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Muhl JR, Pilkington LI, Fedrizzi B, Deed RC. Insights into the relative contribution of four precursors to 3-sulfanylhexan-1-ol and 3-sulfanylhexylacetate biogenesis during fermentation. Food Chem 2024; 449:139193. [PMID: 38604037 DOI: 10.1016/j.foodchem.2024.139193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 03/27/2024] [Accepted: 03/28/2024] [Indexed: 04/13/2024]
Abstract
The desirable wine aroma compounds 3-sulfanylhexan-1-ol (3SH) and 3-sulfanylhexyl acetate (3SHA) are released during fermentation from non-volatile precursors present in the grapes. This work explores the relative contribution of four precursors (E-2-hexenal, 3-S-glutathionylhexan-1-ol, 3-S-glutathionylhexanal, and 3-S-cysteinylhexan-1-ol) to 3SH and 3SHA. Through the use of isotopically labelled analogues of these precursors in defined fermentation media, new insights into the role of each precursor have been identified. E-2-Hexenal was shown to contribute negligible amounts of thiols, while 3-S-glutathionylhexan-1-ol was the main precursor of both 3SH and 3SHA. The glutathionylated precursors were both converted to 3SHA more efficiently than 3-S-cysteinylhexan-1-ol. Interestingly, 3-S-glutathionylhexanal generated 3SHA without detectable concentrations of 3SH, suggesting possible differences in the way this precursor is metabolised compared to 3-S-glutathionylhexan-1-ol and 3-S-cysteinylhexan-1-ol. We also provide the first evidence for chemical conversion of 3-S-glutathionylhexan-1-ol to 3-S-(γ-glutamylcysteinyl)-hexan-1-ol in an oenological system.
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Affiliation(s)
- Jennifer R Muhl
- School of Chemical Sciences, The University of Auckland | Waipapa Taumata Rau, 23 Symonds Street, Auckland, New Zealand.
| | - Lisa I Pilkington
- School of Chemical Sciences, The University of Auckland | Waipapa Taumata Rau, 23 Symonds Street, Auckland, New Zealand; Te Pūnaha Matatini, Auckland 1010, New Zealand.
| | - Bruno Fedrizzi
- School of Chemical Sciences, The University of Auckland | Waipapa Taumata Rau, 23 Symonds Street, Auckland, New Zealand.
| | - Rebecca C Deed
- School of Chemical Sciences, The University of Auckland | Waipapa Taumata Rau, 23 Symonds Street, Auckland, New Zealand; School of Biological Sciences, The University of Auckland | Waipapa Taumata Rau, 3 Symonds Street, Auckland, New Zealand.
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2
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Hegde SG, Kashyap S, Devi S, Kumar P, Michael Raj A J, Kurpad AV. Estimation of exocrine pancreatic insufficiency in children with acute pancreatitis using the 13C mixed triglyceride breath test. Pancreatology 2023; 23:601-606. [PMID: 37481340 DOI: 10.1016/j.pan.2023.07.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 07/10/2023] [Accepted: 07/16/2023] [Indexed: 07/24/2023]
Abstract
BACKGROUND /Objective: The extent of exocrine pancreatic insufficiency (EPI) in the paediatric population with acute pancreatitis (AP) is unknown. The primary objective was to use a 6 h stable-isotope breath test to determine the prevalence of EPI in children with AP. The secondary objective was to determine the diagnostic ability of a 4 h abbreviated breath test in the detection of EPI. METHODS 13C-mixed triglyceride (MTG) breath test was used to measure fat digestibility in 12 children with AP and 12 normal children. EPI was diagnosed based on a cumulative dose percentage recovery (cPDR) cut-off value < 26.8% present in literature. To reduce the test burden, the diagnostic accuracy of an abbreviated 4 h test was evaluated, using a cPDR cut-off that was the 2.5th percentile of its distribution in control children. RESULTS The cPDR of cases was significantly lower than that of controls (27.71 ± 7.88% vs 36.37 ± 4.70%, p = 0.005). The cPDR during acute illness was not significantly different to that at 1 month follow up (24.69 ± 6.83% vs 26.98 ± 11.10%, p = 0.52). The 4 h and 6 h breath test results correlated strongly (r = 0.93, p < 0.001) with each other. The new 4 h test had 87.5% sensitivity and 93.8% specificity for detecting EPI. CONCLUSION Two-thirds (66.7%) of this sample of children with AP had EPI during admission, which persisted at 1 month follow up. The 4 h abbreviated 13C-MTG breath test has good diagnostic ability to detect EPI in children and may improve its clinical utility in this age group.
