Plasmids of Xylella fastidiosa mulberry-infecting strains share extensive sequence identity and gene complement with pVEIS01 from the earthworm symbiont Verminephrobacter eiseniae

Abstract

A ∼25 kbp plasmid was present in each of four Californian strains of Xylella fastidiosa from mulberry affected with leaf scorch disease. Fragments of each plasmid were cloned into Escherichia coli, sequenced, and assembled into circular contigs of 25,105 bp (pXF-RIV11 and pXF-RIV16) or 24,372 bp (pXF-RIV19 and pXF-RIV25). The four plasmids shared >99.8% sequence identity, excluding a 732 bp insertion common to pXF-RIV11 and pXF-RIV16. BLAST searches identified seven regions (totaling 19,252 bp) sharing ≥75% nucleotide sequence identity with pVEIS01, a 31 kbp plasmid from the earthworm symbiont Verminephrobacter eiseniae. Using pXF-RIV11 as a query in BLASTX searches, putative functions of plasmid-encoded open reading frames (ORFs) were identified. Fourteen ORFs were associated with DNA transfer (Type IV secretion), four with plasmid stability (plasmid toxin/anti-toxin addiction), one with protein export (Type II secretion), one with plasmid DNA replication initiation ( trfA), and the remaining ORFs associated with other or unknown functions. The putative origin of DNA replication ( oriV) was located adjacent to the trfA ORF and was similar in structure to that of plasmids belonging to the incP-1 incompatibility group. E. coli plasmids bearing fragments of pXF-RIV11 and the nptII gene as a selectable marker were tested for replication in X. fastidiosa strain Temecula1. Only fragments bearing oriV and trfA were competent for replication in X. fastidiosa. Collectively, these results indicate that mulberry strains of X. fastidiosa harbor plasmids encoding genes associated with DNA transfer and plasmid stability not previously identified on the chromosome of sequenced X. fastidiosa strains and that ancestors of distantly related bacterial species occupying different niches appear to have exchanged genetic material.