101
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Wang L, Zhu W, Lu G, Wu P, Wei Y, Su Y, Jia T, Li L, Guo X, Huang M, Yang Q, Huang D, Liu B. In silico species identification and serotyping for Cronobacter isolates by use of whole-genome sequencing data. Int J Food Microbiol 2021; 358:109405. [PMID: 34563883 DOI: 10.1016/j.ijfoodmicro.2021.109405] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 09/15/2021] [Accepted: 09/16/2021] [Indexed: 10/20/2022]
Abstract
Cronobacter spp. are foodborne pathogens that can cause severe infections in neonates through contaminated powdered infant formula. Accurate and rapid pathogen identification and serotyping are crucial to limit the detrimental effects of bacterial infections, and to prevent outbreaks and sporadic infections. Conventional serotyping is tedious, laborious, and time-consuming; however, with whole-genome sequencing (WGS) becoming faster and cheaper, WGS has vast potential in routine typing and surveillance. Hence, in this study, we developed a publicly available tool, CroTrait (CronobacterTraits), for in silico species identification and O serotyping of Cronobacter isolates based on WGS data. CroTrait showed excellent performance in species identification and O serotyping when 810 genomes with known species identities and 276 genomes with known O serotype were tested. Moreover, CroTrait allows rapid prediction of new potential O serotypes. We identified 11 novel potential O serotypes of Cronobacter using CroTrait. Therefore, CroTrait is a convenient and promising tool for species identification and O serotyping of Cronobacter isolates.
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Affiliation(s)
- Lu Wang
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, People's Republic of China
| | - Wenxuan Zhu
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, People's Republic of China
| | - Gege Lu
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, People's Republic of China
| | - Pan Wu
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, People's Republic of China
| | - Yi Wei
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, People's Republic of China
| | - Yingying Su
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, People's Republic of China
| | - Tianyuan Jia
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, People's Republic of China
| | - Linxing Li
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, People's Republic of China
| | - Xi Guo
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, People's Republic of China
| | - Min Huang
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, People's Republic of China
| | - Qian Yang
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, People's Republic of China
| | - Di Huang
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, People's Republic of China.
| | - Bin Liu
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, People's Republic of China; The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Tianjin, People's Republic of China; Center for Microbial Functional Genomics and Detection Technology, Ministry of Education, Tianjin, People's Republic of China.
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102
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Doorduijn DJ, Heesterbeek DAC, Ruyken M, de Haas CJC, Stapels DAC, Aerts PC, Rooijakkers SHM, Bardoel BW. Polymerization of C9 enhances bacterial cell envelope damage and killing by membrane attack complex pores. PLoS Pathog 2021; 17:e1010051. [PMID: 34752492 PMCID: PMC8604303 DOI: 10.1371/journal.ppat.1010051] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 11/19/2021] [Accepted: 10/20/2021] [Indexed: 11/21/2022] Open
Abstract
Complement proteins can form membrane attack complex (MAC) pores that directly kill Gram-negative bacteria. MAC pores assemble by stepwise binding of C5b, C6, C7, C8 and finally C9, which can polymerize into a transmembrane ring of up to 18 C9 monomers. It is still unclear if the assembly of a polymeric-C9 ring is necessary to sufficiently damage the bacterial cell envelope to kill bacteria. In this paper, polymerization of C9 was prevented without affecting binding of C9 to C5b-8, by locking the first transmembrane helix domain of C9. Using this system, we show that polymerization of C9 strongly enhanced damage to both the bacterial outer and inner membrane, resulting in more rapid killing of several Escherichia coli and Klebsiella strains in serum. By comparing binding of wildtype and ‘locked’ C9 by flow cytometry, we also show that polymerization of C9 is impaired when the amount of available C9 per C5b-8 is limited. This suggests that an excess of C9 is required to efficiently form polymeric-C9. Finally, we show that polymerization of C9 was impaired on complement-resistant E. coli strains that survive killing by MAC pores. This suggests that these bacteria can specifically block polymerization of C9. All tested complement-resistant E. coli expressed LPS O-antigen (O-Ag), compared to only one out of four complement-sensitive E. coli. By restoring O-Ag expression in an O-Ag negative strain, we show that the O-Ag impairs polymerization of C9 and results in complement-resistance. Altogether, these insights are important to understand how MAC pores kill bacteria and how bacterial pathogens can resist MAC-dependent killing. In this paper, we focus on how complement proteins, an essential part of the immune system, kill Gram-negative bacteria via so-called membrane attack complex (MAC) pores. The MAC is a large pore that consists of five different proteins. The final component, C9, assembles a ring of up to 18 C9 molecules that damages the bacterial cell envelope. Here, we aimed to better understand if this polymeric-C9 ring is necessary to kill bacteria and if bacteria can interfere in its assembly. We uncover that polymerization of C9 increased the damage to the entire bacterial cell envelope, which resulted in more rapid killing of several Gram-negative species. We also show that some clinical Escherichia coli strains can block polymerization of C9 and survive MAC-dependent killing by modifying sugars in the bacterial cell envelope, namely the O-antigen of lipopolysaccharide. These insights help us to better understand how the immune system kills bacteria and how pathogenic bacteria can survive killing.
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Affiliation(s)
- Dennis J. Doorduijn
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Dani A. C. Heesterbeek
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Maartje Ruyken
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Carla J. C. de Haas
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Daphne A. C. Stapels
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Piet C. Aerts
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Suzan H. M. Rooijakkers
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Bart W. Bardoel
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
- * E-mail:
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103
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Faust C, Beil C, Dittrich W, Rao E, Langer T. Impact of lipopolysaccharides on cultivation and recombinant protein expression in human embryonal kidney (HEK-293) cells. Eng Life Sci 2021; 21:778-785. [PMID: 34764829 PMCID: PMC8576075 DOI: 10.1002/elsc.202100065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 08/25/2021] [Accepted: 09/17/2021] [Indexed: 11/08/2022] Open
Abstract
The human embryonal kidney 293 cell (HEK-293) is a widely used expression host for transient gene expression. The genes or plasmids used for the transient transfections are usually propagated and extracted from the gram-negative bacterium Escherichia coli, the workhorse for molecular biologists. As a gram-negative bacterium E. coli has an outer membrane (OM) containing lipopolysaccharides (LPS) or endotoxins. LPS are very potent inducers of inflammatory cytokines in the body. In early research phases DNA intended for transient transfections is not routinely checked for LPS-levels. In this study we addressed the question whether LPS has an impact on the cultivation and production of a recombinant antibody. At high concentrations the presence of LPS has a detrimental impact on cell viability and recombinant protein expression. But low LPS concentrations are tolerated and might even enhance protein expression levels.
