title: An extensive (co-)expression analysis tool for the cytochrome P450 superfamily in Arabidopsis thaliana.
abstract: BACKGROUND
  Sequencing of the first plant genomes has revealed that cytochromes P450 have evolved to become the largest family of enzymes in secondary metabolism. The proportion of P450 enzymes with characterized biochemical function(s) is however very small. If P450 diversification mirrors evolution of chemical diversity, this points to an unexpectedly poor understanding of plant metabolism. We assumed that extensive analysis of gene expression might guide towards the function of P450 enzymes, and highlight overlooked aspects of plant metabolism.
  
  
  RESULTS
  We have created a comprehensive database, 'CYPedia', describing P450 gene expression in four data sets: organs and tissues, stress response, hormone response, and mutants of Arabidopsis thaliana, based on public Affymetrix ATH1 microarray expression data. P450 expression was then combined with the expression of 4,130 re-annotated genes, predicted to act in plant metabolism, for co-expression analyses. Based on the annotation of co-expressed genes from diverse pathway annotation databases, co-expressed pathways were identified. Predictions were validated for most P450s with known functions. As examples, co-expression results for P450s related to plastidial functions/photosynthesis, and to phenylpropanoid, triterpenoid and jasmonate metabolism are highlighted here.
  
  
  CONCLUSIONS
  The large scale hypothesis generation tools presented here provide leads to new pathways, unexpected functions, and regulatory networks for many P450s in plant metabolism. These can now be exploited by the community to validate the proposed functions experimentally using reverse genetics, biochemistry, and metabolic profiling.
authors.affiliation: Institute of Plant Molecular Biology, Centre National de la Recherche Scientifique UPR 2357, Université Louis Pasteur, 28 rue Goethe, 67000 Strasbourg, France. juergen.ehlting@ibmp-ulp.u-strasbg.fr
authors.forename: Jürgen
authors.initials: J
authors.lastname: Ehlting
authors.forename: Vincent
authors.initials: V
authors.lastname: Sauveplane
authors.forename: Alexandre
authors.initials: A
authors.lastname: Olry
authors.forename: Jean-François
authors.initials: JF
authors.lastname: Ginglinger
authors.forename: Nicholas J
authors.initials: NJ
authors.lastname: Provart
authors.forename: Danièle
authors.initials: D
authors.lastname: Werck-Reichhart
mesh_terms: D017360:Arabidopsis / Q000187:drug effects / Q000201:enzymology* / Q000235:genetics*; D003517:Cyclopentanes / Q000378:metabolism; D003577:Cytochrome P-450 Enzyme System / Q000235:genetics*; D020869:Gene Expression Profiling / Q000379:methods*; D015971:Gene Expression Regulation, Enzymologic / Q000187:drug effects; D018506:Gene Expression Regulation, Plant / Q000187:drug effects; D017343:Genes, Plant; D005822:Genetic Vectors; D020407:Internet; D005810:Multigene Family / Q000235:genetics*; D009154:Mutation / Q000235:genetics; D009928:Organ Specificity / Q000187:drug effects; D054883:Oxylipins / Q000378:metabolism; D010937:Plant Growth Regulators / Q000096:biosynthesis / Q000494:pharmacology; D018087:Plastids / Q000201:enzymology / Q000235:genetics; D015203:Reproducibility of Results; D014315:Triterpenes / Q000378:metabolism
chemical_list: D003517:Cyclopentanes; D054883:Oxylipins; D010937:Plant Growth Regulators; D014315:Triterpenes; C011006:jasmonic acid; D003577:Cytochrome P-450 Enzyme System