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Structure and gene cluster of the O-antigen of Enterobacter cloacae G3422. Carbohydr Res 2021; 510:108440. [PMID: 34619615 DOI: 10.1016/j.carres.2021.108440] [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: 07/14/2021] [Revised: 09/05/2021] [Accepted: 09/06/2021] [Indexed: 11/20/2022]
Abstract
The O-polysaccharide (OPS) was isolated by mild acid degradation of the lipopolysaccharide of Enterobacter cloacae G3422 and studied by chemical methods, including sugar analyses, Smith degradation, and solvolysis with anhydrous trifluoroacetic acid, along with 1H and 13C NMR spectroscopy. The following structure of the branched tetrasaccharide repeating unit was established: The O-antigen gene cluster of Enterobacter cloacae G3422 was sequenced. The gene functions were tentatively assigned by comparison with sequences in the available databases and found to be in a good agreement with the O-antigen structure.
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Liu B, Furevi A, Perepelov AV, Guo X, Cao H, Wang Q, Reeves PR, Knirel YA, Wang L, Widmalm G. Structure and genetics of Escherichia coli O antigens. FEMS Microbiol Rev 2020; 44:655-683. [PMID: 31778182 PMCID: PMC7685785 DOI: 10.1093/femsre/fuz028] [Citation(s) in RCA: 121] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 11/22/2019] [Indexed: 02/07/2023] Open
Abstract
Escherichia coli includes clonal groups of both commensal and pathogenic strains, with some of the latter causing serious infectious diseases. O antigen variation is current standard in defining strains for taxonomy and epidemiology, providing the basis for many serotyping schemes for Gram-negative bacteria. This review covers the diversity in E. coli O antigen structures and gene clusters, and the genetic basis for the structural diversity. Of the 187 formally defined O antigens, six (O31, O47, O67, O72, O94 and O122) have since been removed and three (O34, O89 and O144) strains do not produce any O antigen. Therefore, structures are presented for 176 of the 181 E. coli O antigens, some of which include subgroups. Most (93%) of these O antigens are synthesized via the Wzx/Wzy pathway, 11 via the ABC transporter pathway, with O20, O57 and O60 still uncharacterized due to failure to find their O antigen gene clusters. Biosynthetic pathways are given for 38 of the 49 sugars found in E. coli O antigens, and several pairs or groups of the E. coli antigens that have related structures show close relationships of the O antigen gene clusters within clades, thereby highlighting the genetic basis of the evolution of diversity.
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Affiliation(s)
- Bin Liu
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, 23 Hongda Street, TEDA, Tianjing 300457, China
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, 23 Hongda Street, TEDA, Tianjin 300457, China
- Tianjin Key Laboratory of Microbial Functional Genomics, 23 Hongda Street, TEDA, Tianjin 300457, China
| | - Axel Furevi
- Department of Organic Chemistry, Arrhenius Laboratory, Svante Arrhenius väg 16C, Stockholm University, S-106 91 Stockholm, Sweden
| | - Andrei V Perepelov
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospect, 47, Moscow, Russia
| | - Xi Guo
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, 23 Hongda Street, TEDA, Tianjing 300457, China
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, 23 Hongda Street, TEDA, Tianjin 300457, China
- Tianjin Key Laboratory of Microbial Functional Genomics, 23 Hongda Street, TEDA, Tianjin 300457, China
| | - Hengchun Cao
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, 23 Hongda Street, TEDA, Tianjing 300457, China
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, 23 Hongda Street, TEDA, Tianjin 300457, China
- Tianjin Key Laboratory of Microbial Functional Genomics, 23 Hongda Street, TEDA, Tianjin 300457, China
| | - Quan Wang
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, 23 Hongda Street, TEDA, Tianjing 300457, China
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, 23 Hongda Street, TEDA, Tianjin 300457, China
- Tianjin Key Laboratory of Microbial Functional Genomics, 23 Hongda Street, TEDA, Tianjin 300457, China
| | - Peter R Reeves
- School of Molecular and Microbial Bioscience, University of Sydney, 2 Butilin Ave, Darlington NSW 2008, Sydney, Australia
| | - Yuriy A Knirel
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospect, 47, Moscow, Russia
| | - Lei Wang
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, 23 Hongda Street, TEDA, Tianjing 300457, China
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, 23 Hongda Street, TEDA, Tianjin 300457, China
- Tianjin Key Laboratory of Microbial Functional Genomics, 23 Hongda Street, TEDA, Tianjin 300457, China
| | - Göran Widmalm
- Department of Organic Chemistry, Arrhenius Laboratory, Svante Arrhenius väg 16C, Stockholm University, S-106 91 Stockholm, Sweden
