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Nehls C, Schröder M, Haubenthal T, Haas A, Gutsmann T. The mechanistic basis of the membrane-permeabilizing activities of the virulence-associated protein A (VapA) from Rhodococcus equi. Mol Microbiol 2024; 121:578-592. [PMID: 38308564 DOI: 10.1111/mmi.15233] [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: 06/20/2023] [Revised: 01/12/2024] [Accepted: 01/17/2024] [Indexed: 02/05/2024]
Abstract
Pathogenic Rhodococcus equi release the virulence-associated protein A (VapA) within macrophage phagosomes. VapA permeabilizes phagosome and lysosome membranes and reduces acidification of both compartments. Using biophysical techniques, we found that VapA interacts with model membranes in four steps: (i) binding, change of mechanical properties, (ii) formation of specific membrane domains, (iii) permeabilization within the domains, and (iv) pH-specific transformation of domains. Biosensor data revealed that VapA binds to membranes in one step at pH 6.5 and in two steps at pH 4.5 and decreases membrane fluidity. The integration of VapA into lipid monolayers was only significant at lateral pressures <20 mN m-1 indicating preferential incorporation into membrane regions with reduced integrity. Atomic force microscopy of lipid mono- and bilayers showed that VapA increased the surface heterogeneity of liquid disordered domains. Furthermore, VapA led to the formation of a new microstructured domain type and, at pH 4.5, to the formation of 5 nm high domains. VapA binding, its integration and lipid domain formation depended on lipid composition, pH, protein concentration and lateral membrane pressure. VapA-mediated permeabilization is clearly distinct from that caused by classical microbial pore formers and is a key contribution to the multiplication of Rhodococcus equi in phagosomes.
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Affiliation(s)
- Christian Nehls
- Division of Biophysics, Research Center Borstel - Leibniz Lung Center, Borstel, Germany
- Centre for Structural Systems Biology (CSSB), Hamburg, Germany
- Kiel Nano, Surface and Interface Science KiNSIS, Kiel University, Kiel, Germany
| | - Marcel Schröder
- Division of Biophysics, Research Center Borstel - Leibniz Lung Center, Borstel, Germany
| | | | - Albert Haas
- Cell Biology Institute, University of Bonn, Bonn, Germany
| | - Thomas Gutsmann
- Division of Biophysics, Research Center Borstel - Leibniz Lung Center, Borstel, Germany
- Centre for Structural Systems Biology (CSSB), Hamburg, Germany
- Kiel Nano, Surface and Interface Science KiNSIS, Kiel University, Kiel, Germany
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2
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Miranda-CasoLuengo R, Yerlikaya Z, Luo H, Cheng C, Blanco A, Haas A, Meijer WG. The N-terminal domain is required for cell surface localisation of VapA, a member of the Vap family of Rhodococcus equi virulence proteins. PLoS One 2024; 19:e0298900. [PMID: 38421980 PMCID: PMC10903876 DOI: 10.1371/journal.pone.0298900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 01/31/2024] [Indexed: 03/02/2024] Open
Abstract
Rhodococcus equi pneumonia is an important cause of mortality in foals worldwide. Virulent equine isolates harbour an 80-85kb virulence plasmid encoding six virulence-associated proteins (Vaps). VapA, the main virulence factor of this intracellular pathogen, is known to be a cell surface protein that creates an intracellular niche for R. equi growth. In contrast, VapC, VapD and VapE are secreted into the intracellular milieu. Although these Vaps share very high degree of sequence identity in the C-terminal domain, the N-terminal domain (N-domain) of VapA is distinct. It has been proposed that this domain plays a role in VapA surface localization but no direct experimental data provides support to such hypothesis. In this work, we employed R. equi 103S harbouring an unmarked deletion of vapA (R. equi ΔvapA) as the genetic background to express C-terminal Strep-tagged Vap-derivatives integrated in the chromosome. The surface localization of these proteins was assessed by flow cytometry using the THE2122;-NWSHPQFEK Tag FITC-antibody. We show that VapA is the only cell surface Vap encoded in the virulence plasmid. We present compelling evidence for the role of the N-terminal domain of VapA on cell surface localization using fusion proteins in which the N-domain of VapD was exchanged with the N-terminus of VapA. Lastly, using an N-terminally Strep-tagged VapA, we found that the N-terminus of VapA is exposed to the extracellular environment. Given the lack of a lipobox in VapA and the exposure of the N-terminal Strep-tag, it is possible that VapA localization on the cell surface is mediated by interactions between the N-domain and components of the cell surface. We discuss the implications of this work on the light of the recent discovery that soluble recombinant VapA added to the extracellular medium functionally complement the loss of VapA.
