Bacteriophage T4 Genome

Miller, Eric S.; Kutter, Elizabeth; Mosig, Gisela; Arisaka, Fumio; Kunisawa, Takashi; Rüger, Wolfgang

doi:10.1128/mmbr.67.1.86-156.2003

Cited by 674 publications

(840 citation statements)

References 1,118 publications

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“…comm.). Furthermore, given that bacteriophages can carry genes for de novo nucleotide synthesis and recycle degraded host nucleic acid (Miller et al 2003) and that RNA-containing viruses would not be labeled, the TdR technique can at best provide only a lower limit estimate for VP. Nevertheless, comparison of the FLV and TdR approaches demonstrates that when the high conversion factor (2.1 × 10 21 viruses mol -1 TdR incorporated) is used VP estimates tend to be in closer agreement.…”

Section: Methods Evaluationmentioning

confidence: 99%

Evaluation of incubation-based methods for estimating virioplankton production in estuaries

Helton¹,

Cottrell²,

Kirchman³

et al. 2005

Aquat. Microb. Ecol.

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Assessment of the role of viral lysis in aquatic microbial communities requires a robust means of estimating viral production (VP). Here, 3 incubation-based VP methods (fluorescently labeled viruses [FLV], dilution [DIL], and thymidine incorporation [TdR]) were evaluated in water samples from the Delaware and Chesapeake Bays. In Chesapeake Bay samples, average VP rates were 10-fold higher for FLV and DIL (~3 to 25 × 10 10 viruses l -1 d -1 ) than for TdR (~0.2 to 3 × 10 10 viruses l -1 d -1 ). Estimates of viral-mediated bacterial mortality (VMM) indicate that FLV overestimates VP in eutrophic waters, since >100% of bacterial production (BP) would have been consumed through viral lysis. DIL and TdR VP methods gave more realistic estimates of VMM with respect to BP. The FLV method provides estimates of both VP and virus removal rates; however, it requires preparation of a viral tracer and twice as many microscopic enumerations as the DIL method. DIL was the least difficult and most efficient method; however, bacterial loss during vacuum diafiltration resulted in poor replicability. TdR gave similar VP estimates to DIL, but requires use of a large and poorly constrained conversion factor. With methodological improvements in bacterial cell recovery, DIL should be the most widely applicable method for estimation of VP in highly productive estuarine waters. KEY WORDS: Viral production · Bacteriophage · Marine viruses · Marine microbial ecologyResale or republication not permitted without written consent of the publisher

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Section: Methods Evaluationmentioning

confidence: 99%

Evaluation of incubation-based methods for estimating virioplankton production in estuaries

Helton¹,

Cottrell²,

Kirchman³

et al. 2005

Aquat. Microb. Ecol.

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“…Much of the knowledge concerning phage-host interactions comes from studies in Escherichia coli. Both lysogenic and lytic coliphages initially promote similar alterations in host metabolism (Calendar, 2006) that halt host cell DNA synthesis (Kazmierczak and Rothman-Denes, 2006), degrade host DNA (Miller et al, 2003) and assemble the machinery for viral production (Taylor, 1995). These activities drastically alter aspects of host metabolism in a specific manner that favors virus replication (see, for example, Poranen et al, 2006).…”

Section: Introductionmentioning

confidence: 99%

Phage infection of an environmentally relevant marine bacterium alters host metabolism and lysate composition

Ankrah

May²,

Middleton³

et al. 2013

The ISME Journal

123

126

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Viruses contribute to the mortality of marine microbes, consequentially altering biological species composition and system biogeochemistry. Although it is well established that host cells provide metabolic resources for virus replication, the extent to which infection reshapes host metabolism at a global level and the effect of this alteration on the cellular material released following viral lysis is less understood. To address this knowledge gap, the growth dynamics, metabolism and extracellular lysate of roseophage-infected Sulfitobacter sp. 2047 was studied using a variety of techniques, including liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based metabolomics. Quantitative estimates of the total amount of carbon and nitrogen sequestered into particulate biomass indicate that phage infection redirects B75% of nutrients into virions. Intracellular concentrations for 82 metabolites were measured at seven time points over the infection cycle. By the end of this period, 71% of the detected metabolites were significantly elevated in infected populations, and stable isotope-based flux measurements showed that these cells had elevated metabolic activity. In contrast to simple hypothetical models that assume that extracellular compounds increase because of lysis, a profile of metabolites from infected cultures showed that 470% of the 56 quantified compounds had decreased concentrations in the lysate relative to uninfected controls, suggesting that these small, labile nutrients were being utilized by surviving cells. These results indicate that virus-infected cells are physiologically distinct from their uninfected counterparts, which has implications for microbial community ecology and biogeochemistry.

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“…Similarly, in Lactobacillus casei phage A2, the two different-sized capsid proteins are translated from the same gene (Garcia et al, 2003b). On the other hand, in E. coli phage T4, the head proteins gp23 and gp24 have evolved via gene duplication (Kutter et al, 1995;Miller et al, 2003). Predicted from the nucleotide sequences of their genes, both structural proteins sp24 and sp46 are apparently proteolytically processed during phage maturation.…”

mentioning

confidence: 99%

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

et al. 2005

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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...

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Bacteriophage T4 Genome

Cited by 674 publications

References 1,118 publications

Evaluation of incubation-based methods for estimating virioplankton production in estuaries

Evaluation of incubation-based methods for estimating virioplankton production in estuaries

Phage infection of an environmentally relevant marine bacterium alters host metabolism and lysate composition

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

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