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The family of\n                    <jats:underline>\n                      <jats:bold>e<\/jats:bold>\n                    <\/jats:underline>\n                    rythromycin\n                    <jats:underline>\n                      <jats:bold>r<\/jats:bold>\n                    <\/jats:underline>\n                    esistance\n                    <jats:underline>\n                      <jats:bold>m<\/jats:bold>\n                    <\/jats:underline>\n                    ethyltransferases (Erm) invariantly install either one or two methyl groups onto the\n                    <jats:italic>N<\/jats:italic>\n                    <jats:sup>6,6<\/jats:sup>\n                    -adenosine of 2058 nucleotide (m\n                    <jats:sup>6<\/jats:sup>\n                    A2058) of the bacterial 23S rRNA, leading to bacterial cross-resistance to all MLS antibiotics. Despite extensive structural studies on the mechanism of Erm-mediated MLS resistance, how the m\n                    <jats:sup>6<\/jats:sup>\n                    A epitranscriptomic mark affects ribosome function and bacterial physiology is not well understood. Here, we show that\n                    <jats:italic>Staphylococcus aureus<\/jats:italic>\n                    cells harboring m\n                    <jats:sup>6<\/jats:sup>\n                    A2058 ribosomes are outcompeted by cells carrying unmodified ribosomes during infections and are severely impaired in colonization in the absence of an unmodified counterpart. The competitive advantage of m\n                    <jats:sup>6<\/jats:sup>\n                    A2058 ribosomes is manifested only upon antibiotic challenge. Using ribosome profiling (Ribo-Seq) and a dual-fluorescence reporter to measure ribosome occupancy and translational fidelity, we found that specific genes involved in host interactions, metabolism, and information processing are disproportionally deregulated in mRNA translation. This dysregulation is linked to a substantial reduction in translational capacity and fidelity in m\n                    <jats:sup>6<\/jats:sup>\n                    A2058 ribosomes. These findings point to a general \u201cinefficient translation\u201d mechanism of trade-offs associated with multidrug-resistant ribosomes.\n                  <\/jats:p>","DOI":"10.1371\/journal.ppat.1011968","type":"journal-article","created":{"date-parts":[[2024,1,22]],"date-time":"2024-01-22T13:29:11Z","timestamp":1705930151000},"page":"e1011968","update-policy":"https:\/\/doi.org\/10.1371\/journal.ppat.corrections_policy","source":"Crossref","is-referenced-by-count":18,"title":["Epitranscriptional m6A modification of rRNA negatively impacts translation and host colonization in Staphylococcus aureus"],"prefix":"10.1371","volume":"20","author":[{"given":"Kathryn E.","family":"Shields","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David","family":"Ranava","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yongjun","family":"Tan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dapeng","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4213-4050","authenticated-orcid":true,"given":"Mee-Ngan F.","family":"Yap","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2024,1,22]]},"reference":[{"issue":"1","key":"ppat.1011968.ref001","doi-asserted-by":"crossref","first-page":"e1691","DOI":"10.1002\/wrna.1691","article-title":"RNA nucleotide methylation: 2021 update.","volume":"13","author":"Y 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coli Ribosomal RNA Methyltransferases.","volume":"11","author":"P Pletnev","year":"2020","journal-title":"Front Genet"},{"issue":"18","key":"ppat.1011968.ref012","doi-asserted-by":"crossref","first-page":"8897","DOI":"10.1093\/nar\/gkw699","article-title":"Antibiotic resistance evolved via inactivation of a ribosomal RNA methylating enzyme","volume":"44","author":"V Stojkovi\u0107","year":"2016","journal-title":"Nucleic Acids Res"},{"issue":"8","key":"ppat.1011968.ref013","doi-asserted-by":"crossref","DOI":"10.3390\/genes12081125","article-title":"RNA Modifications in Pathogenic Bacteria: Impact on Host Adaptation and Virulence.","volume":"12","author":"L Antoine","year":"2021","journal-title":"Genes (Basel)."