KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Rabbit polyclonal anti-CysRS antibodies | (Masuda et al., 2021) | N/A |
| Rabbit polyclonal anti-TrmD antibodies | (Li and Bjork, 1999) | N/A |
| Goat polyclonal anti-rabbit IgG antibodies peroxidase conjugate | Sigma-Aldrich | Cat. #A0545; RRID: AB_257896 |
| Bacterial and virus strains | ||
| Escherichia coli strain K-12 substrain MG1655 | ATCC | Cat. #700926 |
| E. coli strain BW25113 | The Coli Genetic Stock Center (CGSC) | CGSC#: 7636 |
| E. coli strain XAC | (Jakowec et al., 1988) | N/A |
| E. coli strain BL21(DE3) | Millipore | Cat. #69450 |
| E. coli strain ArcticExpress (DE3) | Agilent Technologies | Cat. #230191 |
| E. coli strain K-12 substrain MG1655, proS D98N (trmD + or trmD−) | This paper | N/A |
| E. coli strain K-12 substrain MG1655, proS G107C (trmD + or trmD−) | This paper | N/A |
| E. coli strain K-12 substrain MG1655, proS S123R (trmD + or trmD−) | This paper | N/A |
| E. coli strain K-12 substrain MG1655, proS T199I (trmD + or trmD−) | This paper | N/A |
| E. coli strain K-12 substrain MG1655, proS T199S (trmD + or trmD−) | This paper | N/A |
| E. coli strain K-12 substrain MG1655, proS Q211L (trmD + or trmD−) | This paper | N/A |
| E. coli strain K-12 substrain MG1655, proS A231E (trmD + or trmD−) | This paper | N/A |
| E. coli strain K-12 substrain MG1655, proS N232S (trmD + or trmD−) | This paper | N/A |
| E. coli strain K-12 substrain MG1655, proS A236E (trmD + or trmD−) | This paper | N/A |
| E. coli strain K-12 substrain MG1655, proS D98N, trmD−, pACYC-araC-PC-PBAD-human trm5, proK− | This paper | N/A |
| E. coli strain K-12 substrain MG1655, proS D98N, trmD−, pACYC-araC-PC-PBAD-human trm5, proL− | This paper | N/A |
| E. coli strain K-12 substrain MG1655, proS T199I, trmD−, pACYC-araC-PC-PBAD-human trm5, proK− | This paper | N/A |
| E. coli strain K-12 substrain MG1655, proS T199I, trmD−, pACYC-araC-PC-PBAD-human trm5, proL− | This paper | N/A |
| E. coli strain K-12 substrain MG1655, proS N232S, trmD−, pACYC-araC-PC-PBAD-human trm5, proK− | This paper | N/A |
| E. coli strain K-12 substrain MG1655, proS N232S, trmD−, pACYC-araC-PC-PBAD-human trm5, proL− | This paper | N/A |
| Bacteriophage P1vir | CGSC | CGSC#: 12,133 |
| Chemicals, peptides, and recombinant proteins | ||
| L-Arabinose | Gold Biotechnology | Cat. #A-300-250 |
| BamHI | New England BioLabs | Cat. #R0136 |
| EcoRI | New England BioLabs | Cat. #R0101 |
| NdeI | New England BioLabs | Cat. #R0111 |
| PstI | New England BioLabs | Cat. #R0140 |
| XhoI | New England BioLabs | Cat. #R0146 |
| PfuUltraII fusion HS DNA polymerase | Agilent Technologies | Cat. #600670 |
| Phusion™ High-Fidelity DNA Polymerase | ThermoFisher Scientific | Cat. #F530 |
| NEBuilder® HiFi DNA Assembly Cloning Kit | New England BioLabs | Cat. #E5520S |
| T4 DNA ligase | New England Biolabs | Cat. #M0202 |
| T4 polynucleotide kinase | New England Biolabs | Cat. #M0201 |
| Ampicillin | Fisher Scientific | Cat. #BP1760 |
| Chloramphenicol | Gold Biotechnology | Cat. #G-105 |
| Kanamycin | Gemini Bio-products | Cat. #400-114P |
| Anhydrous tetracycline hydrochloride | Cayman Chemicals | Cat. #10009542 |
| [γ-32P]-ATP | PerkinElmer | Cat. #NEG002A |
| [3H]-Proline | PerkinElmer | Cat. #NET483005MC |
| Critical commercial assays | ||
| SuperSignal West Pico Chemiluminescent Substrate | ThermoFisher Scientific | Cat. #34080 |
| ONE-Glo™ Luciferase Assay System | Promega | Cat. #E6120 |
| Deposited data | ||
