Biology subjects

Rhee, S. Y.

Publications and source records attributed to Rhee, S. Y..

At least 19 recordsLinked to original sources

bioRxiv2026

Extreme cooling enables survival in extreme heat

Complex, multicellular extremophiles face intense challenges in coordinating their cells, tissues, and organs to function in harsh environments. Tidestromia oblongifolia is a desert plant that thrives in Death Valley, where air temperatures exceed 49 {degrees}C. Using natural collections of T. oblongifolia seed, we identified individuals that survive in daily air temperature regimens at the eukaryotic upper thermal limit of 60 {degrees}C. Genome-wide association testing detected genetic variation for survival in extreme heat, and transcriptomics implicated pathways regulating leaf cooling. High-throughput infrared imaging revealed that survival was enabled by leaf cooling far below air temperature, identifying a physiological mechanism of thermophily in a multicellular organism. These discoveries provide insights into mechanisms of extreme heat adaptation that could be leveraged to engineer heat-resilient crops.

plant biology↗

bioRxiv2026

CO2 fixation mediated by the carbon concentrating mechanism enables a rapid response to nitrogen deprivation in cyanobacteria

Cyanobacteria are leading biomass producers of the ocean whose ecological success relies on their ability to respond to dynamic availability of nutrients like CO2 and nitrogen, which require distinct adaptive mechanisms. To survive nitrogen deprivation, cyanobacteria undergo a reversible transition to a dormant mode. Under low CO2 levels, a CO2 concentrating mechanism (CCM) supports their CO2 fixation. While the CCM and nitrogen assimilation have been shown to share some regulatory pathways, how the CCM impacts the response to nitrogen deprivation remains underexplored. In this study, by using mutants of the coastal cyanobacteria Synechococcus sp. PCC 7002 lacking a CCM component, we show that the high rate of carbon fixation mediated by the CCM tunes the speed of the nitrogen deprivation response in {beta}-cyanobacteria. We first show that CCM mutants are deficient in inducing their typical nitrogen deprivation response under atmospheric CO2. However, at higher CO2 concentrations, the CCM mutants induce the nitrogen deprivation response. By combining Rubisco kinetics modeling with measurement of the response speed to nitrogen in various CO2 concentrations, we show that the speed of the nitrogen deprivation response increases linearly with Rubiscos carboxylation rate. We further reveal that the regulation of nitrogen response by the CCM is also present in the distantly related freshwater cyanobacteria Synechococcus elongatus PCC 7942, suggesting a widespread role of this regulation across {beta}-cyanobacteria. This study demonstrates that CO2 fixation by the cyanobacterial CCM is a key regulator of the nitrogen deprivation response, favoring a rapid response to dynamic environments.

plant biology↗

bioRxiv2025

Single-cell-level response to drought in Sorghum bicolor reveals novel targets for improving water use efficiency

Increasing drought threatens global agriculture, especially in water-limited regions. Sorghum bicolor, a drought-tolerant C4 grass, is a promising bioenergy crop for cultivation on marginal lands, yet its molecular drought responses remain poorly understood. To uncover single-cell-level transcriptional responses to drought, we performed single-nucleus RNA sequencing on mature sorghum leaves under well-watered and drought conditions. We identified major cell types and analyzed differential gene expression across mesophyll, bundle sheath, epidermal, vascular, and stomatal cells. Surprisingly, drought effects on transcriptomes exceeded differences due to cell identity, revealing a shared response across cell types. We leveraged this convergence to identify candidate regulators of drought-responsive gene expression. These findings advance our understanding of sorghum drought adaptation and offer new targets for engineering enhanced water use efficiency in bioenergy crops.

plant biology↗

bioRxiv2025

Sorghum Metabolic Atlas: Large-Scale Mapping of Subcellular Enzyme Localization in Sorghum bicolor

