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Sun WS, Torrens G, ter Beek J, Cava F, Berntsson RPA. Breaking barriers: pCF10 type 4 secretion system relies on a self-regulating muramidase to modulate the cell wall. mBio 2024; 15:e0048824. [PMID: 38940556 PMCID: PMC11323569 DOI: 10.1128/mbio.00488-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 05/29/2024] [Indexed: 06/29/2024] Open
Abstract
Conjugative type 4 secretion systems (T4SSs) are the main driver for the spread of antibiotic resistance genes and virulence factors in bacteria. To deliver the DNA substrate to recipient cells, it must cross the cell envelopes of both donor and recipient bacteria. In the T4SS from the enterococcal conjugative plasmid pCF10, PrgK is known to be the active cell wall degrading enzyme. It has three predicted extracellular hydrolase domains: metallo-peptidase (LytM), soluble lytic transglycosylase (SLT), and cysteine, histidine-dependent amidohydrolases/peptidases (CHAP). Here, we report the structure of the LytM domain and show that its active site is degenerate and lacks the active site metal. Furthermore, we show that only the predicted SLT domain is functional in vitro and that it unexpectedly has a muramidase instead of a lytic transglycosylase activity. While we did not observe any peptidoglycan hydrolytic activity for the LytM or CHAP domain, we found that these domains downregulated the SLT muramidase activity. The CHAP domain was also found to be involved in PrgK dimer formation. Furthermore, we show that PrgK interacts with PrgL, which likely targets PrgK to the rest of the T4SS. The presented data provides important information for understanding the function of Gram-positive T4SSs.IMPORTANCEAntibiotic resistance is a large threat to human health and is getting more prevalent. One of the major contributors to the spread of antibiotic resistance among different bacteria is type 4 secretion systems (T4SS). However, mainly T4SSs from Gram-negative bacteria have been studied in detail. T4SSs from Gram-positive bacteria, which stand for more than half of all hospital-acquired infections, are much less understood. The significance of our research is in identifying the function and regulation of a cell wall hydrolase, a key component of the pCF10 T4SS from Enterococcus faecalis. This system is one of the best-studied Gram-positive T4SSs, and this added knowledge aids in our understanding of horizontal gene transfer in E. faecalis as well as other medically relevant Gram-positive bacteria.
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Affiliation(s)
- Wei-Sheng Sun
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
- Wallenberg Centre for Molecular Medicine and Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden
| | - Gabriel Torrens
- Department of Molecular Biology and Laboratory for Molecular Infection Medicine Sweden, Umeå Centre for Microbial Research, SciLifeLab, Umeå University, Umeå, Sweden
| | - Josy ter Beek
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
- Wallenberg Centre for Molecular Medicine and Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden
| | - Felipe Cava
- Department of Molecular Biology and Laboratory for Molecular Infection Medicine Sweden, Umeå Centre for Microbial Research, SciLifeLab, Umeå University, Umeå, Sweden
| | - Ronnie P.-A. Berntsson
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
- Wallenberg Centre for Molecular Medicine and Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden
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2
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Costa TRD, Patkowski JB, Macé K, Christie PJ, Waksman G. Structural and functional diversity of type IV secretion systems. Nat Rev Microbiol 2024; 22:170-185. [PMID: 37814112 PMCID: PMC11290344 DOI: 10.1038/s41579-023-00974-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/13/2023] [Indexed: 10/11/2023]
Abstract
Considerable progress has been made in recent years in the structural and molecular biology of type IV secretion systems in Gram-negative bacteria. The latest advances have substantially improved our understanding of the mechanisms underlying the recruitment and delivery of DNA and protein substrates to the extracellular environment or target cells. In this Review, we aim to summarize these exciting structural and molecular biology findings and to discuss their functional implications for substrate recognition, recruitment and translocation, as well as the biogenesis of extracellular pili. We also describe adaptations necessary for deploying a breadth of processes, such as bacterial survival, host-pathogen interactions and biotic and abiotic adhesion. We highlight the functional and structural diversity that allows this extremely versatile secretion superfamily to function under different environmental conditions and in different bacterial species. Additionally, we emphasize the importance of further understanding the mechanism of type IV secretion, which will support us in combating antimicrobial resistance and treating type IV secretion system-related infections.
