1
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Podkowik M, Perault AI, Putzel G, Pountain A, Kim J, DuMont AL, Zwack EE, Ulrich RJ, Karagounis TK, Zhou C, Haag AF, Shenderovich J, Wasserman GA, Kwon J, Chen J, Richardson AR, Weiser JN, Nowosad CR, Lun DS, Parker D, Pironti A, Zhao X, Drlica K, Yanai I, Torres VJ, Shopsin B. Quorum-sensing agr system of Staphylococcus aureus primes gene expression for protection from lethal oxidative stress. eLife 2024; 12:RP89098. [PMID: 38687677 PMCID: PMC11060713 DOI: 10.7554/elife.89098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2024] Open
Abstract
The agr quorum-sensing system links Staphylococcus aureus metabolism to virulence, in part by increasing bacterial survival during exposure to lethal concentrations of H2O2, a crucial host defense against S. aureus. We now report that protection by agr surprisingly extends beyond post-exponential growth to the exit from stationary phase when the agr system is no longer turned on. Thus, agr can be considered a constitutive protective factor. Deletion of agr resulted in decreased ATP levels and growth, despite increased rates of respiration or fermentation at appropriate oxygen tensions, suggesting that Δagr cells undergo a shift towards a hyperactive metabolic state in response to diminished metabolic efficiency. As expected from increased respiratory gene expression, reactive oxygen species (ROS) accumulated more in the agr mutant than in wild-type cells, thereby explaining elevated susceptibility of Δagr strains to lethal H2O2 doses. Increased survival of wild-type agr cells during H2O2 exposure required sodA, which detoxifies superoxide. Additionally, pretreatment of S. aureus with respiration-reducing menadione protected Δagr cells from killing by H2O2. Thus, genetic deletion and pharmacologic experiments indicate that agr helps control endogenous ROS, thereby providing resilience against exogenous ROS. The long-lived 'memory' of agr-mediated protection, which is uncoupled from agr activation kinetics, increased hematogenous dissemination to certain tissues during sepsis in ROS-producing, wild-type mice but not ROS-deficient (Cybb-/-) mice. These results demonstrate the importance of protection that anticipates impending ROS-mediated immune attack. The ubiquity of quorum sensing suggests that it protects many bacterial species from oxidative damage.
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Affiliation(s)
- Magdalena Podkowik
- Department of Medicine, Division of Infectious Diseases, NYU Grossman School of MedicineNew YorkUnited States
- Antimicrobial-Resistant Pathogens Program, New York University School of MedicineNew YorkUnited States
| | - Andrew I Perault
- Antimicrobial-Resistant Pathogens Program, New York University School of MedicineNew YorkUnited States
- Department of Microbiology, NYU Grossman School of MedicineNew YorkUnited States
| | - Gregory Putzel
- Antimicrobial-Resistant Pathogens Program, New York University School of MedicineNew YorkUnited States
- Department of Microbiology, NYU Grossman School of MedicineNew YorkUnited States
- Microbial Computational Genomic Core Lab, NYU Grossman School of MedicineNew YorkUnited States
| | - Andrew Pountain
- Institute for Systems Genetics; NYU Grossman School of MedicineNew YorkUnited States
| | - Jisun Kim
- Department of Pathology, Immunology and Laboratory Medicine, Center for Immunity and Inflammation, Rutgers New Jersey Medical SchoolNewarkUnited States
| | - Ashley L DuMont
- Department of Medicine, Division of Infectious Diseases, NYU Grossman School of MedicineNew YorkUnited States
| | - Erin E Zwack
- Department of Microbiology, NYU Grossman School of MedicineNew YorkUnited States
| | - Robert J Ulrich
- Department of Medicine, Division of Infectious Diseases, NYU Grossman School of MedicineNew YorkUnited States
| | - Theodora K Karagounis
- Antimicrobial-Resistant Pathogens Program, New York University School of MedicineNew YorkUnited States
- Ronald O. Perelman Department of Dermatology; NYU Grossman School of MedicineNew YorkUnited States
| | - Chunyi Zhou
- Department of Medicine, Division of Infectious Diseases, NYU Grossman School of MedicineNew YorkUnited States
- Antimicrobial-Resistant Pathogens Program, New York University School of MedicineNew YorkUnited States
| | - Andreas F Haag
- School of Medicine, University of St AndrewsSt AndrewsUnited Kingdom
| | - Julia Shenderovich
- Antimicrobial-Resistant Pathogens Program, New York University School of MedicineNew YorkUnited States
- Department of Microbiology, NYU Grossman School of MedicineNew YorkUnited States
| | - Gregory A Wasserman
- Department of Surgery, Northwell Health Lenox Hill HospitalNew YorkUnited States
| | - Junbeom Kwon
- Department of Medicine, Division of Infectious Diseases, NYU Grossman School of MedicineNew YorkUnited States
| | - John Chen
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of SingaporeSingaporeSingapore
| | - Anthony R Richardson
- Department of Microbiology and Molecular Genetics, University of PittsburghPittsburghUnited States
| | - Jeffrey N Weiser
- Department of Microbiology, NYU Grossman School of MedicineNew YorkUnited States
| | - Carla R Nowosad
- Department of Pathology, NYU Grossman School of MedicineNew YorkUnited States
| | - Desmond S Lun
- Center for Computational and Integrative Biology and Department of Computer Science, Rutgers UniversityCamdenUnited States
| | - Dane Parker
- Department of Pathology, Immunology and Laboratory Medicine, Center for Immunity and Inflammation, Rutgers New Jersey Medical SchoolNewarkUnited States
| | - Alejandro Pironti
- Antimicrobial-Resistant Pathogens Program, New York University School of MedicineNew YorkUnited States
- Department of Microbiology, NYU Grossman School of MedicineNew YorkUnited States
- Microbial Computational Genomic Core Lab, NYU Grossman School of MedicineNew YorkUnited States
| | - Xilin Zhao
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen UniversityXiamenChina
| | - Karl Drlica
- Public Health Research Institute, New Jersey Medical School, Rutgers UniversityNew YprkUnited States
- Department of Microbiology, Biochemistry & Molecular Genetics, New Jersey Medical School, Rutgers UniversityNewarkUnited States
| | - Itai Yanai
- Institute for Systems Genetics; NYU Grossman School of MedicineNew YorkUnited States
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of MedicineNew YorkUnited States
| | - Victor J Torres
- Antimicrobial-Resistant Pathogens Program, New York University School of MedicineNew YorkUnited States
- Department of Microbiology, NYU Grossman School of MedicineNew YorkUnited States
| | - Bo Shopsin
- Department of Medicine, Division of Infectious Diseases, NYU Grossman School of MedicineNew YorkUnited States
- Antimicrobial-Resistant Pathogens Program, New York University School of MedicineNew YorkUnited States
- Department of Microbiology, NYU Grossman School of MedicineNew YorkUnited States
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2
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Podkowik M, Perault AI, Putzel G, Pountain A, Kim J, Dumont A, Zwack E, Ulrich RJ, Karagounis TK, Zhou C, Haag AF, Shenderovich J, Wasserman GA, Kwon J, Chen J, Richardson AR, Weiser JN, Nowosad CR, Lun DS, Parker D, Pironti A, Zhao X, Drlica K, Yanai I, Torres VJ, Shopsin B. Quorum-sensing agr system of Staphylococcus aureus primes gene expression for protection from lethal oxidative stress. bioRxiv 2024:2023.06.08.544038. [PMID: 37333372 PMCID: PMC10274873 DOI: 10.1101/2023.06.08.544038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
The agr quorum-sensing system links Staphylococcus aureus metabolism to virulence, in part by increasing bacterial survival during exposure to lethal concentrations of H2O2, a crucial host defense against S. aureus. We now report that protection by agr surprisingly extends beyond post-exponential growth to the exit from stationary phase when the agr system is no longer turned on. Thus, agr can be considered a constitutive protective factor. Deletion of agr increased both respiration and fermentation but decreased ATP levels and growth, suggesting that Δagr cells assume a hyperactive metabolic state in response to reduced metabolic efficiency. As expected from increased respiratory gene expression, reactive oxygen species (ROS) accumulated more in the agr mutant than in wild-type cells, thereby explaining elevated susceptibility of Δagr strains to lethal H2O2 doses. Increased survival of wild-type agr cells during H2O2 exposure required sodA, which detoxifies superoxide. Additionally, pretreatment of S. aureus with respiration-reducing menadione protected Δagr cells from killing by H2O2. Thus, genetic deletion and pharmacologic experiments indicate that agr helps control endogenous ROS, thereby providing resilience against exogenous ROS. The long-lived "memory" of agr-mediated protection, which is uncoupled from agr activation kinetics, increased hematogenous dissemination to certain tissues during sepsis in ROS-producing, wild-type mice but not ROS-deficient (Nox2-/-) mice. These results demonstrate the importance of protection that anticipates impending ROS-mediated immune attack. The ubiquity of quorum sensing suggests that it protects many bacterial species from oxidative damage.
