Kinome Expansion in the Fusarium oxysporum Species Complex Driven by Accessory Chromosomes

Abstract

The Fusarium oxysporum species complex (FOSC) is a group of soilborne pathogens causing severe disease in more than 100 plant hosts, while individual strains exhibit strong host specificity. Both chromosome transfer and comparative genomics experiments have demonstrated that lineage-specific (LS) chromosomes contribute to the host-specific pathogenicity. However, little is known about the functional importance of genes encoded in these LS chromosomes. Focusing on signaling transduction, this study compared the kinomes of 12 F. oxysporum isolates, including both plant and human pathogens and 1 nonpathogenic biocontrol strain, with 7 additional publicly available ascomycete genomes. Overall, F. oxysporum kinomes are the largest, facilitated in part by the acquisitions of the LS chromosomes. The comparative study identified 99 kinases that are present in almost all examined fungal genomes, forming the core signaling network of ascomycete fungi. Compared to the conserved ascomycete kinome, the expansion of the F. oxysporum kinome occurs in several kinase families such as histidine kinases that are involved in environmental signal sensing and target of rapamycin (TOR) kinase that mediates cellular responses. Comparative kinome analysis suggests a convergent evolution that shapes individual F. oxysporum isolates with an enhanced and unique capacity for environmental perception and associated downstream responses.IMPORTANCE Isolates of Fusarium oxysporum are adapted to survive a wide range of host and nonhost conditions. In addition, F. oxysporum was recently recognized as the top emerging opportunistic fungal pathogen infecting immunocompromised humans. The sensory and response networks of these fungi undoubtedly play a fundamental role in establishing the adaptability of this group. We have examined the kinomes of 12 F. oxysporum isolates and highlighted kinase families that distinguish F. oxysporum from other fungi, as well as different isolates from one another. The amplification of kinases involved in environmental signal relay and regulating downstream cellular responses clearly sets Fusarium apart from other Ascomycetes Although the functions of many of these kinases are still unclear, their specific proliferation highlights them as a result of the evolutionary forces that have shaped this species complex and clearly marks them as targets for exploitation in order to combat disease.

Keywords: Fusarium oxysporum species complex; TOR kinase; accessory chromosome; histidine kinase; kinome.

FIG 1

Kinomes across Ascomycota. (a) A neighbor-joining tree constructed from conserved genome genes showing the phylogenetic relationship among the Fusarium species used in this study. (b) Kinases were broken up into major families and abundance per family plotted per species. The individual groups are indicated by colors as shown in the color key. (c) Total gene count plotted against kinome size in each genome. The origin coordinates are y = 100 and x = 2,500. The shortened genome names used in panels a to c are given in Table 1. (d) By eliminating kinases missing from more than one species, we compiled “conserved kinomes” for Ascomycetes (all fungi here), filamentous fungi (all but S. cerevisiae and S. pombe), the genus Fusarium, and the FOSC. Some families remain relatively stable across species (group i [AGC, CAMK, CK, Other, and STE]), while others expand due to increased copy number or increased subfamily number (group ii [Atypical, CMGC, and HisK]). The total sizes of conserved kinomes follow: 99 for ascomycetes, 108 for filamentous fungi, 126 for fusaria, and 128 for FOSC.

FIG 2

TOR kinase expansion through the LS genome. (a) A phylogenetic tree of TOR kinases constructed by the neighbor-joining (NJ) algorithm using TOR kinase protein sequence alignment based on the kinase domain. The core and LS clades of TOR kinase in Fusarium oxysporum are shown in boxes. (b) To the right of the tree is a protein domain image showing the relative structure of each TOR kinase. A red vertical line inside the kinase domain indicates the M2345L mutation. The domains shown are as follows: HEAT repeats (red), FAT domain (blue), RFB domain (white), kinase domain (gray), and FATC domain (black). (c) Measurement in reduction of radial growth of six F. oxysporum (Fo) strains to 50 ng/ml rapamycin on plates containing minimal medium (MM) amended with antibiotic compared to no-antibiotic MM plate controls. Three biological replicates were done for each treatment. Groups that are statistically different from one another using a t test comparison between all groups are indicated by the letters a to d. (d) Pictures of fungal growth on minimal medium with and without antibiotic (rapamycin [Rap]) at 7 days postinoculation. Plates for the most resistant (Fo4287) and least resistant (Fo47) strains are shown.

FIG 3

Histidine kinases are expanded in the fusaria. A phylogenetic tree was constructed for all two-component signaling histidine kinase nucleotide sequences and labeled according to their class (family) (neighbor-joining algorithm). Some kinases were excluded, as they lacked a large portion of the aligned conserved sequence among HisKs. Kinases that are part of the conserved ascomycete kinome (gray background), filamentous kinome (black background), and Fusarium kinome (white background) and kinases that are found only in fusaria in this study (orange background) are indicated. Fusarium oxysporum (Fo) gene identifiers (IDs) are colored red, and Fusarium graminearum (Fg) and Fusarium verticillioides (Fv) gene IDs are colored blue. All bootstrap values above 80% are shown. The domain structure for the class I and class IV HisKs are shown along with a heatmap of the copy number for each class among the fusaria.