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1. Compound ID: 9737
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a-D-GlcpA-(1-3)-a-L-Fucp-(1-4)-+
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-3)-b-D-GlcpNAc-(1-3)-a-L-Fucp-(1-3)-b-D-GlcpNAc-(1- |
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Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide, O-antigen
Contained glycoepitopes: IEDB_115136,IEDB_135813,IEDB_136045,IEDB_137340,IEDB_140630,IEDB_141807,IEDB_142489,IEDB_144562,IEDB_145669,IEDB_150092,IEDB_151531,IEDB_152214,IEDB_174333,IEDB_423096,IEDB_490056,SB_86
The structure is contained in the following publication(s):
- Article ID: 4079
Ovchinnikova OG, Kocharova NA, Kondakova AN, Bialczak-Kokot M, Shashkov AS, Knirel YA, Rozalski A "Structure of the O-polysaccharide from the lipopolysaccharide of Providencia alcalifaciens O28" -
Carbohydrate Research 346(16) (2011) 2638-2641
An O-polysaccharide and oligosaccharides were isolated by GPC following mild acid degradation of the lipopolysaccharide of Providencia alcalifaciens O28. The O-polysaccharide was studied by sugar and methylation analyses, (1)H and (13)C NMR spectroscopy, including 2D ROESY and H-detected (1)H,(13)C HSQC and HMBC experiments, and the following structure of the branched pentasaccharide repeating unit was established: [see formula in text]. This structure was confirmed by ESI MS of the isolated tridecasaccharide consisting of the lipopolysaccharide core and one O-polysaccharide repeat. The ESI mass spectrum also enabled inferring the composition of the core oligosaccharide.
Lipopolysaccharide, core oligosaccharide, O-polysaccharide, Providencia alcalifaciens, bacterial polysaccharide structure
NCBI PubMed ID: 21978611Publication DOI: 10.1016/j.carres.2011.09.008Journal NLM ID: 0043535Publisher: Elsevier
Correspondence: olga.ovchinnikova@gmail.com
Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
Methods: 13C NMR, 1H NMR, NMR-2D, methylation, GLC-MS, sugar analysis, acid hydrolysis, ESI-FT-MS
- Article ID: 4328
Knirel YA "Structure of O-antigens" -
Book: Bacterial lipopolysaccharides: Structure, chemical synthesis, biogenesis and interaction with host cells (2011) Chapter 3, 41-115
The lipopolysaccharide (LPS) is the major constituent of the outer leaflet of the outer membrane of Gram-negative bacteria. Its lipid A moiety is embedded in the membrane and serves as an anchor for the rest of the LPS molecule. The outermost repetitive glycan region of the LPS is linked to the lipid A through a core oligosaccharide (OS), and is designated as the O-specific polysaccharide (O-polysaccharide, OPS) or O-antigen. The O-antigen is the most variable portion of the LPS and provides serological specificity, which is used for bacterial serotyping. The OPS also provides protection to the microorganisms from host defenses such as complement mediated killing and phagocytosis, and is involved in interactions of bacteria with plants and bacteriophages. Studies of the OPSs ranging from the elucidation of their chemical structures and conformations to their biological and physico-chemical properties help improving classification schemes of Gram-negative bacteria. Furthermore, these studies contributed to a better understanding of the mechanisms of pathogenesis of infectious diseases, as well as provided information to develop novel vaccines and diagnostic reagents.
Lipopolysaccharide, synthesis, lipopolysaccharides, structure, Bacterial, host, O-antigen, O antigen, cell, O antigens, O-antigens, chemical, interaction, cells, PDF, chemical synthesis, biogenesis
Publication DOI: 10.1007/978-3-7091-0733-1_3Publisher: Springer
Correspondence: knirel@ioc.ac.ru
Editors: Knirel YA, Valvano MA
Institutions: Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
- Article ID: 4361
Ovchinnikova OG, Liu B, Guo D, Kocharova NA, Shashkov AS, Chen M, Feng L, Rozalski A, Knirel YA, Wang L "Localization and molecular characterization of putative O-antigen gene clusters of Providencia species" -
Microbiology 158(4) (2012) 1024-1036
Enterobacteria of the genus Providencia are opportunistic human pathogens associated with urinary tract and wound infections, as well as enteric diseases. The lipopolysaccharide (LPS) O antigen confers major antigenic variability upon the cell surface and is used for serotyping of Gram-negative bacteria. Recently, Providencia O antigen structures have been extensively studied, but no data on the location and organization of the O antigen gene cluster have been reported. In this study, the four Providencia genome sequences available were analysed, and the putative O antigen gene cluster was identified in the polymorphic locus between the cpxA and yibK genes. This finding provided the necessary information for designing primers, and cloning and sequencing the O antigen gene clusters from five more Providencia alcalifaciens strains. The gene functions predicted in silico were in agreement with the known O antigen structures; furthermore, annotation of the genes involved in the three-step synthesis of GDP-colitose (gmd, colD and colC) was supported by cloning and biochemical characterization of the corresponding enzymes. In one strain (P. alcalifaciens O39), no polysaccharide product of the gene cluster in the cpxA-yibK locus was found, and hence genes for synthesis of the existing O antigen are located elsewhere in the genome. In addition to the putative O antigen synthesis genes, homologues of wza, wzb, wzc and (in three strains) wzi, required for the surface expression of capsular polysaccharides, were found upstream of yibK in all species except Providencia rustigianii, suggesting that the LPS of these species may be attributed to the so-called K LPS (K(LPS)). The data obtained open a way for development of a PCR-based typing method for identification of Providencia isolates.
Lipopolysaccharide, Providencia alcalifaciens, O-antigen gene cluster, O-Polysaccharide structure
NCBI PubMed ID: 22282517Publication DOI: 10.1099/mic.0.055210-0Journal NLM ID: 0376646Publisher: Washington, DC: Kluwer Academic/Plenum Publishers
Correspondence: wanglei@nankai.edu.cn; yknirel@gmail.com
Institutions: TEDA School of Biological Sciences and Biotechnology, Nankai University, 23 Hongda Street, TEDA, 300457 Tianjin, PR China
Methods: 13C NMR, 1H NMR, NMR-2D, PCR, DNA sequencing, SDS-PAGE, glycosyltransferase assays, 31P NMR, ESI-MS, genetic methods, HPLC
- Article ID: 4588
Ovchinnikova OG, Rozalski A, Liu B, Knirel YA "O-Antigens of bacteria of the genus Providencia: structure, serology, genetics, and biosynthesis" -
Biochemistry (Moscow) 78(7) (2013) 798-817
The genus Providencia consists of eight species of opportunistic pathogenic enterobacteria that can cause enteric diseases and urinary tract infections. The existing combined serological classification scheme of three species, P. alcalifaciens, P. stuartii, and P. rustigianii, is based on the specificity of O-antigens (O-polysaccharides) and comprises 63 O-serogroups. Differences between serogroups are related to polymorphism at a specific genome locus, the O-antigen gene cluster, responsible for O-antigen biosynthesis. This review presents data on structures of 36 O-antigens of Providencia, many of which contain unusual monosaccharides and non-carbohydrate components. The structural data correlate with the immunospecificity of the O-antigens and enable substantiation on a molecular level of serological relationships within the genus Providencia and between strains of Providencia and bacteria of the genera Proteus, Escherichia, and Salmonella. Peculiar features of the O-antigen gene cluster organization in 10 Providencia serogroups and biosynthetic pathways of nucleotide precursors of specific monosaccharide components of the O-antigens also are discussed.
