Choreographing root architecture and rhizosphere interactions through synthetic biology

Abstract

Climate change is driving extreme changes to the environment, posing substantial threats to global food security and bioenergy. Given the direct role of plant roots in mediating plant-environment interactions, engineering the form and function of root systems and their associated microbiota may mitigate these effects. Synthetic genetic circuits have enabled sophisticated control of gene expression in microbial systems for years and a surge of advances has heralded the extension of this approach to multicellular plant species. Targeting these tools to affect root structure, exudation, and microbe activity on root surfaces provide multiple strategies for the advancement of climate-ready crops.

Fig. 1. Two-input logic gates controlling tissue-specific gene expression in roots.

Native promoters such as the a SMB promoter (columella and lateral root cap) and b PIN4 promoter (columella and stele) can be used to drive tissue-specific expression of genes. By combining these promoters with synthetic activators and repressors, Brophy et al. generated circuits that can perform Boolean logic operations, creating novel patterns of gene expression not found in nature. c In the NOR gate, GFP is expressed only in tissues where both the PIN4 and SMB promoter are not active. d In the NIMPLY gate, GFP is expressed only where SMB is active, but PIN4 is not.

Fig. 2. Controlling expression through buffer gates and recombinase-based circuits.

Successful engineering of plant form will require fine control over gene expression, both in terms of magnitude and spatial patterning. a Circuits implementing buffer gates to tune expression of slr-1 (inhibits lateral root formation), allowed Brophy et al. to control the number of lateral roots formed. b Guiziou et al. utilized a serine integrase to create a circuit that permanently switches its output when the integrase is expressed, creating a form of cellular memory that records past gene activity.

Fig. 3. Tuning the rhizosphere through root and microbial engineering.

Future climate conditions will exacerbate abiotic (salt, drought, etc.) and biotic (pathogens and pests) stressors that negatively impact crop yield. Through synthetic biology, root form, function, and microbial interactions can be altered to create new crops better equipped to grow in these more challenging conditions. a Custom root system architectures can be created by changing branch rate and gravity setpoint angle, resulting in root systems more suited for water and nutrient acquisition. Modulating suberin deposition can limit the uptake of toxic sodium and metal ions, while insulating roots against nutrient loss. Each panel represents a trait to target for engineering. Left of the dashed line are roots resulting from decreasing the target trait. Right of the dashed line represents an increasing target trait. b Primary and lateral root apices are the main interfaces at which plants modify the local soil environment, and by extension the composition of their microbiome, through the process of rhizodeposition. Control over root cap shedding dynamics and mucilage release can potentially improve root penetration into soil and drought resistance. These features, as well as the release of certain sugars and other metabolites, are also attractive engineering targets for controlling the composition of the root microbiome. Each panel represents a trait to target for engineering. Left of the dashed line is the wild type condition. Right of the dashed line depicts an engineered root. c The plant root microbiome expands the genetic repertoire available to the plant, providing a plethora of beneficial functions to their host. The metabolic flexibility of bacteria allows for the potential engineering of a myriad of actuators to improve plant biotic and abiotic stress tolerance, nutrient acquisition, and carbon sequestration.