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1. Compound ID: 13578
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b-D-Glcp-(1-6)-b-D-GalpNAc-(1-4)-+
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-3)-a-D-Galp-(1-6)-b-D-Galp-(1-3)-b-D-GalpNAc-(1- |
Show graphically |
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_21,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: 5497
Shashkov AS, Cahill SM, Arbatsky NP, Westacott AC, Kasimova AA, Shneider MM, Popova AV, Shagin DA, Shelenkov AA, Mikhailova YV, Yanushevich YG, Edelstein MV, Kenyon JJ, Knirel YA "Acinetobacter baumannii K116 capsular polysaccharide structure is a hybrid of the K14 and revised K37 structures" -
Carbohydrate Research 484 (2019) 107774
The genome of Acinetobacter baumannii clinical isolate, MAR-303, recovered in Russia was sequenced and found to contain a novel gene cluster at the A. baumannii K locus for capsule biosynthesis. The gene cluster, designated KL116, included four genes for glycosyltransferases (Gtrs) and a gene for a Wzy polymerase responsible for joining oligosaccharide K units into the capsular polysaccharide (CPS). The arrangement of KL116 was a hybrid of previously described A. baumannii gene clusters, with two gtr genes and the wzy gene shared by KL37 and the two other gtr genes found in KL14. The structure of the K116 CPS was established by sugar analysis and Smith degradation, along with one- and two-dimensional 1H and 13C NMR spectroscopy. The CPS is composed of branched pentasaccharide K units containing only neutral sugars, with three monosaccharides in the main chain and a disaccharide side chain. The K116 unit shares internal sugar linkages with the K14 and K37 units, corresponding to the presence of shared gtr genes in the gene clusters. However, the specific linkage formed by Wzy was discrepant between K116 and the previously reported K37 CPS produced by A. baumannii isolate NIPH146. The K37 structure was therefore revised in this study, and the corrected Wzy linkage found to be identical to the Wzy linkage in K116. The KL116, KL14 and KL37 gene clusters were found in genomes of a variety of A. baumannii strain backgrounds, indicating their global distribution.
Acinetobacter baumannii, capsular polysaccharide, K locus, K116, K14, Revised K37
NCBI PubMed ID: 31421354Publication DOI: 10.1016/j.carres.2019.107774Journal 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, 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, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russiag State Research Center for Applied Microbiology and Biotechnology, Obolensk, Moscow Region, Russiah Central Scientific Research Institute of Epidemiology, Moscow, Russia
Methods: 13C NMR, 1H NMR, gel filtration, NMR-2D, sugar analysis, Smith degradation, ion-exchange chromatography, bioinformatic analysis, sequencing
- 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: 6078
Kasimova AA, Cahill SM, Shpirt AM, Dudnik AG, Shneider MM, Popova AV, Shelenkov AA, Mikhailova YV, Chizhov AO, Kenyon JJ, Knirel YA "The K139 capsular polysaccharide produced by Acinetobacter baumannii MAR17-1041 belongs to a group of related structures including K14, K37 and K116" -
International Journal of Biological Macromolecules 193(PtB) (2021) 2297-2302
Capsular polysaccharide (CPS) is a key target for bacteriophage and vaccine therapies currently being developed for treatment of infections caused by the extensively antibiotic resistant bacterial species, Acinetobacter baumannii. Identification of new CPS structures and the genetics that drive their synthesis underpins tailored treatment strategies. A novel CPS biosynthesis gene cluster, designated KL139, was identified in the whole genome sequence of a multiply antibiotic resistant clinical isolate, A. baumannii MAR-17-1041, recovered in Russia in 2017. CPS material extracted from A. baumannii MAR-17-1041 was studied by sugar analysis and Smith degradation along with one- and two-dimensional 1H and 13C NMR spectroscopy, and the structure was found to include a branched pentasaccharide repeating unit containing neutral carbohydrates. This structure closely resembles the topology of the A. baumannii K14 CPS but differs in the presence of d-Glcp in place of a d-Galp sugar in the repeat-unit main chain. The difference was attributed to a change in the sequence for two glycosyltransferases. These two proteins are also encoded by the A. baumannii KL37 gene cluster, and a multiple sequence alignment of KL139 with KL14 and KL37 revealed a hybrid relationship. The global distribution of KL139 was also assessed by probing 9065 A. baumannii genomes available in the NCBI non-redundant and WGS databases for the KL139 gene cluster. KL139 was found in 16 genomes from four different countries. Eleven of these isolates belong to the multidrug resistant global lineage, ST25.