},{"issue":"11","key":"ppat.1011968.ref014","doi-asserted-by":"crossref","first-page":"1335","DOI":"10.1134\/S000629792011005X","article-title":"rRNA Methylation and Antibiotic Resistance","volume":"85","author":"IA Osterman","year":"2020","journal-title":"Biochemistry 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Roberts","year":"1999","journal-title":"Antimicrob Agents Chemother"},{"issue":"2","key":"ppat.1011968.ref027","first-page":"151","article-title":"Phylogenetic analysis of rRNA methyltransferases, Erm and KsgA, as related to antibiotic resistance","volume":"309","author":"AK Park","year":"2010","journal-title":"FEMS microbiology letters"},{"issue":"2","key":"ppat.1011968.ref028","doi-asserted-by":"crossref","first-page":"369","DOI":"10.1128\/AAC.39.2.369","article-title":"Prevalence of erm gene classes in erythromycin-resistant Staphylococcus aureus strains isolated between 1959 and 1988","volume":"39","author":"H Westh","year":"1995","journal-title":"Antimicrob Agents Chemother"},{"key":"ppat.1011968.ref029","doi-asserted-by":"crossref","first-page":"203","DOI":"10.3389\/fmicb.2011.00203","article-title":"Acquired antibiotic resistance genes: an overview.","volume":"2","author":"AH van Hoek","year":"2011","journal-title":"Front Microbiol."},{"issue":"18","key":"ppat.1011968.ref030","doi-asserted-by":"crossref","first-page":"9807","DOI":"10.1021\/acs.est.6b00262","article-title":"Antimicrobial Chemicals Are Associated with Elevated Antibiotic Resistance Genes in the Indoor Dust Microbiome","volume":"50","author":"EM Hartmann","year":"2016","journal-title":"Environ Sci Technol"},{"issue":"7","key":"ppat.1011968.ref031","first-page":"e00153","article-title":"Emerging erm(B)-Mediated Macrolide Resistance Associated with Novel Multidrug Resistance Genomic Islands in Campylobacter.","volume":"63","author":"D Liu","year":"2019","journal-title":"Antimicrob Agents Chemother"},{"issue":"10","key":"ppat.1011968.ref032","doi-asserted-by":"crossref","first-page":"pii: a025395","DOI":"10.1101\/cshperspect.a025395","article-title":"Resistance to Macrolide Antibiotics in Public Health Pathogens.","volume":"6","author":"C Fyfe","year":"2016","journal-title":"Cold Spring Harbor perspectives in medicine."},{"issue":"1","key":"ppat.1011968.ref033","doi-asserted-by":"crossref","first-page":"175","DOI":"10.1186\/s12879-019-3779-8","article-title":"Staphylococcus aureus with an erm-mediated constitutive macrolide-lincosamide-streptogramin B resistance phenotype has reduced susceptibility to the new ketolide, solithromycin.","volume":"19","author":"W Yao","year":"2019","journal-title":"BMC Infect Dis"},{"issue":"1","key":"ppat.1011968.ref034","doi-asserted-by":"crossref","first-page":"6089","DOI":"10.1038\/s41598-019-42423-3","article-title":"Azithromycin resistance levels and mechanisms in Escherichia coli.","volume":"9","author":"C Gomes","year":"2019","journal-title":"Sci Rep"},{"issue":"4","key":"ppat.1011968.ref035","doi-asserted-by":"crossref","first-page":"811","DOI":"10.1111\/j.1365-2958.2008.06576.x","article-title":"Programmed drug-dependent ribosome stalling","volume":"71","author":"H Ramu","year":"2009","journal-title":"Mol Microbiol"},{"issue":"2","key":"ppat.1011968.ref036","doi-asserted-by":"crossref","first-page":"190","DOI":"10.1016\/j.molcel.2008.02.026","article-title":"Molecular mechanism of drug-dependent ribosome stalling","volume":"30","author":"N Vazquez-Laslop","year":"2008","journal-title":"Mol Cell"},{"issue":"3","key":"ppat.1011968.ref037","doi-asserted-by":"crossref","first-page":"577","DOI":"10.1128\/AAC.39.3.577","article-title":"Erythromycin resistance by ribosome modification","volume":"39","author":"B. Weisblum","year":"1995","journal-title":"Antimicrob Agents Chemother"},{"key":"ppat.1011968.ref038","doi-asserted-by":"crossref","first-page":"12026","DOI":"10.1038\/ncomms12026","article-title":"A combined cryo-EM and molecular dynamics approach reveals the mechanism of ErmBL-mediated translation arrest.","volume":"7","author":"S Arenz","year":"2016","journal-title":"Nat Commun."