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Affiliation(s)
- Christine Faust
- R&D Biologics Research, Building H811Sanofi‐Aventis Deutschland GmbHFrankfurt am MainGermany
| | - Christian Beil
- R&D Biologics Research, Building H811Sanofi‐Aventis Deutschland GmbHFrankfurt am MainGermany
| | - Werner Dittrich
- R&D Biologics Research, Building H811Sanofi‐Aventis Deutschland GmbHFrankfurt am MainGermany
| | - Ercole Rao
- R&D Biologics Research, Building H811Sanofi‐Aventis Deutschland GmbHFrankfurt am MainGermany
| | - Thomas Langer
- R&D Biologics Research, Building H811Sanofi‐Aventis Deutschland GmbHFrankfurt am MainGermany
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104
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Maffei E, Shaidullina A, Burkolter M, Heyer Y, Estermann F, Druelle V, Sauer P, Willi L, Michaelis S, Hilbi H, Thaler DS, Harms A. Systematic exploration of Escherichia coli phage-host interactions with the BASEL phage collection. PLoS Biol 2021; 19:e3001424. [PMID: 34784345 PMCID: PMC8594841 DOI: 10.1371/journal.pbio.3001424] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Accepted: 09/27/2021] [Indexed: 01/08/2023] Open
Abstract
Bacteriophages, the viruses infecting bacteria, hold great potential for the treatment of multidrug-resistant bacterial infections and other applications due to their unparalleled diversity and recent breakthroughs in their genetic engineering. However, fundamental knowledge of the molecular mechanisms underlying phage-host interactions is mostly confined to a few traditional model systems and did not keep pace with the recent massive expansion of the field. The true potential of molecular biology encoded by these viruses has therefore remained largely untapped, and phages for therapy or other applications are often still selected empirically. We therefore sought to promote a systematic exploration of phage-host interactions by composing a well-assorted library of 68 newly isolated phages infecting the model organism Escherichia coli that we share with the community as the BASEL (BActeriophage SElection for your Laboratory) collection. This collection is largely representative of natural E. coli phage diversity and was intensively characterized phenotypically and genomically alongside 10 well-studied traditional model phages. We experimentally determined essential host receptors of all phages, quantified their sensitivity to 11 defense systems across different layers of bacterial immunity, and matched these results to the phages' host range across a panel of pathogenic enterobacterial strains. Clear patterns in the distribution of phage phenotypes and genomic features highlighted systematic differences in the potency of different immunity systems and suggested the molecular basis of receptor specificity in several phage groups. Our results also indicate strong trade-offs between fitness traits like broad host recognition and resistance to bacterial immunity that might drive the divergent adaptation of different phage groups to specific ecological niches. We envision that the BASEL collection will inspire future work exploring the biology of bacteriophages and their hosts by facilitating the discovery of underlying molecular mechanisms as the basis for an effective translation into biotechnology or therapeutic applications.
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Affiliation(s)
- Enea Maffei
- Biozentrum, University of Basel, Basel, Switzerland
| | | | | | - Yannik Heyer
- Biozentrum, University of Basel, Basel, Switzerland
| | | | | | | | - Luc Willi
- Biozentrum, University of Basel, Basel, Switzerland
| | - Sarah Michaelis
- Institute of Medical Microbiology, University of Zürich, Zürich, Switzerland
| | - Hubert Hilbi
- Institute of Medical Microbiology, University of Zürich, Zürich, Switzerland
| | - David S. Thaler
- Biozentrum, University of Basel, Basel, Switzerland
- Program for the Human Environment, Rockefeller University, New York City, New York, United States of America
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105
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Relationship Between Antibiotic Resistance Patterns and O-Serogroups in Uropathogenic Escherichia coli Strains Isolated from Iraqi Patients. Jundishapur J Microbiol 2021. [DOI: 10.5812/jjm.118833] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Background: The O-antigen is one of the uropathogenic Escherichia coli (UPEC) virulence factors used as a biomarker to classify E. coli strains. Objectives: In this study, the relationship between antibiotic resistance patterns and O-serogroups was investigated in UPEC strains isolated from patients with urinary tract infections (UTIs) in southern Iraq. Methods: A total of 100 UPEC isolates from the urine specimens of patients with UTIs within the age range of 4 months to 78 years in various southern Iraqi hospitals were collected (May 2017 to January 2018) and confirmed using biochemical tests (e.g., Analytical Profile Index 20E). Antibiotic susceptibility tests were performed using the disk diffusion method according to the Clinical and Laboratory Standards Institute guidelines. The multiple polymerase chain reaction technique was applied to investigate the prevalence of O-serogroups. Results: The most frequent serogroups in the E. coli isolates were O8 (27.7%) and O25 (24.4%); however, serogroup O83 was not observed in the samples. Serogroups O75, O6, O16, and O18 had the lowest frequency (1.1%) among the examined isolates. Furthermore, 10% of the isolates did not belong to any of the examined serogroups. The phenotypic tests showed that the highest and the lowest resistance belonged to piperacillin (92%) and imipenem (5%), respectively. Serogroups O4 and O21 showed the highest drug resistance; nevertheless, serogroups O75, O18, and O1 showed the lowest drug resistance. Additionally, 94% of the isolates were resistant to three or more classes of antibiotics. Conclusions: According to the results, UPEC isolates showed high resistance to common antibiotics; however, they were sensitive to imipenem and amikacin. Serogroups O8 and O25 were the most common among UPEC isolates. Moreover, O4 and O21 showed the highest drug resistance. There was a direct relationship between antimicrobial resistance and O-serogroups in UPEC isolates.
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106
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Verde A, Mangini M, Managò S, Tramontano C, Rea I, Boraschi D, Italiani P, De Luca AC. SERS Sensing of Bacterial Endotoxin on Gold Nanoparticles. Front Immunol 2021; 12:758410. [PMID: 34691081 PMCID: PMC8530015 DOI: 10.3389/fimmu.2021.758410] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 09/22/2021] [Indexed: 12/29/2022] Open
Abstract
Engineered gold nanoparticles (AuNPs) find application in several fields related to human activities (i.e., food and cosmetic industry or water purification) including medicine, where they are employed for diagnosis, drug delivery and cancer therapy. As for any material/reagent for human use, the safety of AuNPs needs accurate evaluation. AuNPs are prone to contamination by bacterial endotoxin (lipopolysaccharide, LPS), a potent elicitor of inflammatory responses in mammals. It is therefore important, when assessing AuNP immunosafety and immune-related effects, to discriminate between inflammatory effects intrinsic to the NPs from those caused by an undeliberate and undetected LPS contamination. Detection of LPS contamination in AuNP preparations poses different problems when using the current LPS detection assays, given the general interference of NPs, similar to other particulate agents, with the assay reagents and endpoints. This leads to time-consuming search for optimal assay conditions for every NP batch, with unpredictable results, and to the use in parallel of different assays, each with its weaknesses and unpredictability. Thus, the development of highly sensitive, quantitative and accurate assays able to detect of LPS on AuNPs is very important, in view of their medical applications. Surface-enhanced Raman spectroscopy (SERS) is a label-free, sensitive, chemical-specific, nondestructive and fast technique that can be used to directly obtain molecular fingerprint information and a quantitative analysis of LPS adsorbed on AuNPs. Within this study, we describe the use of SERS for the label-free identification and quantitative evaluation - down to few attograms - of the LPS adsorbed on the surface of 50 nm AuNPs. We thus propose SERS as an efficient tool to detect LPS on the AuNP surface, and as the basis for the development of a new sensitive and specific LPS-detection sensor based on the use of AuNPs and SERS.
