Differentially Expressed Metabolites Research Articles

Metabolomics-based comparative study of breast colostrum and mature breast milk

Breast milk is the safest and most complete natural food for babies. Although breast milk is crucial to the health and development of infants, the metabolites in breast milk during lactation period have not been characterized. Therefore, we examined and compared the metabolites in breast colostrum and mature breast milk using gas chromatography-time-of-flight-mass spectrometry-based metabolomics. A total of 159 metabolites were characterized, of which 72 were differentially expressed metabolites (DEMs), including 17 upregulated and 55 downregulated DEMs in breast colostrum compared to those in mature breast milk. Metabolic pathway analysis revealed that these DEMs were related to glycine, serine, and threonine metabolism; glyoxylate and dicarboxylate metabolism; alanine, aspartate, and glutamate metabolism; pentose and glucuronate interconversions; and aminoacyl-tRNA biosynthesis. Our results improve the understanding of breast milk composition and provide a theoretical basis for optimizing infant formula to closely imitate the nutrients required for proper growth and development of babies.

Integrated Physiological and Metabolomic Analyses of the Effect of Potassium Fertilizer on Citrus Fruit Splitting.

Potassium (K) nutrition plays a key role in alleviating a variety of peel disorders in tree fruit, but the effect of this nutrient on the physiological and metabolic profiles involved in the fruit splitting of citrus remains unclear. Three levels of K were used to treat citrus ‘Ehime Kashi 34’ (Citrus Nishinoka × C. Shiranui), a hybrid cultivar with fruit that easily split. The results showed that the roots of the treatment with K fertilizer increased the contents of calcium (Ca2+), nitrogen (N), and K in the skin and flesh, the fruit firmness ratio of the peel to the flesh, photosynthetic rate, stomatal conductance, and concentration of intercellular CO2. In contrast, it decreases the relative chlorophyll index and content of Ca2+ in the leaves. Simultaneously, 59 and 13 differentially expressed metabolites (DEMs) were detected in the peel and flesh, respectively, after treatment with K. Of them, five compounds were upregulated, including the synthesis of various amino acids in the peel and the accumulation of various glycoside metabolites in the flesh which were upregulated. The accumulation of levels of gibberellin and glycoside were downregulated. That could be the main reason why potassium alleviates fruit splitting.

Armillaria mellea Symbiosis Drives Metabolomic and Transcriptomic Changes in Polyporus umbellatus Sclerotia.

Sclerotia, the medicinal part of Polyporus umbellatus, play important roles in diuresis and renal protection, with steroids and polysaccharides as the main active ingredients. The sclerotia grow and develop only after symbiosis with Armillaria sp. In this study, a systematic metabolomics based on non-targeted UPLC-MS method was carried out between the infected part of the separated cavity wall of the sclerotia (QR) and the uninfected part (the control group, CK) to find and identify differential metabolites. The biosynthetic pathway of characteristic steroids in sclerotia of P. umbellatus was deduced and the content of ergosterol, polyporusterone A and B in the QR and CK groups were detected with the High Performance Liquid Chromatography (HPLC). Furthermore, the expression patterns of putative genes associated with steroid biosynthesis pathway were also performed with quantitative real-time PCR. The results showed that a total of 258 metabolites originated from fungi with the fragmentation score more than 45 and high resolution mass were identified, based on UPLC-MS metabolomic analysis, and there were 118 differentially expressed metabolites (DEMs) between both groups. The metabolic pathways indicated that steroids, fatty acid and carbohydrate were active and enriched during P. umbellatus sclerotia infected by A. mellea. The content of ergosterol, polyporusterone A and B in the QR group increased by 32.2, 75.0, and 20.0%, in comparison to that of the control group. The qRT-PCR analysis showed that series of enzymes including C-8 sterol isomerase (ERG2), sterol C-24 methyltransferase (ERG6) and sterol 22-desaturase (ERG5), which played important roles in the final steps of ergosterol biosynthesis, all presented up-regulated patterns in the QR group in P. umbellatus. The comprehensive metabolomic and transcriptomic information will contribute to further study concerning the mechanisms of P. umbellatus sclerotial formation infected by A. mellea in the future.

