Syndicate content

Laser Scissors and Next-Gen Sequencing Allow Analysis of Gene Activty in Entire Fungal Genomes

With a combination of microscopic laser scissors and modern sequencing methods, biologists at the Ruhr-Universität Bochum (RUB) in Germany have analyzed the activity of genes in the entire genomes of a certain fungi in one fell swoop. Especially with organisms in the millimetre size range, this is a particular challenge because little cell material is available. The scientists of the RUB Department of General and Molecular Botany took advantage of the combined methods to investigate the development of small, multicellular fungi. The results were reported on September 27, 2012 in the open-access journal BMC Genomics. In multicellular organisms, each cell contains the same genetic material, however, often only a fraction of the genes are active (expressed). These differences in gene expression are the cause of variations in the structure and physiology of cells. Gene expression is therefore the key to understanding the development of multicellular organisms. "In large organisms such as plants, it is usually not a problem to get enough starting material to study gene expression," explains Dr. Minou Nowrousian. "In the case of microorganisms, organs often consist of only a few cells, and might be embedded in other tissues from which they are difficult to separate." Therefore, biologists of the research groups of Professor Ulrich Kück and Dr. Nowrousian combined laser microdissection with modern sequencing technologies to analyze the gene activity during the development of certain, just 0.5 millimeters large, sexual structures of fungi. In laser microdissection, scientists cut defined regions of a sample under the light microscope with a laser beam. With this laser mini-scissors, the RUB researchers collected the fruiting bodies, i.e., the sexual structures of the fungus Sordaria macrospora, which has been used for decades as a model organism in developmental biology. From the fruiting bodies, they isolated the RNA which represents the gene activity. With the help of "next-generation" sequencing, they characterized the activity of all genes of the genome simultaneously. The Bochum researchers compared the wild-type fungus with a mutant form that has no mature fruiting bodies, in other words is not able to reproduce sexually. For this purpose, they studied gene expression in young, immature fruiting bodies. They showed that some fruiting body-specific genes are not activated in the mutant. The defective gene contains the "building instructions" for a so-called transcription factor - a protein that turns other genes on or off. The RUB team also found that the fruiting body has a completely different genetic activity pattern to non-reproductive tissue. "With the new combination of methods, we want to investigate the activity of genes in other mutants and developmental stages to better understand the molecular mechanisms of multicellular development in fungi," said Professor Kück. Fungi have a big impact on virtually all ecosystems. They make significant contributions to the reduction of animal and vegetable waste products and thereby contribute to the global carbon cycle. Some species live in symbiosis with plants or animals, other species are pathogens. In the chemical and pharmaceutical industry, fungi are used for the production of antibiotics and enzymes. The formation of pathogenic or symbiotic interactions and the production of medicines or biotechnology-related substances are often tied to specific stages in the life cycle of a fungus. The analysis of fungal development is therefore crucial not only for basic research but also for industrial applications. [Press release] [BMC Genomics abstract]