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Maxson T, Overholt WA, Chivukula V, Caban-Figueroa V, Kongphet-Tran T, Medina Cordoba LK, Cherney B, Rishishwar L, Conley A, Sue D. Genetic basis of clarithromycin resistance in Bacillus anthracis. Microbiol Spectr 2024; 12:e0418023. [PMID: 38666793 PMCID: PMC11237603 DOI: 10.1128/spectrum.04180-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 03/26/2024] [Indexed: 06/06/2024] Open
Abstract
The high-consequence pathogen Bacillus anthracis causes human anthrax and often results in lethal infections without the rapid administration of effective antimicrobial treatment. Antimicrobial resistance profiling is therefore critical to inform post-exposure prophylaxis and treatment decisions, especially during emergencies such as outbreaks or where intentional release is suspected. Whole-genome sequencing using a rapid long-read sequencer can uncover antimicrobial resistance patterns if genetic markers of resistance are known. To identify genomic markers associated with antimicrobial resistance, we isolated B. anthracis derived from the avirulent Sterne strain with elevated minimal inhibitory concentrations to clarithromycin. Mutants were characterized both phenotypically through broth microdilution susceptibility testing and observations during culturing, as well as genotypically with whole-genome sequencing. We identified two different in-frame insertions in the L22 ribosomal protein-encoding gene rplV, which were subsequently confirmed to be involved in clarithromycin resistance through the reversion of the mutant gene to the parent (drug-susceptible) sequence. Detection of the rplV insertions was possible with rapid long-read sequencing, with a time-to-answer within 3 h. The mutations associated with clarithromycin resistance described here will be used in conjunction with known genetic markers of resistance for other antimicrobials to strengthen the prediction of antimicrobial resistance in B. anthracis.IMPORTANCEThe disease anthrax, caused by the pathogen Bacillus anthracis, is extremely deadly if not treated quickly and appropriately. Clarithromycin is an antibiotic recommended for the treatment and post-exposure prophylaxis of anthrax by the Centers for Disease Control and Prevention; however, little is known about the ability of B. anthracis to develop resistance to clarithromycin or the mechanism of that resistance. The characterization of clarithromycin-resistant isolates presented here provides valuable information for researchers and clinicians in the event of a release of the resistant strain. Additionally, knowledge of the genetic basis of resistance provides a foundation for susceptibility prediction through rapid genome sequencing to inform timely treatment decisions.
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Affiliation(s)
- Tucker Maxson
- Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Will A. Overholt
- Applied Bioinformatics Laboratory (ASRT, Inc.; IHRC, Inc.), Atlanta, Georgia, USA
| | - Vasanta Chivukula
- Applied Bioinformatics Laboratory (ASRT, Inc.; IHRC, Inc.), Atlanta, Georgia, USA
| | | | - Thiphasone Kongphet-Tran
- Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Luz K. Medina Cordoba
- Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Blake Cherney
- Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Lavanya Rishishwar
- Applied Bioinformatics Laboratory (ASRT, Inc.; IHRC, Inc.), Atlanta, Georgia, USA
| | - Andrew Conley
- Applied Bioinformatics Laboratory (ASRT, Inc.; IHRC, Inc.), Atlanta, Georgia, USA
| | - David Sue
- Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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Law CTY, Nivesvivat T, Xiong Q, Kulkeaw K, Shi L, Ruenchit P, Suwanpakdee D, Suwanpakdee P, Tongkrajang N, Sarasombath PT, Tsui SKW. Mitochondrial genome diversity of Balamuthia mandrillaris revealed by a fatal case of granulomatous amoebic encephalitis. Front Microbiol 2023; 14:1162963. [PMID: 37213512 PMCID: PMC10196457 DOI: 10.3389/fmicb.2023.1162963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 04/06/2023] [Indexed: 05/23/2023] Open
Abstract
Introduction Balamuthia (B.) mandrillaris is a free-living amoeba that can cause rare yet fatal granulomatous amoebic encephalitis (GAE). However, efficacious treatment for GAE is currently unavailable, especially when genomic studies on B. mandrillaris are limited. Methods In this study, B. mandrillaris strain KM-20 was isolated from the brain tissue of a GAE patient, and its mitochondrial genome was de novo assembled using high-coverage Nanopore long reads and Illumina short reads. Results and Discussion Phylogenetic and comparative analyses revealed a range of diversification in the mitochondrial genome of KM-20 and nine other B. mandrillaris strains. According to the mitochondrial genome alignment, one of the most variable regions was observed in the ribosomal protein S3 (rps3), which was caused by an array of novel protein tandem repeats. The repeating units in the rps3 protein tandem region present significant copy number variations (CNVs) among B. mandrillaris strains and suggest KM-20 as the most divergent strain for its highly variable sequence and highest copy number in rps3. Moreover, mitochondrial heteroplasmy was observed in strain V039, and two genotypes of rps3 are caused by the CNVs in the tandem repeats. Taken together, the copy number and sequence variations of the protein tandem repeats enable rps3 to be a perfect target for clinical genotyping assay for B. mandrillaris. The mitochondrial genome diversity of B. mandrillaris paves the way to investigate the phylogeny and diversification of pathogenic amoebae.
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Affiliation(s)
- Cherie Tsz-Yiu Law
- School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Thirapa Nivesvivat
- Infectious Disease Unit, Department of Pediatrics, Phramongkutklao Hospital, Bangkok, Thailand
| | - Qing Xiong
- School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Kasem Kulkeaw
- Siriraj Integrative Center for Neglected Parasitic Diseases, Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Ling Shi
- School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Pichet Ruenchit
- Siriraj Integrative Center for Neglected Parasitic Diseases, Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Detchvijitr Suwanpakdee
- Infectious Disease Unit, Department of Pediatrics, Phramongkutklao Hospital, Bangkok, Thailand
| | - Piradee Suwanpakdee
- Neurology Division, Department of Pediatrics, Phramongkutklao Hospital, Bangkok, Thailand
| | - Nongnat Tongkrajang
- Siriraj Integrative Center for Neglected Parasitic Diseases, Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Patsharaporn T. Sarasombath
- Siriraj Integrative Center for Neglected Parasitic Diseases, Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Patsharaporn T. Sarasombath, ;
| | - Stephen Kwok-Wing Tsui
- School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- *Correspondence: Stephen Kwok-Wing Tsui,
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Zimenkov D. Variability of Mycobacterium avium Complex Isolates Drug Susceptibility Testing by Broth Microdilution. Antibiotics (Basel) 2022; 11:antibiotics11121756. [PMID: 36551413 PMCID: PMC9774755 DOI: 10.3390/antibiotics11121756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 11/30/2022] [Accepted: 11/30/2022] [Indexed: 12/09/2022] Open
Abstract
Non-tuberculous mycobacteria are widely distributed in environments and are capable of infecting humans, particularly those with a compromised immune system. The most prevalent species that cause nontuberculous mycobacterial lung diseases are slow-growing bacteria from the Mycobacterium avium complex (MAC), mainly M. avium or M. intracellulare. The key treatment of MAC infections includes macrolides, ethambutol, and rifampicin; however, the therapy outcomes are unsatisfactory. Phenotypic drug susceptibility testing is a conditional recommendation prior to treatment, and critical concentrations for clarithromycin, amikacin, moxifloxacin, and linezolid have been established. In this review, data from studies on the determination of MIC of clinical isolates using the broth microdilution method were summarized. A significant variation in the MIC distributions from different studies was found. The main reasons could impact the findings: insufficient reproducibility of the phenotypic testing and variation in species lineages identified in different laboratories, which could have various intrinsic susceptibility to drugs. For most of the drugs analyzed, the MICs are too high, which could undermine the treatment efficiency. Further improvement of treatment outcomes demands the validation of microbiological resistance criteria together with the identification of molecular mechanisms of resistance.
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Affiliation(s)
- Danila Zimenkov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
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Goltermann L, Andersen KL, Johansen HK, Molin S, La Rosa R. Macrolide therapy in Pseudomonas aeruginosa infections causes uL4 ribosomal protein mutations leading to high-level resistance. Clin Microbiol Infect 2022; 28:1594-1601. [PMID: 35988850 DOI: 10.1016/j.cmi.2022.08.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 07/05/2022] [Accepted: 08/06/2022] [Indexed: 01/26/2023]
Abstract
OBJECTIVES Pseudomonas aeruginosa colonizes the cystic fibrosis (CF) airways causing chronic bacterial lung infections. CF patients are routinely treated with macrolides, however, P. aeruginosa is considered insusceptible as consequence of inadequate susceptibility testing leaving resistance mechanism completely overlooked. Here, we investigated a new mechanism of macrolide resistance caused by ribosomal protein mutations. METHODS Investigating a longitudinal collection of 529 isolates from CF patients and analysing 5758 protein sequences from different sources, mutations in P. aeruginosa's ribosomal proteins connected to macrolide resistance were identified. Using a modified susceptibility testing protocol, isolates harbouring a mutated uL4 ribosomal protein were tested for resistance against macrolide antibiotics and macrolide-induced quorum sensing modulation. Proteome and ribosome profiling were applied to assess the impact of the mutations on the bacterial physiology. RESULTS Five uL4 mutations were identified in isolates from different CF patients. Most mapped to the conserved loop region of uL4 and resulted in increased macrolide tolerance (>10-fold relative to wt strains). Greater concentrations (>10-fold) of macrolide antibiotic were needed to inhibit the growth, reduce swimming motility, and induce redox sensitivity of the uL4 mutants. 16 proteins involved in ribosome adaptation displayed altered expression possibly to compensate for the uL4 mutations, which changed the ribosome stoichiometry without negatively affecting bacterial physiology. CONCLUSIONS Macrolide antibiotics should, therefore, be considered as active antimicrobial agents against P. aeruginosa and resistance development should be contemplated when patients are treated with prolonged courses of macrolides. Importantly, improved macrolide susceptibility testing is necessary for the detection of resistant bacteria.
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Affiliation(s)
- Lise Goltermann
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark.
| | | | - Helle Krogh Johansen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark; Department of Clinical Microbiology 9301, Rigshospitalet, 2100, Copenhagen, Denmark; Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Søren Molin
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Ruggero La Rosa
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark.
