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All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Plant synthetic biology innovations for biofuels and bioproducts

Plant-based biosynthesis of fuels, chemicals, and materials promotes environmental sustainability, which includes decreases in greenhouse gas emissions, water pollution, and loss of biodiversity. Advances in plant synthetic biology (synbio) should improve precision and efficacy of genetic engineering for sustainability. Applicable synbio innovations include genome editing, gene circuit design, synthetic promoter development, gene stacking technologies, and the design of environmental sensors. Moreover, recent advancements in developing spatially resolved and single-cell omics contribute to the discovery and characterization of cell-type-specific mechanisms and spatiotemporal gene regulations in distinct plant tissues for the expression of cell- and tissue-specific genes, resulting in improved bioproduction. In conclusion, this review highlights recent plant synbio progress and new single-cell molecular profiling towards sustainable biofuel and biomaterial production.

Yang, Yongil↗
DOE OSTI2023

Editorial: Rising stars in plant ROS/redox biology under abiotic stress conditions

Plants are constantly subjected to a wide range of abiotic stresses including salinity, high temperatures, drought, or cold, among others, that negatively impact their growth and development and cause crop yield losses worldwide (Lesk et al., 2016; Bailey-Serres et al., 2019). These stress conditions induce the accumulation of reactive oxygen species (ROS) such as hydrogen peroxide (H 2 O 2 ), superoxide ($O_{2•}$$^—$), singlet oxygen ($^1O_2$), or hydroxyl radical (HO·). ROS play a key role in stress sensing and signaling, as well as in the activation of different mechanism involved in plant acclimation to different stresses (Mittler et al., 2022). However, ROS levels that are too high are cytotoxic (Mittler, 2017). To prevent cellular oxidation by ROS, an interplay between ROS production, scavenging and transport maintains ROS at controlled concentrations, as well as drives ROS signaling responses involved in plant acclimation to stress (Baxter et al., 2014; Mittler et al., 2022).

protein carbonylation↗
DOE OSTI2021

Plant Synthetic Biology Conference – Travel Awardees and Speakers

The overarching goals of the Plant Synthetic Biology (SynBio) Conference, convened by the American Society of Plant Biologists (ASPB), were to raise community consciousness of what SynBio is and what it can do in key areas, including crop productivity, specialty chemicals, biosensors, and microbe-plant interactions. Within that context, the conference had two broad objectives. First, to feature a set of leading university and industry speakers from the US and Europe whose research on plants and microbes spans the SynBio spectrum with respect both to technology and to applications, as well as short talks (selected from submitted abstracts) on cutting-edge topics. And second, to foster exchanges among public sector scientists and industry scientists, whose participation as poster presenters, exhibitors, and sponsors was actively encouraged because so much innovative SynBio work is being carried out at dynamic young companies.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Plant Cell Biology International Meeting 2022

There is a strong need to develop the knowledge base that will enable the rational design of improved crop species for sustainable agriculture and biomass production. To attain this goal, researchers must learn how plant cells integrate metabolism and cellular dynamics during growth and in response to environmental challenges. Meeting these goals require data sharing and the development and training of faculty, post-doctoral fellows, graduate and undergraduate students in state-of-the-art quantitative integrative cell biology methods. The inaugural Plant Cell Biology International (PCBI) meeting capitalized on the interaction between two well-established plant cell biology communities across the Atlantic, the Midwest Plant Cell Dynamics (PCD) and the European Network for Plant Endomembrane Research (ENPER) and provided a framework to meet these goals. The conference took place in person successfully during August 1-5th 2022 in Crete, Greece. The conference offered opportunities for undergraduate and graduate students, postdocs, young investigators across the globe to present their results and interact across different disciplines. The conference provided an open and inclusive forum for oral presentations that allowed all labs to share research results. It was attended over 80 % by students, postdocs and young investigators. Workshops on best practices for image acquisition and processing pipelines, publication guidelines by scientific journal editors, professional development and well-being benefited the participants at large. Overall, this was the inaugural joint Plant Cell Biology International conference that for the first time officially brought together plant cell biologists to discuss opportunities and challenges in the field to gain a mechanistic understanding of complex biological processes and advance sustainable agriculture. Due to its success, it was rescheduled for 2025 in Crete, to continue strengthening the plant cell biology community and exchanging knowledge and expertise across the globe.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Desorption Electrospray Ionization–Mass Spectrometry Imaging Provides Spatiochemical Information on Potential Biocontrol Agents against Phytophthora capsici Infection in Tomato Plants

