Histone modifications and chromatin dynamics: a focus on filamentous fungi

Abstract

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.

Fig. 1

Domain architecture of human and fungal histone lysine methyltransferases (a, b), protein arginine methyltransferases (c), and histone lysine demethylases (d), respectively. The NCBI blast program (http://www.ncbi.nlm.nih.gov/blast/) was used to compare human sequences of protein family members with sequence databases of the genomes of Aspergillus nidulans (An), Neurospora crassa (Nc), Saccharomyces cerevisiae (Sc), Schizosaccharomyces pombe (Sp), and Ustilago maydis (Um). Sequences of human (Hs) proteins were obtained from GenBank. Domain architectures of proteins were identified and analyzed by the Simple Modular Architecture Research Tool (SMART; http://smart.embl-heidelberg.de/) and were compared with human members of each protein family. The corresponding gene IDs, number of amino acids of proteins, and accession numbers are given.

Fig. 1

Domain architecture of human and fungal histone lysine methyltransferases (a, b), protein arginine methyltransferases (c), and histone lysine demethylases (d), respectively. The NCBI blast program (http://www.ncbi.nlm.nih.gov/blast/) was used to compare human sequences of protein family members with sequence databases of the genomes of Aspergillus nidulans (An), Neurospora crassa (Nc), Saccharomyces cerevisiae (Sc), Schizosaccharomyces pombe (Sp), and Ustilago maydis (Um). Sequences of human (Hs) proteins were obtained from GenBank. Domain architectures of proteins were identified and analyzed by the Simple Modular Architecture Research Tool (SMART; http://smart.embl-heidelberg.de/) and were compared with human members of each protein family. The corresponding gene IDs, number of amino acids of proteins, and accession numbers are given.

Fig. 1

Domain architecture of human and fungal histone lysine methyltransferases (a, b), protein arginine methyltransferases (c), and histone lysine demethylases (d), respectively. The NCBI blast program (http://www.ncbi.nlm.nih.gov/blast/) was used to compare human sequences of protein family members with sequence databases of the genomes of Aspergillus nidulans (An), Neurospora crassa (Nc), Saccharomyces cerevisiae (Sc), Schizosaccharomyces pombe (Sp), and Ustilago maydis (Um). Sequences of human (Hs) proteins were obtained from GenBank. Domain architectures of proteins were identified and analyzed by the Simple Modular Architecture Research Tool (SMART; http://smart.embl-heidelberg.de/) and were compared with human members of each protein family. The corresponding gene IDs, number of amino acids of proteins, and accession numbers are given.

Fig. 2

Domain structure of SET-domain proteins in Aspergillus nidulans. Sequences were derived by a search of the Aspergillus nidulans genome database (http://www.broad.mit.edu/annotation/genome/aspergillusnidulans/) for proteins containing SET domains (SM 00317), and domain structures were identified and analyzed by the Simple Modular Architecture Research Tool (SMART; http://smart.embl-heidelberg.de/). Accession numbers are provided, best-matching protein families are given in parentheses, and the number of amino acids of proteins and e-values are shown.

Fig. 3

Phylogenetic relationships within the genus Aspergillus. SUV39H1 homologous proteins in Aspergillus were searched using the Aspergillus Comparative Database from the BROAD Institute (http://www.broad.mit.edu/). Corresponding proteins were identified by a blast search (http://www.ncbi.nlm.nih.gov/blast/) and Multiple Sequence Alignment and building of the dendrogram was performed by the clustalw program (http://clustalw.genome.jp/).

Fig. 4

Domain architecture of histone lysine methyltransferases (a, b), protein arginine methyltransferases (c), and histone demethylases (d) of different Aspergillus species. Aspergillus homologs of human proteins (see Fig. 1) were searched using the Aspergillus Comparative Database from the BROAD Institute (http://www.broad.mit.edu/). Corresponding proteins were identified by a blast search (http://www.ncbi.nlm.nih.gov/blast/) and domain architectures of proteins were analyzed by the Simple Modular Architecture Research Tool (SMART; http://smart.embl-heidelberg.de/). The number of amino acids of proteins is shown. Accession numbers are given in Tables 4 and 5.

Fig. 4

Domain architecture of histone lysine methyltransferases (a, b), protein arginine methyltransferases (c), and histone demethylases (d) of different Aspergillus species. Aspergillus homologs of human proteins (see Fig. 1) were searched using the Aspergillus Comparative Database from the BROAD Institute (http://www.broad.mit.edu/). Corresponding proteins were identified by a blast search (http://www.ncbi.nlm.nih.gov/blast/) and domain architectures of proteins were analyzed by the Simple Modular Architecture Research Tool (SMART; http://smart.embl-heidelberg.de/). The number of amino acids of proteins is shown. Accession numbers are given in Tables 4 and 5.