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Jia T, Guo D, Han Y, Zhou D. Biosynthesis of UDP-2-acetamido-4-formamido-2,4,6-trideoxy-hexose by WekG, WekE, WekF, and WekD: Enzymes in the Wek pathway responsible for O-antigen Assembly in Escherichia coli O119. Carbohydr Res 2021; 507:108388. [PMID: 34271479 DOI: 10.1016/j.carres.2021.108388] [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: 03/16/2021] [Revised: 06/28/2021] [Accepted: 06/28/2021] [Indexed: 11/15/2022]
Abstract
Considering the importance of bacterial glycoconjugates on virulence and host mimicry, there is a need to better understand the biosynthetic pathways of these unusual sugars to identify critical targets involved in bacterial pathogenesis. In this report, we describe the cloning, overexpression, purification, and biochemical characterization of the four central enzymes in the biosynthesis pathway for UDP-2-acetamido-4-formamido-2,4,6-trideoxy-hexose, WekG, WekE, WekF, and WekD. Product peaks from enzyme-substrate reactions were detected by using a combination of capillary electrophoresis (CE) and electrospray ionization-mass spectrometry (ESI-MS). Putative enzyme assignments were provided by protein sequence analysis. Combined with the mass spectrometric characterization of pathway intermediates, we propose a biosynthetic pathway for UDP-2-acetamido-4-formamido-2,4,6-trideoxy-hexose. This process involves C-4, C-6 dehydration, C-4 amination, and formylation. CID-ESI-MSn result confirmed that the final product is a 4 formamido derivative too rather than the 3 formamido derivatives as reported earlier.
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Affiliation(s)
- Tianyuan Jia
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China; School of Medicine, Southern University of Science and Technology, Shenzhen, China; Key Laboratory of Microbial Functional Genomics, Tianjin, China; The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin, China
| | - Dan Guo
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China; Key Laboratory of Microbial Functional Genomics, Tianjin, China; The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin, China
| | - Yanfang Han
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China; Key Laboratory of Microbial Functional Genomics, Tianjin, China; The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin, China
| | - Dawei Zhou
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China; Key Laboratory of Microbial Functional Genomics, Tianjin, China; The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin, China.
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2
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New Insights on the Feature and Function of Tail Tubular Protein B and Tail Fiber Protein of the Lytic Bacteriophage φYeO3-12 Specific for Yersinia enterocolitica Serotype O:3. Molecules 2020; 25:molecules25194392. [PMID: 32987777 PMCID: PMC7582827 DOI: 10.3390/molecules25194392] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 09/21/2020] [Accepted: 09/23/2020] [Indexed: 12/30/2022] Open
Abstract
For the first time, we are introducing TTPBgp12 and TFPgp17 as new members of the tail tubular proteins B (TTPB) and tail fiber proteins (TFP) family, respectively. These proteins originate from Yersinia enterocolitica phage φYeO3-12. It was originally thought that these were structural proteins. However, our results show that they also inhibit bacterial growth and biofilm formation. According to the bioinformatic analysis, TTPBgp12 is functionally and structurally similar to the TTP of Enterobacteria phage T7 and adopts a β-structure. TFPgp17 contains an intramolecular chaperone domain at its C-terminal end. The N-terminus of TFPgp17 is similar to other representatives of the TFP family. Interestingly, the predicted 3D structure of TFPgp17 is similar to other bacterial S-layer proteins. Based on the thermal unfolding experiment, TTPBgp12 seems to be a two-domain protein that aggregates in the presence of sugars such as maltose and N-acetylglucosamine (GlcNAc). These sugars cause two unfolding events to transition into one global event. TFPgp17 is a one-domain protein. Maltose and GlcNAc decrease the aggregation temperature of TFPgp17, while the presence of N-acetylgalactosamine (GalNAc) increases the temperature of its aggregation. The thermal unfolding analysis of the concentration gradient of TTPBgp12 and TFPgp17 indicates that with decreasing concentrations, both proteins increase in stability. However, a decrease in the protein concentration also causes an increase in its aggregation, for both TTPBgp12 and TFPgp17.
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3
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Li T, Noel KD. Synthesis of N-acetyl-d-quinovosamine in Rhizobium etli CE3 is completed after its 4-keto-precursor is linked to a carrier lipid. MICROBIOLOGY-SGM 2017; 163:1890-1901. [PMID: 29165235 DOI: 10.1099/mic.0.000576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Bacterial O-antigens are synthesized on lipid carriers before being transferred to lipopolysaccharide core structures. Rhizobium etli CE3 lipopolysaccharide is a model for understanding O-antigen biological function. CE3 O-antigen structure and genetics are known. However, proposed enzymology for CE3 O-antigen synthesis has been examined very little in vitro, and even the sugar added to begin the synthesis is uncertain. A model based on mutagenesis studies predicts that 2-acetamido-2,6-dideoxy-d-glucose (QuiNAc) is the first O-antigen sugar and that genes wreV, wreQ and wreU direct QuiNAc synthesis and O-antigen initiation. Previously, synthesis of UDP-QuiNAc was shown to occur in vitro with a WreV orthologue (4,6-hexose dehydratase) and WreQ (4-reductase), but the WreQ catalysis in this conventional deoxyhexose-synthesis pathway was very slow. This seeming deficiency was explained in the present study after WreU transferase activity was examined in vitro. Results fit the prediction that WreU transfers sugar-1-phosphate to bactoprenyl phosphate (BpP) to initiate O-antigen synthesis. Interestingly, WreU demonstrated much higher activity using the product of the WreV catalysis [UDP-4-keto-6-deoxy-GlcNAc (UDP-KdgNAc)] as the sugar-phosphate donor than using UDP-QuiNAc. Furthermore, the WreQ catalysis with WreU-generated BpPP-KdgNAc as the substrate was orders of magnitude faster than with UDP-KdgNAc. The inferred product BpPP-QuiNAc reacted as an acceptor substrate in an in vitro assay for addition of the second O-antigen sugar, mannose. These results imply a novel pathway for 6-deoxyhexose synthesis that may be commonly utilized by bacteria when QuiNAc is the first sugar of a polysaccharide or oligosaccharide repeat unit: UDP-GlcNAc → UDP-KdgNAc → BpPP-KdgNAc → BpPP-QuiNAc.
