Found 12 structures.
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1. Compound ID: 2625
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a-L-RhapNAc-(1-4)-+
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-3)-a-L-QuipNAc-(1-3)-a-D-GlcpNAc-(1-3)-a-D-GalpNAcA-(1- |
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Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide
Contained glycoepitopes: IEDB_137340,IEDB_141807,IEDB_151531
The structure is contained in the following publication(s):
- Article ID: 893
Kondakova AN, Kolodziejska K, Zych K, Senchenkova SN, Sidorczyk Z, Shashkov AS, Knirel YA "Structure of the N-acetyl-L-rhamnosamine-containing O-polysaccharide of Proteus vulgaris TG 155 from a new Proteus serogroup, O55" -
Carbohydrate Research 338(19) (2003) 1999-2004
The O-polysaccharide of the lipopolysaccharide (LPS) of Proteus vulgaris TG 155 was found to contain 2-acetamido-2,6-dideoxy-L-mannose (N-acetyl-L-rhamnosamine, L-RhaNAc), a monosaccharide that occurs rarely in Nature. The following structure of the O-polysaccharide was established by NMR spectroscopy, including 2D COSY, TOCSY, ROESY and 1H,13C HSQC experiments, along with chemical methods: [carbohydrate structure in text] Rabbit polyclonal O-antiserum against P. vulgaris TG 155 reacted with both core and O-polysaccharide moieties of the homologous LPS but showed no cross-reactivity with other LPS from the complete set of serologically different Proteus strains. Based on the unique O-polysaccharide structure and the serological data, we propose classifying P. vulgaris TG 155 into a new, separate Proteus O-serogroup, O55.
Lipopolysaccharide, serological classification, Proteus vulgaris, O-Polysaccharide structure, rhamnosamine
NCBI PubMed ID: 14499576Journal NLM ID: 0043535Publisher: Elsevier
Correspondence: knirel@ioc.ac.ru
Institutions: N.D.Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, N.D.Zelinsky Institute of Organic Chemistry, Russian Academy Of Sciences, Moscow, Russie
Methods: NMR, acid hydrolysis, optical rotation measurement
- Article ID: 4049
Knirel YA, Perepelov AV, Kondakova AN, Senchenkova SN, Sidorczyk Z, Rozalski A, Kaca W "Structure and serology of O-antigens as the basis for classification of Proteus strains" -
Innate Immunity 17(1) (2011) 70-96
This review is devoted to structural and serological characteristics of the O-antigens (O-polysaccharides) of the lipopolysaccharides of various Proteus species, which provide the basis for classifying Proteus strains to O-serogroups. The antigenic relationships of Proteus strains within and beyond the genus as well as their O-antigen-related bioactivities are also discussed.
Lipopolysaccharide, O-antigen, Proteus, polysaccharide structure, classification, Serological cross-reactivity, immunospecificity
NCBI PubMed ID: 20305038Publication DOI: 10.1177/1753425909360668Journal NLM ID: 101469670Publisher: Sage Publications
Correspondence: yknirel@gmail.com
Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Institute of Microbiology, Biotechnology and Immunology, University of Lodz, Lodz, Poland, Department of Microbiology, Jan Kochanowski University, Kielce, Poland
- Article ID: 4926
Sanapala SR, Kulkarni SS "Expedient Route To Access Rare Deoxy Amino L-Sugar Building Blocks for the Assembly of Bacterial Glycoconjugates" -
Journal of the American Chemical Society 138(14) (2016) 4938-4947
Bacterial glycoproteins and oligosaccharides contain several rare deoxy amino l-sugars which are virtually absent in the human cells. This structural difference between the bacterial and host cell surface glycans can be exploited for the development of carbohydrate based vaccines and target specific drugs. However, the unusual deoxy amino l-sugars present in the bacterial glycoconjugates are not available from natural sources. Thus, procurement of orthogonally protected rare l-sugar building blocks through efficient chemical synthesis is a crucial step toward the synthesis of structurally well-defined and homogeneous complex glycans. Herein, we report a general and expedient methodology to access a variety of unusual deoxy amino l-sugars starting from readily available l-rhamnose and l-fucose via highly regioselective, one-pot double serial and double parallel displacements of the corresponding 2,4-bistriflates using azide and nitrite anions as nucleophiles. Alternatively, regioselective monotriflation at O2, O3, and O4 of l-rhamnose/l-fucose allowed selective inversions at respective positions leading to diverse rare sugars. The orthogonally protected deoxy amino l-sugar building blocks could be stereoselectively assembled to obtain biologically relevant bacterial O-glycans, as exemplified by the first total synthesis of the amino linker-attached, conjugation-ready tetrasaccharide of O-PS of Yersinia enterocolitica O:50 strain 3229 and the trisaccharide of Pseudomonas chlororaphis subsp. aureofaciens strain M71.
