1
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Brignoli T, Spinsanti M, Laabei M, Duggan S. Editorial: Bacterial surface polymers. Front Cell Infect Microbiol 2024; 14:1415799. [PMID: 38725450 PMCID: PMC11079282 DOI: 10.3389/fcimb.2024.1415799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Accepted: 04/12/2024] [Indexed: 05/12/2024] Open
Affiliation(s)
- Tarcisio Brignoli
- Department of Biosciences, Università degli Studi di Milano, Milan, Italy
| | | | - Maisem Laabei
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
| | - Seána Duggan
- The Medical Research Council Centre for Medical Mycology at the University of Exeter, Exeter, United Kingdom
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2
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Brignoli T, Ferrara S, Bertoni G. Emerging In Vitro Models for the Study of Infection and Pathogenesis of Pseudomonas aeruginosa and Testing of Antibacterial Agents. Methods Mol Biol 2024; 2721:233-239. [PMID: 37819526 DOI: 10.1007/978-1-0716-3473-8_16] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
Several animal models have been developed to study infection strategies and pathogenesis of Pseudomonas aeruginosa. Some of these models are also used in preclinical and clinical research. However, these models are increasingly showing their limitations, including in recapitulating human diseases such as cystic fibrosis, which is strongly linked to P. aeruginosa infection. The emerging field of human organoids and organs-on-a-chip is expected to provide answers to the need for in vitro modeling of human diseases. Here, we describe the first recent efforts that will hopefully provide the basis for the development of advanced in vitro models for the study of P. aeruginosa infection and pathogenesis and the testing of antibacterial agents.
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Affiliation(s)
- Tarcisio Brignoli
- Department of Biosciences, Università degli Studi di Milano, Milan, Italy
| | - Silvia Ferrara
- Department of Biosciences, Università degli Studi di Milano, Milan, Milano, Italy
| | - Giovanni Bertoni
- Department of Biosciences, Università degli Studi di Milano, Milan, Milano, Italy.
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3
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Altwiley D, Brignoli T, Duggan S, Massey RC. Corrigendum: Triclosan-resistant small-colony variants of Staphylococcus aureus produce less capsule, less phenol-soluble modulins, and are attenuated in a Galleria mellonella model of infection. Microbiology (Reading) 2023; 169. [PMID: 38010142 DOI: 10.1099/mic.0.001419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Affiliation(s)
- Dina Altwiley
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
- Department of Biological Sciences, University of Jeddah, Jeddah, Saudi Arabia
| | - Tarcisio Brignoli
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
- Dipartimento di Bioscienze, Università degli studi di Milano, Milan, Italy
| | - Seána Duggan
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
- MRC Centre for Medical Mycology, University of Exeter, Exeter, UK
| | - Ruth C Massey
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
- Schools of Microbiology and Medicine, and the APC Microbiome Ireland, UCC, Cork, Ireland
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4
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Douglas EJA, Palk N, Brignoli T, Altwiley D, Boura M, Laabei M, Recker M, Cheung GYC, Liu R, Hsieh RC, Otto M, O'Brien E, McLoughlin RM, Massey RC. Extensive remodelling of the cell wall during the development of Staphylococcus aureus bacteraemia. eLife 2023; 12:RP87026. [PMID: 37401629 PMCID: PMC10328498 DOI: 10.7554/elife.87026] [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: 07/05/2023] Open
Abstract
The bloodstream represents a hostile environment that bacteria must overcome to cause bacteraemia. To understand how the major human pathogen Staphylococcus aureus manages this we have utilised a functional genomics approach to identify a number of new loci that affect the ability of the bacteria to survive exposure to serum, the critical first step in the development of bacteraemia. The expression of one of these genes, tcaA, was found to be induced upon exposure to serum, and we show that it is involved in the elaboration of a critical virulence factor, the wall teichoic acids (WTA), within the cell envelope. The activity of the TcaA protein alters the sensitivity of the bacteria to cell wall attacking agents, including antimicrobial peptides, human defence fatty acids, and several antibiotics. This protein also affects the autolytic activity and lysostaphin sensitivity of the bacteria, suggesting that in addition to changing WTA abundance in the cell envelope, it also plays a role in peptidoglycan crosslinking. With TcaA rendering the bacteria more susceptible to serum killing, while simultaneously increasing the abundance of WTA in the cell envelope, it was unclear what effect this protein may have during infection. To explore this, we examined human data and performed murine experimental infections. Collectively, our data suggests that whilst mutations in tcaA are selected for during bacteraemia, this protein positively contributes to the virulence of S. aureus through its involvement in altering the cell wall architecture of the bacteria, a process that appears to play a key role in the development of bacteraemia.