Biological control agents can offer an eco-friendly and more sustainable alternative to conventional chemical pesticides, providing protection against destructive pathogens, such as Phytophthora capsici, while reducing potential environmental harm associated with synthetic pesticide use in agricultural systems. This work evaluates the biocontrol effectiveness of Bacillus vallismortis, Bacillus amyloliquefaciens, Bacillus thuringiensis, and Bacillus subtilis, against the widespread plant pathogen Phytophthora capsici. Our studies showed that Bacillus thuringiensis and Bacillus subtilis promote plant growth and provide protection against Phytophthora capsici in both in vitro and in vivo greenhouse studies, while Bacillus vallismortis and Bacillus amyloliquefaciens were effective in vitro but not in vivo. Specifically, Bacillus thuringiensis was observed to both hinder the growth of Phytophthora capsici and enhance plant resilience to this pathogen, with B. thuringiensis-treated, pathogen-exposed plants displaying a 94.4% increase in root length and a 74.0% increase in shoot height compared to plants with only oomycete exposure. To probe the molecular interactions between the biocontrol agent and pathogen, a dual culture of Bacillus thuringiensis and Phytophthora capsici was analyzed in situ using a desorption electrospray ionization–mass spectrometry imaging (DESI-MSI) workflow. This approach interrogated the spatially oriented biochemical interactions that may serve as the molecular foundation for the effectiveness of these biological control agents in crop protection, identifying seven unique phenotypic regions within the dual culture. Herein, we demonstrate the benefits of biological control agent application in tomato cultivation and showcase the strengths of desorption electrospray ionization–mass spectrometry imaging when applied to the spatially resolved molecular characterization of agriculturally relevant microorganisms.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

A pilot oral history of plant synthetic biology

The whole field of synthetic biology (SynBio) is only about 20 years old, and plant SynBio is younger still. Nevertheless, within that short time, SynBio in general has drawn more scientific, philosophical, government, and private-sector interest than anything in biology since the recombinant DNA revolution. Plant SynBio, in particular, is now drawing more and more interest in relation to plants’ potential to help solve planetary problems such as carbon capture and storage and replacing fossil fuels and feedstocks. As plant SynBio is so young and so fast-developing, we felt it was too soon to try to analyze its history. Instead, we set out to capture the essence of plant SynBio's origins and early development through interviews with 8 of the field's founders, representing 5 countries and 3 continents. We then distilled these founders’ personal recollections and reflections into this review, centering the narrative on timelines for pivotal events, articles, funding programs, and quoting from interviews. We have archived the interview recordings and documented timeline entries. This work provides a resource for future historical scholarship.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Dynamic genome evolution in a model fern

The large size and complexity of most fern genomes have hampered efforts to elucidate fundamental aspects of fern biology and land plant evolution through genome-enabled research. Here we present a chromosomal genome assembly and associated methylome, transcriptome and metabolome analyses for the model fern species Ceratopteris richardii. The assembly reveals a history of remarkably dynamic genome evolution including rapid changes in genome content and structure following the most recent whole-genome duplication approximately 60 million years ago. These changes include massive gene loss, rampant tandem duplications and multiple horizontal gene transfers from bacteria, contributing to the diversification of defence-related gene families. The insertion of transposable elements into introns has led to the large size of the Ceratopteris genome and to exceptionally long genes relative to other plants. Gene family analyses indicate that genes directing seed development were co-opted from those controlling the development of fern sporangia, providing insights into seed plant evolution. Our findings and annotated genome assembly extend the utility of Ceratopteris as a model for investigating and teaching plant biology.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Return of the Lemnaceae: duckweed as a model plant system in the genomics and postgenomics era

Abstract The aquatic Lemnaceae family, commonly called duckweed, comprises some of the smallest and fastest growing angiosperms known on Earth. Their tiny size, rapid growth by clonal propagation, and facile uptake of labeled compounds from the media were attractive features that made them a well-known model for plant biology from 1950 to 1990. Interest in duckweed has steadily regained momentum over the past decade, driven in part by the growing need to identify alternative plants from traditional agricultural crops that can help tackle urgent societal challenges, such as climate change and rapid population expansion. Propelled by rapid advances in genomic technologies, recent studies with duckweed again highlight the potential of these small plants to enable discoveries in diverse fields from ecology to chronobiology. Building on established community resources, duckweed is reemerging as a platform to study plant processes at the systems level and to translate knowledge gained for field deployment to address some of society’s pressing needs. This review details the anatomy, development, physiology, and molecular characteristics of the Lemnaceae to introduce them to the broader plant research community. We highlight recent research enabled by Lemnaceae to demonstrate how these plants can be used for quantitative studies of complex processes and for revealing potentially novel strategies in plant defense and genome maintenance.

