1
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Lembo A, Molinaro A, De Castro C, Berti F, Biagini M. Impact of glycosylation on viral vaccines. Carbohydr Polym 2024; 342:122402. [PMID: 39048237 DOI: 10.1016/j.carbpol.2024.122402] [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: 02/26/2024] [Revised: 05/24/2024] [Accepted: 06/11/2024] [Indexed: 07/27/2024]
Abstract
Glycosylation is the most prominent modification important for vaccines and its specific pattern depends on several factors that need to be considered when developing a new biopharmaceutical. Tailor-made glycosylation can be exploited to develop more effective and safer vaccines; for this reason, a deep understanding of both glycoengineering strategies and glycans structures and functions is required. In this review we discuss the recent advances concerning glycoprotein expression systems and the explanation of glycans immunomodulation mechanisms. Furthermore, we highlight how glycans tune the immunological properties among different vaccines platforms (whole virus, recombinant protein, nucleic acid), also comparing commercially available formulations and describing the state-of-the-art analytical technologies for glycosylation analysis. The whole review stresses the aspect of glycoprotein glycans as a potential tool to overcome nowadays medical needs in vaccine field.
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Affiliation(s)
- Antonio Lembo
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy; GSK, Siena, Italy
| | - Antonio Molinaro
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
| | - Cristina De Castro
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy.
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2
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Stanforth KJ, Zakhour MI, Chater PI, Wilcox MD, Adamson B, Robson NA, Pearson JP. The MUC2 Gene Product: Polymerisation and Post-Secretory Organisation-Current Models. Polymers (Basel) 2024; 16:1663. [PMID: 38932019 PMCID: PMC11207715 DOI: 10.3390/polym16121663] [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: 05/22/2024] [Revised: 06/03/2024] [Accepted: 06/10/2024] [Indexed: 06/28/2024] Open
Abstract
MUC2 mucin, the primary gel-forming component of intestinal mucus, is well researched and a model of polymerisation and post-secretory organisation has been published previously. Recently, several significant developments have been made which either introduce new ideas or challenge previous theories. New ideas include an overhaul of the MUC2 C-terminal globular structure which is proposed to harbour several previously unobserved domains, and include a site for an extra intermolecular disulphide bridge dimer between the cysteine 4379 of adjacent MUC2 C-termini. MUC2 polymers are also now thought to be secreted attached to the epithelial surface of goblet cells in the small intestine and removed following secretion via a metalloprotease meprin β-mediated cleavage of the von Willebrand D2 domain of the N-terminus. It remains unclear whether MUC2 forms intermolecular dimers, trimers, or both, at the N-termini during polymerisation, with several articles supporting either trimer or dimer formation. The presence of a firm inner mucus layer in the small intestine is similarly unclear. Considering this recent research, this review proposes an update to the previous model of MUC2 polymerisation and secretion, considers conflicting theories and data, and highlights the importance of this research to the understanding of MUC2 mucus layers in health and disease.
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Affiliation(s)
- Kyle J. Stanforth
- Aelius Biotech, The Medical School, Framlington Place, Newcastle-upon-Tyne NE2 4HH, UK; (P.I.C.); (M.D.W.); (B.A.); (N.A.R.)
| | - Maria I. Zakhour
- Biosciences Institute, Newcastle University Biosciences Institute, Catherine Cookson Building, Framlington Place, Newcastle-upon-Tyne NE2 4HH, UK; (M.I.Z.); (J.P.P.)
| | - Peter I. Chater
- Aelius Biotech, The Medical School, Framlington Place, Newcastle-upon-Tyne NE2 4HH, UK; (P.I.C.); (M.D.W.); (B.A.); (N.A.R.)
| | - Matthew D. Wilcox
- Aelius Biotech, The Medical School, Framlington Place, Newcastle-upon-Tyne NE2 4HH, UK; (P.I.C.); (M.D.W.); (B.A.); (N.A.R.)
| | - Beth Adamson
- Aelius Biotech, The Medical School, Framlington Place, Newcastle-upon-Tyne NE2 4HH, UK; (P.I.C.); (M.D.W.); (B.A.); (N.A.R.)
| | - Niamh A. Robson
- Aelius Biotech, The Medical School, Framlington Place, Newcastle-upon-Tyne NE2 4HH, UK; (P.I.C.); (M.D.W.); (B.A.); (N.A.R.)
| | - Jeffrey P. Pearson
- Biosciences Institute, Newcastle University Biosciences Institute, Catherine Cookson Building, Framlington Place, Newcastle-upon-Tyne NE2 4HH, UK; (M.I.Z.); (J.P.P.)
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3
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Dai J, Ma M, Niu Q, Eisert RJ, Wang X, Das P, Lechtreck KF, Dutcher SK, Zhang R, Brown A. Mastigoneme structure reveals insights into the O-linked glycosylation code of native hydroxyproline-rich helices. Cell 2024; 187:1907-1921.e16. [PMID: 38552624 PMCID: PMC11015965 DOI: 10.1016/j.cell.2024.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 02/06/2024] [Accepted: 03/05/2024] [Indexed: 04/14/2024]
Abstract
Hydroxyproline-rich glycoproteins (HRGPs) are a ubiquitous class of protein in the extracellular matrices and cell walls of plants and algae, yet little is known of their native structures or interactions. Here, we used electron cryomicroscopy (cryo-EM) to determine the structure of the hydroxyproline-rich mastigoneme, an extracellular filament isolated from the cilia of the alga Chlamydomonas reinhardtii. The structure demonstrates that mastigonemes are formed from two HRGPs (a filament of MST1 wrapped around a single copy of MST3) that both have hyperglycosylated poly(hydroxyproline) helices. Within the helices, O-linked glycosylation of the hydroxyproline residues and O-galactosylation of interspersed serine residues create a carbohydrate casing. Analysis of the associated glycans reveals how the pattern of hydroxyproline repetition determines the type and extent of glycosylation. MST3 possesses a PKD2-like transmembrane domain that forms a heteromeric polycystin-like cation channel with PKD2 and SIP, explaining how mastigonemes are tethered to ciliary membranes.
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Affiliation(s)
- Jin Dai
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Meisheng Ma
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
| | - Qingwei Niu
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis School of Medicine, St. Louis, MO, USA; Molecular Cell Biology (MCB) graduate program, Division of Biology & Biomedical Sciences, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
| | - Robyn J Eisert
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Xiangli Wang
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
| | - Poulomi Das
- Department of Cellular Biology, University of Georgia, Athens, GA, USA
| | - Karl F Lechtreck
- Department of Cellular Biology, University of Georgia, Athens, GA, USA
| | - Susan K Dutcher
- Department of Genetics, Washington University in St. Louis, St Louis, MO, USA
| | - Rui Zhang
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis School of Medicine, St. Louis, MO, USA.
| | - Alan Brown
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
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4
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Guan B, Cao X, Yang M, Yue X, Liu D. Comparative Site-Specific O-Glycosylation Analysis of the Milk Fat Globule Membrane Proteome in Donkey Colostrum and Mature Milk. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:1405-1417. [PMID: 38181196 DOI: 10.1021/acs.jafc.3c07805] [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: 01/07/2024]
Abstract
Donkey milk fat globule membrane (MFGM) proteins are a class of membrane-bound secreted proteins with broad-spectrum biofunctional activities; however, their site-specific O-glycosylation landscapes have not been systematically mapped. In this study, an in-depth MFGM O-glycoproteome profile of donkey milk during lactation was constructed based on an intact glycopeptide-centered, label-free glycoproteomics pipeline, with 2137 site-specific O-glycans from 1121 MFGM glycoproteins and 619 site-specific O-glycans from 217 MFGM glycoproteins identified in donkey colostrum and donkey mature milk, respectively. As lactation progressed, the number of site-specific O-glycans from three glycoproteins significantly increased, whereas that of 11 site-specific O-glycans from five glycoproteins significantly decreased. Furthermore, donkey MFGM O-glycoproteins with core-1 and core-2 core structures and Lewis and sialylated branch structures may be involved in regulating apoptosis. The findings of this study reveal the differences in the composition of donkey MFGM O-glycoproteins and their site-specific O-glycosylation modification dynamic change rules during lactation, providing a molecular basis for understanding the complexity and biological functions of donkey MFGM protein O-glycosylation.
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Affiliation(s)
- Boyuan Guan
- College of Biosystems Engineering and Food Science, National-Local Joint Engineering Laboratory of Intelligent Food Technology and Equipment, Zhejiang Key Laboratory for Agro-Food Processing, Zhejiang Engineering Laboratory of Food Technology and Equipment, Fuli Institute of Food Science, Zhejiang University, Hangzhou 310058, China
- Innovation Center of Yangtze River Delta, Zhejiang University, Jiashan 314100, China
| | - Xueyan Cao
- College of Food Science, Shenyang Agricultural University, Shenyang 11086, China
| | - Mei Yang
- College of Food Science, Shenyang Agricultural University, Shenyang 11086, China
| | - Xiqing Yue
- College of Food Science, Shenyang Agricultural University, Shenyang 11086, China
| | - Donghong Liu
- College of Biosystems Engineering and Food Science, National-Local Joint Engineering Laboratory of Intelligent Food Technology and Equipment, Zhejiang Key Laboratory for Agro-Food Processing, Zhejiang Engineering Laboratory of Food Technology and Equipment, Fuli Institute of Food Science, Zhejiang University, Hangzhou 310058, China
- Innovation Center of Yangtze River Delta, Zhejiang University, Jiashan 314100, China
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5
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Chaoua S, Chaouche NK, Songulashvili G, Gares M, Hiligsmann S, Flahaut S. Yellow laccase produced by Trametes versicolor K1 on tomato waste: A comparative study with the blue one produced on semi-synthetic medium. J Biotechnol 2023; 361:99-109. [PMID: 36509383 DOI: 10.1016/j.jbiotec.2022.12.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 11/30/2022] [Accepted: 12/03/2022] [Indexed: 12/13/2022]
Abstract
Laccase production by fungal growth on agrifood waste is still poorly studied. Trametes versicolor K1 isolated from palm bark produced a yellow non glycosylated laccase from tomato waste based medium (TMT) and a blue glycosylated laccase on glucose medium (GLU). Lignocellulosic biomass, such as pinecones (PIN), palm leaves (PLM), olive pomace (OLV), and alfa stems (ALF) have also been used as growth medium for T. versicolor K1. In these conditions, very low or no laccase production was observed. When peptone was supplied in TMT medium, the laccase activity increased from 4170 U/L to 8618 U/L. By increasing the culture volume up to 1 L, laccase production on TMT was 9929 U/L. The yellow laccase (TmtLac) was purified from the supernatant TMT medium and has shown similar characteristics with the blue laccase (GluLac) purified from the GLU medium. Their apparent protein size was 63 kDa. Catalytic activities of the yellow form were not very different from those of the blue form, but specific activity of the purified yellow laccase produced on tomato waste was much higher. The Km and Vm values for four substrates, ABTS, DMP, guaiacol, and pyrogallol were almost similar for both isoenzymes. The optimum pH and temperature were respectively 4.0 and 50 °C. Although the level of glycosylation is clearly different, the thermostability of TmtLac and GluLac are quite similar. TmtLac is even slightly more tolerant at 60 °C for 24 h than GluLac. Moreover TmtLac showed greater stability at alkaline pH after 24 h compared to that of GluLac.We demonstrate that activity of the yellow TmtLac is not significantly affected compared to the blue laccase and that tomato waste is a simple and interesting lignocellulosic substrate to the laccase producer Trametes sp.