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Affiliation(s)
- Edward JA Douglas
- School of Cellular and Molecular Medicine, University of BristolBristolUnited Kingdom
- Department of Life Sciences, University of BathBathUnited Kingdom
| | - Nathanael Palk
- School of Cellular and Molecular Medicine, University of BristolBristolUnited Kingdom
| | - Tarcisio Brignoli
- School of Cellular and Molecular Medicine, University of BristolBristolUnited Kingdom
- Department of Biosciences, Università degli Studi di MilanoMilanItaly
| | - Dina Altwiley
- School of Cellular and Molecular Medicine, University of BristolBristolUnited Kingdom
| | - Marcia Boura
- School of Cellular and Molecular Medicine, University of BristolBristolUnited Kingdom
| | - Maisem Laabei
- Department of Life Sciences, University of BathBathUnited Kingdom
| | - Mario Recker
- Institute of Tropical Medicine, University of TübingenTübingenGermany
- Centre for Ecology and Conservation, University of Exeter, Penryn CampusExeterUnited Kingdom
| | - Gordon YC Cheung
- Laboratory of Bacteriology, National Institute of Allergy and Infectious Diseases (NIAID), US National Institutes of Health (NIH)BethesdaUnited States
| | - Ryan Liu
- Laboratory of Bacteriology, National Institute of Allergy and Infectious Diseases (NIAID), US National Institutes of Health (NIH)BethesdaUnited States
| | - Roger C Hsieh
- Laboratory of Bacteriology, National Institute of Allergy and Infectious Diseases (NIAID), US National Institutes of Health (NIH)BethesdaUnited States
| | - Michael Otto
- Laboratory of Bacteriology, National Institute of Allergy and Infectious Diseases (NIAID), US National Institutes of Health (NIH)BethesdaUnited States
| | - Eoin O'Brien
- Host Pathogen Interactions Group, School of Biochemistry and Immunology, Trinity College DublinDublinIreland
| | - Rachel M McLoughlin
- Host Pathogen Interactions Group, School of Biochemistry and Immunology, Trinity College DublinDublinIreland
| | - Ruth C Massey
- School of Cellular and Molecular Medicine, University of BristolBristolUnited Kingdom
- Schools of Microbiology and Medicine, University College Cork, and APC Microbiome IrelandCorkIreland
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5
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Ferrara S, Brignoli T, Bertoni G. Little reason to call them small noncoding RNAs. Front Microbiol 2023; 14:1191166. [PMID: 37455713 PMCID: PMC10339803 DOI: 10.3389/fmicb.2023.1191166] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 06/14/2023] [Indexed: 07/18/2023] Open
Abstract
Hundreds of different species of small RNAs can populate a bacterial cell. This small transcriptome contains important information for the adaptation of cellular physiology to environmental changes. Underlying cellular networks involving small RNAs are RNA-RNA and RNA-protein interactions, which are often intertwined. In addition, small RNAs can function as mRNAs. In general, small RNAs are referred to as noncoding because very few are known to contain translated open reading frames. In this article, we intend to highlight that the number of small RNAs that fall within the set of translated RNAs is bound to increase. In addition, we aim to emphasize that the dynamics of the small transcriptome involve different functional codes, not just the genetic code. Therefore, since the role of small RNAs is always code-driven, we believe that there is little reason to continue calling them small noncoding RNAs.