Lipopolysaccharide, biosynthesis, O-antigen, gene cluster, Providencia, serological specificity
NCBI PubMed ID: 24010842Publication DOI: 10.1134/S0006297913070110Journal NLM ID: 0376536Publisher: Nauka/Interperiodica
Correspondence: olga.ovchinnikova@gmail.com
Institutions: ND Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Department of Immunobiology of Bacteria, Institute of Microbiology, Biotechnology and Immunology, University of Lodz, PL 90-237 Lodz, Poland, TEDA School of Biological Sciences and Biotechnology, Nankai University, 23 Hongda Street, TEDA, 300457 Tianjin, P. R. China
- Article ID: 5192
Naumenko OI, Xiong Y, Zheng H, Senchenkova SN, Wang H, Shashkov AS, Li Q, Wang J, Knirel YA "Studies on the O-polysaccharide of Escherichia albertii O2 characterized by non-stoichiometric O-acetylation and non-stoichiometric side-chain L-fucosylation" -
Carbohydrate Research 461 (2018) 80-84
An O-polysaccharide was isolated from the lipopolysaccharide of Escherichia albertii O2 and studied by chemical methods and 1D and 2D 1H and 13C NMR spectroscopy. The following structure of the O-polysaccharide was established: [structure: see text]. The O-polysaccharide is characterized by masked regularity owing to a non-stoichiometric O-acetylation of an l-fucose residue in the main chain and a non-stoichiometric side-chain l-fucosylation of a β-GlcNAc residue. A regular linear polysaccharide was obtained by sequential Smith degradation and alkaline O-deacetylation of the O-polysaccharide. The content of the O-antigen gene cluster of E. albertii O2 was found to be essentially consistent with the O-polysaccharide structure established.
O-specific polysaccharide, O-acetylation, bacterial polysaccharide structure, O-antigen gene cluster, Escherichia albertii, l-Fucosylation
NCBI PubMed ID: 29609101Publication DOI: 10.1016/j.carres.2018.02.013Journal NLM ID: 0043535Publisher: Elsevier
Correspondence: xiongyanwen@icdc.cn
Institutions: N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Higher Chemical College of the Russian Academy of Sciences, D. I. Mendeleev University of Chemical Technology of Russia, Moscow, Russia, Zigong Center for Disease Control and Prevention, Zigong, Sichuan Province, China, State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, Zhejiang Province, China
Methods: 13C NMR, 1H NMR, NMR-2D, sugar analysis, GLC, mild acid hydrolysis, Smith degradation, de-O-acetylation, GPC, bioinformatic analysis
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2. Compound ID: 10865
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b-D-GlcpA-(1-4)-+
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-3)-a-D-Galp-(1-3)-a-L-Fucp-(1-4)-b-D-GlcpNAc-(1-3)-a-L-Fucp-(1-3)-b-D-GlcpNAc-(1- |
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Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide, O-antigen
Contained glycoepitopes: IEDB_115136,IEDB_135813,IEDB_136045,IEDB_136906,IEDB_137340,IEDB_137472,IEDB_140630,IEDB_141794,IEDB_141807,IEDB_142489,IEDB_144562,IEDB_145669,IEDB_150092,IEDB_151528,IEDB_151531,IEDB_152214,IEDB_174333,IEDB_190606,IEDB_423096,IEDB_423153,IEDB_490056,SB_173,SB_7,SB_86
The structure is contained in the following publication(s):
- Article ID: 4424
Zhu H, Perepelov AV, Senchenkova SN, Shashkov AS, Wang L, Knirel YA "Structure and gene cluster of the O-antigen of Escherichia coli O41" -
Carbohydrate Research 349 (2012) 86-89
The acidic O-polysaccharide (O-antigen) of Escherichia coli O41 was studied by sugar analysis along with 1D and 2D (1)H and (13)C NMR spectroscopy, and the following structure of the branched hexasaccharide repeating unit was established: This structure is unique among the known structures of bacterial polysaccharides. The O-antigen gene cluster of E. coli O41 was sequenced. The gene functions were tentatively assigned by a comparison with sequences in the available databases and found to be in full agreement with the E. coli O41 O-polysaccharide structure.
Lipopolysaccharide, O-antigen, Escherichia coli, bacterial polysaccharide structure, O-antigen gene cluster
NCBI PubMed ID: 22244340Publication DOI: 10.1016/j.carres.2011.12.009Journal NLM ID: 0043535Publisher: Elsevier
Correspondence: A.V. Perepelov
Institutions: TEDA School of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, China
Methods: 13C NMR, 1H NMR, NMR-2D, methylation, DNA sequencing, sugar analysis, acid hydrolysis, GLC
- Article ID: 5472
Liu B, Furevi A, Perepelov AV, Guo X, Cao H, Wang Q, Reeves PR, Knirel YA, Wang L, Widmalm G "Structure and genetics of Escherichia coli O antigens" -
FEMS Microbiology Reviews 44(6) (2020) 655-683
Escherichia coli includes clonal groups of both commensal and pathogenic strains, with some of the latter causing serious infectious diseases. O antigen variation is current standard in defining strains for taxonomy and epidemiology, providing the basis for many serotyping schemes for Gram-negative bacteria. This review covers the diversity in E. coli O antigen structures and gene clusters, and the genetic basis for the structural diversity. Of the 187 formally defined O antigens, six (O31, O47, O67, O72, O94 and O122) have since been removed and four (O14, O34, O89 and O144) strains do not produce any O antigen. Therefore, structures are presented for 176 of the 181 E. coli O antigens, some of which include subgroups. Most (93%) of these O antigens are synthesized via the Wzx/Wzy pathway, 11 via the ABC transporter pathway, with O20, O57 and O60 still uncharacterized due to failure to find their O antigen gene clusters. Biosynthetic pathways are given for 38 of the 49 sugars found in E. coli O antigens, and several pairs or groups of the E. coli antigens that have related structures show close relationships of the O antigen gene clusters within clades, thereby highlighting the genetic basis of the evolution of diversity.
structure, O antigen, Escherichia coli, gene cluster, serogroup, diversity
NCBI PubMed ID: 31778182Publication DOI: 10.1093/femsre/fuz028Journal NLM ID: 8902526Publisher: Oxford University Press
Correspondence: G. Widmalm
; Lei Wang
Institutions: Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, Sweden, N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Tianjin Key Laboratory of Microbial Functional Genomics, Tianjin, China, The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Tianjin, China, School of Molecular and Microbial Bioscience (G08), University of Sydney, Sydney, Australia, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, China, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
- Article ID: 5760
Dobrochaeva K, Khasbiulina N, Shilova N, Antipova N, Obukhova P, Galanina O, Blixt O, Kunz H, Filatov A, Knirel Y, Le Pendu J, Khaidukov S, Bovin N "Specificity of human natural antibodies referred to as anti-Tn" -
Molecular Immunology 120 (2020) 74-82
To understand the role of human natural IgM known as antibodies against the carbohydrate epitope Tn, the antibodies were isolated using GalNAcα-Sepharose affinity chromatography, and their specificity was profiled using microarrays (a glycan array printed with oligosaccharides and bacterial polysaccharides, as well as a glycopeptide array), flow cytometry, and inhibition ELISA. The antibodies bound a restricted number of GalNAcα-terminated oligosaccharides better than the parent monosaccharide, e.g., 6-O-Su-GalNAcα and GalNAcα1-3Galβ1-3(4)GlcNAcβ. The binding with several bacterial polysaccharides that have no structural resemblance to the affinity ligand GalNAcα was quite unexpected. Given that GalNAcα is considered the key fragment of the Tn antigen, it is surprising that these antibodies bind weakly GalNAcα-OSer and do not bind a wide variety of GalNAcα-OSer/Thr-containing mucin glycopeptides. At the same time, we have observed specific binding to cells having Tn-positive glycoproteins containing similar glycopeptide motifs in a conformationally rigid macromolecule. Thus, specific recognition of the Tn antigen apparently requires that the naturally occurring "anti-Tn" IgM recognize a complex epitope comprising the GalNAcα as an essential component and a fairly long amino acid sequence where the amino acids adjacent to GalNAcα do not contact the antibody paratope; i.e., the antibodies recognize a spatial epitope or a molecular pattern rather than a classical continuous sequence. In addition, we have not found any increase in the binding of natural antibodies when GalNAcα residues were clustered. These results may help in further development of anticancer vaccines based on synthetic Tn constructs.