Acinetobacter baumannii, capsular polysaccharide, K locus, K139
NCBI PubMed ID: 34793811Publication DOI: 10.1016/j.ijbiomac.2021.11.062Journal NLM ID: 7909578Publisher: Butterworth-Heinemann
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, 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, D.I. Mendeleev University of Chemical Technology of Russia, Moscow, Russia
Methods: 13C NMR, 1H NMR, NMR-2D, sugar analysis, GLC, Smith degradation, GPC, bioinformatic analysis, HR-ESI-MS, sequencing
- Article ID: 6128
Popova AV, Shneider MM, Arbatsky NP, Kasimova AA, Senchenkova SN, Shashkov AS, Dmitrenok AS, Chizhov AO, Mikhailova YV, Shagin DA, Sokolova OS, Timoshina OY, Kozlov RS, Miroshnikov KA, Knirel YA "Specific interaction of novel Friunavirus phages encoding tailspike depolymerases with corresponding Acinetobacter baumannii capsular types" -
Journal of Virology 95(5) (2021) e01714-20
Acinetobacter baumannii is one of the most clinically important nosocomial pathogens. The World Health Organisation refers it to its <> category to develop new strategies for effective therapy. This microorganism is capable of producing structurally diverse capsular polysaccharides (CPSs), which serve as primary receptors for A. baumannii bacteriophages carrying polysaccharide-depolymerasing enzymes. In this study, eight novel bacterial viruses that specifically infect A. baumannii strains belonging to K2/K93, K32, K37, K44, K48, K87, K89 and K116 capsular types were isolated and characterized. The overall genomic architecture demonstrated that these viruses are representatives of the Friunavirus genus of the family Autographiviridae The linear double-stranded DNA phage genomes of 41,105-42,402 bp share high nucleotide sequence identity, except for genes encoding structural depolymerases or tailspikes which determine the host specificity. Deletion mutants lacking N-terminal domains of tailspike proteins were cloned, expressed and purified. The structurally defined CPSs of the phage bacterial hosts were cleaved with the specific recombinant depolymerases, and the resultant oligosaccharides that corresponded to monomers or/and dimers of the CPS repeats (K-units) were isolated. Structures of the derived oligosaccharides were established by nuclear magnetic resonance spectroscopy and high-resolution electrospray ionization mass spectrometry. The data obtained showed that all depolymerases studied were glycosidases that cleave specifically the A. baumannii CPSs by the hydrolytic mechanism, in most cases, by the linkage between the K-units.IMPORTANCE Acinetobacter baumannii, a nonfermentative, Gram-negative, aerobic bacterium, is one of the most significant nosocomial pathogens. The pathogenicity of A. baumannii is based on the cooperative action of many factors, one of them being the production of capsular polysaccharides (CPSs) that surround bacterial cells with a thick protective layer. Polymorphism of the chromosomal capsule loci is responsible for the observed high structural diversity of the CPSs. In this study, we describe eight novel lytic phages which have different tailspike depolymerases (TSDs) determining the interaction of the viruses with corresponding A. baumannii capsular types (K-types). Moreover, we elucidate the structures of oligosaccharide products obtained by cleavage of the CPSs by the recombinant depolymerases. We believe that as the TSDs determine phage specificity, the diversity of their structures should be taken into consideration as selection criteria for inclusion of certain phage candidate to the cocktail designed to control A. baumannii with different K-types
