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Skalický V, Antoniadi I, Pěnčík A, Chamrád I, Lenobel R, Kubeš MF, Zatloukal M, Žukauskaitė A, Strnad M, Ljung K, Novák O. Fluorescence-activated multi-organelle mapping of subcellular plant hormone distribution. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:1825-1841. [PMID: 37682018 DOI: 10.1111/tpj.16456] [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: 03/03/2023] [Revised: 08/17/2023] [Accepted: 08/26/2023] [Indexed: 09/09/2023]
Abstract
Auxins and cytokinins are two major families of phytohormones that control most aspects of plant growth, development and plasticity. Their distribution in plants has been described, but the importance of cell- and subcellular-type specific phytohormone homeostasis remains undefined. Herein, we revealed auxin and cytokinin distribution maps showing their different organelle-specific allocations within the Arabidopsis plant cell. To do so, we have developed Fluorescence-Activated multi-Organelle Sorting (FAmOS), an innovative subcellular fractionation technique based on flow cytometric principles. FAmOS allows the simultaneous sorting of four differently labelled organelles based on their individual light scatter and fluorescence parameters while ensuring hormone metabolic stability. Our data showed different subcellular distribution of auxin and cytokinins, revealing the formation of phytohormone gradients that have been suggested by the subcellular localization of auxin and cytokinin transporters, receptors and metabolic enzymes. Both hormones showed enrichment in vacuoles, while cytokinins were also accumulated in the endoplasmic reticulum.
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Affiliation(s)
- Vladimír Skalický
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany of the Czech Academy of Sciences, CZ-78371, Olomouc, Czech Republic
| | - Ioanna Antoniadi
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-90183, Umeå, Sweden
| | - Aleš Pěnčík
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany of the Czech Academy of Sciences, CZ-78371, Olomouc, Czech Republic
| | - Ivo Chamrád
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany of the Czech Academy of Sciences, CZ-78371, Olomouc, Czech Republic
| | - René Lenobel
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany of the Czech Academy of Sciences, CZ-78371, Olomouc, Czech Republic
| | - Martin F Kubeš
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany of the Czech Academy of Sciences, CZ-78371, Olomouc, Czech Republic
| | - Marek Zatloukal
- Department of Chemical Biology, Faculty of Science, Palacký University, CZ-78371, Olomouc, Czech Republic
| | - Asta Žukauskaitė
- Department of Chemical Biology, Faculty of Science, Palacký University, CZ-78371, Olomouc, Czech Republic
| | - Miroslav Strnad
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany of the Czech Academy of Sciences, CZ-78371, Olomouc, Czech Republic
| | - Karin Ljung
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-90183, Umeå, Sweden
| | - Ondřej Novák
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany of the Czech Academy of Sciences, CZ-78371, Olomouc, Czech Republic
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-90183, Umeå, Sweden
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2
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Plasma membrane N-glycoproteome analysis of wheat seedling leaves under drought stress. Int J Biol Macromol 2021; 193:1541-1550. [PMID: 34740685 DOI: 10.1016/j.ijbiomac.2021.10.217] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 10/12/2021] [Accepted: 10/29/2021] [Indexed: 01/23/2023]
Abstract
Protein glycosylation is one of the ubiquitous post-translational modifications in eukaryotic cells, which play important roles in plant growth and adverse response. In this study, we performed the first comprehensive wheat plasma membrane N-glycoproteome analysis under drought stress via glycopeptide HILIC enrichment and LC-MS/MS identification. In total, 414 glycosylated sites corresponding to 407 glycopeptides and 312 unique glycoproteins were identified, of which 173 plasma membrane glycoproteins with 215 N-glycosylation sites were significantly regulated by drought stress. Functional enrichment analysis reveals that the significantly regulated N-glycosylation proteins were particularly related to protein kinase activity involved in the reception and transduction of extracellular signal and plant cell wall remolding. The motifs and sequence structures analysis showed that the significantly regulated N-glycosylation sites were concentrated within [NxT] motif, and 79.5% of them were located on the random coil that is always on the protein surface and flexible regions, which could facilitate protein glycosylated modification and enhance protein structural stability via reducing protein flexibility. PNGase F enzyme digestion and glycosylation site mutation further indicated that N-glycosylated modification could increase protein stability. Therefore, N-glycosylated modification is involved in plant adaptation to drought stress by improving the stability of cell wall remodeling related plasma membrane proteins.
