Understanding and engineering plant form

Choreographing root architecture and rhizosphere interactions through synthetic biology

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.

Synthetic Biology Approaches to Posttranslational Regulation in Plants

To date synthetic biology approaches involving creation of functional genetic modules are used in a wide range of organisms. In plants, such approaches are used both for research in the field of functional genomics and to increase the yield of agricultural crops. Of particular interest are methods that allow controlling genetic apparatus of the plants at post-translational level, which allow reducing non-targeted effects from interference with the plant genome. This review discusses recent advances in the plant synthetic biology for regulation of the plant metabolism at posttranslational level and highlights their future directions.

Genetic Circuit Design in Rhizobacteria

Genetically engineered plants hold enormous promise for tackling global food security and agricultural sustainability challenges. However, construction of plant-based genetic circuitry is constrained by a lack of well-characterized genetic parts and circuit design rules. In contrast, advances in bacterial synthetic biology have yielded a wealth of sensors, actuators, and other tools that can be used to build bacterial circuitry. As root-colonizing bacteria (rhizobacteria) exert substantial influence over plant health and growth, genetic circuit design in these microorganisms can be used to indirectly engineer plants and accelerate the design-build-test-learn cycle. Here, we outline genetic parts and best practices for designing rhizobacterial circuits, with an emphasis on sensors, actuators, and chassis species that can be used to monitor/control rhizosphere and plant processes.

Biological Parts for Plant Biodesign to Enhance Land-Based Carbon Dioxide Removal

A grand challenge facing society is climate change caused mainly by rising CO2 concentration in Earth's atmosphere. Terrestrial plants are linchpins in global carbon cycling, with a unique capability of capturing CO2 via photosynthesis and translocating captured carbon to stems, roots, and soils for long-term storage. However, many researchers postulate that existing land plants cannot meet the ambitious requirement for CO2 removal to mitigate climate change in the future due to low photosynthetic efficiency, limited carbon allocation for long-term storage, and low suitability for the bioeconomy. To address these limitations, there is an urgent need for genetic improvement of existing plants or construction of novel plant systems through biosystems design (or biodesign). Here, we summarize validated biological parts (e.g., protein-encoding genes and noncoding RNAs) for biological engineering of carbon dioxide removal (CDR) traits in terrestrial plants to accelerate land-based decarbonization in bioenergy plantations and agricultural settings and promote a vibrant bioeconomy. Specifically, we first summarize the framework of plant-based CDR (e.g., CO2 capture, translocation, storage, and conversion to value-added products). Then, we highlight some representative biological parts, with experimental evidence, in this framework. Finally, we discuss challenges and strategies for the identification and curation of biological parts for CDR engineering in plants.

Exploring the interdependence between self-organization and functional morphology in cellular systems

All living matter is subject to continuous adaptation and functional optimization via natural selection. Consequentially, structures with close morphological resemblance repeatedly appear across the phylogenetic tree. How these designs emerge at the cellular level is not fully understood. Here, we explore core concepts of functional morphology and discuss its cause and consequences, with a specific focus on emerging properties of self-organizing systems as the potential driving force. We conclude with open questions and limitations that are present when studying shape-function interdependence in single cells and cellular ensembles.

Developmental Responses to Water and Salinity in Root Systems

Roots provide the primary mechanism that plants use to absorb water and nutrients from their environment. These functions are dependent on developmental mechanisms that direct root growth and branching into regions of soil where these resources are relatively abundant. Water is the most limiting factor for plant growth, and its availability is determined by the weather, soil structure, and salinity. In this review, we define the developmental pathways that regulate the direction of growth and branching pattern of the root system, which together determine the expanse of soil from which a plant can access water. The ability of plants to regulate development in response to the spatial distribution of water is a focus of many recent studies and provides a model for understanding how biological systems utilize positional cues to affect signaling and morphogenesis. A better understanding of these processes will inform approaches to improve crop water use efficiency to more sustainably feed a growing population.

Control of Meristem Size

A fascinating feature of plant growth and development is that plants initiate organs continually throughout their lifespan. The ability to do this relies on specialized groups of pluripotent stem cells termed meristems, which allow for the elaboration of the shoot, root, and vascular systems. We now have a deep understanding of the genetic networks that control meristem initiation and stem cell maintenance, including the roles of receptors and their ligands, transcription factors, and integrated hormonal and chromatin control. This review describes these networks and discusses how this knowledge is being applied to improve crop productivity by increasing fruit size and seed number.