cancer, glycans, natural antibodies, anti-glycan antibodies, Tn antigen
NCBI PubMed ID: 32087569Publication DOI: 10.1016/j.molimm.2020.02.005Journal NLM ID: 7905289Publisher: Elsevier
Correspondence: professorbovin@yandex.ru
Institutions: Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya, Moscow, Russian Federation, Semiotik LLC, 16/10 Miklukho-Maklaya, Moscow, Russian Federation, National Medical Research Center for Obstetrics, Gynecology and Perinatology Named after Academician V.I. Kulakov of the Ministry of Healthcare of Russian Federation, Moscow, Russian Federation, National Research University Higher School of Economics, Moscow, Russian Federation, Department of Chemistry, Chemical Biology, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark, Institut Fur Organische Chemie, Johannes Gutenberg-Universitat Mainz, Duesbergweg 10-14, D-55128, Mainz, Germany, Institute of Immunology, Federal Medical-Biological Agency of Russia, Moscow, Russian Federation, University of Nantes, Inserm, U892 IRT UN, 8 Quai MonCousu, BP70721 Nantes, FR 44007, France
Methods: ELISA, affinity chromatography, flow cytometry analysis, printed glycan array (PGA) analysis, FACS assay
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3. Compound ID: 11733
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b-D-Glcp-(1-4)-+
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-3)-a-L-Fucp-(1-3)-a-D-GlcpA-(1-3)-a-L-Fucp2(65%)Ac-(1-3)-b-D-GlcpNAc-(1- |
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Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide
Contained glycoepitopes: IEDB_115136,IEDB_135813,IEDB_136045,IEDB_137340,IEDB_140630,IEDB_141807,IEDB_142488,IEDB_142489,IEDB_144562,IEDB_145669,IEDB_146664,IEDB_150092,IEDB_151531,IEDB_152214,IEDB_174333,IEDB_490056,IEDB_983931,SB_192,SB_86
The structure is contained in the following publication(s):
- Article ID: 4705
Ovchinnikova OG, Shashkov AS, Moryl M, Liu B, Rozalski A, Knirel YA "Structure and gene cluster organization of the O-antigen of Providencia alcalifaciens O45:H25" -
Carbohydrate Research 398 (2014) 72-76
O-Polysaccharide was obtained by mild acid degradation of the lipopolysaccharide of Providencia alcalifaciens O45:H25 and studied by sugar analysis, Smith degradation, and (1)H and (13)C NMR spectroscopy. The following structure of the pentasaccharide repeat of the O-polysaccharide was established: [structure: see text]. The O-antigen gene cluster of P. alcalifaciens O45 was sequenced and found to be in full agreement with the O-polysaccharide structure established.
Lipopolysaccharide, structure, gene, O-antigen, O antigen, cluster, gene cluster, O-polysaccharide, O polysaccharide, Providencia, Providencia alcalifaciens, bacterial polysaccharide structure, organization, O-antigen gene cluster
NCBI PubMed ID: 25240185Publication DOI: 10.1016/j.carres.2014.07.008Journal NLM ID: 0043535Publisher: Elsevier
Correspondence: yknirel@gmail.com (Y.A. Knirel)
Institutions: Department of Immunobiology of Bacteria, Institute of Microbiology, Biotechnology and Immunology, University of Lodz, PL 90-237 Lodz, Poland, TEDA School of Biological Sciences and Biotechnology, Nankai University, TEDA, 300457 Tianjin, PR China, N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
Methods: 13C NMR, 1H NMR, NMR-2D, DNA sequencing, GLC-MS, sugar analysis, GLC, mild acid hydrolysis, Smith degradation, de-O-acetylation, NMR-1D, GPC, function analysis of gene clusters
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4. Compound ID: 11734
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b-D-Glcp-(1-4)-+
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-3)-a-L-Fucp-(1-3)-a-D-GlcpA-(1-3)-a-L-Fucp-(1-3)-b-D-GlcpNAc-(1- |
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Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide
Contained glycoepitopes: IEDB_115136,IEDB_135813,IEDB_136045,IEDB_137340,IEDB_140630,IEDB_141807,IEDB_142488,IEDB_142489,IEDB_144562,IEDB_145669,IEDB_146664,IEDB_150092,IEDB_151531,IEDB_152214,IEDB_174333,IEDB_490056,IEDB_983931,SB_192,SB_86
The structure is contained in the following publication(s):
- Article ID: 4705
Ovchinnikova OG, Shashkov AS, Moryl M, Liu B, Rozalski A, Knirel YA "Structure and gene cluster organization of the O-antigen of Providencia alcalifaciens O45:H25" -
Carbohydrate Research 398 (2014) 72-76
O-Polysaccharide was obtained by mild acid degradation of the lipopolysaccharide of Providencia alcalifaciens O45:H25 and studied by sugar analysis, Smith degradation, and (1)H and (13)C NMR spectroscopy. The following structure of the pentasaccharide repeat of the O-polysaccharide was established: [structure: see text]. The O-antigen gene cluster of P. alcalifaciens O45 was sequenced and found to be in full agreement with the O-polysaccharide structure established.
Lipopolysaccharide, structure, gene, O-antigen, O antigen, cluster, gene cluster, O-polysaccharide, O polysaccharide, Providencia, Providencia alcalifaciens, bacterial polysaccharide structure, organization, O-antigen gene cluster
NCBI PubMed ID: 25240185Publication DOI: 10.1016/j.carres.2014.07.008Journal NLM ID: 0043535Publisher: Elsevier
Correspondence: yknirel@gmail.com (Y.A. Knirel)
Institutions: Department of Immunobiology of Bacteria, Institute of Microbiology, Biotechnology and Immunology, University of Lodz, PL 90-237 Lodz, Poland, TEDA School of Biological Sciences and Biotechnology, Nankai University, TEDA, 300457 Tianjin, PR China, N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
Methods: 13C NMR, 1H NMR, NMR-2D, DNA sequencing, GLC-MS, sugar analysis, GLC, mild acid hydrolysis, Smith degradation, de-O-acetylation, NMR-1D, GPC, function analysis of gene clusters
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5. Compound ID: 11735
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-3)-a-L-Fucp-(1-3)-a-D-GlcpA-(1-3)-a-L-Fucp-(1-3)-b-D-GlcpNAc-(1- |
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Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide
Contained glycoepitopes: IEDB_115136,IEDB_135813,IEDB_136045,IEDB_137340,IEDB_140630,IEDB_141807,IEDB_142489,IEDB_144562,IEDB_145669,IEDB_150092,IEDB_151531,IEDB_152214,IEDB_174333,IEDB_490056,SB_86
The structure is contained in the following publication(s):
- Article ID: 4705
Ovchinnikova OG, Shashkov AS, Moryl M, Liu B, Rozalski A, Knirel YA "Structure and gene cluster organization of the O-antigen of Providencia alcalifaciens O45:H25" -
Carbohydrate Research 398 (2014) 72-76
O-Polysaccharide was obtained by mild acid degradation of the lipopolysaccharide of Providencia alcalifaciens O45:H25 and studied by sugar analysis, Smith degradation, and (1)H and (13)C NMR spectroscopy. The following structure of the pentasaccharide repeat of the O-polysaccharide was established: [structure: see text]. The O-antigen gene cluster of P. alcalifaciens O45 was sequenced and found to be in full agreement with the O-polysaccharide structure established.
