By Karen Weynberg, CSIRO Synthetic Biology Fellow, School of Chemistry and Molecular Biosciences, Faculty of Science, University of Queensland
Synthetic
biology is an emerging field of research set to revolutionise the future of biological
science. To simply summarise synthetic biology can be challenging due to the myriad
of tools, techniques and applications it encompasses. In essence, synthetic
biology involves the use of engineering principles in a biological context. Using DNA-encoded componentry, synthetic biology enables the design and
construction of biological parts, devices, cellular circuits and networks, and
even whole organisms. This exciting new approach holds great promise for many
areas of research, including biomedical efforts to treat cancer and other
diseases, vaccine development, cell therapies, regenerative medicine and
microbiome engineering.
The growing
problem of global antibiotic resistance is another area that synthetic biology
can play a crucial role in. The abuse and misuse of antibiotics in human health
and animal agriculture has resulted in an alarming increase in multi-drug
resistant (MDR) bacterial strains. Future projections predict that antibiotic
resistance could result in as many as 10 million deaths a year by 2050, surpassing
mortality rates due to cancer1. Alternatives to antibiotics are
now being sought, including phage therapy that is based on the natural
mechanisms by which bacteriophages (literally ‘bacteria eaters’) infect and
kill bacteria.
Phage
therapy can be encapsulated by the ancient proverb that states ‘The enemy of my
enemy is my friend’.
Phages were
discovered just over 100 years ago by two independent European researchers, Frederick
Twort and Felix D’Herelle. Since then, phage therapy has been used most notably
in Eastern European countries, such as Russia and Georgia, to treat bacterial
infections in human patients. The discovery of antibiotics led Western medicine
to turn away from phage therapy, but this cheap, natural and targeted treatment
is now increasingly appealing. Phage therapy is poised to be the ‘Next Big
Thing’ in fighting deadly superbug infections, as the recent increase in both fundamental
research and interest from biotech companies attests to. Companies such as
US-based Ampliphi Biosciences, China-based Phage Luxe and France-based
Pherecydes Pharma are directing efforts into developing phage therapy as a
viable alternative to antibiotic treatments.
Typically, a
cocktail comprised of a number of different phages is administered to combat a
bacterial infection. Phage are usually highly specific for a bacterial host so
the unwanted side effects of broad-spectrum antibiotics, such as targeting beneficial
bacteria not just pathogens, are avoided in phage therapy. Although, hurdles
are still to be overcome, including the approval of rigorous advanced clinical
trials, there have been incidences of ‘compassionate cases’ successfully treated
with phage therapy. One such case is described by Dr Steffanie Strathdee in her
TEDx talk on how phage saved her husband’s life from an otherwise fatal MDR
infection – a case that SIG member Dr. Jeremy J. Barr directly contributed to:
Link to Dr
Steffanie Strathdee TEDx talk:
Synthetic
biology can be used to engineer and synthesise phages to increase their natural
capabilities and manipulate their host range. Issues arising from the use of
traditional phage therapy, such as bacterial resistance and limited host range
can be overcome by employing synthetic biology techniques. Wide-ranging
approaches to engineering phage include in
vivo recombineering, CRISPR-Cas mediated genome engineering, whole-genome
synthesis and cell-free transcription-translation systems (for a comprehensive
review see Pires et al. 20162). Yeast-based assembly of phage
genomes also enables the refactoring of phage genomes3,4. Phage genomes can be
redesigned in silico based on natural
phage genome sequence templates. Phage genome PCR products are then captured in
a yeast artificial chromosome (YAC) and propagated within the yeast cell, which
acts an intermediate host, thus avoiding toxicity issues that would arise in a
bacterial host. Once assembled the engineered phage genomes are extracted and
electroporated into a bacterial host, in order to reboot the phage and produce
viral progeny.
Pathogenic
bacteria can persist within a biofilm that is comprised of a multi-species
consortium within a dense extracellular matrix. Biofilms can form within
medical devices, such as catheters leading to health problems including, for
example, urinary tract infections. The formation of biofilms helps bacteria to evade
the host immune response and minimise their exposure to antibiotics. Phage can
be engineered to produce enzymes e.g. dispersins5 to degrade biofilms, thereby making
target bacteria vulnerable to phage lysis, antibiotics and immune responses
such as macrophages. Engineering of phage to produce other degrading enzymes,
such as capsule depolymerases and lysins, can also increase the efficiency of
phage infection.
A recent
review comprehensively describes the wide scope of phage-based applications
that are now feasible using the sophisticated techniques and tools afforded by
synthetic biology6. This field of biological research
is set to greatly accelerate the development of novel phage-based solutions to
a wide range of issues. The future is bright, the future is phage!
References
1 Editors, P. M.
Antimicrobial Resistance: Is the World Unprepared? PLoS medicine 13,
e1002130-e1002130, doi:10.1371/journal.pmed.1002130 (2016).
2 Pires,
D. P., Cleto, S., Sillankorva, S., Azeredo, J. & Lu, T. K. Genetically
Engineered Phages: a Review of Advances over the Last Decade. Microbiology and Molecular Biology Reviews
80, 523 (2016).
3 Ando,
H., Lemire, S., Pires, D. P. & Lu, T. K. Engineering Modular Viral
Scaffolds for Targeted Bacterial Population Editing. Cell Systems 1, 187-196,
doi:10.1016/j.cels.2015.08.013 (2015).
4 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 434, 278-284, doi:10.1016/j.virol.2012.09.020 (2012).
5 Lu,
T. K. & Collins, J. J. Dispersing biofilms with engineered enzymatic
bacteriophage. Proceedings of the
National Academy of Sciences of the United States of America 104, 11197-11202,
doi:10.1073/pnas.0704624104 (2007).
6 Lemire,
S., Yehl, K. M. & Lu, T. K. Phage-Based Applications in Synthetic Biology. Annual Review of Virology 5, 453-476,
doi:10.1146/annurev-virology-092917-043544 (2018).
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