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6
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Douglas EJA, Palk N, Brignoli T, Altwiley D, Boura M, Laabei M, Recker M, Cheung GYC, Liu R, Hsieh RC, Otto M, Oâ Brien E, McLoughlin RM, Massey RC. Extensive re-modelling of the cell wall during the development of Staphylococcus aureus bacteraemia. bioRxiv 2023:2023.02.23.529713. [PMID: 36865143 PMCID: PMC9980097 DOI: 10.1101/2023.02.23.529713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
The bloodstream represents a hostile environment that bacteria must overcome to cause bacteraemia. To understand how the major human pathogen Staphylococcus aureus manages this we have utilised a functional genomics approach to identify a number of new loci that affect the ability of the bacteria to survive exposure to serum, the critical first step in the development of bacteraemia. The expression of one of these genes, tcaA , was found to be induced upon exposure to serum, and we show that it is involved in the elaboration of a critical virulence factor, the wall teichoic acids (WTA), within the cell envelope. The activity of this protein alters the sensitivity of the bacteria to cell wall attacking agents, including antimicrobial peptides, human defence fatty acids, and several antibiotics. This protein also affects the autolytic activity and lysostaphin sensitivity of the bacteria, suggesting that in addition to changing WTA abundance in the cell envelope, it also plays a role in peptidoglycan crosslinking. With TcaA rendering the bacteria more susceptible to serum killing, while simultaneously increasing the abundance of WTA in the cell envelope, it was unclear what effect this protein may have during infection. To explore this, we examined human data and performed murine experimental infections. Collectively, our data suggests that whilst mutations in tcaA are selected for during bacteraemia, this protein positively contributes to the virulence of S. aureus through its involvement in altering the cell wall architecture of the bacteria, a process that appears to play a key role in the development of bacteraemia.
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7
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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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8
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Altwiley D, Brignoli T, Duggan S, Massey RC. Triclosan-resistant small-colony variants of Staphylococcus aureus produce less capsule, less phenol-soluble modulins, and are attenuated in a Galleria mellonella model of infection. Microbiology (Reading) 2023; 169:001277. [PMID: 36748621 PMCID: PMC9993119 DOI: 10.1099/mic.0.001277] [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] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
In recent work we identified genes that confer the slow-growing and antibiotic-resistant small-colony variant (SCV) form of Staphylococcus aureus, as associated with the amount of capsule the bacteria produce. In this study we isolated a triclosan-resistant SCV (tr-SCV) and demonstrated that it produces significantly less capsule, an effect that appears to be mediated at the transcriptional stage. As with other SCVs, we found that the tr-SCV produces less toxins, and when compared to both a capsule and an Agr mutant we found the tr-SCV to be significantly attenuated in an insect model of infection.
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Affiliation(s)
- Dina Altwiley
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK.,Department of Biological Sciences, University of Jeddah, Jeddah, Saudi Arabia
| | - Tarcisio Brignoli
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK.,Dipartimento di Bioscienze, Università degli studi di Milano, Milan, Italy
| | - Seána Duggan
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK.,MRC Centre for Medical Mycology, University of Exeter, Exeter, UK
| | - Ruth C Massey
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK.,Schools of Microbiology and Medicine, and the APC Microbiome Ireland, UCC, Cork, Ireland
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9
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Brignoli T, Recker M, Lee WWY, Dong T, Bhamber R, Albur M, Williams P, Dowsey AW, Massey RC. Diagnostic MALDI-TOF MS can differentiate between high and low toxic Staphylococcus aureus bacteraemia isolates as a predictor of patient outcome. Microbiology (Reading) 2022; 168. [PMID: 35997594 DOI: 10.1099/mic.0.001223] [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] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Staphylococcus aureus bacteraemia (SAB) is a major cause of blood-stream infection (BSI) in both healthcare and community settings. While the underlying comorbidities of a patient significantly contributes to their susceptibility to and outcome following SAB, recent studies show the importance of the level of cytolytic toxin production by the infecting bacterium. In this study we demonstrate that this cytotoxicity can be determined directly from the diagnostic MALDI-TOF mass spectrum generated in a routine diagnostic laboratory. With further development this information could be used to guide the management and improve the outcomes for SAB patients.
