Information can be stored in bacterial genome

With recent advances in nanotechnology, computers and microchips have gotten exponentially smaller and more powerful over the past few decades. In fact, this phenomenon is so well known that it’s been given a name: Moore’s Law, after the scientist who first described it. Many may be doubtful that this trend will continue forever, due to the physical limits of technological materials, but as it turns out, our bodies already contain tiny, natural computing agents — the bacteria Escherichia coli. Recently, scientists at the Massachusetts Institute of Technology (MIT) have come up with a way to store information in this common bacterium.

Scientists have already succeeded in “programming” information into the genome of E. coli. The genetic code is remarkably simple, using only the four DNA bases A, G, C and T, but these bases can be arranged in an incredibly large number of combinations to represent a sequence of data. Overall, the method is similar to how computers store information with only the two numbers of the binary system.

However, the success and stability of bacteria memory systems are usually limited by several factors. First, a vast number of regulatory sequences must be added in order to properly monitor the man-made DNA. Such systems can also only record simple “digital memory,” or whether or not the intended sequence was transformed into the bacterium successfully.

Now, a team of engineers at MIT, led by professor Timothy Lu and graduate student Fahim Farzadfard, has adapted some of the previous methods to turn E. coli into a “genomic tape recorder” that can not only store information but also determine how much there is and when it was inserted. These bacteria can store time-sensitive “analog memory” because they rely on the expression and activity of a recombinase enzyme. It can be engineered to target a predetermined site in the bacterial genome, allowing for the insertion of any sequence of single-stranded DNA and an antibiotic resistance gene. However, this only occurs when the bacterium processes specific extracellular signals — in this case, substances necessary for metabolism, like light.

After the bacteria were allowed to grow and divide, an antibiotic was added that killed off the cells that did not uptake the intended DNA sequence and the antibiotic resistance gene. The scientists were thus able to determine the length of exposure to the signals by measuring the proportion of cells that survived the antibiotic exposure. Using the inserted regulatory sequences as reference points, the remaining bacteria were then sequenced to recover the stored DNA information.

The way in which these altered E. coli store digital information has been likened to a computer hard drive, where memory retrieval depends on a reading of the physical properties of the entire population of cells instead of just a single cell’s DNA sequence. Furthermore, the information can be retained reliably for a long time; it is preserved through cell divisions and growth of the bacteria and can be observed or recovered in the laboratory at any point.

E. coli can be found abundantly in both the environment and animals, making it a perfect candidate for monitoring biological processes and storing chemical information. Bacteria altered in the lab can theoretically be introduced into systems such as the ocean or the human digestive tract, while being simpler and less invasive than mechanical devices or manual methods. The bacteria can also be programmed to incorporate the DNA of other microorganisms into their own genome.