Phage-Based Applications in Synthetic Biology

Literature Cited

1. 1.  Summers WC, Stent G, Twort F 2012. The strange history of phage therapy. Bacteriophage 2:130–33
   [Google Scholar]
2. 2.  Hatfull GF 2008. Bacteriophage genomics. Curr. Opin. Microbiol. 11:447–53
   [Google Scholar]
3. 3.  Hershey AD, Chase M 1952. Independent functions of viral protein and nucleic acid in growth of bacteriophage. J. Gen. Physiol. 36:39–56
   [Google Scholar]
4. 4.  Crick FH, Barnett L, Brenner S, Watts-Tobin RJ 1961. General nature of the genetic code for proteins. Nature 192:1227–32
   [Google Scholar]
5. 5.  Bertani G, Weigle JJ 1953. Host controlled variation in bacterial viruses. J. Bacteriol. 65:113–21
   [Google Scholar]
6. 6.  Weiss B, Richardson CC 1967. Enzymatic breakage and joining of deoxyribonucleic acid. I. Repair of single-strand breaks in DNA by an enzyme system from Escherichia coli infected with T4 bacteriophage. PNAS 57:1021–28
   [Google Scholar]
7. 7.  Chamberlin M, Ring J 1973. Characterization of T7-specific ribonucleic acid polymerase. 1. General properties of the enzymatic reaction and the template specificity of the enzyme. J. Biol. Chem. 248:2235–44
   [Google Scholar]
8. 8.  Barrangou R, Fremaux C, Deveau H, Richards M, Boyaval P et al. 2007. CRISPR provides acquired resistance against viruses in prokaryotes. Science 315:1709–12
   [Google Scholar]
9. 9.  Donohoue PD, Barrangou R, May AP 2018. Advances in industrial biotechnology using CRISPR-Cas systems. Trends Biotechnol 36:134–46
   [Google Scholar]
10. 10.  Sousa R, Mukherjee S 2003. T7 RNA polymerase. Prog. Nucleic Acid Res. Mol. Biol. 73:1–41
    [Google Scholar]
11. 11.  Lenneman B, Rothman-Denes L 2015. Structural and biochemical investigation of bacteriophage N4-encoded RNA polymerases. Biomolecules 5:647–67
    [Google Scholar]
12. 12.  Temme K, Hill R, Segall-Shapiro TH, Moser F, Voigt CA 2012. Modular control of multiple pathways using engineered orthogonal T7 polymerases. Nucleic Acids Res 40:8773–81
    [Google Scholar]
13. 13.  Meyer AJ, Ellefson JW, Ellington AD 2015. Directed evolution of a panel of orthogonal T7 RNA polymerase variants for in vivo or in vitro synthetic circuitry. ACS Synth. Biol. 4:1070–76
    [Google Scholar]
14. 14.  Segall-Shapiro TH, Meyer AJ, Ellington AD, Sontag ED, Voigt CA 2014. A “resource allocator” for transcription based on a highly fragmented T7 RNA polymerase. Mol. Syst. Biol. 10:742
    [Google Scholar]
15. 15.  Pu J, Zinkus-Boltz J, Dickinson BC 2017. Evolution of a split RNA polymerase as a versatile biosensor platform. Nat. Chem. Biol. 13:432–38
    [Google Scholar]
16. 16.  Han T, Chen Q, Liu H 2017. Engineered photoactivatable genetic switches based on the bacterium phage T7 RNA polymerase. ACS Synth. Biol. 6:357–66
    [Google Scholar]
17. 17.  Baumschlager A, Aoki SK, Khammash M 2017. Dynamic blue light-inducible T7 RNA polymerases (opto-T7RNAPs) for precise spatiotemporal gene expression control. ACS Synth. Biol. 6:2157–67
    [Google Scholar]
18. 18.  Hochschild A, Lewis M 2009. The bacteriophage λ CI protein finds an asymmetric solution. Curr. Opin. Struct. Biol. 19:79–86
    [Google Scholar]
19. 19.  Elowitz MB, Leibler S 2000. A synthetic oscillatory network of transcriptional regulators. Nature 403:335–38