Lipopolysaccharide, structure, gene, O-antigen, O antigen, cluster, gene cluster, O-polysaccharide, O polysaccharide, Providencia, Providencia alcalifaciens, bacterial polysaccharide structure, organization, O-antigen gene cluster
NCBI PubMed ID: 25240185Publication DOI: 10.1016/j.carres.2014.07.008Journal NLM ID: 0043535Publisher: Elsevier
Correspondence: yknirel@gmail.com (Y.A. Knirel)
Institutions: Department of Immunobiology of Bacteria, Institute of Microbiology, Biotechnology and Immunology, University of Lodz, PL 90-237 Lodz, Poland, TEDA School of Biological Sciences and Biotechnology, Nankai University, TEDA, 300457 Tianjin, PR China, N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
Methods: 13C NMR, 1H NMR, NMR-2D, DNA sequencing, GLC-MS, sugar analysis, GLC, mild acid hydrolysis, Smith degradation, de-O-acetylation, NMR-1D, GPC, function analysis of gene clusters
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6. Compound ID: 13135
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-3)-b-D-GlcpNAc-(1-3)-b-D-GlcpNAc-(1-3)-a-L-Fucp-(1-3)-b-D-GlcpNAc-(1- |
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Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide, O-antigen
Contained glycoepitopes: IEDB_135813,IEDB_136045,IEDB_137340,IEDB_141807,IEDB_142489,IEDB_144562,IEDB_145669,IEDB_150092,IEDB_151531,IEDB_152214,IEDB_174333,IEDB_490056,SB_86
The structure is contained in the following publication(s):
- Article ID: 5192
Naumenko OI, Xiong Y, Zheng H, Senchenkova SN, Wang H, Shashkov AS, Li Q, Wang J, Knirel YA "Studies on the O-polysaccharide of Escherichia albertii O2 characterized by non-stoichiometric O-acetylation and non-stoichiometric side-chain L-fucosylation" -
Carbohydrate Research 461 (2018) 80-84
An O-polysaccharide was isolated from the lipopolysaccharide of Escherichia albertii O2 and studied by chemical methods and 1D and 2D 1H and 13C NMR spectroscopy. The following structure of the O-polysaccharide was established: [structure: see text]. The O-polysaccharide is characterized by masked regularity owing to a non-stoichiometric O-acetylation of an l-fucose residue in the main chain and a non-stoichiometric side-chain l-fucosylation of a β-GlcNAc residue. A regular linear polysaccharide was obtained by sequential Smith degradation and alkaline O-deacetylation of the O-polysaccharide. The content of the O-antigen gene cluster of E. albertii O2 was found to be essentially consistent with the O-polysaccharide structure established.
O-specific polysaccharide, O-acetylation, bacterial polysaccharide structure, O-antigen gene cluster, Escherichia albertii, l-Fucosylation
NCBI PubMed ID: 29609101Publication DOI: 10.1016/j.carres.2018.02.013Journal NLM ID: 0043535Publisher: Elsevier
Correspondence: xiongyanwen@icdc.cn
Institutions: N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Higher Chemical College of the Russian Academy of Sciences, D. I. Mendeleev University of Chemical Technology of Russia, Moscow, Russia, Zigong Center for Disease Control and Prevention, Zigong, Sichuan Province, China, State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, Zhejiang Province, China
Methods: 13C NMR, 1H NMR, NMR-2D, sugar analysis, GLC, mild acid hydrolysis, Smith degradation, de-O-acetylation, GPC, bioinformatic analysis
- Article ID: 5461
Knirel YA, Naumenko OI, Senchenkova SN, Perepelov AV "Chemical methods for selective cleavage of glycosidic linkages in structural analysis of bacterial polysaccharides" -
Russian Chemical Reviews = Uspekhi Khimii 88(4) (2019) 406-424
This review is devoted to methods for the selective cleavage of glycosidic bonds. The mechanisms of reactions underlying these methods are considered and examples of their practical application in the structural analysis of bacterial polysaccharides are given. Specific methods for the selective cleavage of polysaccharides, remaining relevant for researchers, include the Smith degradation based on destruction of monosaccharides containing vicinal diol groups, dephosphorylation of phosphate-containing polysaccharides with hydrofluoric acid and the hydrolytic cleavage of glycosyl phosphate bonds in the latter compounds. Non-specific methods, including partial acid hydrolysis, acetolysis and solvolysis with anhydrous organic (CF3SO3H, MeSO3H, CF3CO2H) and inorganic (HF) acids do not make any specific demands on the composition and structure of the polysaccharide and are sensitive to its fine structural features. The review addesses the issue of stability of glycosidic bonds in various monosaccharides to reagents used for non-specific selective cleavage.
structural analysis, Bacterial polysaccharide, selective cleavage, glycosidic bond
Publication DOI: 10.1070/RCR4856Journal NLM ID: 0404506Publisher: London: Chemical Society
Correspondence: Yu.A. Knirel
Institutions: N.D. Zelinskii Institute of Organic Chemistry, Russian Academy of Sciences
Methods: partial acid hydrolysis, HF solvolysis, acid hydrolysis, mild acid hydrolysis, alkaline degradation, b-elimination, Smith degradation, deamination, de-O-acetylation, HF treatment, reduction with NaBD4, triflic acid solvolysis, acetolysis, Li/ethylenediamine degradation, hydrazinolysis, reduction with NaBH4, mild acid degradation, trifluoroacetic acid solvolysis, partial solvolysis with anhydrous trifluoroacetic acid, de-N-acetylation with hydrazine, part acid hydrolysis, HF solvolysis; published polymerization frame was shifted for conformity with other records.
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7. Compound ID: 13136
|
a-L-Fucp-(1-4)-+
|
-3)-b-D-GlcpNAc-(1-3)-b-D-GlcpNAc-(1-3)-a-L-Fucp-(1-3)-b-D-GlcpNAc-(1- |
Show graphically |
Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide, O-antigen
Contained glycoepitopes: IEDB_135813,IEDB_136045,IEDB_137340,IEDB_141807,IEDB_142489,IEDB_144562,IEDB_145669,IEDB_150092,IEDB_151531,IEDB_152214,IEDB_174333,IEDB_423096,IEDB_490056,SB_86
The structure is contained in the following publication(s):
- Article ID: 5192
Naumenko OI, Xiong Y, Zheng H, Senchenkova SN, Wang H, Shashkov AS, Li Q, Wang J, Knirel YA "Studies on the O-polysaccharide of Escherichia albertii O2 characterized by non-stoichiometric O-acetylation and non-stoichiometric side-chain L-fucosylation" -
Carbohydrate Research 461 (2018) 80-84
An O-polysaccharide was isolated from the lipopolysaccharide of Escherichia albertii O2 and studied by chemical methods and 1D and 2D 1H and 13C NMR spectroscopy. The following structure of the O-polysaccharide was established: [structure: see text]. The O-polysaccharide is characterized by masked regularity owing to a non-stoichiometric O-acetylation of an l-fucose residue in the main chain and a non-stoichiometric side-chain l-fucosylation of a β-GlcNAc residue. A regular linear polysaccharide was obtained by sequential Smith degradation and alkaline O-deacetylation of the O-polysaccharide. The content of the O-antigen gene cluster of E. albertii O2 was found to be essentially consistent with the O-polysaccharide structure established.
