Genomic clustering and co-regulation of transcriptional networks in the pathogenic fungus Fusarium graminearum.

Katherine Lawler,Kim Hammond-Kosack,Richard Mr Coulson,Alvis Brazma

doi:10.1186/1752-0509-7-52

Abstract

BackgroundGenes for the production of a broad range of fungal secondary metabolites are frequently colinear. The prevalence of such gene clusters was systematically examined across the genome of the cereal pathogen Fusarium graminearum. The topological structure of transcriptional networks was also examined to investigate control mechanisms for mycotoxin biosynthesis and other processes.ResultsThe genes associated with transcriptional processes were identified, and the genomic location of transcription-associated proteins (TAPs) analyzed in conjunction with the locations of genes exhibiting similar expression patterns. Highly conserved TAPs reside in regions of chromosomes with very low or no recombination, contrasting with putative regulator genes. Co-expression group profiles were used to define positionally clustered genes and a number of members of these clusters encode proteins participating in secondary metabolism. Gene expression profiles suggest there is an abundance of condition-specific transcriptional regulation. Analysis of the promoter regions of co-expressed genes showed enrichment for conserved DNA-sequence motifs. Potential global transcription factors recognising these motifs contain distinct sets of DNA-binding domains (DBDs) from those present in local regulators.ConclusionsProteins associated with basal transcriptional functions are encoded by genes enriched in regions of the genome with low recombination. Systematic searches revealed dispersed and compact clusters of co-expressed genes, often containing a transcription factor, and typically containing genes involved in biosynthetic pathways. Transcriptional networks exhibit a layered structure in which the position in the hierarchy of a regulator is closely linked to the DBD structural class.

Highlights

Genes for the production of a broad range of fungal secondary metabolites are frequently colinear
The F. graminearum genes encoding proteins associated with the transcriptional process were identified by protein family detection and profile matching: of the 14,100 protein entries comprising the F. graminearum genome [17], 723 were linked to transcription
Sequences orthologous to these 723 Transcriptionassociated protein (TAP) were obtained from 56 complete eukaryotic genomes through sequence searching (‘Detection of F. graminearum TAP orthologues’ in Methods), and placed into one of five categories derived from the TAP reference set functional annotations, namely basal transcription factors and cofactors (B), RNA polymerase subunits (P), DNA binding (D), chromatin remodelling and histone modification factors (C) and others (O)

Summary

Introduction

Genes for the production of a broad range of fungal secondary metabolites are frequently colinear. The prevalence of such gene clusters was systematically examined across the genome of the cereal pathogen Fusarium graminearum. The genomes of nematodes and trypanosomes exhibit polycistronic transcription of gene clusters [2,3], though most eukaryotic genes are generally considered to be monocistronic, each with its own. This suggests that higher order genome organisation is linked to expression patterns. Co-expression in eukaryotes could reduce stochastic differences in gene expression and synchronise fluctuations, or noise, in the levels of components of pathways and complexes [12]

Methods

Results

Discussion

Conclusion