Yong, Erin
WRIT 340
Section #66804
Professor Marc Aubertin
Illumin Article
Synthetic Biology: Engineering Bacteria
Bacteria continue to fascinate scientists and researchers as one of the most prevalent and
diverse life forms on this planet. Their short life cycle, high reproductive rate, and relatively
simple genome make them ideal subjects and tools for genetic research. A lot of information and
data have been gathered about bacterial genomes, making them the perfect model for the
emerging field of synthetic biology. This relatively new field strives to combine engineering
principles and biology in order to design and build new biological systems that can be applied to
meet human needs. In recent years, scientists and engineers have been working together to
recreate bacteria with functions that can help in the production of clean energy, the preservation
of the environment, and the development of better treatments for human diseases like cancer.
What is Synthetic Biology
To build a functional car, an engineer has to integrate and put together many different
mechanical parts, each with its own function. All the valves, the wires, the electrical circuits, and
the switches have to be connected and built in just the right way for the car to work properly. In
many ways, engineering bacteria is like building a car except with “biological parts” rather than
mechanical ones. Biological parts are simply sequences that encode for biological functions like
protein-coding regions. Synthetic biology strives to incorporate engineering principles in the
design and construction of new biological systems and in the reconstruction of existing systems.
Although it does build on the ideas of genetic engineering, there are clear distinctions.
Traditional genetic engineering involves the modification or the transfer of one or very few
genes. Synthetic biology, on the other hand, involves the combination of multiple genes rather
than just a few and the use of biological parts to construct new biological pathways and functions
[1]. One of the main goals of synthetic biology is to engineer bacteria to carry out new functions
that have beneficial applications in human health and clean energy [2].
Bacteria
It might be hard to believe bacteria can be useful for humans, especially in regards to
health, since most people have suffered at least once from a sickness or an infection caused by
these tiny organisms. Undoubtedly, bacteria are a great health concern, particularly because of
their ability to develop antibiotic resistance relatively quickly. However, the same properties that
make them so troublesome are also the reasons that make them the perfect subjects for synthetic
biology. Their ability to adapt and uptake foreign DNA is very useful in reconstructing their
genome to carry out novel functions.
Bacteria are very diverse unicellular prokaryotes, but most of them share a simple
structure that consists of the cell wall, the plasma membrane, and the nucleoid, a region of
cytoplasm that appears lighter than its surroundings. Their genome consists of circular
chromosomes located in the nucleoid. Most importantly, they also often have small rings of
independently replicating DNA molecules called plasmids that carry very few genes (See Fig. 1)
[3].
Figure 1: This is the general structure of most bacteria. There is the cell wall, the plasma
membrane, the circular chromosomes in the nucleoid, and the plasmid DNA.
These plasmids can have evolutionary benefits for bacteria, because they have the ability to carry
and spread antibiotic resistant genes. Plasmids carrying foreign genes can be integrated into a
host bacterial genome. When bacteria are altered by the uptake of foreign DNA, it is called
transformation and in synthetic biology, biological parts are often carried by plasmids in order to
integrate them into the bacteria genome.
Standardized Biological Parts
Unlike the mechanical parts that go into building a car, biological parts are much more
diverse, fluid, and unpredictable. Types of biological parts include protein-coding regions,
promoters that control gene expression, and ribosome binding sites that initiate protein synthesis
[4]. In an effort to apply engineering principles like standardization and make it easier to
combine parts to form more complex genetic designs, Tom Knight, a student of the
Massachusetts’s Institute of Technology, introduced BioBricks in 2003 [5]. BioBricks are
standardized DNA sequences with a defined structure and function that are created to be
compatible with other standardized parts [6]. He started the Registry of Standard Biological Parts
in order to compile and categorize the BioBricks created. In the beginning, the Registry only had
about a hundred parts, but today it boasts a collection of about two thousand standardized parts
[7]. BioBricks are considered “standard” because the DNA inserts and the plasmids used to carry
them have to meet certain requirements. All BioBrick plasmids have specific restriction enzyme
sites called EcoRI-HF, Xbal, SpeI, and PstI. Restriction enzymes are molecules that cut DNA at
specific recognition sequences. They can extract specified DNA sequences from a plasmid or
genome, and a ligase enzyme can put the extracted sequence back into a new plasmid that has
been cut with the same restriction enzymes. This is possible because the new plasmid has
matching ends to the insertion sequence. In this way, standardized biological parts are joined
together and designed to create novel biological systems that can be inserted into bacteria (see
Fig. 2) [8].
Figure 2: All the standard biological parts shown above have the same restriction enzyme
sites (EcoRI-HF, Xbal, SpeI, PstI). To join the blue insert with the green insert in a new
plasmid, each plasmid must be cut with two specific restriction enzymes. The fragments
can then be joined in the destination plasmid in a way that the resulting composite part
also has the same four restriction enzyme sites.
Such restrictions can be limiting, but standardized parts like BioBricks make synthetic biology
projects much more reproducible. BioBricks are not the only set of standardized biological parts.
Other systems like BglBrick, created by Christopher Anderson in 2010, do exist, but as of now
BioBricks are the most widely used [9]. This is one method of engineering new biological
systems to design bacteria to satisfy human needs.
Engineering Bacteria For Novel Treatments Against Cancer
Knowledge of genetics and the ability to digitize genetic information has grown
exponentially since the first complete DNA sequencing on phage øX174 in 1977 [10]. The
availability of advanced genomic technology allowed the field of synthetic biology to grow
rapidly in recent years. Although it is a relatively new field, there have already been several
breakthroughs in reconstructing bacteria for functions that benefit humans.
