## 2 Results and Discussion
### The Virus Transcriptome Upon Infection  
General overview of P1 phage gene expressionFigure 1, panel B, shows the number of P1_vir_ genes which have been expressed at 10 min and 30 min of infection. Roughly 70-80% of total phage genes are expressed at 10 min of infection. We found that at 30 min post-infection all phage genes are expressed. In our analysis, we plotted the observed changes onto the P1_vir_ genome map (Figure 2). This allowed linking the expression level of each gene at each time point and in each host with several known P1 genetic features, such as the \(\sigma^{70}\) promoters, Lpa-dependent promoters, C1 operator sites, or Rho-independent terminators. The level of gene expression  
Figure 1: Changes in global gene expression in the course of the virus-host interactions. The wild type and the _dksA_ mutant cultures were infected with the P1_vir_ phage at the beginning of the logarithmic phase of growth. Total RNA sequencing (RNA-seq) was performed for three post-infection time-points: 0 min (no-phage control), 10 min (early gene expression), and 30 min (late gene expression). Panel (**A**) presents the heatmap plot of all analyzed RNA-seq samples based on the expression of all detected genes of both hosts (wild type and _dksA_ mutant) and the P1_vir_ virus. Sample replicates (three for each condition) are listed below the heatmap. Gene expression data are presented as Z-score transformed, scaled in rows values. Panel (**B**) shows the number of P1_vir_ phage genes which have been expressed at 10 and 30 min of infection. The Venn diagram below panel B shows the number of P1_vir_ genes upregulated in the wild type and _dksA_ mutant cells. differs between the time points and the hosts (Figure 2, see rows labeled WT and _dksA_). However, we did not find any uniquely expressed phage genes depending on the host. We also did not find an easy to define pattern in the hosts' gene expression upon phage infection. It seems that a much more complex scenario is rolling out here. Even so, we are still able to pinpoint several factors or events that plausibly lead to the improved P1_vir_ development in a DksA-deficient host (discussed below). Figure 2: P1_vir_ bacteriophage gene expression presented on the genome map. Purple ribbons indicate both coding strands (\(+/-\)); black triangles inside ribbons are pointing at a given gene’s transcription start site. P1_vir_ transcriptome analysis upon infection is shown below the genome map. Gene expression fold changes are shown as values and heatmaps—the first two rows present data for the phage infecting the wild-type strain, and the next two rows present data for the phage infecting the _dksA_ mutant; 10 min and 30 min post-infection, respectively. Several P1 genetic features are shown (gray description): \(\sigma^{20}\) promoters (black arrows); Lpa-dependent promoters (thick red arrows); C1 operator sites (yellow pentagon, patterned if C1 binds at dual sites) Rho-independent terminators are marked with brown flags; sequences other than protein-coding or intergenic regions are shown as black boxes; lytic and plasmid replication origins are shown as white arrows above the genome map. Depicted gene lengths are not proportional to their actual size. _The P1 virulence mechanism dilemma._ One of the most striking observations regarding the P1_vir_ transcriptome in the wild type and _dksA_ hosts is the difference in expression levels of phage genes from the C4-ant1/2 region (Figure 2). We found that the _ant1_ gene which co-produces the lytic anti-repressor Ant is highly expressed in the wild-type host at 30 min post-infection. Moreover, the _kilA_ gene, located directly downstream from the _ant1_/2 genes is also highly expressed in the wild-type strain. These two genes show the highest level of expression among all of the phage's genes during infection of the wild-type strain. High expression of the _ant1_ gene can be linked to point mutations detected in the _imm1_ region of the P1_vir_ genome that we described in the accompanying paper [30].