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Affiliation(s)
- Shalini G Hegde
- Department of Paediatric Surgery, St. John's Medical College Hospital, India
| | - Sindhu Kashyap
- Division of Nutrition, St. John's Research Institute, Bangalore, India
| | - Sarita Devi
- Division of Nutrition, St. John's Research Institute, Bangalore, India
| | - Prasanna Kumar
- Department of Paediatric Surgery, St. John's Medical College Hospital, India
| | | | - Anura V Kurpad
- Department of Physiology, St. John's Medical College Hospital, India.
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3
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Favilli L, Griffith CM, Schymanski EL, Linster CL. High-throughput Saccharomyces cerevisiae cultivation method for credentialing-based untargeted metabolomics. Anal Bioanal Chem 2023:10.1007/s00216-023-04724-5. [PMID: 37212869 DOI: 10.1007/s00216-023-04724-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 04/24/2023] [Accepted: 04/28/2023] [Indexed: 05/23/2023]
Abstract
Identifying metabolites in model organisms is critical for many areas of biology, including unravelling disease aetiology or elucidating functions of putative enzymes. Even now, hundreds of predicted metabolic genes in Saccharomyces cerevisiae remain uncharacterized, indicating that our understanding of metabolism is far from complete even in well-characterized organisms. While untargeted high-resolution mass spectrometry (HRMS) enables the detection of thousands of features per analysis, many of these have a non-biological origin. Stable isotope labelling (SIL) approaches can serve as credentialing strategies to distinguish biologically relevant features from background signals, but implementing these experiments at large scale remains challenging. Here, we developed a SIL-based approach for high-throughput untargeted metabolomics in S. cerevisiae, including deep-48 well format-based cultivation and metabolite extraction, building on the peak annotation and verification engine (PAVE) tool. Aqueous and nonpolar extracts were analysed using HILIC and RP liquid chromatography, respectively, coupled to Orbitrap Q Exactive HF mass spectrometry. Of the approximately 37,000 total detected features, only 3-7% of the features were credentialed and used for data analysis with open-source software such as MS-DIAL, MetFrag, Shinyscreen, SIRIUS CSI:FingerID, and MetaboAnalyst, leading to the successful annotation of 198 metabolites using MS2 database matching. Comparable metabolic profiles were observed for wild-type and sdh1Δ yeast strains grown in deep-48 well plates versus the classical shake flask format, including the expected increase in intracellular succinate concentration in the sdh1Δ strain. The described approach enables high-throughput yeast cultivation and credentialing-based untargeted metabolomics, providing a means to efficiently perform molecular phenotypic screens and help complete metabolic networks.
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Affiliation(s)
- Lorenzo Favilli
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Avenue du Swing 6, Belvaux, L-4367, Luxembourg.
| | - Corey M Griffith
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Avenue du Swing 6, Belvaux, L-4367, Luxembourg
| | - Emma L Schymanski
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Avenue du Swing 6, Belvaux, L-4367, Luxembourg
| | - Carole L Linster
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Avenue du Swing 6, Belvaux, L-4367, Luxembourg
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4
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Feuerstein ML, Hernández-Mesa M, Valadbeigi Y, Le Bizec B, Hann S, Dervilly G, Causon T. Critical evaluation of the role of external calibration strategies for IM-MS. Anal Bioanal Chem 2022; 414:7483-7493. [PMID: 35960317 PMCID: PMC9482903 DOI: 10.1007/s00216-022-04263-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 07/11/2022] [Accepted: 08/02/2022] [Indexed: 11/01/2022]
Abstract
The major benefits of integrating ion mobility (IM) into LC-MS methods for small molecules are the additional separation dimension and especially the use of IM-derived collision cross sections (CCS) as an additional ion-specific identification parameter. Several large CCS databases are now available, but outliers in experimental interplatform IM-MS comparisons are identified as a critical issue for routine use of CCS databases for identity confirmation. We postulate that different routine external calibration strategies applied for traveling wave (TWIM-MS) in comparison to drift tube (DTIM-MS) and trapped ion mobility (TIM-MS) instruments is a critical factor affecting interplatform comparability. In this study, different external calibration approaches for IM-MS were experimentally evaluated for 87 steroids, for which TWCCSN2, DTCCSN2 and TIMCCSN2 are available. New reference CCSN2 values for commercially available and class-specific calibrant sets were established using DTIM-MS and the benefit of using consolidated reference values on comparability of CCSN2 values assessed. Furthermore, use of a new internal correction strategy based on stable isotope labelled (SIL) internal standards was shown to have potential for reducing systematic error in routine methods. After reducing bias for CCSN2 between different platforms using new reference values (95% of TWCCSN2 values fell within 1.29% of DTCCSN2 and 1.12% of TIMCCSN2 values, respectively), remaining outliers could be confidently classified and further studied using DFT calculations and CCSN2 predictions. Despite large uncertainties for in silico CCSN2 predictions, discrepancies in observed CCSN2 values across different IM-MS platforms as well as non-uniform arrival time distributions could be partly rationalized.
