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Lazari LC, Santiago VF, de Oliveira GS, Mule SN, Angeli CB, Rosa-Fernandes L, Palmisano G. Glycosort: A Computational Solution to Post-process Quantitative Large-Scale Intact Glycopeptide Analyses. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1443:23-32. [PMID: 38409414 DOI: 10.1007/978-3-031-50624-6_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Protein glycosylation is a post-translational modification involving the addition of carbohydrates to proteins and plays a crucial role in protein folding and various biological processes such as cell recognition, differentiation, and immune response. The vast array of natural sugars available allows the generation of plenty of unique glycan structures in proteins, adding complexity to the regulation and biological functions of glycans. The diversity is further increased by enzymatic site preferences and stereochemical conjugation, leading to an immense amount of different glycan structures. Understanding glycosylation heterogeneity is vital for unraveling the impact of glycans on different biological functions. Evaluating site occupancies and structural heterogeneity aids in comprehending glycan-related alterations in biological processes. Several software tools are available for large-scale glycoproteomics studies; however, integrating identification and quantitative data to assess heterogeneity complexity often requires extensive manual data processing. To address this challenge, we present a python script that automates the integration of Byonic and MaxQuant outputs for glycoproteomic data analysis. The script enables the calculation of site occupancy percentages by glycans and facilitates the comparison of glycan structures and site occupancies between two groups. This automated tool offers researchers a means to organize and interpret their high-throughput quantitative glycoproteomic data effectively.
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Affiliation(s)
- Lucas C Lazari
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Veronica Feijoli Santiago
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Gilberto S de Oliveira
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Simon Ngao Mule
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Claudia B Angeli
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Livia Rosa-Fernandes
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
- Centre for Motor Neuron Disease Research, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, Australia
| | - Giuseppe Palmisano
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.
- School of Natural Sciences, Faculty of Science and Engineering, Sydney, Australia.
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Polasky DA, Nesvizhskii AI. Recent advances in computational algorithms and software for large-scale glycoproteomics. Curr Opin Chem Biol 2023; 72:102238. [PMID: 36525809 DOI: 10.1016/j.cbpa.2022.102238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/12/2022] [Accepted: 11/14/2022] [Indexed: 12/15/2022]
Abstract
Glycoproteomics, or characterizing glycosylation events at a proteome scale, has seen rapid advances in methods for analyzing glycopeptides by tandem mass spectrometry in recent years. These advances have enabled acquisition of far more comprehensive and large-scale datasets, precipitating an urgent need for improved informatics methods to analyze the resulting data. A new generation of glycoproteomics search methods has recently emerged, using glycan fragmentation to split the identification of a glycopeptide into peptide and glycan components and solve each component separately. In this review, we discuss these new methods and their implications for large-scale glycoproteomics, as well as several outstanding challenges in glycoproteomics data analysis, including validation of glycan assignments and quantitation. Finally, we provide an outlook on the future of glycoproteomics from an informatics perspective, noting the key challenges to achieving widespread and reproducible glycopeptide annotation and quantitation.
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Affiliation(s)
- Daniel A Polasky
- University of Michigan Department of Pathology, Ann Arbor, MI, USA.
| | - Alexey I Nesvizhskii
- University of Michigan Department of Pathology, Ann Arbor, MI, USA; University of Michigan Department of Computational Medicine and Bioinformatics, Ann Arbor, MI, USA.
