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Analysis of Genome Sequences from Plant Pathogenic Rhodococcus Reveals Genetic Novelties in Virulence Loci

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  • Members of Gram-positive Actinobacteria cause economically important diseases to plants. Within the Rhodococcus genus, some members can cause growth deformities and persist as pathogens on a wide range of host plants. The current model predicts that phytopathogenic isolates require a cluster of three loci present on a linear plasmid, with the fas operon central to virulence. The Fas proteins synthesize, modify, and activate a mixture of growth regulating cytokinins, which cause a hormonal imbalance in plants, resulting in abnormal growth. We sequenced and compared the genomes of 20 isolates of Rhodococcus to gain insights into the mechanisms and evolution of virulence in these bacteria. Horizontal gene transfer was identified as critical but limited in the scale of virulence evolution, as few loci are conserved and exclusive to phytopathogenic isolates. Although the fas operon is present in most phytopathogenic isolates, it is absent from phytopathogenic isolate A21d2. Instead, this isolate has a horizontally acquired gene chimera that encodes a novel fusion protein with isopentyltransferase and phosphoribohydrolase domains, predicted to be capable of catalyzing and activating cytokinins, respectively. Cytokinin profiling of the archetypal D188 isolate revealed only one activate cytokinin type that was specifically synthesized in a fas-dependent manner. These results suggest that only the isopentenyladenine cytokinin type is synthesized and necessary for Rhodococcus phytopathogenicity, which is not consistent with the extant model stating that a mixture of cytokinins is necessary for Rhodococcus to cause leafy gall symptoms. In all, data indicate that only four horizontally acquired functions are sufficient to confer the trait of phytopathogenicity to members of the genetically diverse clade of Rhodococcus.
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  • Creason AL, Vandeputte OM, Savory EA, Davis EW II, Putnam ML, et al. (2014) Analysis of Genome Sequences from Plant Pathogenic Rhodococcus Reveals Genetic Novelties in Virulence Loci. PLoS ONE 9(7): e101996. doi:10.1371/journal.pone.0101996
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  • 9
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  • 7
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  • This work is supported by a grant from the Agricultural Research Foundation awarded to JHC. EAS is supported by USDA (United States Department of Agriculture) NIFA (National Institute of Food and Agriculture) post-doctoral fellowship #2013-67012-21139. EWD is supported by a Provost’s Distinguished Graduate Fellowship awarded by Oregon State University. This material is based upon work supported by the National Science Foundation Graduate Research Fellowship under Grant No. DGE-1314109 to EWD. Any opinion, findings, and conclusions or recommendations expressed in this material are those of the authors(s) and do not necessarily reflect the views of the National Science Foundation. This work is also supported in part by the Society of American Florists anda cooperative agreement with USDA-ARS (Agricultural Research Service) awarded to MLP. OMV is a Post-doctoral Researcher of the FRS-FNRS (Fonds de la Recherche Scientifique, Belgium) and supported by grants from FRS-FNRS and the Fonds David et Alice Van Buuren (Belgium). MB is a Senior Research Associate of the FRS-FNRS (Fonds de la Recherche Scientifique, Belgium).
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