Phage engineering: how advances in molecular biology and synthetic biology are being utilized to enhance the therapeutic potential of bacteriophages
Russell Brown, Andreas Lengeling, Baojun Wang
Phage engineering: how advances in molecular biology and synthetic biology are being utilized to enhance the therapeutic potential of bacteriophages
Background: The therapeutic potential of bacteriophages has been debated since their first isolation and characterisation in the early 20th century. However, a lack of consistency in application and observed efficacy during their early use meant that upon the discovery of antibiotic compounds research in the field of phage therapy quickly slowed. The rise of antibiotic resistance in bacteria and improvements in our abilities to modify and manipulate DNA, especially in the context of small viral genomes, has led to a recent resurgence of interest in utilising phage as antimicrobial therapeutics.
Results: In this article a number of results from the literature that have aimed to address key issues regarding the utility and efficacy of phage as antimicrobial therapeutics utilising molecular biology and synthetic biology approaches will be introduced and discussed, giving a general view of the recent progress in the field.
Conclusions: Advances in molecular biology and synthetic biology have enabled rapid progress in the field of phage engineering, with this article highlighting a number of promising strategies developed to optimise phages for the treatment of bacterial disease. Whilst many of the same issues that have historically limited the use of phages as therapeutics still exist, these modifications, or combinations thereof, may form a basis upon which future advances can be built. A focus on rigorous in vivo testing and investment in clinical trials for promising candidate phages may be required for the field to truly mature, but there is renewed hope that the potential benefits of phage therapy may finally be realised.
bacteriophage / phage therapy / phage engineering / synthetic biology
[1] |
Summers, W. C. (2012) The strange history of phage therapy. Bacteriophage, 2, 130–133
CrossRef
Pubmed
Google scholar
|
[2] |
Twort, F. W. (1915) An investigation on the nature of ultra-microscopic viruses. Lancet, 186, 1241–1243
CrossRef
Google scholar
|
[3] |
d’Herelle, F. (1917) On an invisible microbe antagonistic to dysentery bacili. CR Acad. Sci. Paris, 165, 373–375
|
[4] |
Abedon, S. T., Kuhl, S. J., Blasdel, B. G. and Kutter, E. M. (2011) Phage treatment of human infections. Bacteriophage, 1, 66–85
CrossRef
Pubmed
Google scholar
|
[5] |
Neu, H. C. (1992) The crisis in antibiotic resistance. Science, 257, 1064–1073
CrossRef
Pubmed
Google scholar
|
[6] |
Davies, J. and Davies, D. (2010) Origins and evolution of antibiotic resistance. Microbiol. Mol. Biol. Rev., 74, 417–433
CrossRef
Pubmed
Google scholar
|
[7] |
Bradley, R. W., Buck, M. and Wang, B. (2016) Tools and principles for microbial gene circuit engineering. J. Mol. Biol., 428, 862–888
CrossRef
Pubmed
Google scholar
|
[8] |
Wang, B. and Buck, M. (2012) Customizing cell signaling using engineered genetic logic circuits. Trends Microbiol., 20, 376–384
CrossRef
Pubmed
Google scholar
|
[9] |
Wang, B., Kitney, R. I., Joly, N. and Buck, M. (2011) Engineering modular and orthogonal genetic logic gates for robust digital-like synthetic biology. Nat. Commun., 2, 508
CrossRef
Pubmed
Google scholar
|
[10] |
Wang, B., Barahona, M. and Buck, M. (2013) A modular cell-based biosensor using engineered genetic logic circuits to detect and integrate multiple environmental signals. Biosens. Bioelectron., 40, 368–376
CrossRef
Pubmed
Google scholar
|
[11] |
