Metabolic Pathway Maps Research Articles

Susceptibility-weighted imaging for metabolic pathway mapping of low-dosage nanoparticles in organisms

Accurate and noninvasive monitoring of nanoparticles' (NPs) distribution and metabolism in organism is important, especially for NPs at low-dosage, but remains challenging due to the insufficient sensitivity and resolution of the existing imaging techniques. Herein, Fe3O4 NPs with different sizes were synthesized for low-dosage NPs' metabolism study with susceptibility weighted imaging (SWI) technique. SWI, as a functional MRI technique with phase postprocessing, can sensitively detect the differences of magnetic susceptibilities between tissues, so can measure the Fe3O4 contents even at low dosage in tissues. After in vivo intravenous injection, Fe3O4 NPs could be visually distinguished in major organs (kidney, liver, spleen) by SWI, and the corresponding content changes over time were also sensitively detected, but cannot be achieved via the conventional T2-weighted imaging (T2WI). With the SWI technique, the metabolic pathways of Fe3O4 NPs in body were mapped, revealing the critical dependence on the sizes of NPs. This is significant for the assessment of NPs’ metabolic time, toxicity risk, and application potentiality. Undoubtedly, SWI is a powerful tool for real-time metabolism low-dose NPs with designed characteristics (shapes, sizes, surface properties, etc.), and noninvasive detection of targets with magnetic nano-sensors in vivo.

Identification of TPD52 and DNAJB1 as two novel bile biomarkers for cholangiocarcinoma by iTRAQ‑based quantitative proteomics analysis.

Cholangiocarcinoma (CCA) represents a type of epithelial cancer with a late diagnosis and poor outcome. However, the molecular mechanisms responsible for the development of CCA have not yet been fully identified. Thus, in this study, we aimed to elucidate some of these mechanisms. For this purpose, isobaric tags for relative and absolute quantification (iTRAQ) was performed to analyze the secretory proteins from the 2 CCA cell lines, TFK1 and HuCCT1, as well as from a normal biliary epithelial cell line, human intrahepatic biliary epithelial cells (HiBECs). Differentially expressed proteins (DEPs) were identified and biological process analysis was performed according to the Gene Ontology (GO) functional classification annotation and KEGG metabolic pathway map analysis. tumor protein D52 (TPD52) and DnaJ heat shock protein family (Hsp40) member B1 (DNAJB1) were validated using RT-qPCR, western blot analysis and immunohistochemistry. In total, 778 proteins were identified as DEPs. Following validation, TPD52 and DNAJB1 were used for further analysis. The expression levels of TPD52 and DNAJB1 were elevated in CCA cell lines, tissues and bile samples, suggesting that these proteins may contribute to tumor pathogenesis. In addition, the expression levels of TPD52 and DNAJB1 were found to be closely associated with the clinical parameters and prognosis of patients with CCA. On the whole, the findings of this study indicate that TPD52 and DNAJB1 may serve as novel bile biomarkers for CCA.

Utilization of Metabolomics to Teach Undergraduate Students Nutritional Metabolism (P07-006-19)

