Synthetic hormone-responsive transcription factors can monitor and reprogram plant development

Arjun Khakhar, Alexander R. Leydon, Andrew C. Lemmex, Eric Klavins, Jennifer L. Nemhauser

Research output: Contribution to journalArticlepeer-review

12 Scopus citations


Developmental programs sculpt plant morphology to meet environmental challenges, and these same programs have been manipulated to increase agricultural productivity (Doebley et al., 1997; Khush, 2001). Hormones coordinate these programs, creating chemical circuitry (Vanstraelen and Benková, 2012) that has been represented in mathematical models (Refahi et al., 2016; Prusinkiewicz et al., 2009); however, model-guided engineering of plant morphology has been limited by a lack of tools (Parry et al., 2009; Voytas and Gao, 2014). 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 models (Refahi et al., 2016; Prusinkiewicz et al., 2009).

Original languageEnglish (US)
Article numbere34702
StatePublished - May 1 2018
Externally publishedYes

Bibliographical note

Funding Information:
We thank Dr. Takato Imazumi for sharing resources and advice, particularly on luciferase imaging; Dr. Dominic Loque for materials to build the yeast artificial chromosomes ahead of publication; Ms. Mrunmayee Shete and the Aquarium team for technical assistance; Dr. Mallorie Taylor-Teeples for resources and advice related to phyllotactic patterning; and Dr. Hardik Gala for advice on microscopy. We would like to thank Mr. Randolph Lopez and Dr. Clay Wright for commenting on the manuscript, and all members of the Klavins, Seelig and Nemhauser labs for their advice and input. This work was supported by shared grants to EK and JLN from the National Science Foundation (MCB-1411949) and the National Institutes of Health (R01-GM107084), as well as support from the Howard Hughes Medical Institute Faculty Scholars Program to JLN.

Publisher Copyright:
© Khakhar et al.


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