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Affiliation(s)
- Tiago R D Costa
- Centre for Bacterial Resistance Biology, Department of Life Sciences, Imperial College, London, UK.
| | - Jonasz B Patkowski
- Centre for Bacterial Resistance Biology, Department of Life Sciences, Imperial College, London, UK
| | - Kévin Macé
- Institute of Structural and Molecular Biology, Birkbeck and UCL, London, UK
- Institut de Génétique et Développement de Rennes (IGDR), Université de Rennes and CNRS, Rennes, France
| | - Peter J Christie
- Department of Microbiology and Molecular Genetics, McGovern Medical School at UTHealth, Houston, TX, USA.
| | - Gabriel Waksman
- Institute of Structural and Molecular Biology, Birkbeck and UCL, London, UK.
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3
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Zehra M, Heo J, Chung JM, Durie CL. Comparative Analysis of T4SS Molecular Architectures. J Microbiol Biotechnol 2023; 33:1543-1551. [PMID: 37528551 PMCID: PMC10772558 DOI: 10.4014/jmb.2307.07006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 07/21/2023] [Accepted: 07/24/2023] [Indexed: 08/03/2023]
Abstract
The recently published high-resolution R388 T4SS structure provides exciting new details about the complete complex of T4SS, including the components making up the stalk and arches, numerous symmetry mismatches between regions of the complex, and an intriguing interpretation of the closed stalk and radial symmetry of the inner membrane complex, which is related to pilus biogenesis assembly. However, there are a few unidentified densities in the electron microscopy map and portions of the identified component sequences for which the structure is not yet known. It is also unclear how well this minimized DNA-transporting T4SS predicts the structure of other T4SSs, such as expanded systems and those that transport proteins rather than DNA. In this review, we evaluate what can be inferred from the recent high-resolution structure of the R388 T4SS with respect to the Cag and Dot/Icm systems. These systems were selected because, given what is currently known about these systems, we expect them to present most structural differences compared to the R388 T4SS structure. Furthermore, we discuss bacterial physiology and diversity, the T4SS structures and their variations between different bacterial species. These insights may prove beneficial for researchers who elucidate the structure and functions of T4SS in different bacterial species.
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Affiliation(s)
- Mishghan Zehra
- Department of Biochemistry, University of Missouri, Columbia, Missouri, USA
| | - Jiwon Heo
- Department of Biotechnology, The Catholic University of Korea, Bucheon-si 14662, Gyeonggi, Republic of Korea
| | - Jeong Min Chung
- Department of Biotechnology, The Catholic University of Korea, Bucheon-si 14662, Gyeonggi, Republic of Korea
| | - Clarissa L Durie
- Department of Biochemistry, University of Missouri, Columbia, Missouri, USA
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4
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Allard N, Collette A, Paquette J, Rodrigue S, Côté JP. Systematic investigation of recipient cell genetic requirements reveals important surface receptors for conjugative transfer of IncI2 plasmids. Commun Biol 2023; 6:1172. [PMID: 37973843 PMCID: PMC10654706 DOI: 10.1038/s42003-023-05534-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 11/01/2023] [Indexed: 11/19/2023] Open
Abstract
Bacterial conjugation is a major horizontal gene transfer mechanism. While the functions encoded by many conjugative plasmids have been intensively studied, the contribution of recipient chromosome-encoded genes remains largely unknown. Here, we analyzed the genetic requirement of recipient cells for conjugation of IncI2 plasmid TP114, which was recently shown to transfer at high rates in the gut microbiota. We performed transfer assays with ~4,000 single-gene deletion mutants of Escherichia coli. When conjugation occurs on a solid medium, we observed that recipient genes impairing transfer rates were not associated with a specific cellular function. Conversely, transfer assays performed in broth were largely dependent on the lipopolysaccharide biosynthesis pathway. We further identified specific structures in lipopolysaccharides used as recipient cell surface receptors by PilV adhesins associated with the type IVb accessory pilus of TP114. Our strategy is applicable to study other mobile genetic elements and understand important host cell factors for their dissemination.
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Affiliation(s)
- Nancy Allard
- Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, QC, J1K 2R1, Canada
| | - Arianne Collette
- Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, QC, J1K 2R1, Canada
| | - Josianne Paquette
- Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, QC, J1K 2R1, Canada
| | - Sébastien Rodrigue
- Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, QC, J1K 2R1, Canada.
| | - Jean-Philippe Côté
- Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, QC, J1K 2R1, Canada.
