1
|
Jørgensen JB, Djurhuus AM, Carstens AB, Kot W, Neve H, Morris CE, Hansen LH. Presentation of Three Novel Tailed Phages Targeting Multiple Strains of Pseudomonas syringae. Phage (New Rochelle) 2020; 1:245-250. [PMID: 36147285 PMCID: PMC9041480 DOI: 10.1089/phage.2020.0040] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Background: Pseudomonas syringae are ubiquitous epiphytic plant pathogens infecting a wide range of important agricultural plant species. Bacteriophages has been proposed as biocontrol agents against plant pathogens, however, in order to utilize this approach, a deeper understanding of phage diversity and phage-host interactions is required. Materials and Methods: Phages targeting P. syringae GAW0113 were isolated from organic waste samples. Three distinct phage isolates were purified and subjected to whole-genome sequencing, comparative genomics, transmission electron microscopy and host-range assay using a wide selection of diverse P. syringae isolates. Results: The three phage isolates, Pseudomonas phage Bertil, Misse, and Strit, were shown to have podovirus morphology with a short tail stub and isometric head. They had double-stranded DNA ranging from 41,342 to 41,374 bp in size comprising 50-51 open reading frames. The three phage genomes were highly similar and genomic comparison analyses showed that they all belong to the Autographiviridae family of the order Caudovirales. All three phages were shown to have a narrow host-range. Conclusions: The three phages were shown to share morphological and genomic features with other phages in the Autographiviridae family, however, based on the limited nucleotide similarity we propose that the phages constitute a novel genus. All three phages were found to infect multiple strains of P. syringae covering several phylogroups.
Collapse
Affiliation(s)
- Jacob B. Jørgensen
- Department of Plant and Environmental Science, University of Copenhagen, Frederiksberg, Denmark
| | - Amaru M. Djurhuus
- Department of Plant and Environmental Science, University of Copenhagen, Frederiksberg, Denmark
| | - Alexander B. Carstens
- Department of Plant and Environmental Science, University of Copenhagen, Frederiksberg, Denmark
| | - Witold Kot
- Department of Plant and Environmental Science, University of Copenhagen, Frederiksberg, Denmark
| | - Horst Neve
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Kiel, Germany
| | | | - Lars H. Hansen
- Department of Plant and Environmental Science, University of Copenhagen, Frederiksberg, Denmark
- Address correspondence to: Lars H. Hansen, PhD, Department of Plant and Environmental Science, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg 1871, Denmark
| |
Collapse
|
2
|
Kot W, Olsen NS, Nielsen TK, Hutinet G, de Crécy-Lagard V, Cui L, Dedon PC, Carstens AB, Moineau S, Swairjo MA, Hansen LH. Detection of preQ0 deazaguanine modifications in bacteriophage CAjan DNA using Nanopore sequencing reveals same hypermodification at two distinct DNA motifs. Nucleic Acids Res 2020; 48:10383-10396. [PMID: 32941607 PMCID: PMC7544227 DOI: 10.1093/nar/gkaa735] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 08/19/2020] [Accepted: 08/26/2020] [Indexed: 12/22/2022] Open
Abstract
In the constant evolutionary battle against mobile genetic elements (MGEs), bacteria have developed several defense mechanisms, some of which target the incoming, foreign nucleic acids e.g. restriction-modification (R-M) or CRISPR-Cas systems. Some of these MGEs, including bacteriophages, have in turn evolved different strategies to evade these hurdles. It was recently shown that the siphophage CAjan and 180 other viruses use 7-deazaguanine modifications in their DNA to evade bacterial R-M systems. Among others, phage CAjan genome contains a gene coding for a DNA-modifying homolog of a tRNA-deazapurine modification enzyme, together with four 7-cyano-7-deazaguanine synthesis genes. Using the CRISPR-Cas9 genome editing tool combined with the Nanopore Sequencing (ONT) we showed that the 7-deazaguanine modification in the CAjan genome is dependent on phage-encoded genes. The modification is also site-specific and is found mainly in two separate DNA sequence contexts: GA and GGC. Homology modeling of the modifying enzyme DpdA provides insight into its probable DNA binding surface and general mode of DNA recognition.
