## 2 Results and Discussion
### The Host Transcriptome Upon Infection  
Host transcriptomic data for the wild type and _dksA_ strains upon P1_vir_ infection at 0, 10, and 30 min time points were obtained from the same experiment as described above. General overview of the host transcriptomeThe number of downregulated genes of the wild type and _dksA_ mutant strains is presented in Figure 3A. For both host strains, at 10 min of infection, we see a much smaller pool of downregulated genes in comparison to 30 min of infection. A slightly higher number of downregulated genes is noted for the wild-type strain (381) when comparing to the _dksA_ strain (360) at 30 min post-infection. On the other hand, at 10 min the number of downregulated host genes of the _dksA_ mutant is twice that of the wild-type strain. Analysis of the distribution of these genes shows that certain gene sets overlap between the hosts and time points, while others are uniquely downregulated solely in the wild type strain or solely in the _dksA_ mutant; this mainly concerns the genes expressed at 30 min post-infection (Figure 3A, Venn diagram). We observe a similar situation concerning the number of host genes that are upregulated upon phage infection (Figure 3B). For both tested host strains, at 10 min of infection, we see a much smaller number of upregulated genes when compared to 30 min post-infection. A higher number of upregulated genes appears in the wild type strain (409) when compared to the _dksA_ host (305) at 30 min of infection, however, much more genes are upregulated in the _dksA_ mutant (83) at the 10 min time point than in the wild type strain (34). Analysis of the distribution of upregulated genes between the hosts and time points shows that some upregulated genes overlap, but others are uniquely upregulated in the wild type of strain (mostly at 30 min) or the _dksA_ mutant (at both, 10 min and 30 min of infection) (Figure 3B, Venn diagram). Since the number of genes (in both hosts) that are up- or downregulated is very large, it is impossible to present them here one-by-one, and thus we decided to discuss here only the top ten genes with the lowest expression level (downregulated) and the top ten genes with the highest expression level (upregulated) for each host and each time-point (Figure 3C,D, respectively). For further details, see Supplementary Materials of the accompanying paper [30]. Figure 3: General overview of the host transcriptome upon P1\(\ddot{v}\)\(\ddot{v}\)r infection. Panel **(A)** shows the number of downregulated genes of both, the wild type and _dksA_ mutant hosts at 10 min and 30 min post-P1\(\ddot{v}\)r infection. Panel **(B)** shows the number of upregulated genes of both hosts at selected time points upon P1\(\ddot{v}\)r infection. Venn diagrams below panels A and B show the distribution of up- or downregulated genes. Panel **(C)** shows the downregulation level of the top ten genes with the lowest expression at each time-point and host. Panel **(D)** shows the upregulation level of the top ten genes with the highest expression at each time-point and host. Genes with Fold Change (FC) > 1.5 were selected for further analysis. Gene descriptions are in the text and Appendix A, Table A1. Interestingly, we found that the _cspA_ gene encoding the cold shock protein A (CspA) was the most downregulated gene at each time-point and each host. CspA is the major cold-shock protein whose mRNA is very unstable at 37 \({}^{\circ}\)C and its levels rapidly decrease during growth; its expression levels change in response to temperature fluctuations [41; 42; 43]. It was shown that _cspA_ is expressed only during the early-log-phase of growth at 37 \({}^{\circ}\)C and during the log phase after a shift from 37 \({}^{\circ}\)C to 10 \({}^{\circ}\)C [44; 45]. However, _cspA_ is also expressed at 37 \({}^{\circ}\)C under nutritional up-shift conditions, before the cells start to divide [46].