    [Google Scholar]
20. 20.  Brödel AK, Jaramillo A, Isalan M 2016. Engineering orthogonal dual transcription factors for multi-input synthetic promoters. Nat. Commun. 7:13858
    [Google Scholar]
21. 21.  Kotula JW, Kerns SJ, Shaket LA, Siraj L, Collins JJ et al. 2014. Programmable bacteria detect and record an environmental signal in the mammalian gut. PNAS 111:4838–43
    [Google Scholar]
22. 22.  Stirling F, Bitzan L, O'Keefe S, Redfield E, Oliver JWK et al. 2017. Rational design of evolutionarily stable microbial kill switches. Mol. Cell 68:686–97
    [Google Scholar]
23. 23.  Noman N, Inniss M, Iba H, Way JC 2016. Pulse detecting genetic circuit—a new design approach. PLOS ONE 11:e0167162
    [Google Scholar]
24. 24.  Yang L, Nielsen AAK, Fernandez-Rodriguez J, McClune CJ, Laub MT et al. 2014. Permanent genetic memory with >1-byte capacity. Nat. Methods 11:1261–66
    [Google Scholar]
25. 25.  Fogg PCM, Colloms S, Rosser S, Stark M, Smith MCM 2014. New applications for phage integrases. J. Mol. Biol. 426:2703–16
    [Google Scholar]
26. 26.  Inniss MC, Bandara K, Jusiak B, Lu TK, Weiss R et al. 2017. A novel Bxb1 integrase RMCE system for high fidelity site-specific integration of mAb expression cassette in CHO cells. Biotechnol. Bioeng. 114:1837–46
    [Google Scholar]
27. 27.  Zhu F, Gamboa M, Farruggio AP, Hippenmeyer S, Tasic B et al. 2014. DICE, an efficient system for iterative genomic editing in human pluripotent stem cells. Nucleic Acids Res 42:e34
    [Google Scholar]
28. 28.  Matreyek KA, Stephany JJ, Fowler DM 2017. A platform for functional assessment of large variant libraries in mammalian cells. Nucleic Acids Res 45:e102
    [Google Scholar]
29. 29.  Siuti P, Yazbek J, Lu TK 2013. Synthetic circuits integrating logic and memory in living cells. Nat. Biotechnol. 31:448–52
    [Google Scholar]
30. 30.  Hsiao V, Hori Y, Rothemund PW, Murray RM 2016. A population-based temporal logic gate for timing and recording chemical events. Mol. Syst. Biol. 12:869
    [Google Scholar]
31. 31.  Siuti P, Yazbek J, Lu TK 2014. Engineering genetic circuits that compute and remember. Nat. Protoc. 9:1292–300
    [Google Scholar]
32. 32.  Daniel R, Rubens JR, Sarpeshkar R, Lu TK 2013. Synthetic analog computation in living cells. Nature 497:619–23
    [Google Scholar]
33. 33.  Roquet N, Soleimany AP, Ferris AC, Aaronson S, Lu TK 2016. Synthetic recombinase-based state machines in living cells. Science 353:aad8559
    [Google Scholar]
34. 34.  Weinberg BH, Pham NTH, Caraballo LD, Lozanoski T, Engel A et al. 2017. Large-scale design of robust genetic circuits with multiple inputs and outputs for mammalian cells. Nat. Biotechnol. 35:453–62
    [Google Scholar]
35. 35.  Fenno LE, Mattis J, Ramakrishnan C, Hyun M, Lee SY et al. 2014. Targeting cells with single vectors using multiple-feature Boolean logic. Nat. Methods 11:763–72
    [Google Scholar]
36. 36.  Calendar R, Abedon S 2006. The Bacteriophages Oxford, UK: Oxford Univ. Press
37. 37.  Marinelli LJ, Piuri M, Swigonová Z, Balachandran A, Oldfield LM et al. 2008. BRED: a simple and powerful tool for constructing mutant and recombinant bacteriophage genomes. PLOS ONE 3:e3957
    [Google Scholar]