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Affiliation(s)
- Tarcisio Brignoli
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD, UK
| | - Mario Recker
- Centre for Ecology and Conservation, University of Exeter, Penryn, TR10 9FE, UK
- Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany
| | - Winnie W Y Lee
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD, UK
| | - Tim Dong
- Department of Population Health Sciences and Bristol Veterinary School, University of Bristol, Bristol, BS8 2BN, UK
| | - Ranjeet Bhamber
- Department of Population Health Sciences and Bristol Veterinary School, University of Bristol, Bristol, BS8 2BN, UK
| | | | - Philip Williams
- UK Health Security Agency, and University Hospitals Bristol & Weston NHS Trust
| | - Andrew W Dowsey
- Department of Population Health Sciences and Bristol Veterinary School, University of Bristol, Bristol, BS8 2BN, UK
| | - Ruth C Massey
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD, UK
- Schools of Microbiology and Medicine and APC Microbiome Ireland, UCC, Cork, Ireland
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10
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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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11
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Stevens EJ, Morse DJ, Bonini D, Duggan S, Brignoli T, Recker M, Lees JA, Croucher NJ, Bentley S, Wilson DJ, Earle SG, Dixon R, Nobbs A, Jenkinson H, van Opijnen T, Thibault D, Wilkinson OJ, Dillingham MS, Carlile S, McLoughlin RM, Massey RC. Targeted control of pneumolysin production by a mobile genetic element in Streptococcus pneumoniae. Microb Genom 2022; 8:000784. [PMID: 35416147 PMCID: PMC9453066 DOI: 10.1099/mgen.0.000784] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Streptococcus pneumoniae is a major human pathogen that can cause severe invasive diseases such as pneumonia, septicaemia and meningitis. Young children are at a particularly high risk, with an estimated 3-4 million cases of severe disease and between 300 000 and 500 000 deaths attributable to pneumococcal disease each year. The haemolytic toxin pneumolysin (Ply) is a primary virulence factor for this bacterium, yet despite its key role in pathogenesis, immune evasion and transmission, the regulation of Ply production is not well defined. Using a genome-wide association approach, we identified a large number of potential affectors of Ply activity, including a gene acquired horizontally on the antibiotic resistance-conferring Integrative and Conjugative Element (ICE) ICESp23FST81. This gene encodes a novel modular protein, ZomB, which has an N-terminal UvrD-like helicase domain followed by two Cas4-like domains with potent ATP-dependent nuclease activity. We found the regulatory effect of ZomB to be specific for the ply operon, potentially mediated by its high affinity for the BOX repeats encoded therein. Using a murine model of pneumococcal colonization, we further demonstrate that a ZomB mutant strain colonizes both the upper respiratory tract and lungs at higher levels when compared to the wild-type strain. While the antibiotic resistance-conferring aspects of ICESp23FST81 are often credited with contributing to the success of the S. pneumoniae lineages that acquire it, its ability to control the expression of a major virulence factor implicated in bacterial transmission is also likely to have played an important role.
