Found 426 structures.
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1. Compound ID: 32
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b-D-Glcp-(1-6)-a-D-Glcp-(1-6)-+
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-3)-b-D-Glcp-(1-4)-b-D-2daraHexpA-(1-4)-b-D-Glcp-(1-4)-a-L-Rha-(1- |
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Structure type: polymer chemical repeating unit
Compound class: EPS
Contained glycoepitopes: IEDB_136105,IEDB_141806,IEDB_142488,IEDB_144998,IEDB_146664,IEDB_189517,IEDB_225177,IEDB_885823,IEDB_983931,SB_192
The structure is contained in the following publication(s):
- Article ID: 12
Bian W, Chandrasekaran R, Rinaudo M "Molecular structure of the rhamsan-like exocellular polysaccharide RMDP17 from Sphingomonas paucimobilis" -
Carbohydrate Research 337(1) (2002) 45-56
X-Ray diffraction analysis of the sodium salt of the polysaccharide RMDP17, a 2-deoxy rhamsan analog, reveals that it adopts a gellan-like, half-staggered, threefold, left handed, double helix of pitch 57.4 A. The side chain of the branched polymer is hydrogen bonded to the main chain. Sodium ions, linked to the carboxylate groups, promote the association of helices via water molecules. Two helices of opposite polarity occupy a trigonal unit cell of dimensions a=17.6 and c=28.7 A. The packing arrangement displays a series of hydrogen bonds involving main chain and side chain atoms, as well as some water bridges, between the helices.
structure, branched, polysaccharide, analysis, RMDP17, X-ray diffraction, Three-dimensional structure, Rhamsan analog, 2-deoxy, association, carbohydrate, cell, chain, exocellular, exocellular polysaccharide, food, group, helix, hydrogen, hydrogen bond, ion, linked, molecular, Molecular Structure, molecule, polymer, Research, rhamsan, salt, side chain, Sphingomonas, Sphingomonas paucimobilis, water, X-ray
NCBI PubMed ID: 11755911Publication DOI: 10.1016/s0008-6215(01)00277-4Journal NLM ID: 0043535Publisher: Elsevier
Correspondence: chandra@purdue.edu
Institutions: Whistler Center for Carbohydrate Research, 1160 Food Science Building, Purdue University, 47907-1160, West Lafayette, IN, USA
Methods: X-ray
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2. Compound ID: 140
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a-D-Glcp-(1-4)-+
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a-D-Glcp-(1-6)-+ | P-6)-+ P-2)-+ a-Kdop-(2-4)-+
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a-L-Rhap-(1-4)-a-D-GalpNAcA3Ac6NH2-(1-4)-a-D-GalpNFoA6NH2-(1-3)-b-D-QuipNAc-(1-3)-a-L-Rhap-(1-3)-b-D-Glcp-(1-3)-a-D-GalpN-(1-3)-L-gro-a-D-manHepp7Cm-(1-3)-L-gro-a-D-manHepp-(1-5)-a-Kdop-(2--/lipid A/
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L-Ala-(1-2)-+ P-4)-+ |
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Structure type: oligomer
Aglycon: lipid A
Trivial name: glycoform 2 core oligosaccharide with O-unit
Contained glycoepitopes: IEDB_130650,IEDB_130659,IEDB_136105,IEDB_137473,IEDB_140088,IEDB_142488,IEDB_144998,IEDB_146664,IEDB_189517,IEDB_2189047,IEDB_225177,IEDB_885823,IEDB_983931,SB_192
The structure is contained in the following publication(s):
- Article ID: 29
Bystrova OV, Shashkov AS, Kocharova NA, Knirel YA, Lindner B, Zähringer U, Pier GB "Structural studies on the core and the O-polysaccharide repeating unit of Pseudomonas aeruginosa immunotype 1 lipopolysaccharide" -
European Journal of Biochemistry 269(8) (2002) 2194-2203
The structure of the lipopolysaccharide (LPS) of Pseudomonas aeruginosa immunotype 1 was studied after mild acid and strong alkaline degradations by MS and NMR spectroscopy. Three types of LPS molecules were found, including those with an unsubstituted glycoform 1 core (A) or an isomeric glycoform 2 core substituted with one O-polysaccharide repeating unit (B) or with a long-chain O-polysaccharide. Therefore, of two core glycoforms, only glycoform 2 accepts the O-polysaccharide. In the structures A and B, Kdo, Hep, Hep7Cm, GalNAcAN3Ac, GalNFoAN, QuiNAc, GalNAla represent 3-deoxy-d-manno-octulosonic acid, l-glycero-d-manno-heptose, 7-O-carbamoyl-l-glycero-d-manno-heptose, 2-acetamido-3-O-acetyl-2-deoxygalacturonamide, 2-formamido-2-deoxygalacturonamide, 2-acetamido-2,6-dideoxyglucose and 2-(l-alanylamino)-2-deoxygalactose, respectively; all sugars are in the pyranose form and have the d configuration unless otherwise stated. One or more phosphorylation sites may be occupied by diphosphate groups. In a minority of the LPS molecules, an O-acetyl group is present in the outer core region at unknown position. The site and the configuration of the linkage between the O-polysaccharide and the core and the structure of the O-polysaccharide repeating unit were defined in P. aeruginosa immunotype 1. The QuiNAc residue linked to the Rha residue of the core was found to have the beta configuration, whereas in the interior repeating units of the O-polysaccharide this residue is in the α-configuration. The data obtained are in accordance with the initiation of biosynthesis of the O-polysaccharide of P. aeruginosa O6, which is closely related to immunotype 1, by transfer of d-QuiNAc-1-P to undecaprenyl phosphate followed by synthesis of the repeating O-antigen tetrasaccharide
Lipopolysaccharide, structure, repeating unit, Pseudomonas aeruginosa, core oligosaccharide, O-polysaccharide
NCBI PubMed ID: 11985598Journal NLM ID: 0107600Publisher: Oxford, UK: Blackwell Science Ltd. on behalf of the Federation of European Biochemical Societies
Correspondence: knirel@ioc.ac.ru
Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Research Center Borstel, Center for Medicine and Biosciences, Borstel, Germany, Channing Laboratory, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
Methods: 13C NMR, 1H NMR, NMR-2D, 31P NMR, ESI-MS, GLC, mild acid hydrolysis, alkaline degradation
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3. Compound ID: 142
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a-D-Glcp-(1-4)-+
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a-D-Glcp-(1-6)-+ | P-6)-+ P-2)-+ a-Kdop-(2-4)-+ P-4)-+
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b-L-4dthrHexp4enNA-(1-3)-b-D-QuipN-(1-3)-a-L-Rhap-(1-3)-b-D-Glcp-(1-3)-a-D-GalpN-(1-3)-L-gro-a-D-manHepp-(1-3)-L-gro-a-D-manHepp-(1-5)-a-Kdop-(2-6)-b-D-GlcpN-(1-6)-a-D-GlcpN-(1-P
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P-4)-+ |
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Structure type: oligomer
Trivial name: glycoform 2 core oligosaccharide with O-unit
Compound class: core oligosaccharide with O-unit
Contained glycoepitopes: IEDB_130650,IEDB_130659,IEDB_135394,IEDB_136105,IEDB_137340,IEDB_137473,IEDB_140088,IEDB_141807,IEDB_142488,IEDB_144998,IEDB_146664,IEDB_150908,IEDB_151531,IEDB_189517,IEDB_2189047,IEDB_225177,IEDB_885823,IEDB_983931,SB_192
The structure is contained in the following publication(s):
- Article ID: 29
Bystrova OV, Shashkov AS, Kocharova NA, Knirel YA, Lindner B, Zähringer U, Pier GB "Structural studies on the core and the O-polysaccharide repeating unit of Pseudomonas aeruginosa immunotype 1 lipopolysaccharide" -
European Journal of Biochemistry 269(8) (2002) 2194-2203
The structure of the lipopolysaccharide (LPS) of Pseudomonas aeruginosa immunotype 1 was studied after mild acid and strong alkaline degradations by MS and NMR spectroscopy. Three types of LPS molecules were found, including those with an unsubstituted glycoform 1 core (A) or an isomeric glycoform 2 core substituted with one O-polysaccharide repeating unit (B) or with a long-chain O-polysaccharide. Therefore, of two core glycoforms, only glycoform 2 accepts the O-polysaccharide. In the structures A and B, Kdo, Hep, Hep7Cm, GalNAcAN3Ac, GalNFoAN, QuiNAc, GalNAla represent 3-deoxy-d-manno-octulosonic acid, l-glycero-d-manno-heptose, 7-O-carbamoyl-l-glycero-d-manno-heptose, 2-acetamido-3-O-acetyl-2-deoxygalacturonamide, 2-formamido-2-deoxygalacturonamide, 2-acetamido-2,6-dideoxyglucose and 2-(l-alanylamino)-2-deoxygalactose, respectively; all sugars are in the pyranose form and have the d configuration unless otherwise stated. One or more phosphorylation sites may be occupied by diphosphate groups. In a minority of the LPS molecules, an O-acetyl group is present in the outer core region at unknown position. The site and the configuration of the linkage between the O-polysaccharide and the core and the structure of the O-polysaccharide repeating unit were defined in P. aeruginosa immunotype 1. The QuiNAc residue linked to the Rha residue of the core was found to have the beta configuration, whereas in the interior repeating units of the O-polysaccharide this residue is in the α-configuration. The data obtained are in accordance with the initiation of biosynthesis of the O-polysaccharide of P. aeruginosa O6, which is closely related to immunotype 1, by transfer of d-QuiNAc-1-P to undecaprenyl phosphate followed by synthesis of the repeating O-antigen tetrasaccharide
Lipopolysaccharide, structure, repeating unit, Pseudomonas aeruginosa, core oligosaccharide, O-polysaccharide
NCBI PubMed ID: 11985598Journal NLM ID: 0107600Publisher: Oxford, UK: Blackwell Science Ltd. on behalf of the Federation of European Biochemical Societies
Correspondence: knirel@ioc.ac.ru
Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Research Center Borstel, Center for Medicine and Biosciences, Borstel, Germany, Channing Laboratory, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
Methods: 13C NMR, 1H NMR, NMR-2D, 31P NMR, ESI-MS, GLC, mild acid hydrolysis, alkaline degradation
- Article ID: 3207
Bystrova OV, Knirel YA, Lindner B, Kocharova NA, Kondakova AN, Zähringer U, Pier GB "Structures of the core oligosaccharide and O-units in the R- and SR-type lipopolysaccharides of reference strains of Pseudomonas aeruginosa O-serogroups" -
FEMS Immunology and Medical Microbiology 46(1) (2006) 85-99
Highly phosphorylated core oligosaccharides and those substituted with one O-antigen repeating unit were obtained by mild acid degradation or strong alkaline hydrolysis of lipopolysaccharide samples from 23 reference strains representing all Pseudomonas aeruginosa O-serogroups. Studies by high-resolution electrospray ionization mass spectrometry and two-dimensional NMR spectroscopy revealed both conserved and variable structural features of the lipopolysaccharides of various O-serogroups. The upstream terminal saccharide of the O-antigen, which contributes most to the immunospecificity of the bacteria, was defined in 11 from a total of 13 O-serogroups. The data obtained link together the known biosynthesis pathways, genetics and serology of the P. aeruginosa lipopolysaccharide.
