REAGENT or RESOURCE	SOURCE	IDENTIFIER
Bacterial and Virus Strains
Escherichia coli TOP10: F- mcrA Δ(mrr-hsdRMS-mcrBC) Φ80lacZΔM15 ΔlacX74 recA1 araD139 Δ(araleu)7697 galU galK rpsL (StrR) endA1 nupG	Invitrogen, Thermo Fischer Scientific	Cat#C404003
Escherichia coli MG1655: wild-type: F-, lambda-, rph-1	DZMS-German Collection of Microorganisms and Cell Cultures	DSM-No.: 18039
MG1655: argA∗:F-, lambda-, rph-1, argA(H15Y)	This study	N/A
MG1655: ilvA∗:F-, lambda-, rph-1, ilvA(L447F)	This study	N/A
MG1655: hisG∗:F-, lambda-, rph-1, hisG(E271K)	This study	N/A
MG1655: leuA∗:F-, lambda-, rph-1, leuA(G462D)	This study	N/A
MG1655: proB∗:F-, lambda-, rph-1, proB(D107N)	This study	N/A
MG1655: thrA∗:F-, lambda-, rph-1, thrA(S345F)	This study	N/A
MG1655: trpE∗:F-, lambda-, rph-1, trpE(S40F)	This study	N/A
MG1655: ΔargR: F-, lambda-, rph-1, ΔargR	This study	N/A
MG1655: ΔtrpR: F-, lambda-, rph-1, ΔtrpR	This study	N/A
MG1655: ΔhisL: F-, lambda-, rph-1, ΔhisL	This study	N/A
Escherichia coli BW25113: JW2000-1: F-, Δ (araD-araB)567, ΔlacZ4787(::rrnB-3), λ-,ΔhisL787::kan, rph-1, Δ(rhaD-rhaB)568, hsdR514	CGSC	CGSC#9646
MG1655: wild-type CRISPRi-ctrl: F-, lambda-, rph-1, pNUT1533-ctrl	This study	N/A
MG1655: wild-type CRISPRi-argE: F-, lambda-, rph-1, pNUT1533-argE	This study	N/A
MG1655: wild-type CRISPRi-hisB: F-, lambda-, rph-1, pNUT1533-hisB	This study	N/A
MG1655: wild-type CRISPRi-trpA: F-, lambda-, rph-1, pNUT1533-trpA	This study	N/A
MG1655: argA∗ CRISPRi-ctrl: F-, lambda-, rph-1, argA (H15Y) pNUT1533-ctrl	This study	N/A
MG1655: argA∗ CRISPRi-argE: F-, lambda-, rph-1, argA (H15Y) pNUT1533-argE	This study	N/A
MG1655: argA∗ CRISPRi-hisB: F-, lambda-, rph-1, argA (H15Y) pNUT1533-hisB	This study	N/A
MG1655: argA∗ CRISPRi-trpA: F-, lambda-, rph-1, argA (H15Y) pNUT1533-trpA	This study	N/A
MG1655: hisG∗ CRISPRi-ctrl: F-, lambda-, rph-1, hisG (E271K) pNUT1533-ctrl	This study	N/A
MG1655: hisG∗ CRISPRi-hisB: F-, lambda-, rph-1, hisG (E271K) pNUT1533-hisB	This study	N/A
MG1655: hisG∗ CRISPRi-argE: F-, lambda-, rph-1, hisG (E271K) pNUT1533-argE	This study	N/A
MG1655: hisG∗ CRISPRi-trpA: F-, lambda-, rph-1, hisG (E271K) pNUT1533-trpA	This study	N/A
MG1655: trpE∗ CRISPRi-ctrl: F-, lambda-, rph-1, trpE (S40F) pNUT1533-ctrl	This study	N/A
MG1655: trpE∗ CRISPRi-trpA: F-, lambda-, rph-1, trpE (S40F) pNUT1533-trpA	This study	N/A
MG1655: trpE∗ CRISPRi-argE: F-, lambda-, rph-1, trpE (S40F) pNUT1533-argE	This study	N/A
MG1655: trpE∗ CRISPRi-hisB: F-, lambda-, rph-1, trpE (S40F) pNUT1533-hisB	This study	N/A
MG1655: pPargA-gfp: F-, lambda-, rph-1,	This study	N/A
MG1655: argA∗ pPargA-gfp: F-, lambda-, rph-1, argA (H15Y)	This study	N/A
MG1655: pPtrpL-gfp: F-, lambda-, rph-1,	This study	N/A
MG1655: trpE∗ pPtrpL-gfp: F-, lambda-, rph-1, trpE (S40F)	This study	N/A
