Table of Contents

Volume 2, Issue 2

  April/May/June 2012

  Pages 61 - 133

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 Issue Catalogue (MARC XML)

RESEARCH PAPERS

Open Access Article

Detection of TNT-derivatives with recombinant phages

Mladen Simonovicá and Branislav Simonovicá
Pages 61 - 69
http://dx.doi.org/10.4161/bact.20408
Abstract | Full Text | PDF

New immunoreagents for detection of TNT-derivatives TNP and TNP-Tris were developed using phage display technique. The monovalent and pentavalent recombinant phages carrying scFv specific for TNT were constructed and compared with each other to define the impact of valency and molecule dimension on antibody binding in immunoassay. Also, the bifunctional phages were generated, which carried TNT-specific scFvs as well as enzyme β-lactamase as a model marker on its surface. The most sensitive recombinant phages were selected and used for detection of TNP-Tris in a competitive ELISA based on immobilized antigen. Preincubation and partial phages saturation with a sample containing antigen allowed competition with immobilized hapten and displacement of free antigen. The phages exposing enzyme were used as immunoreagents for single step detection. The other phages were detected with specific marked antibodies. To date, the results presented in this paper are the first ever published regarding the recombinant phages for the detection of TNT.

Open Access Article

Mobilization of pathogenicity islands by Staphylococcus aureus strain Newman bacteriophages

Altaira D. Dearborn and Terje Dokland
Pages 70 - 78
Abstract | Full Text | PDF

Staphylococcus aureus pathogenicity islands (SaPIs) are mobile genetic elements that encode virulence factors and depend on helper phages for their mobilization. Such mobilization is specific and depends on the ability of a phage protein to inactivate the SaPI repressor Stl. Phage 80α can mobilize several SaPIs, including SaPI1 and SaPIbov1, via its Sri and Dut proteins, respectively. In many cases, the capsids formed in the presence of the SaPI are smaller than those normally produced by the phage. Two SaPI-encoded proteins, CpmA and CpmB, are involved in this size determination process. S. aureus strain Newman contains four prophages, named φNM1 through φNM4. Phages φNM1 and φNM2 are very similar to phage 80α in the structural genes, and encode almost identical Sri proteins, while their Dut proteins are highly divergent. We show that φNM1 and φNM2 are able to mobilize both SaPI1 and SaPIbov1 and yield infectious transducing particles. The majority of the capsids formed in all cases are small, showing that both SaPIs can redirect the capsid size of both φNM1 and φNM2.

Open Access Article

Biochemical characterization of L1 repressor mutants with altered operator DNA binding activity

Amitava Bandhu, Tridib Ganguly, Biswanath Jana, Amritangshu Chakravarty, Anindya Biswas and Subrata Sau
Pages 79 - 88
Abstract | Full Text | PDF

A mycobacteriophage-specific repressor with the enhanced operator DNA binding activity at 32°C and no activity at 42°C has not been generated yet though it has potential in developing a temperature-controlled expression vector for mycobacterial system. To create such an invaluable repressor, here we have characterized four substitution mutants of mycobacteriophage L1 repressor by various probes. The W69C repressor mutant displayed no operator DNA binding activity, whereas, P131L repressor mutant exhibited very little DNA binding at 32°C. In contrast, both E36K and E39Q repressor mutants showed significantly higher DNA binding activity at 32°C, particularly, under in vivo conditions. Various mutations also had different effects on the structure, stability and the dimerization ability of L1 repressor. While the W69C mutant possessed a distorted tertiary structure, the P131L mutant dimerized poorly in solution at 32°C. Interestingly, both these mutants lost their two-domain structure and aggregated rapidly at 42°C. Of the native and mutant L1 repressor proteins, W69C and E36K mutants appeared to be the least stable at 32°C. Studies together suggest that the mutants, particularly P131L and E39Q mutants, could be used for creating a high affinity temperature-sensitive repressor in the future.

Open Access Article

Inducible Clostridium perfringens bacteriophages ΦS9 and ΦS63: Different genome structures and a fully functional sigK intervening element

Kwang-Pyo Kim, Yannick Born, Rudi Lurz, Fritz Eichenseher, Markus Zimmer, Martin J. Loessner and Jochen Klumpp
Pages 89 - 97
http://dx.doi.org/10.4161/bact.21363
Abstract | Full Text | PDF

