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Plants are the most important sources of food for humans, as well as supplying many ingredients that are of great importance for human health. Developing an understanding of the functional components of plant metabolism has attracted considerable attention. The rapid development of liquid chromatography and gas chromatography, coupled with mass spectrometry, has allowed the detection and characterization of many thousands of metabolites of plant origin. Nowadays, elucidating the detailed biosynthesis and degradation pathways of these metabolites represents a major bottleneck in our understanding. Recently, the decreased cost of genome and transcriptome sequencing rendered it possible to identify the genes involving in metabolic pathways. Here, we review the recent research which integrates metabolomic with different omics methods, to comprehensively identify structural and regulatory genes of the primary and secondary metabolic pathways. Finally, we discuss other novel methods that can accelerate the process of identification of metabolic pathways and, ultimately, identify metabolite function(s).

PLIP lipases can initiate jasmonic acid (JA) biosynthesis. However, little is known about the transcriptional regulation of this process. In this study, an ERF transcription factor (CsESE3) was found to be co-expressed with all necessary genes for JA biosynthesis and several key genes for wax biosynthesis in transcriptomes of ‘Newhall’ navel orange. CsESE3shows partial sequence similarity to the well-known wax regulator SHINEs (SHNs), but lacks a complete MM protein domain. Ectopic overexpression of CsESE3in tomato (OE) resulted in reduction of fruit surface brightness and dwarf phenotype compared to the wild type. The OE tomato lines also showed significant increases in the content of wax and JA and the expression of key genes related to their biosynthesis. Overexpression of CsESE3in citrus callus and fruit enhanced the JA content and the expression of JA biosynthetic genes. Furthermore, CsESE3could bind to and activate the promoters of two phospholipases from the PLIP gene family to initiate JA biosynthesis. Overall, this study indicated that CsESE3could mediate JA biosynthesis by activating PLIPgenes and positively modulate wax biosynthesis. The findings provide important insights into the coordinated control of two defense strategies of plants represented by wax and JA biosynthesis.

Mass spectrometry-based metabolomics approaches can enable detection and quantification of many thousands of metabolite features simultaneously. However, compound identification and reliable quantification are greatly complicated owing to the chemical complexity and dynamic range of the metabolome. Simultaneous quantification of many metabolites within complex mixtures can additionally be complicated by ion suppression, fragmentation and the presence of isomers. Here we present guidelines covering sample preparation, replication and randomization, quantification, recovery and recombination, ion suppression and peak misidentification, as a means to enable high-quality reporting of liquid chromatography– and gas chromatography–mass spectrometry-based metabolomics-derived data.

As one of the most popular beverages globally, tea has enormous economic, cultural, and medicinal importance that necessitates a comprehensive metabolomics study of this species. In this study, a large-scale targeted metabolomics analysis on two types of leaf tissues of nine tea cultivars from five representative geographical origins within China was carried out using the liquid chromatography-mass spectrometry technique. RNA-seq-based transcriptomic analysis was in parallel conducted on the same samples, and gene expression and metabolic differentiation between tissues as well as between the multiple tea cultivars were investigated. The data obtained provide an accessible resource for further studies of naturally occurring metabolic variation of tea plants, which will aid in thoroughly interpreting the underlying genetic and molecular mechanisms of biosynthesis of specialized metabolites in this critical species. Candidate genes including a transcription factor (CsMYB5-like), which were highly correlated with both the content of flavonoids and the expression level of genes participating in the phenylpropanoid and flavonoid biosynthesis pathway, were identified as potential targets for quality improvement of tea.

We examined the impact of autophagy activation on bacterial translocation (BT) and tight junction (TJ) proteins in the intestinal mucosa of patients with severe acute pancreatitis (SAP).

