Skip to main content
SpringerLink
Log in

Synthetic Biology to Engineer Bacteriophage Genomes

  • Protocol
  • First Online:
Bacteriophage Therapy

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2734))

Abstract

Recent advances in the synthetic biology field have enabled the development of new molecular biology techniques used to build specialized bacteriophages with new functionalities. Bacteriophages have been engineered toward a wide range of applications, including pathogen control and detection, targeted drug delivery, or even assembly of new materials.

In this chapter, two strategies that have been successfully used to genetically engineer bacteriophage genomes will be addressed: the bacteriophage recombineering of electroporated DNA (BRED) and the yeast-based phage-engineering platform.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 149.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Hardcover Book
USD 199.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Clark JR, March JB (2006) Bacteriophages and biotechnology: vaccines, gene therapy and antibacterials. Trends Biotechnol 24:212–218

    Article  CAS  PubMed  Google Scholar 

  2. Kutter E, De Vos D, Gvasalia G et al (2010) Phage therapy in clinical practice: treatment of human infections. Curr Pharm Biotechnol 11:69–86

    Article  CAS  PubMed  Google Scholar 

  3. Endersen L, O’Mahony J, Hill C et al (2014) Phage therapy in the food industry. Annu Rev Food Sci Technol 5:327–349

    Article  CAS  Google Scholar 

  4. Jones JB, Jackson LE, Balogh B et al (2007) Bacteriophages for plant disease control. Annu Rev Phytopathol 45:245–262

    Article  CAS  PubMed  Google Scholar 

  5. Monk AB, Rees CD, Barrow P et al (2010) Bacteriophage applications: where are we now? Lett Appl Microbiol 51:363–369

    Article  CAS  PubMed  Google Scholar 

  6. Kilcher S, Loessner MJ (2019) Engineering bacteriophages as versatile biologics. Trends Microbiol 27:355–367

    Article  CAS  PubMed  Google Scholar 

  7. Schmelcher M, Loessner MJ (2014) Application of bacteriophages for detection of foodborne pathogens. Bacteriophage 4:e28137

    Article  PubMed  PubMed Central  Google Scholar 

  8. Lu TK, Bowers J, Koeris MS (2013) Advancing bacteriophage-based microbial diagnostics with synthetic biology. Trends Biotechnol 31:325–327

    Article  CAS  PubMed  Google Scholar 

  9. Yacoby I, Bar H, Benhar I (2007) Targeted drug-carrying bacteriophages as antibacterial nanomedicines. Antimicrob Agents Chemother 51:2156–2163

    Article  CAS  PubMed Central  Google Scholar 

  10. Ju Z, Sun W (2017) Drug delivery vectors based on filamentous bacteriophages and phage-mimetic nanoparticles. Drug Deliv 24:1898

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Pires DP, Cleto S, Sillankorva S et al (2016) Genetically engineered phages: a review of advances over the last decade. Microbiol Mol Biol Rev 80:523–543

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Mahler M, Costa AR, van Beljouw SPB et al (2022) Approaches for bacteriophage genome engineering. Trends Biotechnol 41:669

    Article  PubMed  Google Scholar 

  13. Marinelli LJ, Piuri M, Swigonová Z et al (2008) BRED: a simple and powerful tool for constructing mutant and recombinant bacteriophage genomes. PLoS One 3:e3957

    Article  PubMed  PubMed Central  Google Scholar 

  14. Marinelli LJ, Hatfull GF, Piuri M (2012) Recombineering: a powerful tool for modification of bacteriophage genomes. Bacteriophage 2:5–14

    Article  PubMed  PubMed Central  Google Scholar 

  15. Fehér T, Karcagi I, Blattner FR et al (2012) Bacteriophage recombineering in the lytic state using the lambda red recombinases. Microb Biotechnol 5:466–476

    Article  PubMed  PubMed Central  Google Scholar 

  16. Nobrega FL, Costa AR, Santos JF et al (2016) Genetically manipulated phages with improved pH resistance for oral administration in veterinary medicine. Sci Rep 6:1–12

    Article  Google Scholar 

  17. Ramirez-Chamorro L, Boulanger P, Rossier O (2021) Strategies for bacteriophage T5 mutagenesis: expanding the toolbox for phage genome engineering. Front Microbiol 12:667332

    Article  PubMed  PubMed Central  Google Scholar 

  18. Hupfeld M, Trasanidou D, Ramazzini L et al (2018) A functional type II-A CRISPR–Cas system from Listeria enables efficient genome editing of large non-integrating bacteriophage. Nucleic Acids Res 46:6920

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Møller-Olsen C, Ho SFS, Shukla RD et al (2018) Engineered K1F bacteriophages kill intracellular Escherichia coli K1 in human epithelial cells. Sci Reports 81(8):1–18

    Google Scholar 

  20. Bari SMN, Walker FC, Cater K et al (2017) Strategies for editing virulent staphylococcal phages using CRISPR-Cas10. ACS Synth Biol 6:2316–2325

    Article  CAS  PubMed  Google Scholar 

  21. Box AM, McGuffie MJ, O’Hara BJ et al (2016) Functional analysis of bacteriophage immunity through a type I-E CRISPR-Cas system in Vibrio cholerae and its application in bacteriophage genome engineering. J Bacteriol 198:578–590

