Key Resources Table

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Rabbit polyclonal anti-LolB antibodies	(Matsuyama et al., 1997)	N/A
Rabbit polyclonal anti-CysRS antibodies	This paper	N/A
Rabbit polyclonal anti-TrmD antibodies	(Li and Bjork, 1999)	N/A
Rabbit polyclonal anti-hTrm5 antibodies	Sigma-Aldrich	Cat.#SAB2102581; QC18187
Rabbit polyclonal anti-OmpA antibodies	(Tani et al., 1990)	N/A
Goat polyclonal anti-rabbit IgG antibodies peroxidase conjugate	Sigma-Aldrich	Cat. #A0545
Bacterial and Virus Strains
Escherichia coli strain K-12 substrain MG1655	ATCC	700926
E. coli strain BW25113	The Coli Genetic Stock Center (CGSC)	CGSC#: 7636
E. coli ΔacrB	CGSC	JW0451–2
E. coli Δefp	CGSC	JW4107–1
E. coli ΔtolC	CGSC	JW5503–1
Salmonella enterica serovar Typhimurium strain LT2	ATCC	700720
Bacteriophage P1vir	Goulian lab collection	N/A
Bacteriophage P22	ATCC	97540
Chemicals, Peptides, and Recombinant Proteins
L-(+)-arabinose	Acros Organics	Cat. #365181000
D-(+)-glucose	MG Scientific	Cat. #MAL4912
EcoRI	New England BioLabs	Cat. #R0101S
Pstl	New England BioLabs	Cat. #R0140S
PfuUltrall fusion HS DNA polymerase	Agilent Technologies	Cat. #600670
Nuclease P1	Sigma-Aldrich	Cat. #N8630
Alkaline phosphatase	Sigma-Aldrich	Cat. #P5931
1-methylguanosine (QQQ standard)	Boc Sciences	Cat. #2140–65–0
Guanosine (QQQ standard)	Sigma-Aldrich	Cat. #G6752
[γ-32P]-ATP	PerkinElmer	Cat. #NEG002A
T4 polynucleotide kinase	New England Biolabs	Cat. #M0201
AlamarBlue Dye	Invitrogen	Cat. #DAL1025
Hoechst 33342 (H33342)	Sigma-Aldrich	Cat. #B2261
Carbonyl cyanide m-chlorophenyl hydrazine (CCCP)	Sigma-Aldrich	Cat. #C2759
Ethidium bromide	Sigma-Aldrich	Cat. #E7637
Nile Red	Acros Organics	Cat. #415711000
Thioflavin T	Sigma-Aldrich	Cat. #T3516
Sorbitol	Sigma-Aldrich	Cat. #S1876
Ampicillin	Fisher Scientific	Cat. #BP1760
Carbenicillin	Fisher Scientific	Cat. #BP2648
Chloramphenicol	Gold Biotechnology	Cat. #G-105
Ciprofloxacin	Sigma-Aldrich	Cat. #17850
Gentamicin	Gold Biotechnology	Cat. #G-400
Kanamycin	Gemini Bio-products	Cat. #400–114P
Novobiocin	Sigma-Aldrich	Cat. #N 1628
Paromomycin	Sigma-Aldrich	Cat. #P5057
Polymyxin B	Sigma-Aldrich	Cat. #P4932
Rifampicin	Sigma-Aldrich	Cat. #R3501
Vancomycin	Sigma-Aldrich	Cat. #SBR00001
Critical Commercial Assays
SuperSignal West Pico Chemiluminescent Substrate	Thermo Fisher Scientific	Cat. #34080
Experimental Models: Organisms/Strains
E. coli BL21(DE3) trmD-KD	(Gamper et al., 2015a)	N/A
E. coli MG1655 trmD-KD	This paper	N/A
Salmonella enterica serovar Typhymurium LT2 trmD-KD	This paper	N/A
E. coli MG1655 cysS-KD	This paper	N/A
E. coli MG 1655 proS-KD	This paper	N/A
E. coli proM-KD C37-UGG tRNA	This paper	N/A
E. coli trmD-KD codon-engineered lolB	This paper	N/A
Salmonella trmD-KD codon-engineered tolC	This paper	N/A
Oligonucleotides
Oligo DNA primers for strain construction, plasmid construction, codon engineering, primer extension and affinity tRNA purification	Table S1	N/A
Recombinant DNA
pKD4	CGSC	CGSC #7632
pKD46	CGSC	CGSC #7634
PCP20	CGSC	CGSC #7629
pZS2R	(Kelsic et al., 2015)	N/A
pACYC-araC-PC-PBAD-human trm5	(Gamper et al., 2015a)	N/A
pACYC-araC-PC-PBAD-Ec cysS-His-deg	This paper	N/A
pACYC-araC-Pc-PBAD-Ec proS-His-deg	This paper	N/A
pKK223-3 E. coli G37-UGG tRNA	This paper	N/A
pKK223-3 E. coli C37-UGG tRNA	This paper	N/A
pZS2R-PlolB-YFP	This paper	N/A
Software and Algorithms
MaxQuant v. 1.5.3.30	(Tyanova et al., 2016)	http://www.biochem.rnpg.de/5111795/maxquant
tRNA MS analysis software v.B.07.00	MassHunter Workstation, qualitative analysis	N/A
Image Lab v. 6.0	BIO-RAD	http://www.bio-rad.com/en-us/product/image-lab-software
ImageJ v. 1.51	NIH	https://imagej.nih.gov
Felix32	Photon Technology International	N/A
μManager v. 1.4	(Edelstein et al.,2014)	N/A
MATLAB 2016b	MathWorks	https://www.mathworks.com/products/matlab.html
Other
NucleoSpin Gel and PCR Clean-up	Macherey-Nagel	Cat. #740609
Gibson Assembly Master Mix	New England BioLabs	Cat. #E2611L
MicroPulser Electroporator	BIO-RAD	Cat. #1652100
NucleoBond AX 2000	Macherey-Nagel	Cat. #740525
Impact II Qtof Mass Spectrometer	Bruker Daltonics	N/A
0.22-μm filter	Millipore	SLGV004SL
6410 QQQ triple-quadrupole LC mass spectrometer	Agilent	N/A
Immobilon-P PVDF Membrane	Millipore	IPVH00010
Bransonic 1210 Ultrasonic Cleaner	Branson	N/A
Chemi-Doc XRS+ System	BIO-RAD	Cat. #1708265
Typhoon IP Imaging system	GE Healthcare	N/A
Infinite M200 PRO plate reader	Tecan	N/A
Black opaque 96-well microplate	Greiner Bio-One	Cat. #655077
Transparent sealing film	Excel Scientific	Cat. #STR-SEAL-PLT
Synergy H1 Hybrid Multi-Mode Reader	BioTek	N/A
Quartz cuvette	Starna Cells	Cat. #3-Q-10
QuantaMaster 220 spectrofluorometer	Photon Technology International	N/A
Microfluidic perfusion plates	CellASIC	Cat. #B04a
ONIX microfluidic platform	CellASIC	N/A
Nikon Eclipse Ti-E inverted fluorescence microscope	Nikon	N/A
DU885 electron multiplying charged coupled device camera	Andor	N/A
Active-control environmental chamber	Haison Technology	N/A