Flap endonuclease of bacteriophage T7

Mitsunobu, Hitoshi; Zhu, Bin; Lee, Seung-Joo; Tabor, Stanley; Richardson, Charles C.

doi:10.4161/bact.28507

Cited by 6 publications

(3 citation statements)

References 33 publications

(47 reference statements)

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“… The DNA synthesis, regulation and replication gene products include the Xre family transcriptional regulator (Gp30c; Gp32c), the DNA helicase (Gp36; Gp38) that unwinds the DNA to create template for DNA replication [ 69 ], and another repressor (Gp35; Gp37) likely involved in gene regulation. The putative HNH endonucleases (Gp38, Gp45 and Gp51; Gp40, Gp47 and Gp53) may play a variety of roles in replication, recombination, and repair pathways [ 70 ]. Finally, the antiterminator protein (Gp41; Gp43) renders RNA polymerase resistant to termination signals [ 71 ].…”

Section: Resultsmentioning

confidence: 99%

Identification and Functional Analysis of Temperate Siphoviridae Bacteriophages of Acinetobacter baumannii

Badawy

Pajunen

Haiko

et al. 2020

Viruses

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Acinetobacter baumannii is an opportunistic pathogen that presents a serious clinical challenge due to its increasing resistance to all available antibiotics. Phage therapy has been introduced recently to treat antibiotic-incurable A. baumannii infections. In search for new A. baumannii specific bacteriophages, 20 clinical A. baumannii strains were used in two pools in an attempt to enrich phages from sewage. The enrichment resulted in induction of resident prophage(s) and three temperate bacteriophages, named vB_AbaS_fEg-Aba01, vB_AbaS_fLi-Aba02 and vB_AbaS_fLi-Aba03, all able to infect only one strain (#6597) of the 20 clinical strains, were isolated. Morphological characteristics obtained by transmission electron microscopy together with the genomic information revealed that the phages belong to the family Siphoviridae. The ca. 35 kb genomic sequences of the phages were >99% identical to each other. The linear ds DNA genomes of the phages contained 10 nt cohesive end termini, 52–54 predicted genes, an attP site and one tRNA gene each. A database search revealed an >99% identical prophage in the genome of A. baumannii strain AbPK1 (acc. no. CP024576.1). Over 99% identical prophages were also identified from two of the original 20 clinical strains (#5707 and #5920) and both were shown to be spontaneously inducible, thus very likely being the origins of the isolated phages. The phage vB_AbaS_fEg-Aba01 was also able to lysogenize the susceptible strain #6597 demonstrating that it was fully functional. The phages showed a very narrow host range infecting only two A. baumannii strains. In conclusion, we have isolated and characterized three novel temperate Siphoviridae phages that infect A. baumannii.

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Section: Resultsmentioning

confidence: 99%

Identification and Functional Analysis of Temperate Siphoviridae Bacteriophages of Acinetobacter baumannii

Badawy

Pajunen

Haiko

et al. 2020

Viruses

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“…Loss of nucleases, or mutations in their structural or functional domains, can have disastrous effects on the health of an organism. The impact of these mutations could affect resection rates or binding affinity to the DNA or interacting partners, and we posit that this assay may be sensitive enough to capture and compare these characteristics 71,76,77 . Many nucleases have been well-characterised, including those used in the optimisation of this assay, while many more have yet to be characterised at all.…”

Section: Discussionmentioning

confidence: 99%

A universal fluorescence-based toolkit for real-time quantification of DNA and RNA nuclease activity

Sheppard

Rogers

Harmer

et al. 2019

Sci Rep

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DNA and RNA nucleases play a critical role in a growing number of cellular processes ranging from DNA repair to immune surveillance. Nevertheless, many nucleases have unknown or poorly characterized activities. Elucidating nuclease substrate specificities and co-factors can support a more definitive understanding of cellular mechanisms in physiology and disease. Using fluorescence-based methods, we present a quick, safe, cost-effective, and real-time versatile nuclease assay, which uniquely studies nuclease enzyme kinetics. In conjunction with a substrate library we can now analyse nuclease catalytic rates, directionality, and substrate preferences. The assay is sensitive enough to detect kinetics of repair enzymes when confronted with DNA mismatches or DNA methylation sites. We have also extended our analysis to study the kinetics of human single-strand DNA nuclease TREX2, DNA polymerases, RNA, and RNA:DNA nucleases. These nucleases are involved in DNA repair, immune regulation, and have been associated with various diseases, including cancer and immune disorders.

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“…In addition to proteins already annotated as structural proteins, several enzymes or proteins with other functions were also detected by LC-MS/MS (Tables S3 and S4). These included DNA polymerase (Stab21 gene g145, Figure 6), glycerophosphoryl diester phosphodiesterase (g193) likely involved in cell wall teichoic acid hydrolysis [45,46], nicotinamide phosphosribosyltransferase (g207) that augments nucleotide synthesis [47], ribonucleotide reductases (g138-g140) that are also involved in dNTP synthesis [48], endo-and exonucleases (g130, g132) playing role in host DNA degradation and provision of nucleoside 5 -monophosphate precursors for synthesis of phage DNA progeny [49]. The sigma factor (g151) will quide the host RNA-polymerase to start transcription from phage promoters.…”

Section: Analysis Of Stab Phage Particle Proteomesmentioning

confidence: 99%

Bioprospecting Staphylococcus Phages with Therapeutic and Bio-Control Potential

Oduor

Kadija

Nyachieo

et al. 2020

Viruses

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Emergence of antibiotic-resistant bacteria is a serious threat to the public health. This is also true for Staphylococcus aureus and other staphylococci. Staphylococcus phages Stab20, Stab21, Stab22, and Stab23, were isolated in Albania. Based on genomic and phylogenetic analysis, they were classified to genus Kayvirus of the subfamily Twortvirinae. In this work, we describe the in-depth characterization of the phages that electron microscopy confirmed to be myoviruses. These phages showed tolerance to pH range of 5.4 to 9.4, to maximum UV radiation energy of 25 µJ/cm2, to temperatures up to 45 °C, and to ethanol concentrations up to 25%, and complete resistance to chloroform. The adsorption rate constants of the phages ranged between 1.0 × 10−9 mL/min and 4.7 × 10−9 mL/min, and the burst size was from 42 to 130 plaque-forming units. The phages Stab20, 21, 22, and 23, originally isolated using Staphylococcus xylosus as a host, demonstrated varied host ranges among different Staphylococcus strains suggesting that they could be included in cocktail formulations for therapeutic or bio-control purpose. Phage particle proteomes, consisting on average of ca 60–70 gene products, revealed, in addition to straight-forward structural proteins, also the presence of enzymes such DNA polymerase, helicases, recombinases, exonucleases, and RNA ligase polymer. They are likely to be injected into the bacteria along with the genomic DNA to take over the host metabolism as soon as possible after infection.

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Flap endonuclease of bacteriophage T7

Cited by 6 publications

References 33 publications

Identification and Functional Analysis of Temperate Siphoviridae Bacteriophages of Acinetobacter baumannii

Identification and Functional Analysis of Temperate Siphoviridae Bacteriophages of Acinetobacter baumannii

A universal fluorescence-based toolkit for real-time quantification of DNA and RNA nuclease activity

Bioprospecting Staphylococcus Phages with Therapeutic and Bio-Control Potential

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