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The photosynthetic system of maize (Zea mays) leaves is sensitive to low temperatures and suffers from irreversible damage induced by cold exposure, making cold stress a major factor limiting maize yield. Identifying genes that improve the recovery of photosynthesis from low temperatures in maize will help enhance the cold tolerance of this crop and ensure stable yields. Here, we demonstrate the role of starch phosphorylase 2 (ZmPHOH) in promoting photosynthetic recovery from cold damage. Chlorotic leaf3 (chl3), a null mutant of ZmPHOH, which undergoes chlorophyll degradation and chlorosis earlier than under normal growth conditions after brief exposure to 8 °C and restoration to normal. We determined that chl3 plants could not repair the damage to their photosynthetic system caused by short-term cold exposure after the temperature returned to normal. Metabolome and transcriptome profiling indicated that the soluble sugar content in chl3 leaves was significantly increased after cold treatment and could not be catabolized promptly, leading to repression of photosynthetic gene expression. Our results reveal that ZmPHOH enhances post-cold photosynthetic recovery by promoting the decomposition and metabolism of soluble sugars, thereby regulating the low-temperature resilience in maize, which provides new insights into the chilling tolerance mechanism of maize. [ABSTRACT FROM AUTHOR]

Background: Hepatitis-E virus (HEV)-induced liver failure during pregnancy leads to maternal and fetal complications. This study investigates the HEV-associated metabolomic and immunological changes to elucidate the worsening of obstetric outcomes in patients with acute liver failure (ALF) due to HEV. Methods: Pregnant women with (i) acute viral hepatitis, IgM HEV positive (AVH-E, n = 31, Gr.I), (ii) acute liver failure (ALF-E, n = 15, Gr.II), (iii) acute hepatitis but negative for viral infections (non-HEV, n = 30, Gr.III), and healthy (HC, n = 21, Gr.IV) were evaluated at delivery for plasma untargeted metabolomics, cytokine, and immune profiling. Results: AVH-E and ALF-E (Gr.I, II) showed elevated TNF-α, IL-1β, IL-9, IL-22, and IL-33 compared to HC. In addition, in ALF-E, IFN-γ and IL-12p70 were decreased, but MIP-1α, fractalkine, SDF-1α, IL-22, and IL-33 were increased compared to AVH-E. Both AVH-E and ALF-E had decreased choline, sn-glycero-3-phosphocholine, O -palmitoyl- r -carnitine, and increased taurocholic acid. However, patients with ALF-E had a 2–5-fold decline in these metabolites with raised taurochenodeoxycholic acid. ALF-E showed increased naive T/B cells, decreased CD4, CD8 Tcm, Tem, and plasmablasts, compared to AVH-E contributing to higher failed inductions, preterm births, maternal complications like eclampsia, disseminated intravascular coagulation, preterm premature rupture of membranes, small-for-gestational-age infants, higher rates of intrauterine death, abortion, and mortality. Conclusions: HEV infection reduces choline, phosphocholine, and palmitoyl carnitine, enhancing inflammation in ALF-E, while increasing taurocholic and taurochenodeoxycholic acids impairs the immune response. These factors together likely contribute to severe obstetric complications, including higher failed inductions, intrauterine death, and maternal and fetal mortality in ALF-E. [ABSTRACT FROM AUTHOR]

Salt stress severely inhibits crop growth and production. The native turfgrass species Carex rigescens in northern China, exhibits extraordinary tolerance to multiple abiotic stresses. However, little is known about its specific metabolites and pathways under salt stress. To explore the molecular metabolic mechanisms under salt stress, we conducted metabolome analysis combined with transcriptome analysis of two varieties of Carex rigescens with differing salt tolerances: salt-sensitive Lvping NO.1 and salt-tolerant Lvping NO.2. After 5 days of salt treatment, 114 and 131 differentially abundant metabolites (DAMs) were found in Lvping NO.1 and Lvping NO.2, respectively. Among them, six amino acids involved in the amino acid biosynthesis pathway, namely, valine, phenylalanine, isoleucine, tryptophan, threonine, and serine, were accumulated after treatment. Furthermore, most DAMs related to phenylalanine biosynthesis, metabolism, and phenylpropanoid biosynthesis increased under salt stress in both varieties. The expression profiles of metabolism-associated genes were consistent with the metabolic profiles. However, genes including HCT, β-glucosidases, and F5H, and metabolite 4-hydroxycinnamic acid, of the two varieties may account for the differences in salt tolerance. Our study provides new insights into the mechanisms underlying salt tolerance in Carex rigescens and reveals potential metabolites and genes to improve crop resilience to saline environments. [ABSTRACT FROM AUTHOR]

Salt stress severely inhibits crop growth and production. The native turfgrass species Carex rigescens in northern China, exhibits extraordinary tolerance to multiple abiotic stresses. However, little is known about its specific metabolites and pathways under salt stress. To explore the molecular metabolic mechanisms under salt stress, we conducted metabolome analysis combined with transcriptome analysis of two varieties of Carex rigescens with differing salt tolerances: salt-sensitive Lvping NO.1 and salt-tolerant Lvping NO.2. After 5 days of salt treatment, 114 and 131 differentially abundant metabolites (DAMs) were found in Lvping NO.1 and Lvping NO.2, respectively. Among them, six amino acids involved in the amino acid biosynthesis pathway, namely, valine, phenylalanine, isoleucine, tryptophan, threonine, and serine, were accumulated after treatment. Furthermore, most DAMs related to phenylalanine biosynthesis, metabolism, and phenylpropanoid biosynthesis increased under salt stress in both varieties. The expression profiles of metabolism-associated genes were consistent with the metabolic profiles. However, genes including HCT, β-glucosidases, and F5H, and metabolite 4-hydroxycinnamic acid, of the two varieties may account for the differences in salt tolerance. Our study provides new insights into the mechanisms underlying salt tolerance in Carex rigescens and reveals potential metabolites and genes to improve crop resilience to saline environments.

Marrubium species have been used since ancient times as food additives and curative treatments. Their phytochemical composition and various pharmacological activities were the focus of a number of scientific investigations but no comprehensive metabolome profiling to identify the numerous primary and secondary metabolites has been performed so far. This study aimed to generate a comprehensive picture of the total metabolite content of two Marrubium species—M. peregrinum and M. friwaldskyanum—to provide detailed information about the main primary and secondary metabolites. In addition, the elemental composition was also evaluated. For this purpose, non-targeted metabolomic analyses were conducted using GC-MS, UPLC-MS/MS and ICP-MS approaches. Nearly 500 compounds and 12 elements were detected and described. The results showed a strong presence of phenolic acids, flavonoids and their glucosides, which are generally of great interest due to their various pharmacological activities. Furthermore, tissue-specific analyses for M. friwaldskyanum stem, leaves and flowers were carried out in order to outline the sources of potentially important bioactive molecules. The results generated from this study depict the Marrubium metabolome and reveal its dual scientific importance—from one side, providing information about the metabolites that is fundamental and vital for the survival of these species, and from the other side, defining the large diversity of secondary substances that are a potential source of phytotherapeutic agents. [ABSTRACT FROM AUTHOR]

The deletion of orphan response regulator CovR reduces the growth rate of Streptococcus suis serotype 2 (S. suis 2). In this study, metabolome and transcriptome profiling were performed to study the mechanisms underlying the poor growth of S. suis 2 caused by the deletion of orphan response regulator CovR. By comparing S. suis 2 (ΔcovR) and S. suis 2 (SC19), 146 differentially accumulated metabolites (upregulated: 83 and downregulated: 63) and 141 differentially expressed genes (upregulated: 86 and downregulated: 55) were identified. Metabolome and functional annotation analysis revealed that the growth of ΔcovR was inhibited by the imbalance aminoacyl tRNA biosynthesis (the low contents of L-lysine, L-aspartic acid, L-glutamine, and L-glutamic acid, and the high content of L-methionine). These results provide a new insight into the underlying poor growth of S. suis 2 caused by the deletion of orphan response regulator CovR. Metabolites and candidate genes regulated by the orphan response regulator CovR and involved in the growth of S. suis 2 were reported in this study.

