A trispecies Aspergillus microarray: Comparative transcriptomics of three Aspergillus species. Export

@article{citeulike:2517579, abstract = {The full-genome sequencing of the filamentous fungi Aspergillus nidulans, Aspergillus niger, and Aspergillus oryzae has opened possibilities for studying the cellular physiology of these fungi on a systemic level. As a tool to explore this, we are making available an Affymetrix GeneChip developed for transcriptome analysis of any of the three above-mentioned aspergilli. Transcriptome analysis of triplicate batch cultivations of all three aspergilli on glucose and xylose media was used to validate the performance of the microarray. Gene comparisons of all three species and cross-analysis with the expression data identified 23 genes to be a conserved response across Aspergillus sp., including the xylose transcriptional activator XlnR. A promoter analysis of the up-regulated genes in all three species indicates the conserved XlnR-binding site to be 5'-GGNTAAA-3'. The composition of the conserved gene-set suggests that xylose acts as a molecule, indicating the presence of complex carbohydrates such as hemicellulose, and triggers an array of degrading enzymes. With this case example, we present a validated tool for transcriptome analysis of three Aspergillus species and a methodology for conducting cross-species evolutionary studies within a genus using comparative transcriptomics.}, address = {Center for Microbial Biotechnology, BioCentrum-DTU, Technical University of Denmark, DK-2800 Kgs Lyngby, Denmark.}, author = {Andersen, Mikael R R. and Vongsangnak, Wanwipa and Panagiotou, Gianni and Salazar, Margarita P P. and Lehmann, Linda and Nielsen, Jens}, citeulike-article-id = {2517579}, citeulike-linkout-0 = {http://dx.doi.org/10.1073/pnas.0709964105}, citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/18332432}, citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=18332432}, day = {10}, doi = {10.1073/pnas.0709964105}, issn = {1091-6490}, journal = {Proc Natl Acad Sci U S A}, keywords = {aspergillus, expression-data}, month = {March}, posted-at = {2009-04-01 01:11:20}, priority = {2}, title = {A trispecies Aspergillus microarray: Comparative transcriptomics of three Aspergillus species.}, url = {http://dx.doi.org/10.1073/pnas.0709964105}, year = {2008} }

TY - JOUR ID - citeulike:2517579 L3 - citeulike-article-id:2517579 N2 - The full-genome sequencing of the filamentous fungi Aspergillus nidulans, Aspergillus niger, and Aspergillus oryzae has opened possibilities for studying the cellular physiology of these fungi on a systemic level. As a tool to explore this, we are making available an Affymetrix GeneChip developed for transcriptome analysis of any of the three above-mentioned aspergilli. Transcriptome analysis of triplicate batch cultivations of all three aspergilli on glucose and xylose media was used to validate the performance of the microarray. Gene comparisons of all three species and cross-analysis with the expression data identified 23 genes to be a conserved response across Aspergillus sp., including the xylose transcriptional activator XlnR. A promoter analysis of the up-regulated genes in all three species indicates the conserved XlnR-binding site to be 5'-GGNTAAA-3'. The composition of the conserved gene-set suggests that xylose acts as a molecule, indicating the presence of complex carbohydrates such as hemicellulose, and triggers an array of degrading enzymes. With this case example, we present a validated tool for transcriptome analysis of three Aspergillus species and a methodology for conducting cross-species evolutionary studies within a genus using comparative transcriptomics. JF - Proc Natl Acad Sci U S A SN - 1091-6490 AD - Center for Microbial Biotechnology, BioCentrum-DTU, Technical University of Denmark, DK-2800 Kgs Lyngby, Denmark. TI - A trispecies Aspergillus microarray: Comparative transcriptomics of three Aspergillus species. KW - aspergillus KW - expression-data AU - Andersen, Mikael R AU - Vongsangnak, Wanwipa AU - Panagiotou, Gianni AU - Salazar, Margarita P AU - Lehmann, Linda AU - Nielsen, Jens PY - 2008/03/10/ UR - http://dx.doi.org/10.1073/pnas.0709964105 ER -