Ellen Youngsoo Rim

All Publications

• Integration of crop modeling and sensing into molecular breeding for nutritional quality and stress tolerance. TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik Berlingeri, J., Fuentes, A., Ranario, E., Yun, H., Rim, E. Y., Garrett, O., Howard, A., LaPorte, M. F., Lo, S., Pauli, D., Hershberger, J., Earles, M., Van Deynze, A., Brummer, E. C., Michelmore, R., Wong, C. Y., Magney, T. S., Ronald, P. C., Runcie, D. E., Bailey, B. N., Diepenbrock, C. H. 2025; 138 (9): 205

  Abstract

  Integrating innovative technologies into plant breeding is critical to bolster food and nutritional security under biotic and abiotic stresses in changing climates. While breeding efforts have focused primarily on yield and stress tolerance, emerging evidence highlights the need to also prioritize nutritional quality. Advanced molecular breeding approaches have enhanced our ability to develop improved crop varieties and could be substantially informed by the routine integration of crop modeling and remote sensing technologies. This review article discusses the potential of combining crop modeling and sensing with molecular breeding to address the dual challenge of nutritional quality and stress tolerance. We provide overviews of stress response strategies, challenges in breeding for quality traits, and the use of environmental data in genomic prediction. We also describe the status of crop modeling and sensing technologies in grain legumes, rice, and leafy greens, alongside the status of -omics tools in these crops and the use of AI with directed evolution to identify novel resistance genes. We describe the pairwise and three-way integration of AI-enabled sensing and biophysically and empirically constrained crop modeling into breeding to enable prediction of phenotypic and breeding values and dissection of genotype-by-environment-by-management interactions with increasing fidelity, efficiency, and temporal/spatial resolution to inform selection decisions. This article highlights current initiatives and future trends that focus on leveraging these advancements to develop more climate-resilient and nutritionally dense crops, ultimately enhancing the effectiveness of molecular breeding.

  View details for DOI 10.1007/s00122-025-04984-y

  View details for PubMedID 40781147

  View details for PubMedCentralID PMC12334538

• APEX2-Mediated Proximity Labeling of Wnt Receptor Interactors Upon Pathway Activation. microPublication biology Rim, E. Y., Nusse, R. 2023; 2023

  Abstract

  The Wnt signaling pathway regulates metazoan development, tissue homeostasis, and regeneration. Many outstanding questions in Wnt signal transduction revolve around the molecular events immediately following Wnt-receptor interactions. To identify binding partners of the Wnt receptor Frizzled 7 (Fzd7) upon pathway activation, we tagged Fzd7 with APEX2, an enzyme that allows biotinylation of proximal interactors with high temporal and spatial resolution. Upon confirming proper localization and signaling activity of APEX2-tagged Fzd7, we labeled proximal interactors of Fzd7 with or without Wnt3a stimulation. Mass spectrometry analysis of biotinylated interactors identified several known Wnt pathway proteins. Top interactors enriched upon Wnt treatment were involved in actin cytoskeleton regulation, vesicle trafficking, or phospholipid modification. Proteins enriched in the Wnt-activated Fzd7 interactome that are without established roles in Wnt signaling warrant further examination.

  View details for DOI 10.17912/micropub.biology.000817

  View details for PubMedID 37260921

  View details for PubMedCentralID PMC10227642

• Climate change challenges, plant science solutions PLANT CELL Eckardt, N. A., Ainsworth, E. A., Bahuguna, R. N., Broadley, M. R., Busch, W., Carpita, N. C., Castrillo, G., Chory, J., DeHaan, L. R., Duarte, C. M., Henry, A., Jagadish, S., Langdale, J. A., Leakey, A. D. B., Liao, J. C., Lu, K., McCann, M. C., McKay, J. K., Odeny, D. A., de Oliveira, E., Platten, J., Rabbi, I., Rim, E., Ronald, P. C., Salt, D. E., Shigenaga, A. M., Wang, E., Wolfe, M., Zhang, X. 2023; 35 (1): 24-66

  Abstract

  Climate change is a defining challenge of the 21st century, and this decade is a critical time for action to mitigate the worst effects on human populations and ecosystems. Plant science can play an important role in developing crops with enhanced resilience to harsh conditions (e.g. heat, drought, salt stress, flooding, disease outbreaks) and engineering efficient carbon-capturing and carbon-sequestering plants. Here, we present examples of research being conducted in these areas and discuss challenges and open questions as a call to action for the plant science community.