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Affiliation(s)
- Tiezheng Li
- Present address: Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA.,Department of Biological Sciences, Marquette University, Milwaukee, WI 53233, USA
| | - K Dale Noel
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53233, USA
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4
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Chaudhury A, Ghosh R. A target oriented expeditious approach towards synthesis of certain bacterial rare sugar derivatives. Org Biomol Chem 2017; 15:1444-1452. [DOI: 10.1039/c6ob02670b] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A 3-step sequential one-pot protection profile manipulation on suitable d-glucosamine/d-mannose derivatives led to the diversity oriented synthesis of rare sugar derivatives.
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Affiliation(s)
| | - Rina Ghosh
- Department of Chemistry
- Jadavpur University
- Kolkata-700 032
- India
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5
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Leskinen K, Blasdel BG, Lavigne R, Skurnik M. RNA-Sequencing Reveals the Progression of Phage-Host Interactions between φR1-37 and Yersinia enterocolitica. Viruses 2016; 8:111. [PMID: 27110815 PMCID: PMC4848604 DOI: 10.3390/v8040111] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 04/05/2016] [Accepted: 04/13/2016] [Indexed: 01/05/2023] Open
Abstract
Despite the expanding interest in bacterial viruses (bacteriophages), insights into the intracellular development of bacteriophage and its impact on bacterial physiology are still scarce. Here we investigate during lytic infection the whole-genome transcription of the giant phage vB_YecM_φR1-37 (φR1-37) and its host, the gastroenteritis causing bacterium Yersinia enterocolitica. RNA sequencing reveals that the gene expression of φR1-37 does not follow a pattern typical observed in other lytic bacteriophages, as only selected genes could be classified as typically early, middle or late genes. The majority of the genes appear to be expressed constitutively throughout infection. Additionally, our study demonstrates that transcription occurs mainly from the positive strand, while the negative strand encodes only genes with low to medium expression levels. Interestingly, we also detected the presence of antisense RNA species, as well as one non-coding intragenic RNA species. Gene expression in the phage-infected cell is characterized by the broad replacement of host transcripts with phage transcripts. However, the host response in the late phase of infection was also characterized by up-regulation of several specific bacterial gene products known to be involved in stress response and membrane stability, including the Cpx pathway regulators, ATP-binding cassette (ABC) transporters, phage- and cold-shock proteins.
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Affiliation(s)
- Katarzyna Leskinen
- Department of Bacteriology and Immunology, Medicum, and Research Programs Unit, Immunobiology, University of Helsinki, P.O.Box 21 (Haartmaninkatu 3), FIN-00014 HY Helsinki, Finland.
| | - Bob G Blasdel
- Laboratory of Gene Technology, KU Leuven, BE-3001 Leuven, Belgium.
| | - Rob Lavigne
- Laboratory of Gene Technology, KU Leuven, BE-3001 Leuven, Belgium.
| | - Mikael Skurnik
- Department of Bacteriology and Immunology, Medicum, and Research Programs Unit, Immunobiology, University of Helsinki, P.O.Box 21 (Haartmaninkatu 3), FIN-00014 HY Helsinki, Finland.
- Division of Clinical Microbiology, Helsinki University Hospital, HUSLAB, FIN-00270 Helsinki, Finland.
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Kasperkiewicz K, Swierzko AS, Bartlomiejczyk MA, Cedzynski M, Noszczynska M, Duda KA, Michalski M, Skurnik M. Interaction of human mannose-binding lectin (MBL) with Yersinia enterocolitica lipopolysaccharide. Int J Med Microbiol 2015; 305:544-52. [PMID: 26188838 DOI: 10.1016/j.ijmm.2015.07.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The lipopolysaccharide (LPS) is involved in the interaction between Gram-negative pathogenic bacteria and host. Mannose-binding lectin (MBL), complement-activating soluble pattern-recognition receptor targets microbial glycoconjugates, including LPS. We studied its interactions with a set of Yersinia enterocolitica O:3 LPS mutants. The wild-type strain LPS consists of lipid A (LA) substituted with an inner core oligosaccharide (IC) which in turn is substituted either with the O-specific polysaccharide (OPS) or the outer core hexasaccharide (OC), and sometimes also with the enterobacterial common antigen (ECA). The LPS mutants produced truncated LPS, missing OPS, OC or both, or, in addition, different IC constituents or ECA. MBL bound to LA-IC, LA-IC-OPS and LA-IC-ECA but not LA-IC-OC structures. Moreover, LA-IC substitution with both OPS and ECA prevented the lectin binding. Sequential truncation of the IC heptoses demonstrated that the MBL targets the IC heptose region. Furthermore, microbial growth temperature influenced MBL binding; binding was stronger to bacteria grown at room temperature (22°C) than to bacteria grown at 37°C. In conclusion, our results demonstrate that MBL can interact with Y. enterocolitica LPS, however, the in vivo significance of that interaction remains to be elucidated.
