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bioRxiv · 10.1101/2025.09.18.676983

RE3DB: A multi-omics phylogenomics platform for rice E3 ubiquitin ligases identifies novel regulators of pollen germination

Hwang, W.·Jung, K.-H.
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Abstract

The ubiquitin proteasome system (UPS) shapes rice development and stress responses through E3 ubiquitin ligases, yet roles of E3 ligases in male gametophyte function remain undiscovered and plant-focused functional informatics resource is absent. We developed the Rice E3 Ubiquitin Ligase Database (RE3DB; https://re3db.khu.ac.kr/) and used it to nominate F-box ligases involved in rice (Oryza sativa) pollen germination. RE3DB combines 15 published datasets comprising 1,602 rice E3-ligase genes; RNA-seq across 25 tissues and stress conditions; protein-to-transcript ratios from 14 tissues; six high-confidence protein-protein interaction resources; and family level phylogenies. Integrated modules provide (i) classification/annotation, (ii) E3-substrate prediction from interaction evidence, co-expression and coordinated proteolytic turnover, and (iii) functional-redundancy assessment using phylogenetic heatmaps. Applying RE3DB, we found extensive reproductive enrichment: 284 F-box genes are preferentially expressed in mature anthers. Comparative transcriptomics across nine male-sterile rice mutants identified 111 F-box genes significantly downregulated in at least one mutant (log2 fold change < -1), resolving distinct co-regulation clusters. Integration with a literature-curated regulatory network positions previously uncharacterized F-box genes within modules governing pollen-tube initiation and elongation, consistent with regulation by the RUPO receptor-like kinase and the OsMADS62/63/68 transcription-factor complex. RE3DB is the first comprehensive multi-omics web platform dedicated to functional characterization of rice E3 ligases. By unifying classification, interaction and expression-based inference, and redundancy analysis, it accelerates hypothesis-driven discovery and guides targeted mutagenesis in molecular plant science. The prioritized F-box cohort provides testable candidates for UPS-mediated control of pollen germination and tube growth, and the framework is readily extensible to other crops, holding significant potential for agricultural biotechnology.

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Hwang, W., Jung, K.-H.. 2025-09-20. RE3DB: A multi-omics phylogenomics platform for rice E3 ubiquitin ligases identifies novel regulators of pollen germination. https://doi.org/10.1101/2025.09.18.676983

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