38. 38.  Oppenheim AB, Rattray AJ, Bubunenko M, Thomason LC, Court DL 2004. In vivo recombineering of bacteriophage λ by PCR fragments and single-strand oligonucleotides. Virology 319:185–89
    [Google Scholar]
39. 39.  Fehér T, Karcagi I, Blattner FR, Pósfai G 2012. Bacteriophage recombineering in the lytic state using the lambda red recombinases. Microb. Biotechnol. 5:466–76
    [Google Scholar]
40. 40.  Thomason L, Court DL, Bubunenko M, Costantino N, Wilson H et al. 2007. Recombineering: genetic engineering in bacteria using homologous recombination. Curr. Protoc. Mol. Biol. 106:1.16.1–39
    [Google Scholar]
41. 41.  Pouillot F, Blois H, Iris F 2010. Genetically engineered virulent phage banks in the detection and control of emergent pathogenic bacteria. Biosecur. Bioterrorism Biodefense Strateg. Pract. Sci. 8:155–69
    [Google Scholar]
42. 42.  Swingle B, Bao Z, Markel E, Chambers A, Cartinhour S 2010. Recombineering using RecTE from Pseudomonas syringae. Appl. Environ. . Microbiol 76:4960–68
    [Google Scholar]
43. 43.  Martel B, Moineau S 2014. CRISPR-Cas: an efficient tool for genome engineering of virulent bacteriophages. Nucleic Acids Res 42:9504–13
    [Google Scholar]
44. 44.  Kiro R, Shitrit D, Qimron U 2014. Efficient engineering of a bacteriophage genome using the type I-E CRISPR-Cas system. RNA Biol 11:42–44
    [Google Scholar]
45. 45.  Lemay ML, Tremblay DM, Moineau S 2017. Genome engineering of virulent lactococcal phages using CRISPR-Cas9. ACS Synth. Biol. 6:1351–58
    [Google Scholar]
46. 46.  Tao P, Wu X, Tang WC, Zhu J, Rao V 2017. Engineering of bacteriophage T4 genome using CRISPR-Cas9. ACS Synth. Biol. 6:1952–61
    [Google Scholar]
47. 47.  Jaschke PR, Lieberman EK, Rodriguez J, Sierra A, Endy D 2012. A fully decompressed synthetic bacteriophage øX174 genome assembled and archived in yeast. Virology 434:278–84
    [Google Scholar]
48. 48.  Ando H, Lemire S, Pires DP, Lu TK 2015. Engineering modular viral scaffolds for targeted bacterial population editing. Cell Syst 1:187–96
    [Google Scholar]
49. 49.  Allan EJ, Hoischen C, Gumpert J 2009. Bacterial L‐forms. Adv. Appl. Microbiol. 68:1–39
    [Google Scholar]
50. 50.  Kilcher S, Studer P, Muessner C, Klumpp J, Loessner MJ 2018. Cross-genus rebooting of custom-made, synthetic bacteriophage genomes in L-form bacteria. PNAS 115:567–72
    [Google Scholar]
51. 51.  Gibson DG, Young L, Chuang R, Venter JC, Hutchinson CA III, Smith HO 2009. Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat. Methods 6:343–45
    [Google Scholar]
52. 52.  Garamella J, Marshall R, Rustad M, Noireaux V 2016. The all E. coli TX-TL toolbox 2.0: a platform for cell-free synthetic biology. ACS Synth. Biol. 5:344–55
    [Google Scholar]
53. 53.  Kutter E, De Vos D, Gvasalia G, Alavidze Z, Gogokhia L et al. 2010. Phage therapy in clinical practice: treatment of human infections. Curr. Pharm. Biotechnol. 11:69–86
    [Google Scholar]
54. 54.  Cooper CJ, Khan Mirzaei M, Nilsson AS 2016. Adapting drug approval pathways for bacteriophage-based therapeutics. Front. Microbiol. 7:1209
    [Google Scholar]
55. 55.  Canchaya C, Proux C, Fournous G, Bruttin A, Bru H 2003. Prophage genomics. Microbiol. Mol. Biol. Rev. 67:238–76
    [Google Scholar]
56. 56.  Górski A, Międzybrodzki R, Borysowski J, Dąbrowska K, Wierzbicki P et al. 2012. Phage as a modulator of immune responses. Adv. Virus Res. 83:41–71
