Abstract
Identification of enzymes, regulators and transporters involved in different metabolic processes is the foundation to understand how organisms function. There are, however, many difficulties in identifying candidate genes as well as in proving their in vivo roles. In this review, we describe different approaches utilized in Arabidopsis thaliana to identify gene candidates and experiments required to prove the function of a given candidate. For example, we use the production of methionine-derived aliphatic glucosinolates that represent major defence compounds in A. thaliana. Nearly all biosynthetic genes, as well as the first sets of regulators and transporters, have been identified. An array of approaches, i.e. classical mapping, quantitative trait loci (QTL) mapping, eQTL mapping, co-expression, genome wide association studies (GWAS), mutant screens and phylogenetic analyses, has been exploited to increase the number of identified genes. Here we summarize the lessons learned from the different approaches used over the years with the aim to help designing and combining new approaches in the future.
About the authors
Lea Møller Jensen holds an MSc in Biology-Biotechnology from 2010 received her PhD degree from the Faculty of Science at the University of Copenhagen in 2014. Her research interests lies within understanding the regulatory networks controlling glucosinolate biosynthesis and how these link to other phenotypes crucial for plant survival. The research aims at understanding how natural variation impacts the link from genotype-to-phenotype. Elucidation of the underlying molecular mechanisms is a necessity for understanding variation and changes in these regulatory networks.
Barbara Ann Halkier, Head of DynaMo Center of Excellence at the University of Copenhagen, is leading in the field within pathway elucidation, identification of biosynthetic genes, and transporters of glucosinolates. She is actively pursuing pathway engineering in various host organisms, and has produced glucosinolates in yeast on a robust platform based on stable genomic expression. She has identified the NPF family as transporter family for secondary metabolites, exemplified by the glucosinolate transporters AtGTR1 and AtGTR2. She has generated highly valuable tool in the form of transporter cDNA libraries to be expressed in Xenopus oocytes and screened for uptake of small molecules. She has advanced ligase-independent USER cloning technologies for high-throughput transfer of cDNAs in systems biology.
Meike Burow is renowned for contributions to our understanding of the biosynthesis and activation of glucosinolates. In particular, her studies on plant specifier proteins gave new insights in the evolution and ecological functions the glucosinolate-myrosinase system. Her current research spans protein biochemistry, protein-protein interaction studies, regulatory networks and RNA-mediated regulation to exploit the well-studied biosynthetic pathway to glucosinolates as model system for studying complex regulatory mechanisms and their genetic bases in plants.
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