trisaccharide, Pseudomonas, glycoconjugates, vaccines, L-rhamnose, L-fucose, Yersinia enterocolitica, chemical synthesis, O-glycans
NCBI PubMed ID: 27002789Publication DOI: 10.1021/jacs.6b01823Journal NLM ID: 7503056Publisher: American Chemical Society
Correspondence: suvarn@chem.iitb.ac.in
Institutions: Department of Chemistry, Indian Institute of Technology Bombay , Powai, Mumbai 400076, India
Methods: 13C NMR, 1H NMR, TLC, GLC, chemical synthesis, chemical methods, MS, glycosylation
- Article ID: 6440
Paul A, Kulkarni SS "Total Synthesis of the Repeating Units of Proteus penneri 26 and Proteus vulgaris TG155 via a Common Disaccharide" -
Organic Letters 25(23) (2023) 4400-4405
Herein, we report the first total synthesis of the trisaccharide and tetrasaccharide repeating units of P. penneri 26 and P. vulgaris TG155, respectively, having a common disaccharide unit, 3-aloha-l-QuipNAc-(1 > 3)-alpha-d-GlcpNAc-(1 >. Striking features of the targets are the presence of rare sugar units, l-quinovosamine and l-rhamnosamine, all joined through alpha-glycosidic linkages. Major challenges in the formation of 1,2-cis glycosidic linkages in the case of d-glucosamine, l-quinovosamine, and d-galactosamine have been addressed.
repeating unit, total synthesis, Proteus penneri 26, Proteus vulgaris TG155
NCBI PubMed ID: 37284758Publication DOI: 10.1021/acs.orglett.3c01618Journal NLM ID: 100890393Publisher: American Chemical Society
Correspondence: S.S. Kulkarni
Institutions: Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai, Maharashtra 400076, India
Methods: 13C NMR, 1H NMR, TLC, chemical synthesis, FTIR, UV, glycosylation, optical rotation measurement, CC, HR-ESI-MS
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2. Compound ID: 2626
Structure type: monomer
The structure is contained in the following publication(s):
- Article ID: 893
Kondakova AN, Kolodziejska K, Zych K, Senchenkova SN, Sidorczyk Z, Shashkov AS, Knirel YA "Structure of the N-acetyl-L-rhamnosamine-containing O-polysaccharide of Proteus vulgaris TG 155 from a new Proteus serogroup, O55" -
Carbohydrate Research 338(19) (2003) 1999-2004
The O-polysaccharide of the lipopolysaccharide (LPS) of Proteus vulgaris TG 155 was found to contain 2-acetamido-2,6-dideoxy-L-mannose (N-acetyl-L-rhamnosamine, L-RhaNAc), a monosaccharide that occurs rarely in Nature. The following structure of the O-polysaccharide was established by NMR spectroscopy, including 2D COSY, TOCSY, ROESY and 1H,13C HSQC experiments, along with chemical methods: [carbohydrate structure in text] Rabbit polyclonal O-antiserum against P. vulgaris TG 155 reacted with both core and O-polysaccharide moieties of the homologous LPS but showed no cross-reactivity with other LPS from the complete set of serologically different Proteus strains. Based on the unique O-polysaccharide structure and the serological data, we propose classifying P. vulgaris TG 155 into a new, separate Proteus O-serogroup, O55.
Lipopolysaccharide, serological classification, Proteus vulgaris, O-Polysaccharide structure, rhamnosamine
NCBI PubMed ID: 14499576Journal NLM ID: 0043535Publisher: Elsevier
Correspondence: knirel@ioc.ac.ru
Institutions: N.D.Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, N.D.Zelinsky Institute of Organic Chemistry, Russian Academy Of Sciences, Moscow, Russie
Methods: NMR, acid hydrolysis, optical rotation measurement
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3. Compound ID: 3121
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a-L-RhapNAc-(1-4)-+
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-3)-a-D-FucpNAc-(1-3)-a-D-GalpNAcA-(1-3)-a-L-QuipNAc-(1- |
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Structure type: polymer chemical repeating unit
Compound class: CPS
Contained glycoepitopes: IEDB_1870740
The structure is contained in the following publication(s):
- Article ID: 1136
Reddy GP, Hayat U, Xu QW, Reddy KV, Wang YH, Chiu KW, Morris JG, Bush CA "Structure determination of the capsular polysaccharide from Vibrio vulnificus strain 6353" -
European Journal of Biochemistry 255(1) (1998) 279-288
Vibrio vulnificus is a pathogenic gram-negative bacterium, endemic to brackish waters, which is often isolated from sediments, from the water column or from shellfish. It is associated with wound infections and septicemia in humans and the virulence of V. vulnificus has been strongly associated with encapsulation. The capsular polysaccharide purified from a virulent strain of V. vulnificus 6353 did not show cross reactivity with antibodies to the capsular polysaccharide of a related pathogenic strain of V. vulnificus (MO6-24) the structure of which was recently reported. NMR spectroscopic analysis of the purified polysaccharide from strain 6353 showed that the polymer is composed of four sugar residues per repeating subunit including 2,6-dideoxy-2-N-acetylamino-α-D-glucose (QuiNAc), 2-deoxy-2-N-acetylamino-α-D-galactose (α-D-GalNAc), 2-deoxy-2-N-acetylamino-α-D-galcturonic acid (α-D-GalNAcA) and 2-N-acetylamino-α-D-glucuronamide (α-D-GlcNAcANH2). The 1H- and 13C NMR spectra were completely assigned by homonuclear and heteronuclear NMR spectroscopy. Sugar types and anomeric configurations were determined from proton homonuclear coupling constants and glycosidic linkages were determined from 1H-13C heteronuclear multiple bond correlation spectra. Sugar identities were confirmed by high performance anion-exchange chromatography and absolute configurations were determined by gas chromatography in combination with molecular modeling and NMR spectroscopy. The structure of the polysaccharide repeating unit is: [→4)-α-D-GalpNAc-(1→3)-α-D-GalpNAcA-(1→3)-α-D-QuipNAc-(1→]n α-D-GlcpNAcANH2(1→4)-→. While there are some common features shared among the structures of the capsular polysaccharides of pathogenic strains of V. vulnificus, there are distinct differences in the detailed structures.
