Conservation and Expansion of Transcriptional Factor Repertoire in the Fusarium oxysporum Species Complex

Abstract

The Fusarium oxysporum species complex (FOSC) includes both plant and human pathogens that cause devastating plant vascular wilt diseases and threaten public health. Each F. oxysporum genome comprises core chromosomes (CCs) for housekeeping functions and accessory chromosomes (ACs) that contribute to host-specific adaptation. This study inspects global transcription factor profiles (TFomes) and their potential roles in coordinating CC and AC functions to accomplish host-specific interactions. Remarkably, we found a clear positive correlation between the sizes of TFomes and the proteomes of an organism. With the acquisition of ACs, the FOSC TFomes were larger than the other fungal genomes included in this study. Among a total of 48 classified TF families, 14 families involved in transcription/translation regulations and cell cycle controls were highly conserved. Among the 30 FOSC expanded families, Zn2-C6 and Znf_C2H2 were most significantly expanded to 671 and 167 genes per family including well-characterized homologs of Ftf1 (Zn2-C6) and PacC (Znf_C2H2) that are involved in host-specific interactions. Manual curation of characterized TFs increased the TFome repertoires by 3% including a disordered protein Ren1. RNA-Seq revealed a steady pattern of expression for conserved TF families and specific activation for AC TFs. Functional characterization of these TFs could enhance our understanding of transcriptional regulation involved in FOSC cross-kingdom interactions, disentangle species-specific adaptation, and identify targets to combat diverse diseases caused by this group of fungal pathogens.

The differential virulence of Fusarium strains causing corneal infections and plant diseases is associated with accessory chromosome composition

“…Importantly, these ACs carry strain-specific genes that contribute to plant and human virulence, respectively. Intriguingly, ACs from both genomes also encode proteins with shared functions, including protein phosphorylation and transcriptional regulation, as supported by our previous finding (65,26) that kinase and transcription factor genes have proportionally expanded according to the sizes of AC genes in a genome. In the current study, we discovered the enrichment of AC genes contributing to chromatin assembly/disassembly in both strains.…”

“…The copyright holder for this preprint (which this version posted May 27, 2024. ; https://doi.org/10.1101/2024.05. 23.595639 doi: bioRxiv preprint ACs (also referred to as pathogenicity chromosomes) encode several functionally validated virulence factors toward plant hosts, such as Secreted in Xylem (SIX) effectors (25), transcription factors (26), and kinases (27,28). The importance of F. oxysporum ACs was demonstrated by the finding that a non-pathogenic F. oxysporum strain became virulent upon receiving ACs from a pathogenic strain (21,29,30).…”