Arabidopsis as a model for translational research

PlantGPT: An Arabidopsis-Based Intelligent Agent that Answers Questions about Plant Functional Genomics

Research into plant gene function is crucial for developing strategies to increase crop yields. The recent introduction of large language models (LLMs) offers a means to aggregate large amounts of data into a queryable format, but the output can contain inaccurate or false claims known as hallucinations. To minimize such hallucinations and produce high-quality knowledge-based outputs, the abstracts of over 60 000 plant research articles are compiled into a Chroma database for retrieval-augmented generation (RAG). Then linguistic data are used from 13 993 Arabidopsis (Arabidopsis thaliana) phenotypes and 23 323 gene functions to fine-tune the LLM Llama3-8B, producing PlantGPT, a virtual expert in Arabidopsis phenotype-gene research. By evaluating answers to test questions, it is demonstrated that PlantGPT outperforms general LLMs in answering specialized questions. The findings provide a blueprint for functional genomics research in food crops and demonstrate the potential for developing LLMs for plant research modalities. To provide broader access and facilitate adoption, the online tool http://www.plantgpt.icu is developed, which will allow researchers to use PlantGPT in their scientific investigations.

In defense of funding foundational plant science

Plants are essential for life as we know it on Earth. They oxygenate the atmosphere, regulate the climate, and comprise much of the primary producers underpinning complex food systems. In the 1980s, a multinational group of plant scientists chose the small angiosperm-Arabidopsis thaliana-to serve as the model flowering plant for genetic and molecular studies that would be leveraged to produce vast new datasets, resources, and tools. The rationale they used to persuade funding agencies to make significant investments and focus intense effort on this single plant species was to produce a deep fundamental knowledge of the biology of plants and to apply this knowledge to valuable, but typically less tractable, plant species. Over the past 40 yr, Arabidopsis has emerged as the most powerful and versatile plant model to uncover core biological principles and served as a prototyping system to test advanced molecular and genetic concepts. We argue that the emerging challenges of accelerating climate instability and a rapidly growing global population call for renewed and robust investments in fundamental plant biology research. Leveraging the power of Arabidopsis research, resources, datasets, and global collaborative community is more important than ever. This commentary lays out a vigorous defense of foundational, i.e. "basic," plant science research; describes that often, Arabidopsis is preferable to working directly in crops; highlights several transformative applications generated from basic plant research; and makes the argument that plant science is vital to the survival of humanity.

Challenges of translating Arabidopsis insights into crops

The significance of research conducted on Arabidopsis thaliana cannot be overstated. This focus issue showcases how insights from Arabidopsis have opened new areas of biology and directly advanced our understanding of crops. Here, experts intimately involved in bridging between Arabidopsis and crops share their perspectives on the challenges and opportunities for translation. First, we examine the translatability of genetic modules from Arabidopsis into maize, emphasizing the need to publish well-executed translational experiments, regardless of outcome. Second, we highlight the landmark success of HB4, the first GM wheat cultivar on the market, whose abiotic tolerance is borne from direct translation and based on strategies first outlined in Arabidopsis. Third, we discuss the decades-long journey to engineer oilseed crops capable of producing omega-3 fish oils, with Arabidopsis serving as a critical intermediary. Fourth, we explore how direct translation of starch synthesizing proteins characterized in Arabidopsis helped uncover novel mechanisms and functions in crops, with potential valuable applications. Finally, we illustrate how shared molecular factors between Arabidopsis and barley exhibit distinct molecular wiring as exemplified in cuticular and stomatal development. Together, these vignettes underscore the pivotal role of Arabidopsis as a foundational model plant while highlighting the challenges of translating discoveries into field-ready, commercial cultivars with enhanced knowledge-based traits.

The Manifestation of the Dual ROS-Processing and Redox Signaling Roles of Glutathione Peroxidase-like Enzymes in Development of Arabidopsis Seedlings