NMR, structure, polysaccharide, bacteria, Vibrio, Vibrio vulnificus
NCBI PubMed ID: 9692929Publication DOI: 10.1046/j.1432-1327.1998.2550279.xJournal NLM ID: 0107600Publisher: Oxford, UK: Blackwell Science Ltd. on behalf of the Federation of European Biochemical Societies
Correspondence: bush@umbc.edu
Institutions: Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore MD, USA, Departments of Medicine and Pathology, University of Maryland School of Medicine and Veterans Affairs Medical Center, Baltimore MD, USA
Methods: 13C NMR, 1H NMR, NMR-2D, HPLC
- Article ID: 4926
Sanapala SR, Kulkarni SS "Expedient Route To Access Rare Deoxy Amino L-Sugar Building Blocks for the Assembly of Bacterial Glycoconjugates" -
Journal of the American Chemical Society 138(14) (2016) 4938-4947
Bacterial glycoproteins and oligosaccharides contain several rare deoxy amino l-sugars which are virtually absent in the human cells. This structural difference between the bacterial and host cell surface glycans can be exploited for the development of carbohydrate based vaccines and target specific drugs. However, the unusual deoxy amino l-sugars present in the bacterial glycoconjugates are not available from natural sources. Thus, procurement of orthogonally protected rare l-sugar building blocks through efficient chemical synthesis is a crucial step toward the synthesis of structurally well-defined and homogeneous complex glycans. Herein, we report a general and expedient methodology to access a variety of unusual deoxy amino l-sugars starting from readily available l-rhamnose and l-fucose via highly regioselective, one-pot double serial and double parallel displacements of the corresponding 2,4-bistriflates using azide and nitrite anions as nucleophiles. Alternatively, regioselective monotriflation at O2, O3, and O4 of l-rhamnose/l-fucose allowed selective inversions at respective positions leading to diverse rare sugars. The orthogonally protected deoxy amino l-sugar building blocks could be stereoselectively assembled to obtain biologically relevant bacterial O-glycans, as exemplified by the first total synthesis of the amino linker-attached, conjugation-ready tetrasaccharide of O-PS of Yersinia enterocolitica O:50 strain 3229 and the trisaccharide of Pseudomonas chlororaphis subsp. aureofaciens strain M71.
trisaccharide, Pseudomonas, glycoconjugates, vaccines, L-rhamnose, L-fucose, Yersinia enterocolitica, chemical synthesis, O-glycans
NCBI PubMed ID: 27002789Publication DOI: 10.1021/jacs.6b01823Journal NLM ID: 7503056Publisher: American Chemical Society
Correspondence: suvarn@chem.iitb.ac.in
Institutions: Department of Chemistry, Indian Institute of Technology Bombay , Powai, Mumbai 400076, India
Methods: 13C NMR, 1H NMR, TLC, GLC, chemical synthesis, chemical methods, MS, glycosylation
- Article ID: 5791
Knirel YA, Van Calsteren M "Bacterial exopolysaccharides" -
Book: Comprehensive Glycoscience: From Chemistry to Systems Biology. Reference Module in Chemistry, Molecular Sciences and Chemical Engineering (2021) 1-75
Bacterial extracellular polysaccharides are known as a cell-bound capsule, a sheath, or a slime, which is excreted into the environment. They play an important role in virulence of medical bacteria and plant-to-symbiont interaction and are used for serotyping of bacteria and production of vaccines. Some exopolysaccharides have commercial applications in industry, and claims of health benefits have been documented for an increasing number of them. Exopolysaccharides have diverse composition and structure, and some contain sugar and non-sugar components that are found in bacterial carbohydrates only. The present article provides an updated collection of the data on exopolysaccharides of various classes of gram-negative and gram-positive bacteria reported until the end of 2019. When known, biosynthesis pathways of exopolysaccharides are treated in a summary manner. References are made to structure and biosynthesis relatedness between exopolysaccharides of different bacterial taxa as well as between bacterial polysaccharides and mammalian glycosaminoglycans.
