1
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Chen J, Lou Y, Liu Y, Deng B, Zhu Z, Yang S, Chen D. Advances in Chromatographic and Mass Spectrometric Techniques for Analyzing Reducing Monosaccharides and Their Phosphates in Biological Samples. Crit Rev Anal Chem 2024:1-23. [PMID: 38855933 DOI: 10.1080/10408347.2024.2364232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Reducing monosaccharides and their phosphates are critical metabolites in the central carbon metabolism pathway of living organisms. Variations in their content can indicate abnormalities in metabolic pathways and the onset of certain diseases, necessitating their analysis and detection. Reducing monosaccharides and their phosphates exhibit significant variations in content within biological samples and are present in many isomers, which makes the accurate quantification of reducing monosaccharides and their phosphates in biological samples a challenging task. Various analytical methods such as spectroscopy, fluorescence detection, colorimetry, nuclear magnetic resonance spectroscopy, sensor-based techniques, chromatography, and mass spectrometry are employed to detect monosaccharides and phosphates. In comparison, chromatography and mass spectrometry are highly favored for their ability to simultaneously analyze multiple components and their high sensitivity and selectivity. This review thoroughly evaluates the current chromatographic and mass spectrometric methods used for detecting reducing monosaccharides and their phosphates from 2013 to 2023, highlighting their efficacy and the advancements in these analytical technologies.
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Affiliation(s)
- Jiaqi Chen
- Zhengzhou Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Yifeng Lou
- Zhengzhou Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Yuwei Liu
- Zhengzhou Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Bowen Deng
- Zhengzhou Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Zheng Zhu
- Zhengzhou Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Sen Yang
- Zhengzhou Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
- Henan Key Laboratory of Nanomedicine for Targeting Diagnosis and Treatment, Zhengzhou University, Zhengzhou, China
| | - Di Chen
- Zhengzhou Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
- Henan Key Laboratory of Nanomedicine for Targeting Diagnosis and Treatment, Zhengzhou University, Zhengzhou, China
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2
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Westhoff P, Weber APM. The role of metabolomics in informing strategies for improving photosynthesis. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:1696-1713. [PMID: 38158893 DOI: 10.1093/jxb/erad508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 12/29/2023] [Indexed: 01/03/2024]
Abstract
Photosynthesis plays a vital role in acclimating to and mitigating climate change, providing food and energy security for a population that is constantly growing, and achieving an economy with zero carbon emissions. A thorough comprehension of the dynamics of photosynthesis, including its molecular regulatory network and limitations, is essential for utilizing it as a tool to boost plant growth, enhance crop yields, and support the production of plant biomass for carbon storage. Photorespiration constrains photosynthetic efficiency and contributes significantly to carbon loss. Therefore, modulating or circumventing photorespiration presents opportunities to enhance photosynthetic efficiency. Over the past eight decades, substantial progress has been made in elucidating the molecular basis of photosynthesis, photorespiration, and the key regulatory mechanisms involved, beginning with the discovery of the canonical Calvin-Benson-Bassham cycle. Advanced chromatographic and mass spectrometric technologies have allowed a comprehensive analysis of the metabolite patterns associated with photosynthesis, contributing to a deeper understanding of its regulation. In this review, we summarize the results of metabolomics studies that shed light on the molecular intricacies of photosynthetic metabolism. We also discuss the methodological requirements essential for effective analysis of photosynthetic metabolism, highlighting the value of this technology in supporting strategies aimed at enhancing photosynthesis.
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Affiliation(s)
- Philipp Westhoff
- CEPLAS Plant Metabolomics and Metabolism Laboratory, Heinrich-Heine-University, Universitätsstrasse 1, D-40225 Düsseldorf, Germany
| | - Andreas P M Weber
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Science (CEPLAS), Heinrich-Heine-University, Universitätsstrasse 1, D-40225 Düsseldorf, Germany
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3
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Ofoe R, Thomas RH, Abbey L. Coordinated Regulation of Central Carbon Metabolism in Pyroligneous Acid-Treated Tomato Plants under Aluminum Stress. Metabolites 2023; 13:770. [PMID: 37367927 DOI: 10.3390/metabo13060770] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 06/15/2023] [Accepted: 06/17/2023] [Indexed: 06/28/2023] Open
Abstract
Aluminum (Al) toxicity is a major threat to global crop production in acidic soils, which can be mitigated by natural substances such as pyroligneous acid (PA). However, the effect of PA in regulating plant central carbon metabolism (CCM) under Al stress is unknown. In this study, we investigated the effects of varying PA concentrations (0, 0.25 and 1% PA/ddH2O (v/v)) on intermediate metabolites involved in CCM in tomato (Solanum lycopersicum L., 'Scotia') seedlings under varying Al concentrations (0, 1 and 4 mM AlCl3). A total of 48 differentially expressed metabolites of CCM were identified in the leaves of both control and PA-treated plants under Al stress. Calvin-Benson cycle (CBC) and pentose phosphate pathway (PPP) metabolites were considerably reduced under 4 mM Al stress, irrespective of the PA treatment. Conversely, the PA treatment markedly increased glycolysis and tricarboxylic acid cycle (TCA) metabolites compared to the control. Although glycolysis metabolites in the 0.25% PA-treated plants under Al stress were comparable to the control, the 1% PA-treated plants exhibited the highest accumulation of glycolysis metabolites. Furthermore, all PA treatments increased TCA metabolites under Al stress. Electron transport chain (ETC) metabolites were higher in PA-treated plants alone and under 1 mM, Al but were reduced under a higher Al treatment of 4 mM. Pearson correlation analysis revealed that CBC metabolites had a significantly strong positive (r = 0.99; p < 0.001) association with PPP metabolites. Additionally, glycolysis metabolites showed a significantly moderate positive association (r = 0.76; p < 0.05) with TCA metabolites, while ETC metabolites exhibited no association with any of the determined pathways. The coordinated association between CCM pathway metabolites suggests that PA can stimulate changes in plant metabolism to modulate energy production and biosynthesis of organic acids under Al stress conditions.
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Affiliation(s)
- Raphael Ofoe
- Department of Plant, Food, and Environmental Sciences, Faculty of Agriculture, Dalhousie University, 50 Pictou Road, Bible Hill, NS B2N 5E3, Canada
| | - Raymond H Thomas
- Department of Biology, Faculty of Science, Western University 2025E Biological & Geological Sciences Building, 1151 Richmond Street, London, ON N6A 5B7, Canada
| | - Lord Abbey
- Department of Plant, Food, and Environmental Sciences, Faculty of Agriculture, Dalhousie University, 50 Pictou Road, Bible Hill, NS B2N 5E3, Canada
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4
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Liu S, Lai Z, Zhang M, Tian H, Zhou J, Li Z. Facile synthesis of amino-functionalized magnetic materials for efficient enrichment of anionic metabolites from biological samples. Anal Chim Acta 2023; 1250:340977. [PMID: 36898822 DOI: 10.1016/j.aca.2023.340977] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 02/14/2023] [Accepted: 02/14/2023] [Indexed: 02/17/2023]
Abstract
The analysis of biological samples is often affected by the background matrix. Proper sample preparation is a critical step in the analytical procedure for complex samples. In this study, a simple and efficient enrichment strategy based on Amino-functionalized Polymer-Magnetic MicroParticles (NH2-PMMPs) with coral-like porous structures was developed to enable the detection of 320 anionic metabolites, providing detailed coverage of phosphorylation metabolism. Among them, 102 polar phosphate metabolites including nucleotides, cyclic nucleotides, sugar nucleotides, phosphate sugars, and phosphates, were enriched and identified from serum, tissues, and cells. Furthermore, the detection of 34 previously unknown polar phosphate metabolites in serum samples demonstrates the advantages of this efficient enrichment method for mass spectrometric analysis. The limit of detections (LODs) were between 0.02 and 4 nmol/L for most anionic metabolites and its high sensitivity enabled the detection of 36 polar anion metabolites from 10 cell equivalent samples. This study has provided a promising tool for the efficient enrichment and analysis of anionic metabolites in biological samples with high sensitivity and broad coverage, facilitating the knowledge of the phosphorylation processes of life.
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Affiliation(s)
- Shuai Liu
- Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China
| | - Zhizhen Lai
- Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China
| | - Mo Zhang
- Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China
| | - Hongtao Tian
- Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China
| | - Jiang Zhou
- Analytical Instrumentation Center, College of Chemistry and Molecular Engineering, Peking University, 292 Chengfu Road, Beijing, 100871, China.
| | - Zhili Li
- Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China.
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5
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Su M, Serafimov K, Li P, Knappe C, Lämmerhofer M. Isomer selectivity of one- and two-dimensional approaches of mixed-mode and hydrophilic interaction liquid chromatography coupled to tandem mass spectrometry for sugar phosphates of glycolysis and pentose phosphate pathways. J Chromatogr A 2023; 1688:463727. [PMID: 36566570 DOI: 10.1016/j.chroma.2022.463727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 12/16/2022] [Accepted: 12/17/2022] [Indexed: 12/23/2022]
Abstract
In this study, the chromatographic behavior of mixed-mode and hydrophilic interaction liquid chromatography (HILIC) with the mixed-mode HILIC/strong anion-exchange (SAX) column HILICpak VT-50 2D and the two HILIC columns Atlantis Premier BEH Z-HILIC and Acquity Premier BEH Amide was assessed with regard to their separation capability of the metabolites from the glycolysis and pentose phosphate pathways. Chromatographic conditions were evaluated with the aim of achieving separation of the isomeric glycolytic phosphorylated carbohydrate metabolites free from isomeric interferences and thus allowing for selective targeted analysis by liquid chromatography with tandem mass spectrometry (MS/MS) using multiple reaction monitoring acquisition. The effects of pH values (8.0/9.0/10.0) of the ammonium bicarbonate buffer and gradient time were investigated during HILIC-MS/MS analysis, with the optimal conditions found at pH = 10.0. Separation of the pentose phosphate isomers (ribose 5- and 1-phosphate, xylulose 5-phosphate and ribulose 5-phosphate) was achieved on the mixed-mode HILIC/SAX (HILICpak VT-50 2D) column and HILIC BEH Amide column. Column performance was evaluated based on the direct comparison of chromatographic parameters, i.e. peak width at 50% and peak tailing factors of the individual metabolites. Parity plots were generated allowing a direct comparison between the normalized retention times and assessment of orthogonality of all 3 stationary phases evaluated. Separation of 7 biologically relevant hexose monophosphates metabolites turned out to be challenging by HILIC-MS/MS, with the BEH Amide providing the best individual results for such a separation. However, fructose 6-phosphate and glucose 1-phosphate co-eluted. Therefore, an on-line heart-cutting HILIC-Mixed Mode 2D-LC-QToF experiment was conducted, allowing the separation of this critical isomer pair. In this setup, the BEH Amide column in the 1D separated the majority of target metabolites, while a heart-cut of the peak from totally coeluted fructose 6-phosphate and glucose 1-phosphate was separated in the 2D with HILICpak VT50-2D column, thus allowing undisturbed determination of the glycolytic phosphorylated carbohydrate metabolites due to their chromatographic separation from hexose monophosphate metabolites. The assay specificity towards 7 common hexose monophosphates was characterized (glucose 1- and 6-phosphate, galactose 1- and 6-phosphate, fructose 6-phosphate, mannose 1- and 6-phosphate). The selectivity of some rare hexose monophosphates (allose 6-phosphate, tagatose 6-phosphate, sorbose 1-phosphate) was also tested.
