Decoys provide a scalable platform for identification of plant E3 ubiquitin ligases that regulate circadian function
- Yale University, United States
- South China University of Technology, China
Abstract
The circadian clock relies on regulated degradation of clock proteins to maintain rhythmicity. Despite this, we know few components that mediate protein degradation. This is due to high levels of functional redundancy within plant E3 ubiquitin ligase families. In order to overcome this issue and discover E3 ubiquitin ligases that control circadian function, we generated a library of transgenic Arabidopsis plants expressing dominant-negative 'decoy' E3 ubiquitin ligases. We determined their effects on the circadian clock and identified dozens of new potential regulators of circadian function. To demonstrate the potency of the decoy screening methodology to overcome redundancy and identify bona fide clock regulators, we performed follow-up studies on MAC3A (PUB59) and MAC3B (PUB60). We show that they redundantly control circadian period by regulating splicing. This work demonstrates the viability of ubiquitin ligase decoys as a screening platform to overcome genetic challenges and discover E3 ubiquitin ligases that regulate plant development.
Data availability
All data generated or analyzed during this study are included in the manuscript and supporting files. Source data is provided for Figures 2,3,4,6, S1 and S2.
Article and author information
Author details
Funding
National Science Foundation (EAGER #1548538)
- Joshua M Gendron
National Institutes of Health (R35 GM128670)
- Joshua M Gendron
Gruber Foundation
- Ann Feke
Rudolph J. Anderson Fund
- Chin-Mei Lee
Forest B.H. and Elizabeth D.W. Brown Fund
- Wei Liu
- Chin-Mei Lee
National Science Foundation (GRFP DGE-1122492)
- Ann Feke
National Institutes of Health (T32 GM007499)
- Ann Feke
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Reviewing Editor
- Jürgen Kleine-Vehn, University of Natural Resources and Life Sciences, Austria
Publication history
- Received: December 20, 2018
- Accepted: April 4, 2019
- Accepted Manuscript published: April 5, 2019 (version 1)
- Version of Record published: April 25, 2019 (version 2)
Copyright
© 2019, Feke et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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Decoys provide a scalable platform for identification of plant E3 ubiquitin ligases that regulate circadian function
eLife 8:e44558.
https://doi.org/10.7554/eLife.44558
Further reading
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- Plant Biology
Plant genomes encode hundreds of secreted peptides; however, relatively few have been characterised. We report here an uncharacterised, stress-induced family of plant signalling peptides, which we call CTNIPs. Based on the role of the common co-receptor BRASSINOSTEROID INSENSITIVE 1-ASSOCIATED KINASE 1 (BAK1) in CTNIP-induced responses, we identified in Arabidopsis thaliana the orphan receptor kinase HAESA-LIKE 3 (HSL3) as the CTNIP receptor via a proteomics approach. CTNIP-binding, ligand-triggered complex formation with BAK1, and induced downstream responses all involve HSL3. Notably, the HSL3-CTNIP signalling module is evolutionarily conserved amongst most extant angiosperms. The identification of this novel signalling module will further shed light on the diverse functions played by plant signalling peptides and will provide insights into receptor-ligand co-evolution.
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- Developmental Biology
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Positional information is a central concept in developmental biology. In developing organs, positional information can be idealized as a local coordinate system that arises from morphogen gradients controlled by organizers at key locations. This offers a plausible mechanism for the integration of the molecular networks operating in individual cells into the spatially coordinated multicellular responses necessary for the organization of emergent forms. Understanding how positional cues guide morphogenesis requires the quantification of gene expression and growth dynamics in the context of their underlying coordinate systems. Here, we present recent advances in the MorphoGraphX software (Barbier de Reuille et al., 2015) that implement a generalized framework to annotate developing organs with local coordinate systems. These coordinate systems introduce an organ-centric spatial context to microscopy data, allowing gene expression and growth to be quantified and compared in the context of the positional information thought to control them.
