Synthetic genetic clock checks the thermometer

(Press-News.org) Contact information: Jeff Falk
jfalk@rice.edu
713-348-6775
Rice University
Synthetic genetic clock checks the thermometer Rice University leads study to counter effects of temperature on synthetic gene circuits

HOUSTON – (Jan. 7, 2014) – Genetic systems run like clockwork, attuned to temperature, time of day and many other factors as they regulate living organisms. Scientists at Rice University and the University of Houston have opened a window onto one aspect of the process that has confounded researchers for decades: the mechanism by which genetic regulators adjust to changing temperature.

Until now, synthetic biologists have not been able to duplicate this marvel, but Rice biochemist Matthew Bennett and his team developed a robust synthetic genetic clock that allows Escherichia coli bacteria to accurately keep time in a wide temperature range. The clock, which regulates the production of proteins, does not speed up or slow down with changing temperatures, and offers one possible solution to a problem that has hindered the advance of synthetic biology.

The results were published this week in the Proceedings of the National Academy of Sciences.

The revelation will be of interest to biologists who study regulatory systems, particularly circadian rhythms, but it may be most valuable to synthetic biologists who wish to reprogram cellular regulatory mechanisms for biotechnology, Bennett said.

"One of the problems we've had is that the genetic circuits we build are fragile," he said. "We can build systems that do what we want, but they often do not work well in other people's hands, or if we change the media or temperature. We wanted to create a system that should work independently of the parameters that might be hard for a synthetic biologist to control. We want to show we can build robust circuits, not just by making the architecture of the system more complicated, but by using the right proteins."

The ability to regulate for temperature comes naturally in mammals, but not all life is warm-blooded, and temperature generally affects biochemistry.

"The warmer things are, the more biochemistry speeds up," Bennett said. "This manifests in a lot of ways: Enzymes work faster and biochemical rates are faster."

He said that E. coli, for instance, shows dramatic changes in behavior even within its comfort zone of about 30 to 41 degrees Celsius (86 to 105 degrees Fahrenheit).

"For every 10 degrees Celsius increase in temperature, there's about a doubling in the cell cycle speed," Bennett said.

Among biological processes, there's a notable exception: circadian clocks that keep a steady beat despite the temperature. "We have genetically controlled clocks that help us determine the time of day and coordinate our response to the day-night cycle, changing hormone levels and our alertness. And we're not the only organisms that have them," he said.

"Plants and fungi and even some bacteria that do not have internal temperature regulation also have circadian clocks. For those organisms, it's very important that the period of their circadian clocks remains the same regardless of temperature changes. Your crops, no matter whether it's hot or cold, always keep to the same day-night cycle."

But circadian clocks are also biochemical. "As it gets colder, circadian clocks should slow down, and as it gets warmer, speed up, but they do not," he said. "It's been a mystery as to why that doesn't happen."

Bennett suspected the clocks take their cues from a combination of cellular feedback loops and temperature-sensitive proteins. "Instead of looking at circadian clocks in humans or plants, however, we decided to build a system from the ground up," he said.

His research group started with a synthetic gene oscillator that was built to run in E. coli. Then, by altering a single amino acid of a key protein – LacI, the lactose repressor – the researchers made that protein temperature-sensitive and provided the synthetic clock a guide to compensate for changing conditions.

Bennett noted in the paper that engineers have struggled with temperature compensation for a long time, perhaps most famously in the search for a device to give sailors at sea their longitude.

"Temperature compensation is a problem with timekeeping in general," said the researcher, whose first paper as an undergraduate also touched upon the longitude problem. "Metals expand and contract in response to temperature changes, thus altering the period of mechanical clocks.

"This was a major obstacle for early naval chronometers. The man who invented those chronometers, John Harrison, had to compensate for temperature effects. It was a big problem in engineering back then, and we're still finding it to be a problem when we build gene circuits in bacteria today."



INFORMATION:

Faiza Hussain, a postdoctoral fellow at Rice, is the paper's lead author. Other Rice co-authors are Andrew Hirning, graduate student, and Kathleen Matthews, the Stewart Memorial Professor of Biochemistry and Cell Biology. University of Houston co-authors are Chinmaya Gupta, postdoctoral fellow, Krešimir Josić, associate professor of mathematics, and William Ott, assistant professor of mathematics.

The research was supported by the National Institutes of Health through the joint National Science Foundation/National Institute of General Medical Sciences Mathematical Biology Program, the Robert A. Welch Foundation and the John S. Dunn Foundation Collaborative Research Award Program administered by the Gulf Coast Consortia.

In this video, E. coli cells containing the dual-feedback oscillator are outlined in blue and red tracked as they grow in a microfluidic device at 32 degrees Celsius, left, and 41 degrees Celsius, right. The periods of the cells' fluorescent-tagged "clock" proteins, tracked in the graph at bottom, match despite the change in temperature. (Credit: Bennett Lab/Rice University)

Read the abstract at http://www.pnas.org/cgi/doi/10.1073/pnas.1316298111

This news release can be found online at http://news.rice.edu/2014/01/07/synthetic-genetic-clock-checks-the-thermometer-2/

Follow Rice News and Media Relations via Twitter @RiceUNews.

Related Materials:

The Bennett Lab: http://biodesign.rice.edu

"Huygens's clocks": http://rspa.royalsocietypublishing.org/content/458/2019/563.abstract

University of Houston Department of Mathematics: http://www.mathematics.uh.edu

Images/video:

http://news.rice.edu/wp-content/uploads/2014/01/Composite-horizontal-web.jpg

A vertical version of this image is available here:

http://news.rice.edu/wp-content/uploads/2014/01/Composite-vertical-web.jpg

Rice University scientists engineered a synthetic genetic clock inside a mutant Escherichia coli bacteria that keeps time despite rising or falling temperature. In an experiment, the researchers isolated a small number of engineered bacteria under a fluorescent microscope and captured images over three hours as a single cell (yellow arrow) oscillated at a regular clip between states despite changing conditions. They found altering one amino acid to make a regulator protein sensitive to temperature provided the right feedback to the bacteria's circadian clock. (Credit: Bennett Lab/Rice University)

http://youtu.be/KZDZNANGL3c

In this video, E. coli cells containing the dual-feedback oscillator are outlined in blue and red and tracked as they grow in a microfluidic device at 32 degrees Celsius, left, and 41 degrees Celsius, right. The periods of the cells' fluorescent-tagged "clock" proteins, tracked in the graph at bottom, match despite the change in temperature. (Credit: Bennett Lab/Rice University)

Located on a 300-acre forested campus in Houston, Rice University is consistently ranked among the nation's top 20 universities by U.S. News & World Report. Rice has highly respected schools of Architecture, Business, Continuing Studies, Engineering, Humanities, Music, Natural Sciences and Social Sciences and is home to the Baker Institute for Public Policy. With 3,708 undergraduates and 2,374 graduate students, Rice's undergraduate student-to-faculty ratio is 6-to-1. Its residential college system builds close-knit communities and lifelong friendships, just one reason why Rice has been ranked No. 1 for best quality of life multiple times by the Princeton Review and No. 2 for "best value" among private universities by Kiplinger's Personal Finance. To read "What they're saying about Rice," go to http://tinyurl.com/AboutRiceU.



Jeff Falk
713-348-6775
jfalk@rice.edu

Mike Williams
713-348-6728
mikewilliams@rice.edu