Abstract
A ∼38kB plasmid (pXF-RIV5) was present in the Riv5 strain of Xylella fastidiosa subsp. multiplex isolated from ornamental plum in southern California. The complete nucleotide sequence of pXF-RIV5 is almost identical to that of pXFAS01 from X. fastidiosa subsp. fastidiosa strain M23; the two plasmids vary at only 6 nucleotide positions. BLAST searches and phylogenetic analyses indicate pXF-RIV5 and pXFAS01 share some similarity to chromosomal and plasmid (pXF51) sequences of X. fastidiosa subsp. pauca strain 9a5c and more distant similarity to plasmids from a wide variety of bacteria. Both pXF-RIV5 and pXFAS01 encode homologues of a complete Type IV secretion system involved in conjugation and DNA transfer among bacteria. Mating pair formation proteins (Trb) from Yersinia pseudotuberculosis IP31758 are the mostly closely related non-X. fastidiosa proteins to most of the Trb proteins encoded by pXF-RIV5 and pXFAS01. Unlike many bacterial conjugative plasmids, pXF-RIV5 and pXFAS01 do not carry homologues of known accessory modules that confer selective advantage on host bacteria. However, both plasmids encode seven hypothetical proteins of unknown function and possess a small transposon-associated region encoding a putative transposase and associated factor. Vegetative replication of pXF-RIV5 and pXFAS01 appears to be under control of RepA protein and both plasmids have an origin of DNA replication (oriV) similar to that of pRP4 and pR751 from Escherichia coli. In contrast, conjugative plasmids commonly encode TrfA and have an oriV similar to those found in IncP-1 incompatibility group plasmids. The presence of nearly identical plasmids in single strains from two distinct subspecies of X. fastidiosa is indicative of recent horizontal transfer, probably subsequent to the introduction of subspecies fastidiosa to the United States in the late 19th century.
Highlights
Horizontal gene transfer plays a critical role in bacterial adaptation and evolution
Riv5 is a strain of subspecies multiplex Genomic DNA sequences used for multi-locus sequence typing (MLST) of strain Riv5 were deposited as GenBank Accessions JX679700-JX67907
Phylogeny of concatenated sequences of the eight genes examined by MLST indicated that strain Riv5 clustered with X. fastidiosa strains of subspecies multiplex, including the fully-sequenced multiplex strain M12
Summary
Horizontal gene transfer plays a critical role in bacterial adaptation and evolution. One of the most common mechanisms for DNA exchange is via conjugative plasmids that encode type IV secretion systems (T4SS), a broad class of macromolecular translocation machinery. There are three main types of T4SS: i) conjugation systems that transfer DNA and, in some instances, DNA-binding proteins; ii) effector translocator systems that deliver proteins and other effectors to eukaryotic cells during bacterial infection of eukaryotic hosts; and iii) DNA uptake or release systems that move DNA between the interior of the cell and the extracellular environment [2]. For VirB/D4, the translocation system consists of VirB2-11 proteins forming the secretion channel, the VirD4 substrate receptor or type IV coupling protein (T4CP), and proteins for pilus formation and DNA substrate processing [2]. Many conjugative plasmids contain accessory modules encoding cargo proteins which act as virulence factors, confer resistance to antibiotics/heavy metals, or catabolize toxic organic substances [4]
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