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Affiliation(s)
- Min Su
- Pharmaceutical (Bio-)Analysis, Institute of Pharmaceutical Sciences, University of Tübingen, Auf der Morgenstelle 8, Tübingen 72076, Germany
| | - Kristian Serafimov
- Pharmaceutical (Bio-)Analysis, Institute of Pharmaceutical Sciences, University of Tübingen, Auf der Morgenstelle 8, Tübingen 72076, Germany
| | - Peng Li
- Pharmaceutical (Bio-)Analysis, Institute of Pharmaceutical Sciences, University of Tübingen, Auf der Morgenstelle 8, Tübingen 72076, Germany
| | - Cornelius Knappe
- Pharmaceutical (Bio-)Analysis, Institute of Pharmaceutical Sciences, University of Tübingen, Auf der Morgenstelle 8, Tübingen 72076, Germany
| | - Michael Lämmerhofer
- Pharmaceutical (Bio-)Analysis, Institute of Pharmaceutical Sciences, University of Tübingen, Auf der Morgenstelle 8, Tübingen 72076, Germany.
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6
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Li S, Zhang Z, Liu FL, Yuan BF, Liu TG, Feng YQ. Comprehensive Profiling of Phosphomonoester Metabolites in Saccharomyces cerevisiae by the Chemical Isotope Labeling-LC-MS Method. J Proteome Res 2023; 22:114-122. [PMID: 36484485 DOI: 10.1021/acs.jproteome.2c00507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Phosphomonoesters are important biosynthetic and energy metabolism intermediates in microorganisms. A comprehensive analysis of phosphomonoester metabolites is of great significance for the understanding of their metabolic phosphorylation process and inner mechanism. In this study, we established a pair of isotope reagent d0/d5-2-diazomethyl-N-methyl-phenyl benzamide-labeling-based LC-MS method for the comprehensive analysis of phosphomonoester metabolites. By this method, the labeled phosphomonoester metabolites specifically produced characteristic isotope paired peaks with an m/z difference of 5.0314 in the MS1 spectra and a pair of diagnostic ions (m/z 320.0693/325.1077) in the MS2 spectra. Based on this, a diagnostic ion-based strategy was established for the rapid screening, identification, and relative quantification of phosphomonoester metabolites. Using this strategy, 42 phosphomonoester metabolites were highly accurately identified fromSaccharomyces cerevisiae (S. cerevisiae). Notably, two phosphomonoesters were first detected fromS. cerevisiae. The relative quantification results indicated that the contents of nine phosphomonoester metabolites including two intermediates (Ru5P and S7P) in the pentose phosphate pathway (PPP) were significantly different between lycopene-producible and wild-type S. cerevisiae. A further enzyme assay indicated that the activity of the PPP was closely related to the production of lycopene. Our findings provide new perspectives for the related mechanism study and valuable references for making informed microbial engineering decisions.
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Affiliation(s)
- Sha Li
- Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Zheng Zhang
- Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Fei-Long Liu
- Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Bi-Feng Yuan
- School of Public Health, Wuhan University, Wuhan 430071, China
| | - Tian-Gang Liu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Yu-Qi Feng
- Department of Chemistry, Wuhan University, Wuhan 430072, China.,School of Public Health, Wuhan University, Wuhan 430071, China
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7
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Inhibition of mTOR improves malnutrition induced hepatic metabolic dysfunction. Sci Rep 2022; 12:19948. [PMID: 36402829 PMCID: PMC9675758 DOI: 10.1038/s41598-022-24428-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 11/15/2022] [Indexed: 11/21/2022] Open
Abstract
Severe malnutrition accounts for half-a-million deaths annually in children under the age of five. Despite improved WHO guidelines, inpatient mortality remains high and is associated with metabolic dysfunction. Previous studies suggest a correlation between hepatic metabolic dysfunction and impaired autophagy. We aimed to determine the role of mTORC1 inhibition in a murine model of malnutrition-induced hepatic dysfunction. Wild type weanling C57/B6 mice were fed a 18 or 1% protein diet for two weeks. A third low-protein group received daily rapamycin injections, an mTORC1 inhibitor. Hepatic metabolic function was assessed by histology, immunofluorescence, gene expression, metabolomics and protein levels. Low protein-fed mice manifested characteristics of severe malnutrition, including weight loss, hypoalbuminemia, hypoglycemia, hepatic steatosis and cholestasis. Low protein-fed mice had fewer mitochondria and showed signs of impaired mitochondrial function. Rapamycin prevented hepatic steatosis, restored ATP levels and fasted plasma glucose levels compared to untreated mice. This correlated with increased content of LC3-II, and decreased content mitochondrial damage marker, PINK1. We demonstrate that hepatic steatosis and disturbed mitochondrial function in a murine model of severe malnutrition can be partially prevented through inhibition of mTORC1. These findings suggest that stimulation of autophagy could be a novel approach to improve metabolic function in severely malnourished children.
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8
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Targeted profiling of polar metabolites in cancer metabolic reprogramming by hydrophilic interaction liquid chromatography-tandem mass spectrometry. J Chromatogr A 2022; 1686:463654. [DOI: 10.1016/j.chroma.2022.463654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 11/09/2022] [Accepted: 11/16/2022] [Indexed: 11/19/2022]
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9
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Targeted analysis of sugar phosphates from glycolysis pathway by phosphate methylation with liquid chromatography coupled to tandem mass spectrometry. Anal Chim Acta 2022; 1221:340099. [DOI: 10.1016/j.aca.2022.340099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 06/12/2022] [Accepted: 06/14/2022] [Indexed: 11/18/2022]
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10
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Camprubi E, Harrison SA, Jordan SF, Bonnel J, Pinna S, Lane N. Do Soluble Phosphates Direct the Formose Reaction towards Pentose Sugars? ASTROBIOLOGY 2022; 22:981-991. [PMID: 35833833 DOI: 10.1089/ast.2021.0125] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The formose reaction has been a leading hypothesis for the prebiotic synthesis of sugars such as ribose for many decades but tends to produce complex mixtures of sugars and often tars. Channeling the formose reaction towards the synthesis of biologically useful sugars such as ribose has been a holy grail of origins-of-life research. Here, we tested the hypothesis that a simple, prebiotically plausible phosphorylating agent, acetyl phosphate, could direct the formose reaction towards ribose through phosphorylation of intermediates in a manner resembling gluconeogenesis and the pentose phosphate pathway. We did indeed find that addition of acetyl phosphate to a developing formose reaction stabilized pentoses, including ribose, such that after 5 h of reaction about 10-fold more ribose remained compared with control runs. But mechanistic analyses using liquid chromatography-mass spectrometry showed that, far from being directed towards ribose by phosphorylation, the formose reaction was halted by the precipitation of Ca2+ ions as phosphate minerals such as apatite and hydroxyapatite. Adding orthophosphate had the same effect. Phosphorylated sugars were only detected below the limit of quantification when adding acetyl phosphate. Nonetheless, our findings are not strictly negative. The sensitivity of the formose reaction to geochemically reasonable conditions, combined with the apparent stability of ribose under these conditions, serves as a valuable constraint on possible pathways of sugar synthesis at the origin of life.
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Affiliation(s)
- E Camprubi
- Origins Center, Department of Earth Sciences, Utrecht University, Utrecht, The Netherlands
- Centre for Life's Origins and Evolution (CLOE), Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - S A Harrison
- Centre for Life's Origins and Evolution (CLOE), Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - S F Jordan
- Centre for Life's Origins and Evolution (CLOE), Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - J Bonnel
- Centre for Life's Origins and Evolution (CLOE), Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - S Pinna
- Centre for Life's Origins and Evolution (CLOE), Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - N Lane
- Centre for Life's Origins and Evolution (CLOE), Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
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11
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Liu S, Zhang M, Lai Z, Tian H, Qiu Y, Li Z. Coral-like Magnetic Particles for Chemoselective Extraction of Anionic Metabolites. ACS APPLIED MATERIALS & INTERFACES 2022; 14:32890-32900. [PMID: 35819264 DOI: 10.1021/acsami.2c06922] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
To date, advanced chemical biology tools for chemoselective extraction of metabolites are limited. In this study, unique coral-like polymer particles were synthesized via high concentrations of 1-ethyl-3-(3-(dimethylamino)propyl) carbodiimide hydrochloride (EDC)/N-hydroxysuccinimide (NHS), which are usually used as condensation agents. The polymers can wrap or adhere Fe3O4 nanoparticles (Fe3O4-NPs) to form polymer magnetic microparticles (PMMPs). With abundant NHS-activated moieties on their surface, the coral-like PMMPs could be modified by cystamine for the chemoselective extraction of phosphate/carboxylate anion metabolites from complex biological samples. Finally, 97 metabolites including nucleotides, phosphates, phosphate sugars, carboxylate sugars, and organic acids were extracted and identified from serum, tissues, and cells. These metabolites are involved in four major metabolic pathways including glycolysis, the tricarboxylic acid cycle, the pentose phosphate pathway, and nucleotide metabolism. This study has provided a cost-effective and easy-to-implement preparation of PMMPs with a robust chemoselective extraction ability and versatile applications.