Plant glutathione peroxidase-like (GPXL) enzymes are thiol-based peroxidases that reduce H2O2 or hydroperoxides to water or alcohols using electrons principally from thioredoxin. Arabidopsis thaliana possesses eight isoenzymes (AtGPXL1-8) located in different plant organelles and have various roles in redox-dependent processes. The determination of the redox potential of 6-day-old T-DNA insertional mutants (Atgpxl1-Atgpxl8) using a cytosolic redox-sensitive fluorescent probe (roGFP2) uncovered more oxidized redox status in the shoot and/or root of the untreated mutants, except for Atgpxl5. To investigate the involvement of AtGPXLs in the growth and abiotic stress responses of seedlings, the 4-day-old Atgpxls were exposed to salt and osmotic stresses for two weeks. The evaluation of the reactive oxygen species (ROS) levels of untreated 18-day-old plants using fluorescent microscopy revealed the elevated accumulation of total ROS in the shoots and, in some cases, the roots of the mutants. Regarding the growth of roots, both the length of primary roots and/or the number of lateral roots were affected by the mutation of AtGPXLs. A strong negative correlation was observed between the ROS level of wild type shoots and the development of lateral roots, but it was altered in mutants, while in the case of Atgpxl1, Atgpxl5, and Atgpxl7 seedlings, it disappeared; in other mutants (Atgpxl4, Atgpxl6, and Atgpxl8), the correlation became stronger. Our analysis underpins the discrete role of AtGPXL enzymes in controlling the growth and development of plants by fine tuning the ROS contents and redox status in an organ-specific way. Differences in root phenotype and metabolic activity between Atgpxl mutants and wild type plants highlight the essential role of AtGPXLs in ROS processing to support growth, which is particularly evident when one GPXL isoenzyme is absent or its activity is reduced, both under normal and abiotic stress conditions.

Identification of a drought stress response module in tomato plants commonly induced by fungal endophytes that confer increased drought tolerance

Global climate change exacerbates abiotic stresses, as drought, heat, and salt stresses are anticipated to increase significantly in the coming years. Plants coexist with a diverse range of microorganisms. Multiple inter-organismic relationships are known to confer benefits to plants, including growth promotion and enhanced tolerance to abiotic stresses. In this study, we investigated the mutualistic interactions between three fungal endophytes originally isolated from distinct arid environments and an agronomically relevant crop, Solanum lycopersicum. We demonstrated a significant increase in shoot biomass under drought conditions in co-cultivation with Penicillium chrysogenum isolated from Antarctica, Penicillium minioluteum isolated from the Atacama Desert, Chile, and Serendipita indica isolated from the Thar Desert, India. To elucidate plant gene modules commonly induced by the different endophytes that could explain the observed drought tolerance effect in tomato, a comprehensive transcriptomics analysis was conducted. This analysis led to the identification of a shared gene module in the fungus-infected tomato plants. Within this module, gene network analysis enabled us to identify genes related to abscisic acid (ABA) signaling, ABA transport, auxin signaling, ion homeostasis, proline biosynthesis, and jasmonic acid signaling, providing insights into the molecular basis of drought tolerance commonly mediated by fungal endophytes. Our findings highlight a conserved response in the mutualistic interactions between endophytic fungi isolated from unrelated environments and tomato roots, resulting in improved shoot biomass production under drought stress.

Rice A20/AN1 protein, OsSAP10, confers water-deficit stress tolerance via proteasome pathway and positive regulation of ABA signaling in Arabidopsis

KEY MESSAGE

Overexpression of rice A20/AN1 zinc-finger protein, OsSAP10, improves water-deficit stress tolerance in Arabidopsis via interaction with multiple proteins. Stress-associated proteins (SAPs) constitute a class of A20/AN1 zinc-finger domain containing proteins and their genes are induced in response to multiple abiotic stresses. The role of certain SAP genes in conferring abiotic stress tolerance is well established, but their mechanism of action is poorly understood. To improve our understanding of SAP gene functions, OsSAP10, a stress-inducible rice gene, was chosen for the functional and molecular characterization. To elucidate its role in water-deficit stress (WDS) response, we aimed to functionally characterize its roles in transgenic Arabidopsis, overexpressing OsSAP10. OsSAP10 transgenics showed improved tolerance to water-deficit stress at seed germination, seedling and mature plant stages. At physiological and biochemical levels, OsSAP10 transgenics exhibited a higher survival rate, increased relative water content, high osmolyte accumulation (proline and soluble sugar), reduced water loss, low ROS production, low MDA content and protected yield loss under WDS relative to wild type (WT). Moreover, transgenics were hypersensitive to ABA treatment with enhanced ABA signaling and stress-responsive genes expression. The protein-protein interaction studies revealed that OsSAP10 interacts with proteins involved in proteasomal pathway, such as OsRAD23, polyubiquitin and with negative and positive regulators of stress signaling, i.e., OsMBP1.2, OsDRIP2, OsSCP and OsAMTR1. The A20 domain was found to be crucial for most interactions but insufficient for all interactions tested. Overall, our investigations suggest that OsSAP10 is an important candidate for improving water-deficit stress tolerance in plants, and positively regulates ABA and WDS signaling via protein-protein interactions and modulation of endogenous genes expression in ABA-dependent manner.