polysaccharide structure, Gram-negative bacteria, capsule, Biofilm, polysaccharide biosynthesis, gram-positive bacteria, Monosaccharide composition, Bacterial exopolysaccharide, non-sugar component
Publication DOI: 10.1016/B978-0-12-819475-1.00005-5Publisher: Elsevier
Correspondence: marie-rose.vancalsteren@canada.ca; yknirel@gmail.com
Editors: Barchi J, Kamerling H
Institutions: N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Saint-Hyacinthe Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Hyacinthe, QC, Canada
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4. Compound ID: 4180
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b-L-RhapNAc-(1-4)-+ a-D-Glcp-(1-4)-+
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-3)-b-D-GlcpNAc-(1-3)-a-D-Galp-(1-3)-b-D-GlcpNAc-(1- |
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Structure type: suggested polymer biological repeating unit
Compound class: O-polysaccharide, O-antigen
Contained glycoepitopes: IEDB_135813,IEDB_136906,IEDB_137340,IEDB_137472,IEDB_141794,IEDB_141807,IEDB_142488,IEDB_144998,IEDB_146664,IEDB_151528,IEDB_151531,IEDB_190606,IEDB_983931,SB_173,SB_192,SB_7
The structure is contained in the following publication(s):
- Article ID: 1548
Olsson U, Lycknert K, Stenutz R, Weintraub A, Widmalm G "Structural analysis of the O-antigen polysaccharide from Escherichia coli O152" -
Carbohydrate Research 340(1) (2005) 167-171
The structure of the O-antigen polysaccharide (PS) from Escherichia coli O152 has been determined. Component analysis together with (1)H, (13)C and (31)P NMR spectroscopy were used to elucidate the structure. Inter-residue correlations were determined by (1)H,(31)P COSY, (1)H,(1)H NOESY and (1)H,(13)C heteronuclear multiple-bond correlation experiments. The PS is composed of pentasaccharide repeating units with the following structure: The structure is similar to that of the O-antigen polysaccharide from E. coli O173. The cross-reactivity between E. coli O152 and E. coli O3 may be explained by structural similarities in the branching region of their O-antigen polysaccharides
NMR, structure, chemistry, correlation, structural, polysaccharide, O-antigen, repeating unit, analysis, O antigen, Escherichia, Escherichia coli, NMR spectroscopy, structural analysis, polysaccharides, region, spectroscopy, pentasaccharide, component, similarity, cross-reactivity, crossreactivity, organic, NOESY, COSY, heteronuclear
NCBI PubMed ID: 15620681Publication DOI: 10.1016/j.carres.2004.11.008Journal NLM ID: 0043535Publisher: Elsevier
Institutions: Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, Sweden, Karolinska Institute, Department of Laboratory Medicine, Division of Clinical Bacteriology, F-82 Karolinska University Hospital, Huddinge Stockholm, Sweden
Methods: NMR, composition analysis
- Article ID: 3197
Stenutz R, Weintraub A, Widmalm G "The structures of Escherichia coli O-polysaccharide antigens" -
FEMS Microbiology Reviews 30(3) (2006) 382-403
Escherichia coli is usually a non-pathogenic member of the human colonic flora. However, certain strains have acquired virulence factors and may cause a variety of infections in humans and in animals. There are three clinical syndromes caused by E. coli: (i) sepsis/meningitis; (ii) urinary tract infection and (iii) diarrhoea. Furthermore the E. coli causing diarrhoea is divided into different 'pathotypes' depending on the type of disease, i.e. (i) enterotoxigenic; (ii) enteropathogenic; (iii) enteroinvasive; (iv) enterohaemorrhagic; (v) enteroaggregative and (vi) diffusely adherent. The serotyping of E. coli based on the somatic (O), flagellar (H) and capsular polysaccharide antigens (K) is used in epidemiology. The different antigens may be unique for a particular serogroup or antigenic determinants may be shared, resulting in cross-reactions with other serogroups of E. coli or even with other members of the family Enterobacteriacea. To establish the uniqueness of a particular serogroup or to identify the presence of common epitopes, a database of the structures of O-antigenic polysaccharides has been created. The E. coli database (ECODAB) contains structures, nuclear magnetic resonance chemical shifts and to some extent cross-reactivity relationships. All fields are searchable. A ranking is produced based on similarity, which facilitates rapid identification of strains that are difficult to serotype (if known) based on classical agglutinating methods. In addition, results pertinent to the biosynthesis of the repeating units of O-antigens are discussed. The ECODAB is accessible to the scientific community at http://www.casper.organ.su.se/ECODAB/
NMR, structure, serotype, O-antigen, Enterobacteriacea, database
NCBI PubMed ID: 16594963Publication DOI: 10.1111/j.1574-6976.2006.00016.xJournal NLM ID: 8902526Publisher: Oxford University Press
Correspondence: andrej.weintraub@ki.se
Institutions: Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, Sweden
- Article ID: 3539
Ren Y, Liu B, Cheng J, Liu F, Feng L, Wang L "Characterization of Escherichia coli O3 and O21 O antigen gene clusters and development of serogroup-specific PCR assays" -
Journal of Microbiological Methods 75(2) (2008) 329-334
Escherichia coli O3 and O21 are associated with enteroaggregative E. coli (EAEC). EAEC strains are often non-typable using the routine agglutination method due to their aggregative phenotype. Typing of E. coli O3 and O21 may also be impeded by cross-reactions with O152 or O83. In this study, the O antigen gene clusters of E. coli O3 and O21 were characterized, and PCR assays based on O antigen specific genes wzx (encoding O unit flippase) and wzy (encoding O unit polymerase) from each strain were developed. By screening against all 186 known E. coli O serotypes, the PCR assays were shown to be highly specific to O3 and O21 respectively. The sensitivity of the assays was determined to be 1 pg per mul of chromosomal DNA and 2 CFU per 10 g of water samples. The PCR assays were also applied to 658 clinical E. coli isolates, and 100% of detection accuracy was obtained. The PCR assays developed here are suitable for the detection and identification of E. coli O3 and O21 strains in environmental and clinical samples
PCR, O antigen, O-serotype, wzx, wzy, E.coli 03, E.coli 021
NCBI PubMed ID: 18700154Journal NLM ID: 8306883Correspondence: wanglei@nankai.edu.cn (L. Wang)
Institutions: TEDA School of Biological Sciences and Biotechnology, Nankai University, 23 HongDa Street, TEDA, Tianjin, China, Tianjin Key Laboratory of Microbial Functional Genomics, 23 Hongda Street, TEDA, Tianjin, China
Methods: PCR, genetic methods
- Article ID: 4916
Chen C, Liu B, Xu Y, Utkina N, Zhou D, Danilov L, Torgov V, Veselovsky V, Feng L "Biochemical characterization of the novel a-1,3-galactosyltransferase WclR from Escherichia coli O3" -
Carbohydrate Research 430 (2016) 36-43
Glycosyltransferases (GTs) catalyze the formation of regio- and stereo-specific glycosidic linkages between specific sugar donors and recipients. In this study, the function of the gene wclR from the Escherichia coli O3 O-antigen gene cluster that encodes an ? 1, 3-galactosyltransferase (GalT) that acts on the linkage Gal α1,3-GlcNAc was biochemically characterized. WclR was expressed in E.coli BL21 (DE3), and the enzymatic product was identified by liquid chromatography-mass spectrometry (LC-MS), collision-induced dissociation electrospray ionization ion trap multiple tandem MS (CID-ESI-IT-MS(n)) and galactosidase digestion, using UDP-Gal as the donor substrate and the synthetic acceptor substrate GlcNAc-PP-De (decyl diphosphate N-acetylglucosamine). The physiochemical properties and the substrate specificity of WclR were investigated. WclR is the first bacterial GalT characterized that acts on the linkage Gal α1,3-GlcNAc. This study enhanced our knowledge of the diversified functions of GTs and provided a novel enzyme source for possible pharmaceutical application.