},{"issue":"3","key":"ppat.1011968.ref039","doi-asserted-by":"crossref","first-page":"153","DOI":"10.1038\/nchembio.1998","article-title":"Nascent peptide assists the ribosome in recognizing chemically distinct small molecules","volume":"12","author":"P Gupta","year":"2016","journal-title":"Nat Chem Biol"},{"issue":"12","key":"ppat.1011968.ref040","doi-asserted-by":"crossref","first-page":"7178","DOI":"10.1128\/AAC.01806-16","article-title":"The expression of antibiotic resistance methyltransferase correlates with mRNA stability independently of ribosome stalling","volume":"60","author":"E Dzyubak","year":"2016","journal-title":"Antimicrob Agents Chemother"},{"key":"ppat.1011968.ref041","doi-asserted-by":"crossref","first-page":"690744","DOI":"10.3389\/fmicb.2021.690744","article-title":"Translational Attenuation Mechanism of ErmB Induction by Erythromycin Is Dependent on Two Leader Peptides.","volume":"12","author":"S Wang","year":"2021","journal-title":"Front Microbiol"},{"issue":"12","key":"ppat.1011968.ref042","doi-asserted-by":"crossref","first-page":"1154","DOI":"10.1007\/BF02969307","article-title":"ErmK leader peptide: amino acid sequence critical for induction by erythromycin","volume":"29","author":"AR Kwon","year":"2006","journal-title":"Arch Pharm Res"},{"issue":"3","key":"ppat.1011968.ref043","doi-asserted-by":"crossref","first-page":"377","DOI":"10.1007\/s12272-001-1167-8","article-title":"Molecular analysis of constitutive mutations in ermB and ermA selected in vitro from inducibly MLSB-resistant Enterococci","volume":"31","author":"YH Min","year":"2008","journal-title":"Arch Pharm Res"},{"issue":"11","key":"ppat.1011968.ref044","doi-asserted-by":"crossref","first-page":"3415","DOI":"10.1128\/AAC.47.11.3415-3420.2003","article-title":"Heterogeneity of macrolide-lincosamide-streptogramin B resistance phenotypes in enterococci","volume":"47","author":"YH Min","year":"2003","journal-title":"Antimicrob Agents Chemother"},{"issue":"1","key":"ppat.1011968.ref045","doi-asserted-by":"crossref","first-page":"42","DOI":"10.1093\/jac\/dkn432","article-title":"Unusual resistance patterns in macrolide-resistant Streptococcus pyogenes harbouring erm(A).","volume":"63","author":"S Malhotra-Kumar","year":"2009","journal-title":"J Antimicrob Chemother"},{"issue":"4","key":"ppat.1011968.ref046","doi-asserted-by":"crossref","first-page":"559","DOI":"10.1093\/jac\/43.4.559","article-title":"Inducible or constitutive expression of resistance in clinical isolates of streptococci and enterococci cross-resistant to erythromycin and 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and lincosamides","volume":"418","author":"H Vicarini","year":"1997","journal-title":"Adv Exp Med Biol"},{"issue":"2","key":"ppat.1011968.ref050","doi-asserted-by":"crossref","first-page":"72","DOI":"10.4161\/mge.20109","article-title":"The diversity of inducible and constitutively expressed erm(C) genes and association to different replicon types in staphylococci plasmids.","volume":"2","author":"LE de Vries","year":"2012","journal-title":"Mobile genetic elements."},{"issue":"2","key":"ppat.1011968.ref051","first-page":"147","article-title":"Novel 10-bp deletion in the translational attenuator of a constitutively expressed erm(A) gene from Staphylococcus epidermidis.","volume":"10","author":"L Millan","year":"2007","journal-title":"International microbiology: the official journal of the Spanish Society for Microbiology"},{"issue":"10","key":"ppat.1011968.ref052","doi-asserted-by":"crossref","first-page":"6661","DOI":"10.1128\/AAC.01103-15","article-title":"Constitutive and inducible expression of the rRNA methylase gene erm(B) in Campylobacter.","volume":"59","author":"F Deng","year":"2015","journal-title":"Antimicrob Agents Chemother"},{"issue":"6","key":"ppat.1011968.ref053","doi-asserted-by":"crossref","first-page":"1506","DOI":"10.1111\/j.1365-2958.2007.05744.x","article-title":"Acquisition