Comprehensive Transcriptome-Metabolome Analysis and Evaluation of the Dark_Pur Gene from Brassica juncea that Controls the Differential Regulation of Anthocyanins in Brassica rapa.

Chinese cabbage (Brassica rapa) is a major vegetable crop in China. The accumulation of anthocyanins improves the quality and flavor of Brassica crops and is beneficial for human health. There has been great research interest in breeding purple Chinese cabbage, for which it is necessary to study the key genes and mechanisms of anthocyanin accumulation. Through distant hybridization between purple mustard (Brassica juncea) and green Chinese cabbage (B. rapa), purple Chinese cabbage plants were obtained. Furthermore, the Dark_Pur gene was cloned in the purple Chinese cabbage plants, which came from purple mustard and may be responsible for the purple phenotype in purple Chinese cabbage plants. Through particle bombardment of isolated microspores from Chinese cabbage to transform the Dark_Pur gene, the transformed purple Chinese cabbage plant was obtained, thus verifying the function of the Dark_Pur gene. To further study the Dark_Pur gene regulatory mechanism of anthocyanin accumulation in Chinese cabbage, the purple/green Chinese cabbage lines and purple/green mustard lines were subjected to transcriptome–metabolome analysis. Three stages (cotyledon, seedling, and large-leaf stages) of the purple/green Chinese cabbage lines and purple/green mustard lines were selected for analysis. The results indicated that the expression level of the transcription factor genes BraA09g028560.3C, BraA03g019460.3C, and BraA07g035710.3C may be induced by the Dark_Pur gene and they play an important role in purple Chinese cabbage, and BjuB010898 and BjuO006089 may be responsible for anthocyanin accumulation in mustard. Studying the structural genes of the purple Chinese cabbage showed that PAL, C4H, 4CL, CHS, CHI, F3H, F3’H, FLS, DFR, ANS, and UGT were up-regulated in three growth periods. There were 22 and 10 differentially expressed metabolites (DEMs) in seedling and large-leaf stages between purple/green Chinese cabbage, respectively, and 12 and 14 differentially expressed metabolites (DEMs) in seedling and large-leaf stages between purple/green mustard, respectively, which may indicate that the Dark_Pur gene from purple mustard greatly regulates anthocyanin accumulation in purple Chinese cabbage. This study provides a foundation for further elucidating anthocyanin regulation.

Distinct molecular impact patterns of abamectin on Apis mellifera ligustica and Apis cerana cerana

The effects of insecticides on bee health are a topic of intensive research. Although abamectin is toxic to bees, the molecular impact of abamectin needs to be clarified. Here, we found that Apis cerana cerana exhibited a higher mortality rate when exposed to abamectin than Apis mellifera ligustica. In addition, A. cerana cerana had markedly higher numbers of differentially expressed genes (DEGs), differentially expressed proteins (DEPs) and differentially expressed metabolites (DEMs) than A. mellifera ligustica during exposure to abamectin. These results indicate that abamectin exposure exerts stronger effects on A. cerana cerana than on A. mellifera ligustica. In addition, six DEGs, two DEPs and two DEMs overlapped between the two bee species under abamectin exposure; however, some genes or proteins from the zinc finger protein, superoxide dismutase and peroxiredoxin families and the energy metabolism pathway were only unregulated in A. cerana cerana, which indicates a significant difference in the impact of abamectin on the two bee species. Despite these differences, several of the same gene families, such as heat shock proteins, cytochrome P450, odorant-binding proteins and cuticle proteins, and pathways, including the carbohydrate metabolism, immune system, lipid metabolism, amino acid metabolism, sensory system, locomotion and development pathways, were influenced by abamectin exposure in both A. cerana cerana and A. mellifera ligustica. Together, our results indicate that abamectin causes adverse effects on bees and thus poses a risk to bee populations and that abamectin exposure affects A. cerana cerana more strongly than A. mellifera ligustica. These findings improve our understanding of the behavioural and physiological effects of abamectin on bees.

