Analysis of a Novel Bacteriophage vB_AchrS_AchV4 Highlights the Diversity of Achromobacter Viruses

Abstract

Achromobacter spp. are ubiquitous in nature and are increasingly being recognized as emerging nosocomial pathogens. Nevertheless, to date, only 30 complete genome sequences of Achromobacter phages are available in GenBank, and nearly all of those phages were isolated on Achromobacter xylosoxidans. Here, we report the isolation and characterization of bacteriophage vB_AchrS_AchV4. To the best of our knowledge, vB_AchrS_AchV4 is the first virus isolated from Achromobacter spanius. Both vB_AchrS_AchV4 and its host, Achromobacter spanius RL_4, were isolated in Lithuania. VB_AchrS_AchV4 is a siphovirus, since it has an isometric head (64 ± 3.2 nm in diameter) and a non-contractile flexible tail (232 ± 5.4). The genome of vB_AchrS_AchV4 is a linear dsDNA molecule of 59,489 bp with a G+C content of 62.8%. It contains no tRNA genes, yet it includes 82 protein-coding genes, of which 27 have no homologues in phages. Using bioinformatics approaches, 36 vB_AchrS_AchV4 genes were given a putative function. A further four were annotated based on the results of LC–MS/MS. Comparative analyses revealed that vB_AchrS_AchV4 is a singleton siphovirus with no close relatives among known tailed phages. In summary, this work not only describes a novel and unique phage, but also advances our knowledge of genetic diversity and evolution of Achromobacter bacteriophages.

SGP-C: A Broad Host Range Temperate Bacteriophage; Against Salmonella gallinarum

“…Bioinformatics approaches allowed identification of genes encoding for proteins involved in DNA metabolism that were not clustered together on genome. SGPC phage DNA was observed to be semiautonomous and likely to borrow many of the host replisome proteins for metabolism ( Kaliniene et al, 2021 ). ORF 53 for DNA polymerase I (DNA_pol_A domain), Putative helicases at ORF 59 having Hom_end-associated Hint domain, restriction endonucleases at ORF 56 and ORF 58 having VRR_NUC and HNH_3 domains, respectively were not found co-localized on the genome.…”

“…It included the DNA single-strand annealing proteins related to Rad52, such as RecT, Red-beta and ERF that function in RecA-dependent as well as RecA-independent DNA recombination pathways. Notably, according to the SCOP family, another ORF 48 apart from domain RecA protein-like (ATPase domain), specific domains of Rad51 or helicases was identified ( Kaliniene et al, 2021 ).…”

“…It included the DNA single-strand annealing proteins related to Rad52, such as RecT, Red-beta and ERF that function in RecA-dependent as well as RecA-independent DNA recombination pathways. Notably, according to the SCOP family, another ORF 48 apart from domain RecA protein-like (ATPase domain), specific domains of Rad51 or helicases was identified(Kaliniene et al, 2021).SGP-C exhibited two central components of lysogeny module with 2.4 bp region apart. These components commit for the outcome of "lysis versus lysogeny" decision: λ repressor cI gene for lysogeny and a bistable genetic switch Cro gene for lytic growth.…”

Mining of thousands of prokaryotic genomes reveals high abundance of prophage signals

“…Furthermore, analysis of Average Amino acid Identity (AAI) was carried out based on a pairwise comparison of the dereplicated prophage sequences (clustered prophages) using CompareM (https://github.com/dparks1134/CompareM ). We considered relatedness at genus level for those prophages with an AAI value ≥ 80, as previously reported [27,28]. The prophage relatedness was visualized as an AAI network using Cytoscape v.3.8 [29].…”

“…We also wanted to determine the relatedness between prophages. For this, we performed an AAI pairwise comparison analysis on the clustered prophages, since AAI was established as a reliable metric to obtain phylogenetic relationship between phages [27,28]. Here, we retrieved 2,485 prophages that showed >80% of AAI (where phages with >80% of AAI could be associated to the same genus [28]), and most of them were identified within Proteobacteria, Actinobacteria, Bacteroides and Firmicutes; of these, most of the prophages with AAI of >80% were prophages from hosts with the same taxonomic affiliation (Figure 4A).…”