A quantitative proteome study using the stable isotope labeling with amino acids in cell culture technique was performed on bovine kidney cells after infection with the alphaherpesvirus pseudorabies virus (PrV), the etiological agent of Aujeszky's disease. To enhance yields of proteins to be identified, raw extracts were fractionated by affinity solid-phase extraction with a combination of a cibacron blue F3G-A and a heparin matrix and with a phosphoprotein-specific matrix. After two-dimensional gel electrophoresis in different pH ranges between pH 3 and pH 10, 2,600 proteins representing 565 genes were identified by mass spectrometry and screened for virus-induced changes in relative protein levels. Four hours after infection, significant quantitative variations were found for constituents of the nuclear lamina, representatives of the heterogeneous nuclear ribonucleoproteins, proteins involved in membrane trafficking and intracellular transport, a ribosomal protein, and heat shock protein 27. Several proteins were present in multiple charge variants that were differentially affected by infection with PrV. As a common pattern for all these proteins, a mass shift in favor of the more acidic isoforms was observed, suggesting the involvement of viral or cellular kinases.Herpesviral genes are generally expressed in three kinetic classes (18,19), which are regulated sequentially by a number of positive and negative feedback mechanisms exerted by virusencoded proteins. However, herpesvirus infection also influences the expression of cellular genes, e.g., by host cell shutoff mechanisms that target the integrity of cellular mRNA and thus block the synthesis of cellular proteins. Herpes simplex virus type 1 (HSV-1), the prototypical alphaherpesvirus, expresses two shutoff proteins, ICP27 and pUL41. Whereas ICP27 interferes with mRNA splicing (16, 17), pUL41 degrades mRNA by virtue of its endoribonucleolytic activity (10, 29, 54), with specificity for mRNAs containing AU-rich elements (11). Homologs of both proteins are also present in pseudorabies virus (PrV), an alphaherpesvirus causing Aujeszky's disease. PrV, whose main host is the pig, infects numerous mammalian species except higher primates including humans. In contrast to HSV-1 ICP27, the PrV homolog pUL54 is dispensable for virus replication in cell culture (47,49). Transcript analyses of PrV-infected rat (44), human (6), and porcine (12) cells demonstrated alterations in the abundance of individual cellular transcripts, which resulted in the depletion or accumulation of specific mRNAs. Of the 9,850 genes examined in one study (6), the number of significantly up-or downregulated genes increased from approximately 1,000 to over 2,400 between 6 and 9 h after infection. Evaluation of the functions annotated for highly regulated cellular genes shows that PrV infection influences numerous cellular pathways and that genes involved in protein and nucleic acid metabolism, signaling, transport, cell cycle control, adhesion, transcription, the stress response, and innate ...