Fungal wilt pathogen’s epigenetic toolkit mapped in first genome-wide HDAC survey

Fusarium oxysporum is one of the most destructive plant pathogens on Earth, a soil-borne fungus that invades the vascular tissue of more than 100 crops, from tomatoes and bananas to cotton, and inflicts losses measured in billions of dollars every year. Now, researchers publishing in the journal IMA Fungus have delivered the first systematic, genome-wide portrait of the epigenetic machinery that helps this pathogen grow, sporulate, and survive hostile environments. Their target: the histone deacetylase gene family, a set of enzymes that chemically strip acetyl groups from histone proteins, tightening DNA around its protein scaffold and silencing genes in the process.

Histone deacetylases, or HDACs, are among the most conserved epigenetic regulators in biology. By removing acetyl groups from lysine residues on the N-terminal tails of histones H2A, H2B, H3, and H4, they establish transcriptionally repressive chromatin states. In fungi, these enzymes fall into three broad classes based on their yeast counterparts: zinc-dependent Class I RPD3-type enzymes, zinc-dependent Class II HDA1-type enzymes, and NAD+-dependent Class III enzymes known as sirtuins. Previous work in other fungi has shown that Class I members govern growth and virulence, Class II members are indispensable for host colonization and stress tolerance, and sirtuins regulate asexual development, nutrient utilization, and resistance to thermal and ultraviolet stress.

Using the genome of the F. oxysporum strain Fo47 as a starting point, the team searched NCBI and UniProt databases with hidden Markov models built on conserved HDAC and sirtuin domain profiles, applying a stringent significance threshold. The search identified exactly 11 FoHDAC genes. Phylogenetic reconstruction, comparing the fungal sequences with reference HDACs from budding yeast, Arabidopsis, and humans, sorted the family into three subfamilies: two Class I genes, two Class II genes, and a strikingly dominant SIR2 subfamily containing seven members. That expansion of the sirtuin clade stands out, because related fungi such as Alternaria alternata and Candida albicans carry only six to eight HDAC genes in total.

Structural analysis reinforced the phylogenetic picture. Three-dimensional alignments in PyMOL yielded root-mean-square deviation values between FoHDACs and their orthologs ranging from 0.312 to 3.397 angstroms. One protein, corresponding to FoRPD3, showed exceptional structural similarity to yeast RPD3, with a conserved catalytic pocket geometry that validated the evolutionary clustering. Another, FoClr3, diverged more substantially from yeast HDA1 yet retained its critical active-site residues, a pattern the authors interpret as structural plasticity that may facilitate functional adaptation to environmental pressures. Motif analysis with the MEME Suite uncovered ten conserved signatures, with Class I and II enzymes universally sharing Motifs 3 and 5, while sirtuins uniformly retain Motifs 1, 2, 4, 6, and 8, hinting at deep evolutionary conservation of their catalytic cores.

Physicochemical profiling revealed a family of considerable diversity. Protein lengths ranged from 298 to 1,087 amino acids, corresponding to molecular masses between roughly 32.8 and 117.8 kilodaltons, and isoelectric points split the family into acidic, basic, and near-neutral members. Subcellular localization predictions placed six proteins in the nucleus, three in the cytoplasm, and two, FoSIR5 and FoSIR4, in mitochondria, indicating that the family’s regulatory reach extends across organelles. All members were hydrophilic, and the team observed a significant negative correlation between hydrophilicity and aliphatic index, suggesting that reduced non-polar amino acid content enhances solubility and may favor protein-nucleic acid interactions.

Chromosomal mapping showed the 11 genes distributed asymmetrically across six chromosomes, with chromosomes 1 and 4 each hosting three genes, chromosome 8 two, and chromosomes 5 and 12 one apiece, while six chromosomes carried none at all. Synteny analysis ruled out recent segmental duplications as drivers of family expansion, pointing instead to functional specialization as the route to diversification. Comparative genomics across Fusarium graminearum and Fusarium solani revealed strict one-to-one orthology for all 11 genes, but only three sirtuin-class genes showed cross-family orthology with the rice blast fungus Magnaporthe oryzae, underscoring the exceptional conservation of core sirtuin machinery across fungal lineages.

