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Evseev PV, Sukhova AS, Tkachenko NA, Skryabin YP, Popova AV. Lytic Capsule-Specific Acinetobacter Bacteriophages Encoding Polysaccharide-Degrading Enzymes. Viruses 2024; 16:771. [PMID: 38793652 PMCID: PMC11126041 DOI: 10.3390/v16050771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 05/09/2024] [Accepted: 05/10/2024] [Indexed: 05/26/2024] Open
Abstract
The genus Acinetobacter comprises both environmental and clinically relevant species associated with hospital-acquired infections. Among them, Acinetobacter baumannii is a critical priority bacterial pathogen, for which the research and development of new strategies for antimicrobial treatment are urgently needed. Acinetobacter spp. produce a variety of structurally diverse capsular polysaccharides (CPSs), which surround the bacterial cells with a thick protective layer. These surface structures are primary receptors for capsule-specific bacteriophages, that is, phages carrying tailspikes with CPS-depolymerizing/modifying activities. Phage tailspike proteins (TSPs) exhibit hydrolase, lyase, or esterase activities toward the corresponding CPSs of a certain structure. In this study, the data on all lytic capsule-specific phages infecting Acinetobacter spp. with genomes deposited in the NCBI GenBank database by January 2024 were summarized. Among the 149 identified TSPs encoded in the genomes of 143 phages, the capsular specificity (K specificity) of 46 proteins has been experimentally determined or predicted previously. The specificity of 63 TSPs toward CPSs, produced by various Acinetobacter K types, was predicted in this study using a bioinformatic analysis. A comprehensive phylogenetic analysis confirmed the prediction and revealed the possibility of the genetic exchange of gene regions corresponding to the CPS-recognizing/degrading parts of different TSPs between morphologically and taxonomically distant groups of capsule-specific Acinetobacter phages.
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Affiliation(s)
- Peter V. Evseev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia;
- State Research Center for Applied Microbiology and Biotechnology, City District Serpukhov, Moscow Region, 142279 Obolensk, Russia; (A.S.S.); (Y.P.S.)
- Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Anastasia S. Sukhova
- State Research Center for Applied Microbiology and Biotechnology, City District Serpukhov, Moscow Region, 142279 Obolensk, Russia; (A.S.S.); (Y.P.S.)
| | - Nikolay A. Tkachenko
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia;
| | - Yuriy P. Skryabin
- State Research Center for Applied Microbiology and Biotechnology, City District Serpukhov, Moscow Region, 142279 Obolensk, Russia; (A.S.S.); (Y.P.S.)
| | - Anastasia V. Popova
- State Research Center for Applied Microbiology and Biotechnology, City District Serpukhov, Moscow Region, 142279 Obolensk, Russia; (A.S.S.); (Y.P.S.)
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Roshini J, Patro LPP, Sundaresan S, Rathinavelan T. Structural diversity among Acinetobacter baumannii K-antigens and its implication in the in silico serotyping. Front Microbiol 2023; 14:1191542. [PMID: 37415807 PMCID: PMC10320297 DOI: 10.3389/fmicb.2023.1191542] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 05/30/2023] [Indexed: 07/08/2023] Open
Abstract
Acinetobacter baumannii is an emerging opportunistic pathogen. It exhibits multi-, extreme-, and pan-drug resistance against several classes of antibiotics. Capsular polysaccharide (CPS or K-antigen) is one of the major virulence factors which aids A. baumannii in evading the host immune system. K-antigens of A. baumannii exploit the Wzx/Wzy-dependent pathway that involves 13 different proteins for its assembly and transport onto the outer membrane. A total of 64 (out of 237 K-locus(KL) types) known K-antigen sugar repeating structures are discussed here and are classified into seven groups based on their initial sugars, QuiNAc4NAc, GalNAc, GlcNAc, Gal, QuiNAc/FucNAc, FucNAc, and GlcNAc along with Leg5Ac7Ac/Leg5Ac7R. Thus, the corresponding seven initializing glycosyltransferases (ItrA1, ItrA2, ItrA3, ItrA4, ItrB1, ItrB3, and ItrA3 along with ItrB2) exhibit serotype specificity. The modeled 3D-structural repository of the 64 K-antigens can be accessed at https://project.iith.ac.in/ABSD/k_antigen.html. The topology of K-antigens further reveals the presence of 2-6 and 0-4 sugar monomers in the main and side chains, respectively. The presence of negatively (predominant) or neutrally charged K-antigens is observed in A. baumannii. Such diversity in the K-antigen sugar composition provides the K-typing specificity (viz., 18-69% in terms of reliability) for Wza, Wzb, Wzc, Wzx, and Wzy proteins involved in the Wzx/Wzy-dependent pathway. Interestingly, the degree of uniqueness of these proteins among different K-types is estimated to be 76.79%, considering the 237 reference sequences. This article summarizes the A. baumannii K-antigen structural diversity and creation of a K-antigen digital repository and provides a systematic analysis of the K-antigen assembly and transportation marker proteins.
