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Abstract
Organisms are constantly exposed to microbial pathogens in their environments. When a pathogen meets its host, a series of intricate intracellular interactions shape the outcome of the infection. The understanding of these host–pathogen interactions is crucial for the development of treatments and preventive measures against infectious diseases. Over the past decade, proteomic approaches have become prime contributors to the discovery and understanding of host–pathogen interactions that represent anti‐ and pro‐pathogenic cellular responses. Here, we review these proteomic methods and their application to studying viral and bacterial intracellular pathogens. We examine approaches for defining spatial and temporal host–pathogen protein interactions upon infection of a host cell. Further expanding the understanding of proteome organization during an infection, we discuss methods that characterize the regulation of host and pathogen proteomes through alterations in protein abundance, localization, and post‐translational modifications. Finally, we highlight bioinformatic tools available for analyzing such proteomic datasets, as well as novel strategies for integrating proteomics with other omic tools, such as genomics, transcriptomics, and metabolomics, to obtain a systems‐level understanding of infectious diseases.
Highlights
Molecular Systems Biology 13When studying host–pathogen associations, advantages of immunoaffinity purification coupled to mass spectrometry (IP-MS) are that experiments can be performed in relevant cellular model systems and in the context of viral infection to enable unbiased detection of protein–protein interactions (PPIs), as reviewed in Greco et al (2014)
Organisms are constantly exposed to microbial pathogens in their environments
We review the current state of proteomics approaches to elucidate host–pathogen protein interaction networks, alterations in the composition and organization of the host cell proteome, and infection-induced post-translational regulation
Summary
When studying host–pathogen associations, advantages of IP-MS are that experiments can be performed in relevant cellular model systems and in the context of viral infection to enable unbiased detection of PPIs, as reviewed in Greco et al (2014) These studies can be performed from the pathogen perspective, for example, isolating a viral protein to understand what host factors are targeted by the virus to ensure its replication or suppress host defense. Several studies have utilized ectopic expression of tagged viral proteins outside the context of infection to acquire information of potential viral-host PPIs that can be pursued with biological analyses This approach was shown valuable for studying the function of the Ebola virus matrix protein, VP40 (Yamayoshi et al, 2008). A continuous effort remains to study tagged proteins in the context of infection, such as a recent study using a scanning mutagenesis
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