It’s the tiniest tape recorder in the world – and could the the door for a massive change in everything from disease diagnosis to environmental monitoring.
Researchers at Columbia University Medical Center have converted a natural bacterial immune system into a microscopic data recorder.
By modifying a strain of the ubiquitous human gut microbe E. coli, the enabled it to not only record their interactions with the environment but also time-stamp the events.
Columbia researchers used gene editing to enable e. Coli bacteria to not only record their interactions with the environment but also time-stamp the events.
‘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,’ says Harris Wang of CUMC, the senior author of the Science paper.
Other applications could include environmental sensing and basic studies in ecology and microbiology, where bacteria could monitor otherwise invisible changes without disrupting their surroundings.
The researchers created the microscopic data recorder by using 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 recognize and eliminate them.
‘The CRISPR-Cas system is a natural biological memory device,’ says 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.’
Over a dozen clinical trials are now underway to treat various diseases through CRISPR-Cas gene therapy.
But Ravi Sheth, a graduate student in Wang’s laboratory, saw unrealized 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?’ says Sheth.
To build their microscopic recorder, Sheth and other members of the Wang 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.
WHAT IS CRISPR-CAS9?
CRISPR-Cas9 is a tool for making precise edits in DNA, discovered in bacteria.
The acronym stands for ‘Clustered Regularly Inter-Spaced Palindromic Repeats’.
The technique involves a DNA cutting enzyme and a small tag which tells the enzyme where to cut.
By editing this tag, scientists are able to target the enzyme to specific regions of DNA and make precise cuts, wherever they like.
The CRISPR/Cas9 technqiue uses tags which identify the location of the mutation, and an enzyme, which acts as tiny scissors, to cut DNA in a precise place, allowing small portions of a gene to be removed
It has been used to ‘silence’ genes – effectively switching them off.
When cellular machinery repairs the DNA break, it removes a small snip of DNA.
In this way, researchers can precisely turn off specific genes in the genome.
The approach has been used previously to edit the HBB gene responsible for a condition called β-thalassaemia.
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.
The current paper proves the system can handle at least three simultaneous signals and record for days.
‘Now we’re planning to look at various markers that might be altered under changes in natural or disease states, in the gastrointestinal system or elsewhere,’ says Dr. Wang.
Synthetic biologists have previously used CRISPR to store poems, books, and images in DNA, but this is the first time CRISPR has been used to record cellular activity and the timing of those events.