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5
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Tran SC, McClain MS, Cover TL. Role of the CagY antenna projection in Helicobacter pylori Cag type IV secretion system activity. Infect Immun 2023; 91:e0015023. [PMID: 37638724 PMCID: PMC10501215 DOI: 10.1128/iai.00150-23] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 07/07/2023] [Indexed: 08/29/2023] Open
Abstract
Helicobacter pylori strains containing the cag pathogenicity island (PAI) are associated with the development of gastric adenocarcinoma and peptic ulcer disease. The cag PAI encodes a secreted effector protein (CagA) and a type IV secretion system (Cag T4SS). Cag T4SS activity is required for the delivery of CagA and non-protein substrates into host cells. The Cag T4SS outer membrane core complex (OMCC) contains a channel-like domain formed by helix-loop-helix elements (antenna projections, AP) from 14 copies of the CagY protein (a VirB10 ortholog). Similar VirB10 antenna regions are present in T4SS OMCCs from multiple bacterial species and are predicted to span the outer membrane. In this study, we investigated the role of the CagY antenna region in Cag T4SS OMCC assembly and Cag T4SS function. An H. pylori mutant strain with deletion of the entire CagY AP (∆AP) retained the capacity to produce CagY and assemble an OMCC, but it lacked T4SS activity (CagA translocation and IL-8 induction in AGS gastric epithelial cells). In contrast, a mutant strain with Gly-Ser substitutions in the unstructured CagY AP loop retained Cag T4SS activity. Mutants containing CagY AP loops with shortened lengths were defective in CagA translocation and exhibited reduced IL-8-inducing activity compared to control strains. These data indicate that the CagY AP region is required for Cag T4SS activity and that Cag T4SS activity can be modulated by altering the length of the CagY AP unstructured loop.
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Affiliation(s)
- Sirena C. Tran
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Mark S. McClain
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Timothy L. Cover
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Veterans Affairs Tennessee Valley Healthcare System, Nashville, Tennessee, USA
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6
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Drehkopf S, Scheibner F, Büttner D. Functional characterization of VirB/VirD4 and Icm/Dot type IV secretion systems from the plant-pathogenic bacterium Xanthomonas euvesicatoria. Front Cell Infect Microbiol 2023; 13:1203159. [PMID: 37593760 PMCID: PMC10432156 DOI: 10.3389/fcimb.2023.1203159] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 07/17/2023] [Indexed: 08/19/2023] Open
Abstract
Introduction Many Gram-negative plant- and animal-pathogenic bacteria employ type IV secretion (T4S) systems to transport proteins or DNA/protein complexes into eukaryotic or bacterial target cells. T4S systems have been divided into minimized and expanded T4S systems and resemble the VirB/VirD4 T4S system from the plant pathogen Agrobacterium tumefaciens and the Icm/Dot T4S system from the human pathogen Legionella pneumophila, respectively. The only known plant pathogen with both types of T4S systems is Xanthomonas euvesicatoria which is the causal agent of bacterial spot disease on pepper and tomato plants. Results and discussion In the present study, we show that virB/virD4 and icm/dot T4S genes are expressed and encode components of oligomeric complexes corresponding to known assemblies of VirB/VirD4 and Icm/Dot proteins. Both T4S systems are dispensable for the interaction of X. euvesicatoria with its host plants and do not seem to confer contact-dependent lysis of other bacteria, which was previously shown for the chromosomally encoded VirB/VirD4 T4S system from Xanthomonas axonopodis pv. citri. The corresponding chromosomal T4S gene cluster from X. euvesicatoria is incomplete, however, the second plasmid-localized vir gene cluster encodes a functional VirB/VirD4 T4S system which contributes to plasmid transfer. In agreement with this finding, we identified the predicted relaxase TraI as substrate of the T4S systems from X. euvesicatoria. TraI and additional candidate T4S substrates with homology to T4S effectors from X. axonopodis pv. citri interact with the T4S coupling protein VirD4. Interestingly, however, the predicted C-terminal VirD4-binding sites are not sufficient for T4S, suggesting the contribution of additional yet unknown mechanisms to the targeting of T4S substrates from X. euvesicatoria to both VirB/VirD4 and Icm/Dot T4S systems.