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Affiliation(s)
- Magdalena Podkowik
- Department of Medicine, Division of Infectious Diseases, NYU Grossman School of Medicine, New York, NY, USA
- Antimicrobial-Resistant Pathogens Program, New York University School of Medicine, New York, NY, USA
| | - Andrew I. Perault
- Antimicrobial-Resistant Pathogens Program, New York University School of Medicine, New York, NY, USA
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY, USA
| | - Gregory Putzel
- Antimicrobial-Resistant Pathogens Program, New York University School of Medicine, New York, NY, USA
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY, USA
- Microbial Computational Genomic Core Lab, NYU Grossman School of Medicine, New York, NY, USA
| | - Andrew Pountain
- Institute for Systems Genetics; NYU Grossman School of Medicine, New York, NY, USA
| | - Jisun Kim
- Department of Pathology, Immunology and Laboratory Medicine, Center for Immunity and Inflammation, Rutgers New Jersey Medical School Cancer Center, Newark, NJ, USA
| | - Ashley Dumont
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY, USA
| | - Erin Zwack
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY, USA
| | - Robert J. Ulrich
- Department of Medicine, Division of Infectious Diseases, NYU Grossman School of Medicine, New York, NY, USA
| | - Theodora K. Karagounis
- Antimicrobial-Resistant Pathogens Program, New York University School of Medicine, New York, NY, USA
- Ronald O. Perelman Department of Dermatology; NYU Grossman School of Medicine, New York, NY, USA
| | - Chunyi Zhou
- Department of Medicine, Division of Infectious Diseases, NYU Grossman School of Medicine, New York, NY, USA
- Antimicrobial-Resistant Pathogens Program, New York University School of Medicine, New York, NY, USA
| | - Andreas F. Haag
- School of Medicine, University of St Andrews, St Andrews, UK
| | - Julia Shenderovich
- Antimicrobial-Resistant Pathogens Program, New York University School of Medicine, New York, NY, USA
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY, USA
| | | | - Junbeom Kwon
- Department of Medicine, Division of Infectious Diseases, NYU Grossman School of Medicine, New York, NY, USA
| | - John Chen
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Anthony R. Richardson
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jeffrey N. Weiser
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY, USA
| | - Carla R. Nowosad
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, USA
| | - Desmond S. Lun
- Center for Computational and Integrative Biology and Department of Computer Science, Rutgers University, Camden, NJ, USA
| | - Dane Parker
- Department of Pathology, Immunology and Laboratory Medicine, Center for Immunity and Inflammation, Rutgers New Jersey Medical School Cancer Center, Newark, NJ, USA
| | - Alejandro Pironti
- Antimicrobial-Resistant Pathogens Program, New York University School of Medicine, New York, NY, USA
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY, USA
- Microbial Computational Genomic Core Lab, NYU Grossman School of Medicine, New York, NY, USA
| | - Xilin Zhao
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen, Fujian Province, China
| | - Karl Drlica
- Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, NJ, USA
- Department of Microbiology, Biochemistry & Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, NJ, USA
| | - Itai Yanai
- Institute for Systems Genetics; NYU Grossman School of Medicine, New York, NY, USA
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, USA
| | - Victor J. Torres
- Antimicrobial-Resistant Pathogens Program, New York University School of Medicine, New York, NY, USA
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY, USA
| | - Bo Shopsin
- Department of Medicine, Division of Infectious Diseases, NYU Grossman School of Medicine, New York, NY, USA
- Antimicrobial-Resistant Pathogens Program, New York University School of Medicine, New York, NY, USA
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY, USA
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3
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Thabet MA, Penadés JR, Haag AF. The ClpX protease is essential for inactivating the CI master repressor and completing prophage induction in Staphylococcus aureus. Nat Commun 2023; 14:6599. [PMID: 37852980 PMCID: PMC10584840 DOI: 10.1038/s41467-023-42413-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 10/10/2023] [Indexed: 10/20/2023] Open
Abstract
Bacteriophages (phages) are the most abundant biological entities on Earth, exerting a significant influence on the dissemination of bacterial virulence, pathogenicity, and antimicrobial resistance. Temperate phages integrate into the bacterial chromosome in a dormant state through intricate regulatory mechanisms. These mechanisms repress lytic genes while facilitating the expression of integrase and the CI master repressor. Upon bacterial SOS response activation, the CI repressor undergoes auto-cleavage, producing two fragments with the N-terminal domain (NTD) retaining significant DNA-binding ability. The process of relieving CI NTD repression, essential for prophage induction, remains unknown. Here we show a specific interaction between the ClpX protease and CI NTD repressor fragment of phages Ф11 and 80α in Staphylococcus aureus. This interaction is necessary and sufficient for prophage activation after SOS-mediated CI auto-cleavage, defining the final stage in the prophage induction cascade. Our findings unveil unexpected roles of bacterial protease ClpX in phage biology.
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Affiliation(s)
- Mohammed A Thabet
- School of Infection & Immunity, University of Glasgow, G12 8TA, Glasgow, UK
- Department of Biology, Faculty of Science, Al-Baha University, Al-Baha city, Al Aqiq, 65779, Kingdom of Saudi Arabia
| | - José R Penadés
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, SW7 2AZ, UK
| | - Andreas F Haag
- School of Infection & Immunity, University of Glasgow, G12 8TA, Glasgow, UK.
- School of Medicine, University of St Andrews, North Haugh, St Andrews, KY16 9TF, UK.
