HdaA, a major class 2 histone deacetylase of Aspergillus nidulans, affects growth under conditions of oxidative stress

Histone modifications and chromatin dynamics: a focus on filamentous fungi

The readout of the genetic information of eukaryotic organisms is significantly regulated by modifications of DNA and chromatin proteins. Chromatin alterations induce genome-wide and local changes in gene expression and affect a variety of processes in response to internal and external signals during growth, differentiation, development, in metabolic processes, diseases, and abiotic and biotic stresses. This review aims at summarizing the roles of histone H1 and the acetylation and methylation of histones in filamentous fungi and links this knowledge to the huge body of data from other systems. Filamentous fungi show a wide range of morphologies and have developed a complex network of genes that enables them to use a great variety of substrates. This fact, together with the possibility of simple and quick genetic manipulation, highlights these organisms as model systems for the investigation of gene regulation. However, little is still known about regulation at the chromatin level in filamentous fungi. Understanding the role of chromatin in transcriptional regulation would be of utmost importance with respect to the impact of filamentous fungi in human diseases and agriculture. The synthesis of compounds (antibiotics, immunosuppressants, toxins, and compounds with adverse effects) is also likely to be regulated at the chromatin level.

Histone deacetylase activity regulates chemical diversity in Aspergillus

Bioactive small molecules are critical in Aspergillus species during their development and interaction with other organisms. Genes dedicated to their production are encoded in clusters that can be located throughout the genome. We show that deletion of hdaA, encoding an Aspergillus nidulans histone deacetylase (HDAC), causes transcriptional activation of two telomere-proximal gene clusters--and subsequent increased levels of the corresponding molecules (toxin and antibiotic)--but not of a telomere-distal cluster. Introduction of two additional HDAC mutant alleles in a DeltahdaA background had minimal effects on expression of the two HdaA-regulated clusters. Treatment of other fungal genera with HDAC inhibitors resulted in overproduction of several metabolites, suggesting a conserved mechanism of HDAC repression of some secondary-metabolite gene clusters. Chromatin regulation of small-molecule gene clusters may enable filamentous fungi to successfully exploit environmental resources by modifying chemical diversity.

A systems biology analysis of protein-protein interactions between yeast superoxide dismutases and DNA repair pathways

Superoxide dismutases (SODs) are widely distributed in eukaryotic and prokaryotic species and are responsible for O(2)(.-) scavenging and dismutation to H(2)O(2) and O(2). Mutations in the cytoplasmic (Sod1p) or mitochondrial (Sod2p) form of SODs result in aging, neurodegenerative diseases, and carcinogenesis. Diminished activity of SODs leads to reduced activity of DNA repair pathways, and overexpression of SODs in cells defective for DNA repair increases their level of chromatin damage. Unfortunately, little is understood regarding the interplay between SODs and DNA repair proteins and their role in protecting the genome from oxidative damage. To elucidate the association between yeast SODs and DNA repair mechanisms, a systems biology study was performed employing algorithms of literature data mining and the construction of physical protein-protein interactions from large yeast protein databases. The results obtained in this work allow us to draw two models suggesting that yeast SODs act as O(2)(.-) sensors under conditions of redox imbalance, activating and controlling specific DNA repair mechanisms (e.g., recombinational and excision repair pathways), chromatin remodeling, and synthesis of dNTPs.