###### Abstract  
The virus-host interaction requires a complex interplay between the phage strategy of reprogramming the host machinery to produce and release progeny virions, and the host defense against infection. Using RNA sequencing, we investigated the phage-host interaction to resolve the phenomenon of improved lytic development of P1_vir_ phage in a DksA-deficient _E. coli_ host. Expression of the _ant1_ and _kilA_ P1_vir_ genes in the wild-type host was the highest among all and most probably leads to phage virulence. Interestingly, in a DksA-deficient host, P1_vir_ genes encoding lysozyme and holin are downregulated, while antiholins are upregulated. Gene expression of RepA, a protein necessary for replication initiating at the phage _ori_R region, is increased in the _dksA_ mutant; this is also true for phage genes responsible for viral morphogenesis and architecture. Still, it seems that P1_vir_ is taking control of the bacterial protein, sugar, and lipid metabolism in both, the wild type and _dksA\({}^{-}\)_ hosts. Generally, bacterial hosts are reacting by activating their SOS response or unregulating the heat shock proteins. However, only DksA-deficient cells upregulate their sulfur metabolism and downregulate proteolysis upon P1_vir_ infection. We conclude that P1_vir_ development is enhanced in the _dksA_ mutant due to several improvements, including replication and virion assembly, as well as a less efficient lysis. P1_vir_ bacteriophage; DksA; RNA-seq analysis; phage development; host-virus interaction; transcriptomics +
Footnote †: journal: Molecular Sciences  
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The Icd protein also facilitates phage development by blocking bacterial cell division. The lytic cycle involves phage DNA replication initiated from the _oriL_ region (while _oriR_ serves as an origin to maintain lysogenic P1 plasmid replication) by the RepL initiatory protein. The host cell division is also blocked by the _kilA_ gene product, encoded in the same operon with _repL_[6], ensuring that cellular resources are redirected to phage development. While the above-mentioned early genes are mainly responsible for regulatory processes and phage DNA replication, expression of the late genes is required for assembly of phage particles and subsequent host cell lysis; their expression is dependent on phage-encoded factor Lpa, which modulates transcriptional activity of the host RNA polymerase [7]. Phage lysozyme, controlled by a holin-antiholin system, ensures the timely and effective lysis of bacterial cells [1]. Transcription of the phage early genes is typically completed after 20 min of infection and the late genes are expressed without intermediate stages by 40 min, followed by cell lysis [1]. As is typical for intracellular parasites, P1 bacteriophage development depends on the host proteins in addition to phage-encoded regulatory and enzymatic apparatus. For example, P1 does not encode its own RNA polymerase [8]. Instead, it employs the host enzyme and directs bacterial transcription machinery, assisted by phage regulators (to express phage genes e.g., _c1_, _lpa_). In addition, the host-encoded SspA protein is required for transcription of the P1 late genes [9]. Thus, overall it can be assumed that modifications of host proteins involved in gene expression would directly affect bacteriophage development. Among bacterial transcription factors that bind to RNA polymerase is DksA, which was first identified in _E. coli_ as a multicopy suppressor of a temperature sensitivity phenotype due to mutations in chaperone-encoding genes, _dnA_ and _dnaj_[10]. Some years later, this protein attracted more attention due to its function in transcription regulation. DksA was reported to act as a cofactor for the stringent response alarmone, (p)ppGpp, resulting in amplification of its negative or positive regulatory effects on transcription, depending on the specificity of a given promoter [11; 12].