Abstract
It is well known that bacteriophages play crucial roles in many aspects, such as controlling the number and the diversity of bacteria and participating in horizontal gene transfer, which is a key process in the evolution of bacteria. However, so far, the number of temperate bacteriophages is still limited, and their life processes are severely unknown, except for members of the lambdoid family of coliphages. In this study, a novel temperate phage of Pseudomonas aeruginosa, YA3 (vB_PaeP_YA3), was isolated from waste water. The morphology of YA3 suggested that it is a Podoviridae. The YA3 genome is a circular double-stranded DNA of 45,253 bp, with an average G + C content of 57.2%. A total of 65 open reading frames (ORFs) were predicted according to the sequence of YA3’s genome, of which only 32 (49.2%) ORFs were assigned with putative functions and 13 ORFs were confirmed by the structural proteome. Genome and proteome analyses confirmed the lysogenic nature of this phage, which encodes the typical lysogen-related proteins integrase, CI, Cro, and Q protein. The genome of YA3 is most closely related with that of temperate phage vB_PaeP_Tr60_Ab31, whereas the homology coverage is just 48%. There are many critical differences between their genomes, involving promoters, lysis pathways, and regulation patterns. YA3 is capable of stably lysogenizing its host P. aeruginosa PA14, targeting the integration site within the serine tRNA gene (PA14_RS20820), which is similar with phage vB_PaeP_Tr60_Ab31. The phylogenetic analysis is more complicated than we thought. Based on phage terminase large subunit (TerL) and CI proteins, phage YA3 is related with phage lambda, while their genome coverage is extremely low (<1%). Therefore, phage YA3 is a considerably novel lambda-like temperate phage, and a further study of its genome may deepen our understanding of the interaction between lysogenic phages and their bacterial hosts.
Highlights
Pseudomonas aeruginosa (P. aeruginosa) is one of the most common opportunistic human pathogens with a high diversity
We demonstrate that YA3 is a novel temperate phage of P. aeruginosa and a new member of the lambdoid family
The results showed that YA3 only infects P. aeruginosa PA14 strain but not P. aeruginosa PAO1 or E. coli MG1655 (Supplementary Table S1)
Summary
Pseudomonas aeruginosa (P. aeruginosa) is one of the most common opportunistic human pathogens with a high diversity. Because of its broad ecological range, P. aeruginosa can colonize various habitats, including soil, water, and the animate surfaces of plants, animals, and humans. By forming biofilms, it can even adhere strongly to the surface of medical devices—breathing tubes and catheters, for example, which makes it an important bacteria that cause nosocomial infections (Crull et al, 2018). P. aeruginosa owns multiple resistance mechanisms to antibiotics, so its drug resistance rate is extremely high and has been growing rapidly due to the plentiful use of antibiotics (Hauser, 2009; Zowalaty et al, 2015). The emergence of multidrug-resistant and pan-drugresistant P. aeruginosa strains makes the treatment of its infection a thorny problem
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