of a natural resistance gene renders a clinical strain of methicillin-resistant Staphylococcus aureus resistant to the synthetic antibiotic linezolid","volume":"64","author":"SM Toh","year":"2007","journal-title":"Mol Microbiol"},{"issue":"5","key":"ppat.1011968.ref054","doi-asserted-by":"crossref","first-page":"1745","DOI":"10.1073\/pnas.1814265116","article-title":"Sequential evolution of virulence and resistance during clonal spread of community-acquired methicillin-resistant Staphylococcus aureus","volume":"116","author":"R Copin","year":"2019","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"1","key":"ppat.1011968.ref055","doi-asserted-by":"crossref","DOI":"10.1128\/mBio.02287-17","article-title":"Staphylococcus aureus HemX Modulates Glutamyl-tRNA Reductase Abundance To Regulate Heme Biosynthesis.","volume":"9","author":"JE Choby","year":"2018","journal-title":"MBio."},{"key":"ppat.1011968.ref056","doi-asserted-by":"crossref","first-page":"8125","DOI":"10.1038\/ncomms9125","article-title":"Counter inhibition between leukotoxins attenuates Staphylococcus aureus virulence.","volume":"6","author":"P Yoong","year":"2015","journal-title":"Nat Commun"},{"key":"ppat.1011968.ref057","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.plasmid.2014.08.001","article-title":"Single-copy vectors for integration at the SaPI1 attachment site for Staphylococcus aureus","volume":"76","author":"J Chen","year":"2014","journal-title":"Plasmid"},{"issue":"1","key":"ppat.1011968.ref058","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1111\/j.1574-695X.2012.00937.x","article-title":"Virulence strategies of the dominant USA300 lineage of community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA).","volume":"65","author":"LR Thurlow","year":"2012","journal-title":"FEMS Immunol Med Microbiol"},{"issue":"2","key":"ppat.1011968.ref059","doi-asserted-by":"crossref","first-page":"498","DOI":"10.1073\/pnas.84.2.498","article-title":"Induced mRNA stability in Bacillus subtilis","volume":"84","author":"DH Bechhofer","year":"1987","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ppat.1011968.ref060","doi-asserted-by":"crossref","first-page":"1984","DOI":"10.1038\/ncomms2984","article-title":"Deregulation of translation due to post-transcriptional modification of rRNA explains why erm genes are inducible.","volume":"4","author":"P Gupta","year":"2013","journal-title":"Nat Commun."},{"issue":"1","key":"ppat.1011968.ref061","doi-asserted-by":"crossref","first-page":"187","DOI":"10.1128\/MMBR.00031-15","article-title":"Staying in Shape: the Impact of Cell Shape on Bacterial Survival in Diverse Environments","volume":"80","author":"DC Yang","year":"2016","journal-title":"Microbiol Mol Biol Rev"},{"issue":"17","key":"ppat.1011968.ref062","doi-asserted-by":"crossref","first-page":"e134","DOI":"10.1093\/nar\/gku671","article-title":"Translation inhibitors cause abnormalities in ribosome profiling experiments","volume":"42","author":"MV Gerashchenko","year":"2014","journal-title":"Nucleic Acids Res"},{"key":"ppat.1011968.ref063","doi-asserted-by":"crossref","first-page":"e42591","DOI":"10.7554\/eLife.42591","article-title":"A systematically-revised ribosome profiling method for bacteria reveals pauses at single-codon resolution.","volume":"8","author":"F Mohammad","year":"2019","journal-title":"Elife"},{"issue":"10","key":"ppat.1011968.ref064","doi-asserted-by":"crossref","first-page":"4881","DOI":"10.1093\/nar\/gkw180","article-title":"Ribosome hibernation factor promotes Staphylococcal survival and differentially represses translation","volume":"44","author":"A Basu","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"ppat.1011968.ref065","doi-asserted-by":"crossref","first-page":"723","DOI":"10.1038\/s41467-017-00753-8","article-title":"The cryo-EM structure of hibernating 100S ribosome dimer from pathogenic Staphylococcus aureus.","volume":"8","author":"D Matzov","year":"2017","journal-title":"Nat Commun."