Alterations of RNA maps of IncP-7 plasmid pCAR1 in various Pseudomonas bacteria

RNA transcripts from 199-kb incompatibility P-7 plasmid pCAR1 were analyzed using microarrays with evenly tiled probes with a nine-nucleotide offset in six different Pseudomonas host strains. We re-annotated 12 ORFs based on their RNA maps and on the comparisons with other sequenced IncP-7 plasmids. Ninety six of two hundred ORFs were identified on the IncP-7 backbone related to basic functions of the plasmid (replication, partition and conjugative transfer). More than 90% ORFs on the backbone were transcribed in each host strain, suggesting their importance for the plasmid survival in the host strains. Genes related to partition and conjugative transfer were differentially transcribed host by host, whereas the repA gene encoding replication initiation protein was transcribed at comparable level in each host. As for other plasmid ‘accessory genes’ of pCAR1 encoding carbazole degradation, putative transporter, or transposase were also differentially transcribed among different host strains. These differences may have resulted in distinct behaviors of the plasmid or of its host strain, and RNA maps of pCAR1 give us important information to understand the plasmid behaviors in different environments.

► RNA maps of IncP-7 plasmid pCAR1 were compared in various Pseudomonas hosts.
► According to the maps, eight ORFs were newly identified on pCAR1.
► Most ORFs conserved in other IncP-7 plasmids were transcribed in every host strain.
► Several unknown ORFs were differently transcribed by changing the hosts.
► The RNA maps are valuable to understand plasmid behaviors in different hosts.