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systems biology represents a shift in studying Mathematical modelling is a tool that writing genomes progresses, the new chal-
integrated components from the more tra- enables quantitative predictions or the lenges lie in system design and selection
ditional reductionist approach taken in bio- understanding of data. It is applicable to for new functions, and efficient replication
logical research. Computational modelling is both areas, as are other tools such as mass and production. Additional challenges
an important tool in both fields but used to spectroscopy to measure protein levels arise from how to anticipate, simulate and
achieve different objectives. In systems biol- or transfection methods to move DNA improve highly diverse or personalized
ogy, computational models are used to make into cells. technologies and their impact on complex
predictions about the behaviour of a system, physiological and ecological systems9
whereas modelling is used to direct design in (discussed below).
synthetic biology. Synthetic biology is an
Synthetic biology has expanded and engineering discipline — there is M.B.E. We have come a long way as a field:
evolved substantially from its initial rather a desire to build things that do we have built several generations of oscil-
narrow focus to appreciate and use more lators35-38 and genetic switches4,39 that work
fully the diversity of mechanisms found in not yet exist. with diverse cellular components and
natural biological systems. For example, regulatory mechanisms, and which interact
early work focused largely on transcription with endogenous gene circuits40. Complex
factor-based regulatory networks designed What have been the main achievements metabolic pathways have been engineered
to exhibit dynamic behaviour (such as of synthetic biology so far in basic to produce useful products, and signalling
oscillator and ‘toggle switch’ behaviours)1, research, and what are the challenges to be met?
pathways have been rewired to alter their
whereas designs now routinely incorporate dynamic behaviours in predictable ways.
other levels of regulation, including RNA- R.W. Over the past decade or so, synthetic However, synthetic biology remains
based regulators, post-translational modifi- biology has helped to transform the bio- extremely primitive owing both to technical
cations and molecular scaffolds2. As another logical sciences into a true engineering dis- challenges and, even more, to fundamen-
example, mutation and evolution were cipline. Notable achievements include the tal inadequacies in our understanding of
widely viewed as an obstacle to system per- creation of a registry of composable parts, biological circuit design.
formance and something to be minimized, revolutionary advances in gene synthesis On the technical side, synthesizing
whereas newer approaches are beginning technologies and faster and more efficient genetic circuits and transferring them
to exploit this unique aspect of biological modular DNA assembly methods. By into cells remains far too slow and idio
systems and to design for evolution and integrating these rapidly developing tech- syncratic, especially in animal cells. How-
adaptation3. nologies with computational modelling ever, several new methods, such as those
approaches, a synthetic biologist can now based on the CRISPR system, are extremely
Christopher A. Voigt. The early ambitions engineer biological systems top-down in a encouraging.
in the field were around the creation of (somewhat) predictable manner. On the fundamental side, we still have
cells that could go through a series of What is critically lacking, however, with little understanding of how circuit designs
programmed tasks; for example, Adam respect to mammalian synthetic biology can function effectively in cells and tissues
Arkin envisioned an engineered bacterium (an area that my laboratory is currently and much to learn from natural examples.
that could move through the human body most focused on), are ‘real-world’ applica- In particular, one of the greatest challenges
and could identify microenvironments, and tions. We must now make an effort to tran- is to move synthetic biology from circuits
carry out therapeutic functions4. Doing this sition from developing ‘toy’ applications operating in individual microorganisms
requires control over when and under what to creating actual applications for cancer to circuits that function in a truly multi
conditions genes are turned on, which in therapies, vaccination and engineered cellular fashion, for example, circuits suffi-
turn requires synthetic regulation — in other tissues that society can directly benefit cient to implement self-patterning of cells.
words, circuitry. This was, and remains, from. Arguably, the main challenge here If successful, we may be able to understand
one of the most difficult aspects of genetic is how to safely deliver synthetic circuits multicellular development from a totally
engineering. into mammalian organisms. I predict that new point of view that could inform tissue
Synthetic biology is an engineering the development of RNA-based delivery engineering and regeneration.
