Genomic and proteomic analysis of phiEco32, a novel Escherichia coli bacteriophage

The use of genomic signature distance between bacteriophages and their hosts displays evolutionary relationships and phage growth cycle determination

BACKGROUND

Bacteriophage classification is mainly based on morphological traits and genome characteristics combined with host information and in some cases on phage growth lifestyle. A lack of molecular tools can impede more precise studies on phylogenetic relationships or even a taxonomic classification. The use of methods to analyze genome sequences without the requirement for homology has allowed advances in classification.

RESULTS

Here, we proposed to use genome sequence signature to characterize bacteriophages and to compare them to their host genome signature in order to obtain host-phage relationships and information on their lifestyle. We analyze the host-phage relationships in the four most representative groups of Caudoviridae, the dsDNA group of phages. We demonstrate that the use of phage genomic signature and its comparison with that of the host allows a grouping of phages and is also able to predict the host-phage relationships (lytic vs. temperate).

CONCLUSIONS

We can thus condense, in relatively simple figures, this phage information dispersed over many publications.

The role of interactions between phage and bacterial proteins within the infected cell: a diverse and puzzling interactome

Interactions between bacteriophage proteins and bacterial proteins are important for efficient infection of the host cell. The phage proteins involved in these bacteriophage-host interactions are often produced immediately after infection. A survey of the available set of published bacteriophage-host interactions reveals the targeted host proteins are inhibited, activated or functionally redirected by the phage protein. These interactions protect the bacteriophage from bacterial defence mechanisms or adapt the host-cell metabolism to establish an efficient infection cycle. Regrettably, a large majority of bacteriophage early proteins lack any identified function. Recent research into the antibacterial potential of bacteriophage-host interactions indicates that phage early proteins seem to target a wide variety of processes in the host cell - many of them non-essential. Since a clear understanding of such interactions may become important for regulations involving phage therapy and in biotechnological applications, increased scientific emphasis on the biological elucidation of such proteins is warranted.

Morphological and genetic analysis of three bacteriophages of Serratia marcescens isolated from environmental water

Increases in multidrug-resistant strains of Serratia marcescens are of great concern in pediatrics, especially in neonatal intensive care units. In the search for bacteriophages to control infectious diseases caused by multidrug-resistant S. marcescens, three phages (KSP20, KSP90, and KSP100) were isolated from environmental water and were characterized morphologically and genetically. KSP20 and KSP90 belonged to morphotype A1 of the family Myoviridae, and KSP100 belonged to morphotype C3 of the family Podoviridae. Analysis of the DNA region coding virion proteins, together with their morphological features, indicated that KSP20, KSP90, and KSP100 were related to the P2-like phage (temperate), T4-type phage (virulent), and phiEco32 phage (virulent), respectively. Based on amino acid sequences of the major capsid protein, KSP90 formed a new branch with a Stenotrophomonas maltophilia phage, Smp14, in the T4-type phage phylogeny. Both Smp14 and phiEco32 have been reported as potential therapeutic phages. These results suggest that KSP90 and KSP100 may be candidate therapeutic phages to control S. marcescens infection.

The intron-containing genome of the lytic Pseudomonas phage LUZ24 resembles the temperate phage PaP3

The virulent Pseudomonas aeruginosa bacteriophage LUZ24 (45,625 bp) was isolated from hospital sewage. It belongs to the family of the Podoviridae, and carries a bidirectionally transcribed dsDNA genome delineated by two direct terminal repeats of 184 bp. In vitro transcriptional analysis identified seven sigma(70) promoters, revealing a bias towards stronger promoter strength in the late genomic region. Reverse transcription demonstrated in vivo splicing of a 668 bp Group I intron embedded inside the DNA polymerase gene. Using mass spectrometry, nine structural proteins were identified as part of the phage particle. The lytic characteristics of LUZ24 are evaluated against its genomic content, which displays an overall 71% sequence similarity to the temperate phage PaP3.