Free amino acids (FAAs) positively determine the tea quality, notably theanine (Thea), endowing umami taste of tea infusion, which is the profoundly prevalent research in albino tea genetic resources. Therefore, 339 tea accessions were collected to study FAAs level for deciphering its variation and accumulation mechanism. Interestingly, alanine (Ala) and Thea which had the highest diversity index (H′) value among three varieties of Camellia sinensis(L.) O. Kuntze were significantly higher than wild relatives (P< 0.05). The intraspecific arginine (Arg) and glutamine (Gln) contents in C. sinensis var.assamicawere significantly lower than sinensisand pubilimbavarieties. Moreover, the importance of interdependencies operating across FAAs and chlorophyll levels were highlighted via the cell ultrastructure, metabolomics, and transcriptome analysis. We then determined that the association between phytochrome interacting factor 1 (CsPIF1) identified by weighted gene co-expression network analysis (WGCNA) and Thea content. Intriguingly, transient knock-down CsPIF1expression increased Thea content in tea plant, and the function verification of CsPIF1in Arabidopsisalso indicated that CsPIF1acts as a negative regulator of Thea content by mainly effecting the genes expression related to Thea biosynthesis, transport, and hydrolysis, especially glutamate synthase (CsGOGAT), which was validated to be associated with Thea content with a nonsynonymous SNP by Kompetitive Allele-Specific PCR (KASP). We also investigated the interspecific and geographical distribution of this SNP. Taken together, these results help us to understand and clarify the variation and profile of major FAAs in tea germplasms and promote efficient utilization in tea genetic improvement and breeding.

ABSTRACTThe interaction between adherent-invasive Escherichia coli(AIEC) and intestinal macrophages is implicated in the pathogenesis of Crohn’s disease (CD). However, its role in intestinal fibrogenesis and the underlying molecular mechanisms are poorly understood. In addition, miRNAs such as let-7b may participate in AIEC-macrophage interactions. In this study, we identified that the colonization of AIEC in the ileum was associated with enhanced intestinal fibrosis and reduced let-7b expression by enrolling a prospective cohort of CD patients undergoing ileocolectomy. Besides, AIEC-infected IL-10−/−mice presented more severe intestinal fibrosis and could be improved by exogenous let-7b. Mechanistically, intestinal macrophages were found to be the main target of let-7b. Transferring let-7b-overexpressing macrophages to AIEC-infected IL-10−/−mice significantly alleviated intestinal fibrosis. In vitro, AIEC suppressed exosomal let-7b derived from intestinal epithelial cells (IECs), instead of the direct inhibition of let-7b in macrophages, to promote macrophages to a fibrotic phenotype. Finally, TGFβR1 was identified as one target of let-7b that regulates macrophage polarization. Overall, the results of our work indicate that AIEC is associated with enhanced intestinal fibrosis in CD. AIEC could inhibit exosomal let-7b from IECs to promote intestinal macrophages to a fibrotic phenotype and then contributed to fibrogenesis. Thus, anti-AIEC or let-7b therapy may serve as novel therapeutic approaches to ameliorate intestinal fibrosis.

ABSTRACTPolyunsaturated fatty acids (PUFAs) have been shown to exacerbate Crohn’s disease (CD) by promoting lipid peroxidation (LPO) of intestinal epithelial cells (IECs). Dysbiosis of the gut microbiota may play a crucial role in this process. CD patients often exhibit an increased abundance of Escherichia coli(E. coli) in the gut, and the colonization of adherent-invasive E. coli(AIEC) is implicated in the initiation of intestinal inflammation in CD. However, the impact of AIEC on LPO remains unclear. In this study, we observed that AIEC colonization in the terminal ileum of CD patients was associated with decreased levels of glutathione peroxidase 4 (GPX4) and ferritin heavy chain (FTH) in the intestinal epithelium, along with elevated levels of 4-Hydroxynonenal (4-HNE). In vitroexperiments demonstrated that AIEC infection reduced the levels of GPX4 and FTH, increased LPO, and induced ferroptosis in IECs. Furthermore, arachidonic acid (AA) and docosahexaenoic acid (DHA) supplementation in AIEC-infected IECs significantly aggravated LPO and ferroptosis. However, overexpression of GPX4 rescued AIEC-induced LPO and ferroptosis in IECs. Our results further confirmed that AIEC with AA supplementation, associated with excessive LPO and cell death in IECs, worsened colitis in the DSS mouse model and induced enteritis in the antibiotic cocktail pre-treatment mouse model in vivo. Moreover, treatment with ferrostatin-1, a ferroptosis inhibitor, alleviated AIEC with AA supplementation-induced enteritis in mice, accompanied by reduced LPO and cell death in IECs. Our findings suggest that AIEC, in combination with PUFA supplementation, can induce and exacerbate intestinal inflammation, primarily through increased LPO and ferroptosis in IECs.

