## 2 Results and Discussion
### The Virus Transcriptome Upon Infection
It was claimed previously that the P1\(vir\) phage is unable to enter the lysogenic cycle due to a mutation located in the immunity region \(imml\)[31]. We show that in the _dksA_ strain expression of the \(antl\) and \(ant2\) genes located in this region is downregulated at both post-infection timepoints (Figure 2). Moreover, \(icd\), another gene of the \(imml\) region, is downregulated in the _dksA_ strain at 30 min post-infection (Figure 2); expression of this gene causes reversible inhibition of cell division and apparently is required for \(ant\) expression [1; 33; 34]. Intriguingly, the \(c8\) gene is upregulated in the _dksA_ strain at both time points of infection. Previously published data suggested that the \(c8\) gene is probably involved in the establishment of lysogeny [35; 36], thus, its upregulation may be difficult to explain because P1\(vir\) can solely undergo lytic development. We speculate that the enhanced expression of the lysogeny-related genes even in the lytic-only P1\(vir\) phage is leading to a higher phage yield in the _dksA_ strain. _Minor improvements in the phage development._ Although very attractive, gentle lysis of the host may not be enough on its own to allow the production of more virion particles. Literally, phages need more parts to build up the virions. First, more copies of phage genomes would be needed to produce more progeny phages. Indeed, we observed an enhanced replication of the mini-P1 replicon in the _dksA_ mutant strain (see accompanying paper [30]). Additionally, transcriptome analysis revealed that the _repA_ gene expression is increased in the _dksA_ mutant when compared to the wild-type strain. RepA is necessary for DNA replication initiating at the phage \(oriR\) region and it is needed at the early stages of P1 development, as well as during lysogeny. P1 also has another replication origin--\(oriL\), but the expression of _repL_, a gene encoding the initiator protein of \(oriL\)-driven replication, is not enhanced in the _dksA\({}^{-}\)_ strain when comparing to the wild type cells (Figure 2). Phage DNA from both of these origins is replicating by the theta model, however, in the late stages of lytic development replication switches to the sigma model. It should not be assumed that one origin (\(oriR\)) is strictly lysogenic and the other (\(oriL\)) is strictly lytic; again, the regulation of P1 replication is complex and shows some flexibility [1]. Nevertheless, we can assume that stimulation of replication from at least one origin will lead to a higher copy number of phage genomes that can be used to assemble progeny virions in the _dksA_ host. Upregulation of genes that are involved in viral particle formation could also explain the improved phage lytic development observed in the _dksA\({}^{-}\)_ strain. To produce more phages, more virion parts would be needed. Indeed, we noticed, that several morphogenesis and viral architecture genes are expressed during phage development. In the DksA-deficient strain, 30 min post-infection, expression of several phage genes whose functions are linked to capsid development is substantially upregulated (Figure 2); these include the following genes: 5--encodes the baseplate; 6--encodes all length determinant; 25--encodes tail stabilizing protein [37]; \(prt\)--encodes portal protein; \(pro\)--encodes putative head processing protease and kinase and is required for head morphogenesis [1]; \(ddra\)--encodes viral architecture determinant but its full function is uncertain [38]; \(U\)--encodes the virion protein \(gpU^{\prime}\) when expressed in (+) orientation; \(U^{\prime}\)--variable gene of tail fiber operon, encodes tail fiber assembly chaperone when expressed in (-) orientation [1]; \(R\)--tail fiber structure or assembly [39]. Overall, the transcriptome analysis of P1\(vir\) infection shows that changes in phage gene expression result from a complex interplay between the phage and the host. This situation could be explained in the light of P1 phage biology.