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Affiliation(s)
- Shuai Liu
- Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, 5 Dongdan San Tiao, Beijing 100005, China
| | - Mo Zhang
- Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, 5 Dongdan San Tiao, Beijing 100005, China
| | - Zhizhen Lai
- Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, 5 Dongdan San Tiao, Beijing 100005, China
| | - Hongtao Tian
- Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, 5 Dongdan San Tiao, Beijing 100005, China
| | - Yuming Qiu
- Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, 5 Dongdan San Tiao, Beijing 100005, China
| | - Zhili Li
- Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, 5 Dongdan San Tiao, Beijing 100005, China
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12
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Quantification of Glucose, fructose and 1,5-Anhydroglucitol in plasma of diabetic patients by ultra performance liquid chromatography tandem mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci 2022; 1200:123277. [PMID: 35533424 DOI: 10.1016/j.jchromb.2022.123277] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 04/11/2022] [Accepted: 05/01/2022] [Indexed: 11/20/2022]
Abstract
Type 2 diabetes mellitus (T2DM), a worldwide disease that affects the quality of human life and social development. Glucose, fructose and 1,5-anhydroglucitol are closely related to diabetes mellitus. However, few methods have been reported to achieve these three carbohydrates in the blood simultaneously. In this study, a UPLC-MS/MS method allowing to quantify glucose, fructose, and 1,5-anhydroglucitol simultaneously in human plasma was developed. The analysis was performed by UPLC-MS/MS system with HILIC column. This new method provided satisfactory results in terms of calibration curves with good linearity (R2 > 0.99) over 3 order of magnitude range, precision (coefficient of variation of intra-day and inter-day: 0.72-10.23% and 2.21-13.8%), accuracy (results of intra-day and inter-day: 97-113%, 100-107%), matrix effects (87-109%), recovery (93-119%), carry-over (0.004-0.014%), as well as stability (0.04-6.9%) within the acceptance criteria. The reproducible, precise and accurate method with suitable dynamic ranges was successfully applied to the analysis of glucose, fructose and 1,5-anhydroglucitol in T2DM under different pathophysiological conditions.
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13
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Li S, Liu FL, Zhang Z, Yin XM, Ye TT, Yuan BF, Feng YQ. Ultrasensitive Determination of Sugar Phosphates in Trace Samples by Stable Isotope Chemical Labeling Combined with RPLC-MS. Anal Chem 2022; 94:4866-4873. [PMID: 35274930 DOI: 10.1021/acs.analchem.2c00346] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Sugar phosphates are important metabolic intermediates in organisms and play a vital role in energy and central carbon metabolism. Profiling of sugar phosphates is of great significance but full of challenges due to their high structural similarity and low sensitivities in liquid chromatography (LC)-mass spectrometry (MS). In this study, we developed a novel stable isotope chemical labeling combined with the reversed-phase (RP)LC-MS method for ultrasensitive determination of sugar phosphates at the single-cell level. By chemical derivatization with 2-(diazo-methyl)-N-methyl-N-phenyl-benzamide (2-DMBA) and d5-2-DMBA, sugar phosphate isomers can obtain better separation and identification, and the detection sensitivities of sugar phosphates increased by 3.5-147 folds. The obtained limits of detection of sugar phosphates ranged from 5 to 16 pg/mL. Using this method, we achieved ultrasensitive and accurate quantification of 12 sugar phosphates in different trace biological samples. Benefiting from the improved separation and detection sensitivity, we successfully quantified five sugar phosphates (d-glucose 1-phosphate, d-mannose 6-phosphate, d-fructose 6-phosphate, d-glucose 6-phosphate, and seduheptulose 7-phosphate) in a single protoplast of Arabidopsis thaliana.
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Affiliation(s)
- Sha Li
- Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Fei-Long Liu
- Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Zheng Zhang
- School of Life Sciences and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei 430079, China
| | - Xiao-Ming Yin
- Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Tian-Tian Ye
- Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Bi-Feng Yuan
- Department of Chemistry, Wuhan University, Wuhan 430072, China.,School of Public Health, Wuhan University, Wuhan 430071, China
| | - Yu-Qi Feng
- Department of Chemistry, Wuhan University, Wuhan 430072, China.,School of Public Health, Wuhan University, Wuhan 430071, China
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14
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Lozinski BM, Frederick B, Li Y, Saqui-Salces M, Shurson GC, Urriola PE, Wilson ML, Johnston LJ. Effects of water quality on growth performance and health of nursery pigs. Transl Anim Sci 2022; 6:txac002. [PMID: 35155995 PMCID: PMC8827558 DOI: 10.1093/tas/txac002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 01/12/2022] [Indexed: 11/13/2022] Open
Abstract
An experiment was conducted to determine the effects of providing drinking water of differing qualities on growth performance and health of nursery pigs. Weanling pigs (n = 450; 150 pigs/group; 10 pigs/pen) were assigned randomly to one of three experimental groups consisting of three water sources of varying qualities: 1) Water source A containing 1,410 ppm hardness (CaCO3 equivalent), 1,120 ppm sulfates, and 1,500 ppm total dissolved solids (TDS); 2) Water source B containing 909 ppm hardness (CaCO3 equivalent), 617 ppm sulfates, and 1,050 ppm TDS; and 3) Water source C containing 235 ppm hardness (CaCO3 equivalent), 2 ppm sulfates, and 348 ppm TDS. Pigs were provided ad libitum access to their respective water sources for the duration of the study which began at weaning (21 d of age) and ended 40 d later (61 d of age). Individual pig weights were recorded weekly along with feed intake on a pen basis. Occurrences of morbidity and mortality were recorded daily. Subjective fecal scores were assigned on a pen basis and blood samples were used to evaluate blood chemistry, cytokine concentrations, and phagocytic activity. A differential sugar absorption test was used to assess intestinal permeability. Fecal grab samples were used to establish diet digestibility, and drinking behavior was video-recorded to assess pigs’ acceptance of water sources provided. The statistical model considered fixed effects of water source, room, and their interaction with the random effect of pen. A repeated measures analysis was conducted to determine the effects of water quality over time. There were no differences (P > 0.440) among water sources in average daily gain (A, 0.46 kg/d; B, 0.46 kg/d; C, 0.47 kg/d) or average daily feed intake (A, 0.68 kg/d; B, 0.69 kg/d; C, 0.71 kg/d). Overall mortality of pigs was 0.44% and did not differ across the three water sources. There were no differences in apparent total tract digestibility of the diet, intestinal permeability, immune parameters, or blood chemistry attributable to quality of water consumed by pigs. Pigs did not show an aversion to the water sources provided, because total time pigs spent at the drinker did not differ (P > 0.750) among water sources on days 1 through 3 of the experiment. These data indicate that the water sources of differing quality studied did not affect growth performance or health of nursery pigs.
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Affiliation(s)
- B M Lozinski
- Department of Animal Science, University of Minnesota, St. Paul, United States of America
| | - B Frederick
- Christensen Family Farms, Sleepy Eye, MN, United States of America
| | - Y Li
- Department of Animal Science, University of Minnesota, St. Paul, United States of America
- West Central Research and Outreach Center, University of Minnesota, Morris, United States of America
| | - M Saqui-Salces
- Department of Animal Science, University of Minnesota, St. Paul, United States of America
| | - G C Shurson
- Department of Animal Science, University of Minnesota, St. Paul, United States of America
| | - P E Urriola
- Department of Animal Science, University of Minnesota, St. Paul, United States of America
| | - M L Wilson
- Department of Soil, Water, and Climate, University of Minnesota, St. Paul, United States of America
| | - L J Johnston
- Department of Animal Science, University of Minnesota, St. Paul, United States of America
- West Central Research and Outreach Center, University of Minnesota, Morris, United States of America
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15
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Coupling Mixed Mode Chromatography/ESI Negative MS Detection with Message-Passing Neural Network Modeling for Enhanced Metabolome Coverage and Structural Identification. Metabolites 2021; 11:metabo11110772. [PMID: 34822429 PMCID: PMC8620857 DOI: 10.3390/metabo11110772] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 10/28/2021] [Accepted: 11/08/2021] [Indexed: 11/16/2022] Open
Abstract
A key unmet need in metabolomics continues to be the specific, selective, accurate detection of traditionally difficult to retain molecules including simple sugars, sugar phosphates, carboxylic acids, and related amino acids. Designed to retain the metabolites of central carbon metabolism, this Mixed Mode (MM) chromatography applies varied pH, salt concentration and organic content to a positively charged quaternary amine polyvinyl alcohol stationary phase. This MM method is capable of separating glucose from fructose, and four hexose monophosphates a single chromatographic run. Coupled to a QExactive Orbitrap Mass Spectrometer with negative ESI, linearity, LLOD, %CV, and mass accuracy were assessed using 33 metabolite standards. The standards were linear on average >3 orders of magnitude (R2 > 0.98 for 30/33) with LLOD < 1 pmole (26/33), median CV of 12% over two weeks, and median mass accuracy of 0.49 ppm. To assess the breadth of metabolome coverage and better define the structural elements dictating elution, we injected 607 unique metabolites and determined that 398 are well retained. We then split the dataset of 398 documented RTs into training and test sets and trained a message-passing neural network (MPNN) to predict RT from a featurized heavy atom connectivity graph. Unlike traditional QSAR methods that utilize hand-crafted descriptors or pre-defined structural keys, the MPNN aggregates atomic features across the molecular graph and learns to identify molecular subgraphs that are correlated with variations in RTs. For sugars, sugar phosphates, carboxylic acids, and isomers, the model achieves a predictive RT error of <2 min on 91%, 50%, 77%, and 72% of held-out compounds from these subsets, with overall root mean square errors of 0.11, 0.34, 0.18, and 0.53 min, respectively. The model was then applied to rank order metabolite IDs for molecular features altered by GLS2 knockout in mouse primary hepatocytes.
