1
|
Ostenfeld LJ, Sørensen AN, Neve H, Vitt A, Klumpp J, Sørensen MCH. A hybrid receptor binding protein enables phage F341 infection of Campylobacter by binding to flagella and lipooligosaccharides. Front Microbiol 2024; 15:1358909. [PMID: 38380094 PMCID: PMC10877375 DOI: 10.3389/fmicb.2024.1358909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 01/18/2024] [Indexed: 02/22/2024] Open
Abstract
Flagellotropic bacteriophages are interesting candidates as therapeutics against pathogenic bacteria dependent on flagellar motility for colonization and causing disease. Yet, phage resistance other than loss of motility has been scarcely studied. Here we developed a soft agar assay to study flagellotropic phage F341 resistance in motile Campylobacter jejuni. We found that phage adsorption was prevented by diverse genetic mutations in the lipooligosaccharides forming the secondary receptor of phage F341. Genome sequencing showed phage F341 belongs to the Fletchervirus genus otherwise comprising capsular-dependent C. jejuni phages. Interestingly, phage F341 encodes a hybrid receptor binding protein (RBP) predicted as a short tail fiber showing partial similarity to RBP1 encoded by capsular-dependent Fletchervirus, but with a receptor binding domain similar to tail fiber protein H of C. jejuni CJIE1 prophages. Thus, C. jejuni prophages may represent a genetic pool from where lytic Fletchervirus phages can acquire new traits like recognition of new receptors.
Collapse
Affiliation(s)
- Line Jensen Ostenfeld
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | | | - Horst Neve
- Department of Microbiology and Biotechnology, Max-Rubner Institut, Kiel, Germany
| | - Amira Vitt
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Jochen Klumpp
- Institute for Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | | |
Collapse
|
2
|
Orellana R, Arancibia A, Badilla L, Acosta J, Arancibia G, Escar R, Ferrada G, Seeger M. Ecophysiological Features Shape the Distribution of Prophages and CRISPR in Sulfate Reducing Prokaryotes. Microorganisms 2021; 9:microorganisms9050931. [PMID: 33925267 PMCID: PMC8146710 DOI: 10.3390/microorganisms9050931] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 04/18/2021] [Accepted: 04/23/2021] [Indexed: 12/28/2022] Open
Abstract
Sulfate reducing prokaryotes (SRP) are a phylogenetically and physiologically diverse group of microorganisms that use sulfate as an electron acceptor. SRP have long been recognized as key players of the carbon and sulfur cycles, and more recently, they have been identified to play a relevant role as part of syntrophic and symbiotic relations and the human microbiome. Despite their environmental relevance, there is a poor understanding about the prevalence of prophages and CRISPR arrays and how their distribution and dynamic affect the ecological role of SRP. We addressed this question by analyzing the results of a comprehensive survey of prophages and CRISPR in a total of 91 genomes of SRP with several genotypic, phenotypic, and physiological traits, including genome size, cell volume, minimum doubling time, cell wall, and habitat, among others. Our analysis discovered 81 prophages in 51 strains, representing the 56% of the total evaluated strains. Prophages are non-uniformly distributed across the SRP phylogeny, where prophage-rich lineages belonged to Desulfovibrionaceae and Peptococcaceae. Furthermore, our study found 160 CRISPR arrays in 71 SRP, which is more abundant and widely spread than previously expected. Although there is no correlation between presence and abundance of prophages and CRISPR arrays at the strain level, our analysis showed that there is a directly proportional relation between cellular volumes and number of prophages per cell. This result suggests that there is an additional selective pressure for strains with smaller cells to get rid of foreign DNA, such as prophages, but not CRISPR, due to less availability of cellular resources. Analysis of the prophage genes encoding viral structural proteins reported that 44% of SRP prophages are classified as Myoviridae, and comparative analysis showed high level of homology, but not synteny, among prophages belonging to the Family Desulfovibrionaceae. We further recovered viral-like particles and structures that resemble outer membrane vesicles from D. vulgaris str. Hildenborough. The results of this study improved the current understanding of dynamic interactions between prophages and CRISPR with their hosts in both cultured and hitherto-uncultured SRP strains, and how their distribution affects the microbial community dynamics in several sulfidogenic natural and engineered environments.
Collapse
Affiliation(s)
- Roberto Orellana
- Laboratorio de Biología Celular y Ecofisiología Microbiana, Facultad de Ciencias Naturales y Exactas, Universidad de Playa Ancha, Leopoldo Carvallo 270, Valparaíso 2360001, Chile; (A.A.); (L.B.)
