title: A dual-genome Symbiosis Chip for coordinate study of signal exchange and development in a prokaryote-host interaction.
abstract: The soil-dwelling alpha-proteobacterium Sinorhizobium meliloti engages in a symbiosis with legumes: S. meliloti elicits the formation of plant root nodules where it converts dinitrogen to ammonia for use by the plant in exchange for plant photosynthate. To study the coordinate differentiation of S. meliloti and its legume partner during nodule development, we designed a custom Affymetrix GeneChip with the complete S. meliloti genome and approximately 10,000 probe sets for the plant host, Medicago truncatula. Expression profiling of free-living S. meliloti grown with the plant signal molecule luteolin in defined minimal and rich media or of strains altered in the expression of key regulatory proteins (NodD1, NodD3, and RpoN) confirms previous data and identifies previously undescribed regulatory targets. Analyses of root nodules show that this Symbiosis Chip allows the study of gene expression in both partners simultaneously. Our studies detail nearly 5,000 transcriptome changes in symbiosis and document complex transcriptional profiles of S. meliloti in different environments.
authors.affiliation: Department of Biological Sciences, Stanford University, Stanford, CA 94305-5020, USA.
authors.forename: Melanie J
authors.initials: MJ
authors.lastname: Barnett
authors.forename: Carol J
authors.initials: CJ
authors.lastname: Toman
authors.forename: Robert F
authors.initials: RF
authors.lastname: Fisher
authors.forename: Sharon R
authors.initials: SR
authors.lastname: Long
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics; D004251:DNA Transposable Elements / Q000235:genetics; D004269:DNA, Bacterial / Q000235:genetics; D004268:DNA-Binding Proteins / Q000235:genetics; D012321:DNA-Directed RNA Polymerases / Q000235:genetics; D015870:Gene Expression / Q000187:drug effects; D016680:Genome, Bacterial; D018745:Genome, Plant; D047311:Luteolin / Q000494:pharmacology; D046913:Medicago truncatula / Q000235:genetics / Q000382:microbiology; D009154:Mutation; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D016133:Polymerase Chain Reaction; D051877:RNA Polymerase Sigma 54; D012808:Sigma Factor / Q000235:genetics; D015398:Signal Transduction / Q000235:genetics; D016962:Sinorhizobium meliloti / Q000235:genetics; D013559:Symbiosis / Q000235:genetics*; D015534:Trans-Activators / Q000235:genetics; D014157:Transcription Factors / Q000235:genetics
chemical_list: D001426:Bacterial Proteins; D004251:DNA Transposable Elements; D004269:DNA, Bacterial; D004268:DNA-Binding Proteins; C061268:NodD3 protein, Sinorhizobium meliloti; D012808:Sigma Factor; D015534:Trans-Activators; D014157:Transcription Factors; D012321:DNA-Directed RNA Polymerases; D051877:RNA Polymerase Sigma 54; D047311:Luteolin