ObjectivesMetabolomics, the comprehensive study of metabolites in biological fluids and tissues, offers the ability to observe metabolic changes in a more comprehensive context to identify metabolites altered by intervention. Traditionally, nutritional metabolism has been taught using book and journal article information. Due to the emergence of metabolomics research on University campuses, an opportunity exists to utilize this tool for the purpose of educating students. The objective of this study was to assess the feasibility and effectiveness of involving students in a feeding research study using metabolomics analyses for the purpose of improving student learning of nutritional metabolism. MethodsThe study consisted of two groups (n = 19/group) of nutrient metabolism students: (1) 12 hr fasting blood draw; (2) 2 hr postprandial blood draw following a breakfast meal. Plasma samples were analyzed using LC-MS targeted assays for primary metabolomics, aminomics, and lipidomics. Pre- and post-course questionnaires were completed by students in order to assess the educational interest and effectiveness of the activity. ResultsThe feeding intervention, sample and data analysis were completed within the first 4 wk of the academic quarter. A total of 221 metabolites were identified in the plasma. Altered metabolites included sugars, energetic pathway intermediates, triglycerides, bile acids, amino acids and acylcarnitines. Results were periodically presented in lecture and discussed using interactive group activities throughout the duration of the academic quarter immediately following review of related principle concepts of carbohydrate, protein, and lipid metabolism. Course exams included essay questions requiring explanation of the potential metabolic pathway alterations connected to observed study results. An assigned project required inclusion of study results within an integrated metabolic pathway map. Student questionnaires indicated there was an increase in knowledge, in addition to an increased interest in research (P < 0.05). ConclusionsThe inclusion of metabolomics in University courses may increase student interest and effectively improve student learning of nutritional metabolism and research. Future studies are needed to test this concept for use in other courses. Funding SourcesCalifornia Polytechnic State University, San Luis Obispo Food Science and Nutrition Department.

The "great" controlling nucleotide coenzymes.

Nucleotide coenzymes dot the map of metabolic pathways providing energy to drive the reactions of the pathway and play an important role in regulating and controlling energy metabolism through their shared potential energy, which is widely unobserved due to the paradox that the energy in the coenzyme pools cannot be determined from the concentration of the coenzyme couples. The potential energy of the nucleotide couples in the mitochondria or the cytoplasm is expressed in the enzyme reactions in which they take part. The energy in these couples, [NAD+]/[NADH], [NADP+]/[NADPH], [acetyl CoA]/[CoA], and [ATP]/[ADP]x[Pi], regulates energy metabolism. The energy contained in the couples can be altered by suppling energy equivalents in the form of ketones, such as, D‐β‐hydroxybutyrate to overcome insulin resistance, to restore antioxidants capacity, to form potential treatments for Alzheimer's and Parkinson's diseases, to enhance life span, and to increase physiological performance. © 2019 IUBMB Life, 71(5):565–579, 2019

Targeted Metabolomics with Quantitative Dissolution Dynamic Nuclear Polarization.

Metabolite profiles and their isotopomer distributions can be studied noninvasively in complex mixtures with NMR. The advent of hyperpolarized 13C-NMR using quantitative dissolution Dynamic Nuclear Polarization (qdDNP) and isotope enrichment add sensitivity to such metabolic studies, enabling mapping and quantification of metabolic pathways and networks. Here we describe a sample preparation method, including cell incubation, extraction, and signal enhancement, for reproducible and quantitative analysis of hyperpolarized 13C-NMR metabolite spectra. We further illustrate how qdDNP can be applied to gain metabolic insights into living cells.

Composition of Mycelia and Basidiomata of the Culinary-Medicinal Golden Oyster Mushroom, Pleurotus citrinopileatus (Agaricomycetes) by Nuclear Magnetic Resonance Spectroscopy.

Nuclear magnetic resonance (NMR) spectroscopy has been used to obtain the profile of soluble metabolites on fungus. To enhance the ergothioneine content in Pleurotus citrinopileatus mycelium, amino acid precursors were used for submerged fermentation. The study aimed to analyze the metabolites of high-ergothioneine and regular P. citrinopileatus mycelia (HEPM and RPM) and P. citrinopileatus basidiomata (PCB) using NMR spectroscopy. Principal component analysis (PCA) was applied to differentiate and to describe the differences among three sets of metabolites. The results showed that 55 water-soluble metabolites of PCB, HEPM, and RPM were identified and classified into five groups including amino acids, carbohydrates, organic acids, purines and pyrimidines, and others. Contents of total soluble metabolites were in descending order as follows: PCB (135 mg/g) > HEPM (58 mg/g) > RPM (44 mg/g). The score plot and loading plot separated using PCA showed that the first two components were responsible for R2X = 97.1% and the variance [R2X(1) = 74% for principal component PC1 and R2X(2) = 23.1% for PC2]. A metabolic pathway map of P. citrinopileatus mycelium was established and the differences in the metabolites of RPM and HEPM with precursors added were illuminated.

