Plant synthetic biology: from inspiration to augmentation

A molecular representation system with a common reference frame for analyzing triterpenoid structural diversity

Researchers have uncovered hundreds of thousands of natural products, many of which contribute to medicine, materials, and agriculture. However, missing knowledge about the biosynthetic pathways of these products hinders their expanded use. Nucleotide sequencing is key to pathway elucidation efforts, and analyses of the molecular structures of natural products, although seldom discussed explicitly, also play an important role by suggesting hypothetical pathways for testing. Structural analyses are also important in drug discovery, for which many molecular representation systems-methods of representing molecular structures in a computer-friendly format-have been developed. Unfortunately, pathway elucidation investigations seldom use these representation systems. This gap likely occurs because those systems are primarily built to document molecular connectivity and topology rather than the absolute positions of bonds and atoms in a common reference frame, which would enable chemical structures to be connected with potential underlying biosynthetic steps. Here, we expand on recently developed skeleton-based molecular representation systems by implementing a common-reference-frame-oriented system. We tested this system using triterpenoid structures as a case study and explored its applications in biosynthesis and structural diversity tasks. The common-reference-frame system can identify structural regions of high or low variability on the scale of atoms and bonds and enable hierarchical clustering that is closely connected to underlying biosynthesis. Combined with information on phylogenetic distribution, the system illuminates distinct sources of structural variability, such as different enzyme families operating in the same pathway. These characteristics outline the potential of common-reference-frame molecular representation systems to support large-scale pathway elucidation efforts.

Maize2035: A decadal vision for intelligent maize breeding

Maize, a cornerstone of global food security, has undergone remarkable transformations through breeding, yet further increase in global maize production faces mounting challenges in a changing world. In this Perspective paper, we overview the historical successes of maize breeding that laid the foundation for present opportunities. We examine both the specific and shared breeding goals related to diverse geographies and end-use demands. Achieving these coordinated breeding objectives requires a holistic approach to trait improvement for sustainable agriculture. We discuss cutting-edge solutions, including multi-omics approaches from single-cell analysis to holobionts, smart breeding with advanced technologies and algorithms, and the transformative potential of rational design with synthetic biology approaches. A transition toward a data-driven future is currently underway, with large-scale precision agriculture and autonomous systems poised to revolutionize farming practice. Realizing these futuristic opportunities hinges on collaborative efforts spanning scientific discoveries, technology translations, and socioeconomic considerations in maximizing human and environmental well-being.

Prospects for synthetic biology in 21st Century agriculture

Plant synthetic biology has emerged as a transformative field in agriculture, offering innovative solutions to enhance food security, provide resilience to climate change, and transition to sustainable farming practices. By integrating advanced genetic tools, computational modeling, and systems biology, researchers can precisely modify plant genomes to enhance traits such as yield, stress tolerance, and nutrient use efficiency. The ability to design plants with specific characteristics tailored to diverse environmental conditions and agricultural needs holds great potential to address global food security challenges. Here, we highlight recent advancements and applications of plant synthetic biology in agriculture, focusing on key areas such as photosynthetic efficiency, nitrogen fixation, drought tolerance, pathogen resistance, nutrient use efficiency, biofortification, climate resilience, microbiology engineering, synthetic plant genomes, and the integration of artificial intelligence (AI) with synthetic biology. These innovations aim to maximize resource use efficiency, reduce reliance on external inputs, and mitigate environmental impacts associated with conventional agricultural practices. Despite challenges related to regulatory approval and public acceptance, the integration of synthetic biology in agriculture holds immense promise for creating more resilient and sustainable agricultural systems, contributing to global food security and environmental sustainability. Rigorous multi-field testing of these approaches will undoubtedly be required to ensure reproducibility.

Designed to breathe: synthetic biology applications in plant hypoxia

Over the past years, plant hypoxia research has produced a considerable number of new resources to monitor low oxygen responses in model species, mainly Arabidopsis thaliana. Climate change urges the development of effective genetic strategies aimed at improving plant resilience during flooding events. This need pushes forward the search for optimized tools that can reveal the actual oxygen available to plant cells, in different organs or under various conditions, and elucidate the mechanisms underlying plant hypoxic responses, complementing the existing transcriptomics, proteomics, and metabolic analysis methods. Oxygen-responsive reporters, dyes, and nanoprobes are under continuous development, as well as novel synthetic strategies that make precision control of plant hypoxic responses realistic. In this review, we summarize the recent progress made in the definition of tools for oxygen response monitoring in plants, either adapted from bacterial and animal research or peculiar to plants. Moreover, we highlight how adoption of a synthetic biology perspective has enabled the design of novel genetic circuits for the control of oxygen-dependent responses in plants. Finally, we discuss the current limitations and challenges toward the implementation of synbio solutions in the plant low-oxygen biology field.

