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bioRxiv · 10.1101/2020.06.19.162511

Comparative analysis reveals the modular functional build-up of megaplasmid pTTS12 of Pseudomonas putida S12: a paradigm for transferable traits, plasmid stability and inheritance?

Kusumawardhani, H.·Hosseini, R.·de Winde, J. H.
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Abstract

The Pseudomonas putida S12 genome contains 583 kbp megaplasmid pTTS12 that carries over 600 genes enabling tolerance to various stress conditions, including the solvent extrusion pump SrpABC. We performed a comparative analysis of pTTS12 against 28915 plasmids from NCBI databases. We investigated putative roles of genes encoded on pTTS12 and further elaborated on its role in the establishment and maintenance of several stress conditions, specifically focusing on solvent tolerance in P. putida strains. The backbone of pTTS12 was found to be closely related to that of the carbapenem-resistance plasmid pOZ176, member of the IncP-2 incompatibility group, although remarkably the carbapenem resistance cassette is absent from pTTS12. Megaplasmid pTTS12 contains multiple transposon-flanked cassettes mediating resistance to various heavy metals such as tellurite, chromate (Tn7), and mercury (Tn5053 and Tn5563). Additionally, pTTS12 also contains a P-type, Type IV secretion system (T4SS) supporting self-transfer to other P. putida strains. This study increases our understanding in the build-up of IncP-2 plasmids and several promising exchangeable gene clusters to construct robust microbial hosts for biotechnology applications. ImportanceOriginating from various environmental niches, large numbers of bacterial plasmids have been found carrying heavy metal and antibiotic resistance genes, degradation pathways and specific transporters for organic solvents or aromatic compounds. Such genes may constitute promising candidates for novel synthetic biology applications. Our systematic analysis of gene clusters encoded on megaplasmid pTTS12 underscores that a large portion of its genes is involved in stress response increasing survival under harsh conditions like heavy metal and organic solvent resistance. We show that pTTS12 belongs to the IncP-2 plasmid family. Comparative analysis of pTTS12 provides thorough insight into the structural and functional build-up of members of the IncP-2 plasmid family. pTTS12 is highly stable and carries a complex arrangement of transposable elements containing heavy metal resistance clusters as well as distinct aromatic degradation pathways and solvent-extrusion pump. This offers interesting insight into the evolution of solvent tolerance in the P. putida family.

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Kusumawardhani, H., Hosseini, R., de Winde, J. H.. 2020-06-20. Comparative analysis reveals the modular functional build-up of megaplasmid pTTS12 of Pseudomonas putida S12: a paradigm for transferable traits, plasmid stability and inheritance?. https://doi.org/10.1101/2020.06.19.162511

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