Rice Science

Rice Science

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RE3DB: A Multi-Omics Phylogenomics Platform for Rice E3 Ubiquitin-Ligase-System Genes and Candidate F-Box Genes Associated with Pollen Germination

  1. Graduate School of Green-Bio Science and Crop Biotechnology Institute, Kyung Hee University, Yongin 17104, Republic of Korea; Research Centre for Plant Plasticity, Seoul 08826, Republic of Korea
  • Contact: Ki-Hong JUNG
  • Supported by:

    This study was supported by the grant from the New Breeding Technologies Development Program, the Rural Development Administration of the Republic of Korea to Sunok Moon (Grant No. RS-2024-00322278), and the National Research Foundation of Korea to Ki-Hong Jung (Grant Nos. RS-2021-NR060084 and RS-2021-NR059380). We are grateful to Professor Woo-Jong Hong for generously providing both the source code used to implement phylogenetic heatmap and server infrastructure that enabled us to host and maintain RE3DB.

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Abstract: The ubiquitin-proteasome system (UPS) shapes rice (Oryza sativa) development and stress responses through the actions of E3 ubiquitin ligases; however, the functions of most plant E3s remain unresolved, and integrative, rice-focused multi-omics resources to prioritize E3 ligases remain limited. We developed the Rice E3 Ubiquitin Ligase Database (RE3DB; https://re3db.khu.ac.kr/) as a rice-focused platform for exploration and prioritization of E3 ubiquitin-ligase-system genes. RE3DB consolidates 1 602 curated E3 ubiquitin-ligase-system genes with 15 published datasets, including RNA-seq from 25 tissues and diverse stress conditions, protein-to-transcript ratios (PTRs) from 14 tissues, 6 high-confidence protein-protein interaction resources, and family-level phylogenies. Interactive modules enable (i) classification and functional annotation, (ii) prioritization of candidate E3-substrate relationships based on interaction evidence, co-expression, and coordinated proteolytic turnover, and (iii) assessment of potential functional redundancy using phylogenetic heatmaps. As a resource-use case study, we analyzed tissue- or organ-specific expression profiles of rice E3-system genes, observing strong enrichment of F-box genes in reproductive tissues, including 284 F-box genes preferentially expressed in mature anthers. Comparative transcriptomics across 9 male-sterile rice mutants prioritized 111 F-box candidates that were downregulated in at least one mutant with defects in pollen germination or tube growth, forming distinct co-regulation clusters. Integrating these candidates with a literature-curated regulatory network highlighted previously uncharacterized F-box genes within modules associated with pollen-tube initiation and elongation, consistent with regulation by the RUPO receptor-like kinase and the OsMADS62/63/68 transcription-factor complex. RE3DB provides a rice-focused resource to support hypothesis generation and candidate prioritization for ubiquitin signaling, with potential applications in understanding fertility and yield stability.

Key words: E3 ligase, multi-omics, rice, pollen germination, F-box, phylogenomics