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Affiliation(s)
- Alessandro Verde
- Institute for Experimental Endocrinology and Oncology, "G. Salvatore" (IEOS), Second Unit, Consiglio Nazionale Delle Ricerche (CNR), Napoli, Italy.,Institute of Biochemistry and Cell Biology (IBBC), Consiglio Nazionale Delle Ricerche (CNR), Napoli, Italy
| | - Maria Mangini
- Institute for Experimental Endocrinology and Oncology, "G. Salvatore" (IEOS), Second Unit, Consiglio Nazionale Delle Ricerche (CNR), Napoli, Italy.,Institute of Biochemistry and Cell Biology (IBBC), Consiglio Nazionale Delle Ricerche (CNR), Napoli, Italy
| | - Stefano Managò
- Institute for Experimental Endocrinology and Oncology, "G. Salvatore" (IEOS), Second Unit, Consiglio Nazionale Delle Ricerche (CNR), Napoli, Italy
| | - Chiara Tramontano
- Institute of Applied Sciences and Intelligent Systems (ISASI), Unit of Napoli, Consiglio Nazionale Delle Ricerche (CNR), Napoli, Italy
| | - Ilaria Rea
- Institute of Applied Sciences and Intelligent Systems (ISASI), Unit of Napoli, Consiglio Nazionale Delle Ricerche (CNR), Napoli, Italy
| | - Diana Boraschi
- Institute of Biochemistry and Cell Biology (IBBC), Consiglio Nazionale Delle Ricerche (CNR), Napoli, Italy.,Department of Biology and Evolution of Marine Organisms, Stazione Zoologica "Anton Dohrn", Napoli, Italy.,The Shenzhen Institutes of Advanced Technology (SIAT), Chinese Academy of Science (CAS), Shenzhen, China
| | - Paola Italiani
- Institute of Biochemistry and Cell Biology (IBBC), Consiglio Nazionale Delle Ricerche (CNR), Napoli, Italy
| | - Anna Chiara De Luca
- Institute for Experimental Endocrinology and Oncology, "G. Salvatore" (IEOS), Second Unit, Consiglio Nazionale Delle Ricerche (CNR), Napoli, Italy.,Institute of Biochemistry and Cell Biology (IBBC), Consiglio Nazionale Delle Ricerche (CNR), Napoli, Italy
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107
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Navarro A, van der Ploeg C, Rogé A, Licona-Moreno D, Delgado G, Morales-Espinosa R, Cravioto A, Eslava C. Diversity of Potentially Pathogenic Escherichia coli O104 and O9 Serogroups Isolated before 2011 from Fecal Samples from Children from Different Geographic Regions. Microorganisms 2021; 9:2227. [PMID: 34835353 PMCID: PMC8619403 DOI: 10.3390/microorganisms9112227] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 10/20/2021] [Accepted: 10/22/2021] [Indexed: 11/21/2022] Open
Abstract
In 2011, an outbreak of hemorrhagic colitis and hemolytic uremic syndrome (HUS) was reported in Europe that was related to a hybrid STEAEC of Escherichia coli (E. coli) O104:H4 strain. The current study aimed to analyze strains of E. coli O104 and O9 isolated before 2011. The study included 47 strains isolated from children with and without diarrhea between 1986 and 2009 from different geographic regions, as well as seven reference strains. Serotyping was carried out on 188 anti-O and 53 anti-H sera. PCR was used to identify DEC genes and phylogenetic groups. Resistance profiles to antimicrobials were determined by diffusion in agar, while PFGE was used to analyze genomic similarity. Five serotypes of E. coli O104 and nine of O9 were identified, as well as an antigenic cross-reaction with one anti-E. coli O9 serum. E. coli O104 and O9 presented diarrheagenic E. coli (DEC) genes in different combinations and were located in commensal phylogenetic groups with different antimicrobial resistance. PFGE showed that O104:H4 and O9:(H4, NM) strains from SSI, Bangladesh and México belong to a diverse group located in the same subgroup. E. coli O104 and O9 were classified as commensal strains containing DEC genes. The groups were genetically diverse with pathogenic potential making continued epidemiologic surveillance important.
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Affiliation(s)
- Armando Navarro
- Public Health Department, Faculty of Medicine, Universidad Nacional Autónoma de México, Avenida Universidad 3000, Ciudad Universitaria, México City 04510, Mexico;
| | - Claudia van der Ploeg
- Servicio de Antígenos y Antisueros, Instituto Nacional de Producción de Biológicos (INPB)—ANLIS “Dr. Carlos G. Malbrán”, Buenos Aires 1282, Argentina; (C.v.d.P.); (A.R.)
| | - Ariel Rogé
- Servicio de Antígenos y Antisueros, Instituto Nacional de Producción de Biológicos (INPB)—ANLIS “Dr. Carlos G. Malbrán”, Buenos Aires 1282, Argentina; (C.v.d.P.); (A.R.)
| | - Delia Licona-Moreno
- Public Health Department, Faculty of Medicine, Universidad Nacional Autónoma de México, Avenida Universidad 3000, Ciudad Universitaria, México City 04510, Mexico;
| | - Gabriela Delgado
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, México City 04510, Mexico; (G.D.); (R.M.-E.)
| | - Rosario Morales-Espinosa
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, México City 04510, Mexico; (G.D.); (R.M.-E.)
| | - Alejandro Cravioto
- Faculty of Medicine, Universidad Nacional Autónoma de México, México City 04510, Mexico;
| | - Carlos Eslava
- Peripheral Unit of Basic and Clinical Research in Infectious Diseases, Public Health Department, Research Division, Faculty of Medicine Universidad Nacional Autónoma de México, Bacterial Pathogenicity Laboratory, Hemato-Oncology and Research Unit, Children’s Hospital of Mexico Federico Gómez, Dr. Márquez 162, Col. De los Doctores, México City 06720, Mexico;
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108
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Zheng M, Zheng M, Epstein S, Harnagel AP, Kim H, Lupoli TJ. Chemical Biology Tools for Modulating and Visualizing Gram-Negative Bacterial Surface Polysaccharides. ACS Chem Biol 2021; 16:1841-1865. [PMID: 34569792 DOI: 10.1021/acschembio.1c00341] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Bacterial cells present a wide diversity of saccharides that decorate the cell surface and help mediate interactions with the environment. Many Gram-negative cells express O-antigens, which are long sugar polymers that makeup the distal portion of lipopolysaccharide (LPS) that constitutes the surface of the outer membrane. This review highlights chemical biology tools that have been developed in recent years to facilitate the modulation of O-antigen synthesis and composition, as well as related bacterial polysaccharide pathways, and the detection of unique glycan sequences. Advances in the biochemistry and structural biology of O-antigen biosynthetic machinery are also described, which provide guidance for the design of novel chemical and biomolecular probes. Many of the tools noted here have not yet been utilized in biological systems and offer researchers the opportunity to investigate the complex sugar architecture of Gram-negative cells.
