MIT researchers have engineered bacteria with 'multicolour vision' — E. coli that recognise RGB light and, in response to each colour, express different genes that perform different biological functions. To showcase the technology, the researchers produced several coloured images on culture plates — one of which spells out 'MIT' — by using RGB lights to control the pigment produced by the bacteria. Outside of the lab, the technology could also prove useful for commercial, pharmaceutical, and other applications.
The E. coli is programmed with a protein- and enzyme-based system, analogous to a computer chip, with several different modules to process the light input and produce a biological output.
In computing terms, a 'sensor array' first becomes activated in the presence of either red, green, or blue light, and a “circuit” processes the signal. Then, a 'resource allocator' connects the processed information to 'actuators' that implement the corresponding biological function.
Think of the new E. coli as microbial marionettes, with coloured light instead of puppet strings making the bacteria act in a certain way, says MIT professor of biological engineering Chris Voigt, co-author of a paper in Nature describing the technology.
“Using different colours, we can control different genes that are being expressed,” he says. The paper’s co-authors are former postdocs Jesus Fernandez-Rodriguez, Felix Moser, and Miryoung Song.
To make the new colour images, the researchers programmed bacteria to produce the same pigment as the red, green, or blue light shone upon them. In an incubator, the researchers coated a petri dish with bacteria that are genetically identical. “You can think of it like undeveloped film, where you have the petri dish with bacteria on it,” Voigt says, “and the camera is the incubator.”
At the top of the incubator is a hole, where a stenciled image is projected onto the plate. Over time, the bacteria grow, producing an enzyme that produces a pigment corresponding to whichever RBG colour they’re illuminated by. In addition to the MIT logo, the researchers produced images of various patterns, multicoloured fruit, and the video game character Super Mario.
The engineered bacteria could also be used to rapidly start and stop the chemical reactions of microbes in industrial fermentation processes, which are used to make pharmaceuticals and other products. Today, controlling such chemical reactions requires dumping different chemical additives into large fermenting vats, which is time-consuming and inefficient.
In their paper, the researchers demonstrated this 'chemicals on-demand' concept on a small scale. Using CRISPR gene-editing tools, they modified three genes that produce acetate — a sometimes-unwanted byproduct of various bioprocesses — to produce less of the chemical in response to RGB lights.
“Individually, and in combination with one another, the different colours of light reduce acetate production without sacrificing biomass accumulation,” the researchers wrote in their paper.
Voigt has coined an amusing name for these industrial microbes. “I refer to them as ‘disco bacteria,’” he says, “because different coloured lights are flashing inside the fermenter and controlling the cells.”
A future application, Voigt adds, could be in controlling cells to form various materials and structures. Researchers, including some at MIT, have started programming cells to assemble into living materials that one day could be used to design solar cells, self-healing materials, or diagnostic sensors.
“It’s amazing when you look at the world and see all the different materials,” Voigt says. “Things like cellulose, silk proteins, metals, nanowires, and living materials like organs — all these different things in nature we get from cells growing into different patterns. You can imagine using different colours of light to tell the cells how they should be growing as part of building that material.”
The research was funded by the National Science Foundation’s Synthetic Biology Engineering Research Center, the Office of Naval Research’s Multidisciplinary University Research Initiative, and the National Institutes of Health.