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Bereznicka A, Mikolajczyk K, Szymczak-Kulus K, Kapczynska K, Majorczyk E, Modlinska A, Piasecki T, Kaczmarek R, Czerwinski M. Two Paralogous Gb3/CD77 Synthases in Birds Show Different Preferences for Their Glycoprotein and Glycosphingolipid Substrates. Int J Mol Sci 2021; 22:9761. [PMID: 34575935 PMCID: PMC8466213 DOI: 10.3390/ijms22189761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 09/06/2021] [Accepted: 09/06/2021] [Indexed: 11/22/2022] Open
Abstract
Most glycosyltransferases show remarkable gross and fine substrate specificity, which is reflected in the old one enzyme-one linkage paradigm. While human Gb3/CD77 synthase is a glycosyltransferase that synthesizes the Galα1→4Gal moiety mainly on glycosphingolipids, its pigeon homolog prefers glycoproteins as acceptors. In this study, we characterized two Gb3/CD77 synthase paralogs found in pigeons (Columba livia). We evaluated their specificities in transfected human teratocarcinoma 2102Ep cells by flow cytofluorometry, Western blotting, high-performance thin-layer chromatography, mass spectrometry and metabolic labelling with 14C-galactose. We found that the previously described pigeon Gb3/CD77 synthase (called P) can use predominately glycoproteins as acceptors, while its paralog (called M), which we serendipitously discovered while conducting this study, efficiently synthesizes Galα1→4Gal caps on both glycoproteins and glycosphingolipids. These two paralogs may underlie the difference in expression profiles of Galα1→4Gal-terminated glycoconjugates between neoavians and mammals.
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Affiliation(s)
- Anna Bereznicka
- Laboratory of Glycobiology, Department of Immunochemistry, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wroclaw, Poland; (A.B.); (K.M.); (K.S.-K.); (R.K.)
| | - Krzysztof Mikolajczyk
- Laboratory of Glycobiology, Department of Immunochemistry, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wroclaw, Poland; (A.B.); (K.M.); (K.S.-K.); (R.K.)
| | - Katarzyna Szymczak-Kulus
- Laboratory of Glycobiology, Department of Immunochemistry, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wroclaw, Poland; (A.B.); (K.M.); (K.S.-K.); (R.K.)
| | - Katarzyna Kapczynska
- Laboratory of Medical Microbiology, Department of Immunology of Infectious Diseases, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wroclaw, Poland;
| | - Edyta Majorczyk
- Faculty of Physical Education and Physiotherapy, Opole University of Technology, 45-758 Opole, Poland;
| | - Anna Modlinska
- Department of Epizootiology and Clinic of Birds and Exotic Animals, Wroclaw University of Environmental Sciences, 50-366 Wroclaw, Poland; (A.M.); (T.P.)
| | - Tomasz Piasecki
- Department of Epizootiology and Clinic of Birds and Exotic Animals, Wroclaw University of Environmental Sciences, 50-366 Wroclaw, Poland; (A.M.); (T.P.)
| | - Radoslaw Kaczmarek
- Laboratory of Glycobiology, Department of Immunochemistry, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wroclaw, Poland; (A.B.); (K.M.); (K.S.-K.); (R.K.)
| | - Marcin Czerwinski
- Laboratory of Glycobiology, Department of Immunochemistry, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wroclaw, Poland; (A.B.); (K.M.); (K.S.-K.); (R.K.)
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2
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Siukstaite L, Imberty A, Römer W. Structural Diversities of Lectins Binding to the Glycosphingolipid Gb3. Front Mol Biosci 2021; 8:704685. [PMID: 34381814 PMCID: PMC8350385 DOI: 10.3389/fmolb.2021.704685] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 07/08/2021] [Indexed: 12/18/2022] Open
Abstract
Glycolipids are present on the surfaces of all living cells and thereby represent targets for many protein receptors, such as lectins. Understanding the interactions between lectins and glycolipids is essential for investigating the functions of lectins and the dynamics of glycolipids in living membranes. This review focuses on lectins binding to the glycosphingolipid globotriaosylceramide (Gb3), an attractive host cell receptor, particularly for pathogens and pathogenic products. Shiga toxin (Stx), from Shigella dysenteriae or Escherichia coli, which is one of the most virulent bacterial toxins, binds and clusters Gb3, leading to local negative membrane curvature and the formation of tubular plasma membrane invaginations as the initial step for clathrin-independent endocytosis. After internalization, it is embracing the retrograde transport pathway. In comparison, the homotetrameric lectin LecA from Pseudomonas aeruginosa can also bind to Gb3, triggering the so-called lipid zipper mechanism, which results in membrane engulfment of the bacterium as an important step for its cellular uptake. Notably, both lectins bind to Gb3 but induce distinct plasma membrane domains and exploit mainly different transport pathways. Not only, several other Gb3-binding lectins have been described from bacterial origins, such as the adhesins SadP (from Streptococcus suis) and PapG (from E. coli), but also from animal, fungal, or plant origins. The variety of amino acid sequences and folds demonstrates the structural versatilities of Gb3-binding lectins and asks the question of the evolution of specificity and carbohydrate recognition in different kingdoms of life.
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Affiliation(s)
- Lina Siukstaite
- Faculty of Biology, University of Freiburg, Freiburg, Germany.,Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - Anne Imberty
- CNRS, CERMAV, Université Grenoble Alpes, Grenoble, France
| | - Winfried Römer
- Faculty of Biology, University of Freiburg, Freiburg, Germany.,Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany.,Freiburg Institute for Advanced Studies (FRIAS), University of Freiburg, Freiburg, Germany
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3
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Morimoto K, Suzuki N, Tanida I, Kakuta S, Furuta Y, Uchiyama Y, Hanada K, Suzuki Y, Yamaji T. Blood group P1 antigen-bearing glycoproteins are functional but less efficient receptors of Shiga toxin than conventional glycolipid-based receptors. J Biol Chem 2020; 295:9490-9501. [PMID: 32409578 DOI: 10.1074/jbc.ra120.013926] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 05/12/2020] [Indexed: 12/29/2022] Open
Abstract
Shiga toxin (STx) is a virulence factor produced by enterohemorrhagic Escherichia coli. STx is taken up by mammalian host cells by binding to the glycosphingolipid (GSL) globotriaosylceramide (Gb3; Galα1-4Galβ1-4Glc-ceramide) and causes cell death after its retrograde membrane transport. However, the contribution of the hydrophobic portion of Gb3 (ceramide) to STx transport remains unclear. In pigeons, blood group P1 glycan antigens (Galα1-4Galβ1-4GlcNAc-) are expressed on glycoproteins that are synthesized by α1,4-galactosyltransferase 2 (pA4GalT2). To examine whether these glycoproteins can also function as STx receptors, here we constructed glycan-remodeled HeLa cell variants lacking Gb3 expression but instead expressing pA4GalT2-synthesized P1 glycan antigens on glycoproteins. We compared STx binding and sensitivity of these variants with those of the parental, Gb3-expressing HeLa cells. The glycan-remodeled cells bound STx1 via N-glycans of glycoproteins and were sensitive to STx1 even without Gb3 expression, indicating that P1-containing glycoproteins also function as STx receptors. However, these variants were significantly less sensitive to STx than the parent cells. Fluorescence microscopy and correlative light EM revealed that the STx1 B subunit accumulates to lower levels in the Golgi apparatus after glycoprotein-mediated than after Gb3-mediated uptake but instead accumulates in vacuole-like structures probably derived from early endosomes. Furthermore, coexpression of Galα1-4Gal on both glycoproteins and GSLs reduced the sensitivity of cells to STx1 compared with those expressing Galα1-4Gal only on GSLs, probably because of competition for STx binding or internalization. We conclude that lipid-based receptors are much more effective in STx retrograde transport and mediate greater STx cytotoxicity than protein-based receptors.