    [Google Scholar]
57. 57.  Lu TK, Collins JJ 2007. Dispersing biofilms with engineered enzymatic bacteriophage. PNAS 104:11197–202
    [Google Scholar]
58. 58.  Lin H, Paff ML, Molineux IJ, Bull JJ 2017. Therapeutic application of phage capsule depolymerases against K1, K5, and K30 capsulated E. coli in mice. Front. Microbiol. 8:2257
    [Google Scholar]
59. 59.  Fleming D, Rumbaugh KP 2017. Approaches to dispersing medical biofilms. Microorganisms 5:E15
    [Google Scholar]
60. 60.  Born Y, Fieseler L, Thöny V, Leimer N, Duffy B, Loessner MJ 2017. Engineering of bacteriophages Y2::dpoL1-C and Y2::luxAB for efficient control and rapid detection of the fire blight pathogen, Erwinia amylovora. Appl. Environ. Microbiol. 83:e00341–17
    [Google Scholar]
61. 61.  Silva JB, Storms Z, Sauvageau D 2016. Host receptors for bacteriophage adsorption. FEMS Microbiol. Lett. 363:fnw002
    [Google Scholar]
62. 62.  Yu P, Mathieu J, Li M, Dai Z, Alvarez PJJ 2015. Isolation of polyvalent bacteriophages by sequential multiple-host approaches. Appl. Environ. Microbiol. 82:808–15
    [Google Scholar]
63. 63.  Hamdi S, Rousseau GM, Labrie SJ, Tremblay DM, Kourda RS et al. 2017. Characterization of two polyvalent phages infecting Enterobacteriaceae. Sci. . Rep 7:40349
    [Google Scholar]
64. 64.  Matsuda T, Freeman TA, Hilbert DW, Duff M, Fuortes M et al. 2005. Lysis-deficient bacteriophage therapy decreases endotoxin and inflammatory mediator release and improves survival in a murine peritonitis model. Surgery 137:639–46
    [Google Scholar]
65. 65.  Murooka Y, Takizawa N, Harada T 1981. Introduction of bacteriophage Mu into bacteria of various genera and intergeneric gene transfer by RP4::Mu. J. Bacteriol. 145:358–68
    [Google Scholar]
66. 66.  Murooka Y, Harada T 1979. Expansion of the host range of coliphage P1 and gene transfer from enteric bacteria to other gram-negative bacteria. Appl. Environ. Microbiol. 38:754–57
    [Google Scholar]
67. 67.  Krom RJ, Bhargava P, Lobritz MA, Collins JJ 2015. Engineered phagemids for nonlytic, targeted antibacterial therapies. Nano Lett 15:4808–13
    [Google Scholar]
68. 68.  Citorik RJ, Mimee M, Lu TK 2014. Sequence-specific antimicrobials using efficiently delivered RNA-guided nucleases. Nat. Biotechnol. 32:1141–45
    [Google Scholar]
69. 69.  Chung YB, Hinkle DC 1990. Bacteriophage T7 DNA packaging. I. Plasmids containing a T7 replication origin and the T7 concatemer junction are packaged into transducing particles during phage infection. J. Mol. Biol. 216:911–26
    [Google Scholar]
70. 70.  Hashimoto C 1988. Packaging and transduction of non-T3 DNA by bacteriophage T3. Virology 439:432–39
    [Google Scholar]
71. 71.  Yosef I, Goren MG, Globus R, Molshanski-Mor S, Qimron U 2017. Extending the host range of bacteriophage particles for DNA transduction. Mol. Cell 66:721–28
    [Google Scholar]
72. 72.  Brüssow H 2012. What is needed for phage therapy to become a reality in Western medicine?. Virology 434:138–42
    [Google Scholar]
73. 73.  Hargreaves KR, Clokie MRJ 2014. Clostridium difficile phages: still difficult?. Front. Microbiol. 5:184
    [Google Scholar]
