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Cited by 21Bacteriophages and microbial interactionsCRISPR and Genetic EngineeringVirus-based gene therapy research

Synthetic and Functional Engineering of Bacteriophages: Approaches for Tailored Bactericidal, Diagnostic, and Delivery Platforms

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Alessa, Ola, Aiba, Yoshifumi, Arbaah, Mahmoud, Hidaka, Yuya, Watanabe, Shinya, Miyanaga, Kazuhiko, Wannigama, Dhammika Leshan, Cui, Longzhu·2025·Molecules
DOI 10.3390/molecules30153132PMC PMC12348365
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Abstract

Bacteriophages (phages), the most abundant biological entities on Earth, have long served as both model systems and therapeutic tools. Recent advances in synthetic biology and genetic engineering have revolutionized the capacity to tailor phages with enhanced functionality beyond their natural capabilities. This review outlines the current landscape of synthetic and functional engineering of phages, encompassing both in-vivo and in-vitro strategies. We describe in-vivo approaches such as phage recombineering systems, CRISPR-Cas-assisted editing, and bacterial retron-based methods, as well as synthetic assembly platforms including yeast-based artificial chromosomes, Gibson, Golden Gate, and iPac assemblies. In addition, we explore in-vitro rebooting using TXTL (transcription–translation) systems, which offer a flexible alternative to cell-based rebooting but are less effective for large genomes or structurally complex phages. Special focus is given to the design of customized phages for targeted applications, including host range expansion via receptor-binding protein modifications, delivery of antimicrobial proteins or CRISPR payloads, and the construction of biocontained, non-replicative capsid systems for safe clinical use. Through illustrative examples, we highlight how these technologies enable the transformation of phages into programmable bactericidal agents, precision diagnostic tools, and drug delivery vehicles. Together, these advances establish a powerful foundation for next-generation antimicrobial platforms and synthetic microbiology.

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  • Advances in synthetic biology allow phages to be engineered as programmable anticancer agents capable of remodeling the microbiome or delivering immunomodulatory payloads.

    “Advances in synthetic biology now allow phages to be engineered as programmable anticancer agents, capable of remodeling the microbiome or delivering immunomodulatory payloads [30–33]”

    From Phage therapy in oncology: opportunities for cancer prevention and treatment (2026) · cites this paper as [30]

    The Introduction (§1) describes engineered phages as programmable platforms for targeting and payload delivery, and the Conclusions (§5) envisage microbiome editing. Section 4.4 discusses antimicrobial proteins and gene editors as payloads, but the paper does not establish that these phages are programmable anticancer agents or deliver immunomodulatory payloads. Page numbers are not provided in our copy. (LLM, conf=0.85)

    Experimental — accuracy not yet measured

  • Phages can deliver targeted therapeutic payloads.

    “Phages can eliminate cancer-associated bacteria, remodel the tumor microenvironment, enhance antitumor immunity, and deliver targeted therapeutic payloads.”

    From Phage therapy in oncology: opportunities for cancer prevention and treatment (2026) · cites this paper as [30]

