Characterization of the Genome, Proteome, and Structure of Yersiniophage ϕR1-37

Abstract

The bacteriophage vB_YecM-R1-37 (R1-37) is a lytic yersiniophage that can propagate naturally in different Yersinia species carrying the correct lipopolysaccharide receptor. This large-tailed phage has deoxyuridine (dU) instead of thymidine in its DNA. In this study, we determined the genomic sequence of phage R1-37, mapped parts of the phage transcriptome, characterized the phage particle proteome, and characterized the virion structure by cryo-electron microscopy and image reconstruction. The 262,391-bp genome of R1-37 is one of the largest sequenced phage genomes, and it contains 367 putative open reading frames (ORFs) and 5 tRNA genes. Mass-spectrometric analysis identified 69 phage particle structural proteins with the genes scattered throughout the genome. A total of 269 of the ORFs (73%) lack homologues in sequence databases. Based on terminator and promoter sequences identified from the intergenic regions, the phage genome was predicted to consist of 40 to 60 transcriptional units. Image reconstruction revealed that the R1-37 capsid consists of hexameric capsomers arranged on a T‫72؍‬ lattice similar to the bacteriophage KZ. The tail of R1-37 has a contractile sheath. We conclude that phage R1-37 is a representative of a novel phage type that carries the dU-containing genome in a KZ-like head. Bacteriophages, the viruses that infect bacteria, are the most abundant organisms on Earth, and it is estimated that for each microbial isolate at least 10 different phages exist (19,35). Present knowledge indicates that phages are extremely diverse in nature (7a). Studies on bacteriophages have escalated, since they are excellent targets for genomic and evolutionary research and as models for systems biology studies; in addition, they are important vehicles in horizontal gene transfer. Phages are used as tools in bacterial genetics, and phage gene products are used as tools in molecular biology. Furthermore, their potential as therapeutic agents during the increasing emergence of antibiotic resistance is being reexamined (45,46). In summary, a thorough knowledge of the bacteriophage and its biology is considered essential to all phage research.We have isolated several Yersinia enterocolitica-specific bacteriophages that use different parts of lipopolysaccharide (LPS) as receptors and used them to study the molecular biology and genetics of LPS biosynthesis (2,23,24,33,34,(46)(47)(48). The bacteriophage vB_YecM-R1-37 (R1-37) was isolated from sewage based on its ability to infect Y. enterocolitica strain YeO3-R1, an O-polysaccharide (O-PS)-lacking Y. enterocolitica serotype O:3 strain (44, 48). The host range of R1-37, as well as genetic and structural data, showed that the LPS outer core (OC) hexasaccharide of Y. enterocolitica O:3 is the phage receptor (23,37,38,48).Electron microscopy and analysis of its genome indicated that R1-37 is an exceptionally large-tailed phage with an estimated genome size of 270 kb (23). Structural studies on large bacteriophages with contractile tails are currently limited to the Pse...

Isolation, characterization and complete genome sequence of PhaxI: a phage of Escherichia coli O157 : H7

“…The number of phage particle-associated proteins is much higher than predicted based on SDS-PAGE analysis. Similar findings have been reported for other large bacteriophages such as WKZ and WR1-37 (Skurnik et al, 2012;Thomas et al, 2012).…”

Development of Giant Bacteriophage ϕKZ Is Independent of the Host Transcription Apparatus

“…Inspection of the KZ genome sequence revealed 28 such highly conserved motifs. These motifs have been assumed to act as phage-specific promoters (25,29,(39)(40)(41). Indeed, our RNA-seq data clearly indicate that after 5 min of KZ infection, all transcription is performed on the leading strand and is exclusively associated with these motifs (Fig.…”

“…Intriguingly, three virion proteins, gp178, gp80, and gp180, were found to resemble bacterial RNAP ␤ and ␤= subunits. It was hypothesized that these proteins form a highly unusual virion RNAP, are coinjected with the phage DNA, and participate in early transcription, possibly through recruitment of host-encoded factors (26)(27)(28)(29). Two other KZ proteins, Gp73 and Gp74, also resemble ␤/␤=-like subunits but are not associated with virions, suggesting that the phage encodes an additional, nonvirion RNAP (nvRNAP) (25).…”

Isolation of Yersinia enterocolitica Bacteriophage From Hospital Wastewater

“…To date, bacteriophages φYeO3-12 [8][9][10] and BYenP-AP5 11 specific to Y. enterocolitica, O:3, phage PY54 specific to Y. enterocolitica O:5, 12 and phage φR1-37 specific to Y. enterocolitica have been detected. 13,14 Studies have shown that the receptor for _R1-37 is Y. enterocolitic O:3 LPS outer core (OC) hexasaccharide. [15][16][17][18][19] The host receptor for phages _YeO3-12 and vB_YenP_AP5 has been defined to be the LPS O antigen of serotype O:3, comprising of the sugar 6-deoxy-L-altropyranose.…”