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Affiliation(s)
- Samah Chaoua
- Laboratoire de Mycologie, de Biotechnologie et de l'Activité Microbienne (LaMyBAM), Département de Biologie Appliquée, Université des Frères Mentouri Constantine 1, Constantine, Algeria; Laboratoire de Microbiologie Appliquée, Université Libre de Bruxelles, Brussels, Belgium.
| | - Noreddine Kacem Chaouche
- Laboratoire de Mycologie, de Biotechnologie et de l'Activité Microbienne (LaMyBAM), Département de Biologie Appliquée, Université des Frères Mentouri Constantine 1, Constantine, Algeria
| | - George Songulashvili
- Laboratoire de Microbiologie Appliquée, Université Libre de Bruxelles, Brussels, Belgium
| | - Maroua Gares
- Laboratoire de Mycologie, de Biotechnologie et de l'Activité Microbienne (LaMyBAM), Département de Biologie Appliquée, Université des Frères Mentouri Constantine 1, Constantine, Algeria
| | - Serge Hiligsmann
- Bioengineering Department, CELABOR Research Center, Herve, Belgium
| | - Sigrid Flahaut
- Laboratoire de Microbiologie Appliquée, Université Libre de Bruxelles, Brussels, Belgium
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6
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Roberts DS, Mann M, Li BH, Kim D, Braiser AR, Jin S, Ge Y. Distinct core glycan and O-glycoform utilization of SARS-CoV-2 Omicron variant Spike protein RBD revealed by top-down mass spectrometry. Chem Sci 2022; 13:10944-10949. [PMID: 36320702 PMCID: PMC9491206 DOI: 10.1039/d2sc02132c] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 08/30/2022] [Indexed: 09/21/2023] Open
Abstract
The SARS-CoV-2 Omicron (B.1.1.529) variant possesses numerous spike (S) mutations particularly in the S receptor-binding domain (S-RBD) that significantly improve transmissibility and evasion of neutralizing antibodies. But exactly how the mutations in the Omicron variant enhance viral escape from immunological protection remains to be understood. The S-RBD remains the principal target for neutralizing antibodies and therapeutics, thus new structural insights into the Omicron S-RBD and characterization of the post-translational glycosylation changes can inform rational design of vaccines and therapeutics. Here we report the molecular variations and O-glycoform changes of the Omicron S-RBD variant as compared to wild-type (WA1/2020) and Delta (B.1.617.2) variants using high-resolution top-down mass spectrometry (MS). A novel O-glycosite (Thr376) unique to the Omicron variant is identified. Moreover, we have directly quantified the Core 1 and Core 2 O-glycan structures and characterized the O-glycoform structural heterogeneity of the three variants. Our findings reveal high resolution detail of Omicron O-glycoforms and their utilization to provide direct molecular evidence of proteoform alterations in the Omicron variant which could shed light on how this variant escapes immunological protection.
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Affiliation(s)
- David S Roberts
- Department of Chemistry, University of Wisconsin-Madison WI 53706 USA
| | - Morgan Mann
- Department of Medicine, School of Medicine and Public Health University of Wisconsin-Madison WI 53705 USA
| | - Brad H Li
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison WI 53705 USA
| | - Donguk Kim
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison WI 53705 USA
| | - Allan R Braiser
- Department of Medicine, School of Medicine and Public Health University of Wisconsin-Madison WI 53705 USA
- Institute for Clinical and Translational Research, University of Wisconsin-Madison WI 53705 USA
| | - Song Jin
- Department of Chemistry, University of Wisconsin-Madison WI 53706 USA
| | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison WI 53706 USA
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison WI 53705 USA
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7
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Lebart MC, Trousse F, Valette G, Torrent J, Denus M, Mestre-Frances N, Marcilhac A. Reg-1α, a New Substrate of Calpain-2 Depending on Its Glycosylation Status. Int J Mol Sci 2022; 23:ijms23158591. [PMID: 35955718 PMCID: PMC9369050 DOI: 10.3390/ijms23158591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/21/2022] [Accepted: 07/25/2022] [Indexed: 12/10/2022] Open
Abstract
Reg-1α/lithostathine, a protein mainly associated with the digestive system, was previously shown to be overexpressed in the pre-clinical stages of Alzheimer’s disease. In vitro, the glycosylated protein was reported to form fibrils at physiological pH following the proteolytic action of trypsin. However, the nature of the protease able to act in the central nervous system is unknown. In the present study, we showed that Reg-1α can be cleaved in vitro by calpain-2, the calcium activated neutral protease, overexpressed in neurodegenerative diseases. Using chemical crosslinking experiments, we found that the two proteins can interact with each other. Identification of the cleavage site using mass spectrometry, between Gln4 and Thr5, was found in agreement with the in silico prediction of the calpain cleavage site, in a position different from the one reported for trypsin, i.e., Arg11-Ile12 peptide bond. We showed that the cleavage was impeded by the presence of the neighboring glycosylation of Thr5. Moreover, in vitro studies using electron microscopy showed that calpain-cleaved protein does not form fibrils as observed after trypsin cleavage. Collectively, our results show that calpain-2 cleaves Reg-1α in vitro, and that this action is not associated with fibril formation.
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Affiliation(s)
- Marie-Christine Lebart
- MMDN, Univ Montpellier, EPHE, INSERM, 34095 Montpellier, France; (F.T.); (J.T.); (M.D.); (N.M.-F.); (A.M.)
- EPHE, PSL Research University, 75014 Paris, France
- Correspondence: ; Tel.: +33-4-6714-3889
| | - Françoise Trousse
- MMDN, Univ Montpellier, EPHE, INSERM, 34095 Montpellier, France; (F.T.); (J.T.); (M.D.); (N.M.-F.); (A.M.)
- EPHE, PSL Research University, 75014 Paris, France
| | | | - Joan Torrent
- MMDN, Univ Montpellier, EPHE, INSERM, 34095 Montpellier, France; (F.T.); (J.T.); (M.D.); (N.M.-F.); (A.M.)
- INM, Univ Montpellier, INSERM, 34095 Montpellier, France
| | - Morgane Denus
- MMDN, Univ Montpellier, EPHE, INSERM, 34095 Montpellier, France; (F.T.); (J.T.); (M.D.); (N.M.-F.); (A.M.)
| | - Nadine Mestre-Frances
- MMDN, Univ Montpellier, EPHE, INSERM, 34095 Montpellier, France; (F.T.); (J.T.); (M.D.); (N.M.-F.); (A.M.)
- EPHE, PSL Research University, 75014 Paris, France
| | - Anne Marcilhac
- MMDN, Univ Montpellier, EPHE, INSERM, 34095 Montpellier, France; (F.T.); (J.T.); (M.D.); (N.M.-F.); (A.M.)
- EPHE, PSL Research University, 75014 Paris, France
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8
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Roberts DS, Mann M, Li BH, Kim D, Brasier AR, Jin S, Ge Y. Distinct Core Glycan and O-Glycoform Utilization of SARS-CoV-2 Omicron Variant Spike Protein RBD Revealed by Top-Down Mass Spectrometry. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.02.09.479776. [PMID: 35475171 PMCID: PMC9040677 DOI: 10.1101/2022.02.09.479776] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The SARS-CoV-2 Omicron (B.1.1.529) variant possesses numerous spike (S) mutations particularly in the S receptor-binding domain (S-RBD) that significantly improve transmissibility and evasion of neutralizing antibodies. But exactly how the mutations in the Omicron variant enhance viral escape from immunological protection remains to be understood. The S-RBD remains the principal target for neutralizing antibodies and therapeutics, thus new structural insights into the Omicron S-RBD and characterization of the post-translational glycosylation changes can inform rational design of vaccines and therapeutics. Here we report the molecular variations and O-glycoform changes of the Omicron S-RBD variant as compared to wild-type (WA1/2020) and Delta (B.1.617.2) variants using high-resolution top-down mass spectrometry (MS). A novel O-glycosite (Thr376) unique to the Omicron variant is identified. Moreover, we have directly quantified the Core 1 and Core 2 O-glycan structures and characterized the O-glycoform structural heterogeneity of the three variants. Our findings reveal high resolution detail of Omicron O-glycoforms and their utilization to provide direct molecular evidence of proteoform alterations in the Omicron variant which could shed light on how this variant escapes immunological protection.
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9
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Wang Y, Wu Z, Hu W, Hao P, Yang S. Impact of Expressing Cells on Glycosylation and Glycan of the SARS-CoV-2 Spike Glycoprotein. ACS OMEGA 2021; 6:15988-15999. [PMID: 34179644 PMCID: PMC8204757 DOI: 10.1021/acsomega.1c01785] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Accepted: 06/02/2021] [Indexed: 05/09/2023]
Abstract
The spike glycoprotein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the first point of contact for the virus to recognize and bind to host receptors, is the focus of biomedical research seeking to effectively prevent and treat coronavirus disease (COVID-19). The mass production of spike glycoproteins is usually carried out in different cell systems. Studies have been shown that different expression cell systems alter protein glycosylation of hemagglutinin and neuraminidase in the influenza virus. However, it is not clear whether the cellular system affects the spike protein glycosylation. In this work, we investigated the effect of an expression system on the glycosylation of the spike glycoprotein and its receptor-binding domain. We found that there are significant differences in the glycosylation and glycans attached at each glycosite of the spike glycoprotein obtained from different expression cells. Since glycosylation at the binding site and adjacent amino acids affects the interaction between the spike glycoprotein and the host cell receptor, we recognize that caution should be taken when selecting an expression system to develop inhibitors, antibodies, and vaccines.
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Affiliation(s)
- Yan Wang
- Mass
Spectrometry Facility, National Institute
of Dental and Craniofacial Research, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Zhen Wu
- State
Key Laboratory of Genetic Engineering, Department of Biochemistry,
School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Wenhua Hu
- Center
for Clinical Mass Spectrometry, Department of Pharmaceutical Analysis, Soochow University, Suzhou, Jiangsu 215123, China
| | - Piliang Hao
- School
of Life Science and Technology, ShanghaiTech
University, Shanghai 201210, China
| | - Shuang Yang
- Center
for Clinical Mass Spectrometry, Department of Pharmaceutical Analysis, Soochow University, Suzhou, Jiangsu 215123, China
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10
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Shajahan A, Archer-Hartmann S, Supekar NT, Gleinich AS, Heiss C, Azadi P. Comprehensive characterization of N- and O- glycosylation of SARS-CoV-2 human receptor angiotensin converting enzyme 2. Glycobiology 2021; 31:410-424. [PMID: 33135055 PMCID: PMC7665489 DOI: 10.1093/glycob/cwaa101] [Citation(s) in RCA: 106] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 10/21/2020] [Accepted: 10/21/2020] [Indexed: 12/17/2022] Open
Abstract
The emergence of the COVID-19 pandemic caused by SARS-CoV-2 has created the need for development of new therapeutic strategies. Understanding the mode of viral attachment, entry and replication has become a key aspect of such interventions. The coronavirus surface features a trimeric spike (S) protein that is essential for viral attachment, entry and membrane fusion. The S protein of SARS-CoV-2 binds to human angiotensin converting enzyme 2 (hACE2) for entry. Herein, we describe glycomic and glycoproteomic analysis of hACE2 expressed in HEK293 cells. We observed high glycan occupancy (73.2 to 100%) at all seven possible N-glycosylation sites and surprisingly detected one novel O-glycosylation site. To deduce the detailed structure of glycan epitopes on hACE2 that may be involved in viral binding, we have characterized the terminal sialic acid linkages, the presence of bisecting GlcNAc, and the pattern of N-glycan fucosylation. We have conducted extensive manual interpretation of each glycopeptide and glycan spectrum, in addition to using bioinformatics tools to validate the hACE2 glycosylation. Our elucidation of the site-specific glycosylation and its terminal orientations on the hACE2 receptor, along with the modeling of hACE2 glycosylation sites can aid in understanding the intriguing virus-receptor interactions and assist in the development of novel therapeutics to prevent viral entry. The relevance of studying the role of ACE2 is further increased due to some recent reports about the varying ACE2 dependent complications with regard to age, sex, race, and pre-existing conditions of COVID-19 patients.
