Bacteriophage recombination systems and biotechnical applications

Nafissi, Nafiseh; Slavcev, Roderick A.

doi:10.1007/s00253-014-5512-2

Cited by 37 publications

(35 citation statements)

References 47 publications

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“…Schematic of a CdSe/ZnS core/shell QD surfacefunctionalized with the DHLA-CL4 ligand whose structure is provided above. PTE is ratiometrically self-assembled to the QD surface by its terminal hexahistidine (His) 6 sequence. The average number of PTE per QD is controlled through the molar stoichiometry added during assembly and the conjugates are directly utilized without subsequent purification.…”

Section: Resultsmentioning

confidence: 99%

Understanding How Nanoparticle Attachment Enhances Phosphotriesterase Kinetic Efficiency

Breger

Ancona²,

Walper³

et al. 2015

ACS Nano

173

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As a specific example of the enhancement of enzymatic activity that can be induced by nanoparticles, we investigate the hydrolysis of the organophosphate paraoxon by phosphotriesterase (PTE) when the latter is displayed on semiconductor quantum dots (QDs). PTE conjugation to QDs underwent extensive characterization including structural simulations, electrophoretic mobility shift assays, and dynamic light scattering to confirm orientational and ratiometric control over enzyme display which appears to be necessary for enhancement. PTE hydrolytic activity was then examined when attached to ca. 4 and 9 nm diameter QDs in comparison to controls of freely diffusing enzyme alone. The results confirm that the activity of the QD conjugates significantly exceeded that of freely diffusing PTE in both initial rate (∼4-fold) and enzymatic efficiency (∼2-fold). To probe kinetic acceleration, various modified assays including those with increased temperature, presence of a competitive inhibitor, and increased viscosity were undertaken to measure the activation energy and dissociation rates. Cumulatively, the data indicate that the higher activity is due to an acceleration in enzyme-product dissociation that is presumably driven by the markedly different microenvironment of the PTE-QD bioconjugate's hydration layer. This report highlights how a specific change in an enzymatic mechanism can be both identified and directly linked to its enhanced activity when displayed on a nanoparticle. Moreover, the generality of the mechanism suggests that it could well be responsible for other examples of nanoparticle-enhanced catalysis.

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Section: Resultsmentioning

confidence: 99%

Understanding How Nanoparticle Attachment Enhances Phosphotriesterase Kinetic Efficiency

Breger

Ancona²,

Walper³

et al. 2015

ACS Nano

173

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“…For CDMK9, these are three proteins of unknown function (CDS 59, 67, and 68) and a predicted recombination protein with a lambda Bet-like RecT superfamily domain [55,56] encoded in the DNA replication region. For CDKM15, the unique CDS encodes eight hypothetical proteins (CDS 11, 18, 19, 21, 22, 50, 78, and 79), a predicted anti-repressor (CDS 49) and its terminase small subunit (CDS 1).…”

Section: Resultsmentioning

confidence: 99%

Two Novel Myoviruses from the North of Iraq Reveal Insights into Clostridium difficile Phage Diversity and Biology

Rashid

Barylski

Hargreaves

et al. 2016

Viruses

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Bacteriophages (phages) are increasingly being explored as therapeutic agents to combat bacterial diseases, including Clostridium difficile infections. Therapeutic phages need to be able to efficiently target and kill a wide range of clinically relevant strains. While many phage groups have yet to be investigated in detail, those with new and useful properties can potentially be identified when phages from newly studied geographies are characterised. Here, we report the isolation of C. difficile phages from soil samples from the north of Iraq. Two myoviruses, CDKM15 and CDKM9, were selected for detailed sequence analysis on the basis of their broad and potentially useful host range. CDKM9 infects 25/80 strains from 12/20 C. difficile ribotypes, and CDKM15 infects 20/80 strains from 9/20 ribotypes. Both phages can infect the clinically relevant ribotypes R027 and R001. Phylogenetic analysis based on whole genome sequencing revealed that the phages are genetically distinct from each other but closely related to other long-tailed myoviruses. A comparative genomic analysis revealed key differences in the genes predicted to encode for proteins involved in bacterial infection. Notably, CDKM15 carries a clustered regularly interspaced short palindromic repeat (CRISPR) array with spacers that are homologous to sequences in the CDKM9 genome and of phages from diverse localities. The findings presented suggest a possible shared evolutionary past for these phages and provides evidence of their widespread dispersal.

