Show legend Show as text

Structure type: polymer chemical repeating unit
Compound class: CPS
Contained glycoepitopes: IEDB_115136,IEDB_125613,IEDB_133754,IEDB_135813,IEDB_135849,IEDB_136105,IEDB_137340,IEDB_140630,IEDB_141807,IEDB_141815,IEDB_151531,IEDB_225177,IEDB_423153,IEDB_885823

• Article ID: 6025
  Arbatsky NP, Shashkov AS, Chizhov AO, Timoshina OY, Shneider MM, Knirel YA "Structure of the capsular polysaccharide of Acinetobacter baumannii MAR 55-66" - Russian Chemical Bulletin = Izvestiia Akademii nauk. Seriia khimicheskaia 70(3) (2021) 592-599
  

  A capsular polysaccharide was isolated from cells of opportunistic bacterial pathogen Acinetobacter baumannii strain MAR 55-66. According to carbohydrate analysis and 1H and 13C NMR spectroscopy, it is composed of heptasaccharide repeating units, which include five l-rhamnose (Rha) residues and one residue each of d-glucuronic acid (GlcA) and N-acetyl-d-glucosamine (GlcNAc). For structural analysis of this polysaccharide, the Smith degradation, depolymerization with a recombinant endo-glycosidase from a specific bacteriophage, and selective solvolysis with CF3CO2H were applied. The two last methods resulted in formation of the same linear heptasaccharide, which was subjected to the following chemical modifications: borohydride reduction, β-elimination with alkali, and partial acid hydrolysis. The resulting oligosaccharides were isolated by gel-permeation chromatography, and their structures were established by 1H and 13C NMR spectroscopy including 2D 1H-1H and 1H-13C NMR correlation experiments, as well as high-resolution electrospray ionization mass spectrometry. Based on the data obtained, the structure of the branched heptasaccharide repeating unit containing three Rha residues and one GlcNAc residue in the main chain along with two Rha residues and one GlcA residue in the side chain was established. The polysaccharide studied belongs to a group of structurally similar capsular polysaccharides of A. baumannii, which are built up of branched oligosaccharide repeating units that include four or five l-Rha residues and one residue each of d-GlcA and d-GlcNAc.

  oligosaccharide, structure, Acinetobacter baumannii, capsular polysaccharide, depolymerization

  Publication DOI: 10.1007/s11172-021-3130-6
  Journal NLM ID: 100912060
  Publisher: New York: Consultants Bureau
  Correspondence: chizhov@ioc.ac.ru
  Institutions: N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 47 Leninsky prosp., Moscow, Russian Federation, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, 16/10 ul. Miklukho-Maklaya, 117997, Moscow, Russian Federation
  Methods: 13C NMR, 1H NMR, NMR-2D, sugar analysis, mild acid hydrolysis, Smith degradation, HPLC, GPC, NaBH4 reduction, phage depolymerisation, solvolysis with trifluoroacetic acid, HR-ESI-MS
  
   
  
  Acinetobacter baumannii MAR 55-66
  CSDB ID 10816 (all data & tools)
• Article ID: 6084
  Kenyon JJ, Kasimova AA, Sviridova AN, Shpirt AM, Shneider MM, Mikhailova YV, Shelenkov AA, Popova AV, Perepelov AV, Shashkov AS, Dmitrenok AS, Chizhov AO, Knirel YA "Correlation of Acinetobacter baumannii K144 and K86 capsular polysaccharide structures with genes at the K locus reveals the involvement of a novel multifunctional rhamnosyltransferase for structural synthesis" - International Journal of Biological Macromolecules (2021) 1294-1300
  