Our previous study has demonstrated that the nuclear-origin supplementation of the PSII core subunit D1 protein stimulates growth and increases grain yields in transgenic rice plants by enhancing photosynthetic efficiency. In this study, the underlying mechanisms have been explored regarding how the enhanced photosynthetic capacity affects metabolic activities in the transgenic plants of rice harboring the integrated transgene RbcSPTP-OspsbA cDNA, cloned from rice, under control of the AtHsfA2 promoter and N-terminal fused with the plastid-transit peptide sequence (PTP) cloned from the AtRbcS. Here, a comparative metabolomic analysis was performed using LC-MS in flag leaves of the transgenic rice plants during the grain-filling stage. Critically, the dramatic reduction in the quantities of nucleotides and certain free amino acids was detected, suggesting that the increased photosynthetic assimilation and grain yield in the transgenic plants correlates with the reduced contents of free nucleotides and the amino acids such as glutamine and glutamic acid, which are cellular nitrogen sources. These results suggest that enhanced photosynthesis needs consuming more free nucleotides and nitrogen sources to support the increase in biomass and yields, as exhibited in transgenic rice plants. Unexpectedly, dramatic changes were measured in the contents of flavonoids in the flag leaves, suggesting that a tight and coordinated relationship exists between increasing photosynthetic assimilation and flavonoid biosynthesis. Consistent with the enhanced photosynthetic efficiency, the substantial increase was measured in the content of starch, which is the primary product of the Calvin–Benson cycle, in the transgenic rice plants under field growth conditions. [ABSTRACT FROM AUTHOR]

The ability to monitor patients plays a major role in the success of kidney transplants. However, transplant monitoring still depends on relatively outdated, inadequate technologies. The aim of this study was to reveal the metabolomic profile of the kidney allograft using the metabolomic screening technique and to identify specific eGFRbased biomarkers to monitor individuals with different levels of post-transplantation graft dysfunction. In the current study, urine samples from 131 unique kidney transplant recipients were collected and analyzed by ultra-high performance liquid chromatography and benchtop QTof mass spectrometer (Xevo G2 XS QTof). Acquired data were first pre-processed by Progenesis QI 2.3 (Nonlinear Dynamics, Waters, UK). Putative annotation was performed against the HMDB database following multivariate statistical analysis. Post-transplant biomarker panels that can distinguish stages of renal dysfunction were created by combining the significant markers and taking their ratios. Overall, 8 metabolites were significantly altered within three groups of kidney transplant recipients:4,5-Dihydroorotic acid, N2-Succinyl-L-glutamic acid 5-semialdehyde, Valyl-Arginine, Pantothenic acid, L-phenylalanyl-L-hydroxyproline, MG(0:0/24:0/0:0), QYNAD and 12-Hydroxy-13-O-D-glucuronoside-octadec-9Z-enoate as biomarker candidates (p<0.05). The ratio of 4,5-Dihydroorotic acid to Pantothenic acid (panel-1) can be used to monitor kidney function. Specifically, these metabolite ratios were found to be more sensitive to changes in kidney function than panel-2, which consisted of 7 metabolites, excluding QYNAD, of the 8 major metabolites. Our results may contribute to the monitoring of kidney transplant patients based on post-transplant eGFR-based kidney function stages, thus providing a method for the early evaluation and monitoring of the kidney transplant recipient after transplantation for kidney transplant patient management. [ABSTRACT FROM AUTHOR]

Red and blue light-emitting diodes (LEDs) affect the quality of sweet potato leaves and their nutritional profile. Vines cultivated under blue LEDs had higher soluble protein contents, total phenolic compounds, flavonoids, and total antioxidant activity. Conversely, chlorophyll, soluble sugar, protein, and vitamin C contents were higher in leaves grown under red LEDs. Red and blue light increased the accumulation of 77 and 18 metabolites, respectively. Alpha-linoleic and linolenic acid metabolism were the most significantly enriched pathways based on Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses. A total of 615 genes were differentially expressed between sweet potato leaves exposed to red and blue LEDs. Among these, 510 differentially expressed genes were upregulated in leaves grown under blue light compared with those grown under red light, while the remaining 105 genes were expressed at higher levels in the latter than in the former. Among the KEGG enrichment pathways, blue light significantly induced anthocyanin and carotenoid biosynthesis structural genes. This study provides a scientific reference basis for using light to alter metabolites to improve the quality of edible sweet potato leaves. [ABSTRACT FROM AUTHOR]

Red and blue light-emitting diodes (LEDs) affect the quality of sweet potato leaves and their nutritional profile. Vines cultivated under blue LEDs had higher soluble protein contents, total phenolic compounds, flavonoids, and total antioxidant activity. Conversely, chlorophyll, soluble sugar, protein, and vitamin C contents were higher in leaves grown under red LEDs. Red and blue light increased the accumulation of 77 and 18 metabolites, respectively. Alpha-linoleic and linolenic acid metabolism were the most significantly enriched pathways based on Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses. A total of 615 genes were differentially expressed between sweet potato leaves exposed to red and blue LEDs. Among these, 510 differentially expressed genes were upregulated in leaves grown under blue light compared with those grown under red light, while the remaining 105 genes were expressed at higher levels in the latter than in the former. Among the KEGG enrichment pathways, blue light significantly induced anthocyanin and carotenoid biosynthesis structural genes. This study provides a scientific reference basis for using light to alter metabolites to improve the quality of edible sweet potato leaves.

Acanthus ilicifolius is an important medicinal plant in mangrove forests, which is rich in secondary metabolites with various biological activities. In this study, we used transcriptomic analysis to obtain differentially expressed genes in the flavonoid metabolic pathway and metabolomic methods to detect changes in the types and content in the flavonoid metabolic synthesis pathway. The results showed that DEGs were identified in the mature roots vs. leaves comparison (9001 up-regulated and 8910 down-regulated), mature roots vs. stems comparison (5861 up-regulated and 7374 down-regulated), and mature stems vs. leaves comparison (10,837 up-regulated and 11,903 down-regulated). Furthermore, two AiCHS genes and four AiCHI genes were up-regulated in the mature roots vs. stems of mature A. ilicifolius, and were down-regulated in mature stems vs. leaves, which were highly expressed in the A. ilicifolius stems. A total of 215 differential metabolites were found in the roots vs. leaves of mature A. ilicifolius, 173 differential metabolites in the roots vs. stems, and 228 differential metabolites in the stems vs. leaves. The metabolomic results showed that some flavonoids in A. ilicifolius stems were higher than in the roots. A total of 18 flavonoid differential metabolites were detected in the roots, stems, and leaves of mature A. ilicifolius. In mature leaves, quercetin-3-O-glucoside-7-O-rhamnoside, gossypitrin, isoquercitrin, quercetin 3,7-bis-O-β-D-glucoside, and isorhamnetin 3-O-β-(2″-O-acetyl-β-D-glucuronide) were found in a high content, while in mature roots, di-O-methylquercetin and isorhamnetin were the major compounds. The combined analysis of the metabolome and transcriptome revealed that DEGs and differential metabolites were related to flavonoid biosynthesis. This study provides a theoretical basis for analyzing the molecular mechanism of flavonoid synthesis in A. ilicifolius and provides a reference for further research and exploitation of its medicinal value. [ABSTRACT FROM AUTHOR]