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Affiliation(s)
- Max L Feuerstein
- Department of Chemistry, Institute of Analytical Chemistry, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria
| | | | - Younes Valadbeigi
- Department of Chemistry, Institute of Analytical Chemistry, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria
| | | | - Stephan Hann
- Department of Chemistry, Institute of Analytical Chemistry, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria
| | | | - Tim Causon
- Department of Chemistry, Institute of Analytical Chemistry, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria.
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Dietze J, van Pijkeren A, Egger AS, Ziegler M, Kwiatkowski M, Heiland I. Natural isotope correction improves analysis of protein modification dynamics. Anal Bioanal Chem 2021; 413:7333-7340. [PMID: 34705077 PMCID: PMC8626371 DOI: 10.1007/s00216-021-03732-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 09/21/2021] [Accepted: 10/12/2021] [Indexed: 12/02/2022]
Abstract
Stable isotope labelling in combination with high-resolution mass spectrometry approaches are increasingly used to analyze both metabolite and protein modification dynamics. To enable correct estimation of the resulting dynamics, it is critical to correct the measured values for naturally occurring stable isotopes, a process commonly called isotopologue correction or deconvolution. While the importance of isotopologue correction is well recognized in metabolomics, it has received far less attention in proteomics approaches. Although several tools exist that enable isotopologue correction of mass spectrometry data, the majority is tailored for the analysis of low molecular weight metabolites. We here present PICor which has been developed for isotopologue correction of complex isotope labelling experiments in proteomics or metabolomics and demonstrate the importance of appropriate correction for accurate determination of protein modifications dynamics, using histone acetylation as an example.
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Affiliation(s)
- Jörn Dietze
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, 9037, Tromsø, Norway
| | - Alienke van Pijkeren
- Institute of Biochemistry and Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, 6020, Austria.,Department of Analytical Biochemistry, Groningen Research Institute of Pharmacy, Groningen, The Netherlands
| | - Anna-Sophia Egger
- Institute of Biochemistry and Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, 6020, Austria
| | - Mathias Ziegler
- Department of Biomedicine, University of Bergen, 5020, Bergen, Norway
| | - Marcel Kwiatkowski
- Institute of Biochemistry and Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, 6020, Austria
| | - Ines Heiland
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, 9037, Tromsø, Norway. .,Department of Clinical Medicine, University of Bergen, Bergen, Norway.
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Kunze M, Steiner T, Chen F, Huber C, Rydzewski K, Stämmler M, Heuner K, Eisenreich W. Metabolic adaption of Legionella pneumophila during intracellular growth in Acanthamoeba castellanii. Int J Med Microbiol 2021; 311:151504. [PMID: 33906075 DOI: 10.1016/j.ijmm.2021.151504] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 03/19/2021] [Accepted: 04/15/2021] [Indexed: 11/15/2022] Open
Abstract
The metabolism of Legionella pneumophila strain Paris was elucidated during different time intervals of growth within its natural host Acanthamoeba castellanii. For this purpose, the amoebae were supplied after bacterial infection (t =0 h) with 11 mM [U-13C6]glucose or 3 mM [U-13C3]serine, respectively, during 0-17 h, 17-25 h, or 25-27 h of incubation. At the end of these time intervals, bacterial and amoebal fractions were separated. Each of these fractions was hydrolyzed under acidic conditions. 13C-Enrichments and isotopologue distributions of resulting amino acids and 3-hydroxybutyrate were determined by gas chromatography - mass spectrometry. Comparative analysis of the labelling patterns revealed the substrate preferences, metabolic pathways, and relative carbon fluxes of the intracellular bacteria and their amoebal host during the time course of the infection cycle. Generally, the bacterial infection increased the usage of exogenous glucose via glycolysis by A. castellanii. In contrast, carbon fluxes via the amoebal citrate cycle were not affected. During the whole infection cycle, intracellular L. pneumophila incorporated amino acids from their host into the bacterial proteins. However, partial bacterial de novo biosynthesis from exogenous 13C-Ser and, at minor rates, from 13C-glucose could be shown for bacterial Ala, Asp, Glu, and Gly. More specifically, the catabolic usage of Ser increased during the post-exponential phase of intracellular growth, whereas glucose was utilized by the bacteria throughout the infection cycle and not only late during infection as assumed on the basis of earlier in vitro experiments. The early usage of 13C-glucose by the intracellular bacteria suggests that glucose availability could serve as a trigger for replication of L. pneumophila inside the vacuoles of host cells.