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Auxin Metabolome Profiling in the Arabidopsis Endoplasmic Reticulum Using an Optimised Organelle Isolation Protocol. Int J Mol Sci 2021; 22:ijms22179370. [PMID: 34502279 PMCID: PMC8431077 DOI: 10.3390/ijms22179370] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 08/20/2021] [Accepted: 08/25/2021] [Indexed: 11/17/2022] Open
Abstract
The endoplasmic reticulum (ER) is an extensive network of intracellular membranes. Its major functions include proteosynthesis, protein folding, post-transcriptional modification and sorting of proteins within the cell, and lipid anabolism. Moreover, several studies have suggested that it may be involved in regulating intracellular auxin homeostasis in plants by modulating its metabolism. Therefore, to study auxin metabolome in the ER, it is necessary to obtain a highly enriched (ideally, pure) ER fraction. Isolation of the ER is challenging because its biochemical properties are very similar to those of other cellular endomembranes. Most published protocols for ER isolation use density gradient ultracentrifugation, despite its suboptimal resolving power. Here we present an optimised protocol for ER isolation from Arabidopsis thaliana seedlings for the subsequent mass spectrometric determination of ER-specific auxin metabolite profiles. Auxin metabolite analysis revealed highly elevated levels of active auxin form (IAA) within the ER compared to whole plants. Moreover, samples prepared using our optimised isolation ER protocol are amenable to analysis using various “omics” technologies including analyses of both macromolecular and low molecular weight compounds from the same sample.
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Lísa M, Řehulková H, Hančová E, Řehulka P. Lipidomic analysis using hydrophilic interaction liquid chromatography microgradient fractionation of total lipid extracts. J Chromatogr A 2021; 1653:462380. [PMID: 34348208 DOI: 10.1016/j.chroma.2021.462380] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 05/07/2021] [Accepted: 06/26/2021] [Indexed: 01/04/2023]
Abstract
Lipidomic samples are complex mixtures of structurally different species of a wide range of concentrations providing challenges in their characterization. In this work, we present a proof of concept for the application of a simple microgradient liquid chromatography device on the detailed analysis of lipid classes. Our lipidomic analysis is based on a lipid class microgradient fractionation of a total lipid extract using an in-house-prepared hydrophilic interaction liquid chromatography microcolumn followed by RP-LC/MS of the collected lipid class fractions. The final fractionation method uses a 40-mm-long microcolumn of 500 μm ID with silica stationary phase obtained from a commercially available chromatographic column and the microgradient of the mobile phase prepared in a microsyringe using methyl tert-butyl ether (MTBE) - methanol - water - ammonium acetate mixtures of various elution strengths. MTBE total lipid extract is directly separated by microgradient elution into lipid classes according to their polarity, which enables the collection of isolated fractions of most lipid classes. The method has been applied to the fractionation of porcine brain extract into nonpolar lipids, hexosylceramides, phosphoethanolamines, phosphocholines, sphingomyelins, and lysophosphocholines classes. Achieved repeatability, recovery, and advanced lipid coverage prove the applicability of the microgradient fractionation of total lipid extract for the comprehensive lipidomic analysis.
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Affiliation(s)
- Miroslav Lísa
- University of Hradec Králové, Faculty of Science, Department of Chemistry, Rokitanského 62, 50003 Hradec Králové, Czech Republic.