Differential Metabolomic Responses of Kentucky Bluegrass Cultivars to Low Nitrogen Stress.

Kentucky bluegrass (Poa pratensis L.) is a cool-season turfgrass species that responds strongly to nitrogen (N), but the metabolomic responses of this grass species to N supply is unknown. The N-tolerant cultivar Bluemoon and N-sensitive cultivar Balin were exposed to normal N (15 mM) and low N (0.5 mM) for 21 days for identification of differentially expressed metabolites (DEMs) between normal N and low N treatments. Balin had more reductions of chlorophyll and total soluble protein concentrations and a higher accumulation of superoxide radicals under low N stress. A total of 99 known DEMs were identified in either cultivar or both including 22 amino acids and derivatives, 16 carbohydrates, 29 organic acids, and 32 other metabolites. In Bluemoon, β-alanine metabolism was most enriched, followed by alanine, aspartate, and glutamate metabolism, biosynthesis of valine, leucine, and isoleucine biosynthesis, and glycine, serine, and threonine metabolism. In Balin, alanine, aspartate, and glutamate metabolism were most enriched, followed by the tricarboxylic acid (TCA), glyoxylate and decarbohydrate metabolism, and carbon fixation. Bluemoon generally maintained higher TCA cycle capacity and had more downregulated amino acids, while changes in more organic acids occurred in Balin under low N stress. Some metabolite changes by low-N stress were cultivar-specific. The results suggested that regulation of metabolites related to energy production or energy saving could contribute to low N tolerance in Kentucky bluegrass.

Integration of Metabolome and Transcriptome Studies Reveals Flavonoids, Abscisic Acid, and Nitric Oxide Comodulating the Freezing Tolerance in Liriope spicata.

Liriope spicata is an evergreen perennial ornamental groundcover with a strong freezing tolerance. However, the molecular mechanism underlying the freezing tolerance in L. spicata remains unclear. In this study, a comprehensive investigation of L. spicata freezing tolerance was conducted at the levels of physiology and biochemistry, metabolite, and transcript during the stress treatment. There were 581 unique differentially expressed metabolites (DEMs) and 10,444 unique differentially expressed genes (DEGs) between freezing treatment and normal cultured plant in leaves. Integrated analysis of metabolomics and transcriptomics showed that flavonoid biosynthesis, carbohydrate metabolism, amino acid metabolism, lipid metabolism, and signal transduction pathways were prominently enriched in response to the freezing stress in L. spicata. Now, we identified genes and metabolites involved in the flavonoid pathway, abscisic acid (ABA) biosynthesis, and the oxidative synthesis pathway of nitric oxide (NO), which may form a regulatory network and play a synergistic effect in osmotic adjustment, reactive oxygen species (ROS) homeostasis, and stomatal closure under freezing stress. These results offer a comprehensive network of flavonoids, ABA, and NO comodulating the freezing tolerance in L. spicata.

Combined Transcriptomics and Metabolomics Analysis Reveals the Molecular Mechanism of Salt Tolerance of Huayouza 62, an Elite Cultivar in Rapeseed (Brassica napus L.).

Soil salinity is one of the most significant abiotic stresses affecting crop yield around the world. To explore the molecular mechanism of salt tolerance in rapeseed (Brassica napus L.), the transcriptome analysis and metabolomics analysis were used to dissect the differentially expressed genes and metabolites in two rapeseed varieties with significant differences in salt tolerance; one is an elite rapeseed cultivar, Huayouza 62. A total of 103 key differentially expressed metabolites (DEMs) and 53 key differentials expressed genes (DEGs) that might be related to salt stress were identified through metabolomics and transcriptomics analysis. GO and KEGG analysis revealed that the DEGs were mainly involved in ion transport, reactive oxygen scavenging, osmotic regulation substance synthesis, and macromolecular protein synthesis. The DEMs were involved in TCA cycle, proline metabolism, inositol metabolism, carbohydrate metabolic processes, and oxidation-reduction processes. In addition, overexpression of BnLTP3, which was one of the key DEGs, could increase tolerance to salt stress in Arabidopsis plants. This study reveals that the regulation mechanism of salt tolerance in rapeseed at the transcriptome and metabolism level and provides abundant data for further in-depth identification of essential salt tolerance genes.