Escherichia coli, mass spectrometry, galactosyltransferase, O-antigen gene cluster, WclR
NCBI PubMed ID: 27196310Publication DOI: 10.1016/j.carres.2016.04.012Journal NLM ID: 0043535Publisher: Elsevier
Correspondence: fenglu63@nankai.edu.cn
Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin, China, The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Tianjin, China
Methods: PCR, Western blotting, genetic methods, biochemical methods, enzyme assay, LC-ESI-MS, CID-ESI-IT-MS
- 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
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5. Compound ID: 4467
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a-L-RhapNAc-(1-4)-+
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-3)-a-L-FucpNAc-(1-3)-a-D-GalpNAcA-(1-3)-a-L-QuipNAc-(1- |
Show graphically |
Structure type: polymer chemical repeating unit
Compound class: CPS
The structure is contained in the following publication(s):
- Article ID: 1685
Reddy GP, Hayat U, Bush CA, Morris JG (Jr) "Capsular polysaccharide structure of a clinical isolate of Vibrio vulnificus strain BO62316 determined by heteronuclear NMR spectroscopy and high-performance anion-exchange chromatography" -
Analytical Biochemistry 214 (1993) 106-115
Journal NLM ID: 0370535Publisher: Academic Press
Methods: NMR
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6. Compound ID: 5426
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a-D-Fucp3NAc-(1-2)-+
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-3)-a-D-Rhap4NAc-(1-3)-a-D-RhapNAc-(1-3)-b-D-Rhap-(1-3)-a-D-RhapNAc-(1- |
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Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide, O-antigen
Contained glycoepitopes: IEDB_1394181
The structure is contained in the following publication(s):
- Article ID: 2268
Winn AM, Galbraith L, Temple GS, Wilkinson SG "Structure of the O19 antigen of Xanthomonas maltophilia" -
Carbohydrate Research 247 (1993) 249-254
The O-specific polymer from a strain of Xanthomonas maltophilia O19 contains D-glucose, L-rhamnose, and D-fucose. By means of chemical degradations and NMR studies, the repeating unit of the polymer was determined to be a branched tetrasaccharide of the structure shown. [formula: see text]
NCBI PubMed ID: 7693347Publication DOI: 10.1016/0008-6215(93)84257-7Journal NLM ID: 0043535Publisher: Elsevier
Institutions: School of Chemistry, University of Hull, United Kingdom
Methods: 13C NMR, 1H NMR
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7. Compound ID: 5655
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b-L-RhapNAc-(1-4)-+ a-D-Glcp-(1-4)-+
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-3)-b-D-GlcpNAc-(1-3)-a-D-Galp-(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_136906,IEDB_137340,IEDB_137472,IEDB_141794,IEDB_141807,IEDB_142488,IEDB_144998,IEDB_146664,IEDB_151528,IEDB_151531,IEDB_190606,IEDB_983931,SB_173,SB_192,SB_7
The structure is contained in the following publication(s):
- Article ID: 2458
Medina ES, Widmalm G, Weintraub A, Vial PA, Levine MM, Lindberg AA "Structural studies of the O-antigenic polysaccharides of Escherichia coli O3 and the enteroaggregative Escherichia coli strain 17-2" -
European Journal of Biochemistry 224 (1994) 191-196
Journal NLM ID: 0107600Publisher: Oxford, UK: Blackwell Science Ltd. on behalf of the Federation of European Biochemical Societies
Methods: 13C NMR, 1H NMR
- Article ID: 5027
Naumenko OI, Zheng H, Senchenkova SN, Wang H, Li Q, Shashkov AS, Wang J, Knirel YA, Xiong Y "Structures and gene clusters of the O-antigens of Escherichia albertii O3, O4, O6, and O7" -
Carbohydrate Research 449 (2017) 17-22
The O-specific polysaccharides (OPSs) called O-antigens were obtained by mild acid degradation of the lipopolysaccharides of Escherichia albertii serotypes O3, O4, O6, and O7 and studied by sugar analysis along with 1D and 2D 1H and 13C NMR spectroscopy. The following structure was established for the OPS of E. albertii O4, which, to our knowledge, is unique among known bacterial polysaccharide structures: -2)-α-l-Rhap-(1-2)-α-l-Fucp-(1-2)-β-d-Galp-(1-3)-α-d-GalpNAc-(1-3)-β-d-GlcpNAc-(1- The OPS structure of the strain of E. albertii O7 studied was identical to that of strain LMG 20973 (= Albert 10457), whose structure has been reported earlier (R. Eserstam et al. Eur. J. Biochem. 269 (2002) 3289-3295). E. albertii O3 and O6 shared the OPS structures with Escherichia coli O181 and O3, respectively, except for the lack of O-acetylation in E. albertii O3, which is present in E. coli O181. The gene clusters driving the O-antigen biosynthesis of the E. albertii strains were sequenced, the genes were annotated by comparison with sequences in the available databases, and the predicted functions of the encoded proteins were found to be consistent with the OPS structures established. In accordance with the relatedness of the OPS structures, the O-antigen gene clusters of E. albertii O3 and O6 contain the same genes and have the same organization as those of E. coli O181 and O3, the entire gene clusters being 83% and 98% identical, respectively.