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  1. [1]Hankin M.E. L’action Bactéricide Des Eaux de La et Du Gange Sur Le Vibrion Du Choléra Ann. Inst. Pasteur 1896 10 511 523 10.4161/bact.1.3.16736 · DOI
  2. [2]Sulakvelidze A. Alavidze Z. Morris J. Bacteriophage Therapy Antimicrob. Agents Chemother. 2001 45 649 659 10.1128/AAC.45.3.649-659.2001 11181338 PMC90351 · DOI
  3. [3]Twort F.W. An investigation on the nature of ultra-microscopic viruses Lancet 1915 186 1241 1243 10.1016/S0140-6736(01)20383-3 PMC2170983 20475326 · DOI
  4. [4]D’Herelle F. On an invisible microbe antagonistic toward dysenteric bacilli: Brief note by Mr. F. D’Herelle, presented by Mr. Roux. 1917 Res. Microbiol. 2007 158 553 554 10.1016/j.resmic.2007.07.005 17855060 · DOI
  5. [5]Wollman E. The phenomenon of twort-d’hérelle and its significance Lancet 1935 226 1312 1314 10.1016/S0140-6736(00)47383-6 · DOI
  6. [6]Chanishvili N. Phage Therapy—History from Twort and d’Herelle Through Soviet Experience to Current Approaches Adv. Virus Res. 2012 83 3 40 10.1016/B978-0-12-394438-2.00001-3 22748807 · DOI
  7. [7]Peitzman S.J. Félix d’Hérelle and the Origins of Molecular Biology (Review) Bull. Hist. Med. 2001 75 159 161 10.1353/bhm.2001.0036 · DOI
  8. [8]Summers W.C. The Strange History of Phage Therapy Bacteriophage 2012 2 130 133 10.4161/bact.20757 23050223 PMC3442826 · DOI
  9. [9]Hershey A.D. Chase M.M. Independent Functions of Viral Protein and Nucleic Acid in Growth of Bacteriophage J. Gen. Physiol. 1952 36 39 56 10.1085/jgp.36.1.39 12981234 PMC2147348 · DOI
  10. [10]Van Valen D. Wu D. Chen Y.J. Tuson H. Wiggins P. Phillips R. A Single-Molecule Hershey-Chase Experiment Curr. Biol. 2012 22 1339 1343 10.1016/j.cub.2012.05.023 22727695 PMC3462812 · DOI
  11. [11]Hershey A.D. Rotman R. Genetic Recombination between Host-Range and Plaque-Type Mutants of Bacteriophage in Single Bacterial Cells Genetics 1949 34 44 10.1093/genetics/34.1.44 17247304 PMC1209435 · DOI
  12. [12]Harshey R.M. The Mu Story: How a Maverick Phage Moved the Field Forward Mob. DNA 2012 3 21 10.1186/1759-8753-3-21 23217166 PMC3562280 · DOI · Paper page
  13. [13]Pingoud A. Wilson G.G. Wende W. Type II Restriction Endonucleases—A Historical Perspective and More Nucleic Acids Res. 2014 42 7489 7527 10.1093/nar/gku447 24878924 PMC4081073 · DOI
  14. [14]Rossi R. Montecucco A. Ciarrocchi G. Biamonti G. Functional Characterization of the T4 DNA Ligase: A New Insight into the Mechanism of Action Oxford University Press Oxford, UK 1997 Volume 25 10.1093/nar/25.11.2106 PMC146716 9153309 · DOI
  15. [15]Sanger F. Air G.M. Barrell B.G. Brown N.L. Coulson A.R. Fiddes J.C. Hutchison C.A. Slocombe P.M. Smith M. Nucleotide Sequence of Bacteriophage Φx174 DNA Nature 1977 265 687 695 10.1038/265687a0 870828 · DOI
  16. [16]Navarro F. Muniesa M. Phages in the Human Body Front. Microbiol. 2017 8 566 10.3389/fmicb.2017.00566 28421059 PMC5378999 · DOI
  17. [17]Breitbart M. Rohwer F. Here a Virus, There a Virus, Everywhere the Same Virus? Trends Microbiol. 2005 13 278 284 10.1016/j.tim.2005.04.003 15936660 · DOI
  18. [18]Dion M.B. Oechslin F. Moineau S. Phage Diversity, Genomics and Phylogeny Nat. Rev. Microbiol. 2020 18 125 138 10.1038/s41579-019-0311-5 32015529 · DOI
  19. [19]Uyttebroek S. Chen B. Onsea J. Ruythooren F. Debaveye Y. Devolder D. Spriet I. Depypere M. Wagemans J. Lavigne R. Safety and Efficacy of Phage Therapy in Difficult-to-Treat Infections: A Systematic Review Lancet Infect. Dis. 2022 22 e208 e220 10.1016/S1473-3099(21)00612-5 35248167 · DOI
  20. [20]Azam A.H. Tan X.E. Veeranarayanan S. Kiga K. Cui L. Bacteriophage Technology and Modern Medicine Antibiotics 2021 10 999 10.3390/antibiotics10080999 34439049 PMC8388951 · DOI
  21. [21]Pirnay J.P. Djebara S. Steurs G. Griselain J. Cochez C. De Soir S. Glonti T. Spiessens A. Vanden Berghe E. Green S. Personalized Bacteriophage Therapy Outcomes for 100 Consecutive Cases: A Multicentre, Multinational, Retrospective Observational Study Nat. Microbiol. 2024 9 1434 1453 10.1038/s41564-024-01705-x 38834776 PMC11153159 · DOI
  22. [22]Brödel A.K. Charpenay L.H. Galtier M. Fuche F.J. Terrasse R. Poquet C. Havránek J. Pignotti S. Krawczyk A. Arraou M. In Situ Targeted Base Editing of Bacteria in the Mouse Gut Nature 2024 632 877 884 10.1038/s41586-024-07681-w 38987595 PMC11338833 · DOI
  23. [23]Galtier M. Krawczyk A. Fuche F.J. Charpenay L.H. Stzepourginski I. Pignotti S. Arraou M. Terrasse R. Brödel A.K. Poquet C. Treatment of STEC Infection via CRISPR-Cas Targeted Cleavage of the Shiga Toxin Gene in Animal Models bioRxiv 2025 10.1101/2025.02.28.640725 42202049 · DOI
  24. [24]Cunliffe T.G. Parker A.L. Jaramillo A. Pseudotyping Bacteriophage P2 Tail Fibers to Extend the Host Range for Biomedical Applications ACS Synth. Biol. 2022 11 3207 3215 10.1021/acssynbio.1c00629 36084285 PMC9594776 · DOI
  25. [26]Lu T.K. Collins J.J. Dispersing Biofilms with Engineered Enzymatic Bacteriophage Proc. Natl. Acad. Sci. USA 2007 104 11197 11202 10.1073/pnas.0704624104 17592147 PMC1899193 · DOI · Paper page
  26. [27]Cheng L. Deng Z. Tao H. Song W. Xing B. Liu W. Kong L. Yuan S. Ma Y. Wu Y. Harnessing Stepping-Stone Hosts to Engineer, Select, and Reboot Synthetic Bacteriophages in One Pot Cell Rep. Methods 2022 2 100217 10.1016/j.crmeth.2022.100217 35637913 PMC9142689 · DOI
  27. [28]Eghbalpoor F. Gorji M. Alavigeh M.Z. Moghadam M.T. Genetically Engineered Phages and Engineered Phage-Derived Enzymes to Destroy Biofilms of Antibiotics Resistance Bacteria Heliyon 2024 10 e35666 10.1016/j.heliyon.2024.e35666 39170521 PMC11336853 · DOI
  28. [29]Meile S. Du J. Staubli S. Grossmann S. Koliwer-Brandl H. Piffaretti P. Leitner L. Matter C.I. Baggenstos J. Hunold L. Engineered Reporter Phages for Detection of Escherichia Coli, Enterococcus, and Klebsiella in Urine Nat. Commun. 2023 14 4336 10.1038/s41467-023-39863-x 37474554 PMC10359277 · DOI
  29. [30]Kim J. Kim M. Kim S. Ryu S. Sensitive Detection of Viable Escherichia coli O157:H7 from Foods Using a Luciferase-Reporter Phage PhiV10lux Int. J. Food Microbiol. 2017 254 11 17 10.1016/j.ijfoodmicro.2017.05.002 28511109 · DOI
  30. [31]Tamura A. Azam A.H. Nakamura T. Lee K. Iyoda S. Kondo K. Ojima S. Chihara K. Yamashita W. Cui L. Synthetic Phage-Based Approach for Sensitive and Specific Detection of Escherichia coli O157 Commun. Biol. 2024 7 535 10.1038/s42003-024-06247-w 38710842 PMC11074155 · DOI
  31. [32]Pulkkinen E.M. Hinkley T.C. Nugen S.R. Utilizing In Vitro DNA Assembly to Engineer a Synthetic T7 Nanoluc Reporter Phage for Escherichia coli Detection Integr. Biol. 2019 11 63 68 10.1093/intbio/zyz005 30927414 · DOI
  32. [33]Baker Z.R. Zhang Y. Zhang H. Franklin H.C. Serpa P.B.S. Southard T. Li L. Hsu B.B. Sustained in Situ Protein Production and Release in the Mammalian Gut by an Engineered Bacteriophage Nat. Biotechnol. 2025 1 10 10.1038/s41587-025-02570-7 39966654 PMC12353956 · DOI
  33. [34]Dhasmana N. Ram G. McAllister K.N. Chupalova Y. Lopez P. Ross H.F. Novick R.P. Dynamics of Antibacterial Drone Establishment in Staphylococcus Aureus: Unexpected Effects of Antibiotic Resistance Genes mBio 2021 12 e0208321 10.1128/mBio.02083-21 34781740 PMC8593670 · DOI
  34. [35]Fa-Arun J. Huan Y.W. Darmon E. Wang B. Tail-Engineered Phage P2 Enables Delivery of Antimicrobials into Multiple Gut Pathogens ACS Synth. Biol. 2023 12 596 607 10.1021/acssynbio.2c00615 36731126 PMC9942202 · DOI
