In a step that brings closer the day of cellular computers, a team of US scientists from Johns Hopkins University School of Medicine in the US has engineered living cells to behave like logic gates, or simple biological computational units that produce certain outputs in response to certain combinations of inputs.
In the May issue of Nature Chemical Biology, senior author Takanari Inoue, an assistant professor in the Department of Cell Biology at Johns Hopkins, and member of the University’s Institute of Basic Biomedical Sciences’ Center for Cell Dynamics, and colleagues, describe how they got mammalian cells to behave like AND and OR logic gates.
At the heart of every digital computer are “logic gates” that perform Boolean or logical operations such as NOT, AND and OR. These gates recognize and respond by understanding just two states: True (1) and False (0).
For example, the AND gate has two inputs, and outputs a 1 only when both inputs are 1. So for this gate, out of the four possible input combinations 00, 01, 10 and 11, only the combination 11 produces a 1; the other three combinations result in a 0.
The OR gate also has two inputs, but it outputs a 1 when either or both of them is a 1. So from the four possible combinations 00, 01, 10 and 11, only the 00 leads to 0, for the other three combinations, the OR gate outputs a 1.
In electronic computers the logic gates are silicon-based components, and the states True and False (1 and 0) are represented by the presence or absence of an electrical current.
Now imagine you could make a similar logical processor inside a cell. What components and features could you use? One approach is to use the genetic machinery inside cells, indeed this has been done already. Previous studies have used trascription, the process through which cells read genes to make proteins, to generate outputs. But this is slow and can take from minutes to days. And the need for speed is a key driver in this research, as Inoue explained:
“People like to have speedy computation. We were hoping to achieve computation in cells on the order of seconds, which is significantly faster than what people have achieved thus far.”
So Inoue and colleagues decided to try and develop a system based on cellular proteins.
They achieved this by using a a technique called chemically inducible dimerization (CID) that deploys natural biological mechanisms to fuse two proteins into a complex in the presence of a chemical.
Since AND and OR gates create outputs based on two different inputs, either together or separately, the team needed two different CID systems that didn’t compete or overlap with each other.
They relied on one CID system that’s been studied for years, which brings the animal proteins FRB and FKBP together in the presence of a drug called rapamycin which is derived from bacteria.
In addition, they used a second CID system that brings together the two plant proteins GID1 and GAI, in the presence of a plant hormone called gibberellin.
Inoue explained that since the gibberellin system is based on plants, it doesn’t compete with the animal-based rapamycin one.
He and his colleagues engineered mammalian cells that make all four proteins, as well as a response, when the right two proteins come together.
Thus, when either FRB and FKBP or GID1 and GAI came together, the cell’s membrane developed “ruffles” that were easy to see under a microscope.
To make the OR gate, FRB and GAI were bound together at the cell membrane, while FKBP and GID1 were bound together floating freely in the cell. The OR operation occured by adding either rapamycin OR gibberellin OR both, because any of these resulted in the free-floating pair linking up to the pair at the membrane, to make the output signal.
To make the AND gate, the team put just GAI at the cell membrane, and just had FRB and a combination of FKBP and GID1 free-floating in the cell. In this system, all four proteins had to link up to generate an output signal, which only occured when both rapamycin AND gibberellin were present.
When they tested these systems, the team found they produced the required responses fast, in just a few seconds.
As second proof of principle, they also tested the system using fluorescence as the required output signal. They found this was just as quick.
Inoue said eventually it might be possible to use these methods to build larger, more complex logic circuits and for computers to be based on cells.
In the meantime these systems could be put to good use more or less as they are: for instance they could produce specific outputs in the presence of certain chemicals, a useful diagnostic tool.
Another potential use is for studying how cells naturally produce outputs to regulate bodily functions.
Funds from the National Institute of Health (NIH), the National Science Foundation, and the National Center for Research Resources of the NIH and NIH Roadmap for Medical Research, helped pay for the study.
Written by Catharine Paddock PhD