Bradley, R. W. and Wang, B. (2015) Designer cell signal processing circuits for biotechnology. N. Biotechnol., 32, 635–643
CrossRef
Pubmed
Google scholar
|
[12] |
Haellman, V. and Fussenegger, M. (2016) Synthetic biology—toward therapeutic solutions. J. Mol. Biol., 428, 945–962
CrossRef
Pubmed
Google scholar
|
[13] |
Smith, H. O., Hutchison, C. A. III, Pfannkoch, C. and Venter, J. C. (2003) Generating a synthetic genome by whole genome assembly: ΦX174 bacteriophage from synthetic oligonucleotides. Proc. Natl. Acad. Sci. USA, 100, 15440–15445
CrossRef
Pubmed
Google scholar
|
[14] |
Chan, L.Y., Kosuri, S., and Endy, D. (2005) Refactoring bacteriophage T7. Mol. Syst. Biol. 1, 2005. 0018
CrossRef
Google scholar
|
[15] |
Lu, T. K. and Koeris, M. S. (2011) The next generation of bacteriophage therapy. Curr. Opin. Microbiol., 14, 524–531
CrossRef
Pubmed
Google scholar
|
[16] |
Pires, D. P., Cleto, S., Sillankorva, S., Azeredo, J. and Lu, T. K. (2016) Genetically engineered phages: a review of advances over the last decade. Microbiol. Mol. Biol. Rev., 80, 523–543
CrossRef
Pubmed
Google scholar
|
[17] |
Rakhuba, D. V., Kolomiets, E. I., Dey, E. S. and Novik, G. I. (2010) Bacteriophage receptors, mechanisms of phage adsorption and penetration into host cell. Pol. J. Microbiol., 59, 145–155
Pubmed
|
[18] |
Crawford, J. T. and Goldberg, E. B. (1977) The effect of baseplate mutations on the requirement for tail-fiber binding for irreversible adsorption of bacteriophage T4. J. Mol. Biol., 111, 305–313
CrossRef
Pubmed
Google scholar
|
[19] |
Crawford, J. T. and Goldberg, E. B. (1980) The function of tail fibers in triggering baseplate expansion of bacteriophage T4. J. Mol. Biol., 139, 679–690
CrossRef
Pubmed
Google scholar
|
[20] |
Arscott, P. G. and Goldberg, E. B. (1976) Cooperative action of the T4 tail fibers and baseplate in triggering conformational change and in determining host range. Virology, 69, 15–22
CrossRef
Pubmed
Google scholar
|
[21] |
Molineux, I. J. (2001) No syringes please, ejection of phage T7 DNA from the virion is enzyme driven. Mol. Microbiol., 40, 1–8
CrossRef
Pubmed
Google scholar
|
[22] |
Kemp, P., Garcia, L. R. and Molineux, I. J. (2005) Changes in bacteriophage T7 virion structure at the initiation of infection. Virology, 340, 307–317
CrossRef
Pubmed
Google scholar
|
[23] |
Heller, K. and Braun, V. (1979) Accelerated adsorption of bacteriophage T5 to Escherichia coli F, resulting from reversible tail fiber-lipopolysaccharide binding. J. Bacteriol., 139, 32–38
Pubmed
|
[24] |
Heller, K. and Braun, V. (1982) Polymannose O-antigens of Escherichia coli, the binding sites for the reversible adsorption of bacteriophage T5+ via the L-shaped tail fibers. J. Virol., 41, 222–227
Pubmed
|
[25] |
Riede, I., Degen, M. and Henning, U. (1985) The receptor specificity of bacteriophages can be determined by a tail fiber modifying protein. EMBO J., 4, 2343–2346
Pubmed
|
[26] |
Montag, D., Riede, I., Eschbach, M.-L., Degen, M. and Henning, U. (1987) Receptor-recognizing proteins of T-even type bacteriophages: constant and hypervariable regions and an unusual case of evolution. J. Mol. Biol., 196, 165–174
CrossRef
Pubmed
Google scholar
|
[27] |
Moody, M. F. (1973) Sheath of bacteriophage T4: III. contraction mechanism deduced from partially contracted sheaths. J. Mol. Biol., 80, 613–635
CrossRef
Pubmed
Google scholar
|
[28] |
Wright, A., Hawkins, C. H., Änggård, E. E. and Harper, D. R. (2009) A controlled clinical trial of a therapeutic bacteriophage preparation in chronic otitis due to antibiotic-resistant Pseudomonas aeruginosa; a preliminary report of efficacy. Clin. Otolaryngol., 34, 349–357
CrossRef
Pubmed
Google scholar
|
[29] |
Gu, J., Liu, X., Li, Y., Han, W., Lei, L., Yang, Y., Zhao, H., Gao, Y., Song, J., Lu, R.,