Integrative analysis of the metabolome and transcriptome provides insights into the mechanisms of flavonoid biosynthesis in blackberry

Blackberry fruit is rich in anthocyanins, showing incomparable nutritional and health value. Anthocyanins are flavonoids that are downstream products of the flavonoid biosynthesis pathway. They are important secondary metabolites with antioxidant and anticancer functions. Therefore, we performed combined transcriptome and metabolome analyses of unripe and ripe blackberry fruits to identify the molecular mechanisms of flavonoid biosynthesis. Herein, we identified 997 differentially expressed metabolites (DEMs) in positive-ion mode, 411 DEMs in negative-ion mode, and 17,566 differentially expressed genes (DEGs). Eight DEMs and 16 DEGs were annotated to the flavonoid biosynthesis pathway. Four DEGs related to flavonoids (unigene 0028088, unigene 0039337, unigene 0063209, and unigene 0014842) were positively correlated with related flavonoid DEMs. Interestingly, 8 DEGs and 11 flavonoid-related DEMs showed significant negative correlations. This study lays a foundation for further research on the biosynthesis and metabolism of flavonoid, providing a reference for the future breeding and cultivation of excellent high-flavonoid germplasm resources and the blackberry-related pharmaceutical industry.

Untargeted Metabolomics Reveals Multiple Phytometabolites in the Agricultural Waste Materials and Medicinal Materials of Codonopsis pilosula

Codonopsis pilosula has been used in traditional Chinese medicine for hundreds of years, where it has been used to treat anaemia, fatigue, a weak spleen, and stomach problems, among other ailments. The roots of C. pilosula are considered medicinal, while the aerial parts are always directly discarded after harvest in autumn or winter. Some studies have shown that the stems and leaves of C. pilosula also contain a variety of active metabolites, including saponins, flavonoids, terpenoids, and polysaccharides. To efficiently utilise resources, waste products from C. pilosula leaves and stems were analysed by untargeted metabolomics and chemometrics. A total of 1508 metabolites were detected and annotated, of which 463 were identified as differentially expressed metabolites (DEMs). These DEMs were grouped into classes, such as carboxylic acids and derivatives, steroids, organic oxygen compounds, fatty acyls, prenol lipids, and flavonoids. Metabolic profiling of C. pilosula tissues showed that the contents of polyacetylenes, polyenes, flavonoids, some alkaloids, steroids, terpenoids, and organic acids were higher in stems and leaves, whereas the contents of the main lignans and some alkaloids were more enriched in roots. Moreover, C. pilosula stems and leaves also contained a lobetyolin, syringin and atractylenolide III, which were detected by LC-MS/MS and HPLC-UV. The extracts of C. pilosula aerial parts also showed stronger antioxidant properties than roots. C. pilosula stems and leaves were rich in active ingredients and might have great value for development and utilisation.

Proteomic and lipidomics analyses of high fatty acid AhDGAT3 transgenic soybean reveals the key lipase gene associated with the lipid internal mechanism.