  View details for DOI 10.1093/plcell/koac303

  View details for Web of Science ID 000913710300006

  View details for PubMedID 36222573

  View details for PubMedCentralID PMC9806663

• Plant immunity: Rice XA21-mediated resistance to bacterial infection PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Ercoli, M., Luu, D., Rim, E., Shigenaga, A., de Araujo, A., Chern, M., Jain, R., Ruan, R., Joe, A., Stewart, V., Ronald, P. 2022; 119 (8)

  Abstract

  In this article, we describe the development of the plant immunity field, starting with efforts to understand the genetic basis for disease resistance, which ∼30 y ago led to the discovery of diverse classes of immune receptors that recognize and respond to infectious microbes. We focus on knowledge gained from studies of the rice XA21 immune receptor that recognizes RaxX (required for activation of XA21 mediated immunity X), a sulfated microbial peptide secreted by the gram-negative bacterium Xanthomonas oryzae pv. oryzae. XA21 is representative of a large class of plant and animal immune receptors that recognize and respond to conserved microbial molecules. We highlight the complexity of this large class of receptors in plants, discuss a possible role for RaxX in Xanthomonas biology, and draw attention to the important role of sulfotyrosine in mediating receptor-ligand interactions.

  View details for DOI 10.1073/pnas.2121568119

  View details for Web of Science ID 000766922200014

  View details for PubMedID 35131901

  View details for PubMedCentralID PMC8872720

• The Wnt Pathway: From Signaling Mechanisms to Synthetic Modulators ANNUAL REVIEW OF BIOCHEMISTRY Rim, E., Clevers, H., Nusse, R. 2022; 91: 571-598

  Abstract

  The Wnt pathway is central to a host of developmental and disease-related processes. The remarkable conservation of this intercellular signaling cascade throughout metazoan lineages indicates that it coevolved with multicellularity to regulate the generation and spatial arrangement of distinct cell types. By regulating cell fate specification, mitotic activity, and cell polarity, Wnt signaling orchestrates development and tissue homeostasis, and its dysregulation is implicated in developmental defects, cancer, and degenerative disorders. We review advances in our understanding of this key pathway, from Wnt protein production and secretion to relay of the signal in the cytoplasm of the receiving cell. We discuss the evolutionary history of this pathway as well as endogenous and synthetic modulators of its activity. Finally, we highlight remaining gaps in our knowledge of Wnt signal transduction and avenues for future research.

  View details for DOI 10.1146/annurev-biochem-040320-103615

  View details for Web of Science ID 000819173400023

  View details for PubMedID 35303793

• Beta-catenin-mediated Wnt signal transduction proceeds through an endocytosis-independent mechanism. Molecular biology of the cell Rim, E. Y., Kinney, L. K., Nusse, R. 2020: mbcE20020114

  Abstract

  The Wnt pathway is a key intercellular signaling cascade that regulates development, tissue homeostasis, and regeneration. However, gaps remain in our understanding of the molecular events that take place between ligand-receptor binding and target gene transcription. We used a novel tool for quantitative, real-time assessment of endogenous pathway activation, measured in single cells, to answer an unresolved question in the field - whether receptor endocytosis is required for Wnt signal transduction. We combined knockdown or knockout of essential components of Clathrin-mediated endocytosis with quantitative assessment of Wnt signal transduction in mouse embryonic stem cells (mESCs). Disruption of Clathrin-mediated endocytosis did not affect accumulation and nuclear translocation of beta-catenin, as measured by single-cell live imaging of endogenous beta-catenin, and subsequent target gene transcription. Disruption of another receptor endocytosis pathway, Caveolin-mediated endocytosis, did not affect Wnt pathway activation in mESCs. Additional results in multiple cell lines support that endocytosis is not a requirement for Wnt signal transduction. We show that off-target effects of a drug used to inhibit endocytosis may be one source of the discrepancy among reports on the role of endocytosis in Wnt signaling.