Multiplex Expression Cassette Assembly: A flexible and versatile method for building complex genetic circuits in conventional vectors

The manipulation of multiple transcription units for simultaneous and coordinated expression is not only key to building complex genetic circuits to accomplish diverse functions in synthetic biology, but is also important in crop breeding for significantly improved productivity and overall performance. However, building constructs with multiple independent transcription units for fine-tuned and coordinated regulation is complicated and time-consuming. Here, we introduce the Multiplex Expression Cassette Assembly (MECA) method, which modifies canonical vectors compatible with Golden Gate Assembly, and then uses them to produce multi-cassette constructs. By embedding the junction syntax in primers that are used to amplify functional elements, MECA is able to make complex constructs using only one intermediate vector and one destination vector via two rounds of one-pot Golden Gate assembly reactions, without the need for dedicated vectors and a coherent library of standardized modules. As a proof-of-concept, we modified eukaryotic and prokaryotic expression vectors to generate constructs for transient expression of green fluorescent protein and β-glucuronidase in Nicotiana benthamiana, genome editing to block monoterpene metabolism in tomato glandular trichomes, production of betanin in tobacco and synthesis of β-carotene in Escherichia coli. Additionally, we engineered the stable production of thymol and carvacrol, bioactive compounds from Lamiaceae family plants, in glandular trichomes of tobacco. These results demonstrate that MECA is a flexible, efficient and versatile method for building complex genetic circuits, which will not only play a critical role in plant synthetic biology, but also facilitate improving agronomic traits and pyramiding traits for the development of next-generation elite crops.

Engineering Plant Metabolism for Synthesizing Amino Acid Derivatives of Animal Origin Using a Synthetic Modular Approach

The biosynthesis of amino acid derivatives of animal origin in plants represents a promising frontier in synthetic biology, offering a sustainable and eco-friendly approach to enhancing the nutritional value of plant-based diets. This study leverages the versatile capabilities of Nicotiana benthamiana as a transient expression system to test a synthetic modular framework for the production of creatine, carnosine, and taurine-compounds typically absent in plants but essential for human health. By designing and stacking specialized synthetic modules, we successfully redirected the plant metabolic flux toward the synthesis of these amino acid derivatives of animal origin. Our results revealed the expression of a standalone creatine module resulted in the production of 2.3 μg/g fresh weight of creatine in N. benthamiana leaves. Integrating two modules significantly carnosine yield increased by 3.8-fold and minimized the impact on plant amino acid metabolism compared to individual module application. Unexpectedly, introducing the taurine module caused a feedback-like inhibition of plant cysteine biosynthesis, revealing complex metabolic adjustments that can occur when introducing foreign pathways. Our findings underline the potential for employing plants as biofactories for the sustainable production of essential nutrients of animal origin.

Enzymatic Characterization of SpPAL Genes in S. polyrhiza and Overexpression of the SpPAL3

Phenylalanine ammonia-lyase (PAL, EC 4.3.1.5) catalyzes the deamination of phenylalanine, which is the initial step in the biosynthesis of phenylpropanoids. It serves as a crucial enzyme that facilitates the transfer of carbon from primary to secondary metabolism in plants. Duckweed is regarded as a promising chassis plant in synthetic biology research and application, due to its being rich in secondary metabolites and other advantages. The genes encoding PAL in Spirodela polyrhiza (L.) Schleid, the giant duckweed, were investigated in this study. Three SpPAL genes (SpPAL1-SpPAL3) were identified and cloned. All of them were successfully expressed in E. coli, and their recombinant proteins all showed PAL activity. In addition, SpPAL1 and SpPAL2 proteins could also utilize tyrosine as substrate, although the activity was low. A qRT-PCR analysis demonstrated that the expression of SpPAL3 was most pronounced in young fronds. It was found that the expression of SpPAL1 and SpPAL3 was significantly induced by MeJA treatment. Overexpression of SpPAL3 in Lemna turionifera inhibited the growth of fronds and adventitious roots in the transgenic plants, indicating the importance of SpPAL3 in duckweed besides its involvement in the secondary metabolism.

Improvement and application of vacuum-infiltration system in tomato

The Agrobacterium-mediated transient expression system has been developed and applied to various plants as an alternative to stable transformation. However, its application in tomatoes is still limited due to low expression efficiency. In this study, we describe an improved vacuum-infiltration system that can be used in both tomato fruits and leaves. Notably, this study is the first report of vacuum infiltration in attached tomato fruits. The feasibility of the improved vacuum-infiltration system in Micro-Tom tomato was confirmed by various assays, including multiple fluorescent protein expression analysis, β-glucuronidase activity analysis, and RUBY reporter visualization. Subsequently, the improved vacuum-infiltration system was successfully applied to tomato biotechnology research. Herein, a trichome-specific promoter in tomato was identified that can drive the directional synthesis of specific plant natural products (PNPs). Additionally, based on the assessment results of the improved vacuum-infiltration system, we obtained a flavonoid-rich tomato variety through the stable transformation of AmRosea and AmDelila. In a significant practical application, we successfully synthesized the high-value scutellarin in tomato, which provides an alternative route for the production of PNPs from plants. In addition, the improved vacuum-infiltration system has been demonstrated to be suitable for commercial tomato varieties ('Emerald' and 'Provence') as well. The improved vacuum-infiltration system not only speeds up fundamental and applied research in tomato but also offers an additional powerful tool for advancing tomato synthetic biology research.