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Affiliation(s)
- Meng Zheng
- Department of Chemistry, New York University, New York, 10003 New York, United States
| | - Maggie Zheng
- Department of Chemistry, New York University, New York, 10003 New York, United States
| | - Samuel Epstein
- Department of Chemistry, New York University, New York, 10003 New York, United States
| | - Alexa P. Harnagel
- Department of Chemistry, New York University, New York, 10003 New York, United States
| | - Hanee Kim
- Department of Chemistry, New York University, New York, 10003 New York, United States
| | - Tania J. Lupoli
- Department of Chemistry, New York University, New York, 10003 New York, United States
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109
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Wang J, Jiao H, Zhang X, Zhang Y, Sun N, Yang Y, Wei Y, Hu B, Guo X. Two Enteropathogenic Escherichia coli Strains Representing Novel Serotypes and Investigation of Their Roles in Adhesion. J Microbiol Biotechnol 2021; 31:1191-1199. [PMID: 34261855 PMCID: PMC9705854 DOI: 10.4014/jmb.2105.05016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 07/05/2021] [Accepted: 07/14/2021] [Indexed: 12/15/2022]
Abstract
Enteropathogenic Escherichia coli (EPEC), which belongs to the attaching and effacing diarrheagenic E. coli strains, is a major causative agent of life-threatening diarrhea in infants in developing countries. Most EPEC isolates correspond to certain O serotypes; however, many strains are nontypeable. Two EPEC strains, EPEC001 and EPEC080, which could not be serotyped during routine detection, were isolated. In this study, we conducted an in-depth characterization of their putative O-antigen gene clusters (O-AGCs) and also performed constructed mutagenesis of the O-AGCs for functional analysis of O-antigen (OAg) synthesis. Sequence analysis revealed that the occurrence of O-AGCs in EPEC001 and E. coli O132 may be mediated by recombination between them, and EPEC080 and E. coli O2/O50 might acquire each O-AGC from uncommon ancestors. We also indicated that OAgknockout bacteria were highly adhesive in vitro, except for the EPEC001 wzy derivative, whose adherent capability was less than that of its wild-type strain, providing direct evidence that OAg plays a key role in EPEC pathogenesis. Together, we identified two EPEC O serotypes in silico and experimentally, and we also studied the adherent capabilities of their OAgs, which highlighted the fundamental and pathogenic role of OAg in EPEC.
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Affiliation(s)
- Jing Wang
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, 23 Hongda Street, TEDA, Tianjin 300457, P.R. China,The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, 23 Hongda Street, TEDA, Tianjin 300457, P.R. China
| | - HongBo Jiao
- LanLing Center for Disease Control and Prevention, 1 City Huibao Road, Lanling 276000, Lanling Shandong, P.R. China
| | - XinFeng Zhang
- Taian Center for Disease Control and Prevention, 33 Changcheng Road, Taian 271000, Shandong, P.R. China
| | - YuanQing Zhang
- Jinan KeJia Medical Laboratory, Inc., 800 Minghu West Road, Jinan 250001, Shandong, P.R. China
| | - Na Sun
- Shandong Center for Disease Control and Prevention, 16992 City Ten Road, Jinan 250014, Shandong, P.R. China
| | - Ying Yang
- Shandong Center for Disease Control and Prevention, 16992 City Ten Road, Jinan 250014, Shandong, P.R. China
| | - Yi Wei
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, 23 Hongda Street, TEDA, Tianjin 300457, P.R. China,The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, 23 Hongda Street, TEDA, Tianjin 300457, P.R. China
| | - Bin Hu
- Shandong Center for Disease Control and Prevention, 16992 City Ten Road, Jinan 250014, Shandong, P.R. China,Corresponding authors B. Hu Phone: +86-0531-82679738 Fax: +86-531-82679750 E-mail:
| | - Xi Guo
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, 23 Hongda Street, TEDA, Tianjin 300457, P.R. China,The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, 23 Hongda Street, TEDA, Tianjin 300457, P.R. China,
X. Guo Phone: +86-22-66229574 Fax: +86-22-66229584 E-mail:
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110
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Wang L, Lowary TL. Synthesis of structurally-defined polymeric glycosylated phosphoprenols as potential lipopolysaccharide biosynthetic probes. Chem Sci 2021; 12:12192-12200. [PMID: 34667585 PMCID: PMC8457389 DOI: 10.1039/d1sc03852d] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 08/13/2021] [Indexed: 11/24/2022] Open
Abstract
The biosynthesis of lipopolysaccharide (LPS), a key immunomodulatory molecule produced by gram-negative bacteria, has been a topic of long-term interest. To date, the chemical probes used as tools to study LPS biosynthetic pathways have consisted primarily of small fragments of the larger structure (e.g., the O-chain repeating unit). While such compounds have helped to provide significant insight into many aspects of LPS assembly, understanding other aspects will require larger, more complex probes. For example, the molecular interactions between polymeric LPS biosynthetic intermediates and the proteins that transfer them across the inner and outer membrane remain largely unknown. We describe the synthesis of two lipid-linked polysaccharides, containing 11 and 27 monosaccharide residues, that are related to LPS O-chain biosynthesis in Escherichia coli O9a. This work has led not only to multi-milligram quantities of two biosynthetic probes, but also provided insights into challenges that must be overcome in the chemical synthesis of structurally-defined polysaccharides. The synthesis of lipid-linked polysaccharides containing 11 and 27 monosaccharides via a ‘frame-shift’ strategy is described. The work provides biosynthetic probes and highlights challenges in synthesizing structurally-defined polymeric glycans.![]()
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Affiliation(s)
- Lei Wang
- Department of Chemistry, University of Alberta Edmonton AB T6G 2G2 Canada
| | - Todd L Lowary
- Department of Chemistry, University of Alberta Edmonton AB T6G 2G2 Canada .,Institute of Biological Chemistry, Academia Sinica Academia Road, Section 2, #128, Nangang Taipei 11529 Taiwan.,Institute of Biochemical Sciences, National Taiwan University Section 4, #1, Roosevelt Road. Taipei 10617 Taiwan
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111
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Sørensen AN, Woudstra C, Sørensen MCH, Brøndsted L. Subtypes of tail spike proteins predicts the host range of Ackermannviridae phages. Comput Struct Biotechnol J 2021; 19:4854-4867. [PMID: 34527194 PMCID: PMC8432352 DOI: 10.1016/j.csbj.2021.08.030] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 08/19/2021] [Accepted: 08/19/2021] [Indexed: 12/01/2022] Open
Abstract
Phages belonging to the Ackermannviridae family encode up to four tail spike proteins (TSPs), each recognizing a specific receptor of their bacterial hosts. Here, we determined the TSPs diversity of 99 Ackermannviridae phages by performing a comprehensive in silico analysis. Based on sequence diversity, we assigned all TSPs into distinctive subtypes of TSP1, TSP2, TSP3 and TSP4, and found each TSP subtype to be specifically associated with the genera (Kuttervirus, Agtrevirus, Limestonevirus, Taipeivirus) of the Ackermannviridae family. Further analysis showed that the N-terminal XD1 and XD2 domains in TSP2 and TSP4, hinging the four TSPs together, are preserved. In contrast, the C-terminal receptor binding modules were only conserved within TSP subtypes, except for some Kuttervirus TSP1s and TSP3s that were similar to specific TSP4s. A conserved motif in TSP1, TSP3 and TSP4 of Kuttervirus phages may allow recombination between receptor binding modules, thus altering host recognition. The receptors for numerous uncharacterized phages expressing TSPs in the same subtypes were predicted using previous host range data. To validate our predictions, we experimentally determined the host recognition of three of the four TSPs expressed by kuttervirus S117. We confirmed that S117 TSP1 and TSP2 bind to their predicted host receptors, and identified the receptor for TSP3, which is shared by 51 other Kuttervirus phages. Kuttervirus phages were thus shown encode a vast genetic diversity of potentially exchangeable TSPs influencing host recognition. Overall, our study demonstrates that comprehensive in silico and host range analysis of TSPs can predict host recognition of Ackermannviridae phages.
