 DEGs in each SSN and STN sample, which confirms the transcriptomic results. These results surmise that anatomical changes and higher K+/Na+ ratios are essential for mitigating salt stress in sorghum apart from the genes that are differentially up- and downregulated in contrasting genotypes.

Revealing the response of community structure and metabolic pathway to varying organic matter stress in a dissolved oxygen-differentiated airlift internal circulation partial nitritation-anammox system

In practice, the influent organic matter is often pre-treated to reduce the impact on partial nitritation-anammox (PNA) process. However, the influent organics may also drive the denitrification process and improve total nitrogen removal efficiency of the PNA process. Thus, we designed and operated a novel dissolved oxygen-differentiated airlift internal circulation PNA (PNA-DOAIC) system in this study at various influent C/N ratios of 0–4.0. Nitrogen removal performance, microbial activity and community, and metabolic pathways in response to varying organic matter stress were investigated via the continuous experiment combined with batch test. The results showed that the optimum influent C/N ratio was 2.0 in this system, and the efficient and stable operation was still maintained at the C/N ratios of 0–3. At this time, the TN removal efficiency and removal rate could reach 95.1 % and 0.93 kg-N/m3/d, respectively, while COD efficiency remained at 95.4 %. Efficient removal performance was achieved via the PNA coupled with denitrification. However, the anammox bacteria (AnAOB) activity and abundance declined persistently as the influent C/N ratio was further raised, and heterotrophic bacteria gradually replaced AnAOB as dominate genus. Meanwhile, metabolic functions involving the material exchange and organic degradation were significantly enhanced. Nitrogen removal pathways changed from PNA to the nitrification-denitrification process. This study provides deep insights into effects of organic matter on the PNA process and can expand the application scope of this novel PNA-DOAIC bioreactor.

Large-Scale Qualitative and Quantitative Assessment of Dityrosine Crosslinking Omics in Response to Endogenous and Exogenous Hydrogen Peroxide in Escherichia coli.

Excessive hydrogen peroxide causes oxidative stress in cells. The oxidation of two tyrosine residues in proteins can generate o,o'-dityrosine, a putative biomarker for protein oxidation, which plays critical roles in a variety of organisms. Thus far, few studies have investigated dityrosine crosslinking under endogenous or exogenous oxidative conditions at the proteome level, and its physiological function remains largely unknown. In this study, to investigate qualitative and quantitative dityrosine crosslinking, two mutant Escherichia coli strains and one mutant strain supplemented with H2O2 were used as models for endogenous and exogenous oxidative stress, respectively. By integrating high-resolution liquid chromatography-mass spectrometry and bioinformatic analysis, we created the largest dityrosine crosslinking dataset in E. coli to date, identifying 71 dityrosine crosslinks and 410 dityrosine loop links on 352 proteins. The dityrosine-linked proteins are mainly involved in taurine and hypotaurine metabolism, citrate cycle, glyoxylate, dicarboxylate metabolism, carbon metabolism, etc., suggesting that dityrosine crosslinking may play a critical role in regulating the metabolic pathways in response to oxidative stress. In conclusion, we have reported the most comprehensive dityrosine crosslinking in E. coli for the first time, which is of great significance in revealing its function in oxidative stress.

Integrated transcriptome and metabonomic analysis of key metabolic pathways in response to cadmium stress in novel buckwheat and cultivated species.

Buckwheat (Fagopyrum tataricum), an important food crop, also has medicinal uses. It is widely planted in Southwest China, overlapping with planting areas remarkably polluted by cadmium (Cd). Therefore, it is of great significance to study the response mechanism of buckwheat under Cd stress and further develop varieties with excellent Cd tolerance. In this study, two critical periods of Cd stress treatment (days 7 and 14 after Cd treatment) of cultivated buckwheat (Pinku-1, named K33) and perennial species (F. tatari-cymosum Q.F. Chen) (duoku, named DK19) were analyzed using transcriptome and metabolomics. The results showed that Cd stress led to changes in reactive oxygen species (ROS) and the chlorophyll system. Moreover, Cd-response genes related to stress response, amino acid metabolism, and ROS scavenging were enriched or activated in DK19. Transcriptome and metabolomic analyses highlighted the important role of galactose, lipid (glycerophosphatide metabolism and glycerophosphatide metabolism), and glutathione metabolism in response to Cd stress in buckwheat, which are significantly enriched at the gene and metabolic levels in DK19. The results of the present study provide valuable information for a better understanding of the molecular mechanisms underlying Cd tolerance in buckwheat and useful clues for the genetic improvement of drought tolerance in buckwheat.

Transcriptomic analysis reveals mechanisms for the different drought tolerance of sweet potatoes.

Drought is a common environmental stress with great negative impacts on plant growth, development and geographical distribution as well as agriculture and food production. Sweet potato is characterized by starchy, fresh and pigmented tuber, and is regarded as the seventh most important food crop. However, there has been no comprehensive study of the drought tolerance mechanism of different sweet potato cultivars to date. Here, we studied the mechanism for drought response of seven sweet potato drought-tolerant cultivars using the drought coefficients, physiological indicators and transcriptome sequencing. The seven sweet potato cultivars were classified into four groups of drought tolerance performance. A large number of new genes and transcripts were identified, with an average of about 8000 new genes per sample. Alternative splicing events in sweet potato, which were dominated by first exon and last exon alternative splicing, were not conserved among different cultivars and not significantly affected by drought stress. Furthermore, different drought-tolerance mechanisms were revealed through differentially expressed gene analysis and functional annotation. Two drought-sensitive cultivars, Shangshu-9 and Xushu-22, mainly resisted drought stress by up-regulating plant signal transduction. The other drought-sensitive cultivar Jishu-26 responded to drought stress by down-regulating isoquinoline alkaloid biosynthesis and nitrogen/carbohydrate metabolism. In addition, the drought-tolerant cultivar Chaoshu-1 and drought-preferred cultivar Z15-1 only shared 9% of differentially expressed genes, as well as many opposite metabolic pathways in response to drought. They mainly regulated flavonoid and carbohydrate biosynthesis/metabolism in response to drought, while Z15-1 increased photosynthesis and carbon fixation capacity. The other drought-tolerant cultivar Xushu-18 responded to drought stress by regulating the isoquinoline alkaloid biosynthesis and nitrogen/carbohydrate metabolism. The extremely drought-tolerant cultivar Xuzi-8 was almost unaffected by drought stress and responded to drought environment only by regulating the cell wall. These findings provide important information for the selection of sweet potatoes for specific purposes.