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Affiliation(s)
- Mareike Kunze
- Working Group: Cellular Interactions of Bacterial Pathogens, Centre for Biological Threats and Special Pathogens, ZBS 2, Robert Koch Institute, Berlin, Germany
| | - Thomas Steiner
- Bavarian NMR Center - Structural Membrane Biochemistry, Department of Chemistry, Technische Universität München, Garching, Germany
| | - Fan Chen
- Bavarian NMR Center - Structural Membrane Biochemistry, Department of Chemistry, Technische Universität München, Garching, Germany
| | - Claudia Huber
- Bavarian NMR Center - Structural Membrane Biochemistry, Department of Chemistry, Technische Universität München, Garching, Germany
| | - Kerstin Rydzewski
- Working Group: Cellular Interactions of Bacterial Pathogens, Centre for Biological Threats and Special Pathogens, ZBS 2, Robert Koch Institute, Berlin, Germany
| | - Maren Stämmler
- Proteomics and Spectroscopy, ZBS 6, Robert Koch Institute, Berlin, Germany
| | - Klaus Heuner
- Working Group: Cellular Interactions of Bacterial Pathogens, Centre for Biological Threats and Special Pathogens, ZBS 2, Robert Koch Institute, Berlin, Germany.
| | - Wolfgang Eisenreich
- Bavarian NMR Center - Structural Membrane Biochemistry, Department of Chemistry, Technische Universität München, Garching, Germany.
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Valk E, Maljavin A, Loog M. Detection of Multisite Phosphorylation of Intrinsically Disordered Proteins Using Quantitative Mass-Spectrometry. Methods Mol Biol 2020; 2141:819-33. [PMID: 32696391 DOI: 10.1007/978-1-0716-0524-0_42] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) within proteins have attracted considerable attention in recent years. Several important biological signaling mechanisms including protein-protein interactions and post-translational modifications can be easily mediated by IDPs and IDRs due to their flexible structure. These regions can encode linear sequences that are indispensable in cell-signaling networks and circuits. For example, the linear multisite phosphorylation networks encoded in disordered protein sequences play a key role in cell-cycle regulation where the phosphorylation of proteins controls the orchestration of all major mechanisms. While elucidating a systems-level understanding of this process and other multisite phosphorylation processes, we extensively used mass-spectrometry and found it to be an ideal tool to identify, characterize, and quantify phosphorylation dynamics within IDPs. Here, we describe a quantitative proteomics method, together with a detailed protocol to analyze dynamic multisite phosphorylation processes within IDPs using an in vitro protein phosphorylation assay with "light" gamma-16O ATP and "heavy" gamma-18O ATP, combined with liquid chromatography mass spectrometry.
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Cheng Z, Sun H, Sidhu HS, Sy ND, Gan J. Metabolism of mono-(2-ethylhexyl) phthalate in Arabidopsis thaliana: Exploration of metabolic pathways by deuterium labeling. Environ Pollut 2020; 265:114886. [PMID: 32505963 DOI: 10.1016/j.envpol.2020.114886] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Revised: 05/25/2020] [Accepted: 05/25/2020] [Indexed: 06/11/2023]
Abstract
Mono-(2-ethylhexyl) phthalate (MEHP) is the primary monoester transformation product of the commonly used plasticizer, di-2-ethylhexyl phthalate (DEHP), and has been frequently detected in various environmental compartments (e.g., soil, biosolids, plants). Plants growing in contaminated soils can take up MEHP, and consumption of the contaminated plants may result in unintended exposure for humans and other organisms. The metabolism of MEHP in plants is poorly understood, but critical for evaluating the potential human and environmental health risks. The present study represents the first attempt to explore the metabolic fate of MEHP in plants. We used Arabidopsis thaliana cells as a plant model and explored metabolic pathways of MEHP using deuterium stable isotope labelling (SIL) coupled with time-of-flight high resolution mass spectrometer (TOF-HRMS). A. thaliana rapidly took up MEHP from the culture medium and mediated extensive metabolism of MEHP. Combining SIL with TOF-HRMS analysis was proved as a powerful method for identification of unknown MEHP metabolites. Four phase Ⅰ and three phase Ⅱ metabolites were confirmed or tentatively identified. Based on the detected transformation products, hydroxylation, oxidation, and malonylation are proposed as the potential MEHP metabolism pathways. In cells, the maximum fraction of each transformation product accounted for 2.8-56.5% of the total amount of metabolites during the incubation. For individual metabolites, up to 2.9-100% was found in the culture medium, suggesting plant excretion. The results in the cell culture experiments were further confirmed in cabbage and A. thaliana seedlings. The findings suggest active metabolism of MEHP in plants and highlight the need to include metabolites in refining environmental risk assessment of plasticizers in the agro-food systems.
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Affiliation(s)
- Zhipeng Cheng
- Department of Environmental Science, University of California, Riverside, CA, 92521, United States; MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin, 300350, China
| | - Hongwen Sun
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin, 300350, China
| | - Harmanpreet S Sidhu
- Department of Environmental Science, University of California, Riverside, CA, 92521, United States
| | - Nathan Darlucio Sy
- Department of Environmental Science, University of California, Riverside, CA, 92521, United States
| | - Jay Gan
- Department of Environmental Science, University of California, Riverside, CA, 92521, United States.