  35. [36]Kiga K. Tan X.E. Ibarra-Chávez R. Watanabe S. Aiba Y. Sato’o Y. Li F.Y. Sasahara T. Cui B. Kawauchi M. Development of CRISPR-Cas13a-Based Antimicrobials Capable of Sequence-Specific Killing of Target Bacteria Nat. Commun. 2020 11 2934 10.1038/s41467-020-16731-6 32523110 PMC7287087 · DOI
  36. [37]Shimamori Y. Tan X.E. Li F.Y. Nishikawa Y. Watanabe S. Sasahara T. Miyanaga K. Aiba Y. Veeranarayanan S. Thitiananpakorn K. Efficient Synthesis of CRISPR-Cas13a-Antimicrobial Capsids against MRSA Facilitated by Silent Mutation Incorporation Sci. Rep. 2024 14 16225 10.1038/s41598-024-67193-5 39003336 PMC11246472 · DOI
  37. [38]Li F.Y. Tan X.E. Shimamori Y. Kiga K. Veeranarayanan S. Watanabe S. Nishikawa Y. Aiba Y. Sato’o Y. Miyanaga K. Phagemid-Based Capsid System for CRISPR-Cas13a Antimicrobials Targeting Methicillin-Resistant Staphylococcus Aureus Commun. Biol. 2024 7 1 11 10.1038/s42003-024-06754-w 39271957 PMC11399120 · DOI
  38. [39]Mcgillin M. Tokman J.I. Hsu E. Alcaine S.D. Denes T.G. Assessment of Resistance to Colicinogenic Synthetic Phage Antimicrobial System Microbiol. Spectr. 2024 12 e0079324 10.1128/spectrum.00793-24 39405458 PMC11537092 · DOI
  39. [40]Kiga K. Sato’o Y. Tan X.-E. Miyanaga K. Nguyen H.M. Li F.-Y. Azam A.H. Veeranarayanan S. Watanabe S. Aiba Y. Development of a Non-Replicative Phage-Based DNA Delivery System and Its Application to Antimicrobial Therapies PNAS Nexus 2025 4 pgaf176 10.1093/pnasnexus/pgaf176 40491552 PMC12147096 · DOI
  40. [41]Zhu J. Batra H. Ananthaswamy N. Mahalingam M. Tao P. Wu X. Guo W. Fokine A. Rao V.B. Design of Bacteriophage T4-Based Artificial Viral Vectors for Human Genome Remodeling Nat. Commun. 2023 14 2928 10.1038/s41467-023-38364-1 37253769 PMC10229621 · DOI
  41. [42]Wan H. Zhong X. Yang S. Deng J. Song X. Liu Y. Li Y. Yin Z. Zhao X. Enhancing the Therapeutic Potential of Peptide Antibiotics Using Bacteriophage Mimicry Strategies Adv. Sci. 2024 12 2411753 10.1002/advs.202411753 PMC11744576 39587836 · DOI
  42. [43]He Y. Chen J. CRISPR/Cas9-Mediated Genome Editing of T4 Bacteriophage for High-Throughput Antimicrobial Susceptibility Testing Anal. Chem. 2024 96 18301 18310 10.1021/acs.analchem.4c05177 39474820 PMC11561875 · DOI
  43. [44]Huan Y.W. Torraca V. Brown R. Fa-Arun J. Miles S.L. Oyarzún D.A. Mostowy S. Wang B. P1 Bacteriophage-Enabled Delivery of CRISPR-Cas9 Antimicrobial Activity Against Shigella flexneri ACS Synth. Biol. 2023 12 709 721 10.1021/acssynbio.2c00465 36802585 PMC10028697 · DOI
  44. [45]Valencia-Toxqui G. Ramsey J. How to Introduce a New Bacteriophage on the Block: A Short Guide to Phage Classification J. Virol. 2024 98 e0182123 10.1128/jvi.01821-23 39264154 PMC11494874 · DOI
  45. [46]Ackermann H.W. 5500 Phages Examined in the Electron Microscope Arch. Virol. 2007 152 227 243 10.1007/s00705-006-0849-1 17051420 · DOI
  46. [47]Nguyen H.M. Watanabe S. Sharmin S. Kawaguchi T. Tan X.E. Wannigama D.L. Cui L. RNA and Single-Stranded DNA Phages: Unveiling the Promise from the Underexplored World of Viruses Int. J. Mol. Sci. 2023 24 17029 10.3390/ijms242317029 38069353 PMC10707117 · DOI
  47. [48]Albrycht K. Rynkiewicz A.A. Harasymczuk M. Barylski J. Zielezinski A. Daily Reports on Phage-Host Interactions Front. Microbiol. 2022 13 946070 10.3389/fmicb.2022.946070 35910653 PMC9329054 · DOI
  48. [49]Yuan Y. Gao M. Jumbo Bacteriophages: An Overview Front. Microbiol. 2017 8 403 10.3389/fmicb.2017.00403 28352259 PMC5348500 · DOI
  49. [50]Michniewski S. Rihtman B. Cook R. Jones M.A. Wilson W.H. Scanlan D.J. Millard A. A New Family of “Megaphages” Abundant in the Marine Environment ISME Commun. 2021 1 58 10.1038/s43705-021-00064-6 37938293 PMC9723777 · DOI
  50. [51]Zrelovs N. Dislers A. Kazaks A. Motley Crew: Overview of the Currently Available Phage Diversity Front. Microbiol. 2020 11 579452 10.3389/fmicb.2020.579452 33193205 PMC7658105 · DOI
  51. [52]Olszak T. Latka A. Roszniowski B. Valvano M.A. Drulis-Kawa Z. Phage Life Cycles Behind Bacterial Biodiversity Curr. Med. Chem. 2017 24 3987 4001 10.2174/0929867324666170413100136 28412903 · DOI
  52. [53]Shkoporov A.N. Khokhlova E.V. Stephens N. Hueston C. Seymour S. Hryckowian A.J. Scholz D. Ross R.P. Hill C. Long-Term Persistence of CrAss-like Phage CrAss001 Is Associated with Phase Variation in Bacteroides Intestinalis BMC Biol. 2021 19 163 10.1186/s12915-021-01084-3 34407825 PMC8375218 · DOI
  53. [54]Dougherty P.E. Bernard C. Carstens A.B. Stanford K. McAllister T.A. Rocha E.P.C. Hansen L.H. Persistent Virulent Phages Exist in Bacterial Isolates bioRxiv 2025 10.1101/2024.12.31.630880 41461921 · DOI
  54. [55]Łobocka M.B. Rose D.J. Plunkett G. Rusin M. Samojedny A. Lehnherr H. Yarmolinsky M.B. Blattner F.R. Genome of Bacteriophage P1 J. Bacteriol. 2004 186 7032 10.1128/JB.186.21.7032-7068.2004 15489417 PMC523184 · DOI
  55. [56]Marvin D.A. Symmons M.F. Straus S.K. Structure and Assembly of Filamentous Bacteriophages Prog. Biophys. Mol. Biol. 2014 114 80 122 10.1016/j.pbiomolbio.2014.02.003 24582831 · DOI
  56. [57]Fujisawa H. Morita M. Phage DNA Packaging Genes Cells 1997 2 537 545 10.1046/j.1365-2443.1997.1450343.x 9413995 · DOI
  57. [58]Casjens S.R. Gilcrease E.B. Determining DNA Packaging Strategy by Analysis of the Termini of the Chromosomes in Tailed-Bacteriophage Virions Methods Mol. Biol. 2009 502 91 111 10.1007/978-1-60327-565-1_7 19082553 PMC3082370 · DOI
  58. [59]Merrill B.D. Ward A.T. Grose J.H. Hope S. Software-Based Analysis of Bacteriophage Genomes, Physical Ends, and Packaging Strategies BMC Genom. 2016 17 679 10.1186/s12864-016-3018-2 PMC5000459 27561606 · DOI
  59. [60]Garneau J.R. Depardieu F. Fortier L.C. Bikard D. Monot M. PhageTerm: A Tool for Fast and Accurate Determination of Phage Termini and Packaging Mechanism Using next-Generation Sequencing Data Sci. Rep. 2017 7 8292 10.1038/s41598-017-07910-5 28811656 PMC5557969 · DOI
  60. [61]Apjok G. Számel M. Christodoulou C. Seregi V. Vásárhelyi B.M. Stirling T. Eszenyi B. Sári T. Vidovics F. Nagrand E. Characterization of Antibiotic Resistomes by Reprogrammed Bacteriophage-Enabled Functional Metagenomics in Clinical Strains Nat. Microbiol. 2023 8 410 423 10.1038/s41564-023-01320-2 36759752 PMC9981461 · DOI
  61. [62]Dunne M. Prokhorov N.S. Loessner M.J. Leiman P.G. Reprogramming Bacteriophage Host Range: Design Principles and Strategies for Engineering Receptor Binding Proteins Curr. Opin. Biotechnol. 2021 68 272 281 10.1016/j.copbio.2021.02.006 33744824 PMC10163921 · DOI
  62. [63]Taslem Mourosi J. Awe A. Guo W. Batra H. Ganesh H. Wu X. Zhu J. Understanding Bacteriophage Tail Fiber Interaction with Host Surface Receptor: The Key “Blueprint” for Reprogramming Phage Host Range Int. J. Mol. Sci. 2022 23 12146 10.3390/ijms232012146 36292999 PMC9603124 · DOI
  63. [64]Leprince A. Mahillon J. Phage Adsorption to Gram-Positive Bacteria Viruses 2023 15 196 10.3390/v15010196 36680236 PMC9863714 · DOI
  64. [65]Bennett N.J. Gagic D. Sutherland-Smith A.J. Rakonjac J. Characterization of a Dual-Function Domain That Mediates Membrane Insertion and Excision of Ff Filamentous Bacteriophage J. Mol. Biol. 2011 411 972 985 10.1016/j.jmb.2011.07.002 21763316 · DOI