74. 74.  Pastagia M, Schuch R, Fischetti VA, Huang DB 2013. Lysins: the arrival of pathogen-directed anti-infectives. J. Med. Microbiol. 62:Pt. 101506–16
    [Google Scholar]
75. 75.  Lukacik P, Barnard TJ, Keller PW, Chaturvedi KS, Seddiki N et al. 2012. Structural engineering of a phage lysin that targets gram-negative pathogens. PNAS 109:9857–62
    [Google Scholar]
76. 76.  Briers Y, Walmagh M, Van Puyenbroeck V, Cornelissen A, Cenens W et al. 2014. Engineered endolysin-based “Artilysins” to combat multidrug-resistant gram-negative pathogens. mBio 5:e01379–14
    [Google Scholar]
77. 77.  Defraine V, Schuermans J, Grymonprez B, Govers SK, Aertsen A et al. 2016. Efficacy of Artilysin Art-175 against resistant and persistent Acinetobacter baumannii. Antimicrob. . Agents Chemother 60:3480–88
    [Google Scholar]
78. 78.  Piuri M, Jacobs WR, Hatfull GF 2009. Fluoromycobacteriophages for rapid, specific, and sensitive antibiotic susceptibility testing of Mycobacterium tuberculosis. . PLOS ONE 4:e4870
    [Google Scholar]
79. 79.  O'Donnell MR, Pym A, Jain P, Munsamy V, Wolf A et al. 2015. A novel reporter phage to detect tuberculosis and rifampin resistance in a high-HIV-burden population. J. Clin. Microbiol. 53:2188–94
    [Google Scholar]
80. 80.  Jain P, Hartman TE, Eisenberg N, O'Donnell MR, Kriakov J et al. 2012. ϕ²GFP10, a high-intensity fluorophage, enables detection and rapid drug susceptibility testing of Mycobacterium tuberculosis directly from sputum samples. J. Clin. Microbiol. 50:1362–69
    [Google Scholar]
81. 81.  Jacobs WR, Barletta RG, Udani R, Chan J, Kalkut G et al. 1993. Rapid assessment of drug susceptibilities of Mycobacterium tuberculosis by means of luciferase reporter phages. Science 260:819–22
    [Google Scholar]
82. 82.  Sarkis GJ, Jacobs WR, Hatfull GF 1995. L5 luciferase reporter mycobacteriophages: a sensitive tool for the detection and assay of live mycobacteria. Mol. Microbiol. 15:1055–67
    [Google Scholar]
83. 83.  Pearson RE, Jurgensen S, Sarkis GJ, Hatfull GF, Jacobs WR 1996. Construction of D29 shuttle phasmids and luciferase reporter phages for detection of mycobacteria. Gene 183:129–36
    [Google Scholar]
84. 84.  Kumar V, Loganathan P, Sivaramakrishnan G, Kriakov J, Dusthakeer A et al. 2008. Characterization of temperate phage Che12 and construction of a new tool for diagnosis of tuberculosis. Tuberculosis 88:616–23
    [Google Scholar]
85. 85.  Peng Y, Jin Y, Lin H, Wang J, Khan MN 2014. Application of the VPp1 bacteriophage combined with a coupled enzyme system in the rapid detection of Vibrio parahaemolyticus. J. Microbiol. . Methods 98:99–104
    [Google Scholar]
86. 86.  Kim S, Kim M, Ryu S 2014. Development of an engineered bioluminescent reporter phage for the sensitive detection of viable Salmonella Typhimurium. Anal. Chem. 86:5858–64
    [Google Scholar]
87. 87.  Vandamm JP, Rajanna C, Sharp NJ, Molineux IJ, Schofield DA 2014. Rapid detection and simultaneous antibiotic susceptibility analysis of Yersinia pestis directly from clinical specimens by use of reporter phage. J. Clin. Microbiol. 52:2998–3003
    [Google Scholar]
88. 88.  Schofield DA, Wray DJ, Molineux IJ 2015. Isolation and development of bioluminescent reporter phages for bacterial dysentery. Eur. J. Clin. Microbiol. Infect. Dis. 34:395–403
    [Google Scholar]
