1. Plant Biology
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Synthetic hormone-responsive transcription factors can monitor and re-program plant development

  1. Arjun Khakhar
  2. Alexander R Leydon
  3. Andrew C Lemmex
  4. Eric Klavins
  5. Jennifer L Nemhauser  Is a corresponding author
  1. University of Washington, United States
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Cite this article as: eLife 2018;7:e34702 doi: 10.7554/eLife.34702

Abstract

Developmental programs sculpt plant morphology to meet environmental challenges, and these same programs have been manipulated to increase agricultural productivity1,2. Hormones coordinate these programs, creating chemical circuitry3 that has been represented in mathematical models4,5; however, model-guided engineering of plant morphology has been limited by a lack of tools6,7. Here, we introduce a novel set of synthetic and modular hormone activated Cas9-based repressors (HACRs) in Arabidopsis thaliana that respond to three hormones: auxin, gibberellins and jasmonates. We demonstrate that HACRs are sensitive to both exogenous hormone treatments and local differences in endogenous hormone levels associated with development. We further show that this capability can be leveraged to reprogram development in an agriculturally relevant manner by changing how the hormonal circuitry regulates target genes. By deploying a HACR to re-parameterize the auxin-induced expression of the auxin transporter PIN-FORMED1 (PIN1), we decreased shoot branching and phyllotactic noise, as predicted by existing models4,5.

Data availability

Links to all plasmid sequences are in manuscript and data analysis code is available on github.

Article and author information

Author details

  1. Arjun Khakhar

    Department of Electrical Engineering, University of Washington, Seattle, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-4676-6533
  2. Alexander R Leydon

    Department of Biology, University of Washington, Seattle, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Andrew C Lemmex

    Department of Biology, University of Washington, Seattle, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Eric Klavins

    Department of Electrical Engineering, University of Washington, Seattle, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. Jennifer L Nemhauser

    Department of Biology, University of Washington, Seattle, United States
    For correspondence
    jn7@uw.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-8909-735X

Funding

National Science Foundation (MCB-1411949)

  • Eric Klavins

National Institutes of Health (R01-GM107084)

  • Jennifer L Nemhauser

Howard Hughes Medical Institute (Faculty Scholars Program)

  • Jennifer L Nemhauser

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Dominique C Bergmann, Stanford University/HHMI, United States

Publication history

  1. Received: January 2, 2018
  2. Accepted: April 30, 2018
  3. Accepted Manuscript published: May 1, 2018 (version 1)
  4. Version of Record published: May 30, 2018 (version 2)

Copyright

© 2018, Khakhar 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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Further reading

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    Sonia Accossato et al.
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    Chloroplast biogenesis describes the transition of non-photosynthetic proplastids to photosynthetically active chloroplasts in the cells of germinating seeds. Chloroplast biogenesis requires the import of thousands of nuclear-encoded preproteins by essential import receptor TOC159. We demonstrate that the small ubiquitin-related modifier (SUMO) pathway crosstalks with the ubiquitin–proteasome pathway to affect TOC159 stability during early plant development. We identified a SUMO3-interacting motif (SIM) in the TOC159 GTPase domain and a SUMO3 covalent SUMOylation site in the membrane domain. A single K to R substitution (K1370R) in the M-domain disables SUMOylation. Compared to wild-type TOC159, TOC159K1370R was destabilized under UPS-inducing stress conditions. However, TOC159K1370R recovered to same protein level as wild-type TOC159 in the presence of a proteasome inhibitor. Thus, SUMOylation partially stabilizes TOC159 against UPS-dependent degradation under stress conditions. Our data contribute to the evolving model of tightly controlled proteostasis of the TOC159 import receptor during proplastid to chloroplast transition.

    1. Cell Biology
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    Research Article Updated

    The chloroplast proteome contains thousands of different proteins that are encoded by the nuclear genome. These proteins are imported into the chloroplast via the action of the TOC translocase and associated downstream systems. Our recent work has revealed that the stability of the TOC complex is dynamically regulated by the ubiquitin-dependent chloroplast-associated protein degradation pathway. Here, we demonstrate that the TOC complex is also regulated by the small ubiquitin-like modifier (SUMO) system. Arabidopsis mutants representing almost the entire SUMO conjugation pathway can partially suppress the phenotype of ppi1, a pale-yellow mutant lacking the Toc33 protein. This suppression is linked to increased abundance of TOC proteins and improvements in chloroplast development. Moreover, data from molecular and biochemical experiments support a model in which the SUMO system directly regulates TOC protein stability. Thus, we have identified a regulatory link between the SUMO system and the chloroplast protein import machinery.