  65. [66]Kleinbeck F. Kuhn A. Membrane Insertion of the M13 Minor Coat Protein G3p Is Dependent on Yidc and the Secayeg Translocase Viruses 2021 13 1414 10.3390/v13071414 34372619 PMC8310372 · DOI
  66. [67]Chang C. Guo W. Yu X. Guo C. Zhou N. Guo X. Huang R.L. Li Q. Zhu Y. Engineered M13 Phage as a Novel Therapeutic Bionanomaterial for Clinical Applications: From Tissue Regeneration to Cancer Therapy Mater. Today Bio 2023 20 100612 10.1016/j.mtbio.2023.100612 PMC10102448 37063776 · DOI
  67. [68]Raetz C.R.H. Whitfield C. Lipopolysaccharide Endotoxins Annu. Rev. Biochem. 2002 71 635 700 10.1146/annurev.biochem.71.110601.135414 12045108 PMC2569852 · DOI · Paper page
  68. [69]Washizaki A. Yonesaki T. Otsuka Y. Characterization of the Interactions between Escherichia coli Receptors, LPS and OmpC, and Bacteriophage T4 Long Tail Fibers Microbiologyopen 2016 5 1003 1015 10.1002/mbo3.384 27273222 PMC5221442 · DOI
  69. [70]Montag D. Schwarz H. Henning U. A Component of the Side Tail Fiber of Escherichia Coli Bacteriophage Lambda Can Functionally Replace the Receptor-Recognizing Part of a Long Tail Fiber Protein of the Unrelated Bacteriophage T4 J. Bacteriol. 1989 171 4378 4384 10.1128/jb.171.8.4378-4384.1989 2526805 PMC210215 · DOI
  70. [71]González-García V.A. Pulido-Cid M. Garcia-Doval C. Bocanegra R. Van Raaij M.J. Martín-Benito J. Cuervo A. Carrascosa J.L. Conformational Changes Leading to T7 DNA Delivery upon Interaction with the Bacterial Receptor J. Biol. Chem. 2015 290 10038 10044 10.1074/jbc.M114.614222 25697363 PMC4400320 · DOI
  71. [72]Witte S. Zinsli L.V. Gonzalez-Serrano R. Matter C.I. Loessner M.J. van Mierlo J.T. Dunne M. Structural and Functional Characterization of the Receptor Binding Proteins of Escherichia coli O157 Phages EP75 and EP335 Comput. Struct. Biotechnol. J. 2021 19 3416 3426 10.1016/j.csbj.2021.06.001 34194667 PMC8217332 · DOI
  72. [73]Oats M.F. Coronel-Aguilera C.P. Applegate B.M. Csonka L.N. Bhunia A.K. Gehring A.G. Paoli G.C. Determination of the Infection Dynamics of Escherichia Coli O157:H7 by Bacteriophage ΦV10 Foods 2025 14 617 10.3390/foods14040617 40002061 PMC11854483 · DOI
  73. [74]Marti R. Zurfluh K. Hagens S. Pianezzi J. Klumpp J. Loessner M.J. Long Tail Fibres of the Novel Broad-Host-Range T-Even Bacteriophage S16 Specifically Recognize Salmonella OmpC Mol. Microbiol. 2013 87 818 834 10.1111/mmi.12134 23289425 · DOI
  74. [75]Baxa U. Steinbacher S. Miller S. Weintraub A. Huber R. Seckler R. Interactions of Phage P22 Tails with Their Cellular Receptor, Salmonella O-Antigen Polysaccharide Biophys. J. 1996 71 2040 2048 10.1016/S0006-3495(96)79402-X 8889178 PMC1233670 · DOI
  75. [76]Ando H. Lemire S. Pires D.P. Lu T.K. Engineering Modular Viral Scaffolds for Targeted Bacterial Population Editing Cell Syst. 2015 1 187 196 10.1016/j.cels.2015.08.013 26973885 PMC4785837 · DOI
  76. [77]Scholl D. Cooley M. Williams S.R. Gebhart D. Martin D. Bates A. Mandrell R. An Engineered R-Type Pyocin Is a Highly Specific and Sensitive Bactericidal Agent for the Food-Borne Pathogen Escherichia coli O157:H7 Antimicrob. Agents Chemother. 2009 53 3074 3080 10.1128/AAC.01660-08 19349519 PMC2704633 · DOI
  77. [78]Mitsunaka S. Yamazaki K. Pramono A.K. Ikeuchi M. Kitao T. Ohara N. Kubori T. Nagai H. Ando H. Synthetic Engineering and Biological Containment of Bacteriophages Proc. Natl. Acad. Sci. USA 2022 119 e2206739119 10.1073/pnas.2206739119 36409909 PMC9860248 · DOI
  78. [79]Luria S.E. Dulbecco R. Genetic Recombinations Leading to Production of Active Bacteriophage from Ultraviolet Inactivated Bacteriophage Particles Genetics 1949 34 93 10.1093/genetics/34.2.93 17247312 PMC1209443 · DOI
  79. [80]Duong M.M. Carmody C.M. Ma Q. Peters J.E. Nugen S.R. Optimization of T4 Phage Engineering via CRISPR/Cas9 Sci. Rep. 2020 10 18229 10.1038/s41598-020-75426-6 33106580 PMC7588440 · DOI
  80. [81]Filsinger G.T. Wannier T.M. Pedersen F.B. Lutz I.D. Zhang J. Stork D.A. Debnath A. Gozzi K. Kuchwara H. Volf V. Characterizing the Portability of Phage-Encoded Homologous Recombination Proteins Nat. Chem. Biol. 2021 17 394 402 10.1038/s41589-020-00710-5 33462496 PMC7990699 · DOI
  81. [82]Fishman C.B. Crawford K.D. Bhattarai-Kline S. Poola D. Zhang K. González-Delgado A. Rojas-Montero M. Shipman S.L. Continuous Multiplexed Phage Genome Editing Using Recombitrons Nat. Biotechnol. 2024 1 12 10.1038/s41587-024-02370-5 39237706 PMC11880354 · DOI
  82. [83]Marinelli L.J. Piuri M. Swigoňová Z. Balachandran A. Oldfield L.M. van Kessel J.C. Hatfull G.F. BRED: A Simple and Powerful Tool for Constructing Mutant and Recombinant Bacteriophage Genomes PLoS ONE 2008 3 e3957 10.1371/journal.pone.0003957 19088849 PMC2597740 · DOI
  83. [84]Poteete A.R. What Makes the Bacteriophage λ Red System Useful for Genetic Engineering: Molecular Mechanism and Biological Function FEMS Microbiol. Lett. 2001 201 9 14 10.1016/s0378-1097(01)00242-7 11445160 · DOI
  84. [85]Clark A.J. Margulies A.D. Isolation and characterization of recombination-deficient mutants of Escherichia coli K12 Proc. Natl. Acad. Sci. USA 1965 53 451 459 10.1073/pnas.53.2.451 14294081 PMC219534 · DOI
  85. [86]Maresca M. Erler A. Fu J. Friedrich A. Zhang Y. Stewart A.F. Single-Stranded Heteroduplex Intermediates in λ Red Homologous Recombination BMC Mol. Biol. 2010 11 54 10.1186/1471-2199-11-54 20670401 PMC2918612 · DOI
  86. [87]Marinelli L.J. Hatfull G.F. Piuri M. Recombineering Bacteriophage 2012 2 5 14 10.4161/bact.18778 22666652 PMC3357384 · DOI
  87. [88]Subramanian K. Rutvisuttinunt W. Scott W. Myers R.S. The Enzymatic Basis of Processivity in Lambda Exonuclease Nucleic Acids Res. 2003 31 1585 1596 10.1093/nar/gkg266 12626699 PMC152868 · DOI
  88. [89]Erler A. Wegmann S. Elie-Caille C. Bradshaw C.R. Maresca M. Seidel R. Habermann B. Muller D.J. Stewart A.F. Conformational Adaptability of Redβ during DNA Annealing and Implications for Its Structural Relationship with Rad52 J. Mol. Biol. 2009 391 586 598 10.1016/j.jmb.2009.06.030 19527729 · DOI
  89. [90]Court R. Cook N. Saikrishnan K. Wigley D. The Crystal Structure of Lambda-Gam Protein Suggests a Model for RecBCD Inhibition J. Mol. Biol. 2007 371 25 33 10.1016/j.jmb.2007.05.037 17544443 · DOI
  90. [91]Datsenko K.A. Wanner B.L. One-Step Inactivation of Chromosomal Genes in Escherichia coli K-12 Using PCR Products Proc. Natl. Acad. Sci. USA 2000 97 6640 6645 10.1073/pnas.120163297 10829079 PMC18686 · DOI
  91. [92]Karlinsey J.E. Λ-Red Genetic Engineering in Salmonella Enterica Serovar Typhimurium Methods Enzymol. 2007 421 199 209 10.1016/S0076-6879(06)21016-4 17352924 · DOI
  92. [93]Zhang Y. Buchholz F. Muyrers J.P.P. Francis Stewart A. A New Logic for DNA Engineering Using Recombination in Escherichia coli Nat. Genet. 1998 20 123 128 10.1038/2417 9771703 · DOI
  93. [94]Oppenheim A.B. Rattray A.J. Bubunenko M. Thomason L.C. Court D.L. In Vivo Recombineering of Bacteriophage λ by PCR Fragments and Single-Strand Oligonucleotides Virology 2004 319 185 189 10.1016/j.virol.2003.11.007 14980479 · DOI
  94. [95]Serra-Moreno R. Acosta S. Hernalsteens J.P. Jofre J. Muniesa M. Use of the Lambda Red Recombinase System to Produce Recombinant Prophages Carrying Antibiotic Resistance Genes BMC Mol. Biol. 2006 7 31 10.1186/1471-2199-7-31 16984631 PMC1626079 · DOI
  95. [96]Fehér T. Karcagi I. Blattner F.R. Pósfai G. Bacteriophage Recombineering in the Lytic State Using the Lambda Red Recombinases Microb. Biotechnol. 2012 5 466 476 10.1111/j.1751-7915.2011.00292.x 21910851 PMC3815324 · DOI