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16
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Progress and Challenges in Quantifying Carbonyl-Metabolomic Phenomes with LC-MS/MS. Molecules 2021; 26:molecules26206147. [PMID: 34684729 PMCID: PMC8541004 DOI: 10.3390/molecules26206147] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 09/30/2021] [Accepted: 10/01/2021] [Indexed: 12/17/2022] Open
Abstract
Carbonyl-containing metabolites widely exist in biological samples and have important physiological functions. Thus, accurate and sensitive quantitative analysis of carbonyl-containing metabolites is crucial to provide insight into metabolic pathways as well as disease mechanisms. Although reversed phase liquid chromatography electrospray ionization mass spectrometry (RPLC-ESI-MS) is widely used due to the powerful separation capability of RPLC and high specificity and sensitivity of MS, but it is often challenging to directly analyze carbonyl-containing metabolites using RPLC-ESI-MS due to the poor ionization efficiency of neutral carbonyl groups in ESI. Modification of carbonyl-containing metabolites by a chemical derivatization strategy can overcome the obstacle of sensitivity; however, it is insufficient to achieve accurate quantification due to instrument drift and matrix effects. The emergence of stable isotope-coded derivatization (ICD) provides a good solution to the problems encountered above. Thus, LC-MS methods that utilize ICD have been applied in metabolomics including quantitative targeted analysis and untargeted profiling analysis. In addition, ICD makes multiplex or multichannel submetabolome analysis possible, which not only reduces instrument running time but also avoids the variation of MS response. In this review, representative derivatization reagents and typical applications in absolute quantification and submetabolome profiling are discussed to highlight the superiority of the ICD strategy for detection of carbonyl-containing metabolites.
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17
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Liu FL, Ye TT, Ding JH, Yin XM, Yang XK, Huang WH, Yuan BF, Feng YQ. Chemical Tagging Assisted Mass Spectrometry Analysis Enables Sensitive Determination of Phosphorylated Compounds in a Single Cell. Anal Chem 2021; 93:6848-6856. [PMID: 33882236 DOI: 10.1021/acs.analchem.1c00915] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Polar phosphorylated metabolites are involved in a variety of biological processes and play vital roles in energetic metabolism, cofactor regeneration, and nucleic acid synthesis. However, it is often challenging to interrogate polar phosphorylated metabolites and compounds from biological samples. Liquid chromatography-mass spectrometry (LC/MS) now plays a central role in metabolomic studies. However, LC/MS-based approaches have been hampered by the issues of the low ionization efficiencies, low in vivo concentrations, and less chemical stability of polar phosphorylated metabolites. In this work, we synthesized paired reagents of light and heavy isotopomers, 2-(diazomethyl)phenyl)(9-methyl-1,3,4,9-tetrahydro-2H-pyrido[3,4-b]indol-2-yl)methanone (DMPI) and d3-(2-(diazomethyl)phenyl)(9-methyl-1,3,4,9-tetrahydro-2H-pyrido[3,4-b]indol-2-yl)methanone (d3-DMPI). The paired reagents of DMPI and d3-DMPI carry diazo groups that can efficiently and selectively react with the phosphate group on polar phosphorylated metabolites under mild conditions. As a proof of concept, we found that the transfer of the indole heterocycle group from DMPI/d3-DMPI to ribonucleotides led to the significant increase of ionization efficiencies of ribonucleotides during LC/MS analysis. The detection sensitivities of these ribonucleotides increased by 25-1137-fold upon DMPI tagging with the limits of detection (LODs) being between 7 and 150 amol. With the developed method, we achieved the determination of all the 12 ribonucleotides from a single mammalian cell and from a single stamen of Arabidopsis thaliana. The method provides a valuable tool to investigate the dynamic changes of polar phosphorylated metabolites in a single cell under particular conditions.
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Affiliation(s)
- Fei-Long Liu
- Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Tian-Tian Ye
- Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Jiang-Hui Ding
- Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Xiao-Ming Yin
- Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Xiao-Ke Yang
- Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Wei-Hua Huang
- Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Bi-Feng Yuan
- Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University, Wuhan 430072, China.,School of Health Sciences, Wuhan University, Wuhan 430071, China
| | - Yu-Qi Feng
- Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University, Wuhan 430072, China.,School of Health Sciences, Wuhan University, Wuhan 430071, China
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18
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Qu M, Ma S, Huang Y, Yuan H, Zhang S, Ouyang G, Zhao Y. LC-MS/MS-based non-isotopically paired labeling (NIPL) strategy for the qualification and quantification of monosaccharides. Talanta 2021; 231:122336. [PMID: 33965016 DOI: 10.1016/j.talanta.2021.122336] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 03/08/2021] [Accepted: 03/18/2021] [Indexed: 01/03/2023]
Abstract
Investigation into monosaccharides is critical for studies of oligosaccharides structure and function in biological processes. However, monosaccharides quantification is still challenge due to their isomeric structure and high hydrophilic properties. Besides, it was difficult to obtain isotopic internal standards (IS) of each monosaccharide in complex matrixes. Herein, we developed a novel strategy for the qualification and quantification of monosaccharides in urine using two structure analogs 1-(4-methylphenyl)-3-methyl-5-pyrazolone (MPMP) and1-phenyl-3-methyl-5-pyrazolone (PMP) as non-isotopically paired labeling (NIPL) reagents by liquid chromatograph-tandem mass spectrometry (LC-MS/MS). The derivatized monosaccharides by NIPL method not only had sufficient retention time differences on reversed-phase column, but also exhibited predominant product ion pairs (m/z 189 & m/z 175) in the multiple reaction monitoring (MRM) mode. In this method, PMP labeled standards were adopted as one-to-one internal standards (ISs). 12 urinary monosaccharides were successfully determined and the linear ranges expanded five orders of magnitude with limit of quantification (LOQ) varied from 0.09 ng mL-1 to 0.36 ng mL-1 as well as the accuracy higher than 98.15% and the relative standard derivation (RSD) lower than 7.92%. With assistance of multivariate analysis, the targeted monosaccharide biomarkers were firstly obtained for the diagnosis of bladder cancer. By the inexpensive NIPL reagents-MPMP/PMP, the developed strategy possessed the specific advantages of low cost, simple operation, high sensitivity and high accuracy for the qualification and quantitation of monosaccharides. As expected, this method will provide an alternative application potential for targeted metabolomics analysis.
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Affiliation(s)
- Mengyuan Qu
- College of Chemistry, Zhengzhou University, China
| | - Shanshan Ma
- College of Chemistry, Zhengzhou University, China
| | - Yanjie Huang
- Department of Pediatrics, Henan University of CM, China
| | - Hang Yuan
- College of Chemistry, Zhengzhou University, China.
| | | | | | - Yufen Zhao
- College of Chemistry, Zhengzhou University, China
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19
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Jandova J, Wondrak GT. Genomic GLO1 deletion modulates TXNIP expression, glucose metabolism, and redox homeostasis while accelerating human A375 malignant melanoma tumor growth. Redox Biol 2021; 39:101838. [PMID: 33360689 PMCID: PMC7772567 DOI: 10.1016/j.redox.2020.101838] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 11/29/2020] [Accepted: 12/02/2020] [Indexed: 12/26/2022] Open
Abstract
Glyoxalase 1 (encoded by GLO1) is a glutathione-dependent enzyme detoxifying the glycolytic byproduct methylglyoxal (MG), an oncometabolite involved in metabolic reprogramming. Recently, we have demonstrated that GLO1 is overexpressed in human malignant melanoma cells and patient tumors and substantiated a novel role of GLO1 as a molecular determinant of invasion and metastasis in melanoma. Here, employing NanoString™ gene expression profiling (nCounter™ 'PanCancer Progression Panel'), we report that CRISPR/Cas 9-based GLO1 deletion from human A375 malignant melanoma cells alters glucose metabolism and redox homeostasis, observable together with acceleration of tumorigenesis. Nanostring™ analysis identified TXNIP (encoding thioredoxin-interacting protein), a master regulator of cellular energy metabolism and redox homeostasis, displaying the most pronounced expression change in response to GLO1 elimination, confirmed by RT-qPCR and immunoblot analysis. TXNIP was also upregulated in CRISPR/Cas9-engineered DU145 prostate carcinoma cells lacking GLO1, and treatment with MG or a pharmacological GLO1 inhibitor (TLSC702) mimicked GLO1_KO status, suggesting that GLO1 controls TXNIP expression through regulation of MG. GLO1_KO status was characterized by (i) altered oxidative stress response gene expression, (ii) attenuation of glucose uptake and metabolism with downregulation of gene expression (GLUT1, GFAT1, GFAT2, LDHA) and depletion of related key metabolites (glucose-6-phosphate, UDP-N-acetylglucosamine), and (iii) immune checkpoint modulation (PDL1). While confirming our earlier finding that GLO1 deletion limits invasion and metastasis with modulation of EMT-related genes (e.g. TGFBI, MMP9, ANGPTL4, TLR4, SERPINF1), we observed that GLO1_KO melanoma cells displayed a shortened population doubling time, cell cycle alteration with increased M-phase population, and enhanced anchorage-independent growth, a phenotype supported by expression analysis (CXCL8, CD24, IL1A, CDKN1A). Concordantly, an accelerated growth rate of GLO1_KO tumors, accompanied by TXNIP overexpression and metabolic reprogramming, was observable in a SCID mouse melanoma xenograft model, demonstrating that A375 melanoma tumor growth and metastasis can be dysregulated in opposing ways as a consequence of GLO1 elimination.
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Affiliation(s)
- Jana Jandova
- Department of Pharmacology and Toxicology, College of Pharmacy and UA Cancer Center, University of Arizona, Tucson, AZ, USA
| | - Georg T Wondrak
- Department of Pharmacology and Toxicology, College of Pharmacy and UA Cancer Center, University of Arizona, Tucson, AZ, USA.