Plant synthetic biology for human health: advances in producing medicines in heterologous expression systems

Plant synthetic biology has the capability to provide solutions to global challenges in the production and supply of medicines. Recent advances in 'omics' technologies have accelerated gene discoveries in medicinal plant research so that even multistep biosynthetic pathways for bioactive plant natural products with high structural complexity can be reconstituted in heterologous plant expression systems more rapidly. This review provides an overview of concept and strategies used to produce high-value plant natural products in heterologous plant systems and highlights recent successes in engineering the biosynthesis of conventional and new medicines in alternative plant hosts.

Strategies, Achievements, and Potential Challenges of Plant and Microbial Chassis in the Biosynthesis of Plant Secondary Metabolites

Diverse secondary metabolites in plants, with their rich biological activities, have long been important sources for human medicine, food additives, pesticides, etc. However, the large-scale cultivation of host plants consumes land resources and is susceptible to pest and disease problems. Additionally, the multi-step and demanding nature of chemical synthesis adds to production costs, limiting their widespread application. In vitro cultivation and the metabolic engineering of plants have significantly enhanced the synthesis of secondary metabolites with successful industrial production cases. As synthetic biology advances, more research is focusing on heterologous synthesis using microorganisms. This review provides a comprehensive comparison between these two chassis, evaluating their performance in the synthesis of various types of secondary metabolites from the perspectives of yield and strategies. It also discusses the challenges they face and offers insights into future efforts and directions.

Sugarcane breeding: a fantastic past and promising future driven by technology and methods

Sugarcane is the most important sugar and energy crop in the world. During sugarcane breeding, technology is the requirement and methods are the means. As we know, seed is the cornerstone of the development of the sugarcane industry. Over the past century, with the advancement of technology and the expansion of methods, sugarcane breeding has continued to improve, and sugarcane production has realized a leaping growth, providing a large amount of essential sugar and clean energy for the long-term mankind development, especially in the face of the future threats of world population explosion, reduction of available arable land, and various biotic and abiotic stresses. Moreover, due to narrow genetic foundation, serious varietal degradation, lack of breakthrough varieties, as well as long breeding cycle and low probability of gene polymerization, it is particularly important to realize the leapfrog development of sugarcane breeding by seizing the opportunity for the emerging Breeding 4.0, and making full use of modern biotechnology including but not limited to whole genome selection, transgene, gene editing, and synthetic biology, combined with information technology such as remote sensing and deep learning. In view of this, we focus on sugarcane breeding from the perspective of technology and methods, reviewing the main history, pointing out the current status and challenges, and providing a reasonable outlook on the prospects of smart breeding.

Running the numbers on plant synthetic biology solutions to global problems

Synthetic biology and metabolic engineering promise to deliver sustainable solutions to global problems such as phasing out fossil fuels and replacing industrial nitrogen fixation. While this promise is real, scale matters, and so do knock-on effects of implementing solutions. Both scale and knock-on effects can be estimated by 'Fermi calculations' (aka 'back-of-envelope calculations') that use uncontroversial input data plus simple arithmetic to reach rough but reliable conclusions. Here, we illustrate how this is done and how informative it can be using two cases: oilcane (sugarcane engineered to accumulate triglycerides instead of sugar) as a source of bio-jet fuel, and nitrogen fixation by bacteria in mucilage secreted by maize aerial roots. We estimate that oilcane could meet no more than about 1% of today's U.S. jet fuel demand if grown on all current U.S. sugarcane land and that, if cane land were expanded to meet two-thirds of this demand, the fertilizer and refinery requirements would create a large carbon footprint. Conversely, we estimate that nitrogen fixation in aerial-root mucilage could replace up to 10% of the fertilizer nitrogen applied to U.S. maize, that 2% of plant carbon income used for growth would suffice to fuel the fixation, and that this extra carbon consumption would likely reduce grain yield only slightly.

Advances in plant synthetic biology approaches to control expression of gene circuits

The applications of synthetic biology range from creating simple circuits to monitor an organism's state to complex circuits capable of reconstructing aspects of life. The latter has the potential to be used in plant synthetic biology to address current societal issues by reforming agriculture and enhancing production of molecules of increased demand. For this reason, development of efficient tools to precisely control gene expression of circuits must be prioritized. In this review, we report the latest efforts towards characterization, standardization and assembly of genetic parts into higher-order constructs, as well as available types of inducible systems to modulate their transcription in plant systems. Subsequently, we discuss recent developments in the orthogonal control of gene expression, Boolean logic gates and synthetic genetic toggle-like switches. Finally, we conclude that by combining different means of controlling gene expression, we can create complex circuits capable of reshaping plant life.