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Affiliation(s)
- Asif Shajahan
- Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Rd, Athens, GA 30602, USA
| | - Stephanie Archer-Hartmann
- Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Rd, Athens, GA 30602, USA
| | - Nitin T Supekar
- Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Rd, Athens, GA 30602, USA
| | - Anne S Gleinich
- Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Rd, Athens, GA 30602, USA
| | - Christian Heiss
- Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Rd, Athens, GA 30602, USA
| | - Parastoo Azadi
- Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Rd, Athens, GA 30602, USA
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11
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Antiviral strategies should focus on stimulating the biosynthesis of heparan sulfates, not their inhibition. Life Sci 2021; 277:119508. [PMID: 33865880 PMCID: PMC8046744 DOI: 10.1016/j.lfs.2021.119508] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 03/31/2021] [Accepted: 04/06/2021] [Indexed: 12/23/2022]
Abstract
Antiviral strategies for viruses that utilize proteoglycan core proteins (syndecans and glypicans) as receptors should focus on heparan sulfate (HS) biosynthesis rather than on inhibition of these sugar chains. Here, we show that heparin and certain xylosides, which exhibit in vitro viral entry inhibitory properties against HSV-1, HSV-2, HPV-16, HPV-31, HVB, HVC, HIV-1, HTLV-1, SARS-CoV-2, HCMV, DENV-1, and DENV-2, stimulated HS biosynthesis at the cell surface 2- to 3-fold for heparin and up to 10-fold for such xylosides. This is consistent with the hypothesis from a previous study that for core protein attachment, viruses are glycosylated at HS attachment sites (i.e., serine residues intended to receive the D-xylose molecule for initiating HS chains). Heparanase overexpression, endocytic entry, and syndecan shedding enhancement, all of which are observed during viral infection, lead to glycocalyx deregulation and appear to be direct consequences of this hypothesis. In addition to the appearance of type 2 diabetes and the degradation of HS observed during viral infection, we linked this hypothesis to that proposed in a previous publication.
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12
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Kawahara R, Recuero S, Srougi M, Leite KRM, Thaysen-Andersen M, Palmisano G. The Complexity and Dynamics of the Tissue Glycoproteome Associated With Prostate Cancer Progression. Mol Cell Proteomics 2021; 20:100026. [PMID: 33127837 PMCID: PMC8010466 DOI: 10.1074/mcp.ra120.002320] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 10/19/2020] [Accepted: 10/30/2020] [Indexed: 12/30/2022] Open
Abstract
The complexity and dynamics of the immensely heterogeneous glycoproteome of the prostate cancer (PCa) tumor microenvironment remain incompletely mapped, a knowledge gap that impedes our molecular-level understanding of the disease. To this end, we have used sensitive glycomics and glycoproteomics to map the protein-, cell-, and tumor grade-specific N- and O-glycosylation in surgically removed PCa tissues spanning five histological grades (n = 10/grade) and tissues from patients with benign prostatic hyperplasia (n = 5). Quantitative glycomics revealed PCa grade-specific alterations of the oligomannosidic-, paucimannosidic-, and branched sialylated complex-type N-glycans, and dynamic remodeling of the sialylated core 1- and core 2-type O-glycome. Deep quantitative glycoproteomics identified ∼7400 unique N-glycopeptides from 500 N-glycoproteins and ∼500 unique O-glycopeptides from nearly 200 O-glycoproteins. With reference to a recent Tissue and Blood Atlas, our data indicate that paucimannosidic glycans of the PCa tissues arise mainly from immune cell-derived glycoproteins. Furthermore, the grade-specific PCa glycosylation arises primarily from dynamics in the cellular makeup of the PCa tumor microenvironment across grades involving increased oligomannosylation of prostate-derived glycoproteins and decreased bisecting GlcNAcylation of N-glycans carried by the extracellular matrix proteins. Furthermore, elevated expression of several oligosaccharyltransferase subunits and enhanced N-glycoprotein site occupancy were observed associated with PCa progression. Finally, correlations between the protein-specific glycosylation and PCa progression were observed including increased site-specific core 2-type O-glycosylation of collagen VI. In conclusion, integrated glycomics and glycoproteomics have enabled new insight into the complexity and dynamics of the tissue glycoproteome associated with PCa progression generating an important resource to explore the underpinning disease mechanisms.
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Affiliation(s)
- Rebeca Kawahara
- Departamento de Parasitologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, USP, São Paulo, Brazil; Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia; Biomolecular Discovery Research Centre, Macquarie University, Sydney, NSW, Australia
| | - Saulo Recuero
- Laboratório de Investigação Médica da Disciplina de Urologia da Faculdade de Medicina da USP, São Paulo, Brazil
| | - Miguel Srougi
- Laboratório de Investigação Médica da Disciplina de Urologia da Faculdade de Medicina da USP, São Paulo, Brazil
| | - Katia R M Leite
- Laboratório de Investigação Médica da Disciplina de Urologia da Faculdade de Medicina da USP, São Paulo, Brazil
| | - Morten Thaysen-Andersen
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia; Biomolecular Discovery Research Centre, Macquarie University, Sydney, NSW, Australia.
| | - Giuseppe Palmisano
- Departamento de Parasitologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, USP, São Paulo, Brazil.
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13
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Shajahan A, Supekar NT, Gleinich AS, Azadi P. Deducing the N- and O-glycosylation profile of the spike protein of novel coronavirus SARS-CoV-2. Glycobiology 2020; 30:981-988. [PMID: 32363391 PMCID: PMC7239183 DOI: 10.1093/glycob/cwaa042] [Citation(s) in RCA: 367] [Impact Index Per Article: 91.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Revised: 04/15/2020] [Accepted: 04/15/2020] [Indexed: 12/25/2022] Open
Abstract
The current emergence of the novel coronavirus pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) demands the development of new therapeutic strategies to prevent rapid progress of mortalities. The coronavirus spike (S) protein, which facilitates viral attachment, entry and membrane fusion is heavily glycosylated and plays a critical role in the elicitation of the host immune response. The spike protein is comprised of two protein subunits (S1 and S2), which together possess 22 potential N-glycosylation sites. Herein, we report the glycosylation mapping on spike protein subunits S1 and S2 expressed on human cells through high-resolution mass spectrometry. We have characterized the quantitative N-glycosylation profile on spike protein and interestingly, observed unexpected O-glycosylation modifications on the receptor-binding domain of spike protein subunit S1. Even though O-glycosylation has been predicted on the spike protein of SARS-CoV-2, this is the first report of experimental data for both the site of O-glycosylation and identity of the O-glycans attached on the subunit S1. Our data on the N- and O-glycosylation are strengthened by extensive manual interpretation of each glycopeptide spectra in addition to using bioinformatics tools to confirm the complexity of glycosylation in the spike protein. The elucidation of the glycan repertoire on the spike protein provides insights into the viral binding studies and more importantly, propels research toward the development of a suitable vaccine candidate.
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Affiliation(s)
- Asif Shajahan
- Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Rd, Athens, GA 30602, USA
| | - Nitin T Supekar
- Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Rd, Athens, GA 30602, USA
| | - Anne S Gleinich
- Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Rd, Athens, GA 30602, USA
| | - Parastoo Azadi
- Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Rd, Athens, GA 30602, USA
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14
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Affiliation(s)
- Hayden Wilkinson
- NIBRT GlycoScience Group, National Institute for Bioprocessing, Research and Training, Blackrock, Dublin, Ireland
- CÚRAM, SFI Research Centre for Medical Devices, National University of Ireland, Galway, Ireland
- UCD School of Medicine, College of Health and Agricultural Science, University College Dublin, Dublin, Ireland
| | - Radka Saldova
- NIBRT GlycoScience Group, National Institute for Bioprocessing, Research and Training, Blackrock, Dublin, Ireland
- CÚRAM, SFI Research Centre for Medical Devices, National University of Ireland, Galway, Ireland
- UCD School of Medicine, College of Health and Agricultural Science, University College Dublin, Dublin, Ireland
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15
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Febbraio F, Ionata E, Marcolongo L. Forty years of study on the thermostable β-glycosidase from S. solfataricus: Production, biochemical characterization and biotechnological applications. Biotechnol Appl Biochem 2020; 67:602-618. [PMID: 32621790 DOI: 10.1002/bab.1982] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The aim of this paper is to make the point on the fortieth years study on the β-glycosidase from Sulfolobus solfataricus. This enzyme represents one of the thermophilic biocatalysts, which is more extensively studied as witnessed by the numerous literature reports available since 1980. Comprehensive biochemical studies highlighted its broad substrate specificity for β-d-galacto-, gluco-, and fuco-sides and also showed its remarkable exo-glucosidase and transglycosidase activities. The enzyme demonstrated to be active and stable over a wide range of temperature and pHs, withstanding to several drastic conditions comprising solvents and detergents. Over the years, a great deal of studies were focused on its homotetrameric tridimensional structure, elucidating several structural features involved in the enzyme stability, such as ion pairs and post-translational modifications. Several β-glycosidase mutants were produced in the years in order to understand its peculiar behavior in extreme conditions and/or to improve its functional properties. The β-glycosidase overproduction was also afforded reporting numerous studies dealing with its production in the mesophilic host Escherichia coli, Saccharomyces cerevisiae, Pichia pastoris, and Lactococcus lactis. Relevant applications in food, beverages, bioenergy, pharmaceuticals, and nutraceutical fields of this enzyme, both in free and immobilized forms, highlighted its biotechnological relevance.
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Affiliation(s)
- Ferdinando Febbraio
- Institute of Biochemistry and Cell Biology, National Research Council (CNR), Naples, Italy
| | - Elena Ionata
- Research Institute on Terrestrial Ecosystems, National Research Council (CNR), Naples, 80131, Italy
| | - Loredana Marcolongo
- Research Institute on Terrestrial Ecosystems, National Research Council (CNR), Naples, 80131, Italy
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16
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Choi YJ, Ohn JH, Kim N, Kim W, Park K, Won S, Sael L, Shin CM, Lee SM, Lee S, An HJ, Jang DM, Han BW, Lee HS, Kang SJ, Kim JS, Lee DH. Family-based exome sequencing combined with linkage analyses identifies rare susceptibility variants of MUC4 for gastric cancer. PLoS One 2020; 15:e0236197. [PMID: 32701958 PMCID: PMC7377420 DOI: 10.1371/journal.pone.0236197] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 06/30/2020] [Indexed: 12/24/2022] Open
Abstract
Genome-wide association studies of gastric cancer (GC) cases have revealed common gastric cancer susceptibility loci with low effect size. We investigated rare variants with high effect size via whole-exome sequencing (WES) of subjects with familial clustering of gastric cancer. WES of DNAs from the blood of 19 gastric cancer patients and 36 unaffected family members from 14 families with two or more gastric cancer patients were tested. Linkage analysis combined with association tests were performed using Pedigree Variant Annotation, Analysis, and Search Tool (pVAAST) software. Based on the logarithm of odds (LOD) and permutation-based composite likelihood ratio test (CLRT) from pVAAST, MUC4 was identified as a predisposing gene (LOD P-value = 1.9×10-5; permutation-based P-value of CLRT ≤ 9.9×10-9). In a larger cohort consisting of 597 GC patients and 9,759 healthy controls genotyped with SNP array, we discovered common variants in MUC4 regions (rs148735556, rs11717039, and rs547775645) significantly associated with GC supporting the association of MUC4 with gastric cancer. And the MUC4 variants were found in higher frequency in The Cancer Genome Atlas Study (TCGA) germline samples of patients with multiple cancer types. Immunohistochemistry indicated that MUC4 was downregulated in the noncancerous gastric mucosa of subjects with MUC4 germline missense variants, suggesting that loss of the protective function of MUC4 predisposes an individual to gastric cancer. Rare variants in MUC4 can be novel gastric cancer susceptibility loci in Koreans possessing the familial clustering of gastric cancer.
