Abstract
We isolated and characterized a new Pseudomonas aeruginosa myovirus named PaP1. The morphology of this phage was visualized by electron microscopy and its genome sequence and ends were determined. Finally, genomic and proteomic analyses were performed. PaP1 has an icosahedral head with an apex diameter of 68–70 nm and a contractile tail with a length of 138–140 nm. The PaP1 genome is a linear dsDNA molecule containing 91,715 base pairs (bp) with a G+C content of 49.36% and 12 tRNA genes. A strategy to identify the genome ends of PaP1 was designed. The genome has a 1190 bp terminal redundancy. PaP1 has 157 open reading frames (ORFs). Of these, 143 proteins are homologs of known proteins, but only 38 could be functionally identified. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis and high-performance liquid chromatography-mass spectrometry allowed identification of 12 ORFs as structural protein coding genes within the PaP1 genome. Comparative genomic analysis indicated that the Pseudomonas aeruginosa phage PaP1, JG004, PAK_P1 and vB_PaeM_C2-10_Ab1 share great similarity. Besides their similar biological characteristics, the phages contain 123 core genes and have very close phylogenetic relationships, which distinguish them from other known phage genera. We therefore propose that these four phages be classified as PaP1-like phages, a new phage genus of Myoviridae that infects Pseudomonas aeruginosa.
Highlights
Bacteriophages are ubiquitous in the biosphere [1]
6300 different phages have been examined by electron microscopy [7]; only 759 of these (721 infecting bacteria and 38 infecting archaea) have been completely sequenced based on data from the National Center for Biotechnology Information (NCBI; http://www.ncbi.nlm.nih.gov/; Bethesda, MA, USA, Oct. 2012)
Based on comparative genomic analysis, we propose that P. aeruginosa phages PaP1, JG004, PAK_P1, and vB_PaeM_C2-10_Ab1 be classified as a new genus named ‘‘PaP1-like phages’’ within the Myoviridae family
Summary
Bacteriophages (phages) are ubiquitous in the biosphere [1]. Estimations of phage numbers, ranging from 1030 to 1032 in total, are approximately tenfold higher than those of bacteria [2]. The four identified PaP1 structural proteins, tape measure, tail fiber, baseplate, and major capsid, with molecular weight ranging from 40 kDa to 80 kDa, are important for phage PaP1 particle formation. The genomic comparison indicated that phages PaP1, JG004, PAK_P1, and vB_PaeM_C2-10_Ab1 are closely related. To investigate this further, protein homology analysis was performed. This observation is in accordance with the data listed, in which myoviruses of P. aeruginosa have been assigned to several phage genera, except for PaP1, JG004, PAK_P1, and Figure 8. PaP1, JG004, PAK_P1, and vB_PaeM_C2-10_Ab1 should be grouped as a new phage genus: ‘‘PaP1-like phages’’ (Figure 10)
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