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Affiliation(s)
- Raúl Miranda-CasoLuengo
- UCD School of Biomolecular and Biomedical Science and UCD Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Dublin, Ireland
| | - Zeynep Yerlikaya
- UCD School of Biomolecular and Biomedical Science and UCD Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Dublin, Ireland
- Department of Microbiology, School of Veterinary Medicine, Firat University, Elazığ, Türkiye
| | - Haixia Luo
- UCD School of Biomolecular and Biomedical Science and UCD Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Dublin, Ireland
| | - Cheng Cheng
- UCD School of Biomolecular and Biomedical Science and UCD Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Dublin, Ireland
| | - Alfonso Blanco
- Flow Cytometry Core Technology, UCD Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Dublin, Ireland
| | - Albert Haas
- Institute for Cell Biology, University of Bonn, Bonn, Germany
| | - Wim G. Meijer
- UCD School of Biomolecular and Biomedical Science and UCD Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Dublin, Ireland
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3
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Hansen P, Haubenthal T, Reiter C, Kniewel J, Bosse-Plois K, Niemann HH, von Bargen K, Haas A. Differential Effects of Rhodococcus equi Virulence-Associated Proteins on Macrophages and Artificial Lipid Membranes. Microbiol Spectr 2023; 11:e0341722. [PMID: 36786596 PMCID: PMC10100859 DOI: 10.1128/spectrum.03417-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 01/06/2023] [Indexed: 02/15/2023] Open
Abstract
Virulence-associated protein A (VapA) of Rhodococcus equi is a pathogenicity factor required for the multiplication of virulent R. equi strains within spacious macrophage vacuoles. The production of VapA is characteristic for R. equi isolates from pneumonic foals. VapB and VapN proteins in R. equi isolates from infected pig (VapB) and cattle (VapN) have amino acid sequences very similar to VapA and consequently have been assumed to be its functional correlates. Using model membrane experiments, phagosome pH acidification analysis, lysosome size measurements, protein partitioning, and degradation assays, we provide support for the view that VapA and VapN promote intracellular multiplication of R. equi by neutralizing the pH of the R. equi-containing vacuole. VapB does not neutralize vacuole pH, is not as membrane active as VapA, and does not support intracellular multiplication. This study also shows that the size of the sometimes enormous R. equi-containing vacuoles or the partitioning of purified Vaps into organic phases are not features that have predictive value for virulence of R. equi, whereas the ability of Vaps to increase phagosome pH is coupled to virulence. IMPORTANCE Rhodococcus equi is a major cause of life-threatening pneumonia in foals and occasionally in immunocompromised persons. Virulence-associated protein A (VapA) promotes R. equi multiplication in lung macrophages, which are the major host cells during foal infection. In this study, we compare cellular, biochemical, and biophysical phenotypes associated with VapA to those of VapB (typically produced by isolates from pigs) or VapN (isolates from cattle). Our data support the hypothesis that only some Vaps support multiplication in macrophages by pH neutralization of the phagosomes that R. equi inhabit.