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Puranik A, Goswami R, Sutar P, Tupe D, Rasam P, Dandekar P, Jain R. Mass spectrometry-based glycoprofiling of biopharmaceuticals by using an automated data processing tool: SimGlycan ®. J Sep Sci 2023; 46:e2200521. [PMID: 36463509 DOI: 10.1002/jssc.202200521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 11/15/2022] [Accepted: 11/22/2022] [Indexed: 12/05/2022]
Abstract
The therapeutic and immunological properties of biopharmaceuticals are governed by the glycoforms contained in them. Thus, bioinformatics tools capable of performing comprehensive characterization of glycans are significantly important to the biopharma industry. The primary structural elucidation of glycans using mass spectrometry is tricky and tedious in terms of spectral interpretation. In this study, the biosimilars of a therapeutic monoclonal antibody and an Fc-fusion protein with moderate and heavy glycosylation, respectively, were employed as representative biopharmaceuticals for released glycan analysis using liquid chromatography-tandem mass spectrometry instead of conventional mass spectrometry-based analysis. SimGlycan® is a software with proven ability to process tandem MS data for released glycans could identify eight additional glycoforms in Fc-fusion protein biosimilar, which were not detected during mass spectrometry analysis of released glycans or glyco-peptide mapping of the same molecule. Thus, liquid chromatography-tandem mass spectrometry analysis of released glycans not only complements conventional liquid chromatography-mass spectrometry-based glycan profiling but can also identify additional glycan structures that may otherwise be omitted during conventional liquid chromatography-tandem mass spectrometry based analysis of mAbs. The mass spectrometry data processing tools, such as PMI Byos™, SimGlycan® , etc., can display pivotal analytical capabilities in automated liquid chromatography-mass spectrometry and liquid chromatography-tandem mass spectrometry-based glycan analysis workflows, especially for high-throughput structural characterization of glycoforms in biopharmaceuticals.
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Affiliation(s)
- Amita Puranik
- Department of Chemical Engineering, Institute of Chemical Technology, Mumbai, India
| | | | | | - Devika Tupe
- Shimadzu Analytical (India) Private Limited, Mumbai, India
| | - Pratap Rasam
- Shimadzu Analytical (India) Private Limited, Mumbai, India
| | - Prajakta Dandekar
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Mumbai, India
| | - Ratnesh Jain
- Department of Chemical Engineering, Institute of Chemical Technology, Mumbai, India
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Lubisch M, Moyzio S, Kaiser CS, Krafeld I, Leusder D, Scholz M, Hoepfner L, Hippler M, Liebau E, Kahl J. Using Caenorhabditis elegans to produce functional secretory proteins of parasitic nematodes. Acta Trop 2022; 225:106176. [PMID: 34627755 DOI: 10.1016/j.actatropica.2021.106176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/31/2021] [Accepted: 09/25/2021] [Indexed: 11/29/2022]
Abstract
The expression of antigens in their immunologically-active form remains a challenge, both in the analysis of regulatory pathways exploited by parasitic nematodes or in the development of vaccines. Despite the success of native proteins to induce protective immunity, recombinant proteins expressed in bacteria, yeast or insect cells offer only limited protective capacities, presumably due to incorrect folding or missing complex posttranslational modifications. The present study investigates the feasibility of using the free-living nematode Caenorhabditis elegans as an alternative expression system for proteins found in the secretome of parasitic nematodes. Exemplified by the expression of the extracellular superoxide dismutase from Haemonchus contortus (HcSODe) and the extracellular and glycosylated glutathione S-transferase from the filarial parasite Onchocerca volvulus (OvGST1), we continue our efforts to improve production and purification of recombinant proteins expressed in C. elegans. We demonstrate that sufficient quantities of functional proteins can be expressed in C. elegans for subsequent immunological and biochemical studies.
