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1. Compound ID: 13577
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b-D-Glcp-(1-6)-b-D-GalpNAc-(1-6)-+
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-4)-a-D-Galp-(1-6)-b-D-Galp-(1-3)-b-D-GalpNAc-(1- |
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Structure type: polymer chemical repeating unit
Compound class: CPS
Contained glycoepitopes: IEDB_130648,IEDB_134624,IEDB_134627,IEDB_136044,IEDB_136906,IEDB_137472,IEDB_137473,IEDB_141794,IEDB_142488,IEDB_146664,IEDB_147450,IEDB_151528,IEDB_190606,IEDB_742248,IEDB_983931,SB_163,SB_165,SB_166,SB_187,SB_192,SB_195,SB_23,SB_24,SB_25,SB_7,SB_8,SB_88
The structure is contained in the following publication(s):
- Article ID: 5397
Arbatsky NP, Kasimova AA, Shashkov AS, Shneider MM, Popova AV, Shagin DA, Shelenkov AA, Mikhailova YV, Yanushevich YG, Azizov IS, Edelstein MV, Hall RM, Kenyon JJ, Knirel YA "Structure of the K128 capsular polysaccharide produced by Acinetobacter baumannii KZ-1093 from Kazakhstan" -
Carbohydrate Research 485 (2019) 107814
The structure of the K128 capsular polysaccharide (CPS) produced by Acinetobacter baumannii isolate KZ-1093 from Kazakhstan was established by sugar analysis and Smith degradation along with 1D and 2D 1H and 13C NMR spectroscopy. The CPS was found to consist of branched pentasaccharide repeating units containing only neutral sugars, and its composition and topology are closely related to those of the A. baumannii K116 CPS. The K128 and K116 oligosaccharide units differ in the linkage between the disaccharide side chain and the main chain, with a β-(1→6) linkage in K128 replacing a β-(1→4) linkage in K116. The linkages between the repeating units in the K128 and K116 CPSs are also different, with K128 units linked by β-d-GalpNAc-(1→4)-d-Galp, and β-d-GalpNAc-(1→3)-d-Galp linkages between K116 units. The KZ-1093 genome was sequenced and the CPS biosynthesis gene cluster at the chromosomal K locus was designated KL128. Consistent with the CPS structures, KL128 differs from KL116 in one glycosyltransferase gene and the gene for the Wzy polymerase. In KL128, the gtr200 glycosyltransferase gene replaces gtr76 in KL116, and Gtr200 was therefore assigned to the different β-d-GalpNAc-(1→6)-d-Galp linkage in K128. Similarly, the WzyK128 polymerase could be assigned to the β-d-GalpNAc-(1→4)-d-Galp linkage between the K128 units.
Acinetobacter baumannii, capsular polysaccharide, glycosyltransferase, Wzy polymerase, K locus
NCBI PubMed ID: 31539669Publication DOI: 10.1016/j.carres.2019.107814Journal NLM ID: 0043535Publisher: Elsevier
Correspondence: J.J. Kenyon
Institutions: N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, M. M. Shemyakin & Y. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia, State Research Center for Applied Microbiology and Biotechnology, Obolensk, Moscow Region, Russia, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Australia, Higher Chemical College of the Russian Academy of Sciences, D. I. Mendeleev University of Chemical Technology of Russia, Moscow, Russia, Institute of Antimicrobial Chemotherapy, Smolensk State Medical University, Smolensk, Russia, Central Scientific Research Institute of Epidemiology, Moscow, Russia, School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
Methods: 13C NMR, 1H NMR, NMR-2D, DNA sequencing, sugar analysis, chemical analysis, ion-exchange chromatography, bioinformatic analysis
- 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: 6199
Arbatsky NP, Kasimova AA, Shashkov AS, Shneider MM, Popova AV, Shagin DA, Shelenkov AS, Mikhailova YV, Yanushevich YG, Hall RM, Kenyon JJ "Involvement of a Phage-Encoded Wzy Protein in the Polymerization of K127 Units To Form the Capsular Polysaccharide of Acinetobacter baumannii Isolate 36-1454" -
Microbiology Spectrum 10(3) (2022) e0150321