Metabolic Analysis Reveals Altered Long-Chain Fatty Acid Metabolism in the Host by Huanglongbing Disease.

Candidatus Liberibacter asiaticus (CLas) is the presumed causal agent of Huanglongbing, one of the most destructive diseases in citrus. However, the lipid metabolism component of host response to this pathogen has not been investigated well. Here, metabolic profiling of a variety of long-chain fatty acids and their oxidation products was first performed to elucidate altered host metabolic responses of disease. Fatty acid signals were found to decrease obviously in response to disease regardless of cultivar. Several lipid oxidation products strongly correlated with those fatty acids were also consistently reduced in the diseased group. Using a series of statistical methods and metabolic pathway mapping, we found significant markers contributing to the pathological symptoms and identified their internal relationships and metabolic network. Our findings suggest that the infection of CLas may cause the altered metabolism of long-chain fatty acids, possibly leading to manipulation of the host's defense derived from fatty acids.

PathQuant: A bioinformatic tool to quantitatively annotate the relationship between genes and metabolites through metabolic pathway mapping

Background &amp; ObjectiveThe integration of genome wide association studies (GWAS) with metabolomics, termed mGWAS, offers a tremendous opportunity to gain insights into the genetic control of metabolism. A current bottleneck of mGWAS is the biological interpretation of the large amount of generated data, which include associations between SNP‐annotated genes and metabolites. This project aimed at developing a robust bioinformatic package to quantitatively annotate gene‐metabolite association pairs through metabolic pathway mapping.Methods &amp; ResultsA R package, PathQuant, has been developed following Bioconductor guidelines to ensure reproducibility of results and easy growth. The current version of PathQuant uses as input a list of gene‐metabolite associations pairs and enables: (i) gene classification into enzymatic vs. non‐enzymatic category using the Enzyme Commission number (EC) as annotation; (ii) mapping of metabolic gene‐metabolite pairs on a graph model of human KEGG metabolic pathway maps, where genes are edges and metabolites are nodes, and (iii) calculation of shortest reactional distances between gene‐metabolite pairs with either graphical visualization or textual tables as outputs. As a proof‐of concept, PathQuant was used to map mGWAS gene‐metabolite associations data from Shin et al. (2014) using all KEGG metabolism pathway maps, which include the metabolism reconstruction overview map and specific individual pathway maps. We applied the method for 86 reported associations between 50 enzymatic genes and 66 metabolites measured in plasma. When mapped to KEGG metabolism overview (Fig. 1), these associations are mostly found in “Energy” (purple), “Amino acids” (orange) and “Nucleotides” (green) pathway classes. PathQuant annotated finite numerical distances between 28 genes and 31 metabolites involved in 38 associations of which 36 had a short distance, between 0 and 5, which indicates that the reaction catalyzed by the gene encoded enzyme was not more than 5 reactions apart from that involving its associated metabolite. For 17 genes and 27 metabolites, representing 27 pairs, we were unable to calculate finite numerical distances using PathQuant, which is attributed to current limitations of human KEGG pathway maps, such as (i) missing enzymes annotated in humans creating disconnected subgraphs within the maps, (ii) the presence of a gene and a metabolite from a given pair on different maps and (iii) limited coverage of lipid metabolic diversity in KEGG pathway maps (Fig. 1). While improvement of the tool's capacity for annotation could address limitations (i) and (ii), there were, however, 4 genes and 12 metabolites (21 pairs) that were not present on any KEGG pathways.ConclusionPathQuant provides a high‐throughput approach to link and objectively annotate gene‐metabolite pairs. Future work aims at upgrading PathQuant by refining the annotation and improving coverage of pathway classes by including other pathway databases than KEGG as well as to expand the annotation to genes involved in cell signaling pathways.Support or Funding InformationGenome Canada, Genome Québec, Genome British Columbia, Agilent Technologies, CIHR, Crohn's and Colitis Canada, Government of Canada.

