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Hlozáková TK, Gálová Z, Šliková S, Leišová-Svobodová L, Beinhauer J, Dyčka F, Šebela M, Zetochová E, Gregová E. Molecular Characterization of Novel x-Type HMW Glutenin Subunit 1B × 6.5 in Wheat. PLANTS 2021; 10:plants10102108. [PMID: 34685917 PMCID: PMC8541187 DOI: 10.3390/plants10102108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 09/30/2021] [Accepted: 09/30/2021] [Indexed: 11/29/2022]
Abstract
A novel high molecular weight glutenin subunit encoded by the Glu-1B locus was identified in the French genotype Bagou, which we named 1B × 6.5. This subunit differed in SDS-PAGE from well-known 1B × 6 and 1B × 7 subunits, which are also encoded at this locus. Subunit 1B × 6.5 has a theoretical molecular weight of 88,322.83 Da, which is more mobile than 1B × 6 subunit, and isoelectric point (pI) of about 8.7, which is lower than that for 1B × 6 subunit. The specific primers were designed to amplify and sequence 2476 bp of the Glu-1B locus from genotype Bagou. A high level of similarity was found between the sequence encoding 1B × 6.5 and other x-type encoding alleles of this locus.
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Affiliation(s)
- Tímea Kuťka Hlozáková
- Faculty of Biotechnology and Food Science, Slovak University of Agriculture, Tr. A. Hlinku 2, 949 76 Nitra, Slovakia; (T.K.H.); (Z.G.)
| | - Zdenka Gálová
- Faculty of Biotechnology and Food Science, Slovak University of Agriculture, Tr. A. Hlinku 2, 949 76 Nitra, Slovakia; (T.K.H.); (Z.G.)
| | - Svetlana Šliková
- National Agriculture and Food Centre, Research Institute of Plant Production, Bratislavská Cesta 122, 921 01 Piešťany, Slovakia; (S.Š.); (E.Z.)
| | | | - Jana Beinhauer
- Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelu 27, 783 71 Olomouc, Czech Republic; (J.B.); (F.D.); (M.Š.)
| | - Filip Dyčka
- Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelu 27, 783 71 Olomouc, Czech Republic; (J.B.); (F.D.); (M.Š.)
| | - Marek Šebela
- Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelu 27, 783 71 Olomouc, Czech Republic; (J.B.); (F.D.); (M.Š.)
| | - Erika Zetochová
- National Agriculture and Food Centre, Research Institute of Plant Production, Bratislavská Cesta 122, 921 01 Piešťany, Slovakia; (S.Š.); (E.Z.)
| | - Edita Gregová
- National Agriculture and Food Centre, Research Institute of Plant Production, Bratislavská Cesta 122, 921 01 Piešťany, Slovakia; (S.Š.); (E.Z.)
- Correspondence:
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Perutka Z, Kaduchová K, Chamrád I, Beinhauer J, Lenobel R, Petrovská B, Bergougnoux V, Vrána J, Pecinka A, Doležel J, Šebela M. Proteome Analysis of Condensed Barley Mitotic Chromosomes. FRONTIERS IN PLANT SCIENCE 2021; 12:723674. [PMID: 34497629 PMCID: PMC8419432 DOI: 10.3389/fpls.2021.723674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 07/21/2021] [Indexed: 06/13/2023]
Abstract
Proteins play a major role in the three-dimensional organization of nuclear genome and its function. While histones arrange DNA into a nucleosome fiber, other proteins contribute to higher-order chromatin structures in interphase nuclei, and mitotic/meiotic chromosomes. Despite the key role of proteins in maintaining genome integrity and transferring hereditary information to daughter cells and progenies, the knowledge about their function remains fragmentary. This is particularly true for the proteins of condensed chromosomes and, in particular, chromosomes of plants. Here, we purified barley mitotic metaphase chromosomes by a flow cytometric sorting and characterized their proteins. Peptides from tryptic protein digests were fractionated either on a cation exchanger or reversed-phase microgradient system before liquid chromatography coupled to tandem mass spectrometry. Chromosomal proteins comprising almost 900 identifications were classified based on a combination of software prediction, available database localization information, sequence homology, and domain representation. A biological context evaluation indicated the presence of several groups of abundant proteins including histones, topoisomerase 2, POLYMERASE 2, condensin subunits, and many proteins with chromatin-related functions. Proteins involved in processes related to DNA replication, transcription, and repair as well as nucleolar proteins were found. We have experimentally validated the presence of FIBRILLARIN 1, one of the nucleolar proteins, on metaphase chromosomes, suggesting that plant chromosomes are coated with proteins during mitosis, similar to those of human and animals. These results improve significantly the knowledge of plant chromosomal proteins and provide a basis for their functional characterization and comparative phylogenetic analyses.