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Multiple Mechanisms Confer Resistance to Azithromycin in Shigella in Bangladesh: a Comprehensive Whole Genome-Based Approach. Microbiol Spectr 2022; 10:e0074122. [PMID: 35876510 PMCID: PMC9430107 DOI: 10.1128/spectrum.00741-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Shigella is the second leading cause of diarrheal deaths worldwide. Azithromycin (AZM) is a potential treatment option for Shigella infection; however, the recent emergence of AZM resistance in Shigella threatens the current treatment strategy. Therefore, we conducted a comprehensive whole genome-based approach to identify the mechanism(s) of AZM resistance in Shigella. We performed antimicrobial susceptibility tests, polymerase chain reaction (PCR), Sanger (amplicon) sequencing, and whole genome-based bioinformatics approaches to conduct the study. Fifty-seven (38%) of the Shigella isolates examined were AZM resistant; Shigella sonnei exhibited the highest rate of resistance against AZM (80%). PCR amplification for 15 macrolide resistance genes (MRGs) followed by whole-genome analysis of 13 representative Shigella isolates identified two AZM-modifying genes, mph(A) (in all Shigella isolates resistant to AZM) and mph(E) (in 2 AZM-resistant Shigella isolates), as well as one 23S rRNA-methylating gene, erm(B) (41% of AZM-resistant Shigella isolates) and one efflux pump mediator gene, msr(E) [in the same two Shigella isolates that harbored the mph(E) gene]. This is the first report of msr(E) and mph(E) genes in Shigella. Moreover, we found that an IncFII-type plasmid predominates and can possess all four MRGs. We also detected two plasmid-borne resistance gene clusters: IS26-mph(A)-mrx(A)-mph(R)(A)-IS6100, which is linked to global dissemination of MRGs, and mph(E)-msr(E)-IS482-IS6, which is reported for the first time in Shigella. In conclusion, this study demonstrates that MRGs in association with pathogenic IS6 family insertion sequences generate resistance gene clusters that propagate through horizontal gene transfer (HGT) in Shigella. IMPORTANCEShigella can frequently transform into a superbug due to uncontrolled and rogue administration of antibiotics and the emergence of HGT of antimicrobial resistance factors. The advent of AZM resistance in Shigella has become a serious concern in the treatment of shigellosis. However, there is an obvious scarcity of clinical data and research on genetic mechanisms that induce AZM resistance in Shigella, particularly in low- and middle-income countries. Therefore, this study is an approach to raise the alarm for the next lifeline. We show that two key MRGs [mph(A) and erm(B)] and the newly identified MRGs [mph(E) and msr(E)], with their origination in plasmid-borne pathogenic islands, are fundamental mechanisms of AZM resistance in Shigella in Bangladesh. Overall, this study predicts an abrupt decrease in the effectiveness of AZM against Shigella in the very near future and suggests prompt focus on seeking a more effective treatment alternative to AZM for shigellosis.
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Handel F, Kulik A, Wex KW, Berscheid A, Saur J, Winkler A, Wibberg D, Kalinowski J, Brötz-Oesterhelt H, Mast Y. Ψ-Footprinting approach for the identification of protein synthesis inhibitor producers. NAR Genom Bioinform 2022; 4:lqac055. [PMID: 35855324 PMCID: PMC9290621 DOI: 10.1093/nargab/lqac055] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 06/21/2022] [Accepted: 07/06/2022] [Indexed: 11/20/2022] Open
Abstract
Today, one of the biggest challenges in antibiotic research is a targeted prioritization of natural compound producer strains and an efficient dereplication process to avoid undesired rediscovery of already known substances. Thereby, genome sequence-driven mining strategies are often superior to wet-lab experiments because they are generally faster and less resource-intensive. In the current study, we report on the development of a novel in silico screening approach to evaluate the genetic potential of bacterial strains to produce protein synthesis inhibitors (PSI), which was termed the protein synthesis inhibitor ('psi’) target gene footprinting approach = Ψ-footprinting. The strategy is based on the occurrence of protein synthesis associated self-resistance genes in genome sequences of natural compound producers. The screening approach was applied to 406 genome sequences of actinomycetes strains from the DSMZ strain collection, resulting in the prioritization of 15 potential PSI producer strains. For twelve of them, extract samples showed protein synthesis inhibitory properties in in vitro transcription/translation assays. For four strains, namely Saccharopolyspora flava DSM 44771, Micromonospora aurantiaca DSM 43813, Nocardioides albertanoniae DSM 25218, and Geodermatophilus nigrescens DSM 45408, the protein synthesis inhibitory substance amicoumacin was identified by HPLC-MS analysis, which proved the functionality of the in silico screening approach.
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Affiliation(s)
- Franziska Handel
- Department of Microbiology/Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine, Faculty of Science, University of Tübingen , Auf der Morgenstelle 28, 72076 Tübingen, Germany
- German Center for Infection Research (DZIF) , Partner Site Tübingen, Tübingen , Germany
| | - Andreas Kulik
- Department of Microbiology/Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine, Faculty of Science, University of Tübingen , Auf der Morgenstelle 28, 72076 Tübingen, Germany
- Department of Microbial Bioactive Compounds; Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen ; Tübingen , Baden-Württemberg 72076 , Germany
| | - Katharina W Wex
- Department of Microbial Bioactive Compounds; Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen ; Tübingen , Baden-Württemberg 72076 , Germany
- German Center for Infection Research (DZIF) , Partner Site Tübingen, Tübingen , Germany
| | - Anne Berscheid
- Department of Microbial Bioactive Compounds; Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen ; Tübingen , Baden-Württemberg 72076 , Germany
- German Center for Infection Research (DZIF) , Partner Site Tübingen, Tübingen , Germany
| | - Julian S Saur
- Biomolecular Chemistry, Institute of Organic Chemistry, University of Tübingen , Tübingen , Baden-Württemberg 72076 , Germany
| | - Anika Winkler
- Center for Biotechnology (CeBiTec), Bielefeld University , Universitätsstraße 27, 33615 Bielefeld , Germany
| | - Daniel Wibberg
- Center for Biotechnology (CeBiTec), Bielefeld University , Universitätsstraße 27, 33615 Bielefeld , Germany
| | - Jörn Kalinowski
- Center for Biotechnology (CeBiTec), Bielefeld University , Universitätsstraße 27, 33615 Bielefeld , Germany
| | - Heike Brötz-Oesterhelt
- Department of Microbial Bioactive Compounds; Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen ; Tübingen , Baden-Württemberg 72076 , Germany
- German Center for Infection Research (DZIF) , Partner Site Tübingen, Tübingen , Germany
- Cluster of Excellence Controlling Microbes to Fight Infection , Germany
| | - Yvonne Mast
- Department of Microbiology/Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine, Faculty of Science, University of Tübingen , Auf der Morgenstelle 28, 72076 Tübingen, Germany
- German Center for Infection Research (DZIF) , Partner Site Tübingen, Tübingen , Germany
- Department Bioresources for Bioeconomy and Health Research, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures , Inhoffenstraße 7B, 38124 Braunschweig , Germany
- Technical University Braunschweig, Department of Microbiology , Rebenring 56, 38106 Braunschweig , Germany
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A Survey of Spontaneous Antibiotic-Resistant Mutants of the Halophilic, Thermophilic Bacterium Rhodothermus marinus. Antibiotics (Basel) 2021; 10:antibiotics10111384. [PMID: 34827322 PMCID: PMC8614978 DOI: 10.3390/antibiotics10111384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 11/08/2021] [Accepted: 11/10/2021] [Indexed: 11/17/2022] Open
Abstract
Rhodothermus marinus is a halophilic extreme thermophile, with potential as a model organism for studies of the structural basis of antibiotic resistance. In order to facilitate genetic studies of this organism, we have surveyed the antibiotic sensitivity spectrum of R. marinus and identified spontaneous antibiotic-resistant mutants. R. marinus is naturally insensitive to aminoglycosides, aminocylitols and tuberactinomycins that target the 30S ribosomal subunit, but is sensitive to all 50S ribosomal subunit-targeting antibiotics examined, including macrolides, lincosamides, streptogramin B, chloramphenicol, and thiostrepton. It is also sensitive to kirromycin and fusidic acid, which target protein synthesis factors. It is sensitive to rifampicin (RNA polymerase inhibitor) and to the fluoroquinolones ofloxacin and ciprofloxacin (DNA gyrase inhibitors), but insensitive to nalidixic acid. Drug-resistant mutants were identified using rifampicin, thiostrepton, erythromycin, spiramycin, tylosin, lincomycin, and chloramphenicol. The majority of these were found to have mutations that are similar or identical to those previously found in other species, while several novel mutations were identified. This study provides potential selectable markers for genetic manipulations and demonstrates the feasibility of using R. marinus as a model system for studies of ribosome and RNA polymerase structure, function, and evolution.
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Mutational Activation of Antibiotic-Resistant Mechanisms in the Absence of Major Drug Efflux Systems of Escherichia coli. J Bacteriol 2021; 203:e0010921. [PMID: 33972351 DOI: 10.1128/jb.00109-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mutations are one of the common means by which bacteria acquire resistance to antibiotics. In an Escherichia coli mutant lacking major antibiotic efflux pumps AcrAB and AcrEF, mutations can activate alternative pathways that lead to increased antibiotic resistance. In this work, we isolated and characterized compensatory mutations of this nature mapping in four different regulatory genes, baeS, crp, hns, and rpoB. The gain-of-function mutations in baeS constitutively activated the BaeSR two-component regulatory system to increase the expression of the MdtABC efflux pump. Missense or insertion mutations in crp and hns caused derepression of an operon coding for the MdtEF efflux pump. Interestingly, despite the dependence of rpoB missense mutations on MdtABC for their antibiotic resistance phenotype, neither the expression of the mdtABCD-baeSR operon nor that of other known antibiotic efflux pumps went up. Instead, the transcriptome sequencing (RNA-seq) data revealed a gene expression profile resembling that of a "stringent" RNA polymerase where protein and DNA biosynthesis pathways were downregulated but pathways to combat various stresses were upregulated. Some of these activated stress pathways are also controlled by the general stress sigma factor RpoS. The data presented here also show that compensatory mutations can act synergistically to further increase antibiotic resistance to a level similar to the efflux pump-proficient parental strain. Together, the findings highlight a remarkable genetic ability of bacteria to circumvent antibiotic assault, even in the absence of a major intrinsic antibiotic resistance mechanism. IMPORTANCE Antibiotic resistance among bacterial pathogens is a chronic health concern. Bacteria possess or acquire various mechanisms of antibiotic resistance, and chief among them is the ability to accumulate beneficial mutations that often alter antibiotic targets. Here, we explored E. coli's ability to amass mutations in a background devoid of a major constitutively expressed efflux pump and identified mutations in several regulatory genes that confer resistance by activating specific or pleiotropic mechanisms.