structure, Acinetobacter baumannii, capsular polysaccharide, bacteriophage, glycosidase, capsular type, tailspike depolymerase
NCBI PubMed ID: 33268523Publication DOI: 10.1128/JVI.01714-20Journal NLM ID: 0113724Correspondence: popova.av@mipt.ru; popova_nastya86@mail.ru
Institutions: Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, State Research Center for Applied Microbiology and Biotechnology, Obolensk, Moscow Region, Russia, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia, Institute of Antimicrobial Chemotherapy, Smolensk State Medical University, Smolensk, Russia, Central Scientific Research Institute of Epidemiology, Moscow, Russia, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Moscow Region, Russia, Pirogov Russian National Research Medical University, Moscow, Russia, Lomonosov Moscow State University, Moscow, Russia
Methods: 13C NMR, 1H NMR, NMR-2D, DNA techniques, GPC, phage depolymerisation, HR-ESI-MS, TEM, phage isolation, phage infection inhibition assay, phage genome analysis
- 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: 6474
Timoshina OY, Kasimova AA, Shneider MM, Arbatsky NP, Shashkov AS, Shelenkov AA, Mikhailova YV, Popova AV, Hall RM, Knirel YA, Kenyon JJ "Loss of a Branch Sugar in the Acinetobacter baumannii K3-Type Capsular Polysaccharide Due To Frameshifts in the gtr6 Glycosyltransferase Gene Leads To Susceptibility To Phage APK37.1" -
Microbiology Spectrum 11(1) (2023) e0363122
The type of capsular polysaccharide (CPS) on the cell surface of Acinetobacter baumannii can determine the specificity of lytic bacteriophage under consideration for therapeutic use. Here, we report the isolation of a phage on an extensively antibiotic resistant ST2 A. baumannii isolate AB5001 that carries the KL3 CPS biosynthesis gene cluster predicting a K3-type CPS. As the phage did not infect isolates carrying KL3 or KL22 and known to produce K3 CPS, the structure of the CPS isolated from A. baumannii AB5001 was determined. AB5001 produced a variant CPS form, K3-v1, that lacks the β-d-GlсpNAc side chain attached to the d-Galp residue in the K3 structure. Inspection of the KL3 sequence in the genomes of AB5001 and other phage-susceptible isolates with a KL3 locus revealed single-base deletions in gtr6, causing loss of the Gtr6 glycosyltransferase that adds the missing d-GlсpNAc side chain to the K3 CPS. Hence, the presence of this sugar profoundly restricts the ability of the phage to digest the CPS. The 41-kb linear double-stranded DNA (dsDNA) phage genome was identical to the genome of a phage isolated on a K37-producing isolate and thus was named APK37.1. APK37.1 also infected isolates carrying KL116. Consistent with this, K3-v1 resembles the K37 and K116 structures. APK37.1 is a Friunavirus belonging to the Autographiviridae family. The phage-encoded tail spike depolymerase DpoAPK37.1 was not closely related to Dpo encoded by other sequenced Friunaviruses, including APK37 and APK116. IMPORTANCE Lytic bacteriophage have potential for the treatment of otherwise untreatable extensively antibiotic-resistant bacteria. For Acinetobacter baumannii, most phage exhibit specificity for the type of capsular polysaccharide (CPS) produced on the cell surface. However, resistance can arise via mutations in CPS genes that abolish this phage receptor. Here, we show that single-base deletions in a CPS gene result in alteration of the final structure rather than deletion of the capsule layer and hence affect the ability of a newly reported podophage to infect strains producing the K3 CPS.