CrossRef
Pubmed
Google scholar
|
[30] |
Oliveira, A., Sereno, R. and Azeredo, J. (2010) In vivo efficiency evaluation of a phage cocktail in controlling severe colibacillosis in confined conditions and experimental poultry houses. Vet. Microbiol., 146, 303–308
CrossRef
Pubmed
Google scholar
|
[31] |
Jaiswal, A., Koley, H., Ghosh, A., Palit, A. and Sarkar, B. (2013) Efficacy of cocktail phage therapy in treating Vibrio cholerae infection in rabbit model. Microbes Infect., 15, 152–156
CrossRef
Pubmed
Google scholar
|
[32] |
Chan, B. K. and Abedon, S. T. (2012). Chapter 1 – Phage therapy pharmacology: phage cocktails. In Advances in Applied Microbiology, Laskin, A.I., Sariaslani, S. and Gadd, G.M. ed. 1–23. Massachusetts: Academic Press
|
[33] |
Chan, B. K., Abedon, S. T. and Loc-Carrillo, C. (2013) Phage cocktails and the future of phage therapy. Future Microbiol., 8, 769–783
CrossRef
Pubmed
Google scholar
|
[34] |
Gill, J. J. and Hyman, P. (2010) Phage choice, isolation, and preparation for phage therapy. Curr. Pharm. Biotechnol., 11, 2–14
CrossRef
Pubmed
Google scholar
|
[35] |
Merabishvili, M., Pirnay, J.-P., Verbeken, G., Chanishvili, N., Tediashvili, M., Lashkhi, N., Glonti, T., Krylov, V., Mast, J., Van Parys, L.,
CrossRef
Pubmed
Google scholar
|
[36] |
Kutter, E., De Vos, D., Gvasalia, G., Alavidze, Z., Gogokhia, L., Kuhl, S. and Abedon, S. T. (2010) Phage therapy in clinical practice: treatment of human infections. Curr. Pharm. Biotechnol., 11, 69–86
CrossRef
Pubmed
Google scholar
|
[37] |
Mahichi, F., Synnott, A. J., Yamamichi, K., Osada, T. and Tanji, Y. (2009) Site-specific recombination of T2 phage using IP008 long tail fiber genes provides a targeted method for expanding host range while retaining lytic activity. FEMS Microbiol. Lett., 295, 211–217
CrossRef
Pubmed
Google scholar
|
[38] |
Yoichi, M., Abe, M., Miyanaga, K., Unno, H. and Tanji, Y. (2005) Alteration of tail fiber protein gp38 enables T2 phage to infect Escherichia coli O157:H7. J. Biotechnol., 115, 101–107
CrossRef
Pubmed
Google scholar
|
[39] |
Pouillot, F., Blois, H. and Iris, F. (2010) Genetically engineered virulent phage banks in the detection and control of emergent pathogenic bacteria. Biosecur. Bioterror., 8, 155–169
CrossRef
Pubmed
Google scholar
|
[40] |
Krüger, D. H. and Schroeder, C. (1981) Bacteriophage T3 and bacteriophage T7 virus-host cell interactions. Microbiol. Rev., 45, 9–51
Pubmed
|
[41] |
Lin, T. -Y., Lo, Y. -H., Tseng, P. -W., Chang, S. -F., Lin, Y. -T. and Chen, T. -S. (2012) A T3 and T7 recombinant phage acquires efficient adsorption and a broader host range. PLoS One, 7, e30954
CrossRef
Pubmed
Google scholar
|
[42] |
Ando, H., Lemire, S., Pires, D. P. and Lu, T. K. (2015) Engineering modular viral scaffolds for targeted bacterial population editing. Cell Syst., 1, 187–196
CrossRef
Pubmed
Google scholar
|
[43] |
Friedman, D. I. (1992) Interaction between bacteriophage l and its Escherichia coli host. Curr. Opin. Genet. Dev., 2, 727–738
CrossRef
Pubmed
Google scholar
|
[44] |
Casjens, S. R., Gilcrease, E. B., Winn-Stapley, D. A., Schicklmaier, P., Schmieger, H., Pedulla, M. L., Ford, M. E., Houtz, J. M., Hatfull, G. F. and Hendrix, R. W. (2005) The generalized transducing Salmonella bacteriophage ES18: complete genome sequence and DNA packaging strategy. J. Bacteriol., 187, 1091–1104
CrossRef
Pubmed
Google scholar
|
[45] |
Casjens, S. (2003) Prophages and bacterial genomics: what have we learned so far? Mol. Microbiol., 49, 277–300
CrossRef
Pubmed
Google scholar
|
[46] |
Esvelt, K. M., Carlson, J. C. and Liu, D. R. (2011) A system for the continuous directed evolution of biomolecules. Nature, 472, 499–503
CrossRef
Pubmed
Google scholar
|
[47] |