Escherichia coli and Staphylococcus aureus are globally among the most prominent bacterial strains associated with antibacterial resistance-caused deaths. Naturally occurring polyphenols, such as hydrolyzable tannins, have been shown to potently inhibit E. coli and S. aureus. The current study investigated the metabolome changes of E. coli and S. aureus cultures after treatments with different hydrolyzable tannins using an NMR metabolomics approach. Additionally, the effect of these tannin treatments influencing a more complex bacterial system was studied in a biomimetic setting with fecal samples inoculated into the growth medium. Metabolite concentration changes were observed in all three scenarios: E. coli, S. aureus, and fecal batch culture. The metabolome of E. coli was more altered by the tannin treatments than S. aureus when compared to control cultures. A dimeric hydrolyzable tannin, rugosin D, was found to be the most effective of the studied compounds in influencing bacterial metabolome changes and in inhibiting E. coli and S. aureus growth. It was also observed that the tannin structure should have both hydrophobic and hydrophilic regions to efficiently influence E. coli and S. aureus growth. [ABSTRACT FROM AUTHOR]

Introduction: Colored-leaf plants are increasingly popular for their aesthetic, ecological, and social value, which are important materials for research on the regulation of plant pigments. However, anthocyanin components and the molecular mechanisms of anthocyanin biosynthesis in colored-leaf poplar remain unclear. Consequently, an integrative analysis of transcriptome and metabolome is performed to identify the key metabolic pathways and key genes, which could contribute to themolecularmechanism of anthocyanin biosynthesis in the coloredleaf cultivars poplar. Methods: In this study, integrated metabolite and transcriptome analysis was performed to explore the anthocyanin composition and the specific regulatory network of anthocyanin biosynthesis in the purple leaves of the cultivars ‘Quanhong’ (QHP) and ‘Zhongshanyuan’ (ZSY). Correlation analysis between RNAseq data and metabolite profiles were also performed to explore the candidate genes associated with anthocyanin biosynthesis. R2R3-MYB and bHLH TFs with differential expression levels were used to perform a correlation analysis with differentially accumulated anthocyanins. Results and discussion: A total of 39 anthocyanin compounds were detected by LC-MS/MS analysis. Twelve cyanidins, seven pelargonidins, five delphinidins, and five procyanidins were identified as the major anthocyanin compounds, which were differentially accumulated in purple leaves of QHP and ZSY. The major genes associated with anthocyanin biosynthesis, including structural genes and transcription factors, were differentially expressed in purple leaves of QHP and ZSY through RNA-sequencing (RNA-seq) data analysis, which was consistent with quantitative real-time PCR analysis results. Correlation analysis between RNA-seq data and metabolite profiles showed that the expression patterns of certain differentially expressed genes in the anthocyanin biosynthesis pathway were strongly correlated with the differential accumulation of anthocyanins. One R2R3- MYB subfamily member in the SG5 subgroup, Podel.04G021100, showed a similar expression pattern to some structural genes. This gene was strongly correlated with 16 anthocyanin compounds, indicating that Podel.04G021100 might be involved in the regulation of anthocyanin biosynthesis. These results contribute to a systematic and comprehensive understanding of anthocyanin accumulation and to the molecular mechanisms of anthocyanin biosynthesis in QHP and ZSY. [ABSTRACT FROM AUTHOR]

Physalis peruviana is an edible fruit becoming of increasing economic interest for its nutritional and beneficial health effects that even several countries targeted its cultivation recently to fulfill export demands taking the advantage of its adaptable nature to different soil types. Despite previous reports on its chemical content, little or no studies used metabolomics to reveal its chemical reservoir. Herein, the first comprehensive metabolome profiling of P. peruviana fruits via HR-UPLC/MS in both ionization modes that enabled detection of 71 metabolites including first-time reported compounds belonging to flavonoids, coumarins and withanolides. Additionally, 43 lipoidal compounds were identified via GC/MS and quantification of fat-/water-soluble vitamins was performed via HPLC. New evidence on its crude extract antiarthritic activity is presented as well for the first time using bovine serum albumin as it significantly inhibited protein denaturation at 500µg/ml and 1000µg/ml by 86.5± 0.422 % and 99.49 ± 0.426 %, respectively compared to 78.72 ± 1.23% and 97.80 ± 0.393 % for the standard drug acetyl salicylic acid at the same concentration, respectively, with comparable IC 50 values of 246.35 µg/ml and 229.69 µg/ml for the extract and standard drug, respectively; supporting its folk use in treatment of arthritis. [Display omitted] • First metabolome profiling of Physalis peruviana fruit primary and secondary metabolites. • 71 metabolites were detected via HR-UPLC/MS including several first reported compounds that belong to flavonoids, withanolides and coumarins. • Total ethanol fruit extract possesses significant antarthritic activity via inhibition of protein denaturation supporting its folk use in treatment of arthritis. [ABSTRACT FROM AUTHOR]

Lecanicillium gracile is a recently described micromycete species isolated from mineral-based building materials (plaster and limestone) in interiors of cultural heritage sites in Russia. In this work, the composition of L. gracile metabolites, as well as of the culture liquid, have been characterized. The results suggest that L. gracile is a promising candidate for the search for novel biologically active compounds. During the exponential growth phase, the diversity of metabolites in the mycelium was low; the metabolome profile demonstrated predominant accumulation of monosaccharides and polyols. In the stationary phase, the metabolite diversity in the L. gracile mycelium was high; apparently, at this stage biosynthesis dominated over energy-producing processes. L. gracile synthesized extracellular polymer compounds and shifted medium рН to the alkaline range. When fungi are developing on rock substrates, their extracellular polymer matrix not only serves to facilitate the formation of biofilms with other microorganisms of lithobiont communities, but also, at alkaline pH values, it promotes the formation of secondary calcite on calcium-containing substrates, such as limestone and marble. That is, L. gracile possesses certain biochemical traits that facilitate its long-term growth on rock substrates and reflect the specific character of interactions between the fungus and the substrate materials. [ABSTRACT FROM AUTHOR]

Simple Summary: Low-molecular-weight substances are participants in all biochemical processes occurring in the body. Therefore, by measuring them we can obtain new knowledge about aging mechanisms. At the same time, various animals, which are distinguished by different life expectancies, are excellent objects for such studies, and modern science, known as metabolomics, offers efficient methods to measure them, taking into account their huge diversity. This review describes the aging data accumulated today, obtained by such methods in various animal models and humans. Organism aging is closely related to systemic metabolic changes. However, due to the multilevel and network nature of metabolic pathways, it is difficult to understand these connections. Today, scientists are trying to solve this problem using one of the main approaches of metabolomics—untargeted metabolome profiling. The purpose of this publication is to review metabolomic studies based on such profiling, both in animal models and in humans. This review describes metabolites that vary significantly across age groups and include carbohydrates, amino acids, carnitines, biogenic amines, and lipids. Metabolic pathways associated with the aging process are also shown, including those associated with amino acid, lipid, and energy metabolism. The presented data reveal the mechanisms of aging and can be used as a basis for monitoring biological age and predicting age-related diseases in the early stages of their development. [ABSTRACT FROM AUTHOR]

