Scientists are using engineered gene circuits in plants to control gene expression and root architecture

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Controlling gene activity is an important step in plant engineering for the improvement of bioenergy crops. This research has developed synthetic genes that can be combined to achieve specific patterns of gene expression in the plant. Synthetic gene expression is programmed in the form of Boolean (“AND”, “OR”, and “NOT”) logic gates that operate similarly to computer circuit boards. Using synthetic gene circuits, researchers have succeeded in creating new predictable expression patterns of fluorescent proteins. Finally, they used similar gene circuits to redesign root architecture by adjusting the number of root branches.

To understand biological functions and design new biotechnology applications, scientists must precisely manipulate gene expression. It is the process that converts DNA instructions into proteins and other products that allow cells to do their jobs in an organism. Controlling specific gene expression patterns in plants is a challenge. One potential solution lies in synthetic genetic circuits. However, tuning circuit activity across different plant cell types has proven difficult. This research has made it possible to develop new genetic circuits allowing precise control of root architecture. As roots are important for water and nutrient uptake, this approach will allow the design of tailored root architectures. This in turn will help researchers design bioenergy crops with improved traits for growing in marginal lands.

To establish synthetic gene circuits capable of predictably regulating gene expression in plants, scientists have adapted a large collection of bacterial gene regulators for use as synthetic activators or repressors of gene expression in plants. plants, also called transcription factors. Using a transient expression system, researchers demonstrated that synthetic transcription factors and their target DNA sequences (promoters) are able to direct specific and tunable control of gene expression. They designed synthetic promoters that responded to a synthetic transcription factor to function as simple logic gates that responded to one input, while more complex gates required synthetic promoters that responded to multiple inputs. The research revealed that these logic gates controlled expression in predictable ways according to the specific Boolean rules encoded in the modified genes.

To set up synthetic gene circuits in a multicellular context, the researchers used Arabidopsis roots as a model system where endogenous promoters drove the tissue-specific expression of synthetic transcription factors. Gene circuits generated new expression patterns that were the result of successful logical operations. The researchers further used one of the logic gates to quantitatively control the expression of a hormone signaling regulator to adjust the amount of root branching in the root system of Arabidopsis. These results demonstrate that it is now possible to program gene expression across plant cell types using genetic circuits, providing a roadmap for designing more resilient bioenergetic crops.

Funding was provided by the Department of Energy’s Scientific, Biological, and Environmental Research Program; the Burroughs Wellcome Fund Career Fellowships at the Scientific Interface; Chan Zuckerberg’s Biohub; the Howard Hughes Medical Institute; and the Simons Foundation.

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Material provided by DOE/US Department of Energy. Note: Content may be edited for style and length.

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