89. 89.  Sharp NJ, Vandamm JP, Molineux IJ, Schofield DA 2015. Rapid detection of Bacillus anthracis in complex food matrices using phage-mediated bioluminescence. J. Food Prot. 78:963–68
    [Google Scholar]
90. 90.  Sharp NJ, Molineux IJ, Page MA, Schofield DA 2016. Rapid detection of viable Bacillus anthracis spores in environmental samples by using engineered reporter phages. Appl. Environ. Microbiol. 82:2380–87
    [Google Scholar]
91. 91.  Zhang D, Coronel-Aguilera CP, Romero PL, Perry L, Minocha U et al. 2016. The use of a novel NanoLuc-based reporter phage for the detection of Escherichia coli O157:H7. Sci. Rep. 6:33235
    [Google Scholar]
92. 92.  Kim J, Kim M, Kim S, Ryu S 2017. Sensitive detection of viable Escherichia coli O157:H7 from foods using a luciferase-reporter phage ϕV10 lux. Int. J. Food Microbiol. 254:11–17
    [Google Scholar]
93. 93.  Oosterik LH, Tuntufye HN, Tsonos J, Luyten T, Noppen S et al. 2016. Bioluminescent avian pathogenic Escherichia coli for monitoring colibacillosis in experimentally infected chickens. Vet. J. 216:87–92
    [Google Scholar]
94. 94.  Loessner MJ, Rudolf M, Scherer S 1997. Evaluation of luciferase reporter bacteriophage A511::luxAB for detection of Listeria monocytogenes in contaminated foods. Appl. Environ. Microbiol. 63:2961–65
    [Google Scholar]
95. 95.  Schmidt A, Rabsch W, Broeker NK, Barbirz S 2016. Bacteriophage tailspike protein based assay to monitor phase variable glucosylations in Salmonella O-antigens. BMC Microbiol 16:207
    [Google Scholar]
96. 96.  Schmelcher M, Shabarova T, Eugster MR, Eichenseher F, Tchang VS et al. 2010. Rapid multiplex detection and differentiation of Listeria cells by use of fluorescent phage endolysin cell wall binding domains. Appl. Environ. Microbiol. 76:5745–56
    [Google Scholar]
97. 97.  Na H, Kong M, Ryu S 2016. Characterization of LysPBC4, a novel Bacillus cereus-specific endolysin of bacteriophage PBC4. FEMS Microbiol. Lett. 363:fnw092
    [Google Scholar]
98. 98.  Gómez-Torres N, Dunne M, Garde S, Meijers R, Narbad A et al. 2018. Development of a specific fluorescent phage endolysin for in situ detection of Clostridium species associated with cheese spoilage. Microb. Biotechnol. 11:332–45
    [Google Scholar]
99. 99.  Benešík M, Nováček J, Janda L, Dopitová R, Pernisová M et al. 2018. Role of SH3b binding domain in a natural deletion mutant of Kayvirus endolysin LysF1 with a broad range of lytic activity. Virus Genes 54:130–39
    [Google Scholar]
100. 100.  Ugorcakova J, Medzova L, Solteszova B, Bukovska G 2015. Characterization of a ϕBP endolysin encoded by the Paenibacillus polymyxa CCM 7400 phage. FEMS Microbiol. Lett. 362:fnv098
     [Google Scholar]
101. 101.  Kovacs EW, Hooker JM, Romanini DW, Holder PG, Berry KE, Francis MB 2007. Dual-surface-modified bacteriophage MS2 as an ideal scaffold for a viral capsid-based drug delivery system. Bioconjug. Chem. 18:1140–47
     [Google Scholar]
102. 102.  Ashley CE, Carnes EC, Phillips GK, Durfee PN, Buley MD et al. 2011. Cell-specific delivery of diverse cargos by bacteriophage MS2 virus-like particles. ACS Nano 5:5729–45
     [Google Scholar]
103. 103.  Rhee JK, Baksh M, Nycholat C, Paulson JC, Kitagishi H, Finn MG 2012. Glycan-targeted virus-like nanoparticles for photodynamic therapy. Biomacromolecules 13:2333–38