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Balbontín R, Frazão N, Gordo I. DNA Breaks-Mediated Fitness Cost Reveals RNase HI as a New Target for Selectively Eliminating Antibiotic-Resistant Bacteria. Mol Biol Evol 2021; 38:3220-3234. [PMID: 33830249 PMCID: PMC8321526 DOI: 10.1093/molbev/msab093] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Antibiotic resistance often generates defects in bacterial growth called fitness cost. Understanding the causes of this cost is of paramount importance, as it is one of the main determinants of the prevalence of resistances upon reducing antibiotics use. Here we show that the fitness costs of antibiotic resistance mutations that affect transcription and translation in Escherichia coli strongly correlate with DNA breaks, which are generated via transcription–translation uncoupling, increased formation of RNA–DNA hybrids (R-loops), and elevated replication–transcription conflicts. We also demonstrated that the mechanisms generating DNA breaks are repeatedly targeted by compensatory evolution, and that DNA breaks and the cost of resistance can be increased by targeting the RNase HI, which specifically degrades R-loops. We further show that the DNA damage and thus the fitness cost caused by lack of RNase HI function drive resistant clones to extinction in populations with high initial frequency of resistance, both in laboratory conditions and in a mouse model of gut colonization. Thus, RNase HI provides a target specific against resistant bacteria, which we validate using a repurposed drug. In summary, we revealed key mechanisms underlying the fitness cost of antibiotic resistance mutations that can be exploited to specifically eliminate resistant bacteria.
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Affiliation(s)
| | | | - Isabel Gordo
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
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Salehi N, Attaran B, Zare-Mirakabad F, Ghadiri B, Esmaeili M, Shakaram M, Tashakoripour M, Eshagh Hosseini M, Mohammadi M. The outward shift of clarithromycin binding to the ribosome in mutant Helicobacter pylori strains. Helicobacter 2020; 25:e12731. [PMID: 32794288 DOI: 10.1111/hel.12731] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 06/30/2020] [Accepted: 07/03/2020] [Indexed: 02/06/2023]
Abstract
OBJECTIVES Disruption of protein synthesis, by drug-mediated restriction of the ribosomal nascent peptide exit tunnel (NPET), may inhibit bacterial growth. Here, we have studied the secondary and tertiary structures of domain V of the 23S rRNA in the wild-type and mutant (resistant) H. pylori strains and their mechanisms of interaction with clarithromycin (CLA). METHODS H pylori strains, isolated from cultured gastric biopsies, underwent CLA susceptibility testing by E test, followed by PCR amplification and sequencing of domain V of 23S rRNA. The homology model of this domain in H pylori, in complex with L4 and L22 accessory proteins, was determined based on the E. coli ribosome 3D structure. The interactions between CLA and 23S rRNA complex were determined by molecular docking studies. RESULTS Of the 70 H pylori strains, isolated from 200 dyspeptic patients, 11 (16%) were CLA-resistant. DNA sequencing identified categories with no (A), A2142G (B), and A2143G (C) mutations. Docking studies of our homology model of 23S rRNA complex with CLA showed deviated positions for categories B and C, in reference to category A, with 12.19 Å and 7.92 Å RMSD values, respectively. In both mutant categories, CLA lost its interactions at positions 2142 and 2587 and gained two new bonds with the L4 accessory protein. CONCLUSION Our data suggest that, in mutant H pylori strains, once the nucleotides at positions 2142 and 2587 are detached from the drug, CLA interacts with and is peeled back by the L4 accessory protein, removing the drug-imposed spatial restriction of the NPET.
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Affiliation(s)
- Najmeh Salehi
- Department of Bioinformatics, Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Bahareh Attaran
- HPGC Research Group, Department of Medical Biotechnology, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran.,Department of Microbiology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran
| | - Fatemeh Zare-Mirakabad
- Department of Mathematics and Computer Science, Amirkabir University of Technology, Tehran, Iran
| | - Bahareh Ghadiri
- HPGC Research Group, Department of Medical Biotechnology, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Maryam Esmaeili
- HPGC Research Group, Department of Medical Biotechnology, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Mohadeseh Shakaram
- HPGC Research Group, Department of Medical Biotechnology, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Mohammad Tashakoripour
- Gastroenterology Department, Amiralam Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Mahmoud Eshagh Hosseini
- Gastroenterology Department, Amiralam Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Marjan Mohammadi
- HPGC Research Group, Department of Medical Biotechnology, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
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Lynch CT, Lynch H, Burke S, Hawkins K, Buttimer C, Mc Carthy C, Egan J, Whyte P, Bolton D, Coffey A, Lucey B. Antimicrobial Resistance Determinants Circulating among Thermophilic Campylobacter Isolates Recovered from Broilers in Ireland Over a One-Year Period. Antibiotics (Basel) 2020; 9:E308. [PMID: 32521746 PMCID: PMC7344827 DOI: 10.3390/antibiotics9060308] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 06/04/2020] [Accepted: 06/05/2020] [Indexed: 02/07/2023] Open
Abstract
Campylobacteriosis is the leading cause of human bacterial gastroenteritis, very often associated with poultry consumption. Thermophilic Campylobacter (Campylobacter jejuni and Campylobacter coli) isolates (n = 158) recovered from broiler neck skin and caecal contents in Ireland over a one-year period, resistant to at least one of three clinically relevant antimicrobial classes, were screened for resistance determinants. All ciprofloxacin-resistant isolates (n = 99) harboured the C257T nucleotide mutation (conferring the Thr-86-Ile substitution) in conjunction with other synonymous and nonsynonymous mutations, which may have epidemiological value. The A2075G nucleotide mutation and amino acid substitutions in L4 and L22 were detected in all erythromycin-resistant isolates (n = 5). The tetO gene was detected in 100% (n = 119) of tetracycline-resistant isolates and three of which were found to harbour the mosaic tetracycline resistance gene tetO/32/O. Two streptomycin-resistant C. jejuni isolates (isolated from the same flock) harboured ant(6)-Ib, located in a multidrug resistance genomic island, containing aminoglycoside, streptothricin (satA) and tetracycline resistance genes (truncated tetO and mosaic tetO/32/O). The ant(6)-Ie gene was identified in two streptomycin-resistant C. coli isolates. This study highlights the widespread acquisition of antimicrobial resistance determinants among chicken-associated Campylobacter isolates, through horizontal gene transfer or clonal expansion of resistant lineages. The stability of such resistance determinants is compounded by the fluidity of mobile genetic element.
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Affiliation(s)
- Caoimhe T. Lynch
- Department of Biological Sciences, Cork Institute of Technology, Bishopstown, T12 P928 Cork, Ireland; (C.T.L.); (S.B.); (K.H.); (C.M.C.); (A.C.)
| | - Helen Lynch
- NRL Campylobacter, Backweston Laboratory Complex, Young’s Cross, Celbridge, W23 X3PH Kildare, Ireland; (H.L.); (J.E.)
- School of Veterinary Medicine, University College Dublin, Belfield, D04 V1W8 Dublin 4, Ireland;
| | - Sarah Burke
- Department of Biological Sciences, Cork Institute of Technology, Bishopstown, T12 P928 Cork, Ireland; (C.T.L.); (S.B.); (K.H.); (C.M.C.); (A.C.)
| | - Kayleigh Hawkins
- Department of Biological Sciences, Cork Institute of Technology, Bishopstown, T12 P928 Cork, Ireland; (C.T.L.); (S.B.); (K.H.); (C.M.C.); (A.C.)
| | - Colin Buttimer
- APC Microbiome Ireland, University College Cork, T12 YT20 Cork, Ireland;
| | - Conor Mc Carthy
- Department of Biological Sciences, Cork Institute of Technology, Bishopstown, T12 P928 Cork, Ireland; (C.T.L.); (S.B.); (K.H.); (C.M.C.); (A.C.)
| | - John Egan
- NRL Campylobacter, Backweston Laboratory Complex, Young’s Cross, Celbridge, W23 X3PH Kildare, Ireland; (H.L.); (J.E.)
| | - Paul Whyte
- School of Veterinary Medicine, University College Dublin, Belfield, D04 V1W8 Dublin 4, Ireland;
| | - Declan Bolton
- Teagasc Food Research Centre, Ashtown, D15 DY05 Dublin 15, Ireland;
| | - Aidan Coffey
- Department of Biological Sciences, Cork Institute of Technology, Bishopstown, T12 P928 Cork, Ireland; (C.T.L.); (S.B.); (K.H.); (C.M.C.); (A.C.)
- APC Microbiome Ireland, University College Cork, T12 YT20 Cork, Ireland;
| | - Brigid Lucey
- Department of Biological Sciences, Cork Institute of Technology, Bishopstown, T12 P928 Cork, Ireland; (C.T.L.); (S.B.); (K.H.); (C.M.C.); (A.C.)