discipline — there is a desire to build things methods could be a game changer in
that do not yet exist5,6. Systems biology is overcoming the regulatory hurdles and C.D.S. One of the important effects of
a basic science, where the goal is to better required safety guarantees associated with synthetic biology on basic research is that
understand natural biology. The relationship traditional gene therapy. it has driven the advancement of a variety
is similar to biological engineering and of methods to support the construction
biology, or chemical engineering and chem- G.M.C. In addition to some applications of large-scale genetic programmes and
istry. There can be similar language, but the (discussed below), the achievements genome engineering, including DNA syn-
motivation is different. For example, both include new tools enabling rapid exponen- thesis. Other advances include elucidating
synthetic and systems biology are interested tial improvements in genome sequencing, frameworks that support the rational design
in modularity7. For natural cells, genetics and harvesting DNA from chips for libraries, and precise control over activities, such as
regulatory networks may or may not be mod- multiplex-automated genome engineering gene regulatory and enzyme activities10–12,
ular, perhaps depending on how you frame (MAGE)8 of natural and artificial chromo as well as early steps in pushing standards
the question. By contrast, engineers can somes (mainly in Escherichia coli) and in metrology and data reporting13,14. One
continue to strive to create synthetic genetics Cas9–CRISPR technology for genome edit- big challenge in the field remains to develop
and circuits that are increasingly modular. ing of nearly any genome. As reading and measurement technologies that enable the
high-throughput, non-invasive quantifi- generation of products is large. Some nota- One of the challenges in applications
cation of activities that are not encoded ble examples produced by large companies is harnessing cells to build complex func-
in fluorescent reporter proteins15. As the include insecticides (for example, spinosyn) tional materials. Cells are natural atomic
field has shifted towards favouring design by Dow AgroSciences, USA, and the anti- architects and we already exploit this, as
approaches that generate diversity within malarial artemisinin by Amyris, USA, many in‑use materials are from biology.
the genetic programmes, there has not been and Sanofi, France. Small companies are The examples above are all relatively simple
a corresponding emphasis on the develop developing products; for example, Geno- chemicals, natural products or individual
ment of technologies that enable the char- matica, USA, produces butanediol (BDO) proteins. Obtaining more complex prod-
acterization of the resulting diversity of and Refactored Materials, USA, produces ucts will require synthetic gene circuits
genetic designs. As such, the shift towards a recombinant spider silk. There are many and the ability to control many, possibly
‘design smarter’ approach (versus a ‘design examples, and I am only highlighting a few. hundreds, of genes simultaneously.
more’ approach) is limited by our inability
to learn from current design approaches.
more tailored advanced biologics. Progress happen when researchers can routinely con-
Glossary
in this area may benefit from a closer con- trol and read out systems of multiple inter-
CRISPR nection between the mammalian synthetic acting genes and proteins in living cells and
(Clustered regularly interspaced short palindromic
biology community and the biopharmaceuti- organisms — effectively changing the unit of
repeats). An adaptive immune system that is found in
bacteria and archaea, which is based on an RNA-guided cal industry. The second is the creation of routine genetic engineering from the gene to
nuclease (Cas9). Components of the CRISPR system are synthetic gene circuit therapies that match the gene circuit!
being repurposed to provide powerful, flexible and precise the complexity of biological systems. Systems
genome engineering, and regulatory systems across biology is helping us to decipher the com- C.D.S. Synthetic biology is bringing new
diverse species.
plexity of living organisms by unravelling tools and approaches to applications in
Genetic switches regulatory networks and crosstalk between clinical therapies and biotechnology. For
Natural or synthetic systems for regulating gene these networks. It has also taught us that the production of drugs and fuels, synthetic
expression in response to one or more external or internal biological diseases themselves, such as biology is both advancing the complexity of
signals. The output of genetic switches is often a complex
cancer, or metabolic, immunological, neuro- biosynthetic processes that can be engineered
logical function of input signals that in many cases can
provide a persistent response to transient inputs or logical or psychiatric disorders, are equally and increasing the diversity of molecules
other capabilities. sophisticated and complex. I believe that that can be manufactured through biological
such complex diseases will be best treated by processes. Harnessing the full manufacturing
Genomically recoded organisms modulating our bodies with correspondingly capacity of biology is a big future opportu-
(GROs). Changing every instance in a genome of one or
more of the 64 codons in the genetic code for higher
sophisticated synthetic gene circuit encoded nity, providing us access to more complex
safety and productivity. in therapeutic agents. With its incredible scaffolds and materials. Synthetic biology
pace of research, mammalian synthetic biol- tools also bring the potential to develop safer
Multiplex-automated genome engineering ogy will soon be able to find flagship applica- and more effective clinical therapies, by ena-
(MAGE). Efficient genome editing that is capable of making
tions that will win over the support and trust bling control over the delivery and dosing of
dozens of changes per genome and billions of genomes by
inserting short (90 bases long) single-stranded DNA into of the general public. therapeutic activities in a dynamic temporal
the cellular replication fork with one or more DNA changes. and spatial manner within a patient. Current
G.M.C. Examples include the efficient bio- efforts have focused on cell-based platforms
Optogenetics production of the anti-malarial drug arte- such as immunotherapies and probiotics29.
