Analysis of Genome Sequences from Plant Pathogenic <i>Rhodococcus</i> Reveals Genetic Novelties in Virulence Loci

<div><p>Members of Gram-positive Actinobacteria cause economically important diseases to plants. Within the <i>Rhodococcus</i> 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 <i>fas</i> 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 <i>Rhodococcus</i> 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 <i>fas</i> 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 <i>fas</i>-dependent manner. These results suggest that only the isopentenyladenine cytokinin type is synthesized and necessary for <i>Rhodococcus</i> phytopathogenicity, which is not consistent with the extant model stating that a mixture of cytokinins is necessary for <i>Rhodococcus</i> 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 <i>Rhodococcus</i>.</p></div>