Bassalo, M. C., Liu, R. and Gill, R. T. (2016) Directed evolution and synthetic biology applications to microbial systems. Curr. Opin. Biotechnol., 39, 126–133
CrossRef
Pubmed
Google scholar
|
[48] |
Prins, J. M., van Deventer, S. J., Kuijper, E. J. and Speelman, P. (1994) Clinical relevance of antibiotic-induced endotoxin release. Antimicrob. Agents Chemother., 38, 1211–1218
CrossRef
Pubmed
Google scholar
|
[49] |
Slopek, S., Durlakowa, I., Weber-Dabrowska, B., Kucharewicz-Krukowska, A., Dabrowski, M. and Bisikiewicz, R. (1983) Results of bacteriophage treatment of suppurative bacterial infections. I. General evaluation of the results. Arch. Immunol. Ther. Exp. (Warsz.), 31, 267–291
Pubmed
|
[50] |
Gamage, S. D., Patton, A. K., Hanson, J. F. and Weiss, A. A. (2004) Diversity and host range of Shiga toxin-encoding phage. Infect. Immun., 72, 7131–7139
CrossRef
Pubmed
Google scholar
|
[51] |
Krylov, V. N. (2001) Phagotherapy in terms of bacteriophage genetics: hopes, perspectives, safety, limitations. Genetika, 37, 869–887
Pubmed
|
[52] |
Jerne, N. K. and Avegno, P. (1956) The development of the phage-inactivating properties of serum during the course of specific immunization of an animal: reversible and irreversible inactivation. J. Immunol., 76, 200–208
Pubmed
|
[53] |
Hodyra-Stefaniak, K., Miernikiewicz, P., Drapała, J., Drab, M., Jończyk-Matysiak, E., Lecion, D., Kaźmierczak, Z., Beta, W., Majewska, J., Harhala, M.,
CrossRef
Pubmed
Google scholar
|
[54] |
Sokoloff, A. V., Zhang, G., Sebestyén, M. G. and Wolff, J. A. (2000) The interactions of peptides with the innate immune system studied with use of T7 phage peptide display. Mol. Ther., 2, 131–139
CrossRef
Pubmed
Google scholar
|
[55] |
Merril, C. R., Biswas, B., Carlton, R., Jensen, N. C., Creed, G. J., Zullo, S. and Adhya, S. (1996) Long-circulating bacteriophage as antibacterial agents. Proc. Natl. Acad. Sci. USA, 93, 3188–3192
CrossRef
Pubmed
Google scholar
|
[56] |
Vitiello, C. L., Merril, C. R. and Adhya, S. (2005) An amino acid substitution in a capsid protein enhances phage survival in mouse circulatory system more than a 1000-fold. Virus Res., 114, 101–103
CrossRef
Pubmed
Google scholar
|
[57] |
Capparelli, R., Ventimiglia, I., Roperto, S., Fenizia, D. and Iannelli, D. (2006) Selection of an Escherichia coli O157:H7 bacteriophage for persistence in the circulatory system of mice infected experimentally. Clin. Microbiol. Infect., 12, 248–253
CrossRef
Pubmed
Google scholar
|
[58] |
Capparelli, R., Parlato, M., Borriello, G., Salvatore, P. and Iannelli, D. (2007) Experimental phage therapy against Staphylococcus aureus in mice. Antimicrob. Agents Chemother., 51, 2765–2773
CrossRef
Pubmed
Google scholar
|
[59] |
Łusiak-Szelachowska, M., Żaczek, M., Weber-Dąbrowska, B., Międzybrodzki, R., Kłak, M., Fortuna, W., Letkiewicz, S., Rogóż, P., Szufnarowski, K., Jończyk-Matysiak, E.,
CrossRef
Pubmed
Google scholar
|
[60] |
Loc-Carrillo, C. and Abedon, S. T. (2011) Pros and cons of phage therapy. Bacteriophage, 1, 111–114
CrossRef
Pubmed
Google scholar
|
[61] |
Hagens, S. and Bläsi, U. (2003) Genetically modified filamentous phage as bactericidal agents: a pilot study. Lett. Appl. Microbiol., 37, 318–323
CrossRef
Pubmed
Google scholar
|
[62] |
Hagens, S., Habel, A., von Ahsen, U., von Gabain, A. and Bläsi, U. (2004) Therapy of experimental pseudomonas infections with a nonreplicating genetically modified phage. Antimicrob. Agents Chemother., 48, 3817–3822
CrossRef
Pubmed
Google scholar
|
[63] |
Matsuda, T., Freeman, T. A., Hilbert, D. W., Duff, M., Fuortes, M., Stapleton, P. P. and Daly, J. M. (2005) Lysis-deficient bacteriophage therapy decreases endotoxin and inflammatory mediator release and improves survival in a murine peritonitis model. Surgery, 137, 639–646