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Affiliation(s)
- Philipp Hansen
- Institute for Cell Biology, University of Bonn, Bonn, Germany
| | | | - Caroline Reiter
- Institute for Cell Biology, University of Bonn, Bonn, Germany
| | - Jana Kniewel
- Institute for Cell Biology, University of Bonn, Bonn, Germany
| | | | | | | | - Albert Haas
- Institute for Cell Biology, University of Bonn, Bonn, Germany
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4
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Geerds C, Haas A, Niemann HH. Conformational changes of loops highlight a potential binding site in Rhodococcus equi VapB. Acta Crystallogr F Struct Biol Commun 2021; 77:246-253. [PMID: 34341190 PMCID: PMC8329714 DOI: 10.1107/s2053230x2100738x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 07/16/2021] [Indexed: 12/04/2022] Open
Abstract
Virulence-associated proteins (Vaps) contribute to the virulence of the pathogen Rhodococcus equi, but their mode of action has remained elusive. All Vaps share a conserved core of about 105 amino acids that folds into a compact eight-stranded antiparallel β-barrel with a unique topology. At the top of the barrel, four loops connect the eight β-strands. Previous Vap structures did not show concave surfaces that might serve as a ligand-binding site. Here, the structure of VapB in a new crystal form was determined at 1.71 Å resolution. The asymmetric unit contains two molecules. In one of them, the loop regions at the top of the barrel adopt a different conformation from other Vap structures. An outward movement of the loops results in the formation of a hydrophobic cavity that might act as a ligand-binding site. This lends further support to the hypothesis that the structural similarity between Vaps and avidins suggests a potential binding function for Vaps.
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Affiliation(s)
- Christina Geerds
- Department of Chemistry, Bielefeld University, Universitaetsstrasse 25, 33615 Bielefeld, Germany
| | - Albert Haas
- Institute for Cell Biology, University of Bonn, Ulrich-Haberland-Strasse 61a, 53121 Bonn, Germany
| | - Hartmut H. Niemann
- Department of Chemistry, Bielefeld University, Universitaetsstrasse 25, 33615 Bielefeld, Germany
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5
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Vázquez-Boland JA, Meijer WG. The pathogenic actinobacterium Rhodococcus equi: what's in a name? Mol Microbiol 2019; 112:1-15. [PMID: 31099908 PMCID: PMC6852188 DOI: 10.1111/mmi.14267] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/25/2019] [Indexed: 12/17/2022]
Abstract
Rhodococcus equi is the only recognized animal pathogenic species within an extended genus of metabolically versatile Actinobacteria of considerable biotechnological interest. Best known as a horse pathogen, R. equi is commonly isolated from other animal species, particularly pigs and ruminants, and causes severe opportunistic infections in people. As typical in the rhodococci, R. equi niche specialization is extrachromosomally determined, via a conjugative virulence plasmid that promotes intramacrophage survival. Progress in the molecular understanding of R. equi and its recent rise as a novel paradigm of multihost adaptation has been accompanied by an unusual nomenclatural instability, with a confusing succession of names: "Prescottia equi", "Prescotella equi", Corynebacterium hoagii and Rhodococcus hoagii. This article reviews current advances in the genomics, biology and virulence of this pathogenic actinobacterium with a unique mechanism of plasmid‐transferable animal host tropism. It also discusses the taxonomic and nomenclatural issues around R. equi in the light of recent phylogenomic evidence that confirms its membership as a bona fide Rhodococcus.