lipopolysaccharides, oligosaccharide, structure, core, strain, O-antigen, Pseudomonas, Pseudomonas aeruginosa, core oligosaccharide, reference, lipopolysaccharide structure, preparation, PDF, O-unit
NCBI PubMed ID: 16420601Publication DOI: 10.1111/j.1574-695X.2005.00004.xJournal NLM ID: 9315554Publisher: Elsevier
Correspondence: olgabv@ioc.ac.ru
Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Research Center Borstel, Center for Medicine and Biosciences, Borstel, Germany, Channing Laboratory, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Channing Laboratory, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston,MA, USA
Methods: NMR-2D, mild acid hydrolysis, alkaline degradation, ESI-FTICR-MS
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4. Compound ID: 145
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a-D-Glcp-(1-4)-+
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a-D-Glcp-(1-6)-+ | P-6)-+ P-2)-+ a-Kdop-(2-4)-+ P-4)-+
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b-D-4dthrHex4enNA-(1-3)-b-D-QuipN-(1-3)-a-L-Rhap-(1-3)-b-D-Glcp-(1-3)-a-D-GalpN-(1-3)-L-gro-a-D-manHepp-(1-3)-L-gro-a-D-manHepp-(1-5)-a-Kdop-(2-6)-b-D-GlcpN-(1-6)-a-D-GlcpN-(1-P
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P-4)-+ |
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Structure type: oligomer
Trivial name: glycoform 2 core oligosaccharide with O-unit
Contained glycoepitopes: IEDB_130650,IEDB_130659,IEDB_135394,IEDB_136105,IEDB_137340,IEDB_137473,IEDB_140088,IEDB_141807,IEDB_142488,IEDB_144998,IEDB_146664,IEDB_150908,IEDB_151531,IEDB_189517,IEDB_2189047,IEDB_225177,IEDB_885823,IEDB_983931,SB_192
The structure is contained in the following publication(s):
- Article ID: 30
Bystrova OV, Shashkov AS, Kocharova NA, Knirel YA, Zähringer U, Pier GB "Elucidation of the structure of the lipopolysaccharide core and the linkage between the core and the O-antigen in Pseudomonas aeruginosa immunotype 5 using strong alkaline degradation of the lipopolysaccharide" -
Biochemistry (Moscow) 68(8) (2003) 918-925
The products of the strong alkaline degradation of the lipopolysaccharide (LPS) of Pseudomonas aeruginosa immunotype 5 were separated by anion-exchange HPLC and studied by electrospray ionization mass spectrometry and NMR spectroscopy. It was found that two major products have the same inner core region and lipid A carbohydrate backbone but different outer core regions. The difference is in the position of a rhamnose residue, which is substituted with either an additional glucose residue or a disaccharide remainder of the degraded O-polysaccharide. The site and the configuration of the linkage between the O-polysaccharide and the core were determined and, together with published data, the structure of the so-called biological repeating unit of the O-antigen was defined. The glycosidic linkage of the 2-acetamido-2,6-dideoxy-D-glucose (N-acetyl-D-quinovosamine) residue is ? when it links the O-polysaccharide to the core and ? when it connects the interior repeating units of the O-polysaccharide to each other
Lipopolysaccharide, O-antigen, repeating unit, Pseudomonas aeruginosa, core oligosaccharide
NCBI PubMed ID: 12948393Publication DOI: 10.1023/a:1025759217501Journal NLM ID: 0376536Publisher: Nauka/Interperiodica
Correspondence: knirel@ioc.ac.ru
Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Research Center Borstel, Center for Medicine and Biosciences, Borstel, Germany, Channing Laboratory, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
Methods: 13C NMR, 1H NMR, NMR-2D, 31P NMR, ESI-MS, GLC, alkaline degradation
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5. Compound ID: 147
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a-D-Glcp-(1-4)-+
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a-D-Glcp-(1-6)-+ | P-6)-+ P-2)-+ a-Kdop-(2-4)-+ P-4)-+
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a-L-Rhap-(1-3)-b-D-Glcp-(1-3)-a-D-GalpN-(1-3)-L-gro-a-D-manHepp-(1-3)-L-gro-a-D-manHepp-(1-5)-a-Kdop-(2-6)-b-D-GlcpN-(1-6)-a-D-GlcpN-(1-P
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P-4)-+ |
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Structure type: oligomer
Trivial name: glycoform 2 core, glycoform 2
Compound class: core oligosaccharide, core + lipid A
Contained glycoepitopes: IEDB_130650,IEDB_130659,IEDB_135394,IEDB_136105,IEDB_137340,IEDB_137473,IEDB_140088,IEDB_141807,IEDB_142488,IEDB_144998,IEDB_146664,IEDB_150908,IEDB_151531,IEDB_189517,IEDB_2189047,IEDB_225177,IEDB_885823,IEDB_983931,SB_192
The structure is contained in the following publication(s):
- Article ID: 31
Bystrova OV, Lindner B, Moll H, Kocharova NA, Knirel YA, Zähringer U, Pier GB "Structure of the biological repeating unit of the O-antigen of Pseudomonas aeruginosa immunotype 4 containing both 2-acetamido-2,6-dideoxy-D-glucose and 2-acetamido-2,6-dideoxy-D-galactose" -
Carbohydrate Research 338(17) (2003) 1801-1806
A phosphorylated core-lipid A backbone oligosaccharide that carries a disaccharide remainder of the first O-antigen repeating unit was derived by strong alkaline degradation following mild hydrazinolysis of the lipopolysaccharide of Pseudomonas aeruginosa immunotype 4 (serogroup O-1). The structure of the oligosaccharide was determined using ESI MS and NMR spectroscopy and it was demonstrated that 2-acetamido-2,6-dideoxy-D-glucose is the first monosaccharide of the O-polysaccharide that is linked to the LPS core. These data define the structure of the biological repeating unit of the O-antigen
Lipopolysaccharide, structure, O-antigen, repeating unit, Pseudomonas aeruginosa, O-polysaccharide, 2-acetamido-2, 6-dideoxy-D-galactose
NCBI PubMed ID: 12892948Publication DOI: 10.1016/S0008-6215(03)00262-3Journal NLM ID: 0043535Publisher: Elsevier
Correspondence: knirel@ioc.ac.ru
Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Research Center Borstel, Center for Medicine and Biosciences, Borstel, Germany, Channing Laboratory, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
Methods: 13C NMR, 1H NMR, NMR-2D, 31P NMR, ESI-MS, GLC, alkaline degradation
- Article ID: 32
Bystrova OV, Lindner B, Moll H, Kocharova NA, Knirel YA, Zähringer U, Pier GB "Structure of the lipopolysaccharide of Pseudomonas aeruginosa O-12 with a randomly O-acetylated core region" -
Carbohydrate Research 338(18) (2003) 1895-1905
The lipopolysaccharide of Pseudomonas aeruginosa O-12 was studied by strong alkaline and mild acid degradations and dephosphorylation followed by fractionation of the products by GPC and high-performance anion-exchange chromatography and analyses by ESI FT-MS and NMR spectroscopy. The structures of the lipopolysaccharide core and the O-polysaccharide repeating unit were elucidated and the site and the configuration of the linkage between the O-polysaccharide and the core established. The core was found to be randomly O-acetylated, most O-acetyl groups being located on the terminal rhamnose residue of the outer core region
Lipopolysaccharide, Pseudomonas aeruginosa, core structures, O-antigen repeating unit, O-acetylation
NCBI PubMed ID: 12932374Publication DOI: 10.1016/S0008-6215(03)00290-8Journal NLM ID: 0043535Publisher: Elsevier
Correspondence: knirel@ioc.ac.ru
Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Research Center Borstel, Center for Medicine and Biosciences, Borstel, Germany, Channing Laboratory, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
Methods: 13C NMR, 1H NMR, NMR-2D, dephosphorylation, 31P NMR, GLC, mild acid hydrolysis, alkaline degradation, HPAEC, ESI-FT-MS
- Article ID: 3207
Bystrova OV, Knirel YA, Lindner B, Kocharova NA, Kondakova AN, Zähringer U, Pier GB "Structures of the core oligosaccharide and O-units in the R- and SR-type lipopolysaccharides of reference strains of Pseudomonas aeruginosa O-serogroups" -
FEMS Immunology and Medical Microbiology 46(1) (2006) 85-99
Highly phosphorylated core oligosaccharides and those substituted with one O-antigen repeating unit were obtained by mild acid degradation or strong alkaline hydrolysis of lipopolysaccharide samples from 23 reference strains representing all Pseudomonas aeruginosa O-serogroups. Studies by high-resolution electrospray ionization mass spectrometry and two-dimensional NMR spectroscopy revealed both conserved and variable structural features of the lipopolysaccharides of various O-serogroups. The upstream terminal saccharide of the O-antigen, which contributes most to the immunospecificity of the bacteria, was defined in 11 from a total of 13 O-serogroups. The data obtained link together the known biosynthesis pathways, genetics and serology of the P. aeruginosa lipopolysaccharide.