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12
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Noda M, Danshiitsoodol N, Inoue Y, Okamoto T, Sultana N, Sugiyama M. Antibiotic susceptibility of plant-derived lactic acid bacteria conferring health benefits to human. J Antibiot (Tokyo) 2019; 72:834-842. [PMID: 31399643 DOI: 10.1038/s41429-019-0218-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Revised: 07/09/2019] [Accepted: 07/25/2019] [Indexed: 12/29/2022]
Abstract
Lactic acid bacteria (LAB) confer health benefits to human when administered orally. We have recently isolated several species of LAB strains from plant sources, such as fruits, vegetables, flowers, and medicinal plants. Since antibiotics used to treat bacterial infection diseases induce the emergence of drug-resistant bacteria in intestinal microflora, it is important to evaluate the susceptibility of LAB strains to antibiotics to ensure the safety and security of processed foods. The aim of the present study is to determine the minimum inhibitory concentration (MIC) of antibiotics against several plant-derived LAB strains. When aminoglycoside antibiotics, such as streptomycin (SM), kanamycin (KM), and gentamicin (GM), were evaluated using LAB susceptibility test medium (LSM), the MIC was higher than when using Mueller-Hinton (MH) medium. Etest, which is an antibiotic susceptibility assay method consisting of a predefined gradient of antibiotic concentrations on a plastic strip, is used to determine the MIC of antibiotics world-wide. In the present study, we demonstrated that Etest was particularly valuable while testing LAB strains. We also show that the low susceptibility of the plant-derived LAB strains against each antibiotic tested is due to intrinsic resistance and not acquired resistance. This finding is based on the whole-genome sequence information reflecting the horizontal spread of the drug-resistance genes in the LAB strains.
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Affiliation(s)
- Masafumi Noda
- Department of Probiotic Science for Preventive Medicine, Graduate School of Biomedical and Health Sciences, Hiroshima University, Kasumi 1-2-3, Minami-ku, Hiroshima, 734-8551, Japan
| | - Narandalai Danshiitsoodol
- Department of Probiotic Science for Preventive Medicine, Graduate School of Biomedical and Health Sciences, Hiroshima University, Kasumi 1-2-3, Minami-ku, Hiroshima, 734-8551, Japan
| | - Yusuke Inoue
- Mitsui Sugar Co., Ltd., Hakozaki-cho 36-2, Nihonbashi, Chuo-ku, Tokyo, 103-0015, Japan
| | - Tomoko Okamoto
- Department of Probiotic Science for Preventive Medicine, Graduate School of Biomedical and Health Sciences, Hiroshima University, Kasumi 1-2-3, Minami-ku, Hiroshima, 734-8551, Japan
| | - Nasrin Sultana
- Department of Probiotic Science for Preventive Medicine, Graduate School of Biomedical and Health Sciences, Hiroshima University, Kasumi 1-2-3, Minami-ku, Hiroshima, 734-8551, Japan
| | - Masanori Sugiyama
- Department of Probiotic Science for Preventive Medicine, Graduate School of Biomedical and Health Sciences, Hiroshima University, Kasumi 1-2-3, Minami-ku, Hiroshima, 734-8551, Japan.
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13
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Structure of Dirithromycin Bound to the Bacterial Ribosome Suggests New Ways for Rational Improvement of Macrolides. Antimicrob Agents Chemother 2019; 63:AAC.02266-18. [PMID: 30936109 DOI: 10.1128/aac.02266-18] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Accepted: 03/19/2019] [Indexed: 11/20/2022] Open
Abstract
Although macrolides are known as excellent antibacterials, their medical use has been significantly limited due to the spread of bacterial drug resistance. Therefore, it is necessary to develop new potent macrolides to combat the emergence of drug-resistant pathogens. One of the key steps in rational drug design is the identification of chemical groups that mediate binding of the drug to its target and their subsequent derivatization to strengthen drug-target interactions. In the case of macrolides, a few groups are known to be important for drug binding to the ribosome, such as desosamine. Search for new chemical moieties that improve the interactions of a macrolide with the 70S ribosome might be of crucial importance for the invention of new macrolides. For this purpose, here we studied a classic macrolide, dirithromycin, which has an extended (2-methoxyethoxy)-methyl side chain attached to the C-9/C-11 atoms of the macrolactone ring that can account for strong binding of dirithromycin to the 70S ribosome. By solving the crystal structure of the 70S ribosome in complex with dirithromycin, we found that its side chain interacts with the wall of the nascent peptide exit tunnel in an idiosyncratic fashion: its side chain forms a lone pair-π stacking interaction with the aromatic imidazole ring of the His69 residue in ribosomal protein uL4. To our knowledge, the ability of this side chain to form a contact in the macrolide binding pocket has not been reported previously and potentially can open new avenues for further exploration by medicinal chemists developing next-generation macrolide antibiotics active against resistant pathogens.
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14
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Increased freedom of movement in the nascent chain results in dynamic changes in the structure of the SecM arrest motif. Biosci Rep 2019; 39:BSR20181246. [PMID: 30563926 PMCID: PMC6340945 DOI: 10.1042/bsr20181246] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 12/07/2018] [Accepted: 12/07/2018] [Indexed: 12/13/2022] Open
Abstract
Ribosomes are responsible for the synthesis of all cellular proteins. Due to the diversity of sequence and properties, it was initially believed that translating nascent chains would travel unhindered through the ribosome exit tunnel, however a small but increasing number of proteins have been identified that interact with the exit tunnel to induce translational arrest, Escherichia coli (E. coli) secretion monitor (SecM) is one such stalling peptide. How and why these peptides interact with the exit tunnel is not fully understood, however key features required for stalling appear to be an essential peptide arrest motif at the C-terminus and compaction of the nascent chain within the exit tunnel upon stalling. Mutagenesis of the SecM arrest sequence has identified three conservative point mutations that can retain a degree of stalling in this highly conserved sequence. This level of stalling is further increased when coupled with mutation of a non-essential arrest motif residue P153A. Further analysis of these mutants by pegylation assays indicates that this increase in stalling activity during translation is due to the ability of the P153A mutation to reintroduce compaction of the nascent chain within the exit tunnel possibly due to the improved flexibility of the nascent chain provided by the removal of a restrictive proline residue. The data presented here suggest that arrest sequences may be more prevalent and less highly conserved than previously thought, and highlight the significance of the interactions between the nascent chain and the exit tunnel to affecting translation arrest.
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15
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Han D, Liu Y, Li J, Liu C, Gao Y, Feng J, Lu H, Yang G. Twenty-seven-nucleotide repeat insertion in the rplV gene confers specific resistance to macrolide antibiotics in Staphylococcus aureus. Oncotarget 2018; 9:26086-26095. [PMID: 29899844 PMCID: PMC5995244 DOI: 10.18632/oncotarget.25441] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 04/28/2018] [Indexed: 11/29/2022] Open
Abstract
Macrolide antibiotics are used for treatment of soft-tissue infection caused by Staphylococcus aureus in humans. However, infections with S. aureus are increasingly difficult to treat owing to the emergence and rapid spread of multiple-drug resistant S. aureus. Resistance to macrolide in S. aureus is mostly due to the modification of 23 S rRNA by methylases encoded by erm genes. Here, we have identified that a 27-nucleotide repeat sequence insertion in the rplV gene induced a specific resistance to macrolide antibiotics. An erythromycin-resistant strain, 8325ER+, was screened by resistance to erythromycin from the macrolide-sensitive strain 8325-4. Comparative genome sequencing analysis showed that 8325ER+ contained a 27-nt repeat sequence insertion in the rplV gene that encodes the ribosomal protein L22, when compared to its parent strain. The 27-nt repeat sequence led to an insertion of 9 amino acids in L22, which had been identified to reduce the sensitivity to erythromycin and other macrolide antibiotics. Moreover, we show that the ectopic expression of the mutated rplV gene containing the 27-nt repeat sequence insertion in several susceptible strains specifically conferred resistance to macrolide antibiotics. Our findings present a potential mechanism of resistance to macrolide antibiotics in S. aureus.
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Affiliation(s)
- Dianpeng Han
- Beijing Institute of Basic Medical Sciences, Beijing, China.,State Key Laboratory of Toxicology and Medical Countermeasures, Beijing, China
| | - Yu Liu
- Beijing Institute of Basic Medical Sciences, Beijing, China.,State Key Laboratory of Toxicology and Medical Countermeasures, Beijing, China
| | - Jingjing Li
- Henan University School of Basic Medical Science, Kaifeng, China
| | - Chenghua Liu
- Beijing Institute of Basic Medical Sciences, Beijing, China.,State Key Laboratory of Toxicology and Medical Countermeasures, Beijing, China
| | - Yaping Gao
- Beijing Institute of Basic Medical Sciences, Beijing, China.,State Key Laboratory of Toxicology and Medical Countermeasures, Beijing, China
| | - Jiannan Feng
- Beijing Institute of Basic Medical Sciences, Beijing, China.,State Key Laboratory of Toxicology and Medical Countermeasures, Beijing, China
| | - Huizhe Lu
- Department of Applied Chemistry, College of Science, China Agricultural University, Beijing, China
| | - Guang Yang
- Beijing Institute of Basic Medical Sciences, Beijing, China.,State Key Laboratory of Toxicology and Medical Countermeasures, Beijing, China
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16
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Nikulin AD. Structural Aspects of Ribosomal RNA Recognition by Ribosomal Proteins. BIOCHEMISTRY (MOSCOW) 2018; 83:S111-S133. [DOI: 10.1134/s0006297918140109] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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17
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Antibiotic resistance trends and mechanisms in the foodborne pathogen,Campylobacter. Anim Health Res Rev 2017; 18:87-98. [DOI: 10.1017/s1466252317000135] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
AbstractCampylobacteris a major foodborne pathogen and is commonly present in food producing animals. This pathogenic organism is highly adaptable and has become increasingly resistant to various antibiotics. Recently, both the Centers for Disease Control and Prevention and the World Health Organization have designated antibiotic-resistantCampylobacteras a serious threat to public health. For the past decade, multiple mechanisms conferring resistance to clinically important antibiotics have been described inCampylobacter, and new resistance mechanisms constantly emerge in the pathogen. Some of the recent examples include theerm(B)gene conferring macrolide resistance, thecfr(C)genes mediating resistance to florfenicol and other antimicrobials, and a functionally enhanced variant of the multidrug resistance efflux pump, CmeABC. The continued emergence of new resistance mechanisms illustrates the extraordinary adaptability ofCampylobacterto antibiotic selection pressure and demonstrate the need for innovative strategies to control antibiotic-resistantCampylobacter. In this review, we will briefly summarize the trends of antibiotic resistance inCampylobacterand discuss the mechanisms of resistance to antibiotics used for animal production and important for clinical therapy in humans. A special emphasis will be given to the newly discovered antibiotic resistance.
