Project description:Here, we use proximity labeling and localization mapping to systematically identify proteins associated with the major nuclear shell protein chimallin (ChmA) and other distinctive structures assembled by these phages. We identify six uncharacterized nuclear shell-associated proteins, one of which directly interacts with self-assembled ChmA. The structure and protein-protein interaction network of this protein, which we term ChmB, suggests that it forms pores in the ChmA lattice that serve as docking sites for pro-capsid genome packaging, and may also participate in mRNA and/or protein transport.

2024-01-26 | PXD041684 | Pride

Proteomic characterization of bacteriophage peptides from mastitis producer Staphylococcus aureus by LC-ESI-MS/MS and their bacteriophage phylogenomic analysis

Project description:The present work describes LC-ESI-MS/MS analyses of tryptic digestion peptides from phages that infect Staphylococcus aureus-causing mastitis, and isolated from dairy products. A total of 1935 non-redundant peptides belonging to 1282 proteins were identified and analyzed. Among them, 80 staphylococcal peptides from phages were confirmed. These peptides belong to proteins such as phage repressors, structural phage proteins, uncharacterized phage proteins and complement inhibitors. Moreover, of the phage origin peptides found, eighteen of them were specific to S. aureus strains. These diagnostic peptides could be useful for the identification and characterization of S. aureus strains that cause mastitis. Furthermore, a study of bacteriophage phylogeny and the relationship among the identified phage peptides and the bacteria they infect was also performed. The results show the specific peptides which are present in closely related phages, and the existing links between bacteriophage phylogeny and the respective Staphylococcus spp. infected.

2021-03-25 | PXD023530 | Pride

The component parts of bacteriophage virions accurately defined by a new machine-learning approach built on evolutionary features.

Project description:Klebsiella pneumoniae has risen to prominence as a major threat to human health, with hypervirulent and drug-resistant lineages spreading globally. Given their antimicrobial resistant phenotypes, new therapies are required for the treatment of these infections, and bacteriophages (phages) that kill Klebsiella are being identified for use in phage therapy. In order to circumvent the evolution of phage-resistance taking hold the way that drug-resistance has, clear and considered actions are needed in selecting the phages that would be used in therapeutic cocktails. It is known that annotation of phage genomes is poor, potentially obscuring those phages with the most therapeutic potential. Here we show that phages isolated from infrequently sampled environments have features of therapeutic potential and developed a computational tool called STEP3 to understand the evolutionary features that distinguish the component parts of diverse phages, features that proved particularly suitable to detection of virion proteins with only distantly related homologies. These features were integrated into an ensemble framework to achieve a stable and robust prediction performance by STEP3. Proteomics-based analysis of two phages validated the prediction accuracy of STEP3 and revealed the virions contain component parts that include DNA-binding factors, otherwise unrecognizable capsule degradation enzymes and membrane translocation factors.

2021-04-30 | PXD020607 | Pride

Project description:Aeromonas phages - DMD/UST

| PRJNA870248 | ENA

Bacteriophage

Project description:Natural phages isolated from holy rivers of Kathmandu against multi-drug resistant human pathogen (Escherichia coli, Klebsiella and Salmonella) collected from hospital. Genome sequencing

| PRJNA383466 | ENA

Bacteriophage sp.

Project description:Computational and Experimental Resources for Virome Analysis in Inflammatory Bowel Disease (CERVAID)

| PRJNA737576 | ENA