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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. Microbiol Spectr 2023; 11:e0363122. [PMID: 36651782 PMCID: PMC9927144 DOI: 10.1128/spectrum.03631-22] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 12/21/2022] [Indexed: 01/19/2023] Open
Abstract
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.
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Affiliation(s)
- Olga Y. Timoshina
- M. M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Anastasiya A. Kasimova
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Mikhail M. Shneider
- M. M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Nikolay P. Arbatsky
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Alexander S. Shashkov
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | | | | | - Anastasiya V. Popova
- State Research Center for Applied Microbiology and Biotechnology, Obolensk, Russia
| | - Ruth M. Hall
- School of Life and Environmental Science, University of Sydney, Sydney, Australia
| | - Yuriy A. Knirel
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Johanna J. Kenyon
- Centre for Immunology and Infection Control, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Australia
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Knirel YA, Kasimova AA, Arbatsky NP, Shneider MM, Popova AV, Brovko FA, Shashkov AS, Senchenkova SN, Perepelov AV, Shpirt AM. 5,7-Diamino-3,5,7,9-tetradeoxynon-2-ulosonic Acids in the Capsular Polysaccharides of Acinetobacter baumannii. BIOCHEMISTRY (MOSCOW) 2023; 88:202-210. [PMID: 37072328 DOI: 10.1134/s0006297923020049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
The polysaccharide capsule surrounding bacterial cell plays an important role in pathogenesis of infections caused by the opportunistic pathogen Acinetobacter baumannii by providing protection from external factors. The structures of the capsular polysaccharide (CPS) produced by A. baumannii isolates and the corresponding CPS biosynthesis gene clusters are highly diverse, although many of them are related. Many types of A. baumannii CPSs contain isomers of 5,7-diamino-3,5,7,9-tetradeoxynon-2-ulosonic acid (DTNA). Three of these isomers, namely acinetaminic acid (l-glycero-l-altro isomer), 8-epiacinetaminic acid (d-glycero-l-altro isomer), and 8-epipseudaminic acid (d-glycero-l-manno isomer), have not been found so far in naturally occurring carbohydrates from other species. In A. baumannii CPSs, DTNAs carry N-acyl substituents at positions 5 and 7; in some CPSs, both N-acetyl and N-(3-hydroxybutanoyl) groups are present. Remarkably, pseudaminic acid carries the (R)-isomer and legionaminic acid carries the (S)-isomer of the 3-hydroxybutanoyl group. The review addresses the structure and genetics of biosynthesis of A. baumannii CPSs containing di-N-acyl derivatives of DTNA.
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Affiliation(s)
- Yuriy A Knirel
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, 117913, Russia.
| | - Anastasia A Kasimova
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, 117913, Russia.
| | - Nikolay P Arbatsky
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, 117913, Russia.
| | - Mikhail M Shneider
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.
| | - Anastasia V Popova
- State Research Center for Applied Microbiology and Biotechnology, Obolensk, Moscow Region, 142279, Russia.
| | - Fedor A Brovko
- Branch of the Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry in Pushchino, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia.
| | - Aleksander S Shashkov
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, 117913, Russia.
| | - Sofia N Senchenkova
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, 117913, Russia.
| | - Andrei V Perepelov
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, 117913, Russia.
| | - Anna M Shpirt
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, 117913, Russia.