| | - Helena Řehulková
- University of Hradec Králové, Faculty of Science, Department of Chemistry, Rokitanského 62, 50003 Hradec Králové, Czech Republic
| | - Eliška Hančová
- University of Hradec Králové, Faculty of Science, Department of Chemistry, Rokitanského 62, 50003 Hradec Králové, Czech Republic
| | - Pavel Řehulka
- University of Defence, Faculty of Military Health Sciences, Department of Molecular Pathology and Biology, Trebešská 1575, 50001 Hradec Králové, Czech Republic
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Kouřil R, Nosek L, Opatíková M, Arshad R, Semchonok DA, Chamrád I, Lenobel R, Boekema EJ, Ilík P. Unique organization of photosystem II supercomplexes and megacomplexes in Norway spruce. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 104:215-225. [PMID: 32654240 PMCID: PMC7590091 DOI: 10.1111/tpj.14918] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 06/26/2020] [Indexed: 05/28/2023]
Abstract
Photosystem II (PSII) complexes are organized into large supercomplexes with variable amounts of light-harvesting proteins (Lhcb). A typical PSII supercomplex in plants is formed by four trimers of Lhcb proteins (LHCII trimers), which are bound to the PSII core dimer via monomeric antenna proteins. However, the architecture of PSII supercomplexes in Norway spruce[Picea abies (L.) Karst.] is different, most likely due to a lack of two Lhcb proteins, Lhcb6 and Lhcb3. Interestingly, the spruce PSII supercomplex shares similar structural features with its counterpart in the green alga Chlamydomonas reinhardtii [Kouřil et al. (2016) New Phytol. 210, 808-814]. Here we present a single-particle electron microscopy study of isolated PSII supercomplexes from Norway spruce that revealed binding of a variable amount of LHCII trimers to the PSII core dimer at positions that have never been observed in any other plant species so far. The largest spruce PSII supercomplex, which was found to bind eight LHCII trimers, is even larger than the current largest known PSII supercomplex from C. reinhardtii. We have also shown that the spruce PSII supercomplexes can form various types of PSII megacomplexes, which were also identified in intact grana membranes. Some of these large PSII supercomplexes and megacomplexes were identified also in Pinus sylvestris, another representative of the Pinaceae family. The structural variability and complexity of LHCII organization in Pinaceae seems to be related to the absence of Lhcb6 and Lhcb3 in this family, and may be beneficial for the optimization of light-harvesting under varying environmental conditions.
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Affiliation(s)
- Roman Kouřil
- Department of BiophysicsCentre of the Region Haná for Biotechnological and Agricultural ResearchFaculty of SciencePalacký UniversityŠlechtitelů 27Olomouc783 71Czech Republic
| | - Lukáš Nosek
- Department of BiophysicsCentre of the Region Haná for Biotechnological and Agricultural ResearchFaculty of SciencePalacký UniversityŠlechtitelů 27Olomouc783 71Czech Republic
| | - Monika Opatíková
- Department of BiophysicsCentre of the Region Haná for Biotechnological and Agricultural ResearchFaculty of SciencePalacký UniversityŠlechtitelů 27Olomouc783 71Czech Republic
| | - Rameez Arshad
- Department of BiophysicsCentre of the Region Haná for Biotechnological and Agricultural ResearchFaculty of SciencePalacký UniversityŠlechtitelů 27Olomouc783 71Czech Republic
- Electron Microscopy GroupGroningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenNijenborgh 7Groningen9747 AGThe Netherlands
| | - Dmitry A. Semchonok
- Electron Microscopy GroupGroningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenNijenborgh 7Groningen9747 AGThe Netherlands
| | - Ivo Chamrád
- Department of Protein Biochemistry and ProteomicsCentre of the Region Haná for Biotechnological and Agricultural ResearchFaculty of SciencePalacký UniversityŠlechtitelů 27Olomouc783 71Czech Republic
| | - René Lenobel
- Department of Protein Biochemistry and ProteomicsCentre of the Region Haná for Biotechnological and Agricultural ResearchFaculty of SciencePalacký UniversityŠlechtitelů 27Olomouc783 71Czech Republic
| | - Egbert J. Boekema
- Electron Microscopy GroupGroningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenNijenborgh 7Groningen9747 AGThe Netherlands
| | - Petr Ilík
- Department of BiophysicsCentre of the Region Haná for Biotechnological and Agricultural ResearchFaculty of SciencePalacký UniversityŠlechtitelů 27Olomouc783 71Czech Republic
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6
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Ondrej M, Rehulka P, Rehulkova H, Kupcik R, Tichy A. Fractionation of Enriched Phosphopeptides Using pH/Acetonitrile-Gradient-Reversed-Phase Microcolumn Separation in Combination with LC-MS/MS Analysis. Int J Mol Sci 2020; 21:ijms21113971. [PMID: 32492839 PMCID: PMC7312998 DOI: 10.3390/ijms21113971] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 05/28/2020] [Accepted: 05/28/2020] [Indexed: 12/20/2022] Open
Abstract
Mass spectrometry (MS) is a powerful and sensitive method often used for the identification of phosphoproteins. However, in phosphoproteomics, there is an identified need to compensate for the low abundance, insufficient ionization, and suppression effects of non-phosphorylated peptides. These may hamper the subsequent liquid chromatography–mass spectrometry/mass spectrometry (LC–MS/MS) analysis, resulting in incomplete phosphoproteome characterization, even when using high-resolution instruments. To overcome these drawbacks, we present here an effective microgradient chromatographic technique that yields specific fractions of enriched phosphopeptides compatible with LC–MS/MS analysis. The purpose of our study was to increase the number of identified phosphopeptides, and thus, the coverage of the sample phosphoproteome using the reproducible and straightforward fractionation method. This protocol includes a phosphopeptide enrichment step followed by the optimized microgradient fractionation of enriched phosphopeptides and final LC–MS/MS analysis of the obtained fractions. The simple fractionation system consists of a gas-tight microsyringe delivering the optimized gradient mobile phase to reversed-phase microcolumn. Our data indicate that combining the phosphopeptide enrichment with the microgradient separation is a promising technique for in-depth phosphoproteomic analysis due to moderate input material requirements and more than 3-fold enhanced protein identification.
