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Establishing a Pipeline for Exploration of Chemical Space in Plant Secondary Metabolomes


Researchers in the lab of Professor Cynthia K. Larive at the University of California, Riverside are establishing a pipeline for rapid screening, analysis, and characterization of plant secondary compounds. These specialized molecules are produced in biochemical pathways regulated during development and by environmental cues. Many of plant secondary compounds are known to provide health benefits to humans. Some secondary compounds are produced to deter or recruit other organisms whereas others protect against environmental (abiotic) threats to survival. Plant secondary compounds are immensely variable, with thousands of unique molecules present in a single plant. To some extent, the diversity in chemical structure of these compounds results from an evolutionary arms race between plants and the stresses they encounter.

Kayla A. Kaiser, a fellow supported by the NSF-ChemGen Integrative Graduate Education and Research Trainee Program at University of California, Riverside performed a summer internship at the Max-Planck Institute for Chemical Ecology in Jena, Germany where she received additional training in natural product isolation and characterization in the lab of Professor Bernd Schneider. These skills have been applied to an ongoing collaboration with University of California, Riverside Professor Julia Bailey-Serres utilizing a model plant Arabidopsis thaliana to unravel metabolic strategies for survival of low oxygen stress. Kayla’s cross-disciplinary project has enabled her to become proficient in both analytical chemistry and basic methods in plant molecular genetics. In her hands, plant cultivation and application of stress, analytical method development, data and workflow management have been optimized to allow maximum biological information to be recorded in each experiment. She implements statistical analyses to form new hypotheses in an iterative process. Her studies with Arabidopsis thaliana have been extended to analyses of human foodstuffs including rice, citrus, and pomegranate. IGERT fellows Gregory Barding and Daniel Orr are contributors to this project.

Address Goals

Our work in plant metabolomics utilizes the latest techniques in molecular biology, genetics, analytical and organic chemistry, chemometrics and bioinformatics. The comingling of state-of-the-art laboratory approaches as well as financial and administrative support specifically for interdisciplinary work has brought us closer to our goal of plant metabolomic coverage. There are several centers of research excellence in this field; Western Australia, London, Geneva, Tokyo, and Berlin. Our work has maintained the reputation of University of California as one of the world’s leading contributors to advancing our understanding of basic plant biology.

As we currently work in a post-genomic era, researchers in all types of model organisms are taking new strategies to functional annotation of genes. Metabolomics represents one important approach to this task. It is estimated that 15-20% of Arabidopsis genes encode enzymes of secondary metabolism, facilitating the evolutionary arms race that plants engage in with their environment. Without analytical strategies for metabolite identification and quantification, as well as data management strategies for extracting knowledge out of huge amounts of data, we cannot make progress with discoveries in this area. The potential benefits of understanding plant primary and secondary metabolism lie in genetic engineering of crops or medicinal plants with enhanced desirable properties and reduced undesirable traits or enhanced survivability under environmental pressure, providing food of higher quality and in greater yield. This will maintain the US’ reputation as a research leader as well as protecting the security of our citizens.