ArticleThe Plant cell2024
Quantitative proteomics reveals extensive lysine ubiquitination and transcription factor stability states in Arabidopsis.
Article in The Plant cell, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Omics-driven plant breeding through phenomics-enviromics crosstalk.Nature communications · 2026Review
- Salicylic acid modulates its catabolic enzymes via proteasomal degradation linked to SCF-associated proximity networks.Nature communications · 2026Article
- Ubiquitin-Mediated Proteolysis as a Regulator of the Plant Defense-Growth Balance.Plants (Basel, Switzerland) · 2026Review
- Dynamic ASK1 proximity networks uncover SCF-dependent and noncanonical roles in ABA and drought adaptation.bioRxiv : the preprint server for biology · 2025Article
- Dissecting usuranme biquitin-mediated circadian clock regulation in Arabidopsis via high-throughput yeast screens.Journal of experimental botany · 2025Article
- The Emerging Role of the Salt Tolerance-Related Protein in the Abiotic Stress Response ofPlants (Basel, Switzerland) · 2025Review
- A phosphorylation-driven ubiquitination switch fine-tunes Alfin-like 7-induced ROS signaling in plant immunity.Science advances · 2025Article
- Intrinsic and extrinsic regulators of Aux/IAA protein degradation dynamics.Trends in biochemical sciences · 2022Review
- To the proteome and beyond: advances in single-cell omics profiling for plant systems.Plant physiology · 2022Article
- Shotgun Proteomics as a Powerful Tool for the Study of the Proteomes of Plants, Their Pathogens, and Plant-Pathogen Interactions.Proteomes · 2022Review
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Authors and funding
9 authors.
Funding
Abstract
Protein activity, abundance, and stability can be regulated by post-translational modification including ubiquitination. Ubiquitination is conserved among eukaryotes and plays a central role in modulating cellular function; yet, we lack comprehensive catalogs of proteins that are modified by ubiquitin in plants. In this study, we describe an antibody-based approach to enrich ubiquitinated peptides coupled with isobaric labeling to enable quantification of up to 18-multiplexed samples. This approach identified 17,940 ubiquitinated lysine sites arising from 6,453 proteins from Arabidopsis (Arabidopsis thaliana) primary roots, seedlings, and rosette leaves. Gene ontology analysis indicated that ubiquitinated proteins are associated with numerous biological processes including hormone signaling, plant defense, protein homeostasis, and metabolism. We determined ubiquitinated lysine residues that directly regulate the stability of three transcription factors, CRYPTOCHROME-INTERACTING BASIC-HELIX-LOOP-HELIX 1 (CIB1), CIB1 LIKE PROTEIN 2 (CIL2), and SENSITIVE TO PROTON RHIZOTOXICITY1 (STOP1) using in vivo degradation assays. Furthermore, codon mutation of CIB1 to create a K166R conversion to prevent ubiquitination, via CRISPR/Cas9-derived adenosine base editing, led to an early flowering phenotype and increased expression of FLOWERING LOCUS T (FT). These comprehensive site-level ubiquitinome profiles provide a wealth of data for future functional studies related to modulation of biological processes mediated by this post-translational modification in plants.
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