lipopolysaccharides, oligosaccharide, structure, core, strain, O-antigen, Pseudomonas, Pseudomonas aeruginosa, core oligosaccharide, reference, lipopolysaccharide structure, preparation, PDF, O-unit
NCBI PubMed ID: 16420601Publication DOI: 10.1111/j.1574-695X.2005.00004.xJournal NLM ID: 9315554Publisher: Elsevier
Correspondence: olgabv@ioc.ac.ru
Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Research Center Borstel, Center for Medicine and Biosciences, Borstel, Germany, Channing Laboratory, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Channing Laboratory, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston,MA, USA
Methods: NMR-2D, mild acid hydrolysis, alkaline degradation, ESI-FTICR-MS
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6. Compound ID: 148
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a-D-Glcp-(1-4)-+
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a-D-Glcp-(1-6)-+ | P-6)-+ P-2)-+ a-Kdop-(2-4)-+ P-4)-+
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a-D-FucpN-(1-3)-b-D-QuipN-(1-3)-a-L-Rhap-(1-3)-b-D-Glcp-(1-3)-a-D-GalpN-(1-3)-L-gro-a-D-manHepp-(1-3)-L-gro-a-D-manHepp-(1-5)-a-Kdop-(2-6)-b-D-GlcpN-(1-6)-a-D-GlcpN-(1-P
|
P-4)-+ |
Show graphically |
Structure type: oligomer
Trivial name: glycoform 2 core oligosaccharide with O-unit
Compound class: core oligosaccharide with O-unit
Contained glycoepitopes: IEDB_130650,IEDB_130659,IEDB_135394,IEDB_136105,IEDB_137340,IEDB_137473,IEDB_140088,IEDB_141807,IEDB_142488,IEDB_144998,IEDB_146664,IEDB_150908,IEDB_151531,IEDB_189517,IEDB_2189047,IEDB_225177,IEDB_885823,IEDB_983931,SB_192
The structure is contained in the following publication(s):
- Article ID: 31
Bystrova OV, Lindner B, Moll H, Kocharova NA, Knirel YA, Zähringer U, Pier GB "Structure of the biological repeating unit of the O-antigen of Pseudomonas aeruginosa immunotype 4 containing both 2-acetamido-2,6-dideoxy-D-glucose and 2-acetamido-2,6-dideoxy-D-galactose" -
Carbohydrate Research 338(17) (2003) 1801-1806
A phosphorylated core-lipid A backbone oligosaccharide that carries a disaccharide remainder of the first O-antigen repeating unit was derived by strong alkaline degradation following mild hydrazinolysis of the lipopolysaccharide of Pseudomonas aeruginosa immunotype 4 (serogroup O-1). The structure of the oligosaccharide was determined using ESI MS and NMR spectroscopy and it was demonstrated that 2-acetamido-2,6-dideoxy-D-glucose is the first monosaccharide of the O-polysaccharide that is linked to the LPS core. These data define the structure of the biological repeating unit of the O-antigen
Lipopolysaccharide, structure, O-antigen, repeating unit, Pseudomonas aeruginosa, O-polysaccharide, 2-acetamido-2, 6-dideoxy-D-galactose
NCBI PubMed ID: 12892948Publication DOI: 10.1016/S0008-6215(03)00262-3Journal NLM ID: 0043535Publisher: Elsevier
Correspondence: knirel@ioc.ac.ru
Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Research Center Borstel, Center for Medicine and Biosciences, Borstel, Germany, Channing Laboratory, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
Methods: 13C NMR, 1H NMR, NMR-2D, 31P NMR, ESI-MS, GLC, alkaline degradation
- Article ID: 3207
Bystrova OV, Knirel YA, Lindner B, Kocharova NA, Kondakova AN, Zähringer U, Pier GB "Structures of the core oligosaccharide and O-units in the R- and SR-type lipopolysaccharides of reference strains of Pseudomonas aeruginosa O-serogroups" -
FEMS Immunology and Medical Microbiology 46(1) (2006) 85-99
Highly phosphorylated core oligosaccharides and those substituted with one O-antigen repeating unit were obtained by mild acid degradation or strong alkaline hydrolysis of lipopolysaccharide samples from 23 reference strains representing all Pseudomonas aeruginosa O-serogroups. Studies by high-resolution electrospray ionization mass spectrometry and two-dimensional NMR spectroscopy revealed both conserved and variable structural features of the lipopolysaccharides of various O-serogroups. The upstream terminal saccharide of the O-antigen, which contributes most to the immunospecificity of the bacteria, was defined in 11 from a total of 13 O-serogroups. The data obtained link together the known biosynthesis pathways, genetics and serology of the P. aeruginosa lipopolysaccharide.
lipopolysaccharides, oligosaccharide, structure, core, strain, O-antigen, Pseudomonas, Pseudomonas aeruginosa, core oligosaccharide, reference, lipopolysaccharide structure, preparation, PDF, O-unit
NCBI PubMed ID: 16420601Publication DOI: 10.1111/j.1574-695X.2005.00004.xJournal NLM ID: 9315554Publisher: Elsevier
Correspondence: olgabv@ioc.ac.ru
Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Research Center Borstel, Center for Medicine and Biosciences, Borstel, Germany, Channing Laboratory, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Channing Laboratory, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston,MA, USA
Methods: NMR-2D, mild acid hydrolysis, alkaline degradation, ESI-FTICR-MS
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7. Compound ID: 151
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a-D-Glcp-(1-4)-+
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a-D-Glcp-(1-6)-+ | P-6)-+ P-2)-+ a-Kdop-(2-4)-+ P-4)-+
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a-8eLegp-(2-3)-a-L-FucpN-(1-3)-b-D-QuipN(20%)Ac-(1-3)-a-L-Rhap-(1-3)-b-D-Glcp-(1-3)-a-D-GalpN-(1-3)-L-gro-a-D-manHepp-(1-3)-L-gro-a-D-manHepp-(1-5)-a-Kdop-(2-6)-b-D-GlcpN-(1-6)-a-D-GlcpN-(1-P
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P-4)-+ |
Show graphically |
Structure type: oligomer
Trivial name: glycoform 2 core oligosaccharide with O-unit
Contained glycoepitopes: IEDB_130650,IEDB_130659,IEDB_135394,IEDB_136105,IEDB_137340,IEDB_137473,IEDB_140088,IEDB_141807,IEDB_142488,IEDB_144998,IEDB_146664,IEDB_150908,IEDB_151531,IEDB_189517,IEDB_2189047,IEDB_225177,IEDB_885823,IEDB_983931,SB_192
The structure is contained in the following publication(s):
- Article ID: 32
Bystrova OV, Lindner B, Moll H, Kocharova NA, Knirel YA, Zähringer U, Pier GB "Structure of the lipopolysaccharide of Pseudomonas aeruginosa O-12 with a randomly O-acetylated core region" -
Carbohydrate Research 338(18) (2003) 1895-1905
The lipopolysaccharide of Pseudomonas aeruginosa O-12 was studied by strong alkaline and mild acid degradations and dephosphorylation followed by fractionation of the products by GPC and high-performance anion-exchange chromatography and analyses by ESI FT-MS and NMR spectroscopy. The structures of the lipopolysaccharide core and the O-polysaccharide repeating unit were elucidated and the site and the configuration of the linkage between the O-polysaccharide and the core established. The core was found to be randomly O-acetylated, most O-acetyl groups being located on the terminal rhamnose residue of the outer core region
Lipopolysaccharide, Pseudomonas aeruginosa, core structures, O-antigen repeating unit, O-acetylation
NCBI PubMed ID: 12932374Publication DOI: 10.1016/S0008-6215(03)00290-8Journal NLM ID: 0043535Publisher: Elsevier
Correspondence: knirel@ioc.ac.ru
Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Research Center Borstel, Center for Medicine and Biosciences, Borstel, Germany, Channing Laboratory, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
Methods: 13C NMR, 1H NMR, NMR-2D, dephosphorylation, 31P NMR, GLC, mild acid hydrolysis, alkaline degradation, HPAEC, ESI-FT-MS
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8. Compound ID: 257
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b-D-Glcp-(1-6)-a-D-Glcp-(1-6)-+
|
-4)-b-D-Glcp-(1-4)-a-L-Rhap-(1-3)-b-D-Glcp-(1-4)-b-D-2daraHexpA-(1- |
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Structure type: polymer chemical repeating unit
Trivial name: exocellular polysaccharide
Compound class: EPS
Contained glycoepitopes: IEDB_136105,IEDB_141806,IEDB_142488,IEDB_144998,IEDB_146664,IEDB_189517,IEDB_225177,IEDB_885823,IEDB_983931,SB_192
The structure is contained in the following publication(s):
- Article ID: 67
Falk C, Jansson P, Rinaudo M, Heyraud A, Widmalm G, Hebbar P "Structural studies of the exocellular polysaccharide from Sphingomonas paucimobilis strain I-886" -
Carbohydrate Research 285 (1996) 69-79
