Not all Is SET for Methylation: Evolution of Eukaryotic Protein Methyltransferases.

Dynamic posttranslational modifications to canonical histones that constitute the nucleosome (H2A, H2B, H3, and H4) control all aspects of enzymatic transactions with DNA. Histone methylation has been studied heavily for the past 20 years, and our mechanistic understanding of the control and function of individual methylation events on specific histone arginine and lysine residues has been greatly improved over the past decade, driven by excellent new tools and methods. Here, we will summarize what is known about the distribution and some of the functions of protein methyltransferases from all major eukaryotic supergroups. The main conclusion is that protein, and specifically histone, methylation is an ancient process. Many taxa in all supergroups have lost some subfamilies of both protein arginine methyltransferases (PRMT) and the heavily studied SET domain lysine methyltransferases (KMT). Over time, novel subfamilies, especially of SET domain proteins, arose. We use the interactions between H3K27 and H3K36 methylation as one example for the complex circuitry of histone modifications that make up the "histone code," and we discuss one recent example (Paramecium Ezl1) for how extant enzymes that may resemble more ancient SET domain KMTs are able to modify two lysine residues that have divergent functions in plants, fungi, and animals. Complexity of SET domain KMT function in the well-studied plant and animal lineages arose not only by gene duplication but also acquisition of novel DNA- and histone-binding domains in certain subfamilies.

Application of the Cre/lox System to Construct Auxotrophic Markers for Quantitative Genetic Analyses in Fusarium graminearum.

The bacteriophage P1 Cre/lox system has been utilized in diverse fungi for marker recycling and exchange, generation of targeted chromosome translocations, and targeted deletion of interstitial chromosome segments. Here we show the application of this tool in the wheat and maize pathogen, Fusarium graminearum. We explored three different ways to introduce Cre into strains with floxed genes, namely transformation with an episomal or integrative plasmid (pLC28), fusion of protoplasts of strains carrying floxed genes with strains expressing Cre by forcing heterokaryons, and crosses between strains with floxed genes and strains expressing Cre to isolate progeny in which the target genes had been deleted during the cross. We used this system for the construction of strains bearing auxotrophic markers that were generated by gene replacement with positively selectable markers followed by Cre-mediated marker excision. In addition, updated protocols for transformation and crosses for F. graminearum are provided. In combination, strains and tools developed here add to the arsenal of methods that can be used to carry out molecular genetics with F. graminearum.

A Matter of Scale and Dimensions: Chromatin of Chromosome Landmarks in the Fungi.

Chromatin and chromosomes of fungi are highly diverse and dynamic, even within species. Much of what we know about histone modification enzymes, RNA interference, DNA methylation, and cell cycle control was first addressed in Saccharomyces cerevisiae, Schizosaccharomyces pombe, Aspergillus nidulans, and Neurospora crassa. Here, we examine the three landmark regions that are required for maintenance of stable chromosomes and their faithful inheritance, namely, origins of DNA replication, telomeres and centromeres. We summarize the state of recent chromatin research that explains what is required for normal function of these specialized chromosomal regions in different fungi, with an emphasis on the silencing mechanism associated with subtelomeric regions, initiated by sirtuin histone deacetylases and histone H3 lysine 27 (H3K27) methyltransferases. We explore mechanisms for the appearance of "accessory" or "conditionally dispensable" chromosomes and contrast what has been learned from studies on genome-wide chromosome conformation capture in S. cerevisiae, S. pombe, N. crassa, and Trichoderma reesei. While most of the current knowledge is based on work in a handful of genetically and biochemically tractable model organisms, we suggest where major knowledge gaps remain to be closed. Fungi will continue to serve as facile organisms to uncover the basic processes of life because they make excellent model organisms for genetics, biochemistry, cell biology, and evolutionary biology.