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Knirel YA, Naumenko OI, Senchenkova SN, Perepelov AV. Chemical methods for selective cleavage of glycosidic bonds in the structural analysis of bacterial polysaccharides. RUSSIAN CHEMICAL REVIEWS 2019. [DOI: 10.1070/rcr4856] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Knirel YA, Ivanov PA, Senchenkova SN, Naumenko OI, Ovchinnikova OO, Shashkov AS, Golomidova AK, Babenko VV, Kulikov EE, Letarov AV. Structure and gene cluster of the O antigen of Escherichia coli F17, a candidate for a new O-serogroup. Int J Biol Macromol 2019; 124:389-395. [DOI: 10.1016/j.ijbiomac.2018.11.149] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 11/08/2018] [Accepted: 11/15/2018] [Indexed: 01/18/2023]
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Perepelov AV, Li X, Xu C, Filatov AV, Shashkov AS, Senchenkova SN, Liu B. Structure elucidation and gene cluster characterization of the O-antigen of Vibrio cholerae O14. Carbohydr Res 2019; 474:67-71. [DOI: 10.1016/j.carres.2019.01.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 12/31/2018] [Accepted: 01/14/2019] [Indexed: 10/27/2022]
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Senchenkova SN, Guo X, Naumenko OI, Shashkov AS, Perepelov AV, Liu B, Knirel YA. Structure and genetics of the O-antigens of Escherichia coli O182-O187. Carbohydr Res 2016; 435:58-67. [PMID: 27710814 DOI: 10.1016/j.carres.2016.09.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 08/22/2016] [Accepted: 09/21/2016] [Indexed: 11/25/2022]
Abstract
O-polysaccharides (OPSs) were obtained by mild acid degradation of the lipopolysaccharides of Escherichia coli O182-O187, and their structures were established by sugar analysis, Smith degradation, and 1H and 13C NMR spectroscopy. In addition to the monosaccharides that occur often in E. coli OPSs (d-Glc, d-Gal, d-Man, d-GlcNAc, d-GalNAc, d-GlcA, l-Fuc, d-Rib), a number of less common components were identified as the OPS constituents, including 2-acetamido-2-deoxy-l-quinovose and 4-deoxy-4-[(S)-3-hydroxybutanoyl-l-alanyl]-d-quinovose (O186), 3-acetamido-3-deoxy-d-fucose (O187), 3-deoxy-3-[(R)-3-hydroxybutanoyl]-d-fucose (O184), and 2,3-diacetamido-2,3-dideoxy-l-rhamnose (O182). The OPS structures of E. coli O183 and O182 are identical to those of the OPS of Shigella boydii type 10 and the capsular polysaccharide of E. coli K48, respectively. The OPSs of E. coli O186 and O123 are closely related differing in the presence of a Glc residue in the former in place of a GlcNAc residue in the latter. The O-antigen gene clusters of the bacteria studied were analyzed and their contents were found to be consistent with the OPS structures. Predicted glycosyltransferases encoded in the gene clusters were tentatively assigned to glycosidic linkages based on similarities to sequences of other E. coli O-serogroups available from GenBank and taking into account the OPS structures established.
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Affiliation(s)
- Sof'ya N Senchenkova
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 119991, Moscow, Russian Federation
| | - Xi Guo
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, 300457, Tianjin, PR China
| | - Olesya I Naumenko
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 119991, Moscow, Russian Federation
| | - Alexander S Shashkov
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 119991, Moscow, Russian Federation
| | - Andrei V Perepelov
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 119991, Moscow, Russian Federation
| | - Bin Liu
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, 300457, Tianjin, PR China
| | - Yuriy A Knirel
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 119991, Moscow, Russian Federation.
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Solvolysis with trifluoroacetic acid: an efficient method for selective cleavage of polysaccharides. MENDELEEV COMMUNICATIONS 2016. [DOI: 10.1016/j.mencom.2016.07.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Perepelov AV, Filatov AV, Wang M, Shashkov AS, Wang L, Knirel YA. Structure and gene cluster of the O-antigen of Enterobacter cloacae G3421. Carbohydr Res 2016; 427:55-9. [DOI: 10.1016/j.carres.2016.03.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 03/10/2016] [Accepted: 03/12/2016] [Indexed: 10/22/2022]
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Sigida EN, Fedonenko YP, Shashkov AS, Arbatsky NP, Zdorovenko EL, Konnova SA, Ignatov VV, Knirel YA. Elucidation of a masked repeating structure of the O-specific polysaccharide of the halotolerant soil bacteria Azospirillum halopraeferens Au4. Beilstein J Org Chem 2016; 12:636-42. [PMID: 27340454 PMCID: PMC4902059 DOI: 10.3762/bjoc.12.62] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Accepted: 03/16/2016] [Indexed: 01/14/2023] Open
Abstract
An O-specific polysaccharide was obtained by mild acid hydrolysis of the lipopolysaccharide isolated by the phenol-water extraction from the halotolerant soil bacteria Azospirillum halopraeferens type strain Au4. The polysaccharide was studied by sugar and methylation analyses, selective cleavages by Smith degradation and solvolysis with trifluoroacetic acid, one- and two-dimensional (1)H and (13)C NMR spectroscopy. The following masked repeating structure of the O-specific polysaccharide was established: →3)-α-L-Rhap2Me-(1→3)-[β-D-Glcp-(1→4)]-α-D-Fucp-(1→2)-β-D-Xylp-(1→, where non-stoichiometric substituents, an O-methyl group (~45%) and a side-chain glucose residue (~65%), are shown in italics.