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Affiliation(s)
- Martin Ondrej
- Department of Radiobiology, Faculty of Military Health Sciences, University of Defense in Brno, 500 01 Hradec Kralove, Czech Republic; (M.O.); (H.R.)
| | - Pavel Rehulka
- Department of Molecular Biology and Pathology, Faculty of Military Health Sciences, University of Defense in Brno, 500 01 Hradec Kralove, Czech Republic;
| | - Helena Rehulkova
- Department of Radiobiology, Faculty of Military Health Sciences, University of Defense in Brno, 500 01 Hradec Kralove, Czech Republic; (M.O.); (H.R.)
| | - Rudolf Kupcik
- Department of Biological and Biochemical Sciences, Faculty of Chemical Technology, University of Pardubice, 532 10 Pardubice, Czech Republic;
| | - Ales Tichy
- Department of Radiobiology, Faculty of Military Health Sciences, University of Defense in Brno, 500 01 Hradec Kralove, Czech Republic; (M.O.); (H.R.)
- Correspondence: ; Tel.: +420-973-253-216
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7
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Stratilová B, Klaudiny J, Řehulka P, Stratilová E, Mészárosová C, Garajová S, Pavlatovská B, Řehulková H, Kozmon S, Šesták S, Firáková Z, Vadkertiová R. Characterization of a long-chain α-galactosidase from Papiliotrema flavescens. World J Microbiol Biotechnol 2018; 34:19. [PMID: 29302817 DOI: 10.1007/s11274-017-2403-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 12/22/2017] [Indexed: 11/30/2022]
Abstract
α-Galactosidases are assigned to the class of hydrolases and the subclass of glycoside hydrolases (GHs). They belong to six GH families and include the only characterized α-galactosidases from yeasts (GH 27, Saccharomyces cerevisiae). The present study focuses on an investigation of the lactose-inducible α-galactosidase produced by Papiliotrema flavescens. The enzyme was present on the surface of cells and in the cytosol. Its temperature optimum was about 60 °C and the pH optimum was 4.8; the pH stability ranged from 3.2 to 6.6. This α-galactosidase also exhibited transglycosylation activity. The cytosol α-galactosidase with a molecular weight about 110 kDa, was purified using a combination of liquid chromatography techniques. Three intramolecular peptides were determined by the partial structural analysis of the sequences of the protein isolated, using MALDI-TOF/TOF mass spectrometry. The data obtained recognized the first yeast α-galactosidase, which belongs to the GH 36 family. The bioinformatics analysis and homology modeling of a 210 amino acids long C-terminal sequence (derived from cDNA) confirmed the correctness of these findings. The study was also supplemented by the screening of capsular cryptococcal yeasts, which produce the surface lactose-inducible α- and β-galactosidases. The production of the lactose-inducible α-galactosidases was not found to be a general feature within the yeast strains examined and, therefore, the existing hypothesis on the general function of this enzyme in cryptococcal capsule rearrangement cannot be confirmed.