    Article  CAS  PubMed Central  Google Scholar 

  22. Guan J, Bosch AO, Mendoza SD et al (2022) RNA targeting with CRISPR-Cas13a facilitates bacteriophage genome engineering. 2022.02.14.480438

    Google Scholar 

  23. Adler BA, Hessler T, Cress BF et al (2022) Broad-spectrum CRISPR-Cas13a enables efficient phage genome editing. Nat Microbiol 712(7):1967–1979

    Article  Google Scholar 

  24. Ando H, Lemire S, Pires DP et al (2015) Engineering modular viral scaffolds for targeted bacterial population editing. Cell Syst 1:187–196

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Pires DP, Monteiro R, Mil-Homens D et al (2021) Designing P. aeruginosa synthetic phages with reduced genomes. Sci Rep 11:2164

    Article  CAS  PubMed Central  Google Scholar 

  26. Latka A, Lemire S, Grimon D et al (2021) Engineering the modular receptor-binding proteins of Klebsiella phages switches their capsule serotype specificity. MBio 12:e00455-21

    Article  PubMed Central  Google Scholar 

  27. Kilcher S, Studer P, Muessner C et al (2018) Cross-genus rebooting of custom-made, synthetic bacteriophage genomes in L-form bacteria. Proc Natl Acad Sci U S A 115:567–572

    Article  CAS  PubMed Central  Google Scholar 

  28. Dunne M, Rupf B, Tala M et al (2019) Reprogramming bacteriophage host range through structure-guided design of chimeric receptor binding proteins. Cell Rep 29:1336–1350.e4

    Article  PubMed  Google Scholar 

  29. Shin J, Jardine P, Noireaux V (2012) Genome replication, synthesis, and assembly of the bacteriophage T7 in a single cell-free reaction. ACS Synth Biol 1:408–413

    Article  CAS  PubMed  Google Scholar 

  30. Garamella J, Marshall R, Rustad M et al (2016) The All E. coli TX-TL toolbox 2.0: a platform for cell-free synthetic biology. ACS Synth Biol 5:344–355

    Article  CAS  Google Scholar 

  31. Rustad M, Eastlund A, Jardine P et al (2018) Cell-free TXTL synthesis of infectious bacteriophage T4 in a single test tube reaction. Synth Biol 3:ysy002

    Article  CAS  Google Scholar 

  32. Emslander Q, Vogele K, Braun P et al (2022) Cell-free production of personalized therapeutic phages targeting multidrug-resistant bacteria. Cell Chem Biol 29:1434–1445.e7

    Article  PubMed  Google Scholar 

  33. Liang J, Zhang H, Tan YL et al (2022) Directed evolution of replication-competent double-stranded DNA bacteriophage toward new host specificity. ACS Synth Biol 11:634–643

    Article  CAS  PubMed  Google Scholar 

  34. Murphy KC (2007) The λ gam protein inhibits RecBCD binding to dsDNA ends. J Mol Biol 371:19–24

    Article  CAS  PubMed  Google Scholar 

  35. Court R, Cook N, Saikrishnan K et al (2007) The crystal structure of λ-gam protein suggests a model for RecBCD inhibition. J Mol Biol 371:25–33

    Article  CAS  PubMed  Google Scholar 

  36. Datsenko KA, Wanner BL (2000) One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc Natl Acad Sci U S A 97:6640–6645

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Hanahan D (1983) Studies on transformation of Escherichia coli with plasmids. J Mol Biol 166:557–580

    Article  CAS  PubMed  Google Scholar 

  38. Xu K, Hua J, Roberts KJ et al (2012) Production of recombineering substrates with standard-size PCR primers. FEMS Microbiol Lett 337:97

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgments

The authors acknowledge the financial support from the Portuguese Foundation for Science and Technology (FCT) under the scope of the project EXPL/EMD-EMD/1142/2021, the strategic funding of UIDB/04469/2020 unit, and by LABBELS – Associate Laboratory in Biotechnology, Bioengineering and Microelectromechnaical Systems, LA/P/0029/2020.

Author information

Authors and Affiliations

  1. Department of Bionanoscience, Delft University of Technology, Delft, the Netherlands

    Ana Rita Costa

  2. CEB – Centre of Biological Engineering, University of Minho, Braga, Portugal

    Joana Azeredo & Diana Priscila Pires

  3. LABBELS – Associate Laboratory, Braga, Guimarães, Portugal

    Joana Azeredo & Diana Priscila Pires

Authors
  1. Ana Rita Costa
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Joana Azeredo
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Diana Priscila Pires
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Diana Priscila Pires .

Editor information

Editors and Affiliations

  1. Centre of Biological Engineering, University of Minho, Braga, Portugal

    Joana Azeredo

  2. International Iberian Nanotechnology Laboratory, Braga, Portugal

    Sanna Sillankorva

Rights and permissions

Reprints and permissions

Copyright information

© 2024 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature

About this protocol

Check for updates. Verify currency and authenticity via CrossMark

Cite this protocol

Costa, A.R., Azeredo, J., Pires, D.P. (2024). Synthetic Biology to Engineer Bacteriophage Genomes. In: Azeredo, J., Sillankorva, S. (eds) Bacteriophage Therapy. Methods in Molecular Biology, vol 2734. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3523-0_17

Download citation

  • DOI: https://doi.org/10.1007/978-1-0716-3523-0_17

  • Published:

  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-3522-3

  • Online ISBN: 978-1-0716-3523-0

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation