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Chen S, Wang Y, Cui T, Zheng Y, Zhang F, Ma Q, Zhang C, Liu X. Characterization of three non-canonical N-glycosylation motifs indicates N glyco-A reduces DNA N6-methyladenine and N glyco-D alters G/F actin ratio in Phytophthora sojae. Int J Biol Macromol 2024; 277:133943. [PMID: 39025174 DOI: 10.1016/j.ijbiomac.2024.133943] [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: 04/08/2024] [Revised: 07/08/2024] [Accepted: 07/15/2024] [Indexed: 07/20/2024]
Abstract
Asparagine (Asn, N)-linked glycosylation is an abundant post-translational modification in which Asn, typically in Nglyco-X-S/T; X ≠ P motifs, are modified with N-glycans. It has essential regulatory roles in multicellular organisms. In this study, we systematically investigate the function of three N-glycosylation motifs (Nglyco-A, Nglyco-D and Nglyco-S) previously identified in Phytophthora sojae, through site-directed mutagenesis and functional assays. In P. sojae expressing glycosylation-dead variants pre-PsDMAP1N70A (Nglyco-A motif) or PsADFN64A (Nglyco-D motif), zoospore release or cyst germination is impaired. In particular, the pre-PsDMAP1N70A mutant reduces DNA methylation levels, and the PsADFN64A mutant disrupts the actin forms, which could explain the decrease in pathogenicity after N-glycosylation is destroyed. Similarly, P. sojae expressing PsNRXN132A (Nglyco-S motif) shows increased sensitivity to H2O2 and heat. Through autophagy or 26S proteasome pathway inhibition assays, we found that unglycosylated pre-PsDMAP1N70A and PsADFN64A are degraded via the 26S proteasome pathway, while the autophagy pathway is responsible for PsNRXN132A clearance. These findings demonstrate that glycosylation of these motifs regulates the stability and function of glycoproteins necessary for P. sojae growth, reproduction and pathogenicity, which expands the scope of known N-glycosylation regulatory functions in oomycetes.
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Affiliation(s)
- Shanshan Chen
- Department of Plant Pathology, China Agricultural University, Beijing 100193, China
| | - Yuke Wang
- Department of Plant Pathology, China Agricultural University, Beijing 100193, China
| | - Tongshan Cui
- Department of Plant Pathology, China Agricultural University, Beijing 100193, China
| | - Yuxin Zheng
- Department of Plant Pathology, China Agricultural University, Beijing 100193, China
| | - Fan Zhang
- Department of Plant Pathology, China Agricultural University, Beijing 100193, China
| | - Quanhe Ma
- Department of Plant Pathology, China Agricultural University, Beijing 100193, China
| | - Can Zhang
- Department of Plant Pathology, China Agricultural University, Beijing 100193, China.
| | - Xili Liu
- Department of Plant Pathology, China Agricultural University, Beijing 100193, China; State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling 712100, China.
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2
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Aguilar Díaz de león JS, Thirumurty M, Ly N. Surface plasmon resonance microscopy identifies glycan heterogeneity in pancreatic cancer cells that influences mucin-4 binding interactions. PLoS One 2024; 19:e0304154. [PMID: 38776309 PMCID: PMC11111020 DOI: 10.1371/journal.pone.0304154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 05/07/2024] [Indexed: 05/24/2024] Open
Abstract
Membrane proteins are the main targets of therapeutic drugs and most of them are glycosylated. Glycans play pivotal roles in several biological processes, and glycosylation changes are a well-established hallmark of several types of cancer, including pancreatic cancer, that contribute to tumor growth. Mucin-4 (MUC-4) is a membrane glycoprotein which is associated with pancreatic cancer and metastasis, and it has been targeted as a promising vaccine candidate. In this study, Surface Plasmon Resonance Microscopy (SPRM) was implemented to study complex influences of the native N-glycan cellular environment on binding interactions to the MUC-4 receptor as this is currently the only commercially available label-free technique with high enough sensitivity and resolution to measure binding kinetics and heterogeneity on single cells. Such unique capability enables for a more accurate understanding of the "true" binding interactions on human cancer cells without disrupting the native environment of the target MUC-4 receptor. Removal of N-linked glycans in pancreatic cancer cells using PNGase F exposed heterogeneity in Concanavalin (Con A) binding by revealing three new binding populations with higher affinities than the glycosylated control cells. Anti-MUC-4 binding interactions of enzymatically N-linked deglycosylated pancreatic cancer cells produced a 25x faster association and 37x higher affinity relative to the glycosylated control cells. Lastly, four interaction modes were observed for Helix Pomatia Agglutinin (HPA) binding to the glycosylated control cells, but shifted and increased in activity upon removal of N-linked glycans. These results identified predominant interaction modes of glycan and MUC-4 in pancreatic cancer cells, the kinetics of their binding interactions were quantified, and the influence of N-linked glycans in MUC-4 binding interactions was revealed.
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Affiliation(s)
| | - Miyuki Thirumurty
- Biosensing Instrument Inc., Tempe, Arizona, United States of America
| | - Nguyen Ly
- Biosensing Instrument Inc., Tempe, Arizona, United States of America
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3
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Trbojević-Akmačić I, Lageveen-Kammeijer GSM, Heijs B, Petrović T, Deriš H, Wuhrer M, Lauc G. High-Throughput Glycomic Methods. Chem Rev 2022; 122:15865-15913. [PMID: 35797639 PMCID: PMC9614987 DOI: 10.1021/acs.chemrev.1c01031] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Glycomics aims to identify the structure and function of the glycome, the complete set of oligosaccharides (glycans), produced in a given cell or organism, as well as to identify genes and other factors that govern glycosylation. This challenging endeavor requires highly robust, sensitive, and potentially automatable analytical technologies for the analysis of hundreds or thousands of glycomes in a timely manner (termed high-throughput glycomics). This review provides a historic overview as well as highlights recent developments and challenges of glycomic profiling by the most prominent high-throughput glycomic approaches, with N-glycosylation analysis as the focal point. It describes the current state-of-the-art regarding levels of characterization and most widely used technologies, selected applications of high-throughput glycomics in deciphering glycosylation process in healthy and disease states, as well as future perspectives.
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Affiliation(s)
| | | | - Bram Heijs
- Center
for Proteomics and Metabolomics, Leiden
University Medical Center, PO Box 9600, 2300 RC Leiden, The Netherlands
| | - Tea Petrović
- Genos,
Glycoscience Research Laboratory, Borongajska cesta 83H, 10 000 Zagreb, Croatia
| | - Helena Deriš
- Genos,
Glycoscience Research Laboratory, Borongajska cesta 83H, 10 000 Zagreb, Croatia
| | - Manfred Wuhrer
- Center
for Proteomics and Metabolomics, Leiden
University Medical Center, PO Box 9600, 2300 RC Leiden, The Netherlands
| | - Gordan Lauc
- Genos,
Glycoscience Research Laboratory, Borongajska cesta 83H, 10 000 Zagreb, Croatia
- Faculty
of Pharmacy and Biochemistry, University
of Zagreb, A. Kovačića 1, 10 000 Zagreb, Croatia
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4
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Kovács N, Farsang R, Szigeti M, Vonderviszt F, Jankovics H. Enhanced Recombinant Protein Production of Soluble, Highly Active and Immobilizable PNGase F. Mol Biotechnol 2022; 64:914-918. [PMID: 35244857 PMCID: PMC9259526 DOI: 10.1007/s12033-022-00464-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 02/11/2022] [Indexed: 11/30/2022]
Abstract
High resolution analysis of N-glycans can be performed after their endoglycosidase mediated removal from proteins. N-glycosidase F peptide (PNGase F) is one the most frequently used enzyme for this purpose. Because of the significant demand for PNGase F both in basic and applied research, rapid and inexpensive methods are of great demand for its large-scale production, preferably in immobilizable form to solid supports or surfaces. In this paper, we report on the high-yield production of N-terminal 6His-PNGase F enzyme in a bacterial Escherichia coli SHuffle expression system. The activity profile of the generated enzyme was compared to commercially available PNGase F enzymes, featuring higher activity for the former. The method described here is thus suitable for the cost-effective production of PNGase F in an active, immobilizable form.
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Affiliation(s)
- Noémi Kovács
- Bio-Nanosystems Laboratory, Research Institute of Biomolecular and Chemical Engineering, University of Pannonia, 10 Egyetem Street, Veszprém, 8200, Hungary
| | - Róbert Farsang
- Translational Glycomics Research Group, Research Institute of Biomolecular and Chemical Engineering, University of Pannonia, 10 Egyetem Street, Veszprém, 8200, Hungary
| | - Márton Szigeti
- Translational Glycomics Research Group, Research Institute of Biomolecular and Chemical Engineering, University of Pannonia, 10 Egyetem Street, Veszprém, 8200, Hungary
| | - Ferenc Vonderviszt
- Bio-Nanosystems Laboratory, Research Institute of Biomolecular and Chemical Engineering, University of Pannonia, 10 Egyetem Street, Veszprém, 8200, Hungary
| | - Hajnalka Jankovics
- Bio-Nanosystems Laboratory, Research Institute of Biomolecular and Chemical Engineering, University of Pannonia, 10 Egyetem Street, Veszprém, 8200, Hungary.
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5
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Carroll DJ, Burns MWN, Mottram L, Propheter DC, Boucher A, Lessen GM, Kumar A, Malaker SA, Xing C, Hooper LV, Yrlid U, Kohler JJ. Interleukin-22 regulates B3GNT7 expression to induce fucosylation of glycoproteins in intestinal epithelial cells. J Biol Chem 2022; 298:101463. [PMID: 34864058 PMCID: PMC8808068 DOI: 10.1016/j.jbc.2021.101463] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 11/24/2021] [Accepted: 11/27/2021] [Indexed: 12/13/2022] Open
Abstract
Interleukin (IL)-22 is a cytokine that plays a critical role in intestinal epithelial homeostasis. Its downstream functions are mediated through interaction with the heterodimeric IL-22 receptor and subsequent activation of signal transducer and activator of transcription 3 (STAT3). IL-22 signaling can induce transcription of genes necessary for intestinal epithelial cell proliferation, tissue regeneration, tight junction fortification, and antimicrobial production. Recent studies have also implicated IL-22 signaling in the regulation of intestinal epithelial fucosylation in mice. However, whether IL-22 regulates intestinal fucosylation in human intestinal epithelial cells and the molecular mechanisms that govern this process are unknown. Here, in experiments performed in human cell lines and human-derived enteroids, we show that IL-22 signaling regulates expression of the B3GNT7 transcript, which encodes a β1-3-N-acetylglucosaminyltransferase that can participate in the synthesis of poly-N-acetyllactosamine (polyLacNAc) chains. Additionally, we find that IL-22 signaling regulates levels of the α1-3-fucosylated Lewis X (Lex) blood group antigen, and that this glycan epitope is primarily displayed on O-glycosylated intestinal epithelial glycoproteins. Moreover, we show that increased expression of B3GNT7 alone is sufficient to promote increased display of Lex-decorated carbohydrate glycan structures primarily on O-glycosylated intestinal epithelial glycoproteins. Together, these data identify B3GNT7 as an intermediary in IL-22-dependent induction of fucosylation of glycoproteins and uncover a novel role for B3GNT7 in intestinal glycosylation.
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Affiliation(s)
- Daniela J Carroll
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Mary W N Burns
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Lynda Mottram
- Department of Microbiology and Immunology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Daniel C Propheter
- Department of Immunology, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Andrew Boucher
- Department of Microbiology and Immunology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Gabrielle M Lessen
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Ashwani Kumar
- Eugene McDermott Center for Human Growth and Development, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Stacy A Malaker
- Department of Chemistry, Yale University, New Haven, Connecticut, USA
| | - Chao Xing
- Eugene McDermott Center for Human Growth and Development, The University of Texas Southwestern Medical Center, Dallas, Texas, USA; Department of Bioinformatics, The University of Texas Southwestern Medical Center, Dallas, Texas, USA; Department of Population and Data Sciences, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Lora V Hooper
- Department of Immunology, The University of Texas Southwestern Medical Center, Dallas, Texas, USA; Howard Hughes Medical Institute, Department of Immunology, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Ulf Yrlid
- Department of Microbiology and Immunology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Jennifer J Kohler
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, USA.
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6
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Frensch M, Jäger C, Müller PF, Tadić A, Wilhelm I, Wehrum S, Diedrich B, Fischer B, Meléndez AV, Dengjel J, Eibel H, Römer W. Bacterial lectin BambL acts as a B cell superantigen. Cell Mol Life Sci 2021; 78:8165-8186. [PMID: 34731252 PMCID: PMC8629787 DOI: 10.1007/s00018-021-04009-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 10/03/2021] [Accepted: 10/21/2021] [Indexed: 11/29/2022]
Abstract
B cell superantigens crosslink conserved domains of B cell receptors (BCRs) and cause dysregulated, polyclonal B cell activation irrespective of normal BCR-antigen complementarity. The cells typically succumb to activation-induced cell death, which can impede the adaptive immune response and favor infection. In the present study, we demonstrate that the fucose-binding lectin of Burkholderia ambifaria, BambL, bears functional resemblance to B cell superantigens. By engaging surface glycans, the bacterial lectin activated human peripheral blood B cells, which manifested in the surface expression of CD69, CD54 and CD86 but became increasingly cytotoxic at higher concentrations. The effects were sensitive to BCR pathway inhibitors and excess fucose, which corroborates a glycan-driven mode of action. Interactome analyses in a model cell line suggest BambL binds directly to glycans of the BCR and regulatory coreceptors. In vitro, BambL triggered BCR signaling and induced CD19 internalization and degradation. Owing to the lectin's six binding sites, we propose a BCR activation model in which BambL functions as a clustering hub for receptor glycans, modulates normal BCR regulation, and induces cell death through exhaustive activation.
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Affiliation(s)
- Marco Frensch
- Faculty of Biology, University of Freiburg, Freiburg, Germany
- Signaling Research Centers BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
- International Max Planck Research School for Molecular and Cellular Biology (IMPRS-MCB), Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Christina Jäger
- Faculty of Biology, University of Freiburg, Freiburg, Germany
- Signaling Research Centers BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - Peter F Müller
- Faculty of Biology, University of Freiburg, Freiburg, Germany
- Signaling Research Centers BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - Annamaria Tadić
- Faculty of Biology, University of Freiburg, Freiburg, Germany
- Signaling Research Centers BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - Isabel Wilhelm
- Faculty of Biology, University of Freiburg, Freiburg, Germany
- Signaling Research Centers BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany
| | - Sarah Wehrum
- Faculty of Biology, University of Freiburg, Freiburg, Germany
- Signaling Research Centers BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - Britta Diedrich
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- Department of Dermatology, University Medical Center and University of Freiburg, Freiburg, Germany
| | - Beate Fischer
- Center for Chronic Immunodeficiency, CCI and University Medical Center Freiburg, Freiburg, Germany
| | - Ana Valeria Meléndez
- Faculty of Biology, University of Freiburg, Freiburg, Germany
- Signaling Research Centers BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany
| | - Joern Dengjel
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- Department of Dermatology, University Medical Center and University of Freiburg, Freiburg, Germany
| | - Hermann Eibel
- Center for Chronic Immunodeficiency, CCI and University Medical Center Freiburg, Freiburg, Germany.
| | - Winfried Römer
- Faculty of Biology, University of Freiburg, Freiburg, Germany.
- Signaling Research Centers BIOSS and CIBSS, University of Freiburg, Freiburg, Germany.
- International Max Planck Research School for Molecular and Cellular Biology (IMPRS-MCB), Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany.
- Freiburg Institute for Advanced Studies (FRIAS), University of Freiburg, Freiburg, Germany.
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7
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Plasma membrane N-glycoproteome analysis of wheat seedling leaves under drought stress. Int J Biol Macromol 2021; 193:1541-1550. [PMID: 34740685 DOI: 10.1016/j.ijbiomac.2021.10.217] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 10/12/2021] [Accepted: 10/29/2021] [Indexed: 01/23/2023]
Abstract
Protein glycosylation is one of the ubiquitous post-translational modifications in eukaryotic cells, which play important roles in plant growth and adverse response. In this study, we performed the first comprehensive wheat plasma membrane N-glycoproteome analysis under drought stress via glycopeptide HILIC enrichment and LC-MS/MS identification. In total, 414 glycosylated sites corresponding to 407 glycopeptides and 312 unique glycoproteins were identified, of which 173 plasma membrane glycoproteins with 215 N-glycosylation sites were significantly regulated by drought stress. Functional enrichment analysis reveals that the significantly regulated N-glycosylation proteins were particularly related to protein kinase activity involved in the reception and transduction of extracellular signal and plant cell wall remolding. The motifs and sequence structures analysis showed that the significantly regulated N-glycosylation sites were concentrated within [NxT] motif, and 79.5% of them were located on the random coil that is always on the protein surface and flexible regions, which could facilitate protein glycosylated modification and enhance protein structural stability via reducing protein flexibility. PNGase F enzyme digestion and glycosylation site mutation further indicated that N-glycosylated modification could increase protein stability. Therefore, N-glycosylated modification is involved in plant adaptation to drought stress by improving the stability of cell wall remodeling related plasma membrane proteins.
