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

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.

革兰氏阳性放线菌（Gram-positive Actinobacteria）可引发具有重大经济影响的植物病害。在红球菌属（Rhodococcus）中，部分类群可引发植物生长畸形，并可作为病原菌在多种寄主植物上定殖存活。现有研究模型推测，植物致病性红球菌分离株需要携带位于线性质粒上的三个基因座簇，其中fas操纵子（fas operon）是致病性的核心。Fas蛋白可合成、修饰并激活一组调控植物生长的细胞分裂素混合物，该混合物会引发植物体内激素失衡，进而导致植株异常生长。本研究对20株红球菌分离株的基因组进行了测序与比较分析，以深入解析这类细菌的致病机制与致病性演化过程。研究发现，水平基因转移（horizontal gene transfer）在致病性演化中至关重要，但演化规模有限：仅少数基因座在植物致病性分离株中保守且为其专属。尽管fas操纵子存在于大多数植物致病性分离株中，但植物致病性分离株A21d2却缺失该操纵子。取而代之的是，该分离株携带一个经水平基因转移获得的基因嵌合体，其编码一种兼具异戊烯基转移酶（isopentyltransferase）与磷酸核糖水解酶（phosphoribohydrolase）结构域的新型融合蛋白，据预测可分别催化细胞分裂素并激活其活性。对模式菌株D188分离株的细胞分裂素谱分析显示，仅存在一种以fas依赖方式特异性合成的活化型细胞分裂素。上述结果表明，红球菌的致病性仅需要合成并依赖异戊烯基腺嘌呤型细胞分裂素，这与现有模型相悖——现有模型认为，红球菌引发叶瘿症状需要多种细胞分裂素的混合作用。综上，本研究数据表明，仅需四个经水平基因转移获得的功能元件，即可使遗传多样性丰富的红球菌演化支系成员获得植物致病性性状。