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Affiliation(s)
- Milena Lubisch
- Department of Molecular Physiology, Institute of Animal Physiology, Westfälische Wilhelms-University, Schlossplatz 8, 48143 Münster, Germany
| | - Sven Moyzio
- Department of Molecular Physiology, Institute of Animal Physiology, Westfälische Wilhelms-University, Schlossplatz 8, 48143 Münster, Germany
| | - Charlotte Sophia Kaiser
- Department of Molecular Physiology, Institute of Animal Physiology, Westfälische Wilhelms-University, Schlossplatz 8, 48143 Münster, Germany
| | - Isabel Krafeld
- Department of Molecular Physiology, Institute of Animal Physiology, Westfälische Wilhelms-University, Schlossplatz 8, 48143 Münster, Germany
| | - Dustin Leusder
- Department of Molecular Physiology, Institute of Animal Physiology, Westfälische Wilhelms-University, Schlossplatz 8, 48143 Münster, Germany
| | - Martin Scholz
- Plant Biochemistry and Biotechnology, Institute of Plant Biology and Biotechnology, Westfälische Wilhelms-University, Schlossplatz 8, 48143 Münster, Germany
| | - Lara Hoepfner
- Plant Biochemistry and Biotechnology, Institute of Plant Biology and Biotechnology, Westfälische Wilhelms-University, Schlossplatz 8, 48143 Münster, Germany
| | - Michael Hippler
- Plant Biochemistry and Biotechnology, Institute of Plant Biology and Biotechnology, Westfälische Wilhelms-University, Schlossplatz 8, 48143 Münster, Germany
| | - Eva Liebau
- Department of Molecular Physiology, Institute of Animal Physiology, Westfälische Wilhelms-University, Schlossplatz 8, 48143 Münster, Germany.
| | - Janina Kahl
- Department of Molecular Physiology, Institute of Animal Physiology, Westfälische Wilhelms-University, Schlossplatz 8, 48143 Münster, Germany
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Gong Y, Qin S, Dai L, Tian Z. The glycosylation in SARS-CoV-2 and its receptor ACE2. Signal Transduct Target Ther 2021; 6:396. [PMID: 34782609 PMCID: PMC8591162 DOI: 10.1038/s41392-021-00809-8] [Citation(s) in RCA: 102] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 10/10/2021] [Accepted: 10/24/2021] [Indexed: 02/05/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19), a highly infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has infected more than 235 million individuals and led to more than 4.8 million deaths worldwide as of October 5 2021. Cryo-electron microscopy and topology show that the SARS-CoV-2 genome encodes lots of highly glycosylated proteins, such as spike (S), envelope (E), membrane (M), and ORF3a proteins, which are responsible for host recognition, penetration, binding, recycling and pathogenesis. Here we reviewed the detections, substrates, biological functions of the glycosylation in SARS-CoV-2 proteins as well as the human receptor ACE2, and also summarized the approved and undergoing SARS-CoV-2 therapeutics associated with glycosylation. This review may not only broad the understanding of viral glycobiology, but also provide key clues for the development of new preventive and therapeutic methodologies against SARS-CoV-2 and its variants.
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Affiliation(s)
- Yanqiu Gong
- National Clinical Research Center for Geriatrics and Department of General Practice, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, 610041, Chengdu, China
| | - Suideng Qin
- School of Chemical Science & Engineering, Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University, 200092, Shanghai, China
| | - Lunzhi Dai
- National Clinical Research Center for Geriatrics and Department of General Practice, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, 610041, Chengdu, China.
| | - Zhixin Tian
- School of Chemical Science & Engineering, Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University, 200092, Shanghai, China.
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Comprehensive glycoproteomics shines new light on the complexity and extent of glycosylation in archaea. PLoS Biol 2021; 19:e3001277. [PMID: 34138841 PMCID: PMC8241124 DOI: 10.1371/journal.pbio.3001277] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 06/29/2021] [Accepted: 05/10/2021] [Indexed: 12/19/2022] Open
Abstract
Glycosylation is one of the most complex posttranslational protein modifications. Its importance has been established not only for eukaryotes but also for a variety of prokaryotic cellular processes, such as biofilm formation, motility, and mating. However, comprehensive glycoproteomic analyses are largely missing in prokaryotes. Here, we extend the phenotypic characterization of N-glycosylation pathway mutants in Haloferax volcanii and provide a detailed glycoproteome for this model archaeon through the mass spectrometric analysis of intact glycopeptides. Using in-depth glycoproteomic datasets generated for the wild-type (WT) and mutant strains as well as a reanalysis of datasets within the Archaeal Proteome Project (ArcPP), we identify the largest archaeal glycoproteome described so far. We further show that different N-glycosylation pathways can modify the same glycosites under the same culture conditions. The extent and complexity of the Hfx. volcanii N-glycoproteome revealed here provide new insights into the roles of N-glycosylation in archaeal cell biology. A comprehensive glycoproteomic analysis of Haloferax volcanii reveals the extent and complexity of glycosylation in archaea and provides new insights into the roles of this post-translational modification in various cellular processes, including cell shape determination.