Acinetobacter baumannii, capsular polysaccharide, K locus, APK37.1, K3-v1, KL3
NCBI PubMed ID: 36651782Publication DOI: 10.1128/spectrum.03631-22Journal NLM ID: 101634614Publisher: Washington, DC: ASM Press
Correspondence: J.J.Kenyon
Institutions: N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, 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, State Research Center for Applied Microbiology and Biotechnology, Obolensk, Russia, M. M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia, School of Life and Environmental Science, University of Sydney, Sydney, Australia
Methods: 13C NMR, 1H NMR, NMR-2D, chemical analysis, GLC, Smith degradation, de-O-acetylation, GPC, bioinformatic analysis, phage isolation, phage propagation, phage sequencing
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2. Compound ID: 15846
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b-D-Glcp-(1-6)-b-D-GalpNAc-(1-4)-a-D-Galp-(1-6)-b-D-Galp-(1-3)-b-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_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: 6128
Popova AV, Shneider MM, Arbatsky NP, Kasimova AA, Senchenkova SN, Shashkov AS, Dmitrenok AS, Chizhov AO, Mikhailova YV, Shagin DA, Sokolova OS, Timoshina OY, Kozlov RS, Miroshnikov KA, Knirel YA "Specific interaction of novel Friunavirus phages encoding tailspike depolymerases with corresponding Acinetobacter baumannii capsular types" -
Journal of Virology 95(5) (2021) e01714-20
Acinetobacter baumannii is one of the most clinically important nosocomial pathogens. The World Health Organisation refers it to its <> category to develop new strategies for effective therapy. This microorganism is capable of producing structurally diverse capsular polysaccharides (CPSs), which serve as primary receptors for A. baumannii bacteriophages carrying polysaccharide-depolymerasing enzymes. In this study, eight novel bacterial viruses that specifically infect A. baumannii strains belonging to K2/K93, K32, K37, K44, K48, K87, K89 and K116 capsular types were isolated and characterized. The overall genomic architecture demonstrated that these viruses are representatives of the Friunavirus genus of the family Autographiviridae The linear double-stranded DNA phage genomes of 41,105-42,402 bp share high nucleotide sequence identity, except for genes encoding structural depolymerases or tailspikes which determine the host specificity. Deletion mutants lacking N-terminal domains of tailspike proteins were cloned, expressed and purified. The structurally defined CPSs of the phage bacterial hosts were cleaved with the specific recombinant depolymerases, and the resultant oligosaccharides that corresponded to monomers or/and dimers of the CPS repeats (K-units) were isolated. Structures of the derived oligosaccharides were established by nuclear magnetic resonance spectroscopy and high-resolution electrospray ionization mass spectrometry. The data obtained showed that all depolymerases studied were glycosidases that cleave specifically the A. baumannii CPSs by the hydrolytic mechanism, in most cases, by the linkage between the K-units.IMPORTANCE Acinetobacter baumannii, a nonfermentative, Gram-negative, aerobic bacterium, is one of the most significant nosocomial pathogens. The pathogenicity of A. baumannii is based on the cooperative action of many factors, one of them being the production of capsular polysaccharides (CPSs) that surround bacterial cells with a thick protective layer. Polymorphism of the chromosomal capsule loci is responsible for the observed high structural diversity of the CPSs. In this study, we describe eight novel lytic phages which have different tailspike depolymerases (TSDs) determining the interaction of the viruses with corresponding A. baumannii capsular types (K-types). Moreover, we elucidate the structures of oligosaccharide products obtained by cleavage of the CPSs by the recombinant depolymerases. We believe that as the TSDs determine phage specificity, the diversity of their structures should be taken into consideration as selection criteria for inclusion of certain phage candidate to the cocktail designed to control A. baumannii with different K-types
structure, Acinetobacter baumannii, capsular polysaccharide, bacteriophage, glycosidase, capsular type, tailspike depolymerase
NCBI PubMed ID: 33268523Publication DOI: 10.1128/JVI.01714-20Journal NLM ID: 0113724Correspondence: popova.av@mipt.ru; popova_nastya86@mail.ru
Institutions: Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, State Research Center for Applied Microbiology and Biotechnology, Obolensk, Moscow Region, Russia, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia, Institute of Antimicrobial Chemotherapy, Smolensk State Medical University, Smolensk, Russia, Central Scientific Research Institute of Epidemiology, Moscow, Russia, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Moscow Region, Russia, Pirogov Russian National Research Medical University, Moscow, Russia, Lomonosov Moscow State University, Moscow, Russia