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Affiliation(s)
- Yoon Jin Choi
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, South Korea
| | - Jung Hun Ohn
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, South Korea
| | - Nayoung Kim
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, South Korea
- Department of Internal Medicine and Liver Research Institute, Seoul National University College of Medicine, Seoul, South Korea
- Tumor Microenvironment Global Core Research Center, College of Pharmacy, Seoul National University, Seoul, South Korea
- * E-mail:
| | - Wonji Kim
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, United States of America
| | - Kyungtaek Park
- Interdisciplinary Program of Bioinformatics, Seoul National University, Seoul, South Korea
| | - Sungho Won
- Interdisciplinary Program of Bioinformatics, Seoul National University, Seoul, South Korea
- Department of Public Health Sciences, Seoul National University, Seoul, South Korea
- Institute of Health and Environment, Seoul National University, Seoul, South Korea
| | - Lee Sael
- Department of Artificial Intelligence and Data Science, Ajou University, Seoul, South Korea
| | - Cheol Min Shin
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, South Korea
| | - Sun Min Lee
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, South Korea
| | - Sejoon Lee
- Department of Pathology, Seoul National University Bundang Hospital, Seongnam, South Korea
| | - Hyun Joo An
- Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, South Korea
| | - Dong Man Jang
- Tumor Microenvironment Global Core Research Center, College of Pharmacy, Seoul National University, Seoul, South Korea
| | - Byung Woo Han
- Tumor Microenvironment Global Core Research Center, College of Pharmacy, Seoul National University, Seoul, South Korea
| | - Hye Seung Lee
- Department of Pathology, Seoul National University Bundang Hospital, Seongnam, South Korea
| | - Seung Joo Kang
- Department of Internal Medicine and Healthcare Research Institute, Healthcare System Gangnam Center, Seoul National University Hospital, Seoul, South Korea
| | - Joo Sung Kim
- Department of Internal Medicine and Liver Research Institute, Seoul National University College of Medicine, Seoul, South Korea
- Department of Internal Medicine and Healthcare Research Institute, Healthcare System Gangnam Center, Seoul National University Hospital, Seoul, South Korea
| | - Dong Ho Lee
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, South Korea
- Department of Internal Medicine and Liver Research Institute, Seoul National University College of Medicine, Seoul, South Korea
- Tumor Microenvironment Global Core Research Center, College of Pharmacy, Seoul National University, Seoul, South Korea
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17
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Park GW, Lee JW, Lee HK, Shin JH, Kim JY, Yoo JS. Classification of Mucin-Type O-Glycopeptides Using Higher-Energy Collisional Dissociation in Mass Spectrometry. Anal Chem 2020; 92:9772-9781. [PMID: 32584546 DOI: 10.1021/acs.analchem.0c01218] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Changes in mucin-type O-glycosylation of human proteins affect protein function, immune response, and cancer progression. Since O-glycoproteins are characterized by the microheterogeneity of diverse O-glycans with no conserved sequence and the macroheterogeneity of multiple glycosylation sites on serine and/or threonine in human proteins, the assessment of different mucin types, such as Tn-antigen, core 1, and core 2, and their extended core types in O-glycopeptides, is extremely challenging. Here, we present an O-GlycoProteome Analyzer (O-GPA) that automatically classifies mucin-type O-glycosylation using higher-energy collisional dissociation (HCD) in mass spectrometry. First, we estimated the number of GlcNAc residues using the intensity ratio of GlcNAc-specific fragment ions (HexNAc-CH6O3 and HexNAc-2H2O) over GalNAc-specific fragment ions (HexNAc-C2H6O3 and HexNAc-C2H4O2) in the HCD spectrum. Furthermore, we classified the different mucin types of O-glycopeptides from characteristic B2 (HexNAc2) or Y2α (PEP + HexNAc2), and Y2β (PEP + HexNAcHex) fragment ions, along with the number of GlcNAc. Furthermore, O-GPA automatically determined single or multiple O-glycosylation, regardless of the mucin types. The mucin type of O-glycopeptides from human urine and plasma was confirmed with an overall accuracy of 96%. We found 97 core 1, 56 core 2, 13 extended core 1, and 12 extended core 2 glycopeptides from urine; and 22 core 1, 13 core 2, 7 extended core 1, 1 extended core 2, and 1 Tn-antigen from plasma. Our strategy can be used to successfully characterize specific mucin types of O-glycoproteins in human biological samples.
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Affiliation(s)
- Gun Wook Park
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Cheongju, Ochang-eup 28119, Republic of Korea
| | - Ji Won Lee
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Cheongju, Ochang-eup 28119, Republic of Korea.,Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Hyun Kyoung Lee
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Cheongju, Ochang-eup 28119, Republic of Korea.,Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Jong Hwan Shin
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Cheongju, Ochang-eup 28119, Republic of Korea
| | - Jin Young Kim
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Cheongju, Ochang-eup 28119, Republic of Korea
| | - Jong Shin Yoo
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Cheongju, Ochang-eup 28119, Republic of Korea.,Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, 34134, Republic of Korea
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18
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Kelly MI, Dodds ED. Parallel Determination of Polypeptide and Oligosaccharide Connectivities by Energy-Resolved Collison-Induced Dissociation of Protonated O-Glycopeptides Derived from Nonspecific Proteolysis. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:624-632. [PMID: 32126781 PMCID: PMC7164384 DOI: 10.1021/jasms.9b00065] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Collision-induced dissociation (CID) is by far the most broadly applied dissociation method used for tandem mass spectrometry (MS/MS). This includes MS/MS-based structural interrogation of glycopeptides for applications in glycoproteomics. The end goal of such measurements is to determine the monosaccharide connectivity of the glycan, the amino acid sequence of the peptide, and the site of glycosylation for each glycopeptide of interest. In turn, this allows inferences with respect to the glycoprofile of the intact glycoprotein. For glycopeptide analysis, CID is best known for the ability to determine glycosidic topology of the oligosaccharide group; however, CID has also been shown to produce amide bond cleavage of the polypeptide group. Whether structural information is obtained for the glycan or the peptide has been found to depend on the applied collision energy. While these energy-resolved fragmentation pathways have been the subject of several studies on N-linked glycopeptides, there remains a dearth of similar work on O-linked glycopeptides. In this study, MS/MS via CID was shown to provide substantial peptide backbone fragmentation, in addition to glycosidic fragmentation, in an energy-dependent manner. While qualitatively similar to previous findings for N-glycopeptides, the energy-resolved CID (ER-CID) of O-glycopeptides was found to be substantially more sensitive to the collision energy setting. Thus, deliberately obtaining either glycan or peptide dissociation is a more delicate undertaking for O-glycopeptides. Establishing a more complete understanding of O-glycopeptide ER-CID is likely to have a substantive impact on how O-glycoproteomic analysis is approached in the future.
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Affiliation(s)
- Maia I. Kelly
- Department of Chemistry, University of Nebraska – Lincoln, Lincoln, NE, 68588-0304, USA
| | - Eric D. Dodds
- Department of Chemistry, University of Nebraska – Lincoln, Lincoln, NE, 68588-0304, USA
- Nebraska Center for Integrated Biomolecular Communication, University of Nebraska – Lincoln, Lincoln, NE, 68588-0304, USA
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19
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Abstract
Few approaches exist for the stable and controllable synthesis of customized mucin glycoproteins for glycocalyx editing in eukaryotic cells. Taking advantage of custom gene synthesis and a biology-by-parts approach to cDNA construction, we build a library of swappable DNA bricks for mucin leader tags, membrane anchors, cytoplasmic motifs, and optical reporters, as well as codon-optimized native mucin repeats and newly designed domains for synthetic mucins. We construct a library of over 50 mucins, each with unique chemical, structural, and optical properties and describe how additional permutations could readily be constructed. We apply the library to explore sequence-specific effects on glycosylation for engineering of mucins. We find that the extension of the immature α-GalNAc Tn-antigen to Core 1 and Core 2 glycan structures depends on the underlying peptide backbone sequence. Glycosylation could also be influenced through recycling motifs on the mucin cytoplasmic tail. We expect that the mucin parts inventory presented here can be broadly applied for glycocalyx research and mucin-based biotechnologies.
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Affiliation(s)
- Hao Pan
- Field of Biophysics, Cornell University, Ithaca, New York 14853, United States
| | | | - Nitin T. Supekar
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, United States
| | - Parastoo Azadi
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, United States
| | - Matthew J. Paszek
- Field of Biophysics, Cornell University, Ithaca, New York 14853, United States
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York 14853, United States
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20
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Turupcu A, Poliak P, Margreitter C, Oostenbrink C, Staudacher E. UDP-N-acetyl-α-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase from the snail Biomphalaria glabrata - structural reflections. Glycoconj J 2019; 37:15-25. [PMID: 31396754 PMCID: PMC6994419 DOI: 10.1007/s10719-019-09886-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 07/02/2019] [Accepted: 07/18/2019] [Indexed: 11/26/2022]
Abstract
UDP-GalNAc:polypeptide GalNAc transferase (ppGalNAcT; EC 2.4.1.41) is the initiating enzyme for mucin-type O-glycosylation in animals. Members of this highly conserved glycosyltransferase family catalyse a single glycosidic linkage. They transfer an N-acetylgalactosamine (GalNAc) residue from an activated donor (UDP-GalNAc) to a serine or threonine of an acceptor polypeptide chain. A ppGalNAcT from the freshwater snail Biomphalaria glabrata is the only characterised member of this enzyme family from mollusc origin. In this work, we interpret previously published experimental characterization of this enzyme in the context of in silico models of the enzyme and its acceptor substrates. A homology model of the mollusc ppGalNAcT is created and various substrate peptides are modelled into the active site. We hypothesize about possible molecular interpretations of the available experimental data and offer potential explanations for observed substrate and cofactor specificity. Here, we review and synthesise the current knowledge of Bge-ppGalNAcT, supported by a molecular interpretation of the available data.
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Affiliation(s)
- Aysegül Turupcu
- Institute for Molecular Modeling and Simulation, Department of Material Sciences and Process Engineering, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190, Vienna, Austria
| | - Peter Poliak
- Institute for Molecular Modeling and Simulation, Department of Material Sciences and Process Engineering, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190, Vienna, Austria
- Department of Chemical Physics, Faculty of Chemical and Food Technology, Slovak University of Technology in Bratislava, Radlinského 9, SK-812 37, Bratislava, Slovakia
| | - Christian Margreitter
- Randall Centre for Cell & Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London, SE1 9RT, UK
| | - Chris Oostenbrink
- Institute for Molecular Modeling and Simulation, Department of Material Sciences and Process Engineering, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190, Vienna, Austria
| | - Erika Staudacher
- Department of Chemistry, Glycobiology, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190, Vienna, Austria.
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21
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Pothukuchi P, Agliarulo I, Russo D, Rizzo R, Russo F, Parashuraman S. Translation of genome to glycome: role of the Golgi apparatus. FEBS Lett 2019; 593:2390-2411. [PMID: 31330561 DOI: 10.1002/1873-3468.13541] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 07/12/2019] [Accepted: 07/15/2019] [Indexed: 12/16/2022]
Abstract
Glycans are one of the four biopolymers of the cell and they play important roles in cellular and organismal physiology. They consist of both linear and branched structures and are synthesized in a nontemplated manner in the secretory pathway of mammalian cells with the Golgi apparatus playing a key role in the process. In spite of the absence of a template, the glycans synthesized by a cell are not a random collection of possible glycan structures but a distribution of specific glycans in defined quantities that is unique to each cell type (Cell type here refers to distinct cell forms present in an organism that can be distinguished based on morphological, phenotypic and/or molecular criteria.) While information to produce cell type-specific glycans is encoded in the genome, how this information is translated into cell type-specific glycome (Glycome refers to the quantitative distribution of all glycan structures present in a given cell type.) is not completely understood. We summarize here the factors that are known to influence the fidelity of glycan biosynthesis and integrate them into known glycosylation pathways so as to rationalize the translation of genetic information to cell type-specific glycome.