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Affiliation(s)
- Katarzyna Kasperkiewicz
- Department of Microbiology, University of Silesia, Jagiellonska 28, PL 40-032 Katowice, Poland
| | - Anna S Swierzko
- Laboratory of Immunobiology of Infections, Institute of Medical Biology, Polish Academy of Sciences, Lodowa 106, PL 93-232 Lodz, Poland
| | - Marcin A Bartlomiejczyk
- Laboratory of Immunobiology of Infections, Institute of Medical Biology, Polish Academy of Sciences, Lodowa 106, PL 93-232 Lodz, Poland
| | - Maciej Cedzynski
- Laboratory of Immunobiology of Infections, Institute of Medical Biology, Polish Academy of Sciences, Lodowa 106, PL 93-232 Lodz, Poland.
| | - Magdalena Noszczynska
- Department of Microbiology, University of Silesia, Jagiellonska 28, PL 40-032 Katowice, Poland
| | - Katarzyna A Duda
- Division of Structural Biochemistry, Research Center Borstel, Priority Area Asthma and Allergies, Leibniz Center for Medicine and Biosciences, Parkallee 4a/c, D 23845 Borstel, Germany
| | - Mateusz Michalski
- Laboratory of Immunobiology of Infections, Institute of Medical Biology, Polish Academy of Sciences, Lodowa 106, PL 93-232 Lodz, Poland
| | - Mikael Skurnik
- Department of Bacteriology and Immunology, Haartman Institute, Research Programs Unit, Immunobiology, University of Helsinki, PO Box 21, Haartmaninkatu 3, FIN 00014 Helsinki, Finland; Helsinki University Central Hospital Laboratory Diagnostics, PO Box 21, Haartmaninkatu 3, FIN 00014 Helsinki, Finland
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7
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Saeui CT, Urias E, Liu L, Mathew MP, Yarema KJ. Metabolic glycoengineering bacteria for therapeutic, recombinant protein, and metabolite production applications. Glycoconj J 2015; 32:425-41. [PMID: 25931032 DOI: 10.1007/s10719-015-9583-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 03/16/2015] [Accepted: 03/19/2015] [Indexed: 12/12/2022]
Abstract
Metabolic glycoengineering is a specialization of metabolic engineering that focuses on using small molecule metabolites to manipulate biosynthetic pathways responsible for oligosaccharide and glycoconjugate production. As outlined in this article, this technique has blossomed in mammalian systems over the past three decades but has made only modest progress in prokaryotes. Nevertheless, a sufficient foundation now exists to support several important applications of metabolic glycoengineering in bacteria based on methods to preferentially direct metabolic intermediates into pathways involved in lipopolysaccharide, peptidoglycan, teichoic acid, or capsule polysaccharide production. An overview of current applications and future prospects for this technology are provided in this report.
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Affiliation(s)
- Christopher T Saeui
- Department of Biomedical Engineering and the Translational Tissue Engineering Center, The Johns Hopkins University, Baltimore, MD, USA
| | - Esteban Urias
- Department of Biomedical Engineering and the Translational Tissue Engineering Center, The Johns Hopkins University, Baltimore, MD, USA
| | - Lingshu Liu
- Department of Biomedical Engineering and the Translational Tissue Engineering Center, The Johns Hopkins University, Baltimore, MD, USA
| | - Mohit P Mathew
- Department of Biomedical Engineering and the Translational Tissue Engineering Center, The Johns Hopkins University, Baltimore, MD, USA
| | - Kevin J Yarema
- Department of Biomedical Engineering and the Translational Tissue Engineering Center, The Johns Hopkins University, Baltimore, MD, USA.
- Translational Tissue Engineering Center, The Johns Hopkins University, 5029 Robert H. & Clarice Smith Building, 400 North Broadway, Baltimore, MD, 21231, USA.