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Key Words
- ANI, Average nucleotide identity
- Ackermannviridae family
- Bacteriophage
- CPS, Capsular polysaccharide
- EOP, Efficiency of plating
- Escherichia coli O:157
- Host range
- LB, Luria-Bertani
- LPS, Lipopolysaccharide
- NCBI, National Center for Biotechnology Information
- O-antigen
- ORF, Open reading frame
- PFU, Plaque formation unit
- RBP, Receptor binding protein
- Receptor-binding proteins
- Salmonella
- TSP, Tail spike protein
- Tail spike proteins
- VriC, Virulence-associated protein
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Affiliation(s)
- Anders Nørgaard Sørensen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, 1870 Frederiksberg C, Denmark
| | - Cedric Woudstra
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, 1870 Frederiksberg C, Denmark
| | - Martine C Holst Sørensen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, 1870 Frederiksberg C, Denmark
| | - Lone Brøndsted
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, 1870 Frederiksberg C, Denmark
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112
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Rogé AD, Celi Castillo AB, van der Ploeg CA, Bordagorría XL, Padín VM, Bruno SB. Identification of Two New Sequences of Flagellin-Encoding Gene in Escherichia coli Using PCR and Sequencing-Based Methods. Foodborne Pathog Dis 2021; 19:31-35. [PMID: 34491107 DOI: 10.1089/fpd.2021.0033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Escherichia coli has traditionally been serotyped using antisera against the O and H antigens. However, a proportion of E. coli isolates are nonmotile and, in addition, some isolates do not react with the currently available H-typing sera. Alternative molecular methods have been developed based on the detection of genes encoding for H antigens. In this study, we studied 13 serologically nontypable H antigen E. coli strains using polymerase chain reaction (PCR) and sequencing-based methods. We found two new sequences of flagellin-encoding gene, for each of which a specific antiserum was produced to confirm their expression. Sequencing of the flagellin gene offers a rapid determination of E. coli H antigens and could be used to detect potential novel flagellar antigens.
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Affiliation(s)
- Ariel Diego Rogé
- Servicio Antígenos y Antisueros, Instituto Nacional de Producción de Biológicos, ANLIS "Dr. Carlos G. Malbrán," Ciudad Autónoma de Buenos Aires, Argentina
| | - Ana Beatriz Celi Castillo
- Servicio Antígenos y Antisueros, Instituto Nacional de Producción de Biológicos, ANLIS "Dr. Carlos G. Malbrán," Ciudad Autónoma de Buenos Aires, Argentina
| | - Claudia Andrea van der Ploeg
- Servicio Antígenos y Antisueros, Instituto Nacional de Producción de Biológicos, ANLIS "Dr. Carlos G. Malbrán," Ciudad Autónoma de Buenos Aires, Argentina
| | - Ximena Luciana Bordagorría
- Servicio Antígenos y Antisueros, Instituto Nacional de Producción de Biológicos, ANLIS "Dr. Carlos G. Malbrán," Ciudad Autónoma de Buenos Aires, Argentina
| | - Valeria M Padín
- Servicio Antígenos y Antisueros, Instituto Nacional de Producción de Biológicos, ANLIS "Dr. Carlos G. Malbrán," Ciudad Autónoma de Buenos Aires, Argentina
| | - Susana Beatriz Bruno
- Servicio Antígenos y Antisueros, Instituto Nacional de Producción de Biológicos, ANLIS "Dr. Carlos G. Malbrán," Ciudad Autónoma de Buenos Aires, Argentina
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113
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Miroshnikov KA, Evseev PV, Lukianova AA, Ignatov AN. Tailed Lytic Bacteriophages of Soft Rot Pectobacteriaceae. Microorganisms 2021; 9:1819. [PMID: 34576713 PMCID: PMC8472413 DOI: 10.3390/microorganisms9091819] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 08/23/2021] [Accepted: 08/24/2021] [Indexed: 02/07/2023] Open
Abstract
The study of the ecological and evolutionary traits of Soft Rot Pectobacteriaceae (SRP) comprising genera Pectobacterium and Dickeya often involves bacterial viruses (bacteriophages). Bacteriophages are considered to be a prospective tool for the ecologically safe and highly specific protection of plants and harvests from bacterial diseases. Information concerning bacteriophages has been growing rapidly in recent years, and this has included new genomics-based principles of taxonomic distribution. In this review, we summarise the data on phages infecting Pectobacterium and Dickeya that are available in publications and genomic databases. The analysis highlights not only major genomic properties that assign phages to taxonomic families and genera, but also the features that make them potentially suitable for phage control applications. Specifically, there is a discussion of the molecular mechanisms of receptor recognition by the phages and problems concerning the evolution of phage-resistant mutants.