Vegetable oil is one of the most important components of human nutrition. Soybean (Glycine max) is an important oil crop worldwide and contains rich unsaturated fatty acids. Diacylglycerol acyltransferase (DGAT) is a key rate-limiting enzyme in the Kennedy pathway from diacylglycerol (DAG) to triacylglycerol (TAG). In this study, we conducted further research using T3 AhDGAT3 transgenic soybean. A high-performance gas chromatography flame ionization detector showed that oleic acid (18:1) content and total fatty acid content of transgenic soybean were significantly higher than those of the wild type (WT). However, linoleic acid (18:2) was much lower than that in the WT. For further mechanistic studies, 20 differentially expressed proteins (DEPs) and 119 differentially expressed metabolites (DEMs) were identified between WT (JACK) and AhDGAT3 transgenic soybean mature seeds using proteomic and lipidomics analyses. Combined proteomic and lipidomics analyses showed that the upregulation of the key DEP (lipase GDSL domain-containing protein) in lipid transport and metabolic process induced an increase in the total fatty acid and 18:1 composition, but a decrease in the 18:2 composition of fatty acids. Our study provides new insights into the deep study of molecular mechanism underlying the enhancement of fatty acids in transgenic soybeans, especially oleic acid and total fatty acid, which are enhanced by over-expression of AhDGAT3.

Integrated Metabolomics and Transcriptomic Analysis of Hepatopancreas in Different Living Status Macrobrachium nipponense in Response to Hypoxia.

As the basic element of aerobic animal life, oxygen participates in most physiological activities of animals. Hypoxia stress is often the subject of aquatic animal research. Macrobrachium nipponense, an economically important aquatic animal in southern China, has been affected by hypoxia for many years and this has resulted in a large amount of economic loss due to its sensitivity to hypoxia; Metabolism and transcriptome data were combined in the analysis of the hepatopancreas of M. nipponense in different physiological states under hypoxia; A total of 108, 86, and 48 differentially expressed metabolites (DEMs) were found in three different comparisons (survived, moribund, and dead shrimps), respectively. Thirty-two common DEMs were found by comparing the different physiological states of M. nipponense with the control group in response to hypoxia. Twelve hypoxia-related genes were identified by screening and analyzing common DEMs. GTP phosphoenolpyruvate carboxykinase (PEPCK) was the only differentially expressed gene that ranked highly in transcriptome analysis combined with metabolome analysis. PEPCK ranked highly both in transcriptome analysis and in combination with metabolism analysis; therefore, it was considered to have an important role in hypoxic response. This manuscript fills the one-sidedness of the gap in hypoxia transcriptome analysis and reversely deduces several new genes related to hypoxia from metabolites. This study contributes to the clarification of the molecular process associated with M. nipponense under hypoxic stress.

Unraveling the Association between Metabolic Changes in Inter-Genus and Intra-Genus Bacteria to Mitigate Clubroot Disease of Chinese Cabbage

Clubroot disease caused by the obligate parasite Plasmodiophora brassicae is a serious threat to cabbage production worldwide. Current clubroot control primarily relies on a fungicide, but this has a negative impact on the environment and the use of a single biocontrol agent cannot efficiently control the disease. Thus, the combined application of different biocontrol agents has been proposed as a promising alternative. In this study, we used bacterial biocontrol agents as a co-culture (inter-genus and intra-genus) and mono-culture to mitigate the clubroot disease of Chinese cabbage. We evaluated their biocontrol effect and plant growth promoter (PGP) traits in in vitro and in vivo experiments. This study revealed that the inter-genus bacterial co-culture significantly suppresses the incidence of clubroot disease and enhances plant growth compared with intra-genus and mono-culture. In pairwise interaction, we observed that Bacillus cereus BT-23 promotes the growth of Lysobacter antibioticus 13-6 (inter-genus bacterial co-culture), whereas L. capsici ZST1-2 and L. antibioticus 13-6 (intra-genus microbial co-culture) are antagonists to each other. Furthermore, a total of 5575 metabolites, 732 differentially expressed metabolites (DEMs), and 510 unique metabolites were detected through the LC-MS/MS technique in the bacterial co-culture. The number of unique metabolites in inter-genus bacterial co-culture (393 metabolites) was significantly higher than in the intra-genus bacterial co-culture (117 metabolites). Further analysis of DEMs showed that the DEMs were mainly involved in four kinds of metabolism pathways, i.e., carbohydrate metabolism, amino metabolism, nucleotide metabolism, and metabolism of cofactors and vitamins. The contents of some secondary metabolites with biocontrol activity and plant growth-promoting functions were increased in inter-genus bacterial co-culture, indicating that inter-genus bacterial co-culture has a solid potential to suppress clubroot disease. We conclude that the inter-genus bacterial interaction changes the community metabolism and improves several secondary metabolites functions with respect to disease control and PGP ability.