A comprehensive understanding of capsular polysaccharide (CPS) diversity is critical to implementation of phage therapy to treat panresistant Acinetobacter baumannii infections. Predictions from genome sequences can assist identification of the CPS type but can be complicated if genes outside the K locus (CPS biosynthesis gene cluster) are involved. Here, the CPS produced by A. baumannii clinical isolate 36-1454 carrying a novel K locus, KL127, was determined and compared to other CPSs. KL127 differs from KL128 in only two of the glycosyltransferase (gtr) genes. The K127 unit in 36-1454 CPS was the pentasaccharide β-D-Glcp-(1→6)-D-β-GalpNAc-(1→6)-α-D-Galp-(1→6)-β-D-Glсp-(1→3)-β-D-GalpNAc in which D-Glcp at position 4 replaces d-Galp in K128, and the glycosyltransferases encoded by the different gtr genes form the surrounding linkages. However, although the KL127 and KL128 gene clusters encode nearly identical Wzy polymerases, the linkages between K units that form the CPS chains are different, i.e., β-D-GalpNAc-(1→3)-D-Galp in 36-1454 (K127) and β-D-GalpNAc-(1→4)-D-Galp in KZ-1093 (K128). The linkage between K127 units in 36-1454 is the same as the K-unit linkage in five known CPS structures, and a gene encoding a Wzy protein related to the Wzy of the corresponding K loci was found encoded in a prophage genome in the 36-1454 chromosome. Closely related Wzy proteins were encoded in unrelated phage in available KL127-carrying genomes. However, a clinical isolate, KZ-1257, carrying KL127 but not the prophage was found, and K127 units in the KZ-1257 CPS were β-D-GalpNAc-(1→4)-D-Galp linked, confirming that WzyKL127 forms this linkage and thus that the phage-encoded WzyPh1 forms the β-D-GalpNAc-(1→3)-D-Galp linkage in 36-1454. IMPORTANCE Bacteriophage therapy is an attractive innovative treatment for infections caused by extensively drug resistant Acinetobacter baumannii, for which there are few effective antibiotic treatments remaining. Capsular polysaccharide (CPS) is a primary receptor for many lytic bacteriophages, and thus knowledge of the chemical structures of CPS produced by the species will underpin the identification of suitable phages for therapeutic cocktails. However, recent research has shown that some isolates carry additional genes outside of the CPS biosynthesis K locus, which can modify the CPS structure. These changes can subsequently alter phage receptor sites and may be a method utilized for natural phage resistance. Hence, it is critical to understand the genetics that drive CPS synthesis and the extent to which genes outside of the K locus can affect the CPS structure.
Acinetobacter baumannii, capsular polysaccharide, phage, Wzy polymerase, K locus, K127
NCBI PubMed ID: 35475638Publication DOI: 10.1128/spectrum.01503-21Journal NLM ID: 101634614Publisher: Washington, DC: ASM Press
Correspondence: J.J. Kenyon
Institutions: Institute of Antimicrobial Chemotherapy, Smolensk State Medical University, Smolensk, Russia, Central Scientific Research Institute of Epidemiology, Moscow, Russia, Centre for Immunology and Infection Control, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Australia, N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciencesgrid.4886.2, Moscow, Russia, M. M. Shemyakin & Y. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciencesgrid.4886.2, Moscow, Russia, State Research Center for Applied Microbiology and Biotechnology, Obolensk, Moscow, Russia, School of Life and Environmental Sciences, University of Sydneygrid.1013.3, Sydney, Australia
Methods: 13C NMR, 1H NMR, NMR-2D, sugar analysis, acid hydrolysis, Smith degradation, GPC, function analysis of gene clusters, sequencing
- Article ID: 6309
Rudenko N, Karatovskaya A, Zamyatina A, Shepelyakovskaya A, Semushina S, Brovko F, Shpirt A, Torgov V, Kolotyrkina N, Zinin A, Kasimova A, Perepelov A, Shneider M, Knirel Y "Immune Response to Conjugates of Fragments of the Type K9 Capsular Polysaccharide of Acinetobacter baumannii with Carrier Proteins" -
Microbiology Spectrum 10(5) (2022) e0167422
