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

Area of Science:

• Plant Pathology
• Bacterial Genomics
• Molecular Evolution

Background:

• The acquisition of pathogenicity plasmids, such as pPATH encoding a type III secretion system (T3SS), is crucial for bacterial pathogen evolution.
• Pantoea agglomerans pv. gypsophilae (Pag) and P. agglomerans pv. betae (Pab) are tumorigenic pathogens causing galls on gypsophila and sugar beet, with Pab affecting both hosts.
• Previous draft genome sequences provided partial insights into the type III effectors (T3Es) of Pab and Pag.

Purpose of the Study:

• To fully assemble and comparatively analyze the genomes and pathogenicity plasmids (pPATHpag and pPATHpab) of Pag and Pab.
• To identify novel T3Es, T3SS-associated proteins, and mobile genetic elements contributing to the evolution of these pathovars.
• To elucidate the genetic basis for host specificity and recent divergence of Pag and Pab.

Main Methods:

• Full genome assembly of Pag and Pab using PacBio sequencing technology.
• Comparative sequence analysis of the pPATHpag and pPATHpab plasmids.
• Identification and characterization of coding sequences (CDSs), including T3SS components, T3Es, chaperones, insertion sequences (ISs), and transposons (Tns).

Main Results:

• Complete genome assemblies revealed ~4 Mbp chromosomes and multiple plasmids for both Pag and Pab.
• The pPATHpag and pPATHpab plasmids (~156 kb and ~131 kb) exhibit high sequence identity (97%) and share gene clusters for T3SS, auxin, and cytokinin biosynthesis.
• Three novel T3Es in Pab and one in Pag were identified, along with two novel T3SS-associated chaperones (ShcV and CesT families). Mobile genetic elements (ISs and Tns) were also characterized, with some unique to Pab.

Conclusions:

• The high similarity and shared genetic features of the pPATH plasmids strongly support the hypothesis of recent co-evolution of Pag and Pab into host-specific pathogens.
• The identified novel T3Es and chaperones likely play significant roles in the virulence and host interaction mechanisms of these pathovars.
• The presence of insertion sequences and transposons suggests their contribution to the genomic plasticity and diversification of Pag and Pab.