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Affiliation(s)
| | | | - Daniela Büttner
- Institute for Biology, Department of Genetics, Martin-Luther University Halle-Wittenberg, Halle (Saale), Germany
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7
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Wiehlmann L, Klockgether J, Hammerbacher AS, Salunkhe P, Horatzek S, Munder A, Peilert JF, Gulbins E, Eberl L, Tümmler B. A VirB4 ATPase of the mobile accessory genome orchestrates core genome-encoded features of physiology, metabolism, and virulence of Pseudomonas aeruginosa TBCF10839. Front Cell Infect Microbiol 2023; 13:1234420. [PMID: 37577372 PMCID: PMC10413270 DOI: 10.3389/fcimb.2023.1234420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Accepted: 07/10/2023] [Indexed: 08/15/2023] Open
Abstract
Pseudomonas aeruginosa TBCF10839 is a highly virulent strain that can persist and replicate in human neutrophils. Screening of a signature-tagged mutagenesis (STM) TBCF10839 transposon library in phagocytosis tests identified a mutant that carried the transposon in the VirB4 homolog 5PG21 of an integrative and conjugative element (ICE)-associated type IV secretion system of the pKLC102 subtype. 5P21 TBCF10839 insertion mutants were deficient in metabolic versatility, secretion, quorum sensing, and virulence. The mutants were efficiently killed in phagocytosis tests in vitro and were avirulent in an acute murine airway infection model in vivo. The inactivation of 5PG21 silenced the rhl, las, and pqs operons and the gene expression for the synthesis of hydrogen cyanide, the antimetabolite l-2-amino-4-methoxy-trans-3-butenoic acid, and the H2- and H3-type VI secretion systems and their associated effectors. The mutants were impaired in the utilization of carbon sources and stored compounds that are not funneled into intermediary metabolism. This showcase demonstrates that a single gene of the mobile accessory genome can become an essential element to operate the core genome-encoded features of metabolism and virulence.
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Affiliation(s)
- Lutz Wiehlmann
- Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
- Research Core Unit Genomics, Hannover Medical School, Hannover, Germany
| | - Jens Klockgether
- Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Anna-Silke Hammerbacher
- Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Prabhakar Salunkhe
- Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Sonja Horatzek
- Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Antje Munder
- Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
- Biomedical Research in Endstage and Obstructive Lung Disease, German Center for Lung Research, Hannover, Germany
| | | | - Erich Gulbins
- Department of Surgery, University of Cincinnati College of Medicine, Cincinnati, OH, United States
- Institute of Molecular Biology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Leo Eberl
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Burkhard Tümmler
- Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
- Biomedical Research in Endstage and Obstructive Lung Disease, German Center for Lung Research, Hannover, Germany
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8
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Murthy AC, Aleksanyan N, Morton GM, Toyoda HC, Kalashyan M, Chen S, Ragucci AE, Broulidakis MP, Swerdlow KJ, Bui MNN, Muccioli M, Berkmen MB. Characterization of ConE, the VirB4 Homolog of the Integrative and Conjugative Element ICE Bs1 of Bacillus subtilis. J Bacteriol 2023; 205:e0003323. [PMID: 37219457 PMCID: PMC10294652 DOI: 10.1128/jb.00033-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 05/03/2023] [Indexed: 05/24/2023] Open
Abstract
Conjugation is a major form of horizontal gene transfer, contributing to bacterial evolution and the acquisition of new traits. During conjugation, a donor cell transfers DNA to a recipient through a specialized DNA translocation channel classified as a type IV secretion system (T4SS). Here, we focused on the T4SS of ICEBs1, an integrative and conjugative element in Bacillus subtilis. ConE, encoded by ICEBs1, is a member of the VirB4 family of ATPases, the most conserved component of T4SSs. ConE is required for conjugation and localizes to the cell membrane, predominantly at the cell poles. In addition to Walker A and B boxes, VirB4 homologs have conserved ATPase motifs C, D, and E. Here, we created alanine substitutions in five conserved residues within or near ATPase motifs in ConE. Mutations in all five residues drastically decreased conjugation frequency but did not affect ConE protein levels or localization, indicating that an intact ATPase domain is critical for DNA transfer. Purified ConE is largely monomeric with some oligomers and lacks enzymatic activity, suggesting that ATP hydrolysis may be regulated or require special solution conditions. Finally, we investigated which ICEBs1 T4SS components interact with ConE using a bacterial two-hybrid assay. ConE interacts with itself, ConB, and ConQ, but these interactions are not required to stabilize ConE protein levels and largely do not depend on conserved residues within the ATPase motifs of ConE. The structure-function characterization of ConE provides more insight into this conserved component shared by all T4SSs. IMPORTANCE Conjugation is a major form of horizontal gene transfer and involves the transfer of DNA from one bacterium to another through the conjugation machinery. Conjugation contributes to bacterial evolution by disseminating genes involved in antibiotic resistance, metabolism, and virulence. Here, we characterized ConE, a protein component of the conjugation machinery of the conjugative element ICEBs1 of the bacterium Bacillus subtilis. We found that mutations in the conserved ATPase motifs of ConE disrupt mating but do not alter ConE localization, self-interaction, or levels. We also explored which conjugation proteins ConE interacts with and whether these interactions contribute to stabilizing ConE. Our work contributes to the understanding of the conjugative machinery of Gram-positive bacteria.