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Affiliation(s)
- Konstantin A Miroshnikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, 117997 Moscow, Russia
- Timiryazev Agricultural Academy, Russian State Agrarian University, Timiryazevskaya Str., 49, 127434 Moscow, Russia
| | - Peter V Evseev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, 117997 Moscow, Russia
| | - Anna A Lukianova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, 117997 Moscow, Russia
- Timiryazev Agricultural Academy, Russian State Agrarian University, Timiryazevskaya Str., 49, 127434 Moscow, Russia
- Department of Biology, Lomonosov Moscow State University, Leninskie Gory, 1, bldg. 12, 119234 Moscow, Russia
| | - Alexander N Ignatov
- Timiryazev Agricultural Academy, Russian State Agrarian University, Timiryazevskaya Str., 49, 127434 Moscow, Russia
- Agrobiotechnology Department, Agrarian and Technological Institute, RUDN University, Miklukho-Maklaya Str., 6, 117198 Moscow, Russia
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114
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Luong P, Dube DH. Dismantling the bacterial glycocalyx: Chemical tools to probe, perturb, and image bacterial glycans. Bioorg Med Chem 2021; 42:116268. [PMID: 34130219 DOI: 10.1016/j.bmc.2021.116268] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Revised: 05/27/2021] [Accepted: 06/01/2021] [Indexed: 12/20/2022]
Abstract
The bacterial glycocalyx is a quintessential drug target comprised of structurally distinct glycans. Bacterial glycans bear unusual monosaccharide building blocks whose proper construction is critical for bacterial fitness, survival, and colonization in the human host. Despite their appeal as therapeutic targets, bacterial glycans are difficult to study due to the presence of rare bacterial monosaccharides that are linked and modified in atypical manners. Their structural complexity ultimately hampers their analytical characterization. This review highlights recent advances in bacterial chemical glycobiology and focuses on the development of chemical tools to probe, perturb, and image bacterial glycans and their biosynthesis. Current technologies have enabled the study of bacterial glycosylation machinery even in the absence of detailed structural information.
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Affiliation(s)
- Phuong Luong
- Department of Chemistry & Biochemistry, Bowdoin College, 6600 College Station, Brunswick, ME 04011, USA
| | - Danielle H Dube
- Department of Chemistry & Biochemistry, Bowdoin College, 6600 College Station, Brunswick, ME 04011, USA.
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115
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A Potentiometric Electronic Tongue as a Discrimination Tool of Water-Food Indicator/Contamination Bacteria. CHEMOSENSORS 2021. [DOI: 10.3390/chemosensors9060143] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Microorganism assessment plays a key role in food quality and safety control but conventional techniques are costly and/or time consuming. Alternatively, electronic tongues (E-tongues) can fulfill this critical task. Thus, a potentiometric lab-made E-tongue (40 lipid sensor membranes) was used to differentiate four common food contamination bacteria, including two Gram positive (Enterococcus faecalis, Staphylococcus aureus) and two Gram negative (Escherichia coli, Pseudomonas aeruginosa). Principal component analysis and a linear discriminant analysis-simulated annealing algorithm (LDA-SA) showed that the potentiometric signal profiles acquired during the analysis of aqueous solutions containing known amounts of each studied bacteria allowed a satisfactory differentiation of the four bacterial strains. An E-tongue-LDA-SA model (12 non-redundant sensors) correctly classified 98 ± 5% of the samples (repeated K-fold-CV), the satisfactory performance of which can be attributed to the capability of the lipid membranes to establish electrostatic interactions/hydrogen bonds with hydroxyl, amine and/or carbonyl groups, which are comprised in the bacteria outer membranes. Furthermore, multiple linear regression models, based on selected subsets of E-tongue sensors (12–15 sensors), also allowed quantifying the bacteria contents in aqueous solutions (0.993 ± 0.011 ≤ R2 ≤ 0.998 ± 0.005, for repeated K-fold-CV). In conclusion, the E-tongue could be of great value as a preliminary food quality and safety diagnosis tool.
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116
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Witte S, Zinsli LV, Gonzalez-Serrano R, Matter CI, Loessner MJ, van Mierlo JT, Dunne M. Structural and functional characterization of the receptor binding proteins of Escherichia coli O157 phages EP75 and EP335. Comput Struct Biotechnol J 2021; 19:3416-3426. [PMID: 34194667 PMCID: PMC8217332 DOI: 10.1016/j.csbj.2021.06.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 05/31/2021] [Accepted: 06/01/2021] [Indexed: 12/16/2022] Open
Abstract
Bacteriophages (phages) are widely used as biocontrol agents in food and as antibacterial agents for treatment of food production plant surfaces. An important feature of such phages is broad infectivity towards a given pathogenic species. Phages attach to the surfaces of bacterial cells using receptor binding proteins (RBPs), namely tail fibers or tailspikes (TSPs). The binding range of RBPs is the primary determinant of phage host range and infectivity, and therefore dictates a phage's suitability as an antibacterial agent. Phages EP75 and EP335 broadly infect strains of E. coli serotype O157. To better understand host recognition by both phages, here we focused on characterizing the structures and functions of their RBPs. We identified two distinct tail fibers in the genome of the podovirus EP335: gp12 and gp13. Using fluorescence microscopy, we reveal how gp13 recognizes strains of E. coli serotypes O157 and O26. Phage EP75 belongs to the Kuttervirus genus within the Ackermannviridae family and features a four TSP complex (TSPs 1-4) that is universal among such phages. We demonstrate enzymatic activity of TSP1 (gp167) and TSP2 (gp168) toward the O18A and O157 O-antigens of E. coli, respectively, as well as TSP3 activity (gp169.1) against O4, O7, and O9 Salmonella O-antigens. TSPs of EP75 present high similarity to TSPs from E. coli phages CBA120 (TSP2) and HK620 (TSP1) and Salmonella myovirus Det7 (TSP3), which helps explain the cross-genus infectivity observed for EP75.
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Affiliation(s)
- Sander Witte
- Micreos Food Safety B.V., Wageningen, Nieuwe Kanaal 7P, 6709PA, The Netherlands
| | - Léa V. Zinsli
- Institute of Food Nutrition and Health, ETH Zürich, Schmelzbergstrasse 7, 8092 Zürich, Switzerland
| | | | - Cassandra I. Matter
- Institute of Food Nutrition and Health, ETH Zürich, Schmelzbergstrasse 7, 8092 Zürich, Switzerland
| | - Martin J. Loessner
- Institute of Food Nutrition and Health, ETH Zürich, Schmelzbergstrasse 7, 8092 Zürich, Switzerland
| | - Joël T. van Mierlo
- Micreos Food Safety B.V., Wageningen, Nieuwe Kanaal 7P, 6709PA, The Netherlands
| | - Matthew Dunne
- Institute of Food Nutrition and Health, ETH Zürich, Schmelzbergstrasse 7, 8092 Zürich, Switzerland
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117
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Henderson PJF, Maher C, Elbourne LDH, Eijkelkamp BA, Paulsen IT, Hassan KA. Physiological Functions of Bacterial "Multidrug" Efflux Pumps. Chem Rev 2021; 121:5417-5478. [PMID: 33761243 DOI: 10.1021/acs.chemrev.0c01226] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Bacterial multidrug efflux pumps have come to prominence in human and veterinary pathogenesis because they help bacteria protect themselves against the antimicrobials used to overcome their infections. However, it is increasingly realized that many, probably most, such pumps have physiological roles that are distinct from protection of bacteria against antimicrobials administered by humans. Here we undertake a broad survey of the proteins involved, allied to detailed examples of their evolution, energetics, structures, chemical recognition, and molecular mechanisms, together with the experimental strategies that enable rapid and economical progress in understanding their true physiological roles. Once these roles are established, the knowledge can be harnessed to design more effective drugs, improve existing microbial production of drugs for clinical practice and of feedstocks for commercial exploitation, and even develop more sustainable biological processes that avoid, for example, utilization of petroleum.