A technique to control and perturb cellular behaviour
using light and genetically encoded light-sensitive proteins.
misinin by Amyris and Sanofi and the ‘green- As the field progresses to tackle spatiotem-
It has been extensively used to precisely control neuronal chemistry’ replacement of petrochemicals27 poral programming and pattern formation,
activity spatially and temporally through light. by LS9, USA, and Joule Unlimited, USA. long-term applications of synthetic biology in
In the future, we will see increased use of the clinic should extend to tissue engineering
Oscillator
synthetic biology for therapeutics: moving and regenerative medicine.
Produces oscillations that underlie diverse biological
behaviours from neurobiology to multicellular from random transgenic insertions to precise
development. Synthetic biology has shown that Cas9‑based genome editing28; from antibiotic C.A.V. In the short term, the tools of syn-
remarkably simple circuit designs can produce clock-like carpet-bombing to skin and gut microbial thetic biology can be directly applied to
oscillations of protein levels in individual living cells. therapies; from blunt brain ablations and exploit natural products, including pharma-
drugs to optogenetics and other bio-nano ceuticals, human performance enhancers,
neurotherapies. Bio-nano-materials are industrial chemicals, energetic materials
Some applications of synthetic biology atomically precise and more than a million and agricultural products (for example,
have steered development of new times more energy efficient than current insecticides and pesticides). The potential
clinical therapies and of biotechnology electronic circuits for handling information. of accessing the natural diversity that is
for the production of drugs and fuels. already present in large strain banks and
What advantages have such approaches M.B.E. The work in all of these areas is the sequence databases is extraordinary30.
brought, and what do you foresee for the extremely exciting. Although we have been The DNA sequence information is available,
future of such applications? successful in engineering microorganisms to and bioinformatics can predict gene clusters
produce important products, these platforms that encode the machinery for producing
R.W. Synthetic biology has certainly revolu- are designed to work under well-controlled high value chemicals. DNA synthesis enables
tionized the field of metabolic engineering, laboratory conditions. One key challenge is the conversion of the sequence information
enabling the production of drugs and other figuring out how to engineer cells that can back to physical DNA. However, the host
small biomolecules inspired by natural prod- act as programmable devices and function organism is often long lost, cannot be manip-
ucts. With respect to mammalian synthetic safely in complex natural environments, ulated or the genes are ‘silent’. Overcoming
biology in particular, as I mentioned above, including the human body. Recent cell-based this requires synthetic regulation and tools
despite the great recent progress in the field, therapy results suggest the potential power from synthetic biology. We are at the early
very few applications have actually come to of such approaches. However, we need the phase of a gold rush of mining the databases
fruition so far. However, this is probably in ability to routinely synthesize multi-gene and strain banks for valuable products. There
large part owing to the field being so new. circuits, integrate them precisely in cells and will also be deep enzyme mining (that is, the
I see largely two areas to which mammalian control their behaviour quantitatively. Right high-throughput identification, printing and
synthetic biology will contribute applications now this design cycle remains tediously slow, screening of genes from databases) to diver-
in the future. The first is the use of numer- and this dramatically limits the diversity sify the chemical structures. This may lead
ous recently developed genome engineering of designs and ideas that we can explore. to ‘the dream’ of having enzymes that can be
tools to create next-generation programmed Having said that, I think that a lot of these as flexible as synthetic chemistry in building
mammalian cell lines for the production of problems are solvable. Just imagine what will arbitrary chemical structures.
The use of cells as therapeutics offers the We can finally construct genomically recoded George M. Church is at the Department of Genetics,
Harvard Medical School, Harvard University,
advantage of being able to harness the sens- organisms (GROs)32,33 that cannot exchange
77 Avenue Louis Pasteur,
ing and signal processing capabilities of the functions with natural genomes, and at the Boston, Massachusetts 02115, USA.
cell, as well as the capability to synthesize other end of the spectrum, genes that inten-
Michael Elowitz is at the Division of Biology and
multiple chemical and protein effectors at a tionally spread to control parasites, disease Biological Engineering and Department of
site of interest. vectors and invasive species (for example, Applied Physics, Howard Hughes Medical Institute,
malaria, mosquitoes, kudzu and carp). California Institute of Technology (Caltech),
Technical advances have made it M/C 114‑96, Pasadena, California 91125, USA.
e-mail: melowitz@caltech.edu
possible to write entire synthetic M.B.E. There is a lot we do not yet know
genomes. However, the possibility of creating about what will or will not become possible Christina D. Smolke is at the Stanford University School
of Medicine, 473 Via Ortega, University of Stanford,
synthetic forms of life has raised public with the technologies of synthetic biology.