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Affiliation(s)
- Kanta Morimoto
- Department of Biochemistry and Cell Biology, National Institute of Infectious Diseases, Tokyo, Japan.,Department of Materials and Applied Chemistry, College of Science and Technology, Nihon University, Tokyo, Japan
| | - Noriko Suzuki
- Graduate School of Science and Technology, Niigata University, Niigata, Japan
| | - Isei Tanida
- Department of Cellular and Molecular Neuropathology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Soichiro Kakuta
- Department of Cellular and Molecular Neuropathology, Juntendo University Graduate School of Medicine, Tokyo, Japan.,Laboratory of Morphology and Image Analysis, Biomedical Research Center, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Yoko Furuta
- Department of Cellular and Molecular Neuropathology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Yasuo Uchiyama
- Department of Cellular and Molecular Neuropathology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Kentaro Hanada
- Department of Biochemistry and Cell Biology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yusuke Suzuki
- Department of Materials and Applied Chemistry, College of Science and Technology, Nihon University, Tokyo, Japan
| | - Toshiyuki Yamaji
- Department of Biochemistry and Cell Biology, National Institute of Infectious Diseases, Tokyo, Japan
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4
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Suzuki N. Glycan diversity in the course of vertebrate evolution. Glycobiology 2020; 29:625-644. [PMID: 31287538 DOI: 10.1093/glycob/cwz038] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 04/29/2019] [Accepted: 05/15/2019] [Indexed: 11/12/2022] Open
Abstract
Vertebrates are estimated to have arisen over 500 million years ago in the Cambrian Period. Species that survived the Big Five extinction events at a global scale underwent repeated adaptive radiations along with habitat expansions from the sea to the land and sky. The development of the endoskeleton and neural tube enabled more complex body shapes. At the same time, vertebrates became suitable for the invasion and proliferation of foreign organisms. Adaptive immune systems were acquired for responses to a wide variety of pathogens, and more sophisticated systems developed during the evolution of mammals and birds. Vertebrate glycans consist of common core structures and various elongated structures, such as Neu5Gc, Galα1-3Gal, Galα1-4Gal, and Galβ1-4Gal epitopes, depending on the species. During species diversification, complex glycan structures were generated, maintained or lost. Whole-genome sequencing has revealed that vertebrates harbor numerous and even redundant glycosyltransferase genes. The production of various glycan structures is controlled at the genetic level in a species-specific manner. Because cell surface glycans are often targets of bacterial and viral infections, glycan structural diversity is presumed to be protective against infections. However, the maintenance of apparently redundant glycosyltransferase genes and investment in species-specific glycan structures, even in higher vertebrates with highly developed immune systems, are not well explained. This fact suggests that glycans play important roles in unknown biological processes.
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Affiliation(s)
- Noriko Suzuki
- Graduate School of Science and Technology, Niigata University, Niigata, Japan
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5
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Sanes JT, Hinou H, Lee YC, Nishimura SI. Glycoblotting of Egg White Reveals Diverse N-Glycan Expression in Quail Species. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:531-540. [PMID: 30537828 DOI: 10.1021/acs.jafc.8b04782] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The glycan part of glycoproteins is known to be involved in the structure and modulatory functions of glycoproteins, serving as ligands for cell-to-cell interactions, and as specific ligands for cell-to-microbe interactions. It is believed that intraspecies and interspecies variations in glycosylation exist. As an approach to better understand glycan diversity, egg whites (EW) from four different quail species are studied by the well-established glycoblotting procedure, a glycan enrichment and analysis method. N-Glycans were classified and the profiles were established for quail egg white samples which showed 21 relevant glycan peaks; 18 peaks were expressed significantly, and 10 glycan peaks are found to be abundant in certain species. The result establishes glycan profiles for Blue Scaled, Bobwhite, Japanese, and Mountain Quail egg whites and shows a unique difference among glycan expressions, particularly, high mannose in Japanese Quail and tetra-antennary glycan structure for other quail species.
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Affiliation(s)
- Jurgen T Sanes
- Faculty of Advanced Life Science and Graduate School of Life Science , Hokkaido University , N21, W11, Kita-ku , Sapporo 001-0021 , Japan
| | - Hiroshi Hinou
- Faculty of Advanced Life Science and Graduate School of Life Science , Hokkaido University , N21, W11, Kita-ku , Sapporo 001-0021 , Japan
| | - Yuan Chuan Lee
- Biology Department , Johns Hopkins University , 3400 North Charles Street , Baltimore , Maryland 21218 , United States
| | - Shin-Ichiro Nishimura
- Faculty of Advanced Life Science and Graduate School of Life Science , Hokkaido University , N21, W11, Kita-ku , Sapporo 001-0021 , Japan
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6
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Utratna M, Annuk H, Gerlach JQ, Lee YC, Kane M, Kilcoyne M, Joshi L. Rapid screening for specific glycosylation and pathogen interactions on a 78 species avian egg white glycoprotein microarray. Sci Rep 2017; 7:6477. [PMID: 28743896 PMCID: PMC5526940 DOI: 10.1038/s41598-017-06797-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 06/16/2017] [Indexed: 12/20/2022] Open
Abstract
There is an urgent need for discovery of novel antimicrobials and carbohydrate-based anti-adhesive strategies are desirable as they may not promote resistance. Discovery of novel anti-adhesive molecules from natural product libraries will require the use of a high throughput screening platform. Avian egg white (EW) provides nutrition for the embryo and protects against infection, with glycosylation responsible for binding certain pathogens. In this study, a microarray platform of 78 species of avian EWs was developed and profiled for glycosylation using a lectin panel with a wide range of carbohydrate specificities. The dominating linkages of sialic acid in EWs were determined for the first time using the lectins MAA and SNA-I. EW glycosylation similarity among the different orders of birds did not strictly depend on phylogenetic relationship. The interactions of five strains of bacterial pathogens, including Escherichia coli, Staphylococcus aureus and Vibrio cholera, identified a number of EWs as potential anti-adhesives, with some as strain- or species-specific. Of the two bacterial toxins examined, shiga-like toxin 1 subunit B bound to ten EWs with similar glycosylation more intensely than pigeon EW. This study provides a unique platform for high throughput screening of natural products for specific glycosylation and pathogen interactions. This platform may provide a useful platform in the future for discovery of anti-adhesives targeted for strain and species specificity.
