Genomic analysis and relatedness of P2-like phages of the Burkholderia cepacia complex

Abstract

BackgroundThe Burkholderia cepacia complex (BCC) is comprised of at least seventeen Gram-negative species that cause infections in cystic fibrosis patients. Because BCC bacteria are broadly antibiotic resistant, phage therapy is currently being investigated as a possible alternative treatment for these infections. The purpose of our study was to sequence and characterize three novel BCC-specific phages: KS5 (vB_BceM-KS5 or vB_BmuZ-ATCC 17616), KS14 (vB_BceM-KS14) and KL3 (vB_BamM-KL3 or vB_BceZ-CEP511).ResultsKS5, KS14 and KL3 are myoviruses with the A1 morphotype. The genomes of these phages are between 32317 and 40555 base pairs in length and are predicted to encode between 44 and 52 proteins. These phages have over 50% of their proteins in common with enterobacteria phage P2 and so can be classified as members of the Peduovirinae subfamily and the "P2-like viruses" genus. The BCC phage proteins similar to those encoded by P2 are predominantly structural components involved in virion morphogenesis. As prophages, KS5 and KL3 integrate into an AMP nucleosidase gene and a threonine tRNA gene, respectively. Unlike other P2-like viruses, the KS14 prophage is maintained as a plasmid. The P2 E+E' translational frameshift site is conserved among these three phages and so they are predicted to use frameshifting for expression of two of their tail proteins. The lysBC genes of KS14 and KL3 are similar to those of P2, but in KS5 the organization of these genes suggests that they may have been acquired via horizontal transfer from a phage similar to λ. KS5 contains two sequence elements that are unique among these three phages: an ISBmu2-like insertion sequence and a reverse transcriptase gene. KL3 encodes an EcoRII-C endonuclease/methylase pair and Vsr endonuclease that are predicted to function during the lytic cycle to cleave non-self DNA, protect the phage genome and repair methylation-induced mutations.ConclusionsKS5, KS14 and KL3 are the first BCC-specific phages to be identified as P2-like. As KS14 has previously been shown to be active against Burkholderia cenocepacia in vivo, genomic characterization of these phages is a crucial first step in the development of these and similar phages for clinical use against the BCC.

Bacteriophages of Ralstonia solanacearum: Their Diversity and Utilization as Biocontrol Agents in Agriculture

“…1). This generates a racket-frame-like structure that resembles the morphology reported for Burkholderia cepacia phage KS5 (Seed and Dennis, 2005;Lynch et al, 2010). A tail sheath was often observed attached at the bottom of the tail, but sometimes at intermediate position along the tail, suggesting a movable nature of the sheath along the tail.…”

Bacteriophage Orphan DNA Methyltransferases: Insights from Their Bacterial Origin, Function, and Occurrence

“…Burkholderia cepacia phage KL3 carries a gene that encodes an MTase that appears to be part of a functional defense module. Gene 47 encodes an EcoRII MTase associated with not only a cognate endonuclease but also a Vsr endonuclease (74). It has been proposed that the MTase functions in phage protection and that the endonuclease functions in bacterial DNA digestion, while the Vsr protein is thought to be responsible for postmethylation mismatch repair, the latter of which has been shown to be controlled by DAM-mediated methylation in bacterial cells as mentioned above (74).…”

Identification and characterization of ϕH111-1

“…The dissimilarity of the tail fiber protein (predicted to be the phage anti-receptor) is expected based on the differences in host specificity. 20 Based on CGUG analysis, ϕH111-1 encodes a protein similar to each P2 tail protein excluding E/E+E´, H, R, and S ( Table 2). The ϕH111-1 capsid morphogenesis and DNA packaging proteins are more closely related to those of AcaML1 than the "Vhmllikevirus" phages.…”