},{"issue":"2","key":"ppat.1011968.ref066","doi-asserted-by":"crossref","first-page":"178","DOI":"10.1093\/bfgp\/elq008","article-title":"Transcription attenuation in bacteria: theme and variations","volume":"9","author":"M Naville","year":"2010","journal-title":"Brief Funct 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Kiedrowski","year":"2014","journal-title":"PLoS One."},{"issue":"6","key":"ppat.1011968.ref073","doi-asserted-by":"crossref","first-page":"1259","DOI":"10.1111\/mmi.12733","article-title":"Deletion of membrane-associated Asp23 leads to upregulation of cell wall stress genes in Staphylococcus aureus","volume":"93","author":"M M\u00fcller","year":"2014","journal-title":"Mol Microbiol"},{"issue":"2","key":"ppat.1011968.ref074","doi-asserted-by":"crossref","first-page":"267","DOI":"10.1016\/0092-8674(92)90101-H","article-title":"Sorting of protein A to the staphylococcal cell wall","volume":"70","author":"O Schneewind","year":"1992","journal-title":"Cell"},{"key":"ppat.1011968.ref075","first-page":"e0081421","article-title":"Growth and Stress Tolerance Comprise Independent Metabolic Strategies Critical for Staphylococcus aureus Infection.","volume":"2021","author":"GL Kim","journal-title":"mBio."},{"issue":"21","key":"ppat.1011968.ref076","doi-asserted-by":"crossref","first-page":"5663","DOI":"10.1128\/JB.00628-10","article-title":"Role of surface protein SasG in biofilm formation by Staphylococcus aureus","volume":"192","author":"JA Geoghegan","year":"2010","journal-title":"J Bacteriol"},{"issue":"8","key":"ppat.1011968.ref077","doi-asserted-by":"crossref","first-page":"355","DOI":"10.1016\/j.tibs.2014.06.002","article-title":"Protein mistranslation: friend or foe","volume":"39","author":"L Ribas de Pouplana","year":"2014","journal-title":"Trends Biochem Sci"},{"issue":"6","key":"ppat.1011968.ref078","doi-asserted-by":"crossref","first-page":"2877","DOI":"10.1093\/nar\/gkad104","article-title":"When translation elongation is impaired, the mRNA is uniformly destabilized by the RNA degradosome, while the concentration of mRNA is altered along the molecule","volume":"51","author":"MP Duviau","year":"2023","journal-title":"Nucleic Acids 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limiting ABCE1 concentration involves frameshifting and inhibits nonsense-mediated mRNA decay","author":"G Annibaldis","year":"2020","journal-title":"Nucleic Acids Res"},{"issue":"6","key":"ppat.1011968.ref083","doi-asserted-by":"crossref","first-page":"e1004178","DOI":"10.1371\/journal.pmed.1004178","article-title":"Global incidence in hospital-associated infections resistant to antibiotics: An analysis of point prevalence surveys from 99 countries.","volume":"20","author":"R Balasubramanian","year":"2023","journal-title":"PLoS Med.PubMed Central PMCID"},{"key":"ppat.1011968.ref084","article-title":"Global burden of bacterial antimicrobial resistance in 2019: a systematic analysis.","author":"AR Collaborators","year":"2022","journal-title":"Lancet"},{"issue":"7","key":"ppat.1011968.ref085","doi-asserted-by":"crossref","first-page":"190051","DOI":"10.1098\/rsob.190051","article-title":"Translational control of antibiotic resistance.","volume":"9","author":"A Witzky","year":"2019","journal-title":"Open Biol."},{"issue":"6","key":"ppat.1011968.ref086","doi-asserted-by":"crossref","first-page":"1123","DOI":"10.1038\/s41564-023-01393-z","article-title":"Atlas of mRNA translation and decay for bacteria","volume":"8","author":"S Huch","year":"2023","journal-title":"Nature microbiology"},{"issue":"5","key":"ppat.1011968.ref087","doi-asserted-by":"crossref","first-page":"521","DOI":"10.1261\/rna.069823.118","article-title":"Does Functional Specialization of Ribosomes Really Exist?","volume":"25","author":"MB Ferretti","year":"2019","journal-title":"RNA"},{"issue":"3","key":"ppat.1011968.ref088","doi-asserted-by":"crossref","first-page":"364","DOI":"10.1016\/j.molcel.2018.07.018","article-title":"The Discovery of Ribosome Heterogeneity and Its Implications for Gene Regulation and Organismal Life","volume":"71","author":"NR Genuth","year":"2018","journal-title":"Mol