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Affiliation(s)
- Marta Utratna
- Glycoscience Group, National Centre for Biomedical Engineering Science, National University of Ireland Galway, Galway, Ireland
| | - Heidi Annuk
- Glycoscience Group, National Centre for Biomedical Engineering Science, National University of Ireland Galway, Galway, Ireland
| | - Jared Q Gerlach
- Glycoscience Group, National Centre for Biomedical Engineering Science, National University of Ireland Galway, Galway, Ireland.,Regenerative Medicine Institute, National University of Ireland Galway, Galway, Ireland
| | - Yuan C Lee
- Department of Biology, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland, 21218, USA
| | - Marian Kane
- Glycoscience Group, National Centre for Biomedical Engineering Science, National University of Ireland Galway, Galway, Ireland
| | - Michelle Kilcoyne
- Carbohydrate Signalling Group, Microbiology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland.
| | - Lokesh Joshi
- Glycoscience Group, National Centre for Biomedical Engineering Science, National University of Ireland Galway, Galway, Ireland.
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7
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Kuo FY, Chang BY, Wu CY, Mong KKT, Chen YC. Magnetic Nanoparticle-Based Platform for Characterization of Shiga-like Toxin 1 from Complex Samples. Anal Chem 2015; 87:10513-20. [PMID: 26447488 DOI: 10.1021/acs.analchem.5b02712] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Foodborne illness outbreaks resulting from contamination of Escherichia coli O157:H7 remain a serious concern in food safety. E. coli O157:H7 can cause bloody diarrhea, hemolytic uremic syndrome, or even death. The pathogenicity of E. coli O157:H7 is mainly caused by the expression of Shiga-like toxins (SLTs), i.e., SLT-1 and SLT-2. SLTs are pentamers composed of a single A and five B subunits. In this study, we propose a magnetic nanoparticle (MNP)-based platform to rapidly identify SLT-1 from the complex cell lysate of E. coli O157:H7. The core of the MNPs is made of iron oxide, whereas the surface of the core is coated with a thin layer of alumina (Fe3O4@Al2O3 MNPs). The Fe3O4@Al2O3 MNPs are functionalized with pigeon ovalbumin (POA), which contains Gal-α(1→4)-Gal-β(1→4)-GlcNAc termini that can bind SLT-1B selectively. Furthermore, POA is a phosphate protein. Thus, it can be easily immobilized on the surface of the Fe3O4@Al2O3 MNPs through aluminum phosphate chelation under microwave heating within 1.5 min. The generated POA-Fe3O4@Al2O3 MNPs are capable of effectively enriching SLT-1B from complex cell lysates simply by pipetting 20 μL of the sample in and out of the tip in a vial for ∼1 min. To release SLT-1 from the MNPs, Gal-α(1→4)-Gal disaccharides were used for displacement. The released target species are sufficient to be identified by matrix-assisted laser desorption/ionization mass spectrometry. Although the sample volume used in this approach is small (20 μL) and the enrichment time is short (1 min), the selectivity of this approach toward SLT-1B is quite good. We have demonstrated the effectiveness of this approach for rapid determination of the presence of SLT-1 from complex cell lysates and ham/juice samples based on the detection of SLT-1B.
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Affiliation(s)
- Fang-Yin Kuo
- Department of Applied Chemistry, National Chiao Tung University , Hsinchu 300, Taiwan
| | - Bo-Yao Chang
- Department of Applied Chemistry, National Chiao Tung University , Hsinchu 300, Taiwan
| | - Ching-Yi Wu
- Department of Applied Chemistry, National Chiao Tung University , Hsinchu 300, Taiwan
| | - Kwok-Kong Tony Mong
- Department of Applied Chemistry, National Chiao Tung University , Hsinchu 300, Taiwan
| | - Yu-Chie Chen
- Department of Applied Chemistry, National Chiao Tung University , Hsinchu 300, Taiwan
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8
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Jégouzo SAF, Feinberg H, Dungarwalla T, Drickamer K, Weis WI, Taylor ME. A Novel Mechanism for Binding of Galactose-terminated Glycans by the C-type Carbohydrate Recognition Domain in Blood Dendritic Cell Antigen 2. J Biol Chem 2015; 290:16759-71. [PMID: 25995448 PMCID: PMC4505424 DOI: 10.1074/jbc.m115.660613] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2015] [Indexed: 11/06/2022] Open
Abstract
Blood dendritic cell antigen 2 (BDCA-2; also designated CLEC4C or CD303) is uniquely expressed on plasmacytoid dendritic cells. Stimulation of BDCA-2 with antibodies leads to an anti-inflammatory response in these cells, but the natural ligands for the receptor are not known. The C-type carbohydrate recognition domain in the extracellular portion of BDCA-2 contains a signature motif typical of C-type animal lectins that bind mannose, glucose, or GlcNAc, yet it has been reported that BDCA-2 binds selectively to galactose-terminated, biantennary N-linked glycans. A combination of glycan array analysis and binding competition studies with monosaccharides and natural and synthetic oligosaccharides have been used to define the binding epitope for BDCA-2 as the trisaccharide Galβ1-3/4GlcNAcβ1-2Man. X-ray crystallography and mutagenesis studies show that mannose is ligated to the conserved Ca(2+) in the primary binding site that is characteristic of C-type carbohydrate recognition domains, and the GlcNAc and galactose residues make additional interactions in a wide, shallow groove adjacent to the primary binding site. As predicted from these studies, BDCA-2 binds to IgG, which bears galactose-terminated glycans that are not commonly found attached to other serum glycoproteins. Thus, BDCA-2 has the potential to serve as a previously unrecognized immunoglobulin Fc receptor.