CrossRef
Pubmed
Google scholar
|
[64] |
Westwater, C., Kasman, L. M., Schofield, D. A., Werner, P. A., Dolan, J. W., Schmidt, M. G. and Norris, J. S. (2003) Use of genetically engineered phage to deliver antimicrobial agents to bacteria: an alternative therapy for treatment of bacterial infections. Antimicrob. Agents Chemother., 47, 1301–1307
CrossRef
Pubmed
Google scholar
|
[65] |
Moradpour, Z., Sepehrizadeh, Z., Rahbarizadeh, F., Ghasemian, A., Yazdi, M. T. and Shahverdi, A. R. (2009) Genetically engineered phage harbouring the lethal catabolite gene activator protein gene with an inducer-independent promoter for biocontrol of Escherichia coli. FEMS Microbiol. Lett., 296, 67–71
CrossRef
Pubmed
Google scholar
|
[66] |
Kasman, L. M., Kasman, A., Westwater, C., Dolan, J., Schmidt, M. G. and Norris, J. S. (2002) Overcoming the phage replication threshold: a mathematical model with implications for phage therapy. J. Virol., 76, 5557–5564
CrossRef
Pubmed
Google scholar
|
[67] |
Krom, R. J., Bhargava, P., Lobritz, M. A. and Collins, J. J. (2015) Engineered phagemids for nonlytic, targeted antibacterial therapies. Nano Lett., 15, 4808–4813
CrossRef
Pubmed
Google scholar
|
[68] |
Tamma, P. D., Cosgrove, S. E. and Maragakis, L. L. (2012) Combination therapy for treatment of infections with gram-negative bacteria. Clin. Microbiol. Rev., 25, 450–470
CrossRef
Pubmed
Google scholar
|
[69] |
Gaj, T., Gersbach, C. A. and Barbas, C. F. III (2013) ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering. Trends Biotechnol., 31, 397–405
CrossRef
Pubmed
Google scholar
|
[70] |
Citorik, R. J., Mimee, M. and Lu, T. K. (2014) Sequence-specific antimicrobials using efficiently delivered RNA-guided nucleases. Nat. Biotechnol., 32, 1141–1145
CrossRef
Pubmed
Google scholar
|
[71] |
Bikard, D., Euler, C., Jiang, W., Nussenzweig, P. M., Goldberg, G. W., Duportet, X., Fischetti, V. A. and Marraffini,L. A. (2014) Development of sequence-specific antimicrobials based on programmable CRISPR-Cas nucleases. Nat. Biotechnol., 32, 1146–1150
CrossRef
Pubmed
Google scholar
|
[72] |
Yosef, I., Manor, M., Kiro, R. and Qimron, U. (2015) Temperate and lytic bacteriophages programmed to sensitize and kill antibiotic-resistant bacteria. Proc. Natl. Acad. Sci. USA, 112, 7267–7272
CrossRef
Pubmed
Google scholar
|
[73] |
Yacoby, I., Bar, H. and Benhar, I. (2007) Targeted drug-carrying bacteriophages as antibacterial nanomedicines. Antimicrob. Agents Chemother., 51, 2156–2163
CrossRef
Pubmed
Google scholar
|
[74] |
Lu, T. K. and Collins, J. J. (2009) Engineered bacteriophage targeting gene networks as adjuvants for antibiotic therapy. Proc. Natl. Acad. Sci. USA, 106, 4629–4634
CrossRef
Pubmed
Google scholar
|
[75] |
Edgar, R., Friedman, N., Molshanski-Mor, S. and Qimron, U. (2012) Reversing bacterial resistance to antibiotics by phage-mediated delivery of dominant sensitive genes. Appl. Environ. Microbiol., 78, 744–751
CrossRef
Pubmed
Google scholar
|
[76] |
Libis, V. K., Bernheim, A. G., Basier, C., Jaramillo-Riveri, S., Deyell, M., Aghoghogbe, I., Atanaskovic, I., Bencherif, A. C., Benony, M., Koutsoubelis, N.,
CrossRef
Pubmed
Google scholar
|
[77] |
Bárdy, P., Pantůček, R., Benešík, M. and Doškař, J. (2016) Genetically modified bacteriophages in applied microbiology. J. Appl. Microbiol., 121, 618–633
CrossRef
Pubmed
Google scholar
|
[78] |
Frey, J. (2007) Biological safety concepts of genetically modified live bacterial vaccines. Vaccine, 25, 5598–5605
CrossRef
Pubmed
Google scholar
|
[79] |
http://www.fda.gov/BiologicsBloodVaccines/Vaccines/ApprovedProducts/ucm293952.htm
|
[80] |
http://www.ema.europa.eu/docs/en_GB/document_library/EPAR_-_Public_assessment_report/human/002617/WC500158413.pdf
|
/
〈 | 〉 |