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20
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Mass Spectrometry-based Metabolomics in Translational Research. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1310:509-531. [PMID: 33834448 DOI: 10.1007/978-981-33-6064-8_19] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Metabolomics is the systematic study of metabolite profiles of complex biological systems, and involves the systematic identification and quantification of metabolites. Metabolism is integrated with all biochemical reactions in biological systems; thus metabolite profiles provide collective information on biochemical processes induced by genetic or environmental perturbations. Transcriptomes or proteomes may not be functionally active and not always reflect phenotypic variations. The metabolome, however, consists of the biomolecules closest to the phenotype of living organisms, and is often called the molecular phenotype of biological systems. Thus, metabolome alterations can easily result in disease states, providing important clues to understand pathophysiological mechanisms contributing to various biomedical symptoms. The metabolome and metabolomics have been emphasized in translational research related to biomarker discovery, drug target discovery, drug responses, and disease mechanisms. This review describes the basic concepts, workflows, and applications of mass spectrometry-based metabolomics in translational research.
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21
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Gangi Setty T, Sarkar A, Coombes D, Dobson RCJ, Subramanian R. Structure and Function of N-Acetylmannosamine Kinases from Pathogenic Bacteria. ACS OMEGA 2020; 5:30923-30936. [PMID: 33324800 PMCID: PMC7726757 DOI: 10.1021/acsomega.0c03699] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Accepted: 10/20/2020] [Indexed: 06/12/2023]
Abstract
Several pathogenic bacteria import and catabolize sialic acids as a source of carbon and nitrogen. Within the sialic acid catabolic pathway, the enzyme N-acetylmannosamine kinase (NanK) catalyzes the phosphorylation of N-acetylmannosamine to N-acetylmannosamine-6-phosphate. This kinase belongs to the ROK superfamily of enzymes, which generally contain a conserved zinc-finger (ZnF) motif that is important for their structure and function. Previous structural studies have shown that the ZnF motif is absent in NanK of Fusobacterium nucleatum (Fn-NanK), a Gram-negative bacterium that causes the gum disease gingivitis. However, the effect in loss of the ZnF motif on the kinase activity is unknown. Using kinetic and thermodynamic studies, we have studied the functional properties of Fn-NanK to its substrates ManNAc and ATP, compared its activity with other ZnF motif-containing NanK enzymes from closely related Gram-negative pathogenic bacteria Haemophilus influenzae (Hi-NanK), Pasteurella multocida (Pm-NanK), and Vibrio cholerae (Vc-NanK). Our studies show a 10-fold decrease in substrate binding affinity between Fn-NanK (apparent KM ≈ 700 μM) and ZnF motif-containing NanKs (apparent KM ≈ 60 μM). To understand the structural features that combat the loss of the ZnF motif in Fn-NanK, we solved the crystal structures of functionally homologous ZnF motif-containing NanKs from P. multocida and H. influenzae. Here, we report Pm-NanK:unliganded, Pm-NanK:AMPPNP, Pm-NanK:ManNAc, Hi-NanK:ManNAc, and Hi-NanK:ManNAc-6P:ADP crystal structures. Structural comparisons of Fn-NanK with Hi-NanK, Pm-NanK, and hMNK (human N-acetylmannosamine kinase domain of UDP-N-acetylglucosamine-2-epimerase/N-acetylmannosamine kinase, GNE) show that even though there is less sequence identity, they have high degree of structural similarity. Furthermore, our structural analyses highlight that the ZnF motif of Fn-NanK is substituted by a set of hydrophobic residues, which forms a hydrophobic cluster that helps the proper orientation of ManNac in the active site. In summary, ZnF-containing and ZnF-lacking NanK enzymes from different Gram-negative pathogenic bacteria are functionally very similar but differ in their metal requirement. Our structural studies unveil the structural modifications in Fn-NanK that compensate the loss of the ZnF motif in comparison to other NanK enzymes.
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Affiliation(s)
- Thanuja Gangi Setty
- Institute for Stem
Cell Science and Regenerative Medicine, GKVK Post, Bangalore, KA 560065, India
- The University of Trans-Disciplinary Health Sciences
& Technology (TDU), Bangalore, KA 560064, India
| | - Arunabha Sarkar
- National Centre for Biological Sciences − TIFR, Bangalore 560065, India
| | - David Coombes
- Biomolecular Interaction Centre and School
of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
| | - Renwick C. J. Dobson
- Biomolecular Interaction Centre and School
of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
- Bio21 Molecular Science and Biotechnology
Institute, Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Ramaswamy Subramanian
- Institute for Stem
Cell Science and Regenerative Medicine, GKVK Post, Bangalore, KA 560065, India
- Department of Biological
Sciences and Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana 47907, United States
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22
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Oyama Y, Bartman CM, Bonney S, Lee JS, Walker LA, Han J, Borchers CH, Buttrick PM, Aherne CM, Clendenen N, Colgan SP, Eckle T. Intense Light-Mediated Circadian Cardioprotection via Transcriptional Reprogramming of the Endothelium. Cell Rep 2020; 28:1471-1484.e11. [PMID: 31390562 PMCID: PMC6708043 DOI: 10.1016/j.celrep.2019.07.020] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 05/15/2019] [Accepted: 07/08/2019] [Indexed: 01/10/2023] Open
Abstract
Consistent daylight oscillations and abundant oxygen availability are fundamental to human health. Here, we investigate the intersection between light-sensing (Period 2 [PER2]) and oxygen-sensing (hypoxia-inducible factor [HIF1A]) pathways in cellular adaptation to myocardial ischemia. We demonstrate that intense light is cardioprotective via circadian PER2 amplitude enhancement, mimicking hypoxia-elicited adenosine- and HIF1A-metabolic adaptation to myocardial ischemia under normoxic conditions. Whole-genome array from intense light-exposed wild-type or Per2-/- mice and myocardial ischemia in endothelial-specific PER2-deficient mice uncover a critical role for intense light in maintaining endothelial barrier function via light-enhanced HIF1A transcription. A proteomics screen in human endothelia reveals a dominant role for PER2 in metabolic reprogramming to hypoxia via mitochondrial translocation, tricarboxylic acid (TCA) cycle enzyme activity regulation, and HIF1A transcriptional adaption to hypoxia. Translational investigation of intense light in human subjects identifies similar PER2 mechanisms, implicating the use of intense light for the treatment of cardiovascular disease.
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Affiliation(s)
- Yoshimasa Oyama
- Mucosal Inflammation Program, Departments of Medicine and Anesthesiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Colleen M Bartman
- Mucosal Inflammation Program, Departments of Medicine and Anesthesiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA; Graduate Training Program in Cell Biology, Stem Cells, and Development, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Stephanie Bonney
- Mucosal Inflammation Program, Departments of Medicine and Anesthesiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA; Graduate Training Program in Cell Biology, Stem Cells, and Development, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - J Scott Lee
- Mucosal Inflammation Program, Departments of Medicine and Anesthesiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Lori A Walker
- Division of Cardiology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Jun Han
- Department of Biochemistry and Microbiology, Genome BC Proteomics Centre, University of Victoria, Victoria, BC, Canada
| | - Christoph H Borchers
- Department of Biochemistry and Microbiology, Genome BC Proteomics Centre, University of Victoria, Victoria, BC, Canada; Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, Quebec, Canada; Gerald Bronfman Department of Oncology, Jewish General Hospital, McGill University, Montreal, Quebec, Canada
| | - Peter M Buttrick
- Division of Cardiology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Carol M Aherne
- Mucosal Inflammation Program, Departments of Medicine and Anesthesiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Nathan Clendenen
- Mucosal Inflammation Program, Departments of Medicine and Anesthesiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Sean P Colgan
- Mucosal Inflammation Program, Departments of Medicine and Anesthesiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Tobias Eckle
- Mucosal Inflammation Program, Departments of Medicine and Anesthesiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA; Division of Cardiology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA; Graduate Training Program in Cell Biology, Stem Cells, and Development, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
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23
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Challenges in Analysis of Hydrophilic Metabolites Using Chromatography Coupled with Mass Spectrometry. JOURNAL OF ANALYSIS AND TESTING 2020. [DOI: 10.1007/s41664-020-00126-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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24
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Olson AK, Bouchard B, Zhu WZ, Chatham JC, Des Rosiers C. First characterization of glucose flux through the hexosamine biosynthesis pathway (HBP) in ex vivo mouse heart. J Biol Chem 2020; 295:2018-2033. [PMID: 31915250 PMCID: PMC7029105 DOI: 10.1074/jbc.ra119.010565] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Revised: 01/06/2020] [Indexed: 12/31/2022] Open
Abstract
The hexosamine biosynthesis pathway (HBP) branches from glycolysis and forms UDP-GlcNAc, the moiety for O-linked β-GlcNAc (O-GlcNAc) post-translational modifications. An inability to directly measure HBP flux has hindered our understanding of the factors regulating protein O-GlcNAcylation. Our goals in this study were to (i) validate a LC-MS method that assesses HBP flux as UDP-GlcNAc (13C)-molar percent enrichment (MPE) and concentration and (ii) determine whether glucose availability or workload regulate cardiac HBP flux. For (i), we perfused isolated murine working hearts with [U-13C6]glucosamine (1, 10, 50, or 100 μm), which bypasses the rate-limiting HBP enzyme. We observed a concentration-dependent increase in UDP-GlcNAc levels and MPE, with the latter reaching a plateau of 56.3 ± 2.9%. For (ii), we perfused isolated working hearts with [U-13C6]glucose (5.5 or 25 mm). Glycolytic efflux doubled with 25 mm [U-13C6]glucose; however, the calculated HBP flux was similar among the glucose concentrations at ∼2.5 nmol/g of heart protein/min, representing ∼0.003–0.006% of glycolysis. Reducing cardiac workload in beating and nonbeating Langendorff perfusions had no effect on the calculated HBP flux at ∼2.3 and 2.5 nmol/g of heart protein/min, respectively. To the best of our knowledge, this is the first direct measurement of glucose flux through the HBP in any organ. We anticipate that these methods will enable foundational analyses of the regulation of HBP flux and protein O-GlcNAcylation. Our results suggest that in the healthy ex vivo perfused heart, HBP flux does not respond to acute changes in glucose availability or cardiac workload.