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Affiliation(s)
- Sabine A F Jégouzo
- the Department of Life Sciences, Imperial College, London SW7 2AZ, United Kingdom
| | - Hadar Feinberg
- From the Departments of Structural Biology and Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, California 94305 and
| | - Tabassum Dungarwalla
- the Department of Life Sciences, Imperial College, London SW7 2AZ, United Kingdom
| | - Kurt Drickamer
- the Department of Life Sciences, Imperial College, London SW7 2AZ, United Kingdom
| | - William I Weis
- From the Departments of Structural Biology and Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, California 94305 and
| | - Maureen E Taylor
- the Department of Life Sciences, Imperial College, London SW7 2AZ, United Kingdom
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9
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van Eerde A, Grahn EM, Winter HC, Goldstein IJ, Krengel U. Atomic-resolution structure of the -galactosyl binding Lyophyllum decastes lectin reveals a new protein family found in both fungi and plants. Glycobiology 2014; 25:492-501. [DOI: 10.1093/glycob/cwu136] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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10
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Yang Y, Barendregt A, Kamerling JP, Heck AJR. Analyzing protein micro-heterogeneity in chicken ovalbumin by high-resolution native mass spectrometry exposes qualitatively and semi-quantitatively 59 proteoforms. Anal Chem 2013; 85:12037-45. [PMID: 24229052 PMCID: PMC3880056 DOI: 10.1021/ac403057y] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Accepted: 11/14/2013] [Indexed: 01/18/2023]
Abstract
Taking chicken Ovalbumin as a prototypical example of a eukaryotic protein we use high-resolution native electrospray ionization mass spectrometry on a modified Exactive Orbitrap mass analyzer to qualitatively and semiquantitatively dissect 59 proteoforms in the natural protein. This variety is largely induced by the presence of multiple phosphorylation sites and a glycosylation site that we find to be occupied by at least 45 different glycan structures. Mass analysis of the intact protein in its native state is straightforward and fast, requires very little sample preparation, and provides a direct view on the stoichiometry of all different coappearing modifications that are distinguishable in mass. As such, this proof-of-principal analysis shows that native electrospray ionization mass spectrometry in combination with an Orbitrap mass analyzer offers a means to characterize proteins in a manner highly complementary to standard bottom-up shot-gun proteome analysis.
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Affiliation(s)
- Yang Yang
- Biomolecular Mass
Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research
and Utrecht Institute for Pharmaceutical Sciences, University
of Utrecht, Padualaan
8, 3584 CH Utrecht, The Netherlands
- Netherlands
Proteomics Center, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Arjan Barendregt
- Biomolecular Mass
Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research
and Utrecht Institute for Pharmaceutical Sciences, University
of Utrecht, Padualaan
8, 3584 CH Utrecht, The Netherlands
- Netherlands
Proteomics Center, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Johannis P. Kamerling
- Biomolecular Mass
Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research
and Utrecht Institute for Pharmaceutical Sciences, University
of Utrecht, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Albert J. R. Heck
- Biomolecular Mass
Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research
and Utrecht Institute for Pharmaceutical Sciences, University
of Utrecht, Padualaan
8, 3584 CH Utrecht, The Netherlands
- Netherlands
Proteomics Center, Padualaan
8, 3584 CH Utrecht, The Netherlands
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11
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Day CJ, Tram G, Hartley-Tassell LE, Tiralongo J, Korolik V. Assessment of glycan interactions of clinical and avian isolates of Campylobacter jejuni. BMC Microbiol 2013; 13:228. [PMID: 24119179 PMCID: PMC3852789 DOI: 10.1186/1471-2180-13-228] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Accepted: 09/27/2013] [Indexed: 03/08/2023] Open
Abstract
BACKGROUND Campylobacter jejuni strain 11168 was demonstrated to have a broad specificity for eukaryotic surface glycosylation using glycan array analysis. The initial screen indicated that sialic acid and mannose are important binding partners after environmental stress, while galactose and fucose structures are likely to be involved in persistent infection. RESULTS In this broader study, five additional human/clinical isolates and six chicken isolates were fully assessed to determine their glycan binding capacity using an extended glycan array. C. jejuni 11168 was rescreened here due to the presence of glycoaminoglycan (GAG) and other structures that were not available on our previous glycan array. The current array analysis of additional C. jejuni strains confirmed the growth condition dependent differences in glycan binding that was previously observed for C. jejuni 11168. We noted strain to strain variations, particularly for the human isolates C. jejuni 520 and 81116 and the chicken isolate C. jejuni 331, with the majority of differences observed in galactose, mannose and GAG binding. Chicken isolates were found to bind to a broader range of glycans compared to the human isolates, recognising branched mannose and carageenan (red seaweed) glycans. Glycan array data was confirmed using cell-based lectin inhibition assays with the fucose (UEA-I) and mannose (ConA) binding lectins. CONCLUSIONS This study confirms that all C. jejuni strains tested bind to a broad range of glycans, with the majority of strains (all except 81116) altering recognition of sialic acid and mannose after environmental stress. Galactose and fucose structures were bound best by all strains when C. jejuni was grown under host like conditions confirming the likelihood of these structures being involved in persistent infection.
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Affiliation(s)
- Christopher J Day
- Institute for Glycomics, G26, Griffith University Gold Coast Campus, Queensland 4222, Australia.
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12
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Suzuki N, Nawa D, Su TH, Lin CW, Khoo KH, Yamamoto K. Distribution of the Galβ1-4Gal epitope among birds: species-specific loss of the glycan structure in chicken and its relatives. PLoS One 2013; 8:e59291. [PMID: 23527153 PMCID: PMC3602017 DOI: 10.1371/journal.pone.0059291] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Accepted: 02/13/2013] [Indexed: 01/15/2023] Open
Abstract
The Galβ1-4Gal epitope is rarely found in mammals, and the natural antibody against Galβ1-4Gal is rich in human. In contrast, we have previously demonstrated the presence of Galβ1-4Gal in pigeon and ostrich, and the absence of this epitope in chicken. Here, to further investigate the expression of this glycan among birds, egg white glycoproteins and egg yolk IgG from nine species of birds, namely, chicken, duck, emu, guineafowl, ostrich, peafowl, pigeon, quail, and turkey, were analyzed by western blot using an anti-(Galβ1-4Gal) antibody. The results indicated that some egg white glycoproteins from emu, ostrich, and quail, and heavy chains of IgG from all of the birds, except chicken and quail, were stained with the antibody. The presence of Galβ1-4Gal on N-glycans of IgGs from guineafowl, peafowl, and turkey were confirmed by mass spectrometry (MS), MS/MS, and MS(n) analyses. In quail, the presence of Galβ1-4Gal was confirmed by detecting the activities of UDP-galactose: β-galactoside β1,4-galactosyltransferase (β4GalT(Gal)) in various tissues, and by detecting Galβ1-4Gal by western blotting. In contrast, bamboo partridge, which is a close relative of chicken, did not show any detectable activities of β4GalT(Gal) or Galβ1-4Gal on glycoproteins. Because quail, peafowl, turkey, chicken, and bamboo partridge belong to the same family, i.e., Phasianidae, expression of Galβ1-4Gal was most likely differentiated within this family. Considering that Galβ1-4Gal is also expressed in ostrich, emu, and pigeon, which are phylogenetically distant relatives within modern birds, Galβ1-4Gal expression appears to be widely distributed among birds, but might have been abolished in the ancestors of chicken and bamboo partridge.