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Affiliation(s)
- Zdeněk Perutka
- Department of Protein Biochemistry and Proteomics, Faculty of Science, Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University Olomouc, Olomouc, Czechia
| | - Kateřina Kaduchová
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
| | - Ivo Chamrád
- Department of Protein Biochemistry and Proteomics, Faculty of Science, Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University Olomouc, Olomouc, Czechia
| | - Jana Beinhauer
- Department of Protein Biochemistry and Proteomics, Faculty of Science, Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University Olomouc, Olomouc, Czechia
| | - René Lenobel
- Department of Protein Biochemistry and Proteomics, Faculty of Science, Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University Olomouc, Olomouc, Czechia
| | - Beáta Petrovská
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
| | - Véronique Bergougnoux
- Department of Molecular Biology, Faculty of Science, Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University Olomouc, Olomouc, Czechia
| | - Jan Vrána
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
| | - Ales Pecinka
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
| | - Jaroslav Doležel
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
| | - Marek Šebela
- Department of Protein Biochemistry and Proteomics, Faculty of Science, Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University Olomouc, Olomouc, Czechia
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O'Rourke MB, Viengkhou B, Smith CC, Sonderegger L, Padula MP, Sutherland GT, Hofer MJ, Crossett B. Matrix phase fractionation: Investigating the compromise between dynamic range of analyte extraction and spatial resolution in mass spectrometry imaging. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2021; 35:e9106. [PMID: 33860568 DOI: 10.1002/rcm.9106] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 02/26/2021] [Accepted: 03/31/2021] [Indexed: 06/12/2023]
Abstract
RATIONALE Matrix-assisted laser desorption ionisation with mass spectrometry imaging (MSI) has seen rapid development in recent years and as such is becoming an important technique for the mapping of biomolecules from the surface of tissues. One key area of development is the optimisation of analyte extraction by using modified matrices or mixes of common ones. METHODS A series of serial sections were prepared for lipid MSI by either dry coating (sublimation) or by wet spray application of several matrices. These samples were then evaluated for analyte extraction, delocalisation and dynamic range. RESULTS We have shown that the spraying and sublimation methods of matrix application can be used complementarily. This creates large datasets, with each preparation method applied narrowly and then interpreted as a 'fraction' of the whole. Once combined, the dynamic range is significantly increased. We have dubbed this technique 'matrix phase fractionation'. CONCLUSIONS We have found that, by utilising matrix phase fractionation for the detection of lipids in brain tissue, it is possible to create a significantly more comprehensive dataset than would otherwise be possible with traditional 'single-run' workflows.
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Affiliation(s)
- Matthew B O'Rourke
- Northern Clinical School, Bowel Cancer & Biomarker Lab, Faculty of Medicine and Health, The University of Sydney Level 8, Kolling Institute, Royal North Shore Hospital, NSW, 2065, Australia
| | - Barney Viengkhou
- School of Life and Environmental Sciences, Charles Perkins Centre and The Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, NSW, 2006, Australia
| | - Caine C Smith
- Neuropathology Group, Discipline of Pathology, School of Medical Sciences and Charles Perkins Centre, Faculty of Medicine and Health, The University of Sydney, NSW, 2006, Australia
| | - Lorenz Sonderegger
- Shimadzu Australasia, Unit F, 10-16 South Street, Rydalmere, NSW, 2116, Australia
| | - Matthew P Padula
- School of Life Science and Proteomics Core Facility, Faculty of Science, The University of Technology Sydney, Ultimo, 2007, Australia
| | - Greg T Sutherland
- Neuropathology Group, Discipline of Pathology, School of Medical Sciences and Charles Perkins Centre, Faculty of Medicine and Health, The University of Sydney, NSW, 2006, Australia
| | - Markus J Hofer
- School of Life and Environmental Sciences, Charles Perkins Centre and The Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, NSW, 2006, Australia
