By tinkering with its DNA, scientists have converted the common gut bacterium E. coli into the world’s smallest tape recorder. The newly designed microbes are engineered in such a way that they are capable of documenting and storing memories from their environment which can then be retrieved at a later date. The idea behind these living data storage devices is that one day, they could be used as tiny health monitors or environmental sensors.
Scientists have attempted to store useful information in bacterial DNA before, but only managed to successfully record all-or-nothing memories, such as whether a particular stimulus is present in the environment or not. These digital memories could not therefore inform us of how long the exposure was, or how much of the stimulus was present, i.e. analog information. These new cells, however, are capable of doing just that.
To create their living memory recorders, scientists from the Massachusetts Institute of Technology (MIT) turned to sequences of DNA found in certain species of bacteria called retrons. Retrons carry the genetic information for the production of enzymes (biological catalysts) which generate single strands of DNA that are then inserted into the bacterium’s genome. Usually, these strands are used by the bacteria to manipulate their host.
By tinkering with their DNA sequence, the researchers were able to make retrons that only produce unique DNA sequences when a particular stimulus, such as light or a chemical, is present. These strands, which are effectively a record of the experience, are then inserted into a specific target site within the genome.
“We can target it anywhere in the genome,” says lead scientist Timothy Lu, “which is why we’re viewing it as a tape recorder, because you can direct it where that signal is written.”
Because the sequence can be passed on from generation to generation, the memory gradually accumulates and is stored for the lifetime of the population. Scientists can then recover this stored information by sequencing the genome of the organism. By determining how many of the cells within the population contain the new DNA sequence, they can work out the magnitude and duration of the signal. The higher the proportion containing the sequence, the greater the exposure.
The ultimate goal for the researchers is to use this system as a monitoring device for different environments. Because scientists can design the cells to respond to a variety of different stimuli, the potential applications are vast. The organisms could be placed in the ocean to measure levels of CO2 or pollution, for example. Alternatively, they could be used in medicine to monitor disease progression, such as the spread of cancers, by picking up stimuli that are released by diseased cells.