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Affiliation(s)
- Barbora Stratilová
- Institute of Chemistry, Center for Glycomics, Slovak Academy of Sciences, Dúbravská cesta 9, 845 38, Bratislava, Slovakia.,Department of Physical and Theoretical Chemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Mlynská dolina, Ilkovičova 6, 842 15, Bratislava, Slovakia
| | - Jaroslav Klaudiny
- Institute of Chemistry, Center for Glycomics, Slovak Academy of Sciences, Dúbravská cesta 9, 845 38, Bratislava, Slovakia
| | - Pavel Řehulka
- Institute of Molecular Pathology, Faculty of Military Health Sciences, University of Defence, Třebešská 1575, 50001, Hradec Králové, Czech Republic
| | - Eva Stratilová
- Institute of Chemistry, Center for Glycomics, Slovak Academy of Sciences, Dúbravská cesta 9, 845 38, Bratislava, Slovakia
| | - Csilla Mészárosová
- Institute of Chemistry, Center for Glycomics, Slovak Academy of Sciences, Dúbravská cesta 9, 845 38, Bratislava, Slovakia
| | - Soňa Garajová
- Institute of Chemistry, Center for Glycomics, Slovak Academy of Sciences, Dúbravská cesta 9, 845 38, Bratislava, Slovakia
| | - Barbora Pavlatovská
- Institute of Food Chemistry and Biotechnology, Faculty of Chemistry, Brno University of Technology, Purkyňova 118, 612 00, Brno, Czech Republic
| | - Helena Řehulková
- Institute of Molecular Pathology, Faculty of Military Health Sciences, University of Defence, Třebešská 1575, 50001, Hradec Králové, Czech Republic
| | - Stanislav Kozmon
- Institute of Chemistry, Center for Glycomics, Slovak Academy of Sciences, Dúbravská cesta 9, 845 38, Bratislava, Slovakia
| | - Sergej Šesták
- Institute of Chemistry, Center for Glycomics, Slovak Academy of Sciences, Dúbravská cesta 9, 845 38, Bratislava, Slovakia
| | - Zuzana Firáková
- Institute of Chemistry, Center for Glycomics, Slovak Academy of Sciences, Dúbravská cesta 9, 845 38, Bratislava, Slovakia
| | - Renáta Vadkertiová
- Institute of Chemistry, Center for Glycomics, Slovak Academy of Sciences, Dúbravská cesta 9, 845 38, Bratislava, Slovakia.
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Harvey DJ. Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2011-2012. MASS SPECTROMETRY REVIEWS 2017; 36:255-422. [PMID: 26270629 DOI: 10.1002/mas.21471] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Accepted: 01/15/2015] [Indexed: 06/04/2023]
Abstract
This review is the seventh update of the original article published in 1999 on the application of MALDI mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2012. General aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, and fragmentation are covered in the first part of the review and applications to various structural types constitute the remainder. The main groups of compound are oligo- and poly-saccharides, glycoproteins, glycolipids, glycosides, and biopharmaceuticals. Much of this material is presented in tabular form. Also discussed are medical and industrial applications of the technique, studies of enzyme reactions, and applications to chemical synthesis. © 2015 Wiley Periodicals, Inc. Mass Spec Rev 36:255-422, 2017.
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Affiliation(s)
- David J Harvey
- Department of Biochemistry, Oxford Glycobiology Institute, University of Oxford, Oxford, OX1 3QU, UK
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Beinhauer J, Lenobel R, Loginov D, Chamrád I, Řehulka P, Sedlářová M, Marchetti-Deschmann M, Allmaier G, Šebela M. Identification ofBremia lactucaeandOidium neolycopersiciproteins extracted for intact spore MALDI mass spectrometric biotyping. Electrophoresis 2016; 37:2940-2952. [DOI: 10.1002/elps.201600144] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Revised: 07/19/2016] [Accepted: 08/17/2016] [Indexed: 01/26/2023]
Affiliation(s)
- Jana Beinhauer
- Department of Protein Biochemistry and Proteomics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science; Palacký University; Olomouc Czech Republic
| | - René Lenobel
- Department of Protein Biochemistry and Proteomics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science; Palacký University; Olomouc Czech Republic
| | - Dmitry Loginov
- Department of Protein Biochemistry and Proteomics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science; Palacký University; Olomouc Czech Republic
| | - Ivo Chamrád
- Department of Protein Biochemistry and Proteomics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science; Palacký University; Olomouc Czech Republic
| | - Pavel Řehulka
- Institute of Molecular Pathology, Faculty of Military Health Sciences; University of Defence; Hradec Králové Czech Republic
| | - Michaela Sedlářová
- Department of Botany, Faculty of Science; Palacký University; Olomouc Czech Republic
| | | | - Günter Allmaier
- Institute of Chemical Technologies and Analytics; Vienna University of Technology (TU Wien); Vienna Austria