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Affiliation(s)
- José A Vázquez-Boland
- Microbial Pathogenesis Group, Edinburgh Medical School (Biomedical Sciences - Infection Medicine), University of Edinburgh, Chancellor's Building, Little France campus, Edinburgh, EH16 4SB, UK
| | - Wim G Meijer
- UCD School of Biomolecular and Biomedical Science, University College Dublin, Dublin 4, Ireland
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6
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Bargen K, Scraba M, Krämer I, Ketterer M, Nehls C, Krokowski S, Repnik U, Wittlich M, Maaser A, Zapka P, Bunge M, Schlesinger M, Huth G, Klees A, Hansen P, Jeschke A, Bendas G, Utermöhlen O, Griffiths G, Gutsmann T, Wohlmann J, Haas A. Virulence‐associated protein A fromRhodococcus equiis an intercompartmental pH‐neutralising virulence factor. Cell Microbiol 2018; 21:e12958. [DOI: 10.1111/cmi.12958] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 08/17/2018] [Accepted: 09/04/2018] [Indexed: 12/26/2022]
Affiliation(s)
- Kristine Bargen
- Division of Biophysics, Cell Biology InstituteUniversity of Bonn Bonn Germany
| | - Mirella Scraba
- Division of Biophysics, Cell Biology InstituteUniversity of Bonn Bonn Germany
| | - Ina Krämer
- Division of Biophysics, Cell Biology InstituteUniversity of Bonn Bonn Germany
| | - Maren Ketterer
- Division of Biophysics, Cell Biology InstituteUniversity of Bonn Bonn Germany
| | | | - Sina Krokowski
- Division of Biophysics, Cell Biology InstituteUniversity of Bonn Bonn Germany
| | - Urska Repnik
- Department of BiosciencesUniversity of Oslo Oslo Norway
| | - Michaela Wittlich
- Division of Biophysics, Cell Biology InstituteUniversity of Bonn Bonn Germany
| | - Anna Maaser
- Division of Biophysics, Cell Biology InstituteUniversity of Bonn Bonn Germany
| | - Pia Zapka
- Division of Biophysics, Cell Biology InstituteUniversity of Bonn Bonn Germany
| | - Madeleine Bunge
- Division of Biophysics, Cell Biology InstituteUniversity of Bonn Bonn Germany
| | | | - Gitta Huth
- Division of Biophysics, Cell Biology InstituteUniversity of Bonn Bonn Germany
| | - Annette Klees
- Division of Biophysics, Cell Biology InstituteUniversity of Bonn Bonn Germany
| | - Philipp Hansen
- Division of Biophysics, Cell Biology InstituteUniversity of Bonn Bonn Germany
| | - Andreas Jeschke
- Division of Biophysics, Cell Biology InstituteUniversity of Bonn Bonn Germany
| | - Gerd Bendas
- Pharmaceutical InstituteUniversity of Bonn Bonn Germany
| | - Olaf Utermöhlen
- Institute for Medical Microbiology, Immunology and Hygiene, University Medical Center, and Center for Molecular Medicine Köln, and German Center for Infection Research (DCIF) Cologne Germany
| | | | | | - Jens Wohlmann
- Division of Biophysics, Cell Biology InstituteUniversity of Bonn Bonn Germany
- Department of BiosciencesUniversity of Oslo Oslo Norway
| | - Albert Haas
- Division of Biophysics, Cell Biology InstituteUniversity of Bonn Bonn Germany
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7
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Willingham-Lane JM, Coulson GB, Hondalus MK. Identification of a VapA virulence factor functional homolog in Rhodococcus equi isolates housing the pVAPB plasmid. PLoS One 2018; 13:e0204475. [PMID: 30286098 PMCID: PMC6171844 DOI: 10.1371/journal.pone.0204475] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 09/07/2018] [Indexed: 11/30/2022] Open
Abstract
Rhodococcus equi is a facultative intracellular bacterium of macrophages and is an important pathogen of animals and immunocompromised people wherein disease results in abcessation of the lungs and other sites. Prior work has shown that the presence of the major virulence determinant, VapA, encoded on the pVAPA-type plasmid, disrupts normal phagosome development and is essential for bacterial replication within macrophages. pVAPA- type plasmids are typical of R. equi strains derived from foals while strains from pigs carry plasmids of the pVAPB-type, lacking vapA, and those from humans harbor various types of plasmids including pVAPA and pVAPB. Through the creation and analysis of a series of gene deletion mutants, we found that vapK1 or vapK2 is required for optimal intracellular replication of an R. equi isolate carrying a pVAPB plasmid type. Complementation analysis of a ΔvapA R. equi strain with vapK1 or vapK2 showed the VapK proteins of the pVAPB-type plasmid could restore replication capacity to the macrophage growth-attenuated ΔvapA strain. Additionally, in contrast to the intracellular growth capabilities displayed by an equine R. equi transconjugant strain carrying a pVAPB-type plasmid, a transconjugant strain carrying a pVAPB-type plasmid deleted of vapK1 and vapK2 proved incapable of replication in equine macrophages. Cumulatively, these data indicate that VapK1 and K2 are functionally equivalent to VapA.