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Bartoli J, Citerne S, Mouille G, Bouveret E, Field B. Quantification of guanosine triphosphate and tetraphosphate in plants and algae using stable isotope-labelled internal standards. Talanta 2020; 219:121261. [PMID: 32887152 DOI: 10.1016/j.talanta.2020.121261] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 06/03/2020] [Indexed: 12/20/2022]
Abstract
Guanosine tetraphosphate (G4P) and guanosine pentaphosphate (G5P) are signalling nucleotides found in bacteria and photosynthetic eukaryotes that are implicated in a wide-range of processes including stress acclimation, developmental transitions and growth control. Measurements of G4P/G5P levels are essential for studying the diverse roles of these nucleotides. However, G4P/G5P quantification is particularly challenging in plants and algae due to lower cellular concentrations, compartmentalization and high metabolic complexity. Despite recent advances the speed and accuracy of G4P quantification in plants and algae can still be improved. Here, we report a new approach for rapid and accurate G4P quantification which relies on the use of synthesized stable isotope-labelled as internal standards. We anticipate that this approach will accelerate research into the function of G4P signaling in plants, algae and other organisms.
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Szabo Z, Khan SH, Widdowson PJ, Reusch D, Viner R, Carillo S, Huhmer A, Bones J. A streamlined workflow for twoplexing of N-linked glycan analysis using light ( 12C 6) and heavy ( 13C 6) isotopologues of 3-aminobenzenesulfonic acid. Anal Chim Acta 2020; 1099:155-64. [PMID: 31986272 DOI: 10.1016/j.aca.2019.11.055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 11/21/2019] [Accepted: 11/22/2019] [Indexed: 11/20/2022]
Abstract
Comparative glycosylation analysis of biopharmaceuticals requires the development of methods that deliver the necessary throughput, support structural elucidation and relative quantitation of glycans released from therapeutics. The current study presents the development and applicability assessment of a twoplex approach using light and heavy isotopolouges of 3-aminobenzenesulfonic acid (3-ASA) under wet labeling conditions followed by UHPLC-MS analysis in data dependent acquisition mode. Excellent labelling efficiency, >90%, was achieved for both the light and heavy variants of the reagent. Glycan distributions of two human IgG lots labeled by light and heavy isotopolouges were identical, demonstrating no labeling bias introduced by either of the isotopologues. Peak area distributions of glycan profiles of two human IgG lots were compared to 2-aminobenzamide (2-AB) and RapiFluor-MS protocols. The comparison led to identical results in peak area distribution across the three dyes, but differences in chromatographic selectivity attributed to the different tags. MS1 based relative quantitation was further validated by releasing glycans from the same lot of human IgG, with glycan pools obtained labeled with light and heavy isotopologues separately, followed by mixing and clean-up of the same amount of light and heavy labeled glycan pools. MS analyses of each glycan resulted in a ratio of light and heavy XIC in the range of 0.97 ≤ x ≤ 1.05, demonstrating the method is amenable for the relative quantitation of glycans. Excellent correlation between the relative quantitation data of N-glycans from two human IgG N-glycan pools using the twoplex approach and ratios from peak area distribution calculated from the fluorescent chromatogram was observed (r = 0.986), further corroborating the reliability of the method and its potential applicability in the biopharmaceutical industry. Highly informative HCD-MS2 spectra dominated mostly by Y- and Z-type single and double glycosidic fragment ions facilitate structural interpretation of the oligosaccharides.
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Abstract
Stable isotope labeling is a generally applicable method of quantifying cell dynamics. Its advent has opened up the way for the quantitative study of T cells in humans. However, the literature is confusing as estimates vary by orders of magnitude between studies. In this short review we aim to explain the reasons for the discrepancies in estimates, clarify which estimates have been superseded and why and highlight the current best estimates. We focus on stable isotope labeling of T cell subsets in healthy humans. Current best estimates of the proliferation and production of CD4+ and CD8+ T cell subsets. Explanation of why estimates vary between studies and which estimates have been superseded. Discussion of the implications of model choice.