Soft corals are recognized as an abundant source of diverse secondary metabolites with unique chemical features and physiologic capabilities. However, the discovery of these metabolites is usually hindered by the traditional protocol which requires a large quantity of living tissue for isolation and spectroscopic investigations. In order to overcome this problem, untargeted metabolomics protocols have been developed. The latter have been applied here to study the chemodiversity of common Egyptian soft coral species, using only minute amounts of coral biomass. Spectral similarity networks, based on high-resolution tandem mass spectrometry data, were employed to explore and highlight the metabolic biodiversity of nine Egyptian soft coral species. Species-specific metabolites were highlighted for future prioritization of soft coral species for MS-guided chemical investigation. Overall, 79 metabolites were tentatively assigned, encompassing diterpenes, sesquiterpenes, and sterols. Simultaneously, the methodology assisted in shedding light on newly-overlooked chemical diversity with potential undescribed scaffolds. For instance, glycosylated fatty acids, nitrogenated aromatic compounds, and polyketides were proposed in Sinularia leptoclados, while alkaloidal terpenes and N-acyl amino acids were proposed in both Sarcophyton roseum and Sarcophyton acutum. [ABSTRACT FROM AUTHOR]

Abstract Background Sesame (Sesamum indicum L.) leaves, flowers, especially seeds are used in traditional medicine to prevent or cure various diseases. Its seed’s market is expanding. However, the other tissues are still underexploited due to the lack of information related to metabolites distribution and variability in the plant. Herein, the metabolite profiles of five sesame tissues (leaves, fresh seeds, white and purple flowers, and fresh carpels) have been investigated using ultra-high-performance liquid chromatography-mass spectrometry (UPLC-MS/MS)-based widely targeted metabolomics analysis platform. Results In total, 776 metabolites belonging to diverse classes were qualitatively and quantitatively identified. The different tissues exhibited obvious differences in metabolites composition. The majority of flavonoids predominantly accumulated in flowers. Amino acids and derivatives, and lipids were identified predominantly in fresh seeds followed by flowers. Many metabolites, including quinones, coumarins, tannins, vitamins, terpenoids and some bioactive phenolic acids (acteoside, isoacteoside, verbascoside, plantamajoside, etc.) accumulated mostly in leaves. Lignans were principally detected in seeds. 238 key significantly differential metabolites were filtered out. KEGG annotation and enrichment analyses of the differential metabolites revealed that flavonoid biosynthesis, amino acids biosynthesis, and phenylpropanoid biosynthesis were the main differently regulated pathways. In addition to the tissue-specific accumulation of metabolites, we noticed a cooperative relationship between leaves, fresh carpels, and developing seeds in terms of metabolites transfer. Delphinidin-3-O-(6ʺ-O-p-coumaroyl)glucoside and most of the flavonols were up-regulated in the purple flowers indicating they might be responsible for the purple coloration. Conclusion This study revealed that the metabolic processes in the sesame tissues are differently regulated. It offers valuable resources for investigating gene-metabolites interactions in sesame tissues and examining metabolic transports during seed development in sesame. Furthermore, our findings provide crucial knowledge that will facilitate sesame biomass valorization.

Our previous study has demonstrated that the nuclear-origin supplementation of the PSII core subunit D1 protein stimulates growth and increases grain yields in transgenic rice plants by enhancing photosynthetic efficiency. In this study, the underlying mechanisms have been explored regarding how the enhanced photosynthetic capacity affects metabolic activities in the transgenic plants of rice harboring the integrated transgene RbcSPTP-OspsbA cDNA, cloned from rice, under control of the AtHsfA2 promoter and N-terminal fused with the plastid-transit peptide sequence (PTP) cloned from the AtRbcS. Here, a comparative metabolomic analysis was performed using LC-MS in flag leaves of the transgenic rice plants during the grain-filling stage. Critically, the dramatic reduction in the quantities of nucleotides and certain free amino acids was detected, suggesting that the increased photosynthetic assimilation and grain yield in the transgenic plants correlates with the reduced contents of free nucleotides and the amino acids such as glutamine and glutamic acid, which are cellular nitrogen sources. These results suggest that enhanced photosynthesis needs consuming more free nucleotides and nitrogen sources to support the increase in biomass and yields, as exhibited in transgenic rice plants. Unexpectedly, dramatic changes were measured in the contents of flavonoids in the flag leaves, suggesting that a tight and coordinated relationship exists between increasing photosynthetic assimilation and flavonoid biosynthesis. Consistent with the enhanced photosynthetic efficiency, the substantial increase was measured in the content of starch, which is the primary product of the Calvin–Benson cycle, in the transgenic rice plants under field growth conditions.

Cultivated peanut (Arachis hypogaea L.) is an important source of edible oil and protein. Peanut testa (seed coat) provides protection for seeds and serves as a carrier for diversity metabolites necessary for human health. There is significant diversity available for testa color in peanut germplasms. However, the kinds and type of metabolites in peanut testa has not been comprehensively investigated. In this study, we performed metabolite profiling using UPLC-MS/MS for four peanut germplasm lines with different testa colors, including pink, purple, red, and white. A total of 85 metabolites were identified in four peanuts. Comparative metabolomics analysis identified 78 differentially accumulated metabolites (DAMs). Some metabolites showed significant correlation with other metabolites. For instance, proanthocyanidins were positively correlated with cyanidin 3-O-rutinoside and malvin, and negatively correlated with pelargonidin-3-glucoside. We observed that the total proanthocyanidins are most abundant in pink peanut variety WH10. The red testa accumulated more isoflavones, flavonols and anthocyanidins compared with that in pink testa. These results provided valuable information about differential accumulation of metabolites in testa with different color, which are helpful for further investigation of the molecular mechanism underlying biosynthesis and accumulation of these metabolites in peanut. [ABSTRACT FROM AUTHOR]

A comprehensive analysis of crucial metabolites in seabuckthorn (Hippophae rhamnoides L.) was conducted by analyzing the methanolic extract of berries originating from 37 geographical sites of the Indian Himalayas by using 1H NMR-based metabolome profiling. The concentration of 103 metabolites was annotated, of which two, spermidine and beta-alanine, were reported for the first time in higher concentrations in berries collected from Himachal Pradesh and Jammu and Kashmir. The quantified peak intensity matched with standard compounds present in the different databases, including Madison-Qingdao Metabolomics Consortium Database (MMCD), Human Metabolome Database (HMDB), and Spectral Database of Organic Compounds (SBDS). Multivariate data analysis was performed, and a heat map was generated, which provided direct visualization of the prevailing metabolomic diversity allowing the identification of metabolomic discriminators of seabuckthorn berries representing different geographical regions. The overall results indicated higher expression of metabolites in the Jammu and Kashmir region, excluding some metabolites such as spermidine and beta-alanine, which showed a higher expression in Himachal Pradesh. The metabolomic information generated from seabuckthorn berries originating from different regions provides a valuable resource, which food industrialists could exploit to identify metabolites related to the assessment of food safety and quality of different food products, nutraceuticals, pharmaceuticals, and cosmeceuticals. Furthermore, our findings demonstrate that 1H NMR-based metabolomics is a promising approach for comprehensive metabolome profiling, source discrimination, and quality assessment in plant species. [ABSTRACT FROM AUTHOR]

Escherichia coli and Staphylococcus aureus are globally among the most prominent bacterial strains associated with antibacterial resistance-caused deaths. Naturally occurring polyphenols, such as hydrolyzable tannins, have been shown to potently inhibit E. coli and S. aureus. The current study investigated the metabolome changes of E. coli and S. aureus cultures after treatments with different hydrolyzable tannins using an NMR metabolomics approach. Additionally, the effect of these tannin treatments influencing a more complex bacterial system was studied in a biomimetic setting with fecal samples inoculated into the growth medium. Metabolite concentration changes were observed in all three scenarios: E. coli, S. aureus, and fecal batch culture. The metabolome of E. coli was more altered by the tannin treatments than S. aureus when compared to control cultures. A dimeric hydrolyzable tannin, rugosin D, was found to be the most effective of the studied compounds in influencing bacterial metabolome changes and in inhibiting E. coli and S. aureus growth. It was also observed that the tannin structure should have both hydrophobic and hydrophilic regions to efficiently influence E. coli and S. aureus growth.