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Affiliation(s)
| | - Garry B. Coulson
- Department of Infectious Disease, University of Georgia, Athens, Georgia, United States of America
| | - Mary K. Hondalus
- Department of Infectious Disease, University of Georgia, Athens, Georgia, United States of America
- * E-mail:
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8
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Wright LM, Carpinone EM, Bennett TL, Hondalus MK, Starai VJ. VapA of Rhodococcus equi binds phosphatidic acid. Mol Microbiol 2017; 107:428-444. [PMID: 29205554 DOI: 10.1111/mmi.13892] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 11/28/2017] [Accepted: 12/03/2017] [Indexed: 12/30/2022]
Abstract
Rhodococcus equi is a multihost, facultative intracellular bacterial pathogen that primarily causes pneumonia in foals less than six months in age and immunocompromised people. Previous studies determined that the major virulence determinant of R. equi is the surface bound virulence associated protein A (VapA). The presence of VapA inhibits the maturation of R. equi-containing phagosomes and promotes intracellular bacterial survival, as determined by the inability of vapA deletion mutants to replicate in host macrophages. While the mechanism of action of VapA remains elusive, we show that soluble recombinant VapA32-189 both rescues the intramacrophage replication defect of a wild type R. equi strain lacking the vapA gene and enhances the persistence of nonpathogenic Escherichia coli in macrophages. During macrophage infection, VapA was observed at both the bacterial surface and at the membrane of the host-derived R. equi containing vacuole, thus providing an opportunity for VapA to interact with host constituents and promote alterations in phagolysosomal function. In support of the observed host membrane binding activity of VapA, we also found that rVapA32-189 interacted specifically with liposomes containing phosphatidic acid in vitro. Collectively, these data demonstrate a lipid binding property of VapA, which may be required for its function during intracellular infection.
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Affiliation(s)
- Lindsay M Wright
- Department of Infectious Diseases, University of Georgia, Athens, GA 30602, USA
| | - Emily M Carpinone
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA
| | - Terry L Bennett
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA
| | - Mary K Hondalus
- Department of Infectious Diseases, University of Georgia, Athens, GA 30602, USA
| | - Vincent J Starai
- Department of Infectious Diseases, University of Georgia, Athens, GA 30602, USA.,Department of Microbiology, University of Georgia, Athens, GA 30602, USA
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9
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Rofe AP, Davis LJ, Whittingham JL, Latimer-Bowman EC, Wilkinson AJ, Pryor PR. The Rhodococcus equi virulence protein VapA disrupts endolysosome function and stimulates lysosome biogenesis. Microbiologyopen 2016; 6. [PMID: 27762083 PMCID: PMC5387311 DOI: 10.1002/mbo3.416] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 09/09/2016] [Accepted: 09/20/2016] [Indexed: 12/11/2022] Open
Abstract
Rhodococcus equi (R. equi) is an important pulmonary pathogen in foals that often leads to the death of the horse. The bacterium harbors a virulence plasmid that encodes numerous virulence‐associated proteins (Vaps) including VapA that is essential for intracellular survival inside macrophages. However, little is known about the precise function of VapA. Here, we demonstrate that VapA causes perturbation to late endocytic organelles with swollen endolysosome organelles having reduced Cathepsin B activity and an accumulation of LBPA, LC3 and Rab7. The data are indicative of a loss of endolysosomal function, which leads cells to upregulate lysosome biogenesis to compensate for the loss of functional endolysosomes. Although there is a high degree of homology of the core region of VapA to other Vap proteins, only the highly conserved core region of VapA, and not VapD of VapG, gives the observed effects on endolysosomes. This is the first demonstration of how VapA works and implies that VapA aids R. equi survival by reducing the impact of lysosomes on phagocytosed bacteria.