Collapse
Affiliation(s)
- Witold Kot
- Department of Plant and Environmental Science, University of Copenhagen, Denmark
| | - Nikoline S Olsen
- Department of Environmental Science, Aarhus University, Roskilde, Denmark
| | - Tue K Nielsen
- Department of Plant and Environmental Science, University of Copenhagen, Denmark
| | - Geoffrey Hutinet
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL USA
| | - Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL USA.,Genetics Institute, University of Florida, Gainesville, FL, USA
| | - Liang Cui
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore
| | - Peter C Dedon
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Alexander B Carstens
- Department of Plant and Environmental Science, University of Copenhagen, Denmark
| | - Sylvain Moineau
- Département de biochimie, de microbiologie et de bio-informatique, Université Laval, Québec City, PQ, Canada.,Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, PQ, Canada.,Félix d'Hérelle Reference Center for Bacterial Viruses, Université Laval, Québec City, PQ, Canada
| | - Manal A Swairjo
- Department of Chemistry and Biochemistry and the Viral Information Institute, San Diego State University, San Diego, CA, USA
| | - Lars H Hansen
- Department of Plant and Environmental Science, University of Copenhagen, Denmark
| |
Collapse
|
3
|
Hylling O, Carstens AB, Kot W, Hansen M, Neve H, Franz CMAP, Johansen A, Ellegaard-Jensen L, Hansen LH. Two novel bacteriophage genera from a groundwater reservoir highlight subsurface environments as underexplored biotopes in bacteriophage ecology. Sci Rep 2020; 10:11879. [PMID: 32681144 PMCID: PMC7368026 DOI: 10.1038/s41598-020-68389-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 06/12/2020] [Indexed: 11/09/2022] Open
Abstract
Although bacteriophages are central entities in bacterial ecology and population dynamics, there is currently no literature on the genomes of bacteriophages isolated from groundwater. Using a collection of bacterial isolates from an aquifer as hosts, this study isolated, sequenced and characterised two bacteriophages native to the groundwater reservoir. Host phylogenetic analyses revealed that the phages targeted B. mycoides and a novel Pseudomonas species. These results suggest that both bacteriophages represent new genera, highlighting that groundwater reservoirs, and probably other subsurface environments as well, are underexplored biotopes in terms of the presence and ecology of bacteriophages.
Collapse
Affiliation(s)
- Ole Hylling
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, 4000, Roskilde, Denmark
| | - Alexander B Carstens
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, 4000, Roskilde, Denmark.,Department of Plant- and Environmental Sciences, Section for Microbial Ecology and Biotechnology, University of Copenhagen, Copenhagen, Denmark
| | - Witold Kot
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, 4000, Roskilde, Denmark.,Department of Plant- and Environmental Sciences, Section for Microbial Ecology and Biotechnology, University of Copenhagen, Copenhagen, Denmark
| | - Martin Hansen
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, 4000, Roskilde, Denmark
| | - Horst Neve
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Hermann-Weigmann-Straße 1, 24103, Kiel, Germany
| | - Charles M A P Franz
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Hermann-Weigmann-Straße 1, 24103, Kiel, Germany
| | - Anders Johansen
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, 4000, Roskilde, Denmark
| | - Lea Ellegaard-Jensen
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, 4000, Roskilde, Denmark
| | - Lars H Hansen
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, 4000, Roskilde, Denmark. .,Department of Plant- and Environmental Sciences, Section for Microbial Ecology and Biotechnology, University of Copenhagen, Copenhagen, Denmark.
| |
Collapse
|
4
|
Hutinet G, Kot W, Cui L, Hillebrand R, Balamkundu S, Gnanakalai S, Neelakandan R, Carstens AB, Fa Lui C, Tremblay D, Jacobs-Sera D, Sassanfar M, Lee YJ, Weigele P, Moineau S, Hatfull GF, Dedon PC, Hansen LH, de Crécy-Lagard V. 7-Deazaguanine modifications protect phage DNA from host restriction systems. Nat Commun 2019; 10:5442. [PMID: 31784519 PMCID: PMC6884629 DOI: 10.1038/s41467-019-13384-y] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 11/04/2019] [Indexed: 12/14/2022] Open
Abstract
Genome modifications are central components of the continuous arms race between viruses and their hosts. The archaeosine base (G+), which was thought to be found only in archaeal tRNAs, was recently detected in genomic DNA of Enterobacteria phage 9g and was proposed to protect phage DNA from a wide variety of restriction enzymes. In this study, we identify three additional 2'-deoxy-7-deazaguanine modifications, which are all intermediates of the same pathway, in viruses: 2'-deoxy-7-amido-7-deazaguanine (dADG), 2'-deoxy-7-cyano-7-deazaguanine (dPreQ0) and 2'-deoxy-7- aminomethyl-7-deazaguanine (dPreQ1). We identify 180 phages or archaeal viruses that encode at least one of the enzymes of this pathway with an overrepresentation (60%) of viruses potentially infecting pathogenic microbial hosts. Genetic studies with the Escherichia phage CAjan show that DpdA is essential to insert the 7-deazaguanine base in phage genomic DNA and that 2'-deoxy-7-deazaguanine modifications protect phage DNA from host restriction enzymes.