The exocellular polysaccharide from Sphingomonas paucimobilis strain I-886 has been studied using methylation analysis, Smith degradation, partial acid hydrolysis, NMR spectroscopy, and mass spectrometry as the principal methods. It is concluded that the repeating unit has the following structure: [formula: see text] The absolute configuration of the uronic acid was deduced from 1H NMR chemical shifts and is most likely D. Some preparations of the polysaccharide also contain phosphate and O-acyl groups which have not been identified or localised
Sphingomonas paucimobilis, capsular polysaccharide structure, deoxyglucuronic acid
NCBI PubMed ID: 9011378Journal NLM ID: 0043535Publisher: Elsevier
Institutions: Clinical Research Centre, Karolinska Institute, Huddinge Hospital, Sweden, Centre de Recherches sur les Macromolecules Vegetales, Grenoble, France, Departement of Organic Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, Sweden, Centre de Pedologie Biologique, Vandouevre les Nancy, France
Methods: NMR-2D, methylation, partial acid hydrolysis, NMR, sugar analysis, Smith degradation
- 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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9. Compound ID: 411
|
R-Pyr-(2-6:2-4)-a-D-Galp-(1-2)-+
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-3)-a-L-Rhap-(1-3)-b-D-Glcp-(1-3)-a-L-Rhap-(1-3)-a-L-Rhap-(1-3)-a-L-Rhap-(1-2)-a-D-Glcp-(1- |
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Structure type: polymer chemical repeating unit
Compound class: EPS
Contained glycoepitopes: IEDB_136105,IEDB_136906,IEDB_137472,IEDB_141794,IEDB_142488,IEDB_144998,IEDB_146664,IEDB_151528,IEDB_151770,IEDB_151771,IEDB_158539,IEDB_189517,IEDB_190606,IEDB_225177,IEDB_885823,IEDB_983931,SB_192,SB_7
The structure is contained in the following publication(s):
- Article ID: 141
Van Calsteren MR, Pau-Roblot C, Begin A, Roy D "Structure determination of the exopolysaccharide produced by Lactobacillus rhamnosus strains RW-9595M and R" -
Biochemical Journal (2002) 7-17
Exopolysaccharides (EPSs) were isolated and purified from Lactobacillus rhamnosus strains RW-9595M, which has been shown to possess cytokine-stimulating activity, and R grown under various fermentation conditions (carbon source, incubation temperature and duration). Identical (1)H NMR spectra were obtained in all cases. Molecular masses were determined by gel permeation chromatography. The primary structure was elucidated using chemical and spectroscopic techniques. Organic acid, monosaccharide and absolute configuration analyses gave the following composition: pyruvate, 1; D-glucose, 2; D-galactose, 1; and l-rhamnose, 4. Methylation analysis indicated the presence of three residues of 3-linked rhamnose, and one residue each of 2,3-linked rhamnose, 2-linked glucose, 3-linked glucose and 4,6-linked galactose. The EPS was submitted to periodate oxidation followed by borohydride reduction. Monosaccharide analysis of the resulting polysaccharide gave the new composition: rhamnose, 4; and glucose, 1. Methylation analysis confirmed the loss of the 2-linked glucose and 4,6-linked galactose residues. On the basis of one- and two-dimensional (1)H and (13)C NMR data, the structure of the native EPS was consistent with the following heptasaccharide repeating unit: {3Rhaα-3Glcβ-3[Gal4,6(R)Pyα- 2]Rhaα-3Rhaα-3Rhaα-2Glcα-}(n) where Rha corresponds to rhamnose (6-deoxymannose) and Py corresponds to pyruvate acetal. Complete (1)H and (13)C assignments are reported for the native and the corresponding pyruvate-hydrolysed polysaccharide. Electrospray MS and MS/MS data are given for the oligosaccharide produced by Smith degradation.
NMR, Lactic acid bacteria, sequence, heptasaccharide repeating unit, pyruvate substituent
NCBI PubMed ID: 11903041Publication DOI: 10.1016/S0008-6215(99)00181-0Journal NLM ID: 2984726RPublisher: London, UK : Published by Portland Press on behalf of the Biochemical Society
Correspondence: vancalsteren@em.agr.ca
Institutions: Centre de recherche et de developpement sur les aliments, Agriculture et Agroalimentaire Canada, 3600 boulevard Casavant Ouest, Saint- Hyacinthe, Quebec, Canada J2S 8E3
Methods: NMR-2D, methylation, NMR, mild acid hydrolysis, Smith degradation
- Article ID: 5067
Birch J, Harðarson HK, Khan S, Van Calsteren MR, Ipsen R, Garrigues C, Almdal K, Hachem MA, Svensson B "Effect of repeat unit structure and molecular mass of lactic acid bacteria hetero-exopolysaccharides on binding to milk proteins" -
Carbohydrate Polymers 177 (2017) 406-414
Interactions of exopolysaccharides and proteins are of great importance in food science, but complicated to analyze and quantify at the molecular level. A surface plasmon resonance procedure was established to characterize binding of seven structure-determined, branched hetero-exopolysaccharides (HePSs) of 0.14-4.9MDa from lactic acid bacteria to different milk proteins (β-casein, κ-casein, native and heat-treated β-lactoglobulin) at pH 4.0-5.0. Maximum binding capacity (RUmax) and apparent affinity (KA,app) were HePS- and protein-dependent and varied for example 10- and 600-fold, respectively, in the complexation with native β-lactoglobulin at pH 4.0. Highest RUmax and KA,app were obtained with heat-treated β-lactoglobulin and β-casein, respectively. Overall, RUmax and KA,app decreased 6- and 20-fold, respectively, with increasing pH from 4.0 to 5.0. KA,app was influenced by ionic strength and temperature, indicating that polar interactions stabilize HePS-protein complexes. HePS size as well as oligosaccharide repeat structure, conferring chain flexibility and hydrogen bonding potential, influence the KA,app.
Binding parameters, Dynamic light scattering (DLS), Hetero-exopolysaccharides (HePSs), Surface plasmon resonance (SPR), β- and κ-casein, β-lactoglobulin
NCBI PubMed ID: 28962786Publication DOI: 10.1016/j.carbpol.2017.08.055Journal NLM ID: 8307156Publisher: Elsevier
Correspondence: B. Svensson
Institutions: Enzyme and Protein Chemistry, Department of Biotechnology and Biomedicine, Technical University of Denmark, Elektrovej, building 375, DK-2800 Kgs. Lyngby, Denmark, Department of Micro- and Nanotechnology, Technical University of Denmark, Produktionstorvet, building 423, DK-2800 Kgs. Lyngby, Denmark, Saint-Hyacinthe Research and Development Centre, Agriculture and Agri-Food Canada, 3600 Casavant Boulevard West, Saint-Hyacinthe, Quebec J2S 8E3, Canada, Department of Food Science, University of Copenhagen, Rolighedsvej 26, DK-1958 Frederiksberg C, Denmark, CED-Discovery, Chr Hansen A/S, DK-2970 Hørsholm, Denmark
Methods: gel filtration, 13C NMR, 1H NMR, sugar analysis, ESI-MS, acid hydrolysis, GC, MS/MS, methanolysis, reduction with NaBD4, acetylation, SPR, protein immobilization, dynamic light scattering
- 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
- Article ID: 5880
De Vuyst L, De Vin F "Exopolysaccharides from Lactic Acid Bacteria" -
Book: Comprehensive Glycoscience: From Chemistry to Systems Biology. Reference Module in Chemistry, Molecular Sciences and Chemical Engineering (2007) 477-519
carbohydrates, polysaccharides, Lactic acid bacteria, exopolysaccharides, glycolipids, glycoproteins, Glycomics
Publication DOI: 10.1016/B978-044451967-2/00129-XPublisher: Elsevier
Correspondence: ldvuyst@vub.ac.be
Editors: Barchi J, Kamerling H
Institutions: Department of Applied Biological Sciences and Engineering, Research Group of Industrial Microbiology and Food Biotechnology, Vrije Universiteit Brussel, Brussels, Belgium
- Article ID: 6301
Qin CJ, Ding MR, Tian GZ, Zou XP, Fu JJ, Hu J, Yin J "Chemical approaches towards installation of rare functional groups in bacterial surface glycans" -
Chinese Journal of Natural Medicines = Zhongguo Tianran Yaowu 20(6) (2022) 401-420
Bacterial surface glycans perform a diverse and important set of biological roles, and have been widely used in the treatment of bacterial infectious diseases. The majority of bacterial surface glycans are decorated with diverse rare functional groups, including amido, acetamidino, carboxamido and pyruvate groups. These functional groups are thought to be important constituents for the biological activities of glycans. Chemical synthesis of glycans bearing these functional groups or their variants is essential for the investigation of structure-activity relationships by a medicinal chemistry approach. To date, a broad choice of synthetic methods is available for targeting the different rare functional groups in bacterial surface glycans. This article reviews the structures of naturally occurring rare functional groups in bacterial surface glycans, and the chemical methods used for installation of these groups.
