Synthetic biologists are a new breed of researchers: part-scientist, part-engineer. Building on the work of more traditional biologists, synthetic biologists try to use what we know about biology to engineer new functions into living things, such as producing useful chemical compounds (like drugs) and generating biofuels. The hope is there, but engineering organisms to do these things remains a challenge due to the inherent complexities of living things and their constituent cells. Our current understanding focuses on the basics of how, when, and where proteins are made. Proteins are the molecules that carry out most biological functions and chemical reactions inside cells, and they are encoded by stretches of DNA sequences called genes. Synthetic biologists know how to manipulate genes and move them between organisms thereby allowing them to engineer organisms with new functions. This type of work has already lead to some astonishing successes, but much work, including standardization of techniques and generation of systems where it is easier to manipulate genes, still needs to be done before cells can be as easily engineered as traditional machines.
One of synthetic biology’s earliest and most lauded successes was the production of a precursor to the anti-malarial drug, artemisinin, in yeast. Artemisinin is a compound normally produced in a plant called Artemisia annua L., commonly known as the annual wormwood. In the wormwood, a group of proteins carry out a series of chemical reactions that lead to the production of artemisinin. Researchers in Professor Jay Keasling’s lab at Berkeley introduced the wormwood genes encoding these proteins into yeast, then they optimized the amount of protein produced from each gene in order to synthesize the drug-precursor properly. This process has the potential to greatly lower the cost of artemisinin, a drug that is crucial for treatment of malaria (1).
In order to make cells that carry out complex functions like the production of the artemisinin precursor, researchers are developing biological circuits. The basic idea is that we can model the way genes and their encoded proteins interact in a similar way to how electrical flow in a computer is modeled by electrical circuits. In electronic circuits, different inputs are processed by a series of components to produce specific outputs (e.g. what you see on the screen). In a biological circuit, the input could be something like a chemical compound, while the circuit components are made up of a series of protein-gene interactions. The resulting output is usually the production of the target protein or chemical. Creating synthetic biological circuits allows us to engineer new functions into cells. For instance, just as we can make lights blink or turn them on and off using a switch, we can make biological circuits that cause protein production to increase or decrease in response to an external signal. For example, with a protein like green fluorescent protein (GFP), which fluoresces green when excited by a particular wavelength of light, we can actually see if biological circuits function as designed by monitoring GFP production (Movie 1). Researchers use GFP to show that they can use circuits to produce proteins in a predictable manner. Once this is done with GFP, a circuit can theoretically be used to produce any protein in the pattern specific to the circuit, allowing the design and manipulation of more complicated protein patterns to carry out specific functions. For instance, patterns of protein production during out own development determine what cells will become different parts of our body. Creating biological circuits puts us on the path toward understanding how to produce proteins in similarly complicated patterns so that we too may one day make cellular structures like organs.
Movie 1: A biological circuit was designed that causes cells to produce a modified version GFP in pulses in synchrony (2).
Creating even simple circuits that function properly in cells is a huge challenge because cells contain many non-designed, natural components that can interfere with biological circuits. Synthetic biologists are currently working to make standard synthetic biological circuits with their component genes, proteins, and patterns of protein production showing reproducible functions in different systems. Having a set of fully characterized and functioning parts will expedite the process of making cells that do useful things. Similar to electronic engineering, where having standards on computer chips and circuit boards greatly enhances the creativity of electrical engineers, synthetic biologists hope that a set of standardized parts will allow them to build new systems without having to worry about the component parts fitting together. In the future, circuits will not need to be designed from the ground up but will simply be adapted for use in new processes.
No such set of fully characterized parts exists yet, but there are research groups working on cataloguing circuits, making them easier to produce, and making them publicly available for researchers around the world. Primary among these groups are the BioBricks foundation and the BIOFAB (International Open Facility Advancing Biotechnology). The BioBricks foundation has established a standard method for putting together and designing components of biological circuits. The BIOFAB seeks to make, prototype, test, and characterize biological parts that synthetic biologists can later use to build circuits. These parts and those created in other labs that are part of the BioBricks Foundation are being compiled in the MIT Registry of Standard Biological Parts. Though many of the parts in the registry are poorly characterized, having the goal of standardization is a significant step toward making synthetic biology easier to do.
