This would contain some hundred carbon sources, and fifty to hundred nitrogen sources, sulphur and phosphorous sources, and eventually also include different pH and aeration conditions. Since macronutrients are the major determinants of the fungal phenotype, a comprehensive profiling system should ideally include the maximum number of various nutrient sources in a single assay. Therefore, a (semi)high-throughput and comprehensive phenotypic assay would greatly accelerate a functional genomic approach. As such, phenotypes are the ultimate goal in strain improvement in biotechnology during the screening of fungi for new processes or products. Phenotype is the manifested attribute of an organism, the joint product of its genes and their environment during ontogeny. To comprehend, however, how the gene initially is encoded in the genome is ultimately displayed at the cellular level the phenotype must be considered. These technologies allow for global analysis of the information flow from DNA to RNA to protein. The most well known “global” approaches are DNA-microarrays for transcriptomics (Fodor et al., 1993 Kahmann and Basse, 2001) and two-dimensional gel electrophoresis (O′Farrell, 1975) for proteomics. In addition to investigation systems, which focus on specific genes, pathways, or processes, functional genomic methods attempt to study the impact of altered genes on the phenotype of the organism, using technologies that provide a cell-wide perspective. For many conidial fungi, facilitated methods for production of knockout mutants have already been established (Sweigard et al., 1999 Chaveroche et al., 2000 Hamer et al., 2001), but new approaches for wide-domain functional characterization of the gene of interest need further elaboration. To this end, “high-throughput methods”, capable of studying all these traits, have and are being developed. To understand the information stored in the genome, one must understand the production of knockout mutants and the consequence for the organism biology, learn the conditions for the expression of the gene, and have knowledge of the stability, compartmentation, and modification of the gene’s translation product. Genome sequencing, however, is only the first step towards the identification and validation of the function of the genes of an organism. Their importance for humankind has consequently led to an increasing number of fungi for which genomic sequences are now available (>130 at as noticed on Dec.
This characteristic has been exploited extensively to study metabolic pathways and their regulation in model fungi such as Aspergillus nidulans and Neurospora crassa. Conidial fungi are capable of metabolizing a wide variety of nutrients. Some conidial fungi are responsible for the production of industrially important enzymes, antibiotics, secondary metabolites and foods (e.g., cheeses, sake, and soya sauce), whereas others produce toxins contaminating food products and/or resulting in food spoilage.
We also report examples of the versatility of this tool.Ĭonidial fungi (mitosporic Dikarya, also informally called imperfect fungi or Fungi Imperfecti), commonly known as molds and mildews, represent a diverse and economically important biological group of organisms that include animal and plant pathogens, as well as organisms used in biotechnology. In this article, we review the background of PM applications for fungi and the methodic requirements to obtain reliable results. More recently, Phenotype MicroArray (PM) technology has been introduced as a tool to characterize the metabolism of a (wild) fungal strain or a mutant. This allows for global analysis of the information flow from DNA to RNA to protein, but it is usually not sufficient for the description of the global phenotype of an organism. Functional genomics and proteomics widely exploit the genomic information to study the cell-wide impact of altered genes on the phenotype of an organism and its function. These various applications and extremely versatile natural phenotypes have led to the constantly growing list of complete genomes which are now available. They are also important pathogens of animals including humans and agricultural crops. Conidial fungi or molds and mildews are widely used in modern biotechnology as producers of antibiotics and other secondary metabolites, industrially important enzymes, chemicals and food.
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