Target genes for plant productivity improvement

The use of chemical fertilizers and pesticides, as well as the development of high-yielding varieties enabled substantial increase in crop productivity during the 20th century. However, the increase in yield over the last two decades has been slower. It is thought that further improvement in productivity of the major crop species using traditional cultivation methods is limited. Therefore, the use of genetic engineering seems to be a promising approach. There is ongoing research concerning genes that have an impact on plant growth, development and yield. The proteins and miRNAs encoded by these genes participate in a variety of processes, such as growth regulation, assimilate transport and partitioning as well as macronutrient uptake and metabolism. This paper presents the major directions in research concerning genes that may be targets of genetic engineering aimed to improve plant productivity.

Synthetic hormone-responsive transcription factors can monitor and re-program plant development

Developmental programs sculpt plant morphology to meet environmental challenges, and these same programs have been manipulated to increase agricultural productivity (Doebley et al., 1997; Khush, 2001). Hormones coordinate these programs, creating chemical circuitry (Vanstraelen and Benková, 2012) that has been represented in mathematical models (Refahi et al., 2016; Prusinkiewicz et al., 2009); however, model-guided engineering of plant morphology has been limited by a lack of tools (Parry et al., 2009; Voytas and Gao, 2014). Here, we introduce a novel set of synthetic and modular hormone activated Cas9-based repressors (HACRs) in Arabidopsis thaliana that respond to three hormones: auxin, gibberellins and jasmonates. We demonstrate that HACRs are sensitive to both exogenous hormone treatments and local differences in endogenous hormone levels associated with development. We further show that this capability can be leveraged to reprogram development in an agriculturally relevant manner by changing how the hormonal circuitry regulates target genes. By deploying a HACR to re-parameterize the auxin-induced expression of the auxin transporter PIN-FORMED1 (PIN1), we decreased shoot branching and phyllotactic noise, as predicted by existing models (Refahi et al., 2016; Prusinkiewicz et al., 2009).

The genetic information of plants contains sets of instructions that shape a growing seedling. These ‘developmental programs’ are under the control of a range of hormones, such as auxin. Typically, the information from the hormones is relayed to the genetic material through proteins called transcription factors, which can act on DNA to turn specific genes on or off. Scientists have a good understanding of the roles of hormones, and they have created mathematical models that predict how changes in hormone levels affect the shape of a plant. However, it is still difficult to manipulate hormones inside a plant and test these models.

Here, Khakhar et al. created artificial transcription factors, referred to as HACRs, and put them into a plant called Arabidopsis thaliana. An HACR is made of different molecular modules stitched together. Each module has a precise role; for example, one turns off a specific gene, while another targets the HACR for destruction if a given hormone is present.

First, Khakhar et al. showed that HACRs could help track the levels of auxin in a developing plant. Arabidopsis plants were genetically engineered so that they would always produce a fluorescent protein. Then, an HACR was created that would switch off the gene for that fluorescent protein, so that no fluorescence would be present in the cell. If auxin was present, the HACR would get degraded, meaning fluorescence would appear. This helped to finely assess the amount of the hormone in various parts of the plant. By changing the modules in the HACRs, this approach could be applied to at least three other types of hormones.

Second, HACRs were used to reprogram Arabidopsis and change its appearance. For example, it is well known that auxin controls the number and location of branches on a plant. This complex process depends on how strongly auxin promotes the expression of a gene called PIN1. Khakhar et al. engineered an HACR that represses PIN1, and created a mathematical model that described the impact of this intervention. As predicted by the simulation, the HACR changed the strength of the relationship between PIN1 and auxin, which resulted in plants with fewer branches – a trait that is of interest in farming.

HACRs are a new type of technology that is likely to work in a wide range of species. Ultimately, these artificial transcription factors could help to engineer plants that can face the disruptions brought by climate change, which would ensure better food security for people around the world.

Q&A: How do gene regulatory networks control environmental responses in plants?

A gene regulatory network (GRN) describes the hierarchical relationship between transcription factors, associated proteins, and their target genes. Studying GRNs allows us to understand how a plant's genotype and environment are integrated to regulate downstream physiological responses. Current efforts in plants have focused on defining the GRNs that regulate functions such as development and stress response and have been performed primarily in genetically tractable model plant species such as Arabidopsis thaliana. Future studies will likely focus on how GRNs function in non-model plants and change over evolutionary time to allow for adaptation to extreme environments. This broader understanding will inform efforts to engineer GRNs to create tailored crop traits.