Stanford, California 94305, USA.
concerns about the potential development of I worry in particular about the potential for e-mail: csmolke@stanford.edu
infectious agents or effects on biodiversity. misunderstanding, sometimes increased by
Christopher A. Voigt is at the Synthetic Biology Center,
What challenges lie ahead for this field, and a misleading hype. Great efforts have been Department of Biological Engineering,
what are the key ethical and regulatory issues made to improve the information gap, for Massachusetts Institute of Technology (MIT),
that must be addressed? example by the Sloan Foundation, USA, 500 Technology Square,
and the US National Academy of Sciences. Cambridge, Massachusetts 02139, USA.
e-mail: cavoigt@gmail.com
R.W. It is interesting to consider entirely new Ultimately, we scientists must collectively
forms of life — and these may eventually be ‘keep it real,’ focus on the most critical Ron Weiss is at the Synthetic Biology Center,
Department of Biological Engineering, Department of
possible. However, the majority of synthetic risks seriously and thoughtfully in a way
Electrical Engineering and Computer Science,
biology projects are focused on improving that is grounded in reality, engage with the Massachusetts Institute of Technology (MIT),
existing strains by adding new functionality larger community and make the most of NE47‑223, 500 Technology Square,
to bacterial, yeast or mammalian cells that the unique opportunity we now have for Cambridge, Massachusetts 02139, USA.
are useful to the biotechnology industry. fundamental discovery and understanding. e-mail: rweiss@mit.edu
18. Gibson, D. G. et al. Complete chemical synthesis, 28. Mali, P., Esvelt, K. M. & Church, G. M. Cas9 as a 39. Gardner, T. S., Cantor, C. R. & Collins, J. J.
assembly, and cloning of a Mycoplasma genitalium versatile tool for engineering biology. Nature Methods Construction of a genetic toggle switch in
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20. Xia, B., Leguia, M., Anderson, J. C. & Densmore, D. (2011). integrated gene circuits. Science 333, 1244–1248
Eugene — a domain specific language for specifying 30. de Jager, V. et al. antiSMASH: rapid identification, (2011).
and constraining synthetic biological parts, devices, annotation and analysis of secondary metabolite
and systems. PloS ONE 6, e18882 (2011). biosynthesis gene clusters in bacterial and fungal Acknowledgements
21. Czar, M. J., Cai, Y. & Peccoud, J. Writing DNA with genome sequences. Nucleic Acids Res. 39, G.M.C. is supported by grants from the US Department of
GenoCAD™. Nucleic Acids Res. 37, W40–W47 (2009). W339–346 (2011). Energy (DOE), US Defense Advanced Research Projects
22. Hillson, N. J., Rosengarten, R.D. & Keasling, J.D. j5 31. Tumpey, T. M. et al. Characterization of the Agency (DARPA), US National Human Genome Research
DNA assembly design automation software. ACS reconstructed 1918 spanish influenza pandemic virus. Institute (NHGRI), US National Science Foundation (NSF) and
Synth. Biol. 1, 14–21 (2011). Science 310, 77–80 (2005). Personal Genome Project (PGP). C.D.S. is supported by funds
23. Tran, A. B., Paull, M., Keasling, J. D., Arkin, A. P. & 32. Lajoie, M. J. et al. Genomically recoded organisms from the US National Institutes of Health (NIH), NSF, DARPA,
Endy, D. Precise and reliable gene expression via impart new biological functions. Science 342, Human Frontiers Science Program (HFSP), and Bill and
standard transcription and translation initiation 357–360 (2013). Melinda Gates Foundation.
elements. Nature Methods 10, 354–360 (2013). 33. Lajoie, M. J. et al. Probing the limits of genetic
24. Brophy, J. A. N., Clancy, K., Peterson, T. & Voigt, C. A. recoding in essential genes. Science 342, 361–363 Competing interests statement
Characterization of 582 natural and synthetic (2013). The authors declare no competing interests.
terminators and quantification of their design 34. Elowitz, M. & Lim, W. A. Build life to understand it.
constraints. Nature Methods 10, 659–664 (2013). Nature 468, 889–890 (2010).
35.
25. Rhodius, V. A. et al. Design of orthogonal genetic Danino, T. et al. A synchronized quorum of genetic FURTHER INFORMATION
switches based on a crosstalk map of σs, anti-σs, and clocks. Nature 463, 326–330 (2010). George M. Church’s homepage:
promoters. Mol. Syst. Biol. 9, 1–13 (2013). 36. Stricker, J. et al. A fast, robust and tunable synthetic http://www.arep.med.harvard.edu
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