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Shashkov AS, Kasimova AA, Arbatsky NP, Senchenkova SN, Perepelov AV, Dmitrenok AS, Chizhov AO, Knirel YA, Shneider MM, Popova AV, Kenyon JJ. Complete chemical structure of the K135 capsular polysaccharide produced by Acinetobacter baumannii RES-546 that contains 5,7-di-N-acetyl-8-epipseudaminic acid. Carbohydr Res 2023; 523:108726. [PMID: 36446189 DOI: 10.1016/j.carres.2022.108726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 11/09/2022] [Accepted: 11/15/2022] [Indexed: 11/24/2022]
Abstract
A structurally diverse capsular polysaccharide (CPS) in the outer cell envelope plays an important role in the virulence of the important bacterial pathogen, Acinetobacter baumannii. More than 75 different CPS structures have been determined for the species to date, and many CPSs include isomers of a higher sugar, namely 5,7-diamino-3,5,7,9-tetradeoxynon-2-ulosonic acid. Recently, a novel isomer having the d-glycero-l-manno configuration (5,7-di-N-acetyl-8-epipseudaminic acid; 8ePse5Ac7Ac) has been identified in the CPS from A. baumannii clinical isolate RES-546 [Carbohydr. Res. 513 (2022) 108,531]. Here, the complete chemical structure of this CPS, designated K135, was elucidated. The CPS was found to have a branched tetrasaccharide K unit and to include the higher sugar as part of a 8ePse5Ac7Ac-(2 → 6)-α-Gal disaccharide branching from a →3)-α-D-GlcpNAc-(1 → 3)-β-D-GlcpNAc-(1→ main chain. Assignment of glycosyltransferases encoded by the CPS biosynthesis gene cluster in the RES-546 genome enabled the first sugar of the K unit, and hence the topology of the K135 CPS, to be determined.
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Affiliation(s)
- Alexander S Shashkov
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Anastasiya A Kasimova
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Nikolay P Arbatsky
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Sof'ya N Senchenkova
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Andrei V Perepelov
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Andrei S Dmitrenok
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Alexander O Chizhov
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Yuriy A Knirel
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Mikhail M Shneider
- M.M. Shemyakin & Y. A Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Anastasia V Popova
- State Research Center for Applied Microbiology and Biotechnology, Obolensk, Moscow, Region, Russia
| | - Johanna J Kenyon
- Centre for Immunology and Infection Control, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Australia.
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Insights into mucoid Acinetobacter baumannii: A review of microbiological characteristics, virulence, and pathogenic mechanisms in a threatening nosocomial pathogen. Microbiol Res 2022; 261:127057. [DOI: 10.1016/j.micres.2022.127057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 04/29/2022] [Accepted: 04/29/2022] [Indexed: 01/25/2023]
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Kasimova AA, Dudnik AG, Shashkov AS, Shneider MM, Christofferson A, Shelenkov AA, Mikhailova YV, Kenyon JJ, Knirel YA. The K218 capsular polysaccharide produced by Acinetobacter baumannii isolate 52-249 includes 5,7-di-N-acetylpseudaminic acid linked by a KpsS3 glycosyltransferase. Int J Biol Macromol 2022; 218:310-316. [PMID: 35872309 DOI: 10.1016/j.ijbiomac.2022.07.135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 06/28/2022] [Accepted: 07/18/2022] [Indexed: 11/17/2022]
Abstract
Two acylated forms of the higher sugar, 5,7-diamino-3,5,7,9-tetradeoxy-l-glycero-l-manno-non-2-ulosonic acid called pseudaminic acid, Pse5Ac7Ac and Pse5Ac7RHb where R indicates (R)-3-hydroxybutanoyl, have been found to occur in many capsular polysaccharide (CPS) types produced by isolates of an important human pathogen, Acinetobacter baumannii. The presence of either a psaABCEDF or psaABCGHF gene module at the K locus (KL) for CPS biosynthesis determines the type of the variant produced. Here, an A. baumannii clinical isolate 52-249, recovered in 2015 in Moscow, Russia, was found to include a novel psaABCIJF gene module in the KL218 sequence at the K locus. The CPS from 52-249 was extracted and studied by sugar analysis and partial acid hydrolysis along with one- and two-dimensional 1H and 13C NMR spectroscopy. A branched tetrasaccharide repeating unit was identified, which included a →3)-α-d-Galp-(1→6)-α-d-GlcpNAc-(1→3)-β-d-GalpNAc-(1→ main chain and Pse5Ac7Ac attached as a side branch, indicating that the psaABCIJF gene module is associated with synthesis of this variant. The K218 CPS was found to be structurally related to the K46 CPS of A. baumannii, and a comparison of the two structures enabled the assignment of glycosyltransferases. A KpsS3 protein for the α-(2→6) linkage of the Pse5Ac7Ac residue to D-Galp in K218 was identified.