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Haag AF, Liljeroos L, Donato P, Pozzi C, Brignoli T, Bottomley MJ, Bagnoli F, Delany I. In Vivo Gene Expression Profiling of Staphylococcus aureus during Infection Informs Design of Stemless Leukocidins LukE and -D as Detoxified Vaccine Candidates. Microbiol Spectr 2023; 11:e0257422. [PMID: 36688711 PMCID: PMC9927290 DOI: 10.1128/spectrum.02574-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 01/02/2023] [Indexed: 01/24/2023] Open
Abstract
Staphylococcus aureus is a clinically important bacterial pathogen that has become resistant to treatment with most routinely used antibiotics. Alternative strategies, such as vaccination and phage therapy, are therefore actively being investigated to prevent or combat staphylococcal infections. Vaccination requires that vaccine targets are expressed at sufficient quantities during infection so that they can be targeted by the host's immune system. While our knowledge of in vitro expression levels of putative vaccine candidates is comprehensive, crucial in vivo expression data are scarce and promising vaccine candidates during in vitro assessment often prove ineffective in preventing S. aureus infection. Here, we show how a newly developed high-throughput quantitative reverse transcription-PCR (qRT-PCR) assay monitoring the expression of 84 staphylococcal genes encoding mostly virulence factors can inform the selection and design of effective vaccine candidates against staphylococcal infections. We show that this assay can accurately quantify mRNA expression levels of these genes in several host organs relying only on very limited amounts of bacterial mRNA in each sample. We selected two highly expressed genes, lukE and lukD, encoding pore-forming leukotoxins, to inform the design of detoxified recombinant proteins and showed that immunization with recombinant genetically detoxified LukED antigens conferred protection against staphylococcal skin infection in mice. Consequently, knowledge of in vivo-expressed virulence determinants can be successfully deployed to identify and select promising candidates for optimized design of effective vaccine antigens against S. aureus. Notably, this approach should be broadly applicable to numerous other pathogens. IMPORTANCE Vaccination is an attractive strategy for preventing bacterial infections in an age of increased antimicrobial resistance. However, vaccine development frequently suffers significant setbacks when candidate antigens that show promising results in in vitro experimentation fail to protect from disease. An alluring strategy is to focus resources on developing bacterial virulence factors that are expressed during disease establishment or maintenance and are critical for bacterial in-host survival as vaccine targets. While expression profiles of many virulence factors have been characterized in detail in vitro, our knowledge of their in vivo expression profiles is still scarce. Here, using a high-throughput qRT-PCR approach, we identified two highly expressed leukotoxins in a murine infection model and showed that genetically detoxified derivatives of these elicited a protective immune response in a murine skin infection model. Therefore, in vivo gene expression can inform the selection of promising candidates for the design of effective vaccine antigens.
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Affiliation(s)
- Andreas F. Haag
- GSK, Siena, Italy
- School of Medicine, University of St. Andrews, St. Andrews, United Kingdom
| | | | | | | | - Tarcisio Brignoli
- GSK, Siena, Italy
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
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5
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Borghi S, Antunes A, Haag AF, Spinsanti M, Brignoli T, Ndoni E, Scarlato V, Delany I. Multilayer Regulation of Neisseria meningitidis NHBA at Physiologically Relevant Temperatures. Microorganisms 2022; 10:microorganisms10040834. [PMID: 35456883 PMCID: PMC9031163 DOI: 10.3390/microorganisms10040834] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 04/03/2022] [Accepted: 04/13/2022] [Indexed: 11/16/2022] Open
Abstract
Neisseria meningitidis colonizes the nasopharynx of humans, and pathogenic strains can disseminate into the bloodstream, causing septicemia and meningitis. NHBA is a surface-exposed lipoprotein expressed by all N. meningitidis strains in different isoforms. Diverse roles have been reported for NHBA in heparin-mediated serum resistance, biofilm formation, and adherence to host tissues. We determined that temperature controls the expression of NHBA in all strains tested, with increased levels at 30−32 °C compared to 37 °C. Higher NHBA expression at lower temperatures was measurable both at mRNA and protein levels, resulting in higher surface exposure. Detailed molecular analysis indicated that multiple molecular mechanisms are responsible for the thermoregulated NHBA expression. The comparison of mRNA steady-state levels and half-lives at 30 °C and 37 °C demonstrated an increased mRNA stability/translatability at lower temperatures. Protein stability was also impacted, resulting in higher NHBA stability at lower temperatures. Ultimately, increased NHBA expression resulted in higher susceptibility to complement-mediated killing. We propose that NHBA regulation in response to temperature downshift might be physiologically relevant during transmission and the initial step(s) of interaction within the host nasopharynx. Together these data describe the importance of NHBA both as a virulence factor and as a vaccine antigen during neisserial colonization and invasion.
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Affiliation(s)
- Sara Borghi
- Immune Monitoring Laboratory, NYU Langone Health, 550 First Avenue, New York, NY 10016, USA;
- Department of Pathology, NYU Grossman School of Medicine, 550 First Avenue, New York, NY 10016, USA
- GlaxoSmithKline (GSK) Vaccines, 53100 Siena, Italy;
| | - Ana Antunes
- MabDesign, 69007 Lyon, France;
- GlaxoSmithKline (GSK) Vaccines, 53100 Siena, Italy;
| | - Andreas F. Haag
- School of Medicine, University of St Andrews, North-Haugh, St Andrews KY16 9TF, UK;
- Institute of Infection, Immunity and Inflammation, University of Glasgow, 120 University Place, Glasgow G12 8TA, UK
- GlaxoSmithKline (GSK) Vaccines, 53100 Siena, Italy;
| | | | - Tarcisio Brignoli
- School of Cellular and Molecular Medicine, University of Bristol, Bristol BS8 1TH, UK;
- GlaxoSmithKline (GSK) Vaccines, 53100 Siena, Italy;
| | - Enea Ndoni
- Lonza Group AG, 4057 Basel, Switzerland;
- GlaxoSmithKline (GSK) Vaccines, 53100 Siena, Italy;
| | - Vincenzo Scarlato
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, 40126 Bologna, Italy;
| | - Isabel Delany
- GlaxoSmithKline (GSK) Vaccines, 53100 Siena, Italy;
- Correspondence:
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6
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Ibarra-Chávez R, Brady A, Chen J, Penadés JR, Haag AF. Phage-inducible chromosomal islands promote genetic variability by blocking phage reproduction and protecting transductants from phage lysis. PLoS Genet 2022; 18:e1010146. [PMID: 35344558 PMCID: PMC8989297 DOI: 10.1371/journal.pgen.1010146] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 04/07/2022] [Accepted: 03/14/2022] [Indexed: 11/18/2022] Open
Abstract
Phage-inducible chromosomal islands (PICIs) are a widespread family of highly mobile genetic elements that disseminate virulence and toxin genes among bacterial populations. Since their life cycle involves induction by helper phages, they are important players in phage evolution and ecology. PICIs can interfere with the lifecycle of their helper phages at different stages resulting frequently in reduced phage production after infection of a PICI-containing strain. Since phage defense systems have been recently shown to be beneficial for the acquisition of exogenous DNA via horizontal gene transfer, we hypothesized that PICIs could provide a similar benefit to their hosts and tested the impact of PICIs in recipient strains on host cell viability, phage propagation and transfer of genetic material. Here we report an important role for PICIs in bacterial evolution by promoting the survival of phage-mediated transductants of chromosomal or plasmid DNA. The presence of PICIs generates favorable conditions for population diversification and the inheritance of genetic material being transferred, such as antibiotic resistance and virulence genes. Our results show that by interfering with phage reproduction, PICIs can protect the bacterial population from phage attack, increasing the overall survival of the bacterial population as well as the transduced cells. Moreover, our results also demonstrate that PICIs reduce the frequency of lysogenization after temperate phage infection, creating a more genetically diverse bacterial population with increased bet-hedging opportunities to adapt to new niches. In summary, our results identify a new role for the PICIs and highlight them as important drivers of bacterial evolution.