A Systematic Approach to Time-series Metabolite Profiling and RNA-seq Analysis of Chinese Hamster Ovary Cell Culture

Chinese hamster ovary (CHO) cells are the primary host used for biopharmaceutical protein production. The engineering of CHO cells to produce higher amounts of biopharmaceuticals has been highly dependent on empirical approaches, but recent high-throughput “omics” methods are changing the situation in a rational manner. Omics data analyses using gene expression or metabolite profiling make it possible to identify key genes and metabolites in antibody production. Systematic omics approaches using different types of time-series data are expected to further enhance understanding of cellular behaviours and molecular networks for rational design of CHO cells. This study developed a systematic method for obtaining and analysing time-dependent intracellular and extracellular metabolite profiles, RNA-seq data (enzymatic mRNA levels) and cell counts from CHO cell cultures to capture an overall view of the CHO central metabolic pathway (CMP). We then calculated correlation coefficients among all the profiles and visualised the whole CMP by heatmap analysis and metabolic pathway mapping, to classify genes and metabolites together. This approach provides an efficient platform to identify key genes and metabolites in CHO cell culture.

Testing and evaluation: the present and future of the assessment of medical professionals.

The aim of this review is to highlight recent and potential future enhancements to the United States Licensing Examination (USMLE) program. The USMLE program is co-owned by the National Board of Medical Examiners (NBME) and the Federation of State Medical Boards. The USMLE includes four examinations: Step 1, Step 2 Clinical Knowledge, Step 2 Clinical Skills, and Step 3; every graduate of Liaison Committee on Medical Education-accredited allopathic medical schools and all international medical graduates must pass this examination series to practice medicine in the United States. From 2006 to 2009, the program underwent an indepth review resulting in five accepted recommendations. These recommendations have been the primary driver for many of the recent enhancements, such as an increased emphasis on foundational science and changes in the clinical skills examination, including more advanced communication skills assessment. These recommendations will continue to inform future changes such as access to references (e.g., a map of metabolic pathways) or decision-making tools for use during the examination. The NBME also provides assessment services globally to medical schools, students, residency programs, and residents. In 2015, >550,000 assessments were provided through the subject examination program, NBME self-assessment services, and customized assessment services.

Meal-insulin cycle: A visual summary of the biochemical events between meals.

In the present article, a scheme that summarizes the biochemical events occurring in the human body after the consumption of a meal is proposed. The scheme illustrates the metabolic sequence as a series of counteracting components occupying opposite positions in a cycle, indicating their opposite actions or physiological states, such as meal versus energy consumption, increase versus decrease of blood glucose levels, and excretion of insulin versus excretion of glucagon. Furthermore, the cycle is complemented by a table indicating the acceleration or inhibition of selected metabolic pathways and actions. Since the cycle demonstrates the effects of a meal and of insulin on metabolism it was named "the meal-insulin cycle." Evaluation of the implementation in the classroom by postgraduate students of Nutrition showed that the proposed summarized visualization improved the understanding of the events between meals of all students, both holders of a Nutrition degree as well as graduates of another science division. Moreover, the representation as a perpetuating cycle throughout our lifespan was new to the students. The students recognized the graphical illustration as the most helpful feature. The proposed scheme may be used in teaching metabolism or biochemistry in a students' course or in a diabetes care course, it can be found on the internet, at the URL www.metpath.teithe.gr/meal_insulin_cycle and is linked to an interactive map of metabolic pathways. © 2016 by The International Union of Biochemistry and Molecular Biology, 45(3):279-284, 2017.

Metabolic response induced by parasitic plant-fungus interactions hinder amino sugar and nucleotide sugar metabolism in the host.