| | - Marek Šebela
- Department of Protein Biochemistry and Proteomics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science; Palacký University; Olomouc Czech Republic
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Xue X, Zhao Y, Zhang X, Zhang C, Kumar A, Zhang X, Zou G, Wang PC, Zhang J, Liang XJ. Phenylboronic acid-functionalized magnetic nanoparticles for one-step saccharides enrichment and mass spectrometry analysis. BIOPHYSICS REPORTS 2015; 1:61-70. [PMID: 26942220 PMCID: PMC4762129 DOI: 10.1007/s41048-015-0002-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2015] [Accepted: 04/01/2015] [Indexed: 11/16/2022] Open
Abstract
Abstract In this work, 2-(2-aminoethoxy) ethanol-blocked phenylboronic acid-functionalized magnetic nanoparticles (blocked PMNPs) were fabricated for selective enrichment of different types of saccharides. The phenylboronic acid was designed for capturing the cis-diols moieties on saccharides molecules, and the 2-(2-aminoethoxy) ethanol can deplete the nonspecific absorption of peptides and proteins which always coexisted with saccharides. For mass spectrometry analysis, the PMNPs bound saccharides can be directly applied onto the MALDI plate with matrix without removing the PMNPs. By PMNPs, the simple saccharide (glucose) could be detected in pmol level. The complex saccharides can also be reliably purified and analyzed; 16 different N-glycans were successfully identified from ovalbumin, and the high-abundance N-glycans can be detected even when the ovalbumin was in very low concentration (2 μg). In human milk, ten different oligosaccharides were identified, and the lactose can still be detected when the human milk concentration was low to 0.01 μL. Graphical Abstract ![]()
Electronic supplementary material The online version of this article (doi:10.1007/s41048-015-0002-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xiangdong Xue
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, Beijing, 100190 China
| | - Yuanyuan Zhao
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, Beijing, 100190 China
| | - Xu Zhang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, Beijing, 100190 China
| | - Chunqiu Zhang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, Beijing, 100190 China
| | - Anil Kumar
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, Beijing, 100190 China
| | - Xiaoning Zhang
- Laboratory of Pharmaceutics, School of Medicine, Tsinghua University, Beijing, 100084 China
| | - Guozhang Zou
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, Beijing, 100190 China
| | - Paul C Wang
- Fu Jen Catholic University, Taipei, 24205 China
| | - Jinchao Zhang
- College of Chemistry & Environmental Science, Chemical Biology Key Laboratory of Hebei Province, Hebei University, Baoding, 071002 China
| | - Xing-Jie Liang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, Beijing, 100190 China
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11
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Kolli V, Dodds ED. Energy-resolved collision-induced dissociation pathways of model N-linked glycopeptides: implications for capturing glycan connectivity and peptide sequence in a single experiment. Analyst 2014; 139:2144-53. [DOI: 10.1039/c3an02342g] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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12
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Franc V, Řehulka P, Raus M, Stulík J, Novak J, Renfrow MB, Šebela M. Elucidating heterogeneity of IgA1 hinge-region O-glycosylation by use of MALDI-TOF/TOF mass spectrometry: role of cysteine alkylation during sample processing. J Proteomics 2013; 92:299-312. [PMID: 23891555 DOI: 10.1016/j.jprot.2013.07.013] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2013] [Revised: 06/19/2013] [Accepted: 07/11/2013] [Indexed: 12/22/2022]
Abstract
UNLABELLED Determining disease-associated changes in protein glycosylation provides a better understanding of pathogenesis. This work focuses on human immunoglobulin A1 (IgA1), where aberrant O-glycosylation plays a key role in the pathogenesis of IgA nephropathy (IgAN). Normal IgA1 hinge region carries 3 to 6 O-glycans consisting of N-acetylgalactosamine (GalNAc) and galactose (Gal); both sugars may be sialylated. In IgAN patients, some O-glycans on a fraction of IgA1 molecules are Gal-deficient. Here we describe a sample preparation protocol with optimized cysteine alkylation of a Gal-deficient polymeric IgA1 myeloma protein prior to in-gel digestion and analysis of the digest by MALDI-TOF/TOF mass spectrometry (MS). Following a novel strategy, IgA1 hinge-region O-glycopeptides were fractionated by reversed-phase liquid chromatography using a microgradient device and identified by MALDI-TOF/TOF tandem MS (MS/MS). The acquired MS/MS spectra were interpreted manually and by means of our own software. This