title: Integration of bioinformatics and synthetic promoters leads to the discovery of novel elicitor-responsive cis-regulatory sequences in Arabidopsis.
abstract: A combination of bioinformatic tools, high-throughput gene expression profiles, and the use of synthetic promoters is a powerful approach to discover and evaluate novel cis-sequences in response to specific stimuli. With Arabidopsis (Arabidopsis thaliana) microarray data annotated to the PathoPlant database, 732 different queries with a focus on fungal and oomycete pathogens were performed, leading to 510 up-regulated gene groups. Using the binding site estimation suite of tools, BEST, 407 conserved sequence motifs were identified in promoter regions of these coregulated gene sets. Motif similarities were determined with STAMP, classifying the 407 sequence motifs into 37 families. A comparative analysis of these 37 families with the AthaMap, PLACE, and AGRIS databases revealed similarities to known cis-elements but also led to the discovery of cis-sequences not yet implicated in pathogen response. Using a parsley (Petroselinum crispum) protoplast system and a modified reporter gene vector with an internal transformation control, 25 elicitor-responsive cis-sequences from 10 different motif families were identified. Many of the elicitor-responsive cis-sequences also drive reporter gene expression in an Agrobacterium tumefaciens infection assay in Nicotiana benthamiana. This work significantly increases the number of known elicitor-responsive cis-sequences and demonstrates the successful integration of a diverse set of bioinformatic resources combined with synthetic promoter analysis for data mining and functional screening in plant-pathogen interaction.
authors: Institut für Genetik, Technische Universität Braunschweig, 38106 Braunschweig, Germany.
authors: Jeannette
authors: J
authors: Koschmann
authors: Fabian
authors: F
authors: Machens
authors: Marlies
authors: M
authors: Becker
authors: Julia
authors: J
authors: Niemeyer
authors: Jutta
authors: J
authors: Schulze
authors: Lorenz
authors: L
authors: Bülow
authors: Dietmar J
authors: DJ
authors: Stahl
authors: Reinhard
authors: R
authors: Hehl
mesh_terms: D016960:Agrobacterium tumefaciens / Q000472:pathogenicity; D017360:Arabidopsis / Q000235:genetics* / Q000378:metabolism / Q000382:microbiology; D001665:Binding Sites; D019295:Computational Biology / Q000379:methods*; D017124:Conserved Sequence; D018744:DNA, Plant / Q000235:genetics; D057225:Data Mining / Q000379:methods; D030541:Databases, Genetic; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D005813:Genes, Synthetic; D005822:Genetic Vectors / Q000235:genetics / Q000378:metabolism; D054884:Host-Pathogen Interactions; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D059372:Nucleotide Motifs; D020411:Oligonucleotide Array Sequence Analysis; D028528:Petroselinum / Q000166:cytology / Q000378:metabolism; D018515:Plant Leaves / Q000235:genetics / Q000378:metabolism / Q000382:microbiology; D010957:Plasmids / Q000235:genetics / Q000378:metabolism; D011401:Promoter Regions, Genetic; D011523:Protoplasts / Q000166:cytology / Q000378:metabolism; D012045:Regulatory Sequences, Nucleic Acid; D012689:Sequence Homology, Nucleic Acid; D014026:Nicotiana / Q000235:genetics / Q000378:metabolism / Q000382:microbiology; D014170:Transformation, Genetic
chemical_list: D018744:DNA, Plant