A fragile lattice: replacing bacteriophage λ's head stability gene D with the shp gene of phage 21 generates the Mg2+-dependent virus, λ shp

Wendt, Jennifer L.; Feiss, Michael

doi:10.1016/j.virol.2004.05.024

Cited by 18 publications

(20 citation statements)

References 18 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…orf26 (Sf1) and orf6 (Sf3), members of pham n. 6, were classified as bacteriophage lambda head decoration protein D. Since the protein allows for the display of many copies of a foreign protein, which is advantageous for displaying weak ligands for affinity selection, a useful platform for phage polypeptide display was recently developed [78]. Interestingly, orf32 in Sf1 and orf12 in Sf3 were not assigned functions previously, although they belong to the pham n. 12 together with orf 1 (Sf1) which is classified as terminase_4.…”

Section: Resultsmentioning

confidence: 99%

Functional and comparative genome analysis of novel virulent actinophages belonging to Streptomyces flavovirens

et al. 2017

View full text Add to dashboard Cite

BackgroundNext Generation Sequencing (NGS) technologies provide exciting possibilities for whole genome sequencing of a plethora of organisms including bacterial strains and phages, with many possible applications in research and diagnostics. No Streptomyces flavovirens phages have been sequenced to date; there is therefore a lack in available information about S. flavovirens phage genomics. We report biological and physiochemical features and use NGS to provide the complete annotated genomes for two new strains (Sf1 and Sf3) of the virulent phage Streptomyces flavovirens, isolated from Egyptian soil samples.ResultsThe S. flavovirens phages (Sf1 and Sf3) examined in this study show higher adsorption rates (82 and 85%, respectively) than other actinophages, indicating a strong specificity to their host, and latent periods (15 and 30 min.), followed by rise periods of 45 and 30 min. As expected for actinophages, their burst sizes were 1.95 and 2.49 virions per mL. Both phages were stable and, as reported in previous experiments, showed a significant increase in their activity after sodium chloride (NaCl) and magnesium chloride (MgCl2.6H2O) treatments, whereas after zinc chloride (ZnCl2) application both phages showed a significant decrease in infection.The sequenced phage genomes are parts of a singleton cluster with sizes of 43,150 bp and 60,934 bp, respectively. Bioinformatics analyses and functional characterizations enabled the assignment of possible functions to 19 and 28 putative identified ORFs, which included phage structural proteins, lysis components and metabolic proteins.Thirty phams were identified in both phages, 10 (33.3%) of them with known function, which can be used in cluster prediction. Comparative genomic analysis revealed significant homology between the two phages, showing the highest hits among Sf1, Sf3 and the closest Streptomyces phage (VWB phages) in a specific 13Kb region. However, the phylogenetic analysis using the Major Capsid Protein (MCP) sequences highlighted that the isolated phages belong to the BG Streptomyces phage group but are clearly separated, representing a novel sub-cluster.ConclusionThe results of this study provide the first physiological and genomic information for S. flavovirens phages and will be useful for pharmaceutical industries based on S. flavovirens and future phage evolution studies.

show abstract

Section: Resultsmentioning

confidence: 99%

Functional and comparative genome analysis of novel virulent actinophages belonging to Streptomyces flavovirens

et al. 2017

View full text Add to dashboard Cite

show abstract

“…The gpD protein of bacteriophage lambda and gpShp of bacteriophage 21 function as head stabilization proteins (57,59). DNA packaging in bacteriophage lambda is accompanied by expansion of the prohead to an icosahedral shape and the binding of gpD.…”

Section: Resultsmentioning

confidence: 99%

Structural Characterization of the UL25 DNA-Packaging Protein from Herpes Simplex Virus Type 1

Bowman

Welschhans

Jayaram

et al. 2006

J Virol

View full text Add to dashboard Cite

Herpesviruses replicate their double stranded DNA genomes as high-molecular-weight concatemers which are subsequently cleaved into unit-length genomes by a complex mechanism that is tightly coupled to DNA insertion into a preformed capsid structure, the procapsid. The herpes simplex virus type 1 UL25 protein is incorporated into the capsid during DNA packaging, and previous studies of a null mutant have demonstrated that its function is essential at the late stages of the head-filling process, either to allow packaging to proceed to completion or for retention of the viral genome within the capsid. We have expressed and purified an N-terminally truncated form of the 580-residue UL25 protein and have determined the crystallographic structure of the region corresponding to amino acids 134 to 580 at 2.1-Å resolution. This structure, the first for any herpesvirus protein involved in processing and packaging of viral DNA, reveals a novel fold, a distinctive electrostatic distribution, and a unique "flexible" architecture in which numerous flexible loops emanate from a stable core. Evolutionary trace analysis of UL25 and its homologues in other herpesviruses was used to locate potentially important amino acids on the surface of the protein, leading to the identification of four putative docking regions for protein partners.

