## 2 Results and Discussion
### The Host Transcriptome Upon Infection
Gene Set Annotation--analysis of Gene Ontology terms.Since it is impossible to analyze all genes one by one in each gene set, we performed a Gene Set Annotation which provided summarized information about biological processes that were down- and upregulated at selected time-points and hosts upon P1_vir_ phage infection (Figure 4). Biological processes regulated in hosts upon phage infection.We found that the host gene expression changes (both, up- and downregulated pool of genes) are more pronounced at 30 min of infection in comparison to 10 min (Figure 3), and this is also reflected in Gene Ontology terms analysis. In the wild-type strain, only one biological process--the cation transmembrane transport--is downregulated at 10 min post-infection (Figure 4A). In the _dksA\({}^{-}\)_ strain we have also found only a small set of downregulated biological processes (Figure 4A). Among upregulated biological processes at 10 min of infection, we found six GO terms for the wild type and five for the _dksA_ strain (Figure 4B). Changes occur in more biological processes (up- and downregulated) at 30 min of infection--this applies to both, the wild type and the _dksA_ mutant strains (Figure 4A, B). Downregulated biological processes in the host cell.Based on the GO term analysis, we found many similarities in the downregulation of metabolic processes between both hosts upon P1_vir_ infection. In both hosts, we found downregulation of amino acid import across the plasma membrane, cation transmembrane transport, cellular amino acid biosynthetic process, cellular protein modification process, cellular response to DNA damage stimulus, rRNA modification (Figure 4A). The first response to phage infection is shutting down biosynthesis of macromolecules (including proteins) and some transmembrane transporters--it appears that the energy-consuming systems are downregulated and host metabolism starts to be reprogrammed for phage purposes. That kind of strategy is general for many viruses, including phages, however, it may differ in details and execution [1; 53; 60]. On the other hand, another important phage strategy upon infection is the downregulation of cellular response to DNA damage stimulus which we found in both hosts (Figure 4A)--this may result from phage DNA maintenance and protection. Those processes also fit well with the phage proceeding to take over cellular metabolism [1; 6; 53]. In the wild type.Unique to the wild-type host, we observed downregulation of siderophore-dependent iron import into the cell, cellular polysaccharide biosynthesis process, purine nucleotide biosynthesis process, response to cold, and ribosomal large subunit assembly (Figure 4). In general, we can observe more detailed scenarios for energy conserving processes, such as reduced synthesis of poly- and oligosaccharides, complex compounds or their modifications, assembly, or de novo synthesis of basic compounds. In the _dksA\({}^{-}\) strain.Unique to the _dksA_ host, we observed downregulation of the peptidoglycan process, inosine monophosphate (IMP) biosynthetic process, lipopolysaccharide biosynthetic process, signal transduction, nucleobase metabolic process, cell wall organization and regulation of cell shape, and proteolysis (Figure 4A). We see that here the scenario of conserving energy and resources is a little bit different in execution than in the wild-type host. Downregulation of proteolysis in the _dksA_ mutant cells infected with P1_vir_ is particularly interesting, as two other bacteriophages--A and T4--have been also shown to affect proteolysis in an infected cell by acting on the host-encoded proteases (reviewed in [27]). However the phenomenon of increased phage T4 yield in a _dksA\({}^{-}\)_ mutant was described only partially--the host transcription was not performed in the analysis [61].