Two testbeds will serve to demonstrate the utility of synthetic biology and the tools constructed in our thrusts and will drive development of the thrusts:

• construction of a bacterium to swim to a chemical or biological agent and destroy it
• development of a bacterium for customized chemical synthesis. 

The underlying goal of our research is not just to deliver systems that fulfill these two testbed applications, but rather to develop the foundational infrastructure that is needed to make routine the design and construction of any engineered biological system. 

View a graphic of how each testbed is integrated with the three thrust areas.

RESEARCH HIGHLIGHT
	Designing cancer-killing bacteria

One of the testbeds for SynBERC will be designing and engineering modules that will be integrated to construct a bacterium capable of moving to and attacking a chemical or biological entity; for example, a tumor or a chemical warfare agent. There are a number of environmental cues that bacteria could use to distinguish a tumor from healthy tissue. The environment is hypoxic and more nutritious, and bacteria grow to significantly higher cell densities (Yu et a, 2003). Components that sense these differences can be linked to genetic circuits that integrate the information. The circuits will activate engineered pathways that control bacterial chemotaxis and the interaction between the bacterium and a mammalian cell. These systems will be engineered into a non-pathogenic E. coli chassis.

Towards this goal, we have constructed a strain that links the lux quorum sensing system from Vibrio fischeri and the inv gene from Yersinia pseudotuberculosis. It has been previously demonstrated that invasin (inv) will induce invasion into mammalian cells when expressed in E. coli (Isberg et al, 1987). When linked to the quorum system, we demonstrated that invasion into HeLa cells only occurs when the density of bacteria crosses a threshold of 3´108 cfu/ml (Anderson et al, 2005). This may be a mechanism by which the bacteria can sense the low concentrations associated with healthy tissues (<106 cfu/g) and high concentrations in tumors (109 cfu/g) (Toso, 2002). The significance of this work is that it demonstrates how the interaction of a bacterium with a eukaryotic cell can be programmed to respond to heterologous signals.

2. Building a microbial chemical factory
Testbed leader: Kristala Jones Prather

The assignment of biological functions according to defined parts enables the construction of custom-designed microbes to serve as chemical factories. Metabolic enzymes, or “Metabolism and Materials Parts” (MMPs), are defined based on the chemical conversions they catalyze. Parts specific to the expression of proteins, such as promoters and ribosome binding sites, can be combined with MMPs to construct devices that result in the in vivo conversion of substrates to products. The inclusion of transport protein parts facilitates the secretion of valuable products into the extracellular medium. Such devices can be assembled based on known, naturally-occurring biosynthetic pathways, or according to synthetic schemes developed for the production of un-natural compounds. The goal of this testbed is to integrate devices for synthesis of a variety of important natural product precursors and un-natural small molecules into a single chassis.

The devices assembled for natural product precursor biosynthesis will include but not be limited to systems for the production of terpenoids, polyketides, and alkaloids. The ready availability of higher-level devices (multi-step pathways) for precursor synthesis and assembly of these precursors into hybrid molecules would allow, among other things, production of existing or novel antibiotics to combat potential bioterror agents and a wide variety of chemicals, including some of the most complicated natural products that are used by the pharmaceutical industry. For novel natural products discovered in rare, protected, or uncultivable organisms, these biosynthetic devices would alleviate the need for complicated and/or environmentally-harmful chemical synthesis and could reduce the cost of drugs by orders-of-magnitude. When used in conjunction with the other systems constructed in the two testbeds, these chemical synthesis devices would enable the synthetic biologist to engineer into a bacterium capable of moving to a tumor the ability to produce a complex chemotherapeutic (e.g., Taxol) when the bacterium reaches its target.