Infestation by the biotrophic pathogen Gymnosporangium asiaticum can be devastating for plant of the family Rosaceae. However, the phytopathology of this process has not been thoroughly elucidated. Using a metabolomics approach, we discovered the intrinsic activities that induce disease symptoms after fungal invasion in terms of microbe-induced metabolic responses. Through metabolic pathway enrichment and mapping, we found that the host altered its metabolite levels, resulting in accumulation of tetrose and pentose sugar alcohols, in response to this fungus. We then used a multiple linear regression model to evaluate the effect of the interaction between this abnormal accumulation of sugar alcohol and the group variable (control/parasitism). The results revealed that this accumulation resulted in deficiency in the supply of specific sugars, which led to a lack of amino sugar and nucleotide sugar metabolism. Halting this metabolism could hamper pivotal functions in the plant host, including cell wall synthesis and lesion repair. In conclusion, our findings indicate that altered metabolic responses that occur during fungal parasitism can cause deficiency in substrates in pivotal pathways and thereby trigger pathological symptoms.

Plasma, urine and ligament tissue metabolite profiling reveals potential biomarkers of ankylosing spondylitis using NMR-based metabolic profiles.

BackgroundAnkylosing spondylitis (AS) is an autoimmune rheumatic disease mostly affecting the axial skeleton. Currently, anti-tumour necrosis factor α (anti-TNF-α) represents an effective treatment for AS that may delay the progression of the disease and alleviate the symptoms if the diagnosis can be made early. Unfortunately, effective diagnostic biomarkers for AS are still lacking; therefore, most patients with AS do not receive timely and effective treatment. The intent of this study was to determine several key metabolites as potential biomarkers of AS using metabolomic methods to facilitate the early diagnosis of AS.MethodsFirst, we collected samples of plasma, urine, and ligament tissue around the hip joint from AS and control groups. The samples were examined by nuclear magnetic resonance spectrometry, and multivariate data analysis was performed to find metabolites that differed between the groups. Subsequently, according to the correlation coefficients, variable importance for the projection (VIP) and P values of the metabolites obtained in the multivariate data analysis, the most crucial metabolites were selected as potential biomarkers of AS. Finally, metabolic pathways involving the potential biomarkers were determined using the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, and the metabolic pathway map was drawn.ResultsForty-four patients with AS agreed to provide plasma and urine samples, and 30 provided ligament tissue samples. An equal number of volunteers were recruited for the control group. Multidimensional statistical analysis suggested significant differences between the patients with AS and control subjects, and the models exhibited good discrimination and predictive ability. A total of 20 different metabolites ultimately met the requirements for potential biomarkers. According to KEGG analysis, these marker metabolites were primarily related to fat metabolism, intestinal microbial metabolism, glucose metabolism and choline metabolism pathways, and they were also probably associated with immune regulation.ConclusionsOur work demonstrates that the potential biomarkers that were identified appeared to have diagnostic value for AS and deserve to be further investigated. In addition, this work also suggests that the metabolomic profiling approach is a promising screening tool for the diagnosis of patients with AS.

1H NMR-based metabolic study reveals the improvements of bitter melon (Momordica charantia) on energy metabolism in diet-induced obese mouse