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Affiliation(s)
- Anastasiya A Kasimova
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Aleksandra G Dudnik
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Alexander S Shashkov
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Mikhail M Shneider
- M. M. Shemyakin & Y. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Alex Christofferson
- Centre for Immunology and Infection Control, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Australia
| | | | | | - Johanna J Kenyon
- Centre for Immunology and Infection Control, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Australia.
| | - Yuriy A Knirel
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
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Arbatsky NP, Shashkov AS, Shneider MM, Popova AV, Kasimova AA, Miroshnikov KA, Knirel YA, Hall RM, Kenyon JJ. The K89 capsular polysaccharide produced by Acinetobacter baumannii LUH5552 consists of a pentameric repeat-unit that includes a 3-acetamido-3,6-dideoxy-d-galactose residue. Int J Biol Macromol 2022; 217:515-521. [PMID: 35843396 DOI: 10.1016/j.ijbiomac.2022.07.085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 06/17/2022] [Accepted: 07/11/2022] [Indexed: 11/17/2022]
Abstract
Acinetobacter baumannii isolate LUH5552 carries the KL89 capsule biosynthesis gene cluster. Capsular polysaccharide (CPS) isolated from LUH5552 was analyzed by sugar analysis, Smith degradation, and one- and two-dimensional 1H and 13C NMR spectroscopy. The K89 CPS structure has not been seen before in A. baumannii CPS structures resolved to date and includes a 3-acetamido-3,6-dideoxy-d-galactose (d-Fucp3NAc) residue which is rare amongst A. baumannii CPS. The K89 CPS has a →3)-α-d-GalpNAc-(1→3)-β-d-GlcpNAc-(1→ main chain with a β-d-Glcp-(1→2)-β-d-Fucp3NAc-(1→6)-d-Glcp side branch that is α-(1→4) linked to d-GalpNAc. The roles of the Wzy polymerase and the four glycosyltransferases encoded by the KL89 gene cluster in the biosynthesis of the K89 CPS were assigned. Two glycosyltransferases, Gtr121 and Gtr122, link the d-Fucp3NAc to its neighboring sugars.
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Affiliation(s)
- Nikolay P Arbatsky
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Alexander S Shashkov
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Mikhail M Shneider
- M. M. Shemyakin & Y. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Anastasiya V Popova
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia; State Research Center for Applied Microbiology and Biotechnology, Obolensk, Moscow Region, Russia
| | - Anastasiya A Kasimova
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Konstantin A Miroshnikov
- M. M. Shemyakin & Y. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Yuriy A Knirel
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Ruth M Hall
- School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia
| | - Johanna J Kenyon
- Centre for Immunology and Infection Control, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Australia.
