vB_BcM_Sam46 and vB_BcM_Sam112, members of a new bacteriophage genus with unusual small terminase structure

One of the serious public health concerns is food contaminated with pathogens and their vital activity products such as toxins. Bacillus cereus group of bacteria includes well-known pathogenic species such as B. anthracis, B. cereus sensu stricto (ss), B. cytotoxicus and B. thuringiensis. In this report, we describe the Bacillus phages vB_BcM_Sam46 and vB_BcM_Sam112 infecting species of this group. Electron microscopic analyses indicated that phages Sam46 and Sam112 have the myovirus morphotype. The genomes of Sam46 and Sam112 comprise double-stranded DNA of 45,419 bp and 45,037 bp in length, respectively, and have the same GC-content. The genome identity of Sam46 and Sam112 is 96.0%, indicating that they belong to the same phage species. According to the phylogenetic analysis, these phages form a distinct clade and may be members of a new phage genus, for which we propose the name ‘Samaravirus’. In addition, an interesting feature of the Sam46 and Sam112 phages is the unusual structure of their small terminase subunit containing N-terminal FtsK_gamma domain.

DeephageTP: A Convolutional Neural Network Framework For Identifying Phage-Specific Proteins From Metagenomic Sequencing Data

Backgroud: Bacteriophage (phage) is the most abundant and diverse biological entity on the Earth. This makes it a challenge to identify and annotate phage genomes efficiently on a large scale.Results: Portal (portal protein), TerL (large terminase subunit protein), and TerS (small terminase subunit protein) are the three specific proteins of the tailed phage. Here, we develop a CNN (convolutional neural network)-based framework, DeephageTP, to identify the three protein sequences encoded by the metagenome data. The framework takes one-hot encoding data of the original protein sequences as the input and extracts the predictive features in the process of modeling. To overcome the false positive problem, a cutoff-loss-value strategy is introduced based on the distributions of the loss values of the sequences within the same category. The proposed model with the set of cutoff-loss-values demonstrates high performance in terms of Precision in identifying TerL and Portal sequences (94% and 90%, respectively) from the mimic metagenomic dataset. Finally, we tested the efficacy of the framework using three real metagenomic datasets, and the result shows that compared to the conventional alignment-based methods, our proposed framework has a particular advantage in identifying the novel phage-specific protein sequences of portal and TerL with remote homology to their counterparts in the training dataset.Conclusions: In summary, our study for the first time develops a CNN-based framework for identifying the phage-specific protein sequences with high complexity and low conservation, and this framework will help us find novel phages in metagenomic sequencing data. The DeephageTP is available at https://github.com/chuym726/DeephageTP.

Biophysical analysis of Pseudomonas-phage PaP3 small terminase suggests a mechanism for sequence-specific DNA-binding by lateral interdigitation

The genome packaging motor of tailed bacteriophages and herpesviruses is a powerful nanomachine built by several copies of a large (TerL) and a small (TerS) terminase subunit. The motor assembles transiently at the portal vertex of an empty precursor capsid (or procapsid) to power genome encapsidation. Terminase subunits have been studied in-depth, especially in classical bacteriophages that infect Escherichia coli or Salmonella, yet, less is known about the packaging motor of Pseudomonas-phages that have increasing biomedical relevance. Here, we investigated the small terminase subunit from three Podoviridae phages that infect Pseudomonas aeruginosa. We found TerS is polymorphic in solution but assembles into a nonamer in its high-affinity heparin-binding conformation. The atomic structure of Pseudomonas phage PaP3 TerS, the first complete structure for a TerS from a cos phage, reveals nine helix-turn-helix (HTH) motifs asymmetrically arranged around a β-stranded channel, too narrow to accommodate DNA. PaP3 TerS binds DNA in a sequence-specific manner in vitro. X-ray scattering and molecular modeling suggest TerS adopts an open conformation in solution, characterized by dynamic HTHs that move around an oligomerization core, generating discrete binding crevices for DNA. We propose a model for sequence-specific recognition of packaging initiation sites by lateral interdigitation of DNA.

DeephageTP: A Convolutional Neural Network Framework for Identifying Phage-specific Proteins from metagenomic sequencing data

Background: Bacteriophage (phage) is the most abundant and diverse biological entity on the Earth. This makes it a challenge to identify and annotate phage genomes efficiently on a large scale. Portal (portal protein), TerL (large terminase subunit protein) and TerS (small terminase subunit protein) are the three specific proteins of the tailed phage. Here, we develop a CNN (convolutional neural network)-based framework, DeephageTP, to identify these three proteins from metagenome data. The framework takes one-hot encoding data of the original protein sequences as the input and extracts the predictive features in the process of modeling. The cutoff loss value for each protein category was determined by exploiting the distributions of the loss values of the sequences within the same category. Finally, we tested the efficacy of the framework using three real metagenomic datasets. Result: The proposed multiclass classification CNN-based model was trained by the training datasets and shows relatively high prediction performance ( A ccuracy : Portal, 98.8%; TerL, 98.6%; TerS, 97.8%) for the three protein categories, respectively. The experiments using the independent mimic dataset demonstrate that the performance of the model could become worse along with the increase of the data size. To address this issue, we determined and set the cutoff loss values (i.e., TerL: -5.2, Portal: -4.2, TerS: -2.9) for each of the three categories, respectively. With these values, the model obtains high performance in terms of Precision in identifying the TerL and Portal sequences (i.e, ~ 94% and ~ 90%, respectively) from the mimic dataset that is 20 times larger than the training dataset. More interestingly, the framework identified from the three real metagenomic datasets many novel phage sequences that are not detectable by the two alignment-based methods (i.e., DIAMOND and HMMER). Conclusion: Compared to the conventional alignment-based methods, our proposed framework shows high performance in identifying phage-specific protein sequences with a particular advantage in identifying the novel protein sequences with remote homology to their known counterparts in public databases. Indeed, our method could also be applied for identifying the other protein sequences with the characteristic of high complexity and low conservation. The DeephageTP is available at https://github.com/chuym726/DeephageTP .

Geno- and Phenotypic Characterization of Human Cytomegalovirus Mutants SelectedIn Vitroafter Letermovir (AIC246) Exposure

ABSTRACTLetermovir is a novel antiviral compound currently in clinical development for the prevention of human cytomegalovirus (HCMV) infections. In contrast to all currently approved anti-HCMV drugs that target the viral DNA polymerase, letermovir acts via a distinct mode of action involving the viral terminase subunit pUL56. To extend our understanding of potential letermovir resistance mechanisms, we used marker transfer to characterize mutations identified in letermovir-resistant HCMV variants that were selected in cell culture.

The 1.58 Å resolution structure of the DNA-binding domain of bacteriophage SF6 small terminase provides new hints on DNA binding

DNA packaging in tailed bacteriophages and in evolutionarily related herpesviruses is controlled by a viral-encoded terminase. As in a number of other phages, in theBacillus subtilisbacteriophages SF6 and SPP1 the terminase complex consists of two proteins: G1P and G2P. The crystal structure of the N-terminal DNA-binding domain of the bacteriophage SF6 small terminase subunit G1P is reported. Structural comparison with other DNA-binding proteins allows a general model for the interaction of G1P with the packaging-initiation site to be proposed.