KEY RESOURCES TABLE.

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Bacterial and Virus Strains
For the list of bacterial strains generated in this work, see Supplemental Table 1	this study	Supplemental Table 1
Chemicals, Peptides, and Recombinant Proteins
For the list of chemicals used in the chemical-genetic screen, see Supplemental Table 2	this study	Supplemental Table 2
Trizol LS	Invitrogen	Catalog No. 10296028
T4 RNA ligase buffer	NEB	Catalog No. B0216L
T4 RNA ligase 2 truncated KQ	NEB	Catalog No. M0373L
T4 Polynucleotide Kinase (PNK)	NEB	Catalog No. M0201L
T4 RNA Ligase 1	NEB	Catalog No. M0204L
SuperScript IV	Thermo Fisher Scientific	Catalog No. 18090010
HCC-amino-D-alanine (HADA)	Michael vanNieuwenhze lab	N/A
Teknova EZ rich defined media kit (EZ-RDM)	Teknova	Catalog No. M2105
Critical Commercial Assays
Ribo-Zero rRNA removal kit (Gram-negative bacteria)	Illumina	MRZGN126
Deposited Data
Images and data from the paper	this study	https://doi.org/10.5061/dryad.z612jm68q
Raw sequences and processed data for gene expression analysis of β-P153L.	this study	GSE151022 (NCBI GEO)
Raw sequences for whole genome resequencing of ΔmreB strains.	this study	PRJNA632897 (NCBI SRA)
Code Ocean compute capsule: Generating the chemical genetic interaction dataset (Supplemental Dataset 1)	this study	https://doi.org/10.24433/CO.9507705.v1
Code Ocean compute capsule: Running DESeq2 on RNA-seq counts.	this study	https://doi.org/10.24433/CO.2313056.v1
Code Ocean compute capsule: Generating Supplemental Dataset 2, figures, and statistics cited in the main text of the paper.	this study	https://doi.org/10.24433/CO.8886448.v3
Code Ocean compute capsule: Generating the list of conditions and concentrations used in the screen. (Supplemental Table 2)	this study	https://doi.org/10.24433/CO.2239948.v1
Code Ocean compute capsule: Generating the enrichment tables. (Supplemental Table 3)	this study	https://doi.org/10.24433/CO.1521219.v3
Code Ocean compute capsule: Generating mutation reports using breseq. (Supplemental Table 4)	this study	https://doi.org/10.24433/CO.6559033.v1
Code Ocean compute capsule: Collating the table of gene expression changes in genes of interest. (Supplemental Table 5)	this study	https://doi.org/10.24433/CO.3392553.v1
Code Ocean compute capsule: Generating chemical genetic interaction datasets for the marker-only alleles. (Supplemental Dataset 3 and Supplemental Figure 4)	this study	https://doi.org/10.24433/CO.5034235.v1
Code Ocean compute capsule: Comparing the results of hierarchical clustering with a cut-off to k-means clustering with k=23. (Supplemental Figure 5)	this study	https://doi.org/10.24433/CO.3570885.v2
Oligonucleotides
For the list of oligonucleotides and plasmids used in this study, see Supplemental Table 6	this study	Supplemental Table 6
Software and Algorithms
MATLAB R2020b v. 9.9.0.1495850	Mathworks	https://www.mathworks.com
Python v. 3.7.3	Python Software Foundation	https://www.python.org/
R v. 3.5.1	R Foundation for Statistical Computing	https://www.r-project.org/
Gene Set Enrichment Analysis v. 3.0	(Subramanian et al., 2005)	https://www.gsea-msigdb.org/gsea/index.jsp
Cytoscape v. 3.7.2	(Shannon et al., 2003)	https://cytoscape.org/
Gen5 ™ v. 3.04	BioTek ®	https://www.biotek.com/products/software-robotics-software/gen5-software-features-for-imaging-microscopy/
Iris v. 0.9.4	(Kritikos et al., 2017)	http://critichu.github.io/Iris
breseq v. 0.333.2	(Deatherage and Barrick, 2014)	https://github.com/barricklab/breseq
DESeq2 v. 1.22.2	(Love et al., 2014)	http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html
shake v. 5.0	(Jos(10584), 2019)	https://www.mathworks.com/matlabcentral/fileexchange/10067-shake
ami v. 1.0.0.0	(Nguyen, 2021)	https://www.mathworks.com/matlabcentral/fileexchange/33144-the-adjusted-mutual-information
venn v. 1.7.0.0	(Darik, 2011)	https://www.mathworks.com/matlabcentral/fileexchange/22282-venn
Other
Data browser for chemical-genetic interaction dataset	this study	https://microbialphenotypes.org/wiki/index.php?title=Special:RNAPchemicalgenetics