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Open Access Highly Accessed Research article

Comparison of transcriptome technologies in the pathogenic fungus Aspergillus fumigatus reveals novel insights into the genome and MpkA dependent gene expression

Sebastian Müller1, Clara Baldin23, Marco Groth4, Reinhard Guthke1, Olaf Kniemeyer235, Axel A Brakhage23 and Vito Valiante2*

Author Affiliations

1 Department of Systems Biology / Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Beutenbergstr. 11a, Jena 07745, Germany

2 Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Beutenbergstr. 11a, Jena 07745, Germany

3 Department of Microbiology and Molecular Biology, Institute of Microbiology, Friedrich Schiller University Jena, Beutenbergstr. 11a, Jena 07745, Germany

4 Department of Genome Analysis, Leibniz Institute for Age Research - Fritz Lipmann Institute, Beutenbergstr. 11a, Jena 07745, Germany

5 Integrated Research and Treatment Center, Center for Sepsis Control and Care Jena, University Hospital (CSCC), Jena 07747, Germany

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BMC Genomics 2012, 13:519  doi:10.1186/1471-2164-13-519

Published: 2 October 2012

Abstract

Background

The filamentous fungus Aspergillus fumigatus has become the most important airborne fungal pathogen causing life-threatening infections in immuno-compromised patients. Recently developed high-throughput transcriptome and proteome technologies, such as microarrays, RNA deep-sequencing, and LC-MS/MS of peptide mixtures, are of enormous value for systematically investigating pathogenic organisms. In the field of infection biology, one of the priorities is to collect and standardise data, in order to generate datasets that can be used to investigate and compare pathways and gene responses involved in pathogenicity. The “omics” era provides a multitude of inputs that need to be integrated and assessed. We therefore evaluated the potential of paired-end mRNA-Seq for investigating the regulatory role of the central mitogen activated protein kinase (MpkA). This kinase is involved in the cell wall integrity signalling pathway of A. fumigatus and essential for maintaining an intact cell wall in response to stress.

Results

The comparison of the transcriptome and proteome of an A. fumigatus wild-type strain with an mpkA null mutant strain revealed that 70.4% of the genome was found to be expressed and that MpkA plays a significant role in the regulation of many genes involved in cell wall remodelling, oxidative stress and iron starvation response, and secondary metabolite biosynthesis. Moreover, absence of the mpkA gene also strongly affects the expression of genes involved in primary metabolism. The data were further processed to evaluate the potential of the mRNA-Seq technique. We comprehensively matched up our data to published transcriptome studies and were able to show an improved data comparability of mRNA-Seq experiments independently of the technique used. Analysis of transcriptome and proteome data revealed only a weak correlation between mRNA and protein abundance.

Conclusions

High-throughput analysis of MpkA-dependent gene expression confirmed many previous findings that this kinase is important for regulating many genes involved in metabolic pathways. Our analysis showed more than 2000 differentially regulated genes. RNA deep-sequencing is less error-prone than established microarray-based technologies. It also provides additional information in A. fumigatus studies and as a result is more suitable for the creation of extensive datasets.

Keywords:
Aspergillus fumigatus; mRNA-Seq; Transcriptome; Proteome; Secondary metabolite gene clusters; Cell wall integrity pathway