Methyltransferase CclA-dependent control of secondary metabolite gene clusters and stress response in Aspergillus...

Aspergillus species generate diverse secondary metabolites (SMs), including commercially valuable compounds and mycotoxins that affect food safety. The biosynthesis of these SMs is regulated through gene clusters controlled by epigenetic and transcriptional mechanisms. However, the function of the histone H3 lysine 4 (H3K4) methyltransferase CclA across different metabolic stages remains poorly understood during the metabolic switch from primary to secondary metabolism. We performed integrated transcriptomic, proteomic, and RT-qPCR analyses of a ΔcclA mutant and wild type Aspergillus nidulans during late exponential growth phase (20h) where primary metabolism (PM) is predominant and stationary phase (48 h) where secondary metabolism (SM) is predominant. At the PM stage, 2971 genes (∼25% of the genome) were upregulated in ΔcclA, including SM clusters for sterigmatocystin (ST), monodictyphenone, emodin, orsellinic acid, austinol, and emericellamides, as well as genes involved in xylan metabolism and oxidative stress response. Conversely, genes controlling cell wall biosynthesis, filamentation, and sexual development were downregulated. At the SM stage, 2798 genes (∼24% of the genome) were upregulated, but ST and terrequinone clusters were markedly downregulated, revealing CclA's dual role as a global repressor and selective activator of SMs. Proteomic assessment confirmed coherent expression patterns (Pearson r = 0.71-0.77) with transcriptomic data, and RT-qPCR validated important regulatory and SM genes (r = 0.9). Phenotypic tests demonstrated that ΔcclA exhibited improved resistance to oxidative, osmotic, and cell wall stress while maintaining conidiation and growth. Overall, these results identify CclA as a principal regulator of SM, development, and stress adaptation. Understanding its dual functions gives a foundation for reducing mycotoxin contamination and enhancing the production of valuable metabolites.