- Correspondence:
| | - Alejandra Arancibia
- Laboratorio de Biología Celular y Ecofisiología Microbiana, Facultad de Ciencias Naturales y Exactas, Universidad de Playa Ancha, Leopoldo Carvallo 270, Valparaíso 2360001, Chile; (A.A.); (L.B.)
| | - Leonardo Badilla
- Laboratorio de Biología Celular y Ecofisiología Microbiana, Facultad de Ciencias Naturales y Exactas, Universidad de Playa Ancha, Leopoldo Carvallo 270, Valparaíso 2360001, Chile; (A.A.); (L.B.)
| | - Jonathan Acosta
- Departamento de Estadística, Pontificia Universidad Católica de Chile, Avda. Vicuña Mackenna 4860, Santiago 7820436, Chile;
| | - Gabriela Arancibia
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química & Centro de Biotecnología Daniel Alkalay-Lowitt, Universidad Técnica Federico Santa María, Avenida España 1680, Valparaíso 2390123, Chile; (G.A.); (R.E.); (G.F.); (M.S.)
| | - Rodrigo Escar
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química & Centro de Biotecnología Daniel Alkalay-Lowitt, Universidad Técnica Federico Santa María, Avenida España 1680, Valparaíso 2390123, Chile; (G.A.); (R.E.); (G.F.); (M.S.)
| | - Gustavo Ferrada
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química & Centro de Biotecnología Daniel Alkalay-Lowitt, Universidad Técnica Federico Santa María, Avenida España 1680, Valparaíso 2390123, Chile; (G.A.); (R.E.); (G.F.); (M.S.)
| | - Michael Seeger
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química & Centro de Biotecnología Daniel Alkalay-Lowitt, Universidad Técnica Federico Santa María, Avenida España 1680, Valparaíso 2390123, Chile; (G.A.); (R.E.); (G.F.); (M.S.)
| |
Collapse
|
3
|
Dunstan RA, Pickard D, Dougan S, Goulding D, Cormie C, Hardy J, Li F, Grinter R, Harcourt K, Yu L, Song J, Schreiber F, Choudhary J, Clare S, Coulibaly F, Strugnell RA, Dougan G, Lithgow T. The flagellotropic bacteriophage YSD1 targets Salmonella Typhi with a Chi-like protein tail fibre. Mol Microbiol 2019; 112:1831-1846. [PMID: 31556164 DOI: 10.1111/mmi.14396] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/23/2019] [Indexed: 11/29/2022]
Abstract
The discovery of a Salmonella-targeting phage from the waterways of the United Kingdom provided an opportunity to address the mechanism by which Chi-like bacteriophage (phage) engages with bacterial flagellae. The long tail fibre seen on Chi-like phages has been proposed to assist the phage particle in docking to a host cell flagellum, but the identity of the protein that generates this fibre was unknown. We present the results from genome sequencing of this phage, YSD1, confirming its close relationship to the original Chi phage and suggesting candidate proteins to form the tail structure. Immunogold labelling in electron micrographs revealed that YSD1_22 forms the main shaft of the tail tube, while YSD1_25 forms the distal part contributing to the tail spike complex. The long curling tail fibre is formed by the protein YSD1_29, and treatment of phage with the antibodies that bind YSD1_29 inhibits phage infection of Salmonella. The host range for YSD1 across Salmonella serovars is broad, but not comprehensive, being limited by antigenic features of the flagellin subunits that make up the Salmonella flagellum, with which YSD1_29 engages to initiate infection.