| | - Ben Crossett
- Sydney Mass Spectrometry, Charles Perkins Centre, The University of Sydney, Camperdown, NSW, 2006, Australia
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Scolari F, Valerio F, Benelli G, Papadopoulos NT, Vaníčková L. Tephritid Fruit Fly Semiochemicals: Current Knowledge and Future Perspectives. INSECTS 2021; 12:insects12050408. [PMID: 33946603 PMCID: PMC8147262 DOI: 10.3390/insects12050408] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 04/23/2021] [Accepted: 04/27/2021] [Indexed: 12/14/2022]
Abstract
The Dipteran family Tephritidae (true fruit flies) comprises more than 5000 species classified in 500 genera distributed worldwide. Tephritidae include devastating agricultural pests and highly invasive species whose spread is currently facilitated by globalization, international trade and human mobility. The ability to identify and exploit a wide range of host plants for oviposition, as well as effective and diversified reproductive strategies, are among the key features supporting tephritid biological success. Intraspecific communication involves the exchange of a complex set of sensory cues that are species- and sex-specific. Chemical signals, which are standing out in tephritid communication, comprise long-distance pheromones emitted by one or both sexes, cuticular hydrocarbons with limited volatility deposited on the surrounding substrate or on the insect body regulating medium- to short-distance communication, and host-marking compounds deposited on the fruit after oviposition. In this review, the current knowledge on tephritid chemical communication was analysed with a special emphasis on fruit fly pest species belonging to the Anastrepha, Bactrocera, Ceratitis, and Rhagoletis genera. The multidisciplinary approaches adopted for characterising tephritid semiochemicals, and the real-world applications and challenges for Integrated Pest Management (IPM) and biological control strategies are critically discussed. Future perspectives for targeted research on fruit fly chemical communication are highlighted.
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Affiliation(s)
- Francesca Scolari
- Institute of Molecular Genetics IGM-CNR “Luigi Luca Cavalli-Sforza”, I-27100 Pavia, Italy
- Correspondence: (F.S.); (L.V.); Tel.: +39-0382-986421 (F.S.); +420-732-852-528 (L.V.)
| | - Federica Valerio
- Department of Biology and Biotechnology, University of Pavia, I-27100 Pavia, Italy;
| | - Giovanni Benelli
- Department of Agriculture, Food and Environment, University of Pisa, Via del Borghetto 80, 56124 Pisa, Italy;
| | - Nikos T. Papadopoulos
- Department of Agriculture Crop Production and Rural Environment, University of Thessaly, Fytokou st., N. Ionia, 38446 Volos, Greece;
| | - Lucie Vaníčková
- Department of Chemistry and Biochemistry, Faculty of AgriSciences Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic
- Department of Forest Botany, Dendrology and Geobiocoenology, Faculty of Forestry and Wood Technology, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic
- Correspondence: (F.S.); (L.V.); Tel.: +39-0382-986421 (F.S.); +420-732-852-528 (L.V.)
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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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O'Rourke MB, Djordjevic SP, Padula MP. The quest for improved reproducibility in MALDI mass spectrometry. MASS SPECTROMETRY REVIEWS 2018; 37:217-228. [PMID: 27420733 DOI: 10.1002/mas.21515] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 05/19/2016] [Accepted: 06/16/2016] [Indexed: 05/18/2023]
Abstract
Reproducibility has been one of the biggest hurdles faced when attempting to develop quantitative protocols for MALDI mass spectrometry. The heterogeneous nature of sample recrystallization has made automated sample acquisition somewhat "hit and miss" with manual intervention needed to ensure that all sample spots have been analyzed. In this review, we explore the last 30 years of literature and anecdotal evidence that has attempted to address and improve reproducibility in MALDI MS. Though many methods have been attempted, we have discovered a significant publication history surrounding the use of nitrocellulose as a substrate to improve homogeneity of crystal formation and therefore reproducibility. We therefore propose that this is the most promising avenue of research for developing a comprehensive and universal preparation protocol for quantitative MALDI MS analysis. © 2016 Wiley Periodicals, Inc. Mass Spec Rev 37:217-228, 2018.