Making Biology Simpler
Standardization will undoubtedly make it easier to build biological circuits, but one could argue that standardization is currently infeasible because our knowledge of even the most basic organisms is incomplete. One of the simplest systems synthetic biologists have attempted to engineer is the bacterium Escherichia coli. Even though this simple, single-celled organism has been studied and used in research labs for decades, we still don’t knows what every gene in E. coli does, and we have even less understanding of how all the proteins encoded by these genes interact. E. coli only have about 5,000 genes, a small (but still daunting) number compared to the roughly 25,000 genes humans have. When synthetic biologists make circuits in E. coli or use them to produce useful compounds, they have to take into account the effects the circuit will have on all these genes and how these genes will, in turn, affect the circuit. From these 5,000 different genes, E. coli can produce 5,000 different proteins in many different combinations. With this much complexity, it is nearly impossible to predict exactly what will happen (though we are getting better at it).
It is due to these complexities that some in the field are working toward making synthetic organisms with a defined set of genes of known functionality. If researchers can make an organism with an entirely known set of genes that are engineered to produce known proteins under known conditions, this could give us much greater control over the organism and simplify how we do synthetic biology. In 2010, a group led by Craig Venter who played a major role in sequencing the human genome (the complete genetic information of a single organism), put together many small, chemically synthesized pieces of DNA to construct a genome modeled (nearly exactly) after the genome of a small bacterium. This man-made genome was assembled by introducing these pieces of DNA into yeast, which then stitched these pieces together using natural biological processes. The complete genome product was then placed into a host bacterium. Upon dividing, the host bacterium was able to transfer the synthetic genome to one of its offspring. This offspring adopted the size and shape of the bacterium its synthetic genome was modeled after and expressed most of the proteins appropriate to this bacterium (4). While this did not constitute the complete design of a synthetic organism, nor was it “artificial life” as hyped up by some in the media, it showed that we can use completely man-made DNA sequences to substitute for natural genomes. Researchers may someday be able to use the techniques pioneered by Venter and his colleagues to piece together a rationally designed synthetic genome for a synthetic organism.
There are many exciting possibilities in the field of synthetic biology. If we can make a well-characterized set of biological circuits and easily controllable synthetic organisms, this may allow us to engineer new functionalities into organisms quickly and cost-effectively. Keep your eyes and ears open. If the dreams of synthetic biologists are fully realized, we will one day think about cells as useful little machines that fight cancer, provide energy for our automobiles, and produce drugs cheaply enough that those who need them can actually afford them.
Tyler J. Ford is a graduate student at Harvard Medical School.
Links of Interest:
BioBricks Website — www.bbf.openwetware.org
BIOFAB Website — www.biofab.org
1. Ro DK, Paradise EM, Ouellet M, Fisher KJ, Newman KL, Ndungu JM, Ho KA, Eachus RA, Ham TS, Kirby J, Chang MC, Withers ST, Shiba Y, Sarpong R, Keasling JD. (2006) Production of the antimalarial drug precursor artemisinic acid in engineered yeast. Nature. 440 (7086): 940-943.
2. Danino T, Mondragón-Palomino O, Tsimring L, Hasty J. A synchronized quorum of genetic clocks. Nature. 463 (7279): 326-330.
3. Gibson DG, Glass JI, Lartigue C, Noskov VN, Chuang RY, Algire MA, Benders GA, Montague MG, Ma L, Moodie MM, Merryman C, Vashee S, Krishnakumar R, Assad-Garcia N, Andrews-Pfannkoch C, Denisova EA, Young L, Qi ZQ, Segall-Shapiro TH, Calvey CH, Parmar PP, Hutchinson CA 3rd, Smith HO, Venter JC. (2010). Creation of a bacterial cell controlled by a chemically synthesized genome. Science. 329 (5987): 52-56.