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Affiliation(s)
- Aaron K Olson
- Division of Cardiology, Department of Pediatrics, University of Washington, Seattle, Washington 98105; Seattle Children's Research Institute, Seattle, Washington 98101.
| | - Bertrand Bouchard
- Montreal Heart Institute Research Center and Department of Nutrition, Université de Montréal, Montreal, Québec H1T 1C8, Canada
| | - Wei Zhong Zhu
- Seattle Children's Research Institute, Seattle, Washington 98101
| | - John C Chatham
- Division of Molecular and Cellular Pathology, Department of Pathology, University of Alabama, Birmingham, Alabama 35294
| | - Christine Des Rosiers
- Montreal Heart Institute Research Center and Department of Nutrition, Université de Montréal, Montreal, Québec H1T 1C8, Canada
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25
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Pfannkuch L, Hurwitz R, Traulsen J, Sigulla J, Poeschke M, Matzner L, Kosma P, Schmid M, Meyer TF. ADP heptose, a novel pathogen-associated molecular pattern identified in Helicobacter pylori. FASEB J 2019; 33:9087-9099. [PMID: 31075211 PMCID: PMC6662969 DOI: 10.1096/fj.201802555r] [Citation(s) in RCA: 103] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The gastric pathogen Helicobacter pylori activates the NF-κB pathway in human epithelial cells via the recently discovered α-kinase 1 TRAF-interacting protein with forkhead-associated domain (TIFA) axis. We and others showed that this pathway can be triggered by heptose 1,7-bisphosphate (HBP), an LPS intermediate produced in gram-negative bacteria that represents a new pathogen-associated molecular pattern (PAMP). Here, we report that our attempts to identify HBP in lysates of H. pylori revealed surprisingly low amounts, failing to explain NF-κB activation. Instead, we identified ADP-glycero-β-D-manno-heptose (ADP heptose), a derivative of HBP, as the predominant PAMP in lysates of H. pylori and other gram-negative bacteria. ADP heptose exhibits significantly higher activity than HBP, and cells specifically sensed the presence of the β-form, even when the compound was added extracellularly. The data lead us to conclude that ADP heptose not only constitutes the key PAMP responsible for H. pylori–induced NF-κB activation in epithelial cells, but it acts as a general gram-negative bacterial PAMP.—Pfannkuch, L., Hurwitz, R., Traulsen, J., Sigulla, J., Poeschke, M., Matzner, L., Kosma, P., Schmid, M., Meyer, T. F. ADP heptose, a novel pathogen-associated molecular pattern identified in Helicobacter pylori.
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Affiliation(s)
- Lennart Pfannkuch
- Department of Molecular Biology, Max Planck Institute for Infection Biology, Berlin, Germany.,Department of Infectious Diseases and Pulmonary Medicine, Charité, University Hospital Berlin, Berlin, Germany.,Berlin Institute of Health, Berlin, Germany
| | - Robert Hurwitz
- Department of Molecular Biology, Max Planck Institute for Infection Biology, Berlin, Germany
| | - Jan Traulsen
- Department of Molecular Biology, Max Planck Institute for Infection Biology, Berlin, Germany
| | - Janine Sigulla
- Department of Molecular Biology, Max Planck Institute for Infection Biology, Berlin, Germany
| | - Marcella Poeschke
- Department of Molecular Biology, Max Planck Institute for Infection Biology, Berlin, Germany
| | - Laura Matzner
- Department of Molecular Biology, Max Planck Institute for Infection Biology, Berlin, Germany
| | - Paul Kosma
- Department of Chemistry, University of Natural Resources and Life Sciences-Vienna, Vienna, Austria
| | - Monika Schmid
- Department of Molecular Biology, Max Planck Institute for Infection Biology, Berlin, Germany
| | - Thomas F Meyer
- Department of Molecular Biology, Max Planck Institute for Infection Biology, Berlin, Germany
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26
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Shumilina J, Kusnetsova A, Tsarev A, Janse van Rensburg HC, Medvedev S, Demidchik V, Van den Ende W, Frolov A. Glycation of Plant Proteins: Regulatory Roles and Interplay with Sugar Signalling? Int J Mol Sci 2019; 20:E2366. [PMID: 31086058 PMCID: PMC6539852 DOI: 10.3390/ijms20092366] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Revised: 05/08/2019] [Accepted: 05/09/2019] [Indexed: 02/06/2023] Open
Abstract
Glycation can be defined as an array of non-enzymatic post-translational modifications of proteins formed by their interaction with reducing carbohydrates and carbonyl products of their degradation. Initial steps of this process rely on reducing sugars and result in the formation of early glycation products-Amadori and Heyns compounds via Schiff base intermediates, whereas their oxidative degradation or reactions of proteins with α-dicarbonyl compounds yield a heterogeneous group of advanced glycation end products (AGEs). These compounds accompany thermal processing of protein-containing foods and are known to impact on ageing, pathogenesis of diabetes mellitus and Alzheimer's disease in mammals. Surprisingly, despite high tissue carbohydrate contents, glycation of plant proteins was addressed only recently and its physiological role in plants is still not understood. Therefore, here we summarize and critically discuss the first steps done in the field of plant protein glycation during the last decade. We consider the main features of plant glycated proteome and discuss them in the context of characteristic metabolic background. Further, we address the possible role of protein glycation in plants and consider its probable contribution to protein degradation, methylglyoxal and sugar signalling, as well as interplay with antioxidant defense.
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Affiliation(s)
- Julia Shumilina
- Department of Biochemistry, St. Petersburg State University, Saint Petersburg 199034, Russia.
| | - Alena Kusnetsova
- Department of Biochemistry, St. Petersburg State University, Saint Petersburg 199034, Russia.
- Department of Biotechnology, St. Petersburg Chemical Pharmaceutical University, Saint Petersburg 197022, Russia.
| | - Alexander Tsarev
- Department of Biochemistry, St. Petersburg State University, Saint Petersburg 199034, Russia.
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, 06120 Halle, Germany.
| | | | - Sergei Medvedev
- Department of Plant Physiology and Biochemistry, St. Petersburg State University, Saint Petersburg 199034, Russia.
| | - Vadim Demidchik
- Department of Plant Cell Biology and Bioengineering, Belarusian State University, 220030 Minsk, Belarus.
- Department of Horticulture, Foshan University, Foshan 528231, China.
| | - Wim Van den Ende
- Laboratory of Molecular Plant Biology, KU Leuven, 3001 Leuven, Belgium.
| | - Andrej Frolov
- Department of Biochemistry, St. Petersburg State University, Saint Petersburg 199034, Russia.
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, 06120 Halle, Germany.
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27
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Abstract
Phosphorylated carbohydrates are central metabolites involved in key plant metabolic pathways, such as glycolysis and central carbon metabolism. Such pathways influence plant growth, development, and stress responses to environmental changes, and ultimately, reflect the plant's energy status. The high polarity of these metabolites, the variety of isomeric structures (e.g., glucose-1-phosphate (G1P)/fructose-6-phosphate (F6P)/mannose-6-phosphate (M6P)/G6P, sucrose-6-phosphate (S6P)/T6P), and rapid metabolic turnover makes their analysis particularly challenging. In this chapter, we describe the use of a set of known phosphorylated carbohydrates to develop and validate a hydrophilic interaction chromatography (HILIC) triple quadrupole (QqQ) tandem mass spectrometry (MS/MS) method in the highly sensitive and selective multiple reaction monitoring (MRM) mode for the target analysis of G1P, F6P, M6P, G6P, S6P, T6P, and the sugar nucleotide uridine 5-diphospho-glucose (UDPG). We present detailed information regarding HILIC column chemistry and practical considerations when coupling it with a QqQ-MS system.
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28
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Rende U, Niittylä T, Moritz T. Two-step derivatization for determination of sugar phosphates in plants by combined reversed phase chromatography/tandem mass spectrometry. PLANT METHODS 2019; 15:127. [PMID: 31719834 PMCID: PMC6836659 DOI: 10.1186/s13007-019-0514-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Accepted: 10/29/2019] [Indexed: 05/14/2023]
Abstract
BACKGROUND Sugar phosphates are important intermediates of central carbon metabolism in biological systems, with roles in glycolysis, the pentose-phosphate pathway, tricarboxylic acid (TCA) cycle, and many other biosynthesis pathways. Understanding central carbon metabolism requires a simple, robust and comprehensive analytical method. However, sugar phosphates are notoriously difficult to analyze by traditional reversed phase liquid chromatography. RESULTS Here, we show a two-step derivatization of sugar phosphates by methoxylamine and propionic acid anhydride after chloroform/methanol (3:7) extraction from Populus leaf and developing wood that improves separation, identification and quantification of sugar phosphates by ultra high performance liquid chromatography-electrospray ionization-mass spectrometry (UHPLC-ESI-MS). Standard curves of authentic sugar phosphates were generated for concentrations from pg to ng/μl with a correlation coefficient R 2 > 0.99. The method showed high sensitivity and repeatability with relative standard deviation (RSD) < 20% based on repeated extraction, derivatization and detection. The analytical accuracy for Populus leaf extracts, determined by a two-level spiking approach of selected metabolites, was 79-107%. CONCLUSION The results show the reliability of combined reversed phase liquid chromatography-tandem mass spectrometry for sugar phosphate analysis and demonstrate the presence of two unknown sugar phosphates in Populus extracts.