Plasmodiophora brassicae, an obligate biotrophic pathogen-causing clubroot disease, can seriously affect Brassica crops worldwide, especially Chinese cabbage. Understanding the transcriptome and metabolome profiling changes during the infection of P. brassicae will provide key insights in understanding the defense mechanism in Brassica crops. In this study, we estimated the phytohormones using targeted metabolome assays and transcriptomic changes using RNA sequencing (RNA-seq) in the roots of resistant (BrT24) and susceptible (Y510-9) plants at 0, 3, 9, and 20 days after inoculation (DAI) with P. brassicae. Differentially expressed genes (DEGs) in resistant vs. susceptible lines across different time points were identified. The weighted gene co-expression network analysis of the DEGs revealed six pathways including “Plant–pathogen interaction” and “Plant hormone signal transduction” and 15 hub genes including pathogenic type III effector avirulence factor gene (RIN4) and auxin-responsive protein (IAA16) to be involved in plants immune response. Inhibition of Indoleacetic acid, cytokinin, jasmonate acid, and salicylic acid contents and changes in related gene expression in R-line may play important roles in regulation of clubroot resistance (CR). Based on the combined metabolome profiling and hormone-related transcriptomic responses, we propose a general model of hormone-mediated defense mechanism. This study definitely enhances our current understanding and paves the way for improving CR in Brassica rapa.

Plasmodiophora brassicae , an obligate biotrophic pathogen-causing clubroot disease, can seriously affect Brassica crops worldwide, especially Chinese cabbage. Understanding the transcriptome and metabolome profiling changes during the infection of P. brassicae will provide key insights in understanding the defense mechanism in Brassica crops. In this study, we estimated the phytohormones using targeted metabolome assays and transcriptomic changes using RNA sequencing (RNA-seq) in the roots of resistant (BrT24) and susceptible (Y510-9) plants at 0, 3, 9, and 20 days after inoculation (DAI) with P. brassicae. Differentially expressed genes (DEGs) in resistant vs. susceptible lines across different time points were identified. The weighted gene co-expression network analysis of the DEGs revealed six pathways including "Plant–pathogen interaction" and "Plant hormone signal transduction" and 15 hub genes including pathogenic type III effector avirulence factor gene (RIN4) and auxin-responsive protein (IAA16) to be involved in plants immune response. Inhibition of Indoleacetic acid, cytokinin, jasmonate acid, and salicylic acid contents and changes in related gene expression in R-line may play important roles in regulation of clubroot resistance (CR). Based on the combined metabolome profiling and hormone-related transcriptomic responses, we propose a general model of hormone-mediated defense mechanism. This study definitely enhances our current understanding and paves the way for improving CR in Brassica rapa. [ABSTRACT FROM AUTHOR]

Abstract Background The dry root and rhizome of Salvia miltiorrhiza Bunge, or Danshen, is a well-known, traditional Chinese medicine. Tanshinones are active compounds that accumulate in the periderm, resulting in red-colored roots. However, lines with orange roots have been observed in cultivated fields. Here, we performed metabolome and transcriptome analyses to investigate the changes of orange-rooted Danshen. Methods Metabolome analysis was performed by ultra-high-performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UPLC/Q-Tof–MS) to investigate the metabolites variation between orange Danshen and normal Danshen. RNA sequencing and KEGG enrichment analysis were performed to analyzing the differentially expressed genes between orange-rooted and normal Danshen. Results In total, 40 lipophilic components were detected in metabolome analysis, and seven compounds were significantly decreased in the orange Danshen, including the most abundant active compounds, tanshinone IIA and tanshinone I in normal Danshen. Systematic analysis of transcriptome profiles revealed that the down-regulated genes related to catalytic dehydrogenation was not detected. However, two genes related to stress resistance, and four genes related to endoplasmic reticulum (ER)-associated degradation of proteins were up-regulated in orange Danshen. Conclusions Decreases in the content of dehydrogenated furan ring tanshinones such as tanshinone IIA resulted in phenotypic changes and quality degradation of Danshen. Transcriptome analysis indicated that incorrect folding and ER-associated degradation of corresponding enzymes, which could catalyze C15-C16 dehydrogenase, might be contributed to the decrease in dehydrogenated furan ring tanshinones, rather than lower expression of the relative genes. This limited dehydrogenation of cryptotanshinone and dihydrotanshinone I into tanshinones IIA and I products, respectively, led to a reduced quality of Danshen in cultivated fields.

Soft corals are recognized as an abundant source of diverse secondary metabolites with unique chemical features and physiologic capabilities. However, the discovery of these metabolites is usually hindered by the traditional protocol which requires a large quantity of living tissue for isolation and spectroscopic investigations. In order to overcome this problem, untargeted metabolomics protocols have been developed. The latter have been applied here to study the chemodiversity of common Egyptian soft coral species, using only minute amounts of coral biomass. Spectral similarity networks, based on high-resolution tandem mass spectrometry data, were employed to explore and highlight the metabolic biodiversity of nine Egyptian soft coral species. Species-specific metabolites were highlighted for future prioritization of soft coral species for MS-guided chemical investigation. Overall, 79 metabolites were tentatively assigned, encompassing diterpenes, sesquiterpenes, and sterols. Simultaneously, the methodology assisted in shedding light on newly-overlooked chemical diversity with potential undescribed scaffolds. For instance, glycosylated fatty acids, nitrogenated aromatic compounds, and polyketides were proposed in Sinularia leptoclados, while alkaloidal terpenes and N-acyl amino acids were proposed in both Sarcophyton roseum and Sarcophyton acutum.

Background: Sesame (Sesamum indicum L.) leaves, flowers, especially seeds are used in traditional medicine to prevent or cure various diseases. Its seed's market is expanding. However, the other tissues are still underexploited due to the lack of information related to metabolites distribution and variability in the plant. Herein, the metabolite profiles of five sesame tissues (leaves, fresh seeds, white and purple flowers, and fresh carpels) have been investigated using ultra-high-performance liquid chromatography-mass spectrometry (UPLC-MS/MS)-based widely targeted metabolomics analysis platform. Results: In total, 776 metabolites belonging to diverse classes were qualitatively and quantitatively identified. The different tissues exhibited obvious differences in metabolites composition. The majority of flavonoids predominantly accumulated in flowers. Amino acids and derivatives, and lipids were identified predominantly in fresh seeds followed by flowers. Many metabolites, including quinones, coumarins, tannins, vitamins, terpenoids and some bioactive phenolic acids (acteoside, isoacteoside, verbascoside, plantamajoside, etc.) accumulated mostly in leaves. Lignans were principally detected in seeds. 238 key significantly differential metabolites were filtered out. KEGG annotation and enrichment analyses of the differential metabolites revealed that flavonoid biosynthesis, amino acids biosynthesis, and phenylpropanoid biosynthesis were the main differently regulated pathways. In addition to the tissue-specific accumulation of metabolites, we noticed a cooperative relationship between leaves, fresh carpels, and developing seeds in terms of metabolites transfer. Delphinidin-3-O-(6ʺ-O-p-coumaroyl)glucoside and most of the flavonols were up-regulated in the purple flowers indicating they might be responsible for the purple coloration. Conclusion: This study revealed that the metabolic processes in the sesame tissues are differently regulated. It offers valuable resources for investigating gene-metabolites interactions in sesame tissues and examining metabolic transports during seed development in sesame. Furthermore, our findings provide crucial knowledge that will facilitate sesame biomass valorization. [ABSTRACT FROM AUTHOR]