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Affiliation(s)
- Peter J F Henderson
- School of Biomedical Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Claire Maher
- School of Environmental and Life Sciences, University of Newcastle, Callaghan 2308, New South Wales, Australia
| | - Liam D H Elbourne
- Department of Biomolecular Sciences, Macquarie University, Sydney 2109, New South Wales, Australia.,ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney 2019, New South Wales, Australia
| | - Bart A Eijkelkamp
- College of Science and Engineering, Flinders University, Bedford Park 5042, South Australia, Australia
| | - Ian T Paulsen
- Department of Biomolecular Sciences, Macquarie University, Sydney 2109, New South Wales, Australia.,ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney 2019, New South Wales, Australia
| | - Karl A Hassan
- School of Environmental and Life Sciences, University of Newcastle, Callaghan 2308, New South Wales, Australia.,ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney 2019, New South Wales, Australia
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118
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Structure of a full-length bacterial polysaccharide co-polymerase. Nat Commun 2021; 12:369. [PMID: 33446644 PMCID: PMC7809406 DOI: 10.1038/s41467-020-20579-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 12/08/2020] [Indexed: 01/29/2023] Open
Abstract
Lipopolysaccharides are important components of the bacterial cell envelope that among other things act as a protective barrier against the environment and toxic molecules such as antibiotics. One of the most widely disseminated pathways of polysaccharide biosynthesis is the inner membrane bound Wzy-dependent pathway. Here we present the 3.0 Å structure of the co-polymerase component of this pathway, WzzB from E. coli solved by single-particle cryo-electron microscopy. The overall architecture is octameric and resembles a box jellyfish containing a large bell-shaped periplasmic domain with the 2-helix transmembrane domain from each protomer, positioned 32 Å apart, encircling a large empty transmembrane chamber. This structure also reveals the architecture of the transmembrane domain, including the location of key residues for the Wzz-family of proteins and the Wzy-dependent pathway present in many Gram-negative bacteria, explaining several of the previous biochemical and mutational studies and lays the foundation for future investigations.
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119
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Su T, Nakamoto R, Chun YY, Chua WZ, Chen JH, Zik JJ, Sham LT. Decoding capsule synthesis in Streptococcus pneumoniae. FEMS Microbiol Rev 2020; 45:6041728. [PMID: 33338218 DOI: 10.1093/femsre/fuaa067] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 12/07/2020] [Indexed: 12/20/2022] Open
Abstract
Streptococcus pneumoniae synthesizes more than one hundred types of capsular polysaccharides (CPS). While the diversity of the enzymes and transporters involved is enormous, it is not limitless. In this review, we summarized the recent progress on elucidating the structure-function relationships of CPS, the mechanisms by which they are synthesized, how their synthesis is regulated, the host immune response against them, and the development of novel pneumococcal vaccines. Based on the genetic and structural information available, we generated provisional models of the CPS repeating units that remain unsolved. In addition, to facilitate cross-species comparisons and assignment of glycosyltransferases, we illustrated the biosynthetic pathways of the known CPS in a standardized format. Studying the intricate steps of pneumococcal CPS assembly promises to provide novel insights for drug and vaccine development as well as improve our understanding of related pathways in other species.
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Affiliation(s)
- Tong Su
- Infectious Diseases Translational Research Programme, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, 117545, Singapore
| | - Rei Nakamoto
- Infectious Diseases Translational Research Programme, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, 117545, Singapore
| | - Ye Yu Chun
- Infectious Diseases Translational Research Programme, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, 117545, Singapore
| | - Wan Zhen Chua
- Infectious Diseases Translational Research Programme, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, 117545, Singapore
| | - Jia Hui Chen
- Infectious Diseases Translational Research Programme, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, 117545, Singapore
| | - Justin J Zik
- Infectious Diseases Translational Research Programme, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, 117545, Singapore
| | - Lok-To Sham
- Infectious Diseases Translational Research Programme, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, 117545, Singapore
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120
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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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121
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Lipopolysaccharide-Linked Enterobacterial Common Antigen (ECA LPS) Occurs in Rough Strains of Escherichia coli R1, R2, and R4. Int J Mol Sci 2020; 21:ijms21176038. [PMID: 32839412 PMCID: PMC7504096 DOI: 10.3390/ijms21176038] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 08/18/2020] [Accepted: 08/20/2020] [Indexed: 12/26/2022] Open
Abstract
Enterobacterial common antigen (ECA) is a conserved surface antigen characteristic for Enterobacteriaceae. It is consisting of trisaccharide repeating unit, →3)-α-d-Fucp4NAc-(1→4)-β-d-ManpNAcA-(1→4)-α-d-GlcpNAc-(1→, where prevailing forms include ECA linked to phosphatidylglycerol (ECAPG) and cyclic ECA (ECACYC). Lipopolysaccharide (LPS)-associated form (ECALPS) has been proved to date only for rough Shigella sonnei phase II. Depending on the structure organization, ECA constitutes surface antigen (ECAPG and ECALPS) or maintains the outer membrane permeability barrier (ECACYC). The existence of LPS was hypothesized in the 1960–80s on the basis of serological observations. Only a few Escherichia coli strains (i.e., R1, R2, R3, R4, and K-12) have led to the generation of anti-ECA antibodies upon immunization, excluding ECAPG as an immunogen and conjecturing ECALPS as the only immunogenic form. Here, we presented a structural survey of ECALPS in E. coli R1, R2, R3, and R4 to correlate previous serological observations with the presence of ECALPS. The low yields of ECALPS were identified in the R1, R2, and R4 strains, where ECA occupied outer core residues of LPS that used to be substituted by O-specific polysaccharide in the case of smooth LPS. Previously published observations and hypotheses regarding the immunogenicity and biosynthesis of ECALPS were discussed and correlated with presented herein structural data.
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122
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Structural analysis of the O-antigen polysaccharide from Escherichia coli O188. Carbohydr Res 2020; 498:108051. [PMID: 33075674 DOI: 10.1016/j.carres.2020.108051] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 05/26/2020] [Accepted: 05/26/2020] [Indexed: 02/07/2023]
Abstract
The structure of the O-antigen from Escherichia coli reference strain O188 (E. coli O188:H10) has been investigated. The lipopolysaccharide shows a typical nonrandom modal chain-length distribution and the sugar and absolute configuration analysis revealed d-Man, d-Glc, d-GlcN and d-GlcA as major components. The structure of the O-specific polysaccharide was determined using one- and two-dimensional 1H and 13C NMR spectroscopy experiments, where inter-residue correlations were identified by 1H,13C-heteronuclear multiple-bond correlation and 1H,1H-NOESY experiments, which revealed that it consists of pentasaccharide repeating units with the following structure: Biosynthetic aspects and NMR analysis are consistent with the presented structure as the biological repeating unit. The O-antigen of Shigella boydii type 16 differs only in that it carries O-acetyl groups to ~50% at O6 of the branch-point mannose residues. A molecular model of the E. coli O188 O-antigen containing 20 repeating units extends ~100 Å, which is similar to the height of the periplasmic portion of polysaccharide co-polymerase Wzz proteins that regulate the O-antigen chain length of lipopolysaccharides in the Wzx/Wzy biosynthetic pathway.