Plant metabolism drives traits essential for productivity and resilience, yet understanding metabolic networks requires subcellular, cellular, and tissue-level spatial context that remains limited, particularly in crop species. Experimentally-derived subcellular localization data for enzymes are sparse, constraining analyses of metabolic organization in the cell. We developed a high-throughput protoplast transformation and fluorescent protein (FP) tagging system optimized for Sorghum bicolor, a climate-resilient C4 crop. Using this platform, we experimentally determined the subcellular localization of 234 metabolic enzymes spanning 184 pathways. The sorghum enzymes we characterized localize to 12 subcellular compartments. Comparison with computational predictions highlights variable accuracy across compartments, and cross-species comparison with Arabidopsis thaliana shows partial agreement with available experimental data. All data are accessible through the Sorghum Metabolic Atlas (www.sorghummetabolicatlas.org) web platform, enabling search, visualization, and download. This study presents a large-scale experimental dataset of enzyme localization in sorghum, providing a resource for studies of plant metabolic organization and comparative analyses.

plant biology↗

bioRxiv2025

FLOE1 maintains cellular viscosity in rehydrating Arabidopsis embryos

Most plant embryos can survive for years in a dry state of less than 10% water(1). Rehydration during seed germination is critical but risky-too little environmental water can dehydrate and kill the developing embryo. Plants avoid this by germinating only when sufficient water is present. However, the mechanisms by which sufficient water is sensed and how it triggers germination remain unknown. FLOE1 suppresses seed germination under water limitation by undergoing reversible phase changes in response to water potential(2). To understand how FLOE1 affects germination, we compared water behavior in wild type and floe1-1 null mutants. While both had similar amounts of water when dry, floe1-1 seeds hydrated less than the wild type after imbibition. Additionally, bound water was less restricted in floe1-1 embryos, suggesting FLOE1 promotes macromolecular water binding. By developing plant-compatible versions of Genetically Encoded Multimeric nanoparticles (GEMs)(3), we show that FLOE1 increases cytoplasmic viscosity during embryo rehydration. FLOE1 in yeast was sufficient to increase cytoplasmic viscosity. FLOE1 also increased cytoplasmic viscosity during hyperosmotic stress in yeast, and this ability was ablated by FLOE1 domain deletions. Our study identifies FLOE1 as a regulator of water content, dynamics, and cytoplasmic viscosity, linking molecular water control to cellular physical properties.

plant biology↗

bioRxiv2025

Satiety, TAX-4, and OSM-9 Tune the Attraction of C. elegans Nematodes to Microbial Fermentation Products

Animals are sensitive to selective pressures associated with nutrient acquisition, underscoring the evolutionary significance of chemosensation in foraging and its intersection with satiety. For the model nematode Caenorhabditis elegans, isoamyl alcohol (3-methyl-1-butanol) and 2-methyl-1-butanol are produced by microbial fermentation and present in bacterial food sources collected from the natural environments. Both compounds, which are structural isomers of one another, elicit strong attraction in laboratory settings. Using laboratory chemotaxis assays, we show that starvation attenuates attraction to both compounds. Well-fed C. elegans is largely insensitive to the biosynthetic precursors of both alcohols, with the exception of 4-methyl-2-oxovaleric acid, which is a mild repellent. C. elegans chemosensation relies on expression of tax-4 cyclic nucleotide-gated (CNG) and osm-9 transient receptor potential, vanilloid (TRPV) ion channels and animals lacking both genes are taste- and smell-blind. Animals lacking tax-4 fail to attract isoamyl alcohol and 2-methyl-1-butanol and those lacking osm-9 exhibit stronger attraction than the wild-type. Starvation not only attenuates attraction, but also enhances repulsion to 4-methyl-2-oxovaleric acid and uncovers repulsion in tax-4 mutants absent in their well-fed counterparts. Collectively, these findings implicate satiety in regulating response strength, tax-4-dependent chemotaxis in attraction to isoamyl alcohol and 2-methyl-1-butanol, and osm-9-dependent chemotaxis in suppressing responses to biosynthetic precursors.

neuroscience↗

bioRxiv2025

Phosphorus Availability Modulates Flowering Time Through Subcellular Reprogramming of bGLU25 and GRP7 in Flowering Plants