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Affiliation(s)
- Noriko Suzuki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Japan.
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Springer SA, Gagneux P. Glycan evolution in response to collaboration, conflict, and constraint. J Biol Chem 2013; 288:6904-11. [PMID: 23329843 DOI: 10.1074/jbc.r112.424523] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Glycans, oligo- and polysaccharides secreted or attached to proteins and lipids, cover the surfaces of all cells and have a regulatory capacity and structural diversity beyond any other class of biological molecule. Glycans may have evolved these properties because they mediate cellular interactions and often face pressure to evolve new functions rapidly. We approach this idea two ways. First, we discuss evolutionary innovation. Glycan synthesis, regulation, and mode of chemical interaction influence the spectrum of new forms presented to evolution. Second, we describe the evolutionary conflicts that arise when alleles and individuals interact. Glycan regulation and diversity are integral to these biological negotiations. Glycans are tasked with such an amazing diversity of functions that no study of cellular interaction can begin without considering them. We propose that glycans predominate the cell surface because their physical and chemical properties allow the rapid innovation required of molecules on the frontlines of evolutionary conflict.
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Affiliation(s)
- Stevan A Springer
- Glycobiology Research and Training Center and Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California 92093-0687 USA
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Suzuki N, Nawa D, Tateno H, Yasuda T, Oda S, Mitani H, Nishimaki T, Katsumura T, Oota H, Hanihara T, Oga A, Hirabayashi J, Yamamoto K. Generation of monoclonal antibodies against the Gal 1-4Gal epitope: A key tool in studies of species-specific glycans expressed in fish, amphibians and birds. Glycobiology 2012; 23:91-105. [DOI: 10.1093/glycob/cws129] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Hirose K, Amano M, Hashimoto R, Lee YC, Nishimura SI. Insight into Glycan Diversity and Evolutionary Lineage Based on Comparative Avio-N-glycomics and Sialic Acid Analysis of 88 Egg Whites of Galloanserae. Biochemistry 2011; 50:4757-74. [DOI: 10.1021/bi101940x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Kazuko Hirose
- Graduate School of Life Science, Hokkaido University, Sapporo 001-0021, Japan
| | - Maho Amano
- Graduate School of Life Science, Hokkaido University, Sapporo 001-0021, Japan
- Division of Quantification of Health State (Feel Fine Co.), Graduate School of Life Science, Hokkaido University, Sapporo 001-0021, Japan
| | - Ryo Hashimoto
- Graduate School of Life Science, Hokkaido University, Sapporo 001-0021, Japan
| | - Yuan Chuan Lee
- Department of Biology, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Shin-Ichiro Nishimura
- Graduate School of Life Science, Hokkaido University, Sapporo 001-0021, Japan
- Division of Quantification of Health State (Feel Fine Co.), Graduate School of Life Science, Hokkaido University, Sapporo 001-0021, Japan
- Ezose Sciences, Inc., 25 Riverside Drive, Pine Brook, New Jersey 07058, United States
- Medicinal Chemistry Pharmaceuticals, LLC, 1-715, N7, W4, Kita-ku, Sapporo 060-0807, Japan
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Hreggvidsson GO, Dobruchowska JM, Fridjonsson OH, Jonsson JO, Gerwig GJ, Aevarsson A, Kristjansson JK, Curti D, Redgwell RJ, Hansen CE, Kamerling JP, Debeche-Boukhit T, Suzuki N, Nawa D, Yamamoto K, Ju T, Xia B, Aryal RP, Wang W, Wang Y, Ding X, Mi R, He M, Cummings RD. Errata. Glycobiology 2011. [DOI: 10.1093/glycob/cwr035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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17
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Suzuki N, Nawa D, Yamamoto K. Distinct expression profiles of UDP-galactose: β-D-galactoside α1,4-galactosyltransferase and UDP-galactose: β-D-galactoside β1,4-galactosyltransferase in pigeon, ostrich and chicken. Glycobiology 2010; 21:283-94. [PMID: 20959391 DOI: 10.1093/glycob/cwq163] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
We previously identified two novel enzymes in pigeon, α1,4- and β1,4-galactosyltransferases (GalTs), which are responsible for the biosynthesis of the Galα1-4Gal and Galβ1-4Gal sequences on glycoproteins, respectively. No such glycan structures and/or enzymes have been found in mammals, suggesting that the expression of these enzymes diverged during the course of vertebrate evolution. To compare their expression profiles among avian species, we first established a method for detecting the activities of these two GalTs based on the two-dimensional high pressure liquid chromatography mapping technique, using 2-aminopyridine-derivatized asialo-biantennary N-glycans as an acceptor substrate. When we analyzed the activities of GalTs in pigeon liver extracts in the presence of UDP-Gal, 13 different products containing Galα1-4Galβ1-4GlcNAc, Galβ1-4Galβ1-4GlcNAc and/or Galα1-4Galβ1-4Galβ1-4GlcNAc branches were identified. The newly formed glycosidic linkages of the enzymatic products were determined by nuclear magnetic resonance and methylation analysis, as well as by galactosidase digestions. The activities of both α1,4- and β1,4-GalTs were detected in various tissues in pigeon, although their relative activities were different in each tissue. In contrast, ostrich expressed β1,4-GalT, but not α1,4-GalT, in all tissues analyzed, whereas neither α1,4- nor β1,4-GalT activity was detected in chicken. These results indicate that α1,4- and β1,4-GalTs are expressed in a species-specific manner and are distributed throughout the entire body of pigeon or ostrich when the enzymes are present.
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Affiliation(s)
- Noriko Suzuki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Chiba 277-8562, Japan.
