Abstract
We studied the dynamics of the proteome of influenza virus A/PR/8/34 (H1N1) infected Madin-Darby canine kidney cells up to 12 hours post infection by mass spectrometry based quantitative proteomics using the approach of stable isotope labeling by amino acids in cell culture (SILAC). We identified 1311 cell proteins and, apart from the proton channel M2, all major virus proteins. Based on their abundance two groups of virus proteins could be distinguished being in line with the function of the proteins in genesis and formation of new virions. Further, the data indicate a correlation between the amount of proteins synthesized and their previously determined copy number inside the viral particle. We employed bioinformatic approaches such as functional clustering, gene ontology, and pathway (KEGG) enrichment tests to uncover co-regulated cellular protein sets, assigned the individual subsets to their biological function, and determined their interrelation within the progression of viral infection. For the first time we are able to describe dynamic changes of the cellular and, of note, the viral proteome in a time dependent manner simultaneously. Through cluster analysis, time dependent patterns of protein abundances revealed highly dynamic up- and/or down-regulation processes. Taken together our study provides strong evidence that virus infection has a major impact on the cell status at the protein level.
Highlights
The evolution of viruses is accompanied by an opposing evolution through constant interaction with their host
The matrix protein 1 (M1) forms a layer beneath the viral membrane, enveloping eight different RNA segments. These segments are associated with the nucleoprotein (NP) as well as the three polymerase subunits (PA, PB1, PB2) forming viral ribonucleoprotein complexes
The genome is further encoding for two regulatory proteins: the nonstructural protein 1 (NS1) which is expressed in the host cell but is not a component of the virion itself, and the nuclear export protein (NEP, synonymous NS2) which is represented in the virus particle in small quantities [2]
Summary
The evolution of viruses is accompanied by an opposing evolution through constant interaction with their host. This increase is accompanied by reduction of ribosome biogenesis, rRNA processing, and translational elongation (cluster 6) indicating enhanced virus protein expression at the expense of expression of cellular proteins Among these proteins characterized by a strong and constant increase in abundance were those connected to viral functions and replication cycle: GO terms enriched in cluster 2 (Figure 3) include ‘‘localization and transport’’, ‘‘protein import into nucleus’’, ‘‘translational initiation’’, ‘‘actin filament organization’’ (actin is involved in the formation of budding zones [56]) and ‘‘COPI vesicles’’ (required for post-translational modification of the viral surface proteins and their transport to the plasma membrane [57]). Subsequent studies will unravel whether those checkpoints may serve as targets for antiviral drugs
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