The clonal bacterial species Acinetobacter baumannii is an emerging multidrug-resistant pathogen which causes high-lethality infections. Cells of A. baumannii are surrounded by the type-specific capsular polysaccharide (CPS), which provides resistance to the protective mechanisms of the host and is considered a target for immunization. The conjugates of three inert carrier proteins and A. baumannii type K9 CPS fragments, which contained various numbers of oligosaccharide repeats (K-units), were synthesized by periodate oxidation and squaric acid chemistry. The conjugates were applied to immunize mice, and chemical synthesis by squaric acid was shown to significantly improve the immunogenic properties of glycoconjugate. In BALB/c mice, IgG antibodies were predominant among type K9 CPS reactive antibodies, and their total content was several times higher than that of IgM. Immune sera were characterized by their opsonization ability during practically the entire lives of the experimental mice. The sera were cross-reactive, but the highest specificity was observed against the antigen (type K9 CPS) used for immunization. The immunization of BALB/c and ICR-1 mice with a glycoconjugate without adjuvants led to varying degrees of stimulation of IL-10, IL-17A, and TNF-alpha production, but not IL-4 production in the ICR-1 mice. This is in contrast to the BALB/c mice, in which gamma-IFN production was also activated. The protective effectiveness of the glycoconjugates obtained by squaric acid chemistry was demonstrated by experiments that involved challenging immunized and nonimmunized animals with a lethal dose of A. baumannii K9. IMPORTANCE Immunization by glycoconjugates with A. baumannii type K9 CPS fragments induced a high level of antibodies (predominantly IgG) in sera, which reacted specifically with the CPS of A. baumannii type K9, as well as a long immunological memory. The sera of immunized animals efficiently opsonized A. baumannii type K9. Immunization resulted in the balanced production of pro/anti-inflammatory lymphokines and protective antibodies to ensure the survival of the mice infected with A. baumannii. The level of specific antibodies was sufficient to provide protective immunity against the challenge by A. baumannii, making this approach applicable in the development of vaccine preparations.
carbohydrates, carbohydrate, Acinetobacter baumannii, capsular polysaccharide, glycoconjugate, immunochemistry, interleukins, opsonisation assay
NCBI PubMed ID: 35980044Publication DOI: 10.1128/spectrum.01674-22Journal NLM ID: 101634614Publisher: Washington, DC: ASM Press
Correspondence: N.Rudenko
Institutions: Laboratory of Immunochemistry, Pushchino Branch, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Pushchino, Moscow Region, Russia, Laboratory of Carbohydrates and Biocides, N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Laboratory of Molecular Bioengineering, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
Methods: periodate oxidation, EIA, chemical synthesis, MALDI-TOF MS, statistical analysis, immunization, HR-ESI-MS, opsonization assay
- Article ID: 6475
Timoshina OY, Kasimova AA, Shneider MM, Matyuta IO, Nikolaeva AY, Evseev PV, Arbatsky NP, Shashkov AS, Chizhov AO, Shelenkov AA, Mikhailova YV, Slukin PV, Volozhantsev NV, Boyko KM, Knirel YA, Miroshnikov KA, Popova AV "Friunavirus Phage-Encoded Depolymerases Specific to Different Capsular Types of Acinetobacter baumannii" -
International Journal of Molecular Sciences 24(10) (2023) 9100
Acinetobacter baumannii is a critical priority nosocomial pathogen that produces a variety of capsular polysaccharides (CPSs), the primary receptors for specific depolymerase-carrying phages. In this study, the tailspike depolymerases (TSDs) encoded in genomes of six novel Friunaviruses, APK09, APK14, APK16, APK86, APK127v, APK128, and one previously described Friunavirus phage, APK37.1, were characterized. For all TSDs, the mechanism of specific cleavage of corresponding A. baumannii capsular polysaccharides (CPSs) was established. The structures of oligosaccharide fragments derived from K9, K14, K16, K37/K3-v1, K86, K127, and K128 CPSs degradation by the recombinant depolymerases have been determined. The crystal structures of three of the studied TSDs were obtained. A significant reduction in mortality of Galleria mellonella larvae infected with A. baumannii of K9 capsular type was shown in the example of recombinant TSD APK09_gp48. The data obtained will provide a better understanding of the interaction of phage-bacterial host systems and will contribute to the formation of principles of rational usage of lytic phages and phage-derived enzymes as antibacterial agents.
