获得编码Ⅲ型分泌系统（T3SS）和效应子（T3Es）的致病性质粒pPATH的获得很可能导致了非致病细菌向致瘤病原体Pantoea agglomerans的转变。P. agglomerans pv. gypsophilae（Pag）在铁线莲（Gypsophila paniculata）上形成瘤，并在甜菜（Beta vulgaris）上触发免疫反应，而P. agglomerans pv. betae（Pab）在铁线莲和甜菜上形成瘤。之前使用MiSeq Illumina技术产生了Pag和Pab基因组的草稿序列，并用于确定Pab和Pag的部分T3E库存。在这里，我们使用PacBio技术对Pab和Pag基因组进行了完全组装，并对Pab和Pag的致病性质粒pPATHpag和pPATHpab进行了比较序列分析。Pab和Pag基因组的组装揭示出一个约为4 Mbp的染色体，GC含量为55%，以及Pab和Pag中的三个和四个质粒，分别。 pPATHpag和pPATHpab在74%的范围内具有97%的相似性，并且具有相似的GC含量（51%）；它们的大小分别为约156 kb和约131 kb，并且分别由198个和155个编码序列（CDSs）组成。在这两个质粒中，我们确认了编码T3SS的高度相似基因群的存在，以及生长素和细胞分裂素合成酶的存在。在Pab中鉴定了三个假定的新T3E，在Pag中鉴定了一个。在Pag和Pab编码的T3SS相关蛋白中，我们鉴定了ShcV和CesT家族的两个新转运蛋白，在两个病原方差中具有很高的相似性。我们还鉴定出可能有助于两个病原方差进化的插入序列（ISs）和转座子（Tns）。这包括七个共享的IS元素，以及三个仅在Pab中存在的IS和两个转座子。最后，比较序列分析揭示了仅存在于pPATHpab或pPATHpag中的质粒区域和CDS。pPATH质粒的高度相似性和共同特征支持了这两个菌株最近演化为特定宿主致病菌的假设。版权所有 © 2023 Geraffi, Gupta, Wagner, Barash, Pupko and Sessa.

Acquisition of the pathogenicity plasmid pPATH that encodes a type III secretion system (T3SS) and effectors (T3Es) has likely led to the transition of a non-pathogenic bacterium into the tumorigenic pathogen Pantoea agglomerans. P. agglomerans pv. gypsophilae (Pag) forms galls on gypsophila (Gypsophila paniculata) and triggers immunity on sugar beet (Beta vulgaris), while P. agglomerans pv. betae (Pab) causes galls on both gypsophila and sugar beet. Draft sequences of the Pag and Pab genomes were previously generated using the MiSeq Illumina technology and used to determine partial T3E inventories of Pab and Pag. Here, we fully assembled the Pab and Pag genomes following sequencing with PacBio technology and carried out a comparative sequence analysis of the Pab and Pag pathogenicity plasmids pPATHpag and pPATHpab. Assembly of Pab and Pag genomes revealed a ~4 Mbp chromosome with a 55% GC content, and three and four plasmids in Pab and Pag, respectively. pPATHpag and pPATHpab share 97% identity within a 74% coverage, and a similar GC content (51%); they are ~156 kb and ~131 kb in size and consist of 198 and 155 coding sequences (CDSs), respectively. In both plasmids, we confirmed the presence of highly similar gene clusters encoding a T3SS, as well as auxin and cytokinins biosynthetic enzymes. Three putative novel T3Es were identified in Pab and one in Pag. Among T3SS-associated proteins encoded by Pag and Pab, we identified two novel chaperons of the ShcV and CesT families that are present in both pathovars with high similarity. We also identified insertion sequences (ISs) and transposons (Tns) that may have contributed to the evolution of the two pathovars. These include seven shared IS elements, and three ISs and two transposons unique to Pab. Finally, comparative sequence analysis revealed plasmid regions and CDSs that are present only in pPATHpab or in pPATHpag. The high similarity and common features of the pPATH plasmids support the hypothesis that the two strains recently evolved into host-specific pathogens.Copyright © 2023 Geraffi, Gupta, Wagner, Barash, Pupko and Sessa.