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Shashkov AS, Arbatsky NP, Senchenkova SN, Perepelov AV, Chizhov AO, Dmitrenok AS, Shneider MM, Knirel YA. NoteIdentification of 5,7-diacetamido-3,5,7,9-tetradeoxy-d-glycero-l-manno-non-2-ulosonic acid (di-N-acetyl-8-epipseudaminic acid) in the capsular polysaccharide of Acinetobacter baumannii Res546. Carbohydr Res 2022; 513:108531. [PMID: 35245711 DOI: 10.1016/j.carres.2022.108531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 02/27/2022] [Indexed: 11/02/2022]
Abstract
A structurally diverse capsular polysaccharide that surrounds the bacterial cell plays an important role in virulence of Acinetobacter baumannii, a cause of nosocomial infections worldwide. Various isomers of 5,7-diacylamido-3,5,7,9-tetradeoxynon-2-ulosonic acid have been identified as components of bacterial polysaccharides. In this work, we report on the identification of a new isomer having the d-glycero-l-manno configuration (8-epipseudaminic acid) in the capsular polysaccharide of A. baumannii Res546. The higher sugar was isolated by Smith degradation of the polysaccharide followed by mild acid hydrolysis and identified by a comparison with all isomers using NMR spectroscopy and optical rotation.
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Affiliation(s)
- Alexander S Shashkov
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia.
| | - Nikolay P Arbatsky
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Sof'ya N Senchenkova
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Andrei V Perepelov
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Alexander O Chizhov
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Andrei S Dmitrenok
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Mikhail M Shneider
- M.M. Shemyakin & Y.A Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Yuriy A Knirel
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
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Structure of the K87 capsular polysaccharide and KL87 gene cluster of Acinetobacter baumannii LUH5547 reveals a heptasaccharide repeating unit. Carbohydr Res 2021; 509:108439. [PMID: 34555685 DOI: 10.1016/j.carres.2021.108439] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 08/09/2021] [Accepted: 08/31/2021] [Indexed: 12/31/2022]
Abstract
K87 capsular polysaccharide (CPS) was isolated from Acinetobacter baumannii isolate LUH5547 that carries the KL87 capsule biosynthesis gene cluster at the chromosomal K locus. Studies by sugar analysis, selective chemical cleavages, and 1D and 2D 1H and 13C NMR spectroscopy showed that the CPS has a branched heptasaccharide repeat (K unit) containing one residue each of d-glucose (d-Glсp), d-glucuronic acid (d-GlсpA), N-acetyl-d-glucosamine (d-GlсpNAc), 6-deoxy-l-talose (l-6dTalp), and three residues of l-rhamnose (l-Rhap). The following structure of the CPS was established: →3)-α-L-Rhap-(1→2)-α-L-Rhap-(1→3)-α-L-6dTalp-(1→3)-β-D-GlcpNAc-(1→2↑1β-D-GlcpA-(4←1)-α-D-Glcp(2←1)-α-L-Rhap The position of a minor O-acetyl group present in the CPS was not determined. Functions of enzymes coded by genes in the KL87 gene cluster were tentatively assigned and found to be consistent with the CPS structure.
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Specific Interaction of Novel Friunavirus Phages Encoding Tailspike Depolymerases with Corresponding Acinetobacter baumannii Capsular Types. J Virol 2021; 95:JVI.01714-20. [PMID: 33268523 PMCID: PMC8092837 DOI: 10.1128/jvi.01714-20] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Acinetobacter baumannii is one of the most clinically important nosocomial pathogens. The World Health Organisation refers it to its «critical priority» 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.
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Involvement of a multifunctional rhamnosyltransferase in the synthesis of three related Acinetobacter baumannii capsular polysaccharides, K55, K74 and K85. Int J Biol Macromol 2020; 166:1230-1237. [PMID: 33159946 DOI: 10.1016/j.ijbiomac.2020.11.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 07/22/2020] [Accepted: 11/02/2020] [Indexed: 12/17/2022]
Abstract
KL55, KL74, and KL85 capsular polysaccharide (CPS) biosynthesis loci in Acinetobacter baumannii BAL_204, BAL_309, and LUH5543 genomes, respectively, are related and each contains genes for l-Rhap and d-GlcpA synthesis. The CPSs were isolated and studied by sugar analysis, Smith degradation, and 1H and 13C NMR spectroscopy. The K55 and K74 CPSs are built up of branched octasaccharide repeats (K units) containing one residue each of d-GlcpA and d-GlcpNAc and six residues of l-Rhap. The K55 unit differs from the K74 unit in the linkage between D-GlcpA and an l-Rhap residue in the K unit (1 → 3 versus 1 → 2) and linkage between K units. However, most K units in the isolated K74 CPS were modified by β-elimination of a side-chain α-l-Rhap-(1 → 3)-α-l-Rhap disaccharide from position 4 of GlcA to give 4-deoxy-l-threo-hex-4-enuronic acid (1:~3 ratio of intact and modified units). The K85 CPS has a branched heptasaccharide K unit similar to the K74 unit but with one fewer α-l-Rhap residue in the side chain. In contrast to previous findings on A. baumannii CPSs, each K locus includes fewer glycosyltransferase (Gtr) genes than the number required to form all linkages in the K units. Hence, one Gtr appears to be multifunctional catalysing formation of two 1 → 2 and one 1 → 3 linkages between the l-Rha residues.