Identification of Differentially Expressed Genes and Pathways Involved in Growth and Development of Mesona chinensis Benth Under Red- and Blue-Light Conditions.

Mesona chinensis Benth (MCB) is an important Chinese herbal medicine. The plant factories might be one of the ways to solve the shortage of MCB supply. In this study, the MCB seedlings were treated under the red (R) and blue (B) lights in the plant factory. Results showed that the red light promoted the growth and development of MCB in comparison with the blue light. Under the red-light condition, the biomass, plant height, and root characteristics were significantly higher than those under blue-light condition, while the soil and plant analyzer development (SPAD) under the red-light treatment was significantly lower than that under the blue-light treatment. Red light also significantly promoted the content of soluble sugar and pectin of MCB compared with blue light. Transcriptome analysis showed that a total of 4,165 differentially expressed genes (DEGs) were detected including 2,034 upregulated and 2,131 downregulated. Of these, 1,112 DEGs including 410 upregulated and 702 downregulated genes were associated with 111 pathways. Moreover, a total of 8,723 differentially expressed transcription factors (TFs) were identified in R vs. B, and these TFs were distributed in 56 gene families. Metabonomic results revealed that a total of 184 metabolites and 99 differentially expressed metabolites (DEMs) (42 upregulated and 57 downregulated) were identified in the red- and blue-light treatments. Integrative analysis of transcriptome and metabolome unveiled that a total of 24 pathways included 70 compounds (metabolites) and were associated with 28 unigenes. In particular, these pathways included starch and sucrose metabolism, phenylpropanoid biosynthesis, cysteine and methionine metabolism, glycolysis/gluconeogenesis, and pentose and glucuronate interconversions. The unigenes included asparagine synthetase (AS), thymidine kinase (TK), alpha, alpha-trehalose-phosphate synthase (TPS), phosphatase IMPL1 (IMPL1), dihydroflavonol 4-reductase (D4R), and 4-coumarate-CoA ligase-like 6 (4CL6), bifunctional aspartokinase-homoserine dehydrogenase 1 (thrA), and abscisic acid 8′-hydroxylase 2 isoform X1 (ABA8). It was indicated that these pathways and genes might play important roles in the growth and development of MCB. This study laid a foundation for the future research of MCB.

Integrative analyses of metabolome and transcriptome reveals metabolomic variations and candidate genes involved in sweet cherry (Prunus avium L.) fruit quality during development and ripening.

Sweet cherry (Prunus avium L.), one of the most appreciated and most important commercial temperate fruits, has high sensory quality and nutritional value. Investigating its metabolic variations provides valuable information on the formation of fruit quality. In this study, widely targeted LC-MS/MS based metabolomics was used to identify and quantify metabolic changes during ‘Black Pearl’ sweet cherry development and ripening. A total of 263 significant differentially expressed metabolites (DEMs) were detected during the four fruit-development stages. Significant differences were observed in the composition and content of compounds in the four stages of cherry development, especially sugars, organic acids, and flavonoids. Moreover, transcriptome analysis provided a molecular basis for metabolic variations during fruit development. A total of 6724 significant differentially expressed genes (DEGs) were identified. Further correlation analysis of major DEMs and DEGs showed that 19 key DEGs were involved in sugar metabolism, 23 key DEGs in organic acid metabolism, and 13 key DEGs in flavonoid metabolism. The upregulated genes involved in the flavonoid pathway probably play an important role in regulating the rapid increase of anthocyanin content during fruit development. These comprehensive analysis data provide a better understanding to improve fruit quality traits based on molecular and metabolic levels.

Placental metabolic profiling in gestational diabetes mellitus: An important role of fatty acids.

