Synthetic gene circuits with a memory!

Imagine having a USB port in the body that we could use to insert a "flash drive" and transfer genetic data, therapies, or monitoring devices. The flash drive would have to be some kind of removable biological entity that has no problem getting in and out of the body. If you think about it, bacteria are the perfect candidates to be such devices. So, what if bacteria could be used as storage for genetic memory?

This is not so far-fetched if you think that recent studies have shown for example that genes expressed by bacteria in our guts can affect our propensity to be lean or fat. Bacteria have genes that "record" and "affect" what's going on in our body. The question is: can we control them?

Bacteria have a way of turning "on" or "off" their genes based on stimuli from the environment. Synthetic biology studies ways of using these "switches" to make "gene circuits". Genetic regulatory circuits are the biological analog of electric circuits, where genes, instead of light bulbs, are being turned on or off (by activating other genes).

Genetic circuits have numerous applications in medicine. For example, Auslaender et al. [1] used synthetic biology to create a pH sensor for cells. The researchers then implanted these cells into mice and used it as a device to detect diabetes. Lack of insulin causes an excess of acidity in the blood, and the pH drops below 7.35. Changes in pH induced by diabetes were quickly detected by the pH-sensor cells in the implanted mice. The pH information was processed and triggered a transgene expression response that resulted in the secretion of alkaline phosphatase to counteract the acidity. Basically, what the cells were able to do in the mice is: (1) detect the drop in pH; (2) trigger a response to restore the pH to normal levels.

In an electrical circuit you assemble elements like resistance and capacity. In a genetic circuit you assemble genes and "operators" able to edit the DNA in order to activate or deactivate the genes. One of such "editors" is a class of enzymes called recombinases. Apparently, there aren't many of these enzymes available, which limits the number of gene circuits one can make.

A recent study published in Science [2], however, presented a new class of such enzymes, derived from the bacteriophage Lambda, which is a virus that infects Escherichia coli. The novelty of the method doesn't stop here. You see, the goal is not just to have a working circuit, but to also make it autonomous. In other words, ideally, one wants a system able to detect responses and readjust the output based on the input it receives. The researchers devised genetic regulatory circuits able to "write", "input" and "read" genetic information.

Farzadfard and Lu [2] "converted genomic DNA into a 'tape recorder' for memorizing information in living cell populations." Their circuit, named SCRIBE (Synthetic Cellular Recorders Integrating Biological Events), responds to gene regulatory signals by generating single-stranded (ssDNA). The ssDNA is then coexpressed with a recombinase and introduces specific mutations in targeted positions of the cell DNA. The fraction of cells in the bacterial culture that carry the introduced mutations represents the biological memory at the population level.

For example, when the researchers exposed the cultures to an exposure input for 12 days (the equivalent of 120 generations in the bacterial population), they found that the

"frequency of mutants in these populations was linearly related to the total exposure time. Furthermore, we demonstrate that SCRIBE-induced mutations can be written and erased and can be used to record multiple inputs across the distributed genomic DNA of bacterial populations [2]."

It's a 'collective memory' embedded in the observed frequency of the mutation in the bacterial population. And the applications are almost infinite. I truly can't wait to see where this kind of research will take us in the future.

[1] Ausländer D, Ausländer S, Charpin-El Hamri G, Sedlmayer F, Müller M, Frey O, Hierlemann A, Stelling J, & Fussenegger M (2014). A synthetic multifunctional mammalian pH sensor and CO2 transgene-control device. Molecular cell, 55 (3), 397-408 PMID: 25018017

[2] Farzadfard, F., & Lu, T. (2014). Genomically encoded analog memory with precise in vivo DNA writing in living cell populations Science, 346 (6211), 1256272-1256272 DOI: 10.1126/science.1256272