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Cahill SM, Arbatsky NP, Shashkov AS, Shneider MM, Popova AV, Hall RM, Kenyon JJ, Knirel YA. Elucidation of the K32 Capsular Polysaccharide Structure and Characterization of the KL32 Gene Cluster of Acinetobacter baumannii LUH5549. BIOCHEMISTRY (MOSCOW) 2020; 85:241-247. [PMID: 32093600 DOI: 10.1134/s000629792002011x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Capsular polysaccharide (CPS), isolated from Acinetobacter baumannii LUH5549 carrying the KL32 capsule biosynthesis gene cluster, was studied by sugar analysis, Smith degradation, and one- and two-dimensional 1H and 13C NMR spectroscopy. The K32 CPS was found to be composed of branched pentasaccharide repeats (K units) containing two residues of β-D-GalpNAc and one residue of β-D-GlcpA (β-D-glucuronic acid) in the main chain and one residue each of β-D-Glcp and α-D-GlcpNAc in the disaccharide side chain. Consistent with the established CPS structure, the KL32 gene cluster includes genes for a UDP-glucose 6-dehydrogenase (Ugd3) responsible for D-GlcA synthesis and four glycosyltransferases that were assigned to specific linkages. Genes encoding an acetyltransferase and an unknown protein product were not involved in CPS biosynthesis. Whilst the KL32 gene cluster has previously been found in the global clone 2 (GC2) lineage, LUH5549 belongs to the sequence type ST354, thus demonstrating horizontal gene transfer between these lineages.
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Affiliation(s)
- S M Cahill
- Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD 4001, Australia
| | - N P Arbatsky
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, 119991, Russia
| | - A S Shashkov
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, 119991, Russia
| | - M M Shneider
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - A V Popova
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia.,State Research Center for Applied Microbiology and Biotechnology, Obolensk, Moscow Region, 142279, Russia
| | - R M Hall
- School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia
| | - J J Kenyon
- Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD 4001, Australia
| | - Y A Knirel
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, 119991, Russia.
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Flack EKP, Chidwick HS, Best M, Thomas GH, Fascione MA. Synthetic Approaches for Accessing Pseudaminic Acid (Pse) Bacterial Glycans. Chembiochem 2020; 21:1397-1407. [PMID: 31944494 DOI: 10.1002/cbic.202000019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Indexed: 12/18/2022]
Abstract
Pseudaminic acids (Pses) are a group of non-mammalian nonulosonic acids (nulOs) that have been shown to be an important virulence factor for a number of pathogenic bacteria, including emerging multidrug-resistant ESKAPE pathogens. Despite their discovery over 30 years ago, relatively little is known about the biological significance of Pse glycans compared with their sialic acid analogues, primarily due to a lack of access to the synthetically challenging Pse architecture. Recently, however, the Pse backbone has been subjected to increasing synthetic exploration by carbohydrate (bio)chemists, and the total synthesis of complex Pse glycans achieved with inspiration from the biosynthesis and subsequent detailed study of chemical glycosylation by using Pse donors. Herein, context is provided for these efforts by summarising recent synthetic approaches pioneered for accessing Pse glycans, which are set to open up this underexplored area of glycoscience to the wider scientific community.
