E.coli become analogue hard drives

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.'