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Affiliation(s)
- Anastasia C. Murthy
- Department of Chemistry and Biochemistry, Suffolk University, Boston, Massachusetts, USA
| | - Naira Aleksanyan
- Department of Chemistry and Biochemistry, Suffolk University, Boston, Massachusetts, USA
| | - Georgeanna M. Morton
- Department of Chemistry and Biochemistry, Suffolk University, Boston, Massachusetts, USA
| | - Hunter C. Toyoda
- Department of Chemistry and Biochemistry, Suffolk University, Boston, Massachusetts, USA
| | - Meri Kalashyan
- Department of Chemistry and Biochemistry, Suffolk University, Boston, Massachusetts, USA
| | - Sirui Chen
- Department of Chemistry and Biochemistry, Suffolk University, Boston, Massachusetts, USA
| | - Adelyn E. Ragucci
- Department of Chemistry and Biochemistry, Suffolk University, Boston, Massachusetts, USA
- Cancer Immunology and Virology Department, Dana Farber Cancer Institute, Boston, Massachusetts, USA
| | - Matthew P. Broulidakis
- Department of Chemistry and Biochemistry, Suffolk University, Boston, Massachusetts, USA
| | - Kyle J. Swerdlow
- Department of Chemistry and Biochemistry, Suffolk University, Boston, Massachusetts, USA
| | - Minh N. N. Bui
- Department of Chemistry and Biochemistry, Suffolk University, Boston, Massachusetts, USA
| | - Maria Muccioli
- Department of Chemistry and Biochemistry, Suffolk University, Boston, Massachusetts, USA
| | - Melanie B. Berkmen
- Department of Chemistry and Biochemistry, Suffolk University, Boston, Massachusetts, USA
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9
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Piscon B, Pia Esposito E, Fichtman B, Samburski G, Efremushkin L, Amselem S, Harel A, Rahav G, Zarrilli R, Gal-Mor O. The Effect of Outer Space and Other Environmental Cues on Bacterial Conjugation. Microbiol Spectr 2023; 11:e0368822. [PMID: 36995224 PMCID: PMC10269834 DOI: 10.1128/spectrum.03688-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 03/11/2023] [Indexed: 03/31/2023] Open
Abstract
Bacterial conjugation is one of the most abundant horizontal gene transfer (HGT) mechanisms, playing a fundamental role in prokaryote evolution. A better understanding of bacterial conjugation and its cross talk with the environment is needed for a more complete understanding of HGT mechanisms and to fight the dissemination of malicious genes between bacteria. Here, we studied the effect of outer space, microgravity, and additional key environmental cues on transfer (tra) gene expression and conjugation efficiency, using the under studied broad-host range plasmid pN3, as a model. High resolution scanning electron microscopy revealed the morphology of the pN3 conjugative pili and mating pair formation during conjugation. Using a nanosatellite carrying a miniaturized lab, we studied pN3 conjugation in outer space, and used qRT-PCR, Western blotting and mating assays to determine the effect of ground physicochemical parameters on tra gene expression and conjugation. We showed for the first time that bacterial conjugation can occur in outer space and on the ground, under microgravity-simulated conditions. Furthermore, we demonstrated that microgravity, liquid media, elevated temperature, nutrient depletion, high osmolarity and low oxygen significantly reduce pN3 conjugation. Interestingly, under some of these conditions we observed an inverse correlation between tra gene transcription and conjugation frequency and found that induction of at least traK and traL can negatively affect pN3 conjugation frequency in a dose-dependent manner. Collectively, these results uncover pN3 regulation by various environmental cues and highlight the diversity of conjugation systems and the different ways in which they may be regulated in response to abiotic signals. IMPORTANCE Bacterial conjugation is a highly ubiquitous and promiscuous process, by which a donor bacterium transfers a large portion of genetic material to a recipient cell. This mechanism of horizontal gene transfer plays an important role in bacterial evolution and in the ability of bacteria to acquire resistance to antimicrobial drugs and disinfectants. Bacterial conjugation is a complex and energy-consuming process, that is tightly regulated and largely affected by various environmental signals sensed by the bacterial cell. Comprehensive knowledge about bacterial conjugation and the ways it is affected by environmental cues is required to better understand bacterial ecology and evolution and to find new effective ways to counteract the threating dissemination of antibiotic resistance genes between bacterial populations. Moreover, characterizing this process under stress or suboptimal growth conditions such as elevated temperatures, high salinity or in the outer space, may provide insights relevant to future habitat environmental conditions.