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Affiliation(s)
- Prathyush Pothukuchi
- Institute of Biochemistry and Cellular Biology, National Research Council of Italy, Napoli, Italy
| | - Ilenia Agliarulo
- Institute of Biochemistry and Cellular Biology, National Research Council of Italy, Napoli, Italy
| | - Domenico Russo
- Institute of Biochemistry and Cellular Biology, National Research Council of Italy, Napoli, Italy
| | - Riccardo Rizzo
- Institute of Biochemistry and Cellular Biology, National Research Council of Italy, Napoli, Italy
| | - Francesco Russo
- Institute of Biochemistry and Cellular Biology, National Research Council of Italy, Napoli, Italy
| | - Seetharaman Parashuraman
- Institute of Biochemistry and Cellular Biology, National Research Council of Italy, Napoli, Italy
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22
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Gana R, Vasudevan S. Ridge regression estimated linear probability model predictions of O-glycosylation in proteins with structural and sequence data. BMC Mol Cell Biol 2019; 20:21. [PMID: 31253080 PMCID: PMC6599295 DOI: 10.1186/s12860-019-0200-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 05/27/2019] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND To-date, no claim regarding finding a consensus sequon for O-glycosylation has been made. Thus, predicting the likelihood of O-glycosylation with sequence and structural information using classical regression analysis is quite difficult. In particular, if a binary response is used to distinguish between O-glycosylated and non-O-glycosylated sequences, an appropriate set of non-O-glycosylatable sequences is hard to find. RESULTS Three sequences from similar post-translational modifications (PTMs) of proteins occurring at, or very near, the S/T-site are analyzed: N-glycosylation, O-mucin type (O-GalNAc) glycosylation, and phosphorylation. Results found include: 1) The consensus composite sequon for O-glycosylation is: ~(W-S/T-W), where "~" denotes the "not" operator. 2) The consensus sequon for phosphorylation is ~(W-S/T/Y/H-W); although W-S/T/Y/H-W is not an absolute inhibitor of phosphorylation. 3) For linear probability model (LPM) estimation, N-glycosylated sequences are good approximations to non-O-glycosylatable sequences; although N - ~P - S/T is not an absolute inhibitor of O-glycosylation. 4) The selective positioning of an amino acid along the sequence, differentiates the PTMs of proteins. 5) Some N-glycosylated sequences are also phosphorylated at the S/T-site in the N - ~P - S/T sequon. 6) ASA values for N-glycosylated sequences are stochastically larger than those for O-GlcNAc glycosylated sequences. 7) Structural attributes (beta turn II, II´, helix, beta bridges, beta hairpin, and the phi angle) are significant LPM predictors of O-GlcNAc glycosylation. The LPM with sequence and structural data as explanatory variables yields a Kolmogorov-Smirnov (KS) statistic of 99%. 8) With only sequence data, the KS statistic erodes to 80%, and 21% of out-of-sample O-GlcNAc glycosylated sequences are mispredicted as not being glycosylated. The 95% confidence interval around this mispredictions rate is 16% to 26%. CONCLUSIONS The data indicates the existence of a consensus sequon for O-glycosylation; and underscores the germaneness of structural information for predicting the likelihood of O-glycosylation.
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Affiliation(s)
- Rajaram Gana
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington D.C, USA.
| | - Sona Vasudevan
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington D.C, USA.
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23
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Toward Spider Glue: Long Read Scaffolding for Extreme Length and Repetitious Silk Family Genes AgSp1 and AgSp2 with Insights into Functional Adaptation. G3-GENES GENOMES GENETICS 2019; 9:1909-1919. [PMID: 30975702 PMCID: PMC6553539 DOI: 10.1534/g3.119.400065] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
An individual orb weaving spider can spin up to seven different types of silk, each with unique functions and material properties. The capture spiral silk of classic two-dimensional aerial orb webs is coated with an amorphous glue that functions to retain prey that get caught in a web. This unique modified silk is partially comprised of spidroins (spider fibroins) encoded by two members of the silk gene family. The glue differs from solid silk fibers as it is a viscoelastic, amorphic, wet material that is responsive to environmental conditions. Most spidroins are encoded by extremely large, highly repetitive genes that cannot be sequenced using short read technology alone, as the repetitive regions are longer than read length. We sequenced for the first time the complete genomic Aggregate Spidroin 1 (AgSp1) and Aggregate Spidroin 2 (AgSp2) glue genes of orb weaving spider Argiope trifasciata using error-prone long reads to scaffold for high accuracy short reads. The massive coding sequences are 42,270 bp (AgSp1) and 20,526 bp (AgSp2) in length, the largest silk genes currently described. The majority of the predicted amino acid sequence of AgSp1 consists of two similar but distinct motifs that are repeated ∼40 times each, while AgSp2 contains ∼48 repetitions of an AgSp1-similar motif, interspersed by regions high in glutamine. Comparisons of AgSp repetitive motifs from orb web and cobweb spiders show regions of strict conservation followed by striking diversification. Glues from these two spider families have evolved contrasting material properties in adhesion (stickiness), extensibility (stretchiness), and elasticity (the ability of the material to resume its native shape), which we link to mechanisms established for related silk genes in the same family. Full-length aggregate spidroin sequences from diverse species with differing material characteristics will provide insights for designing tunable bio-inspired adhesives for a variety of unique purposes.
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Valoskova K, Biebl J, Roblek M, Emtenani S, Gyoergy A, Misova M, Ratheesh A, Reis-Rodrigues P, Shkarina K, Larsen ISB, Vakhrushev SY, Clausen H, Siekhaus DE. A conserved major facilitator superfamily member orchestrates a subset of O-glycosylation to aid macrophage tissue invasion. eLife 2019; 8:e41801. [PMID: 30910009 PMCID: PMC6435326 DOI: 10.7554/elife.41801] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 02/11/2019] [Indexed: 12/29/2022] Open
Abstract
Aberrant display of the truncated core1 O-glycan T-antigen is a common feature of human cancer cells that correlates with metastasis. Here we show that T-antigen in Drosophila melanogaster macrophages is involved in their developmentally programmed tissue invasion. Higher macrophage T-antigen levels require an atypical major facilitator superfamily (MFS) member that we named Minerva which enables macrophage dissemination and invasion. We characterize for the first time the T and Tn glycoform O-glycoproteome of the Drosophila melanogaster embryo, and determine that Minerva increases the presence of T-antigen on proteins in pathways previously linked to cancer, most strongly on the sulfhydryl oxidase Qsox1 which we show is required for macrophage tissue entry. Minerva's vertebrate ortholog, MFSD1, rescues the minerva mutant's migration and T-antigen glycosylation defects. We thus identify a key conserved regulator that orchestrates O-glycosylation on a protein subset to activate a program governing migration steps important for both development and cancer metastasis.
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Affiliation(s)
| | - Julia Biebl
- Institute of Science and Technology AustriaKlosterneuburgAustria
| | - Marko Roblek
- Institute of Science and Technology AustriaKlosterneuburgAustria
| | - Shamsi Emtenani
- Institute of Science and Technology AustriaKlosterneuburgAustria
| | - Attila Gyoergy
- Institute of Science and Technology AustriaKlosterneuburgAustria
| | - Michaela Misova
- Institute of Science and Technology AustriaKlosterneuburgAustria
| | - Aparna Ratheesh
- Institute of Science and Technology AustriaKlosterneuburgAustria
- Centre for Mechanochemical Cell Biology and Division of Biomedical Sciences, Warwick Medical SchoolUniversity of WarwickCoventryUnited Kingdom
| | | | | | - Ida Signe Bohse Larsen
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Sergey Y Vakhrushev
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Henrik Clausen
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Daria E Siekhaus
- Institute of Science and Technology AustriaKlosterneuburgAustria
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25
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Ali A, Baby B, Vijayan R. From Desert to Medicine: A Review of Camel Genomics and Therapeutic Products. Front Genet 2019; 10:17. [PMID: 30838017 PMCID: PMC6389616 DOI: 10.3389/fgene.2019.00017] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 01/14/2019] [Indexed: 12/11/2022] Open
Abstract
Camels have an important role in the lives of human beings, especially in arid regions, due to their multipurpose role and unique ability to adapt to harsh conditions. In spite of its enormous economic, cultural, and biological importance, the camel genome has not been widely studied. The size of camel genome is roughly 2.38 GB, containing over 20,000 genes. The unusual genetic makeup of the camel is the main reason behind its ability to survive under extreme environmental conditions. The camel genome harbors several unique variations which are being investigated for the treatment of several disorders. Various natural products from camels have also been tested and prescribed as adjunct therapy to control the progression of ailments. Interestingly, the camel employs unique immunological and molecular mechanisms against pathogenic agents and pathological conditions. Here, we broadly review camel classification, distribution and breed as well as recent progress in the determination of the camel genome, its size, genetic distribution, response to various physiological conditions, immunogenetics and the medicinal potential of camel gene products.
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Affiliation(s)
| | | | - Ranjit Vijayan
- Department of Biology, College of Science, United Arab Emirates University, Al Ain, United Arab Emirates
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26
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Structural and In Vitro Functional Comparability Analysis of Altebrel™, a Proposed Etanercept Biosimilar: Focus on Primary Sequence and Glycosylation. Pharmaceuticals (Basel) 2019; 12:ph12010014. [PMID: 30658444 PMCID: PMC6469174 DOI: 10.3390/ph12010014] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 12/30/2018] [Accepted: 01/01/2019] [Indexed: 02/07/2023] Open
Abstract
The demand for reliable comparability studies of biosimilars grows with their increased market share. These studies focus on physicochemical, structural, functional and clinical properties to ensure that a biosimilar has no significant differences to the originator product and can be released into the market without extensive clinical trials. In the current study, Enbrel® (etanercept, the originator) and Altebrel™ (the proposed biosimilar) underwent direct comparison. “Bottom-up” mass spectrometric analysis was used for primary sequence analysis, evaluation of N/O-glycosylation sites and quantification of methionine oxidation. N/O-glycans were analyzed after permethylation derivatization and the effect of N-glycans on in-vitro functionality of etanercept was assayed. Three enzyme peptide mapping resulted in complete identification of the primary structure. It was confirmed that total ion chromatograms are valuable datasets for the analysis of the primary structure of biodrugs. New N/O-glycan structures were identified and all the N-glycans were quantified. Finally, investigation of the functional properties of N-deglycosylated and non-modified etanercept samples using surface plasmon resonance analysis and in-vitro bioassay showed that N-glycosylation has no significant effect on its in-vitro functionality. Analysis of etanercept and its biosimilar, revealed a high similarity in terms of glycosylation, primary structure and in-vitro functionality.
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27
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Yang W, Ao M, Hu Y, Li QK, Zhang H. Mapping the O-glycoproteome using site-specific extraction of O-linked glycopeptides (EXoO). Mol Syst Biol 2018; 14:e8486. [PMID: 30459171 PMCID: PMC6243375 DOI: 10.15252/msb.20188486] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 10/16/2018] [Accepted: 10/17/2018] [Indexed: 01/30/2023] Open
Abstract
Protein glycosylation is one of the most abundant post-translational modifications. However, detailed analysis of O-linked glycosylation, a major type of protein glycosylation, has been severely impeded by the scarcity of suitable methodologies. Here, a chemoenzymatic method is introduced for the site-specific extraction of O-linked glycopeptides (EXoO), which enabled the mapping of over 3,000 O-linked glycosylation sites and definition of their glycans on over 1,000 proteins in human kidney tissues, T cells, and serum. This large-scale localization of O-linked glycosylation sites demonstrated that EXoO is an effective method for defining the site-specific O-linked glycoproteome in different types of sample. Detailed structural analysis of the sites identified revealed conserved motifs and topological orientations facing extracellular space, the cell surface, the lumen of the Golgi, and the endoplasmic reticulum (ER). EXoO was also able to reveal significant differences in the O-linked glycoproteome of tumor and normal kidney tissues pointing to its broader use in clinical diagnostics and therapeutics.
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Affiliation(s)
- Weiming Yang
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Minghui Ao
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Yingwei Hu
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Qing Kay Li
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Hui Zhang
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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28
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Raimondi D, Orlando G, Tabaro F, Lenaerts T, Rooman M, Moreau Y, Vranken WF. Large-scale in-silico statistical mutagenesis analysis sheds light on the deleteriousness landscape of the human proteome. Sci Rep 2018; 8:16980. [PMID: 30451933 PMCID: PMC6242909 DOI: 10.1038/s41598-018-34959-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 10/26/2018] [Indexed: 12/18/2022] Open
Abstract
Next generation sequencing technologies are providing increasing amounts of sequencing data, paving the way for improvements in clinical genetics and precision medicine. The interpretation of the observed genomic variants in the light of their phenotypic effects is thus emerging as a crucial task to solve in order to advance our understanding of how exomic variants affect proteins and how the proteins' functional changes affect human health. Since the experimental evaluation of the effects of every observed variant is unfeasible, Bioinformatics methods are being developed to address this challenge in-silico, by predicting the impact of millions of variants, thus providing insight into the deleteriousness landscape of entire proteomes. Here we show the feasibility of this approach by using the recently developed DEOGEN2 variant-effect predictor to perform the largest in-silico mutagenesis scan to date. We computed the deleteriousness score of 170 million variants over 15000 human proteins and we analysed the results, investigating how the predicted deleteriousness landscape of the proteins relates to known functionally and structurally relevant protein regions and biophysical properties. Moreover, we qualitatively validated our results by comparing them with two mutagenesis studies targeting two specific proteins, showing the consistency of DEOGEN2 predictions with respect to experimental data.