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8
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Stevenson-Leggett P, Armstrong S, Keep S, Britton P, Bickerton E. Analysis of the avian coronavirus spike protein reveals heterogeneity in the glycans present. J Gen Virol 2021; 102. [PMID: 34424155 PMCID: PMC8513636 DOI: 10.1099/jgv.0.001642] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Infectious bronchitis virus (IBV) is an economically important coronavirus, causing damaging losses to the poultry industry worldwide as the causative agent of infectious bronchitis. The coronavirus spike (S) glycoprotein is a large type I membrane protein protruding from the surface of the virion, which facilitates attachment and entry into host cells. The IBV S protein is cleaved into two subunits, S1 and S2, the latter of which has been identified as a determinant of cellular tropism. Recent studies expressing coronavirus S proteins in mammalian and insect cells have identified a high level of glycosylation on the protein’s surface. Here we used IBV propagated in embryonated hens’ eggs to explore the glycan profile of viruses derived from infection in cells of the natural host, chickens. We identified multiple glycan types on the surface of the protein and found a strain-specific dependence on complex glycans for recognition of the S2 subunit by a monoclonal antibody in vitro, with no effect on viral replication following the chemical inhibition of complex glycosylation. Virus neutralization by monoclonal or polyclonal antibodies was not affected. Following analysis of predicted glycosylation sites for the S protein of four IBV strains, we confirmed glycosylation at 18 sites by mass spectrometry for the pathogenic laboratory strain M41-CK. Further characterization revealed heterogeneity among the glycans present at six of these sites, indicating a difference in the glycan profile of individual S proteins on the IBV virion. These results demonstrate a non-specific role for complex glycans in IBV replication, with an indication of an involvement in antibody recognition but not neutralisation.
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Affiliation(s)
| | - Stuart Armstrong
- Institute of Infection and Global Health, University of Liverpool, Liverpool L3 5RF, UK
| | - Sarah Keep
- The Pirbright Institute, Woking, Surrey GU24 0NF, UK
| | - Paul Britton
- The Pirbright Institute, Woking, Surrey GU24 0NF, UK
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9
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Zhang C, Cai M, Chen S, Zhang F, Cui T, Xue Z, Wang W, Zhang B, Liu X. The consensus N glyco -X-S/T motif and a previously unknown N glyco -N-linked glycosylation are necessary for growth and pathogenicity of Phytophthora. Environ Microbiol 2021; 23:5147-5163. [PMID: 33728790 DOI: 10.1111/1462-2920.15468] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 03/10/2021] [Accepted: 03/15/2021] [Indexed: 11/26/2022]
Abstract
Asparagine (Asn, N)-linked glycosylation within Nglyco -X-S/T; X ≠ P motif is a ubiquitously distributed post-translational modification that participates in diverse cellular processes. In this work, N-glycosylation inhibitor was shown to prevent Phytophthora sojae growth, suggesting that N-glycosylation is necessary for oomycete development. We conducted a glycoproteomic analysis of P. sojae to identify and map N-glycosylated proteins and to quantify differentially expressed glycoproteins associated with mycelia, asexual cyst, and sexual oospore developmental stages. A total of 355 N-glycosylated proteins was found, containing 496 glycosites, potentially involved in glycan degradation, carbon metabolism, glycolysis, or other metabolic pathways. Through PNGase F deglycosylation assays and site-directed mutagenesis of a GPI transamidase protein (GPI16) upregulated in cysts and a heat shock protein 70 (HSP70) upregulated in oospores, we demonstrated that both proteins were N-glycosylated and that the Nglyco -N motif is a target site for asparagine - oligosaccharide linkage. Glycosite mutations of Asn 94 Nglyco -X-S/T in the GPI16 led to impaired cyst germination and pathogenicity, while mutation of the previously unknown Asn 270 Nglyco -N motif in HSP70 led to decreased oospore production. In addition to providing a map of the oomycete N-glycoproteome, this work confirms that P. sojae has evolved multiple N-glycosylation motifs essential for growth.
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Affiliation(s)
- Can Zhang
- Department of Plant Pathology, China Agricultural University, Beijing, 100193, China
| | - Meng Cai
- Department of Plant Pathology, China Agricultural University, Beijing, 100193, China
| | - Shanshan Chen
- Department of Plant Pathology, China Agricultural University, Beijing, 100193, China
| | - Fan Zhang
- Department of Plant Pathology, China Agricultural University, Beijing, 100193, China
| | - Tongshan Cui
- Department of Plant Pathology, China Agricultural University, Beijing, 100193, China
| | - Zhaolin Xue
- Department of Plant Pathology, China Agricultural University, Beijing, 100193, China
| | - Weizhen Wang
- Department of Plant Pathology, China Agricultural University, Beijing, 100193, China
| | - Borui Zhang
- Department of Plant Pathology, China Agricultural University, Beijing, 100193, China
| | - Xili Liu
- Department of Plant Pathology, China Agricultural University, Beijing, 100193, China.,State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, China
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10
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Shear force sensing of epithelial Na + channel (ENaC) relies on N-glycosylated asparagines in the palm and knuckle domains of αENaC. Proc Natl Acad Sci U S A 2019; 117:717-726. [PMID: 31871197 PMCID: PMC6955349 DOI: 10.1073/pnas.1911243117] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The ability to sense mechanical forces is essential for all living organisms. Extracellular tethers have been proposed to mediate mechanical activation of channels belonging to the epithelial Na+ channel (ENaC)/degenerin protein family. The nature and architecture of the tethers that link the channel protein with the extracellular matrix are unknown. Our study provides experimental evidence that glycosylated asparagines and their N-glycans are part of tethers for mechanical activation of ENaC by shear force. The identified asparagines are also important for arterial blood pressure regulation in vivo. These findings provide insights into how mechanical forces are sensed by mechanosensitive ENaC channels to regulate blood pressure. Mechanosensitive ion channels are crucial for normal cell function and facilitate physiological function, such as blood pressure regulation. So far little is known about the molecular mechanisms of how channels sense mechanical force. Canonical vertebrate epithelial Na+ channel (ENaC) formed by α-, β-, and γ-subunits is a shear force (SF) sensor and a member of the ENaC/degenerin protein family. ENaC activity in epithelial cells contributes to electrolyte/fluid-homeostasis and blood pressure regulation. Furthermore, ENaC in endothelial cells mediates vascular responsiveness to regulate blood pressure. Here, we provide evidence that ENaC’s ability to mediate SF responsiveness relies on the “force-from-filament” principle involving extracellular tethers and the extracellular matrix (ECM). Two glycosylated asparagines, respectively their N-glycans localized in the palm and knuckle domains of αENaC, were identified as potential tethers. Decreased SF-induced ENaC currents were observed following removal of the ECM/glycocalyx, replacement of these glycosylated asparagines, or removal of N-glycans. Endothelial-specific overexpression of αENaC in mice induced hypertension. In contrast, expression of αENaC lacking these glycosylated asparagines blunted this effect. In summary, glycosylated asparagines in the palm and knuckle domains of αENaC are important for SF sensing. In accordance with the force-from-filament principle, they may provide a connection to the ECM that facilitates vascular responsiveness contributing to blood pressure regulation.
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11
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Chatterjee S, Lee LY, Kawahara R, Abrahams JL, Adamczyk B, Anugraham M, Ashwood C, Sumer‐Bayraktar Z, Briggs MT, Chik JHL, Everest‐Dass A, Förster S, Hinneburg H, Leite KRM, Loke I, Möginger U, Moh ESX, Nakano M, Recuero S, Sethi MK, Srougi M, Stavenhagen K, Venkatakrishnan V, Wongtrakul‐Kish K, Diestel S, Hoffmann P, Karlsson NG, Kolarich D, Molloy MP, Muders MH, Oehler MK, Packer NH, Palmisano G, Thaysen‐Andersen M. Protein Paucimannosylation Is an EnrichedN‐Glycosylation Signature of Human Cancers. Proteomics 2019; 19:e1900010. [DOI: 10.1002/pmic.201900010] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 07/25/2019] [Indexed: 01/01/2023]
Affiliation(s)
- Sayantani Chatterjee
- Department of Molecular Sciences and Biomolecular Discovery and Design Research Centre (BDDRC) Macquarie University Sydney 2109 Australia
| | - Ling Y. Lee
- Department of Molecular Sciences and Biomolecular Discovery and Design Research Centre (BDDRC) Macquarie University Sydney 2109 Australia
- ISGlobal, Barcelona Centre for International Health Research (CRESIB) Hospital Clínic–Universitat de Barcelona Barcelona 08193 Spain
| | - Rebeca Kawahara
- Department of Molecular Sciences and Biomolecular Discovery and Design Research Centre (BDDRC) Macquarie University Sydney 2109 Australia
- Department of Parasitology, Institute of Biomedical Sciences University of São Paulo São Paulo 01000 Brazil
| | - Jodie L. Abrahams
- Department of Molecular Sciences and Biomolecular Discovery and Design Research Centre (BDDRC) Macquarie University Sydney 2109 Australia
- Institute for Glycomics, Griffith University Gold Coast 4222 Australia
| | - Barbara Adamczyk
- Department of Medical Biochemistry and Cell Biology Institute of Biomedicine, Sahlgrenska Academy University of Gothenburg Gothenburg SE 405 30 Sweden
| | - Merrina Anugraham