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Affiliation(s)
- Rodrigo Ibarra-Chávez
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
- Department of Biology, Section of Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Aisling Brady
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, United Kingdom
| | - John Chen
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - José R. Penadés
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, United Kingdom
- Universidad CEU Cardenal Herrera, Moncada, Spain
- * E-mail: (JRP); (AFH)
| | - Andreas F. Haag
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
- School of Medicine, University of St Andrews, North Haugh, St Andrews, United Kingdom
- * E-mail: (JRP); (AFH)
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7
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Humphrey S, Fillol-Salom A, Quiles-Puchalt N, Ibarra-Chávez R, Haag AF, Chen J, Penadés JR. Bacterial chromosomal mobility via lateral transduction exceeds that of classical mobile genetic elements. Nat Commun 2021; 12:6509. [PMID: 34750368 PMCID: PMC8575950 DOI: 10.1038/s41467-021-26004-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 09/03/2021] [Indexed: 12/02/2022] Open
Abstract
It is commonly assumed that the horizontal transfer of most bacterial chromosomal genes is limited, in contrast to the frequent transfer observed for typical mobile genetic elements. However, this view has been recently challenged by the discovery of lateral transduction in Staphylococcus aureus, where temperate phages can drive the transfer of large chromosomal regions at extremely high frequencies. Here, we analyse previously published as well as new datasets to compare horizontal gene transfer rates mediated by different mechanisms in S. aureus and Salmonella enterica. We find that the horizontal transfer of core chromosomal genes via lateral transduction can be more efficient than the transfer of classical mobile genetic elements via conjugation or generalized transduction. These results raise questions about our definition of mobile genetic elements, and the potential roles played by lateral transduction in bacterial evolution.
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Affiliation(s)
- Suzanne Humphrey
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, G12 8TA, UK
| | - Alfred Fillol-Salom
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, G12 8TA, UK
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, SW7 2AZ, UK
| | - Nuria Quiles-Puchalt
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, G12 8TA, UK
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, SW7 2AZ, UK
| | - Rodrigo Ibarra-Chávez
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, G12 8TA, UK
- Department of Biology, Section of Microbiology, University of Copenhagen, Universitetsparken 15, Bldg. 1, DK2100, Copenhagen, Denmark
| | - Andreas F Haag
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, G12 8TA, UK
| | - John Chen
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, 5 Science Drive 2, Singapore, Singapore
| | - José R Penadés
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, G12 8TA, UK.
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, SW7 2AZ, UK.
- Departamento de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad CEU Cardenal Herrera, Valencia, 46113, Spain.
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8
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Rapun-Araiz B, Haag AF, Solano C, Lasa I. The impact of two-component sensorial network in staphylococcal speciation. Curr Opin Microbiol 2020; 55:40-47. [PMID: 32199334 PMCID: PMC7322546 DOI: 10.1016/j.mib.2020.02.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 01/31/2020] [Accepted: 02/03/2020] [Indexed: 01/26/2023]
Abstract
Bacteria use two-component systems (TCSs) to sense and respond to their environments. Free-living bacteria usually contain dozens of TCSs, each of them responsible for sensing and responding to a different range of signals. Differences in the content of two-component systems are related with the capacity of the bacteria to colonize different niches or improve the efficiency to grow under the conditions of the existing niche. This review highlights differences in the TCS content between Staphylococcus aureus and Staphylococcus saprophyticus as a case study to exemplify how the ability to sense and respond to the environment is relevant for bacterial capacity to colonize and survive in/on different body surfaces.
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Affiliation(s)
- Beatriz Rapun-Araiz
- Laboratory of Microbial Pathogenesis, Navarrabiomed, Complejo Hospitalario de Navarra (CHN)-Universidad Pública de Navarra (UPNA), IDISNA, Pamplona, 31008, Spain
| | - Andreas F Haag
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, UK
| | - Cristina Solano
- Laboratory of Microbial Pathogenesis, Navarrabiomed, Complejo Hospitalario de Navarra (CHN)-Universidad Pública de Navarra (UPNA), IDISNA, Pamplona, 31008, Spain
| | - Iñigo Lasa
- Laboratory of Microbial Pathogenesis, Navarrabiomed, Complejo Hospitalario de Navarra (CHN)-Universidad Pública de Navarra (UPNA), IDISNA, Pamplona, 31008, Spain.
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9
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Ibarra-Chávez R, Haag AF, Dorado-Morales P, Lasa I, Penadés JR. Rebooting Synthetic Phage-Inducible Chromosomal Islands: One Method to Forge Them All. Biodes Res 2020; 2020:5783064. [PMID: 37849900 PMCID: PMC10530653 DOI: 10.34133/2020/5783064] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 04/17/2020] [Indexed: 10/19/2023] Open
Abstract
Phage-inducible chromosomal islands (PICIs) are a widespread family of mobile genetic elements, which have an important role in bacterial pathogenesis. These elements mobilize among bacterial species at extremely high frequencies, representing an attractive tool for the delivery of synthetic genes. However, tools for their genetic manipulation are limited and timing consuming. Here, we have adapted a synthetic biology approach for rapidly editing of PICIs in Saccharomyces cerevisiae based on their ability to excise and integrate into the bacterial chromosome of their cognate host species. As proof of concept, we engineered several PICIs from Staphylococcus aureus and Escherichia coli and validated this methodology for the study of the biology of these elements by generating multiple and simultaneous mutations in different PICI genes. For biotechnological purposes, we also synthetically constructed PICIs as Trojan horses to deliver different CRISPR-Cas9 systems designed to either cure plasmids or eliminate cells carrying the targeted genes. Our results demonstrate that the strategy developed here can be employed universally to study PICIs and enable new approaches for diagnosis and treatment of bacterial diseases.
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Affiliation(s)
- Rodrigo Ibarra-Chávez
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Andreas F. Haag
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Pedro Dorado-Morales
- Laboratory of Microbial Pathogenesis, Navarrabiomed, Complejo Hospitalario de Navarra-Universidad Pública de Navarra (UPNA), Instituto de Investigación Sanitaria de Navarra (IDISNA), 31008 Pamplona, Spain
| | - Iñigo Lasa
- Laboratory of Microbial Pathogenesis, Navarrabiomed, Complejo Hospitalario de Navarra-Universidad Pública de Navarra (UPNA), Instituto de Investigación Sanitaria de Navarra (IDISNA), 31008 Pamplona, Spain
| | - José R. Penadés
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
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10
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Seib KL, Haag AF, Oriente F, Fantappiè L, Borghi S, Semchenko EA, Schulz BL, Ferlicca F, Taddei AR, Giuliani MM, Pizza M, Delany I. The meningococcal vaccine antigen GNA2091 is an analogue of YraP and plays key roles in outer membrane stability and virulence. FASEB J 2019; 33:12324-12335. [DOI: 10.1096/fj.201900669r] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Kate L. Seib
- Institute for GlycomicsGriffith UniversityGold CoastQueenslandAustralia
| | | | | | | | | | | | - Benjamin L. Schulz
- School of Chemistry and Molecular BiosciencesThe University of QueenslandBrisbaneQueenslandAustralia
| | | | - Anna Rita Taddei
- Interdepartmental Centre of Electron Microscopy (CIME)Tuscia UniversityTusciaItaly
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11
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Brignoli T, Manetti AGO, Rosini R, Haag AF, Scarlato V, Bagnoli F, Delany I. Absence of Protein A Expression Is Associated With Higher Capsule Production in Staphylococcal Isolates. Front Microbiol 2019; 10:863. [PMID: 31133995 PMCID: PMC6523524 DOI: 10.3389/fmicb.2019.00863] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 04/04/2019] [Indexed: 12/19/2022] Open
Abstract
Staphylococcus aureus is a major human pathogen, and a leading cause of soft tissue and blood stream infections. One of the causes of its success as a pathogen is the peculiar array of immune evasion factors through which the bacterium avoids host defenses, where the staphylococcal protein A (SpA) plays a major role thanks to its IgG binding activities. Moreover, SpA has recently been proposed as a promising vaccine antigen. In this study, we evaluated the expression of SpA in a collection of staphylococcal strains, about 7% of which did not express SpA (SpA- strains), despite the presence of the gene. By a comparative genomic analysis, we identified that a mutation in the spa 5′ UTR sequence affecting the RBS is responsible for the loss of SpA in a subset of SpA- strains. Using a high-throughput qRT-PCR approach on a selected panel of virulence-related genes, we identified that the SpA- phenotype is associated with lower spa transcript levels and increased expression and production of capsule as well as other changes in the transcription of several key virulence factors. Our data suggest that the SpA- phenotype has occurred in geographically distinct strains through different molecular mechanisms including both mutation, leading likely to translation alterations, and transcriptional deregulation. Furthermore, we provide evidence that SpA- strains are highly susceptible to phagocytic uptake mediated by anti-capsule antibodies. These data suggest that S. aureus may alter its virulence factor expression pattern as an adaptation to the host or environment. Vaccination strategies targeting both SpA and capsule could therefore result in broader coverage against staphylococcal isolates than SpA alone.