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Affiliation(s)
- Emily J Stevens
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD, UK
| | - Daniel J Morse
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD, UK
| | - Dora Bonini
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD, UK
| | - Seána Duggan
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD, UK
| | - Tarcisio Brignoli
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD, UK
| | - Mario Recker
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Exeter, TR10 9FE, UK.,Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany
| | - John A Lees
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, St. Mary's Campus, Imperial College London, London, W2 1PG, UK
| | - Nicholas J Croucher
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, St. Mary's Campus, Imperial College London, London, W2 1PG, UK
| | - Stephen Bentley
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Daniel J Wilson
- Big Data Institute, Nuffield Department of Population Health, University of Oxford, Oxford, OX3 7LF, UK
| | - Sarah G Earle
- Big Data Institute, Nuffield Department of Population Health, University of Oxford, Oxford, OX3 7LF, UK
| | - Robert Dixon
- Big Data Institute, Nuffield Department of Population Health, University of Oxford, Oxford, OX3 7LF, UK
| | - Angela Nobbs
- Bristol Dental School, University of Bristol, Bristol, BS1 2LY, UK
| | - Howard Jenkinson
- Bristol Dental School, University of Bristol, Bristol, BS1 2LY, UK
| | | | - Derek Thibault
- Biology Department, Boston College, Chestnut Hill, MA, USA
| | - Oliver J Wilkinson
- DNA-Protein Interactions Unit, School of Biochemistry, University of Bristol, Bristol, BS8 1TD, UK
| | - Mark S Dillingham
- DNA-Protein Interactions Unit, School of Biochemistry, University of Bristol, Bristol, BS8 1TD, UK
| | - Simon Carlile
- Host Pathogen Interactions Group, School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, Ireland
| | - Rachel M McLoughlin
- Host Pathogen Interactions Group, School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, Ireland
| | - Ruth C Massey
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD, UK.,Schools of Microbiology and Medicine and APC Microbiome Ireland, University College Cork, Cork, Ireland
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12
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Altwiley D, Brignoli T, Edwards A, Recker M, Lee JC, Massey RC. A functional menadione biosynthesis pathway is required for capsule production by Staphylococcus aureus. Microbiology (Reading) 2021; 167. [PMID: 34825882 PMCID: PMC8743628 DOI: 10.1099/mic.0.001108] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Staphylococcus aureus is a major human pathogen that utilises a wide array of pathogenic and immune evasion strategies to cause disease. One immune evasion strategy, common to many bacterial pathogens, is the ability of S. aureus to produce a capsule that protects the bacteria from several aspects of the human immune system. To identify novel regulators of capsule production by S. aureus, we applied a genome wide association study (GWAS) to a collection of 300 bacteraemia isolates that represent the two major MRSA clones in UK and Irish hospitals: CC22 and CC30. One of the loci associated with capsule production, the menD gene, encodes an enzyme critical to the biosynthesis of menadione. Mutations in this gene that result in menadione auxotrophy induce the slow growing small-colony variant (SCV) form of S. aureus often associated with chronic infections due to their increased resistance to antibiotics and ability to survive inside phagocytes. Utilising such an SCV, we functionally verified this association between menD and capsule production. Although the clinical isolates with polymorphisms in the menD gene in our collections had no apparent growth defects, they were more resistant to gentamicin when compared to those with the wild-type menD gene. Our work suggests that menadione is involved in the production of the S. aureus capsule, and that amongst clinical isolates polymorphisms exist in the menD gene that confer the characteristic increased gentamicin resistance, but not the major growth defect associated with SCV phenotype.
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Affiliation(s)
- Dina Altwiley
- School of Cellular and Molecular Medicine, University of Bristol, BS8 1TD, UK.,University of Jeddah, Saudi Arabia
| | - Tarcisio Brignoli
- School of Cellular and Molecular Medicine, University of Bristol, BS8 1TD, UK
| | - Andrew Edwards
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, SW7 2AZ, UK
| | - Mario Recker
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, TR10 9FE, UK
| | - Jean C Lee
- Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Ruth C Massey
- School of Cellular and Molecular Medicine, University of Bristol, BS8 1TD, UK.,Schools of Microbiology and Medicine, and APC Microbiome Ireland, University College Cork, Ireland
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13
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Douglas EJA, Duggan S, Brignoli T, Massey RC. The MpsB protein contributes to both the toxicity and immune evasion capacity of Staphylococcus aureus. Microbiology (Reading) 2021; 167. [PMID: 34618666 PMCID: PMC8698210 DOI: 10.1099/mic.0.001096] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Understanding the role specific bacterial factors play in the development of severe disease in humans is critical if new approaches to tackle such infections are to be developed. In this study we focus on genes we have found to be associated with patient outcome following bacteraemia caused by the major human pathogen Staphylococcus aureus. By examining the contribution these genes make to the ability of the bacteria to survive exposure to the antibacterial factors found in serum, we identify three novel serum resistance-associated genes, mdeA, mpsB and yycH. Detailed analysis of an MpsB mutant supports its previous association with the slow growing small colony variant (SCV) phenotype of S. aureus, and we demonstrate that the effect this mutation has on membrane potential prevents the activation of the Agr quorum sensing system, and as a consequence the mutant bacteria do not produce cytolytic toxins. Given the importance of both toxin production and immune evasion for the ability of S. aureus to cause disease, we believe that these findings explain the role of the mpsB gene as a mortality-associated locus during human disease.
