The rate of protein turnover can act as a pacemaker to coordinate responses within and between cells, and is frequently dysregulated in human disease. Yet we know remarkably little about what controls substrate degradation kinetics or how these kinetics translate into downstream responses. One possible reason is the lack of available models for high- resolution structure-function analysis of degradation and transcriptional activation. The SCF class of E3 ubiquitin ligases is highly conserved among animals, plants and fungi. We propose to use an SCF involved in auxin response, at the heart of nearly every aspect of plant biology, as a model to investigate general principles underlying E3 function and connect that function to transcriptional activation and morphogenesis. The small-molecule triggered degradation in the auxin pathway offers a unique advantage for these studies, and has facilitated our engineering of auxin-induced degradation and transcriptional activation in yeast. Work with this system has led to our central hypothesis: the auxin system functions as a universal developmental timer in plants, and similar logic circuits likely act in most eukaryotes. To test this hypothesis, we propose to: (1) Define the determinants and relevance of variation in degradation rates. We have already identified several domains of interest in E3 and substrate components, and are using synthetic and computational tools to connect individual residues to degradation dynamics. (2) Quantify the impact of degradation rate on transcriptional repression. We have extended our synthetic assays to include auxin-induced transcription. We can now quantitatively track the molecular events between substrate turnover and downstream responses over time. This technology enables our study of previously intractable problems like how the removal of co-repressors is integrated with transcriptional activation. (3) Couple cellular degradation timers to developmental transitions. We have shown in transgenic plants that substrate degradation rate sets the pace of lateral organ development. We will use multiple, complementary approaches to analyze the transcriptome of these plants to elucidate how the timing of substrate turnover regulates developmental progression in a cell-type-dependent manner. Together, the proposed work will provide a mechanistic framework for E3 function in the auxin response and potentially provide insights into fundamental properties of E3:substrate interactions and downstream events. These insights can inform our understanding of E3s associated with human disease, as well as guiding future design of synthetic circuits using auxin components for therapeutic applications.

Public Health Relevance

Ubiquitin-mediated protein degradation is key to cellular homeostasis and is often disrupted in human disease. The human genome encodes more E3s than protein kinases, and the specificity of E3:substrate interactions makes them attractive drug targets. A structural and biochemical understanding of the dynamic nature of E3:substrate interactions and their link to transcriptional control, especially in a readily-screenable synthetic context, might allow new breakthroughs in this area.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
Project #
Application #
Study Section
Membrane Biology and Protein Processing Study Section (MBPP)
Program Officer
Hoodbhoy, Tanya
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
University of Washington
Schools of Arts and Sciences
United States
Zip Code
de Lange, Orlando; Klavins, Eric; Nemhauser, Jennifer (2018) Synthetic genetic circuits in crop plants. Curr Opin Biotechnol 49:16-22
Khakhar, Arjun; Leydon, Alexander R; Lemmex, Andrew C et al. (2018) Synthetic hormone-responsive transcription factors can monitor and re-program plant development. Elife 7:
Wright, R Clay; Zahler, Mollye L; Gerben, Stacey R et al. (2017) Insights into the Evolution and Function of Auxin Signaling F-Box Proteins in Arabidopsis thaliana Through Synthetic Analysis of Natural Variants. Genetics 207:583-591
Pierre-Jerome, Edith; Wright, R Clay; Nemhauser, Jennifer L (2017) Characterizing Auxin Response Circuits in Saccharomyces cerevisiae by Flow Cytometry. Methods Mol Biol 1497:271-281
Dezfulian, Mohammad H; Jalili, Espanta; Roberto, Don Karl A et al. (2016) Oligomerization of SCFTIR1 Is Essential for Aux/IAA Degradation and Auxin Signaling in Arabidopsis. PLoS Genet 12:e1006301
Taylor-Teeples, Mallorie; Lanctot, Amy; Nemhauser, Jennifer L (2016) As above, so below: Auxin's role in lateral organ development. Dev Biol 419:156-164
Pierre-Jerome, Edith; Moss, Britney L; Lanctot, Amy et al. (2016) Functional analysis of molecular interactions in synthetic auxin response circuits. Proc Natl Acad Sci U S A 113:11354-11359
Nemhauser, Jennifer L; Torii, Keiko U (2016) Plant synthetic biology for molecular engineering of signalling and development. Nat Plants 2:16010
Galli, Mary; Liu, Qiujie; Moss, Britney L et al. (2015) Auxin signaling modules regulate maize inflorescence architecture. Proc Natl Acad Sci U S A 112:13372-7
Yu, Hong; Zhang, Yi; Moss, Britney L et al. (2015) Untethering the TIR1 auxin receptor from the SCF complex increases its stability and inhibits auxin response. Nat Plants 1:

Showing the most recent 10 out of 13 publications