show abstract

“…This marks the first identification of a virion structural protein gene that is transcriptionally upstream of the terminase genes in the lambdoid phage group, which typically have a very stereotyped late operon gene order in which the small terminase subunit gene is the most promoter-proximal virion assembly gene (11,13,28). The two other types of lambdoid phage decoration protein genes, the lambda D gene (61,66) and the ES18 8 gene (10), lie immediately to the left of the coat protein gene. The unusual location of dec might indicate that it has had an evolutionarily recent arrival into the L genome, but on the other hand the stop codon of dec is separated by only 3 bp from the initiation codon of gene 3, suggesting that there has been sufficient time for presumably optimal juxtaposition of these two genes in the L genome.…”

Section: Resultsmentioning

confidence: 99%

“…Previously studied dsDNA tailed bacteriophage decoration proteins are the phage T4 Soc and Hoc proteins (25,33,34,44,47), the phage D protein (17,18,61,66), and the 29 head fiber protein (46,59); the D protein is dispensable only under special low-DNA-content circumstances (54). In addition, adenovirus IX protein (26,41,48) and the herpesvirus VP26 (5, 43) and perhaps triplex (49,52,60) proteins can be classified as decoration proteins.…”

Section: Resultsmentioning

confidence: 99%

Nucleotide Sequence of the Head Assembly Gene Cluster of Bacteriophage L and Decoration Protein Characterization

Gilcrease¹,

Winn-Stapley²,

Hewitt³

et al. 2005

J Bacteriol

View full text Add to dashboard Cite

The temperate Salmonella enterica bacteriophage L is a close relative of the very well studied bacteriophage P22. In this study we show that the L procapsid assembly and DNA packaging genes, which encode terminase, portal, scaffold, and coat proteins, are extremely close relatives of the homologous P22 genes (96.3 to 99.1% identity in encoded amino acid sequence). However, we also identify an L gene, dec, which is not present in the P22 genome and which encodes a protein (Dec) that is present on the surface of L virions in about 150 to 180 molecules/virion. We also show that the Dec protein is a trimer in solution and that it binds to P22 virions in numbers similar to those for L virions. Its binding dramatically stabilizes P22 virions against disruption by a magnesium ion chelating agent. Dec protein binds to P22 coat protein shells that have expanded naturally in vivo or by sodium dodecyl sulfate treatment in vitro but does not bind to unexpanded procapsid shells. Finally, analysis of phage L restriction site locations and a number of patches of nucleotide sequence suggest that phages ST64T and L are extremely close relatives, perhaps the two closest relatives that have been independently isolated to date among the lambdoid phages.Bacteriophage L was reported to have been isolated after it was induced by UV irradiation from Salmonella enterica strain LT2 by Bezdek and Amati (2) in Czechoslovakia in 1967. Curiously, currently used LT2 cultures do not carry this prophage, although they do carry up to four other intact prophages (7, 40), so either extant LT2 strains have lost their L prophage or the strain used by those authors had inadvertently become lysogenized by phage L from the environment. Whatever its exact origin, L is a temperate, short-tailed doublestranded-DNA (dsDNA) bacteriophage that infects Salmonella enterica serovar Typhimurium (2). It is a rather close relative of the well-studied phage P22, with which it can form viable hybrids (2,3,23). It has immunity (C2 and Cro repressors), C1 activator, and replication protein specificities different from those of P22, but P22 regulatory genes c3, 23, and 24, virion assembly genes 1, 2, 3, 5, 8, 9, 10, 16, and 20, and lysis genes 13, 15, and 19 have been shown to be interchangeable between the two phages (2-4, 23, 31, 36, 51). Unlike P22, L does not have an immunity I region (27, 57) or a sieB function (58). DNA heteroduplex analysis (62) as well as physical map (27) and genetic map (56) construction showed that related genes are present in the same order on the P22 and L chromosomes. L virions are very similar in appearance to P22 virions when viewed in the electron microscope with negative staining (2), the two virions contain generally similar structural proteins (2, 27, 39), and their virion DNAs are indistinguishable in length (27). However, L virions have a significantly lighter equilibrium banding density in CsCl gradients than those of P22 (2), and phage L virions contain a major structural protein with a molecular mass of approximately 15 kDa tha...

show abstract

A fragile lattice: replacing bacteriophage λ's head stability gene D with the shp gene of phage 21 generates the Mg2+-dependent virus, λ shp

Cited by 18 publications

References 18 publications

Functional and comparative genome analysis of novel virulent actinophages belonging to Streptomyces flavovirens

Functional and comparative genome analysis of novel virulent actinophages belonging to Streptomyces flavovirens

Structural Characterization of the UL25 DNA-Packaging Protein from Herpes Simplex Virus Type 1

Nucleotide Sequence of the Head Assembly Gene Cluster of Bacteriophage L and Decoration Protein Characterization

Contact Info

Product

Resources

About