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Proteomics

Proteomics

A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term...

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Label-Free Quantitative Proteomics Workflow for Discovery-Driven Host-Pathogen Interactions

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Published on: October 20, 2020

Next-generation proteomics for quantitative Jumbophage-bacteria interaction mapping.

Andrea Fossati^1,2,3, Deepto Mozumdar⁴, Claire Kokontis⁴

¹J. David Gladstone Institutes, San Francisco, 94158, CA, USA.

Nature Communications

|August 24, 2023

Summary

This summary is machine-generated.

Co-fractionation mass spectrometry reveals over 6000 host-pathogen interactions for Pseudomonas aeruginosa jumbophages. This high-throughput method uncovers conserved phage predation mechanisms and identifies novel protein complexes.

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Quantification of Proteins Using Peptide Immunoaffinity Enrichment Coupled with Mass Spectrometry

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Quantification of Proteins Using Peptide Immunoaffinity Enrichment Coupled with Mass Spectrometry

Quantification of Proteins Using Peptide Immunoaffinity Enrichment Coupled with Mass Spectrometry

Published on: July 31, 2011

Area of Science:

Microbiology
Virology
Proteomics

Background:

Host-pathogen interactions are crucial for infection dynamics.
Traditional affinity-purification mass spectrometry has limitations in scalability and biological authenticity for studying these interactions.
Bacteriophages, like jumbophages, offer unique models for dissecting host-pathogen interactions.

Purpose of the Study:

To apply co-fractionation mass spectrometry for high-throughput analysis of host-pathogen interactions during native jumbophage infections.
To characterize the extensive protein-protein interaction networks between Pseudomonas aeruginosa and jumbophages ϕKZ and ϕPA3.
To develop an accessible resource for exploring phage-host interactome data.

Main Methods:

Utilized co-fractionation mass spectrometry to analyze host-pathogen interactions in Pseudomonas aeruginosa infected with jumbophages ϕKZ and ϕPA3.
Quantified and identified over 6000 unique host-pathogen interactions per phage, covering more than 50% of their proteomes.
Developed PhageMAP, an online database for querying, visualizing, and predicting phage-host interactions.

Main Results:

Detected extensive host-pathogen interactions, including phage proteins interacting with the host ribosome.
Identified novel protein complexes for previously uncharacterized phage open reading frames (ORFs).
Revealed conserved interaction patterns across KZ-like phages, suggesting shared predation mechanisms.
Discovered a ϕPA3 complex with structural and sequence similarity to the ϕKZ non-virion RNA polymerase.

Conclusions:

Co-fractionation mass spectrometry is a scalable and effective method for deep profiling of host-pathogen interactomes during viral infections.
The study provides a comprehensive interactome map for jumbophages, revealing conserved mechanisms and novel protein functions.
PhageMAP serves as a valuable resource for the research community, facilitating further investigation into phage biology and host manipulation.