title: Mining the genome of Rhodococcus fascians, a plant growth-promoting bacterium gone astray.
abstract: Rhodococcus fascians is a phytopathogenic Gram-positive Actinomycete with a very broad host range encompassing especially dicotyledonous herbaceous perennials, but also some monocots, such as the Liliaceae and, recently, the woody crop pistachio. The pathogenicity of R. fascians strain D188 is known to be encoded by the linear plasmid pFiD188 and to be dictated by its capacity to produce a mixture of cytokinins. Here, we show that D188-5, the nonpathogenic plasmid-free derivative of the wild-type strain D188 actually has a plant growth-promoting effect. With the availability of the genome sequence of R. fascians, the chromosome of strain D188 was mined for putative plant growth-promoting functions and the functionality of some of these activities was tested. This analysis together with previous results suggests that the plant growth-promoting activity of R. fascians is due to production of plant growth modulators, such as auxin and cytokinin, combined with degradation of ethylene through 1-amino-cyclopropane-1-carboxylic acid deaminase. Moreover, R. fascians has several functions that could contribute to efficient colonization and competitiveness, but there is little evidence for a strong impact on plant nutrition. Possibly, the plant growth promotion encoded by the D188 chromosome is imperative for the epiphytic phase of the life cycle of R. fascians and prepares the plant to host the bacteria, thus ensuring proper continuation into the pathogenic phase.
authors.affiliation: Department of Biology, California State University Bakersfield, Bakersfield, CA 93311, USA.
authors.forename: Isolde M
authors.initials: IM
authors.lastname: Francis
authors.affiliation: Department of Plant Systems Biology, VIB, 9052 Gent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium.
authors.forename: Elisabeth
authors.initials: E
authors.lastname: Stes
authors.affiliation: Department of Plant Pathology, University of Florida, Gainesville, FL 32611, USA.
authors.forename: Yucheng
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: Department of Biology, California State University Bakersfield, Bakersfield, CA 93311, USA.
authors.forename: Diana
authors.initials: D
authors.lastname: Rangel
authors.affiliation: Department of Applied Biosciences, Ghent University, 9000 Gent, Belgium.
authors.forename: Kris
authors.initials: K
authors.lastname: Audenaert
authors.affiliation: Department of Applied Biosciences, Ghent University, 9000 Gent, Belgium. Electronic address: danny.vereecke@ugent.be.
authors.forename: Danny
authors.initials: D
authors.lastname: Vereecke
mesh_terms: D017360:Arabidopsis / Q000254:growth & development / Q000382:microbiology; D001426:Bacterial Proteins / Q000096:biosynthesis / Q000235:genetics; D001709:Biotechnology; D002876:Chromosomes, Bacterial / Q000235:genetics; D003583:Cytokinins / Q000096:biosynthesis / Q000235:genetics; D005030:Ethylenes / Q000378:metabolism; D016680:Genome, Bacterial; D054884:Host-Pathogen Interactions / Q000235:genetics / Q000502:physiology; D007210:Indoleacetic Acids / Q000378:metabolism; D063245:Plant Development; D010935:Plant Diseases / Q000382:microbiology; D010937:Plant Growth Regulators / Q000096:biosynthesis / Q000235:genetics; D010944:Plants / Q000382:microbiology*; D012240:Rhodococcus / Q000235:genetics* / Q000472:pathogenicity* / Q000502:physiology; D014774:Virulence / Q000235:genetics / Q000502:physiology
chemical_list: D001426:Bacterial Proteins; D003583:Cytokinins; D005030:Ethylenes; D007210:Indoleacetic Acids; D010937:Plant Growth Regulators; C036216:ethylene