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Affiliation(s)
- Adam P Rofe
- Department of Biology, Wentworth Way, University of York, York, UK
| | - Luther J Davis
- Cambridge Institute for Medical Research and Department of Clinical Biochemistry, Addenbrooke's Hospital, University of Cambridge, Cambridge
| | - Jean L Whittingham
- Structural Biology Laboratory, Department of Chemistry, University of York, York, UK
| | - Elizabeth C Latimer-Bowman
- Cambridge Institute for Medical Research and Department of Clinical Biochemistry, Addenbrooke's Hospital, University of Cambridge, Cambridge
| | - Anthony J Wilkinson
- Structural Biology Laboratory, Department of Chemistry, University of York, York, UK
| | - Paul R Pryor
- Department of Biology, Wentworth Way, University of York, York, UK.,Hull York Medical School, University of York, York, UK
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10
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Mendes JS, Santiago ADS, Toledo MAS, Rosselli-Murai LK, Favaro MTP, Santos CA, Horta MAC, Crucello A, Beloti LL, Romero F, Tasic L, de Souza AA, de Souza AP. VapD in Xylella fastidiosa Is a Thermostable Protein with Ribonuclease Activity. PLoS One 2015; 10:e0145765. [PMID: 26694028 PMCID: PMC4687846 DOI: 10.1371/journal.pone.0145765] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2015] [Accepted: 12/08/2015] [Indexed: 01/15/2023] Open
Abstract
Xylella fastidiosa strain 9a5c is a gram-negative phytopathogen that is the causal agent of citrus variegated chlorosis (CVC), a disease that is responsible for economic losses in Brazilian agriculture. The most well-known mechanism of pathogenicity for this bacterial pathogen is xylem vessel occlusion, which results from bacterial movement and the formation of biofilms. The molecular mechanisms underlying the virulence caused by biofilm formation are unknown. Here, we provide evidence showing that virulence-associated protein D in X. fastidiosa (Xf-VapD) is a thermostable protein with ribonuclease activity. Moreover, protein expression analyses in two X. fastidiosa strains, including virulent (Xf9a5c) and nonpathogenic (XfJ1a12) strains, showed that Xf-VapD was expressed during all phases of development in both strains and that increased expression was observed in Xf9a5c during biofilm growth. This study is an important step toward characterizing and improving our understanding of the biological significance of Xf-VapD and its potential functions in the CVC pathosystem.