Two inducible temperate bacteriophages ΦS9 and ΦS63 from Clostridium perfringens were sequenced and analyzed. Isometric heads and long non-contractile tails classify ΦS9 and ΦS63 in the Siphoviridae family, and their genomes consist of 39,457 bp (ΦS9) and 33,609 bp (ΦS63) linear dsDNA, respectively. ΦS63 has 3′-overlapping cohesive genome ends, whereas ΦS9 is the first Clostridium phage featuring an experimentally proven terminally redundant and circularly permuted genome. A total of 50 and 43 coding sequences were predicted for ΦS9 and ΦS63, respectively, organized into 6 distinct lifestyle-associated modules typical for temperate Siphoviruses. Putative functions could be assigned to 26 gene products of ΦS9, and to 25 of ΦS63. The ΦS9 attB attachment and insertion site is located in a non-coding region upstream of a putative phosphorylase gene. Interestingly, ΦS63 integrates into the 3′ part of sigK in C. perfringens, and represents the first functional skin-element-like phage described for this genus. With respect to possible effects of lysogeny, we did not obtain evidence that ΦS9 may influence sporulation of a lysogenized host. In contrast, interruption of sigK, a sporulation associated gene in various bacteria, by the ΦS63 prophage insertion is more likely to affect sporulation of its carrier.




METHODS AND PROTOCOLS

Open Access Article

Real-time quantitative PCR to discriminate and quantify lambdoid bacteriophages of Escherichia coli K-12

Dominik Refardt
Pages 98 - 104
http://dx.doi.org/10.4161/bact.20092
Abstract | Full Text | PDF

Quantification of bacteriophages by real-time quantitative PCR (qPCR) is an interesting alternative to the traditional plaque assay. Importantly, the method should in principle be able to discriminate between closely related phages that are indistinguishable by most other means. Here, a method is presented that employs qPCR to discriminate and quantify ten closely related lambdoid phages of Escherichia coli str. K-12. It is shown that (1) treatment of samples with DNase efficiently removes non-encapsidated DNA, while the titer of plaque forming units is not affected, (2) individual phage types can be accurately quantified in mixed lysates, and (3) the detection limit corresponds to that of a plaque assay. The method is used to quantify individual phage types that are released from lysogens that carry up to three different prophages.




REVIEW

Open Access Article

Phage-based platforms for the clinical detection of human bacterial pathogens

David A. Schofield, Natasha J. Sharp and Caroline Westwater
Pages 105 - 283
http://dx.doi.org/10.4161/bact.19274
Abstract | Full Text | PDF

Bacteriophages (phages) have been utilized for decades as a means for uniquely identifying their target bacteria. Due to their inherent natural specificity, ease of use, and straightforward production, phage possess a number of desirable attributes which makes them particularly suited as bacterial detectors. As a result, extensive research has been conducted into the development of phage, or phage-derived products to expedite the detection of human pathogens. However, very few phage-based diagnostics have transitioned from the research lab into a clinical diagnostic tool. Herein we review the phage-based platforms that are currently used for the detection of Mycobacterium tuberculosis, Yersinia pestis, Bacillus anthracis and Staphylococcus aureus in the clinical field. We briefly describe the disease, the current diagnostic options, and the role phage diagnostics play in identifying the cause of infection, and determining antibiotic susceptibility.




VIEWS AND COMMENTARIES

Open Access Article

Murphy's law—if anything can go wrong, it will: Problems in phage electron microscopy

Hans-W. Ackermann and Kenneth L. Tiekotter
Pages 122 - 129
http://dx.doi.org/10.4161/bact.20693
Abstract | Full Text | PDF

The quality of bacteriophage electron microscopy appears to be on a downward course since the 1980s. This coincides with the introduction of digital electron microscopes and a general lowering of standards, possibly due to the disappearance of several world-class electron microscopists The most important problem seems to be poor contrast. Positive staining is frequently not recognized as an undesirable artifact. Phage parts, bacterial debris, and aberrant or damaged phage particles may be misdiagnosed as bacterial viruses. Digital electron microscopes often seem to be operated without magnification control because this is difficult and inconvenient. In summary, most phage electron microscopy problems may be attributed to human failure. Journals are a last-ditch defense and have a heavy responsibility in selecting competent reviewers and rejecting, or not, unsatisfactory articles.

Open Access Article

The strange history of phage therapy

William C. Summers
Pages 130 - 133
http://dx.doi.org/10.4161/bact.20757
Abstract | Full Text | PDF

Since the enlightenment, scientists have enjoyed a self-image as rational actors, guided only by reason, evidence and logic. When the Royal Society of London was founded in 1660 it chose as its motto “nullius in verba” (often translated as “on the word of no one”) a reference to Horace’s Epistles “Nullius addictus iurare in verba magistri…” (being not obliged swear allegiance to any master). Similar to our 21st century contemporaries who embrace the “new evidenced-based medicine,” the “virtuosi” of the Royal Society proclaimed a new era in science based only on observation and direct experience.