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Affiliation(s)
- Bar Piscon
- The Infectious Diseases Research Laboratory, Sheba Medical Center, Tel-Hashomer, Israel
- Department of Clinical Microbiology and Immunology, Tel Aviv University, Tel Aviv, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Eliana Pia Esposito
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Boris Fichtman
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Guy Samburski
- SpacePharma R&D Israel LTD., Herzliya Pituach, Israel & SpacePharma SA, Courgenay, Switzerland
| | - Lihi Efremushkin
- SpacePharma R&D Israel LTD., Herzliya Pituach, Israel & SpacePharma SA, Courgenay, Switzerland
| | - Shimon Amselem
- SpacePharma R&D Israel LTD., Herzliya Pituach, Israel & SpacePharma SA, Courgenay, Switzerland
| | - Amnon Harel
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Galia Rahav
- The Infectious Diseases Research Laboratory, Sheba Medical Center, Tel-Hashomer, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Raffaele Zarrilli
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Ohad Gal-Mor
- The Infectious Diseases Research Laboratory, Sheba Medical Center, Tel-Hashomer, Israel
- Department of Clinical Microbiology and Immunology, Tel Aviv University, Tel Aviv, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
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10
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Breidenstein A, Ter Beek J, Berntsson RPA. Structural and functional characterization of TraI from pKM101 reveals basis for DNA processing. Life Sci Alliance 2023; 6:e202201775. [PMID: 36669792 PMCID: PMC9868005 DOI: 10.26508/lsa.202201775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 01/10/2023] [Accepted: 01/10/2023] [Indexed: 01/21/2023] Open
Abstract
Type 4 secretion systems are large and versatile protein machineries that facilitate the spread of antibiotic resistance and other virulence factors via horizontal gene transfer. Conjugative type 4 secretion systems depend on relaxases to process the DNA in preparation for transport. TraI from the well-studied conjugative plasmid pKM101 is one such relaxase. Here, we report the crystal structure of the trans-esterase domain of TraI in complex with its substrate oriT DNA, highlighting the conserved DNA-binding mechanism of conjugative relaxases. In addition, we present an apo structure of the trans-esterase domain of TraI that includes most of the flexible thumb region. This allows us for the first time to visualize the large conformational change of the thumb subdomain upon DNA binding. We also characterize the DNA binding, nicking, and religation activity of the trans-esterase domain, helicase domain, and full-length TraI. Unlike previous indications in the literature, our results reveal that the TraI trans-esterase domain from pKM101 behaves in a conserved manner with its homologs from the R388 and F plasmids.
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Affiliation(s)
- Annika Breidenstein
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
- Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden
| | - Josy Ter Beek
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
- Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden
| | - Ronnie P-A Berntsson
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
- Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden
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11
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Dutka P, Liu Y, Maggi S, Ghosal D, Wang J, Carter SD, Zhao W, Vijayrajratnam S, Vogel JP, Jensen GJ. Structure and Function of the Dot/Icm T4SS. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.22.533729. [PMID: 36993699 PMCID: PMC10055428 DOI: 10.1101/2023.03.22.533729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
The Legionella pneumophila Dot/Icm type IV secretion system (T4SS) delivers effector proteins into host cells during infection. Despite its significance as a potential drug target, our current understanding of its atomic structure is limited to isolated subcomplexes. In this study, we used subtomogram averaging and integrative modeling to construct a nearly-complete model of the Dot/Icm T4SS accounting for seventeen protein components. We locate and provide insights into the structure and function of six new components including DotI, DotJ, DotU, IcmF, IcmT, and IcmX. We find that the cytosolic N-terminal domain of IcmF, a key protein forming a central hollow cylinder, interacts with DotU, providing insight into previously uncharacterized density. Furthermore, our model, in combination with analyses of compositional heterogeneity, explains how the cytoplasmic ATPase DotO is connected to the periplasmic complex via interactions with membrane-bound DotI/DotJ proteins. Coupled with in situ infection data, our model offers new insights into the T4SS-mediated secretion mechanism.
