Gene-centric discovery of novel secondary metabolite biosynthetic pathways in Arabidopsis thaliana
- Plants have the capacity to produce a vast array of small molecules in order to interact with and reshape their environment. These so-called secondary metabolites can have diverse biological roles, acting in protection against pathogens and abiotic stresses, uptake of nutrients, and interspecies communication, for instance. Understanding how and why specific secondary metabolites are produced is of significant interest not only from a basic biological perspective, but also because it can enable engineering of hardier plant varieties. Such understanding requires elucidation of a specific metabolite's biosynthetic pathway -- the set of enzymes that carry out the chemical transformations needed to generate the metabolite from ubiquitous small molecule building blocks. Pathway discovery has traditionally been tedious due to the inherent complexity of plant metabolism and genomic organization; today, however, the availability of whole genome sequences and global transcriptional datasets promises to greatly accelerate this process. Here, we describe a gene-centric approach for the discovery of novel secondary metabolite biosynthetic pathways of biological interest in the model plant Arabidopsis thaliana. Guided by gene expression evidence, we characterize the biochemical function of candidate enzymes of unknown function by metabolic profiling of knockout mutants, followed by coexpression analysis to identify additional pathway enzymes. Chemical and biological characterization of the secondary metabolites produced allows us to probe their likely ecological functions. Three novel metabolite types discovered using applications of this approach are presented: indole-3-carbonyl nitrile (ICN) and derivatives, indolic alkaloids which function in pathogen defense; sideretin, an oxidized coumarin that facilitates iron acquisition from the soil via a reductive mechanism; and cysteine-rich peptides exuded by roots in response to zinc deficiency, whose biological functions are not yet clear. In the first two cases, we describe the complete biosynthetic pathways of both ICN and sideretin and the chemical syntheses of all pathway products. This work demonstrates the broad applicability of gene-centric approaches that leverage the availability of large-scale datasets for identification of biologically significant secondary metabolite pathways, and paves the way for engineering plant varieties with enhanced tolerance to disease and low micronutrient availability.
|Type of resource
|electronic; electronic resource; remote
|1 online resource.
|Stanford University, Department of Chemical Engineering.
|Khosla, Chaitan, 1964-
|Khosla, Chaitan, 1964-
|Statement of responsibility
|Submitted to the Department of Chemical Engineering.
|Thesis (Ph.D.)--Stanford University, 2016.
- © 2016 by Jakub Rajniak
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