- Department of Molecular Sciences and Biomolecular Discovery and Design Research Centre (BDDRC) Macquarie University Sydney 2109 Australia
- Institute of Biological Chemistry Academia Sinica Taipei 11529 Taiwan
| | - Christopher Ashwood
- Department of Molecular Sciences and Biomolecular Discovery and Design Research Centre (BDDRC) Macquarie University Sydney 2109 Australia
- Department of Biochemistry Medical College of Wisconsin Milwaukee WI 53226 USA
| | - Zeynep Sumer‐Bayraktar
- Department of Molecular Sciences and Biomolecular Discovery and Design Research Centre (BDDRC) Macquarie University Sydney 2109 Australia
- School of Life and Environmental Sciences Charles Perkins Centre (CPC), The University of Sydney Sydney 2006 Australia
| | - Matthew T. Briggs
- Future Industries Institute Mawson Lakes Campus, University of South Australia Adelaide 5005 Australia
| | - Jenny H. L. Chik
- Department of Molecular Sciences and Biomolecular Discovery and Design Research Centre (BDDRC) Macquarie University Sydney 2109 Australia
- International Collaboration on Repair Discoveries Vancouver Coastal Health Research Institute and Department of Pathology and Laboratory Medicine The University of British Columbia Vancouver BC V6T 1Z4 Canada
| | - Arun Everest‐Dass
- Department of Molecular Sciences and Biomolecular Discovery and Design Research Centre (BDDRC) Macquarie University Sydney 2109 Australia
- Institute for Glycomics, Griffith University Gold Coast 4222 Australia
| | - Sarah Förster
- Rudolf‐Becker‐Laboratory Institute of Pathology University Hospital Bonn Bonn 53127 Germany
| | - Hannes Hinneburg
- Department of Molecular Sciences and Biomolecular Discovery and Design Research Centre (BDDRC) Macquarie University Sydney 2109 Australia
| | - Katia R. M. Leite
- Laboratório de Investigação Médica da Disciplina de Urologia (LIM55) Faculdade de Medicina da FMUSP Universidade de Sao Paulo São Paulo 01000 Brazil
| | - Ian Loke
- Department of Molecular Sciences and Biomolecular Discovery and Design Research Centre (BDDRC) Macquarie University Sydney 2109 Australia
- Department of Biological Sciences National University of Singapore Singapore 119077 Singapore
| | - Uwe Möginger
- Department for Biochemistry and Molecular Biology University of Southern Denmark Odense 5230 Denmark
| | - Edward S. X. Moh
- Department of Molecular Sciences and Biomolecular Discovery and Design Research Centre (BDDRC) Macquarie University Sydney 2109 Australia
- ARC Centre for Nanoscale Biophotonics Macquarie University Sydney 2109 Australia
| | - Miyako Nakano
- Department of Molecular Sciences and Biomolecular Discovery and Design Research Centre (BDDRC) Macquarie University Sydney 2109 Australia
- Graduate School of Advanced Sciences of Matter Hiroshima University Hiroshima 739‐8527 Japan
| | - Saulo Recuero
- Laboratório de Investigação Médica da Disciplina de Urologia (LIM55) Faculdade de Medicina da FMUSP Universidade de Sao Paulo São Paulo 01000 Brazil
| | - Manveen K. Sethi
- Department of Molecular Sciences and Biomolecular Discovery and Design Research Centre (BDDRC) Macquarie University Sydney 2109 Australia
- Center for Biomedical Mass Spectrometry Department of Biochemistry Boston University School of Medicine Boston University Boston MA 02215 USA
| | - Miguel Srougi
- Laboratório de Investigação Médica da Disciplina de Urologia (LIM55) Faculdade de Medicina da FMUSP Universidade de Sao Paulo São Paulo 01000 Brazil
| | - Kathrin Stavenhagen
- Department of Molecular Sciences and Biomolecular Discovery and Design Research Centre (BDDRC) Macquarie University Sydney 2109 Australia
- Beth Israel Deaconess Medical Center Department of Surgery and Harvard Medical School Center for Glycoscience Harvard Medical School Boston MA 02215 USA
| | - Vignesh Venkatakrishnan
- Department of Rheumatology and Inflammation Research Institute of Medicine, Sahlgrenska Academy University of Gothenburg Gothenburg SE 405 30 Sweden
| | - Katherine Wongtrakul‐Kish
- Department of Molecular Sciences and Biomolecular Discovery and Design Research Centre (BDDRC) Macquarie University Sydney 2109 Australia
- Bioprocessing Technology Institute A*STAR Singapore 13862 Singapore
| | - Simone Diestel
- Institute of Nutrition and Food Sciences University of Bonn Bonn 53127 Germany
| | - Peter Hoffmann
- Future Industries Institute Mawson Lakes Campus, University of South Australia Adelaide 5005 Australia
| | - Niclas G. Karlsson
- Department of Medical Biochemistry and Cell Biology Institute of Biomedicine, Sahlgrenska Academy University of Gothenburg Gothenburg SE 405 30 Sweden
| | - Daniel Kolarich
- Institute for Glycomics, Griffith University Gold Coast 4222 Australia
| | - Mark P. Molloy
- Department of Molecular Sciences and Biomolecular Discovery and Design Research Centre (BDDRC) Macquarie University Sydney 2109 Australia
- Faculty of Medicine and Health Sydney School of Medicine Royal North Shore Hospital Sydney 2065 Australia
| | - Michael H. Muders
- Rudolf‐Becker‐Laboratory Institute of Pathology University Hospital Bonn Bonn 53127 Germany
| | - Martin K. Oehler
- Department of Gynaecological Oncology Royal Adelaide Hospital Adelaide 5000 Australia
| | - Nicolle H. Packer
- Department of Molecular Sciences and Biomolecular Discovery and Design Research Centre (BDDRC) Macquarie University Sydney 2109 Australia
- Institute for Glycomics, Griffith University Gold Coast 4222 Australia
- ARC Centre for Nanoscale Biophotonics Macquarie University Sydney 2109 Australia
| | - Giuseppe Palmisano
- Department of Parasitology, Institute of Biomedical Sciences University of São Paulo São Paulo 01000 Brazil
| | - Morten Thaysen‐Andersen
- Department of Molecular Sciences and Biomolecular Discovery and Design Research Centre (BDDRC) Macquarie University Sydney 2109 Australia
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12
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Bacteriophage T4 capsid as a nanocarrier for Peptide-N-Glycosidase F immobilization through self-assembly. Sci Rep 2019; 9:4865. [PMID: 30890747 PMCID: PMC6424964 DOI: 10.1038/s41598-019-41378-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 02/13/2019] [Indexed: 11/12/2022] Open
Abstract
Enzyme immobilization is widely applied in biocatalysis to improve stability and facilitate recovery and reuse of enzymes. However, high cost of supporting materials and laborious immobilization procedures has limited its industrial application and commercialization. In this study, we report a novel self-assembly immobilization system using bacteriophage T4 capsid as a nanocarrier. The system utilizes the binding sites of the small outer capsid protein, Soc, on the T4 capsid. Enzymes as Soc fusions constructed with regular molecular cloning technology expressed at the appropriate time during phage assembly and self-assembled onto the capsids. The proof of principle experiment was carried out by immobilizing β-galactosidase, and the system was successfully applied to the immobilization of an important glycomics enzyme, Peptide-N-Glycosidase F. Production of Peptide-N-Glycosidase F and simultaneous immobilization was finished within seven hours. Characterizations of the immobilized Peptide-N-Glycosidase F indicated high retention of activity and well reserved deglycosylation capacity. The immobilized Peptide-N-Glycosidase F was easily recycled by centrifugation and exhibited good stability that sustained five repeated uses. This novel system uses the self-amplified T4 capsid as the nanoparticle-type of supporting material, and operates with a self-assembly procedure, making it a simple and low-cost enzyme immobilization technology with promising application potentials.
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13
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Xu X, Chen F, Huang Z, Ma L, Chen L, Pan Y, Xu J, Kim S, Kinane D, Koo H, Zhou X. Meeting report: a close look at oral biofilms and microbiomes. Int J Oral Sci 2018; 10:28. [PMID: 30111787 PMCID: PMC6093876 DOI: 10.1038/s41368-018-0030-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 06/24/2018] [Indexed: 02/05/2023] Open
Abstract
The "Biofilms, Microbiomes and Oral Diseases: Challenges and Future Perspectives" symposium jointly organized by Penn Dental Medicine and West China School of Stomatology was held on 30 September 2017 at Penn Wharton China Center (PWCC) in Beijing, China. The topics included the pathogenicity of oral biofilms, novel strategies for the control of biofilm-related diseases, oral microbiome and single-cell approaches, and the link between oral diseases and overall health. Researchers from a number of disciplines, representing institutions from China and Penn Dental Medicine, gathered to discuss advances in our understanding of biofilms, as well as future directions for the control of biofilm-related oral and systemic diseases.
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Affiliation(s)
- Xin Xu
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Department of Cariology and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Feng Chen
- Central Laboratory, Peking University School and Hospital of Stomatology, Beijing, China
| | - Zhengwei Huang
- Department of Endodontics, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lvyan Ma
- State Key Laboratory of Microbial Resources Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Li Chen
- Key Laboratory of Medical Molecular Virology, Ministry of Education and Health, Fudan University, Shanghai, China
| | - Yaping Pan
- Department of Periodontics, School of Stomatology, Chinese Medical University, Shenyang, China
| | - Jian Xu
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Syngcuk Kim
- Department of Endodontics, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Denis Kinane
- Department of Periodontics, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Hyun Koo
- Divisions of Pediatric Dentistry and Community Oral Health, Department of Orthodontics, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Xuedong Zhou
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Department of Cariology and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China.