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Affiliation(s)
- Derek C Macallan
- Institute for Infection and Immunity, St George's, University of London, London, UK
| | - Robert Busch
- Department of Life Sciences, University of Roehampton, London, UK
| | - Becca Asquith
- Department of Infectious Disease, Imperial College London, London, UK
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12
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Qian ZY, Chen X, Zhu HT, Shi JZ, Gong TT, Xian QM. Study on the cyanobacterial toxin metabolism of Microcystis aeruginosa in nitrogen-starved conditions by a stable isotope labelling method. J Hazard Mater 2019; 373:558-564. [PMID: 30952000 DOI: 10.1016/j.jhazmat.2019.03.127] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Revised: 03/16/2019] [Accepted: 03/30/2019] [Indexed: 06/09/2023]
Abstract
In this study, the biosynthesis of microcystins (MCs) was investigated after long-term nitrogen-starved conditions in cyanobacterium Microcystis aeruginosa. The results demonstrated that the algal cells were able to survive in a non-growing state with nitrogen starvation for more than one month. The physiological properties of the algal cells were studied to elucidate the mechanisms of viability under nitrogen-deprivation conditions. After the state of nitrogen chlorosis, new toxins could be resynthesized and tracked using 15N-stable isotope-labelled nitrogen. Nitrogen starvation of nutritionally replete cells resulted in a significant increase of microcystin-LY (MC-LY), thereby suggesting that MC-LY may undergo catabolism to provide nitrogen or that MC-LY may be produced to play an important role in the cell in response to nitrogen deprivation. The rank order of different types of nitrogen in algal cells assimilation was N-ammonium > N-urea > N-nitrate > N-alanine. The relationship between the production of toxin variants and various environmental conditions is an interesting issue for future research and may help improve the understanding of the ecological role of cyanobacterial toxins.
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Affiliation(s)
- Zong-Yao Qian
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Xiao Chen
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - He-Te Zhu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Jun-Zhe Shi
- Wuxi Environmental Monitoring Central Station, Wuxi, 214121, China
| | - Ting-Ting Gong
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Qi-Ming Xian
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China.
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Baliu-Piqué M, Otto SA, Borghans JAM, Tesselaar K. In vivo deuterium labelling in mice supports a dynamic model for memory T-cell maintenance in the bone marrow. Immunol Lett 2019; 210:29-32. [PMID: 31004681 DOI: 10.1016/j.imlet.2019.04.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 04/12/2019] [Accepted: 04/16/2019] [Indexed: 10/27/2022]
Abstract
The maintenance and dynamics of memory T-cells in the bone marrow are a matter of ongoing debate. It has been suggested that memory T-cells in the bone marrow are maintained as long-lived, quiescent cells. We have recently shown that memory T-cells isolated from goat bone marrow undergo self-renewal and recirculate via the blood and lymph. Using the well-established memory T-cell markers CD44 and CD62L we here show very similar results in mice. This provides further support for the concept that memory T-cells are continuously self-renewing and recirculating between blood, bone marrow, spleen and lymph nodes.
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Affiliation(s)
- Mariona Baliu-Piqué
- Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Sigrid A Otto
- Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - José A M Borghans
- Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Kiki Tesselaar
- Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht, the Netherlands.
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Baliu-Piqué M, Kurniawan H, Ravesloot L, Verheij MW, Drylewicz J, Lievaart-Peterson K, Borghans JAM, Koets A, Tesselaar K. Age-related distribution and dynamics of T-cells in blood and lymphoid tissues of goats. Dev Comp Immunol 2019; 93:1-10. [PMID: 30550777 DOI: 10.1016/j.dci.2018.12.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Revised: 12/10/2018] [Accepted: 12/10/2018] [Indexed: 06/09/2023]
Abstract
Neonatal mammals have increased disease susceptibility and sub-optimal vaccine responses. This raises problems in both humans and farm animals. The high prevalence of paratuberculosis in goats and the lack of an effective vaccine against it have a strong impact on the dairy sector, and calls for vaccines optimized for the neonatal immune system. We characterized the composition of the T-cell pool in neonatal kids and adult goats and quantified their turnover rates using in vivo deuterium labelling. From birth to adulthood, CD4+ T-cells were the predominant subset in the thymus and lymph nodes, while spleen and bone marrow contained mainly CD8+ lymphocytes. In blood, CD4+ T-cells were the predominant subset during the neonatal period, while CD8+ T-cells predominated in adults. We observed that thymic mass and cellularity increased during the first 5 months after birth, but decreased later in life. Deuterium labelling revealed that T-cell turnover rates in neonatal kids are considerably higher than in adult animals.
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Affiliation(s)
- Mariona Baliu-Piqué
- Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Henry Kurniawan
- Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Lars Ravesloot
- Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Lelystad, the Netherlands; Department of Farm Animal Health, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Myrddin W Verheij
- Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Julia Drylewicz
- Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht, the Netherlands
| | | | - José A M Borghans
- Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Ad Koets
- Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Lelystad, the Netherlands; Department of Farm Animal Health, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Kiki Tesselaar
- Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht, the Netherlands.