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Affiliation(s)
- Edward J A Douglas
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD, UK
| | - Seána Duggan
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD, UK
| | - Tarcisio Brignoli
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD, UK
| | - Ruth C Massey
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD, UK.,Schools of Microbiology and Medicine, University College Cork and APC Microbiome Ireland, Cork, Ireland
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14
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Spinsanti M, Brignoli T, Bodini M, Fontana LE, De Chiara M, Biolchi A, Muzzi A, Scarlato V, Delany I. Deconvolution of intergenic polymorphisms determining high expression of Factor H binding protein in meningococcus and their association with invasive disease. PLoS Pathog 2021; 17:e1009461. [PMID: 33770146 PMCID: PMC8026042 DOI: 10.1371/journal.ppat.1009461] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 09/30/2020] [Revised: 04/07/2021] [Accepted: 03/09/2021] [Indexed: 12/11/2022] Open
Abstract
Neisseria meningitidis is a strictly human pathogen and is the major cause of septicemia and meningitis worldwide. Factor H binding protein (fHbp) is a meningococcal surface-exposed lipoprotein that binds the human Complement factor H allowing the bacterium to evade the host innate immune response. FHbp is also a key antigen in two vaccines against N. meningitidis serogroup B. Although the fHbp gene is present in most circulating meningococcal strains, level of fHbp expression varies among isolates and has been correlated to differences in promoter sequences upstream of the gene. Here we elucidated the sequence determinants that control fHbp expression in globally circulating strains. We analyzed the upstream fHbpintergenic region (fIR) of more than 5800 strains representative of the UK circulating isolates and we identified eleven fIR sequence alleles which represent 88% of meningococcal strains. By engineering isogenic recombinant strains where fHbp expression was under the control of each of the eleven fIR alleles, we confirmed that the fIR sequence determines a specific and distinct level of expression. Moreover, we identified the molecular basis for variation in expression through polymorphisms within key regulatory regions that are known to affect fHbp expression. We experimentally established three expression groups, high–medium–low, that correlated directly with the susceptibility to killing mediated by anti-fHbp antibodies and the ability of the meningococcal strain to survive within human serum. By using this sequence classification and information about the variant, we predicted fHbp expression in the panel of UK strains and we observed that strains with higher expressing fIR alleles are more likely associated with invasive disease. Overall, our findings can contribute to understand and predict vaccine coverage mediated by fHbp as well as to shed light on the role of this virulence factor in determining an invasive phenotype. Complement plays a key role in the immunity against Neisseria meningitidis. The meningococcus uses the Factor H binding protein (fHbp), to bind a negative regulator of the alternative complement pathway, factor H, to its surface thus preventing complement deposition and lysis. The use of fHbp as an antigen in two licensed vaccines highlights its public health relevance. Therefore the levels of this antigen produced by the bacterium are pivotal on the one hand for the survival of N. meningitidis in blood and on the other hand for the susceptibility to vaccine-induced killing antibodies. Here, we identify the predominant nucleotide sequences that drive distinct levels of the fHbp antigen in circulating meningococcal strains. We cluster them into distinct groups with increasing levels and observe that strains expressing higher fHbp amounts are associated with invasive disease. Our findings show that the nucleotide sequence of the fHbp promoter can be used for the prediction of antigen levels of any given strain and consequently for both the assessment of its sensitivity to killing by fHbp antibodies and its likelihood to cause invasive disease.