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14
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Uversky VN, El-Baky NA, El-Fakharany EM, Sabry A, Mattar EH, Uversky AV, Redwan EM. Functionality of intrinsic disorder in tumor necrosis factor-α and its receptors. FEBS J 2017; 284:3589-3618. [PMID: 28746777 DOI: 10.1111/febs.14182] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 06/15/2017] [Accepted: 07/20/2017] [Indexed: 01/02/2023]
Affiliation(s)
- Vladimir N. Uversky
- Department of Biological Sciences; Faculty of Sciences; King Abdulaziz University; Jeddah Saudi Arabia
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute; Morsani College of Medicine; University of South Florida; Tampa FL USA
- Institute for Biological Instrumentation; Russian Academy of Sciences; Pushchino, Moscow Region Russia
| | - Nawal Abd El-Baky
- Protective Proteins Laboratory; Protein Research Department; Genetic Engineering and Biotechnology Research Institute; City for Scientific Research and Technology Applications; New Borg EL-Arab, Alexandria Egypt
| | - Esmail M. El-Fakharany
- Protective Proteins Laboratory; Protein Research Department; Genetic Engineering and Biotechnology Research Institute; City for Scientific Research and Technology Applications; New Borg EL-Arab, Alexandria Egypt
| | - Amira Sabry
- Protective Proteins Laboratory; Protein Research Department; Genetic Engineering and Biotechnology Research Institute; City for Scientific Research and Technology Applications; New Borg EL-Arab, Alexandria Egypt
| | - Ehab H. Mattar
- Department of Biological Sciences; Faculty of Sciences; King Abdulaziz University; Jeddah Saudi Arabia
| | - Alexey V. Uversky
- Center for Data Analytics and Biomedical Informatics; Department of Computer and Information Sciences; College of Science and Technology; Temple University; Philadelphia PA USA
| | - Elrashdy M. Redwan
- Department of Biological Sciences; Faculty of Sciences; King Abdulaziz University; Jeddah Saudi Arabia
- Protective Proteins Laboratory; Protein Research Department; Genetic Engineering and Biotechnology Research Institute; City for Scientific Research and Technology Applications; New Borg EL-Arab, Alexandria Egypt
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15
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Hennigan K, Conroy PJ, Walsh MT, Amin M, O'Kennedy R, Ramasamy P, Gleich GJ, Siddiqui Z, Glynn S, McCabe O, Mooney C, Harvey BJ, Costello RW, McBryan J. Eosinophil peroxidase activates cells by HER2 receptor engagement and β1-integrin clustering with downstream MAPK cell signaling. Clin Immunol 2016; 171:1-11. [PMID: 27519953 PMCID: PMC5070911 DOI: 10.1016/j.clim.2016.08.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 08/02/2016] [Accepted: 08/06/2016] [Indexed: 01/21/2023]
Abstract
Eosinophils account for 1–3% of peripheral blood leukocytes and accumulate at sites of allergic inflammation, where they play a pathogenic role. Studies have shown that treatment with mepolizumab (an anti-IL-5 monoclonal antibody) is beneficial to patients with severe eosinophilic asthma, however, the mechanism of precisely how eosinophils mediate these pathogenic effects is uncertain. Eosinophils contain several cationic granule proteins, including Eosinophil Peroxidase (EPO). The main significance of this work is the discovery of EPO as a novel ligand for the HER2 receptor. Following HER2 activation, EPO induces activation of FAK and subsequent activation of β1-integrin, via inside-out signaling. This complex results in downstream activation of ERK1/2 and a sustained up regulation of both MUC4 and the HER2 receptor. These data identify a receptor for one of the eosinophil granule proteins and demonstrate a potential explanation of the proliferative effects of eosinophils. Eosinophil peroxidase (EPO) is confirmed as a ligand for the HER2 receptor. EPO activation of HER2 leads to activation of FAK, ERK and β1 integrin. EPO induces a sustained upregulation of MUC4 and HER2. Possible mechanism for the proliferative effects of eosinophils is uncovered.
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Affiliation(s)
- Kerrie Hennigan
- Department of Medicine Respiratory Research Division, Royal College of Surgeons in Ireland, Beaumont Hospital, Dublin 9, Ireland
| | - Paul J Conroy
- Biomedical Diagnostics Institute, Dublin City University, Dublin 9, Ireland
| | - Marie-Therese Walsh
- Department of Medicine Respiratory Research Division, Royal College of Surgeons in Ireland, Beaumont Hospital, Dublin 9, Ireland
| | - Mohamed Amin
- Department of Medicine Respiratory Research Division, Royal College of Surgeons in Ireland, Beaumont Hospital, Dublin 9, Ireland
| | - Richard O'Kennedy
- Biomedical Diagnostics Institute, Dublin City University, Dublin 9, Ireland
| | - Patmapriya Ramasamy
- Department of Medicine Respiratory Research Division, Royal College of Surgeons in Ireland, Beaumont Hospital, Dublin 9, Ireland
| | - Gerald J Gleich
- Department of Dermatology, University of Utah, Salt Lake City, USA
| | - Zeshan Siddiqui
- Graduate Entry Medical School, University of Limerick, Ireland
| | - Senan Glynn
- Department of Medicine Respiratory Research Division, Royal College of Surgeons in Ireland, Beaumont Hospital, Dublin 9, Ireland
| | - Olive McCabe
- Department of Molecular Medicine, Royal College of Surgeons in Ireland, Beaumont Hospital, Dublin 9, Ireland
| | - Catherine Mooney
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - Brian J Harvey
- Department of Molecular Medicine, Royal College of Surgeons in Ireland, Beaumont Hospital, Dublin 9, Ireland
| | - Richard W Costello
- Department of Medicine Respiratory Research Division, Royal College of Surgeons in Ireland, Beaumont Hospital, Dublin 9, Ireland.
| | - Jean McBryan
- Department of Molecular Medicine, Royal College of Surgeons in Ireland, Beaumont Hospital, Dublin 9, Ireland
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16
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Weng Y, Sui Z, Jiang H, Shan Y, Chen L, Zhang S, Zhang L, Zhang Y. Releasing N-glycan from peptide N-terminus by N-terminal succinylation assisted enzymatic deglycosylation. Sci Rep 2015; 5:9770. [PMID: 25902405 PMCID: PMC4405948 DOI: 10.1038/srep09770] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Accepted: 03/18/2015] [Indexed: 01/13/2023] Open
Abstract
Due to the important roles of N-glycoproteins in various biological processes, the global N-glycoproteome analysis has been paid much attention. However, by current strategies for N-glycoproteome profiling, peptides with glycosylated Asn at N-terminus (PGANs), generated by protease digestion, could hardly be identified, due to the poor deglycosylation capacity by enzymes. However, theoretically, PGANs occupy 10% of N-glycopeptides in the typical tryptic digests. Therefore, in this study, we developed a novel strategy to identify PGANs by releasing N-glycans through the N-terminal site-selective succinylation assisted enzymatic deglycosylation. The obtained PGANs information is beneficial to not only achieve the deep coverage analysis of glycoproteomes, but also discover the new biological functions of such modification.
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Affiliation(s)
- Yejing Weng
- 1] Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R. &A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China [2] University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhigang Sui
- Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R. &A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Hao Jiang
- 1] Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R. &A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China [2] University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yichu Shan
- Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R. &A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Lingfan Chen
- 1] Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R. &A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China [2] University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shen Zhang
- 1] Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R. &A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China [2] University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lihua Zhang
- Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R. &A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Yukui Zhang
- Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R. &A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
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17
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Mass Production of an Active Peptide-N-Glycosidase F Using Silkworm-Baculovirus Expression System. Mol Biotechnol 2015; 57:735-45. [DOI: 10.1007/s12033-015-9866-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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18
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Koonin EV, Dolja VV, Krupovic M. Origins and evolution of viruses of eukaryotes: The ultimate modularity. Virology 2015; 479-480:2-25. [PMID: 25771806 PMCID: PMC5898234 DOI: 10.1016/j.virol.2015.02.039] [Citation(s) in RCA: 321] [Impact Index Per Article: 35.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Revised: 02/19/2015] [Accepted: 02/20/2015] [Indexed: 01/04/2023]
Abstract
Viruses and other selfish genetic elements are dominant entities in the biosphere, with respect to both physical abundance and genetic diversity. Various selfish elements parasitize on all cellular life forms. The relative abundances of different classes of viruses are dramatically different between prokaryotes and eukaryotes. In prokaryotes, the great majority of viruses possess double-stranded (ds) DNA genomes, with a substantial minority of single-stranded (ss) DNA viruses and only limited presence of RNA viruses. In contrast, in eukaryotes, RNA viruses account for the majority of the virome diversity although ssDNA and dsDNA viruses are common as well. Phylogenomic analysis yields tangible clues for the origins of major classes of eukaryotic viruses and in particular their likely roots in prokaryotes. Specifically, the ancestral genome of positive-strand RNA viruses of eukaryotes might have been assembled de novo from genes derived from prokaryotic retroelements and bacteria although a primordial origin of this class of viruses cannot be ruled out. Different groups of double-stranded RNA viruses derive either from dsRNA bacteriophages or from positive-strand RNA viruses. The eukaryotic ssDNA viruses apparently evolved via a fusion of genes from prokaryotic rolling circle-replicating plasmids and positive-strand RNA viruses. Different families of eukaryotic dsDNA viruses appear to have originated from specific groups of bacteriophages on at least two independent occasions. Polintons, the largest known eukaryotic transposons, predicted to also form virus particles, most likely, were the evolutionary intermediates between bacterial tectiviruses and several groups of eukaryotic dsDNA viruses including the proposed order "Megavirales" that unites diverse families of large and giant viruses. Strikingly, evolution of all classes of eukaryotic viruses appears to have involved fusion between structural and replicative gene modules derived from different sources along with additional acquisitions of diverse genes.
