Quantification of prolyl cis-trans molecular switch as a timing device in auxin-regulated lateral root development in rice

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This project explores a key part of the amazing molecular circuitry that governs how a seed develops into a whole plant, and addresses a major gap in our understanding of how dynamic motions in the molecular world can influence the shape of a living organism. In rice, a specific signal-responsive molecular circuit has been identified that controls the formation of lateral roots that branch off of the main vertical root. This research project will investigate relationships between the sprouting of lateral roots and the rate of a specific molecular switch that regulates the timing of this circuit, thereby linking this molecular rate to the formation of the mature plant. These investigations will foster training of graduate and undergraduate students across multidisciplinary fields, and will be incorporated into a graduate level course on protein structure and function. Importantly, a series of four learning modules that incorporate this scientific research will be produced and then disseminated via the vast network of 4-H chapters across New York state that reaches approximately 189,000 youth in regions that include low-income rural and American Indian populations. The primary potential societal impacts are to train young scientists in an exciting area of investigation, to contribute key insights into how molecular motions govern the development of whole organisms, and to stimulate interest in scientific exploration in youth who otherwise might not be exposed to concepts that span from molecules to plants. The overall goal of this project is to quantitatively investigate the role of a specific prolyl cis-trans molecular switch that acts as a timing device in an auxin-responsive transcription regulatory circuit that governs lateral root development in rice. The specific goals are to tune the molecular switching rate using gene editing, to measure induced changes in rate using NMR spectroscopy, to quantify the resulting changes in circuit dynamics in single cells using confocal fluorescence microscopy, and to observe corresponding changes in phenotype in the whole organism. The results of these experiments will be used to establish a quantitative mathematical model for prediction of the effects of this cis-trans switching rate on cellular dynamics, with impact on phenotype. The potentially transformative aspect of the project is that if successful, it will integrate knowledge across the scales from motions of individual bonds, to the dynamics of a molecular circuit that regulates gene transcription in a single cell, to a well-defined phenotype (i.e., "genotype-to-phenotype"). This project is jointly funded by the Molecular Biophysics and Systems and Synthetic Biology Clusters in the Division of Molecular and Cellular Biosciences.