Cell"},{"issue":"32","key":"ppat.1011968.ref089","doi-asserted-by":"crossref","first-page":"19487","DOI":"10.1073\/pnas.2009607117","article-title":"Selective translation by alternative bacterial ribosomes","volume":"117","author":"YX Chen","year":"2020","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"2","key":"ppat.1011968.ref090","doi-asserted-by":"crossref","first-page":"eaao0665","DOI":"10.1126\/sciadv.aao0665","article-title":"Variant ribosomal RNA alleles are conserved and exhibit tissue-specific expression","volume":"4","author":"MM Parks","year":"2018","journal-title":"Sci Adv"},{"issue":"3","key":"ppat.1011968.ref091","doi-asserted-by":"crossref","first-page":"515","DOI":"10.1038\/s41564-018-0341-1","article-title":"Divergent rRNAs as regulators of gene expression at the ribosome level","volume":"4","author":"W Song","year":"2019","journal-title":"Nature microbiology"},{"issue":"1","key":"ppat.1011968.ref092","doi-asserted-by":"crossref","first-page":"236","DOI":"10.1016\/j.celrep.2018.08.093","article-title":"Endogenous rRNA Sequence Variation Can Regulate Stress Response Gene Expression and Phenotype.","volume":"25","author":"CM Kurylo","year":"2018","journal-title":"Cell Rep"},{"key":"ppat.1011968.ref093","article-title":"The ribosome epitranscriptome: Inert\u2014or a platform for functional plasticity?","author":"JM Georgeson","year":"2021","journal-title":"RNA"},{"issue":"1","key":"ppat.1011968.ref094","doi-asserted-by":"crossref","first-page":"4093","DOI":"10.1038\/s41467-023-39790-x","article-title":"An RNA modification enzyme directly senses reactive oxygen species for translational regulation in Enterococcus faecalis","volume":"14","author":"WL Lee","year":"2023","journal-title":"Nat Commun"},{"key":"ppat.1011968.ref095","doi-asserted-by":"crossref","first-page":"421","DOI":"10.1146\/annurev-biochem-060815-014818","article-title":"How Messenger RNA and Nascent Chain Sequences Regulate Translation Elongation","volume":"87","author":"J Choi","year":"2018","journal-title":"Annu Rev Biochem"},{"key":"ppat.1011968.ref096","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1146\/annurev-biochem-080211-105026","article-title":"Arrest peptides: cis-acting modulators of translation","volume":"82","author":"K Ito","year":"2013","journal-title":"Annu Rev Biochem"},{"issue":"5","key":"ppat.1011968.ref097","doi-asserted-by":"crossref","first-page":"2777","DOI":"10.1093\/nar\/gkaa001","article-title":"Mutational characterization and mapping of the 70S ribosome active site","volume":"48","author":"AE d\u2019Aquino","year":"2020","journal-title":"Nucleic Acids Res"},{"issue":"5924","key":"ppat.1011968.ref098","doi-asserted-by":"crossref","first-page":"255","DOI":"10.1126\/science.1170160","article-title":"Coding-sequence determinants of gene expression in Escherichia coli","volume":"324","author":"G Kudla","year":"2009","journal-title":"Science"},{"issue":"43","key":"ppat.1011968.ref099","doi-asserted-by":"crossref","first-page":"15379","DOI":"10.1073\/pnas.1410356111","article-title":"Sequence selectivity of macrolide-induced translational attenuation","volume":"111","author":"AR Davis","year":"2014","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"45","key":"ppat.1011968.ref100","doi-asserted-by":"crossref","first-page":"15958","DOI":"10.1073\/pnas.1417334111","article-title":"The general mode of translation inhibition by macrolide antibiotics","volume":"111","author":"K Kannan","year":"2014","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"6115","key":"ppat.1011968.ref101","doi-asserted-by":"crossref","first-page":"82","DOI":"10.1126\/science.1228985","article-title":"Translation elongation factor EF-P alleviates ribosome stalling at polyproline stretches","volume":"339","author":"S Ude","year":"2013","journal-title":"Science"},{"issue":"21","key":"ppat.1011968.ref102","doi-asserted-by":"crossref","first-page":"5941","DOI":"10.1093\/emboj\/cdg561","article-title":"Sequences that direct significant levels of frameshifting are frequent in coding regions of Escherichia coli","volume":"22","author":"OL Gurvich","year":"2003","journal-title":"EMBO