Researchers in the US who last year genetically engineered individual bacteria to count time by turning fluorescent proteins inside their cells on and off, have taken their idea a stage further: they have made bacterial colonies of coupled genetic clocks that flash on and off in synchrony, and they have also engineered the bacterial genes so the blinking rate changes in response to changes in the environment.
The researchers, from the University of California, San Diego (UCSD), describe their work in a paper published in the journal Nature on 21 January.
Dr Jeff Hasty, associate professor of biology and bioengineering at UCSD headed the research team with Dr Lev Tsimring, associate director of UCSD’s BioCircuits Institute.
“Programming living cells is one defining goal of the new field of synthetic biology,” Hasty told the media.
Tsimring said that:
“Synchronization plays a crucial role in physics and biology as a way of self-organization of highly regular behavior with less that perfect components.”
“This phenomenon has a myriad of applications in modern technology, from communication networks to GPS. Our study demonstrates how inherently noisy gene oscillators can operate together with beautiful synchronicity and regularity once coupled together in a specific way,” he added.
About ten years ago, scientists defined a new direction for synthetic biology by designing and making a genetic toggle switch and an oscillator: opening the door to introducing many functions normally associated with fields like electromechanics and electronics into living cells. Since then, the field has seen living cell circuits capable of pattern generation, noise shaping, edge detection and event counting.
And now, with this new study, another important step occurs: intercellular coupling that is capable of synchronized oscillations in a growing population of cells.
Martin Fussenegger of the Swiss Federal Institute of Technology Zurich (ETH Zurich) in Basel, who was not involved with the latest research, told NatureNews that:
“For the first time, it is possible to synchronize individual oscillators in different organisms of the same population.”
“If it is implemented in mammalian cells, this could have a tremendous impact in the future,” he added.
Imagine this: an implantable drug dispenser that not only delivers a scheduled dose of a drug, but is also capable of responding to changes in the body, and alters the dose accordingly.
Or this: a genetic sensor that blinks at different rates dependent on temperature, poisons and other hazards it detects in the environment.
The research was backed by grants from the National Institutes of Health’s (NIH) National Institute of General Medical Sciences. James Anderson, who oversees their computational biology grants, said that Hasty and colleagues:
“Have used powerful genetic tools, backed by decades of detailed knowledge of bacterial processes, to create a system that delivers on the promise of synthetic biology – to engineer living organisms to meet pressing societal needs.”
“The oscillating system they engineered sets the stage for the development of highly sensitive sensors that could have multiple applications in basic research, biotechnology and medicine,” said Anderson.
For their study, Hasty, Tsimring and colleagues exploited a type of cellular communication where bacterial cells exchange small molecules; as Hasty explained:
“Many bacteria species are known to communicate by a mechanism known as quorum sensing, that is, relaying between them small molecules to trigger various behaviors.”
“Other bacteria are known to disrupt this communication mechanism by degrading these relay molecules,” he said.
Essentially the researchers exploited this feature from two different organisms: they transferred communication genes from two species of bacteria into the genome of Escherichia coli but wired them up to produce a positive feedback effect and a negative feedback effect that worked together like the pendulum of a clock.
The positive feedback came from the production of a molecule called acyl-homoserine lactone (AHL) that gradually moves into other cells, that then also increase production of AHL. The negative feedback came from the fact that AHL production also triggers a gene that breaks down AHL. The result is a network of coupled oscillators: AHL goes up, AHL goes down, AHL goes up, AHL goes down, with the quorum sensing components allowing the phase information, the oscillations between the bacterial cells, to be relayed across the network.
By genetically latching a fluorescent protein so that it glows brighter when the AHL level is high and dulls when it is low, the researchers could see how the E coli colony’s production of AHL oscillated as the light pulsed.
The researchers also constructed devices that precisely controlled the size of the bacterial colonies: one at a micron scale and the other at a millimeter scale.
Hasty said that the micron scale colonies oscillated synchronously from 50 to 90 minutes, but at the larger scale, the millimeter scale, the time for diffusion of the AHL across the colony became more important, and in this case they could see the signal propagating through it.
Hasty said that:
“The use of quorum sensing is a promising approach to increase the sensitivity and robustness of the dynamic response to external signals.”
“In nature, synchronization typically helps stabilize a desired behavior arising from a network of intrinsically noisy and unreliable elements. We think the synchronized genetic clock sets the stage for the use of microbes as a macroscopic biosensor with oscillatory output, or applications of using a synchronized periodic signal in drug delivery,” he explained.
Fussenegger agreed that “synchronized oscillation is really very important in biology,” and could see how such innovation could lead for example to the design of “brain pacemakers” that restore the coordinated firing of neurons that is essential for thinking and action. We may also begin to understand “how cells synchronize themselves with their neighbours, or maybe how being out of sync has some pathological consequences,” he told NatureNews.
“A synchronized quorum of genetic clocks.”
Tal Danino, Octavio Mondragon-Palomino, Lev Tsimring and Jeff Hasty.
DOI:10.1038/nature08753
Sources: UCSD, NatureNews.
Written by: Catharine Paddock, PhD