     [Google Scholar]
104. 104.  Galaway FA, Stockley PG 2013. MS2 viruslike particles: a robust, semisynthetic targeted drug delivery platform. Mol. Pharm. 10:59–68
     [Google Scholar]
105. 105.  Kato T, Yui M, Deo VK, Park EY 2015. Development of rous sarcoma virus-like particles displaying hCC49 scFv for Specific targeted drug delivery to human colon carcinoma cells. Pharm. Res. 32:3699–707
     [Google Scholar]
106. 106.  Deo VK, Kato T, Park EY 2016. Virus-like particles displaying recombinant short-chain fragment region and interleukin 2 for targeting colon cancer tumors and attracting macrophages. J. Pharm. Sci. 105:1614–22
     [Google Scholar]
107. 107.  Sánchez-Sánchez L, Tapia-Moreno A, Juarez-Moreno K, Patterson DP, Cadena-Nava RD et al. 2015. Design of a VLP-nanovehicle for CYP450 enzymatic activity delivery. J. Nanobiotechnol. 13:66
     [Google Scholar]
108. 108.  Lino CA, Caldeira JC, Peabody DS 2017. Display of single-chain variable fragments on bacteriophage MS2 virus-like particles. J. Nanobiotechnol. 15:13
     [Google Scholar]
109. 109.  Vaks L, Benhar I 2011. Antibacterial application of engineered bacteriophage nanomedicines: antibody-targeted, chloramphenicol prodrug loaded bacteriophages for inhibiting the growth of Staphylococcus aureus bacteria. Methods Mol. Biol. 726:187–206
     [Google Scholar]
110. 110.  Anand P, O'Neil A, Lin E, Douglas T, Holford M 2015. Tailored delivery of analgesic ziconotide across a blood brain barrier model using viral nanocontainers. Sci. Rep. 5:12497
     [Google Scholar]
111. 111.  Qazi S, Miettinen HM, Wilkinson RA, McCoy K, Douglas T, Wiedenheft B 2016. Programmed self-assembly of an active P22-Cas9 nanocarrier system. Mol. Pharm. 13:1191–96
     [Google Scholar]
112. 112.  Jennings GT, Bachmann MF 2008. The coming of age of virus-like particle vaccines. Biol. Chem. 389:521–36
     [Google Scholar]
113. 113.  Lua LHL, Connors NK, Sainsbury F, Chuan YP, Wibowo N, Middelberg APJ 2014. Bioengineering virus-like particles as vaccines. Biotechnol. Bioeng. 111:425–40
     [Google Scholar]
114. 114.  Deng L, Roose K, Job ER, De Rycke R, Van Hamme E et al. 2017. Oral delivery of Escherichia coli persistently infected with M2e-displaying bacteriophages partially protects against influenza A virus. J. Control. Release 264:55–65
     [Google Scholar]
115. 115.  Butterfield GL, Lajoie MJ, Gustafson HH, Sellers DL, Nattermann U et al. 2017. Evolution of a designed protein assembly encapsulating its own RNA genome. Nature 552:415–20
     [Google Scholar]
116. 116.  Han L, Shao C, Liang B, Liu A 2016. Genetically engineered phage-templated MnO₂ nanowires: synthesis and their application in electrochemical glucose biosensor operated at neutral pH condition. ACS Appl. Mater. Interfaces 8:13768–76
     [Google Scholar]
117. 117.  Li Y, Cao B, Yang M, Zhu Y, Suh J, Mao C 2016. Identification of novel short BaTiO₃-binding/nucleating peptides for phage-templated in situ synthesis of BaTiO₃ polycrystalline nanowires at room temperature. ACS Appl. Mater. Interfaces 8:30714–21
     [Google Scholar]
118. 118.  Manivannan S, Kang I, Seo Y, Jin HE, Lee SW, Kim K 2017. M13 virus-incorporated biotemplates on electrode surfaces to nucleate metal nanostructures by electrodeposition. ACS Appl. Mater. Interfaces 9:32965–76