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18
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Florin T, Maracci C, Graf M, Karki P, Klepacki D, Berninghausen O, Beckmann R, Vázquez-Laslop N, Wilson DN, Rodnina MV, Mankin AS. An antimicrobial peptide that inhibits translation by trapping release factors on the ribosome. Nat Struct Mol Biol 2017; 24:752-757. [PMID: 28741611 PMCID: PMC5589491 DOI: 10.1038/nsmb.3439] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 06/21/2017] [Indexed: 12/12/2022]
Abstract
Many antibiotics stop bacterial growth by inhibiting different steps of protein synthesis. However, no specific inhibitors of translation termination are known. Proline-rich antimicrobial peptides, a component of the antibacterial defense system of multicellular organisms, interfere with bacterial growth by inhibiting translation. Here we show that Api137, a derivative of the insect-produced antimicrobial peptide apidaecin, arrests terminating ribosomes using a unique mechanism of action. Api137 binds to the Escherichia coli ribosome and traps release factors 1 or 2 subsequent to release of the nascent polypeptide chain. A high-resolution cryo-EM structure of the ribosome complexed with release factor 1 and Api137 reveals the molecular interactions that lead to release factor trapping. Api137-mediated depletion of the cellular pool of free release factors causes the majority of ribosomes to stall at stop codons prior to polypeptide release, thereby resulting in a global shutdown of translation termination.
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Affiliation(s)
- Tanja Florin
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Cristina Maracci
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Michael Graf
- Gene Center, Department for Biochemistry and Center for Protein Science Munich (CiPSM), University of Munich, Munich, Germany
| | - Prajwal Karki
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Dorota Klepacki
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Otto Berninghausen
- Gene Center, Department for Biochemistry and Center for Protein Science Munich (CiPSM), University of Munich, Munich, Germany
| | - Roland Beckmann
- Gene Center, Department for Biochemistry and Center for Protein Science Munich (CiPSM), University of Munich, Munich, Germany
| | - Nora Vázquez-Laslop
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Daniel N Wilson
- Gene Center, Department for Biochemistry and Center for Protein Science Munich (CiPSM), University of Munich, Munich, Germany.,Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | - Marina V Rodnina
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Alexander S Mankin
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, Illinois, USA
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19
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Wekselman I, Zimmerman E, Davidovich C, Belousoff M, Matzov D, Krupkin M, Rozenberg H, Bashan A, Friedlander G, Kjeldgaard J, Ingmer H, Lindahl L, Zengel JM, Yonath A. The Ribosomal Protein uL22 Modulates the Shape of the Protein Exit Tunnel. Structure 2017; 25:1233-1241.e3. [PMID: 28689968 DOI: 10.1016/j.str.2017.06.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 05/08/2017] [Accepted: 06/02/2017] [Indexed: 10/19/2022]
Abstract
Erythromycin is a clinically useful antibiotic that binds to an rRNA pocket in the ribosomal exit tunnel. Commonly, resistance to erythromycin is acquired by alterations of rRNA nucleotides that interact with the drug. Mutations in the β hairpin of ribosomal protein uL22, which is rather distal to the erythromycin binding site, also generate resistance to the antibiotic. We have determined the crystal structure of the large ribosomal subunit from Deinococcus radiodurans with a three amino acid insertion within the β hairpin of uL22 that renders resistance to erythromycin. The structure reveals a shift of the β hairpin of the mutated uL22 toward the interior of the exit tunnel, triggering a cascade of structural alterations of rRNA nucleotides that propagate to the erythromycin binding pocket. Our findings support recent studies showing that the interactions between uL22 and specific sequences within nascent chains trigger conformational rearrangements in the exit tunnel.
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Affiliation(s)
- Itai Wekselman
- Department of Structural Biology, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ella Zimmerman
- Department of Structural Biology, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Chen Davidovich
- Department of Structural Biology, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Matthew Belousoff
- Department of Structural Biology, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Donna Matzov
- Department of Structural Biology, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Miri Krupkin
- Department of Structural Biology, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Haim Rozenberg
- Department of Structural Biology, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Anat Bashan
- Department of Structural Biology, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Gilgi Friedlander
- The Ilana and Pascal Mantoux Institute for Bioinformatics, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Jette Kjeldgaard
- Department of Veterinary Disease Biology, University of Copenhagen, 1870 Frederiksbergc, Denmark
| | - Hanne Ingmer
- Department of Veterinary Disease Biology, University of Copenhagen, 1870 Frederiksbergc, Denmark
| | - Lasse Lindahl
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, MD 21250, USA
| | - Janice M Zengel
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, MD 21250, USA
| | - Ada Yonath
- Department of Structural Biology, The Weizmann Institute of Science, Rehovot 7610001, Israel.
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20
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Gomes C, Martínez-Puchol S, Palma N, Horna G, Ruiz-Roldán L, Pons MJ, Ruiz J. Macrolide resistance mechanisms in Enterobacteriaceae: Focus on azithromycin. Crit Rev Microbiol 2016; 43:1-30. [DOI: 10.3109/1040841x.2015.1136261] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Cláudia Gomes
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic ? Universitat de Barcelona, Spain
| | - Sandra Martínez-Puchol
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic ? Universitat de Barcelona, Spain
| | - Noemí Palma
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic ? Universitat de Barcelona, Spain
| | - Gertrudis Horna
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic ? Universitat de Barcelona, Spain
- Universidad Peruana Cayetano Heredia, Lima, Peru
| | | | - Maria J Pons
- Universidad Peruana de Ciencias Aplicadas, Lima, Peru
| | - Joaquim Ruiz
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic ? Universitat de Barcelona, Spain
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21
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Schroeder MR, Stephens DS. Macrolide Resistance in Streptococcus pneumoniae. Front Cell Infect Microbiol 2016; 6:98. [PMID: 27709102 PMCID: PMC5030221 DOI: 10.3389/fcimb.2016.00098] [Citation(s) in RCA: 116] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 08/26/2016] [Indexed: 01/21/2023] Open
Abstract
Streptococcus pneumoniae is a common commensal and an opportunistic pathogen. Suspected pneumococcal upper respiratory infections and pneumonia are often treated with macrolide antibiotics. Macrolides are bacteriostatic antibiotics and inhibit protein synthesis by binding to the 50S ribosomal subunit. The widespread use of macrolides is associated with increased macrolide resistance in S. pneumoniae, and the treatment of pneumococcal infections with macrolides may be associated with clinical failures. In S. pneumoniae, macrolide resistance is due to ribosomal dimethylation by an enzyme encoded by erm(B), efflux by a two-component efflux pump encoded by mef (E)/mel(msr(D)) and, less commonly, mutations of the ribosomal target site of macrolides. A wide array of genetic elements have emerged that facilitate macrolide resistance in S. pneumoniae; for example erm(B) is found on Tn917, while the mef (E)/mel operon is carried on the 5.4- or 5.5-kb Mega element. The macrolide resistance determinants, erm(B) and mef (E)/mel, are also found on large composite Tn916-like elements most notably Tn6002, Tn2009, and Tn2010. Introductions of 7-valent and 13-valent pneumococcal conjugate vaccines (PCV-7 and PCV-13) have decreased the incidence of macrolide-resistant invasive pneumococcal disease, but serotype replacement and emergence of macrolide resistance remain an important concern.
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Affiliation(s)
| | - David S Stephens
- Departments of Medicine, Emory UniversityAtlanta, GA, USA; Departments of Microbiology and Immunology, Emory UniversityAtlanta, GA, USA; Departments of Epidemiology, Emory UniversityAtlanta, GA, USA
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22
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Lemieux JE, Tran AD, Freimark L, Schaffner SF, Goethert H, Andersen KG, Bazner S, Li A, McGrath G, Sloan L, Vannier E, Milner D, Pritt B, Rosenberg E, Telford S, Bailey JA, Sabeti PC. A global map of genetic diversity in Babesia microti reveals strong population structure and identifies variants associated with clinical relapse. Nat Microbiol 2016; 1:16079. [PMID: 27572973 DOI: 10.1038/nmicrobiol.2016.79] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 04/28/2016] [Indexed: 11/09/2022]
Abstract
Human babesiosis caused by Babesia microti is an emerging tick-borne zoonosis of increasing importance due to its rising incidence and expanding geographic range(1). Infection with this organism, an intraerythrocytic parasite of the phylum Apicomplexa, causes a febrile syndrome similar to malaria(2). Relapsing disease is common among immunocompromised and asplenic individuals(3,4) and drug resistance has recently been reported(5). To investigate the origin and genetic diversity of this parasite, we sequenced the complete genomes of 42 B. microti samples from around the world, including deep coverage of clinical infections at endemic sites in the continental USA. Samples from the continental USA segregate into a Northeast lineage and a Midwest lineage, with subsequent divergence of subpopulations along geographic lines. We identify parasite variants that associate with relapsing disease, including amino acid substitutions in the atovaquone-binding regions of cytochrome b (cytb) and the azithromycin-binding region of ribosomal protein subunit L4 (rpl4). Our results shed light on the origin, diversity and evolution of B. microti, suggest possible mechanisms for clinical relapse, and create the foundation for further research on this emerging pathogen.
