Bacterial wild-type and dksA strains were cultured in LB broth containing 10 mM CaCl2 to OD600 = 0.2, at 37 °C with shaking. Next, P1vir was added at final MOI = 10. One-ml samples were immediately withdrawn to previously prepared 1.5 mL tubes containing 250 µL of aqua-phenol (5% phenol in 96% ethanol). Samples were withdrawn at 0, 10, and 30 min after P1vir infection. Next, RNA isolation was performed using the RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocol. The elution step was performed twice using 50 µL of RNase-free water on the same column to increase the RNA yields. Thus obtained RNA was digested with a DNase using TURBO DNA-free™ Kit (Ambion, Carlsbad, CA, USA), according to the manufacturer’s protocol. Samples were stored at −80 °C. The purity and integrity of RNA were assessed using the Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA) and Agilent RNA 6000 Nano Kit, according to the manufacturer’s protocol.

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