title: Compartmentalized gene regulatory network of the pathogenic fungus Fusarium graminearum.
abstract: Head blight caused by Fusarium graminearum threatens world-wide wheat production, resulting in both yield loss and mycotoxin contamination. We reconstructed the global F. graminearum gene regulatory network (GRN) from a large collection of transcriptomic data using Bayesian network inference, a machine-learning algorithm. This GRN reveals connectivity between key regulators and their target genes. Focusing on key regulators, this network contains eight distinct but interwoven modules. Enriched for unique functions, such as cell cycle, DNA replication, transcription, translation and stress responses, each module exhibits distinct expression profiles. Evolutionarily, the F. graminearum genome can be divided into core regions shared with closely related species and variable regions harboring genes that are unique to F. graminearum and perform species-specific functions. Interestingly, the inferred top regulators regulate genes that are significantly enriched from the same genomic regions (P < 0.05), revealing a compartmentalized network structure that may reflect network rewiring related to specific adaptation of this plant pathogen. This first-ever reconstructed filamentous fungal GRN primes our understanding of pathogenicity at the systems biology level and provides enticing prospects for novel disease control strategies involving the targeting of master regulators in pathogens. The program can be used to construct GRNs of other plant pathogens.
authors.affiliation: Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA, 01003, USA.
authors.forename: Li
authors.initials: L
authors.lastname: Guo
authors.affiliation: Department of Electrical & Computer Engineering, University of Massachusetts Amherst, Amherst, MA, 01003, USA.
authors.forename: Guoyi
authors.initials: G
authors.lastname: Zhao
authors.affiliation: Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, 47907, USA.
authors.forename: Jin-Rong
authors.initials: JR
authors.lastname: Xu
authors.affiliation: USDA-ARS, Cereal Disease Laboratory, University of Minnesota, St Paul, MN, 55108, USA.
authors.forename: H Corby
authors.initials: HC
authors.lastname: Kistler
authors.affiliation: Department of Electrical & Computer Engineering, University of Massachusetts Amherst, Amherst, MA, 01003, USA.
authors.forename: Lixin
authors.initials: L
authors.lastname: Gao
authors.affiliation: Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA, 01003, USA.
authors.forename: Li-Jun
authors.initials: LJ
authors.lastname: Ma
mesh_terms: D001483:Base Sequence; D005670:Fusarium / Q000235:genetics* / Q000472:pathogenicity*; D053263:Gene Regulatory Networks; D017343:Genes, Plant; D060066:Protein Interaction Maps / Q000235:genetics; D015203:Reproducibility of Results; D013045:Species Specificity; D014157:Transcription Factors / Q000378:metabolism; D014774:Virulence / Q000235:genetics
chemical_list: D014157:Transcription Factors
keywords: Bayesian network inference; Fusarium graminearum; cell circuits; modularity; network rewire and fungal pathogenesis