Virus–Host Interaction Gets <i>Curiouser and Curiouser</i>. PART II: Functional Transcriptomics of the <i>E. coli</i> DksA-Deficient Cell upon Phage P1<i>vir</i> Infection

• Main Authors: Grzegorz M. Cech, Agnieszka Szalewska-Pałasz, Katarzyna Potrykus, Anna Kloska
• Format: Article
• Language: English
• Published: MDPI AG 2021-06-01
• Series: International Journal of Molecular Sciences
• Subjects: P1<i>vir</i> bacteriophage; DksA; RNA-seq analysis; phage development; host-virus interaction; transcriptomics
• Online Access: https://www.mdpi.com/1422-0067/22/11/6159

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<i>vir</i> phage in a DksA-deficient <i>E. coli</i> host. Expression of the <i>ant1</i> and <i>kilA</i> P1<i>vir</i> 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<i>vir</i> genes encoding lysozyme and holin are downregulated, while antiholins are upregulated. Gene expression of RepA, a protein necessary for replication initiating at the phage <i>oriR</i> region, is increased in the <i>dksA</i> mutant; this is also true for phage genes responsible for viral morphogenesis and architecture. Still, it seems that P1<i>vir</i> is taking control of the bacterial protein, sugar, and lipid metabolism in both, the wild type and <i>dksA⁻</i> hosts. Generally, bacterial hosts are reacting by activating their SOS response or upregulating the heat shock proteins. However, only DksA-deficient cells upregulate their sulfur metabolism and downregulate proteolysis upon P1<i>vir</i> infection. We conclude that P1<i>vir</i> development is enhanced in the <i>dksA</i> mutant due to several improvements, including replication and virion assembly, as well as a less efficient lysis.