J"},{"issue":"9","key":"ppat.1011968.ref103","doi-asserted-by":"crossref","first-page":"2332","DOI":"10.1128\/JB.00027-11","article-title":"Whole-genome sequencing of Staphylococcus aureus strain RN4220, a key laboratory strain used in virulence research, identifies mutations that affect not only virulence factors but also the fitness of the strain","volume":"193","author":"D Nair","year":"2011","journal-title":"J Bacteriol"},{"issue":"1","key":"ppat.1011968.ref104","first-page":"e00537","article-title":"A genetic resource for rapid and comprehensive phenotype screening of nonessential Staphylococcus aureus genes.","volume":"4","author":"PD Fey","year":"2013","journal-title":"mBio"},{"issue":"4","key":"ppat.1011968.ref105","first-page":"e00334","article-title":"Hibernation-promoting factor sequesters Staphylococcus aureus ribosomes to antagonize RNase R-mediated nucleolytic degradation.","volume":"2","author":"A Liponska","year":"2021","journal-title":"mBio"},{"issue":"Pt 4","key":"ppat.1011968.ref106","doi-asserted-by":"crossref","first-page":"741","DOI":"10.1099\/00221287-140-4-741","article-title":"Analysis of the induction of general stress proteins of Bacillus subtilis","volume":"140","author":"U V\u00f6lker","year":"1994","journal-title":"Microbiology (Reading)."},{"issue":"4","key":"ppat.1011968.ref107","doi-asserted-by":"crossref","first-page":"402","DOI":"10.1006\/meth.2001.1262","article-title":"Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method.","volume":"25","author":"KJ Livak","year":"2001","journal-title":"Methods."},{"issue":"18","key":"ppat.1011968.ref108","doi-asserted-by":"crossref","first-page":"6053","DOI":"10.1074\/jbc.RA119.012307","article-title":"The hibernating 100S complex is a target of ribosome-recycling factor and elongation factor G in Staphylococcus aureus","volume":"295","author":"A Basu","year":"2020","journal-title":"J Biol Chem"},{"issue":"W1","key":"ppat.1011968.ref109","doi-asserted-by":"crossref","first-page":"W345","DOI":"10.1093\/nar\/gkac247","article-title":"The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update","volume":"50","author":"Galaxy Communuity","year":"2022","journal-title":"Nucleic Acids Res"},{"issue":"11","key":"ppat.1011968.ref110","doi-asserted-by":"crossref","first-page":"2212","DOI":"10.1038\/nprot.2013.133","article-title":"Selective ribosome profiling as a tool for studying the interaction of chaperones and targeting factors with nascent polypeptide chains and ribosomes.","volume":"8","author":"AH Becker","year":"2013","journal-title":"Nat Protoc"},{"key":"ppat.1011968.ref111","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1186\/1741-7007-8-49","article-title":"MochiView: versatile software for genome browsing and DNA motif analysis","volume":"8","author":"OR Homann","year":"2010","journal-title":"BMC Biol"},{"issue":"7","key":"ppat.1011968.ref112","doi-asserted-by":"crossref","first-page":"923","DOI":"10.1093\/bioinformatics\/btt656","article-title":"featureCounts: an efficient general purpose program for assigning sequence reads to genomic features","volume":"30","author":"Y Liao","year":"2014","journal-title":"Bioinformatics"},{"issue":"1","key":"ppat.1011968.ref113","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1093\/bioinformatics\/btp616","article-title":"edgeR: a Bioconductor package for differential expression analysis of digital gene expression data","volume":"26","author":"MD Robinson","year":"2010","journal-title":"Bioinformatics"},{"key":"ppat.1011968.ref114","doi-asserted-by":"crossref","first-page":"218","DOI":"10.1126\/science.1168978","article-title":"Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling","volume":"324","author":"NT Ingolia","year":"2009","journal-title":"Science"},{"issue":"5","key":"ppat.1011968.ref115","doi-asserted-by":"crossref","first-page":"1253","DOI":"10.1128\/AAC.46.5.1253-1261.2002","article-title":"Identification of essential residues in the Erm(B) rRNA methyltransferase of Clostridium perfringens.","volume":"46","author":"KA 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