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Brief report: a new profile of terminal N-acetyllactosamines glycans on pig red blood cells and different expression of alpha-galactose on Sika deer red blood cells and nucleated cells. Glycoconj J 2010; 27:427-33. [PMID: 20422448 DOI: 10.1007/s10719-010-9289-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2008] [Revised: 03/30/2010] [Accepted: 04/07/2010] [Indexed: 10/19/2022]
Abstract
It has been reported that: (1) large variations were found in the number of sialic acid (SA) capped with N-acetyllactosamines (SA-Galbeta1-4GlcNAc-R) and alpha-Gal epitopes (Galalpha1-3Galbeta1-4GlcNAc-R) or uncapped N-acetyllactosamines (Galbeta1-4GlcNAc-R) on different mammalian red blood cells, and on nucleated cells originating from a given tissue in various species; (2) goat, sheep, horse and mouse red blood cells lack alpha-Gal epitopes, despite the expression of this epitope on a variety of nucleated cells in these species, including lymphocytes differentiated from the same hematopoietic origin. In this study, flow cytometry and Western blot analyses of pig red blood cells showed that alpha-Gal epitopes on pig red cells developed concomitantly after treatment with neuraminidase, suggesting that the terminal N-acetyllactosaminide glycans were capped with SA-alpha-Gal epitopes. Whereas, the expression of the alpha-Gal epitopes on red blood cells from Sika deer (Cevus nippon hortulorum) were found to be absent even though the epitopes were present on their white blood cells. Thus, these results add new data not only for the terminal carbohydrate structures on cell surface glycans of various mammalian cells, but also for wide variety of epitope expression on the cells from different tissues, which might be useful for understanding their unique states resulting from differentiation and evolution.
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Yagi H, Yamamoto M, Yu SY, Takahashi N, Khoo KH, Lee YC, Kato K. N-Glycosylation profiling of turtle egg yolk: expression of galabiose structure. Carbohydr Res 2009; 345:442-8. [PMID: 20044081 DOI: 10.1016/j.carres.2009.12.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2009] [Revised: 11/30/2009] [Accepted: 12/05/2009] [Indexed: 11/29/2022]
Abstract
To understand the roles of species-specific carbohydrates, systematic studies of interspecific glycan analyses are imperative. An extensive series of glycomics studies on approximately 180 kinds of bird eggs have demonstrated that 60-70% of the birds, which are closely related in phylogeny, express the alpha-Galp-(1-->4)-Galp structure on their egg glycoproteins. This prompted us to investigate the glycosylation profiles of eggs from an evolutionarily related organism, a sea turtle (reptilian). We performed N-glycosylation profiling of turtle egg yolk by using HPLC mapping in conjunction with mass spectrometric methods and thereby demonstrated that the alpha-Galp-(1-->4)-Galp groups are displayed on approximately 38% of total N-glycans. Our findings suggest that the ability to express the galabiose structure was acquired at an early stage of diversification in amniotes.
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Affiliation(s)
- Hirokazu Yagi
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan
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21
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Suzuki N, Yamamoto K. Molecular cloning of pigeon UDP-galactose:beta-D-galactoside alpha1,4-galactosyltransferase and UDP-galactose:beta-D-galactoside beta1,4-galactosyltransferase, two novel enzymes catalyzing the formation of Gal alpha1-4Gal beta1-4Gal beta1-4GlcNAc sequence. J Biol Chem 2009; 285:5178-87. [PMID: 19959475 DOI: 10.1074/jbc.m109.018663] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
We previously found that pigeon IgG possesses unique N-glycan structures that contain the Gal alpha1-4Gal beta1-4Gal beta1-4GlcNAc sequence at their nonreducing termini. This sequence is most likely produced by putative alpha1,4- and beta1,4-galactosyltransferases (GalTs), which are responsible for the biosynthesis of the Gal alpha1-4Gal and Gal beta1-4Gal sequences on the N-glycans, respectively. Because no such glycan structures have been found in mammalian glycoproteins, the biosynthetic enzymes that produce these glycans are likely to have distinct substrate specificities from the known mammalian GalTs. To study these enzymes, we cloned the pigeon liver cDNAs encoding alpha4GalT and beta4GalT by expression cloning and characterized these enzymes using the recombinant proteins. The deduced amino acid sequence of pigeon alpha4GalT has 58.2% identity to human alpha4GalT and 68.0 and 66.6% identity to putative alpha4GalTs from chicken and zebra finch, respectively. Unlike human and putative chicken alpha4GalTs, which possess globotriosylceramide synthase activity, pigeon alpha4GalT preferred to catalyze formation of the Gal alpha1-4Gal sequence on glycoproteins. In contrast, the sequence of pigeon beta4GalT revealed a type II transmembrane protein consisting of 438 amino acid residues, with no significant homology to the glycosyltransferases so far identified from mammals and chicken. However, hypothetical proteins from zebra finch (78.8% identity), frogs (58.9-60.4%), zebrafish (37.1-43.0%), and spotted green pufferfish (43.3%) were similar to pigeon beta4GalT, suggesting that the pigeon beta4GalT gene was inherited from the common ancestors of these vertebrates. The sequence analysis revealed that pigeon beta4GalT and its homologs form a new family of glycosyltransferases.
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Affiliation(s)
- Noriko Suzuki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Chiba 277-8562, Japan.
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Strategic glycan elution map for the production of human-type N-linked oligosaccharides: the case of hen egg yolk and white. Biosci Biotechnol Biochem 2009; 73:543-51. [PMID: 19270371 DOI: 10.1271/bbb.80598] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Glycans play important roles in various biological phenomena, but the lack of a systematic procedure for producing complex structures of glycans severely restricts their application in the medical and industrial fields. In this paper, we propose a basic strategy for the preparation of substantial amounts (>100 mg) of N-linked oligosaccharides, where the structure of each glycan is mapped with its elution position in liquid chromatography as well as the empirical yield. In model experiments using hen egg white and yolk as starting materials, the former provided a series of agalactosylated complex-type and hybrid-type N-linked oligosaccharides containing bisecting N-acetylglucosamine (GlcNAc) in addition to two high-mannose type glycans. In contrast, egg yolk gave predominantly alpha2-6sialylated biantennary glycans together with a high-mannose type one, reflecting the difference in the origins of the tissues. Due to the total identity of the glycans obtained to human ones, the present strategy should provide a practical scheme for the production of human-type N-linked oligosaccharides.
