Subtractive hybridization reveals a high genetic diversity in the fish pathogen Photobacterium damselae subsp. piscicida: evidence of a SXT-like element

Abstract

Photobacterium damselae subsp. piscicida is the causative agent of fish pasteurellosis, a severe disease affecting cultured marine fish worldwide. In this study, suppression subtractive hybridization was used to identify DNA fragments present in the virulent strain PC554.2, but absent in the avirulent strain EPOY 8803-II. Twenty-one genomic regions of this type (that included twenty-six distinct putative ORFs) were analysed by DNA sequencing. Twenty ORFs encoded proteins with homology to proteins in other bacteria, including four homologues involved in siderophore biosynthesis, and four homologues related to mobile elements; three of these were putative transposases and one was a putative conjugative transposon related to the Vibrio cholerae SXT element. This sequence was shown to be integrated into a prfC gene homologue. Six ORFs showed no significant homology to known bacterial proteins. Among the 21 DNA fragments specific to strain PC554.2, 5 DNA fragments (representing 7 ORFs) were also absent in the avirulent strain ATCC 29690. The analysis of these differential regions, as well as the screening of their presence in a collection of strains, demonstrated the high genetic heterogeneity of this pathogen.

Genomic and Functional Analysis of ICE Pda Spa1, a Fish-Pathogen-Derived SXT-Related Integrating Conjugative Element That Can Mobilize a Virulence Plasmid

“…1). Overall, our assembly and analysis of the complete ICEP daSpa1 genome sequence confirmed the proposal of JuizRio et al (24) that this fish pathogen harbors an SXT-R391 family ICE.…”

“…piscicida isolate, contains homologues of SXT genes that are apparently inserted into prfC, the V. cholerae SXT integration site, and proposed that these genes are likely to be part of a P. damselae subsp. piscicida SXT-like ICE (24). We determined the complete DNA sequence of this SXT-like element (here named ICEPdaSpa1) to further comparative genomic analyses of the SXT-R391 family of ICEs.…”

“…piscicida PC554.2. The cosmid library was propagated in E. coli XLI-Blue MR and screened by colony PCR using primers for the previously described ICEPdaSpa1 int, traI, traC, and traN genes (24).…”

“…piscicida isolate derived from a diseased sole (Solea senegalensis) from a fish farm in Galicia, Spain, appears to contain an SXT-like ICE (24). They found that they could amplify five SXT backbone genes from this virulent P. damselae subsp.…”

DNA-Damaging Agents Induce the RecA-Independent Homologous Recombination Functions of Integrating Conjugative Elements of the SXT/R391 Family

“…Newly identified ICEs are classified in this family based on the conservation of the scaffold of conserved genes, the presence of a conserved P4-like site-specific tyrosine recombinase and on their site-specific integration into the 5= end of prfC, which encodes the peptide chain release factor RF3 (9). Interspersed in intergenic regions of this conserved backbone are variable DNA sequences that confer a wide selection of accessory functions, for instance, antibiotic or heavy metal resistances, and genes involved in modifying cellsignaling pathways (10)(11)(12)(13)(14)(15)(16)(17)(18). Similar to the induction of the lytic cycle of bacteriophage in lysogenic cells, the expression of the transfer genes of SXT/R391 ICEs is derepressed under conditions that trigger the host's SOS response.…”