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Affiliation(s)
- Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
| | - Valerian V Dolja
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA.
| | - Mart Krupovic
- Institut Pasteur, Unité Biologie Moléculaire du Gène chez les Extrêmophiles, Department of Microbiology, Paris 75015, France.
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19
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Sun G, Yu X, Bao C, Wang L, Li M, Gan J, Qu D, Ma J, Chen L. Identification and characterization of a novel prokaryotic peptide: N-glycosidase from Elizabethkingia meningoseptica. J Biol Chem 2015; 290:7452-62. [PMID: 25614628 DOI: 10.1074/jbc.m114.605493] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Peptide:N-glycosidase (PNGase) F, the first PNGase identified in prokaryotic cells, catalyzes the removal of intact asparagine-linked oligosaccharide chains from glycoproteins and/or glycopeptides. Since its discovery in 1984, PNGase F has remained as the sole prokaryotic PNGase. Recently, a novel gene encoding a protein with a predicted PNGase domain was identified from a clinical isolate of Elizabethkingia meningoseptica. In this study, the candidate protein was expressed in vitro and was subjected to biochemical and structural analyses. The results revealed that it possesses PNGase activity and has substrate specificity different from that of PNGase F. The crystal structure of the protein was determined at 1.9 Å resolution. Structural comparison with PNGase F revealed a relatively larger glycan-binding groove in the catalytic domain and an additional bowl-like domain with unknown function at the N terminus of the candidate protein. These structural and functional analyses indicated that the candidate protein is a novel prokaryotic N-glycosidase. The protein has been named PNGase F-II.
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Affiliation(s)
- Guiqin Sun
- From the Key Laboratory of Medical Molecular Virology, Ministry of Education and Health, Shanghai Medical College, Fudan University, Shanghai 200032, China, Zhejiang Chinese Medical University, Hangzhou 310053, China
| | - Xiang Yu
- the State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Celimuge Bao
- From the Key Laboratory of Medical Molecular Virology, Ministry of Education and Health, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Lei Wang
- From the Key Laboratory of Medical Molecular Virology, Ministry of Education and Health, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Meng Li
- From the Key Laboratory of Medical Molecular Virology, Ministry of Education and Health, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Jianhua Gan
- the Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200433, China, and
| | - Di Qu
- From the Key Laboratory of Medical Molecular Virology, Ministry of Education and Health, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Jinbiao Ma
- the State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, China,
| | - Li Chen
- From the Key Laboratory of Medical Molecular Virology, Ministry of Education and Health, Shanghai Medical College, Fudan University, Shanghai 200032, China,
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20
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Jacobsen J, Wind SL, Rasholt EL, van den Brink JM. N-Glycosidase F improves gel firmness in fermented milk products. Int Dairy J 2014. [DOI: 10.1016/j.idairyj.2013.12.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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21
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Wang Y, Zhou X, Yu Q, Duan Y, Huang B, Hong G, Zhou A, Jin L. Prestaining of glycoproteins in sodium dodecyl sulfate polyacrylamide gels by dansylhydrazine. Proteomics 2014; 14:1322-7. [DOI: 10.1002/pmic.201300532] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2013] [Revised: 02/18/2014] [Accepted: 03/18/2014] [Indexed: 01/12/2023]
Affiliation(s)
- Yang Wang
- Department of histology and embryology; Institute of neuroscience; Wenzhou Medical University; Wenzhou Zhejiang P. R. China
| | - Xuan Zhou
- Zhejiang Provincial Key Laboratory of Biopharmaceuticals; Wenzhou Medical University; Wenzhou Zhejiang P. R. China
- Ningbo First Hospital; Ningbo Zhejiang P. R. China
| | - Qing Yu
- Zhejiang Provincial Key Laboratory of Biopharmaceuticals; Wenzhou Medical University; Wenzhou Zhejiang P. R. China
| | - Yuanmeng Duan
- Zhejiang Provincial Key Laboratory of Biopharmaceuticals; Wenzhou Medical University; Wenzhou Zhejiang P. R. China
| | - Binbin Huang
- Zhejiang Provincial Key Laboratory of Biopharmaceuticals; Wenzhou Medical University; Wenzhou Zhejiang P. R. China
| | - Guoying Hong
- Zhejiang Provincial Key Laboratory of Biopharmaceuticals; Wenzhou Medical University; Wenzhou Zhejiang P. R. China
- Wenzhou Undersun Biotechnology Co., Ltd; Wenzhou Zhejiang P. R. China
| | - Ayi Zhou
- Department of histology and embryology; Institute of neuroscience; Wenzhou Medical University; Wenzhou Zhejiang P. R. China
| | - Litai Jin
- Zhejiang Provincial Key Laboratory of Biopharmaceuticals; Wenzhou Medical University; Wenzhou Zhejiang P. R. China
- Wenzhou Undersun Biotechnology Co., Ltd; Wenzhou Zhejiang P. R. China
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22
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Zhou X, Hong GY, Huang BB, Duan YM, Shen JY, Ni MW, Cong WT, Jin LT. Improved conditions for periodate/Schiff's base-based fluorescent staining of glycoproteins with dansylhydrazine in SDS-PAGE. Electrophoresis 2014; 35:1439-47. [DOI: 10.1002/elps.201300595] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Revised: 02/13/2014] [Accepted: 02/24/2014] [Indexed: 11/05/2022]
Affiliation(s)
- Xuan Zhou
- Zhejiang Provincial Key Laboratory of Biopharmaceuticals; Wenzhou Medical University; Wenzhou Zhejiang P. R. China
- Ningbo First Hospital; Ningbo Zhejiang P. R. China
| | - Guo-Ying Hong
- Zhejiang Provincial Key Laboratory of Biopharmaceuticals; Wenzhou Medical University; Wenzhou Zhejiang P. R. China
- Wenzhou Undersun Biotechnology Co., Ltd; Wenzhou Zhejiang P. R. China
| | - Bin-Bin Huang
- Zhejiang Provincial Key Laboratory of Biopharmaceuticals; Wenzhou Medical University; Wenzhou Zhejiang P. R. China
| | - Yuan-Meng Duan
- Zhejiang Provincial Key Laboratory of Biopharmaceuticals; Wenzhou Medical University; Wenzhou Zhejiang P. R. China
| | - Jia-Yi Shen
- Zhejiang Provincial Key Laboratory of Biopharmaceuticals; Wenzhou Medical University; Wenzhou Zhejiang P. R. China
| | - Mao-Wei Ni
- Zhejiang Provincial Key Laboratory of Biopharmaceuticals; Wenzhou Medical University; Wenzhou Zhejiang P. R. China
| | - Wei-Tao Cong
- Zhejiang Provincial Key Laboratory of Biopharmaceuticals; Wenzhou Medical University; Wenzhou Zhejiang P. R. China
- Wenzhou Undersun Biotechnology Co., Ltd; Wenzhou Zhejiang P. R. China
| | - Li-Tai Jin
- Zhejiang Provincial Key Laboratory of Biopharmaceuticals; Wenzhou Medical University; Wenzhou Zhejiang P. R. China
- Wenzhou Undersun Biotechnology Co., Ltd; Wenzhou Zhejiang P. R. China
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23
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Bolduan S, Hubel P, Reif T, Lodermeyer V, Höhne K, Fritz JV, Sauter D, Kirchhoff F, Fackler OT, Schindler M, Schubert U. HIV-1 Vpu affects the anterograde transport and the glycosylation pattern of NTB-A. Virology 2013; 440:190-203. [PMID: 23528733 DOI: 10.1016/j.virol.2013.02.021] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Revised: 02/22/2013] [Accepted: 02/25/2013] [Indexed: 02/07/2023]
Abstract
HIV-1 Vpu induces downregulation of cell surface NTB-A to evade lysis of HIV-1 infected cells by NK cells. Here we show that Vpu affects the anterograde transport and the glycosylation pattern of NTB-A by a mechanism that is distinct from the Vpu induced downregulation of CD4 and tetherin. In the presence of Vpu, only the high mannose form of NTB-A was detectable, suggesting that Vpu prevented the formation of the mature form of NTB-A. This phenomenon is associated with the ability of Vpu to downregulate cell surface NTB-A by retention of NTB-A within the Golgi-compartment. Furthermore, the Vpu-mediated effect on NTB-A glycosylation is highly conserved among Vpu proteins derived from HIV-1 and SIV and corresponds to the level of downregulation of NTB-A. Together, these results suggest that the reduction of NTB-A from the cell surface is associated with the Vpu-mediated effect on the glycosylation pattern of newly synthesized NTB-A molecules.