MG1655: pPthrL-gfp: F-, lambda-, rph-1,	This study	N/A
MG1655: thrA∗ pPthrL-gfp: F-, lambda-, rph-1, thrA (S345F)	This study	N/A
MG1655: pPhisL-gfp: F-, lambda-, rph-1,	This study	N/A
MG1655: hisG∗ pPhisL-gfp: F-, lambda-, rph-1, hisG (E271K)	This study	N/A
MG1655: pPleuL-gfp: F-, lambda-, rph-1,	This study	N/A
MG1655: leuA∗ pPleuL-gfp: F-, lambda-, rph-1, leuA (G462D)	This study	N/A
Chemicals, Peptides, and Recombinant Proteins
Acetonitrile	Honeywell Riedel-de Haën	Cat#14261-2L
Methanol	VWR	Cat#83638.320
Anhydrotetracycline	Sigma-Aldrich	Cat#1035708-25MG
IPTG	Roth	Cat#CN08.2
Ampicillin	Roth	Cat#K029.2
Kanamycin	Roth	Cat#T832.3
Gentamycin	Roth	Cat#0233.3
Spectinomycin	Roth	Cat#HP66.2
Critical Commercial Assays
PierceTM Quantitative Colometric Peptide Assay	Thermo Fisher Scientific	Cat#23275
His GraviTrapTM	Merck	11-0033-99
Deposited Data
Metabolome, proteome and labeling data	This study	Table S7
kcat-values for enzymes in amino-acid biosynthesis (Table S3)	(Schomburg et al., 2013) (Davidi and Milo, 2017)	BRENDA [doi:https://doi.org/10.1016/j.copbio.2017.02.007]
Amino acid requirement of Escherichia coli (Table S4)	(Monk et al., 2017)	[doi:https://doi.org/10.1038/nbt.3956]
Inhibition Constants (Table S5)	(Keseler et al., 2017) (Schomburg et al., 2013); (Gama-Castro et al., 2016)	EcoCyc BRENDA; RegulonDB
Oligonucleotides
Oligonucleotides are listed in Table S6
Recombinant DNA
pKDsgRNA-ack	Reisch and Prather (2015)	Addgene plasmid # 62654
pCas9-CR4	Reisch and Prather (2015)	Addgene plasmid # 62655
pKDsgRNA-p15	Reisch and Prather (2015)	Addgene plasmid # 62656
pdCas9	Larson et al. (2013)	Addgene plasmid # 44249
pgRNA	Larson et al. (2013)	Addgene plasmid # 44251
pKDsgRNA-argA(H15Y)	This study	N/A
pKDsgRNA-ilvA(L447F)	This study	N/A
pKDsgRNA-hisG(E271K)	This study	N/A
pKDsgRNA-leuA(G462D)	This study	N/A
pKDsgRNA-proB(D107N)	This study	N/A
pKDsgRNA-thrA(S345F)	This study	N/A
pKDsgRNA-trpE(S40F)	This study	N/A
pKDsgRNA-ΔargR	This study	N/A
pKDsgRNA-ΔtrpR	This study	N/A
pNUT542	Singh et al. (2017)
pNUT1533-ctrl	This study	N/A
pNUT1533-argE	This study	N/A
pNUT1533-trpA	This study	N/A
pNUT1533-hisA	This study	N/A
pUA66-PargA-gfp: pPargA-gfp	Zaslaver et al. (2006)	N/A
pUA66-PtrpL-gfp: pPtrpL-gfp	Zaslaver et al. (2006)	N/A
pUA66 based plasmid with PhisL	This study	pPhisL-gfp
pUA66 based plasmid with PleuL	This study	pPleuL-gfp
pUA66 based plasmid with PthrA	This study	pPthrA-gfp
Software and Algorithms
MATLAB codes for model analysis	This study	https://github.com/nfarke/Sander_et_al
Matlab Version 9.3.0.713579 (R2017b) for the modelling section and analysis of experimental data	mathworks.com	N/A
BD FACSDiva software version 8.0	BD Biosciences, NJ, USA	N/A
FlowJo v10.4.1	FlowJo LLC, Ashland, OR, USA	N/A