The promoter regions upstream of the FoHDAC genes proved to be dense with regulatory information. Screening 2-kilobase stretches identified 22 putative cis-regulatory elements, including core motifs such as CAAT and TATA boxes alongside antioxidant response elements ARE and as-1, stress response elements known as STRE, dehydration-responsive DRE elements, MYB and MYC recognition sites, and W-boxes targeted by WRKY transcription factors. The as-1 motif was conserved across every family member, pointing to essential roles in mitigating oxidative stress, while selective enrichment of WRE elements in specific genes suggested spatiotemporal specialization for developmental coordination. In essence, the promoters are wired to translate environmental signals, from reactive oxygen species to osmotic shifts, into rapid epigenetic reconfiguration.

Gene Ontology enrichment and molecular docking simulations then connected structure to function. Beyond core deacetylation, the genes were annotated for roles in transcriptional regulation, macromolecular catabolism, and heterochromatin assembly, with FoHST4, FoHST3, and FoClr3 implicated in cellular component organization relevant to sporulation and cell wall biogenesis. Docking against eight histone acetylation marks, including H3K9ac and H4K16ac, produced robust binding affinities at or below minus 5 kilocalories per mole for all FoHDACs. The HDAC-class enzymes employed conserved His/Asp catalytic dyads with distinct substrate preferences, FoHOS3 selectively engaging H4K16ac and FoClr3 targeting multiple sites, while sirtuins displayed broader recognition, with FoHST3 binding every tested site and FoSIR2 showing high affinity for H3K14ac and H3K23ac. Notably, FoHST4, FoHST3, and FoSIR2 also exhibited intrinsic histone acyltransferase activity, marking them as bifunctional enzymes.

Expression profiling by reverse-transcription quantitative PCR across four developmental stages revealed choreographed dynamics. Eight genes peaked in the dormant conidial phase, were suppressed during spore germination, and progressively recovered through mycelial growth and sporulation, while FoHOS3 and FoRPD3 were continuously activated across developmental transitions and FoSIR7 was induced exclusively during sporulation. Under stress, the picture sharpened dramatically. Salt stress broadly repressed transcription, most dramatically a 33.67-fold suppression of FoHST3, whereas cold stress at 4 degrees Celsius triggered an induction of FoHOS3 exceeding 100-fold, accompanied by coordinated activation of FoHOS2, FoRPD3, and FoSIR7. Heat stress upregulated FoHOS3 more than 15-fold, oxidative stress elevated FoHOS3, FoSIR7, and FoSIR5, and fungicide exposure produced compound-specific responses, with fludioxonil activating FoHOS3 and FoSIR7 and hymexazol inducing FoSIR7, FoHST2, and FoSIR5.

Taken together, the findings cast FoHOS3 as a master stress integrator, consistently induced across osmotic, oxidative, thermal, and chemical challenges, with FoSIR7 acting as a broad-spectrum responder and FoHST3 and FoHST4 typically repressed under stress. The authors propose a three-phase epigenetic model of pathogenic progression, spanning dormancy governed by FoHOS2 and FoClr3, virulence activation, and colonization driven by FoSIR7. Because HDACs are dispensable or divergent between fungi and their hosts, the family represents an attractive target for next-generation fungicides designed to disrupt virulence with minimal off-target effects. The team notes that future work combining chromatin accessibility and histone modification mapping will be needed to fully resolve the regulatory networks, but the study establishes a foundation for precision antifungal strategies at a time when climate-stressed agriculture urgently needs them.

Subject of Research: Genome-wide identification and expression profiling of histone deacetylase genes in the plant-pathogenic fungus Fusarium oxysporum

Article Title: Genome-wide identification and expression profiling of the histone deacetylase gene family in Fusarium oxysporum

Article References: Liao, H.-X., Wen, J.-R., Shi, H.-M., Cun, H.-Q., Hong, Y.-J., Hu, Z.-F., Xu, F.-R., Noiprasert, S., Apiwongsrichai, K., Liu, X.-Y., & Dong, X. (2026). Genome-wide identification and expression profiling of the histone deacetylase gene family in Fusarium oxysporum. IMA Fungus, 17, Article e168980. https://doi.org/10.3897/imafungus.17.168980

Image Credits: AI Generated

DOI: 10.3897/imafungus.17.168980

Keywords: Fusarium oxysporum, histone deacetylases, epigenetics, sirtuins, plant pathology, chromatin regulation, gene expression, molecular docking, stress response, fungicides, vascular wilt, genomics