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Affiliation(s)
- Elena N Sigida
- Institute of Biochemistry and Physiology of Plants and Microorganisms, Russian Academy of Sciences, Prospekt Entuziastov 13, Saratov 410049, Russia
| | - Yuliya P Fedonenko
- Institute of Biochemistry and Physiology of Plants and Microorganisms, Russian Academy of Sciences, Prospekt Entuziastov 13, Saratov 410049, Russia
| | - Alexander S Shashkov
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospekt 47, Moscow 119991, Russia
| | - Nikolay P Arbatsky
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospekt 47, Moscow 119991, Russia
| | - Evelina L Zdorovenko
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospekt 47, Moscow 119991, Russia
| | - Svetlana A Konnova
- Institute of Biochemistry and Physiology of Plants and Microorganisms, Russian Academy of Sciences, Prospekt Entuziastov 13, Saratov 410049, Russia
- Chernyshevsky Saratov State University, Ulitsa Astrakhanskaya 83, Saratov 410012, Russia
| | - Vladimir V Ignatov
- Institute of Biochemistry and Physiology of Plants and Microorganisms, Russian Academy of Sciences, Prospekt Entuziastov 13, Saratov 410049, Russia
| | - Yuriy A Knirel
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospekt 47, Moscow 119991, Russia
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Perepelov AV, Guo X, Filatov AV, Liu B, Knirel YA. Structure and gene cluster of the O-antigen of Escherichia coli O43. Carbohydr Res 2015; 416:32-6. [PMID: 26342864 DOI: 10.1016/j.carres.2015.08.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Revised: 07/09/2015] [Accepted: 08/12/2015] [Indexed: 11/26/2022]
Abstract
The O-polysaccharide (O-antigen) of Escherichia coli O43 was isolated from the lipopolysaccharide and studied by chemical methods, including sugar analyses, Smith degradation, and solvolysis with anhydrous trifluoroacetic acid, along with (1)H and (13)C NMR spectroscopy. The following structure of the pentasaccharide repeating unit of the O-polysaccharide was established: [Formula: see text] Functions of genes in the O-antigen gene cluster of E. coli O43 were assigned by a comparison with sequences in the available databases and found to be in agreement with the O-polysaccharide structure.
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Affiliation(s)
- Andrei V Perepelov
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 119991 Moscow, Russian Federation.
| | - Xi Guo
- TEDA Institute of Biological Sciences and Biotechnology, TEDA, Nankai University, 300457 Tianjin, China
| | - Andrei V Filatov
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 119991 Moscow, Russian Federation
| | - Bin Liu
- TEDA Institute of Biological Sciences and Biotechnology, TEDA, Nankai University, 300457 Tianjin, China
| | - Yuriy A Knirel
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 119991 Moscow, Russian Federation
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Jiang L, Perepelov AV, Filatov AV, Liu B, Shashkov AS, Senchenkova SN, Wang L, Knirel YA. Structure and gene cluster of the O-antigen of Escherichia coli O68. Carbohydr Res 2014; 397:27-30. [PMID: 25193381 DOI: 10.1016/j.carres.2014.07.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Revised: 07/28/2014] [Accepted: 07/29/2014] [Indexed: 10/24/2022]
Abstract
The O-polysaccharide (O-antigen) of Escherichia coli O68 was studied by sugar analysis, partial solvolysis with anhydrous trifluoroacetic acid, and 1D and 2D (1)H and (13)C NMR spectroscopies. The following structure of the branched heptasaccharide repeating unit was established: [structure: see text]. The O-antigen gene cluster of E. coli O68 was sequenced. The gene functions were tentatively assigned by comparison with sequences in the available databases and found to be in full agreement with the O-antigen structure.
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Affiliation(s)
- Lingyan Jiang
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, 23 Hongda Street, Tianjin 300457, China; The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Tianjin, China; Tianjin Key Laboratory of Microbial Functional Genomics, Tianjin, China
| | - Andrei V Perepelov
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 119991 Moscow, Russian Federation.
| | - Andrei V Filatov
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 119991 Moscow, Russian Federation
| | - Bin Liu
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Tianjin, China; Tianjin Key Laboratory of Microbial Functional Genomics, Tianjin, China
| | - Alexander S Shashkov
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 119991 Moscow, Russian Federation
| | - Sof'ya N Senchenkova
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 119991 Moscow, Russian Federation
| | - Lei Wang
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Tianjin, China; Tianjin Key Laboratory of Microbial Functional Genomics, Tianjin, China; State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China
| | - Yuriy A Knirel
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 119991 Moscow, Russian Federation
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