Abstract Background Camelina sativa has attracted much interest as alternative renewable resources for biodiesel, other oil-based industrial products and a source for edible oils. Its unique oil attributes attract research to engineering new varieties of improved oil quantity and quality. The overexpression of enzymes catalyzing the synthesis of the glycerol backbone and the sequential conjugation of fatty acids into this backbone is a promising approach for increasing the levels of triacylglycerol (TAG). In a previous study, we co-expressed the diacylglycerol acyltransferase (DGAT1) and glycerol-3-phosphate dehydrogenase (GPD1), involved in TAG metabolism, in Camelina seeds. Transgenic plants exhibited a higher-percentage seed oil content, a greater seed mass, and overall improved seed and oil yields relative to wild-type plants. To further increase seed oil content in Camelina, we utilized metabolite profiling, in conjunction with transcriptome profiling during seed development to examine potential rate-limiting step(s) in the production of building blocks for TAG biosynthesis. Results Transcriptomic analysis revealed approximately 2518 and 3136 transcripts differentially regulated at significant levels in DGAT1 and GPD1 transgenics, respectively. These transcripts were found to be involved in various functional categories, including alternative metabolic routes in fatty acid synthesis, TAG assembly, and TAG degradation. We quantified the relative contents of over 240 metabolites. Our results indicate major metabolic switches in transgenic seeds associated with significant changes in the levels of glycerolipids, amino acids, sugars, and organic acids, especially the TCA cycle and glycolysis intermediates. Conclusions From the transcriptomic and metabolomic analysis of DGAT1, GPD1 and DGAT1 + GPD1 expressing lines of C. sativa, we conclude that TAG production is limited by (1) utilization of fixed carbon from the source tissues supported by the increase in glycolysis pathway metabolites and decreased transcripts levels of transcription factors controlling fatty acids synthesis; (2) TAG accumulation is limited by the activity of lipases/hydrolases that hydrolyze TAG pool supported by the increase in free fatty acids and monoacylglycerols. This comparative transcriptomics and metabolomics approach is useful in understanding the regulation of TAG biosynthesis, identifying bottlenecks, and the corresponding genes controlling these pathways identified as limitations, for generating Camelina varieties with improved seed and oil yields.

Sustainable switchgrass production (Panicum virgatum) as a bioenergy crop hinges partly on efficiently using soil macronutrients, especially nitrogen (N). In this study, switchgrass plants were grown under four different N conditions (6.0 mM KNO3, N-replete control; 2.0 mM, mild limitation; 0.6 mM, moderate limitation; and 0.2 mM, severe limitation). Subsequently, the physiological, metabolic, and transcriptomic responses of switchgrass roots and shoots to N limitation were determined. Moderate N limitation marked a tipping point for large changes in plant growth, root-to-shoot ratio, root system architecture (root surfaces and specific root length - SRL) and total nitrogen content. Integrating metabolic data and transcriptomic analyses revealed that N limitation reduced switchgrass photosynthetic capacity and carbon(C)-fixation activities. Our results indicate that switchgrass balances C-fixation with N-assimilation and N transport and recycles N-compounds by rerouting C-flux from glycolysis, the oxidative branch of the pentose phosphate pathway (OPPP), and from the tricarboxylic acid (TCA) cycle in an organ-specific manner. The energy and reduction power so generated, and C-skeletons appear to be directed towards N uptake, biosynthesis of energy storage compounds with high C/N ratio such as sucrose, non-N-containing lipids, and various branches of secondary metabolism. Taken together, the findings of this study provide new insights into how switchgrass plants adapt to N limitation. • N-level influence C/N allocation for plant growth and RSA maintenance. • Moderate N limitation is the tipping point for significant morphological and molecular changes. • Extensive N-level-dependent reprogramming of genes and metabolites. • Dynamic balance of C-flux with N-assimilation, transport and recycling N-compounds. • N limitation caused a shift from N- to C-rich compounds at a tissue-specific level. [ABSTRACT FROM AUTHOR]

The green microalga Auxenochlorella pyrenoidosa is realized a promising source of alternative protein due to its high protein content and fermentable property, but the deep green color and off-odor are the bottlenecks for its application in foods. Using atmospheric and room temperature plasma (ARTP) mutagenesis, a novel chlorophyll-deficient mutant, A4-1 strain with golden color and better flavor, was successfully obtained in our previous work. In this study, to reveal the formation of the improved flavor in A4-1 strain compared to the wild type (WT), the volatiles basis was analyzed by HS-SPME Arrow-GC-MS, and the potential precursors causing flavor improvement were explored by UPLC-ESI-MS/MS. Results showed the volatiles were mainly composed of hydrocarbons, terpenoids, esters, ketones, alcohols, and aldehydes, and 29 of which were significantly different between the two biomass, largely attributed to variations of primary metabolite content, particularly those enriched in the fatty acids and amino acids. The analysis of relative odor activity value (ROAV) verified that β -ionone, dimethyl trisulfide and (Z)-6-nonenal were the main odorants, in which the lower contributions of dimethyl trisulfide (off-flavor, rancid or cooked oniony) and (Z)-6-nonenal (off-flavor, stink or fishy) were found in A4-1, which made A4-1 biomass become more neutral and superior to WT biomass in terms of odor perception. It is the first report of flavor improvement for green microalgae through breeding technology, and the novel biomass of A4-1 strain will broaden A. pyrenoidosa biomass in food application. [ABSTRACT FROM AUTHOR]

Plants that produce atropine and scopolamine fall under several genera within the nightshade family. Both atropine and scopolamine are used clinically, but they are also important in a forensics context because they are abused recreationally for their psychoactive properties. The accurate species attribution of these plants, which are related taxonomically, and which all contain the same characteristic biomarkers, is a challenging problem in both forensics and horticulture, as the plants are not only mind-altering, but are also important in landscaping as ornamentals. Ambient ionization mass spectrometry in combination with a hierarchical classification workflow is shown to enable species identification of these plants. The hierarchical classification simplifies the classification problem to primarily consider the subset of models that account for the hierarchy taxonomy, instead of having it be based on discrimination between species using a single flat classification model. Accordingly, the seeds of 24 nightshade plant species spanning 5 genera (i.e. Atropa , Brugmansia , Datura , Hyocyamus and Mandragora), were analyzed by direct analysis in real time-high resolution mass spectrometry (DART-HRMS) with minimal sample preparation required. During the training phase using a top-down hierarchical classification algorithm, the best set of discriminating features were selected and evaluated with a partial least square-discriminant analysis (PLS-DA) classifier to discriminate and visualize the data. The method yields species identity through a class hierarchy, and reveals the most significant markers for differentiation. The overall accuracy of the approach for species identification was 95% and 96% using 100X bootstrapping validation and test samples respectively. The method can be extended for the rapid identification of an infinite number of plant species. Image 1 • Seed taxonomy was identified with DART-HRMS data and a hierarchical classifier. • MS spectra were directly generated from seeds representing 24 species (5 genera). • Species are atropine and scopolamine-containing members of the nightshade family. • A top-down hierarchical classification aids in high accurate taxonomy prediction. • Best discriminative features were identified. [ABSTRACT FROM AUTHOR]