Biochemistry & Molecular Biology↗
DOE OSTI2026

Synthetic Biology of Plants and Microbes for Agriculture, Environment, and Future Applications

Agriculture is under pressure to provide food for a growing population and the feedstock required to drive the bioeconomy. Methods to breed and genetically modify plants are inadequate to keep pace. When engineering crops, traits are painstakingly introduced into plants one-at-a-time, combine unpredictably, and are continuously expressed. Synthetic biology is changing these paradigms with new genome construction tools, computer aided design (CAD), and artificial intelligence (AI). “Smart plants” contain circuits that respond to environmental change, alter morphology, or respond to threats. Further, the plant and associated microbes (fungi, bacteria, archaea) are now being viewed by genetic engineers as a holistic system. Historically, plant health has been enhanced by many natural and laboratory-evolved soil microbes marketed to enhance growth, provide nutrients, or confer pest/stress resistance. Synthetic biology has expanded the number of species that can be engineered, increased the complexity of engineered functions, controlled environmental release, and assembled stable consortia. New CAD tools will manage genetic engineering projects spanning multiple plant genomes (nucleus, chloroplast, mitochondrion) and the thousands of genomes of associated bacteria/fungi. Here, this review covers advanced genetic engineering techniques to drive the next agricultural revolution, as well as push plant engineering into new realms for manufacturing, infrastructure, sensing, and remediation.

Clauer, Phillip [Massachusetts Inst. of Technology↗
DOE OSTI2024

Genome organization and botanical diversity

Abstract The rich diversity of angiosperms, both the planet's dominant flora and the cornerstone of agriculture, is integrally intertwined with a distinctive evolutionary history. Here, we explore the interplay between angiosperm genome organization and botanical diversity, empowered by genomic approaches ranging from genetic linkage mapping to analysis of gene regulation. Commonality in the genetic hardware of plants has enabled robust comparative genomics that has provided a broad picture of angiosperm evolution and implicated both general processes and specific elements in contributing to botanical diversity. We argue that the hardware of plant genomes—both in content and in dynamics—has been shaped by selection for rather substantial differences in gene regulation between plants and animals such as maize and human, organisms of comparable genome size and gene number. Their distinctive genome content and dynamics may reflect in part the indeterminate development of plants that puts strikingly different demands on gene regulation than in animals. Repeated polyploidization of plant genomes and multiplication of individual genes together with extensive rearrangement and differential retention provide rich raw material for selection of morphological and/or physiological variations conferring fitness in specific niches, whether natural or artificial. These findings exemplify the burgeoning information available to employ in increasing knowledge of plant biology and in modifying selected plants to better meet human needs.

Biochemistry & Molecular Biology↗
DOE OSTI2024

Plant synthetic biology as a tool to help eliminate hidden hunger

Agricultural systems are under increasing pressure from declining environmental conditions, a growing population, and changes in consumer preferences, resulting in widespread malnutrition-related illnesses. Improving plant nutritional content through biotechnology techniques such as synthetic biology is a promising strategy to help combat hidden hunger caused by the lack of affordable and healthy foods in human diets. Production of compounds usually found in animal-rich diets, such as vitamin D or omega-3 fatty acids, has been recently demonstrated in planta. Here, we review recent biotechnological approaches to biofortifying plants with vitamins, minerals, and other metabolites, and summarise synthetic biology advances that offer the opportunity to build on these early biofortification efforts.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Causes and consequences of experimental variation in Nicotiana benthamiana transient expression

Infiltration of Agrobacterium tumefaciens into Nicotiana benthamiana has become a foundational technique in plant biology, enabling efficient delivery of transgenes in planta with technical ease, robust signal, and relatively high throughput. Despite transient expression’s prevalence in disciplines such as synthetic biology, little work has been done to describe and address the variability inherent in this system, a concern for experiments that rely on highly quantitative readouts. In a comprehensive analysis of N. benthamiana agroinfiltration experiments, we model sources of variability that affect transient expression. Our findings emphasize the need to validate normalization methods under the specific conditions of each study, as distinct normalization schemes do not always reduce variation either within or between experiments. Using a dataset of 1915 plants collected over three years, we develop a model of variation in N. benthamiana transient expression, using power analysis to determine the number of individual plants required for a given effect size. Drawing on our longitudinal data, these findings inform practical guidelines for minimizing variability through strategic experimental design and power analysis, providing a foundation for more robust and reproducible use of N. benthamiana in quantitative plant biology and synthetic biology applications.

