RESUMEN
DNA glycosylases are DNA repair enzymes capable of removing damaged nitrogenous bases, including those formed as a result of UV irradiation with sunlight (approximately 300-400 нм). DNA glycosylases are common not only among bacteria, archaea, and eukaryotes, but some groups of viruses can also encode them. The best-known viral glycosylase is endonuclease V (DenV, Pdg-T4) of Escherichia virus T4, the main substrate of which is cyclobutane pyrimidine dimers. DenV is isolated separately from other large families of glycosylases; it is quite common in nature and has homologs in a number of other viruses and even bacteria. However, the ways of its origin are poorly understood. The best-known DenV homolog is the glycosylase of Chlorella virus strain, PBCV-1 (Cv-pdg). This review contains the main known data on the structure and mechanism of operation of DenV and its homologs. The issues of biological importance and distribution of the enzyme and its homologs among viruses are considered and supplemented separately. Supplementary Information: The online version contains supplementary material available at 10.1007/s12551-022-00972-4.
RESUMEN
[This corrects the article DOI: 10.3389/fmicb.2021.632686.].
RESUMEN
Bacteriophages are bacterial viruses and the most abundant biological entities on Earth. Temperate bacteriophages can form prophages stably maintained in the host population: they either integrate into the host genome or replicate as plasmids in the host cytoplasm. As shown, tailed temperate bacteriophages may form circular plasmid prophages in many bacterial species of the taxa Firmicutes, Gammaproteobacteria and Spirochaetes. The actual number of such prophages is thought to be underestimated for two main reasons: first, in bacterial whole genome-sequencing assemblies, they are difficult to distinguish from actual plasmids; second, there is an absence of experimental studies which are vital to confirm their existence. In Firmicutes, such prophages appear to be especially numerous. In the present study, we identified 23 genomes from species of the Bacillus cereus group that were deposited in GenBank as plasmids and may belong to plasmid prophages with little or no homology to known viruses. We consider these putative prophages worth experimental assays since it will broaden our knowledge of phage diversity and suggest that more attention be paid to such molecules in all bacterial sequencing projects as this will help in identifying previously unknown phages.
Asunto(s)
Bacillus cereus/genética , Plásmidos/genética , Profagos/genética , Bacillus/genética , Bacteriófagos/genética , Bases de Datos Genéticas , Genoma Viral/genéticaRESUMEN
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.
RESUMEN
The Bacillus cereus group of bacteria includes, inter alia, the species known to be associated with human diseases and food poisoning. Here, we describe the Bacillus phage vB_BtS_B83 (abbreviated as B83) infecting the species of this group. Transmission electron microscopy (TEM) micrographs indicate that B83 belongs to the Siphoviridae family. B83 is a temperate phage using an arbitrium system for the regulation of the lysis-lysogeny switch, and is probably capable of forming a circular plasmid prophage. Comparative analysis shows that it has been previously sequenced, but was mistaken for a plasmid. B83 shares common genome organization and >46% of proteins with other the Bacillus phage, BMBtp14. Phylograms constructed using large terminase subunits and a pan-genome presence-absence matrix show that these phages form a clade distinct from the closest viruses. Based on the above, we propose the creation of a new genus named Bembunaquatrovirus that includes B83 and BMBtp14.