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24
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Zhao G, Li G, Zhou X, Matsuo I, Ito Y, Suzuki T, Lennarz WJ, Schindelin H. Structural and mutational studies on the importance of oligosaccharide binding for the activity of yeast PNGase. Glycobiology 2009; 19:118-25. [PMID: 18854368 PMCID: PMC2722417 DOI: 10.1093/glycob/cwn108] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Peptide:N-glycanase (PNGase) is an important component of the endoplasmic reticulum-associated protein degradation pathway in which it de-glycosylates misfolded glycoproteins, thus facilitating their proteasomal degradation. PNGase belongs to the transglutaminase superfamily and features a Cys, His, and Asp catalytic triad, which is essential for its enzymatic activity. An elongated substrate-binding groove centered on the active site Cys191 was visualized in the crystal structure of apo-PNGase, whereas its complex with Z-VAD-fmk, a peptide-based inhibitor of PNGase, revealed that the inhibitor occupied one end of the substrate-binding groove while being covalently linked to the active site Cys. Recently, haloacetamidyl-containing carbohydrate-based inhibitors of PNGase were developed and shown to specifically label the active site Cys. In this study, we describe the crystal structure of yeast PNGase in complex with N,N'-diacetylchitobiose (chitobiose). We found that the chitobiose binds on the side opposite to the peptide binding site with the active site Cys191 being located approximately midway between the carbohydrate and peptide binding sites. Mutagenesis studies confirm the critical role of the chitobiose-interacting residues in substrate binding and suggest that efficient oligosaccharide binding is required for PNGase activity. In addition, the N-terminus of a symmetry-related PNGase was found to bind to the proposed peptide-binding site of PNGase. Together with the bound chitobiose, this enables us to propose a model for glycoprotein binding to PNGase. Finally, deleting the C-terminal residues of yeast PNGase, which are disordered in all structures of this enzyme, results in a significant reduction in enzyme activity, indicating that these residues might be involved in binding of the mannose residues of the glycan chain.
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Affiliation(s)
- Gang Zhao
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA
| | - Guangtao Li
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA
| | - Xiaoke Zhou
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA
| | - Ichiro Matsuo
- RIKEN (The Institute of Physical and Chemical Research), 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Yukishige Ito
- RIKEN (The Institute of Physical and Chemical Research), 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | | | - William J Lennarz
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA
| | - Hermann Schindelin
- To whom correspondence should be addressed: Tel: +49-931-201-48320; Fax: +49-931-201-48309; e-mail:
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25
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Royle L, Dwek RA, Rudd PM. Determining the structure of oligosaccharides N- and O-linked to glycoproteins. CURRENT PROTOCOLS IN PROTEIN SCIENCE 2006; Chapter 12:12.6.1-12.6.45. [PMID: 18429295 DOI: 10.1002/0471140864.ps1206s43] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Many proteins involved in biological events are glycosylated. A glycoprotein consists of a mixture of glycosylation variants of a single polypeptide chain, known as glycoforms. It has become clear that a detailed understanding of the roles which glycosylation plays in the biosynthesis, transport, biological function, and degradation of a glycoprotein can only be achieved when the protein and sugar(s) are viewed as an entity. Many glycoproteins can now be modeled by combining glycan sequencing data and oligosaccharide structural information with protein structural data. Pivotal to this approach is sensitive, state-of-the-art oligosaccharide sequencing technology which can give a rapid insight into the glycosylation of a glycoprotein without the need for sophisticated equipment and expertise. This unit gives a detailed introduction into the analysis of glycans, and the many figures will help the user identify which type of experiment needs to be undertaken. Methods for releasing glycans from glycoproteins are followed by protocols for labeling and purifying (by HPLC) the glycans from the rest of the components. Strategies for N- and O-glycan analysis are also included.
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26
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Benson SD, Bamford JKH, Bamford DH, Burnett RM. Does common architecture reveal a viral lineage spanning all three domains of life? Mol Cell 2005; 16:673-85. [PMID: 15574324 DOI: 10.1016/j.molcel.2004.11.016] [Citation(s) in RCA: 182] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Our discovery that the major coat protein of bacteriophage PRD1 resembles that of human adenovirus raised the unexpected possibility that viruses infecting bacteria could be related by evolution to those infecting animal hosts. We first review the development of this idea. We then describe how we have used structure-based modeling to show that several other viruses with no detectable sequence similarity are likely to have coats constructed from similar proteins-the "double-barrel trimer." There is evidence that the group includes a diversity of viruses infecting very different hosts in all three domains of life: Eukarya; Bacteria; and Archaea that diverged billions of years ago. The current classification of viruses obscures such similarities. We propose that the occurrence of a double-barrel trimer coat protein in an icosahedral dsDNA virus with large facets, irrespective of its host, is a very strong indicator of its membership in a lineage of viruses with a common ancestor.
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Affiliation(s)
- Stacy D Benson
- The Wistar Institute, 3601 Spruce Street, Philadelphia, Pennsylvania 19104, USA
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27
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Hirsch C, Misaghi S, Blom D, Pacold ME, Ploegh HL. Yeast N-glycanase distinguishes between native and non-native glycoproteins. EMBO Rep 2004; 5:201-6. [PMID: 14726951 PMCID: PMC1298977 DOI: 10.1038/sj.embor.7400066] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2003] [Revised: 11/20/2003] [Accepted: 11/20/2003] [Indexed: 11/09/2022] Open
Abstract
N-glycanase from Saccharomyces cerevisiae (Png1) preferentially removes N-glycans from misfolded proteins. The ability of Png1 to distinguish between folded and misfolded glycoproteins is reminiscent of substrate recognition by UDP-glucose glycoprotein glucosyl transferase, an enzyme that possesses this trait. The only known in vivo substrates of Png1 are aberrant glycoproteins that originate in the endoplasmic reticulum, and arrive in the cytoplasm for proteasomal degradation. The substrate specificity of Png1 is admirably suited for this task.
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Affiliation(s)
- Christian Hirsch
- Department of Pathology, Harvard Medical School, 200 Longwood Avenue, Boston, Massachusetts, USA
| | - Shahram Misaghi
- Department of Pathology, Harvard Medical School, 200 Longwood Avenue, Boston, Massachusetts, USA
| | - Daniël Blom
- Department of Pathology, Harvard Medical School, 200 Longwood Avenue, Boston, Massachusetts, USA
| | - Michael E Pacold
- Department of Pathology, Harvard Medical School, 200 Longwood Avenue, Boston, Massachusetts, USA
| | - Hidde L Ploegh
- Department of Pathology, Harvard Medical School, 200 Longwood Avenue, Boston, Massachusetts, USA
- Tel: +1 617 432 4776; Fax: +1 617 432 4775; E-mail:
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28
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Loo T, Patchett ML, Norris GE, Lott JS. Using secretion to solve a solubility problem: high-yield expression in Escherichia coli and purification of the bacterial glycoamidase PNGase F. Protein Expr Purif 2002; 24:90-8. [PMID: 11812228 DOI: 10.1006/prep.2001.1555] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
PNGase F is a widely used deglycosidase, secreted in small amounts by the gram-negative bacterium Flavobacterium meningosepticum. We have designed a T7 promoter-based Escherichia coli expression system to provide a high-yield source of recombinant enzyme. When expressed intracellularly, the enzyme was produced in a largely insoluble state. However, when expressed as a fusion with the leader sequence from the ompA gene, hexahistidine-tagged PNGase F was efficiently processed and exported to the E. coli periplasm. Single-step purification using immobilized metal affinity chromatography yielded 8 mg of pure enzyme per liter of culture, which is fully active on a range of protein and peptide substrates.
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Affiliation(s)
- Trevor Loo
- Institute of Molecular Biosciences, Massey University, Private Bag 11-222, Palmerston North, New Zealand
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29
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Zhou X, Alber F, Folkers G, Gonnet GH, Chelvanayagam G. An analysis of the helix-to-strand transition between peptides with identical sequence. Proteins 2000; 41:248-56. [PMID: 10966577 DOI: 10.1002/1097-0134(20001101)41:2<248::aid-prot90>3.0.co;2-j] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
An analysis of peptide segments with identical sequence but that differ significantly in structure was performed over non-redundant databases of protein structures. We focus on those peptides, which fold into an alpha-helix in one protein but a beta-strand in another. While the study shows that many such structurally ambivalent peptides contain amino acids with a strong helical preference collocated with amino acids with a strong strand preference, the results overwhelmingly indicate that the peptide's environment ultimately dictates its structure. Furthermore, the first naturally occurring structurally ambivalent nonapeptide from evolutionary unrelated proteins is described, highlighting the intrinsic plasticity of peptide sequences. We even find seven proteins that show structural ambivalence under different conditions. Finally, a computer algorithm has been implemented to identify regions in a given sequence where secondary structure prediction programs are likely to make serious mispredictions.