Context: Obesity can be ameliorated by some natural products such as polyphenol, flavones and saponin. As a typical medicinal plant, Momordica charantia L. (Cucurbitaceae) (bitter melon, BM) contains these natural chemicals and reduces diet-induced obesity in mice.Objective: This study evaluates the metabolic effects of dietary BM supplement, investigates a global metabolic profile and determines associated perturbations in metabolic pathways.Materials and methods: Male C57BL/6 mice were fed with low-fat diet (LFD), high-fat diet (HFD) and HFD supplemented with 5% BM based on 37.6 g/kg body weight in average for 12 weeks, respectively. Then energy metabolism was quantified using PhenoMaster/LabMaster. The spectroscopy of urine was acquired by nuclear magnetic resonance and latent biomarkers were identified. Pattern recognition analysis was used to discriminate associated metabolic profiles.Results: Dietary BM supplement reduced body weight gain (−0.15-fold, p < 0.01) and blood glucose levels (−0.19-fold, p < 0.01) in HFD-fed mice. Meanwhile, the levels of energy metabolism were enhanced (0.08–0.11-fold, p < 0.01). According to pattern recognition analysis, dietary BM supplement changed metabolic profiles in HFD-fed mice and the modified profiles were similar to those in LFD-fed mice. Finally, the mapping of metabolic pathways showed that dietary BM supplement primarily affected glucose metabolism-associated pathways.Discussion and conclusion: The results indicated that BM improves weight loss in diet-induced obesity and elevate energy expenditure in HFD-fed mice. The pattern recognition with metabolic study may be used as a noninvasive detection method to assess the effects of dietary BM supplement on mouse energy metabolism.

Metabolic Profiling with Gas Chromatography-Mass Spectrometry and Capillary Electrophoresis-Mass Spectrometry Reveals the Carbon-Nitrogen Status of Tobacco Leaves Across Different Planting Areas.

The interaction between carbon (C) and nitrogen (N) metabolism can reflect plant growth status and environmental factors. Little is known regarding the connections between C-N metabolism and growing regions under field conditions. To comprehensively investigate the relationship in mature tobacco leaves, we established metabolomics approaches based on gas chromatography-mass spectrometry (GC-MS) and capillary electrophoresis-time-of-flight-mass spectrometry (CE-TOF-MS). Approximately 240 polar metabolites were determined. Multivariate statistical analysis revealed that the growing region greatly influenced the metabolic profiles of tobacco leaves. A metabolic correlation network and related pathway maps were used to reveal the global overview of the alteration of C-N metabolism across three typical regions. In Yunnan, sugars and tricarboxylic acid (TCA) cycle intermediates were closely correlated with amino acid pools. Henan tobacco leaves showed positive correlation between the pentose phosphate pathway (PPP) intermediates and C-rich secondary metabolism. In Guizhou, the proline and asparagine had significant links with TCA cycle intermediates and urea cycle, and antioxidant accumulation was observed in response to drought. These results demonstrate that combined analytical approaches have great potential to detect polar metabolites and provide information on C-N metabolism related to planting regional characteristics.

Metabolomics for undergraduates: Identification and pathway assignment of mitochondrial metabolites.

Metabolomics is a key discipline in systems biology, together with genomics, transcriptomics, and proteomics. In this omics cascade, the metabolome represents the biochemical products that arise from cellular processes and is often regarded as the final response of a biological system to environmental or genetic changes. The overall screening approach to identify all the metabolites in a given biological system is called metabolic fingerprinting. Using high-resolution and high-mass accuracy mass spectrometry, large metabolome coverage, sensitivity, and specificity can be attained. Although the theoretical concepts of this methodology are usually provided in life-science programs, hands-on laboratory experiments are not usually accessible to undergraduate students. Even if the instruments are available, there are not simple laboratory protocols created specifically for teaching metabolomics. We designed a straightforward hands-on laboratory experiment to introduce students to this methodology, relating it to biochemical knowledge through metabolic pathway mapping of the identified metabolites. This study focuses on mitochondrial metabolomics since mitochondria have a well-known, medium-sized cellular sub-metabolome. These features facilitate both data processing and pathway mapping. In this experiment, students isolate mitochondria from potatoes, extract the metabolites, and analyze them by high-resolution mass spectrometry (using an FT-ICR mass spectrometer). The resulting mass list is submitted to an online program for metabolite identification, and compounds associated with mitochondrial pathways can be highlighted in a metabolic network map.