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Suzuki N, Su TH, Wu SW, Yamamoto K, Khoo KH, Lee YC. Structural analysis of N-glycans from gull egg white glycoproteins and egg yolk IgG. Glycobiology 2009; 19:693-706. [PMID: 19240272 DOI: 10.1093/glycob/cwp025] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
We previously showed that the expression of (Gal alpha 1-4Gal)-bearing glycoproteins among birds is related to their phylogeny. However, precise structures of (Gal alpha 1-4Gal)-containing N-glycans were only known for pigeon egg white glycoproteins and IgG. To compare structural features of (Gal alpha 1-4Gal)-containing N-glycans from other species, we analyzed N-glycans of gull egg white (GEW)-glycoproteins, ovomucoid, and ovotransferrin, and gull egg yolk IgG by HPLC, mass spectrometry (MS), and MS/MS analyses. GEW-glycoproteins included neutral, monosialyl, and disialyl N-glycans, and some of them contained Gal alpha 1-4Gal sequences. Bi-, tri-, and tetra-antennary oligosaccharides that lacked bisecting GlcNAc were the major core structures, and incomplete alpha-galactosylation and sialylation as well as the presence of diLacNAc on the branches generated microheterogeneity of the N-glycan structures. Moreover, unlike pigeon egg white glycoproteins, the major sialylation in GEW-glycoproteins is alpha2,3-, but not alpha2,6-linked sialic acids (NeuAc). In addition to the complex-type oligosaccharide, hybrid-type oligosaccharides that lack bisecting GlcNAc were also abundant in GEW-glycoproteins. Gull egg yolk IgG also contained Gal alpha 1-4Gal beta 1-4GlcNAc beta 1- sequences, but unlike pigeon IgG, no Gal alpha 1-4Gal beta 1-4Gal beta 1-4GlcNAc beta 1- sequence was detected. Bi- and tri-antennary complex-type oligosaccharides with bisecting GlcNAc and with core fucosylation as well as high-mannose-type oligosaccharides were the major structures in gull IgG. Our data indicated that some N-glycans from both GEW-glycoproteins and gull IgG contain the Gal alpha 1-4Gal beta 1-4GlcNAc beta 1- sequence, but the ratio of alpha-Gal-capped residues to non-alpha-Gal-capped residues in the nonreducing termini of N-glycans is much lower than that in those of pigeon glycoproteins.
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Affiliation(s)
- Noriko Suzuki
- Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA.
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Yamaguchi D, Kawasaki N, Matsuo I, Totani K, Tozawa H, Matsumoto N, Ito Y, Yamamoto K. VIPL has sugar-binding activity specific for high-mannose-type N-glycans, and glucosylation of the α1,2 mannotriosyl branch blocks its binding. Glycobiology 2007; 17:1061-9. [PMID: 17621594 DOI: 10.1093/glycob/cwm074] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
VIP36-like protein (VIPL) was identified as an endoplasmic reticulum (ER) resident protein with homology to VIP36, a cargo receptor involved in the transport of glycoproteins within cells. Although VIPL is structurally similar to VIP36, VIPL is thought not to be a lectin, because its sugar-binding activity has not been detected in several experiments. Here, recombinant soluble VIPL proteins (sVIPL) were expressed in Escherichia coli, biotinylated with biotin ligase and oligomerized with R-phycoerythrin (PE)-labeled streptavidin (SA). As measured with flow cytometry, PE-labeled sVIPL-SA bound to deoxymannojirimycin (DMJ)- or kifunensine (KIF)- but not to swainsonine (SW)-treated HeLaS3 cells in the presence of calcium. A surface plasmon resonance analysis showed that the avidity of sVIPL was enhanced after it formed a complex with SA. The binding of PE-labeled sVIPL-SA was abrogated by endo beta-N-acetylglucosaminidase H treatment of the DMJ- or KIF-treated cells. Competition with several high-mannose-type N-glycans inhibited VIPL binding, and indicated that VIPL recognizes the Manalpha1-2Manalpha1-2Man sequence. Glucosylation of the outer mannose residue of this portion decreased the binding. Although the biochemical characteristics of VIPL are similar to those of VIP36, the sugar-binding activity of VIPL was stronger at neutral pH, corresponding to the pH in the lumen of the ER, than under acidic conditions.
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Affiliation(s)
- Daisuke Yamaguchi
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Bioscience BLD 602, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
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Bishop JR, Gagneux P. Evolution of carbohydrate antigens--microbial forces shaping host glycomes? Glycobiology 2007; 17:23R-34R. [PMID: 17237137 DOI: 10.1093/glycob/cwm005] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Many glycans show remarkably discontinuous distribution across evolutionary lineages. These differences play major roles when organisms belonging to different lineages interact as host-pathogen or host-symbiont. Certain lineage-specific glycans have become important signals for multicellular host organisms, which use them as molecular signatures of their pathogens and symbionts through recognition by a toolkit of innate defense molecules. In turn, pathogens have evolved to exploit host lineage-specific glycans and are constantly shaping the glycomes of their hosts. These interactions take place in the face of numerous critical endogenous functions played by glycans within host organisms. Whether due to simple evolutionary divergence or adaptive changes under natural selection resulting from endogenous functional requirements, once different lineages elaborate on differential glycomes these mutual differences provide opportunities for host exploitation and/or pathogen defense between lineages. Such phylogenetic molecular recognition mechanisms will augment and likely contribute to the maintenance of lineage-specific differences in glycan repertoires.
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Affiliation(s)
- Joseph R Bishop
- Glycobiology Research and Training Center, Cellular and Molecular Medicine-East, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0687, USA
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LIVEZEY BRADLEYC, ZUSI RICHARDL. Higher-order phylogeny of modern birds (Theropoda, Aves: Neornithes) based on comparative anatomy. II. Analysis and discussion. Zool J Linn Soc 2007; 149:1-95. [PMID: 18784798 PMCID: PMC2517308 DOI: 10.1111/j.1096-3642.2006.00293.x] [Citation(s) in RCA: 281] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
In recent years, avian systematics has been characterized by a diminished reliance on morphological cladistics of modern taxa, intensive palaeornithogical research stimulated by new discoveries and an inundation by analyses based on DNA sequences. Unfortunately, in contrast to significant insights into basal origins, the broad picture of neornithine phylogeny remains largely unresolved. Morphological studies have emphasized characters of use in palaeontological contexts. Molecular studies, following disillusionment with the pioneering, but non-cladistic, work of Sibley and Ahlquist, have differed markedly from each other and from morphological works in both methods and findings. Consequently, at the turn of the millennium, points of robust agreement among schools concerning higher-order neornithine phylogeny have been limited to the two basalmost and several mid-level, primary groups. This paper describes a phylogenetic (cladistic) analysis of 150 taxa of Neornithes, including exemplars from all non-passeriform families, and subordinal representatives of Passeriformes. Thirty-five outgroup taxa encompassing Crocodylia, predominately theropod Dinosauria, and selected Mesozoic birds were used to root the trees. Based on study of specimens and the literature, 2954 morphological characters were defined; these characters have been described in a companion work, approximately one-third of which were multistate (i.e. comprised at least three states), and states within more than one-half of these multistate characters were ordered for analysis. Complete heuristic searches using 10 000 