Methods: 13C NMR, 1H NMR, NMR-2D, DNA techniques, GPC, phage depolymerisation, HR-ESI-MS, TEM, phage isolation, phage infection inhibition assay, phage genome analysis
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3. Compound ID: 15847
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b-D-Glcp-(1-6)-b-D-GalpNAc-(1-4)-+
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b-D-Glcp-(1-6)-b-D-GalpNAc-(1-4)-a-D-Galp-(1-6)-b-D-Galp-(1-3)-b-D-GalpNAc-(1-3)-a-D-Galp-(1-6)-b-D-Galp-(1-3)-D-GalpNAc |
Show graphically |
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_21,SB_23,SB_24,SB_25,SB_7,SB_8,SB_88
The structure is contained in the following publication(s):
- Article ID: 6128
Popova AV, Shneider MM, Arbatsky NP, Kasimova AA, Senchenkova SN, Shashkov AS, Dmitrenok AS, Chizhov AO, Mikhailova YV, Shagin DA, Sokolova OS, Timoshina OY, Kozlov RS, Miroshnikov KA, Knirel YA "Specific interaction of novel Friunavirus phages encoding tailspike depolymerases with corresponding Acinetobacter baumannii capsular types" -
Journal of Virology 95(5) (2021) e01714-20
Acinetobacter baumannii is one of the most clinically important nosocomial pathogens. The World Health Organisation refers it to its <> category to develop new strategies for effective therapy. This microorganism is capable of producing structurally diverse capsular polysaccharides (CPSs), which serve as primary receptors for A. baumannii bacteriophages carrying polysaccharide-depolymerasing enzymes. In this study, eight novel bacterial viruses that specifically infect A. baumannii strains belonging to K2/K93, K32, K37, K44, K48, K87, K89 and K116 capsular types were isolated and characterized. The overall genomic architecture demonstrated that these viruses are representatives of the Friunavirus genus of the family Autographiviridae The linear double-stranded DNA phage genomes of 41,105-42,402 bp share high nucleotide sequence identity, except for genes encoding structural depolymerases or tailspikes which determine the host specificity. Deletion mutants lacking N-terminal domains of tailspike proteins were cloned, expressed and purified. The structurally defined CPSs of the phage bacterial hosts were cleaved with the specific recombinant depolymerases, and the resultant oligosaccharides that corresponded to monomers or/and dimers of the CPS repeats (K-units) were isolated. Structures of the derived oligosaccharides were established by nuclear magnetic resonance spectroscopy and high-resolution electrospray ionization mass spectrometry. The data obtained showed that all depolymerases studied were glycosidases that cleave specifically the A. baumannii CPSs by the hydrolytic mechanism, in most cases, by the linkage between the K-units.IMPORTANCE Acinetobacter baumannii, a nonfermentative, Gram-negative, aerobic bacterium, is one of the most significant nosocomial pathogens. The pathogenicity of A. baumannii is based on the cooperative action of many factors, one of them being the production of capsular polysaccharides (CPSs) that surround bacterial cells with a thick protective layer. Polymorphism of the chromosomal capsule loci is responsible for the observed high structural diversity of the CPSs. In this study, we describe eight novel lytic phages which have different tailspike depolymerases (TSDs) determining the interaction of the viruses with corresponding A. baumannii capsular types (K-types). Moreover, we elucidate the structures of oligosaccharide products obtained by cleavage of the CPSs by the recombinant depolymerases. We believe that as the TSDs determine phage specificity, the diversity of their structures should be taken into consideration as selection criteria for inclusion of certain phage candidate to the cocktail designed to control A. baumannii with different K-types
structure, Acinetobacter baumannii, capsular polysaccharide, bacteriophage, glycosidase, capsular type, tailspike depolymerase
NCBI PubMed ID: 33268523Publication DOI: 10.1128/JVI.01714-20Journal NLM ID: 0113724Correspondence: popova.av@mipt.ru; popova_nastya86@mail.ru
Institutions: Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, State Research Center for Applied Microbiology and Biotechnology, Obolensk, Moscow Region, Russia, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia, Institute of Antimicrobial Chemotherapy, Smolensk State Medical University, Smolensk, Russia, Central Scientific Research Institute of Epidemiology, Moscow, Russia, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Moscow Region, Russia, Pirogov Russian National Research Medical University, Moscow, Russia, Lomonosov Moscow State University, Moscow, Russia
Methods: 13C NMR, 1H NMR, NMR-2D, DNA techniques, GPC, phage depolymerisation, HR-ESI-MS, TEM, phage isolation, phage infection inhibition assay, phage genome analysis
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