chemical synthesis, acetamidino group, amido group, bacterial surface glycan, carboxamido group, pyruvyl ketal
NCBI PubMed ID: 35750381Publication DOI: 10.1016/S1875-5364(22)60177-8Journal NLM ID: 101504416Publisher: Beijing: Science Press; Elsevier
Correspondence: J. Yin
Institutions: Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China, Wuxi School of Medicine, Jiangnan University, Wuxi, China
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10. Compound ID: 434
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L-GroA-(1-2)-+
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-3)-b-D-Glcp6(50%)Ac-(1-4)-b-D-GlcpA-(1-4)-b-D-Glcp-(1-4)-a-L-Rhap-(1- |
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Structure type: polymer chemical repeating unit
Trivial name: gellan, gellan gum
Compound class: EPS, CPS
Contained glycoepitopes: IEDB_115136,IEDB_136105,IEDB_140630,IEDB_142488,IEDB_146664,IEDB_189517,IEDB_225177,IEDB_423153,IEDB_885823,IEDB_983931,SB_192
The structure is contained in the following publication(s):
- Article ID: 161
Videira P, Fialho A, Geremia RA, Breton C, Sá-Correia I "Biochemical characterization of the b-1,4-glucuronosyltransferase GelK in the gellan gum-producing strain Sphingomonas paucimobilis ATCC 31461" -
Biochemical Journal 358(2) (2001) 457-464
Biosynthesis of bacterial polysaccharide-repeat units proceeds by sequential transfer of sugars, from the appropriate sugar donor to an activated lipid carrier, by committed glycosyltransferases (GTs). Few studies on the mechanism of action for this type of GT are available. Sphingomonas paucimobilis A.T.C.C. 31461 produces the industrially important polysaccharide gellan gum. We have cloned the gelK gene from S. paucimobilis A.T.C.C. 31461. GelK belongs to family 1 of the GT classification [Campbell, Davies, Bulone, Henrissat (1997) Biochem. J. 326, 929-939]. Sequence similarity studies suggest that GelK consists of two protein modules corresponding to the -NH(2) and -CO(2)H halves, the latter possibly harbouring the GT activity. The gelK gene and the open reading frames coding for the -NH(2) (GelK(NH2)) and -CO(2)H (GelK(COOH)) halves were overexpressed in Escherichia coli. GelK and GelK(NH2) were present in both the soluble and membrane fractions of E. coli, whereas GelK(COOH) was only present in the soluble fraction. GelK catalysed the transfer of [(14)C]glucuronic acid from UDP-[(14)C]glucuronic acid into a glycolipid extracted from S. paucimobilis or E. coli, even in the presence of EDTA, and the radioactive sugar was released from the glycolipid by β-1,4-glucuronidase. GelK was not able to use synthetic glucosyl derivatives as acceptors, indicating that the PP(i)-lipid moiety is needed for enzymic activity. Recombinant GelK(NH2) and GelK(COOH) did not show detectable activity. Based on the biochemical characteristics of GelK and on sequence similarities with N-acetylglucosaminyltransferase, we propose that GT families 1 and 28 form a superfamily.
strain, characterization, Sphingomonas, Sphingomonas paucimobilis, exopolysaccharide, biochemical, bioinformatics, conserved amino acids, gellan, N-acetylglucosaminyltransferase, secondary structure prediction
NCBI PubMed ID: 11513745Journal NLM ID: 2984726RPublisher: London, UK : Published by Portland Press on behalf of the Biochemical Society
Correspondence: roberto.geremia@ujf-grenoble.fr
Institutions: Centra de Engenharia Bioldgica e Quimica, Instituto Superior Tecnico, Av. Rovisco Pais, 1049-001 Lisboa, Portugal, Plasticite et Expression des Genomes Microbiens, Universite Joseph Fourier and Centre National de la Recherche Scientifique FRE 2383, Bat. CERMO, 460 Rue de la Piscine, 38041 Grenoble cedex 9, France, Centre de Recherches sur les Macromolecules Vegetales, CNRS, BP 53X, 38041 Grenoble, France., Centre de Recherches sur les Macromolecules Vegetales, CNRS, BP 53X, 38041 Grenoble, France
Methods: genetic methods, biochemical methods
- Article ID: 1290
Yamazaki M, Thorne L, Mikolajczak M, Armentrout RW, Pollock TJ "Linkage of genes essential for synthesis of a polysaccharide capsule in Sphingomonas strain S88" -
Journal of Bacteriology 178 (1996) 2676-2687
Several structurally related capsular polysaccharides that are secreted by members of the genus Sphingomonas are being developed as aqueous rheological control agents for diverse industrial and food applications. They include gellan (S-60), welan (S-130), rhamsan (S-194), S-657, S-88, S-198, S-7, and NW-11. We refer to these polysaccharides as sphingans, after the genus name. This paper characterizes the first gene cluster isolated from a Sphingomonas species (S88) that is required for capsule synthesis. Overlapping DNA segments which spanned about 50 kbp of S88 DNA restored the synthesis of sphingan S-88 in capsule-negative mutants. The mutations were mapped into functional complementation groups, and the contiguous nucleotide sequence for the 29-kbp cluster was determined. The genetic complementation map and the DNA sequences were interpreted as an extended multicistronic locus containing genes essential for the assembly and secretion of polysaccharide S-88. Many of the deduced amino acid sequences were similar to gene products from other polysaccharide-secreting bacteria such as Rhizobium meliloti (succinoglycan), Xanthomonas campestris (xanthan gum), and Salmonella enterica (O antigen). The S88 locus contained a four-gene operon for the biosynthesis of dTDP-L-rhamnose, an essential precursor for the sphingans. Unexpectedly, there were also two genes for secretion of a lytic or toxin-like protein nested within the polysaccharide cluster. The conservation and linkage of genes that code for a defensive capsule and genes for secretion of an offensive lysin or toxin suggest a heretofore unknown pathogenic life history for Sphingomonas strain S88
biosynthesis, synthesis, gene, strain, polysaccharide, Sphingomonas, linkage, capsule
NCBI PubMed ID: 8626338Journal NLM ID: 2985120RPublisher: American Society for Microbiology
Institutions: Shin-Etsu Bio, Inc., San Diego, California 92121, USA
- Article ID: 1483
Sletmoen M, Maurstad G, Sikorski P, Paulsen BS, Stokke BT "Characterisation of bacterial polysaccharides: steps towards single-molecular studies" -
Carbohydrate Research 338(23) (2003) 2459-2475
Techniques used in studies of polysaccharides, including chemical composition, linkage pattern, and higher order structures are in constant development. They provide information necessary for understanding of the polysaccharide properties and functions. Here, recent advancements in studies of the polysaccharides at the single-molecule level are highlighted. Over the last few years, single-molecule techniques such as force spectroscopy have improved in sensitivity and can today be used to detect forces in the pN range. In addition, these techniques can be used to investigate properties of single molecules close to physiological conditions. The challenges in the interpretation of the observations are aided by control experiments using well-characterised polysaccharides and by data provided by complementary methods. This field is expected to have increasing impact on the further advancement of the molecular understanding of the role of polysaccharides in various biological processes such as recognition and cell adhesion.
X-ray fibre diffraction, AFM, TEM, Force spectroscopy, Single-molecules
NCBI PubMed ID: 14670709Journal NLM ID: 0043535Publisher: Elsevier
Correspondence: bjorn.stokke@phys.ntnu.no
Institutions: Biophysics and Medical Technology, Department of Physics, The Norwegian University of Science and Technology, NTNU, NO-7491 Trondheim, Norway, Department of Pharmacognosy, School of Pharmacy, University of Oslo, P.O. Box 1068 Blindern, NO-0316 Oslo, Norway
- Article ID: 1646
Saksouk N, Pelosi L, Colin-Morel P, Boumedienne M, Abdian PL, Geremia RA "The capsular polysaccharide biosynthesis of Streptococcus pneumoniae serotype 8: functional identification of the glycosyltransferase WciS (Cap8H)" -
Biochemical Journal (2005) 63-72
CPS (capsular polysaccharide) is a major virulence factor in Streptococcus pneumoniae. Biosynthesis of CPS RU (repeat unit) proceeds by sequential transfer of sugar residues from the appropriate sugar donor to an activated lipid carrier by committed GTs (glycosyltransferases). While the nucleotide sequence of many cps loci is already known, the real substrate specificity of the hypothetical GTs, as well as the sequence of sugar addition is unclear. In the present paper, we report the biochemical characterization of one α-Galactosyltransferase, WciS (Cap8H), a member of GT family 4. This enzyme is implicated in the tetrasaccharide RU biosynthetic pathway of Strep. pneumoniae CPS 8 ([→4)-α-D-Glcp-(1→4)-α-D-Galp-(1→4)-β-D-GlcAp-(1→4)-β-D-Glcp-(1→]n). Expression of WciS-His6 in Escherichia coli BL21 (DE3) strains or BL21 (DE3)/∆galU strain resulted in synthesis of a 39 kDa membrane-associated protein identified by N-terminal sequencing and recognized by anti-His6-tag antibody. This protein was capable of adding a galactose residue cellobiuronic acid [β-D-GlcAp-(1→4)-D-Glcp]-pyrophosphate-polyprenol from UDP-Gal. The newly added galactose residue is removed by α-galactosidase, indicating that WciS is a retaining GT. Our results suggest that WciS catalyses the addition of the third sugar residue of the CPS 8 RU. The recombinant WciS-His6 was solubilized and purified as a soluble multimer, opening the way for structural studies.
Streptococcus pneumoniae, capsular polysaccharide, glycosyltransferase, galactosyltransferase, virulence factor, WciS
NCBI PubMed ID: 15766331Journal NLM ID: 2984726RPublisher: London, UK : Published by Portland Press on behalf of the Biochemical Society
Correspondence: rf.elbonerg-fju@aimereg.otrebor)
Institutions: Laboratoire Adaptation et Pathogenie des Micro-organismes, CNRS UMR 5163, Batiment Jean Roget, Faculte de Medecine Pharmacie, La Tronche, France
Methods: biochemical methods
- Article ID: 4321
Jia W, Zhang J, Jiang Y, Zheng Z, Zhan X, Lin C "Structure of oligosaccharide F21 derived from exopolysaccharide WL-26 produced by Sphingomonas sp. ATCC 31555" -
Carbohydrate Polymers 90(1) (2012) 60-66
Mild hydrolysis of Sphingomonas sp. ATCC 31555 polysaccharide WL-26 afforded a new oligosaccharide, F21. Structural resolution based on sugar and methylation analyses as well as NMR data revealed the oligosaccharide to have the following structure: (formula: see text).