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Affiliation(s)
- Przemysław Dutka
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Yuxi Liu
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Stefano Maggi
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
| | - Debnath Ghosal
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Present address: Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, Australia
| | - Jue Wang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Stephen D. Carter
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Present address: MRC-University of Glasgow Centre for Virus Research, School of Infection and Immunity, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, Scotland, UK
| | - Wei Zhao
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | | | - Joseph P. Vogel
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Grant J. Jensen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
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12
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Jia Y, Wang Z, Zhu S, Wang Z, Liu Y. Disinfectants facilitate the transformation of exogenous antibiotic resistance genes via multiple pathways. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 253:114678. [PMID: 36857920 DOI: 10.1016/j.ecoenv.2023.114678] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 02/19/2023] [Accepted: 02/21/2023] [Indexed: 06/18/2023]
Abstract
The prevalence and spread of multidrug-resistant (MDR) bacteria pose a global challenge to public health. Natural transformation is one of the essential ways for horizontal transfer of antibiotic resistance genes (ARGs). Although disinfectants are frequently used during COVID-19, little is known about whether these disinfectants are associated with the transformation of plasmid-borne ARGs. In our study, we assessed the effect of some disinfectants on bacterial transformation using resistance plasmids as extracellular DNA and E. coli DH5α as the recipient bacteria. The results showed that these disinfectants at environmentally relevant concentrations, including benzalkonium bromide (BB), benzalkonium chloride (BC) and polyhexamethylene guanidine hydrochloride (PHMG), significantly enhanced the transformation of plasmid-encoded ARGs. Furthermore, we investigated the mechanisms underlying the promotive effect of disinfectants on transformation. We revealed that the addition of disinfectants significantly increased the membrane permeability and promoted membrane-related genes expression. Moreover, disinfectants led to the boosted bacterial respiration, ATP production and flagellum motility, as well as increased expression of bacterial secretion system-related genes. Together, our findings shed insights into the spread of ARGs through bacterial transformation and indicate potential risks associated with the widespread use of disinfectants.
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Affiliation(s)
- Yuqian Jia
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
| | - Zeyu Wang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
| | - Shuyao Zhu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
| | - Zhiqiang Wang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu, China.
| | - Yuan Liu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu, China; Institute of Comparative Medicine, Yangzhou University, Yangzhou, Jiangsu, China.
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13
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Lai L, Cheung YW, Martinez M, Kixmoeller K, Palao L, Steimle S, Ho MC, Black BE, Lai EM, Chang YW. In Situ Structure Determination of Bacterial Surface Nanomachines Using Cryo-Electron Tomography. Methods Mol Biol 2023; 2646:211-248. [PMID: 36842118 DOI: 10.1007/978-1-0716-3060-0_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2023]
Abstract
Bacterial surface nanomachines are often refractory to structural determination in their intact form due to their extensive association with the cell envelope preventing them from being properly purified for traditional structural biology methods. Cryo-electron tomography (cryo-ET) is an emerging branch of cryo-electron microscopy that can visualize supramolecular complexes directly inside frozen-hydrated cells in 3D at nanometer resolution, therefore posing a unique capability to study the intact structures of bacterial surface nanomachines in situ and reveal their molecular association with other cellular components. Furthermore, the resolution of cryo-ET is continually improving alongside methodological advancement. Here, using the type IV pilus machine in Myxococcus xanthus as an example, we describe a step-by-step workflow for in situ structure determination including sample preparation and screening, microscope and camera tuning, tilt series acquisition, data processing and tomogram reconstruction, subtomogram averaging, and structural analysis.