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Affiliation(s)
- Jacob E Lemieux
- The Broad Institute of MIT Division of Health Sciences and and MIT, Cambridge 02142, Massachusetts, USA.,Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
| | - Alice D Tran
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Lisa Freimark
- The Broad Institute of MIT Division of Health Sciences and and MIT, Cambridge 02142, Massachusetts, USA
| | - Stephen F Schaffner
- The Broad Institute of MIT Division of Health Sciences and and MIT, Cambridge 02142, Massachusetts, USA
| | - Heidi Goethert
- Tufts School of Veterinary Medicine, North Grafton, Massachusetts 01536, USA
| | - Kristian G Andersen
- The Broad Institute of MIT Division of Health Sciences and and MIT, Cambridge 02142, Massachusetts, USA.,The Scripps Research Institute, La Jolla, California 92037, USA
| | - Suzane Bazner
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
| | - Amy Li
- Koch Institute for Integrative Cancer Research at MIT, Cambridge, Massachusetts 02142, USA
| | - Graham McGrath
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
| | - Lynne Sloan
- Department of Pathology, The Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Edouard Vannier
- Division of Geographic Medicine and Infectious Disease, Tufts Medical Center, Boston, Massachusetts 02111, USA
| | - Dan Milner
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
| | - Bobbi Pritt
- Department of Pathology, The Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Eric Rosenberg
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts 02114, USA.,Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
| | - Sam Telford
- Tufts School of Veterinary Medicine, North Grafton, Massachusetts 01536, USA
| | - Jeffrey A Bailey
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA.,Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA
| | - Pardis C Sabeti
- The Broad Institute of MIT Division of Health Sciences and and MIT, Cambridge 02142, Massachusetts, USA.,Department of Evolutionary and Organismic Biology, MIT Division of Health Sciences and University, Cambridge, Massachusetts 02138, USA
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23
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Lawrence MG, Shamsuzzaman M, Kondopaka M, Pascual C, Zengel JM, Lindahl L. The extended loops of ribosomal proteins uL4 and uL22 of Escherichia coli contribute to ribosome assembly and protein translation. Nucleic Acids Res 2016; 44:5798-810. [PMID: 27257065 PMCID: PMC4937340 DOI: 10.1093/nar/gkw493] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2015] [Accepted: 05/21/2016] [Indexed: 11/13/2022] Open
Abstract
Nearly half of ribosomal proteins are composed of a domain on the ribosome surface and a loop or extension that penetrates into the organelle's RNA core. Our previous work showed that ribosomes lacking the loops of ribosomal proteins uL4 or uL22 are still capable of entering polysomes. However, in those experiments we could not address the formation of mutant ribosomes, because we used strains that also expressed wild-type uL4 and uL22. Here, we have focused on ribosome assembly and function in strains in which loop deletion mutant genes are the only sources of uL4 or uL22 protein. The uL4 and uL22 loop deletions have different effects, but both mutations result in accumulation of immature particles that do not accumulate in detectable amounts in wild-type strains. Thus, our results suggest that deleting the loops creates kinetic barriers in the normal assembly pathway, possibly resulting in assembly via alternate pathway(s). Furthermore, deletion of the uL4 loop results in cold-sensitive ribosome assembly and function. Finally, ribosomes carrying either of the loop-deleted proteins responded normally to the secM translation pausing peptide, but the uL4 mutant responded very inefficiently to the cmlAcrb pause peptide.
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Affiliation(s)
- Marlon G Lawrence
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, MD 21250, USA
| | - Md Shamsuzzaman
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, MD 21250, USA
| | - Maithri Kondopaka
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, MD 21250, USA
| | - Clarence Pascual
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, MD 21250, USA
| | - Janice M Zengel
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, MD 21250, USA
| | - Lasse Lindahl
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, MD 21250, USA
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24
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Chellat MF, Raguž L, Riedl R. Targeting Antibiotic Resistance. Angew Chem Int Ed Engl 2016; 55:6600-26. [PMID: 27000559 PMCID: PMC5071768 DOI: 10.1002/anie.201506818] [Citation(s) in RCA: 294] [Impact Index Per Article: 36.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Revised: 10/10/2015] [Indexed: 12/11/2022]
Abstract
Finding strategies against the development of antibiotic resistance is a major global challenge for the life sciences community and for public health. The past decades have seen a dramatic worldwide increase in human-pathogenic bacteria that are resistant to one or multiple antibiotics. More and more infections caused by resistant microorganisms fail to respond to conventional treatment, and in some cases, even last-resort antibiotics have lost their power. In addition, industry pipelines for the development of novel antibiotics have run dry over the past decades. A recent world health day by the World Health Organization titled "Combat drug resistance: no action today means no cure tomorrow" triggered an increase in research activity, and several promising strategies have been developed to restore treatment options against infections by resistant bacterial pathogens.
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Affiliation(s)
- Mathieu F Chellat
- Institute of Chemistry and Biotechnology, Center for Organic and Medicinal Chemistry, Zurich University of Applied Sciences (ZHAW), Einsiedlerstrasse 31, 8820, Wädenswil, Switzerland
| | - Luka Raguž
- Institute of Chemistry and Biotechnology, Center for Organic and Medicinal Chemistry, Zurich University of Applied Sciences (ZHAW), Einsiedlerstrasse 31, 8820, Wädenswil, Switzerland
| | - Rainer Riedl
- Institute of Chemistry and Biotechnology, Center for Organic and Medicinal Chemistry, Zurich University of Applied Sciences (ZHAW), Einsiedlerstrasse 31, 8820, Wädenswil, Switzerland.
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25
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Affiliation(s)
- Mathieu F. Chellat
- Institut für Chemie und Biotechnologie, FS Organische Chemie und Medizinalchemie; Zürcher Hochschule für Angewandte Wissenschaften (ZHAW); Einsiedlerstrasse 31 CH-8820 Wädenswil Schweiz
| | - Luka Raguž
- Institut für Chemie und Biotechnologie, FS Organische Chemie und Medizinalchemie; Zürcher Hochschule für Angewandte Wissenschaften (ZHAW); Einsiedlerstrasse 31 CH-8820 Wädenswil Schweiz
| | - Rainer Riedl
- Institut für Chemie und Biotechnologie, FS Organische Chemie und Medizinalchemie; Zürcher Hochschule für Angewandte Wissenschaften (ZHAW); Einsiedlerstrasse 31 CH-8820 Wädenswil Schweiz
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26
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Abstract
Transfer RNAs (tRNAs) are central players in the protein translation machinery and as such are prominent targets for a large number of natural and synthetic antibiotics. This review focuses on the role of tRNAs in bacterial antibiosis. We will discuss examples of antibiotics that target multiple stages in tRNA biology from tRNA biogenesis and modification, mature tRNAs, aminoacylation of tRNA as well as prevention of proper tRNA function by small molecules binding to the ribosome. Finally, the role of deacylated tRNAs in the bacterial “stringent response” mechanism that can lead to bacteria displaying antibiotic persistence phenotypes will be discussed.
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27
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Gamalinda M, Woolford JL. Deletion of L4 domains reveals insights into the importance of ribosomal protein extensions in eukaryotic ribosome assembly. RNA (NEW YORK, N.Y.) 2014; 20:1725-31. [PMID: 25246649 PMCID: PMC4201825 DOI: 10.1261/rna.046649.114] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Numerous ribosomal proteins have a striking bipartite architecture: a globular body positioned on the ribosomal exterior and an internal loop buried deep into the rRNA core. In eukaryotes, a significant number of conserved r-proteins have evolved extra amino- or carboxy-terminal tail sequences, which thread across the solvent-exposed surface. The biological importance of these extended domains remains to be established. In this study, we have investigated the universally conserved internal loop and the eukaryote-specific extensions of yeast L4. We show that in contrast to findings with bacterial L4, deleting the internal loop of yeast L4 causes severely impaired growth and reduced levels of large ribosomal subunits. We further report that while depleting the entire L4 protein blocks early assembly steps in yeast, deletion of only its extended internal loop affects later steps in assembly, revealing a second role for L4 during ribosome biogenesis. Surprisingly, deletion of the entire eukaryote-specific carboxy-terminal tail of L4 has no effect on viability, production of 60S subunits, or translation. These unexpected observations provide impetus to further investigate the functions of ribosomal protein extensions, especially eukaryote-specific examples, in ribosome assembly and function.
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Affiliation(s)
- Michael Gamalinda
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | - John L Woolford
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
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28
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Lu J, Deutsch C. Regional discrimination and propagation of local rearrangements along the ribosomal exit tunnel. J Mol Biol 2014; 426:4061-4073. [PMID: 25308341 DOI: 10.1016/j.jmb.2014.10.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Revised: 10/01/2014] [Accepted: 10/02/2014] [Indexed: 11/25/2022]
Abstract
All proteins, from bacteria to man, are made in the ribosome and are elongated, one residue at a time, at the peptidyl transferase center. This growing peptide chain wends its way through the ribosomal tunnel to the exit port, ~100Å from the peptidyl transferase center. We have identified locations in the tunnel that sense and respond to single side chains of the nascent peptide to induce local conformational changes. Moreover, side-chain sterics and rearrangements deep in the tunnel influence the disposition of residues 45Å away at the exit port and are consistent with side-chain-induced axial retraction of the peptide backbone. These coupled responses are neither haphazard nor uniform along the tunnel. Rather, they are confined to discriminating zones in the tunnel and are sequence specific. Such discerning communication may contribute to folding events and mechanisms governing sequence-specific signaling between different regions of the tunnel during translation.
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Affiliation(s)
- Jianli Lu
- Department of Physiology, University of Pennsylvania, PA 19104, USA
| | - Carol Deutsch
- Department of Physiology, University of Pennsylvania, PA 19104, USA.
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29
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Krylov AA, Kolontaevsky EE, Mashko SV. Oligonucleotide recombination in corynebacteria without the expression of exogenous recombinases. J Microbiol Methods 2014; 105:109-15. [PMID: 25087479 DOI: 10.1016/j.mimet.2014.07.028] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Revised: 07/21/2014] [Accepted: 07/23/2014] [Indexed: 11/24/2022]
Abstract
Brevibacterium lactofermentum and Corynebacterium glutamicum are important biotechnology species of the genus Corynebacterium. The single-strand DNA annealing protein (SSAP)-independent oligonucleotide-mediated recombination procedure was successfully applied to the commonly used wild-type strains B. lactofermentum AJ1511 and C. glutamicum ATCC13032. When the rpsL gene was used as a target, the optimized protocol yielded up to (1.4±0.3)×10(3) and (6.7±1.3)×10(3) streptomycin-resistant colonies per 10(8) viable cells for the corresponding strains. We tested the influence of several parameters that are known to enhance the efficiency of oligonucleotide-mediated recombination in other bacterial species. Among them, increasing the concentration of oligonucleotides and targeting the lagging strand of the chromosome have proven to have positive effects on both of the tested species. No difference in the efficiency of recombination was observed between the oligonucleotides phosphorothiorated at the 5' ends and the unmodified oligonucleotides or between the oligonucleotides with four mutated nucleotides and those with one mutated nucleotide. The described approach demonstrates that during the adaptation of the recombineering technique, testing SSAP-independent oligonucleotide-mediated recombination could be a good starting point. Such testing could decrease the probability of an incorrect interpretation of the effect of exogenous protein factors (such as SSAP and/or corresponding exonucleases) due to non-optimal experimental conditions. In addition, SSAP-independent recombination itself could be useful in combination with suitable selection/enrichment methods.
