DOI QR코드

DOI QR Code

Isolation and Characterization of a Weizmannia coagulans Bacteriophage Youna2 and Its Endolysin PlyYouna2

  • Bokyung Son (Department of Food Biotechnology, Dong-A University) ;
  • Youna Kim (Department of Food Science and Technology, Seoul National University of Science and Technology) ;
  • Booyoung Yu (Department of Food Science and Technology, Seoul National University of Science and Technology) ;
  • Minsuk Kong (Department of Food Science and Technology, Seoul National University of Science and Technology)
  • Received : 2023.03.16
  • Accepted : 2023.04.27
  • Published : 2023.08.28

Abstract

Weizmannia coagulans (formerly Bacillus coagulans) is Gram-positive, and spore-forming bacteria causing food spoilage, especially in acidic canned food products. To control W. coagulans, we isolated a bacteriophage Youna2 from a sewage sludge sample. Morphological analysis revealed that phage Youna2 belongs to the Siphoviridae family with a non-contractile and flexible tail. Youna2 has 52,903 bp double-stranded DNA containing 61 open reading frames. There are no lysogeny-related genes, suggesting that Youna2 is a virulent phage. plyYouna2, a putative endolysin gene was identified in the genome of Youna2 and predicted to be composed of a N-acetylmuramoyl-L-alanine amidase domain (PF01520) at the N-terminus and unknown function DUF5776 domain (PF19087) at the C-terminus. While phage Youna2 has a narrow host range, infecting only certain strains of W. coagulans, PlyYouna2 exhibited a broad antimicrobial spectrum beyond the Bacillus genus. Interestingly, PlyYouna2 can lyse Gram-negative bacteria such as Escherichia coli, Yersinia enterocolitica, Pseudomonas putida and Cronobacter sakazakii without other additives to destabilize bacterial outer membrane. To the best of our knowledge, Youna2 is the first W. coagulans-infecting phage and we speculate its endolysin PlyYouna2 can provide the basis for the development of a novel biocontrol agent against various foodborne pathogens.

Keywords

Acknowledgement

This work was supported by the National Research Foundation of Korea (NRF) grant funded by the Korean government (MSIT) (No., no. 2020R1C1C1008127, to M.K.) and Green Fusion Technology Program funded by Ministry of Environment, Republic of Korea (to B.S.).

