Synthetic Biologists Create Bacterial ‘Tape Recorder’

A team of synthetic biologists from Columbia University has successfully converted an immune system of the gut bacterium Escherichia coli into a microscopic ‘tape recorder,’ laying the groundwork for a new class of technologies that use bacteria for everything from disease diagnosis to environmental monitoring. The results are published in the journal Science.

Audio signals can be stored in a magnetic tape medium; similarly the microscopic data recorder stores biological signals into a CRISPR tape in bacteria. Image credit: Columbia University Medical Center.

Dr. Harris Wang from the Department of Pathology and Cell Biology and Systems Biology at Columbia University Medical Center and colleagues created the microscopic recorder by taking advantage of CRISPR-Cas, an immune system in many species of bacteria.

“The CRISPR-Cas system is a natural biological memory device. 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,” Dr. Wang said.

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 the darling of gene therapy researchers, who have modified it to make precise changes in the genomes of cultured cells, laboratory animals, and even humans.

Indeed, over a dozen clinical trials are now underway to treat various diseases through CRISPR-Cas gene therapy.

Ravi Sheth, first author of the study and a graduate student at Columbia University, said: “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?”

To build their microscopic recorder, the researchers 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 scientists can then examine the bacterial CRISPR locus and use computational tools to read the recording and its timing.

The system can handle at least three simultaneous signals and record for days, according to the study.

“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,” Dr. Wang explained.

“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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Ravi U. Sheth et al. Multiplex recording of cellular events over time on CRISPR biological tape. Science, published online November 23, 2017; doi: 10.1126/science.aao0958