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15
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Bayram H, Sayadi A, Immonen E, Arnqvist G. Identification of novel ejaculate proteins in a seed beetle and division of labour across male accessory reproductive glands. Insect Biochem Mol Biol 2019; 104:50-57. [PMID: 30529580 DOI: 10.1016/j.ibmb.2018.12.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 12/04/2018] [Accepted: 12/06/2018] [Indexed: 06/09/2023]
Abstract
The male ejaculate contains a multitude of seminal fluid proteins (SFPs), many of which are key reproductive molecules, as well as sperm. However, the identification of SFPs is notoriously difficult and a detailed understanding of this complex phenotype has only been achieved in a few model species. We employed a recently developed proteomic method involving whole-organism stable isotope labelling coupled with proteomic and transcriptomic analyses to characterize ejaculate proteins in the seed beetle Callosobruchus maculatus. We identified 317 proteins that were transferred to females at mating, and a great majority of these showed signals of secretion and were highly male-biased in expression in the abdomen. These male-derived proteins were enriched with proteins involved in general metabolic and catabolic processes but also with proteolytic enzymes and proteins involved in protection against oxidative stress. Thirty-seven proteins showed significant homology with SFPs previously identified in other insects. However, no less than 92 C. maculatus ejaculate proteins were entirely novel, receiving no significant blast hits and lacking homologs in extant data bases, consistent with a rapid and divergent evolution of SFPs. We used 3D micro-tomography in conjunction with proteomic methods to identify 5 distinct pairs of male accessory reproductive glands and to show that certain ejaculate proteins were only recovered in certain male glands. Finally, we provide a tentative list of 231 candidate female-derived reproductive proteins, some of which are likely important in ejaculate processing and/or sperm storage.
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Affiliation(s)
- Helen Bayram
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, Norbyvägen 18D, SE-752 36, Uppsala, Sweden
| | - Ahmed Sayadi
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, Norbyvägen 18D, SE-752 36, Uppsala, Sweden
| | - Elina Immonen
- Department of Ecology and Genetics, Evolutionary Biology, Uppsala University, Norbyvägen 18D, SE-752 36, Uppsala, Sweden
| | - Göran Arnqvist
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, Norbyvägen 18D, SE-752 36, Uppsala, Sweden.
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16
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Keymer A, Huber C, Eisenreich W, Gutjahr C. Tracking Lipid Transfer by Fatty Acid Isotopolog Profiling from Host Plants to Arbuscular Mycorrhiza Fungi. Bio Protoc 2018; 8:e2786. [PMID: 34286009 DOI: 10.21769/bioprotoc.2786] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Revised: 03/13/2018] [Accepted: 03/19/2018] [Indexed: 11/02/2022] Open
Abstract
Lipid transfer from host plants to arbuscular mycorrhiza fungi was hypothesized for several years because sequenced arbuscular mycorrhiza fungal genomes lack genes encoding cytosolic fatty acid synthase ( Wewer et al., 2014 ; Rich et al., 2017 ). It was finally shown by two independent experimental approaches ( Jiang et al., 2017 ; Keymer et al., 2017 ; Luginbuehl et al., 2017 ). One approach used a technique called isotopolog profiling ( Keymer et al., 2017 ). Isotopologs are molecules, which differ only in their isotopic composition. For isotopolog profiling an organism is fed with a heavy isotope labelled precursor metabolite. Subsequently, the labelled isotopolog composition of metabolic products is analysed via mass spectrometry. The detected isotopolog pattern of the metabolite(s) of interest yields information about metabolic pathways and fluxes ( Ahmed et al., 2014 ). The following protocol describes an experimental setup, which enables separate isotopolog profiling of fatty acids in plant roots colonized by arbuscular mycorrhiza fungi and their associated fungal extraradical mycelium, to elucidate fluxes between both symbiotic organisms. We predict that this strategy can also be used to study metabolite fluxes between other organisms if the two interacting organisms can be physically separated.
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Affiliation(s)
- Andreas Keymer
- Genetics, Faculty of Biology, LMU Munich, Biocenter Martinsried, Germany.,Plant Genetics, School of Life Sciences Weihenstephan, Technical University Munich (TUM), Freising, Germany
| | - Claudia Huber
- Biochemistry, Technical University Munich (TUM), Garching, Germany
| | | | - Caroline Gutjahr
- Genetics, Faculty of Biology, LMU Munich, Biocenter Martinsried, Germany.,Plant Genetics, School of Life Sciences Weihenstephan, Technical University Munich (TUM), Freising, Germany
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Ikeya T, Ban D, Lee D, Ito Y, Kato K, Griesinger C. Solution NMR views of dynamical ordering of biomacromolecules. Biochim Biophys Acta Gen Subj 2017; 1862:287-306. [PMID: 28847507 DOI: 10.1016/j.bbagen.2017.08.020] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 08/22/2017] [Accepted: 08/24/2017] [Indexed: 01/01/2023]
Abstract
BACKGROUND To understand the mechanisms related to the 'dynamical ordering' of macromolecules and biological systems, it is crucial to monitor, in detail, molecular interactions and their dynamics across multiple timescales. Solution nuclear magnetic resonance (NMR) spectroscopy is an ideal tool that can investigate biophysical events at the atomic level, in near-physiological buffer solutions, or even inside cells. SCOPE OF REVIEW In the past several decades, progress in solution NMR has significantly contributed to the elucidation of three-dimensional structures, the understanding of conformational motions, and the underlying thermodynamic and kinetic properties of biomacromolecules. This review discusses recent methodological development of NMR, their applications and some of the remaining challenges. MAJOR CONCLUSIONS Although a major drawback of NMR is its difficulty in studying the dynamical ordering of larger biomolecular systems, current technologies have achieved considerable success in the structural analysis of substantially large proteins and biomolecular complexes over 1MDa and have characterised a wide range of timescales across which biomolecular motion exists. While NMR is well suited to obtain local structure information in detail, it contributes valuable and unique information within hybrid approaches that combine complementary methodologies, including solution scattering and microscopic techniques. GENERAL SIGNIFICANCE For living systems, the dynamic assembly and disassembly of macromolecular complexes is of utmost importance for cellular homeostasis and, if dysregulated, implied in human disease. It is thus instructive for the advancement of the study of the dynamical ordering to discuss the potential possibilities of solution NMR spectroscopy and its applications. This article is part of a Special Issue entitled "Biophysical Exploration of Dynamical Ordering of Biomolecular Systems" edited by Dr. Koichi Kato.