NMR, oligosaccharide, structure, chemistry, carbohydrate, polymer, Sphingomonas, exopolysaccharide, PAGE, biotechnology, Polymers, China, structure characterization, oligosaccharide F21, partial acid hydrolysis
Publication DOI: 10.1016/j.carbpol.2012.04.061Journal NLM ID: 8307156Publisher: Elsevier
Correspondence: X.-B. Zhan
Institutions: Key Laboratory of Carbohydrate Chemistry and Biotechnology, School of Biotechnology, Jiangnan University, Wuxi, China
Methods: 13C NMR, 1H NMR, NMR-2D, methylation, partial acid hydrolysis, GC-MS, sugar analysis, mild acid hydrolysis, HPLC, HPAEC-PAD
- Article ID: 4605
Prajapati VD, Jani GK, Zala BS, Khutliwala TA "An insight into the emerging exopolysaccharide gellan gum as a novel polymer" -
Carbohydrate Polymers 93(2) (2013) 670-678
The microbial exopolysaccharides are water-soluble polymers secreted by microorganisms during fermentation. The biopolymer gellan gum is a relatively recent addition to the family of microbial polysaccharides that is gaining much importance in food, pharmaceutical and chemical industries due to its novel properties. It is commercially produced by C.P. Kelco in Japan and the USA. This article presents a critical review of the available information on the gum synthesized by Sphingomonas paucimobilis with special emphasis on its fermentative production. Factors affecting the fermentative production of gellan gum and problems associated with mass transfer have been addressed. Classification and trade names of gellan gum has been specified. Characteristics of gellan gum with respect to its structure, physicochemical properties are discussed. An attempt has also been made to review the current and potential applications of gellan gum in food, pharmaceutical and other industries.
Sphingomonas paucimobilis, Gellan gum, fermentative production
NCBI PubMed ID: 23499110Publication DOI: 10.1016/j.carbpol.2013.01.030Journal NLM ID: 8307156Publisher: Elsevier
Correspondence: vippra2000@yahoo.com
Institutions: Department of Pharmaceutics, S.S.R. College of Pharmacy, Saily-Silvassa Road, Saily, Silvassa, U.T. of Dadra and Nagar Haveli 396 230, India
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11. Compound ID: 467
|
a-L-Rhap-(1-3)-b-D-Glcp-(1-3)-a-L-Rhap-(1-3)-a-L-Rhap-(1-3)-a-L-Rhap-(1-2)-Gro |
Show graphically |
Structure type: oligomer
Compound class: EPS, cell wall polysaccharide
Contained glycoepitopes: IEDB_136105,IEDB_142488,IEDB_146664,IEDB_189517,IEDB_225177,IEDB_885823,IEDB_983931,SB_192
The structure is contained in the following publication(s):
- Article ID: 141
Van Calsteren MR, Pau-Roblot C, Begin A, Roy D "Structure determination of the exopolysaccharide produced by Lactobacillus rhamnosus strains RW-9595M and R" -
Biochemical Journal (2002) 7-17
Exopolysaccharides (EPSs) were isolated and purified from Lactobacillus rhamnosus strains RW-9595M, which has been shown to possess cytokine-stimulating activity, and R grown under various fermentation conditions (carbon source, incubation temperature and duration). Identical (1)H NMR spectra were obtained in all cases. Molecular masses were determined by gel permeation chromatography. The primary structure was elucidated using chemical and spectroscopic techniques. Organic acid, monosaccharide and absolute configuration analyses gave the following composition: pyruvate, 1; D-glucose, 2; D-galactose, 1; and l-rhamnose, 4. Methylation analysis indicated the presence of three residues of 3-linked rhamnose, and one residue each of 2,3-linked rhamnose, 2-linked glucose, 3-linked glucose and 4,6-linked galactose. The EPS was submitted to periodate oxidation followed by borohydride reduction. Monosaccharide analysis of the resulting polysaccharide gave the new composition: rhamnose, 4; and glucose, 1. Methylation analysis confirmed the loss of the 2-linked glucose and 4,6-linked galactose residues. On the basis of one- and two-dimensional (1)H and (13)C NMR data, the structure of the native EPS was consistent with the following heptasaccharide repeating unit: {3Rhaα-3Glcβ-3[Gal4,6(R)Pyα- 2]Rhaα-3Rhaα-3Rhaα-2Glcα-}(n) where Rha corresponds to rhamnose (6-deoxymannose) and Py corresponds to pyruvate acetal. Complete (1)H and (13)C assignments are reported for the native and the corresponding pyruvate-hydrolysed polysaccharide. Electrospray MS and MS/MS data are given for the oligosaccharide produced by Smith degradation.
NMR, Lactic acid bacteria, sequence, heptasaccharide repeating unit, pyruvate substituent
NCBI PubMed ID: 11903041Publication DOI: 10.1016/S0008-6215(99)00181-0Journal NLM ID: 2984726RPublisher: London, UK : Published by Portland Press on behalf of the Biochemical Society
Correspondence: vancalsteren@em.agr.ca
Institutions: Centre de recherche et de developpement sur les aliments, Agriculture et Agroalimentaire Canada, 3600 boulevard Casavant Ouest, Saint- Hyacinthe, Quebec, Canada J2S 8E3
Methods: NMR-2D, methylation, NMR, mild acid hydrolysis, Smith degradation
- Article ID: 5527
Zdorovenko E, Kadykova A, Kiseleva E, Shashkov A, Knirel Y, Plotnikova D, Novik G "Structures of cell-wall glycopolymers of Lactobacillus rhamnosus BIM B-1039" -
Carbohydrate Research 472 (2019) 138-143
Glycopolymers of two types were isolated from the cell wall of Lactobacillus rhamnosus BIM B-1039 by stepwise extraction with cold and hot 10% aq CCl3CO2H followed by anion-exchange gel chromatography. The following structures of the glycopolymers were established by sugar analysis, Smith degradation and 1D and 2D NMR spectroscopy: [structure: see text].
NMR spectroscopy, Lactic acid bacteria, cell wall, glycopolymer, Lactobacillus rhamnosus
Publication DOI: 10.1016/j.carres.2018.12.006Journal NLM ID: 0043535Publisher: Elsevier
Correspondence: E.L. Zdorovenko
Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Institute of Bioorganic chemistry, National Academy of Sciences of Belarus, Minsk, Belarus, Institute of Microbiology, National Academy of Sciences of Belarus, Minsk, Belarus, Higher Chemical College of the Russian Academy of Sciences, D. I. Mendeleev University of Chemical Technology of Russia, Moscow Russia
Methods: 13C NMR, 1H NMR, NMR-2D, sugar analysis, GLC, HPAEC, Smith degradation, GPC, extraction, 13C NMR analysis by GODDESS and GRASS
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12. Compound ID: 493
|
a-L-Rhap-(1-3)-+
|
-3)-b-D-Glcp-(1-4)-b-D-GlcpA-(1-4)-b-D-Glcp-(1-4)-a-L-Rhap-(1- |
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Structure type: polymer chemical repeating unit
Trivial name: sphingan, S-88, welan gum (S-130), wellan, S-130
Compound class: EPS, CPS
Contained glycoepitopes: IEDB_115136,IEDB_136105,IEDB_140630,IEDB_142488,IEDB_146664,IEDB_189517,IEDB_225177,IEDB_423153,IEDB_885823,IEDB_983931,SB_192
The structure is contained in the following publication(s):
- Article ID: 161
Videira P, Fialho A, Geremia RA, Breton C, Sá-Correia I "Biochemical characterization of the b-1,4-glucuronosyltransferase GelK in the gellan gum-producing strain Sphingomonas paucimobilis ATCC 31461" -
Biochemical Journal 358(2) (2001) 457-464
Biosynthesis of bacterial polysaccharide-repeat units proceeds by sequential transfer of sugars, from the appropriate sugar donor to an activated lipid carrier, by committed glycosyltransferases (GTs). Few studies on the mechanism of action for this type of GT are available. Sphingomonas paucimobilis A.T.C.C. 31461 produces the industrially important polysaccharide gellan gum. We have cloned the gelK gene from S. paucimobilis A.T.C.C. 31461. GelK belongs to family 1 of the GT classification [Campbell, Davies, Bulone, Henrissat (1997) Biochem. J. 326, 929-939]. Sequence similarity studies suggest that GelK consists of two protein modules corresponding to the -NH(2) and -CO(2)H halves, the latter possibly harbouring the GT activity. The gelK gene and the open reading frames coding for the -NH(2) (GelK(NH2)) and -CO(2)H (GelK(COOH)) halves were overexpressed in Escherichia coli. GelK and GelK(NH2) were present in both the soluble and membrane fractions of E. coli, whereas GelK(COOH) was only present in the soluble fraction. GelK catalysed the transfer of [(14)C]glucuronic acid from UDP-[(14)C]glucuronic acid into a glycolipid extracted from S. paucimobilis or E. coli, even in the presence of EDTA, and the radioactive sugar was released from the glycolipid by β-1,4-glucuronidase. GelK was not able to use synthetic glucosyl derivatives as acceptors, indicating that the PP(i)-lipid moiety is needed for enzymic activity. Recombinant GelK(NH2) and GelK(COOH) did not show detectable activity. Based on the biochemical characteristics of GelK and on sequence similarities with N-acetylglucosaminyltransferase, we propose that GT families 1 and 28 form a superfamily.
