Yersiniophage ϕR1-37 is a tailed bacteriophage having a 270 kb DNA genome with thymidine replaced by deoxyuridine

Abstract

Yersiniophage wR1-37 is a tailed bacteriophage having a 270 kb DNA genome with thymidine replaced by deoxyuridine Bacteriophage wR1-37 was isolated based on its ability to infect strain YeO3-R1, a virulenceplasmid-cured O antigen-negative derivative of Yersinia enterocolitica serotype O : 3. In this study, the phage receptor was found to be a structure in the outer core hexasaccharide of Y. enterocolitica O : 3 LPS. The phage receptor was present in the outer core of strains of many other Y. enterocolitica serotypes, but also in some Yersinia intermedia strains. Surprisingly, the receptor structure resided in the O antigen of Yersinia pseudotuberculosis O : 9. Electron microscopy demonstrated that wR1-37 particles have an icosahedral head of 88 nm, a short neck of 10 nm, a long contractile tail of 236 nm, and tail fibres of at least 86 nm. This implies that the phage belongs to the order Caudovirales and the family Myoviridae in the ICTV (International Committee for Taxonomy of Viruses) classification. wR1-37 was found to have a lytic life cycle, with eclipse and latent periods of 40 and 50 min, respectively, and a burst size of~80 p.f.u. per infected cell. Restriction digestions and PFGE showed that the wR1-37 genome was dsDNA and~270 kb in size. Enzymically hydrolysed DNA was subjected to HPLC-MS/MS analysis, which demonstrated that the wR1-37 genome is composed of DNA in which thymidine (T) is >99 % replaced by deoxyuridine (dU). The only organisms known to have similar DNA are the Bacillus subtilis-specific bacteriophages PBS1 and PBS2. N-terminal amino acid sequences of four major structural proteins did not show any similarity to (viral) protein sequences in databases, indicating that close relatives of wR1- 37 have not yet been characterized. Genes for two of the structural proteins, p24 and p46, were identified from the partially sequenced wR1-37 genome. INTRODUCTIONYersinia enterocolitica is a Gram-negative bacterium of the family Enterobacteriaceae. The species includes over 30 serotypes, a number of which are human pathogens (Wauters et al., 1991). While the major pathogenic serotypes in Europe, Canada, Japan and South Africa are O : 3 and O : 9; in the United States serotype O : 8 is more prevalent. Y. enterocolitica is widely distributed in nature, swine being the major reservoir of the pathogenic strains (Bottone, 1997).Bacteriophages are the most abundant organisms on Earth, and it is estimated that for each microbial isolate at least 10 different phages can be found (Hendrix, 2002;Pedulla et al., 2003). A number of phages infecting the members of the genus Yersinia have been isolated (Baker & Farmer, 1982;Popp et al., 2000;Stevenson & Airdrie, 1984), but relatively few have been characterized in more detail. Y. enterocolitica O : 3-specific phage wYeO3-12 has been shown to be closely related to Escherichia coli phages T3 and T7 (Pajunen et al., 2000(Pajunen et al., , 2001. Likewise, Yersinia pestis phage wA1122 was recently found to be a close relative of T7 (Garcia et al., 2003a). Bacteriophage...

DNA digestion to deoxyribonucleoside: A simplified one-step procedure

“…Likewise, in vivo experiments in humans, such as examination of the effect of gene polymorphisms [6] and nutritional status [6,7] on DNA metabolism, have used labeled one-carbon donors to label monocyte DNA. Nucleoside hydrolysates of DNA also have been used in determining the base composition of DNA, including investigation of epigenetic modification such as deoxycytosine methylation [8,9], oxidative damage [10,11], or unique DNA composition [12].…”

Intragenus generalized transduction in Staphylococcus spp. by a novel giant phage

“…The methicillin-resistant gene in MRSA is considered to have originated from animal-associated staphylococci (Tsubakishita et al, 2010;Moellering, 2011), so giant myophages such as S6 could contribute to the emergence of new types of MRSA in various environments. Moreover, if RNA is the precursor to life and phages that contain uracilbased DNAs are relics of the RNA world, giant myophages such as phages S6, PBS1 and phiR1-37, may have had important roles in the evolution of bacteria from the last universal common ancestor (Forterre, 2005;Kiljunen et al, 2005). In the future, the experimental evolution of S. aureus into MRSA will be investigated using phage S6 to elucidate the origin and emergence of MRSA.…”

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

“…These include Pseudomonas aeruginosa phage KZ (280 kbp, Mesyanzhinov et al, 2002), EL (211 kbp, Herveldt et al, 2005), and PA3 (309 kbp, Monson et al, 2011), Vibrio parahaemolyticus phage KVP40 (245 kbp, Miller et al, 2003), Stenotrophomonas maltophila phage SMA5 (250 kbp, Chang et al, 2005), and Yersinia enterocolitica phage R1-37 (270 kbp, Kiljunen et al, 2005). Jumbo phages were also reported for Sinorhizobium meliloti (phage N3, 207 kbp, Martin and Long, 1984) and Bacillus megaterium (phage G, 670 kbp, Sun and Serwer, 1997).…”