AimGestational diabetes mellitus (GDM) is the most common metabolic disorder during pregnancy. Accumulating studies have reported metabolites that are significantly associated with the development of GDM. However, studies on the metabolism of placenta, the most important organ of maternal‐fetal energy and material transport, are extremely rare. This study aimed to identify and discuss the relationship between differentially expressed metabolites (DEM) and clinical parameters of the mothers and newborns.MethodsIn this study, metabolites from 63 placenta tissues (32 GDM and 31 normal controls) were assayed by ultra‐performance liquid chromatography‐high resolution mass spectrometry (UPLC‐HRMS).ResultsA total of 1297 annotated metabolites were detected, of which 87 significantly different in GDM placenta. Lipids and lipid‐like molecules accounted for 62.1% of DEM as they were significantly enriched via the “biosynthesis of unsaturated fatty acids” and “fatty acid biosynthesis” pathways. Linoleic acid and α‐linolenic acid appeared to be good biomarkers for the prediction and diagnosis of GDM. In addition, the level of PC(14:0/18:0) was negatively correlated with neonatal weight. 14 metabolites significantly different in male and female offspring, with the most increase in female newborns.ConclusionEven if maternal blood glucose level is well controlled, there are still metabolic abnormalities in GDM. Lipids and lipid‐like molecules were the main differential metabolites, especially unsaturated fatty acids.

Metabolomics Analysis of the Effect of GAT-2 Deficiency on Th1 Cells in Mice.

The classic neurotransmitter γ-aminobutyric acid (GABA) has been shown to shape the activation and function of immune cells. There are four high-affinity GABA transporters (GATs, including GAT-1, GAT-2, GAT-3, and GAT-4) responsible for the transmembrane transport of GABA in mice. To explore the effect of GAT-2 on type 1 helper T (Th1) cells, naïve CD4+ T cells were isolated from splenocytes of GAT-2 knockout (KO) and wild-type (WT) mice and cultured for Th1 cell differentiation, and then, metabolomics analysis of Th1 cells was performed via gas chromatography coupled to time-of-flight mass spectrometry added with multivariate analyses. Based on the variable importance projection value > 1 and P < 0.05, a total of nine differentially expressed metabolites (DEMs) were identified between WT and KO. Then, DEMs were mapped to the KEGG database, and five metabolic pathways were significantly enriched, including the cysteine and methionine metabolism, the riboflavin metabolism, the purine metabolism, the glycerolipid metabolism, and the glycerophospholipid metabolism. Collectively, our metabolomics analysis revealed that deficiency of GAT-2 influenced the metabolomics profile of Th1 cells, which will provide insights into T cell response to GAT-2 deficiency in mice. Data are available via MetaboLights with identifier MTBLS3358.

Transcriptomic and Metabolomic Analyses Provide Insights Into an Aberrant Tissue of Tea Plant (Camellia sinensis).

Tea plant (Camellia sinensis (L.) O. Kuntze) is one of the most important economic crops with multiple mutants. Recently, we found a special tea germplasm that has an aberrant tissue on its branches. To figure out whether this aberrant tissue is associated with floral bud (FB) or dormant bud (DB), we performed tissue section, transcriptome sequencing, and metabolomic analysis of these tissues. Longitudinal sections indicated the aberrant tissue internal structure was more like a special bud (SB), but was similar to that of DB. Transcriptome data analysis showed that the number of heterozygous and homozygous SNPs was significantly different in the aberrant tissue compared with FB and DB. Further, by aligning the unmapped sequences of the aberrant tissue to the Non-Redundant Protein Sequences (NR) database, we observed that 36.13% of unmapped sequences were insect sequences, which suggested that the aberrant tissue might be a variation of dormant bud tissue influenced by the interaction of tea plants and insects or pathogens. Metabolomic analysis showed that the differentially expressed metabolites (DEMs) between the aberrant tissue and DB were significantly enriched in the metabolic pathways of biosynthesis of plant hormones and biosynthesis of phenylpropanoids. Subsequently, we analyzed the differentially expressed genes (DEGs) in the above mentioned two tissues, and the results indicated that photosynthetic capacity in the aberrant tissue was reduced, whereas the ethylene, salicylic acid and jasmonic acid signaling pathways were activated. We speculated that exogenous infection induced programmed cell death (PCD) and increased the lignin content in dormant buds of tea plants, leading to the formation of this aberrant tissue. This study advanced our understanding of the interaction between plants and insects or pathogens, providing important clues about biotic stress factors and key genes that lead to mutations and formation of the aberrant tissue.

