Key resources table.

Reagent type (species) or resource	Designation	Source or reference	Identifiers	Additional information
Strain, strain background (Escherichia coli)	See Supplementary file 4	This study		See Supplementary file 4
Strain, strain background (Vibrio cholerae)	See Supplementary file 4	This study		See Supplementary file 4
Recombinant DNA reagent (plasmids)	See Supplementary file 4	This study		See Supplementary file 4
Sequence-based reagent (oligonucleotides)	See Supplementary file 4	This study		See Supplementary file 4
Antibody	ANTI-FLAG M2 antibody (mouse monoclonal)	Sigma-Aldrich	Cat#F1804; RRID:AB_262044	(Western blot 1:1.000)
Antibody	RNA Polymerase alpha antibody 4RA2 (rabbit monoclonal)	BioLegend	Cat#WP003; RRID:AB_2687386	(1:10.000)
Antibody	anti-mouse IgG HRP (goat polyclonal)	ThermoFischer	Cat#31430; RRID:AB_228307	(1:10.000)
Antibody	anti-rabbit IgG HRP (goat polyclonal)	ThermoFischer	Cat#A16104; RRID:AB_2534776	(1:10.000)
Commercial assay or kit	TURBO DNA-free Kit	Invitrogen	Cat#AM1907
Commercial assay or kit	NEBNext Ultra II Directional RNA Library Prep Kit for Illumina	NEB	Cat#E7760
Commercial assay or kit	Ribo-Zero rRNA Removal Kit (Gram-Negative Bacteria)	Illumina	Cat#MRZGN126
Chemical compound, drug	Protein G Sepharose	Sigma-Aldrich	Cat##P3296
Chemical compound, drug	Bicyclomycin (BCM)	SantaCruz Biotech.	Cat#sc-391755; CAS ID: 38129-37-2
Software, algorithm	MultAlin	Corpet, 1988 (PMID:2849754)		http://multalin.toulouse.inra.fr/multalin
Software, algorithm	RNAhybrid	Rehmsmeier et al., 2004 (PMID:15383676)		http://bibiserv2.cebitec.uni-bielefeld.de RRID:SCR_003252
Software, algorithm	CLC Genomics Workbench	Qiagen		https://qiagenbioinformatics.com RRID:SCR_011853
Software, algorithm	SigmaPlot	SYSTAT		https://systatsoftware.com RRID:SCR_003210
Software, algorithm	GelQuantNET	biochemlabsolutions		http://biochemlabsolutions.com/GelQuantNET.html RRID:SCR_015703
Software, algorithm	BIO-1D	VILBER		http://vilber.de/en/products/analysis-software
Software, algorithm	ImageJ	Schneider et al., 2012 (PMID:22930834)		https://imagej.nih.gov/ij/ RRID:SCR_003070
Software, algorithm	cutadapt	Martin, 2011		https://doi.org/10.14806/ej.17.1.200
Software, algorithm	READemption	Förstner et al., 2014 (PMID:25123900)		https://doi.org/10.5281/zenodo.591469
Software, algorithm	DESeq2	Love et al., 2014 (PMID:25516281)		http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html
Software, algorithm	RNAfold	Lorenz et al., 2011 (PMID:22115189)		http://www.tbi.univie.ac.at/RNA
Software, algorithm	WebLogo	Crooks et al., 2004 (PMID:15173120)		http://weblogo.threeplusone.com/
Software, algorithm	BEDTools	Quinlan and Hall, 2010 (PMID:20110278)		http://code.google.com/p/bedtools