Background: Seed oil content is an important agronomic trait of Brassica napus(B. napus), and metabolites are considered as the bridge between genotype and phenotype for physical traits. Results: Using a widely targeted metabolomics analysis in a natural population of 388 B. napusinbred lines, we quantify 2172 metabolites in mature seeds by liquid chromatography mass spectrometry, in which 131 marker metabolites are identified to be correlated with seed oil content. These metabolites are then selected for further metabolite genome-wide association study and metabolite transcriptome-wide association study. Combined with weighted correlation network analysis, we construct a triple relationship network, which includes 21,000 edges and 4384 nodes among metabolites, metabolite quantitative trait loci, genes, and co-expression modules. We validate the function of BnaA03.TT4, BnaC02.TT4, and BnaC05.UK, three candidate genes predicted by multi-omics analysis, which show significant impacts on seed oil content through regulating flavonoid metabolism in B. napus. Conclusions: This study demonstrates the advantage of utilizing marker metabolites integrated with multi-omics analysis to dissect the genetic basis of agronomic traits in crops.

Naturally, resistant crop germplasms are important resources for managing the issues of agricultural product safety and environment deterioration. We found a spontaneous mutant of ‘Newhall’ navel orange (Citrus sinensisOsbeck) (MT) with broad-spectrum protections against fungal pathogens in the orchard, postharvest-storage, and artificial inoculation conditions. To understand the defense mechanism of MT fruit, we constructed a genome-scale metabolic network that integrated metabolome and transcriptome datasets. The coordinated transcriptomic and metabolic data were enriched in two sub-networks, showing the decrease in very long chain fatty acid (by 41.53%) and cuticular wax synthesis (by 81.34%), and increase in the synthesis of jasmonic acid (JA) (by 95.23%) and JA-induced metabolites such as 5-dimethylnobietin (by 28.37%) in MT. Furthermore, cytological and biochemical analyses confirmed that the response to fungal infection in MT was independent of wax deficiency and was correlated with the levels of jasmonates, and the expression of plant defensin gene PDF1.2. Results of exogenous application of MeJA and JA inhibitors such as propyl gallate proved that JA-mediated defense contributes to the strong tolerance against pathogens in MT. Our results indicated that jasmonate biosynthesis and signaling are stimulated by the fatty acid redirection of MT, and participate in the tolerance of pathogenic fungi. Elevated hormone signaling underpins fungal protection in a naturally occurring variety of orange found in China. Yunjiang Cheng from Huazhong Agricultural 
University in Wuhan, China, and coworkers analyzed all the genes expressed and metabolites produced by a mutant variety of ‘Newhall’ navel orange (Citrus sinensisOsbeck). The researchers found that, compared to wild-type oranges, the fungus-resistant mutant showed a decrease in both fatty acid synthesis and surface wax production, as well as an increase in synthesis of jasmonic acid, a plant hormone involved in anti-microbial defenses. The mutant seems to redirect production of fatty acids to make more jasmonic acid—and it’s this hormone that mediates the plant’s strong tolerance to fungal pathogens. This information could help agronomists breed other varieties of pest-resistant oranges that require less chemical fungicide under field and storage conditions.

Conducting supporters of purified single-walled carbon nanotubes (SWNTs) and graphene oxide (GO) were used to confine pomegranate-structured SnO2nanospheres for forming SnO2-GO-SWNT composites. As anode material for lithium ion batteries (LIBs), this composite exhibits a stable and large reversible capacity together with an excellent rate capability. In addition, an analysis of the AC impedance spectroscopy has been used to confirm the enhanced mechanism for LIB performance. The improved electrochemical performance should be ascribed greatly to the reinforced synergistic effects between GO and SWNT networks, and their enhanced contribution of the conductivity. These results indicate that this composite has potential for utilization in high-rate and durable LIBs.

ABSTRACTMacroautophagy/autophagy is a conserved mechanism responsible for the degradation of unnecessary or dysfunctional components and recycling of the nutrients they contain in order to promote cellular or organismal longevity. In plants photosynthesis is massively impaired under extended darkness stress and the transition to heterotrophic metabolism results in carbon and nitrogen starvation which induces metabolic and autophagic shifts to recycle nutrients for plant survival. The majority of research concerning dark-induced senescence focuses on single genes or pathways, and the global characterization of primary and lipid metabolites and autophagy remains limited. To address these aspects we recently developed a time-resolved genome-wide association-based approach to analyze these shifts following 0 d, 3 d and 6 d of darkness. Six patterns of metabolic shifts and 215 associations with enzymes, transcriptional regulators and autophagy genes (such as AT2G31260/ATG9, AT4G16520/ATG8F, AT5G45900/ATG7and AT2G05630/ATG8D) were identified. Furthermore detailed characterization of candidate genes further demonstrated that the metabolic and autophagic shifts in response to dark-induced senescence is under tightly coordinated genetic regulation.