Comparative cytology combined with transcriptomic and metabolomic analyses of Solanum nigrum L. in response to Cd toxicity

Cadmium (Cd) triggers molecular alterations in plants, perturbs metabolites and damages plant growth. Therefore, understanding the molecular mechanism underlying the Cd tolerance in plants is necessary for assessing the persistent environmental impact of Cd. In this study, Solanum nigrum was selected as the test plant to investigate changes in biomass, Cd translocation, cell ultrastructure, metabolites and genes under hydroponic conditions. The results showed that the plant biomass was significantly decreased under Cd stress, and the plant has a stronger Cd transport capability. Transmission electron microscopy revealed that increased Cd concentration gradually damaged the plant organs (roots, stems and leaves) cell ultrastructure, as evidenced by swollen chloroplasts and deformed cell walls. Additionally, metabolomics analyses revealed that Cd stress mainly affected seven metabolism pathways, including 19 differentially expressed metabolites (DEMs). Moreover, 3908 common differentially expressed genes (DEGs, 1049 upregulated and 2859 downregulated) were identified via RNA-seq among five Cd treatments. Meanwhile, conjoint analysis found several DEGs and DEMs, including laccase, peroxidase, D-fructose, and cellobiose etc., are associated with cell wall biosynthesis, implying the cell wall biosynthesis pathway plays a critical role in Cd detoxification. Our comprehensive investigation using multiple approaches provides a molecular-scale perspective on plant response to Cd stress.

The suppressive mechanism of dietary macroalgae Saccharina japonica against hepatic lipid accumulation in black seabream A. schlegelii

Hepatic lipid accumulation (HLA) is a major risk factor for the development of liver diseases in cultured fish species, which can lead to severe health problems and decrease harvest yields, thus result in economic losses. Macroalgae Saccharina japonica (SJ) has been reported to reduce HLA in mammals, but effects and underlying mechanism of dietary SJ on HLA in fish remain elusive. This study aimed to investigate the effect of dietary SJ on HLA of black seabream (A. schlegelii), an important marine economic fish. Juvenile black seabream (2.78 ± 0.16 g) was fed diets with three levels of SJ (0, 2.5 and 10%) for 90 days, and then blood and liver tissues were extracted for biochemical, histological and multiple-omic analyses. This study demonstrated that dietary supplementation of 2.5% and 10% SJ improved HLA-related parameters, including reducing serum lipid content and the activity of aminotransferase. Meanwhile, histological analysis showed that dietary SJ reduced lipid vacuoles in hepatocytes. The transcriptomic analysis of differentially expressed genes (DEG) showed that all the DEG in primary bile acid biosynthesis and biosynthesis of unsaturated fatty acids were down-regulated in SJ2.5% group and SJ10% group, respectively. Besides, all the DEG in regulation of autophagy were up-regulated in SJ2.5% and SJ10% groups compared with SJ0% group. Moreover, the metabolomic analysis of the differentially expressed metabolites (DEM) found that lipid metabolism was the main type of pathway in SJ supplementation groups. Furthermore, the analysis of both of DEG and DEM co-enriched in Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway related to lipid metabolism found that the significant enriched pathways were primary bile acid biosynthesis, glycerophospholipid metabolism, biosynthesis of unsaturated fatty acids and fatty acid biosynthesis metabolism in SJ2.5% and SJ10% groups compared with SJ0% group. However, there were no pathways co-enriched between SJ10% and SJ2.5% group. In short, 2.5% and 10% SJ supplementation diets may reduce serum lipid content and HLA of black seabream through promoting autophagy and inhibiting the synthesis of fatty acids and bile acids.