O-specific polysaccharide, O-acetylation, bacterial polysaccharide structure, O-antigen gene cluster, Escherichia albertii, l-Fucosylation
NCBI PubMed ID: 29609101Publication DOI: 10.1016/j.carres.2018.02.013Journal NLM ID: 0043535Publisher: Elsevier
Correspondence: xiongyanwen@icdc.cn
Institutions: N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Higher Chemical College of the Russian Academy of Sciences, D. I. Mendeleev University of Chemical Technology of Russia, Moscow, Russia, Zigong Center for Disease Control and Prevention, Zigong, Sichuan Province, China, State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, Zhejiang Province, China
Methods: 13C NMR, 1H NMR, NMR-2D, sugar analysis, GLC, mild acid hydrolysis, Smith degradation, de-O-acetylation, GPC, bioinformatic analysis
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8. Compound ID: 13137
|
70%a-L-Fucp-(1-4)-+
|
-3)-b-D-GlcpNAc-(1-3)-b-D-GlcpNAc-(1-3)-a-L-Fucp4(70%)Ac-(1-3)-b-D-GlcpNAc-(1- |
Show graphically |
Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide, O-antigen
Contained glycoepitopes: IEDB_135813,IEDB_136045,IEDB_137340,IEDB_141807,IEDB_142489,IEDB_144562,IEDB_145669,IEDB_150092,IEDB_151531,IEDB_152214,IEDB_174333,IEDB_423096,IEDB_490056,SB_86
The structure is contained in the following publication(s):
- Article ID: 5192
Naumenko OI, Xiong Y, Zheng H, Senchenkova SN, Wang H, Shashkov AS, Li Q, Wang J, Knirel YA "Studies on the O-polysaccharide of Escherichia albertii O2 characterized by non-stoichiometric O-acetylation and non-stoichiometric side-chain L-fucosylation" -
Carbohydrate Research 461 (2018) 80-84
An O-polysaccharide was isolated from the lipopolysaccharide of Escherichia albertii O2 and studied by chemical methods and 1D and 2D 1H and 13C NMR spectroscopy. The following structure of the O-polysaccharide was established: [structure: see text]. The O-polysaccharide is characterized by masked regularity owing to a non-stoichiometric O-acetylation of an l-fucose residue in the main chain and a non-stoichiometric side-chain l-fucosylation of a β-GlcNAc residue. A regular linear polysaccharide was obtained by sequential Smith degradation and alkaline O-deacetylation of the O-polysaccharide. The content of the O-antigen gene cluster of E. albertii O2 was found to be essentially consistent with the O-polysaccharide structure established.
O-specific polysaccharide, O-acetylation, bacterial polysaccharide structure, O-antigen gene cluster, Escherichia albertii, l-Fucosylation
NCBI PubMed ID: 29609101Publication DOI: 10.1016/j.carres.2018.02.013Journal NLM ID: 0043535Publisher: Elsevier
Correspondence: xiongyanwen@icdc.cn
Institutions: N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Higher Chemical College of the Russian Academy of Sciences, D. I. Mendeleev University of Chemical Technology of Russia, Moscow, Russia, Zigong Center for Disease Control and Prevention, Zigong, Sichuan Province, China, State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, Zhejiang Province, China
Methods: 13C NMR, 1H NMR, NMR-2D, sugar analysis, GLC, mild acid hydrolysis, Smith degradation, de-O-acetylation, GPC, bioinformatic analysis
- Article ID: 5461
Knirel YA, Naumenko OI, Senchenkova SN, Perepelov AV "Chemical methods for selective cleavage of glycosidic linkages in structural analysis of bacterial polysaccharides" -
Russian Chemical Reviews = Uspekhi Khimii 88(4) (2019) 406-424
This review is devoted to methods for the selective cleavage of glycosidic bonds. The mechanisms of reactions underlying these methods are considered and examples of their practical application in the structural analysis of bacterial polysaccharides are given. Specific methods for the selective cleavage of polysaccharides, remaining relevant for researchers, include the Smith degradation based on destruction of monosaccharides containing vicinal diol groups, dephosphorylation of phosphate-containing polysaccharides with hydrofluoric acid and the hydrolytic cleavage of glycosyl phosphate bonds in the latter compounds. Non-specific methods, including partial acid hydrolysis, acetolysis and solvolysis with anhydrous organic (CF3SO3H, MeSO3H, CF3CO2H) and inorganic (HF) acids do not make any specific demands on the composition and structure of the polysaccharide and are sensitive to its fine structural features. The review addesses the issue of stability of glycosidic bonds in various monosaccharides to reagents used for non-specific selective cleavage.
structural analysis, Bacterial polysaccharide, selective cleavage, glycosidic bond
Publication DOI: 10.1070/RCR4856Journal NLM ID: 0404506Publisher: London: Chemical Society
Correspondence: Yu.A. Knirel
Institutions: N.D. Zelinskii Institute of Organic Chemistry, Russian Academy of Sciences
Methods: partial acid hydrolysis, HF solvolysis, acid hydrolysis, mild acid hydrolysis, alkaline degradation, b-elimination, Smith degradation, deamination, de-O-acetylation, HF treatment, reduction with NaBD4, triflic acid solvolysis, acetolysis, Li/ethylenediamine degradation, hydrazinolysis, reduction with NaBH4, mild acid degradation, trifluoroacetic acid solvolysis, partial solvolysis with anhydrous trifluoroacetic acid, de-N-acetylation with hydrazine, part acid hydrolysis, HF solvolysis; published polymerization frame was shifted for conformity with other records.
- Article ID: 5481
Naumenko OI, Senchenkova SN, Knirel YA "O-Specific polysaccharides of a new species of enteric bacteria Escherichia albertii closely related to E. coli" -
Russian Journal of Bioorganic Chemistry 45(6) (2019) 451-462
The data on the structure of O-specific polysaccharides (O-antigens) of all nine known molecular types (potential O-serotypes) of a new type of enterobacteria Escherichia albertii, causative agents of intestinal infections in humans and birds, are presented. The advantages and limitations of structural analysis methods used to determine the structure of E. albertii polysaccharides are discussed. The annotation of genes in gene clusters of biosynthesis of O-antigens of E. albertii was carried out by comparison with the sequences in the available databases. Structural and genetic relationships between O-antigens of E. albertii and closely related species of E. coli are discussed. It was found that, in addition to the O-antigen, E. albertii O9 expresses a mannan of the same structure as the mannan of E. coli O8.
