title: An integrated genomics approach to define niche establishment by Rhodococcus fascians.
abstract: Rhodococcus fascians is a Gram-positive phytopathogen that induces shooty hyperplasia on its hosts through the secretion of cytokinins. Global transcriptomics using microarrays combined with profiling of primary metabolites on infected Arabidopsis (Arabidopsis thaliana) plants revealed that this actinomycete modulated pathways to convert its host into a niche. The transcript data demonstrated that R. fascians leaves a very characteristic mark on Arabidopsis with a pronounced cytokinin response illustrated by the activation of cytokinin perception, signal transduction, and homeostasis. The microarray data further suggested active suppression of an oxidative burst during the R. fascians pathology, and comparison with publicly available transcript data sets implied a central role for auxin in the prevention of plant defense activation. Gene Ontology categorization of the differentially expressed genes hinted at a significant impact of infection on the primary metabolism of the host, which was confirmed by subsequent metabolite profiling. The much higher levels of sugars and amino acids in infected plants are presumably accessed by the bacteria as carbon and nitrogen sources to support epiphytic and endophytic colonization. Hexoses, accumulating from a significantly increased invertase activity, possibly inhibited the expression of photosynthesis genes and photosynthetic activity in infected leaves. Altogether, these changes are indicative of sink development in symptomatic tissues. The metabolomics data furthermore point to the possible occurrence of secondary signaling during the interaction, which might contribute to symptom development. These data are placed in the context of regulation of bacterial virulence gene expression, suppression of defense, infection phenotype, and niche establishment.
authors.affiliation: Department of Plant Systems Biology, Flanders Institute for Biotechnology, 9052 Ghent, Belgium.
authors.forename: Stephen
authors.initials: S
authors.lastname: Depuydt
authors.forename: Sandra
authors.initials: S
authors.lastname: Trenkamp
authors.forename: Alisdair R
authors.initials: AR
authors.lastname: Fernie
authors.forename: Samira
authors.initials: S
authors.lastname: Elftieh
authors.forename: Jean-Pierre
authors.initials: JP
authors.lastname: Renou
authors.forename: Marnik
authors.initials: M
authors.lastname: Vuylsteke
authors.forename: Marcelle
authors.initials: M
authors.lastname: Holsters
authors.forename: Danny
authors.initials: D
authors.lastname: Vereecke
mesh_terms: D000596:Amino Acids / Q000096:biosynthesis; D017360:Arabidopsis / Q000201:enzymology / Q000235:genetics* / Q000382:microbiology*; D002952:Citric Acid Cycle; D016000:Cluster Analysis; D003583:Cytokinins / Q000378:metabolism; D015536:Down-Regulation / Q000235:genetics; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant / Q000235:genetics; D023281:Genomics / Q000379:methods*; D054884:Host-Pathogen Interactions / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis; D010788:Photosynthesis / Q000235:genetics; D018515:Plant Leaves / Q000235:genetics / Q000382:microbiology / Q000648:ultrastructure; D011073:Polyamines / Q000378:metabolism; D012240:Rhodococcus / Q000502:physiology*; D012984:Software; D015854:Up-Regulation / Q000235:genetics; D043324:beta-Fructofuranosidase / Q000235:genetics / Q000378:metabolism
chemical_list: D000596:Amino Acids; D003583:Cytokinins; D011073:Polyamines; D043324:beta-Fructofuranosidase