random-addition replicates recovered a total solution set of 97 well-resolved, most-parsimonious trees (MPTs). The set of MPTs was confirmed by an expanded heuristic search based on 10 000 random-addition replicates and a full ratchet-augmented exploration to ascertain global optima. A strict consensus tree of MPTs included only six trichotomies, i.e. nodes differing topologically among MPTs. Bootstrapping (based on 10 000 replicates) percentages and ratchet-minimized support (Bremer) indices indicated most nodes to be robust. Several fossil Neornithes (e.g. Dinornithiformes, Aepyornithiformes) were placed within the ingroup a posteriori either through unconstrained, heursitic searches based on the complete matrix augmented by these taxa separately or using backbone-constraints. Analysis confirmed the topology among outgroup Theropoda and achieved robust resolution at virtually all levels of the Neornithes. Findings included monophyly of the palaeognathous birds, comprising the sister taxa Tinamiformes and ratites, respectively, and the Anseriformes and Galliformes as monophyletic sister-groups, together forming the sister-group to other Neornithes exclusive of the Palaeognathae (Neoaves). Noteworthy inferences include: (i) the sister-group to remaining Neoaves comprises a diversity of marine and wading birds; (ii) Podicipedidae are the sister-group of Gaviidae, and not closely related to the Phoenicopteridae, as recently suggested; (iii) the traditional Pelecaniformes, including the shoebill (Balaeniceps rex) as sister-taxon to other members, are monophyletic; (iv) traditional Ciconiiformes are monophyletic; (v) Strigiformes and Falconiformes are sister-groups; (vi) Cathartidae is the sister-group of the remaining Falconiformes; (vii) Ralliformes (Rallidae and Heliornithidae) are the sister-group to the monophyletic Charadriiformes, with the traditionally composed Gruiformes and Turniciformes (Turnicidae and Mesitornithidae) sequentially paraphyletic to the entire foregoing clade; (viii) Opisthocomus hoazin is the sister-taxon to the Cuculiformes (including the Musophagidae); (ix) traditional Caprimulgiformes are monophyletic and the sister-group of the Apodiformes; (x) Trogoniformes are the sister-group of Coliiformes; (xi) Coraciiformes, Piciformes and Passeriformes are mutually monophyletic and closely related; and (xii) the Galbulae are retained within the Piciformes. Unresolved portions of the Neornithes (nodes having more than one most-parsimonious solution) comprised three parts of the tree: (a) several interfamilial nodes within the Charadriiformes; (b) a trichotomy comprising the (i) Psittaciformes, (ii) Columbiformes and (iii) Trogonomorphae (Trogoniformes, Coliiformes) + Passerimorphae (Coraciiformes, Piciformes, Passeriformes); and (c) a trichotomy comprising the Coraciiformes, Piciformes and Passeriformes. The remaining polytomies were among outgroups, although several of the highest-order nodes were only marginally supported; however, the majority of nodes were resolved and met or surpassed conventional standards of support. Quantitative comparisons with alternative hypotheses, examination of highly supportive and diagnostic characters for higher taxa, correspondences with prior studies, complementarity and philosophical differences with palaeontological phylogenetics, promises and challenges of palaeogeography and calibration of evolutionary rates of birds, and classes of promising evidence and future directions of study are reviewed. Homology, as applied to avian examples of apparent homologues, is considered in terms of recent theory, and a revised annotated classification of higher-order taxa of Neornithes and other closely related Theropoda is proposed. (c) 2007 The Linnean Society of London, Zoological Journal of the Linnean Society, 2007, 149, 1-95.
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Affiliation(s)
- BRADLEY C LIVEZEY
- Section of Birds, Carnegie Museum of Natural History4400 Forbes Avenue, Pittsburgh, PA 15213-4080, USA
| | - RICHARD L ZUSI
- Division of Birds, National Museum of Natural HistoryWashington, DC 20013-7012, USA
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Lee RT, Lauc G, Lee YC. Glycoproteomics: protein modifications for versatile functions. Meeting on glycoproteomics. EMBO Rep 2006; 6:1018-22. [PMID: 16239927 PMCID: PMC1371038 DOI: 10.1038/sj.embor.7400556] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2005] [Accepted: 09/19/2005] [Indexed: 11/08/2022] Open
Affiliation(s)
- Reiko T. Lee
- Department of Biology, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Gordan Lauc
- Department of Biology, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Yuan C. Lee
- Department of Biology, Johns Hopkins University, Baltimore, Maryland 21218, USA
- Tel: +1 410 516 7041; Fax: +1 410 516 8716;
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Watanabe M, Nikaido M, Tsuda TT, Kobayashi T, Mindell D, Cao Y, Okada N, Hasegawa M. New candidate species most closely related to penguins. Gene 2006; 378:65-73. [PMID: 16806742 DOI: 10.1016/j.gene.2006.05.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2006] [Revised: 05/03/2006] [Accepted: 05/08/2006] [Indexed: 11/28/2022]
Abstract
The phylogenetic position of the order Spenisciformes in Aves remains unclear despite several independent analyses based on morphological and molecular data. To address this issue, we determined the complete mtDNA sequence of rockhopper penguins. The mitochondrial genome, excluding the region from the D-loop to 12SrRNA, was also sequenced for petrel, albatross, frigatebird, loon and grebe, which previous studies suggest are related to penguins. A maximum likelihood analysis of the phylogenetic placement of penguins with 23 birds, including 17 species whose mtDNA sequences were previously reported, suggested that storks are the closest extant relatives of penguins, with 78% and 56% bootstrap supports, depending on the choice of outgroup species. Thus, ciconiiform birds constitute new candidates as the closest extant relatives of penguins (previously proposed candidates were either gaviiform, podicipediform, or procellariiform birds). In addition to this new evidence, our analysis gave evidence to some of ambiguous relationships in the avian tree: our analysis supported a basal split between passerines and other neoavians within Neoaves, and rejected the monophyly of Falconiformes as well as that of loons and grebes.
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Affiliation(s)
- Maiko Watanabe
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Kanagawa 226-8501, Japan
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Suzuki N, Laskowski M, Lee YC. Tracing the history of Galalpha1-4Gal on glycoproteins in modern birds. Biochim Biophys Acta Gen Subj 2005; 1760:538-46. [PMID: 16290275 DOI: 10.1016/j.bbagen.2005.10.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2005] [Revised: 10/10/2005] [Accepted: 10/11/2005] [Indexed: 11/26/2022]
Abstract
Galalpha1-4Gal is typically found in mammalian glycolipids in small quantities, and recognized by some pathogens, such as uropathogenic Escherichia coli. In contrast, glycoproteins containing Galalpha1-4Gal were rarely found in vertebrates except in a few species of birds and amphibians until recently. However, we had previously reported that pigeon (Columba livia) egg white and serum glycoproteins are rich in N-glycans with Galalpha1-4Gal at non-reducing termini. Our investigation with egg white glycoproteins from 181 avian species also revealed that the distribution of (Galalpha1-4Gal)-containing glycoproteins was not rare among avians, and is correlated with the phylogeny of birds. The differentiated expression was most likely emerged at earlier stage of diversification of modern birds, but some birds might have lost the facility for the expression relatively recently.
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Affiliation(s)
- Noriko Suzuki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
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