Collapse
Affiliation(s)
- Rhys A Dunstan
- Infection and Immunity Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, 3800, Australia
| | - Derek Pickard
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK.,Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge, UK
| | - Sam Dougan
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - David Goulding
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Claire Cormie
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Joshua Hardy
- Infection and Immunity Program, Department of Biochemistry & Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, 3800, Australia
| | - Fuyi Li
- Infection and Immunity Program, Department of Biochemistry & Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, 3800, Australia
| | - Rhys Grinter
- Infection and Immunity Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, 3800, Australia.,School of Biological Sciences, Monash University, Clayton, 3800, Australia
| | | | - Lu Yu
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Jiangning Song
- Infection and Immunity Program, Department of Biochemistry & Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, 3800, Australia
| | | | - Jyoti Choudhary
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Simon Clare
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Fasseli Coulibaly
- Infection and Immunity Program, Department of Biochemistry & Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, 3800, Australia
| | - Richard A Strugnell
- Department of Microbiology and Immunology, The Peter Doherty Institute, The University of Melbourne, Parkville, 3052, Australia
| | - Gordon Dougan
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK.,Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge, UK
| | - Trevor Lithgow
- Infection and Immunity Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, 3800, Australia
| |
Collapse
|
5
|
Kropinski AM, Van den Bossche A, Lavigne R, Noben JP, Babinger P, Schmitt R. Genome and proteome analysis of 7-7-1, a flagellotropic phage infecting Agrobacterium sp H13-3. Virol J 2012; 9:102. [PMID: 22650361 PMCID: PMC3517404 DOI: 10.1186/1743-422x-9-102] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2012] [Accepted: 05/04/2012] [Indexed: 11/16/2022] Open
Abstract
Background The flagellotropic phage 7-7-1 infects motile cells of Agrobacterium sp H13-3 by attaching to and traveling along the rotating flagellar filament to the secondary receptor at the base, where it injects its DNA into the host cell. Here we describe the complete genomic sequence of 69,391 base pairs of this unusual bacteriophage. Methods The sequence of the 7-7-1 genome was determined by pyro(454)sequencing to a coverage of 378-fold. It was annotated using MyRAST and a variety of internet resources. The structural proteome was analyzed by SDS-PAGE coupled electrospray ionization-tandem mass spectrometry (MS/MS). Results Sequence annotation and a structural proteome analysis revealed 127 open reading frames, 84 of which are unique. In six cases 7-7-1 proteins showed sequence similarity to proteins from the virulent Burkholderia myovirus BcepB1A. Unique features of the 7-7-1 genome are the physical separation of the genes encoding the small (orf100) and large (orf112) subunits of the DNA packaging complex and the apparent lack of a holin-lysin cassette. Proteomic analysis revealed the presence of 24 structural proteins, five of which were identified as baseplate (orf7), putative tail fibre (orf102), portal (orf113), major capsid (orf115) and tail sheath (orf126) proteins. In the latter case, the N-terminus was removed during capsid maturation, probably by a putative prohead protease (orf114).
Collapse
Affiliation(s)
- Andrew M Kropinski
- Laboratory for Foodborne Zoonoses, Public Health Agency of Canada, Guelph, ON, NIG 3W4, Canada.
| | | | | | | | | | | |
Collapse
|
6
|
Alternative mechanism for bacteriophage adsorption to the motile bacterium Caulobacter crescentus. Proc Natl Acad Sci U S A 2011; 108:9963-8. [PMID: 21613567 DOI: 10.1073/pnas.1012388108] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
2D and 3D cryo-electron microscopy, together with adsorption kinetics assays of Cb13 and CbK phage-infected Caulobacter crescentus, provides insight into the mechanisms of infection. Cb13 and CbK actively interact with the flagellum and subsequently attach to receptors on the cell pole. We present evidence that the first interaction of the phage with the bacterial flagellum takes place through a filament on the phage head. This contact with the flagellum facilitates concentration of phage particles around the receptor (i.e., the pilus portals) on the bacterial cell surface, thereby increasing the likelihood of infection. Phage head filaments have not been well characterized and their function is described here. Phage head filaments may systematically underlie the initial interactions of phages with their hosts in other systems and possibly represent a widespread mechanism of efficient phage propagation.
Collapse
|
7
|
Quintero EJ, Busch K, Weiner RM. Spatial and Temporal Deposition of Adhesive Extracellular Polysaccharide Capsule and Fimbriae by
Hyphomonas
Strain MHS-3. Appl Environ Microbiol 1998; 64:1246-55. [PMID: 16349537 PMCID: PMC106137 DOI: 10.1128/aem.64.4.1246-1255.1998] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
ABSTRACT
Hyphomonas
strain MHS-3, a member of a genus of primary colonizers of surfaces immersed in marine water, synthesizes two structures that mediate adhesion to solid substrata, namely, capsular exopolysaccharide and fimbriae. Specific stains, gold-labelled lectins, and monoclonal antibodies, along with transmission electron microscopy of synchronized populations, revealed that both structures are polarly and temporally expressed. The timed synthesis and placement of the fimbriae and capsule correlated with the timing and locus of MHS-3 adhesion.
Collapse
Affiliation(s)
- E J Quintero
- Department of Microbiology, University of Maryland, College Park, Maryland 20742
| | | | | |
Collapse
|