nemhauser lab
department of biology
university of washington
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Evaluating the impact of evolution on signaling networks

Summary: Approaches for engineering new crop varieties are remarkably crude compared to the design and implementation of non-biological technology (e.g., next-generation aircraft). One strength of engineering is its ability to parse complex systems, such as a Boeing 787, into sub-networks or modules that can be analyzed in isolation. The synthetic auxin response system in yeast, developed by my lab in collaboration with Eric Klavins in the UW Electrical Engineering Department, makes it possible to interrogate the function of plant auxin signaling modules in isolation. This approach has already produced fundamental insights into the mechanisms for tuning response dynamics. In addition, it provides a high efficiency pipeline for engineering altered auxin response in a variety of plants with agricultural and industrial applications.

A comparative approach. Brassica rapa has much to offer as a study system, including the dramatically increased size of its seedlings.
Variation in degradation rate acts as a reprogrammable timer. Our work using synthetic assays of auxin response in yeast led to two conclusions: 1) the rate of auxin-induced degradation is highly variable across the large Arabidopsis Aux/IAA family, and 2) degradation rate is among the most effective tuning knobs for altering downstream transcriptional dynamics. By combining approaches drawn from synthetic and plant biology, we have discovered that we can tune the dynamics of organogenesis by engineering variants of IAA14 with altered turnover rates. We conclude that Aux/IAAs can act as auxin-initiated reprogrammable timers, facilitating context-specific dynamic cell behaviors such as re-entry into mitosis. We are excited to see whether other members of the Aux/IAA family are acting as timers in other contexts (e.g., other tissues, other developmental stages).

Variation of auxin response in plants with distinct evolutionary and ecological histories. We are just beginning to clone auxin response components from a variety of plants to test their function in our synthetic system. This comparative approach may help answer one of the oldest questions in auxin biology: how does such a simple molecule do so many different things?

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