Lipopolysaccharide, O-antigen, Pseudomonas aeruginosa, Escherichia coli, bacterial polysaccharide structure, O-antigen gene cluster, Enterobacter cloacae, Escherichia albertii
NCBI PubMed ID: 28672166Publication DOI: 10.1016/j.carres.2017.06.008Journal 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, China
Methods: 13C NMR, 1H NMR, NMR-2D, sugar analysis, acid hydrolysis, GLC, GPC, acetylation, bioinformatic analysis, sequencing
- 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 trifluoroacetic acid, acid hydrolysis with CF3CO2H
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8. Compound ID: 7930
Structure type: monomer
Trivial name: UDP-β-L-RhaNAc
The structure is contained in the following publication(s):
- Article ID: 3506
Liu B, Knirel YA, Feng L, Perepelov AV, Senchenkova SN, Wang Q, Reeves P, Wang L "Structure and genetics of Shigella O antigens" -
FEMS Microbiology Reviews 32(4) (2008) 627-653
This review covers the O antigens of the 46 serotypes of Shigella, but those of most Shigella flexneri are variants of one basic structure, leaving 34 Shigella distinct O antigens to review, together with their gene clusters. Several of the structures and gene clusters are reported for the first time and this is the first such group for which structures and DNA sequences have been determined for all O antigens. Shigella strains are in effect Escherichia coli with a specific mode of pathogenicity, and 18 of the 34 O antigens are also found in traditional E. coli. Three are very similar to E. coli O antigens and 13 are unique to Shigella strains. The O antigen of Shigella sonnei is quite atypical for E. coli and is thought to have transferred from Plesiomonas. The other 12 O antigens unique to Shigella strains have structures that are typical of E. coli, but there are considerably more anomalies in their gene clusters, probably reflecting recent modification of the structures. Having the complete set of structures and genes opens the way for experimental studies on the role of this diversity in pathogenicity.
structure, O antigen, Shigella, O antigen gene cluster, O antigen diversity
NCBI PubMed ID: 18422615Publication DOI: 10.1111/j.1574-6976.2008.00114.xJournal NLM ID: 8902526Publisher: Oxford University Press
Correspondence: wanglei@nankai.edu.cn
Institutions: TEDA School of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, China, TEDA School of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, China.
Methods: 13C NMR, 1H NMR, NMR-2D, sugar analysis, ESI-MS, serological methods, genetic methods, biochemical methods
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9. Compound ID: 12723
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a-L-RhapNAc-(1-4)-+
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-3)-a-D-GalpNAcA-(1-3)-a-L-QuipNAc-(1-4)-a-D-GlcpNAc-(1- |
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Structure type: polymer biological repeating unit
Compound class: O-antigen
Contained glycoepitopes: IEDB_137340,IEDB_141807,IEDB_151531
The structure is contained in the following publication(s):
- Article ID: 5057
Yu X, Torzewska A, Zhang X, Yin Z, Drzewiecka D, Cao H, Liu B, Knirel YA, Rozalski A, Wang L "Genetic diversity of the O antigens of Proteus species and the development of a suspension array for molecular serotyping" -
PLoS One 12(8) (2017) e0183267
Proteus species are well-known opportunistic pathogens frequently associated with skin wound and urinary tract infections in humans and animals. O antigen diversity is important for bacteria to adapt to different hosts and environments, and has been used to identify serotypes of Proteus isolates. At present, 80 Proteus O-serotypes have been reported. Although the O antigen structures of most Proteus serotypes have been identified, the genetic features of these O antigens have not been well characterized. The O antigen gene clusters of Proteus species are located between the cpxA and secB genes. In this study, we identified 55 O antigen gene clusters of different Proteus serotypes. All clusters contain both the wzx and wzy genes and exhibit a high degree of heterogeneity. Potential functions of O antigen-related genes were proposed based on their similarity to genes in available databases. The O antigen gene clusters and structures were compared, and a number of glycosyltransferases were assigned to glycosidic linkages. In addition, an O serotype-specific suspension array was developed for detecting 31 Proteus serotypes frequently isolated from clinical specimens. To our knowledge, this is the first comprehensive report to describe the genetic features of Proteus O antigens and to develop a molecular technique to identify different Proteus serotypes.
