Regulation of subtelomeric fungal secondary metabolite genes by H3K4me3 regulators CclA and KdmB

Abstract

Summary Studies on the regulation of fungal secondary metabolism highlight the importance of histone H3K4 methylation regulators Set1, CclA (Ash2) and KdmB (KDM5), but it remains unclear whether these proteins act by direct modulation of H3K4me3 at the target genes. In filamentous fungi, secondary metabolite genes are frequently located near telomeres, a site where H3K4 methylation is thought to have a repressive role. Here we analyzed the role of CclA, KdmB and H3K4me3 in regulating the subtelomeric EAS and LTM cluster genes in Epichloë festucae. Depletion of H3K4me3 correlated with transcriptional activation of these genes in ΔcclA, similarly enrichment of H3K4me3 correlated with transcriptional repression of the genes in ΔkdmB which was accompanied by significant reduction in the levels of the agriculturally undesirable lolitrems. These transcriptional changes could only be explained by the alterations in H3K4me3 and not in the subtelomerically‐important marks H3K9me3/K27me3. However, H3K4me3 changes in both mutants were not confined to these regions but occurred genome‐wide, and at other subtelomeric loci there were inconsistent correlations between H3K4me3 enrichment and gene repression. Our study suggests that CclA and KdmB are crucial regulators of secondary metabolite genes, but these proteins likely act via means independent to, or in conjunction with the H3K4me3 mark.

Evidence of a Demethylase-Independent Role for the H3K4-Specific Histone Demethylases in Aspergillus nidulans and Fusarium graminearum Secondary Metabolism

“…In fact, from the analyzed SMs that are affected by the loss of FgKdm5, all of them were found to be downregulated in ∆ fgkdm5 . Similarly, lack of the KDM5 homolog KdmB in Epichloë festucae resulted in reduced expression of the SMGCs involved in lolitrem ( ltm ) as well as ergoalkaloids and indole diterpenes ( eas ) biosynthesis (Lukito et al, 2019). Contrary to A. nidulans but in line with F. fujikuroi (Janevska et al, 2018), Fusarium strains deficient for H3K4 methylation did not phenocopy the ∆ fgkdm5 strain.…”

Host infection by the grass-symbiotic fungusEpichloë festucaerequires catalytically active H3K9 and H3K36 methyltransferases

“…This is not surprising given that H3K9 and H3K36 methylation defects would affect the expression of a large number of genes, resulting in more dramatic phenotypes for these mutants. However, these host colonization and symbiosis defects appear to be specific to these two H3 marks as mutations that affect H3K4 and H3K27 methylation have little or no impact on the host interaction phenotype [8,10].…”

“…Deletion of the cclA gene, which encodes a homolog of the Bre2 component of the COMPASS (Set1) complex responsible for deposition of H3K4me3, also led to transcriptional activation of the IDT and EAS genes in axenic culture. In contrast, deletion of the kdmB gene, which encodes the H3K4me3 demethylase, decreased in planta expression of the IDT and EAS genes, and reduced levels of IDTs in planta [10]. Plants infected with the cclA or kdmB mutants have a host interaction phenotype that is similar to wildtype, demonstrating that loss of the ability to add (DcclA) or remove (DkdmB) H3K4me3 does not impact on the ability of E. festucae to establish a symbiosis.…”

“…These results suggest that the phenotypes observed for ΔsetB were due to the H3K36 methylation defects. The E. festucae ΔclrD mutant, which is defective in H3K9 mono-, di-and tri-methylation, also has a non-infection phenotype [8,10]. However, that analysis did not differentiate lack of infection from lack of persistence as host plants were only examined for infection at 10-12 wpi.…”

“…Histone extraction and western blot were performed as previously described [10]. In brief, fungal tissues were ground to a fine powder in liquid nitrogen, and nuclei were isolated by glycerol gradient centrifugation, sonicated, and histones were subsequently isolated by acid extraction.…”