  96. [97]Thomason L.C. Sawitzke J.A. Li X. Costantino N. Court D.L. Recombineering: Genetic Engineering in Bacteria Using Homologous Recombination Curr. Protoc. Mol. Biol. 2014 106 1.16.1 1.16.39 10.1002/0471142727.mb0116s106 24733238 · DOI
  97. [98]Isaev A. Andriianov A. Znobishcheva E. Zorin E. Morozova N. Severinov K. Editing of Phage Genomes—Recombineering-Assisted SpCas9 Modification of Model Coliphages T7, T5, and T3 Mol. Biol. 2022 56 801 815 10.1134/S0026893322060073 36475474 · DOI
  98. [99]Derbise A. Lesic B. Dacheux D. Ghigo J.M. Carniel E. A Rapid and Simple Method for Inactivating Chromosomal Genes in Yersinia FEMS Immunol. Med. Microbiol. 2003 38 113 116 10.1016/S0928-8244(03)00181-0 13129645 · DOI
  99. [100]Lesic B. Rahme L.G. Use of the Lambda Red Recombinase System to Rapidly Generate Mutants in Pseudomonas Aeruginosa BMC Mol. Biol. 2008 9 20 10.1186/1471-2199-9-20 18248677 PMC2287187 · DOI
  100. [101]Muyrers J.P.P. Zhang Y. Buchholz F. Stewart A.F. RecE/RecT and Redα/Redβ Initiate Double-Stranded Break Repair by Specifically Interacting with Their Respective Partners Genes Dev. 2000 14 1971 10.1101/gad.14.15.1971 10921910 PMC316823 · DOI
  101. [102]Muyrers J.P.P. Zhang Y. Stewart A.F. Techniques: Recombinogenic Engineering–New Options for Cloning and Manipulating DNA Trends Biochem. Sci. 2001 26 325 331 10.1016/S0968-0004(00)01757-6 11343926 · DOI
  102. [103]Van Kessel J.C. Hatfull G.F. Recombineering in Mycobacterium Tuberculosis Nat. Methods 2006 4 147 152 10.1038/nmeth996 17179933 · DOI
  103. [104]Van Kessel J.C. Hatfull G.F. Efficient Point Mutagenesis in Mycobacteria Using Single-Stranded DNA Recombineering: Characterization of Antimycobacterial Drug Targets Mol. Microbiol. 2008 67 1094 1107 10.1111/j.1365-2958.2008.06109.x 18221264 · DOI
  104. [105]Lopes A. Amarir-Bouhram J. Faure G. Petit M.A. Guerois R. Detection of Novel Recombinases in Bacteriophage Genomes Unveils Rad52, Rad51 and Gp2.5 Remote Homologs Nucleic Acids Res. 2010 38 3952 3962 10.1093/nar/gkq096 20194117 PMC2896510 · DOI
  105. [106]Swingle B. Bao Z. Markel E. Chambers A. Cartinhour S. Recombineering Using RecTE from Pseudomonas Syringae Appl. Environ. Microbiol. 2010 76 4960 4968 10.1128/AEM.00911-10 20543050 PMC2916495 · DOI
  106. [107]Jacobs W.R. Snapper S.B. Tuckinan M. Bloom B.R. Mycobacteriophage Vector Systems Rev. Infect. Dis. 1989 11 S404 S410 10.1093/clinids/11.Supplement_2.S404 2652256 · DOI · Paper page
  107. [108]Pearson R.E. Jurgensen S. Sarkis G.J. Hatfull G.F. Jacobs W.R. Construction of D29 Shuttle Phasmids and Luciferase Reporter Phages for Detection of Mycobacteria Gene 1996 183 129 136 10.1016/S0378-1119(96)00530-6 8996097 · DOI
  108. [109]Sarkis G.J. Jacobs W.R. Hatfulll G.F. L5 Luciferase Reporter Mycobacteriophages: A Sensitive Tool for the Detection and Assay of Live Mycobacteria Mol. Microbiol. 1995 15 1055 1067 10.1111/j.1365-2958.1995.tb02281.x 7623662 · DOI
  109. [110]Wetzel K.S. Guerrero-Bustamante C.A. Dedrick R.M. Ko C.C. Freeman K.G. Aull H.G. Divens A.M. Rock J.M. Zack K.M. Hatfull G.F. CRISPY-BRED and CRISPY-BRIP: Efficient Bacteriophage Engineering Sci. Rep. 2021 11 6796 10.1038/s41598-021-86112-6 33762639 PMC7990910 · DOI
  110. [111]Yin J. Zheng W. Gao Y. Jiang C. Shi H. Diao X. Li S. Chen H. Wang H. Li R. Single-Stranded DNA-Binding Protein and Exogenous RecBCD Inhibitors Enhance Phage-Derived Homologous Recombination in Pseudomonas iScience 2019 14 1 10.1016/j.isci.2019.03.007 30921732 PMC6438905 · DOI
  111. [112]Bao Z. Cartinhour S. Swingle B. Substrate and Target Sequence Length Influence RecTEPsy Recombineering Efficiency in Pseudomonas Syringae PLoS ONE 2012 7 e50617 10.1371/journal.pone.0050617 23226333 PMC3511549 · DOI
  112. [113]Zheng W. Xia Y. Wang X. Gao S. Zhou D. Fu J. Li R. Yin J. Cascade-Cas3 Facilitates High-Accuracy Genome Engineering in Pseudomonas Using Phage-Encoded Homologous Recombination Eng. Microbiol. 2022 2 100046 10.1016/j.engmic.2022.100046 39628699 PMC11611027 · DOI
  113. [114]Liang R. Liu J. Scarless and Sequential Gene Modification in Pseudomonas Using PCR Product Flanked by Short Homology Regions BMC Microbiol. 2010 10 209 10.1186/1471-2180-10-209 20682065 PMC2924854 · DOI
  114. [115]Chen Y. Yan B. Chen W. Zhang X. Liu Z. Zhang Q. Li L. Hu M. Zhao X. Xu X. Development of the CRISPR-Cas12a System for Editing of Pseudomonas Aeruginosa Phages iScience 2024 27 110210 10.1016/j.isci.2024.110210 39055914 PMC11269290 · DOI
  115. [116]Yosef I. Goren M.G. Globus R. Molshanski-Mor S. Qimron U. Extending the Host Range of Bacteriophage Particles for DNA Transduction Mol. Cell 2017 66 721 728.e3 10.1016/j.molcel.2017.04.025 28552617 · DOI
  116. [117]Hatoum-Aslan A. Phage Genetic Engineering Using CRISPR–Cas Systems Viruses 2018 10 335 10.3390/v10060335 29921752 PMC6024849 · DOI
  117. [118]Mahler M. Costa A.R. van Beljouw S.P.B. Fineran P.C. Brouns S.J.J. Approaches for Bacteriophage Genome Engineering Trends Biotechnol. 2023 41 669 685 10.1016/j.tibtech.2022.08.008 36117025 · DOI
  118. [119]Hoshiga F. Yoshizaki K. Takao N. Miyanaga K. Tanji Y. Modification of T2 Phage Infectivity toward Escherichia coli O157:H7 via Using CRISPR/Cas9 FEMS Microbiol. Lett. 2019 366 41 10.1093/femsle/fnz041 30801649 · DOI
  119. [120]Dionne E.N. Cornely K. An Application of Mycobacteriophage Genome Engineering Using Bacteriophage Recombineering with Electroporated DNA (BRED) and CRISPR Cas-9 Systems FASEB J. 2022 36 10.1096/fasebj.2022.36.S1.R5326 · DOI
  120. [121]Choi S.Y. Romero-Calle D.X. Cho H.G. Bae H.W. Cho Y.H. Use of Cas9 Targeting and Red Recombination for Designer Phage Engineering J. Microbiol. 2024 62 1 10 10.1007/s12275-024-00107-2 38300409 · DOI
  121. [122]Heler R. Samai P. Modell J.W. Weiner C. Goldberg G.W. Bikard D. Marraffini L.A. Cas9 Specifies Functional Viral Targets during CRISPR-Cas Adaptation Nature 2015 519 199 10.1038/nature14245 25707807 PMC4385744 · DOI
  122. [123]Chatterjee P. Jakimo N. Lee J. Amrani N. Rodríguez T. Koseki S.R.T. Tysinger E. Qing R. Hao S. Sontheimer E.J. An Engineered ScCas9 with Broad PAM Range and High Specificity and Activity Nat. Biotechnol. 2020 38 1154 1158 10.1038/s41587-020-0517-0 32393822 · DOI
  123. [124]Zhao L. Koseki S.R.T. Silverstein R.A. Amrani N. Peng C. Kramme C. Savic N. Pacesa M. Rodríguez T.C. Stan T. PAM-Flexible Genome Editing with an Engineered Chimeric Cas9 Nat. Commun. 2023 14 6175 10.1038/s41467-023-41829-y 37794046 PMC10550912 · DOI · Paper page
  124. [126]Hibshman G.N. Bravo J.P.K. Hooper M.M. Dangerfield T.L. Zhang H. Finkelstein I.J. Johnson K.A. Taylor D.W. Unraveling the Mechanisms of PAMless DNA Interrogation by SpRY-Cas9 Nat. Commun. 2024 15 3663 10.1038/s41467-024-47830-3 38688943 PMC11061278 · DOI
  125. [127]Tao P. Wu X. Tang W.C. Zhu J. Rao V. Engineering of Bacteriophage T4 Genome Using CRISPR-Cas9 ACS Synth. Biol. 2017 6 1952 10.1021/acssynbio.7b00179 28657724 PMC5771229 · DOI
  126. [128]Fernbach J. Baggenstos J. Riedo J. McCallin S. Loessner M.J. Kilcher S. CRISPR-Cas9 Enables Efficient Genome Engineering of the Strictly Lytic, Broad Host-Range Staphylococcal Bacteriophage K bioRxiv 2024 10.1101/2024.03.19.585701 PMC12442396 40757862 · DOI