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8
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Noszczyńska M, Kasperkiewicz K, Duda KA, Podhorodecka J, Rabsztyn K, Gwizdała K, Świerzko AS, Radziejewska-Lebrecht J, Holst O, Skurnik M. Serological characterization of the enterobacterial common antigen substitution of the lipopolysaccharide of Yersinia enterocolitica O : 3. Microbiology (Reading) 2015; 161:219-227. [DOI: 10.1099/mic.0.083493-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Magdalena Noszczyńska
- Department of Microbiology, University of Silesia, Jagiellońska 28, PL- 40-032 Katowice, Poland
| | - Katarzyna Kasperkiewicz
- Department of Microbiology, University of Silesia, Jagiellońska 28, PL- 40-032 Katowice, Poland
| | - Katarzyna Anna Duda
- Division of Structural Biochemistry, Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Borstel, Germany
| | - Joanna Podhorodecka
- Division of Structural Biochemistry, Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Borstel, Germany
- Department of Microbiology, University of Silesia, Jagiellońska 28, PL- 40-032 Katowice, Poland
| | - Kamila Rabsztyn
- Department of Microbiology, University of Silesia, Jagiellońska 28, PL- 40-032 Katowice, Poland
| | - Karolina Gwizdała
- Department of Microbiology, University of Silesia, Jagiellońska 28, PL- 40-032 Katowice, Poland
| | - Anna Stanisława Świerzko
- Department of Immunobiology of Infections, Institute of Medical Biology, PAS, Lodowa 106, PL- 93-232 Łódź, Poland
| | | | - Otto Holst
- Division of Structural Biochemistry, Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Borstel, Germany
| | - Mikael Skurnik
- Helsinki University Central Hospital Laboratory Diagnostics, FIN-00270 Helsinki, Finland
- Department of Bacteriology and Immunology, Haartman Institute, and Research Programs Unit, Immunobiology, University of Helsinki, FIN-00014, Helsinki, Finland
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9
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Li T, Simonds L, Kovrigin EL, Noel KD. In vitro biosynthesis and chemical identification of UDP-N-acetyl-d-quinovosamine (UDP-d-QuiNAc). J Biol Chem 2014; 289:18110-20. [PMID: 24817117 DOI: 10.1074/jbc.m114.555862] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
N-acetyl-d-quinovosamine (2-acetamido-2,6-dideoxy-d-glucose, QuiNAc) occurs in the polysaccharide structures of many Gram-negative bacteria. In the biosynthesis of QuiNAc-containing polysaccharides, UDP-QuiNAc is the hypothetical donor of the QuiNAc residue. Biosynthesis of UDP-QuiNAc has been proposed to occur by 4,6-dehydration of UDP-N-acetyl-d-glucosamine (UDP-GlcNAc) to UDP-2-acetamido-2,6-dideoxy-d-xylo-4-hexulose followed by reduction of this 4-keto intermediate to UDP-QuiNAc. Several specific dehydratases are known to catalyze the first proposed step. A specific reductase for the last step has not been demonstrated in vitro, but previous mutant analysis suggested that Rhizobium etli gene wreQ might encode this reductase. Therefore, this gene was cloned and expressed in Escherichia coli, and the resulting His6-tagged WreQ protein was purified. It was tested for 4-reductase activity by adding it and NAD(P)H to reaction mixtures in which 4,6-dehydratase WbpM had acted on the precursor substrate UDP-GlcNAc. Thin layer chromatography of the nucleotide sugars in the mixture at various stages of the reaction showed that WbpM converted UDP-GlcNAc completely to what was shown to be its 4-keto-6-deoxy derivative by NMR and that addition of WreQ and NADH led to formation of a third compound. Combined gas chromatography-mass spectrometry analysis of acid hydrolysates of the final reaction mixture showed that a quinovosamine moiety had been synthesized after WreQ addition. The two-step reaction progress also was monitored in real time by NMR. The final UDP-sugar product after WreQ addition was purified and determined to be UDP-d-QuiNAc by one-dimensional and two-dimensional NMR experiments. These results confirmed that WreQ has UDP-2-acetamido-2,6-dideoxy-d-xylo-4-hexulose 4-reductase activity, completing a pathway for UDP-d-QuiNAc synthesis in vitro.
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Affiliation(s)
- Tiezheng Li
- From the Departments of Biological Sciences and
| | | | | | - K Dale Noel
- From the Departments of Biological Sciences and
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10
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Emmadi M, Kulkarni SS. Recent advances in synthesis of bacterial rare sugar building blocks and their applications. Nat Prod Rep 2014; 31:870-9. [DOI: 10.1039/c4np00003j] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
This Highlight describes recent advances in the synthesis of the bacterial deoxy amino hexopyranoside building blocks and their application in constructing various biologically important bacterial O-glycans.
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Affiliation(s)
- Madhu Emmadi
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai, India
| | - Suvarn S. Kulkarni
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai, India
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11
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Beczała A, Ovchinnikova OG, Datta N, Mattinen L, Knapska K, Radziejewska-Lebrecht J, Holst O, Skurnik M. Structure and genetic basis of Yersinia similis serotype O:9 O-specific polysaccharide. Innate Immun 2013; 21:3-16. [DOI: 10.1177/1753425913514783] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The O-polysaccharide (OPS, O-Ag) cap of LPS is a major virulence factor of Yersinia species and also serves as a receptor for the binding of lytic bacteriophage φR1-37. Currently, the OPS-based serotyping scheme for the Yersinia pseudotuberculosis complex includes 21 known O-serotypes that follow three distinct lineages: Y. pseudotuberculosis sensu stricto, Y. similis and the Korean group of strains. Elucidation of the Y. pseudotuberculosis complex OPS structures and characterization of the OPS genetics (altogether 18 O-serotypes studied thus far) allows a better understanding of the relationships among the various O serotypes and will facilitate the analysis of the evolutionary processes giving rise to new serotypes. Here we present the characterization of the OPS structure and gene cluster of Y. similis O:9. Bacteriophage φR1-37, which uses the Y. similis O:9 OPS as a receptor, also infects a number of Y. enterocolitica serotypes, including O:3, O:5,27, O:9 and O:50. The Y. similis O:9 OPS structure resembled none of the receptor structures of the Y. enterocolitica strains, suggesting that φR1-37 can recognize several surface receptors, thus promoting broad host specificity.
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Affiliation(s)
- Agnieszka Beczała
- Division of Structural Biochemistry, Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Airway Research Center North (ARCN), Borstel, Germany
- Department of Microbiology, Faculty of Biology and Environmental Protection, University of Silesia, Katowice, Poland
| | - Olga G Ovchinnikova
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Neeta Datta
- Department of Bacteriology and Immunology, Haartman Institute, and Research Programs Unit, Immunobiology, University of Helsinki, Helsinki, Finland
| | - Laura Mattinen
- Department of Bacteriology and Immunology, Haartman Institute, and Research Programs Unit, Immunobiology, University of Helsinki, Helsinki, Finland
| | - Katarzyna Knapska
- Department of Bacteriology and Immunology, Haartman Institute, and Research Programs Unit, Immunobiology, University of Helsinki, Helsinki, Finland
| | - Joanna Radziejewska-Lebrecht
- Department of Microbiology, Faculty of Biology and Environmental Protection, University of Silesia, Katowice, Poland
| | - Otto Holst
- Division of Structural Biochemistry, Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Airway Research Center North (ARCN), Borstel, Germany
| | - Mikael Skurnik
- Department of Bacteriology and Immunology, Haartman Institute, and Research Programs Unit, Immunobiology, University of Helsinki, Helsinki, Finland
- Helsinki University Central Hospital Laboratory Diagnostics, Helsinki, Finland
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12
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Muszyński A, Rabsztyn K, Knapska K, Duda KA, Duda-Grychtoł K, Kasperkiewicz K, Radziejewska-Lebrecht J, Holst O, Skurnik M. Enterobacterial common antigen and O-specific polysaccharide coexist in the lipopolysaccharide of Yersinia enterocolitica serotype O : 3. Microbiology (Reading) 2013; 159:1782-1793. [DOI: 10.1099/mic.0.066662-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Affiliation(s)
- Artur Muszyński
- Department of Microbiology, University of Silesia, Katowice, Poland
| | - Kamila Rabsztyn
- Department of Microbiology, University of Silesia, Katowice, Poland
| | - Katarzyna Knapska
- Department of Bacteriology and Immunology, Haartman Institute, Research Programs Unit, Immunobiology, University of Helsinki, Helsinki, Finland
| | - Katarzyna A. Duda
- Division of Structural Biochemistry, Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Airway Research Center North (ARCN), Member of the German Center for Lung Research (DZL), Borstel, Germany
- Department of Microbiology, University of Silesia, Katowice, Poland
| | | | | | | | - Otto Holst
- Division of Structural Biochemistry, Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Airway Research Center North (ARCN), Member of the German Center for Lung Research (DZL), Borstel, Germany
| | - Mikael Skurnik
- Helsinki University Central Hospital Laboratory Diagnostics, Helsinki, Finland
- Department of Bacteriology and Immunology, Haartman Institute, Research Programs Unit, Immunobiology, University of Helsinki, Helsinki, Finland
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13
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Kokoulin MS, Kalinovsky AI, Komandrova NA, Tovarchi VE, Tomshich SV, Nedashkovskaya OI, Vaskovsky VE. The structure of the O-specific polysaccharide from marine bacterium Litorimonas taeanensis G5T containing 2-acetamido-4-((3S,5S)-3,5-dihydroxyhexanamido)-2,4-dideoxy-d-quinovose and 2-acetamido-2,6-dideoxy-l-xylo-hexos-4-ulose. Carbohydr Res 2013; 375:105-11. [DOI: 10.1016/j.carres.2013.04.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Accepted: 04/03/2013] [Indexed: 10/27/2022]
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14
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Kenyon JJ, Hall RM. Variation in the complex carbohydrate biosynthesis loci of Acinetobacter baumannii genomes. PLoS One 2013; 8:e62160. [PMID: 23614028 PMCID: PMC3628348 DOI: 10.1371/journal.pone.0062160] [Citation(s) in RCA: 208] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2012] [Accepted: 03/19/2013] [Indexed: 01/16/2023] Open
Abstract
Extracellular polysaccharides are major immunogenic components of the bacterial cell envelope. However, little is known about their biosynthesis in the genus Acinetobacter, which includes A. baumannii, an important nosocomial pathogen. Whether Acinetobacter sp. produce a capsule or a lipopolysaccharide carrying an O antigen or both is not resolved. To explore these issues, genes involved in the synthesis of complex polysaccharides were located in 10 complete A. baumannii genome sequences, and the function of each of their products was predicted via comparison to enzymes with a known function. The absence of a gene encoding a WaaL ligase, required to link the carbohydrate polymer to the lipid A-core oligosaccharide (lipooligosaccharide) forming lipopolysaccharide, suggests that only a capsule is produced. Nine distinct arrangements of a large capsule biosynthesis locus, designated KL1 to KL9, were found in the genomes. Three forms of a second, smaller variable locus, likely to be required for synthesis of the outer core of the lipid A-core moiety, were designated OCL1 to OCL3 and also annotated. Each K locus includes genes for capsule export as well as genes for synthesis of activated sugar precursors, and for glycosyltransfer, glycan modification and oligosaccharide repeat-unit processing. The K loci all include the export genes at one end and genes for synthesis of common sugar precursors at the other, with a highly variable region that includes the remaining genes in between. Five different capsule loci, KL2, KL6, KL7, KL8 and KL9 were detected in multiply antibiotic resistant isolates belonging to global clone 2, and two other loci, KL1 and KL4, in global clone 1. This indicates that this region is being substituted repeatedly in multiply antibiotic resistant isolates from these clones.
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Affiliation(s)
- Johanna J. Kenyon
- School of Molecular Bioscience, The University of Sydney, Sydney, New South Wales, Australia
| | - Ruth M. Hall
- School of Molecular Bioscience, The University of Sydney, Sydney, New South Wales, Australia
- * E-mail:
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Li DG, Liu B, Zhou DW. Structural characterization of enzymatic products in the dTDP-d-Qui4NFo biosynthetic pathway using electrospray ionization tandem mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2013; 27:681-690. [PMID: 23418147 DOI: 10.1002/rcm.6501] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2012] [Revised: 12/04/2012] [Accepted: 01/03/2013] [Indexed: 06/01/2023]
Abstract
RATIONALE Structural characterization of biosynthetic precursors is very important in assigning enzymatic function to proteins that have been identified as functional homologs on the basis of sequence homology alone. The objective of this study is to demonstrate the use of electrospray ionization tandem mass spectrometry (ESI-MS/MS) as a powerful technique for the characterization of enzymatic products in the biosynthetic pathway of deoxythymidine 5'-diphosphate-4-formamido-4,6-dideoxy-D-glucose (dTDP-D-Qui4NFo) in Providencia alcalifaciens O30. METHODS The glucose-1-phosphate thymidyltransferase (RmlA), dTDP-d-glucose 4,6-dehydratase (RmlB), dTDP-4-keto-6-deoxy-d-glucose aminotransferase (VioA), and formyltransferase (VioF) catalyzed reactions were directly monitored by ESI-MS, followed by a detailed structural characterization of the final enzymatic products using ESI-MS/MS in the negative-ion mode after minimal cleanup. RESULTS The biosynthetic pathway of dTDP-D-Qui4NFo, beginning from α-D-glucose-1-phosphate in four reaction steps catalyzed by RmlA, RmlB, VioA and VioF, was characterized solely by ESI-MS/MS. The results obtained were in good agreement with that of traditional high-performance liquid chromatography (HPLC) monitoring and preparation, as well as nuclear magnetic resonance (NMR) and ESI-MS structural characterization. CONCLUSIONS MS provides efficient and simple characterization of important unusual dTDP-sugar biosynthetic pathways in the O-chains of bacterial lipopolysaccharides.
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Affiliation(s)
- Dian-Ge Li
- TEDA School of Biological Sciences and Biotechnology, Tianjin Key Laboratory of Microbial Functional Genomics, Tianjin Research Center for Functional Genomics and Biochip, Ministry of Education, Nankai University, 23 Hongda Street, TEDA, Tianjin, 300457, China
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Abstract
The bacteriophage vB_YecM-ϕR1-37 (ϕR1-37) is a lytic yersiniophage that can propagate naturally in different Yersinia species carrying the correct lipopolysaccharide receptor. This large-tailed phage has deoxyuridine (dU) instead of thymidine in its DNA. In this study, we determined the genomic sequence of phage ϕR1-37, mapped parts of the phage transcriptome, characterized the phage particle proteome, and characterized the virion structure by cryo-electron microscopy and image reconstruction. The 262,391-bp genome of ϕR1-37 is one of the largest sequenced phage genomes, and it contains 367 putative open reading frames (ORFs) and 5 tRNA genes. Mass-spectrometric analysis identified 69 phage particle structural proteins with the genes scattered throughout the genome. A total of 269 of the ORFs (73%) lack homologues in sequence databases. Based on terminator and promoter sequences identified from the intergenic regions, the phage genome was predicted to consist of 40 to 60 transcriptional units. Image reconstruction revealed that the ϕR1-37 capsid consists of hexameric capsomers arranged on a T=27 lattice similar to the bacteriophage ϕKZ. The tail of ϕR1-37 has a contractile sheath. We conclude that phage ϕR1-37 is a representative of a novel phage type that carries the dU-containing genome in a ϕKZ-like head.