The transition from vegetative to reproductive growth is vital for plant fitness and crop yield and is strongly influenced by nutrient availability. While nitrogen deficiency accelerates flowering, phosphorus (P) limitation delays it. However, the molecular basis for how P availability regulates flowering time remains unclear. Here, through genome-wide association mapping in Arabidopsis, we uncover genetic variation in {beta}-GLUCOSIDASE 25 (bGLU25) that modulates flowering under P-limited conditions. In P-sufficient environments, bGLU25 localizes to the endoplasmic reticulum. Under P limitation, however, bGLU25 translocates to the cytosol, a process mediated by P-regulated SERINE CARBOXY PEPTIDASE 50 (SCP50). In the cytosol, bGLU25 binds to JACALIN-LECTIN LIKE1 (AtJAC1), preventing the nuclear translocation of the Flowering Locus C (FLC) regulator GLYCINE-RICH RNA-BINDING PROTEIN 7 (GRP7). This cytosolic sequestration of GRP7 under P-deprivation elevates FLC expression, delaying flowering. Moreover, in the monocot rice, the homologs of bGLU25 also modulate flowering responses to P availability, indicating a conserved role for bGLU25 across flowering plants. Our findings provide a molecular framework for breeding strategies aimed at optimizing flowering time in response to P levels.

plant biology↗

bioRxiv2024

UnigeneFinder: An automated pipeline for gene calling from transcriptome assemblies without a reference genome

For most species in nature, transcriptome data is much more readily available than genome data. Without a reference genome, however, gene calling is cumbersome and inaccurate due to the high degree of redundancy in de novo transcriptome assemblies. To simplify and increase the accuracy of de novo transcriptome assembly in the absence of a reference genome, we developed UnigeneFinder. Combining several clustering methods, UnigeneFinder substantially reduces the redundancy typical of raw transcriptome assemblies. This pipeline offers an effective solution to the problem of inflated transcript numbers, achieving a closer representation of the actual underlying genome. UnigeneFinder performs comparably or better, compared to existing tools, on plant species with varying genome complexities. UnigeneFinder is the only available transcriptome redundancy solution that fully automates the generation of primary transcript, coding region, and protein sequences, analogous to those available for high quality reference genomes. These features, coupled with the pipelines cross-platform implementation and focus on automation and an accessible user interface, make UnigeneFinder a useful tool for many downstream sequence-based analyses in non-model organisms lacking a reference genome, including differential gene expression analysis, accurate ortholog identification, functional enrichments, and evolutionary analyses. UnigeneFinder also runs efficiently both on high-performance computing (HPC) systems and personal computers, further reducing barriers to use.

bioinformatics↗

bioRxiv2024

A reference-free algorithm discovers regulation in the plant transcriptome

Most plant genomes and their regulation remain unknown. We used SPLASH - a new, reference-genome free sequence variation detection algorithm - to analyze transcriptional and post-transcriptional regulation from RNA-seq data. We discovered differential homolog expression during maize pollen development, and imbibition-dependent cryptic splicing in Arabidopsis seeds. SPLASH enables discovery of novel regulatory mechanisms, including differential regulation of genes from hybrid parental haplotypes, without the use of alignment to a reference genome.

bioinformatics↗

bioRxiv2024

Arabidopsis thaliana RHAMNOSE 1 condensate formation drives UDP-rhamnose synthesis

Rhamnose is an essential component of the plant cell wall and is synthesized from uridine diphosphate (UDP)-glucose by the RHAMNOSE1 (RHM1) enzyme. RHM1 localizes to biomolecular condensates in plants, but their identity, formation, and function remain elusive. Combining live imaging, genetics, and biochemical approaches in Arabidopsis and heterologous systems, we show that RHM1 alone is sufficient to form enzymatically active condensates, which we name rhamnosomes. Rhamnosome formation is required for UDP-rhamnose synthesis and organ development. Overall, our study demonstrates a novel role for biomolecular condensation in metabolism and organismal development, and provides further support for how organisms have harnessed this biophysical process to regulate small molecule metabolism. One-Sentence SummaryCondensation of RHM1 drives UDP-rhamnose synthesis during plant development.

plant biology↗

bioRxiv2024

Variability in drought gene expression datasets highlight the need for community standardization

Physiologically relevant drought stress is difficult to apply consistently, and the heterogeneity in experimental design, growth conditions, and sampling schemes make it challenging to compare water deficit studies in plants. Here, we re-analyzed hundreds of drought gene expression experiments across diverse model and crop species and quantified the variability across studies. We found that drought studies are surprisingly uncomparable, even when accounting for differences in genotype, environment, drought severity, and method of drying. Many studies, including most Arabidopsis work, lack high-quality phenotypic and physiological datasets to accompany gene expression, making it impossible to assess the severity or in some cases the occurrence of water deficit stress events. From these datasets, we developed supervised learning classifiers that can accurately predict if RNA-seq samples have experienced a physiologically relevant drought stress, and suggest this can be used as a quality control for future studies. Together, our analyses highlight the need for more community standardization, and the importance of paired physiology data to quantify stress severity for reproducibility and future data analyses.