| Whole-genome sequencing data of E. coli trmD-KO suppressor cells | This paper | EMBL-EBI ArrayExpress: E-MTAB-12178 |
| Codes for codon usage and tRNAPro distribution analysis | This paper | https://doi.org/10.5281/zenodo.7093913 |
| List of annotated genome sequences retrieved from public databases | Table S3 | N/A |
| Experimental models: Organisms/strains | ||
| E. coli strain K-12 substrain MG1655 | ATCC | Cat. #700926 |
| Oligonucleotides | ||
| Oligo DNAs for bacterial strain construction, plasmid construction, CRISPR mutagenesis, and Northern blotting | Table S2 | N/A |
| Recombinant DNA | ||
| pKD46 | CGSC | CGSC #7634 |
| pKD46-EctrmD | This paper | N/A |
| pCP20 | CGSC | CGSC #7629 |
| pACYC-araC-PC-PBAD-human trm5 | (Gamper et al., 2015) | N/A |
| pCas9cr4 | (Reisch and Prather, 2015) | N/A |
| pKDsgRNA | (Reisch and Prather, 2015) | N/A |
| pZS2R-mCherry | (Kelsic et al., 2015) | N/A |
| pZS2R-YFP | (Kelsic et al., 2015) | N/A |
| pKK223-3 E. coli Pro(CGG) (proK) | This paper | N/A |
| pKK223-3 E. coli Pro(GGG) (proL) | (Gamper et al., 2015) | N/A |
| pKK223-3 E. coli Pro(UGG) (proM) | (Masuda et al., 2021) | N/A |
| pKK223-3 E. coli Pro(GGG) (proL) with anticodon UGG | (Masuda et al., 2018) | N/A |
| pKK223-3 E. col Met(CAU) (metV) | (Gamper et al., 2015) | N/A |
| Software and algorithms | ||
| FASTQC v 0.11.5 | Andrews S. (2010) | http://www.bioinformatics.babraham.ac.uk/projects/fastqc |
| Burrows-Wheeler Alignment (BWA) tool v 0.7.15 - r1140 | (Li and Durbin, 2009) | N/A |
| SAMtools v 1.3.1 | (Li et al., 2009) | N/A |
| Bcftools | (Li, 2011) | https://samtools.github.io/bcftools/bcftools.html |
| SnpEff | (Cingolani et al., 2012) | N/A |
| Image Lab v. 6.0 | BIO-RAD | http://www.bio-rad.com/en-us/product/image-lab-software |
| PyMOL v. 2.4.1 | Schrödinger | https://pymol.org/ |
| Clustal X v. 2.1 | (Larkin et al., 2007) | N/A |
| Excel v. 2010 | Microsoft | https://www.microsoft.com/ |
| Kaleidagraph v. 4.5 | Synergy software | https://www.synergy.com/ |
| ImageJ v. 1.51 | National Institutes of Health | https://imagej.nih.gov |
| Python v. 3.7.7 | Python Software Foundation | https://www.python.org/ |
| ETE3 v. 3.1.2 | (Huerta-Cepas et al., 2016) | http://etetoolkit.org/ |
| RefSeq release 211 | (OĽeary et al., 2016) | https://www.ncbi.nlm.nih.gov/refseq/ |
| GenBank release 248 | (Sayers et al., 2022) | https://www.ncbi.nlm.nih.gov/genbank/ |
| FastTree v. 2.1.10 | (Price et al., 2009, 2010) | http://www.microbesonline.org/fasttree/ |
| GtRNAdb release 19 | (Chan and Lowe, 2016) | http://gtrnadb.ucsc.edu/ |
| matplotlib v. 3.5.0 | https://doi.org/10.1109/MCSE.2007.55 | https://matplotlib.org/3.1.1/index.html |
| SINA v. 1.2.11 | (Pruesse et al., 2012) | https://www.arb-silva.de/aligner/ |
| SILVA release 89 | (Quast et al., 2013) | https://www.arb-silva.de/ |
| Scipy v.1.9.0 | (Virtanen et al., 2020) | https://scipy.org |
| Other | ||
| NucleoSpin Gel and PCR Clean-up | Macherey-Nagel | Cat. #740609 |
| Hybond™-N + Nitrocellulose Membrane | GE healthcare | Cat. #RPN203B |
| Nextera XT DNA Library Preparation Kit | Illumina | Cat. #FC-131-1024 |
| Trans-Blot® TurboTM Transfer System | BIO-RAD | Cat. #1704150 |
| MicroPulser Electroporator | BIO-RAD | Cat. #1652100 |
| UV Crosslinker | Fisher Scientific | Cat. #FB-UVXL-1000 |
| Tri-Carb 4910 TR Scintillation Counter | PerkinElmer | N/A |
| Immobilon-P PVDF Membrane | Millipore | IPVH00010 |
| ChemiDoc MP Imaging System | BIO-RAD | Cat. #12003154 |
| Typhoon IP Imaging System | GE Healthcare | N/A |
| Infinite M200 PRO Plate Reader | Tecan | N/A |