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Diversity of limestone bacteriophages infecting Dickeya solani isolated in the Czech Republic

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Abstract

Seven novel tailed lytic viruses (Ds3CZ, Ds5CZ, Ds9CZ, Ds16CZ, Ds20CZ, Ds23CZ, Ds25CZ) infecting the bacterium Dickeya solani were isolated in the Czech Republic. Genomes of these viruses are dsDNA, 149,364 to 155,285 bp in length, and the genome arrangement is very similar to that of the type virus Dickeya virus LIMEstone 1. All but the Ds25CZ virus should be regarded as strains of a single species. Most of the sequence differences are due to the presence or absence of homing endonuclease (HE) genes, with 23 HEs found in Ds3CZ, Ds5CZ, and Ds20CZ, 22 in Ds9CZ, 19 in Ds16CZ, 18 in Ds25CZ, and 15 in Ds23CZ.

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References

  1. Tsror L, Lebiush S, Erlich O, Ben-Daniel B, van der Wolf J (2010) First report of latent infection of Cyperus rotundus caused by a biovar 3 Dickeya sp. (Syn. Erwinia chrysanthemi) in Israel. New Dis Rep 22:14. https://doi.org/10.5197/j.2044-0588.2010.022.014

    Article  Google Scholar 

  2. CABI Invasive species compendium (2019) https://www.cabi.org/isc/datasheet/120278#todistribution

  3. Khayi S, Blin P, Pédron J, Chong T, Chan K, Moumni M, Hélias V, Gijsegem F, Faure D (2015) Population genomics reveals additive and replacing horizontal gene transfers in the emerging pathogen Dickeya solani. BMC Genom 16:788. https://doi.org/10.1186/s12864-015-1997-z

    Article  CAS  Google Scholar 

  4. Parkinson N, Pritchard L, Bryant R, Toth I, Elphinstone J (2015) Epidemiology of Dickeya dianthicola and Dickeya solani in ornamental hosts and potato studied using variable number tandem repeat analysis. Eur J Plant Pathol 141:63–70. https://doi.org/10.1007/s10658-014-0523-5

    Article  Google Scholar 

  5. Czajkowski R, de Boer WJ, van Veen JA, van der Wolf JM (2012) Studies on the interaction between the biocontrol agent, Serratia plymuthica A30, and blackleg-causing Dickeya sp. (biovar 3) in potato (Solanum tuberosum). Plant Pathol 61:677–688. https://doi.org/10.1111/j.1365-3059.2011.02565.x

    Article  Google Scholar 

  6. Adriaenssens EM, van Vaerenbergh J, van den Heuvel D, Dunon V, Ceyssens PJ, de Proft M, Kropinski AM, Noben JP, Maes M, Lavigne R (2012) T4-related bacteriophage LIMEstone isolates for the control of soft rot on potato caused by 'Dickeya solani’. PLoS ONE 7:e33227. https://doi.org/10.1371/journal.pone.0033227

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Czajkowski R, Ozymko Z, Zwirowski S, Lojkowska E (2014) Complete genome sequence of a broad-host-range lytic Dickeya spp. bacteriophage phiD5. Arch Virol 159:3153–3155. https://doi.org/10.1007/s00705-014-2170-8

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Czajkowski R, Ozymko Z, Siwinska J, Ossowicki A, de Jager V, Narajczyk M, Lojkowska E (2015) The complete genome, structural proteome, comparative genomics and phylogenetic analysis of a broad host lytic bacteriophage varphiD3 infecting pectinolytic Dickeya spp. Stand Genomic Sci 10:68. https://doi.org/10.1186/s40793-015-0068-z

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Czajkowski R, Ozymko Z, de Jager V, Siwinska J, Smolarska A, Ossowicki A, Narajczyk M, Lojkowska E (2015) Genomic, proteomic and morphological characterization of two novel broad host lytic bacteriophages PhiPD10.3 and PhiPD23.1 infecting pectinolytic Pectobacterium spp. and Dickeya spp. PLoS ONE 10:e0119812. https://doi.org/10.1371/journal.pone.0119812

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Kabanova AP, Shneider MM, Korzhenkov AA, Bugaeva EN, Miroshnikov KK, Zdorovenko EL, Kulikov EE, Toschakov SV, Ignatov AN, Knirel YA, Miroshnikov KA (2019) Host specificity of the Dickeya bacteriophage PP35 is directed by a tail spike interaction with bacterial O-antigen, enabling the infection of alternative non-pathogenic bacterial host. Front Microbiol 9:3288. https://doi.org/10.3389/fmicb.2018.03288

    Article  PubMed  PubMed Central  Google Scholar 

  11. Czajkowski R, Ozymko Z, Lojkowska E (2014) Isolation and characterization of novel soilborne lytic bacteriophages infecting Dickeya spp. Biovar 3 (“D. solani”). Plant Pathol 63:758–772. https://doi.org/10.1111/ppa.12157

    Article  Google Scholar 

  12. Aziz RK, Bartels D, Best AA et al (2008) The RAST server: rapid annotations using subsystems technology. BMC Genom 9:75. https://doi.org/10.1186/1471-2164-9-75

    Article  CAS  Google Scholar 

  13. Kumar S, Stecher G, Tamura K (2016) Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874. https://doi.org/10.1093/molbev/msw054

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Edgell DR, Gibb EA, Belfort M (2010) Mobile DNA elements in T4 and related phages. Virol J 7:290. https://doi.org/10.1186/1743-422X-7-290

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Stoddard BL (2011) Homing endonucleases: from microbial genetic invaders to reagents for targeted DNA modification. Structure 19:7–15. https://doi.org/10.1016/j.str.2010.12.003

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Taylor GK, Stoddard BL (2012) Structural, functional and evolutionary relationships between homing endonucleases and proteins from their host organisms. Nucleic Acids Res 40:5189–5200. https://doi.org/10.1093/nar/gks226

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Kropinski AM, Anany H, Kuhn JH, Tolstoy I, Kutter E, Adriaenssens EM (2017) To create a new bacteriophage family, Ackermann viridae, containing two (2) new subfamilies including four (4) genera. ICTV Taxon Hist Limestonevirus. https://doi.org/10.13140/RG.2.2.29173.88800

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Acknowledgements

This research work was supported by project QK1910028 from the Ministry of Agriculture of the Czech Republic and by institutional funding RVO60077344.

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Authors and Affiliations

  1. Department of Plant Virology, Institute of Plant Molecular Biology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, České Budějovice, Czech Republic

    Karel Petrzik, Sára Brázdová & Igor Koloniuk

  2. PRI Havlíčkův Brod, Dobrovského 2366, 580 01, Havlíčkův Brod, Czech Republic

    Josef Vacek

  3. VŠCHT, Technická 1905/5, Praha 6-Dejvice, 160 00, Prague, Czech Republic

    Rudolf Ševčík

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  1. Karel Petrzik
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  2. Josef Vacek
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  3. Sára Brázdová
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  4. Rudolf Ševčík
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  5. Igor Koloniuk
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Correspondence to Karel Petrzik.

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The authors declare no conflict of interest. The funding sponsors had no role in the design of the study, in the collection, analysis, or interpretation of data, in the writing of the manuscript, or in the decision to publish the results.

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Petrzik, K., Vacek, J., Brázdová, S. et al. Diversity of limestone bacteriophages infecting Dickeya solani isolated in the Czech Republic. Arch Virol 166, 1171–1175 (2021). https://doi.org/10.1007/s00705-020-04926-7

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  • DOI: https://doi.org/10.1007/s00705-020-04926-7

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