strain, characterization, Sphingomonas, Sphingomonas paucimobilis, exopolysaccharide, biochemical, bioinformatics, conserved amino acids, gellan, N-acetylglucosaminyltransferase, secondary structure prediction
NCBI PubMed ID: 11513745Journal NLM ID: 2984726RPublisher: London, UK : Published by Portland Press on behalf of the Biochemical Society
Correspondence: roberto.geremia@ujf-grenoble.fr
Institutions: Centra de Engenharia Bioldgica e Quimica, Instituto Superior Tecnico, Av. Rovisco Pais, 1049-001 Lisboa, Portugal, Plasticite et Expression des Genomes Microbiens, Universite Joseph Fourier and Centre National de la Recherche Scientifique FRE 2383, Bat. CERMO, 460 Rue de la Piscine, 38041 Grenoble cedex 9, France, Centre de Recherches sur les Macromolecules Vegetales, CNRS, BP 53X, 38041 Grenoble, France., Centre de Recherches sur les Macromolecules Vegetales, CNRS, BP 53X, 38041 Grenoble, France
Methods: genetic methods, biochemical methods
- Article ID: 252
Hashimoto W, Murata K "a-L-rhamnosidase of Sphingomonas sp. R1 producing an unusual exopolysaccharide of sphingan" -
Bioscience, Biotechnology, and Biochemistry 62(6) (1998) 1068-1074
A soil bacterium with α-L-rhamnosidase was isolated from a cumulative mixed culture containing a polysaccharide of gellan as a carbon source and identified to be Sphingomonas paucimobilis, known as a potent producer of gellan. The isolate (designated Sphingomonas sp. R1) produced an unusual exopolysaccharide of sphingan (denoted HWR1) distinct from gellan. The rhamnose in gellan was replaced with mannose in HWR1. The bacterium had a peculiar cell surface covered with many complicated plaits. α-L-Rhamnosidase purified from Sphingomonas sp. R1 grown in the presence of naringin was a monomer with a molecular mass of 110 kDa and most active at pH 8.0 and 50 degrees C. The enzyme required divalent metal ions for the activity and released L-rhamnose from various rhamnosyl glycosides.
polysaccharide, Sphingomonas, exopolysaccharide, sphingan, a-L-rhamnosidase
NCBI PubMed ID: 9692187Publication DOI: 10.1271/bbb.62.1068Journal NLM ID: 9205717Publisher: Japan Society for Bioscience, Biotechnology, and Agrochemistry
Correspondence: hasimoto@food2.food.kyoto-u.ac.jp
Institutions: Research Institute for Food Science, Kyoto University, Uji 611-0011, Japan
Methods: SDS-PAGE, TLC, acid hydrolysis, HPLC, electron microscopy, enzyme assay
- Article ID: 908
Kumar NS, Ratnayake RMSK, Widmalm G, Jansson P "Selective cleavage of welan gum (S-130) by oxidative decarboxylation with lead tetraacetate" -
Carbohydrate Research 291 (1996) 109-114
Oxidative decarboxylation of peracetylated welan gum (S-130) with lead tetraacetate resulted in selective cleavage of the glucuronosidic linkages. Products of the degradation were reduced with sodium borohydride, O-deacetylated, and fractionated. Polymeric and oligomeric fractions were separated and analysed by 1H NMR spectroscopy and fast atom bombardment mass spectrometry, and were found to be monomers, dimers, and trimers of the repeating unit. Results show that this method may be used to liberate alditol-terminated multiples of the repeating unit of peracetylated glycuronans by cleavage and degradation of the uronic acid residues. The reaction sequence also confirms the recent finding that welan gum contains repeating units with randomly distributed terminal groups.
degradation, Welan gum, S-130, Lead tetraacetate
NCBI PubMed ID: 8864225Publication DOI: 10.1016/s0008-6215(96)00137-1Journal NLM ID: 0043535Publisher: Elsevier
Institutions: Department of Chemistry, University of Peradeniya, Peradeniya, Sri Lanka
Methods: NMR, oxidative decarboxylation
- Article ID: 1359
Arndt ER, Stevens ES "Vacuum ultraviolet circular dichroism of gellan-family polymer films from water and dimethyl sulfoxide" -
Carbohydrate Research 280 (1996) 15-26
The denaturing effect of dimethyl sulfoxide (Me2SO) on the conformation of the gellan-welan-rhamsan family of microbial polysaccharides is directly demonstrated by circular dichroism (CD). The three polysaccharides display strikingly similar CD spectra (140-210 nm) for films cast from Me2SO. The disrupting effect of Me2SO on gellan and welan conformations has previously been reported by others on the basis of light-scattering and viscosity studies. Films cast from aqueous solutions at room temperature show more-intense CD bands, both at 182 nm, as is also observed for aqueous solutions, and in the 150-175 nm region. These features correspond to the ordered helical chains found by X-ray diffraction studies of similarly prepared films.
polysaccharide, polymer, water, viscosity, physico-chemical, circular dichroism, Dimethyl Sulfoxide, dimethylsulfoxide, film
NCBI PubMed ID: 8581894Publication DOI: 10.1016/0008-6215(95)00285-5Journal NLM ID: 0043535Publisher: Elsevier
Institutions: Department of Chemistry, State University of New York at Binghamton, Binghamton, USA
Methods: vacuum ultraviolet CD
- Article ID: 2044
Jansson PE, Lindberg B, Widmalm G, Sandford PA "Structural studies of an extracellular polysaccharide (S-130) elaborated by Alcaligenes ATCC 31555" -
Carbohydrate Research 139 (1985) 217-223
The structure of an extracellular polysaccharide (S-130) elaborated by Alcaligenes ATCC 31555, has been investigated. It is concluded that the polysaccharide is composed of pentasaccharide units having the following structure: [Formula: see text]. Of these units, approximately two-thirds contain terminal α-L-rhamnopyranosyl groups; the remainder contain α-L-mannopyranosyl groups. Approximately 50% of the units contain an O-acetyl group.
Publication DOI: 10.1016/0008-6215(85)90022-9Journal NLM ID: 0043535Publisher: Elsevier
Institutions: Department of Organic Chemistry, Arrhenius Laboratory, University of Stockholm, Stockholm, Sweden
- Article ID: 2056
O'Neill MA, Selvendran RR, Morris VJ, Eagles J "Structure of the extracellular polysaccharide produced by the bacterium Alcaligenes (ATCC 31555) species" -
Carbohydrate Research 147 (1986) 295-313
The extracellular anionic polysaccharide produced by the bacterium Alcaligenes (ATCC 31555) contains L-mannose, L-rhamnose, D-glucose, and D-glucuronic acid in the molar ratios 1.0:4.5:3.1:2.3. Analysis of the methylated and methylated, carboxyl-reduced polysaccharide indicated terminal non-reducing rhamnose and mannose, (1→4)-linked rhamnose, (1→3)- and (1→3,1→4)-linked glucose, and (1→4)-linked glucuronic acid to be present in the ratios 1.0:0.8:2.1:2.2:2.0:2.2. Partial acid hydrolysis and base-catalysed β-elimination gave a series of oligosaccharides that were isolated as their alkylated alditol derivatives by reverse-phase h.p.l.c. and characterised by f.a.b.-m.s., e.i.-m.s., and 1H-n.m.r. spectroscopy. The repeating unit 1, excluding O-acyl groups, is proposed.[Formula: see text]
Journal NLM ID: 0043535WWW link: http://dx.doi.org/10.1016/S0008-6215(00)90638-4Publisher: Elsevier
Institutions: AFRC Institute of Food Research, Norwich Laboratory, Norwich, UK
- Article ID: 2070
Jansson PE, Kumar NS, Lindberg B "Structural studies of a polysaccharide (S-88) elaborated by Pseudomonas ATCC 31554" -
Carbohydrate Research 156 (1986) 165-172
The structure of the extracellular polysaccharide elaborated by Pseudomonas ATCC 31554 has been investigated, methylation analyses, specific degradations, and 1H-n.m.r. spectroscopy being the main methods used. It is concluded that the polysaccharide is composed of pentasaccharide repeating-units with the structure: →3)-β-D-Glcp-(1→4)-β-D-GlcpA-(1→4)-[α-L-Rha-(1→3)-]-β-D-Glcp-(1→4)-α-L-[Rha or Man]-(1→. An unusual feature is that a sugar residue in the chain may be either L-rhamnose or L-mannose. The polysaccharide also contains O-acetyl groups (approximately 5%) which have not been located.
Publication DOI: 10.1016/S0008-6215(00)90108-3Journal NLM ID: 0043535Publisher: Elsevier
Institutions: Department of Organic Chemistry, Arrhenius Laboratory, University of Stockholm, Stockholm, Sweden
- Article ID: 2558
Lopes L, Milas M, Rinaudo M "Influence of the method of purification on some solution properties of welan gum" -
International Journal of Biological Macromolecules 16 (1994) 253-258
The origin and some consequences of the presence of aggregates and impurities (deriving from the fermentation procedure) on the solution properties of welan gum have been studied. For this purpose, a method of purification was developed for a fermentation welan broth. It was verified that this method is ineffective for the dissociation of aggregates in the commercial product. This demonstrates the irreversible nature of the intermolecular interactions of welan samples isolated by precipitation in the presence of impurities. The purified products were characterized (Mw, [eta], kH) and the results were compared to those obtained from commercial samples of welan. The influence of the method of purification on the rheological properties was analysed.
polysaccharide, Welan gum, aggregates
NCBI PubMed ID: 7893630Journal NLM ID: 7909578Publisher: Butterworth-Heinemann
Institutions: Instituto de Macromoléculas (IMA/UFRJ), Brazil
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13. Compound ID: 893
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L-Gro-(?-2)-+
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-3)-b-D-Glcp6Ac-(1-4)-b-D-GlcpA-(1-4)-b-D-Glcp-(1-4)-a-L-Rhap-(1- |
Show graphically |
Structure type: polymer chemical repeating unit
Trivial name: gellan
Compound class: EPS
Contained glycoepitopes: IEDB_115136,IEDB_136105,IEDB_140630,IEDB_142488,IEDB_146664,IEDB_189517,IEDB_225177,IEDB_423153,IEDB_885823,IEDB_983931,SB_192
The structure is contained in the following publication(s):
- Article ID: 252
Hashimoto W, Murata K "a-L-rhamnosidase of Sphingomonas sp. R1 producing an unusual exopolysaccharide of sphingan" -
Bioscience, Biotechnology, and Biochemistry 62(6) (1998) 1068-1074
A soil bacterium with α-L-rhamnosidase was isolated from a cumulative mixed culture containing a polysaccharide of gellan as a carbon source and identified to be Sphingomonas paucimobilis, known as a potent producer of gellan. The isolate (designated Sphingomonas sp. R1) produced an unusual exopolysaccharide of sphingan (denoted HWR1) distinct from gellan. The rhamnose in gellan was replaced with mannose in HWR1. The bacterium had a peculiar cell surface covered with many complicated plaits. α-L-Rhamnosidase purified from Sphingomonas sp. R1 grown in the presence of naringin was a monomer with a molecular mass of 110 kDa and most active at pH 8.0 and 50 degrees C. The enzyme required divalent metal ions for the activity and released L-rhamnose from various rhamnosyl glycosides.