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Affiliation(s)
- Alexander A Krylov
- Ajinomoto-Genetika Research Institute, 1-st Dorozhny proezd 1, Moscow 117545, Russia.
| | - Egor E Kolontaevsky
- Ajinomoto-Genetika Research Institute, 1-st Dorozhny proezd 1, Moscow 117545, Russia
| | - Sergey V Mashko
- Ajinomoto-Genetika Research Institute, 1-st Dorozhny proezd 1, Moscow 117545, Russia
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30
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Petráčková D, Janeček J, Bezoušková S, Kalachová L, Techniková Z, Buriánková K, Halada P, Haladová K, Weiser J. Fitness and proteome changes accompanying the development of erythromycin resistance in a population of Escherichia coli grown in continuous culture. Microbiologyopen 2013; 2:841-52. [PMID: 23996919 PMCID: PMC3831644 DOI: 10.1002/mbo3.121] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Revised: 07/04/2013] [Accepted: 07/16/2013] [Indexed: 12/27/2022] Open
Abstract
We studied the impact of a sublethal concentration of erythromycin on the fitness and proteome of a continuously cultivated population of Escherichia coli. The development of resistance to erythromycin in the population was followed over time by the gradient plate method and minimum inhibitory concentration (MIC) measurements. We measured the growth rate, standardized efficiency of synthesis of radiolabeled proteins, and translation accuracy of the system. The proteome changes were followed over time in two parallel experiments that differed in the presence or absence of erythromycin. A comparison of the proteomes at each time point (43, 68, and 103 h) revealed a group of unique proteins differing in expression. From all 35 proteins differing throughout the cultivation, only three were common to more than one time point. In the final population, a significant proportion of upregulated proteins was localized to the outer or inner cytoplasmic membranes or to the periplasmic space. In a population growing for more than 100 generations in the presence of antibiotic, erythromycin-resistant bacterial clones with improved fitness in comparison to early resistant culture predominated. This phenomenon was accompanied by distinct changes in protein expression during a stepwise, population-based development of erythromycin resistance.
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Affiliation(s)
- Denisa Petráčková
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
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31
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Mutations in the Escherichia coli ribosomal protein L22 selectively suppress the expression of a secreted bacterial virulence factor. J Bacteriol 2013; 195:2991-9. [PMID: 23625843 DOI: 10.1128/jb.00211-13] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Mutations in the ribosomal protein L22 that impair peptide-mediated translation arrest in Escherichia coli have been shown to reduce the expression of several genes, including secA, which encodes an ATPase that drives protein export via the Sec pathway. Here, we used a comparative proteomic approach to obtain insight into the global effects of the L22(Δ82-84) mutation on gene expression and protein synthesis. While the mutation did not affect or modestly affected the level of most soluble proteins, it dramatically reduced the level of antigen 43 (Ag43), a secreted virulence factor that promotes autoaggregation. The reduced protein concentration correlated with a sharp decrease in the abundance and stability of Ag43 mRNA. We found that the overexpression of secA or the inactivation of genes that encode presecretory and membrane proteins restored Ag43 production in the L22 mutant strain. Furthermore, impairment of the Sec pathway in a wild-type strain reduced Ag43 production but did not significantly affect the synthesis of other presecretory proteins. Taken together, these results indicate that Ag43 gene expression is exquisitely sensitive to the status of the Sec machinery and strongly suggest that the L22 mutation decreases the Ag43 concentration indirectly by reducing secA expression. Our results imply the existence of a novel regulatory mechanism in which the efficiency of protein export is coupled to gene expression and help to explain the modulation of SecA synthesis that has been observed in response to secretion stress.
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32
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Gomes C, Pons MJ, Magallon-Tejada A, Durand D, Lluque A, Mosquito S, Riveros M, Mercado E, Prada A, Ochoa TJ, Ruiz J. In VitroDevelopment and Analysis ofEscherichia coliandShigella boydiiAzithromycin–Resistant Mutants. Microb Drug Resist 2013; 19:88-93. [DOI: 10.1089/mdr.2012.0036] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Cláudia Gomes
- Barcelona Center for International Health Research (CRESIB, Hospital Clínic-Universitat de Barcelona), Barcelona, Spain
| | - Maria J. Pons
- Barcelona Center for International Health Research (CRESIB, Hospital Clínic-Universitat de Barcelona), Barcelona, Spain
| | - Ariel Magallon-Tejada
- Barcelona Center for International Health Research (CRESIB, Hospital Clínic-Universitat de Barcelona), Barcelona, Spain
| | - David Durand
- Institute of Tropical Medicine Alexander von Humboldt, University Cayetano Heredia, Peru
| | - Angela Lluque
- Institute of Tropical Medicine Alexander von Humboldt, University Cayetano Heredia, Peru
| | - Susan Mosquito
- Institute of Tropical Medicine Alexander von Humboldt, University Cayetano Heredia, Peru
| | - Maribel Riveros
- Institute of Tropical Medicine Alexander von Humboldt, University Cayetano Heredia, Peru
| | - Erik Mercado
- Institute of Tropical Medicine Alexander von Humboldt, University Cayetano Heredia, Peru
| | - Ana Prada
- Institute of Tropical Medicine Alexander von Humboldt, University Cayetano Heredia, Peru
| | - Theresa J. Ochoa
- Institute of Tropical Medicine Alexander von Humboldt, University Cayetano Heredia, Peru
- Center for Infectious Diseases, University of Texas School of Public Health, Houston, Texas
| | - Joaquim Ruiz
- Barcelona Center for International Health Research (CRESIB, Hospital Clínic-Universitat de Barcelona), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Spain
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
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33
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Selective Protein Synthesis by Ribosomes with a Drug-Obstructed Exit Tunnel. Cell 2012; 151:508-20. [DOI: 10.1016/j.cell.2012.09.018] [Citation(s) in RCA: 112] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2012] [Revised: 06/18/2012] [Accepted: 09/10/2012] [Indexed: 11/21/2022]
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34
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Poehlsgaard J, Andersen NM, Warrass R, Douthwaite S. Visualizing the 16-membered ring macrolides tildipirosin and tilmicosin bound to their ribosomal site. ACS Chem Biol 2012; 7:1351-5. [PMID: 22563863 DOI: 10.1021/cb300105p] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The veterinary antibiotic tildipirosin (20,23-dipiperidinyl-mycaminosyl-tylonolide, Zuprevo) was developed recently to treat bovine and swine respiratory tract infections caused by bacterial pathogens such as Pasteurella multocida. Tildipirosin is a derivative of the naturally occurring compound tylosin. Here, we define drug-target interactions by combining chemical footprinting with structure modeling and show that tildipirosin, tylosin, and an earlier tylosin derivative, tilmicosin (20-dimethylpiperidinyl-mycaminosyl-tylonolide, Micotil), bind to the same macrolide site within the large subunit of P. multocida and Escherichia coli ribosomes. The drugs nevertheless differ in how they occupy this site. Interactions of the two piperidine components, which are unique to tildipirosin, distinguish this drug from tylosin and tilmicosin. The 23-piperidine of tildipirosin contacts ribosomal residues on the tunnel wall while its 20-piperidine is oriented into the tunnel lumen and is positioned to interfere with the growing nascent peptide.
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Affiliation(s)
- Jacob Poehlsgaard
- Department of Biochemistry & Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Niels M. Andersen
- Department of Biochemistry & Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Ralf Warrass
- MSD Animal
Health Group, Intervet Innovation GmbH,
Zur Propstei, D-55270 Schwabenheim, Germany
| | - Stephen Douthwaite
- Department of Biochemistry & Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
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35
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Imai Y, Fujiwara T, Ochi K, Hosaka T. Development of the ability to produce secondary metabolites in Streptomyces through the acquisition of erythromycin resistance. J Antibiot (Tokyo) 2012; 65:323-6. [DOI: 10.1038/ja.2012.16] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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36
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Kannan K, Mankin AS. Macrolide antibiotics in the ribosome exit tunnel: species-specific binding and action. Ann N Y Acad Sci 2012; 1241:33-47. [PMID: 22191525 DOI: 10.1111/j.1749-6632.2011.06315.x] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Macrolide antibiotics bind in the nascent peptide exit tunnel of the ribosome and inhibit protein synthesis. The majority of information on the principles of binding and action of these antibiotics comes from studies that employed model organisms. However, there is a growing understanding that the binding of macrolides to their target, as well as the mode of inhibition of translation, can be strongly influenced by variations in ribosome structure between bacterial species. Awareness of the existence of species-specific differences in drug action and appreciation of the extent of these differences can stimulate future work on developing better macrolide drugs. In this review, representative cases illustrating the organism-specific binding and action of macrolide antibiotics, as well as species-specific mechanisms of resistance are analyzed.
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Affiliation(s)
- Krishna Kannan
- Center for Pharmaceutical Biotechnology, University of Illinois at Chicago, 60607, USA
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37
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Muroi M, Shima K, Igarashi M, Nakagawa Y, Tanamoto KI. Application of Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry for Discrimination of Laboratory-Derived Antibiotic-Resistant Bacteria. Biol Pharm Bull 2012; 35:1841-5. [DOI: 10.1248/bpb.b12-00465] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Masashi Muroi
- Research Institute of Pharmaceutical Sciences, Musashino University
| | - Keisuke Shima
- Analytical & Measuring Instruments Division, Shimadzu Corporation
| | | | - Yasuyoshi Nakagawa
- Resource Collection Division, National Institute of Technology and Evaluation
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38
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Ribosomal mutations as the main cause of macrolide resistance in Campylobacter jejuni and Campylobacter coli. Antimicrob Agents Chemother 2011; 55:5939-41. [PMID: 21911571 DOI: 10.1128/aac.00314-11] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The aim of this study was to examine macrolide resistance mutations in Campylobacter species. In 76 strains studied, point mutation A to G at position 2059 of the 23S rRNA gene was detected in 30 of the 33 erythromycin-resistant strains. An amino acid insertion in the ribosomal protein L22 was found in one resistant strain without a 23S rRNA mutation. The A2059G mutation is the main cause of macrolide resistance in Campylobacter species.