Cover Picture: Biotechnology Journal 7/2015

AbstractSpecial issue: Mammalian Production Systems. This special issue is edited by Nicole Borth and Lars Nielsen. It focuses on the use of CHO cells and their improvement to produce recombinant proteins. The articles cover the application of CRISPR technology, systems biology and modeling approaches as well as bioinformatics methods. The cover visualizes the highly interconnected metabolic pathway map of CHO cells based on a genome‐scale metabolic reconstruction (blue: reactions, red: molecular species). Image by Michael Hanscho.

Deep questions about the nature of early-life signals: a commentary on Lister (1673) 'A description of certain stones figured like plants'.

In 1673, Martin Lister explored the preservation of ‘St Cuthbert's beads’ plus other fossil crinoid remains from approximately 350 Ma Carboniferous limestone in northern England. He used taphonomic evidence (transport, disarticulation, burial and cementation) to infer an origin as petrified plant remains, in contrast with his views expressed elsewhere that fossil mollusc shells could have formed abiogenically, by ‘plastic forces’ within rock. Lister also observed pentagonal symmetry, now seen as characteristic of living echinoderm skeletons. A postscript from John Ray supports Lister's ‘taphonomic’ observations and accepts the biogenicity of these fossil ‘vegetables’. Ray then concluded with a prophecy, predicting the discovery of comparable living fossils in remote ocean waters. These early discussions compare with current debates about the character of candidate microfossils from the early Earth and Mars. Interesting biomorphs are now tested against the abiogenic null hypotheses, making use of features such as those pioneered by Lister, including evidence for geological context, rules for growth and taphonomy. Advanced techniques now allow us to extend this list of criteria to include the nanoscale mapping of biology-like behaviour patterns plus metabolic pathways. Whereas the science of palaeobiology once began with tests for biogenicity, the same is now true for geobiology and astrobiology. This commentary was written to celebrate the 350th anniversary of the journal Philosophical Transactions of the Royal Society.

Multiomics in grape berry skin revealed specific induction of the stilbene synthetic pathway by ultraviolet-C irradiation.

Grape (Vitis vinifera) accumulates various polyphenolic compounds, which protect against environmental stresses, including ultraviolet-C (UV-C) light and pathogens. In this study, we looked at the transcriptome and metabolome in grape berry skin after UV-C irradiation, which demonstrated the effectiveness of omics approaches to clarify important traits of grape. We performed transcriptome analysis using a genome-wide microarray, which revealed 238 genes up-regulated more than 5-fold by UV-C light. Enrichment analysis of Gene Ontology terms showed that genes encoding stilbene synthase, a key enzyme for resveratrol synthesis, were enriched in the up-regulated genes. We performed metabolome analysis using liquid chromatography-quadrupole time-of-flight mass spectrometry, and 2,012 metabolite peaks, including unidentified peaks, were detected. Principal component analysis using the peaks showed that only one metabolite peak, identified as resveratrol, was highly induced by UV-C light. We updated the metabolic pathway map of grape in the Kyoto Encyclopedia of Genes and Genomes (KEGG) database and in the KaPPA-View 4 KEGG system, then projected the transcriptome and metabolome data on a metabolic pathway map. The map showed specific induction of the resveratrol synthetic pathway by UV-C light. Our results showed that multiomics is a powerful tool to elucidate the accumulation mechanisms of secondary metabolites, and updated systems, such as KEGG and KaPPA-View 4 KEGG for grape, can support such studies.

Protein Arginylation: Over 50 Years of Discovery.

Posttranslational modifications have emerged in recent years as the major biological regulators responsible for the orders of magnitude increase in complexity of protein functions. These "molecular switches" affect nearly every protein in vivo by modulating their protein structure, activity, molecular interactions, and homeostasis. While over 350 protein modifications have been described, only a handful of them have been characterized. Until recently, protein arginylation has belonged to the list of obscure, poorly understood posttranslational modifications, before the recent explosion of studies has put arginylation on the map of intracellular metabolic pathways and biological processes. This chapter contains an overview of all the major milestones in the protein arginylation field, from its original discovery in 1963 to this day.