O-antigen, gene cluster, Proteus, glycosyltransferases, serotyping, genomics, genetic diversity, serotype-specific
NCBI PubMed ID: 28817637Publication DOI: 10.1371/journal.pone.0183267Journal NLM ID: 101285081Publisher: San Francisco, CA: Public Library of Science
Correspondence: Lei Wang
Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, P. R. China, Tianjin Research Center for Functional Genomics and Biochips, TEDA College, Nankai University, Tianjin, P. R. China, Tianjin Key Laboratory of Microbial Functional Genomics, TEDA College, Nankai University, Tianjin, P. R. China, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, TEDA College, Nankai University, Tianjin, P. R. China, Department of Immunobiology of Bacteria, Department of General Microbiology Institute of Microbiology, Biotechnology and Immunology, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
Methods: PCR, DNA sequencing, genetic methods, function analysis of gene clusters, serotyping
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10. Compound ID: 13995
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a-D-Glcp-(1-6)-+ a-L-Rhap-(1-4)-+
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{{{-a-D-Galp-(1-2)-}}}b-D-Glcp-(1-6)-+
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-4)-b-D-Glcp-(1-3)-a-L-RhapNAc-(1-4)-b-D-Glcp-(1-3)-a-L-Rhap2Ac-(1-
|
a-L-Rhap-(1-3)-+ |
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Structure type: polymer chemical repeating unit
; 123600
Compound class: EPS
Contained glycoepitopes: IEDB_130422,IEDB_131186,IEDB_135818,IEDB_136105,IEDB_136906,IEDB_137472,IEDB_141794,IEDB_141806,IEDB_142488,IEDB_144998,IEDB_146664,IEDB_151528,IEDB_189517,IEDB_190606,IEDB_225177,IEDB_241101,IEDB_885823,IEDB_983931,SB_192,SB_7
The structure is contained in the following publication(s):
- Article ID: 5522
Xu YM, Cui YL, Yue FF, Liu LH, Shan YY, Liu BF, Zhou Y, Lü X "Exopolysaccharides produced by lactic acid bacteria and Bifidobacteria: Structures, physiochemical functions and applications in the food industry" -
Food Hydrocolloids 94 (2019) 475-499
Exopolysaccharides (EPSs)-producing lactic acid bacteria (LAB) and Bifidobacteria are widely used as starter cultures to make fermented food products due to their technological benefits. Moreover, LAB-EPSs and bifido-EPSs have been demonstrated to possess various physiological functions such as antioxidant, anticancer, antibacterial and immunological activities, among which the immunoregulatory activity has attracted a lot of scientific interests in recent years. Generally, these functions are closely related to the chemical compositions and configurations of EPSs. This review sheds light on structures and functions of LAB-EPSs and bifido-EPSs. Among them, in vitro and in vivo models used to evaluate the immune effects of EPSs are summarized in detail, with particular emphasis on the structure-immunity relationship of EPSs. Furthermore, the applications of EPSs in the food industry, especially the different roles EPSs played in the yogurt texture, are discussed carefully in this review. Finally, some strategies of EPSs production are also proposed to provide some information about the enhancement of EPSs yield.
structure, exopolysaccharides, immunity, Bifidobacteria, Applications, Functions, Yogurt
Publication DOI: 10.1016/j.foodhyd.2019.03.032Journal NLM ID: 8701770Publisher: New York, NY: Elsevier
Correspondence: X. Lü
Institutions: College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi Province, 712100, China
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11. Compound ID: 14020
|
a-D-Glcp-(1-6)-+ a-L-Rhap-(1-4)-+
| |
{{{-a-D-Galp-(1-2)-}}}b-D-Glcp-(1-6)-+
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-4)-b-D-Glcp-(1-3)-a-L-RhapNAc-(1-4)-b-D-Glcp-(1-3)-a-L-Rhap2Ac-(1-
|
a-L-Rhap-(1-3)-+ |
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Structure type: polymer chemical repeating unit
Compound class: EPS
Contained glycoepitopes: IEDB_130422,IEDB_131186,IEDB_135818,IEDB_136105,IEDB_136906,IEDB_137472,IEDB_141794,IEDB_141806,IEDB_142488,IEDB_144998,IEDB_146664,IEDB_151528,IEDB_189517,IEDB_190606,IEDB_225177,IEDB_241101,IEDB_885823,IEDB_983931,SB_192,SB_7
The structure is contained in the following publication(s):
- Article ID: 5533
Zhou Y, Cui Y, Qu X "Exopolysaccharides of lactic acid bacteria: Structure, bioactivity and associations: A review" -
Carbohydrate Polymers 207 (2019) 317-332
The ability to exhibit various bioactivities is widespread in exopolysaccharide (EPS) of lactic acid bacteria (LAB), and it has been admittedly associated with large structural variability of these polymers. Exceptional bioactivities such as cholesterol-lowering, immunomodulating, antioxidant, antiviral and anticoagulant effects render these biopolymers vast commercial value for global market and application potentials in medicine sector. Therefore, an elaborate understanding of structure-to-function associations will be prerequisite to search natural and artificial EPSs for new applications in functional food, health and medicine fields. In this review, it is presented a significant overview of the latest advances in the field of EPS from genes to application. This review emphasized in the general biosynthesis pathway together with genetic modules, multiple structures, functions, and respective functional mechanisms of LAB-derived EPSs, and the relationships between their structure and bioactivity, which will help to exploit new bioactive drugs from LAB-derived EPS.