polysaccharide, Sphingomonas, exopolysaccharide, sphingan, a-L-rhamnosidase
NCBI PubMed ID: 9692187Publication DOI: 10.1271/bbb.62.1068Journal NLM ID: 9205717Publisher: Japan Society for Bioscience, Biotechnology, and Agrochemistry
Correspondence: hasimoto@food2.food.kyoto-u.ac.jp
Institutions: Research Institute for Food Science, Kyoto University, Uji 611-0011, Japan
Methods: SDS-PAGE, TLC, acid hydrolysis, HPLC, electron microscopy, enzyme assay
- Article ID: 333
Morris ER, Gothard MGE, Hember MWN, Manning CE, Robinson G "Conformational and rheological transitions of welan, rhamsan and acylated gellan" -
Carbohydrate Polymers 30 (1996) 165-175
Native (‘high acyl’) gellan adopts double helix geometry at a much higher temperature than the deacylated polymer (commercial gellan gum), but the resulting gels are weaker, more elastic, and show no thermal hysteresis between formation and melting, indicating that acetyl groups, which are located on the periphery of the helix, prevent aggregation. On progressive removal of glyceryl substituents, which are located in the core of the helix and modify its geometry, the disorder-order transition becomes broader (i.e. less co-operative) and moves to a lower temperature. Eventually a second transition appears at the position characteristic of the fully deacylated polymer. Comparison of the relative magnitudes of the two transitions with the proportion of residual glycerate indicates that conversion from ‘high acyl’ to ‘deacetylated’ geometry requires six consecutive repeating units devoid of glyceryl groups.In welan and rhamsan, the double helix is stabilised to temperatures above 100 °C by incorporation of, respectively, monosaccharide and disaccharide sidechains in the ordered structure. Both have ‘weak gel’ properties similar to those of xanthan. However, ‘true’ gels are formed when the helix structure is dissociated and regenerated (by dissolving welan in dimethyl sulphoxide and adding water, or by heating and cooling deacylated rhamsan in aqueous solution). Our interpretation of this behaviour is that the native structures of both polymers are perfect double helices, with exact pairing of strands along the full length of the participating chains. Dissociation of these ‘perfect’ structures allows development of a cross-linked network by individual chains forming shorter helices with more than one partner.
rhamsan, rheological, conformational, exopolysaccharide, gellan, acylated, physico-chemical, welan
Publication DOI: 10.1016/S0144-8617(96)00059-8Journal NLM ID: 8307156Publisher: Elsevier
Institutions: Department of Food Research & Technology, Silsoe College, Cranfield University, Silsoe, Bedford, MK45 4DT, UK, Unilever Research, Colworth Laboratory, Sharnbrook, Bedford, MK44 1LQ, UK
Methods: X-ray, differential scanning calorimetry (DSC), viscosity measurement
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14. Compound ID: 894
|
/Variants 0/-+
|
-4)-a-L-Rhap-(1-3)-b-D-Glcp2Ac-(1-4)-b-D-GlcpA-(1-4)-b-D-Glcp-(1-
/Variants 0/ is:
a-L-Rhap-(1-3)-
OR (exclusively)
a-L-Manp-(1-3)- |
Show graphically |
Structure type: polymer chemical repeating unit
Trivial name: welan
Compound class: EPS
Contained glycoepitopes: IEDB_115136,IEDB_135849,IEDB_136105,IEDB_1394182,IEDB_140630,IEDB_142488,IEDB_146664,IEDB_189517,IEDB_225177,IEDB_423153,IEDB_885823,IEDB_983930,IEDB_983931,SB_192,SB_61
The structure is contained in the following publication(s):
- Article ID: 252
Hashimoto W, Murata K "a-L-rhamnosidase of Sphingomonas sp. R1 producing an unusual exopolysaccharide of sphingan" -
Bioscience, Biotechnology, and Biochemistry 62(6) (1998) 1068-1074
A soil bacterium with α-L-rhamnosidase was isolated from a cumulative mixed culture containing a polysaccharide of gellan as a carbon source and identified to be Sphingomonas paucimobilis, known as a potent producer of gellan. The isolate (designated Sphingomonas sp. R1) produced an unusual exopolysaccharide of sphingan (denoted HWR1) distinct from gellan. The rhamnose in gellan was replaced with mannose in HWR1. The bacterium had a peculiar cell surface covered with many complicated plaits. α-L-Rhamnosidase purified from Sphingomonas sp. R1 grown in the presence of naringin was a monomer with a molecular mass of 110 kDa and most active at pH 8.0 and 50 degrees C. The enzyme required divalent metal ions for the activity and released L-rhamnose from various rhamnosyl glycosides.
polysaccharide, Sphingomonas, exopolysaccharide, sphingan, a-L-rhamnosidase
NCBI PubMed ID: 9692187Publication DOI: 10.1271/bbb.62.1068Journal NLM ID: 9205717Publisher: Japan Society for Bioscience, Biotechnology, and Agrochemistry
Correspondence: hasimoto@food2.food.kyoto-u.ac.jp
Institutions: Research Institute for Food Science, Kyoto University, Uji 611-0011, Japan
Methods: SDS-PAGE, TLC, acid hydrolysis, HPLC, electron microscopy, enzyme assay
- 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
- Article ID: 6146
Sun X, Zhang J "Bacterial exopolysaccharides: Chemical structures, gene clusters and genetic engineering" -
International Journal of Biological Macromolecules 173 (2021) 481-490
In recent decades, the composition, structure, biosynthesis, and function of bacterial extracellular polysaccharides (EPS) have been extensively studied. EPS are synthesized through different biosynthetic pathways. The genes responsible for EPS synthesis are usually clustered on the genome or large plasmids of bacteria. Generally, different EPS synthesis gene clusters direct the synthesis of EPS with different chemical structures and biological activities. A better understanding of the gene functions involved in EPS biosynthesis is critical for the production of EPS with special biological activities. Genetic engineering methods are usually used to study EPS synthesis related genes. This review organizes the available information on EPS, including their structures, synthesis of related genes, and highlights the research progress of modifying EPS gene clusters through gene-editing methods.
genetic engineering, gene clusters, bacterial extracellular polysaccharides
Publication DOI: 10.1016/j.ijbiomac.2021.01.139Journal NLM ID: 7909578Publisher: Butterworth-Heinemann
Correspondence: jfzhang@mail.njust.edu.cn
Institutions: Center for Molecular Metabolism, Nanjing University of Science & Technology, Nanjing, China
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15. Compound ID: 895
|
a-L-Rhap-(1-4)-a-L-Rhap-(1-3)-+
|
-3)-b-D-Glcp-(1-4)-b-D-GlcpA-(1-4)-b-D-Glcp-(1-4)-a-L-Rhap-(1- |
Show graphically |
Structure type: polymer chemical repeating unit
Trivial name: sphingan, S-657
Compound class: EPS
Contained glycoepitopes: IEDB_115136,IEDB_136105,IEDB_140630,IEDB_142488,IEDB_146664,IEDB_189517,IEDB_225177,IEDB_423153,IEDB_885823,IEDB_983931,SB_192
The structure is contained in the following publication(s):
- Article ID: 252
Hashimoto W, Murata K "a-L-rhamnosidase of Sphingomonas sp. R1 producing an unusual exopolysaccharide of sphingan" -
Bioscience, Biotechnology, and Biochemistry 62(6) (1998) 1068-1074
A soil bacterium with α-L-rhamnosidase was isolated from a cumulative mixed culture containing a polysaccharide of gellan as a carbon source and identified to be Sphingomonas paucimobilis, known as a potent producer of gellan. The isolate (designated Sphingomonas sp. R1) produced an unusual exopolysaccharide of sphingan (denoted HWR1) distinct from gellan. The rhamnose in gellan was replaced with mannose in HWR1. The bacterium had a peculiar cell surface covered with many complicated plaits. α-L-Rhamnosidase purified from Sphingomonas sp. R1 grown in the presence of naringin was a monomer with a molecular mass of 110 kDa and most active at pH 8.0 and 50 degrees C. The enzyme required divalent metal ions for the activity and released L-rhamnose from various rhamnosyl glycosides.
polysaccharide, Sphingomonas, exopolysaccharide, sphingan, a-L-rhamnosidase
NCBI PubMed ID: 9692187Publication DOI: 10.1271/bbb.62.1068Journal NLM ID: 9205717Publisher: Japan Society for Bioscience, Biotechnology, and Agrochemistry
Correspondence: hasimoto@food2.food.kyoto-u.ac.jp
Institutions: Research Institute for Food Science, Kyoto University, Uji 611-0011, Japan
Methods: SDS-PAGE, TLC, acid hydrolysis, HPLC, electron microscopy, enzyme assay
- Article ID: 2079
Chowdhury TA, Lindberg B, Lindquist U, Baird J "Structural studies of an extracellular polysaccharide, S-657, elaborated by Xanthomonas ATCC 53159" -
Carbohydrate Research 164 (1987) 117-122
Journal NLM ID: 0043535Publisher: Elsevier
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