SURF 2018: Synthetic modules for regulation of bacterial growth

2018 SURF project description

• Mentor: Richard Murray
• Co-mentor: Reed McCardell

Complex consortia of microbes occur nearly everywhere in nature, including in the human body, and are implicated in a number of significant environmental and human physiological processes. The composition of microbial communities all over the human body are dynamic in response to changes in the environment around the human host and inside the host itself. In an attempt to build understanding and control of the dynamics of microbial community composition, we are working to design communities with various population level behaviors effected by synthetic regulators of bacterial growth.

The approach we are taking to this goal involves cell-cell communication between bacteria in culture, genetic circuits that translate population information into signals inside each cell and synthetic growth regulators activated or repressed by these intracellular signals. Together, modules performing each of these functions can create a community of bacteria capable of regulating its composition by slowing or speeding up growth of community members.

At the moment, toxin/antitoxin systems, particularly ccdB/ccdA, are the most well-used growth regulators [1,2], but the set of regulators in the syntheic biological toolbox is growing. One important focus of our project to develop synthetic microbial consortia is the development of a collection of growth regulatory systems acting with different mechanisms, dynamic range and effect sizes. We envision using these regulators in combination or individually to enable various population level dynamics in bacterial communities.

Of particular interest are two types of growth regulation that are very relevant to our understanding and control of natural microbial communities. One is regulation via secreted antibiotics, or bacteriocins, and the other is regulation via metabolic interdependency and resource availability. Both these systems are employed widely in natural microbial communities, have seen at least introductory quantitative study [3,4,5,6], and offer improved simplicity, efficiency and power over other growth regulators, as they are capable of both signal transmission (as an intercellular signal) and growth regulatory action as a single genetic module (compared to widely used quorum sensing modules coupled with effectors)

This SURF project will investigate one of these mechanisms of growth regulation with goals:

• High level goal: Design and construct a genetic circuit effecting composition control on a synthetic community of bacteria. With subgoals below...
• Clone at least one effector and all its required component parts (bacteriocin +/- resistance gene; metabolic enzyme inhibitor/activator)
• Assess dynamic range, effect size off/on dynamics of growth regulator(s)
• Develop a mathematical model for the action of growth regulator(s)

The specific growth regulatory systems presented above are ideas from the mentor and co-mentor, but we are open to mechanisms of growth regulation of all types. Students are encouraged to consider growth regulation at any level and investigate systems in which they are interested.

Required skills: Students should be comfortable with basic molecular biological techniques for cloning of genes and bacterial transformation. The work will be performed in E. coli and students should be familiar with bacterial culture. Quantification of growth regulatory parameters is very important for efforts to computationally model growth regulation and skills in programming and data analysis are required. Modeling of growth regulation will be based on differential equations; students should be familiar with the basic mathematics of differential equations.

References

1. You, L., Cox, R. S., Weiss, R. & Arnold, F. H. Programmed population control by cell–cell communication and regulated killing. Nature 428, 868–871 (2004).
2. Balagaddé, F. K. et al. A synthetic Escherichia coli predator-prey ecosystem. Mol. Syst. Biol. 4, 187 (2008).
3. Weber, M. F., Poxleitner, G., Hebisch, E., Frey, E. & Opitz, M. Chemical warfare and survival strategies in bacterial range expansions. J. R. Soc. Interface 11, 20140172 (2014).
4. Kirkup, B. C. & Riley, M. A. Antibiotic-mediated antagonism leads to a bacterial game of rock–paper–scissors in vivo. Nature 428, 412–414 (2004).
5. Kerr, B., Riley, M. A., Feldman, M. W. & Bohannan, B. J. M. Local dispersal promotes biodiversity in a real-life game of rock–paper–scissors. Nature 418, 171–174 (2002).
6. Kerner, A., Park, J., Williams, A. & Lin, X. N. A programmable escherichia coli consortium via tunable symbiosis. PLoS One 7, 1–10 (2012).