In 2006, J. Christopher Anderson was able to reengineer Escherichia coli to invade
cancer cells [11]. Traditional cancer treatments are problematic because they are toxic to both
cancerous and healthy tissues, and they often cannot reach all of the cancer cells in the body.
Certain properties of bacteria, however, offer solutions to these problems. Bacteria have the
ability to sense their environments and target specific cells. Tumors have lower oxygen levels,
higher density, and higher lactic acid concentrations than surrounding tissues. A cancer-killing
organism must be able to carry out several complicated functions. It needs to be able to sense and
respond to the tumor environment, and must only produce toxins when it actually enters the
tumor. In order to create an organism that can carry out all these functions, Anderson took
biological parts from different bacteria and inserted them into Escherichia coli. Invasin from
Yersinia psuedotuberculosis was inserted into E. coli and this enabled it to invade cancer cells of
several types including cervical carcinoma, hapatocarcinoma, and osteosarcoma [11]. To ensure
that the E.coli only attacks cancer cells, invasin was linked to other genes that recognized tumor
characteristics. A lux genetic circuit from Vibrio fischeri has the ability to sense when low
densities changes to high densities. When this was linked to the invasin, E.coli only became
activated when cells reached a certain density [11]. Formate dehydrogenase is a gene in E.coli
that is strongly expressed in anaerobic conditions, and this was another gene that was
synthetically linked to the invasin so that the E.coli only invaded and produced toxins when the
cell density was high and the oxygen levels low. Anderson’s engineered E.coli did prove
successful in selectively invading cancer cells. This new development with synthetic biology has
the potential to exceed the current standard of cancer treatments in the future.
Engineering Bacteria For Production of Clean Energy
Synthetic biology can also be used to engineer bacteria with the ability to produce cleaner
forms of energy. Increasing energy costs and environmental degradation stressed the need for
ways to produce sustainable and renewable fuels. Biodiesel, composed of fatty acid esters, is an
alternate energy source derived from plant and animals oils. It can be used as a substitute for
petroleum-based fuels. Unfortunately, it takes a lot of acres of oilseed crops to produce relatively
little biodiesel [1]. This can become an even heavier environmental burden than the use of
petroleum-based fuels. Scientists are seeking new ways to produce it from more readily available
sugars like sugar cane or corn [1]. In 2010, researchers successfully engineered new pathways in
E.coli to directly converted sugar to biodiesel [1]. E.coli is an ideal subject for this endeavor,
because it naturally produces fatty acids just to grow. They already have the mechanism for the
synthesis of fatty acids. Now with synthetic biology, new pathways can be created and existing
pathways can be modified to increase the ability of E.coli to produce fatty acids. This was mainly
carried out by over expressing certain enzymes, biological catalysts, in order to shift the
equilibrium towards producing more fatty acids from the sugar [12]. Reengineered bacteria could
potentially become an efficient source of clean energy that can replace petroleum fuel in the
future.
Impact
Synthetic biology opens up a lot of possibilities. The ability to alter bacteria and other
organisms on the scale of whole genomes to carry out new functions can have a lot of beneficial
real world applications in health, energy, and the environment. Building organisms that do not
exist in nature from the ground up can also lead to greater understanding of how life works and
how it might have started. A more thorough exploration of possible life forms that have not been
realized by existing organisms is now possible. Inevitably ethical issues regarding the nature of
life will be raised and concerns about unforeseen consequences due to making synthetic genomes
and artificial bacteria will have to be addressed. There are real dangers in large scale DNA
synthesis, particularly since the organisms can potentially become very pathogenic and deadly.
Therefore in order to make sure humans reap the full benefits of synthetic biology, honest
transparency and careful consideration of risks must be upheld. In the end, the risks are worth it
when considering what synthetic biology can do for future generations. More efficient treatments
for cancer are just the tip of the iceberg. Applications of synthesis biology can lead to more
affordable medical care for some select diseases in the future, because it is often cheaper to
produce drugs with engineered bacteria than expensive chemical synthesis reactions. Cleaner
energy and successful cancer treatments without terrible side effects are just a few of the benefits
synthetic biology can offer.
References
[1] Konig, H., Frank, D., Heil, R., & Coenen, C. (2013). Synthetic Genomics and Synthetic
Biology Applications Between Hopes and Concerns . Current Genomics, 14, 11-24.
[2] Thompson, V. (n.d.). Engineering Techniques Repurpose Bacteria | Behind the Scenes |
LiveScience . Science News – Science Articles and Current Events | LiveScience .
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[3] Reece, J. B., & Campbell, N. A. (2011). Campbell biology Jane B. Reece ... [et al.]. (9th ed.).
Boston: Benjamin Cummings.
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[6] Aldhous, P. (2006). Redesigning Life. New Scientist, 190(2552), 43-47.
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http://parts.igem.org/Help:About_the_Registry
[8] Baker, A. (2010). An Introduction to BioBricks. UMI Dissertations , 1, 1-80.
[9] Anderson, C., & Dueber, J. (2010). BglBricks: A flexible standard for biological part
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[11] Anderson, J. C., Clarke, E. J., Arkin, A. P., & Voigt, C. A. (2006). Environmentally
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[12] Band-Watts, Brooks, Robert Bellerose, and Michelle Chang. "Microbial production of
fatty-acid-derived fuels and chemicals from plant biomass." Nature 7 (2011): 222-227.
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[Image]. (n.d.). Hyperphysics. Retrieved October 17, 2013, from http://hyperphysics.phyastr.gsu.edu/hbase/biology/imgbio/cellprokaryote6.gif
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