Localised genetic heterogeneity provides a novel mode of evolution in dsDNA phages

• Published in: Scientific reports Vol. 7; no. 1; pp. 13731 - 8
• Main Authors: Magill, Damian J., Kucher, Phillip A., Krylov, Victor N., Pleteneva, Elena A., Quinn, John P., Kulakov, Leonid A.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 23.10.2017; Nature Publishing Group
• Subjects: 45/22; 45/23; 631/181/735; 631/326/1321; Bacteriophages - enzymology; Bacteriophages - genetics; DNA, Viral - genetics; DNA-directed DNA polymerase; DNA-Directed DNA Polymerase - chemistry; DNA-Directed DNA Polymerase - metabolism; Evolution; Evolution, Molecular; Genetic variability; Genomes; Heterogeneity; High-Throughput Nucleotide Sequencing; Humanities and Social Sciences; Models, Molecular; multidisciplinary; Natural selection; Parasites; Phages; Phenotype; Protein Conformation; Science; Science (multidisciplinary); Sequence Analysis, DNA; Single-nucleotide polymorphism; Viruses
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-017-14285-0

The Red Queen hypothesis posits that antagonistic co-evolution between interacting species results in recurrent natural selection via constant cycles of adaptation and counter-adaptation. Interactions such as these are at their most profound in host-parasite systems, with bacteria and their viruses providing the most intense of battlefields. Studies of bacteriophage evolution thus provide unparalleled insight into the remarkable elasticity of living entities. Here, we report a novel phenomenon underpinning the evolutionary trajectory of a group of dsDNA bacteriophages known as the phiKMVviruses . Employing deep next generation sequencing (NGS) analysis of nucleotide polymorphisms we discovered that this group of viruses generates enhanced intraspecies heterogeneity in their genomes. Our results show the localisation of variants to genes implicated in adsorption processes, as well as variation of the frequency and distribution of SNPs within and between members of the phiKMVviruses . We link error-prone DNA polymerase activity to the generation of variants. Critically, we show trans-activity of this phenomenon (the ability of a phiKMVvirus to dramatically increase genetic variability of a co-infecting phage), highlighting the potential of phages exhibiting such capabilities to influence the evolutionary path of other viruses on a global scale.