     [Google Scholar]
119. 119.  Yi H, Ghosh D, Ham MH, Qi J, Barone PW et al. 2012. M13 phage-functionalized single-walled carbon nanotubes as nanoprobes for second near-infrared window fluorescence imaging of targeted tumors. Nano Lett 12:1176–83
     [Google Scholar]
120. 120.  Szot-Karpińska K, Golec P, Leśniewski A, Pałys B, Marken F et al. 2016. Modified filamentous bacteriophage as a scaffold for carbon nanofiber. Bioconjug. Chem. 27:2900–10
     [Google Scholar]
121. 121.  Golec P, Żelechowska K, Karczewska-Golec J, Karczewski J, Leśniewski A et al. 2017. Bacteriophages as factories for Eu₂O₃ nanoparticle synthesis. Bioconjug. Chem. 28:1834–41
     [Google Scholar]
122. 122.  Lee HK, Lee Y, Kim H, Lee HE, Chang H et al. 2017. Screening of Pro-Asp sequences exposed on bacteriophage M13 as an ideal anchor for gold nanocubes. ACS Synth. Biol. 6:1635–41
     [Google Scholar]
123. 123.  Giessen TW, Silver PA 2016. A catalytic nanoreactor based on in vivo encapsulation of multiple enzymes in an engineered protein nanocompartment. ChemBioChem 17:1931–35
     [Google Scholar]
124. 124.  Myhrvold C, Polka JK, Silver PA 2016. Synthetic lipid-containing scaffolds enhance production by colocalizing enzymes. ACS Synth. Biol. 5:1396–403
     [Google Scholar]
125. 125.  Smith GP 1985. Filamentous fusion phage: novel expression vectors that display cloned antigens on the virion surface. Science 228:1315–17
     [Google Scholar]
126. 126.  Wu CH, Liu IJ, Lu RM, Wu HC 2016. Advancement and applications of peptide phage display technology in biomedical science. J. Biomed. Sci. 23:8
     [Google Scholar]
127. 127.  Esvelt KM, Carlson JC, Liu DR 2011. A system for the continuous directed evolution of biomolecules. Nature 472:499–503
     [Google Scholar]
128. 128.  Carlson JC, Badran AH, Guggiana-Nilo DA, Liu DR 2014. Negative selection and stringency modulation in phage-assisted continuous evolution. Nat. Chem. Biol. 10:216–22
     [Google Scholar]
129. 129.  Bryson DI, Fan C, Guo LT, Miller C, Söll D, Liu DR 2017. Continuous directed evolution of aminoacyl-tRNA synthetases. Nat. Chem. Biol. 13:1253–60
     [Google Scholar]
130. 130.  Packer MS, Rees HA, Liu DR 2017. Phage-assisted continuous evolution of proteases with altered substrate specificity. Nat. Commun. 8:956
     [Google Scholar]
131. 131.  Hubbard BP, Badran AH, Zuris JA, Guilinger JP, Davis KM et al. 2015. Continuous directed evolution of DNA-binding proteins to improve TALEN specificity. Nat. Methods 12:939–42
     [Google Scholar]
132. 132.  Badran AH, Guzov VM, Huai Q, Kemp MM, Vishwanath P et al. 2016. Continuous evolution of Bacillus thuringiensis toxins overcomes insect resistance. Nature 533:58–63
     [Google Scholar]
133. 133.  Farzadfard F, Lu TK 2014. Genomically encoded analog memory with precise in vivo DNA writing in living cell populations. Science 346:1256272
     [Google Scholar]
134. 134.  Sharma U, Paul VD 2017. Bacteriophage lysins as antibacterials. Crit. Care 21:99
     [Google Scholar]
135. 135.  Kauffman KM, Hussain FA, Yang J, Arevalo P, Brown JM et al. 2018. A major lineage of non-tailed dsDNA viruses as unrecognized killers of marine bacteria. Nature 554:118–22
     [Google Scholar]