  View details for DOI 10.1091/mbc.E20-02-0114

  View details for PubMedID 32320321

• MUT-14 and SMUT-1 DEAD Box RNA Helicases Have Overlapping Roles in Germline RNAi and Endogenous siRNA Formation CURRENT BIOLOGY Phillips, C. M., Montgomery, B. E., Breen, P. C., Roovers, E. F., Rim, Y., Ohsumi, T. K., Newman, M. A., van Wolfswinkel, J. C., Ketting, R. F., Ruvkun, G., Montgomery, T. A. 2014; 24 (8): 839-844

  Abstract

  More than 2,000 C. elegans genes are targeted for RNA silencing by the mutator complex, a specialized small interfering RNA (siRNA) amplification module which is nucleated by the Q/N-rich protein MUT-16. The mutator complex localizes to Mutator foci adjacent to P granules at the nuclear periphery in germ cells. Here, we show that the DEAD box RNA helicase smut-1 functions redundantly in the mutator pathway with its paralog mut-14 during RNAi. Mutations in both smut-1 and mut-14 also cause widespread loss of endogenous siRNAs. The targets of mut-14 and smut-1 largely overlap with the targets of other mutator class genes; however, the mut-14 smut-1 double mutant and the mut-16 mutant display the most dramatic depletion of siRNAs, suggesting that they act at a similarly early step in siRNA formation. mut-14 and smut-1 are predominantly expressed in the germline and, unlike other mutator class genes, are specifically required for RNAi targeting germline genes. A catalytically inactive, dominant-negative missense mutant of MUT-14 is RNAi defective in vivo; however, mutator complexes containing the mutant protein retain the ability to synthesize siRNAs in vitro. The results point to a role for mut-14 and smut-1 in initiating siRNA amplification in germ cell Mutator foci, possibly through the recruitment or retention of target mRNAs.

  View details for DOI 10.1016/j.cub.2014.02.060

  View details for Web of Science ID 000334272700019

  View details for PubMedID 24684932

  View details for PubMedCentralID PMC4010136

• PIWI Associated siRNAs and piRNAs Specifically Require the <i>Caenorhabditis elegans</i> HEN1 Ortholog <i>henn</i>-<i>1</i> PLOS GENETICS Montgomery, T. A., Rim, Y., Zhang, C., Dowen, R. H., Phillips, C. M., Fischer, S. E. J., Ruvkun, G. 2012; 8 (4): 72-83

  Abstract

  Small RNAs--including piRNAs, miRNAs, and endogenous siRNAs--bind Argonaute proteins to form RNA silencing complexes that target coding genes, transposons, and aberrant RNAs. To assess the requirements for endogenous siRNA formation and activity in Caenorhabditis elegans, we developed a GFP-based sensor for the endogenous siRNA 22G siR-1, one of a set of abundant siRNAs processed from a precursor RNA mapping to the X chromosome, the X-cluster. Silencing of the sensor is also dependent on the partially complementary, unlinked 26G siR-O7 siRNA. We show that 26G siR-O7 acts in trans to initiate 22G siRNA formation from the X-cluster. The presence of several mispairs between 26G siR-O7 and the X-cluster mRNA, as well as mutagenesis of the siRNA sensor, indicates that siRNA target recognition is permissive to a degree of mispairing. From a candidate reverse genetic screen, we identified several factors required for 22G siR-1 activity, including the chromatin factors mes-4 and gfl-1, the Argonaute ergo-1, and the 3' methyltransferase henn-1. Quantitative RT-PCR of small RNAs in a henn-1 mutant and deep sequencing of methylated small RNAs indicate that siRNAs and piRNAs that associate with PIWI clade Argonautes are methylated by HENN-1, while siRNAs and miRNAs that associate with non-PIWI clade Argonautes are not. Thus, PIWI-class Argonaute proteins are specifically adapted to associate with methylated small RNAs in C. elegans.

  View details for DOI 10.1371/journal.pgen.1002616

  View details for Web of Science ID 000303441800005

  View details for PubMedID 22536158

  View details for PubMedCentralID PMC3334881