ena-PROJECT-goll-30-07-2012-17:11:09:418-65
Comparison of transcriptome technologies in the pathogenic fungus Aspergillus fumigatus reveals novel insights in genome structure and MpkA-dependent gene expression
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 to systematically investigate pathogenic organisms. In the field of infection biology, one of the priorities is to collect and standardize 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. Here, the potential of paired-end RNA-Seq was evaluated and furthermore used to investigate the regulatory role of the central mitogen activated protein kinase MpkA, which is involved in the cell wall integrity signalling pathway of A. fumigatus. Results: The comparison of the transcriptome and proteome of an A. fumigatus wild-type strain with an mpkA null mutant strain confirmed that MpkA plays a role in the regulation of many genes involved in cell wall remodelling, oxidative and iron starvation stress response, and secondary metabolite biosynthesis. More over, lacking of the mpkA gene strongly affects the primary metabolism as well. The data obtained in this study have been further computed to evaluate the potential of RNA-Seq technique. We conducted a comprehensive comparison of our data with previously published transcriptome studies, revealing an improved data comparison of RNA-Seq experiments independent of the used technique. Analysis of transcriptome and proteome data showed that there is a weak correlation between mRNA and protein abundance. Conclusions: High-throughput analysis of MpkA-dependent gene expression confirmed many of the previous finding revealing the importance of this kinase in regulating many genes involved in metabolic pathways. More than 2000 differentially regulated genes have been identified in our analysis. The comparison of RNA deep-sequencing with established microarray-based technologies revealed that this technique is less error-prone and provides additional information in A. fumigatus studies resulting more suitable for the creation of extensive data-sets.
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 to systematically investigate pathogenic organisms. In the field of infection biology, one of the priorities is to collect and standardize 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. Here, the potential of paired-end RNA-Seq was evaluated and furthermore used to investigate the regulatory role of the central mitogen activated protein kinase MpkA, which is involved in the cell wall integrity signalling pathway of A. fumigatus. Results: The comparison of the transcriptome and proteome of an A. fumigatus wild-type strain with an mpkA null mutant strain confirmed that MpkA plays a role in the regulation of many genes involved in cell wall remodelling, oxidative and iron starvation stress response, and secondary metabolite biosynthesis. More over, lacking of the mpkA gene strongly affects the primary metabolism as well. The data obtained in this study have been further computed to evaluate the potential of RNA-Seq technique. We conducted a comprehensive comparison of our data with previously published transcriptome studies, revealing an improved data comparison of RNA-Seq experiments independent of the used technique. Analysis of transcriptome and proteome data showed that there is a weak correlation between mRNA and protein abundance. Conclusions: High-throughput analysis of MpkA-dependent gene expression confirmed many of the previous finding revealing the importance of this kinase in regulating many genes involved in metabolic pathways. More than 2000 differentially regulated genes have been identified in our analysis. The comparison of RNA deep-sequencing with established microarray-based technologies revealed that this technique is less error-prone and provides additional information in A. fumigatus studies resulting more suitable for the creation of extensive data-sets.