Comparative genomic analysis of clinical Acinetobacter nosocomialis isolates from Terengganu, Malaysia led to the discovery of a novel tetracycline-resistant plasmid

Rep_3 plasmids found in Acinetobacter species that include orfX also harbour dif modules

Plasmids found in Acinetobacter species are not found in other Gram-negative species. There are many distinct plasmid types and the majority encode a Rep_3 family RepA replication initiation protein. Among these, a number were known to carry dif modules. Here, the representative plasmid for each of the 78 reported R3 types was examined to identity features of the plasmid backbone that are associated with the carriage of dif modules. A conserved open reading frame designated orfX (IPR047783) was found downstream of repA in 35 of them, and the backbones of those 35 plasmids were bounded by recombination sites recognised by XerC and XerD, known as pdif sites. These plasmid backbones are all equivalent to a C-type dif module as the pdif sites are in the orientation D/C at one end and C/D at the other end, i.e. the XerC binding sites are internal. Hence, to provide the XerD binding sites and generate a complete plasmid at least one D-type dif module is needed. Phylogenies of the RepA and OrfX proteins revealed that plasmids with closely-related RepA proteins are not always associated with closely-related OrfX proteins and vice-versa indicating extensive backbone recombination. Folded structures of diverse OrfX proteins predicted using AlphaFold 3 revealed an N-terminal HTH domain followed by a long α-helix that is predicted to promote dimerization and a disordered C-terminus. Given the correlation between the presence of orfX and one or more dif modules, the possibility that OrfX is involved in dif module movement deserves to be investigated.

Variation in the plasmid backbone and dif module content of R3-T33 Acinetobacter plasmids

The predominant type of plasmids found in Acinetobacter species encode a Rep_3 initiation protein and many of these carry their accessory genes in dif modules. Here, available sequences of the 14 members of the group of Rep_3 plasmids typed as R3-T33, using a threshold of 95% identity in the repA gene, were compiled and compared. These plasmids were from various Acinetobacter species. The pdif sites were identified allowing the backbone and dif modules to be defined. As for other Rep_3 plasmids carrying dif modules, orfX encoding a protein of unknown function was found downstream of repA followed by a pdif site in the orientation XerC binding site-spacer-XerD binding site. Most backbones (n = 12) also included mobA and mobC genes but the two plasmids with the most diverged repA and orfX genes had different backbone contents. Although the gene content of the plasmid backbone was largely conserved, extensive recombinational exchange was detected and only two small groups carried identical or nearly identical backbones. Individual plasmids were associated with 1 to 13 dif modules. Many different dif modules were identified, including ones containing antibiotic or chromate resistance genes and several toxin/antitoxin gene pairs. In some cases, modules carrying the same genes were significantly diverged. Generally, the orientation of the pdif sites alternated such that C modules (XerC binding sites internal) alternated with D modules (XerD binding sites internal). However, fusions of two dif modules via mutational inactivation or loss of a pdif site were also detected.