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E.coli become analogue hard drives

24 November 2014
Appeared in BioNews 781

E.coli have been engineered to record information from their environment by storing it in their DNA, much like a computer's hard drive.

Bacteria have been used to store information before, in a way that allowed scientists to tell if they had been exposed to a certain event. The new system uses analogue storage rather than an on-or-off digital form, meaning more extensive information can be recorded.

'You can store very long term information,' said Professor Timothy Lu, who directed the work at Massachusetts Institute of Technology. 'You could imagine having this system in a bacterium that lives in your gut, or environmental bacteria. You could put this out for days or months, and then come back later and see what happened at a quantitative level.'

The technology, named SCRIBE (Synthetic Cellular Recorders Integrating Biological Events), uses distinctive bacterial DNA structures called retrons. They are able to produce an enzyme that makes new strands of DNA, which are then inserted into the bacterial genome.

The researchers reprogrammed these retrons to insert specific DNA sequences at targeted sites in the genome, but only when the E.coli is exposed to a particular input, such as bright light. These DNA insertions will be passed on as the bacteria multiply, meaning the whole bacterial population can be used to track how long and how often they are exposed to the inputs over time.

Besides direct DNA sequencing, one way to read the bacterial 'hard drive' is to ensure that the inserted DNA sequence activates an antibiotic resistance gene. Since only bacteria that have experienced the input signal will survive antibiotic treatment, the number of surviving bacteria can be used as a read out for the input's strength, or length of exposure.

Dr Shawn Douglas, a bio-nanotechnologist who was not involved with the study, told Genetic Engineering & Biotechnology News: 'This work is very exciting because it integrates many useful capabilities in a single system: long-lasting, analogue, distributed genomic storage with a variety of readout options.'

He added: 'Rather than treating each individual cell as a digital storage device, [the authors] treat an entire population of cells as an analogue 'hard drive', greatly increasing the total amount of information that can be stored and retrieved.'

SCRIBE could have many environmental applications including monitoring the ocean for carbon dioxide levels, acidity, or pollutants. It could also be used to create probiotics that record events in people's guts, such as inflammation.

The stability of the SCRIBE system, however, is a potential concern. Cameron Myhrvold, at Harvard University's Wyss Institute for Biologically Inspired Engineering, told New Scientist that 'retrons might mutate and malfunction in some more challenging cellular environments, which could compromise their ability to record cellular events.'

Bacteria become 'genomic tape recorders'
EurekAlert! (press release) |  13 November 2014
Bacterial Computer’s Analog Memory Stores Environmental Data in DNA
Genetic Engineering and Biotechnology News |  14 November 2014
Cells act like old tape recorders to monitor health
New Scientist |  13 November 2014
Cellular 'computers' gain a hard drive
Nature |  14 November 2014
DNA Tape Recorder
The Scientist |  13 November 2014
Genomically encoded analog memory with precise in vivo DNA writing in living cell populations
Science |  14 November 2014
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