Main conclusion: This study highlights dehydration-mediated temporal changes in physicochemical, transcriptome and metabolome profiles indicating altered gene expression and metabolic shifts, underlying endurance and adaptation to stress tolerance in the marginalized crop, grasspea. Grasspea, often regarded as an orphan legume, is recognized to be fairly tolerant to water-deficit stress. In the present study, 3-week-old grasspea seedlings were subjected to dehydration by withholding water over a period of 144 h. While there were no detectable phenotypic changes in the seedlings till 48 h, the symptoms appeared during 72 h and aggravated upon prolonged dehydration. The physiological responses to water-deficit stress during 72–96 h displayed a decrease in pigments, disruption in membrane integrity and osmotic imbalance. We evaluated the temporal effects of dehydration at the transcriptome and metabolome levels. In total, 5201 genes of various functional classes including transcription factors, cytoplasmic enzymes and structural cell wall proteins, among others, were found to be dehydration-responsive. Further, metabolome profiling revealed 59 dehydration-responsive metabolites including sugar alcohols and amino acids. Despite the lack of genome information of grasspea, the time course of physicochemical and molecular responses suggest a synchronized dehydration response. The cross-species comparison of the transcriptomes and metabolomes with other legumes provides evidence for marked molecular diversity. We propose a hypothetical model that highlights novel biomarkers and explain their relevance in dehydration-response, which would facilitate targeted breeding and aid in commencing crop improvement efforts. [ABSTRACT FROM AUTHOR]

Longan fruit pulp sugar content and sweetness decline after ripening, which affects fruit quality and postharvest storage. Fruit sugar decline research has focused mainly on fruit physiology and biochemistry. To explore the molecular mechanism underlying sugar decline, we conducted transcriptome and metabolome analyses of 'Shixia' longan fruit aril (pulp) tissues at different stages of development. In total, 873 metabolites and 26584 annotated unigenes were identified. Sugar content changes in aril tissues were closely related to gene expression patterns related to starch and sucrose metabolism, such as sucrose phosphate synthase (SPS), invertase (INV), sucrose synthase (SUS), and glucose-6-phosphate isomerase (GPI). Notably, glycolytic pathway gene expression and cellulose and lignin contents increased during the sugar decline stage compared to the sugar accumulation stage. Conversely, sucrose transporter genes, such as DlSWEET2b , DlSWEET10 , and DlSWEET12 , showed the opposite expression pattern, pointing to reduced sucrose transport during sugar decline. These results indicate that longan fruit sugar decline is likely related to an interruption of sugar input (cessation of sucrose transport to the aril) and continued glycolysis and cellulose/lignin biosynthesis. This provides a new way to delay longan fruit sugar decline, by regulating sugar transport instead of inhibiting respiration. • A sudden decrease in sucrose content results in longan sugar receding. • Glycolysis and cellulose and lignin synthesis reduce the sucrose content of longan. • Inhibition of expression of sucrose transporter genes blocks sucrose transport. • Input interruption and continuous consumption of sugar lead to sugar receding. [ABSTRACT FROM AUTHOR]

[Display omitted] • Metabolomics was used to characterize digestion differences between MS and YS. • More bioactive compounds were released in gastric digestion than in intestinal digestion. • YS samples contained more total sugars than MS samples. • Reducing power and anti-inflammatory activity decreased with the increase of total organic and amino acids content. • Pancreatic lipase and cholesterol esterase inhibition activities improved with the increase of total organic acids content. The aim of the present study was to comparatively investigate the relative phytochemical profiles (phenolic content, organic and amino acids, free sugars, and other metabolites using metabolomics approach), and bioactive potentials of young (YS) and mature soybean (MS) upon in vitro simulated gastrointestinal digestion (SGID). Cumulatively, a total of 198 metabolites were identified in MS and YS, 119 metabolites in undigested YS, and a total of 136 metabolites in undigested MS, which further increased to 156 and 152 in YS and MS upon SGID, respectively. Gastric digesta of both YS and MS exhibited higher inhibitory properties towards α-amylase and DPP-IV enzymes than their intestinal digesta. Furthermore, the intestinal digesta of MS showed higher antioxidant and anti-inflammatory activities compared to the YS intestinal digesta. Overall, the results suggested that the gastrointestinal digestion of YS and MS displayed distinctive metabolic profiles together with varied bioactive potentials. [ABSTRACT FROM AUTHOR]

Fish species exhibit great diversity rating of aging (from negligible to rapid), which gives a unique possibility for the discovery of the molecular mechanisms that determine the differences in the rate of aging. A mass spectrometric metabolic profiling of skeletal muscle of fish with various aging rates was carried out by direct injection to a quadrupole time-of-flight mass spectrometer. The first group includes long-lived fish species (pike (Esox Lucius) and sterlet (Acipenser ruthenus); the second group—species with gradual senescence such as that observed in many mammalian species of similar size (zander (Sandra lucioperca) and perch (Perca fluviatilis)) and the third group—species with very short life cycle (chum salmon (Oncorhynchus keta) and pink salmon (Oncorhynchus gorbuscha)). Multivariate analysis of metabolic profiles allowed the detecting of about 80 group-specific features associated with amino acids, lipids, biogenic amines, intermediates of glycolysis, glycogenolysis, and citric acid cycle. Possible roles in the aging process are hypothesized for the biochemical pathways of the metabolites that were altered in the different groups.

There are a number of different animals that belong to long- and short-lived species and show a various rate of ageing, providing an ideal model to investigate mechanisms of longevity. In this work, a metabolome profiling of blood plasma from fishes with various ageing rates—negligible (Pike Esox Lucius and Sterlet Acipenser ruthenus), gradual (Zander Sander lucioperca and Perch Perca fluviatilis) and rapid (Chum Salmon Oncorhynchus keta and Pink Salmon Oncorhynchus gorbuscha)—was assessed by means of direct infusion to quadrupole time-of-flight mass spectrometry. Of the 2056 distinct m/z features detected by a mass spectrometry metabolic profiling of blood plasma samples, fifteen metabolites in the classes of dipeptides, fatty acids, glycerolipids, phosphoethanolamines and phosphatidylcholines were significantly associated with ageing rate, independent of species differences. This is the first study of the metabolome of fishes with various ageing rate, and this untargeted approach highlighted the metabolic conditions that may serve to assess the ageing process.

In order to characterize copepod feeding in relation to microbial plankton community dynamics, we combined metabarcoding and metabolome analyses during a 22-day seawater mesocosm experiment. Nutrient amendment of mesocosms promoted the development of haptophyte ( Phaeocystis pouchetii)- and diatom ( Skeletonema marinoi)-dominated plankton communities in mesocosms, in which Calanus sp. copepods were incubated for 24 h in flow-through chambers to allow access to prey particles (<500 μm). Copepods and mesocosm water sampled six times spanning the experiment were analysed using metabarcoding, while intracellular metabolite profiles of mesocosm plankton communities were generated for all experimental days. Taxon-specific metabarcoding ratios (ratio of consumed prey to available prey in the surrounding seawater) revealed diverse and dynamic copepod feeding selection, with positive selection on large diatoms, heterotrophic nanoflagellates and fungi, while smaller phytoplankton, including P. pouchetii, were passively consumed or even negatively selected according to our indicator. Our analysis of the relationship between Calanus grazing ratios and intracellular metabolite profiles indicates the importance of carbohydrates and lipids in plankton succession and copepod-prey interactions. This molecular characterization of Calanus sp. grazing therefore provides new evidence for selective feeding in mixed plankton assemblages and corroborates previous findings that copepod grazing may be coupled to the developmental and metabolic stage of the entire prey community rather than to individual prey abundances. [ABSTRACT FROM AUTHOR]