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Leonori D, Seeberger PH. De Novo Synthesis of the Bacterial 2-Amino-2,6-Dideoxy Sugar Building Blocks d-Fucosamine, d-Bacillosamine, and d-Xylo-6-deoxy-4-ketohexosamine. Org Lett 2012; 14:4954-7. [DOI: 10.1021/ol3023227] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Daniele Leonori
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany, and Institute for Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195 Berlin, Germany
| | - Peter H. Seeberger
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany, and Institute for Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195 Berlin, Germany
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Bacterial cell surface structures in Yersinia enterocolitica. Arch Immunol Ther Exp (Warsz) 2012; 60:199-209. [PMID: 22484801 DOI: 10.1007/s00005-012-0168-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2011] [Accepted: 01/30/2012] [Indexed: 01/13/2023]
Abstract
Yersinia enterocolitica is a widespread member of the family of Enterobacteriaceae that contains both non-virulent and virulent isolates. Pathogenic Y. enterocolitica strains, especially belonging to serotypes O:3, O:5,27, O:8 and O:9 are etiologic agents of yersiniosis in animals and humans. Y. enterocolitica cell surface structures that play a significant role in virulence have been subject to many investigations. These include outer membrane (OM) glycolipids such as lipopolysaccharide (LPS) and enterobacterial common antigen (ECA) and several cell surface adhesion proteins present only in virulent Y. enterocolitica, i.e., Inv, YadA and Ail. While the yadA gene is located on the Yersinia virulence plasmid the Ail, Inv, LPS and ECA are chromosomally encoded. These structures ensure the correct architecture of the OM, provide adhesive properties as well as resistance to antimicrobial peptides and to host innate immune response mechanisms.
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Pieretti G, Carillo S, Lindner B, Kim KK, Lee KC, Lee JS, Lanzetta R, Parrilli M, Corsaro MM. Characterization of the Core Oligosaccharide and the O-Antigen Biological Repeating Unit from Halomonas stevensii Lipopolysaccharide: The First Case of O-Antigen Linked to the Inner Core. Chemistry 2012; 18:3729-35. [DOI: 10.1002/chem.201102550] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2011] [Indexed: 11/10/2022]
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Skurnik M, Toivonen S. Identification of distinct lipopolysaccharide patterns among Yersinia enterocolitica and Y. enterocolitica-like bacteria. BIOCHEMISTRY (MOSCOW) 2012; 76:823-31. [PMID: 21999544 DOI: 10.1134/s0006297911070133] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The lipopolysaccharide (LPS) of strains representing various serotypes of Yersinia enterocolitica and Y. enterocolitica-like bacteria was studied by deoxycholate-PAGE and silver staining analysis. Four main types of LPS were detected based on the O-polysaccharide (O-PS): (i) LPS with homopolymeric O-PS, (ii) LPS with ladder-forming heteropolymeric O-PS, (iii) LPS with single-length O-PS, and (iv) semi-rough LPS without O-PS. Within the first three types, several subvariants were detected. Selected serotypes representing all above LPS types are sensitive to bacteriophage φR1-37 indicating that they share the phage receptor, a hexasaccharide called outer core in Y. enterocolitica O:3. Whereas phage φR1-37-resistant mutants of homopolymeric O-PS have lost only the outer core, those of ladder-forming or single-length O-PS have lost also the O-PS suggesting that in the latter ones the outer core is bridging between O-PS and lipid A-core. This work forms a basis of further structural, biochemical and genetic studies of these LPSs.
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Affiliation(s)
- M Skurnik
- Department of Bacteriology and Immunology, Haartman Institute, Infection Biology Research Program, University of Helsinki, Finland.
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Skurnik M. Yersinia surface structures and bacteriophages. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 954:293-301. [PMID: 22782776 DOI: 10.1007/978-1-4614-3561-7_37] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Mikael Skurnik
- Department of Bacteriology and Immunology, Haartman Institute, University of Helsinki, Finland.
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Rabsztyn K, Kasperkiewicz K, Duda KA, Li CM, Łukasik M, Radziejewska-Lebrecht J, Skurnik M. Characterization of anti-ECA antibodies in rabbit antiserum against rough Yersinia enterocolitica O:3. BIOCHEMISTRY (MOSCOW) 2011; 76:832-9. [DOI: 10.1134/s0006297911070145] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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23
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Pinta E, Li Z, Batzilla J, Pajunen M, Kasanen T, Rabsztyn K, Rakin A, Skurnik M. Identification of three oligo-/polysaccharide-specific ligases in Yersinia enterocolitica. Mol Microbiol 2011; 83:125-36. [DOI: 10.1111/j.1365-2958.2011.07918.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Ruan X, Loyola DE, Marolda CL, Perez-Donoso JM, Valvano MA. The WaaL O-antigen lipopolysaccharide ligase has features in common with metal ion-independent inverting glycosyltransferases. Glycobiology 2011; 22:288-99. [PMID: 21983211 DOI: 10.1093/glycob/cwr150] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
WaaL is a membrane enzyme that catalyzes a key step in lipopolysaccharide (LPS) synthesis: the glycosidic bonding of a sugar at the proximal end of the undecaprenyl-diphosphate (Und-PP) O-antigen with a terminal sugar of the lipid A-core oligosaccharide (OS). Utilizing an in vitro assay, we demonstrate here that ligation with purified Escherichia coli WaaL occurs without adenosine-5'-triphosphate (ATP) and magnesium ions. Furthermore, E. coli and Pseudomonas aeruginosa WaaL proteins cannot catalyze ATP hydrolysis in vitro. We also show that a lysine substitution of the arginine (Arg)-215 residue renders an active protein, whereas WaaL mutants with alanine replacements in the periplasmic-exposed residues Arg-215, Arg-288 and histidine (His)-338 and also the membrane-embedded aspartic acid-389 are nonfunctional. An in silico approach, combining predicted topological information with the analysis of sequence conservation, confirms the importance of a positive charge at the small periplasmic loop of WaaL, since an Arg corresponding to Arg-215 was found at a similar position in all the WaaL homologs. Also, a universally conserved H[NSQ]X(9)GXX[GTY] motif spanning the C-terminal end of the predicted large periplasmic loop and the membrane boundary of the transmembrane helix was identified. The His residue in this motif corresponds to His-338. A survey of LPS structures in which the linkage between O-antigen and lipid A-core OS was elucidated reveals that it is always in the β-configuration, whereas the sugars bound to Und-PP are in the α-configuration. Together, our biochemical and in silico data argue that WaaL proteins use a common reaction mechanism and share features of metal ion-independent inverting glycosyltransferases.