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Affiliation(s)
- Teppei Ikeya
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, 1-1 Minamiosawa, Hachioji, Tokyo 192-0373, Japan; CREST, Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan.
| | - David Ban
- Department of Medicine, James Graham Brown Cancer Center, University of Louisville, 505 S. Hancock St., Louisville, KY 40202, USA
| | - Donghan Lee
- Department of Medicine, James Graham Brown Cancer Center, University of Louisville, 505 S. Hancock St., Louisville, KY 40202, USA
| | - Yutaka Ito
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, 1-1 Minamiosawa, Hachioji, Tokyo 192-0373, Japan; CREST, Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Koichi Kato
- Okazaki Institute for Integrative Bioscience and Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan; Graduate School of Pharmaceutical Sciences, Nagoya City University, Tanabe-dori 3-1, Mizuho-ku, Nagoya 467-8603, Japan
| | - Christian Griesinger
- Department of Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen 37077, Germany.
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Daloso DM, Antunes WC, Pinheiro DP, Waquim JP, Araújo WL, Loureiro ME, Fernie AR, Williams TCR. Tobacco guard cells fix CO2 by both Rubisco and PEPcase while sucrose acts as a substrate during light-induced stomatal opening. Plant Cell Environ 2015; 38:2353-71. [PMID: 25871738 DOI: 10.1111/pce.12555] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Revised: 04/07/2015] [Accepted: 04/09/2015] [Indexed: 05/21/2023]
Abstract
Transcriptomic and proteomic studies have improved our knowledge of guard cell function; however, metabolic changes in guard cells remain relatively poorly understood. Here we analysed metabolic changes in guard cell-enriched epidermal fragments from tobacco during light-induced stomatal opening. Increases in sucrose, glucose and fructose were observed during light-induced stomatal opening in the presence of sucrose in the medium while no changes in starch were observed, suggesting that the elevated fructose and glucose levels were a consequence of sucrose rather than starch breakdown. Conversely, reduction in sucrose was observed during light- plus potassium-induced stomatal opening. Concomitant with the decrease in sucrose, we observed an increase in the level as well as in the (13) C enrichment in metabolites of, or associated with, the tricarboxylic acid cycle following incubation of the guard cell-enriched preparations in (13) C-labelled bicarbonate. Collectively, the results obtained support the hypothesis that sucrose is catabolized within guard cells in order to provide carbon skeletons for organic acid production. Furthermore, they provide a qualitative demonstration that CO2 fixation occurs both via ribulose-1,5-biphosphate carboxylase/oxygenase (Rubisco) and phosphoenolpyruvate carboxylase (PEPcase). The combined data are discussed with respect to current models of guard cell metabolism and function.
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Affiliation(s)
- Danilo M Daloso
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, 36570-900, Minas Gerais, Brazil
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, 14476, Germany
| | - Werner C Antunes
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, 36570-900, Minas Gerais, Brazil
- Departamento de Biologia, Universidade Estadual de Maringá, Maringá, Paraná, 87020-900, Brazil
| | - Daniela P Pinheiro
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, 36570-900, Minas Gerais, Brazil
| | - Jardel P Waquim
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, 36570-900, Minas Gerais, Brazil
| | - Wagner L Araújo
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, 36570-900, Minas Gerais, Brazil
| | - Marcelo E Loureiro
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, 36570-900, Minas Gerais, Brazil
| | - Alisdair R Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, 14476, Germany
| | - Thomas C R Williams
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, 36570-900, Minas Gerais, Brazil
- Departamento de Botânica, Universidade de Brasilia, Brasilia, Distrito Federal, 70910-900, Brazil
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