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
