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Glowing bacteria shed light on what makes biological clocks tick

Nov 2011
Ashley N. Paddock,

Scientists have long known that plants and animals are governed by circadian rhythm – a 24-hour cycle of alternating light and darkness to guide biological processes. Although we know that our bodies are entrained, or synchronized, by light and would drift out of phase if left in the dark, we have yet to understand exactly how this process works at the molecular level.

To find out, biologists and bioengineers at the University of California developed a model biological system that is simpler than that of an organism. Led by biology professor Jeff Hasty, they created a simple circadian system using a model consisting of glowing, blinking E. coli. The system was detailed in the Sept. 2 issue of Science (doi: 10.1126/science.1205369).

Combining techniques from synthetic biology, microfluidic technology and computational modeling, the researchers built a microfluidic chip containing chambers with E. coli. Within each bacterium, the genetic machinery responsible for the biological clock oscillations was green fluorescent protein, which caused the bacteria to periodically fluoresce.

The researchers modified the bacteria to glow and blink whenever arabinose – a chemical that triggered the oscillatory clock mechanisms of the bacteria – was flushed through the microfluidic chip. This enabled them to simulate day and night cycles over a period of minutes rather than days to better understand how a population of cells synchronizes its biological clocks.

“We studied quantitatively how a minimal genetic oscillator in single cells is capable of picking up the phase of an oscillatory external input and relay it to drive the expression of a gene,” Hasty said. “In contrast, the timekeeping systems of natural organisms use coordinated groups of complex cell oscillators for generating the daily rhythms and processing the environmental inputs to produce the multiple phased signals that coordinate essential cellular and organismal processes.”

Hasty said a similar microfluidic system could be constructed, in principle, with mammalian cells to study how human cells synchronize with light and darkness. In future research, they hope to integrate synthetic clocks with cell processes such as metabolism and cell division to understand how this is achieved in natural settings.

Genetic models such as this could be important because circadian rhythm disruptions have been linked to medical issues such as sleep disorders and diabetes.

“While fluorescence microscopy will continue to be the central tool for the investigation of biological clocks, the use of light to control gene expression in individual cells (optogenetics) will be, without a doubt, an important new resource to learn about the dynamics of synthetic multicellular systems,” Hasty said.

fluorescence microscopy
Observation of samples using excitation produced fluorescence. A sample is placed within the excitation laser and the plane of observation is scanned. Emitted photons from the sample are filtered by a long pass dichroic optic and are detected and recorded for digital image reproduction.
Americasarabinosebiological clock oscillationsbiological clocksBiophotonicsBioScanCaliforniacircadian rhythmcircadian system of E. colicomputational modelingE. coli bacteriafluorescence microscopygenetic oscillatorsGFPgreen fluorescent proteinJeff Hastymammalian cellsmicrofluidic chipMicrofluidic technologyMicroscopyNewsSynthetic biologysynthetic multicellular systemsUniversity of California San Diego

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