Knock‐down of the methyltransferase Kmt6 relieves H3K27me3 and results in induction of cryptic and otherwise silent secondary metabolite gene clusters in Fusarium fujikuroi

Abstract

Summary Filamentous fungi produce a vast array of secondary metabolites (SMs) and some play a role in agriculture or pharmacology. Sequencing of the rice pathogen Fusarium fujikuroi revealed the presence of far more SM-encoding genes than known products. SM production is energy-consuming and thus tightly regulated, leaving the majority of SM gene clusters silent under laboratory conditions. One important regulatory layer in SM biosynthesis involves histone modifications that render the underlying genes either silent or poised for transcription. Here, we show that the majority of the putative SM gene clusters in F. fujikuroi are located within facultative heterochromatin marked by trimethylated lysine 27 on histone 3 (H3K27me3). Kmt6, the methyltransferase responsible for establishing this histone mark, appears to be essential in this fungus, and knock-down of Kmt6 in the KMT6kd strain shows a drastic phenotype affecting fungal growth and development. Transcription of four so far cryptic and otherwise silent putative SM gene clusters was induced in the KMT6kd strain, in which decreased expression of KMT6 is accompanied by reduced H3K27me3 levels at the respective gene loci and accumulation of novel metabolites. One of the four putative SM gene clusters, named STC5, was analysed in more detail thereby revealing a novel sesquiterpene.

A Matter of Scale and Dimensions: Chromatin of Chromosome Landmarks in the Fungi

“…Matching the finding of few active genes, cytological data from plants and animals suggest that B chromosomes are heterochromatic, and most studies suggest that they are enriched for H3K9me2/3 [230, 231]. In fungi the hallmark chromatin feature of accessory chromosomes is H3K27me3 [22, 62, 145, 146], though transposable elements are still covered by H3K9me3 in Fusarium and Z. tritici (Figure 5). Thus, the separating characteristic –at least for now– seems to be the presence of H3K27me3 and facultative heterochromatin on accessory chromosomes.…”

“…This situation is different in F. graminearum , where ~20% of all genes were newly turned on or upregulated when KMT6 was deleted, and where H3K27me3 covers almost a third of the whole genome [145]. In F. fujikuroi deletion of kmt6 is lethal, and effects of derepression of secondary metabolite gene clusters were studied by RNAi-mediated downregulation of kmt6 [146]. Again, H3K27me3 covers almost a third of the whole genome, including almost all of the smaller chromosomes (Figure 5C), the so-called “accessory” chromosomes [22].…”

“…In several Neurospora , Fusarium , and Zymoseptoria species a correlation between subtelomeric blocks of non-syntenic DNA and H3K27me3 has been found [62, 123, 134, 145, 146]. H3K27me3 seems to act like an “immune system” for the fungus, perhaps silencing novel incoming DNA sequences [134], though this idea has been difficult to test, and a sequence-based “signal” for H3K27me3 targeting has yet to emerge from studies with Neurospora or Fusarium .…”

“…The four chromosomes of F. graminearum likely resulted from chromosome fusions of the ancestral 11 or 12 chromosomes that are present in extant sister species [151]. Recombination profiles [151–153] and chromatin structure analyses [145, 146] suggest that the epigenetically defined and usually silent or “cryptic” regions within chromosome arms maintain sequence diversity but also have been maintained as “subtelomeric-like regions” over millennia. What emerges from the combination of the studies discussed in the previous sections is a large variety of regulatory circuits in different taxa, suggesting that we are just at the beginning of uncovering how and why H3K27 methylation is necessary in fungi.…”

Normal chromosome conformation depends on subtelomeric facultative heterochromatin in Neurospora crassa

“…We conclude that subtelomeric facultative heterochromatin is required to maintain the normal genome structure, but normal genome structure is not functionally paramount in N. crassa grown under standard laboratory conditions. Curiously, in Fusarium species that have been examined, deletion of SET-7 homologs causes severe growth defects (25) or is lethal (26).…”