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Affiliation(s)
- Umut Rende
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, 901 83 Umeå, Sweden
| | - Totte Niittylä
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, 901 83 Umeå, Sweden
| | - Thomas Moritz
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, 901 83 Umeå, Sweden
- The NovoNordisk Foundation Centre for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
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29
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Walvekar A, Rashida Z, Maddali H, Laxman S. A versatile LC-MS/MS approach for comprehensive, quantitative analysis of central metabolic pathways. Wellcome Open Res 2018; 3:122. [PMID: 30345389 PMCID: PMC6171562 DOI: 10.12688/wellcomeopenres.14832.1] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/17/2018] [Indexed: 11/23/2022] Open
Abstract
Liquid chromatography-mass spectrometry (LC-MS/MS) based approaches are widely used for the identification and quantitation of specific metabolites, and are a preferred approach towards analyzing cellular metabolism. Most methods developed come with specific requirements such as unique columns, ion-pairing reagents and pH conditions, and typically allow measurements in a specific pathway alone. Here, we present a single column-based set of methods for simultaneous coverage of multiple pathways, primarily focusing on central carbon, amino acid, and nucleotide metabolism. We further demonstrate the use of this method for quantitative, stable isotope-based metabolic flux experiments, expanding its use beyond steady-state level measurements of metabolites. The expected kinetics of label accumulation pertinent to the pathway under study are presented with some examples. The methods discussed here are broadly applicable, minimize the need for multiple chromatographic resolution methods, and highlight how simple labeling experiments can be valuable in facilitating a comprehensive understanding of the metabolic state of cells.
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Affiliation(s)
- Adhish Walvekar
- Institute for Stem Cell biology and Regenerative Medicine (inStem), Bangalore, Karnataka, 560065, India
| | - Zeenat Rashida
- Institute for Stem Cell biology and Regenerative Medicine (inStem), Bangalore, Karnataka, 560065, India
- Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Hemanth Maddali
- Institute for Stem Cell biology and Regenerative Medicine (inStem), Bangalore, Karnataka, 560065, India
| | - Sunil Laxman
- Institute for Stem Cell biology and Regenerative Medicine (inStem), Bangalore, Karnataka, 560065, India
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30
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Whicher A, Camprubi E, Pinna S, Herschy B, Lane N. Acetyl Phosphate as a Primordial Energy Currency at the Origin of Life. ORIGINS LIFE EVOL B 2018; 48:159-179. [PMID: 29502283 PMCID: PMC6061221 DOI: 10.1007/s11084-018-9555-8] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 01/24/2018] [Indexed: 11/30/2022]
Abstract
Metabolism is primed through the formation of thioesters via acetyl CoA and the phosphorylation of substrates by ATP. Prebiotic equivalents such as methyl thioacetate and acetyl phosphate have been proposed to catalyse analogous reactions at the origin of life, but their propensity to hydrolyse challenges this view. Here we show that acetyl phosphate (AcP) can be synthesised in water within minutes from thioacetate (but not methyl thioacetate) under ambient conditions. AcP is stable over hours, depending on temperature, pH and cation content, giving it an ideal poise between stability and reactivity. We show that AcP can phosphorylate nucleotide precursors such as ribose to ribose-5-phosphate and adenosine to adenosine monophosphate, at modest (~2%) yield in water, and at a range of pH. AcP can also phosphorylate ADP to ATP in water over several hours at 50 °C. But AcP did not promote polymerization of either glycine or AMP. The amino group of glycine was preferentially acetylated by AcP, especially at alkaline pH, hindering the formation of polypeptides. AMP formed small stacks of up to 7 monomers, but these did not polymerise in the presence of AcP in aqueous solution. We conclude that AcP can phosphorylate biologically meaningful substrates in a manner analogous to ATP, promoting the origins of metabolism, but is unlikely to have driven polymerization of macromolecules such as polypeptides or RNA in free solution. This is consistent with the idea that a period of monomer (cofactor) catalysis preceded the emergence of polymeric enzymes or ribozymes at the origin of life.
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Affiliation(s)
- Alexandra Whicher
- Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London, WC1E 6BT, UK
| | - Eloi Camprubi
- Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London, WC1E 6BT, UK
| | - Silvana Pinna
- Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London, WC1E 6BT, UK
| | - Barry Herschy
- Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London, WC1E 6BT, UK
| | - Nick Lane
- Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London, WC1E 6BT, UK.
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31
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Zhong F, Xu M, Schelli K, Rutowski J, Holmén BA, Zhu J. Comparing the impact of ultrafine particles from petrodiesel and biodiesel combustion to bacterial metabolism by targeted HPLC-MS/MS metabolic profiling. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2017; 142:164-170. [PMID: 28410499 DOI: 10.1016/j.ecoenv.2017.04.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 03/29/2017] [Accepted: 04/03/2017] [Indexed: 06/07/2023]
Abstract
Alterations of gut bacterial metabolism play an important role in their host metabolism, and can result in diseases such as obesity and diabetes. While many factors were discovered influencing the gut bacterial metabolism, exposure to ultrafine particles (UFPs) from engine combustions were recently proposed to be a potential risk factor for the perturbation of gut bacterial metabolism, and consequentially to obesity and diabetes development. This study focused on evaluation of how UFPs from diesel engine combustions impact gut bacterial metabolism. We hypothesize that UFPs from different type of diesel (petrodiesel vs. biodiesel) will both impact bacterial metabolism, and the degree of impact is also diesel type-dependent. Targeted metabolic profiling of 221 metabolites were applied to three model gut bacteria in vitro, Streptococcus salivarius, Lactobacillus acidophilus and Lactobacillus fermentum. UFPs from two types of fuels, petrodiesel (B0) and a biodiesel blend (B20: 20% soy biodiesel/80% B0 by volume), were exposed to the bacteria and their metabolic changes were compared. For each bacterial strain, metabolites with significantly changed abundance were observed in both perturbations, and all three strains have increased number of altered metabolites detected from B20 UFPs perturbation in comparison to B0 UFPs. Multivariate statistical analysis further confirmed that the metabolic profiles were clearly different between testing groups. Metabolic pathway analyses also demonstrated several important metabolic pathways, including pathways involves amino acids biosynthesis and sugar metabolism, were significantly impacted by UFPs exposure.
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Affiliation(s)
- Fanyi Zhong
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, United States
| | - Mengyang Xu
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, United States
| | - Katie Schelli
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, United States
| | - Joshua Rutowski
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, United States
| | - Britt A Holmén
- School of Engineering, University of Vermont, Burlington, VT 05405, United States
| | - Jiangjiang Zhu
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, United States.
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32
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Mathon C, Barding GA, Larive CK. Separation of ten phosphorylated mono-and disaccharides using HILIC and ion-pairing interactions. Anal Chim Acta 2017; 972:102-110. [DOI: 10.1016/j.aca.2017.03.029] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Revised: 03/05/2017] [Accepted: 03/09/2017] [Indexed: 10/19/2022]
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33
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Analysis of low abundant trehalose-6-phosphate and related metabolites in Medicago truncatula by hydrophilic interaction liquid chromatography–triple quadrupole mass spectrometry. J Chromatogr A 2016; 1477:30-38. [DOI: 10.1016/j.chroma.2016.11.031] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 10/21/2016] [Accepted: 11/20/2016] [Indexed: 11/21/2022]
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34
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Petucci C, Zelenin A, Culver JA, Gabriel M, Kirkbride K, Christison TT, Gardell SJ. Use of Ion Chromatography/Mass Spectrometry for Targeted Metabolite Profiling of Polar Organic Acids. Anal Chem 2016; 88:11799-11803. [PMID: 27782384 DOI: 10.1021/acs.analchem.6b03435] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Organic acids (OAs) serve as metabolites that play pivotal roles in a host of different metabolic and regulatory pathways. The polar nature of many OAs poses a challenge to their measurement using widely practiced analytical methods. In this study, a targeted metabolomics method was developed using ion chromatography/triple quadrupole mass spectrometry (IC/MS) to quantitate 28 polar OAs with limits of quantitation ranging from 0.25 to 50 μM. The interday assay precisions ranged from 1% to 19%, with accuracies ranging from 82% to 115%. The IC/MS assay was used to quantitate OAs in quadriceps muscle from sedentary mice compared to fatigued mice subjected to either a low intensity, long duration (LILD) or high intensity, short duration (HISD) forced treadmill regimen. Among the OAs examined, significant differences were detected for hippuric acid, malic acid, fumaric acid, and 2-ketoglutaric acid between the sedentary and fatigued mice. In conclusion, the IC/MS method enabled the separation and quantitative survey of a broad range of polar OAs that are difficult to analyze by chromatographic techniques.
