In silico prediction and characterisation of secondary metabolite clusters in the plant pathogenic fungus Verticillium dahliae.

Xiaoqian Shi-Kunne,Jasper R L Depotter,Malaika K Ebert,Roger De Pedro Jové,Michael F Seidl,Bart P H J Thomma

doi:10.1093/femsle/fnz081

Abstract

ABSTRACTFungi are renowned producers of natural compounds, also known as secondary metabolites (SMs) that display a wide array of biological activities. Typically, the genes that are involved in the biosynthesis of SMs are located in close proximity to each other in so-called secondary metabolite clusters. Many plant-pathogenic fungi secrete SMs during infection in order to promote disease establishment, for instance as cytocoxic compounds. Verticillium dahliae is a notorious plant pathogen that can infect over 200 host plants worldwide. However, the SM repertoire of this vascular pathogen remains mostly uncharted. To unravel the potential of V. dahliae to produce SMs, we performed in silico predictions and in-depth analyses of its secondary metabolite clusters. Using distinctive traits of gene clusters and the conserved signatures of core genes 25 potential SM gene clusters were identified. Subsequently, phylogenetic and comparative genomics analyses were performed, revealing that two putative siderophores, ferricrocin and TAFC, DHN-melanin and fujikurin may belong to the SM repertoire of V. dahliae.

Highlights

Filamentous fungi are known for their ability to produce a vast array of distinct chemical compounds that are known as secondary metabolites (SMs) (Keller, Turner and Bennett 2005)
The putative secondary metabolite clusters (SMCs) were classified as nine type I polyketides synthases (PKSs), one type III PKS, one PKS-non-ribosomal peptide synthetases (NRPSs), three NRPSs and four terpenes
We found that each of these SMCs contains one core gene

Summary

INTRODUCTION

Filamentous fungi are known for their ability to produce a vast array of distinct chemical compounds that are known as secondary metabolites (SMs) (Keller, Turner and Bennett 2005). Genes involved in the synthesis of SMs are frequently located in close proximity to each other, forming so-called secondary metabolite clusters (SMCs) (Keller and Hohn 1997; Brakhage and Schroeckh 2011; Wiemann and Keller 2014) Most of these SMCs contain one biosynthetic core gene that is flanked by transporter proteins, transcription factors and genes encoding tailoring enzymes that modify the SM structure (Keller and Hohn 1997; Keller, Turner and Bennett 2005). Phylogenetic and comparative genomics analyses are very informative as the number of fungal genomes and characterised SM pathways increases These two approaches are very helpful to identify gene clusters that are involved in the production of SMs that have been characterised in other fungal species and allow subsequent predictions of identical or related compounds that a particular fungal species might produce (Medema , Takano and Breitling 2013; Cairns and Meyer 2017). We conducted an in silico analysis to unravel the potential secondary metabolism of V. dahliae by making use of the gapless genome assembly of strain JR2 (Faino et al 2015)

MATERIALS AND METHODS

RESULTS AND DISCUSSION

CONCLUSIONS