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DNA Bacteriophages01:26

DNA Bacteriophages

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Bacteriophages, or phages, are viruses that specifically infect bacteria, utilizing their genetic material to hijack host cellular machinery for replication. DNA bacteriophages employ single-stranded DNA (ssDNA) or double-stranded DNA (dsDNA) genomes. These phages exhibit diverse replication strategies and host interactions, influencing their ecological roles and applications in biotechnology and medicine.ssDNA BacteriophagesssDNA phages, with their small genomes, utilize unique strategies to...
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Lytic Cycle of Bacteriophages01:30

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Bacteriophages, also known as phages, are specialized viruses that infect bacteria. A key characteristic of phages is their distinctive “head-tail” morphology. A phage begins the infection process (i.e., lytic cycle) by attaching to the outside of a bacterial cell. Attachment is accomplished via proteins in the phage tail that bind to specific receptor proteins on the outer surface of the bacterium. The tail injects the phage’s DNA genome into the bacterial cytoplasm. In the...
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Lysogenic Cycle of Bacteriophages00:43

Lysogenic Cycle of Bacteriophages

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In contrast to the lytic cycle, phages infecting bacteria via the lysogenic cycle do not immediately kill their host cell. Instead, they combine their genome with the host genome, allowing the bacteria to replicate the phage DNA along with the bacterial genome. The incorporated copy of the phage genome is called the prophage. Some prophages can re-activate and enter the lytic cycle. This often occurs in response to a perturbation, such as DNA damage, but can also transpire in the absence of...
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Protein-protein Interfaces02:04

Protein-protein Interfaces

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Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a...
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Viral Replication: Lytic Cycle01:20

Viral Replication: Lytic Cycle

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Bacteriophages, or phages, are viruses that specifically infect bacteria. Among them, T-even bacteriophages, such as T4, exhibit a well-characterized lytic replication cycle in Escherichia coli (E. coli). This process ensures the rapid proliferation of the virus while ultimately leading to the destruction of the bacterial host.Attachment and DNA InjectionThe infection process begins with the recognition and binding of the T4 phage to the E. coli cell surface. Tail fibers of the phage...
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Related Experiment Video

Updated: Jul 22, 2025

Phage Phenomics: Physiological Approaches to Characterize Novel Viral Proteins
09:40

Phage Phenomics: Physiological Approaches to Characterize Novel Viral Proteins

Published on: June 11, 2015

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Protein embeddings improve phage-host interaction prediction.

Mark Edward M Gonzales1,2, Jennifer C Ureta1,2, Anish M S Shrestha1,3,2

  • 1Bioinformatics Laboratory, Advanced Research Institute for Informatics, Computing and Networking, De La Salle University, Manila, Philippines.

Plos One
|July 24, 2023
PubMed
Summary
This summary is machine-generated.

Predicting phage-host interactions is crucial for fighting antimicrobial resistance. Using protein language models to analyze phage receptor-binding proteins significantly improves prediction accuracy over traditional methods.

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Area of Science:

  • Microbiology
  • Bioinformatics
  • Computational Biology

Background:

  • Phage therapy is a promising strategy against antimicrobial resistance.
  • Accurate prediction of phage-host interactions is essential for selecting effective phages.
  • Current computational methods often require manual feature engineering, limiting efficiency.

Purpose of the Study:

  • To develop a more effective computational method for predicting phage-host interactions.
  • To leverage protein language models for automated feature extraction from phage proteins.
  • To assess the performance of receptor-binding protein embeddings in host prediction.

Main Methods:

  • Phage-host interaction prediction framed as a multiclass classification task.
  • Utilized embeddings from protein language models (e.g., ProtT5) for receptor-binding proteins.
  • Compared performance against models using handcrafted genomic and protein sequence features.

Main Results:

  • Protein language model embeddings outperformed handcrafted features for host prediction.
  • The ProtT5 model achieved the highest accuracy.
  • A 3% to 4% increase in weighted F1 and recall scores was observed with ProtT5 embeddings.

Conclusions:

  • Receptor-binding protein embeddings provide a powerful input for phage-host interaction prediction models.
  • Automated feature extraction using protein language models enhances prediction performance.
  • This approach offers a more efficient and accurate method for identifying candidate phages.