Engineering bacterial photographs: now in color!

“Color on the screen is not only more natural than black-and-white, it is more stimulating, more exciting, more dramatic.” said Broadway and color designer Robert Edmond Jones. The same may be said of the leap forward in our ability to engineer bacteria to see and display color. Researchers at MIT gave the bacterium E. coli that ability to take ‘color photographs’.  Color images using reg-green-blue (RGB) sensors and RGB pigments builds on an idea first published in 2005 that used bacteria to make black and white images by sensing red light only.

This idea goes all the way back to a project at the first International Genetically Engineered Machine  (iGEM) contest. Then methods for engineering bacteria were still quite primitive and the widely circulated image actually had more color change to the plate the bacteria grew on rather than the bacteria themselves. Now the parts available to engineer E. coli have matured enough to build more complex circuits.

Engineering advancements for RGB images

The early black and white version images used a red light sensor to control the production of the LacZ enzyme which catalyzes a black precipitate from the chemical S-gal (3,4-cyclohexenoesculetin-beta-D-galactopyranoside). To extend that idea to RGB images required several new synthetic biology parts and more advanced circuity. The first part needed to take a color image is color sensing. The researchers optimized three sensors that turn promoters on or off in response to different wavelengths–or colors–of light: a chimeric histidine kinase (Cph8*) turns a promoter on in infrared (705 nm) light and off in red (650 nm) light, Synechocystis CcaSR turns a promoter on in green (535 nm) light and off in far-red (672 nm) light, and a chimeric histidine kinase (YF1) turns a promoter off off in 470 nm light.

To drive color expression using the two sensors that turn off expression in response to RGB light, they had to use inverters that turn an ‘off’ into an ‘on’. The inverter was a repressor that is controlled by the sensor and controls the output color. That way the light turns off the repressor which means the output is on. Also in between the sensing step and the output step is a resource allocator that had been previously published by the Voigt lab using split T7 RNA polymerase. This step is modular in that it can be connected to the color outputs or produce another gene or RNA.

Applications of the RGB the system

The real accomplishment is not the beautiful color images the team created, but the ability to tune a systems with 18 genes, 14 promoters, and 18 terminators spread across 4 plasmids all in the same bacterial cells. Creating color images in plates of bacteria is probably not industrially relevant–except maybe for a synbio novelty item–but an engineered strain that can rapidly respond to three different light signals can be very useful. It gives three controls that can target different functions, but it also has a few advantages that chemical inducers do not have–precise timing and spatial control.

Using the modularity of the resource allocator promoters, they had the system produce different guide RNAs that control CRISPR-Cas9 repression. By combining the RGB system with CRISPRi–the method of CRISPR interference that uses a catalytically dead Cas9 to repress targeted genes–they were able to control the production of acetate by shining different colors of light.

This type of control could be useful in complex metabolic engineering in which you might want to control several genes over time to optimize production of your product. Another interesting application would be producing biomaterials with temporal and spatial resolution. Temporal resolution might improve the efficiency of material production. Spatial resolution could do some things that would be difficult with chemical inducers. For instance, you could 3D print biomaterials produced by bacteria similar to how a Formlabs 3D printer polymerizes using stereolithography. Light gives much finer temporal and spatial resolution than physically adding or taking away a chemical. Like the addition of color to the movie screen, there are more exciting opportunities when engineered cells can see color.

References and further reading:

Engineering RGB color vision into Escherichia coli – recent research article on color bacterial photographs ($)

Synthetic biology: Engineering Escherichia coli to see light – 2005 research paper on black-and-white bacterial photographs ($)

Bacteria engineered to produce living, full-colour photographs – New Scientist

Bacteria with multicolor vision – MIT News