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Affiliation(s)
- Chris Petucci
- Sanford Burnham Prebys Medical Discovery Institute , 6400 Sanger Road, Orlando, Florida 32827, United States.,Southeast Center for Integrated Metabolomics, Clinical and Translational Sciences Institute, University of Florida , 2004 Mowry Road, Gainesville, Florida 32610, United States
| | - Andrew Zelenin
- Sanford Burnham Prebys Medical Discovery Institute , 6400 Sanger Road, Orlando, Florida 32827, United States.,Southeast Center for Integrated Metabolomics, Clinical and Translational Sciences Institute, University of Florida , 2004 Mowry Road, Gainesville, Florida 32610, United States
| | - Jeffrey A Culver
- Sanford Burnham Prebys Medical Discovery Institute , 6400 Sanger Road, Orlando, Florida 32827, United States.,Southeast Center for Integrated Metabolomics, Clinical and Translational Sciences Institute, University of Florida , 2004 Mowry Road, Gainesville, Florida 32610, United States
| | - Meghan Gabriel
- Sanford Burnham Prebys Medical Discovery Institute , 6400 Sanger Road, Orlando, Florida 32827, United States
| | - Ken Kirkbride
- Thermo Fisher Scientific , 1214 Oakmead Parkway, Sunnyvale, California 94088, United States
| | - Terri T Christison
- Thermo Fisher Scientific , 1214 Oakmead Parkway, Sunnyvale, California 94088, United States
| | - Stephen J Gardell
- Sanford Burnham Prebys Medical Discovery Institute , 6400 Sanger Road, Orlando, Florida 32827, United States.,Southeast Center for Integrated Metabolomics, Clinical and Translational Sciences Institute, University of Florida , 2004 Mowry Road, Gainesville, Florida 32610, United States
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35
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Bround MJ, Wambolt R, Cen H, Asghari P, Albu RF, Han J, McAfee D, Pourrier M, Scott NE, Bohunek L, Kulpa JE, Chen SRW, Fedida D, Brownsey RW, Borchers CH, Foster LJ, Mayor T, Moore EDW, Allard MF, Johnson JD. Cardiac Ryanodine Receptor (Ryr2)-mediated Calcium Signals Specifically Promote Glucose Oxidation via Pyruvate Dehydrogenase. J Biol Chem 2016; 291:23490-23505. [PMID: 27621312 DOI: 10.1074/jbc.m116.756973] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Indexed: 11/06/2022] Open
Abstract
Cardiac ryanodine receptor (Ryr2) Ca2+ release channels and cellular metabolism are both disrupted in heart disease. Recently, we demonstrated that total loss of Ryr2 leads to cardiomyocyte contractile dysfunction, arrhythmia, and reduced heart rate. Acute total Ryr2 ablation also impaired metabolism, but it was not clear whether this was a cause or consequence of heart failure. Previous in vitro studies revealed that Ca2+ flux into the mitochondria helps pace oxidative metabolism, but there is limited in vivo evidence supporting this concept. Here, we studied heart-specific, inducible Ryr2 haploinsufficient (cRyr2Δ50) mice with a stable 50% reduction in Ryr2 protein. This manipulation decreased the amplitude and frequency of cytosolic and mitochondrial Ca2+ signals in isolated cardiomyocytes, without changes in cardiomyocyte contraction. Remarkably, in the context of well preserved contractile function in perfused hearts, we observed decreased glucose oxidation, but not fat oxidation, with increased glycolysis. cRyr2Δ50 hearts exhibited hyperphosphorylation and inhibition of pyruvate dehydrogenase, the key Ca2+-sensitive gatekeeper to glucose oxidation. Metabolomic, proteomic, and transcriptomic analyses revealed additional functional networks associated with altered metabolism in this model. These results demonstrate that Ryr2 controls mitochondrial Ca2+ dynamics and plays a specific, critical role in promoting glucose oxidation in cardiomyocytes. Our findings indicate that partial RYR2 loss is sufficient to cause metabolic abnormalities seen in heart disease.
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Affiliation(s)
- Michael J Bround
- From the Cardiovascular Research Group, Life Sciences Institute and.,Departments of Cellular and Physiological Sciences
| | - Rich Wambolt
- From the Cardiovascular Research Group, Life Sciences Institute and.,the Department of Pathology and Laboratory Medicine, University of British Columbia and the Centre for Heart and Lung Innovation, St. Paul's Hospital, Vancouver, British Columbia V6Z 1Y6
| | - Haoning Cen
- From the Cardiovascular Research Group, Life Sciences Institute and.,Departments of Cellular and Physiological Sciences
| | - Parisa Asghari
- From the Cardiovascular Research Group, Life Sciences Institute and.,Departments of Cellular and Physiological Sciences
| | - Razvan F Albu
- Biochemistry and Molecular Biology, and.,the Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T 1Z4
| | - Jun Han
- the University of Victoria-Genome British Columbia Proteomics Centre, Victoria, British Columbia V8Z 7X8, and
| | - Donald McAfee
- From the Cardiovascular Research Group, Life Sciences Institute and.,Anesthesiology, Pharmacology and Therapeutics, University of British Columbia, Vancouver, British Columbia V6T 1Z3
| | - Marc Pourrier
- From the Cardiovascular Research Group, Life Sciences Institute and.,Anesthesiology, Pharmacology and Therapeutics, University of British Columbia, Vancouver, British Columbia V6T 1Z3
| | - Nichollas E Scott
- Biochemistry and Molecular Biology, and.,the Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T 1Z4
| | - Lubos Bohunek
- the Department of Pathology and Laboratory Medicine, University of British Columbia and the Centre for Heart and Lung Innovation, St. Paul's Hospital, Vancouver, British Columbia V6Z 1Y6
| | | | - S R Wayne Chen
- the Libin Cardiovascular Institute of Alberta, Department of Physiology and Pharmacology, University of Calgary, Calgary, Alberta T2N 2T9, Canada
| | - David Fedida
- From the Cardiovascular Research Group, Life Sciences Institute and.,Anesthesiology, Pharmacology and Therapeutics, University of British Columbia, Vancouver, British Columbia V6T 1Z3
| | | | - Christoph H Borchers
- the University of Victoria-Genome British Columbia Proteomics Centre, Victoria, British Columbia V8Z 7X8, and
| | - Leonard J Foster
- Biochemistry and Molecular Biology, and.,the Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T 1Z4
| | - Thibault Mayor
- Biochemistry and Molecular Biology, and.,the Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T 1Z4
| | - Edwin D W Moore
- From the Cardiovascular Research Group, Life Sciences Institute and.,Departments of Cellular and Physiological Sciences
| | - Michael F Allard
- From the Cardiovascular Research Group, Life Sciences Institute and.,the Department of Pathology and Laboratory Medicine, University of British Columbia and the Centre for Heart and Lung Innovation, St. Paul's Hospital, Vancouver, British Columbia V6Z 1Y6
| | - James D Johnson
- From the Cardiovascular Research Group, Life Sciences Institute and .,Departments of Cellular and Physiological Sciences
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36
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Review of sample preparation strategies for MS-based metabolomic studies in industrial biotechnology. Anal Chim Acta 2016; 938:18-32. [DOI: 10.1016/j.aca.2016.07.033] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 07/22/2016] [Accepted: 07/26/2016] [Indexed: 02/08/2023]
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37
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Qin Q, Wang B, Chang M, Zhou Z, Shi X, Xu G. Highly efficient solid-phase derivatization of sugar phosphates with titanium-immobilized hydrophilic polydopamine-coated silica. J Chromatogr A 2016; 1457:125-33. [PMID: 27371021 DOI: 10.1016/j.chroma.2016.06.046] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 06/11/2016] [Accepted: 06/15/2016] [Indexed: 10/21/2022]
Abstract
Sugar phosphates are a type of key metabolic intermediates of glycolysis, gluconeogenesis and pentose phosphate pathway, which can regulate tumor energetic metabolism. Due to their low endogenous concentrations, poor chromatographic retention properties as well as ionization suppression from complex matrix interference, the determination of sugar phosphates in biological samples is very difficult. In this study, titanium-immobilized hydrophilic polydopamine-coated silica microspheres (SiO2@PD-Ti(4+)) were synthesized for highly efficient solid-phase derivatization of sugar phosphates. Sugar phosphates were selectively captured onto the surface of the SiO2@PD-Ti(4+) microspheres by chelating with phosphate groups, and then reacted with 3-amino-9-ethylcarbazole via reductive amination based on solid-phase derivatization, which could not only increase the retention and resolution of sugar phosphates on reversed-phase liquid chromatography (RPLC), but also improve the mass spectrometry (MS) sensitivity of sugar phosphates. The adsorption capacity of SiO2@PD-Ti(4+) microspheres towards glucose-6-phosphate is 0.76mg/g, which is much larger than that of commercial TiO2. Compared with the traditional liquid-phase derivatization, the solid-phase derivatization based on the SiO2@PD-Ti(4+) microspheres displayed several superiorities including shorter derivatization time (within 10min), higher product purity and much lower limit of detection (up to 38pmol/L). In addition, good linearity (R(2)≥0.99), excellent recovery (80.6-118%) and high precision (RSDs with 2.8-7.8%) were obtained when the developed method was used for quantitative analysis of sugar phosphates. Finally, the SiO2@PD-Ti(4+) microspheres combined with RPLC-MS were successfully applied to the determination of sugar phosphates from hepatocarcinoma cell lines and could even detect the trace sugar phosphates in thousands of cells.
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Affiliation(s)
- Qian Qin
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bohong Wang
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mengmeng Chang
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhihui Zhou
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xianzhe Shi
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
| | - Guowang Xu
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
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Quantitative liquid chromatography–electrospray ionization-mass spectrometry analysis of amine-containing metabolites derivatized with cyanuric chloride and methylamine isotopologues. J Chromatogr A 2015; 1388:60-8. [DOI: 10.1016/j.chroma.2015.01.094] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Revised: 01/13/2015] [Accepted: 01/28/2015] [Indexed: 11/19/2022]
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Chu DB, Troyer C, Mairinger T, Ortmayr K, Neubauer S, Koellensperger G, Hann S. Isotopologue analysis of sugar phosphates in yeast cell extracts by gas chromatography chemical ionization time-of-flight mass spectrometry. Anal Bioanal Chem 2015; 407:2865-75. [PMID: 25673246 DOI: 10.1007/s00216-015-8521-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2014] [Revised: 01/17/2015] [Accepted: 01/27/2015] [Indexed: 01/05/2023]
Abstract
Metabolic flux analysis is based on the measurement of isotopologue ratios. In this work, a new GC-MS-based method was introduced enabling accurate determination of isotopologue distributions of sugar phosphates in cell extracts. A GC-TOFMS procedure was developed involving a two-step online derivatization (ethoximation followed by trimethylsilylation) offering high mass resolution, high mass accuracy and the potential of retrospective data analysis typical for TOFMS. The information loss due to fragmentation intrinsic for isotopologue analysis by electron ionization could be overcome by chemical ionization with methane. A thorough optimization regarding pressure of the reaction gas, emission current, electron energy and temperature of the ion source was carried out. For a substantial panel of sugar phosphates both of the glycolysis and the pentose phosphate pathway, sensitive determination of the protonated intact molecular ions together with low abundance fragment ions was successfully achieved. The developed method was evaluated for analysis of Pichia pastoris cell extracts. The measured isotopologue ratios were in the range of 55:1-2:1. The comparison of the experimental isotopologue fractions with the theoretical fractions was excellent, revealing a maximum bias of 4.6% and an average bias of 1.4%.
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Affiliation(s)
- Dinh Binh Chu
- Division of Analytical Chemistry, Department of Chemistry, University of Natural Resources and Life Sciences, BOKU Vienna, Muthgasse 18, 1190, Vienna, Austria
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