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Affiliation(s)
- Xiang Ruan
- Centre for Human Immunology, Department of Microbiology and Immunology, University of Western Ontario, London, ON, Canada
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Identification of the lipopolysaccharide core of Yersinia pestis and Yersinia pseudotuberculosis as the receptor for bacteriophage φA1122. J Bacteriol 2011; 193:4963-72. [PMID: 21764935 DOI: 10.1128/jb.00339-11] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
φA1122 is a T7-related bacteriophage infecting most isolates of Yersinia pestis, the etiologic agent of plague, and used by the CDC in the identification of Y. pestis. φA1122 infects Y. pestis grown both at 20 °C and at 37 °C. Wild-type Yersinia pseudotuberculosis strains are also infected but only when grown at 37 °C. Since Y. pestis expresses rough lipopolysaccharide (LPS) missing the O-polysaccharide (O-PS) and expression of Y. pseudotuberculosis O-PS is largely suppressed at temperatures above 30 °C, it has been assumed that the phage receptor is rough LPS. We present here several lines of evidence to support this. First, a rough derivative of Y. pseudotuberculosis was also φA1122 sensitive when grown at 22 °C. Second, periodate treatment of bacteria, but not proteinase K treatment, inhibited the phage binding. Third, spontaneous φA1122 receptor mutants of Y. pestis and rough Y. pseudotuberculosis could not be isolated, indicating that the receptor was essential for bacterial growth under the applied experimental conditions. Fourth, heterologous expression of the Yersinia enterocolitica O:3 LPS outer core hexasaccharide in both Y. pestis and rough Y. pseudotuberculosis effectively blocked the phage adsorption. Fifth, a gradual truncation of the core oligosaccharide into the Hep/Glc (L-glycero-D-manno-heptose/D-glucopyranose)-Kdo/Ko (3-deoxy-D-manno-oct-2-ulopyranosonic acid/D-glycero-D-talo-oct-2-ulopyranosonic acid) region in a series of LPS mutants was accompanied by a decrease in phage adsorption, and finally, a waaA mutant expressing only lipid A, i.e., also missing the Kdo/Ko region, was fully φA1122 resistant. Our data thus conclusively demonstrated that the φA1122 receptor is the Hep/Glc-Kdo/Ko region of the LPS core, a common structure in Y. pestis and Y. pseudotuberculosis.
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Pinta E, Duda KA, Hanuszkiewicz A, Salminen TA, Bengoechea JA, Hyytiäinen H, Lindner B, Radziejewska-Lebrecht J, Holst O, Skurnik M. Characterization of the six glycosyltransferases involved in the biosynthesis of Yersinia enterocolitica serotype O:3 lipopolysaccharide outer core. J Biol Chem 2010; 285:28333-42. [PMID: 20595390 DOI: 10.1074/jbc.m110.111336] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Yersinia enterocolitica (Ye) is a gram-negative bacterium; Ye serotype O:3 expresses lipopolysaccharide (LPS) with a hexasaccharide branch known as the outer core (OC). The OC is important for the resistance of the bacterium to cationic antimicrobial peptides and also functions as a receptor for bacteriophage phiR1-37 and enterocoliticin. The biosynthesis of the OC hexasaccharide is directed by the OC gene cluster that contains nine genes (wzx, wbcKLMNOPQ, and gne). In this study, we inactivated the six OC genes predicted to encode glycosyltransferases (GTase) one by one by nonpolar mutations to assign functions to their gene products. The mutants expressed no OC or truncated OC oligosaccharides of different lengths. The truncated OC oligosaccharides revealed that the minimum structural requirements for the interactions of OC with bacteriophage phiR1-37, enterocoliticin, and OC-specific monoclonal antibody 2B5 were different. Furthermore, using chemical and structural analyses of the mutant LPSs, we could assign specific functions to all six GTases and also revealed the exact order in which the transferases build the hexasaccharide. Comparative modeling of the catalytic sites of glucosyltransferases WbcK and WbcL followed by site-directed mutagenesis allowed us to identify Asp-182 and Glu-181, respectively, as catalytic base residues of these two GTases. In general, conclusive evidence for specific GTase functions have been rare due to difficulties in accessibility of the appropriate donors and acceptors; however, in this work we were able to utilize the structural analysis of LPS to get direct experimental evidence for five different GTase specificities.
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Affiliation(s)
- Elise Pinta
- Department of Bacteriology and Immunology, Infection Biology Research Program, Haartman Institute, University of Helsinki, FIN-00014 Helsinki, Finland
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