Nano-crystalline FeOOH particles (5∼10 nm) have been uniformly mixed with electric matrix of single-walled carbon nanotubes (SWNTs) for forming FeOOH/SWNT composite via a facile ultrasonication method. Directly using the FeOOH/SWNT composite (containing 15 wt% SWNTs) as anode material for lithium battery enhances kinetics of the Li+insertion/extraction processes, thereby effectively improving reversible capacity and cycle performance, which delivers a high reversible capacity of 758 mAh·g−1under a current density of 400 mA·g−1even after 180 cycles, being comparable with previous reports in terms of electrochemical performance for FeOOH anode. The good electrochemical performance should be ascribed to the small particle size and nano-crystalline of FeOOH, as well as the good electronic conductivity of SWNT matrix.

A diverse collection of 359 advanced maize (Zea maysL.) inbred lines from the International Maize and Wheat Improvement Center (CIMMYT) and International Institute for Tropical Agriculture (IITA) breeding programs for drought, low N, soil acidity (SA), and pest and disease resistance was genotyped using 1260 single nucleotide polymorphism (SNP) markers. Model‐based population partition, neighbor‐joining (NJ) clustering, and principal component analysis (PCA) based on the genotypic data were employed to classify the lines into subgroups. A subgroup largely consisting of lines developed from La Posta Sequía (LPS) consistently separated from other lines when using different methods based on both SNP and SNP haplotype data. Lines related by pedigree tended to cluster together. Nine main subsets of lines were determined based on pedigree information, environmental adaptation, and breeding scheme. Analysis of molecular variance (AMOVA) revealed that variation within these subsets was much higher than that among subsets. Genetic diversity and linkage disequilibrium (LD) level were tested in the whole panel and within each subset. The potential of the panel for association mapping was tested using 999 SNP markers with minor allelic frequency (MAF) ≥ 0.05 and phenotypic data (grain yield [GY], ears per plant [EPP], and anthesis to silking interval [ASI]). Results show the panel is ideal for association mapping where type I error can be controlled using a mixed linear model (Q+ K). Use of pedigree, heterotic group, and ecological adaptation information together with molecular characterization of this panel presents a valuable genetic resource for stress tolerance breeding in maize.

Both cuticle and membrane lipids play essential roles in quality maintenance and disease resistance in fresh fruits. Many reports have indicated the modification of alternative branch pathways in epicuticular wax mutants; however, the specific alterations concerning lipids have not been clarified thus far. Here, we conducted a comprehensive, time-resolved lipidomic, and transcriptomic analysis on the “Newhall” navel orange (WT) and its glossy mutant (MT) “Gannan No. 1”. The results revealed severely suppressed wax formation accompanied by significantly elevated production of 36-carbon plastid lipids with increasing fruit maturation in MT. Transcriptomics analysis further identified a series of key functional enzymes and transcription factors putatively involved in the biosynthesis pathways of wax and membrane lipids. Moreover, the high accumulation of jasmonic acid (JA) in MT was possibly due to the need to maintain plastid lipid homeostasis, as the expression levels of two significantly upregulated lipases (CsDAD1 and CsDALL2) were positively correlated with plastid lipids and characterized to hydrolyze plastid lipids to increase the JA content. Our results will provide new insights into the molecular mechanisms underlying the natural variation of plant lipids to lay a foundation for the quality improvement of citrus fruit.

A new method was presented for calculating extinction cross-section of electromagnetic wave by the core-shell spherical granule. An equivalent method was used to calculate the equivalent permittivity of the core-shell spherical granule. A concentric core-shell spherical granule can be replaced by a solid granule possessing the same radius with the original coating shell, and the equivalent permittivity is equal to that of the product of equivalent coefficient and the kernel permittivity. Based on the electromagnetic wave theory and the equivalent method, the scattering and absorption characteristics of the electromagnetic wave by a core-shell spherical particle were analyzed under the condition that wavelength was far greater than the particle diameter. The influence of geometrical and dielectric parameters on the scattering and absorption of microwave was discussed numerically in detail.