biosynthesis, structure, O-antigen, Escherichia coli, O-specific polysaccharide, glycosyltransferase, O-antigen gene cluster, selective cleavage, glycosidic bond, Escherichia albertii, bacterial mannan
Publication DOI: 10.1134/S1068162019060293Journal NLM ID: 9420101Publisher: Springer Science and Business Media
Correspondence: YA Knirel
Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
Methods: solvolysis with CF3CO2H, acid hydrolysis with CF3CO2H
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9. Compound ID: 19817
|
D-Manp-(1-?)-+
|
b-D-GlcpNAc-(1-2)-D-Manp-(1-?)-b-D-Manp-(1-4)-b-D-GlcpNAc-(1-4)-b-D-GlcpNAc-(1-?)-L-Fucp-(1--/Pep2; Pep1/ |
Show graphically |
Structure type: oligomer
; 2398,2476 [M+H]+; 2430,2337 [M+H]+
Aglycon: Pep2; Pep1
Compound class: N-glycan
Contained glycoepitopes: IEDB_130701,IEDB_133966,IEDB_135813,IEDB_136045,IEDB_136104,IEDB_137340,IEDB_137485,IEDB_141793,IEDB_141807,IEDB_142489,IEDB_144562,IEDB_144983,IEDB_144995,IEDB_151531,IEDB_152206,IEDB_152214,IEDB_153212,IEDB_174333,IEDB_490056,IEDB_983930,SB_136,SB_196,SB_197,SB_198,SB_44,SB_67,SB_72,SB_74,SB_85,SB_86
The structure is contained in the following publication(s):
- Article ID: 7877
Cao L, Yu L, Guo Z, Shen A, Guo Y, Liang X "N-Glycosylation site analysis of proteins from Saccharomyces cerevisiae by using hydrophilic interaction liquid chromatography-based enrichment, parallel deglycosylation, and mass spectrometry" -
Journal of Proteome Research 13(3) (2014) 1485-1493
N-Glycosylation site analysis of baker's yeast Saccharomyces cerevisiae is of fundamental significance to elucidate the molecular mechanism of human congenital disorders of glycosylation (CDG). Here we present a mass spectrometry (MS)-based workflow for the profiling of N-glycosylated sites in S. cerevisiae proteins. In this workflow, proteolytic glycopeptides were enriched by using a hydrophilic material named Click TE-Cys to improve the glycopeptide selectivity and coverage. To enhance the reliability of the identified results, the enriched glycopeptides were subjected to parallel deglycosylation by using two endoglycosidases (i.e., PNGase F and Endo Hf), respectively, prior to LC-MS/MS analysis. On the basis of the workflow, a total of 135 N-glycosylated sites including 6 known, 93 potential, and 36 novel sites were identified and mapped to 79 proteins. Among the novel-type sites, nine sites from eight proteins, which were simultaneously identified via PNGase F and Endo Hf deglycosylation, are believed to possess high confidence. The established workflow, together with the profile of N-glycosylated sites, will contribute to the improvement of S. cerevisiae model for revealing the pathogenesis of CDG.
mass spectrometry, glycopeptide, Glycoproteomics, Saccharomyces cerevisiae, yeast, hydrophilic interaction liquid chromatography
NCBI PubMed ID: 24527708Publication DOI: 10.1021/pr401049eJournal NLM ID: 101128775Publisher: Washington, DC: American Chemical Society
Correspondence: Liang X
Institutions: Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
Methods: enzymatic digestion, affinity chromatography, cell growth, HILIC, LC−MS, MALDI-QIT-TOF
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10. Compound ID: 19820
|
D-Manp-(1-?)-+
|
b-D-GlcpNAc-(1-2)-D-Manp-(1-?)-b-D-Manp-(1-4)-b-D-GlcpNAc-(1-4)-b-D-GlcpNAc-(1-?)-L-Fucp-(1--/Pep1/ |
Show graphically |
Structure type: oligomer
; 2430,2337 [M+H]+
Aglycon: Pep1
Compound class: N-glycan
Contained glycoepitopes: IEDB_130701,IEDB_133966,IEDB_135813,IEDB_136045,IEDB_136104,IEDB_137340,IEDB_137485,IEDB_141793,IEDB_141807,IEDB_142489,IEDB_144562,IEDB_144983,IEDB_144995,IEDB_151531,IEDB_152206,IEDB_152214,IEDB_153212,IEDB_174333,IEDB_490056,IEDB_983930,SB_136,SB_196,SB_197,SB_198,SB_44,SB_67,SB_72,SB_74,SB_85,SB_86
The structure is contained in the following publication(s):
- Article ID: 7877
Cao L, Yu L, Guo Z, Shen A, Guo Y, Liang X "N-Glycosylation site analysis of proteins from Saccharomyces cerevisiae by using hydrophilic interaction liquid chromatography-based enrichment, parallel deglycosylation, and mass spectrometry" -
Journal of Proteome Research 13(3) (2014) 1485-1493
N-Glycosylation site analysis of baker's yeast Saccharomyces cerevisiae is of fundamental significance to elucidate the molecular mechanism of human congenital disorders of glycosylation (CDG). Here we present a mass spectrometry (MS)-based workflow for the profiling of N-glycosylated sites in S. cerevisiae proteins. In this workflow, proteolytic glycopeptides were enriched by using a hydrophilic material named Click TE-Cys to improve the glycopeptide selectivity and coverage. To enhance the reliability of the identified results, the enriched glycopeptides were subjected to parallel deglycosylation by using two endoglycosidases (i.e., PNGase F and Endo Hf), respectively, prior to LC-MS/MS analysis. On the basis of the workflow, a total of 135 N-glycosylated sites including 6 known, 93 potential, and 36 novel sites were identified and mapped to 79 proteins. Among the novel-type sites, nine sites from eight proteins, which were simultaneously identified via PNGase F and Endo Hf deglycosylation, are believed to possess high confidence. The established workflow, together with the profile of N-glycosylated sites, will contribute to the improvement of S. cerevisiae model for revealing the pathogenesis of CDG.
mass spectrometry, glycopeptide, Glycoproteomics, Saccharomyces cerevisiae, yeast, hydrophilic interaction liquid chromatography
NCBI PubMed ID: 24527708Publication DOI: 10.1021/pr401049eJournal NLM ID: 101128775Publisher: Washington, DC: American Chemical Society
Correspondence: Liang X
Institutions: Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
Methods: enzymatic digestion, affinity chromatography, cell growth, HILIC, LC−MS, MALDI-QIT-TOF
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11. Compound ID: 19821
|
D-Manp-(1-?)-+
|
b-D-Galp-(1-?)-b-D-GlcpNAc-(1-2)-D-Manp-(1-?)-b-D-Manp-(1-4)-b-D-GlcpNAc-(1-4)-b-D-GlcpNAc-(1-?)-L-Fucp-(1--/Pep2; Pep1/ |
Show graphically |
Structure type: oligomer
; 2560,2584 [M+H]+, 2592,2511 [M+H]+
Aglycon: Pep2; Pep1
Compound class: N-glycan
Contained glycoepitopes: IEDB_130646,IEDB_130701,IEDB_133966,IEDB_135813,IEDB_136044,IEDB_136045,IEDB_136104,IEDB_137340,IEDB_137472,IEDB_137485,IEDB_1391962,IEDB_140108,IEDB_140122,IEDB_141793,IEDB_141794,IEDB_141807,IEDB_142078,IEDB_142489,IEDB_143794,IEDB_144562,IEDB_144983,IEDB_144995,IEDB_150899,IEDB_151531,IEDB_152206,IEDB_152214,IEDB_153212,IEDB_174333,IEDB_190606,IEDB_423128,IEDB_490056,IEDB_983930,SB_136,SB_137,SB_165,SB_166,SB_187,SB_195,SB_196,SB_197,SB_198,SB_29,SB_30,SB_44,SB_67,SB_7,SB_72,SB_74,SB_85,SB_86,SB_88
The structure is contained in the following publication(s):
- Article ID: 7877
Cao L, Yu L, Guo Z, Shen A, Guo Y, Liang X "N-Glycosylation site analysis of proteins from Saccharomyces cerevisiae by using hydrophilic interaction liquid chromatography-based enrichment, parallel deglycosylation, and mass spectrometry" -
Journal of Proteome Research 13(3) (2014) 1485-1493
N-Glycosylation site analysis of baker's yeast Saccharomyces cerevisiae is of fundamental significance to elucidate the molecular mechanism of human congenital disorders of glycosylation (CDG). Here we present a mass spectrometry (MS)-based workflow for the profiling of N-glycosylated sites in S. cerevisiae proteins. In this workflow, proteolytic glycopeptides were enriched by using a hydrophilic material named Click TE-Cys to improve the glycopeptide selectivity and coverage. To enhance the reliability of the identified results, the enriched glycopeptides were subjected to parallel deglycosylation by using two endoglycosidases (i.e., PNGase F and Endo Hf), respectively, prior to LC-MS/MS analysis. On the basis of the workflow, a total of 135 N-glycosylated sites including 6 known, 93 potential, and 36 novel sites were identified and mapped to 79 proteins. Among the novel-type sites, nine sites from eight proteins, which were simultaneously identified via PNGase F and Endo Hf deglycosylation, are believed to possess high confidence. The established workflow, together with the profile of N-glycosylated sites, will contribute to the improvement of S. cerevisiae model for revealing the pathogenesis of CDG.
