Northern Blot and qRT-PCR Analysis

For Northern blot analyses, total RNA was prepared and blotted as described previously (Papenfort et al., 2017 (link)). Membranes were hybridized in Roti-Hybri-Quick buffer (Carl Roth, Karlsruhe, Germany) with [³²P]‐labeled DNA oligonucleotides at 42°C or with riboprobes at 63°C. Riboprobes were generated using the MAXIscript T7 Transcription Kit (Thermo Fisher Scientific, Waltham, Massachusetts). Signals were visualized using a Typhoon Phosphorimager (GE Healthcare, Chicago, Illinois) and quantified using GelQuant (RRID:SCR_015703; BioChemLabSolutions, San Francisco, California). Oligonucleotides for Northern blot analyses are provided in Supplementary file 4C. For qRT-PCR, total RNA was isolated with the SV Total RNA Isolation System (Promega, Fitchburg, Wisconsin). qRT–PCR was performed in three biological and two technical replicates using the Luna Universal One‐Step RT‐qPCR Kit (New England BioLabs, Ipswich, Massachusetts) and the MyiQ Single‐Color Real‐Time PCR Detection System (Bio‐Rad, Hercules, California). 5S rRNA and recA were used as reference genes; oligonucleotides used for all qRT-PCR analyses are provided in Supplementary file 4C.