Mathematicians at the University of Houston and biologists at Rice University want to make a gene clock to use in synthetic biology applications that reprogram cellular regulatory mechanisms in the field of biotechnology. The problem with this approach is that “genetic circuits we build are fragile,” said Rice biochemist Matthew Bennett. “We can build systems that do what we want, but they often do not work well… if we change the media or temperature.” Added Krešimir Josić, professor of mathematics at UH, “In E. coli and other bacteria, if you increase the temperature by about 10 degrees the rate of biochemical reactions will double–and therefore genetic clocks will speed up.”
This poses a problem, as accurate timing relies on consistency. “We wanted to create a synthetic gene clock that compensates for this increase in tempo and keeps accurate time, regardless of temperature,” explained Josić. To accomplish this, Josić, Bennett, University of Houston mathematics professor William Ott, and postdoctoral fellow Chinmaya Gupta worked together for the last three years to engineer a “gene circuit not affected by temperature change.” The final model used a modified gene inserted in a plasmid, which was then inserted into E. coli. The mutation was made in the gene for LacI, the lactose repressor in the well-known lac operon of E. coli. A switch in one coded amino acid yielded the desired result: the mutated gene was able to slow down the genetic clock as temperature increased.
To design the necessary features of the plasmid to counteract temperature change, the UH part of the team created a mathematical model that captured the mechanisms essential to counteract the temperature-dependent changes in biochemical reaction rates. “Having a mechanistic model that allows you to determine which features are important and which can be ignored for a genetic circuit to behave in a particular way allows you to more efficiently create circuits with desired properties,” Gupta said. “It allows you to concentrate on the most important factors necessary in the design.” The model indicated that a single mutation could result in a genetic clock with a stable period across a range of temperatures.
While synthetic biologists and mathematicians seem to make an unlikely duo, Josić pointed out that “computational and mathematical tools are essential in all types of engineering,” and asked the question, “Why not for biological engineering?” Their collaboration was funded by the National Institutes of Health through the joint National Science Foundation/National Institute of General Medical Sciences Mathematical Biology Program.