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Affiliation(s)
- X Zhou
- Department of Computer Science, Eidgenössische Technische Hochshule, Zürich, Switzerland
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30
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Ferro V, Weiler L, Withers SG. Convergent synthesis of a fluorescence-quenched glycopeptide as a potential substrate for peptide: N-glycosidases. Carbohydr Res 1998. [DOI: 10.1016/s0008-6215(98)00011-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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31
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Abstract
Structural trees for large protein superfamilies, such as beta proteins with the aligned beta sheet packing, beta proteins with the orthogonal packing of alpha helices, two-layer and three-layer alpha/beta proteins, have been constructed. The structural motifs having unique overall folds and a unique handedness are taken as root structures of the trees. The larger protein structures of each superfamily are obtained by a stepwise addition of alpha helices and/or beta strands to the corresponding root motif, taking into account a restricted set of rules inferred from known principles of the protein structure. Among these rules, prohibition of crossing connections, attention to handedness and compactness, and a requirement for alpha helices to be packed in alpha-helical layers and beta strands in beta layers are the most important. Proteins and domains whose structures can be obtained by stepwise addition of alpha helices and/or beta strands to the same root motif can be grouped into one structural class or a superfamily. Proteins and domains found within branches of a structural tree can be grouped into subclasses or subfamilies. Levels of structural similarity between different proteins can easily be observed by visual inspection. Within one branch, protein structures having a higher position in the tree include the structures located lower. Proteins and domains of different branches have the structure located in the branching point as the common fold.
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Affiliation(s)
- A V Efimov
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region.
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32
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Romero A, Varela PF, Sanz L, Töpfer-Petersen E, Calvete JJ. Crystallization and preliminary X-ray diffraction analysis of boar seminal plasma spermadhesin PSP-I/PSP-II, a heterodimer of two CUB domains. FEBS Lett 1996; 382:15-7. [PMID: 8612739 DOI: 10.1016/0014-5793(96)00133-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Boar spermadhesin PSP-I/PSP-II (M(r) 29 000-30 000), a non-covalent heterodimer of two CUB domains, was crystallized in two crystal forms. Complete diffraction data sets for hexagonal (space group P6(1,5)22) and trigonal (space group P3(1,2)21) crystals have been collected up to 2.9 and 2.5 angstrom resolution, respectively. Cell constants of the hexagonal and trigonal crystal forms are a=b=87.2 angstrom, c=152.4 angstrom, and a=b=96.2 angstrom, c=70.8 angstrom, respectively. The calculated packing parameters (Vm) are 2.8 and 3.2 angstrom(3)/DA for the hexagonal and trigonal crystal forms, respectively, indicating that, in both cases, the asymmetric unit is constituted by one PSP-I/PSP-II heterodimer. This paper reports the first crystals of a protein built up by a CUB domain architecture.
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Affiliation(s)
- A Romero
- Instituto de Química-Física 'Rocasolano' C.S.I.C., Madrid, Spain
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33
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Leonidas DD, Elbert BL, Zhou Z, Leffler H, Ackerman SJ, Acharya KR. Crystal structure of human Charcot-Leyden crystal protein, an eosinophil lysophospholipase, identifies it as a new member of the carbohydrate-binding family of galectins. Structure 1995; 3:1379-93. [PMID: 8747464 DOI: 10.1016/s0969-2126(01)00275-1] [Citation(s) in RCA: 111] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
BACKGROUND The Charcot-Leyden crystal (CLC) protein is a major autocrystallizing constituent of human eosinophils and basophils, comprising approximately 10% of the total cellular protein in these granulocytes. Identification of the distinctive hexagonal bipyramidal crystals of CLC protein in body fluids and secretions has long been considered a hallmark of eosinophil-associated allergic inflammation. Although CLC protein possesses lysophospholipase activity, its role(s) in eosinophil or basophil function or associated inflammatory responses has remained speculative. RESULTS The crystal structure of the CLC protein has been determined at 1.8 A resolution using X-ray crystallography. The overall structural fold of CLC protein is highly similar to that of galectins -1 and -2, members of an animal lectin family formerly classified as S-type or S-Lac (soluble lactose-binding) lectins. This is the first structure of an eosinophil protein to be determined and the highest resolution structure so far determined for any member of the galectin family. CONCLUSIONS The CLC protein structure possesses a carbohydrate-recognition domain comprising most, but not all, of the carbohydrate-binding residues that are conserved among the galectins. The protein exhibits specific (albeit weak) carbohydrate-binding activity for simple saccharides including N-acetyl-D-glucosamine and lactose. Despite CLC protein having no significant sequence or structural similarities to other lysophospholipase catalytic triad has also been identified within the CLC structure, making it a unique dual-function polypeptide. These structural findings suggest a potential intracellular and/or extracellular role(s) for the galectin-associated activities of CLC protein in eosinophil and basophil function in allergic diseases and inflammation.
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Affiliation(s)
- D D Leonidas
- School of Biology and Biochemistry, University of Bath, Claverton Down, UK
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34
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Kuhn P, Guan C, Cui T, Tarentino AL, Plummer TH, Van Roey P. Active site and oligosaccharide recognition residues of peptide-N4-(N-acetyl-beta-D-glucosaminyl)asparagine amidase F. J Biol Chem 1995; 270:29493-7. [PMID: 7493989 DOI: 10.1074/jbc.270.49.29493] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Crystallographic analysis and site-directed mutagenesis have been used to identify the catalytic and oligosaccharide recognition residues of peptide-N4-(N-acetyl-beta-D-glucosaminyl)asparagine amidase F (PNGase F), an amidohydrolase that removes intact asparagine-linked oligosaccharide chains from glycoproteins and glycopeptides. Mutagenesis has shown that three acidic residues, Asp-60, Glu-206, and Glu-118, that are located in a cleft at the interface between the two domains of the protein are essential for activity. The D60N mutant has no detectable activity, while E206Q and E118Q have less than 0.01 and 0.1% of the wild-type activity, respectively. Crystallographic analysis, at 2.0-A resolution, of the complex of the wild-type enzyme with the product, N,N'-diacetylchitobiose, shows that Asp-60 is in direct contact with the substrate at the cleavage site, while Glu-206 makes contact through a bridging water molecule. This indicates that Asp-60 is the primary catalytic residue, while Glu-206 probably is important for stabilization of reaction intermediates. Glu-118 forms a hydrogen bond with O6 of the second N-acetylglucosamine residue of the substrate and the low activity of the E118Q mutant results from its reduced ability to bind the oligosaccharide. This analysis also suggests that the mechanism of action of PNGase F differs from those of L-asparaginase and glycosylasparaginase, which involve a threonine residue as the nucleophile.
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Affiliation(s)
- P Kuhn
- Wadsworth Center, New York State Department of Health, Albany 12201, USA
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35
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Oinonen C, Tikkanen R, Rouvinen J, Peltonen L. Three-dimensional structure of human lysosomal aspartylglucosaminidase. NATURE STRUCTURAL BIOLOGY 1995; 2:1102-8. [PMID: 8846222 DOI: 10.1038/nsb1295-1102] [Citation(s) in RCA: 145] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The high resolution crystal structure of human lysosomal aspartylglucosaminidase (AGA) has been determined. This lysosomal enzyme is synthesized as a single polypeptide precursor, which is immediately post-translationally cleaved into alpha- and beta-subunits. Two alpha- and beta-chains are found to pack together forming the final heterotetrameric structure. The catalytically essential residue, the N-terminal threonine of the beta-chain is situated in the deep pocket of the funnel-shaped active site. On the basis of the structure of the enzyme-product complex we present a catalytic mechanism for this lysosomal enzyme with an exceptionally high pH optimum. The three-dimensional structure also allows the prediction of the structural consequences of human mutations resulting in aspartylglucosaminuria (AGU), a lysosomal storage disease.
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Affiliation(s)
- C Oinonen
- Department of Chemistry, University of Joensuu, Finland
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36
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Roach PL, Clifton IJ, Fülöp V, Harlos K, Barton GJ, Hajdu J, Andersson I, Schofield CJ, Baldwin JE. Crystal structure of isopenicillin N synthase is the first from a new structural family of enzymes. Nature 1995; 375:700-4. [PMID: 7791906 DOI: 10.1038/375700a0] [Citation(s) in RCA: 329] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Penicillin antibiotics are all produced from fermentation-derived penicillins because their chemical synthesis is not commercially viable. The key step in penicillin biosynthesis, in which both the beta-lactam and thiazolidine rings of the nucleus are created, is mediated by isopenicillin N synthase (IPNS), which binds ferrous iron and uses dioxygen as a cosubstrate. In a unique enzymatic step, with no chemical precedent, IPNS catalyses the transfer of four hydrogen atoms from its tripeptide substrate to dioxygen forming, in a single reaction, the complete bicyclic nucleus of the penicillins. We now report the structure of IPNS complexed with manganese, which reveals the active site is unusually buried within a 'jelly-roll' motif and lined by hydrophobic residues, and suggest how this structure permits the process of penicillin formation. Sequence analyses indicate IPNS, 1-aminocyclopropane-1-carboxylic acid oxidase and many of the 2-oxo-acid-dependent oxygenases contain a conserved jelly-roll motif, forming a new structural family of enzymes.
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Affiliation(s)
- P L Roach
- Dyson Perrins Laboratory, University of Oxford, UK
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