The genome and proteome of coliphage T1

AbstractThe genome of enterobacterial phage T1 has been sequenced, revealing that its 50.7-kb terminally redundant, circularly permuted sequence contains 48,836 bp of nonredundant nucleotides. Seventy-seven open reading frames (ORFs) were identified, with a high percentage of small genes located at the termini of the genomes displaying no homology to existing phage or prophage proteins. Of the genes showing homologs (47%), we identified those involved in host DNA degradation (three endonucleases) and T1 replication (DNA helicase, primase, and single-stranded DNA-binding proteins) and recombination (RecE and Erf homologs). While the tail genes showed homology to those from temperate coliphage N15, the capsid biosynthetic genes were unique. Phage proteins were resolved by 2D gel electrophoresis, and mass spectrometry was used to identify several of the spots including the major head, portal, and tail proteins, thus verifying the annotation

Genome of campylobacter coli bacteriophage phiCcoIBB_35

Campylobacter is recognized worldwide as the major etiologic agent in human diarrheoal disease, being Campylobacter jejuni and Campylobacter coli the most prevalent species. Bacteriophages are natural predators of bacteria, ubiquitous in the environment, self-limiting, self- replicating and with a high host-specicity. These make them potentially an important biocontrol agent of foodborne diseases. There are only few reports on Campylobacter bacteriophages, probably due to the fastidious nature of the host Campylobacter which makes the isolation of these phages challenging. Moreover the refractory nature to restriction enzymes digestion of their DNA causes difficulties in characterizing Campylobacter phage genomes by common methods such as restriction fragment length polymorphism. In a previous study Campylobacter phages were isolated from poultry intestinal contents (Carvalho et al., 2010) and one of these phages (phage phiCcoIBB 35) was selected to be genetically sequenced as it showed broad lytic spectra against food and clinical Campylobacter coli and Campylobacter jejuni strains. The PFGE analysis indicates that the genome of phage phiCcoIBB 35 is approximately 204kb. However due to the fact that DNA preparations appeared to contain substances that inhibit Taq and 29 enzymes, the DNA sequence data consists of ve DNA contigs in a total of 172 kb that were not possible to be aligned. Annotation indicates that most of the ORFs are unique and that homology exists with members of the Teequatrovirinae namely for all T4 tail proteins, one head protein (gp23), neck protein (gp20); and baseplate proteins (gp6,gp25, gp48). Moreover homologs were found to T4 proteins involved in morphogenesis, nucleotide metabolism, transcription, DNA replication and recombination. Unique genes involved in the carbohydrate metabolism, pathogenesis and amino acid metabolism were also annotated. Several incidences of gene duplications, split genes with intein and introns and insertion-like sequences were present. To our knowledge this study represents the rst report of the genomic sequence of a lytic Campylobacter phage and therefore is of extreme importance for further comparisons with other phage sequences. Nu

Complete genome sequence of pseudomonas aeruginosa Phage vB_PaeM_CEB_DP1

vB_PaeM_CEB_DP1 is a Pseudomonas aeruginosa bacteriophage (phage) belonging to the Pbunalikevirus genus of the Myoviridae family of phages. It was isolated from hospital sewage. vB_PaeM_CEB_DP1 is a double-stranded DNA (dsDNA) phage, with a genome of 66,158 bp, containing 89 predicted open reading frames.NIH -National Institutes of Health(1DP2OD008435

A roadmap for genome-based phage taxonomy

Bacteriophage (phage) taxonomy has been in flux since its inception over four decades ago. Genome sequencing has put pressure on the classification system and recent years have seen significant changes to phage taxonomy. Here, we reflect on the state of phage taxonomy and provide a roadmap for the future, including the abolition of the order Caudovirales and the families Myoviridae, Podoviridae, and Siphoviridae. Furthermore, we specify guidelines for the demarcation of species, genus, subfamily and family-level ranks of tailed phage taxonomy

Genome sequence and characterization of Streptomyces phage Pablito, representing a new species within the genus Janusvirus

Streptomycetes are ubiquitous soil bacteria. Here we report the complete and annotated genome sequence and characterization of Streptomyces phage Pablito, isolated from a soil sample in Haarlem, the Netherlands using Streptomyces lividans as host. This phage was able to infect a diverse range of Streptomyces strains, but none belonging to the sister genus Kitasatospora. Phage Pablito has double-stranded DNA with a genome length of 49,581 base pairs encoding 76 putative proteins, of which 26 could be predicted. The presence of a serine integrase protein indicated the lysogenic nature of phage Pablito. The phage remained stable over a wide range of temperatures (25--45 \textdegreeC) and at pH\thinspace\thinspace7.0, but lost infectivity at temperatures above 55 \textdegreeC or when the pH dropped below 6.0. This newly isolated phage is closely related to Streptomyces phage Janus and Hank144 and considered a new species classified in the genus Janusvirus, within the subfamily Arquattrovirinae.This work was funded by a VICI grant from the Dutch Research Council (NWO) to DC (Grant Number VI.C.192.002) and an NWO XS grant to AB (Grant Number OCENW.XS.041). Microscope access was supported by the Netherlands Center for Electron Nanoscopy and partially funded by the Netherlands Electron Microscopy Infrastructure Grant 84.034.014.info:eu-repo/semantics/publishedVersio

Characterization of newly isolated lytic bacteriophages active against Acinetobacter baumannii

Based on genotyping and host range, two newly isolated lytic bacteriophages, myovirus vB_AbaM_Acibel004 and podovirus vB_AbaP_Acibel007, active against Acinetobacter baumannii clinical strains, were selected from a new phage library for further characterization. The complete genomes of the two phages were analyzed. Both phages are characterized by broad host range and essential features of potential therapeutic phages, such as short latent period (27 and 21 min, respectively), high burst size (125 and 145, respectively), stability of activity in liquid culture and low frequency of occurrence of phage-resistant mutant bacterial cells. Genomic analysis showed that while Acibel004 represents a novel bacteriophage with resemblance to some unclassified Pseudomonas aeruginosa phages, Acibel007 belongs to the well-characterized genus of the Phikmvlikevirus. The newly isolated phages can serve as potential candidates for phage cocktails to control A. baumannii infections