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Affiliation(s)
- Tarcisio Brignoli
- GSK Vaccines, Siena, Italy.,Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Bologna, Italy
| | | | | | - Andreas F Haag
- GSK Vaccines, Siena, Italy.,Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Vincenzo Scarlato
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Bologna, Italy
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12
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Neamah MM, Mir-Sanchis I, López-Sanz M, Acosta S, Baquedano I, Haag AF, Marina A, Ayora S, Penadés JR. Sak and Sak4 recombinases are required for bacteriophage replication in Staphylococcus aureus. Nucleic Acids Res 2017; 45:6507-6519. [PMID: 28475766 PMCID: PMC5499656 DOI: 10.1093/nar/gkx308] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2016] [Accepted: 05/03/2017] [Indexed: 11/16/2022] Open
Abstract
DNA-single strand annealing proteins (SSAPs) are recombinases frequently encoded in the genome of many bacteriophages. As SSAPs can promote homologous recombination among DNA substrates with an important degree of divergence, these enzymes are involved both in DNA repair and in the generation of phage mosaicisms. Here, analysing Sak and Sak4 as representatives of two different families of SSAPs present in phages infecting the clinically relevant bacterium Staphylococcus aureus, we demonstrate for the first time that these enzymes are absolutely required for phage reproduction. Deletion of the genes encoding these enzymes significantly reduced phage replication and the generation of infectious particles. Complementation studies revealed that these enzymes are required both in the donor (after prophage induction) and in the recipient strain (for infection). Moreover, our results indicated that to perform their function SSAPs require the activity of their cognate single strand binding (Ssb) proteins. Mutational studies demonstrated that the Ssb proteins are also required for phage replication, both in the donor and recipient strain. In summary, our results expand the functions attributed to the Sak and Sak4 proteins, and demonstrate that both SSAPs and Ssb proteins are essential for the life cycle of temperate staphylococcal phages.
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Affiliation(s)
- Maan M Neamah
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8TA, UK.,Department of Microbiology, Faculty of Veterinary Medicine, University of Kufa, Kufa, Iraq
| | - Ignacio Mir-Sanchis
- Departamento de Ciencias Biomédicas, Universidad CEU Cardenal Herrera, 46113 Moncada, Valencia, Spain
| | - María López-Sanz
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, 28049 Madrid, Spain
| | - Sonia Acosta
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, 28049 Madrid, Spain
| | - Ignacio Baquedano
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, 28049 Madrid, Spain
| | - Andreas F Haag
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8TA, UK
| | - Alberto Marina
- Instituto de Biomedicina de Valencia (IBV-CSIC) and CIBER de Enfermedades Raras (CIBERER), 46010 Valencia, Spain
| | - Silvia Ayora
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, 28049 Madrid, Spain
| | - José R Penadés
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8TA, UK
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13
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Scietti L, Sampieri K, Pinzuti I, Bartolini E, Benucci B, Liguori A, Haag AF, Lo Surdo P, Pansegrau W, Nardi-Dei V, Santini L, Arora S, Leber X, Rindi S, Savino S, Costantino P, Maione D, Merola M, Speziale P, Bottomley MJ, Bagnoli F, Masignani V, Pizza M, Scharenberg M, Schlaeppi JM, Nissum M, Liberatori S. Exploring host-pathogen interactions through genome wide protein microarray analysis. Sci Rep 2016; 6:27996. [PMID: 27302108 PMCID: PMC4908583 DOI: 10.1038/srep27996] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 05/23/2016] [Indexed: 12/17/2022] Open
Abstract
During bacterial pathogenesis extensive contacts between the human and the bacterial extracellular proteomes take place. The identification of novel host-pathogen interactions by standard methods using a case-by-case approach is laborious and time consuming. To overcome this limitation, we took advantage of large libraries of human and bacterial recombinant proteins. We applied a large-scale protein microarray-based screening on two important human pathogens using two different approaches: (I) 75 human extracellular proteins were tested on 159 spotted Staphylococcus aureus recombinant proteins and (II) Neisseria meningitidis adhesin (NadA), an important vaccine component against serogroup B meningococcus, was screened against ≈2300 spotted human recombinant proteins. The approach presented here allowed the identification of the interaction between the S. aureus immune evasion protein FLIPr (formyl-peptide receptor like-1 inhibitory protein) and the human complement component C1q, key players of the offense-defense fighting; and of the interaction between meningococcal NadA and human LOX-1 (low-density oxidized lipoprotein receptor), an endothelial receptor. The novel interactions between bacterial and human extracellular proteins here presented might provide a better understanding of the molecular events underlying S. aureus and N. meningitidis pathogenesis.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Seguinde Arora
- Novartis Institutes for Biomedical Research, Novartis Campus, 4056 Basel, Switzerland
| | - Xavier Leber
- Novartis Institutes for Biomedical Research, Novartis Campus, 4056 Basel, Switzerland
| | - Simonetta Rindi
- Department of Molecular Medicine, Unit of Biochemistry, Viale Taramelli 3/b, 27100 Pavia, Italy
| | | | | | | | - Marcello Merola
- GSK Vaccines, Via Fiorentina 1, 53100 Siena, Italy.,University of Naples "Federico II", Department of Biology, via Cinthia 4, 80126 Naples, Italy
| | - Pietro Speziale
- Department of Molecular Medicine, Unit of Biochemistry, Viale Taramelli 3/b, 27100 Pavia, Italy
| | | | | | | | | | - Meike Scharenberg
- Novartis Institutes for Biomedical Research, Novartis Campus, 4056 Basel, Switzerland
| | - Jean-Marc Schlaeppi
- Novartis Institutes for Biomedical Research, Novartis Campus, 4056 Basel, Switzerland
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14
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Liguori A, Malito E, Lo Surdo P, Fagnocchi L, Cantini F, Haag AF, Brier S, Pizza M, Delany I, Bottomley MJ. Molecular Basis of Ligand-Dependent Regulation of NadR, the Transcriptional Repressor of Meningococcal Virulence Factor NadA. PLoS Pathog 2016; 12:e1005557. [PMID: 27105075 PMCID: PMC4841544 DOI: 10.1371/journal.ppat.1005557] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Accepted: 03/17/2016] [Indexed: 11/18/2022] Open
Abstract
Neisseria adhesin A (NadA) is present on the meningococcal surface and contributes to adhesion to and invasion of human cells. NadA is also one of three recombinant antigens in the recently-approved Bexsero vaccine, which protects against serogroup B meningococcus. The amount of NadA on the bacterial surface is of direct relevance in the constant battle of host-pathogen interactions: it influences the ability of the pathogen to engage human cell surface-exposed receptors and, conversely, the bacterial susceptibility to the antibody-mediated immune response. It is therefore important to understand the mechanisms which regulate nadA expression levels, which are predominantly controlled by the transcriptional regulator NadR (Neisseria adhesin A Regulator) both in vitro and in vivo. NadR binds the nadA promoter and represses gene transcription. In the presence of 4-hydroxyphenylacetate (4-HPA), a catabolite present in human saliva both under physiological conditions and during bacterial infection, the binding of NadR to the nadA promoter is attenuated and nadA expression is induced. NadR also mediates ligand-dependent regulation of many other meningococcal genes, for example the highly-conserved multiple adhesin family (maf) genes, which encode proteins emerging with important roles in host-pathogen interactions, immune evasion and niche adaptation. To gain insights into the regulation of NadR mediated by 4-HPA, we combined structural, biochemical, and mutagenesis studies. In particular, two new crystal structures of ligand-free and ligand-bound NadR revealed (i) the molecular basis of ‘conformational selection’ by which a single molecule of 4-HPA binds and stabilizes dimeric NadR in a conformation unsuitable for DNA-binding, (ii) molecular explanations for the binding specificities of different hydroxyphenylacetate ligands, including 3Cl,4-HPA which is produced during inflammation, (iii) the presence of a leucine residue essential for dimerization and conserved in many MarR family proteins, and (iv) four residues (His7, Ser9, Asn11 and Phe25), which are involved in binding 4-HPA, and were confirmed in vitro to have key roles in the regulatory mechanism in bacteria. Overall, this study deepens our molecular understanding of the sophisticated regulatory mechanisms of the expression of nadA and other genes governed by NadR, dependent on interactions with niche-specific signal molecules that may play important roles during meningococcal pathogenesis. Serogroup B meningococcus (MenB) causes fatal sepsis and invasive meningococcal disease, particularly in young children and adolescents, as highlighted by recent MenB outbreaks in universities of the United States and Canada. The Bexsero vaccine protects against MenB and has recently been approved in > 35 countries worldwide. Neisseria adhesin A (NadA) present on the meningococcal surface can mediate binding to human cells and is one of the three MenB vaccine protein antigens. The amount of NadA exposed on the meningococcal surface also influences the antibody-mediated serum bactericidal response measured in vitro. A deep understanding of nadA expression is therefore important, otherwise the contribution of NadA to vaccine-induced protection against meningococcal meningitis may be underestimated. The abundance of surface-exposed NadA is regulated by the ligand-responsive transcriptional repressor NadR. Here, we present functional, biochemical and high-resolution structural data on NadR. Our studies provide detailed insights into how small molecule ligands, such as hydroxyphenylacetate derivatives, found in relevant host niches, modulate the structure and activity of NadR, by ‘conformational selection’ of inactive forms. These findings shed light on the regulation of NadR, a key MarR-family virulence factor of this important human pathogen.
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Affiliation(s)
| | | | | | - Luca Fagnocchi
- Istituto Nazionale di Genetica Molecolare “Romeo ed Enrica Invernizzi”, Milan, Italy
| | - Francesca Cantini
- CERM Magnetic Resonance Centre, University of Florence, Florence, Italy
| | - Andreas F. Haag
- Institute of Infection, Immunity & Inflammation, University of Glasgow, Glasgow, United Kingdom
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15
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Haag AF, Arnold MFF, Myka KK, Kerscher B, Dall'Angelo S, Zanda M, Mergaert P, Ferguson GP. Molecular insights into bacteroid development duringRhizobium–legume symbiosis. FEMS Microbiol Rev 2013; 37:364-83. [DOI: 10.1111/1574-6976.12003] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Revised: 09/12/2012] [Accepted: 09/14/2012] [Indexed: 01/09/2023] Open
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16
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Haag AF, Arnold MFF, Myka KK, Kerscher B, Dall'Angelo S, Zanda M, Mergaert P, Ferguson GP. Molecular insights into bacteroid development duringRhizobium-legume symbiosis. FEMS Microbiol Rev 2012. [DOI: 10.1111/1574-6976.2012.12003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Affiliation(s)
- Andreas F. Haag
- School of Medicine & Dentistry, Institute of Medical Sciences, University of Aberdeen; Aberdeen; UK
| | - Markus F. F. Arnold
- School of Medicine & Dentistry, Institute of Medical Sciences, University of Aberdeen; Aberdeen; UK
| | - Kamila K. Myka
- School of Medicine & Dentistry, Institute of Medical Sciences, University of Aberdeen; Aberdeen; UK
| | - Bernhard Kerscher
- School of Medicine & Dentistry, Institute of Medical Sciences, University of Aberdeen; Aberdeen; UK
| | - Sergio Dall'Angelo
- School of Medical Sciences, Institute of Medical Sciences, University of Aberdeen; Aberdeen; UK
| | | | - Peter Mergaert
- Institut des Sciences du Végétal, Centre National de la Recherche Scientifique; Gif-sur-Yvette Cedex; France
| | - Gail P. Ferguson
- School of Medicine & Dentistry, Institute of Medical Sciences, University of Aberdeen; Aberdeen; UK
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17
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Haag AF, Kerscher B, Dall'Angelo S, Sani M, Longhi R, Baloban M, Wilson HM, Mergaert P, Zanda M, Ferguson GP. Role of cysteine residues and disulfide bonds in the activity of a legume root nodule-specific, cysteine-rich peptide. J Biol Chem 2012; 287:10791-8. [PMID: 22351783 DOI: 10.1074/jbc.m111.311316] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The root nodules of certain legumes including Medicago truncatula produce >300 different nodule-specific cysteine-rich (NCR) peptides. Medicago NCR antimicrobial peptides (AMPs) mediate the differentiation of the bacterium, Sinorhizobium meliloti into a nitrogen-fixing bacteroid within the legume root nodules. In vitro, NCR AMPs such as NCR247 induced bacteroid features and exhibited antimicrobial activity against S. meliloti. The bacterial BacA protein is critical to prevent S. meliloti from being hypersensitive toward NCR AMPs. NCR AMPs are cationic and have conserved cysteine residues, which form disulfide (S-S) bridges. However, the natural configuration of NCR AMP S-S bridges and the role of these in the activity of the peptide are unknown. In this study, we found that either cysteine replacements or S-S bond modifications influenced the activity of NCR247 against S. meliloti. Specifically, either substitution of cysteines for serines, changing the S-S bridges from cysteines 1-2, 3-4 to 1-3, 2-4 or oxidation of NCR247 lowered its activity against S. meliloti. We also determined that BacA specifically protected S. meliloti against oxidized NCR247. Due to the large number of different NCRs synthesized by legume root nodules and the importance of bacterial BacA proteins for prolonged host infections, these findings have important implications for analyzing the function of these novel peptides and the protective role of BacA in the bacterial response toward these peptides.
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Affiliation(s)
- Andreas F Haag
- School of Medicine and Dentistry, Institute of Medical Sciences, University of Aberdeen, Aberdeen AB25 2ZD, United Kingdom.
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18
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Haag AF, Baloban M, Sani M, Kerscher B, Pierre O, Farkas A, Longhi R, Boncompagni E, Hérouart D, Dall’Angelo S, Kondorosi E, Zanda M, Mergaert P, Ferguson GP. Protection of Sinorhizobium against host cysteine-rich antimicrobial peptides is critical for symbiosis. PLoS Biol 2011; 9:e1001169. [PMID: 21990963 PMCID: PMC3186793 DOI: 10.1371/journal.pbio.1001169] [Citation(s) in RCA: 136] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2011] [Accepted: 08/22/2011] [Indexed: 01/01/2023] Open
Abstract
A bacterial membrane protein, BacA, protects Sinorhizobium meliloti against the antimicrobial activity of host peptides, enabling the peptides to induce bacterial persistence rather than bacterial death. Sinorhizobium meliloti differentiates into persisting, nitrogen-fixing bacteroids within root nodules of the legume Medicago truncatula. Nodule-specific cysteine-rich antimicrobial peptides (NCR AMPs) and the bacterial BacA protein are essential for bacteroid development. However, the bacterial factors central to the NCR AMP response and the in planta role of BacA are unknown. We investigated the hypothesis that BacA is critical for the bacterial response towards NCR AMPs. We found that BacA was not essential for NCR AMPs to induce features of S. meliloti bacteroids in vitro. Instead, BacA was critical to reduce the amount of NCR AMP-induced membrane permeabilization and bacterial killing in vitro. Within M. truncatula, both wild-type and BacA-deficient mutant bacteria were challenged with NCR AMPs, but this resulted in persistence of the wild-type bacteria and rapid cell death of the mutant bacteria. In contrast, BacA was dispensable for bacterial survival in an M. truncatula dnf1 mutant defective in NCR AMP transport to the bacterial compartment. Therefore, BacA is critical for the legume symbiosis by protecting S. meliloti against the bactericidal effects of NCR AMPs. Host AMPs are ubiquitous in nature and BacA proteins are essential for other chronic host infections by symbiotic and pathogenic bacteria. Hence, our findings suggest that BacA-mediated protection of bacteria against host AMPs is a critical stage in the establishment of different prolonged host infections. Certain bacterial species have the unique capacity to enter into eukaryotic host cells and establish prolonged infections, which can be beneficial (e.g. bacterial-legume symbiosis) or detrimental (e.g. chronic disease) for the host. However, the mechanisms by which bacteria persist in host cells are poorly understood. Legume peptides and the bacterial BacA membrane protein play essential roles in enabling bacteria to establish prolonged legume infections. However, the biological function of BacA in persistent legume infections has eluded scientists for nearly two decades. In this article, we investigated a potential relationship between legume peptides and BacA in the establishment of prolonged bacterial-legume infections. We found that BacA was critical to protect bacteria against the antimicrobial action of legume peptides, thereby allowing the peptides to induce bacterial persistence within the legume rather than rapid bacterial death. Mammalian hosts also produce peptides in response to invading microorganisms and BacA proteins are critical for medically important bacterial pathogens such as Mycobacterium tuberculosis to form prolonged mammalian infections. Therefore, our results suggest that BacA-mediated protection against host peptides might be a conserved mechanism used by both symbiotic and pathogenic bacterial species to establish long-term host infections.
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Affiliation(s)
- Andreas F. Haag
- School of Medicine & Dentistry, Institute of Medical Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Mikhail Baloban
- Institut des Sciences du Végétal, Centre National de la Recherche Scientifique, Gif-sur-Yvette, France
| | - Monica Sani
- Consiglio Nazionale delle Ricerche–Istituto di Chimica del Riconoscimento Molecolare C.N.R.-I.C.R.M., Milano, Italy
- KemoTech s.r.l., Pula, Italy
| | - Bernhard Kerscher
- School of Medicine & Dentistry, Institute of Medical Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Olivier Pierre
- Interactions Biotiques et Santé Végétale, Institut National de la Recherche Agronomique, Centre National de la Recherche Scientifique, Université de Nice–Sophia Antipolis, Sophia-Antipolis, France
| | - Attila Farkas
- Institute for Plant Genomics, Human Biotechnology and Bioenergy, Bay Zoltan Foundation for Applied Research, Szeged, Hungary
| | - Renato Longhi
- Consiglio Nazionale delle Ricerche–Istituto di Chimica del Riconoscimento Molecolare C.N.R.-I.C.R.M., Milano, Italy
| | - Eric Boncompagni
- Interactions Biotiques et Santé Végétale, Institut National de la Recherche Agronomique, Centre National de la Recherche Scientifique, Université de Nice–Sophia Antipolis, Sophia-Antipolis, France
| | - Didier Hérouart
- Interactions Biotiques et Santé Végétale, Institut National de la Recherche Agronomique, Centre National de la Recherche Scientifique, Université de Nice–Sophia Antipolis, Sophia-Antipolis, France
| | - Sergio Dall’Angelo
- School of Medical Sciences, Institute of Medical Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Eva Kondorosi
- Institut des Sciences du Végétal, Centre National de la Recherche Scientifique, Gif-sur-Yvette, France
- Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - Matteo Zanda
- Consiglio Nazionale delle Ricerche–Istituto di Chimica del Riconoscimento Molecolare C.N.R.-I.C.R.M., Milano, Italy
- School of Medical Sciences, Institute of Medical Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Peter Mergaert
- Institut des Sciences du Végétal, Centre National de la Recherche Scientifique, Gif-sur-Yvette, France
- * E-mail: (PM); (GPF)
| | - Gail P. Ferguson
- School of Medicine & Dentistry, Institute of Medical Sciences, University of Aberdeen, Aberdeen, United Kingdom
- * E-mail: (PM); (GPF)
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19
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Haag AF, Wehmeier S, Muszyński A, Kerscher B, Fletcher V, Berry SH, Hold GL, Carlson RW, Ferguson GP. Biochemical characterization of Sinorhizobium meliloti mutants reveals gene products involved in the biosynthesis of the unusual lipid A very long-chain fatty acid. J Biol Chem 2011; 286:17455-66. [PMID: 21454518 PMCID: PMC3093819 DOI: 10.1074/jbc.m111.236356] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2011] [Revised: 03/25/2011] [Indexed: 11/06/2022] Open
Abstract
Sinorhizobium meliloti forms a symbiosis with the legume alfalfa, whereby it differentiates into a nitrogen-fixing bacteroid. The lipid A species of S. meliloti are modified with very long-chain fatty acids (VLCFAs), which play a central role in bacteroid development. A six-gene cluster was hypothesized to be essential for the biosynthesis of VLCFA-modified lipid A. Previously, two cluster gene products, AcpXL and LpxXL, were found to be essential for S. meliloti lipid A VLCFA biosynthesis. In this paper, we show that the remaining four cluster genes are all involved in lipid A VLCFA biosynthesis. Therefore, we have identified novel gene products involved in the biosynthesis of these unusual lipid modifications. By physiological characterization of the cluster mutant strains, we demonstrate the importance of this gene cluster in the legume symbiosis and for growth in the absence of salt. Bacterial LPS species modified with VLCFAs are substantially less immunogenic than Escherichia coli LPS species, which lack VLCFAs. However, we show that the VLCFA modifications do not suppress the immunogenicity of S. meliloti LPS or affect the ability of S. meliloti to induce fluorescent plant defense molecules within the legume. Because VLCFA-modified lipids are produced by other rhizobia and mammalian pathogens, these findings will also be important in understanding the function and biosynthesis of these unusual fatty acids in diverse bacterial species.