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Affiliation(s)
- Longsheng Lai
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yee-Wai Cheung
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Matthew Martinez
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kathryn Kixmoeller
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Leon Palao
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Stefan Steimle
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Meng-Chiao Ho
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Ben E Black
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Erh-Min Lai
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Yi-Wei Chang
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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14
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Cryo-EM structure of the Agrobacteriumtumefaciens T-pilus reveals the importance of positive charges in the lumen. Structure 2022; 31:375-384.e4. [PMID: 36513067 DOI: 10.1016/j.str.2022.11.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 09/19/2022] [Accepted: 11/14/2022] [Indexed: 12/14/2022]
Abstract
Agrobacterium tumefaciens is a natural genetic engineer that transfers DNA into plants, which is the most applied process for generation of genetically modified plants. DNA transfer is mediated by a type IV secretion system in the cell envelope and extracellular T-pili. We here report the cryo-electron microscopic structures of the T-pilus at 3.2-Å resolution and of the plasmid pKM101-determined N-pilus at 3-Å resolution. Both pili contain a main pilus protein (VirB2 in A. tumefaciens, TraM in pKM101) and phospholipids arranged in a five-start helical assembly. They contain positively charged amino acids in the lumen, and the lipids are positively charged in the T-pilus (phosphatidylcholine) conferring overall positive charge. Mutagenesis of the lumen-exposed Arg91 in VirB2 results in protein destabilization and loss of pilus formation. Our results reveal that different phospholipids can be incorporated into type IV secretion pili and that the charge of the lumen may be of functional importance.
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15
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Abstract
Bacterial conjugation is the fundamental process of unidirectional transfer of DNAs, often plasmid DNAs, from a donor cell to a recipient cell1. It is the primary means by which antibiotic resistance genes spread among bacterial populations2,3. In Gram-negative bacteria, conjugation is mediated by a large transport apparatus—the conjugative type IV secretion system (T4SS)—produced by the donor cell and embedded in both its outer and inner membranes. The T4SS also elaborates a long extracellular filament—the conjugative pilus—that is essential for DNA transfer4,5. Here we present a high-resolution cryo-electron microscopy (cryo-EM) structure of a 2.8 megadalton T4SS complex composed of 92 polypeptides representing 8 of the 10 essential T4SS components involved in pilus biogenesis. We added the two remaining components to the structural model using co-evolution analysis of protein interfaces, to enable the reconstitution of the entire system including the pilus. This structure describes the exceptionally large protein–protein interaction network required to assemble the many components that constitute a T4SS and provides insights on the unique mechanism by which they elaborate pili. Cryo-electron microscopy structures of a 2.8 megadalton bacterial type IV secretion system encoded by the plasmid R388 and comprising 92 polypeptides provide insights into the stepwise mechanism of pilus assembly.
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16
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Lockwood DC, Amin H, Costa TRD, Schroeder GN. The Legionella pneumophila Dot/Icm type IV secretion system and its effectors. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 35639581 DOI: 10.1099/mic.0.001187] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
To prevail in the interaction with eukaryotic hosts, many bacterial pathogens use protein secretion systems to release virulence factors at the host–pathogen interface and/or deliver them directly into host cells. An outstanding example of the complexity and sophistication of secretion systems and the diversity of their protein substrates, effectors, is the Defective in organelle trafficking/Intracellular multiplication (Dot/Icm) Type IVB secretion system (T4BSS) of
Legionella pneumophila
and related species.
Legionella
species are facultative intracellular pathogens of environmental protozoa and opportunistic human respiratory pathogens. The Dot/Icm T4BSS translocates an exceptionally large number of effectors, more than 300 per
L. pneumophila
strain, and is essential for evasion of phagolysosomal degradation and exploitation of protozoa and human macrophages as replicative niches. Recent technological advancements in the imaging of large protein complexes have provided new insight into the architecture of the T4BSS and allowed us to propose models for the transport mechanism. At the same time, significant progress has been made in assigning functions to about a third of
L. pneumophila
effectors, discovering unprecedented new enzymatic activities and concepts of host subversion. In this review, we describe the current knowledge of the workings of the Dot/Icm T4BSS machinery and provide an overview of the activities and functions of the to-date characterized effectors in the interaction of
L. pneumophila
with host cells.
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Affiliation(s)
- Daniel C Lockwood
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, BT9 7BL, Northern Ireland, UK
| | - Himani Amin
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College, London, SW7 2AZ, UK
| | - Tiago R D Costa
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College, London, SW7 2AZ, UK
| | - Gunnar N Schroeder
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, BT9 7BL, Northern Ireland, UK
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