Plant metabolic clusters – from genetics to genomics

Abstract

Summary Plant natural products are of great value for agriculture, medicine and a wide range of other industrial applications. The discovery of new plant natural product pathways is currently being revolutionized by two key developments. First, breakthroughs in sequencing technology and reduced cost of sequencing are accelerating the ability to find enzymes and pathways for the biosynthesis of new natural products by identifying the underlying genes. Second, there are now multiple examples in which the genes encoding certain natural product pathways have been found to be grouped together in biosynthetic gene clusters within plant genomes. These advances are now making it possible to develop strategies for systematically mining multiple plant genomes for the discovery of new enzymes, pathways and chemistries. Increased knowledge of the features of plant metabolic gene clusters – architecture, regulation and assembly – will be instrumental in expediting natural product discovery. This review summarizes progress in this area.

Genome-Wide Prediction of Metabolic Enzymes, Pathways, and Gene Clusters in Plants

“…In bacteria and fungi, which also produce a large array of specialized metabolites, many biosynthetic pathways are organized into physically colocalized metabolic gene clusters (Cimermancic et al, 2014;Wisecaver and Rokas, 2015). Plant metabolic pathways are generally not known to occur in clusters, although there are now about 20 reported cases of specialized metabolic pathways that occur as gene clusters (Boycheva et al, 2014;Nützmann and Osbourn, 2014;Nützmann et al, 2016). Bioinformatic approaches have recently identified hundreds of metabolic gene clusters in Arabidopsis (Arabidopsis thaliana), rice (Oryza sativa), and sorghum (Sorghum bicolor; Chae et al, 2014) and collocated gene pairs between terpene synthases and oxidoreductases in several plant species (Boutanaev et al, 2015).…”

Discovery, Biosynthesis and Stress-Related Accumulation of Dolabradiene-Derived Defenses in Maize

“…The nearly ubiquitous presence of ZmAN2 as a pathogen defense transcript marker is consistent with the essential biosynthetic role in the modular formation of multiple specialized diterpenoid metabolites, including not only A-and B-series kauralexins but also dolabralexins. Notably, ZmAN2 does not cluster with any class I diTPSs in the maize genome, illustrating a different genomic organization of diterpenoid metabolism in maize as compared with rice and tomato (Solanum lycopersicum), where several specialized diterpenoid pathways form functional biosynthetic clusters (Matsuba et al, 2013;Nützmann et al, 2016). However, the presence of the uncharacterized class II diTPSs ZmCPS3 and ZmCPS4 suggests that specialized diterpenoid metabolism in maize likely follows the common modular blueprint of combining different diTPS and P450 enzymes, as shown for rice, wheat, and various other species across the plant kingdom (Xu et al, 2007a;Zhou et al, 2012;Hall et al, 2013;Cui et al, 2015;Zerbe and Bohlmann, 2015).…”

A Metabolic Gene Cluster in the Wheat W1 and the Barley Cer-cqu Loci Determines β-Diketone Biosynthesis and Glaucousness

“…These clusters clearly share a few typical features detected in other metabolic gene clusters to date. These include (1) a typical size of a several hundred kilobases (800 kb in wheat), (2) the presence of at least three genes, (3) the involvement of genes encoding a minimum of three types of biosynthetic enzymes, and (4) the tight coexpression of the clustered genes (Nützmann and Osbourn, 2014;Nützmann et al, 2016). Another common feature of plant metabolic gene clusters is the presence of an enzyme catalyzing the first committed step in the pathway.…”