Viral proteomics: global evaluation of viruses and their interaction with the host

Abstract

Viruses constantly adapt to and modulate the host environment during replication and propagation. Both DNA and RNA viruses encode multifunctional proteins that interact with and modify host cell proteins. While viral genomes were the first complete sequences known, the corresponding proteomes are only now elucidated, with some surprising results. Even more daunting is the task to globally monitor the impact of viral infection on the proteome of the host cell and many technical hurdles must still be overcome in order to facilitate robust and reproducible measurements. Further complicating the picture is the dynamic nature of proteins, including post-translational modifications, enzymatic cleavage and activation or destruction by proteolytic events. Nevertheless, several promising studies have been published using high-throughput methods directly measuring protein abundance. Particularly, quantitative or semiquantitative mass spectrometry-based analysis of viral and cellular proteomes are now being used to characterize viruses and their host interaction. In addition, the full set of interactions between viral and host proteins, the interactome, is beginning to emerge, with often unexpected interactions that need to be carefully validated. In this review, we will discuss two major areas of viral proteomics: first, virion proteomics (such as the protein characterization of viral particles) and second, proteoviromics, including the viral protein interactomics and the quantitative analysis of host cell proteome during viral infection.

Keywords::

• interactomics
• iTRAQ™
• LC-MS/MS
• liquid chromatography
• MALDI
• matrix-assisted laser desorption/ionization
• proteoviromics
• SILAC
• stable isotope labeling of amino acids in cell culture
• tandem affinity purification
• tandem mass spectrometry
• TAP
• virion proteomics
• Y2H
• yeast two hybrid

Financial & competing interests disclosure

This work was supported by NIH grants R21 CA109674, R01 AI 059457 and R01 CA/AI1094011. The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed.

No writing assistance was utilized in the production of this manuscript.