Influence of Non-canonical DNA Bases on the Genomic Diversity of Tevenvirinae

Abstract

The Tevenvirinae viruses are some of the most common viruses on Earth. Representatives of this subfamily have long been used in the molecular biology studies as model organisms – since the emergence of the discipline. Tevenvirinae are promising agents for phage therapy in animals and humans, since their representatives have only lytic life cycle and many of their host bacteria are pathogens. As confirmed experimentally, some Tevenvirinae have non-canonical DNA bases. Non-canonical bases can play an essential role in the diversification of closely related viruses. The article performs a comparative and evolutionary analysis of Tevenvirinae genomes and components of Tevenvirinae genomes. A comparative analysis of these genomes and the genes associated with the synthesis of non-canonical bases allows us to conclude that non-canonical bases have a major influence on the divergence of Tevenvirinae viruses within the same habitats. Supposedly, Tevenvirinae developed a strategy for changing HGT frequency in individual populations, which was based on the accumulation of proteins for the synthesis of non-canonical bases and proteins that used those bases as substrates. Owing to this strategy, ancestors of Tevenvirinae with the highest frequency of HGT acquired genes that allowed them to exist in a certain niche, and ancestors with the lowest HGT frequency preserved the most adaptive of those genes. Given the origin and characteristics of genes associated with the synthesis of non-canonical bases in Tevenvirinae, one can assume that other phages may have similar strategies. The article demonstrates the dependence of genomic diversity of closely related Tevenvirinae on non-canonical bases.

Comparative analysis of Actinobacteria phage-plasmids and their transduction potential

“…In addition, the gene of this methyltransferase is located between the genes of DNA polymerase and helicase. It has been shown in our previous study [44] that this region usually includes genes for the synthesis of some non-canonical DNA bases and their modifications. Taking into account that in Pseudotevenvirsus this gene is located in the other region, further study of the homologs of the genes of this methyltransferase and the regions of bases synthesis may extend our knowledge about diversity of phages due to non-canonical bases.…”

Characteristics of Environmental Klebsiella pneumoniae and Klebsiella oxytoca Bacteriophages and Their Therapeutic Applications

“…A main barrier that protects bacteria from phage infection by the degradation of incoming phage DNA is formed by restriction-modification systems. T4-related phages overcome the action of these systems by various modifications of bases in their DNA (summarized in Nikulin and Zimin [ 104 ] and references therein). Our search of phages Kpn35c1 and Rpl1 predicted gene products for homologs of DNA base modification-associated proteins of T4-even related phages, listed in Nikulin and Zimin [ 104 ] revealed only homologs of two T4 proteins involved in DNA modification, namely dCTPase/dUTPase, and DenA ( Table S2 ).…”

“…T4-related phages overcome the action of these systems by various modifications of bases in their DNA (summarized in Nikulin and Zimin [ 104 ] and references therein). Our search of phages Kpn35c1 and Rpl1 predicted gene products for homologs of DNA base modification-associated proteins of T4-even related phages, listed in Nikulin and Zimin [ 104 ] revealed only homologs of two T4 proteins involved in DNA modification, namely dCTPase/dUTPase, and DenA ( Table S2 ). In phage T4 dCTPase/dUTPase hydrolyzes dCTP and dCDP, preventing its incorporation into phage DNA in place of deoxy-hydroxymethyl-cytosine, which is used by T4 as a substrate for DNA synthesis.…”