Julius Kühn Institute (JKI), Federal Research Centre for Cultivated Plants, Institute for Plant Protection in Horticulture and Urban Green, Braunschweig, Germany.
Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.
Genome Biol Evol. 2023 Aug 1;15(8). doi: 10.1093/gbe/evad133.
Agrobacteria are important plant pathogens responsible for crown/cane gall and hairy root diseases. Crown/cane gall disease is associated with strains carrying tumor-inducing (Ti) plasmids, while hairy root disease is caused by strains harboring root-inducing (Ri) plasmids. In this study, we analyzed the sequences of Ti plasmids of the novel "tumorigenes" clade of the family Rhizobiaceae ("tumorigenes" Ti plasmids), which includes two species, Rhizobium tumorigenes and Rhizobium rhododendri. The sequences of reference Ti/Ri plasmids were also included, which was followed by a comparative analysis of their backbone and accessory regions. The "tumorigenes" Ti plasmids have novel opine signatures compared with other Ti/Ri plasmids characterized so far. The first group exemplified by pTi1078 is associated with production of agrocinopine, nopaline, and ridéopine in plant tumors, while the second group comprising pTi6.2 is responsible for synthesis of leucinopine. Bioinformatic and chemical analyses, including opine utilization assays, indicated that leucinopine associated with pTi6.2 most likely has D,L stereochemistry, unlike the L,L-leucinopine produced in tumors induced by reference strains Chry5 and Bo542. Most of the "tumorigenes" Ti plasmids have conjugative transfer system genes that are unusual for Ti plasmids, composed of avhD4/avhB and traA/mobC/parA regions. Next, our results suggested that "tumorigenes" Ti plasmids have a common origin, but they diverged through large-scale recombination events, through recombination with single or multiple distinct Ti/Ri plasmids. Lastly, we showed that Ti/Ri plasmids could be differentiated based on pairwise Mash or average amino-acid identity distance clustering, and we supply a script to facilitate application of the former approach by other researchers.
农杆菌是重要的植物病原体，可导致冠瘿瘤和发根病。冠瘿瘤病与携带肿瘤诱导（Ti）质粒的菌株有关，而发根病则由携带发根诱导（Ri）质粒的菌株引起。在这项研究中，我们分析了家族根瘤菌科的新型“致瘤”类群的 Ti 质粒序列，该类群包括两个物种，根瘤菌和杜鹃根瘤菌。我们还包括了参考 Ti/Ri 质粒的序列，随后对它们的骨干和附属区域进行了比较分析。与迄今为止表征的其他 Ti/Ri 质粒相比，“致瘤”Ti 质粒具有新颖的植物碱特征。以 pTi1078 为代表的第一组与在植物肿瘤中产生农杆菌素、胭脂碱和里德碱有关，而由 pTi6.2 组成的第二组负责合成亮氨酸。生物信息学和化学分析，包括植物碱利用试验，表明与 pTi6.2 相关的亮氨酸很可能具有 D,L 立体化学，与参考菌株 Chry5 和 Bo542 诱导的肿瘤中产生的 L,L-亮氨酸不同。大多数“致瘤”Ti 质粒具有不寻常的可移动性转移系统基因，由 avhD4/avhB 和 traA/mobC/parA 区域组成。接下来，我们的结果表明，“致瘤”Ti 质粒具有共同的起源，但通过大规模重组事件，通过与单个或多个不同的 Ti/Ri 质粒重组而发生分歧。最后，我们表明 Ti/Ri 质粒可以基于成对 Mash 或平均氨基酸同一性距离聚类来区分，我们提供了一个脚本，以方便其他研究人员应用前者的方法。
