Comparative analysis of \emph{Actinobacteria} phage-plasmids and their transduction potential

N. A. Nikulin ; S. S. Kiselev ; V. V. Panyukov ; Y. Lu ; A. A. Zimin

Matematičeskaâ biologiâ i bioinformatika, Tome 18 (2023) no. 2, pp. 323-346.

Résumé

The genus Streptomyces is the most extensively studied group within actinobacteria, which are widely used for the production of antibiotics and other metabolites. Streptomyces bacteriophages attract a lot of interest to study phage-host coevolution. One of the probable interactions is a bacteriophage-mediated horizontal transfer of genes encoding bacterial metabolites, which are important for humans. In this study, a search for Streptomyces bacteriophages having capacities necessary for efficient horizontal transfer was performed. Groups of bacteriophages of actinobacteria and their plasmids with relatively long GC-rich sequences containing both genes related to viral morphogenesis and plasmid-associated genes were revealed by comparative genome analysis. In one of these groups, homologs of proteins of DNA packaging into a capsid of Punavirus genus phages, that representatives are capable to perform a horizontal transfer of genes with high frequency were identified. Taking it into account, as well as the peculiarities of their genomic structure, horizontal gene transfer by this group of viruses and plasmids was assumed to occur. Considering the genome length and GC-content, it is thought that these viruses could be useful for producers construction. Moreover, some given examples showing the chimerical origin of phage-plasmids allow suggesting that recombination events between considered phages-plasmids occur at high frequency. New representatives of viruses with low similarity to known phage genomes were also detected among plasmids. A wide diversity of actinobacterial phage-plasmids that is related to their variability and a probable existence of a great number of sequences of this type of viruses in databases were found out.

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