EBR1 genomic expansion and its role in virulence of Fusarium species

Abstract

Genome sequencing of Fusarium oxysporum revealed that pathogenic forms of this fungus harbour supernumerary chromosomes with a wide variety of genes, many of which likely encode traits required for pathogenicity or niche specialization. Specific transcription factor gene families are expanded on these chromosomes including the EBR1 family (Enhanced Branching). The significance of the EBR1 family expansion on supernumerary chromosomes and whether EBR1 paralogues are functional is currently unknown. EBR1 is found as a single copy in F.graminearum and other fungi but as multiple paralogues in pathogenic F.oxysporum strains. These paralogues exhibit sequence and copy number variation among different host-specific strains and even between more closely related strains. Relative expression of the EBR1 paralogues depends on growth conditions and on the presence of the single EBR1 gene in the core genome. Deletion of EBR1 in the core genome in different F.oxysporum strains resulted in impaired growth, reduced pathogenicity and slightly reduced biocontrol capacities. To identify genes regulated by EBR1, the transcriptomes of wild-type and Δebr1 strains were compared for both F.oxysporum and F.graminearum. These studies showed that in both species, EBR1 regulates genes involved in general metabolism as well as virulence.

Transcription Factors Encoded on Core and Accessory Chromosomes of Fusarium oxysporum Induce Expression of Effector Genes

“…We found 13 predicted transcription factor genes that cluster into nine families. The transcription factor gene families were numbered TF1 to TF9 and include one homolog of EBR1 ( TF8 ) and three homologs of FTF1 ( TF1 ) (Fig 1, S1 Data: tab ‘TF table’ ) [35,37]. Most gene families encode proteins containing zinc finger DNA binding domains; four are Cys2His2 zinc finger DNA binding domains (Tf3, Tf4, Tf6 and Tf7) and two are Zn(2)Cys(6) zinc finger DNA binding domains (Tf1 and Tf8).…”

“…graminearum , and orthologs of cTF4 and cTF9 are required for pathogenicity of F . graminearum (FGSG_10057, FGSG_10517 and FGSG_06651 respectively) [37,62]. Of these three transcription factors, we have only obtained a DNA binding site for cTf4, which is, like the DNA binding sites of aTf2, aTf5 and aTf7, not enriched among genes up- or down-regulated during infection.…”

Living apart together: crosstalk between the core and supernumerary genomes in a fungal plant pathogen

“…Notable instances include the transcription factor EBR1 [41, 42], key component of the RNA silencing pathway Dicer2 [43] and the secondary metabolite backbone gene PKS8 [44]. In the case of EBR1 , up to 11 duplications were found.…”

“…In F. oxysporum f. sp. lycopersici it has undergone gene duplication on the supernumerary chromosomes [41], which seemingly has independently occurred on the supernumerary chromosomes of F. poae . In Metarhizium , it has been hypothesized that an arrest of RIP was instrumental in the evolution to generalist infection agents [54], and the advantages of a temporary RIP relaxation or arrest may include accelerated evolution and divergence between related species [2].…”

The FTF gene family regulates virulence and expression of SIX effectors in Fusarium oxysporum

“…lycopersici, and thus is part of the core genome, whereas the other EBR paralogues are located in LS chromosomes. Mutants altered in EBR1 showed reduced growth when grown in culture and reduced virulence against tomato plants (Jonkers et al, 2013).…”