'Biological tape recorder' built from microbes

Researchers from Columbia University Medical Center have converted a natural bacterial immune system into what they describe as a microscopic data recorder, laying the groundwork for a class of technologies that use bacterial cells for everything from disease diagnosis to environmental monitoring.

Through a few clever molecular hacks, the researchers modified an ordinary laboratory strain of the human gut microbe E. coli, enabling the bacteria to not only record their interactions with the environment but also time-stamp the events. Their results have been published in the journal Science.

Senior author Dr Harris Wang and members of his laboratory created the microscopic data recorder by taking advantage of CRISPR-Cas, an immune system in many species of bacteria. CRISPR-Cas copies snippets of DNA from invading viruses so that subsequent generations of bacteria can repel these pathogens more effectively. As a result, the CRISPR locus of the bacterial genome accumulates a chronological record of the bacterial viruses that it and its ancestors have survived. When those same viruses try to infect again, the CRISPR-Cas system can recognise and eliminate them.

“The CRISPR-Cas system is a natural biological memory device,” said Dr Wang. “From an engineering perspective that’s actually quite nice, because it’s already a system that has been honed through evolution to be really great at storing information.”

CRISPR-Cas normally uses its recorded sequences to detect and cut the DNA of incoming phages. The specificity of this DNA cutting activity has made CRISPR-Cas invaluable to gene therapy researchers, who have modified it to make precise changes in the genomes of cultured cells, laboratory animals and even humans.

The abilities of CRISPR have not been lost on synthetic biologists, either, who have previously used the system to store poems, books and images in DNA. Yet Ravi Sheth, a graduate student in Dr Wang’s laboratory, saw unrealised potential in CRISPR-Cas’s recording function.

“When you think about recording temporally changing signals with electronics, or an audio recording … that’s a very powerful technology, but we were thinking how can you scale this to living cells themselves?” said Sheth.

To build their microscopic recorder, Sheth and other members of the lab modified a piece of DNA called a plasmid, giving it the ability to create more copies of itself in the bacterial cell in response to an external signal. A separate recording plasmid, which drives the recorder and marks time, expresses components of the CRISPR-Cas system.

In the absence of an external signal, only the recording plasmid is active, and the cell adds copies of a spacer sequence to the CRISPR locus in its genome. When an external signal is detected by the cell, the other plasmid is also activated, leading to insertion of its sequences instead.

The result is a mixture of background sequences that record time and signal sequences that change depending on the cell’s environment. The researchers can then examine the bacterial CRISPR locus and use computational tools to read the recording and its timing.

This is said to be the first time CRISPR has been used to record cellular activity and the timing of those events, with the paper proving the system can handle at least three simultaneous signals and record for days. According to Dr Wang, the researchers are now “planning to look at various markers that might be altered under changes in natural or disease states, in the gastrointestinal system or elsewhere”.

“Such bacteria, swallowed by a patient, might be able to record the changes they experience through the whole digestive tract, yielding an unprecedented view of previously inaccessible phenomena,” he said. Other applications could include environmental sensing and basic studies in ecology and microbiology, where bacteria could monitor otherwise invisible changes without disrupting their surroundings.

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