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Abstract
Glycoproteomics is unquestionably on the rise and its current development benefits from past experience in proteomics, in particular when attending to bioinformatics needs. An extensive range of software solutions is available, but the reproducibility of mass spectrometry data processing remains challenging. One of the key issues in running automated glycopeptide identification software is the selection of a reference glycan composition file. The default choices are often too broad, and a fastidious literature search to properly target this selection can be avoided. This chapter suggests the use of GlyConnect Compozitor to collect relevant information on glycosylation in a given tissue or cell line and shape an appropriate glycan composition set that can be input in the majority of search engines accommodating user-defined compositions.
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Xu N, Oltmanns A, Zhao L, Girot A, Karimi M, Hoepfner L, Kelterborn S, Scholz M, Beißel J, Hegemann P, Bäumchen O, Liu LN, Huang K, Hippler M. Altered N-glycan composition impacts flagella-mediated adhesion in Chlamydomonas reinhardtii. eLife 2020; 9:58805. [PMID: 33300874 PMCID: PMC7759384 DOI: 10.7554/elife.58805] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 12/09/2020] [Indexed: 01/22/2023] Open
Abstract
For the unicellular alga Chlamydomonas reinhardtii, the presence of N-glycosylated proteins on the surface of two flagella is crucial for both cell-cell interaction during mating and flagellar surface adhesion. However, it is not known whether only the presence or also the composition of N-glycans attached to respective proteins is important for these processes. To this end, we tested several C. reinhardtii insertional mutants and a CRISPR/Cas9 knockout mutant of xylosyltransferase 1A, all possessing altered N-glycan compositions. Taking advantage of atomic force microscopy and micropipette force measurements, our data revealed that reduction in N-glycan complexity impedes the adhesion force required for binding the flagella to surfaces. This results in impaired polystyrene bead binding and transport but not gliding of cells on solid surfaces. Notably, assembly, intraflagellar transport, and protein import into flagella are not affected by altered N-glycosylation. Thus, we conclude that proper N-glycosylation of flagellar proteins is crucial for adhering C. reinhardtii cells onto surfaces, indicating that N-glycans mediate surface adhesion via direct surface contact.
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Affiliation(s)
- Nannan Xu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Anne Oltmanns
- Institute for Plant Biology and Biotechnology, University of Münster, Münster, Germany
| | - Longsheng Zhao
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom.,State Key Laboratory of Microbial Technology, and Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Antoine Girot
- Max Planck Institute for Dynamics and Self-Organization (MPIDS), Göttingen, Germany
| | - Marzieh Karimi
- Max Planck Institute for Dynamics and Self-Organization (MPIDS), Göttingen, Germany
| | - Lara Hoepfner
- Institute for Plant Biology and Biotechnology, University of Münster, Münster, Germany
| | - Simon Kelterborn
- Institute of Biology, Experimental Biophysics, Humboldt University of Berlin, Berlin, Germany
| | - Martin Scholz
- Institute for Plant Biology and Biotechnology, University of Münster, Münster, Germany
| | - Julia Beißel
- Institute for Plant Biology and Biotechnology, University of Münster, Münster, Germany
| | - Peter Hegemann
- Institute of Biology, Experimental Biophysics, Humboldt University of Berlin, Berlin, Germany
| | - Oliver Bäumchen
- Max Planck Institute for Dynamics and Self-Organization (MPIDS), Göttingen, Germany.,Experimental Physics V, University of Bayreuth, Bayreuth, Germany
| | - Lu-Ning Liu
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom.,College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Kaiyao Huang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Michael Hippler
- Institute for Plant Biology and Biotechnology, University of Münster, Münster, Germany.,Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
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