  127. [129]Shen J. Zhou J. Chen G.-Q. Xiu Z.-L. Efficient Genome Engineering of a Virulent Klebsiella Bacteriophage Using CRISPR-Cas9 J. Virol. 2018 92 e0053418 10.1128/JVI.00534-18 PMC6096830 29899105 · DOI
  128. [130]Zetsche B. Gootenberg J.S. Abudayyeh O.O. Slaymaker I.M. Makarova K.S. Essletzbichler P. Volz S.E. Joung J. Van Der Oost J. Regev A. Cpf1 Is a Single RNA-Guided Endonuclease of a Class 2 CRISPR-Cas System Cell 2015 163 759 771 10.1016/j.cell.2015.09.038 26422227 PMC4638220 · DOI
  129. [131]Liu Y. Tao P. Genetic Engineering of Bacteriophage Using CRISPR-Cas12a Humana New York, NY, USA 2025 43 53 10.1007/978-1-0716-4358-7_4 · DOI
  130. [132]Yuan S. Li Y. Kou C. Sun Y.C. Ma Y. CRISPR/Cas12a-Based Genome Editing for Cyanophage of Anabeana sp. Synth. Syst. Biotechnol. 2025 10 140 147 10.1016/J.SYNBIO.2024.09.011 39493338 PMC11530783 · DOI
  131. [133]Abudayyeh O.O. Gootenberg J.S. Konermann S. Joung J. Slaymaker I.M. Cox D.B.T. Shmakov S. Makarova K.S. Semenova E. Minakhin L. C2c2 Is a Single-Component Programmable RNA-Guided RNA-Targeting CRISPR Effector Science 2016 353 aaf5573 10.1126/science.aaf5573 27256883 PMC5127784 · DOI
  132. [134]Shmakov S. Abudayyeh O.O. Makarova K.S. Wolf Y.I. Gootenberg J.S. Semenova E. Minakhin L. Joung J. Konermann S. Severinov K. Discovery and Functional Characterization of Diverse Class 2 CRISPR-Cas Systems Mol. Cell 2015 60 385 397 10.1016/j.molcel.2015.10.008 26593719 PMC4660269 · DOI
  133. [135]East-Seletsky A. O’Connell M.R. Knight S.C. Burstein D. Cate J.H.D. Tjian R. Doudna J.A. Two Distinct RNase Activities of CRISPR-C2c2 Enable Guide-RNA Processing and RNA Detection Nature 2016 538 270 273 10.1038/nature19802 27669025 PMC5576363 · DOI
  134. [136]Adler B.A. Hessler T. Cress B.F. Lahiri A. Mutalik V.K. Barrangou R. Banfield J. Doudna J.A. Broad-Spectrum CRISPR-Cas13a Enables Efficient Phage Genome Editing Nat. Microbiol. 2022 7 1967 1979 10.1038/s41564-022-01258-x 36316451 PMC9712115 · DOI
  135. [137]Guan J. Oromí-Bosch A. Mendoza S.D. Karambelkar S. Berry J.D. Bondy-Denomy J. Bacteriophage Genome Engineering with CRISPR–Cas13a Nat. Microbiol. 2022 7 1956 1966 10.1038/s41564-022-01243-4 36316452 PMC9722621 · DOI
  136. [138]Yee T. Furuichi T. Inouye S. Inouye M. Multicopy Single-Stranded DNA Isolated from a Gram-Negative Bacterium, Myxococcus Xanthus Cell 1984 38 203 209 10.1016/0092-8674(84)90541-5 6088065 · DOI
  137. [139]Dhundale A. Lampson B. Furuichi T. Inouye M. Inouye S. Structure of MsDNA from Myxococcus Xanthus: Evidence for a Long, Self-Annealing RNA Precursor for the Covalently Linked, Branched RNA Cell 1987 51 1105 1112 10.1016/0092-8674(87)90596-4 2446773 · DOI
  138. [140]Hsu M.Y. Inouye S. Inouye M. Structural Requirements of the RNA Precursor for the Biosynthesis of the Branched RNA-Linked Multicopy Single-Stranded DNA of Myxococcus Xanthus J. Biol. Chem. 1989 264 6214 6219 10.1016/S0021-9258(18)83336-1 2467910 · DOI
  139. [141]Lampson B.C. Inouye M. Inouye S. Reverse Transcriptase with Concomitant Ribonuclease H Activity in the Cell-Free Synthesis of Branched RNA-Linked MsDNA of Myxococcus Xanthus Cell 1989 56 701 707 10.1016/0092-8674(89)90592-8 2465091 · DOI
  140. [142]Lampson B. Inouye M. Inouye S. The MsDNAs of Bacteria Prog. Nucleic Acid. Res. Mol. Biol. 2001 67 65 91 10.1016/S0079-6603(01)67025-9 11525386 · DOI
  141. [143]Simon A.J. Ellington A.D. Finkelstein I.J. Retrons and Their Applications in Genome Engineering Nucleic Acids Res. 2019 47 11007 11019 10.1093/nar/gkz865 31598685 PMC6868368 · DOI
  142. [144]Millman A. Bernheim A. Stokar-Avihail A. Fedorenko T. Voichek M. Leavitt A. Oppenheimer-Shaanan Y. Sorek R. Bacterial Retrons Function In Anti-Phage Defense Cell 2020 183 1551 1561.e12 10.1016/j.cell.2020.09.065 33157039 · DOI
  143. [145]Lopez S.C. Crawford K.D. Lear S.K. Bhattarai-Kline S. Shipman S.L. Precise Genome Editing across Kingdoms of Life Using Retron-Derived DNA Nat. Chem. Biol. 2022 18 199 206 10.1038/s41589-021-00927-y 34949838 PMC8810715 · DOI
  144. [146]González-Delgado A. Lopez S.C. Rojas-Montero M. Fishman C.B. Shipman S.L. Simultaneous Multi-Site Editing of Individual Genomes Using Retron Arrays Nat. Chem. Biol. 2024 20 1482 1492 10.1038/s41589-024-01665-7 38982310 PMC11512673 · DOI
  145. [147]Jaschke P.R. Lieberman E.K. Rodriguez J. Sierra A. Endy D. A Fully Decompressed Synthetic Bacteriophage ØX174 Genome Assembled and Archived in Yeast Virology 2012 434 278 284 10.1016/j.virol.2012.09.020 23079106 · DOI
  146. [148]Gibson D.G. Young L. Chuang R.Y. Venter J.C. Hutchison C.A. Smith H.O. Enzymatic Assembly of DNA Molecules up to Several Hundred Kilobases Nat. Methods 2009 6 343 345 10.1038/nmeth.1318 19363495 · DOI
  147. [149]Engler C. Kandzia R. Marillonnet S. A One Pot, One Step, Precision Cloning Method with High Throughput Capability PLoS ONE 2008 3 e3647 10.1371/journal.pone.0003647 18985154 PMC2574415 · DOI
  148. [150]Nozaki S. Rapid and Accurate Assembly of Large DNA Assisted by In Vitro Packaging of Bacteriophage ACS Synth. Biol. 2022 11 4113 4122 10.1021/acssynbio.2c00419 36446634 PMC9764419 · DOI
  149. [151]Garenne D. Haines M.C. Romantseva E.F. Freemont P. Strychalski E.A. Noireaux V. Cell-Free Gene Expression Nat. Rev. Methods Primers 2021 1 49 10.1038/s43586-021-00046-x · DOI
  150. [152]Shin J. Jardine P. Noireaux V. Genome Replication, Synthesis, and Assembly of the Bacteriophage T7 in a Single Cell-Free Reaction ACS Synth. Biol. 2012 1 408 413 10.1021/sb300049p 23651338 · DOI
  151. [153]Rustad M. Eastlund A. Jardine P. Noireaux V. Cell-Free TXTL Synthesis of Infectious Bacteriophage T4 in a Single Test Tube Reaction Synth. Biol. 2018 3 ysy002 10.1093/synbio/ysy002 PMC7445788 32995511 · DOI
  152. [154]Burke D.T. Carle G.F. Olson M.V. Cloning of Large Segments of Exogenous DNA into Yeast by Means of Artificial Chromosome Vectors Science 1987 236 806 812 10.1126/science.3033825 3033825 · DOI
  153. [155]Frazer L.A.N. O’Keefe R.T. A New Series of Yeast Shuttle Vectors for the Recovery and Identification of Multiple Plasmids from Saccharomyces Cerevisiae Yeast 2007 24 777 789 10.1002/yea.1509 17597491 · DOI
  154. [156]Gibson D.G. Benders G.A. Axelrod K.C. Zaveri J. Algire M.A. Moodie M. Montague M.G. Venter J.C. Smith H.O. Hutchison C.A. One-Step Assembly in Yeast of 25 Overlapping DNA Fragments to Form a Complete Synthetic Mycoplasma Genitalium Genome Proc. Natl. Acad. Sci. USA 2008 105 20404 20409 10.1073/pnas.0811011106 19073939 PMC2600582 · DOI
  155. [157]Brownstein B.H. Silverman G.A. Little R.D. Burke D.T. Korsmeyer S.J. Schlessinger D. Olson M.V. Isolation of Single-Copy Human Genes from a Library of Yeast Artificial Chromosome Clones Science 1989 244 1348 1351 10.1126/science.2544027 2544027 · DOI
  156. [158]Ipoutcha T. Racharaks R. Huttelmaier S. Wilson C.J. Ozer E.A. Hartmann E.M. A Synthetic Biology Approach to Assemble and Reboot Clinically Relevant Pseudomonas Aeruginosa Tailed Phages Microbiol. Spectr. 2024 12 e0289723 10.1128/spectrum.02897-23 38294230 PMC10913387 · DOI
  157. [159]Kristensen C.S. Petersen A.Ø. Kilstrup M. van der Helm E. Takos A. Cell-Free Synthesis of Infective Phages from in Vitro Assembled Phage Genomes for Efficient Phage Engineering and Production of Large Phage Libraries Synth. Biol. 2024 9 12 10.1093/synbio/ysae012 PMC11409935 39296367 · DOI