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Affiliation(s)
| | - Tarcisio Brignoli
- GSK, Siena, Italy
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Bologna, Italy
| | | | | | | | | | | | - Vincenzo Scarlato
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Bologna, Italy
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15
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Gregorova M, Morse D, Brignoli T, Steventon J, Hamilton F, Albur M, Arnold D, Thomas M, Halliday A, Baum H, Rice C, Avison MB, Davidson AD, Santopaolo M, Oliver E, Goenka A, Finn A, Wooldridge L, Amulic B, Boyton RJ, Altmann DM, Butler DK, McMurray C, Stockton J, Nicholls S, Cooper C, Loman N, Cox MJ, Rivino L, Massey RC. Post-acute COVID-19 associated with evidence of bystander T-cell activation and a recurring antibiotic-resistant bacterial pneumonia. eLife 2020; 9:e63430. [PMID: 33331820 PMCID: PMC7775105 DOI: 10.7554/elife.63430] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [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: 09/24/2020] [Accepted: 12/16/2020] [Indexed: 12/24/2022] Open
Abstract
Here, we describe the case of a COVID-19 patient who developed recurring ventilator-associated pneumonia caused by Pseudomonas aeruginosa that acquired increasing levels of antimicrobial resistance (AMR) in response to treatment. Metagenomic analysis revealed the AMR genotype, while immunological analysis revealed massive and escalating levels of T-cell activation. These were both SARS-CoV-2 and P. aeruginosa specific, and bystander activated, which may have contributed to this patient's persistent symptoms and radiological changes.
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Affiliation(s)
- Michaela Gregorova
- School of Cellular and Molecular Medicine, University of BristolBristolUnited Kingdom
| | - Daniel Morse
- School of Cellular and Molecular Medicine, University of BristolBristolUnited Kingdom
| | - Tarcisio Brignoli
- School of Cellular and Molecular Medicine, University of BristolBristolUnited Kingdom
| | - Joseph Steventon
- School of Cellular and Molecular Medicine, University of BristolBristolUnited Kingdom
| | | | | | | | | | - Alice Halliday
- School of Cellular and Molecular Medicine, University of BristolBristolUnited Kingdom
| | - Holly Baum
- School of Cellular and Molecular Medicine, University of BristolBristolUnited Kingdom
| | - Christopher Rice
- School of Cellular and Molecular Medicine, University of BristolBristolUnited Kingdom
| | - Matthew B Avison
- School of Cellular and Molecular Medicine, University of BristolBristolUnited Kingdom
| | - Andrew D Davidson
- School of Cellular and Molecular Medicine, University of BristolBristolUnited Kingdom
| | - Marianna Santopaolo
- School of Cellular and Molecular Medicine, University of BristolBristolUnited Kingdom
| | - Elizabeth Oliver
- School of Cellular and Molecular Medicine, University of BristolBristolUnited Kingdom
| | - Anu Goenka
- School of Cellular and Molecular Medicine, University of BristolBristolUnited Kingdom
| | - Adam Finn
- School of Cellular and Molecular Medicine, University of BristolBristolUnited Kingdom
| | - Linda Wooldridge
- Bristol Veterinary School in the Faculty of Health SciencesBristolUnited Kingdom
| | - Borko Amulic
- School of Cellular and Molecular Medicine, University of BristolBristolUnited Kingdom
| | - Rosemary J Boyton
- Department of Infectious Disease, Imperial College LondonLondonUnited Kingdom
- Lung Division, Royal Brompton & Harefield NHS Foundation TrustLondonUnited Kingdom
| | - Daniel M Altmann
- Department of Infectious Disease, Imperial College LondonLondonUnited Kingdom
| | - David K Butler
- Department of Infectious Disease, Imperial College LondonLondonUnited Kingdom
| | - Claire McMurray
- Institute of Microbiology and Infection, University of BirminghamBirminghamUnited Kingdom
| | - Joanna Stockton
- Institute of Microbiology and Infection, University of BirminghamBirminghamUnited Kingdom
| | - Sam Nicholls
- Institute of Microbiology and Infection, University of BirminghamBirminghamUnited Kingdom
| | - Charles Cooper
- Institute of Microbiology and Infection, University of BirminghamBirminghamUnited Kingdom
| | - Nicholas Loman