Collapse
Affiliation(s)
- Geoffrey Hutinet
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, 32611, USA.
| | - Witold Kot
- Department of Environmental Science, Aarhus University, Roskilde, Denmark
| | - Liang Cui
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance Interdisciplinary Research Group, Campus for Research Excellence and Technological Enterprise, Singapore, 138602, Singapore
| | - Roman Hillebrand
- Department of Biological Engineering and Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Nitto Denko Avecia, 125 Fortune Boulevard, Milford, MA, 01757, USA
| | - Seetharamsingh Balamkundu
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance Interdisciplinary Research Group, Campus for Research Excellence and Technological Enterprise, Singapore, 138602, Singapore
| | - Shanmugavel Gnanakalai
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance Interdisciplinary Research Group, Campus for Research Excellence and Technological Enterprise, Singapore, 138602, Singapore
| | - Ramesh Neelakandan
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance Interdisciplinary Research Group, Campus for Research Excellence and Technological Enterprise, Singapore, 138602, Singapore
| | | | - Chuan Fa Lui
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Denise Tremblay
- Département de Biochimie, Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, Québec City, QC, G1V 0A6, Canada
- Félix d'Hérelle Reference Center for Bacterial Viruses and Groupe de Recherche en Écologie Buccale, Faculté de Médecine Dentaire, Université Laval, Québec City, QC, G1V 0A6, Canada
| | - Deborah Jacobs-Sera
- Pittsburgh Bacteriophage Institute and Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Mandana Sassanfar
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Yan-Jiun Lee
- Research Department, New England Biolabs, Ipswich, MA, 01938, USA
| | - Peter Weigele
- Research Department, New England Biolabs, Ipswich, MA, 01938, USA
| | - Sylvain Moineau
- Département de Biochimie, Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, Québec City, QC, G1V 0A6, Canada
- Félix d'Hérelle Reference Center for Bacterial Viruses and Groupe de Recherche en Écologie Buccale, Faculté de Médecine Dentaire, Université Laval, Québec City, QC, G1V 0A6, Canada
| | - Graham F Hatfull
- Pittsburgh Bacteriophage Institute and Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Peter C Dedon
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance Interdisciplinary Research Group, Campus for Research Excellence and Technological Enterprise, Singapore, 138602, Singapore
- Department of Biological Engineering and Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Lars H Hansen
- Department of Environmental Science, Aarhus University, Roskilde, Denmark
| | - Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, 32611, USA.
- University of Florida, Genetics Institute, Gainesville, Florida, 32610, USA.
| |
Collapse
|
5
|
Carstens AB, Djurhuus AM, Kot W, Jacobs-Sera D, Hatfull GF, Hansen LH. Unlocking the Potential of 46 New Bacteriophages for Biocontrol of Dickeya Solani. Viruses 2018; 10:E621. [PMID: 30423804 PMCID: PMC6267328 DOI: 10.3390/v10110621] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 11/08/2018] [Accepted: 11/09/2018] [Indexed: 01/12/2023] Open
Abstract
Modern agriculture is expected to face an increasing global demand for food while also needing to comply with higher sustainability standards. Therefore, control of crop pathogens requires new, green alternatives to current methods. Potatoes are susceptible to several bacterial diseases, with infections by soft rot Enterobacteriaceae (SRE) being a significant contributor to the major annual losses. As there are currently no efficient ways of combating SRE, we sought to develop an approach that could easily be incorporated into the potato production pipeline. To this end, 46 phages infecting the emerging potato pathogen Dickeya solani were isolated and thoroughly characterized. The 46 isolated phages were grouped into three different groups based on DNA similarity, representing two distinct clusters and a singleton. One cluster showed similarity to phages previously used to successfully treat soft rot in potatoes, whereas the remaining phages were novel and showed only very limited similarity to previously isolated phages. We selected six diverse phages in order to create the hereto most complex phage cocktail against SRE. The cocktail was applied in a proof-of-principle experiment to treat soft rot in potatoes under simulated storage conditions. We show that the phage cocktail was able to significantly reduce the incidence of soft rot as well as disease severity after 5 days of storage post-infection with Dickeya solani. This confirms results from previous studies that phages represent promising biocontrol agents against SRE infection in potato.
Collapse
Affiliation(s)
- Alexander B Carstens
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, 4000 Roskilde, Denmark.
| | - Amaru M Djurhuus
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, 4000 Roskilde, Denmark.
| | - Witold Kot
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, 4000 Roskilde, Denmark.
| | - Deborah Jacobs-Sera
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA.
| | - Graham F Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA.
| | - Lars H Hansen
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, 4000 Roskilde, Denmark.
| |
Collapse
|