  158. [160]Lu C. He L. Guo Y. Wang T. Ye Y. Lin Z. Synthesis of Headful Packaging Phages Through Yeast Transformation-Associated Recombination Viruses 2025 17 45 10.3390/v17010045 PMC11769102 39861840 · DOI
  159. [161]Assad-Garcia N. D’Souza R. Buzzeo R. Tripathi A. Oldfield L.M. Vashee S. Fouts D.E. Cross-Genus “Boot-Up” of Synthetic Bacteriophage in Staphylococcus Aureus by Using a New and Efficient DNA Transformation Method Appl. Environ. Microbiol. 2022 88 e0148621 10.1128/AEM.01486-21 34818102 PMC8824277 · DOI
  160. [162]Gibson D.G. Enzymatic Assembly of Overlapping DNA Fragments Methods Enzymol. 2011 498 349 361 10.1016/B978-0-12-385120-8.00015-2 21601685 PMC7149801 · DOI
  161. [163]Lin Z. Li H. He L. Jing Y. Pistolozzi M. Wang T. Ye Y. Efficient Genome Editing for Pseudomonas Aeruginosa Using CRISPR-Cas12a Gene 2021 790 145693 10.1016/j.gene.2021.145693 33961975 · DOI
  162. [164]Levrier A. Karpathakis I. Nash B. Bowden S.D. Lindner A.B. Noireaux V. PHEIGES: All-Cell-Free Phage Synthesis and Selection from Engineered Genomes Nat. Commun. 2024 15 2223 10.1038/s41467-024-46585-1 38472230 PMC10933291 · DOI
  163. [165]Wang F.J. Ripley L.S. The Spectrum of Acridine Resistant Mutants of Bacteriophage T4 Reveals Cryptic Effects of the TsL141 DNA Polymerase Allele on Spontaneous Mutagenesis Genetics 1998 148 1655 10.1093/genetics/148.4.1655 9560385 PMC1460093 · DOI
  164. [166]Pryor J.M. Potapov V. Bilotti K. Pokhrel N. Lohman G.J.S. Rapid 40 Kb Genome Construction from 52 Parts through Data-Optimized Assembly Design ACS Synth. Biol. 2022 11 2036 2042 10.1021/acssynbio.1c00525 35613368 PMC9208013 · DOI
  165. [167]Kilcher S. Studer P. Muessner C. Klumpp J. Loessner M.J. Adhya S. Cross-Genus Rebooting of Custom-Made, Synthetic Bacteriophage Genomes in L-Form Bacteria Proc. Natl. Acad. Sci. USA 2018 115 567 572 10.1073/pnas.1714658115 29298913 PMC5776983 · DOI
  166. [168]Nirenberg M.W. Matthaei J.H. The Dependence of Cell-Free Protein Synthesis in E. Coli upon Naturally Occurring or Synthetic Polyribonucleotides Proc. Natl. Acad. Sci. USA 1961 47 1588 1602 10.1073/pnas.47.10.1588 14479932 PMC223178 · DOI
  167. [169]Carlson E.D. Gan R. Hodgman C.E. Jewett M.C. Cell-Free Protein Synthesis: Applications Come of Age Biotechnol. Adv. 2012 30 1185 1194 10.1016/j.biotechadv.2011.09.016 22008973 PMC4038126 · DOI
  168. [170]Gregorio N.E. Levine M.Z. Oza J.P. A User’s Guide to Cell-Free Protein Synthesis Methods Protoc. 2019 2 24 10.3390/mps2010024 31164605 PMC6481089 · DOI
  169. [171]Pizarro-Bauerle J. Ando H. Engineered Bacteriophages for Practical Applications Biol. Pharm. Bull. 2020 43 240 249 10.1248/bpb.b19-00914 32009112 · DOI
  170. [172]Kortright K.E. Chan B.K. Koff J.L. Turner P.E. Phage Therapy: A Renewed Approach to Combat Antibiotic-Resistant Bacteria Cell Host Microbe 2019 25 219 232 10.1016/j.chom.2019.01.014 30763536 · DOI
  171. [173]Borin J.M. Avrani S. Barrick J.E. Petrie K.L. Meyer J.R. Coevolutionary Phage Training Leads to Greater Bacterial Suppression and Delays the Evolution of Phage Resistance Proc. Natl. Acad. Sci. USA 2021 118 e2104592118 10.1073/pnas.2104592118 34083444 PMC8201913 · DOI
  172. [174]Hodyra-Stefaniak K. Lahutta K. Majewska J. Kaźmierczak Z. Lecion D. Harhala M. Kęska W. Owczarek B. Jończyk-Matysiak E. Kłopot A. Bacteriophages Engineered to Display Foreign Peptides May Become Short-Circulating Phages Microb. Biotechnol. 2019 12 730 741 10.1111/1751-7915.13414 31037835 PMC6559017 · DOI
  173. [175]Kim K.P. Cha J.D. Jang E.H. Klumpp J. Hagens S. Hardt W.D. Lee K.Y. Loessner M.J. PEGylation of Bacteriophages Increases Blood Circulation Time and Reduces T-Helper Type 1 Immune Response Microb. Biotechnol. 2008 1 247 257 10.1111/j.1751-7915.2008.00028.x 21261844 PMC3815886 · DOI
  174. [176]Dąbrowska K. Abedon S.T. Pharmacologically Aware Phage Therapy: Pharmacodynamic and Pharmacokinetic Obstacles to Phage Antibacterial Action in Animal and Human Bodies Microbiol. Mol. Biol. Rev. 2019 83 e0001219 10.1128/MMBR.00012-19 PMC6822990 31666296 · DOI
  175. [177]Doud M.B. Robertson J.M. Strathdee S.A. Optimizing Phage Therapy with Artificial Intelligence: A Perspective Front. Cell. Infect. Microbiol. 2025 15 1611857 10.3389/fcimb.2025.1611857 40496019 PMC12149144 · DOI
  176. [178]Boeckaerts D. Stock M. Ferriol-González C. Oteo-Iglesias J. Sanjuán R. Domingo-Calap P. De Baets B. Briers Y. Prediction of Klebsiella Phage-Host Specificity at the Strain Level Nat. Commun. 2024 15 4355 10.1038/s41467-024-48675-6 38778023 PMC11111740 · DOI
  177. [180]Pirnay J.P. Phage Therapy in the Year 2035 Front. Microbiol. 2020 11 1171 10.3389/fmicb.2020.01171 32582107 PMC7284012 · DOI
  178. [181]Cao X. Yu T. Sun Z. Chen M. Xie W. Pang Q. Deng H. Engineered Phages in Anti-Infection and Anti-Tumor Fields: A Review Microb. Pathog. 2025 198 107052 10.1016/j.micpath.2024.107052 39442821 · DOI
  179. [182]Peng H. Chen I.A. Qimron U. Engineering Phages to Fight Multidrug-Resistant Bacteria Chem. Rev. 2025 125 933 971 10.1021/acs.chemrev.4c00681 39680919 PMC11758799 · DOI
  180. [183]Woudstra C. Sørensen A.N. Sørensen M.C.H. Brøndsted L. Strategies for Developing Phages into Novel Antimicrobial Tailocins Trends Microbiol. 2024 32 996 1006 10.1016/j.tim.2024.03.003 38580606 · DOI
  181. [184]Cui L. Watanabe S. Miyanaga K. Kiga K. Sasahara T. Aiba Y. Tan X.-E. Veeranarayanan S. Thitiananpakorn K. Nguyen H.M. A Comprehensive Review on Phage Therapy and Phage-Based Drug Development Antibiotics 2024 13 870 10.3390/antibiotics13090870 39335043 PMC11428490 · DOI
  182. [185]Cui L. Veeranarayanan S. Thitiananpakorn K. Wannigama D.L. Bacteriophage Bioengineering: A Transformative Approach for Targeted Drug Discovery and Beyond Pathogens 2023 12 1179 10.3390/pathogens12091179 37764987 PMC10534869 · DOI · Paper page
  183. [186]Veeranarayanan S. Azam A.H. Kiga K. Watanabe S. Cui L. Bacteriophages as Solid Tumor Theragnostic Agents Int. J. Mol. Sci. 2021 23 402 10.3390/ijms23010402 35008840 PMC8745063 · DOI · Paper page
  184. [187]Pirnay J.P. Kutter E. Bacteriophages: It’s a Medicine, Jim, but Not as We Know It Lancet Infect. Dis. 2021 21 309 311 10.1016/S1473-3099(20)30464-3 32949499 · DOI
  185. [188]Pirnay J.P. Blasdel B.G. Bretaudeau L. Buckling A. Chanishvili N. Clark J.R. Corte-Real S. Debarbieux L. Dublanchet A. De Vos D. Quality and Safety Requirements for Sustainable Phage Therapy Products Pharm. Res. 2015 32 2173 2179 10.1007/s11095-014-1617-7 25585954 PMC4452253 · DOI
  186. [189]Cui L. Kiga K. Kondabagil K. Węgrzyn A. Current and Future Directions in Bacteriophage Research for Developing Therapeutic Innovations Sci. Rep. 2024 14 24404 10.1038/s41598-024-76427-5 39420115 PMC11487266 · DOI · Paper page
  187. [190]Smith G.P. Filamentous Fusion Phage: Novel Expression Vectors That Display Cloned Antigens on the Virion Surface Science 1985 228 1315 1317 10.1126/science.4001944 4001944 · DOI · Paper page
  188. [191]Smith H.O. Hutchison C.A. Pfannkoch C. Venter J.C. Generating a Synthetic Genome by Whole Genome Assembly: ΦX174 Bacteriophage from Synthetic Oligonucleotides Proc. Natl. Acad. Sci. USA 2003 100 15440 15445 10.1073/pnas.2237126100 14657399 PMC307586 · DOI
  189. [192]Garamella J. Marshall R. Rustad M. Noireaux V. The All E. coli TX-TL Toolbox 2.0: A Platform for Cell-Free Synthetic Biology ACS Synth. Biol. 2016 5 344 355 10.1021/acssynbio.5b00296 26818434 · DOI

