Email updates

Keep up to date with the latest news and content from BMC Systems Biology and BioMed Central.

Open Access Highly Accessed Research article

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

Katherine Lawler12*, Kim Hammond-Kosack3, Alvis Brazma1 and Richard MR Coulson14

Author Affiliations

1 European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK

2 Institute for Mathematical and Molecular Biomedicine, King’s College London, Hodgkin Building, London SE1 1UL, UK

3 Department of Plant Biology and Crop Science, Rothamsted Research, Harpenden, Herts AL5 2JQ, UK

4 Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK

For all author emails, please log on.

BMC Systems Biology 2013, 7:52  doi:10.1186/1752-0509-7-52

Published: 27 June 2013

Abstract

Background

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 topological structure of transcriptional networks was also examined to investigate control mechanisms for mycotoxin biosynthesis and other processes.

Results

The 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.

Conclusions

Proteins 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.

Keywords:
Transcriptional networks; DNA-binding domains; mycotoxin biosynthesis; filamentous fungi; gene clusters