References

  1. Clokie MR, Millard AD, Letarov AV, Heaphy S. 2011. Phages in nature. Bacteriophage 1: 31-45. https://doi.org/10.4161/bact.1.1.14942
  2. Garcia P, Martinez B, Obeso J, Rodriguez A. 2008. Bacteriophages and their application in food safety. Lett. Appl. Microbiol. 47: 479-485. https://doi.org/10.1111/j.1472-765X.2008.02458.x
  3. Lu TK, Koeris MS. 2011. The next generation of bacteriophage therapy. Curr. Opin. Microbiol. 14: 524-531. https://doi.org/10.1016/j.mib.2011.07.028
  4. Polaska M, Sokolowska B. 2019. Bacteriophages-a new hope or a huge problem in the food industry. AIMS Microbiol. 5: 324.
  5. Goodridge LD, Bisha B. 2011. Phage-based biocontrol strategies to reduce foodborne pathogens in foods. Bacteriophage 1: 130-137. https://doi.org/10.4161/bact.1.3.17629
  6. Schmelcher M, Donovan DM, Loessner MJ. 2012. Bacteriophage endolysins as novel antimicrobials. Future Microbiol. 7: 1147-1171. https://doi.org/10.2217/fmb.12.97
  7. Bai J, Kim YT, Ryu S, Lee JH. 2016. Biocontrol and rapid detection of food-borne pathogens using bacteriophages and endolysins. Front. Microbiol. 7: 474.
  8. Fischetti VA. 2008. Bacteriophage lysins as effective antibacterials. Curr. Opin. Microbiol. 11: 393-400. https://doi.org/10.1016/j.mib.2008.09.012
  9. Borysowski J, Weber-Dabrowska B, Gorski A. 2006. Bacteriophage endolysins as a novel class of antibacterial agents. Exp. Biol. Med. 231: 366-377. https://doi.org/10.1177/153537020623100402
  10. Loessner MJ. 2005. Bacteriophage endolysins-current state of research and applications. Curr. Opin. Microbiol. 8: 480-487. https://doi.org/10.1016/j.mib.2005.06.002
  11. Andre S, Vallaeys T, Planchon S. 2017. Spore-forming bacteria responsible for food spoilage. Res. Microbiol. 168: 379-387. https://doi.org/10.1016/j.resmic.2016.10.003
  12. Kuroda A, Sugimoto Y, Funahashi T, Sekiguchi J. 1992. Genetic structure, isolation and characterization of a Bacillus licheniformis cell wall hydrolase. Mol. Gen. Genet. 234: 129-137. https://doi.org/10.1007/BF00272354
  13. Lucas R, Grande MJ, Abriouel H, Maqueda M, Omar NB, Valdivia E, et al. 2006. Application of the broad-spectrum bacteriocin enterocin AS-48 to inhibit Bacillus coagulans in canned fruit and vegetable foods. Food Chem. Toxicol. 44: 1774-1781. https://doi.org/10.1016/j.fct.2006.05.019
  14. Konuray G, Erginkaya Z. 2018. Potential use of Bacillus coagulans in the food industry. Foods 7: 92.
  15. Gupta RS, Patel S, Saini N, Chen S. 2020. Robust demarcation of 17 distinct Bacillus species clades, proposed as novel Bacillaceae genera, by phylogenomics and comparative genomic analyses: description of Robertmurraya kyonggiensis sp. nov. and proposal for an emended genus Bacillus limiting it only to the members of the Subtilis and Cereus clades of species. Int. J. Syst. Evol. Microbiol. 70: 5753-5798. https://doi.org/10.1099/ijsem.0.004475
  16. Haberbeck LU, da Silva Riehl CA, Salomao BdCM, De Aragao GMF. 2012. Bacillus coagulans spore inactivation through the application of oregano essential oil and heat. LWT-Food Sci. Technol. 46: 267-273. https://doi.org/10.1016/j.lwt.2011.09.021
  17. Kim JJ, Kim HK. 2021. Antioxidant and antibacterial activity of caprylic acid vanillyl ester produced by lipase-mediated transesterification. J. Microbiol. Biotechnol. 31: 317-326 https://doi.org/10.4014/jmb.2010.10018
  18. Lee JH, Shin H, Son B, Heu S, Ryu S. 2013. Characterization and complete genome sequence of a virulent bacteriophage B4 infecting food-borne pathogenic Bacillus cereus. Arch. Virol. 158: 2101-2108. https://doi.org/10.1007/s00705-013-1719-2
  19. Adams MJ, Lefkowitz EJ, King AM, Harrach B, Harrison RL, Knowles NJ, et al. 2017. 50 years of the International Committee on Taxonomy of Viruses: progress and prospects. Arch. Virol. 162: 1441-1446. https://doi.org/10.1007/s00705-016-3215-y
  20. Wilcox S, Toder R, Foster J. 1996. Rapid isolation of recombinant lambda phage DNA for use in fluorescence in situ hybridization. Chromosome Res. 4: 397-404. https://doi.org/10.1007/BF02257276
  21. McNair K, Aziz RK, Pusch GD, Overbeek R, Dutilh BE, Edwards R. 2018. Phage genome annotation using the RAST pipeline. Methods Mol. Biol. 1681: 231-238. https://doi.org/10.1007/978-1-4939-7343-9_17
  22. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, et al. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25: 3389-3402. https://doi.org/10.1093/nar/25.17.3389
  23. Grant JR, Stothard P. 2008. The CGView Server: a comparative genomics tool for circular genomes. Nucleic Acids Res. 36: W181-W184. https://doi.org/10.1093/nar/gkn179
  24. Jumper J, Evans R, Pritzel A, Green T, Figurnov M, Ronneberger O, et al. 2021. Highly accurate protein structure prediction with AlphaFold. Nature 596: 583-589. https://doi.org/10.1038/s41586-021-03819-2
  25. DeLano WL. 2002. Pymol: an open-source molecular graphics tool. CCP4 Newsl. Protein Crystallogr. 40: 82-92.
  26. Son B, Yun J, Lim JA, Shin H, Heu S, Ryu S. 2012. Characterization of LysB4, an endolysin from the Bacillus cereus-infecting bacteriophage B4. BMC Microbiol. 12: 33.
  27. Ha E, Son B, Ryu S. 2018. Clostridium perfringens virulent bacteriophage CPS2 and its thermostable endolysin lysCPS2. Viruses 10: 251.
  28. Knecht LE, Veljkovic M, Fieseler L. 2020. Diversity and function of phage encoded depolymerases. Front. Microbiol. 10: 2949.
  29. Loessner MJ, Inman RB, Lauer P, Calendar R. 2000. Complete nucleotide sequence, molecular analysis and genome structure of bacteriophage A118 of Listeria monocytogenes: implications for phage evolution. Mol. Microbiol. 35: 324-340. https://doi.org/10.1046/j.1365-2958.2000.01720.x
  30. Shavrina M, Zimin A, Molochkov N, Chernyshov S, Machulin A, Mikoulinskaia G. 2016. In vitro study of the antibacterial effect of the bacteriophage T5 thermostable endolysin on Escherichia coli cells. J. Appl. Microbiol. 121: 1282-1290. https://doi.org/10.1111/jam.13251
  31. Lood R, Winer BY, Pelzek AJ, Diez-Martinez R, Thandar M, Euler CW, et al. 2015. Novel phage lysin capable of killing the multidrug-resistant gram-negative bacterium Acinetobacter baumannii in a mouse bacteremia model. Antimicrob. Agents Chemother. 59: 1983-1991. https://doi.org/10.1128/AAC.04641-14
  32. Lim JA, Shin H, Heu S, Ryu S. 2014. Exogenous lytic activity of SPN9CC endolysin against gram-negative bacteria. J. Microbiol. Biotechnol. 24: 803-811. https://doi.org/10.4014/jmb.1403.03035
  33. Gontijo MTP, Jorge GP, Brocchi M. 2021. Current status of endolysin-based treatments against Gram-negative bacteria. Antibiotics 10: 1143.
  34. Antonova NP, Vasina DV, Lendel AM, Usachev EV, Makarov VV, Gintsburg AL, et al. 2019. Broad bactericidal activity of the Myoviridae bacteriophage lysins LysAm24, LysECD7, and LysSi3 against Gram-negative ESKAPE pathogens. Viruses 11: 284.
  35. Antonova NP, Vasina DV, Rubalsky EO, Fursov MV, Savinova AS, Grigoriev IV, et al. 2020. Modulation of endolysin LysECD7 bactericidal activity by different peptide tag fusion. Biomolecules 10: 440.