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Affiliation(s)
- Matthew B O'Rourke
- Proteomics Core Facility, University of Technology Sydney, Cnr Harris and Thomas St, Ultimo, New South Wales, 2007, Australia
| | - Steven P Djordjevic
- The iThree Institute, University of Technology Sydney, Cnr Harris and Thomas St, Ultimo, New South Wales, 2007, Australia
| | - Matthew P Padula
- Proteomics Core Facility, University of Technology Sydney, Cnr Harris and Thomas St, Ultimo, New South Wales, 2007, Australia
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Eeltink S, Wouters S, Dores-Sousa JL, Svec F. Advances in organic polymer-based monolithic column technology for high-resolution liquid chromatography-mass spectrometry profiling of antibodies, intact proteins, oligonucleotides, and peptides. J Chromatogr A 2017; 1498:8-21. [PMID: 28069168 DOI: 10.1016/j.chroma.2017.01.002] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Revised: 11/22/2016] [Accepted: 01/02/2017] [Indexed: 11/27/2022]
Abstract
This review focuses on the preparation of organic polymer-based monolithic stationary phases and their application in the separation of biomolecules, including antibodies, intact proteins and protein isoforms, oligonucleotides, and protein digests. Column and material properties, and the optimization of the macropore structure towards kinetic performance are also discussed. State-of-the-art liquid chromatography-mass spectrometry biomolecule separations are reviewed and practical aspects such as ion-pairing agent selection and carryover are presented. Finally, advances in comprehensive two-dimensional LC separations using monolithic columns, in particular ion-exchange×reversed-phase and reversed-phase×reversed-phase LC separations conducted at high and low pH, are shown.
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Affiliation(s)
- Sebastiaan Eeltink
- Vrije Universiteit Brussel, Department of Chemical Engineering, Pleinlaan 2, B-1050 Brussels, Belgium.
| | - Sam Wouters
- Vrije Universiteit Brussel, Department of Chemical Engineering, Pleinlaan 2, B-1050 Brussels, Belgium
| | - José Luís Dores-Sousa
- Vrije Universiteit Brussel, Department of Chemical Engineering, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Frantisek Svec
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing, China
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Moravcová D, Rantamäki AH, Duša F, Wiedmer SK. Monoliths in capillary electrochromatography and capillary liquid chromatography in conjunction with mass spectrometry. Electrophoresis 2016; 37:880-912. [PMID: 26800083 DOI: 10.1002/elps.201500520] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 12/18/2015] [Accepted: 12/21/2015] [Indexed: 12/29/2022]
Abstract
Here, we have reviewed separation studies utilizing monolithic capillary columns for separation of compounds preceding MS analysis. The review is divided in two parts according to the used separation method, namely CEC and capillary LC (cLC). Based on our overview, monolithic CEC-MS technique have been more focused on the syntheses of highly specialized and selective separation phase materials for fast and efficient separation of specific types of analytes. In contrast, monolithic cLC-MS is more widely used and is often employed, for instance, in the analysis of oligonucleotides, metabolites, and peptides and proteins in proteomic studies. While poly(styrene-divinylbenzene)-based and silica-based monolithic capillaries found their place in proteomic analyses, the other laboratory-synthesized monoliths still wait for their wider utilization in routine analyses. The development of new monolithic materials will most likely continue due to the demand of more efficient and rapid separation of increasingly complex samples.
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Affiliation(s)
- Dana Moravcová
- Institute of Analytical Chemistry of the CAS, v. v. i, Brno, Czech Republic
| | | | - Filip Duša
- Institute of Analytical Chemistry of the CAS, v. v. i, Brno, Czech Republic
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Šesták J, Moravcová D, Kahle V. Instrument platforms for nano liquid chromatography. J Chromatogr A 2015; 1421:2-17. [DOI: 10.1016/j.chroma.2015.07.090] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 07/23/2015] [Accepted: 07/24/2015] [Indexed: 11/25/2022]
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Wang T, Chen Y, Ma J, Chen M, Nie C, Hu M, Li Y, Jia Z, Fang J, Gao H. Ampholine-functionalized hybrid organic–inorganic silica material as sorbent for solid-phase extraction of acidic and basic compounds. J Chromatogr A 2013; 1308:63-72. [DOI: 10.1016/j.chroma.2013.08.025] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Revised: 08/02/2013] [Accepted: 08/05/2013] [Indexed: 11/26/2022]
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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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Šesták J, Duša F, Moravcová D, Kahle V. Simple automated liquid chromatographic system for splitless nano column gradient separations. J Chromatogr A 2013; 1276:26-32. [DOI: 10.1016/j.chroma.2012.12.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Revised: 12/03/2012] [Accepted: 12/11/2012] [Indexed: 11/24/2022]
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14