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Affiliation(s)
- Juliano S. Mendes
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, SP, Brazil, CEP 13083-875
| | - André da S. Santiago
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, SP, Brazil, CEP 13083-875
| | - Marcelo A. S. Toledo
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, SP, Brazil, CEP 13083-875
| | - Luciana K. Rosselli-Murai
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, SP, Brazil, CEP 13083-875
| | - Marianna T. P. Favaro
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, SP, Brazil, CEP 13083-875
| | - Clelton A. Santos
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, SP, Brazil, CEP 13083-875
| | - Maria Augusta C. Horta
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, SP, Brazil, CEP 13083-875
| | - Aline Crucello
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, SP, Brazil, CEP 13083-875
| | - Lilian L. Beloti
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, SP, Brazil, CEP 13083-875
| | - Fabian Romero
- Departamento de Química Orgânica, Instituto de Química, Universidade Estadual de Campinas, Campinas, SP, Brazil, CEP 13083-970
| | - Ljubica Tasic
- Departamento de Química Orgânica, Instituto de Química, Universidade Estadual de Campinas, Campinas, SP, Brazil, CEP 13083-970
| | | | - Anete P. de Souza
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, SP, Brazil, CEP 13083-875
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, SP, Brazil, CEP 13083-862
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11
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Ariff A, Wise MJ, Kahler CM, Tay CY, Peters F, Perkins TT, Chang BJ. Novel Moraxella catarrhalis prophages display hyperconserved non-structural genes despite their genomic diversity. BMC Genomics 2015; 16:860. [PMID: 26497500 PMCID: PMC4619438 DOI: 10.1186/s12864-015-2104-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 10/16/2015] [Indexed: 11/25/2022] Open
Abstract
Background Moraxella catarrhalis is an important pathogen that often causes otitis media in children, a disease that is not currently vaccine preventable. Asymptomatic colonisation of the human upper respiratory tract is common and lack of clearance by the immune system is likely due to the emergence of seroresistant genetic lineages. No active bacteriophages or prophages have been described in this species. This study was undertaken to identify and categorise prophages in M. catarrhalis, their genetic diversity and the relationship of such diversity with the host-species phylogeny. Results This study presents a comparative analysis of 32 putative prophages identified in 95 phylogenetically variable, newly sequenced M. catarrhalis genomes. The prophages were genotypically classified into four diverse clades. The genetic synteny of each clade is similar to the group 1 phage family Siphoviridae, however, they form genotypic clusters that are distinct from other members of this family. No core genetic sequences exist across the 32 prophages despite clades 2, 3, and 4 sharing the most sequence identity. The analysis of non-structural prophage genes (coding the integrase, and terminase), and portal gene showed that the respective genes were identical for clades 2, 3, and 4, but unique for clade 1. Empirical analysis calculated that these genes are unexpectedly hyperconserved, under purifying selection, suggesting a tightly regulated functional role. As such, it is improbable that the prophages are decaying remnants but stable components of a fluctuating, flexible and unpredictable system ultimately maintained by functional constraints on non-structural and packaging genes. Additionally, the plate encoding genes were well conserved across all four prophage clades, and the tail fibre genes, commonly responsible for receptor recognition, were clustered into three major groups distributed across the prophage clades. A pan-genome of 283,622 bp was identified, and the prophages were mapped onto the diverse M. catarrhalis multi-locus sequence type (MLST) backbone. Conclusion This study has provided the first evidence of putatively mobile prophages in M. catarrhalis, identifying a diverse and fluctuating system dependent on the hyperconservation of a few key, non-structural genes. Some prophages harbour virulence-related genes, and potentially influence the physiology and virulence of M. catarrhalis. Importantly our data will provide supporting information on the identification of novel prophages in other species by adding greater weight to the identification of non-structural genes. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2104-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Amir Ariff
- School of Pathology and Laboratory Medicine, The University of Western Australia, Perth, WA, Australia.
| | - Michael J Wise
- School of Chemistry and Biochemistry, The University of Western Australia, Perth, WA, Australia.
| | - Charlene M Kahler
- School of Pathology and Laboratory Medicine, The University of Western Australia, Perth, WA, Australia.
| | - Chin Yen Tay
- School of Pathology and Laboratory Medicine, The University of Western Australia, Perth, WA, Australia.
| | - Fanny Peters
- School of Pathology and Laboratory Medicine, The University of Western Australia, Perth, WA, Australia.
| | - Timothy T Perkins
- School of Pathology and Laboratory Medicine, The University of Western Australia, Perth, WA, Australia.
| | - Barbara J Chang
- School of Pathology and Laboratory Medicine, The University of Western Australia, Perth, WA, Australia.