Cited by

Sorted by citations

Authors
Alessa, O., Aiba, Y., Arbaah, M., Hidaka, Y., Watanabe, S., Miyanaga, K., Wannigama, D. L., & Cui, L.
Affiliations
  • Jichi Medical University (JP)
  • Yamagata Prefectural Central Hospital (JP)
Corresponding author
Cui, Longzhu
ORCID
Venue
Molecules
Publisher
MDPI AG
Published
2025-07-25
Volume
30
Issue
15
Pages
3132
ISSN
1420-3049 (ISSN-L)
DOI
10.3390/molecules30153132
PMC
PMC12348365
OpenAlex
W4413116955
Cited by
21
References
3
Citations by year
2026: 20 · 2025: 1
FWCI
2.25
Type
journal article
Language
en
Open access
Licence
Locations
  • Molecules (publishedVersion, cc-by)
  • Preprints.org (acceptedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders
  • Japan Agency for Medical Research and Development (JP25ae0121045, JP25gm1610002, JP25fk0108698, JP24H00662, JP25K21731, JP24K22027, JP25K13511, JP25K19273, JPJ009237)
  • JSPS KAKENHI (JP25ae0121045, JP25gm1610002, JP25fk0108698, JP24H00662, JP25K21731, JP24K22027, JP25K13511, JP25K19273, JPJ009237)
  • Moonshot R&D Program for Agriculture, Forestry, Fisheries (JP25ae0121045, JP25gm1610002, JP25fk0108698, JP24H00662, JP25K21731, JP24K22027, JP25K13511, JP25K19273, JPJ009237)
Topics
  • Physical Sciences › Environmental Science › Ecology › Bacteriophages and microbial interactions
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › CRISPR and Genetic Engineering
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Virus-based gene therapy research
Keywords
bacteriophages, phage engineering, phage genome assembly, Golden Gate assembly, Gibson assembly, transcription-translation system, host range expansion, CRISPR delivery, antimicrobial proteins, phage therapy, phage diagnostics, drug carriers
MeSH terms
Gene Editing, Anti-Bacterial Agents, Bacteriophages, Genetic Engineering, Humans, Drug Delivery Systems, Synthetic Biology, CRISPR-Cas Systems

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