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

Abstract

Fungi produce a plethora of secondary metabolites (SMs) involved in cellular protection, defense, and signaling. Like other metabolic processes, transcription of SM biosynthesis genes is tightly regulated to prevent an unnecessary use of resources. Genes involved in SM biosynthesis are usually physically linked, arranged in secondary metabolite gene clusters (SMGCs). Research over the last decades has shown that chromatin structure and posttranslational modifications (PTMs) of histones represent important layers of SMGC regulation. For instance, trimethylation of histone H3 lysine 4 (H3K4me3) is a PTM typically associated with promoter regions of actively transcribed genes. Previously, we have shown that the H3K4me3-specific, JmjC domain-containing histone demethylase KdmB functions not only in repression but also in activation of secondary metabolism in Aspergillus nidulans , suggesting that KdmB has additional functions apart from histone demethylation. In this study, we identified demethylase-independent functions of KdmB in transcriptional regulation of SM gene clusters. Furthermore, we show that this activating and demethylase-independent role of the H3K4 demethylase is also conserved in the phytopathogenic fungus Fusarium graminearum . Lack of FgKdm5 resulted in significant downregulation of five of seven analyzed SMs, whereby only one SMGC depends on a functional JmjC-domain. In A. nidulans strains deficient in H3K4 methylation, i.e., cclA ∆, largely phenocopied kdmB ∆, while this is not the case for most of the SMs analyzed in Fusarium spp. Notably, KdmB could not rescue the demethylase function in ∆ fgkdm5 but restored all demethylase-independent phenotypes.

The COMPASS-like complex modulates fungal development and pathogenesis by regulating H3K4me3-mediated targeted gene expression inMagnaporthe oryzae

“…Recently, some studies have showed that histone demethylases, such as KdmA, an H3K9/36me3 demethylase, play a role in transcriptional regulation in A. nidulans (Agger et a l ., 2007 & 2019; Matthews et al, 2015). This finding suggests that these UTX-like containing COMPASS-like complexes and their associated bivalent H3K9/27 demethylase and H3K4me3 methyltransferase activities may be involved in dynamic target gene activation (Bernstein et al, 2006; Amar et al, 2015;Bachleitner et al, 2019).…”

“…(Connolly et al, 2013; Palmer et al, 2013; Matthews et al, 2016). In F. graminearum , FgSet1 is a Set1 orthologue and is one subunit of the COMPASS-like complex, which also plays an important role in regulating fungal growth and secondary metabolism (Connolly et al, 2013; Liu et al, 2015; Bachleitner et al, 2019).…”

A novel fungal gene regulation system based on inducible VPR-dCas9 and nucleosome map-guided sgRNA positioning

“…Usually, the individual genes within a given BGC are transcriptionally co-regulated, not expressed by default and activated only in response to a “proprietary” expression signal. For most of these clusters, standard laboratory conditions do not generate this critical signal and consequently, their cognate products cannot be identified (Bachleitner et al 2019 ; Chujo and Scott 2014 ; Connolly et al 2013 ; Gacek-Matthews et al 2016 ; Gacek and Strauss 2012 ; Reyes-Dominguez et al 2010 ; Studt et al 2016 ). About 50% of the BGCs contain a gene that encodes a pathway-specific transcriptional activator (Keller 2019 ).…”

Activation of silent secondary metabolite gene clusters by nucleosome map-guided positioning of the synthetic transcription factor VPR-dCas9

“…For most of these clusters, standard laboratory conditions do not generate this critical signal and consequently they are silent. (Bachleitner et al, 2019;Chujo and Scott, 2014;Connolly et al, 2013;Gacek-Matthews et al, 2016;Gacek and Strauss, 2012;Reyes-Dominguez et al, 2010;Studt et al, 2016). In about 50% of the cases the SM BGCs contain a gene that encodes for a transcriptional activator (Keller, 2019).…”

“…Because of these complications and limitations of established techniques there are still hundreds of predicted fungal BGCs awaiting the characterisation of their cognate metabolite (Lyu et al, 2020). Other approaches that interfere with chromatinbased regulators, such as histone deacetylases (Shwab et al, 2007;Studt et al, 2013), histone methyl transferases (Chujo and Scott, 2014;Connolly et al, 2013;Studt et al, 2016),histone demethylases (Bachleitner et al, 2019;Gacek-Matthews et al, 2016), etc. may work for some clusters, but not for others.…”