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Affiliation(s)
- Daniele Raimondi
- Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, La Plaine Campus, Triomflaan, 1050, Brussels, Belgium
- ESAT-STADIUS, KU Leuven, Kasteelpark Arenberg 10, 3001, Leuven, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
| | - Gabriele Orlando
- Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, La Plaine Campus, Triomflaan, 1050, Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
| | - Francesco Tabaro
- Institute of Biosciences and Medical Technology, Arvo Ylpőn katu 34, 33520, Tampere, Finland
| | - Tom Lenaerts
- Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, La Plaine Campus, Triomflaan, 1050, Brussels, Belgium
- Machine Learning Group, ULB, La Plaine Campus, 1050, Brussels, Belgium
| | - Marianne Rooman
- Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, La Plaine Campus, Triomflaan, 1050, Brussels, Belgium
- Department of BioModeling, BioInformatics & BioProcesses, Université Libre de Bruxelles, 1050, Brussels, Belgium
| | - Yves Moreau
- ESAT-STADIUS, KU Leuven, Kasteelpark Arenberg 10, 3001, Leuven, Belgium
- Imec, 3001, Leuven, Belgium
| | - Wim F Vranken
- Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, La Plaine Campus, Triomflaan, 1050, Brussels, Belgium.
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium.
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29
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Salah Ud-Din AIM, Roujeinikova A. Flagellin glycosylation with pseudaminic acid in Campylobacter and Helicobacter: prospects for development of novel therapeutics. Cell Mol Life Sci 2018; 75:1163-1178. [PMID: 29080090 PMCID: PMC11105201 DOI: 10.1007/s00018-017-2696-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 10/10/2017] [Accepted: 10/24/2017] [Indexed: 02/08/2023]
Abstract
Many pathogenic bacteria require flagella-mediated motility to colonise and persist in their hosts. Helicobacter pylori and Campylobacter jejuni are flagellated epsilonproteobacteria associated with several human pathologies, including gastritis, acute diarrhea, gastric carcinoma and neurological disorders. In both species, glycosylation of flagellin with an unusual sugar pseudaminic acid (Pse) plays a crucial role in the biosynthesis of functional flagella, and thereby in bacterial motility and pathogenesis. Pse is found only in pathogenic bacteria. Its biosynthesis via six consecutive enzymatic steps has been extensively studied in H. pylori and C. jejuni. This review highlights the importance of flagella glycosylation and details structural insights into the enzymes in the Pse pathway obtained via a combination of biochemical, crystallographic, and mutagenesis studies of the enzyme-substrate and -inhibitor complexes. It is anticipated that understanding the underlying structural and molecular basis of the catalytic mechanisms of the Pse-synthesising enzymes will pave the way for the development of novel antimicrobials.
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Affiliation(s)
- Abu Iftiaf Md Salah Ud-Din
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, VIC, Australia
| | - Anna Roujeinikova
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, VIC, Australia.
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia.
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30
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Veillon L, Fakih C, Abou-El-Hassan H, Kobeissy F, Mechref Y. Glycosylation Changes in Brain Cancer. ACS Chem Neurosci 2018; 9:51-72. [PMID: 28982002 DOI: 10.1021/acschemneuro.7b00271] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Protein glycosylation is a posttranslational modification that affects more than half of all known proteins. Glycans covalently bound to biomolecules modulate their functions by both direct interactions, such as the recognition of glycan structures by binding partners, and indirect mechanisms that contribute to the control of protein conformation, stability, and turnover. The focus of this Review is the discussion of aberrant glycosylation related to brain cancer. Altered sialylation and fucosylation of N- and O-glycans play a role in the development and progression of brain cancer. Additionally, aberrant O-glycan expression has been implicated in brain cancer. This Review also addresses the clinical potential and applications of aberrant glycosylation for the detection and treatment of brain cancer. The viable roles glycans may play in the development of brain cancer therapeutics are addressed as well as cancer-glycoproteomics and personalized medicine. Glycoprotein alterations are considered as a hallmark of cancer while high expression in body fluids represents an opportunity for cancer assessment.
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Affiliation(s)
- Lucas Veillon
- Department
of Chemistry and Biochemistry, Texas Tech University, Lubbock Texas 79409, United States
| | - Christina Fakih
- Department
of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Hadi Abou-El-Hassan
- Department
of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Firas Kobeissy
- Department
of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Yehia Mechref
- Department
of Chemistry and Biochemistry, Texas Tech University, Lubbock Texas 79409, United States
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31
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Chen X, Nagai Y, Zhu Z, Ruan H, Peehl DM, Greene MI, Zhang H. A spliced form of CD44 expresses the unique glycan that is recognized by the prostate cancer specific antibody F77. Oncotarget 2018; 9:3631-3640. [PMID: 29423071 PMCID: PMC5790488 DOI: 10.18632/oncotarget.23341] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 11/26/2017] [Indexed: 01/08/2023] Open
Abstract
Prostate cancer is the most common cancer occurring in men in the United States. The monoclonal antibody F77 that was originally developed in our laboratory recognizes mainly glycolipids as well as O-linked glycosylation on proteins in prostate cancer cells. We have identified a spliced form of glycoprotein CD44 as one critical protein expressing the F77 antigen. The F77-specific glycosylation occurs on multiple potential glycosylation sites on the CD44 protein encoded by the fourteenth exon. CD44 is a tumor stem cell marker and is known to induce tumor stemness and metastasis. Knockdown of CD44 or FUT1 genes dramatically reduced F77-induced apoptosis in prostate cancer cell lines. We developed an ELISA using both a CD44 antibody and F77 to identify the special form of glycosylated CD44 from prostate cancer cells as well as from serum samples of prostate cancer patients. These results reveal a CD44-dependent mechanism for F77 to induce tumor cell apoptosis, and a new strategy for the detection of glycosylated CD44 proteins secreted by prostate cancer cells.
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Affiliation(s)
- Xi Chen
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yasuhiro Nagai
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Zhiqiang Zhu
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Hang Ruan
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Donna M. Peehl
- Department of Urology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Mark I. Greene
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Hongtao Zhang
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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32
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Darula Z, Medzihradszky KF. Analysis of Mammalian O-Glycopeptides-We Have Made a Good Start, but There is a Long Way to Go. Mol Cell Proteomics 2018; 17:2-17. [PMID: 29162637 PMCID: PMC5750848 DOI: 10.1074/mcp.mr117.000126] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Indexed: 12/18/2022] Open
Abstract
Glycosylation is perhaps the most common post-translational modification. Recently there has been growing interest in cataloging the glycan structures, glycoproteins, and specific sites modified and deciphering the biological functions of glycosylation. Although the results are piling up for N-glycosylation, O-glycosylation is seriously trailing behind. In our review we reiterate the difficulties researchers have to overcome in order to characterize O-glycosylation. We describe how an ingenious cell engineering method delivered exciting results, and what could we gain from "wild-type" samples. Although we refer to the biological role(s) of O-glycosylation, we do not provide a complete inventory on this topic.
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Affiliation(s)
- Zsuzsanna Darula
- From the ‡Laboratory of Proteomics Research, Biological Research Centre, Hungarian Academy of Sciences, H-6726, 62 Temesvari krt, Szeged, Hungary
| | - Katalin F Medzihradszky
- From the ‡Laboratory of Proteomics Research, Biological Research Centre, Hungarian Academy of Sciences, H-6726, 62 Temesvari krt, Szeged, Hungary;
- §Department of Pharmaceutical Chemistry, School of Pharmacy, University of California San Francisco, Genentech Hall, N472A, MC 2240, 600 16th Street, San Francisco, California 94158-2517
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33
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Dutta D, Mandal C, Mandal C. Unusual glycosylation of proteins: Beyond the universal sequon and other amino acids. Biochim Biophys Acta Gen Subj 2017; 1861:3096-3108. [DOI: 10.1016/j.bbagen.2017.08.025] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Revised: 08/03/2017] [Accepted: 08/14/2017] [Indexed: 12/11/2022]
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In-Depth Glyco-Peptidomics Approach Reveals Unexpected Diversity of Glycosylated Peptides and Atypical Post-Translational Modifications in Dendroaspis angusticeps Snake Venom. Int J Mol Sci 2017; 18:ijms18112453. [PMID: 29156586 PMCID: PMC5713420 DOI: 10.3390/ijms18112453] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 11/08/2017] [Accepted: 11/09/2017] [Indexed: 11/16/2022] Open
Abstract
Animal venoms represent a valuable source of bioactive peptides that can be derived into useful pharmacological tools, or even innovative drugs. In this way, the venom of Dendroaspis angusticeps (DA), the Eastern Green Mamba, has been intensively studied during recent years. It mainly contains hundreds of large toxins from 6 to 9 kDa, each displaying several disulfide bridges. These toxins are the main target of venom-based studies due to their valuable activities obtained by selectively targeting membrane receptors, such as ion channels or G-protein coupled receptors. This study aims to demonstrate that the knowledge of venom composition is still limited and that animal venoms contain unexpected diversity and surprises. A previous study has shown that Dendroaspis angusticeps venom contains not only a cocktail of classical toxins, but also small glycosylated peptides. Following this work, a deep exploration of DA glycopeptidome by a dual nano liquid chromatography coupled to electrospray ionization mass spectrometry (nanoLC-ESI-MS) and Matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF-MS) analyses was initiated. This study reveals unsuspected structural diversity of compounds such as 221 glycopeptides, displaying different glycan structures. Sequence alignments underline structural similarities with natriuretic peptides already characterized in Elapidae venoms. Finally, the presence of an S-cysteinylation and hydroxylation of proline on four glycopeptides, never described to date in snake venoms, is also revealed by proteomics and affined by nuclear magnetic resonance (NMR) experiments.
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Azevedo R, Peixoto A, Gaiteiro C, Fernandes E, Neves M, Lima L, Santos LL, Ferreira JA. Over forty years of bladder cancer glycobiology: Where do glycans stand facing precision oncology? Oncotarget 2017; 8:91734-91764. [PMID: 29207682 PMCID: PMC5710962 DOI: 10.18632/oncotarget.19433] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 06/19/2017] [Indexed: 12/19/2022] Open
Abstract
The high molecular heterogeneity of bladder tumours is responsible for significant variations in disease course, as well as elevated recurrence and progression rates, thereby hampering the introduction of more effective targeted therapeutics. The implementation of precision oncology settings supported by robust molecular models for individualization of patient management is warranted. This effort requires a comprehensive integration of large sets of panomics data that is yet to be fully achieved. Contributing to this goal, over 40 years of bladder cancer glycobiology have disclosed a plethora of cancer-specific glycans and glycoconjugates (glycoproteins, glycolipids, proteoglycans) accompanying disease progressions and dissemination. This review comprehensively addresses the main structural findings in the field and consequent biological and clinical implications. Given the cell surface and secreted nature of these molecules, we further discuss their potential for non-invasive detection and therapeutic development. Moreover, we highlight novel mass-spectrometry-based high-throughput analytical and bioinformatics tools to interrogate the glycome in the postgenomic era. Ultimately, we outline a roadmap to guide future developments in glycomics envisaging clinical implementation.
