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Discovery of small molecules that alter plant traits in a beneficial manner


The goal of University of California Riverside’s Center for Plant Cell Biology Chemical Genomics Interdisciplinary Graduate Research and Training (ChemGen IGERT) program, funded by the National Science Foundation (NSF), is to foster productive interactions between biologists, chemists, computer scientists and engineers across traditional disciplinary boundaries. To achieve this, fellows and associates of the ChemGen IGERT program actively research plant and plant pest/pathogen biology using chemical genomics as a tool. Chemical genomics is the systematic discovery of drugs that affect specific biological processes using model organisms. Implementation of this approach requires orchestrated research initiatives in genetics, biochemistry, synthetic organic chemistry, analytical chemistry, computation biology, and bioengineering. The research project of each ChemGen IGERT participant involves at least two of the target disciplines, Biology, Chemistry, Computer Sciences and Engineering, to provide significant exposure to the technologically innovative field of chemical biology.

Several of the ChemGen IGERT students have used a library of 62,000+ distinct small molecules to identify compounds that affect important plant processes including growth, response to environmental stress, and response to pathogens. The chemical genomics strategy taken by participant Sean Cutler that lead to the identification of the receptor of the plant hormone abscisic acid exemplifies the appropriateness of this approach for elucidation of important biological processes in plants. The following descriptions are exemplary research projects that involve ChemGen IGERT PhD students and faculty from multiple disciplines.

ChemGen IGERT fellow Michelle Brown aims to discover the mechanisms that control the trafficking of proteins within endomembranes. As a model for understanding these basic processes, she has focused on the mechanism of response to gravity in plants. Gravitropism requires two key elements: the rapid cycling of proteins that transport the hormone auxin to and from the cell membrane, coupled with the rapid targeting and turnover of these proteins in the central storage vacuoles. Michelle and several postdoctoral researchers under the direction of Professor Natasha Raikhel use chemical genomics to address this question. Michelle was an essential part of a team of four people who used a library of 48,000 compounds to identify 365 small molecules that have an effect on tobacco pollen germination and produce mislocalization of a membrane marker protein at the pollen tip. This part was done at UC Riverside, using compounds purchased with NSF-IGERT program funds, in collaboration with two groups from the Univ. of Gent in Belgium. In addition, 129 compounds that are active on the endomembrane system were identified. These two collections of bioactive compounds will be available for the scientific community at large for further investigations. In addition, Michelle performed a gravitropism screen on the 365 tobacco pollen germination inhibitors and cross-referenced it with the protein localization screen. One of her major achievements is the production of high-resolution movies that capture the effect of chemical compounds on fluorescent markers in live cells. These compound screens are greatly benefited by the chemi-informatic tools produced by IGERT associate Eddie Cao with Professor Thomas Girke.

In a separate project, ChemGen IGERT fellows Colleen Knoth and Melinda Salus, assisted by several undergraduates and guided by Professor Thomas Eulgem, have screened over 62,000 compounds for their ability to promote immune responses in healthy plants. Such synthetic defense elicitors have the potential to reduce infection of crops and their products by devastating pathogens. In the initial screens the potent synthetic elicitor, DCA was identified. The more recent screens have identified new promising compounds. By using mutants defective in the plant defense response, the IGERT fellows have discovered compounds that interfere with defense signaling in distinct manners. One newly identified synthetic elicitor has been tested for its defense inducing activity in Arabidopsis lines, blocked in defense signaling at different levels: nahG, wrky70-3, npr1-3, ndr1, eds1-2, and pad4. In contrast to our previously characterized synthetic elicitor DCA, this new compound is unable to induce defense in nahG plants and, thus, interferes with defense signaling in a manner distinct from DCA. They also identified four active and three inactive analogs of the new synthetic elicitor. The chemical structure of this compound was confirmed via MS, through interactions with analytical chemists at UC Riverside. Both of these activators of plant defense responses hold promise for agriculture in protecting crops and their products from damage by pathogens.

The investigations combine student training in biology, analytical and organic chemistry and bioinformatics. Both projects have included NSF-Research Experience for Undergraduate and UC Riverside undergraduate participants.

Publications and Patents:
Knoth C, Ringler J, Dangl J, Eulgem T (2007) Arabidopsis WRKY70 is required for full RPP4-mediated disease resistance and basal defense against Hyaloperonospora parasitica. Molecular Plant Microbe Interactions 20(2):120-128.

Knoth, C., Eulgem, T. (2008) The oomycete response gene LURP1 is required for defense against Hyaloperonsopora parasitica in Arabidopsis thaliana. Plant J. 2008 55(1):53-64.

Knoth. C., Salus, M., Girke, T., Eulgem, T. (2009) The synthetic elicitor 3,5-Dichloroanthranillic acid (DCA) induces NPR1-dependent and NPR1-independent mechanisms of disease resistance in Arabidopsis thaliana. Plant Physiology, 150, 333-347.

Eulgem, T., Girke, T., Knoth, C. (2008). U. S. Patent Application No. UC2008-084-3 Methods and Compositions for Providing Salicylic Acid-Independent Pathogen Resistance in Plants.

Address Goals

The activity advances basic knowledge of plant biology and may be applicable to improving agricultural productivity. The project fostered cross-disciplinary training of PhD students and undergraduates.