  Whole genome sequence from Acinetobacter baumannii isolate Ab-46-1632 reveals a novel KL144 capsular polysaccharide (CPS) biosynthesis gene cluster, which carries genes for d-glucuronic acid (D-GlcA) and l-rhamnose (l-Rha) synthesis. The CPS was extracted from Ab-46-1632 and studied by 1H and 13C NMR spectroscopy, including a two-dimensional 1H,13C HMBC experiment and Smith degradation. The CPS was found to have a hexasaccharide repeat unit composed of four l-Rhap residues and one residue each of d-GlcpA and N-acetyl-d-glucosamine (D-GlcpNAc) consistent with sugar synthesis genes present in KL144. The K144 CPS structure was established and found to be related to those of A. baumannii K55, K74, K85, and K86. A comparison of the corresponding gene clusters to KL144 revealed a number of shared glycosyltransferase genes correlating to shared glycosidic linkages in the structures. One from the enzymes, encoded by only KL144 and KL86, is proposed to be a novel multifunctional rhamnosyltransfaerase likely responsible for synthesis of a shared α-l-Rhap-(1→2)-α-L-Rhap-(1→3)-L-Rhap trisaccharide fragment in the K144 and K86 structures.

  Acinetobacter baumannii, capsular polysaccharide, K locus, K144, K86, multifunctional glycosyltransferase

  NCBI PubMed ID: 34757131
  Publication DOI: 10.1016/j.ijbiomac.2021.10.178
  Journal NLM ID: 7909578
  Publisher: Butterworth-Heinemann
  Correspondence: asyashpirt@gmail.com
  Institutions: 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, N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Science, Moscow, Russia, M.M. Shemyakin and Y.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Moscow, Russia, State Research Center for Applied Microbiology and Biotechnology, Obolensk, Moscow, Region, Russia
  Methods: 13C NMR, 1H NMR, NMR-2D, sugar analysis, acid hydrolysis, GLC, Smith degradation, GPC, bioinformatic analysis, HR-ESI-MS, sequencing
  
   
  
  Acinetobacter baumannii K86
  CSDB ID 5871 (all data & tools)
• 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: 37240444
  Publication DOI: 10.3390/ijms24109100
  Journal NLM ID: 101092791
  Publisher: 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
  
   
  
  Acinetobacter baumannii K86 MAR 55-66
  CSDB ID 27043 (all data & tools)

Show legend Show as text

Structure type: oligomer
Compound class: CPS
Contained glycoepitopes: IEDB_115136,IEDB_125613,IEDB_133754,IEDB_135813,IEDB_135849,IEDB_136105,IEDB_137340,IEDB_140630,IEDB_141807,IEDB_141815,IEDB_151531,IEDB_225177,IEDB_423153,IEDB_885823

• 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: 37240444
  Publication DOI: 10.3390/ijms24109100
  Journal NLM ID: 101092791
  Publisher: 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
  
   
  
  Acinetobacter baumannii K86 MAR 55-66
  CSDB ID 27044 (all data & tools)

Show legend Show as text

Structure type: oligomer
Compound class: CPS
Contained glycoepitopes: IEDB_115136,IEDB_125613,IEDB_133754,IEDB_135813,IEDB_135849,IEDB_136105,IEDB_137340,IEDB_140630,IEDB_141807,IEDB_141815,IEDB_151531,IEDB_225177,IEDB_423153,IEDB_885823

• 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: 37240444
  Publication DOI: 10.3390/ijms24109100
  Journal NLM ID: 101092791
  Publisher: 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
  
   
  
  Acinetobacter baumannii K86 MAR 55-66
  CSDB ID 27045 (all data & tools)

Show legend Show as text

Structure type: oligomer
Compound class: CPS
Contained glycoepitopes: IEDB_115136,IEDB_125613,IEDB_133754,IEDB_135813,IEDB_135849,IEDB_136105,IEDB_137340,IEDB_140630,IEDB_141807,IEDB_141815,IEDB_151531,IEDB_225177,IEDB_423153,IEDB_885823

• 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: 37240444
  Publication DOI: 10.3390/ijms24109100
  Journal NLM ID: 101092791
  Publisher: 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
  
   
  
  Acinetobacter baumannii K86 MAR 55-66
  CSDB ID 27046 (all data & tools)