mass spectrometry, glycopeptide, Glycoproteomics, Saccharomyces cerevisiae, yeast, hydrophilic interaction liquid chromatography
NCBI PubMed ID: 24527708Publication DOI: 10.1021/pr401049eJournal NLM ID: 101128775Publisher: Washington, DC: American Chemical Society
Correspondence: Liang X
Institutions: Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
Methods: enzymatic digestion, affinity chromatography, cell growth, HILIC, LC−MS, MALDI-QIT-TOF
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12. Compound ID: 19822
|
b-D-GlcpNAc-(1-2)-D-Manp-(1-6)-+
|
b-D-GlcpNAc-(1-2)-D-Manp-(1-3)-b-D-Manp-(1-4)-b-D-GlcpNAc-(1-4)-b-D-GlcpNAc-(1-?)-L-Fucp-(1--/Pep2; Pep1/ |
Show graphically |
Structure type: oligomer
; 2601,2725 [M+H]+, 2633,2410 [M+H]+
Aglycon: Pep2; Pep1
Compound class: N-glycan
Contained glycoepitopes: IEDB_123886,IEDB_130701,IEDB_135813,IEDB_136045,IEDB_137340,IEDB_137485,IEDB_141793,IEDB_141807,IEDB_142489,IEDB_144562,IEDB_144983,IEDB_151531,IEDB_152206,IEDB_152214,IEDB_153212,IEDB_174333,IEDB_490056,IEDB_548907,IEDB_983930,SB_197,SB_198,SB_33,SB_44,SB_67,SB_72,SB_73,SB_74,SB_85,SB_86
The structure is contained in the following publication(s):
- Article ID: 7877
Cao L, Yu L, Guo Z, Shen A, Guo Y, Liang X "N-Glycosylation site analysis of proteins from Saccharomyces cerevisiae by using hydrophilic interaction liquid chromatography-based enrichment, parallel deglycosylation, and mass spectrometry" -
Journal of Proteome Research 13(3) (2014) 1485-1493
N-Glycosylation site analysis of baker's yeast Saccharomyces cerevisiae is of fundamental significance to elucidate the molecular mechanism of human congenital disorders of glycosylation (CDG). Here we present a mass spectrometry (MS)-based workflow for the profiling of N-glycosylated sites in S. cerevisiae proteins. In this workflow, proteolytic glycopeptides were enriched by using a hydrophilic material named Click TE-Cys to improve the glycopeptide selectivity and coverage. To enhance the reliability of the identified results, the enriched glycopeptides were subjected to parallel deglycosylation by using two endoglycosidases (i.e., PNGase F and Endo Hf), respectively, prior to LC-MS/MS analysis. On the basis of the workflow, a total of 135 N-glycosylated sites including 6 known, 93 potential, and 36 novel sites were identified and mapped to 79 proteins. Among the novel-type sites, nine sites from eight proteins, which were simultaneously identified via PNGase F and Endo Hf deglycosylation, are believed to possess high confidence. The established workflow, together with the profile of N-glycosylated sites, will contribute to the improvement of S. cerevisiae model for revealing the pathogenesis of CDG.
mass spectrometry, glycopeptide, Glycoproteomics, Saccharomyces cerevisiae, yeast, hydrophilic interaction liquid chromatography
NCBI PubMed ID: 24527708Publication DOI: 10.1021/pr401049eJournal NLM ID: 101128775Publisher: Washington, DC: American Chemical Society
Correspondence: Liang X
Institutions: Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
Methods: enzymatic digestion, affinity chromatography, cell growth, HILIC, LC−MS, MALDI-QIT-TOF
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13. Compound ID: 19824
|
b-D-GlcpNAc-(1-?)-D-Manp-(1-?)-+
|
b-D-Galp-(1-?)-b-D-GlcpNAc-(1-2)-D-Manp-(1-?)-b-D-Manp-(1-4)-b-D-GlcpNAc-(1-4)-b-D-GlcpNAc-(1-?)-L-Fucp-(1--/Pep2; Pep1/ |
Show graphically |
Structure type: oligomer
; 2763,2676 [M+H]+, 2795,2568 [M+H]+
Aglycon: Pep2; Pep1
Compound class: N-glycan
Contained glycoepitopes: IEDB_130646,IEDB_130701,IEDB_133966,IEDB_135813,IEDB_136044,IEDB_136045,IEDB_136104,IEDB_137340,IEDB_137472,IEDB_137485,IEDB_1391962,IEDB_140108,IEDB_140122,IEDB_141793,IEDB_141794,IEDB_141807,IEDB_142078,IEDB_142489,IEDB_143794,IEDB_144562,IEDB_144983,IEDB_144995,IEDB_150899,IEDB_151531,IEDB_152206,IEDB_152214,IEDB_153212,IEDB_174333,IEDB_190606,IEDB_423128,IEDB_490056,IEDB_983930,SB_136,SB_137,SB_165,SB_166,SB_187,SB_195,SB_196,SB_197,SB_198,SB_29,SB_30,SB_44,SB_67,SB_7,SB_72,SB_74,SB_85,SB_86,SB_88
The structure is contained in the following publication(s):
- Article ID: 7877
Cao L, Yu L, Guo Z, Shen A, Guo Y, Liang X "N-Glycosylation site analysis of proteins from Saccharomyces cerevisiae by using hydrophilic interaction liquid chromatography-based enrichment, parallel deglycosylation, and mass spectrometry" -
Journal of Proteome Research 13(3) (2014) 1485-1493
N-Glycosylation site analysis of baker's yeast Saccharomyces cerevisiae is of fundamental significance to elucidate the molecular mechanism of human congenital disorders of glycosylation (CDG). Here we present a mass spectrometry (MS)-based workflow for the profiling of N-glycosylated sites in S. cerevisiae proteins. In this workflow, proteolytic glycopeptides were enriched by using a hydrophilic material named Click TE-Cys to improve the glycopeptide selectivity and coverage. To enhance the reliability of the identified results, the enriched glycopeptides were subjected to parallel deglycosylation by using two endoglycosidases (i.e., PNGase F and Endo Hf), respectively, prior to LC-MS/MS analysis. On the basis of the workflow, a total of 135 N-glycosylated sites including 6 known, 93 potential, and 36 novel sites were identified and mapped to 79 proteins. Among the novel-type sites, nine sites from eight proteins, which were simultaneously identified via PNGase F and Endo Hf deglycosylation, are believed to possess high confidence. The established workflow, together with the profile of N-glycosylated sites, will contribute to the improvement of S. cerevisiae model for revealing the pathogenesis of CDG.