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Affiliation(s)
- Andreas F. Haag
- From the School of Medicine and Dentistry, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, United Kingdom and
| | - Silvia Wehmeier
- From the School of Medicine and Dentistry, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, United Kingdom and
| | - Artur Muszyński
- the Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602
| | | | - Vivien Fletcher
- From the School of Medicine and Dentistry, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, United Kingdom and
| | - Susan H. Berry
- From the School of Medicine and Dentistry, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, United Kingdom and
| | - Georgina L. Hold
- From the School of Medicine and Dentistry, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, United Kingdom and
| | - Russell W. Carlson
- the Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602
| | - Gail P. Ferguson
- From the School of Medicine and Dentistry, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, United Kingdom and
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20
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Karunakaran R, Haag AF, East AK, Ramachandran VK, Prell J, James EK, Scocchi M, Ferguson GP, Poole PS. BacA is essential for bacteroid development in nodules of galegoid, but not phaseoloid, legumes. J Bacteriol 2010; 192:2920-8. [PMID: 20363949 PMCID: PMC2876491 DOI: 10.1128/jb.00020-10] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2010] [Accepted: 03/22/2010] [Indexed: 01/01/2023] Open
Abstract
BacA is an integral membrane protein, the mutation of which leads to increased resistance to the antimicrobial peptides bleomycin and Bac7(1-35) and a greater sensitivity to SDS and vancomycin in Rhizobium leguminosarum bv. viciae, R. leguminosarum bv. phaseoli, and Rhizobium etli. The growth of Rhizobium strains on dicarboxylates as a sole carbon source was impaired in bacA mutants but was overcome by elevating the calcium level. While bacA mutants elicited indeterminate nodule formation on peas, which belong to the galegoid tribe of legumes, bacteria lysed after release from infection threads and mature bacteroids were not formed. Microarray analysis revealed almost no change in a bacA mutant of R. leguminosarum bv. viciae in free-living culture. In contrast, 45 genes were more-than 3-fold upregulated in a bacA mutant isolated from pea nodules. Almost half of these genes code for cell membrane components, suggesting that BacA is crucial to alterations that occur in the cell envelope during bacteroid development. In stark contrast, bacA mutants of R. leguminosarum bv. phaseoli and R. etli elicited the formation of normal determinate nodules on their bean host, which belongs to the phaseoloid tribe of legumes. Bacteroids from these nodules were indistinguishable from the wild type in morphology and nitrogen fixation. Thus, while bacA mutants of bacteria that infect galegoid or phaseoloid legumes have similar phenotypes in free-living culture, BacA is essential only for bacteroid development in indeterminate galegoid nodules.
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Affiliation(s)
- Ramakrishnan Karunakaran
- Department of Molecular Microbiology, John Innes Centre, Colney Lane, Norwich, NR4 7UH, United Kingdom, Division of Applied Medicine, School of Medicine & Dentistry, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, United Kingdom, School of Biological Sciences, University of Reading, Reading, RG6 6AJ, United Kingdom, EPI Division, Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, United Kingdom, Department of Life Sciences, University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy
| | - Andreas F. Haag
- Department of Molecular Microbiology, John Innes Centre, Colney Lane, Norwich, NR4 7UH, United Kingdom, Division of Applied Medicine, School of Medicine & Dentistry, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, United Kingdom, School of Biological Sciences, University of Reading, Reading, RG6 6AJ, United Kingdom, EPI Division, Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, United Kingdom, Department of Life Sciences, University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy
| | - Alison K. East
- Department of Molecular Microbiology, John Innes Centre, Colney Lane, Norwich, NR4 7UH, United Kingdom, Division of Applied Medicine, School of Medicine & Dentistry, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, United Kingdom, School of Biological Sciences, University of Reading, Reading, RG6 6AJ, United Kingdom, EPI Division, Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, United Kingdom, Department of Life Sciences, University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy
| | - Vinoy K. Ramachandran
- Department of Molecular Microbiology, John Innes Centre, Colney Lane, Norwich, NR4 7UH, United Kingdom, Division of Applied Medicine, School of Medicine & Dentistry, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, United Kingdom, School of Biological Sciences, University of Reading, Reading, RG6 6AJ, United Kingdom, EPI Division, Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, United Kingdom, Department of Life Sciences, University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy
| | - Jurgen Prell
- Department of Molecular Microbiology, John Innes Centre, Colney Lane, Norwich, NR4 7UH, United Kingdom, Division of Applied Medicine, School of Medicine & Dentistry, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, United Kingdom, School of Biological Sciences, University of Reading, Reading, RG6 6AJ, United Kingdom, EPI Division, Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, United Kingdom, Department of Life Sciences, University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy
| | - Euan K. James
- Department of Molecular Microbiology, John Innes Centre, Colney Lane, Norwich, NR4 7UH, United Kingdom, Division of Applied Medicine, School of Medicine & Dentistry, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, United Kingdom, School of Biological Sciences, University of Reading, Reading, RG6 6AJ, United Kingdom, EPI Division, Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, United Kingdom, Department of Life Sciences, University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy
| | - Marco Scocchi
- Department of Molecular Microbiology, John Innes Centre, Colney Lane, Norwich, NR4 7UH, United Kingdom, Division of Applied Medicine, School of Medicine & Dentistry, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, United Kingdom, School of Biological Sciences, University of Reading, Reading, RG6 6AJ, United Kingdom, EPI Division, Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, United Kingdom, Department of Life Sciences, University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy
| | - Gail P. Ferguson
- Department of Molecular Microbiology, John Innes Centre, Colney Lane, Norwich, NR4 7UH, United Kingdom, Division of Applied Medicine, School of Medicine & Dentistry, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, United Kingdom, School of Biological Sciences, University of Reading, Reading, RG6 6AJ, United Kingdom, EPI Division, Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, United Kingdom, Department of Life Sciences, University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy
| | - Philip S. Poole
- Department of Molecular Microbiology, John Innes Centre, Colney Lane, Norwich, NR4 7UH, United Kingdom, Division of Applied Medicine, School of Medicine & Dentistry, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, United Kingdom, School of Biological Sciences, University of Reading, Reading, RG6 6AJ, United Kingdom, EPI Division, Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, United Kingdom, Department of Life Sciences, University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy
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21
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Abstract
We describe the development of a novel positive-selection vector, RHP-AmpS, that is suitable for seamless cloning and high-level protein expression in Escherichia coli. In this vector, beta-lactamase (Bla) was rendered nonfunctional by replacing the codon for the C-terminal amino acid of the beta-lactamase gene (bla) with a stop codon. Insertion of a target gene in the correct orientation (tail to tail) results in the reconstruction of the C-terminal codon (W290) of bla. This restores the function of the gene and allows the selection of positive recombinants on agar plates containing ampicillin. To allow a high level of protein expression, this selection cassette was inserted into the T7 polymerase-based expression cassette of the Novagen pET28a expression vector. To our knowledge, this is the first example of true positive-selection cloning and direct, high-level expression from a single vector.
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Affiliation(s)
- Andreas F Haag
- Department of Biotechnology & Bioinformatics, Weihenstephan University of Applied Sciences, Freising, Germany
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