- Institute of Microbiology and Infection, University of BirminghamBirminghamUnited Kingdom
| | - Michael J Cox
- Lung Division, Royal Brompton & Harefield NHS Foundation TrustLondonUnited Kingdom
| | - Laura Rivino
- School of Cellular and Molecular Medicine, University of BristolBristolUnited Kingdom
| | - Ruth C Massey
- School of Cellular and Molecular Medicine, University of BristolBristolUnited Kingdom
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16
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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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17
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Pepe S, Pinatel E, Fiore E, Puccio S, Peano C, Brignoli T, Vannini A, Danielli A, Scarlato V, Roncarati D. The Helicobacter pylori Heat-Shock Repressor HspR: Definition of Its Direct Regulon and Characterization of the Cooperative DNA-Binding Mechanism on Its Own Promoter. Front Microbiol 2018; 9:1887. [PMID: 30154784 PMCID: PMC6102357 DOI: 10.3389/fmicb.2018.01887] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [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: 12/21/2017] [Accepted: 07/27/2018] [Indexed: 12/12/2022] Open
Abstract
The ability of pathogens to perceive environmental conditions and modulate gene expression accordingly is a crucial feature for bacterial survival. In this respect, the heat-shock response, a universal cellular response, allows cells to adapt to hostile environmental conditions and to survive during stress. In the major human pathogen Helicobacter pylori the expression of chaperone-encoding operons is under control of two auto-regulated transcriptional repressors, HrcA and HspR, with the latter acting as the master regulator of the regulatory circuit. To further characterize the HspR regulon in H. pylori, we used global transcriptome analysis (RNA-sequencing) in combination with Chromatin Immunoprecipitation coupled with deep sequencing (ChIP-sequencing) of HspR genomic binding sites. Intriguingly, these analyses showed that HspR is involved in the regulation of different crucial cellular functions through a limited number of genomic binding sites. Moreover, we further characterized HspR-DNA interactions through hydroxyl-radical footprinting assays. This analysis in combination with a nucleotide sequence alignment of HspR binding sites, revealed a peculiar pattern of DNA protection and highlighted sequence conservation with the HAIR motif (an HspR-associated inverted repeat of Streptomyces spp.). Site-directed mutagenesis demonstrated that the HAIR motif is fundamental for HspR binding and that additional nucleotide determinants flanking the HAIR motif are required for complete binding of HspR to its operator sequence spanning over 70 bp of DNA. This finding is compatible with a model in which possibly a dimer of HspR recognizes the HAIR motif overlapping its promoter for binding and in turn cooperatively recruits two additional dimers on both sides of the HAIR motif.
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Affiliation(s)
- Simona Pepe
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Bologna, Italy
| | - Eva Pinatel
- Institute of Biomedical Technologies, National Research Council, Milan, Italy
| | - Elisabetta Fiore
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Bologna, Italy
| | - Simone Puccio
- Institute of Biomedical Technologies, National Research Council, Milan, Italy.,Humanitas Clinical and Research Center, Milan, Italy
| | - Clelia Peano
- Institute of Biomedical Technologies, National Research Council, Milan, Italy.,Humanitas Clinical and Research Center, Milan, Italy.,Institute of Genetic and Biomedical Research, National Research Council, Milan, Italy
| | - Tarcisio Brignoli
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Bologna, Italy
| | - Andrea Vannini
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Bologna, Italy
| | - Alberto Danielli
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Bologna, Italy
| | - Vincenzo Scarlato
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Bologna, Italy
| | - Davide Roncarati
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Bologna, Italy
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