mass spectrometry, glycopeptide, Glycoproteomics, Saccharomyces cerevisiae, yeast, hydrophilic interaction liquid chromatography
NCBI PubMed ID: 24527708Publication DOI: 10.1021/pr401049eJournal NLM ID: 101128775Publisher: Washington, DC: American Chemical Society
Correspondence: Liang X
Institutions: Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
Methods: enzymatic digestion, affinity chromatography, cell growth, HILIC, LC−MS, MALDI-QIT-TOF
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14. Compound ID: 19826
|
b-D-GlcpNAc-(1-2)-D-Manp-(1-6)-+
|
b-D-GlcpNAc-(1-2)-D-Manp-(1-3)-b-D-Manp-(1-4)-b-D-GlcpNAc-(1-4)-b-D-GlcpNAc-(1-?)-L-Fucp-(1--/Pep2; Pep1/
|
b-D-GlcpNAc-(1-?)-+ |
Show graphically |
Structure type: oligomer
; 2804,2876 [M+H]+, 2836,2574 [M+H]+
Aglycon: Pep2; Pep1
Compound class: N-glycan
Contained glycoepitopes: IEDB_123886,IEDB_130701,IEDB_135813,IEDB_136045,IEDB_137340,IEDB_137485,IEDB_141793,IEDB_141807,IEDB_142489,IEDB_144562,IEDB_144983,IEDB_151531,IEDB_152206,IEDB_152214,IEDB_153212,IEDB_174333,IEDB_490056,IEDB_548907,IEDB_983930,SB_197,SB_198,SB_33,SB_44,SB_67,SB_72,SB_73,SB_74,SB_85,SB_86
The structure is contained in the following publication(s):
- Article ID: 7877
Cao L, Yu L, Guo Z, Shen A, Guo Y, Liang X "N-Glycosylation site analysis of proteins from Saccharomyces cerevisiae by using hydrophilic interaction liquid chromatography-based enrichment, parallel deglycosylation, and mass spectrometry" -
Journal of Proteome Research 13(3) (2014) 1485-1493
N-Glycosylation site analysis of baker's yeast Saccharomyces cerevisiae is of fundamental significance to elucidate the molecular mechanism of human congenital disorders of glycosylation (CDG). Here we present a mass spectrometry (MS)-based workflow for the profiling of N-glycosylated sites in S. cerevisiae proteins. In this workflow, proteolytic glycopeptides were enriched by using a hydrophilic material named Click TE-Cys to improve the glycopeptide selectivity and coverage. To enhance the reliability of the identified results, the enriched glycopeptides were subjected to parallel deglycosylation by using two endoglycosidases (i.e., PNGase F and Endo Hf), respectively, prior to LC-MS/MS analysis. On the basis of the workflow, a total of 135 N-glycosylated sites including 6 known, 93 potential, and 36 novel sites were identified and mapped to 79 proteins. Among the novel-type sites, nine sites from eight proteins, which were simultaneously identified via PNGase F and Endo Hf deglycosylation, are believed to possess high confidence. The established workflow, together with the profile of N-glycosylated sites, will contribute to the improvement of S. cerevisiae model for revealing the pathogenesis of CDG.
mass spectrometry, glycopeptide, Glycoproteomics, Saccharomyces cerevisiae, yeast, hydrophilic interaction liquid chromatography
NCBI PubMed ID: 24527708Publication DOI: 10.1021/pr401049eJournal NLM ID: 101128775Publisher: Washington, DC: American Chemical Society
Correspondence: Liang X
Institutions: Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
Methods: enzymatic digestion, affinity chromatography, cell growth, HILIC, LC−MS, MALDI-QIT-TOF
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15. Compound ID: 19827
|
b-D-Galp-(1-?)-b-D-GlcpNAc-(1-2)-D-Manp-(1-6)-+
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b-D-Galp-(1-?)-b-D-GlcpNAc-(1-2)-D-Manp-(1-3)-b-D-Manp-(1-4)-b-D-GlcpNAc-(1-4)-b-D-GlcpNAc-(1-?)-L-Fucp-(1--/Pep2; Pep1/ |
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Structure type: oligomer
; 2925,2703 [M+H]+, 2957,2582 [M+H]+
Aglycon: Pep2; Pep1
Compound class: N-glycan
Contained glycoepitopes: IEDB_123886,IEDB_130646,IEDB_130701,IEDB_135813,IEDB_136044,IEDB_136045,IEDB_137340,IEDB_137472,IEDB_137485,IEDB_1391962,IEDB_140108,IEDB_140122,IEDB_141793,IEDB_141794,IEDB_141807,IEDB_142078,IEDB_142489,IEDB_143794,IEDB_144562,IEDB_144983,IEDB_150899,IEDB_151531,IEDB_152206,IEDB_152214,IEDB_153212,IEDB_174333,IEDB_190606,IEDB_423128,IEDB_490056,IEDB_540672,IEDB_548907,IEDB_983930,SB_137,SB_165,SB_166,SB_187,SB_195,SB_197,SB_198,SB_29,SB_30,SB_33,SB_44,SB_67,SB_7,SB_72,SB_73,SB_74,SB_85,SB_86,SB_88
The structure is contained in the following publication(s):
- Article ID: 7877
Cao L, Yu L, Guo Z, Shen A, Guo Y, Liang X "N-Glycosylation site analysis of proteins from Saccharomyces cerevisiae by using hydrophilic interaction liquid chromatography-based enrichment, parallel deglycosylation, and mass spectrometry" -
Journal of Proteome Research 13(3) (2014) 1485-1493
N-Glycosylation site analysis of baker's yeast Saccharomyces cerevisiae is of fundamental significance to elucidate the molecular mechanism of human congenital disorders of glycosylation (CDG). Here we present a mass spectrometry (MS)-based workflow for the profiling of N-glycosylated sites in S. cerevisiae proteins. In this workflow, proteolytic glycopeptides were enriched by using a hydrophilic material named Click TE-Cys to improve the glycopeptide selectivity and coverage. To enhance the reliability of the identified results, the enriched glycopeptides were subjected to parallel deglycosylation by using two endoglycosidases (i.e., PNGase F and Endo Hf), respectively, prior to LC-MS/MS analysis. On the basis of the workflow, a total of 135 N-glycosylated sites including 6 known, 93 potential, and 36 novel sites were identified and mapped to 79 proteins. Among the novel-type sites, nine sites from eight proteins, which were simultaneously identified via PNGase F and Endo Hf deglycosylation, are believed to possess high confidence. The established workflow, together with the profile of N-glycosylated sites, will contribute to the improvement of S. cerevisiae model for revealing the pathogenesis of CDG.
mass spectrometry, glycopeptide, Glycoproteomics, Saccharomyces cerevisiae, yeast, hydrophilic interaction liquid chromatography
NCBI PubMed ID: 24527708Publication DOI: 10.1021/pr401049eJournal NLM ID: 101128775Publisher: Washington, DC: American Chemical Society
Correspondence: Liang X
Institutions: Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
Methods: enzymatic digestion, affinity chromatography, cell growth, HILIC, LC−MS, MALDI-QIT-TOF
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