OnlineFirst Articles
Research Papers

Isolation, characterization and genomic analysis of a novel lytic bacteriophage infecting Agrobacterium tumefaciens

PDF
  • Miloud SABRI,
  • kaoutar EL HANDI,
  • Orges CARA,
  • Angelo DE STRADIS,
  • Toufic ELBEAINO
Miloud SABRI
International Centre for Advanced Mediterranean Agronomic Studies (CIHEAM of Bari), Via Ceglie 9, 70010 Valenzano (Ba)
kaoutar EL HANDI
International Centre for Advanced Mediterranean Agronomic Studies (CIHEAM of Bari), Via Ceglie 9, 70010 Valenzano (Ba)
Orges CARA
International Centre for Advanced Mediterranean Agronomic Studies (CIHEAM of Bari), Via Ceglie 9, 70010 Valenzano (Ba)
Angelo DE STRADIS
National Research Council of Italy (CNR), Institute for Sustainable Plant Protection (IPSP), University of Bari, Via Amendola 165/A, 70126 Bari
Toufic ELBEAINO
International Centre for Advanced Mediterranean Agronomic Studies (CIHEAM of Bari), Via Ceglie 9, 70010 Valenzano (Ba)
DOI: https://doi.org/10.36253/phyto-15623
Categories

Published 2024-11-15

Keywords

  • Plant pathogenic bacteria,
  • Biocontrol,
  • crown gall,
  • phage therapy

How to Cite

[1]
M. SABRI, kaoutar EL HANDI, O. CARA, A. DE STRADIS, and T. ELBEAINO, “Isolation, characterization and genomic analysis of a novel lytic bacteriophage infecting Agrobacterium tumefaciens”, Phytopathol. Mediterr., pp. 323–334, Nov. 2024.

Copyright (c) 2024 Miloud SABRI, kaoutar EL HANDI, Orges CARA, Angelo DE STRADIS, Toufic ELBEAINO

Creative Commons License

This work is licensed under a Creative Commons Attribution 4.0 International License.

Crossref
Scopus
Google Scholar
Europe PMC

Abstract

Agrobacterium tumefaciens causes crown gall, and economic losses in important crops, including apple, pear, peach, and almond. Difficulties controlling this disease with conventional pesticides require alternative antibacterial agents. A novel lytic bacteriophage, Agrobacterium phage PAT1 (PAT1), with high lysis potential against A. tumefaciens, was isolated from wastewater. Interaction between PAT1 and A. tumefaciens cells was investigated using transmission electron microscopy. PAT1 adsorbed, infected, and replicated on A. tumefaciens in ≤30 min. Turbidity assays showed that PAT1 [Multiplicity of Infection (MOI) = 1] inhibited A. tumefaciens growth by 82% for 48 hours. PAT1 was resistant to broad ranges of pH (4 to 10) and temperatures (4 to 60°C). Bioinformatics analyses of the PAT1 genomic sequence showed that the bacteriophage was closely related to Atuphduovirus (Autographiviridae) phages. The PAT1 genome size was 45,040 base pairs with a G+C content of 54.5%, consisting of 54 coding sequences (CDS), of which the functions of 23 CDS were predicted, including an endolysin gene which could be used as an antimicrobial against A. tumefaciens. No lysogenic mediated genes or genes encoding virulence factors, antibiotic resistance, or toxins were detected in PAT1 genome. The bacteriophage showed potential as a biocontrol agent against A. tumefaciens infections, expanding the limited catalogue of lytic A. tumefaciens phages, although efficacy for control of crown gall in planta remains to be evaluated.

PDF

Downloads

Download data is not yet available.

Metrics

Metrics Loading ...