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Franc V, Šebela M, Řehulka P, Končitíková R, Lenobel R, Madzak C, Kopečný D. Analysis of N-glycosylation in maize cytokinin oxidase/dehydrogenase 1 using a manual microgradient chromatographic separation coupled offline to MALDI-TOF/TOF mass spectrometry. J Proteomics 2012; 75:4027-37. [DOI: 10.1016/j.jprot.2012.05.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2012] [Revised: 04/13/2012] [Accepted: 05/08/2012] [Indexed: 12/26/2022]
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15
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Duša F, Křenková J, Moravcová D, Kahle V, Šlais K. Divergent-flow isoelectric focusing for separation and preparative analysis of peptides. Electrophoresis 2012; 33:1687-94. [DOI: 10.1002/elps.201100587] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
| | - Jana Křenková
- Institute of Analytical Chemistry of the Academy of Sciences of the Czech Republic; v. v. i.; Brno; Czech Republic
| | - Dana Moravcová
- Institute of Analytical Chemistry of the Academy of Sciences of the Czech Republic; v. v. i.; Brno; Czech Republic
| | - Vladislav Kahle
- Institute of Analytical Chemistry of the Academy of Sciences of the Czech Republic; v. v. i.; Brno; Czech Republic
| | - Karel Šlais
- Institute of Analytical Chemistry of the Academy of Sciences of the Czech Republic; v. v. i.; Brno; Czech Republic
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16
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Sagar S, Gehring C, Minneman KP. Methods to Isolate and Identify New Plant Signaling Peptides. SIGNALING AND COMMUNICATION IN PLANTS 2012. [DOI: 10.1007/978-3-642-27603-3_12] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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17
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Colgrave ML, Goswami H, Howitt CA, Tanner GJ. What is in a Beer? Proteomic Characterization and Relative Quantification of Hordein (Gluten) in Beer. J Proteome Res 2011; 11:386-96. [DOI: 10.1021/pr2008434] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Michelle L. Colgrave
- CSIRO Livestock Industries, CSIRO Livestock Industries, QBP, Building 80, Services Rd, The University of Queensland, St Lucia, QLD 4067, Australia
- CSIRO Food Futures National Research Flagship, GPO Box 1600, Canberra, ACT 2601, Australia
| | - Hareshwar Goswami
- CSIRO Livestock Industries, CSIRO Livestock Industries, QBP, Building 80, Services Rd, The University of Queensland, St Lucia, QLD 4067, Australia
- CSIRO Food Futures National Research Flagship, GPO Box 1600, Canberra, ACT 2601, Australia
| | - Crispin A. Howitt
- CSIRO Food Futures National Research Flagship, GPO Box 1600, Canberra, ACT 2601, Australia
- CSIRO Plant Industry, GPO Box 1600 Canberra, ACT, 2601, Australia
| | - Gregory J. Tanner
- CSIRO Food Futures National Research Flagship, GPO Box 1600, Canberra, ACT 2601, Australia
- CSIRO Plant Industry, GPO Box 1600 Canberra, ACT, 2601, Australia
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18
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Rozenbrand J, van Bennekom WP. Silica-based and organic monolithic capillary columns for LC: recent trends in proteomics. J Sep Sci 2011; 34:1934-44. [PMID: 21710526 DOI: 10.1002/jssc.201100294] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2011] [Revised: 05/03/2011] [Accepted: 05/03/2011] [Indexed: 11/10/2022]
Abstract
The use of monolithic liquid chromatography (LC) columns for proteomics, covering the scientific literature from 2004 to the beginning of 2011, is reviewed. Attention is paid to recent developments in column technology and materials, focusing on silica-based and organic (polystyrene and methacrylate) monolithic capillary columns for proteomics. The applicability of these columns is illustrated by examples of the analysis of (complex) protein digests and proteins conveniently summarized in tables. Furthermore, characteristics of column materials are compared and future trends and prospects are presented.
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Affiliation(s)
- Johan Rozenbrand
- Biomolecular Analysis, Faculty of Science, Department of Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands.
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Namera A, Nakamoto A, Saito T, Miyazaki S. Monolith as a new sample preparation material: Recent devices and applications. J Sep Sci 2011; 34:901-24. [DOI: 10.1002/jssc.201000795] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2010] [Revised: 01/12/2011] [Accepted: 01/15/2011] [Indexed: 11/07/2022]
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20
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Alwael H, Connolly D, Clarke P, Thompson R, Twamley B, O'Connor B, Paull B. Pipette-tip selective extraction of glycoproteins with lectin modified gold nano-particles on a polymer monolithic phase. Analyst 2011; 136:2619-28. [DOI: 10.1039/c1an15137a] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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21
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Porous monoliths: sorbents for miniaturized extraction in biological analysis. Anal Bioanal Chem 2010; 399:3345-57. [DOI: 10.1007/s00216-010-4190-x] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2010] [Revised: 09/01/2010] [Accepted: 09/01/2010] [Indexed: 10/19/2022]
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