plant biology↗

bioRxiv2023

Conflicts in natural selection constrain adaptation to climate change in Arabidopsis thaliana

Climate change has already caused noticeable changes in species-wide traits, such as the well-documented acceleration of spring flowering. Because the evolutionary past has favored certain combinations of traits, some strategies like fast growth with early flowering that are adaptive today are at odds with other plant resilience strategies such as elevated water use efficiency. We know that the evolution of trait combinations is shaped by genomic constraints, but it is unclear whether and how this is affected by natural selection from climate change. Growing hundreds of Arabidopsis thaliana natural populations under different rainfall regimes revealed opposing natural selection on flowering time and water use efficiency, with strong antagonistic genetic correlations and contrasting causal alleles identified by Genome-Wide Association analyses. Inactivation of the central flowering regulator FLC in multiple, diverse accessions relaxed trait correlations in a genetic background-dependent manner and allowed for the emergence of a novel adaptive trait combination--early flowering and intermediate water use efficiency. Future climates are predicted to escalate conflicts in natural selection among adaptive traits, but our work shows that surprisingly simple genetic changes can help solve these conflicts.

evolutionary biology↗

bioRxiv2023

Non-destructive, whole-plant phenotyping reveals dynamic changes in water use efficiency, photosynthetic efficiency, and rhizosphere acidification of sorghum cultivars under osmotic stress

Noninvasive phenotyping can quantify dynamic plant growth processes at higher temporal resolution than destructive phenotyping and can reveal phenomena that would be missed by end-point analysis alone. Additionally, whole-plant phenotyping can identify growth conditions that are optimal for both above- and below-ground tissues. However, noninvasive, whole-plant phenotyping approaches available today are generally expensive, complex, and non-modular. We developed a low-cost and versatile approach to non-invasively measure whole-plant physiology over time by growing plants in isolated hydroponic chambers. We demonstrate the versatility of our approach by measuring whole-plant biomass accumulation, water use, and water use efficiency every two days on unstressed and osmotically-stressed sorghum accessions. We identified relationships between root zone acidification and photosynthetic efficiency on whole-plant water use efficiency over time. Our system can be implemented using cheap, basic components, requires no specific technical expertise, and is suitable for any non-aquatic vascular plant species.

plant biology↗

bioRxiv2023

An efficient behavioral screening platform classifies natural products and other chemical cues according to their chemosensory valence in C. elegans

Throughout history, humans have relied on plants as a source of medication, flavoring, and food. Plants synthesize large chemical libraries and release many of these compounds into the rhizosphere and atmosphere where they affect animal and microbe behavior. To survive, nematodes must have evolved the sensory capacity to distinguish plant-made small molecules (SMs) that are harmful and must be avoided from those that are beneficial and should be sought. This ability to classify chemical cues as a function of their value is fundamental to olfaction, and represents a capacity shared by many animals, including humans. Here, we present an efficient platform based on multi-well plates, liquid handling instrumentation, inexpensive optical scanners, and bespoke software that can efficiently determine the valence (attraction or repulsion) of single SMs in the model nematode, Caenorhabditis elegans. Using this integrated hardware-wetware-software platform, we screened 90 plant SMs and identified 37 that attracted or repelled wild-type animals, but had no effect on mutants defective in chemosensory transduction. Genetic dissection indicates that for at least 10 of these SMs, response valence emerges from the integration of opposing signals, arguing that olfactory valence is often determined by integrating chemosensory signals over multiple lines of information. This study establishes that C. elegans is an effective discovery engine for determining chemotaxis valence and for identifying natural products detected by the chemosensory nervous system.

neuroscience↗

bioRxiv2021

Uncoupling differential water usage from drought resistance in a dwarf Arabidopsis mutant