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“…This putative integrase (gp109) is consistent with the results of our superinfection studies in which Basilisk behaved as a temperate phage (Table 1). High rates of recombination and the presence of recombination systems are a hallmark of tailed bacteriophages (36,(67)(68)(69), and such systems have proven useful for genetic recombineering in both bacteria and phages (70,71). The JL and Shanette genomes also encode a recombination nuclease (SbcCD) that is found in other Bacillus phages, including SPO1 and CampHawk.…”

Section: Figmentioning

confidence: 99%

The Genomes, Proteomes, and Structures of Three Novel Phages That Infect the Bacillus cereus Group and Carry Putative Virulence Factors

Grose

Belnap

Jensen

et al. 2014

J Virol

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This article reports the results of studying three novel bacteriophages, JL, Shanette, and Basilisk, which infect the pathogen Bacillus cereus and carry genes that may contribute to its pathogenesis. We analyzed host range and superinfection ability, mapped their genomes, and characterized phage structure by mass spectrometry and transmission electron microscopy (TEM). The JL and Shanette genomes were 96% similar and contained 217 open reading frames (ORFs) and 220 ORFs, respectively, while Basilisk has an unrelated genome containing 138 ORFs. Mass spectrometry revealed 23 phage particle proteins for JL and 15 for Basilisk, while only 11 and 4, respectively, were predicted to be present by sequence analysis. Structural protein homology to wellcharacterized phages suggested that JL and Shanette were members of the family Myoviridae, which was confirmed by TEM. The third phage, Basilisk, was similar only to uncharacterized phages and is an unrelated siphovirus. Cryogenic electron microscopy of this novel phage revealed a T‫9؍‬ icosahedral capsid structure with the major capsid protein (MCP) likely having the same fold as bacteriophage HK97 MCP despite the lack of sequence similarity. Several putative virulence factors were encoded by these phage genomes, including TerC and TerD involved in tellurium resistance. Host range analysis of all three phages supports genetic transfer of such factors within the B. cereus group, including B. cereus, B. anthracis, and B. thuringiensis. This study provides a basis for understanding these three phages and other related phages as well as their contributions to the pathogenicity of B. cereus group bacteria. IMPORTANCEThe Bacillus cereus group of bacteria contains several human and plant pathogens, including B. cereus, B. anthracis, and B. thuringiensis. Phages are intimately linked to the evolution of their bacterial hosts and often provide virulence factors, making the study of B. cereus phages important to understanding the evolution of pathogenic strains. Herein we provide the results of detailed study of three novel B. cereus phages, two highly related myoviruses (JL and Shanette) and an unrelated siphovirus (Basilisk). The detailed characterization of host range and superinfection, together with results of genomic, proteomic, and structural analyses, reveal several putative virulence factors as well as the ability of these phages to infect different pathogenic species.

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Bacteriophage recombination systems and biotechnical applications

Cited by 37 publications

References 47 publications

Understanding How Nanoparticle Attachment Enhances Phosphotriesterase Kinetic Efficiency

Understanding How Nanoparticle Attachment Enhances Phosphotriesterase Kinetic Efficiency

Two Novel Myoviruses from the North of Iraq Reveal Insights into Clostridium difficile Phage Diversity and Biology

The Genomes, Proteomes, and Structures of Three Novel Phages That Infect the Bacillus cereus Group and Carry Putative Virulence Factors

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