Comparative sequence analysis of pPATH pathogenicity plasmids in Pantoea agglomerans gall-forming bacteria

Abstract

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 pathogenPantoea agglomerans.P. agglomeranspv.gypsophilae(Pag) forms galls on gypsophila (Gypsophila paniculata) and triggers immunity on sugar beet (Beta vulgaris), whileP. agglomeranspv.betae(Pab) causes galls on both gypsophila and sugar beet. Draft sequences of thePagandPabgenomes were previously generated using the MiSeq Illumina technology and used to determine partial T3E inventories ofPabandPag. Here, we fully assembled thePabandPaggenomes following sequencing with PacBio technology and carried out a comparative sequence analysis of thePabandPagpathogenicity plasmids pPATHpagand pPATHpab. Assembly ofPabandPaggenomes revealed a ~4 Mbp chromosome with a 55% GC content, and three and four plasmids inPabandPag, respectively. pPATHpagand pPATHpabshare 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 inPaband one inPag. Among T3SS-associated proteins encoded byPagandPab, 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 toPab. Finally, comparative sequence analysis revealed plasmid regions and CDSs that are present only in pPATHpabor 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.