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12
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Transcriptome reprogramming by plasmid-encoded transcriptional regulators is required for host niche adaption of a macrophage pathogen. Infect Immun 2015; 83:3137-45. [PMID: 26015480 DOI: 10.1128/iai.00230-15] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Accepted: 05/18/2015] [Indexed: 11/20/2022] Open
Abstract
Rhodococcus equi is a facultative intracellular pathogen of macrophages, relying on the presence of a conjugative virulence plasmid harboring a 21-kb pathogenicity island (PAI) for growth in host macrophages. The PAI encodes a family of 6 virulence-associated proteins (Vaps) in addition to 20 other proteins. The contribution of these to virulence has remained unclear. We show that the presence of only 3 virulence plasmid genes (of 73 in total) is required and sufficient for intracellular growth. These include a single vap family member, vapA, and two PAI-located transcriptional regulators, virR and virS. Both transcriptional regulators are essential for wild-type-level expression of vapA, yet vapA expression alone is not sufficient to allow intracellular growth. A whole-genome microarray analysis revealed that VirR and VirS substantially integrate themselves into the chromosomal regulatory network, significantly altering the transcription of 18% of all chromosomal genes. This pathoadaptation involved significant enrichment of select gene ontologies, in particular, enrichment of genes involved in transport processes, energy production, and cellular metabolism, suggesting a major change in cell physiology allowing the bacterium to grow in the hostile environment of the host cell. The results suggest that following the acquisition of the virulence plasmid by an avirulent ancestor of R. equi, coevolution between the plasmid and the chromosome took place, allowing VirR and VirS to regulate the transcription of chromosomal genes in a process that ultimately promoted intracellular growth. Our findings suggest a mechanism for cooption of existing chromosomal traits during the evolution of a pathogenic bacterium from an avirulent saprophyte.
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Okoko T, Blagova EV, Whittingham JL, Dover LG, Wilkinson AJ. Structural characterisation of the virulence-associated protein VapG from the horse pathogen Rhodococcus equi. Vet Microbiol 2015; 179:42-52. [PMID: 25746683 PMCID: PMC4518536 DOI: 10.1016/j.vetmic.2015.01.027] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Revised: 01/30/2015] [Accepted: 01/31/2015] [Indexed: 01/20/2023]
Abstract
The 3-dimensional structure of a Rhodococcus equi virulence protein was determined. VapG comprises a closed beta barrel domain preceded by a natively disordered region. The structures of VapB, VapD and VapG are closely superimposable. The VAP structures lack recognisable ligand or protein binding sites. Phagosome-induced conformational changes may be required for virulence.
Virulence and host range in Rhodococcus equi depends on the variable pathogenicity island of their virulence plasmids. Notable gene products are a family of small secreted virulence-associated proteins (Vaps) that are critical to intramacrophagic proliferation. Equine-adapted strains, which cause severe pyogranulomatous pneumonia in foals, produce a cell-associated VapA that is necessary for virulence, alongside five other secreted homologues. In the absence of biochemical insight, attention has turned to the structures of these proteins to develop a functional hypothesis. Recent studies have described crystal structures for VapD and a truncate of the VapA orthologue of porcine-adapted strains, VapB. Here, we crystallised the full-length VapG and determined its structure by molecular replacement. Electron density corresponding to the N-terminal domain was not visible suggesting that it is disordered. The protein core adopted a compact elliptical, anti-parallel β-barrel fold with β1–β2–β3–β8–β5–β6–β7–β4 topology decorated by a single peripheral α-helix unique to this family. The high glycine content of the protein allows close packing of secondary structural elements. Topologically, the surface has no indentations that indicate a nexus for molecular interactions. The distribution of polar and apolar groups on the surface of VapG is markedly uneven. One-third of the surface is dominated by exposed apolar side-chains, with no ionisable and only four polar side-chains exposed, giving rise to an expansive flat hydrophobic surface. Other surface regions are more polar, especially on or near the α-helix and a belt around the centre of the β-barrel. Possible functional significance of these recent structures is discussed.
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Affiliation(s)
- Tebekeme Okoko
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK
| | - Elena V Blagova
- Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, UK
| | - Jean L Whittingham
- Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, UK.
| | - Lynn G Dover
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK
| | - Anthony J Wilkinson
- Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, UK
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