Acinetobacter baumannii, capsular polysaccharide, crystal structure, bacteriophage, glycosidase, capsular type, tailspike depolymerase
NCBI PubMed ID: 37240444Publication DOI: 10.3390/ijms24109100Journal NLM ID: 101092791Publisher: Basel, Switzerland: MDPI
Correspondence: A.V. Popova
Institutions: Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia, State Research Center for Applied Microbiology and Biotechnology, 142279 Obolensk, Russia, N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 119991 Moscow, Russia, Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia, Center for Photonics and 2D Materials, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia, Complex of NBICS Technologies, National Research Center 'Kurchatov Institute', 123182 Moscow, Russia, Central Scientific Research Institute of Epidemiology, 111123 Moscow, Russia
Methods: 13C NMR, 1H NMR, NMR-2D, PCR, X-ray, DNA techniques, GPC, enzymatic depolymerization, crystallization, HR-ESI-MS, phage isolation, phage genome analysis, phage propagation, phage sequencing
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2. Compound ID: 16695
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b-D-Glcp-(1-6)-b-D-GalpNAc-(1-6)-+
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b-D-Glcp-(1-6)-b-D-GalpNAc-(1-6)-a-D-Galp-(1-6)-b-D-Galp-(1-3)-b-D-GalpNAc-(1-4)-a-D-Galp-(1-6)-b-D-Galp-(1-3)-D-GalpNAc |
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Structure type: oligomer
Compound class: CPS
Contained glycoepitopes: IEDB_130648,IEDB_134624,IEDB_134627,IEDB_136044,IEDB_136906,IEDB_137472,IEDB_137473,IEDB_1391961,IEDB_1391963,IEDB_141584,IEDB_141794,IEDB_142488,IEDB_143260,IEDB_146664,IEDB_147450,IEDB_151528,IEDB_190606,IEDB_742248,IEDB_885822,IEDB_983931,SB_163,SB_165,SB_166,SB_187,SB_192,SB_195,SB_23,SB_24,SB_25,SB_7,SB_8,SB_88
The structure is contained in the following publication(s):
- Article ID: 6475
Timoshina OY, Kasimova AA, Shneider MM, Matyuta IO, Nikolaeva AY, Evseev PV, Arbatsky NP, Shashkov AS, Chizhov AO, Shelenkov AA, Mikhailova YV, Slukin PV, Volozhantsev NV, Boyko KM, Knirel YA, Miroshnikov KA, Popova AV "Friunavirus Phage-Encoded Depolymerases Specific to Different Capsular Types of Acinetobacter baumannii" -
International Journal of Molecular Sciences 24(10) (2023) 9100
Acinetobacter baumannii is a critical priority nosocomial pathogen that produces a variety of capsular polysaccharides (CPSs), the primary receptors for specific depolymerase-carrying phages. In this study, the tailspike depolymerases (TSDs) encoded in genomes of six novel Friunaviruses, APK09, APK14, APK16, APK86, APK127v, APK128, and one previously described Friunavirus phage, APK37.1, were characterized. For all TSDs, the mechanism of specific cleavage of corresponding A. baumannii capsular polysaccharides (CPSs) was established. The structures of oligosaccharide fragments derived from K9, K14, K16, K37/K3-v1, K86, K127, and K128 CPSs degradation by the recombinant depolymerases have been determined. The crystal structures of three of the studied TSDs were obtained. A significant reduction in mortality of Galleria mellonella larvae infected with A. baumannii of K9 capsular type was shown in the example of recombinant TSD APK09_gp48. The data obtained will provide a better understanding of the interaction of phage-bacterial host systems and will contribute to the formation of principles of rational usage of lytic phages and phage-derived enzymes as antibacterial agents.
Acinetobacter baumannii, capsular polysaccharide, crystal structure, bacteriophage, glycosidase, capsular type, tailspike depolymerase
NCBI PubMed ID: 37240444Publication DOI: 10.3390/ijms24109100Journal NLM ID: 101092791Publisher: Basel, Switzerland: MDPI
Correspondence: A.V. Popova
Institutions: Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia, State Research Center for Applied Microbiology and Biotechnology, 142279 Obolensk, Russia, N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 119991 Moscow, Russia, Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia, Center for Photonics and 2D Materials, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia, Complex of NBICS Technologies, National Research Center 'Kurchatov Institute', 123182 Moscow, Russia, Central Scientific Research Institute of Epidemiology, 111123 Moscow, Russia
Methods: 13C NMR, 1H NMR, NMR-2D, PCR, X-ray, DNA techniques, GPC, enzymatic depolymerization, crystallization, HR-ESI-MS, phage isolation, phage genome analysis, phage propagation, phage sequencing
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