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Affiliation(s)
- Emily K P Flack
- Department of Chemistry, University of York, Heslington Road, Heslington, York, YO10 5DD, UK
| | - Harriet S Chidwick
- Department of Chemistry, University of York, Heslington Road, Heslington, York, YO10 5DD, UK
| | - Matthew Best
- Department of Chemistry, University of York, Heslington Road, Heslington, York, YO10 5DD, UK
| | - Gavin H Thomas
- Department of Biology, University of York, Heslington Road, Heslington, York, YO10 5DD, UK
| | - Martin A Fascione
- Department of Chemistry, University of York, Heslington Road, Heslington, York, YO10 5DD, UK
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Structure of the K128 capsular polysaccharide produced by Acinetobacter baumannii KZ-1093 from Kazakhstan. Carbohydr Res 2019; 485:107814. [DOI: 10.1016/j.carres.2019.107814] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 08/20/2019] [Accepted: 09/08/2019] [Indexed: 11/21/2022]
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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. Carbohydr Res 2019; 484:107774. [DOI: 10.1016/j.carres.2019.107774] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 07/22/2019] [Accepted: 08/07/2019] [Indexed: 11/26/2022]
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17
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Kenyon JJ, Arbatsky NP, Shneider MM, Popova AV, Dmitrenok AS, Kasimova AA, Shashkov AS, Hall RM, Knirel YA. The K46 and K5 capsular polysaccharides produced by Acinetobacter baumannii NIPH 329 and SDF have related structures and the side-chain non-ulosonic acids are 4-O-acetylated by phage-encoded O-acetyltransferases. PLoS One 2019; 14:e0218461. [PMID: 31220143 PMCID: PMC6586298 DOI: 10.1371/journal.pone.0218461] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 06/03/2019] [Indexed: 12/01/2022] Open
Abstract
Acinetobacter baumannii isolate NIPH 329 carries a novel capsular polysaccharide (CPS) gene cluster, designated KL46, that is closely related to the KL5 locus in A. baumannii isolate SDF but includes genes for synthesis of 5,7-diacetamido-3,5,7,9-tetradeoxy-l-glycero-l-manno-non-2-ulosonic (di-N-acetylpseudaminic) acid (Pse5Ac7Ac) instead of the corresponding D-glycero-D-galacto isomer (di-N-acetyllegionaminic acid) (Leg5Ac7Ac). In agreement with the genetic content of KL46, chemical studies of the K46 CPS produced by NIPH 329 revealed a branched tetrasaccharide repeat (K unit) with an overall structure the same as K5 from SDF but with â-Pse5Ac7Ac replacing α-Leg5Ac7Ac. As for K5, the K46 unit begins with d-GalpNAc and includes α-d-GlcpNAc-(1→3)-d-GalpNAc and α-d-Galp-(1→6)-d-GlcpNAc linkages, formed by Gtr14 and Gtr15 glycosyltransferases, respectively. The Gtr94K46 glycosyltransferase, which is related to Gtr13K5, links Pse5Ac7Ac to d-Galp in the growing K unit via a â-(2→6) linkage. Nearly identical Wzy enzymes connect the K46 and K5 units via a α-D-GalpNAc-(1→3)-α-D-Galp linkage to form closely related CPSs. Both Pse5Ac7Ac in K46 and Leg5Ac7Ac in K5 are acetylated at O4 but no acetyltransferase gene is present in KL46 or KL5. Related acetyltransferases were found encoded in the NIPH 329 and SDF genomes, but not in other strains carrying an unacetylated Pse or Leg derivative in the CPS. The genes encoding the acetyltransferases were in different putative phage genomes. However, related acetyltransferases were rare among the >3000 publically available genome sequences.
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Affiliation(s)
- Johanna J. Kenyon
- Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Australia
- * E-mail:
| | - Nikolay P. Arbatsky
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Mikhail M. Shneider
- M. M. Shemyakin & Y. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Anastasiya V. Popova
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
- State Research Center for Applied Microbiology and Biotechnology, Obolensk, Moscow Region, Russia
| | - Andrei S. Dmitrenok
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Anastasiya A. Kasimova
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
- Higher Chemical College of the Russian Academy of Sciences, D. I. Mendeleev University of Chemical Technology of Russia, Moscow, Russia
| | - Alexander S. Shashkov
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Ruth M. Hall
- School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia
| | - Yuriy A. Knirel
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
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