title: Comparative transcriptomics of the model mushroom Coprinopsis cinerea reveals tissue-specific armories and a conserved circuitry for sexual development.
abstract: BACKGROUND
  It is well known that mushrooms produce defense proteins and secondary metabolites against predators and competitors; however, less is known about the correlation between the tissue-specific expression and the target organism (antagonist) specificity of these molecules. In addition, conserved transcriptional circuitries involved in developing sexual organs in fungi are not characterized, despite the growing number of gene expression datasets available from reproductive and vegetative tissue. The aims of this study were: first, to evaluate the tissue specificity of defense gene expression in the model mushroom Coprinopsis cinerea and, second, to assess the degree of conservation in transcriptional regulation during sexual development in basidiomycetes.
  
  
  RESULTS
  In order to characterize the regulation in the expression of defense loci and the transcriptional circuitries controlling sexual reproduction in basidiomycetes, we sequenced the poly (A)-positive transcriptome of stage 1 primordia and vegetative mycelium of C. cinerea A43mutB43mut. Our data show that many genes encoding predicted and already characterized defense proteins are differentially expressed in these tissues. The predicted specificity of these proteins with regard to target organisms suggests that their expression pattern correlates with the type of antagonists these tissues are confronted with. Accordingly, we show that the stage 1 primordium-specific protein CC1G_11805 is toxic to insects and nematodes. Comparison of our data to analogous data from Laccaria bicolor and Schizophyllum commune revealed that the transcriptional regulation of nearly 70 loci is conserved and probably subjected to stabilizing selection. A Velvet domain-containing protein was found to be up-regulated in all three fungi, providing preliminary evidence of a possible role of the Velvet protein family in sexual development of basidiomycetes. The PBS-soluble proteome of C. cinerea primordia and mycelium was analyzed by shotgun LC-MS. This proteome data confirmed the presence of intracellular defense proteins in primordia.
  
  
  CONCLUSIONS
  This study shows that the exposure of different tissues in fungi to different types of antagonists shapes the expression pattern of defense loci in a tissue-specific manner. Furthermore, we identify a transcriptional circuitry conserved among basidiomycetes during fruiting body formation that involves, amongst other transcription factors, the up-regulation of a Velvet domain-containing protein.
authors.forename: David Fernando
authors.initials: DF
authors.lastname: Plaza
authors.forename: Chia-Wei
authors.initials: CW
authors.lastname: Lin
authors.forename: Niels Sebastiaan Johannes
authors.initials: NS
authors.lastname: van der Velden
authors.forename: Markus
authors.initials: M
authors.lastname: Aebi
authors.affiliation: Department of Biology, Institute of Microbiology, ETH Zürich, Zürich, Switzerland. markus.kuenzler@micro.biol.ethz.ch.
authors.forename: Markus
authors.initials: M
authors.lastname: Künzler
mesh_terms: D000363:Agaricales / Q000502:physiology*; D000595:Amino Acid Sequence; D001427:Bacterial Toxins / Q000737:chemistry / Q000235:genetics; D016000:Cluster Analysis; D048690:Fruiting Bodies, Fungal / Q000235:genetics; D005656:Fungal Proteins / Q000737:chemistry / Q000235:genetics; D020869:Gene Expression Profiling; D015966:Gene Expression Regulation, Fungal; D053263:Gene Regulatory Networks; D008969:Molecular Sequence Data; D009928:Organ Specificity / Q000235:genetics; D052899:Pore Forming Cytotoxic Proteins / Q000737:chemistry / Q000235:genetics; D040641:Quantitative Trait Loci; D016415:Sequence Alignment; D014158:Transcription, Genetic; D059467:Transcriptome
chemical_list: D001427:Bacterial Toxins; D005656:Fungal Proteins; D052899:Pore Forming Cytotoxic Proteins; C032676:aerolysin