DePolymerase Predictor (DePP): a machine learning tool for the targeted identification of phage depolymerases

Abstract Biofilm production plays a clinically significant role in the pathogenicity of many bacteria, limiting our ability to apply antimicrobial agents and contributing in particular to the pathogenesis of chronic infections. Bacteriophage depolymerases, leveraged by these viruses to circumvent biofilm mediated resistance, represent a potentially powerful weapon in the fight against antibiotic resistant bacteria. Such enzymes are able to degrade the extracellular matrix that is integral to the formation of all biofilms and as such would allow complementary therapies or disinfection procedures to be successfully applied. In this manuscript, we describe the development and application of a machine learning based approach towards the identification of phage depolymerases. We demonstrate that on the basis of a relatively limited number of experimentally proven enzymes and using an amino acid derived feature vector that the development of a powerful model with an accuracy on the order of 90% is possible, showing the value of such approaches in protein functional annotation and the discovery of novel therapeutic agents

Genomic hypervariability of phage Andromeda is unique among known dsDNA viruses

A new lytic bacteriophage Andromeda, specific to the economically important plant pathogen Pseudomonas syringae, was isolated and characterised. It belongs to the Podoviridae family, Autographivirinae subfamily and possesses a linear dsDNA genome of 40,008 bp with four localised nicks. Crucially, Andromeda’s genome has no less than 80 hypervariable sites (SNPs), which show genome wide distribution resulting in heterogenous populations of this phage reminiscent of those of RNA virus quasispecies. Andromeda has no nucleotide sequence homology to phage phiNFS, a member of phiKMVviruses, in which a similar phenomenon was discovered. We show that Andromeda and Andromeda-related phages form a group within the Autographivirinae, designated here as the “ExophiKMVviruses”. The “ExophiKMVviruses” were revealed to share conservation of gene order with core phiKMVviruses despite their sequence-based relationship to SP6-related phages. Our findings suggest that genomic hypervariability might be a feature that occurs among various Autographivirinae groups

Localised genetic heterogeneity provides a novel mode of evolution in dsDNA phages

Abstract The Red Queen hypothesis posits that antagonistic co-evolution between interacting species results in recurrent natural selection via constant cycles of adaptation and counter-adaptation. Interactions such as these are at their most profound in host-parasite systems, with bacteria and their viruses providing the most intense of battlefields. Studies of bacteriophage evolution thus provide unparalleled insight into the remarkable elasticity of living entities. Here, we report a novel phenomenon underpinning the evolutionary trajectory of a group of dsDNA bacteriophages known as the phiKMVviruses. Employing deep next generation sequencing (NGS) analysis of nucleotide polymorphisms we discovered that this group of viruses generates enhanced intraspecies heterogeneity in their genomes. Our results show the localisation of variants to genes implicated in adsorption processes, as well as variation of the frequency and distribution of SNPs within and between members of the phiKMVviruses. We link error-prone DNA polymerase activity to the generation of variants. Critically, we show trans-activity of this phenomenon (the ability of a phiKMVvirus to dramatically increase genetic variability of a co-infecting phage), highlighting the potential of phages exhibiting such capabilities to influence the evolutionary path of other viruses on a global scale

Insights into the structural dynamics of the bacteriophage t7 dna polymerase and its complexes

The T7 DNA polymerase is dependent on the host protein thioredoxin (trx) for its processivity and fidelity. Using all-atom molecular dynamics, we demonstrate the specific interactions between trx and the T7 polymerase, and show that trx docking to its binding domain on the polymerase results in a significant level of stability and exposes a series of basic residues within the domain that interact with the phosphodiester backbone of the DNA template. We also characterize the nature of interactions between the T7 DNA polymerase and its DNA template. We show that the trx-binding domain acts as an intrinsic clamp, constraining the DNA via a two-step hinge motion, and characterize the interactions necessary for this to occur. Together, these insights provide a significantly improved understanding of the interactions responsible for highly processive DNA replication by T7 polymerase

HTGR reactor physics and fuel cycle studies

The high-temperature gas-cooled reactor (HTGR) appears as a good candidate for the next generation of nuclear power plants. In the "HTR-N" project of the European Union Fifth Framework Program, analyses have been performed on a number of conceptual HTGR designs, derived from reference pebble-bed and hexagonal block-type HTGR types. It is shown that several HTGR concepts are quite promising as systems for the incineration of plutonium and possibly minor actinides.These studies were mainly concerned with the investigation and intercomparison of the plutonium and actinide burning capabilities of a number of HTGR concepts and associated fuel cycles, with emphasis on the use of civil plutonium from spent LWR uranium fuel (first generation Pu) and from spent LWR MOX fuel (second generation Pu). Besides, the "HTR-N" project also included activities concerning the validation of computational tools and the qualification of models. Indeed, it is essential that validated analytical tools are available in the European nuclear community to perform conceptual design studies, industrial calculations (reload calculations and the associated core follow), safety analyses for licensing, etc., for new fuel cycles aiming at plutonium and minor actinide (MA) incineration/transinutation without multi-reprocessing of the discharged fuel.These validation and qualification activities have been centred round the two HTGR systems currently in operation, viz. the HTR-10 and the HTTR. The re-calculation of the HTTR first criticality with a Monte Carlo neutron transport code now yields acceptable correspondence with experimental data. Also calculations by 3D diffusion theory codes yield acceptable results. Special attention, however, has to be given to the modelling of neutron streaming effects. For the HTR-10 the analyses focused on first criticality, temperature coefficients and control rod worth. Also in these studies a good correspondence between calculation and experiment is observed for the 3D diffusion theory codes. (c) 2006 Elsevier B.V. All rights reserved

Pangenomic analyses of the <i>Tevenvirinae</i>.

<p>(a) Gene presence/absence matrix plot. Blue regions correspond to genes present in a minimum of two phages on the extreme right hand side and increasing to all phages (if applicable) on the extreme left. (b) A plot of unique genes against the number of genomes. Numbers of unique genes rises with genome number highlighting the fact that individual members of the <i>Tevenvirinae</i> contain a significant quantity of novel genes. (c) A plot of the number of pangenomic genes (those not common to any phages) against number of genomes showing a steady rise in the T4-like pangenome and highlighting the wide array of accessory genes present in this group. (d) Graph showing number of completely new genes against genome number in each successive phage highlighting that despite a steady increase in unique genes across the entire <i>Tevenvirinae</i>, the number of new genes with respect to each additional phage steadily declines showing that there is a limit on the novelty and that there is some commonality across a large majority of members.</p

Electron microscopic images of (a) and (b), bacteriophage pf16 in non-contracted and contracted forms respectively, and (c) and (d) bacteriophage phiPMW.

<p>Scale bar corresponds to 100 nm.</p