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123
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Yan K, Liu T, Duan B, Liu F, Cao M, Peng W, Dai Q, Chen H, Yuan F, Bei W. The CpxAR Two-Component System Contributes to Growth, Stress Resistance, and Virulence of Actinobacillus pleuropneumoniae by Upregulating wecA Transcription. Front Microbiol 2020; 11:1026. [PMID: 32528444 PMCID: PMC7255013 DOI: 10.3389/fmicb.2020.01026] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 04/27/2020] [Indexed: 12/14/2022] Open
Abstract
Actinobacillus pleuropneumoniae is the pathogen of porcine contagious pleuropneumonia. In A. pleuropneumoniae, the CpxAR two-component system is essential for fitness and growth. The O-antigen protrudes from the outer membrane to the exterior of the cell, and the outer membrane serves as a barrier that helps the bacteria to survive in harsh environments. WecA, a undecaprenyl phosphate GlcNAc-1-phosphate transferase, is involved in O-antigen repeating unit biosynthesis. In this study, we investigated the role of CpxAR in the expression of wecA in A. pleuropneumoniae. Our results revealed that CpxR positively regulates wecA expression by directly binding to the putative promoter region of wecA. Wild-type, ΔcpxAR, ΔwecA, and complemented strains were investigated under serum, oxidative, and osmotic stresses. The ΔcpxAR and ΔwecA strains were more susceptible to these stresses than the wild-type, but the complemented strains showed phenotypes similar to those of the wild-type. Mice infected with the ΔcpxAR and ΔwecA strains exhibited lower mortality and bacterial loads in the lung than those infected with the wild-type or complemented strains. This study reveals that the CpxAR two-component system contributes to A. pleuropneumoniae growth, stress resistance, and virulence, by upregulating expression of wecA. Our findings provide new insight into the pathogenesis of A. pleuropneumoniae.
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Affiliation(s)
- Kang Yan
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Ting Liu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Benzhen Duan
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Feng Liu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Manman Cao
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Wei Peng
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Qi Dai
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Huanchun Chen
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Fangyan Yuan
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture), Institute of Animal Husbandry and Veterinary Sciences, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Weicheng Bei
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,State Key Laboratory of Genetically Engineered Veterinary Vaccines, Qingdao, China.,The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
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124
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Whitfield C, Williams DM, Kelly SD. Lipopolysaccharide O-antigens-bacterial glycans made to measure. J Biol Chem 2020; 295:10593-10609. [PMID: 32424042 DOI: 10.1074/jbc.rev120.009402] [Citation(s) in RCA: 87] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 05/17/2020] [Indexed: 01/05/2023] Open
Abstract
Lipopolysaccharides are critical components of bacterial outer membranes. The more conserved lipid A part of the lipopolysaccharide molecule is a major element in the permeability barrier imposed by the outer membrane and offers a pathogen-associated molecular pattern recognized by innate immune systems. In contrast, the long-chain O-antigen polysaccharide (O-PS) shows remarkable structural diversity and fulfills a range of functions, depending on bacterial lifestyles. O-PS production is vital for the success of clinically important Gram-negative pathogens. The biological properties and functions of O-PSs are mostly independent of specific structures, but the size distribution of O-PS chains is particularly important in many contexts. Despite the vast O-PS chemical diversity, most are produced in bacterial cells by two assembly strategies, and the different mechanisms employed in these pathways to regulate chain-length distribution are emerging. Here, we review our current understanding of the mechanisms involved in regulating O-PS chain-length distribution and discuss their impact on microbial cell biology.
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Affiliation(s)
- Chris Whitfield
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Danielle M Williams
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Steven D Kelly
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
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125
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Plattner M, Shneider MM, Arbatsky NP, Shashkov AS, Chizhov AO, Nazarov S, Prokhorov NS, Taylor NMI, Buth SA, Gambino M, Gencay YE, Brøndsted L, Kutter EM, Knirel YA, Leiman PG. Structure and Function of the Branched Receptor-Binding Complex of Bacteriophage CBA120. J Mol Biol 2019; 431:3718-3739. [PMID: 31325442 DOI: 10.1016/j.jmb.2019.07.022] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 07/10/2019] [Accepted: 07/10/2019] [Indexed: 01/21/2023]
Abstract
Bacteriophages recognize their host cells with the help of tail fiber and tailspike proteins that bind, cleave, or modify certain structures on the cell surface. The spectrum of ligands to which the tail fibers and tailspikes can bind is the primary determinant of the host range. Bacteriophages with multiple tailspike/tail fibers are thought to have a wider host range than their less endowed relatives but the function of these proteins remains poorly understood. Here, we describe the structure, function, and substrate specificity of three tailspike proteins of bacteriophage CBA120-TSP2, TSP3 and TSP4 (orf211 through orf213, respectively). We show that tailspikes TSP2, TSP3 and TSP4 are hydrolases that digest the O157, O77, and O78 Escherichia coli O-antigens, respectively. We demonstrate that recognition of the E. coli O157:H7 host by CBA120 involves binding to and digesting the O157 O-antigen by TSP2. We report the crystal structure of TSP2 in complex with a repeating unit of the O157 O-antigen. We demonstrate that according to the specificity of its tailspikes TSP2, TSP3, and TSP4, CBA120 can infect E. coli O157, O77, and O78, respectively. We also show that CBA120 infects Salmonella enterica serovar Minnesota, and this host range expansion is likely due to the function of TSP1. Finally, we describe the assembly pathway and the architecture of the TSP1-TSP2-TSP3-TSP4 branched complex in CBA120 and its related ViI-like phages.
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Affiliation(s)
- Michel Plattner
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555-0647, USA; École Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
| | - Mikhail M Shneider
- Laboratory of Molecular Bioengineering, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 16/10 Miklukho-Maklaya St., 117997 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
| | - Alexander O Chizhov
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Sergey Nazarov
- École Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
| | - Nikolai S Prokhorov
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555-0647, USA
| | - Nicholas M I Taylor
- Structural Biology of Molecular Machines Group, Protein Structure & Function Programme, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, Copenhagen 2200, Denmark
| | - Sergey A Buth
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555-0647, USA
| | - Michela Gambino
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, 1870 Frederiksberg C, Denmark
| | - Yilmaz Emre Gencay
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, 1870 Frederiksberg C, Denmark
| | - Lone Brøndsted
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, 1870 Frederiksberg C, Denmark
| | | | - Yuriy A Knirel
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Petr G Leiman
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555-0647, USA.
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