allowed assigning up to six O-glycosylation sites and demonstration, for the first time, of the distribution of isomeric O-glycoforms having the same molecular mass, but a different glycosylation pattern. The most abundant Gal-deficient O-glycoforms were GalNAc4Gal3 and GalNAc5Gal4 with one Gal-deficient site and GalNAc5Gal3 and GalNAc4Gal2 with two Gal-deficient sites. The most frequent Gal-deficient sites were at Ser230 and/or Thr236. BIOLOGICAL SIGNIFICANCE In this work, we studied the O-glycosylation in the hinge region of human immunoglobulin A1 (IgA1). Aberrant glycosylation of the protein plays a key role in the pathogenesis of IgA nephropathy. Thus identification of the O-glycan composition of IgA1 is important for a deeper understanding of the disease mechanism, biomarker discovery and validation, and implementation and monitoring of disease-specific therapies. We developed a new procedure for elucidating the heterogeneity of IgA1 O-glycosylation. After running a polyacrylamide gel electrophoresis under denaturing conditions, the heavy chain of IgA1 was subjected to in-gel digestion by trypsin. O-glycopeptides were separated from the digest on capillary columns using a microgradient chromatographic device (replacing commonly used liquid chromatographs) and subjected to MALDI-TOF/TOF mass spectrometry (MS) and tandem mass spectrometry (MS/MS) involving post-source decay fragmentation. We show that the complete modification of cysteines by iodoacetamide prior to electrophoresis is critical for successful MS/MS analyses on the way to deciphering the microheterogeneity of O-glycosylation in IgA1. Similarly, the removal of the excess of the reagent is equally important. The acquired MS/MS allowed assigning up to six O-glycosylation sites and identification of isomeric O-glycoforms. We show that our simplified approach is efficient and has a high potential to provide a method for the rapid assessment of IgA1 heterogeneity that is a less expensive and yet corroborating alternative to LC-(high-resolution)-MS protocols. The novelty and biological significance reside in the demonstration, for the first time, of the distribution of the most abundant isoforms of HR O-glycopeptides of IgA1. As another new feature, we introduce a software solution for the interpretation of MS/MS data of O-glycopeptide isoforms, which provides the possibility of fast and easier data processing. This article is part of a Special Issue entitled: Posttranslational Protein modifications in biology and Medicine.
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Affiliation(s)
- Vojtěch Franc
- Department of Protein Biochemistry and Proteomics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 11, CZ-783 71 Olomouc, Czech Republic
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Franc V, Řehulka P, Medda R, Padiglia A, Floris G, Šebela M. Analysis of the glycosylation pattern of plant copper amine oxidases by MALDI-TOF/TOF MS coupled to a manual chromatographic separation of glycans and glycopeptides. Electrophoresis 2013; 34:2357-67. [PMID: 23580492 DOI: 10.1002/elps.201200622] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Revised: 12/30/2012] [Accepted: 01/24/2013] [Indexed: 02/02/2023]
Abstract
The N-glycosylation in pea seedling amine oxidase and lentil seedling amine oxidase was analyzed in the present work. For that purpose, the enzymes were purified as native proteins from their natural sources. An enzymatic deglycosylation of pea seedling amine oxidase by endoglycosidase H under denaturing conditions combined with its proteolytic digestion by trypsin was carried out in order to analyze both N-glycans and "trimmed" N-glycopeptides with a residual N-acetylglucosamine attached at the originally occupied N-glycosylation sites. The released N-glycans were subjected to a manual chromatographic purification followed by MALDI-TOF/TOF MS. MS and MS/MS analyses were also performed directly on peptides and N-glycopeptides generated by proteolytic digestion of the studied enzymes. Sequencing of glycopeptides by MALDI-TOF/TOF MS/MS after their separation on a RP using a microgradient chromatographic device clearly demonstrated binding of paucimannose and hybrid N-glycan structures at Asn558. Such carbohydrates have been reported to exist in many plant N-glycoproteins, e.g. in peroxidases. Although high-mannose glycan structures were identified after the enzymatic deglycosylation, they could not be assigned to a particular N-glycosylation site. The presence of unoccupied glycosylation sites in several peptides was also confirmed from MS/MS results.
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Affiliation(s)
- Vojtěch Franc
- Department of Protein Biochemistry and Proteomics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Olomouc, Czech Republic
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