Mass spectrometry-based metabolome profiling became the method of choice in systems biology approaches and aims to enhance biological understanding of complex biological systems. Genomics, transcriptomics, and proteomics are well established technologies and are commonly used by many scientists. In comparison, metabolomics is an emerging field and has not reached such high-throughput, routine and coverage than other omics technologies. Nevertheless, substantial improvements were achieved during the last years. Integrated data derived from multi-omics approaches will provide a deeper understanding of entire biological systems. Metabolome profiling is mainly hampered by its diversity, variation of metabolite concentration by several orders of magnitude and biological data interpretation. Thus, multiple approaches are required to cover most of the metabolites. No software tool is capable of comprehensively translating all the data into a biologically meaningful context yet. In this review, we discuss the advantages of metabolome profiling and main obstacles limiting progress in systems biology. [ABSTRACT FROM AUTHOR]

Abiotic stresses, including low temperature, can significantly reduce plant yielding. The knowledge on the molecular basis of stress tolerance could help to improve its level in species of relatively high importance to agriculture. Unfortunately, the complex research performed so far mainly on model species and also, to some extent, on cereals does not fully cover the demands of other agricultural plants of temperate climate, including forage grasses. Two Lolium perenne (perennial ryegrass) genotypes with contrasting levels of frost tolerance, the high frost tolerant (HFT) and the low frost tolerant (LFT) genotypes, were selected for comparative metabolomic research. The work focused on the analysis of leaf metabolite accumulation before and after seven separate time points of cold acclimation. Gas chromatography-mass spectrometry (GC/MS) was used to identify amino acids (alanine, proline, glycine, glutamic and aspartic acid, serine, lysine and asparagine), carbohydrates (fructose, glucose, sucrose, raffinose and trehalose) and their derivatives (mannitol, sorbitol and inositol) accumulated in leaves in low temperature. The observed differences in the level of frost tolerance between the analysed genotypes could be partially due to the time point of cold acclimation at which the accumulation level of crucial metabolite started to increase. In the HFT genotype, earlier accumulation was observed for proline and asparagine. The increased amounts of alanine, glutamic and aspartic acids, and asparagine during cold acclimation could be involved in the regulation of photosynthesis intensity in L. perenne. Among the analysed carbohydrates, only raffinose revealed a significant association with the acclimation process in this species. [ABSTRACT FROM AUTHOR]

Background Scale-up to industrial production level of a fermentation process occurs after optimization at small scale, a critical transition for successful technology transfer and commercialization of a product of interest. At the large scale a number of important bioprocess engineering problems arise that should be taken into account to match the values obtained at the small scale and achieve the highest productivity and quality possible. However, the changes of the host strain's physiological and metabolic behavior in response to the scale transition are still not clear. Results Heterogeneity in substrate and oxygen distribution is an inherent factor at industrial scale (10,000 L) which affects the success of process up-scaling. To counteract these detrimental effects, changes in dissolved oxygen and pressure set points and addition of diluents were applied to 10,000 L scale to enable a successful process scale-up. A comprehensive semiquantitative and time-dependent analysis of the exometabolome was performed to understand the impact of the scale-up on the metabolic/physiological behavior of the host microorganism. Intermediates from central carbon catabolism and mevalonate/ergosterol synthesis pathways were found to accumulate in both the 10 L and 10,000 L scale cultures in a time-dependent manner. Moreover, excreted metabolites analysis revealed that hypoxic conditions prevailed at the 10,000 L scale. The specific product yield increased at the 10,000 L scale, in spite of metabolic stress and catabolic-anabolic uncoupling unveiled by the decrease in biomass yield on consumed oxygen. Conclusions An optimized S. cerevisiae fermentation process was successfully scaled-up to an industrial scale bioreactor. The oxygen uptake rate (OUR) and overall growth profiles were matched between scales. The major remaining differences between scales were wet cell weight and culture apparent viscosity. The metabolic and physiological behavior of the host microorganism at the 10,000 L scale was investigated with exometabolomics, indicating that reduced oxygen availability affected oxidative phosphorylation cascading into down- and upstream pathways producing overflow metabolism. Our study revealed striking metabolic and physiological changes in response to hypoxia exerted by industrial bioprocess up-scaling [ABSTRACT FROM AUTHOR]

Kaempferol (KMP) has numerous important biological functions, and we recently showed that it remarkably increased intracellular adenosine triphosphate (ATP) content in C2C12 myotubes under hypoxic conditions. Since intracellular ATP is generated by aerobic energy metabolism or anaerobic glycolysis, hypoxia inducible factor-1α (HIF-1α) has been shown to be associated with metabolic remodeling and causes metabolic shift from aerobic energy metabolism to anaerobic glycolysis in response to hypoxic conditions. Here, we investigate the effects of KMP under hypoxic conditions on the stabilization of HIF-1α in C2C12 myotubes and its underlying molecular mechanisms. Constitutive HIF-1α protein expression was observed in C2C12 myotubes, and its expression under hypoxic conditions was remarkably suppressed by KMP by reducing its stability; thus, resulting in an increase in ATP content. Furthermore, KMP strikingly increased the ubiquitination of HIF-1α and promoted its degradation via the ubiquitin proteasome system. Inhibition of HIF-1α by KMP resulted in the abrogation of the expression of glycolytic enzymes such as lactate dehydrogenase A and pyruvate dehydrogenase kinase isozyme 1. In addition, the metabolome profiling showed that KMP promoted oxidative energy production, while the mitochondrial complex activity assay indicated that KMP increased the activity of mitochondrial complex IV. Finally, we showed that KMP inhibited HIF-1α expression and increased intracellular ATP content in the soleus muscle of rats. Taken together, these results suggest that KMP increases intracellular ATP content under hypoxic conditions by suppressing the HIF-1α stabilization and/or by enhancing the mitochondrial complex IV activity in muscle. [ABSTRACT FROM AUTHOR]

[Display omitted] • 671 metabolites were detected in black, brown, yellow, and white sesame seeds. • 60 key significantly differential metabolites that correlated with the seed coat color variation and antioxidant activities. • Key differently regulated pathways were identified. • The dark sesame seeds showed strong antioxidant efficiency than light sesame seeds. • The variety H16 (Black seed) was suggested for nutritional and quality breeding purposes. Sesame seeds are considered worldwide as a functional food due to their nutritional and therapeutical values. Several physiological functions are being associated with sesame seeds and their derived products. However, the phytochemicals responsible for these various proprieties are not well understood. Thus, to acknowledge the diversity and variability of metabolites in sesame seeds of different colors and reveal key metabolites and pathways contributing to differences in antioxidant activities, black, brown, yellow, and white sesame seeds from 12 varieties were subjected to LC-MS/MS-based widely targeted metabolomics analysis. Totally, 671 metabolites were identified and chemically classified. The metabolic compounds varied significantly with the seed coat color and genotype. Many flavonoids, amino acids, and terpenoids were up-regulated in dark seeds. Sixty key differential metabolites were filtered out. Phenylpropanoid biosynthesis, amino acids biosynthesis, and tyrosine metabolism were the main differently regulated pathways. The DPPH, ABTS, and FRAP assays showed that the antioxidant activities of the seeds increased with the seed coat darkness. Therefore, the pharmacological proprieties of black seeds might be related to their high content of flavonoids and essential amino acids mostly. These findings expand phytochemicals composition information of different colored sesame seeds and provide resources for their comprehensive use and quality improvement. [ABSTRACT FROM AUTHOR]