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Affiliation(s)
- Rita Azevedo
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, Porto, Portugal
- Institute of Biomedical Sciences Abel Salazar, University of Porto, Porto, Portugal
| | - Andreia Peixoto
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, Porto, Portugal
- Institute of Biomedical Sciences Abel Salazar, University of Porto, Porto, Portugal
- New Therapies Group, INEB-Institute for Biomedical Engineering, Porto, Portugal
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Cristiana Gaiteiro
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, Porto, Portugal
| | - Elisabete Fernandes
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, Porto, Portugal
- Institute of Biomedical Sciences Abel Salazar, University of Porto, Porto, Portugal
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- Biomaterials for Multistage Drug and Cell Delivery, INEB-Institute for Biomedical Engineering, Porto, Portugal
| | - Manuel Neves
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, Porto, Portugal
- Institute of Biomedical Sciences Abel Salazar, University of Porto, Porto, Portugal
| | - Luís Lima
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, Porto, Portugal
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- Glycobiology in Cancer, Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
| | - Lúcio Lara Santos
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, Porto, Portugal
- Department of Surgical Oncology, Portuguese Institute of Oncology, Porto, Portugal
| | - José Alexandre Ferreira
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, Porto, Portugal
- Institute of Biomedical Sciences Abel Salazar, University of Porto, Porto, Portugal
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- Glycobiology in Cancer, Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
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36
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Chaffey PK, Guan X, Wang X, Ruan Y, Li Y, Miller SG, Tran AH, Koelsch TN, Pass LF, Tan Z. Quantitative Effects of O-Linked Glycans on Protein Folding. Biochemistry 2017; 56:4539-4548. [DOI: 10.1021/acs.biochem.7b00483] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Patrick K. Chaffey
- Department of Chemistry and
Biochemistry and BioFrontiers Institute, University of Colorado, Boulder, Colorado 80303, United States
| | - Xiaoyang Guan
- Department of Chemistry and
Biochemistry and BioFrontiers Institute, University of Colorado, Boulder, Colorado 80303, United States
| | - Xinfeng Wang
- Department of Chemistry and
Biochemistry and BioFrontiers Institute, University of Colorado, Boulder, Colorado 80303, United States
| | - Yuan Ruan
- Department of Chemistry and
Biochemistry and BioFrontiers Institute, University of Colorado, Boulder, Colorado 80303, United States
| | - Yaohao Li
- Department of Chemistry and
Biochemistry and BioFrontiers Institute, University of Colorado, Boulder, Colorado 80303, United States
| | - Suzannah G. Miller
- Department of Chemistry and
Biochemistry and BioFrontiers Institute, University of Colorado, Boulder, Colorado 80303, United States
| | - Amy H. Tran
- Department of Chemistry and
Biochemistry and BioFrontiers Institute, University of Colorado, Boulder, Colorado 80303, United States
| | - Theo N. Koelsch
- Department of Chemistry and
Biochemistry and BioFrontiers Institute, University of Colorado, Boulder, Colorado 80303, United States
| | - Lomax F. Pass
- Department of Chemistry and
Biochemistry and BioFrontiers Institute, University of Colorado, Boulder, Colorado 80303, United States
| | - Zhongping Tan
- Department of Chemistry and
Biochemistry and BioFrontiers Institute, University of Colorado, Boulder, Colorado 80303, United States
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37
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Sharma A, Ramos‐Tomillero I, El‐Faham A, Rodríguez H, de la Torre BG, Albericio F. Tetrahydropyranyl: A Non-aromatic, Mild-Acid-Labile Group for Hydroxyl Protection in Solid-Phase Peptide Synthesis. ChemistryOpen 2017; 6:206-210. [PMID: 28413752 PMCID: PMC5390794 DOI: 10.1002/open.201600157] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2016] [Revised: 12/12/2016] [Indexed: 11/30/2022] Open
Abstract
The use of the tetrahydropyranyl (Thp) group for the protection of serine and threonine side-chain hydroxyl groups in solid-phase peptide synthesis has not been widely investigated. Ser/Thr side-chain hydroxyl protection with this acid-labile and non-aromatic moiety is presented here. Although Thp reacts with free carboxylic acids, it can be concluded that to introduce Thp ethers at the hydroxyl groups of N-protected Ser and Thr, protection of the C-terminal carboxyl group is unnecessary due to the lability of Thp esters. Thp-protected Ser/Thr-containing tripeptides are synthesized and the removal of Thp studied in low concentrations of trifluoroacetic acid in the presence of cation scavengers. Given its general stability to most non-acidic reagents, improved solubility of its conjugates and ease with which it can be removed, Thp emerges as an effective protecting group for the hydroxyl groups of Ser and Thr in solid-phase peptide synthesis.
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Affiliation(s)
- Anamika Sharma
- Catalysis and Peptide Research UnitSchool of Health SciencesUniversity of KwaZulu-NatalDurban4001South Africa
| | - Iván Ramos‐Tomillero
- Inorganic and Organic DepartmentUniversity of BarcelonaMartí Franqués 1–1108028BarcelonaSpain
| | - Ayman El‐Faham
- Department of ChemistryCollege of ScienceKing Saud UniversityP.O. Box 2455Riyadh11451Saudi Arabia
- Department of ChemistryFaculty of ScienceAlexandria UniversityP.O. Box 426, IbrahimiaAlexandria21321Egypt
| | | | - Beatriz G. de la Torre
- Catalysis and Peptide Research UnitSchool of Health SciencesUniversity of KwaZulu-NatalDurban4001South Africa
- School of Laboratory of Medicine & Medical SciencesUniversity of KwaZulu-NatalDurban4001South Africa
| | - Fernando Albericio
- Catalysis and Peptide Research UnitSchool of Health SciencesUniversity of KwaZulu-NatalDurban4001South Africa
- Inorganic and Organic DepartmentUniversity of BarcelonaMartí Franqués 1–1108028BarcelonaSpain
- Department of ChemistryCollege of ScienceKing Saud UniversityP.O. Box 2455Riyadh11451Saudi Arabia
- School of Chemistry & PhysicsUniversity of KwaZulu-NatalDurban4001South Africa
- CIBER-BBN, Networking Centre on BioengineeringBiomaterials and NanomedicineBarcelona Science ParkBaldiri Reixac 10–1208028BarcelonaSpain
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38
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Chaffey PK, Guan X, Wang LX, Tan Z. Introduction: General Aspects of the Chemical Biology of Glycoproteins. CHEMICAL BIOLOGY OF GLYCOPROTEINS 2017. [DOI: 10.1039/9781782623823-00001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
This chapter is meant to serve as an introduction to the remainder of the book by providing general background on the chemical biology of glycoproteins as well as a brief review of the chapters that follow. The purpose here is to introduce some basic concepts common to many forms of glycosylation for those readers who may be unfamiliar with the field. We begin with a discussion of the strategies and methods used to study protein glycosylation. During the overview, an effort is made to highlight a few relevant aspects of chemical glycobiology, including glycoprotein biosynthesis and a brief description of the synthesis and function of glycoproteins. Finally, we have a summary of the contributions from chemical biology over the years. It is our hope that, after reading this introductory chapter, the reader will have a broad view of the chemical glycobiology field as it currently stands and a deeper appreciation for some of the unique ideas that chemical biology brings to the field.
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Affiliation(s)
- Patrick K. Chaffey
- Department of Chemistry and Biochemistry and BioFrontiers Institute, University of Colorado Boulder CO 80303 USA
| | - Xiaoyang Guan
- Department of Chemistry and Biochemistry and BioFrontiers Institute, University of Colorado Boulder CO 80303 USA
| | - Lai-Xi Wang
- Department of Chemistry and Biochemistry, University of Maryland College Park MD 20742 USA
| | - Zhongping Tan
- Department of Chemistry and Biochemistry and BioFrontiers Institute, University of Colorado Boulder CO 80303 USA
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39
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Issa H, Huc-Claustre E, Reddad T, Bonadé Bottino N, Tropis M, Houssin C, Daffé M, Bayan N, Dautin N. Click-chemistry approach to study mycoloylated proteins: Evidence for PorB and PorC porins mycoloylation in Corynebacterium glutamicum. PLoS One 2017; 12:e0171955. [PMID: 28199365 PMCID: PMC5310785 DOI: 10.1371/journal.pone.0171955] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 01/27/2017] [Indexed: 01/23/2023] Open
Abstract
Protein mycoloylation is a recently identified, new form of protein acylation. This post-translational modification consists in the covalent attachment of mycolic acids residues to serine. Mycolic acids are long chain, α-branched, β-hydroxylated fatty acids that are exclusively found in the cell envelope of Corynebacteriales, a bacterial order that includes important genera such as Mycobacterium, Nocardia or Corynebacterium. So far, only 3 mycoloylated proteins have been identified: PorA, PorH and ProtX from C. glutamicum. Whereas the identity and function of ProtX is unknown, PorH and PorA associate to form a membrane channel, the activity of which is dependent upon PorA mycoloylation. However, the exact role of mycoloylation and the generality of this phenomenon are still unknown. In particular, the identity of other mycoloylated proteins, if any, needs to be determined together with establishing whether such modification occurs in Corynebacteriales genera other than Corynebacterium. Here, we tested whether a metabolic labeling and click-chemistry approach could be used to detect mycoloylated proteins. Using a fatty acid alkyne analogue, we could indeed label PorA, PorH and ProtX and determine ProtX mycoloylation site. Importantly, we also show that two other porins from C. glutamicum, PorB and PorC are mycoloylated.
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Affiliation(s)
- Hanane Issa
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris‐Sud, Université Paris‐Saclay, Gif‐sur‐Yvette Cedex, France
- Holy Spirit University of Kaslik (USEK), Jounieh, Mount Lebanon, Lebanon
| | | | - Thamila Reddad
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris‐Sud, Université Paris‐Saclay, Gif‐sur‐Yvette Cedex, France
| | - Nolwenn Bonadé Bottino
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris‐Sud, Université Paris‐Saclay, Gif‐sur‐Yvette Cedex, France
| | - Maryelle Tropis
- Institute of Pharmacology and Structural Biology (IPBS), UMR 5089, France
| | - Christine Houssin
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris‐Sud, Université Paris‐Saclay, Gif‐sur‐Yvette Cedex, France
| | - Mamadou Daffé
- Institute of Pharmacology and Structural Biology (IPBS), UMR 5089, France
| | - Nicolas Bayan
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris‐Sud, Université Paris‐Saclay, Gif‐sur‐Yvette Cedex, France
| | - Nathalie Dautin
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris‐Sud, Université Paris‐Saclay, Gif‐sur‐Yvette Cedex, France
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40
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Effects of Glycosylation on the Enzymatic Activity and Mechanisms of Proteases. Int J Mol Sci 2016; 17:ijms17121969. [PMID: 27898009 PMCID: PMC5187769 DOI: 10.3390/ijms17121969] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Revised: 11/07/2016] [Accepted: 11/10/2016] [Indexed: 02/06/2023] Open
Abstract
Posttranslational modifications are an important feature of most proteases in higher organisms, such as the conversion of inactive zymogens into active proteases. To date, little information is available on the role of glycosylation and functional implications for secreted proteases. Besides a stabilizing effect and protection against proteolysis, several proteases show a significant influence of glycosylation on the catalytic activity. Glycans can alter the substrate recognition, the specificity and binding affinity, as well as the turnover rates. However, there is currently no known general pattern, since glycosylation can have both stimulating and inhibiting effects on activity. Thus, a comparative analysis of individual cases with sufficient enzyme kinetic and structural data is a first approach to describe mechanistic principles that govern the effects of glycosylation on the function of proteases. The understanding of glycan functions becomes highly significant in proteomic and glycomic studies, which demonstrated that cancer-associated proteases, such as kallikrein-related peptidase 3, exhibit strongly altered glycosylation patterns in pathological cases. Such findings can contribute to a variety of future biomedical applications.
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41
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GlycoMine struct: a new bioinformatics tool for highly accurate mapping of the human N-linked and O-linked glycoproteomes by incorporating structural features. Sci Rep 2016; 6:34595. [PMID: 27708373 PMCID: PMC5052564 DOI: 10.1038/srep34595] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 09/15/2016] [Indexed: 12/13/2022] Open
Abstract
Glycosylation plays an important role in cell-cell adhesion, ligand-binding and subcellular recognition. Current approaches for predicting protein glycosylation are primarily based on sequence-derived features, while little work has been done to systematically assess the importance of structural features to glycosylation prediction. Here, we propose a novel bioinformatics method called GlycoMinestruct(http://glycomine.erc.monash.edu/Lab/GlycoMine_Struct/) for improved prediction of human N- and O-linked glycosylation sites by combining sequence and structural features in an integrated computational framework with a two-step feature-selection strategy. Experiments indicated that GlycoMinestruct outperformed NGlycPred, the only predictor that incorporated both sequence and structure features, achieving AUC values of 0.941 and 0.922 for N- and O-linked glycosylation, respectively, on an independent test dataset. We applied GlycoMinestruct to screen the human structural proteome and obtained high-confidence predictions for N- and O-linked glycosylation sites. GlycoMinestruct can be used as a powerful tool to expedite the discovery of glycosylation events and substrates to facilitate hypothesis-driven experimental studies.