References

  1. Álvarez B., López M.M., Biosca E.G., 2019. Biocontrol of the major plant pathogen Ralstonia solanacearum in irrigation water and host plants by novel waterborne lytic bacteriophages. Frontiers in Microbiology 10, https://doi.org/10.3389/fmicb.2019.02813.
  2. Asghari S., Harighi B., Ashengroph M., Clement C., Aziz A., Esmaeel Q., Ait Barka E., 2020. Induction of systemic resistance to Agrobacterium tumefaciens by endophytic bacteria in grapevine. Plant Pathology 69: 827–837. https://doi.org/10.1111/ppa.13175.
  3. Attai H., Brown P.J.B., 2019. Isolation and characterization T4- and T7-Like phages that infect the bacterial plant pathogen Agrobacterium tumefaciens. Viruses 11: 528. https://doi.org/10.3390/v11060528.
  4. Attai H., Boon M., Phillips K., Noben J.-P., Lavigne R., Brown P.J.B., 2018. Larger than life: Isolation and genomic characterization of a Jumbo phage that infects the bacterial plant pathogen, Agrobacterium tumefaciens. Frontiers in Microbiology 9: 1861. https://doi.org/10.3389/fmicb.2018.01861.
  5. Attai H., Rimbey J., Smith G.P., Brown P.J.B., 2017. Expression of a peptidoglycan hydrolase from lytic bacteriophages Atu_ph02 and Atu_ph03 triggers lysis of Agrobacterium tumefaciens. Applied and Environmental Microbiology, 83: e01498-17. https://doi.org/10.1128/AEM.01498-17.
  6. Borges A.L., 2021. How to train your bacteriophage. Proceedings of the National Academy of Sciences, 118: e2109434118. https://doi.org/10.1073/pnas.2109434118.
  7. Choi O., Bae J., Kang B., Lee Y., Kim S., Fuqua C., Kim J., 2019. Simple and economical biosensors for distinguishing Agrobacterium-mediated plant galls from nematode-mediated root knots. Scientific Reports, Nature Publishing Group 9: 17961. https://doi.org/10.1038/s41598-019-54568-2.
  8. Deschamps S., Mudge J., Cameron C., Ramaraj T., Anand A., Fengler K., Hayes K., Liaca V., Jones T.J., May G., 2016. Characterization, correction and de novo assembly of an Oxford Nanopore genomic dataset from Agrobacterium tumefaciens. Scientific Reports, Nature Publishing Group 6: 28625. https://doi.org/10.1038/srep28625.
  9. Eckardt N.A., 2006. A genomic analysis of tumor development and source-sink relationships in Agrobacterium-induced crown gall disease in Arabidopsis. The Plant Cell 18: 3350–3352. https://doi.org/10.1105/tpc.107.050294.
  10. Egido J.E., Costa A.R., Aparicio-Maldonado C., Haas P.J., Brouns S.J.J., 2022. Mechanisms and clinical importance of bacteriophage resistance. FEMS Microbiology Reviews 46: fuab048. https://doi.org/10.1093/femsre/fuab048.
  11. Etminani F., Harighi B., Mozafari A.A., 2022. Effect of volatile compounds produced by endophytic bacteria on virulence traits of grapevine crown gall pathogen, Agrobacterium tumefaciens. Scientific Reports, Nature Publishing Group 12: 10510. https://doi.org/10.1038/s41598-022-14864-w.
  12. Federici S., Nobs S.P., Elinav E., 2021. Phages and their potential to modulate the microbiome and immunity. Cellular & Molecular Immunology 18: 889–904. https://doi.org/10.1038/s41423-020-00532-4.
  13. Fischetti V.A., 2018. Development of phage lysins as novel therapeutics: A historical perspective. Viruses 10: 310. https://doi.org/10.3390/v10060310.
  14. Fortuna K.J., Holtappels D., Venneman J., Baeyen S., Vallino M., Verwilt P., Rediers H., De Coninck B., Maes M., Van Varenbergh J, Lavigne R., Wagemans J., 2023. Back to therRoots: Agrobacterium-specific phages show potential to disinfect nutrient solution from hydroponic greenhouses. Applied and Environmental Microbiology 89: e00215-23. https://doi.org/10.1128/aem.00215-23.
  15. Gencay Y.E., Jasinskytė D., Robert C., Semsey S., Martínez V., et al., Sommer M.O.A., 2024. Engineered phage with antibacterial CRISPR–Cas selectively reduce E. coli burden in mice. Nature Biotechnology 42: 265–274. https://doi.org/10.1038/s41587-023-01759-y.
  16. Hyman P., Abedon S.T., 2010. Bacteriophage host range and bacterial resistance. Advances in Applied Microbiology 70: 217–248. https://doi.org/10.1016/S0065-2164(10)70007-1.
  17. Jia H.-J., Jia P.-P., Yin S., Bu L.-K., Yang G., Pei D.-S., 2023. Engineering bacteriophages for enhanced host range and efficacy: insights from bacteriophage-bacteria interactions. Frontiers in Microbiology 14. https://doi.org/10.3389/fmicb.2023.1172635.
  18. Kawaguchi A., Nita M., Ishii T., Watanabe M., Noutoshi Y., 2019. Biological control agent Rhizobium (=Agrobacterium) vitis strain ARK-1 suppresses expression of the essential and non-essential vir genes of tumorigenic R. vitis. BMC Research Notes 12: 1. https://doi.org/10.1186/s13104-018-4038-6.