Understanding the molecular and physiological mechanisms of how plants respond to drought is paramount to breeding more drought resistant crops. Certain mutations or allelic variations result in plants with altered water-use requirements. To correctly identify genetic differences which confer a drought phenotype, plants with different genotypes must be subjected to equal levels of drought stress. Many reports of advantageous mutations conferring drought resistance do not control for soil water content variations across genotypes and may therefore need to be re-examined. Here, we reassessed the drought phenotype of the Arabidopsis thaliana dwarf mutant, chiquita1-1 (also called costl), by growing mutant seedlings together with the wild type to ensure uniform soil water availability across genotypes. Our results demonstrate that the dwarf phenotype conferred by loss of CHIQ1 function results in constitutively lower water usage, but not increased drought resistance.

plant biology↗

bioRxiv2021

CHIQUITA1 maintains temporal transition between proliferation and differentiation in Arabidopsis thaliana

Body size varies widely among species, populations, and individuals depending on the environment. Transitioning between proliferation and differentiation is a crucial determinant of final organ size, but how the timing of this transition is established and maintained remains unknown. Using cell proliferation markers and genetic analysis, we show that CHIQUITA1 (CHIQ1) is required to maintain the timing of the transition from proliferation to differentiation in Arabidopsis thaliana. Combining kinematic and cell lineage tracking studies, we found that the number of actively dividing cells in chiquita1-1 plants decreases prematurely compared to wild type plants, suggesting CHIQ1 maintains the proliferative capacity in dividing cells and ensures that cells divide a certain number of times. CHIQ1 belongs to a plant-specific gene family of unknown molecular function and physically and genetically interacts with three close members of its family to control the timing of proliferation exit. Our work reveals the interdependency between cellular and organ-level processes underlying final organ size determination. SignificanceTiming of the transition between proliferation and differentiation is fundamental for determining the final size of organs and organisms. In agriculture, controlling organ and organism size can influence key agronomic traits such as yield and biomass. Dwarfism prevents lodging and was the trait responsible for the Green Revolution. Today, more sophisticated traits are needed for generating crops that are both resilient and sustainable. Revealing the molecular mechanisms that control the temporal transition between proliferation and differentiation will help unlock the potential of next-generation crops. Here, we report that CHIQUITA 1 in Arabidopsis thaliana is needed to maintain the proper timing of the transition between proliferation and differentiation in leaves and roots.

plant biology↗

bioRxiv2021

A Bivalent Chromatin Controls Timing of Expression of Camalexin Biosynthesis Genes in Response to a Pathogen Signal in Arabidopsis

Temporal dynamics of gene expression underpins the responses to internal and environmental stimuli. In eukaryotes, regulation of gene induction includes changing chromatin states at the target genes, and recruitment of the transcriptional machinery that includes transcription factors. As one of the most potent specialized metabolites in Arabidopsis thaliana, camalexin can be rapidly induced by bacterial and fungal infections. Though several transcription factors controlling camalexin biosynthesis genes have been characterized, it remains unknown how the rapid activation of genes in this pathway upon a pathogen signal happens. By combining publicly available epigenomic data with in vivo chromatin mapping, we found that camalexin biosynthesis genes are marked with two epigenetic modifications with opposite effects on gene expression, H3K27me3 (repression) and H3K18ac (activation), to form a bivalent chromatin. Mutants with reduced H3K27m3 or H3K18ac showed that both modifications were required to determine the timing of gene expression and metabolite accumulation at an early stage of the stress response. Our study indicates that this type of bivalent chromatin, which we name a kairostat, plays an important role controlling the timely induction of gene expression upon stimuli in plants.

plant biology↗

bioRxiv2021

Plant Metabolic Network: A multi-species resource of plant metabolic information

Plant metabolism is a pillar of our ecosystem, food security, and economy. To understand and engineer plant metabolism, we first need a comprehensive and accurate annotation of all metabolic information across plant species. As a step towards this goal, we previously created the Plant Metabolic Network (PMN), an online resource of curated and computationally predicted information about the enzymes, compounds, reactions, and pathways that make up plant metabolism. Here we report PMN 15, which contains genome-scale metabolic pathway databases of 126 algal and plant genomes, ranging from model organisms to crops to medicinal plants, and new tools for analyzing and viewing metabolism information across species and integrating omics data in a metabolic context. 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 continued growth and refinement of the PMN resource and demonstrates its wide-ranging utility in integrating metabolism with other areas of plant biology. One-sentence SummaryThe Plant Metabolic Network is a collection of databases containing experimentally-supported and predicted information about plant metabolism spanning many species.

plant biology↗