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Rep_3 plasmids found in Acinetobacter species that include orfX also harbour dif modules
Stephanie J Ambrose1, Carol H Pong1, Ruth M Hall1
1School of Life and Environmental Sciences, The University of Sydney, NSW 2006, Australia.
Plasmid
|April 25, 2025
Summary
Acinetobacter plasmids often contain dif modules, with a conserved orfX gene linked to specific recombination sites. Extensive backbone recombination suggests orfX may play a role in dif module movement.
Area of Science:
- Microbiology
- Molecular Biology
- Genetics
Background:
- Acinetobacter plasmids are distinct among Gram-negative bacteria.
- Many Acinetobacter plasmids utilize a Rep_3 family RepA replication initiation protein.
- Some Acinetobacter plasmids are known to carry dif modules.
Purpose of the Study:
- To identify plasmid backbone features associated with dif module carriage in Acinetobacter.
- To investigate the role of a conserved gene, orfX, in relation to dif modules.
- To understand the evolutionary dynamics and structural properties of these plasmids.
Main Methods:
- Examination of 78 distinct Acinetobacter plasmid types (R3 types).
- Identification of conserved open reading frame orfX downstream of repA.
- Analysis of plasmid backbone recombination sites (pdif sites) recognized by XerC and XerD.
- Phylogenetic analysis of RepA and OrfX proteins.
- Structural prediction of OrfX proteins using AlphaFold 3.
Main Results:
- A conserved orfX gene was found downstream of repA in 35 of the examined plasmids.
- These 35 plasmids possess backbones bounded by XerC/XerD-recognized pdif sites, forming C-type dif modules.
- Phylogenetic analyses indicated extensive backbone recombination between RepA and OrfX.
- Predicted OrfX structures show an N-terminal HTH domain, a dimerization-promoting α-helix, and a disordered C-terminus.
Conclusions:
- The presence of orfX correlates with dif module carriage in Acinetobacter plasmids.
- Extensive recombination suggests complex evolutionary histories for these plasmid backbones.
- OrfX's structure and its association with dif modules warrant further investigation into its potential role in dif module mobilization.