biosynthesis, structure, exopolysaccharide, mechanism, bioactivity, Structure-to-function association
NCBI PubMed ID: 30600013Publication DOI: 10.1016/j.carbpol.2018.11.093Journal NLM ID: 8307156Publisher: Elsevier
Correspondence: Y. Cui
Institutions: Department of Food Science and Engineering, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, China, Institute of Microbiology, Heilongjiang Academy of Sciences, Harbin, China
- Article ID: 5534
Ai L, Guo Q, Ding H, Guo B, Chen W, Cui SW "Structure characterization of exopolysaccharides from Lactobacillus casei LC2W from skim milk" -
Food Hydrocolloids 56 (2016) 134-143
LCP1, a high molecular weight fraction of the EPSs produced by strain LC2W isolated from skim milk, was studied by partial acid hydrolysis, smith degradation, methylation analysis and 1D & 2D NMR spectroscopy to elucidate its main structure feature. Monosaccharides composition analysis revealed the presence of glucose (57.8% mol%), rhamnose (27.7%, mol%) and galactose (14.5%, mol%), respectively. O-acetyl (-OAc) and N-acetyl (-NAc) groups were also evidenced by FTIR and NMR spectroscopies. The linkage patterns of sugar residues were determined by methylation analysis and partial acid hydrolysis. The main sugar residues included: T-Rhmp (18.4%), 3-Rhmp (15.7%) T-Glcp (21.7), 4-Glcp (16.3%), 3,4,6-Glcp (16.3%) and 2,6-Galp (11.9%). 1D and 2D NMR analysis revealed that both -OAc and -NAc were connected to 3-Rhmp at O-2 position. The configuration and glycosidic sequences for sugar residues were established by 2D NMR spectroscopy. A possible structure of LCP1 was proposed.
NMR, structure, Lactic acid bacteria, exopolysaccharides, partial acid hydrolysis
Publication DOI: 10.1016/j.foodhyd.2015.10.023Journal NLM ID: 8701770Publisher: New York, NY: Elsevier
Correspondence: Steve W. Cui
Institutions: School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China, Guelph Food Research Centre, Agriculture and Agri-Food Canada, Guelph, Ontario, N1G 5C9, Canada, State Key Laboratory of Dairy Biotechnology, Technology Center of Bright Dairy & Food Co. Ltd., Shanghai 200436, China, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
Methods: 13C NMR, 1H NMR, methylation, periodate oxidation, NMR-2D, partial acid hydrolysis, GC-MS, sugar analysis, HPAEC, Smith degradation, FTIR, alkaline treatment
- Article ID: 6267
Li J, Yu L, Zhao J, Tian F, Chen W, Zhai Q "Capsular polysaccarides of probiotics and their immunomodulatory roles" -
Food Science and Human Wellness 11(5) (2022) 1111-1120
Studies have determined the immunomodulatory activities of cell-surface polysaccharides of lactic acid bacteria (LAB) and Bacteroides; however, the mechanisms, synthesis, regulation, structure, and functional links have not been systematically discussed. We first introduce the structure of the capsular polysaccharides (CPSs) of commonly studied probiotics and Bacteroides. Wzx-Wzy dependent and ATP-binding cassette (ABC) transporter-dependent pathways are the two main biosynthesis and secretion of CPS pathways. The genes known to be associated with these two pathways are mainly those associated with priming glycosyltransferase (pGT); a variable number of genes encoding for different glycosyl transferases (GTs); Wzx/Wzy-encoding enzymes related to flippases and polymerases; and ABC-transporter genes. In addition, the effects of CPSs on host immunity as well as their related underlying mechanisms are described. Surface polysaccharides on probiotics can serve as a mask to aid in their escape from attacks from the host's immune system. In turn, they also exhibit immunomodulatory activities, such as strengthening the functions of macrophages, promoting the maturation of antigen-presenting cells, and inducing regulatory T cells. All of these effects of cell-surface polysaccharides exhibit their significant protective properties in immunocompromised diseases, such as colitis, arthritis, and dermatitis. Finally, we focused on their structure and functional links.
capsular polysaccharide, Bacteroides, immunomodulation, probiotics
Publication DOI: 10.1016/j.fshw.2022.04.003Journal NLM ID: 101610174Publisher: China: China Food Publishing Company
Correspondence: Q. Zhai
Institutions: State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China, School of Food Science and Technology, Jiangnan University, Wuxi, China
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12. Compound ID: 16598
|
a-L-RhapNAc-(1-4)-+
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a-L-QuipNAc-(1-3)-a-D-GlcpNAc-(1-3)-a-D-GalpNAcA-(1--/3-aminopropyl/ |
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Structure type: oligomer
; 892.3650 [M+Na]+
C35H59N5O20
Aglycon: 3-aminopropyl
Compound class: O-polysaccharide
Contained glycoepitopes: IEDB_137340,IEDB_141807,IEDB_151531
The structure is contained in the following publication(s):
- Article ID: 6440
Paul A, Kulkarni SS "Total Synthesis of the Repeating Units of Proteus penneri 26 and Proteus vulgaris TG155 via a Common Disaccharide" -
Organic Letters 25(23) (2023) 4400-4405
Herein, we report the first total synthesis of the trisaccharide and tetrasaccharide repeating units of P. penneri 26 and P. vulgaris TG155, respectively, having a common disaccharide unit, 3-aloha-l-QuipNAc-(1 > 3)-alpha-d-GlcpNAc-(1 >. Striking features of the targets are the presence of rare sugar units, l-quinovosamine and l-rhamnosamine, all joined through alpha-glycosidic linkages. Major challenges in the formation of 1,2-cis glycosidic linkages in the case of d-glucosamine, l-quinovosamine, and d-galactosamine have been addressed.
repeating unit, total synthesis, Proteus penneri 26, Proteus vulgaris TG155
NCBI PubMed ID: 37284758Publication DOI: 10.1021/acs.orglett.3c01618Journal NLM ID: 100890393Publisher: American Chemical Society
Correspondence: S.S. Kulkarni
Institutions: Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai, Maharashtra 400076, India
Methods: 13C NMR, 1H NMR, TLC, chemical synthesis, FTIR, UV, glycosylation, optical rotation measurement, CC, HR-ESI-MS
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