Tang, Sophia N. [Joint BioEnergy Institute (JBEI),↗
DOE OSTI2021

Plant Metabolic Network 15: A resource of genome-wide metabolism databases for 126 plants and algae

To understand and engineer plant metabolism, we need a comprehensive and accurate annotation of all metabolic information across plant species. As a step towards this goal, we, in this study, generated genome-scale metabolic pathway databases of 126 algal and plant genomes, ranging from model organisms to crops to medicinal plants (https://plantcyc.org). Of these, 104 have not been reported before. We systematically evaluated the quality of the databases, which revealed that our semi-automated validation pipeline dramatically improves the quality. We then compared the metabolic content across the 126 organisms using multiple correspondence analysis and found that Brassicaceae, Poaceae, and Chlorophyta appeared as metabolically distinct groups. To demonstrate the utility of this resource, we used recently published sorghum transcriptomics data to discover previously unreported trends of metabolism underlying drought tolerance. We also used single-cell transcriptomics data from the Arabidopsis root to infer cell type-specific metabolic pathways. This work shows the quality and quantity of our resource and demonstrates its wide-ranging utility in integrating metabolism with other areas of plant biology.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

How to engineer the unknown: Advancing a quantitative and predictive understanding of plant and soil biology to address climate change

Our basic understanding of carbon cycling in the biosphere remains qualitative and incomplete, precluding our ability to effectively engineer novel solutions to climate change. How can we attempt to engineer the unknown? This challenge has been faced before in plant biology, providing a roadmap to guide future efforts. We use examples from over a century of photosynthesis research to illustrate the key principles that will set future plant engineering on a solid footing, namely, an effort to identify the key control variables, quantify the effects of systematically tuning these variables, and use theory to account for these observations. The main contributions of plant synthetic biology will stem not from delivering desired genotypes but from enabling the kind of predictive understanding necessary to rationally design these genotypes in the first place. Only then will synthetic plant biology be able to live up to its promise.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

A century of studying plant secondary metabolism—From “what?” to “where, how, and why?”

Abstract Over the past century, early advances in understanding the identity of the chemicals that collectively form a living plant have led scientists to deeper investigations exploring where these molecules localize, how they are made, and why they are synthesized in the first place. Many small molecules are specific to the plant kingdom and have been termed plant secondary metabolites, despite the fact that they can play primary and essential roles in plant structure, development, and response to the environment. The past 100 yr have witnessed elucidation of the structure, function, localization, and biosynthesis of selected plant secondary metabolites. Nevertheless, many mysteries remain about the vast diversity of chemicals produced by plants and their roles in plant biology. From early work characterizing unpurified plant extracts, to modern integration of ‘omics technology to discover genes in metabolite biosynthesis and perception, research in plant (bio)chemistry has produced knowledge with substantial benefits for society, including human medicine and agricultural biotechnology. Here, we review the history of this work and offer suggestions for future areas of exploration. We also highlight some of the recently developed technologies that are leading to ongoing research advances.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Phytohormones in a universe of regulatory metabolites: lessons from jasmonate

Small-molecule phytohormones exert control over plant growth, development, and stress responses by coordinating the patterns of gene expression within and between cells. Increasing evidence indicates that currently recognized plant hormones are part of a larger group of regulatory metabolites that have acquired signaling properties during the evolution of land plants. This rich assortment of chemical signals reflects the tremendous diversity of plant secondary metabolism, which offers evolutionary solutions to the daunting challenges of sessility and other unique aspects of plant biology. A major gap in our current understanding of plant regulatory metabolites is the lack of insight into the direct targets of these compounds. Here, we illustrate the blurred distinction between classical phytohormones and other bioactive metabolites by highlighting the major scientific advances that transformed the view of jasmonate from an interesting floral scent to a potent transcriptional regulator. Lessons from jasmonate research generally apply to other phytohormones and thus may help provide a broad understanding of regulatory metabolite–protein interactions. In providing a framework that links small-molecule diversity to transcriptional plasticity, we hope to stimulate future research to explore the evolution, functions, and mechanisms of perception of a broad range of plant regulatory metabolites.

59 BASIC BIOLOGICAL SCIENCES↗