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42
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Gastaldello A, Alocci D, Baeriswyl JL, Mariethoz J, Lisacek F. GlycoSiteAlign: Glycosite Alignment Based on Glycan Structure. J Proteome Res 2016; 15:3916-3928. [DOI: 10.1021/acs.jproteome.6b00481] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Alessandra Gastaldello
- Proteome
Informatics Group, SIB Swiss Institute of Bioinformatics, 7 route
de Drize, 1227 Geneva, Switzerland
- Computer
Science Department CUI, University of Geneva, 1227 Geneva, Switzerland
| | - Davide Alocci
- Proteome
Informatics Group, SIB Swiss Institute of Bioinformatics, 7 route
de Drize, 1227 Geneva, Switzerland
- Computer
Science Department CUI, University of Geneva, 1227 Geneva, Switzerland
| | - Jean-Luc Baeriswyl
- Proteome
Informatics Group, SIB Swiss Institute of Bioinformatics, 7 route
de Drize, 1227 Geneva, Switzerland
- Section
of Biology, Faculty of Sciences, University of Geneva, 1211 Geneva, Switzerland
| | - Julien Mariethoz
- Proteome
Informatics Group, SIB Swiss Institute of Bioinformatics, 7 route
de Drize, 1227 Geneva, Switzerland
- Computer
Science Department CUI, University of Geneva, 1227 Geneva, Switzerland
| | - Frederique Lisacek
- Proteome
Informatics Group, SIB Swiss Institute of Bioinformatics, 7 route
de Drize, 1227 Geneva, Switzerland
- Computer
Science Department CUI, University of Geneva, 1227 Geneva, Switzerland
- Section
of Biology, Faculty of Sciences, University of Geneva, 1211 Geneva, Switzerland
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43
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Léger T, Garcia C, Camadro JM. The Metacaspase (Mca1p) Restricts O-glycosylation During Farnesol-induced Apoptosis in Candida albicans. Mol Cell Proteomics 2016; 15:2308-23. [PMID: 27125826 DOI: 10.1074/mcp.m116.059378] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Indexed: 11/06/2022] Open
Abstract
Protein glycolysation is an essential posttranslational modification in eukaryotic cells. In pathogenic yeasts, it is involved in a large number of biological processes, such as protein folding quality control, cell viability and host/pathogen relationships. A link between protein glycosylation and apoptosis was established by the analysis of the phenotypes of oligosaccharyltransferase mutants in budding yeast. However, little is known about the contribution of glycosylation modifications to the adaptive response to apoptosis inducers. The cysteine protease metacaspase Mca1p plays a key role in the apoptotic response in Candida albicans triggered by the quorum sensing molecule farnesol. We subjected wild-type and mca1-deletion strains to farnesol stress and then studied the early phase of apoptosis release in quantitative glycoproteomics and glycomics experiments on cell-free extracts essentially devoid of cell walls. We identified and characterized 62 new glycosylated peptides with their glycan composition: 17 N-glycosylated, 45 O-glycosylated, and 81 additional sites of N-glycosylation. They were found to be involved in the control of protein folding, cell wall integrity and cell cycle regulation. We showed a general increase in the O-glycosylation of proteins in the mca1 deletion strain after farnesol challenge. We identified 44 new putative protein substrates of the metacaspase in the glycoprotein fraction enriched on concanavalin A. Most of these substrates are involved in protein folding or protein resolubilization and in mitochondrial functions. We show here that key Mca1p substrates, such as Cdc48p or Ssb1p, involved in degrading misfolded glycoproteins and in the protein quality control system, are themselves differentially glycosylated. We found putative substrates, such as Bgl2p (validated by immunoblot), Srb1p or Ugp1p, that are involved in the biogenesis of glycans. Our findings highlight a new role of the metacaspase in amplifying cell death processes by affecting several critical protein quality control systems through the alteration of the protein glycosylation machinery.Data are available via ProteomeXchange with identifier PXD003677.
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Affiliation(s)
- Thibaut Léger
- From the ‡Mass Spectrometry Laboratory, Institut Jacques Monod, UMR 7592, Univ Paris Diderot, CNRS, Sorbonne Paris Cité, F-75205 Paris, France
| | - Camille Garcia
- From the ‡Mass Spectrometry Laboratory, Institut Jacques Monod, UMR 7592, Univ Paris Diderot, CNRS, Sorbonne Paris Cité, F-75205 Paris, France
| | - Jean-Michel Camadro
- From the ‡Mass Spectrometry Laboratory, Institut Jacques Monod, UMR 7592, Univ Paris Diderot, CNRS, Sorbonne Paris Cité, F-75205 Paris, France; §Mitochondria, Metals and Oxidative Stress Group, Institut Jacques Monod, UMR 7592, Univ Paris Diderot, CNRS, Sorbonne Paris Cité, F-75205 Paris, France
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44
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Vishwanatha KS, Bäck N, Lam TT, Mains RE, Eipper BA. O-Glycosylation of a Secretory Granule Membrane Enzyme Is Essential for Its Endocytic Trafficking. J Biol Chem 2016; 291:9835-50. [PMID: 26961877 DOI: 10.1074/jbc.m115.711838] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2015] [Indexed: 01/08/2023] Open
Abstract
Peptidylglycine α-amidating monooxygenase (PAM) (EC 1.14.17.3) catalyzes peptide amidation, a crucial post-translational modification, through the sequential actions of its monooxygenase (peptidylglycine α-hydroxylating monooxygenase) and lyase (peptidyl-α-hydroxyglycine α-amidating lyase (PAL)) domains. Alternative splicing generates two different regions that connect the protease-resistant catalytic domains. Inclusion of exon 16 introduces a pair of Lys residues, providing a site for controlled endoproteolytic cleavage of PAM and the separation of soluble peptidylglycine α-hydroxylating monooxygenase from membrane-associated PAL. Exon 16 also includes two O-glycosylation sites. PAM-1 lacking both glycosylation sites (PAM-1/OSX; where OSX is O-glycan-depleted mutant of PAM-1) was stably expressed in AtT-20 corticotrope tumor cells. In PAM-1/OSX, a cleavage site for furin-like convertases was exposed, generating a shorter form of membrane-associated PAL. The endocytic trafficking of PAM-1/OSX differed dramatically from that of PAM-1. A soluble fragment of the cytosolic domain of PAM-1 was produced in the endocytic pathway and entered the nucleus; very little soluble fragment of the cytosolic domain was produced from PAM-1/OSX. Internalized PAM-1/OSX was rapidly degraded; unlike PAM-1, very little internalized PAM-1/OSX was detected in multivesicular bodies. Blue native PAGE analysis identified high molecular weight complexes containing PAM-1; the ability of PAM-1/OSX to form similar complexes was markedly diminished. By promoting the formation of high molecular weight complexes, O-glycans may facilitate the recycling of PAM-1 through the endocytic compartment.
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Affiliation(s)
| | - Nils Bäck
- the Department of Anatomy, Faculty of Medicine, University of Helsinki, Fin-00014, Helsinki, Finland, and
| | - TuKiet T Lam
- the W. M. Keck Foundation Biotechnology Resource Laboratory, Yale/Keck MS and Proteomics Resource, Yale/NIDA Neuroproteomics Center, Yale University, New Haven, Connecticut 06511
| | | | - Betty A Eipper
- From the Departments of Neuroscience and Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, Connecticut 06030,
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45
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Louros NN, Baltoumas FA, Hamodrakas SJ, Iconomidou VA. A β-solenoid model of the Pmel17 repeat domain: insights to the formation of functional amyloid fibrils. J Comput Aided Mol Des 2016; 30:153-64. [PMID: 26754844 DOI: 10.1007/s10822-015-9892-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 12/21/2015] [Indexed: 10/22/2022]
Abstract
Pmel17 is a multidomain protein involved in biosynthesis of melanin. This process is facilitated by the formation of Pmel17 amyloid fibrils that serve as a scaffold, important for pigment deposition in melanosomes. A specific luminal domain of human Pmel17, containing 10 tandem imperfect repeats, designated as repeat domain (RPT), forms amyloid fibrils in a pH-controlled mechanism in vitro and has been proposed to be essential for the formation of the fibrillar matrix. Currently, no three-dimensional structure has been resolved for the RPT domain of Pmel17. Here, we examine the structure of the RPT domain by performing sequence threading. The resulting model was subjected to energy minimization and validated through extensive molecular dynamics simulations. Structural analysis indicated that the RPT model exhibits several distinct properties of β-solenoid structures, which have been proposed to be polymerizing components of amyloid fibrils. The derived model is stabilized by an extensive network of hydrogen bonds generated by stacking of highly conserved polar residues of the RPT domain. Furthermore, the key role of invariant glutamate residues is proposed, supporting a pH-dependent mechanism for RPT domain assembly. Conclusively, our work attempts to provide structural insights into the RPT domain structure and to elucidate its contribution to Pmel17 amyloid fibril formation.
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Affiliation(s)
- Nikolaos N Louros
- Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Panepistimiopolis, 157 01, Athens, Greece
| | - Fotis A Baltoumas
- Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Panepistimiopolis, 157 01, Athens, Greece
| | - Stavros J Hamodrakas
- Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Panepistimiopolis, 157 01, Athens, Greece
| | - Vassiliki A Iconomidou
- Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Panepistimiopolis, 157 01, Athens, Greece.
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46
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Li F, Li C, Wang M, Webb GI, Zhang Y, Whisstock JC, Song J. GlycoMine: a machine learning-based approach for predicting N-, C- and O-linked glycosylation in the human proteome. Bioinformatics 2015; 31:1411-9. [DOI: 10.1093/bioinformatics/btu852] [Citation(s) in RCA: 129] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Accepted: 12/23/2014] [Indexed: 12/31/2022] Open
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47
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Petris G, Bestagno M, Arnoldi F, Burrone OR. New tags for recombinant protein detection and O-glycosylation reporters. PLoS One 2014; 9:e96700. [PMID: 24802141 PMCID: PMC4011882 DOI: 10.1371/journal.pone.0096700] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Accepted: 04/10/2014] [Indexed: 01/24/2023] Open
Abstract
Monoclonal antibodies (mAbs), because of their unique specificity, are irreplaceable tools for scientific research. Precise mapping of the antigenic determinants allows the development of epitope tagging approaches to be used with recombinant proteins for several purposes. Here we describe a new family of tags derived from the epitope recognized by a single highly specific mAb (anti-roTag mAb), which was obtained from a pool of mAbs reacting with the rotavirus nonstructural protein 5 (NSP5). The variable regions of the anti-roTag mAb were identified and their binding capacity verified upon expression as a single-chain/miniAb. The minimal epitope, termed roTag, was identified as a 10 amino acid sequence (SISSSIFKNE). The affinity of the anti-roTag/roTag interaction was found to be comparable to that of the anti-SV5/SV5 tag interaction. roTag was successfully used for detection of several recombinant cytosolic, secretory and membrane proteins. Two additional variants of roTag of 10 and 13 amino acids containing O-glycosylation susceptible sites (termed OG-tag and roTagO) were constructed and characterised. These tags were useful to detect proteins passing through the Golgi apparatus, the site of O-glycosylation.
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Affiliation(s)
- Gianluca Petris
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
| | - Marco Bestagno
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
| | - Francesca Arnoldi
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy
| | - Oscar R. Burrone
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
- * E-mail:
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49
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Woodin CL, Maxon M, Desaire H. Software for automated interpretation of mass spectrometry data from glycans and glycopeptides. Analyst 2013; 138:2793-803. [PMID: 23293784 DOI: 10.1039/c2an36042j] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The purpose of this review is to provide those interested in glycosylation analysis with the most updated information on the availability of automated tools for MS characterization of N-linked and O-linked glycosylation types. Specifically, this review describes software tools that facilitate elucidation of glycosylation from MS data on the basis of mass alone, as well as software designed to speed the interpretation of glycan and glycopeptide fragmentation from MS/MS data. This review focuses equally on software designed to interpret the composition of released glycans and on tools to characterize N-linked and O-linked glycopeptides. Several websites have been compiled and described that will be helpful to the reader who is interested in further exploring the described tools.
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Affiliation(s)
- Carrie L Woodin
- Department of Chemistry, University of Kansas, 2030 Becker Drive, Lawrence, KS 66047, USA
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50
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Spencer D, Novarra S, Zhu L, Mugabe S, Thisted T, Baca M, Depaz R, Barton C. O-xylosylation in a Recombinant Protein is Directed at a Common Motif on Glycine–Serine Linkers. J Pharm Sci 2013; 102:3920-4. [DOI: 10.1002/jps.23733] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Revised: 08/30/2013] [Accepted: 09/03/2013] [Indexed: 11/10/2022]
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