  19. Khan F.M., Rasheed F., Yang Y., Liu B., Zhang R., 2024. Endolysins: a new antimicrobial agent against antimicrobial resistance. Strategies and opportunities in overcoming the challenges of endolysins against Gram-negative bacteria. Frontiers in Pharmacology 15. https://doi.org/10.3389/fphar.2024.1385261.
  20. Kim N.-H., Park W.B., Cho J.E., Choi Y.J., Choi S.J., et al., Kim H.B., 2018. Effects of phage endolysin SAL200 combined with antibiotics on Staphylococcus aureus infection. Antimicrobial Agents and Chemotherapy 62: 10.1128/aac.00731-18. https://doi.org/10.1128/aac.00731-18.
  21. Knezevic P., Aleksic Sabo V., 2019. Combining bacteriophages with other antibacterial agents to combat bacteria. (A. Górski, R. Międzybrodzki and J. Borysowski, ed.), Cham, Springer International Publishing, 257–293. https://doi.org/10.1007/978-3-030-26736-0_10.
  22. Kropinski A.M., Van den Bossche A., Lavigne R., Noben J.-P., Babinger P., Schmitt R., 2012. Genome and proteome analysis of 7-7-1, a flagellotropic phage infecting Agrobacterium sp H13-3. Virology Journal 9: 102. https://doi.org/10.1186/1743-422X-9-102.
  23. Kropinski A.M., Mazzocco A., Waddell T.E., Lingohr E., Johnson R.P., 2009. Enumeration of bacteriophages by double agar overlay plaque assay. Methods in Molecular Biology 501: 69–76. https://doi.org/10.1007/978-1-60327-164-6_7.
  24. Lee C.-W., Efetova M., Engelmann J.C., Kramell R., Wasternack C., et a.,Deeken R., 2009. Agrobacterium tumefaciens promotes tumor induction by modulating pathogen defense in Arabidopsis thaliana. The Plant Cell 21: 2948–2962. https://doi.org/10.1105/tpc.108.064576.
  25. Liu B., Guo Q., Li Z., Guo X., Liu X., 2023. Bacteriophage endolysin: A powerful weapon to control bacterial biofilms. The Protein Journal 42: 463–476. https://doi.org/10.1007/s10930-023-10139-z.
  26. Loc-Carrillo C., Abedon S.T., 2011. Pros and cons of phage therapy. Bacteriophage 1: 111–114. https://doi.org/10.4161/bact.1.2.14590.
  27. Nazir A., Xu X., Liu Y., Chen Y., 2023. Phage endolysins: advances in the world of food safety. Cells 12: 2169. https://doi.org/10.3390/cells12172169.
  28. Nishimura Y., Yoshida T., Kuronishi M., Uehara H., Ogata H., Goto S., 2017. ViPTree: the viral proteomic tree server. Bioinformatics 33: 2379–2380. https://doi.org/10.1093/bioinformatics/btx157.
  29. Nittolo T., Ravindran A., Gonzalez C.F., Ramsey J., 2019. Complete genome sequence of Agrobacterium tumefaciens Myophage Milano. Microbiology Resource Announcements 8: e00587-19. https://doi.org/10.1128/MRA.00587-19.
  30. Penyalver R., Vicedo B., López M.M., 2000. Use of the genetically engineered Agrobacterium strain K1026 for biological control of crown gall. European Journal of Plant Pathology 106: 801–810. DOI : 10.1023/A:1008785813757.
  31. Sabri M., El Handi K., Valentini F., De Stradis A., Achbani E.H., et al., Elbeaino T., 2022. Identification and characterization of Erwinia Phage IT22: A new bacteriophage-based biocontrol against Erwinia amylovora. Viruses 14: 2455. https://doi.org/10.3390/v14112455.
  32. Sabri M., El Handi K., Cara O., De Stradis A., Valentini F., Elbeaino T., 2024. Xylella phage MATE 2: a novel bacteriophage with potent lytic activity against Xylella fastidiosa subsp. pauca. Frontiers in Microbiology 15. https://doi.org/10.3389/fmicb.2024.1412650.
  33. Svircev A., Roach D., Castle A., 2018. Framing the future with bacteriophages in agriculture. Viruses 10: 218. https://doi.org/10.3390/v10050218.
  34. Thompson M.G., Moore W.M., Hummel N.F.C., Pearson A.N., Barnum C.R., et al., Shih P.M., 2020. Agrobacterium tumefaciens: A bacterium primed for synthetic biology. BioDesign Research 8189219. https://doi.org/10.34133/2020/8189219.
  35. Vicedo B., Peñalver R., Asins M.J., López M.M., 1993. Biological control of i, colonization, and pAgK84 transfer with i K84 and the tra- mutant strain K1026. Applied and Environmental Microbiology 59: 309–315.
  36. Vu N.T., Oh C.-S., 2020. Bacteriophage usage for bacterial disease management and diagnosis in plants. The Plant Pathology Journal 36: 204–217. https://doi.org/10.5423/PPJ.RW.04.2020.0074.
  37. Wong K.Y., Megat Mazhar Khair M.H., Song A.A.-L., Masarudin M.J., Chong C.M., et al., Teo M.Y.M., 2022. Endolysins against Streptococci as an antibiotic alternative. Frontiers in Microbiology 13: https://doi.org/10.3389/fmicb.2022.935145.
  38. Xu H.-M., Xu W.-M., Zhang L., 2022. Current status of phage therapy against infectious diseases and potential application beyond infectious diseases. International Journal of Clinical Practice 2022: 4913146. https://doi.org/10.1155/2022/4913146.

Most read articles by the same author(s)

<< < 1 2