## 2 Results and Discussion
### The Virus Transcriptome Upon Infection
This is because mutations located in the promoter region of the C4 antisense RNA or near the C4-antisense-RNA binding site may directly affect the _ant1_ expression; thus, the permanent or extremely enhanced _ant1_ expression forces P1_vir_ to enter the lytic pathway. On the other hand, we must remember that in the wild type strain, although there is a much lesser expression of _ant1_ and _kilA_ genes, those genes are still highly expressed in comparing to the general gene expression in the wild type host, (Figure 2, both hosts in 30 min). As mentioned in the accompanying paper [30], our findings support the hypothesis that originated in the 1980s claiming that the mutation located somewhere within the C4-ant1/2 region is a key to the P1_vir_ obligatory virulence [31]. The KilA protein promotes cellular death, so very high levels of _kilA_ gene expression will promote lytic development. Moreover, KilA has been considered as another anti-repressor of the lytic functions (prof. [PERSON], personal communication). This hypothesis is even more interesting if we consider the expression of the P1_vir_ant1_/2 and _kilA_ genes in the _dksA\({}^{-}\)_ host. Expression of these two genes in the _dksA\({}^{-}\)_ host is also sufficiently high for the P1_vir_ phage to enter the lytic development, but the overall expression level of these genes is much lower in comparison to the one in the wild type host. We hypothesize that lower expression of genes directly responsible for triggering the lytic-only development may result in a less rapid and more gentle lysis. _The gentle lysis hypothesis._ We hypothesize that the lack of DksA protein unlocks a cascade of events which leads to a situation where cell lysis is less efficient and somehow less rapid, thus, maturation of more virion particles may be possible. As we have shown in both, the qPCR (in the accompanying paper [30]) and RNA-seq analysis (this work), the level of phage _lpa_ mRNA decreases more significantly in the DksA-deficient strain. The Lpa protein activates the expression of the so-called Lpa-controlled operons and is required for expression of the P1 late genes, e.g., the lysozyme, structural proteins, and DNA packaging proteins. With some exceptions, genes involved in the late functions are expressed from late promotors and are entirely or partially dependent on Lpa [1]. The level of _lyz_-specific mRNA is lower when the phage infects the _dksA_ mutant than in the wild-type bacteria. Moreover, we have observed upregulation of the phage _lydE_ and _lydB_ gene expression in the _dksA_ host (Figure 2); these genes encode antiholins which are lysis determinants that prevent premature lysis [1]. In contrast, we observed that expression of the phage _lydA_ gene encoding holin, a protein triggering cell lysis, as well as the _kilA_ gene, a protein whose overexpression kills the host cell [32], are substantially downregulated in the _dksA_ mutant in comparison to the wild type host, at 30 min post-infection (Figure 2). We think that the less efficient expression of genes responsible for the host cell lysis may give a chance for more efficient phage DNA replication and virion part assembly before all of cell barriers collapse when cell lysis occurs and progeny virions are released. This potential shift could explain the improved lytic phage development observed in the _dksA\({}^{-}\)_ strain--the longer the bacterial cells are kept in a good condition and the antiholins prevent premature lysis, the more virus particles will be able to mature in a given time. Additionally, RNA-seq analysis proves experimental observation of lower \(c\)1 gene expression under given conditions (the accompanying paper [30]). _P1_vir_ _in a dksA\({}^{-}\) strain--at the brink of lysogeny._ Despite the lysis-only development of P1_vir_, our analysis of phage transcriptome revealed some changes in the expression of genes involved in the lysogenic pathway upon infection of the _dksA_ strain.