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Global nutrient profiling by Phenotype MicroArrays: a tool complementing genomic and proteomic studies in conidial fungi

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Abstract

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. They are also important pathogens of animals including humans and agricultural crops. These various applications and extremely versatile natural phenotypes have led to the constantly growing list of complete genomes which are now available. 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. 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. More recently, Phenotype MicroArray (PM) technology has been introduced as a tool to characterize the metabolism of a (wild) fungal strain or a mutant. In this article, we review the background of PM applications for fungi and the methodic requirements to obtain reliable results. We also report examples of the versatility of this tool.

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Authors and Affiliations

  1. Research Area of Gene Technology and Applied Biochemistry, Institute of Chemical Engineering, Vienna University of Technology, A-1060, Vienna, Austria

    Lea Atanasova & Irina S. Druzhinina

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  1. Lea Atanasova
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  2. Irina S. Druzhinina
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Correspondence to Irina S. Druzhinina.

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Project (No. FWF P-P17859-B06) supported by the Austrian Science Foundation

Introducing editorial board member: Irina S. Druzhinina, the corresponding author of this invited review, is an editorial board member of Journal of Zhejiang University-SCIENCE B (Biomedicine & Biotechnology). Her study is focused on phylogeny and molecular ecology of Hypocreales fungi and on the development of bioinformatic tools for molecular identification of microbes. In the other line of research she is interested in metabolomics of filamentous fungi applying Phenotype MicroArray techniques. In 2001, she gained the doctorate of natural sciences of University of Vienna (Austria). Shortly after, she founded a research group on fungal evolution and functional biodiversity in Vienna University of Technology (Austria) and obtained a position of Assistant Professor in Department of Applied Biochemistry and Gene Technology.

Lea Atanasova, the first author of this invited review, studied biology and ecology at the University of Ljubljana (Slovenia) and has graduated from the University Vienna (Austria). She was awarded for her master thesis by the Austrian Federal Ministry of Agriculture, Forestry, Environment and Water Management as well as by Ecological Society of Germany, Austria and Switzerland. Soon after graduation, she joined the Irina S. Druzhinina’s research group of fungal biodiversity and evolution in Vienna University of Technology (Austria) and started to work on her PhD thesis dedicated to the molecular ecology of soil mycobiota.

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Atanasova, L., Druzhinina, I.S. Global nutrient profiling by Phenotype MicroArrays: a tool complementing genomic and proteomic studies in conidial fungi. J. Zhejiang Univ. Sci. B 11, 151–168 (2010). https://doi.org/10.1631/jzus.B1000007

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  • DOI: https://doi.org/10.1631/jzus.B1000007

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