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Combinations of macrolide resistance determinants in field isolates of Mannheimia haemolytica and Pasteurella multocida. Antimicrob Agents Chemother 2011; 55:4128-33. [PMID: 21709086 DOI: 10.1128/aac.00450-11] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Respiratory tract infections in cattle are commonly associated with the bacterial pathogens Mannheimia haemolytica and Pasteurella multocida. These infections can generally be successfully treated in the field with one of several groups of antibiotics, including macrolides. A few recent isolates of these species exhibit resistance to veterinary macrolides with phenotypes that fall into three distinct classes. The first class has type I macrolide, lincosamide, and streptogramin B antibiotic resistance and, consistent with this, the 23S rRNA nucleotide A2058 is monomethylated by the enzyme product of the erm(42) gene. The second class shows no lincosamide resistance and lacks erm(42) and concomitant 23S rRNA methylation. Sequencing of the genome of a representative strain from this class, P. multocida 3361, revealed macrolide efflux and phosphotransferase genes [respectively termed msr(E) and mph(E)] that are arranged in tandem and presumably expressed from the same promoter. The third class exhibits the most marked drug phenotype, with high resistance to all of the macrolides tested, and possesses all three resistance determinants. The combinations of erm(42), msr(E), and mph(E) are chromosomally encoded and intermingled with other exogenous genes, many of which appear to have been transferred from other members of the Pasteurellaceae. The presence of some of the exogenous genes explains recent reports of resistance to additional drug classes. We have expressed recombinant versions of the erm(42), msr(E), and mph(E) genes within an isogenic Escherichia coli background to assess their individually contributions to resistance. Our findings indicate what types of compounds might have driven the selection for these resistance determinants.
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40
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Desmolaize B, Rose S, Warrass R, Douthwaite S. A novel Erm monomethyltransferase in antibiotic-resistant isolates of Mannheimia haemolytica and Pasteurella multocida. Mol Microbiol 2011; 80:184-94. [PMID: 21371136 DOI: 10.1111/j.1365-2958.2011.07567.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Mannheimia haemolytica and Pasteurella multocida are aetiological agents commonly associated with respiratory tract infections in cattle. Recent isolates of these pathogens have been shown to be resistant to macrolides and other ribosome-targeting antibiotics. Direct analysis of the 23S rRNAs by mass spectrometry revealed that nucleotide A2058 is monomethylated, consistent with a Type I erm phenotype conferring macrolide-lincosamide resistance. The erm resistance determinant was identified by full genome sequencing of isolates. The sequence of this resistance determinant, now termed erm(42), has diverged greatly from all previously characterized erm genes, explaining why it has remained undetected in PCR screening surveys. The sequence of erm(42) is, however, completely conserved in six independent M. haemolytica and P. multocida isolates, suggesting relatively recent gene transfer between these species. Furthermore, the composition of neighbouring chromosomal sequences indicates that erm(42) was acquired from other members of the Pasteurellaceae. Expression of recombinant erm(42) in Escherichia coli demonstrated that the enzyme retains its properties as a monomethyltransferase without any dimethyltransferase activity. Erm(42) is a novel addition to the Erm family: it is phylogenetically distant from the other Erm family members and it is unique in being a bona fide monomethyltransferase that is disseminated between bacterial pathogens.
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Affiliation(s)
- Benoit Desmolaize
- Department of Biochemistry & Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
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41
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Binding and action of CEM-101, a new fluoroketolide antibiotic that inhibits protein synthesis. Antimicrob Agents Chemother 2010; 54:4961-70. [PMID: 20855725 DOI: 10.1128/aac.00860-10] [Citation(s) in RCA: 116] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We characterized the mechanism of action and the drug-binding site of a novel ketolide, CEM-101, which belongs to the latest class of macrolide antibiotics. CEM-101 shows high affinity for the ribosomes of Gram-negative (Escherichia coli) and Gram-positive (Staphylococcus aureus) bacteria. The ketolide shows high selectivity in its inhibitory action and readily interferes with synthesis of a reporter protein in the bacterial but not eukaryotic cell-free translation system. Binding of CEM-101 to its ribosomal target site was characterized biochemically and by X-ray crystallography. The X-ray structure of CEM-101 in complex with the E. coli ribosome shows that the drug binds in the major macrolide site in the upper part of the ribosomal exit tunnel. The lactone ring of the drug forms hydrophobic interactions with the walls of the tunnel, the desosamine sugar projects toward the peptidyl transferase center and interacts with the A2058/A2509 cleft, and the extended alkyl-aryl arm of the drug is oriented down the tunnel and makes contact with a base pair formed by A752 and U2609 of the 23S rRNA. The position of the CEM-101 alkyl-aryl extended arm differs from that reported for the side chain of the ketolide telithromycin complexed with either bacterial (Deinococcus radiodurans) or archaeal (Haloarcula marismortui) large ribosomal subunits but closely matches the position of the side chain of telithromycin complexed to the E. coli ribosome. A difference in the chemical structure of the side chain of CEM-101 in comparison with the side chain of telithromycin and the presence of the fluorine atom at position 2 of the lactone ring likely account for the superior activity of CEM-101. The results of chemical probing suggest that the orientation of the CEM-101 extended side chain observed in the E. coli ribosome closely resembles its placement in Staphylococcus aureus ribosomes and thus likely accurately reflects interaction of CEM-101 with the ribosomes of the pathogenic bacterial targets of the drug. Chemical probing further demonstrated weak binding of CEM-101, but not of erythromycin, to the ribosome dimethylated at A2058 by the action of Erm methyltransferase.
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42
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Gestin B, Valade E, Thibault F, Schneider D, Maurin M. Phenotypic and genetic characterization of macrolide resistance in Francisella tularensis subsp. holarctica biovar I. J Antimicrob Chemother 2010; 65:2359-67. [PMID: 20837574 DOI: 10.1093/jac/dkq315] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
OBJECTIVES Francisella tularensis subsp. holarctica strains are classified as biovars I and II, which are susceptible and naturally resistant to the macrolide erythromycin, respectively. The present study was aimed at both selecting biovar I strains with increased levels of erythromycin resistance and characterizing the underlying genetic mechanisms. METHODS Serial cultures in the presence of increasingly high erythromycin concentrations were performed to select independent high- and intermediate-level erythromycin-resistant mutants from each of three different biovar I strains. The mutants were characterized for cross-resistance to several antibiotics, presence of mutations in the genes encoding the 23S rRNA and the L4 and L22 ribosomal proteins, and overexpression of efflux pumps. RESULTS Mutants displayed cross-resistance to all macrolide compounds tested but not to other classes of antibiotics. We found mutations in domain V of the 23S rRNA gene (G2057A, A2058G, A2058T and C2611T) and in the gene encoding L22, leading to either the G91D substitution or the M82K83R84 deletion. Analysis of mutants with intermediate resistance levels obtained over the course of the selection process revealed both a positive correlation between the number of mutated ribosomal operons and the resistance level, and an additional resistance mechanism in the early steps of selection. CONCLUSIONS We showed that high-level resistance to macrolides can be easily obtained in vitro in F. tularensis subsp. holarctica biovar I strains, thereby suggesting that in vivo selection for resistance may explain reported failures of antibiotic treatment. Ketolides were the most effective macrolides tested, which may limit the risk of selection for resistance.
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Affiliation(s)
- Brieuc Gestin
- CNRS UMR 5163 and Laboratoire Adaptation et Pathogénie des Micro-organismes, Université Joseph Fourier Grenoble 1, BP 170, F-38042 Grenoble Cedex 9, France
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Park KH, Billon-Denis E, Dahmane T, Lebaupain F, Pucci B, Breyton C, Zito F. In the cauldron of cell-free synthesis of membrane proteins: playing with new surfactants. N Biotechnol 2010; 28:255-61. [PMID: 20800706 DOI: 10.1016/j.nbt.2010.08.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2010] [Revised: 07/22/2010] [Accepted: 08/18/2010] [Indexed: 02/06/2023]
Abstract
Cell-free protein synthesis is a well-known technique for the roles it has played in deciphering the genetic code and in the beginnings of signal sequence studies. Since then, many efforts have been made to optimise this technique and, recently, to adapt it to membrane protein production with yields compatible with structural investigations. The versatility of the method allows membrane proteins to be obtained directly stabilised in surfactant micelles or inserted in a lipidic environment (proteoliposome, bicelle, and nanodisc) at the end of synthesis. Among the surfactants used, non-detergent ones such as fluorinated surfactants proved to be a good alternative in terms of colloidal stability and preservation of the integrity of membrane proteins, as shown for Escherichia coli homo-pentameric channel, MscL (Park et al., Biochem. J., 403: 183-187). Here we report cell-free expression of Escherichia coli leader peptidase (a transmembrane protease), Halobacterium salinarium bacteriorhodopsin (a transmembrane protein binding a hydrophobic cofactor) and E. coli MscL in the presence of non-detergent surfactants, amphipols and fluorinated surfactants in comparison to their expression in classical detergents. The results confirm the potentialities of fluorinated surfactants and, although pointing to limitations in using the first generations amphipols, results are discussed in the light of membrane protein refolding, especially in the case of bacteriorhodopsin. Preliminary experiments using new generations of amphipols supports choices made in developing new molecules.
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Affiliation(s)
- Kyu-Ho Park
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, UMR 7099, CNRS and Université Paris-7, Institut de Biologie Physico-Chimique, CNRS FRC 550, F-75005 Paris, France
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Abstract
Protein synthesis is one of the major targets in the cell for antibiotics. This review endeavors to provide a comprehensive "post-ribosome structure" A-Z of the huge diversity of antibiotics that target the bacterial translation apparatus, with an emphasis on correlating the vast wealth of biochemical data with more recently available ribosome structures, in order to understand function. The binding site, mechanism of action, and modes of resistance for 26 different classes of protein synthesis inhibitors are presented, ranging from ABT-773 to Zyvox. In addition to improving our understanding of the process of translation, insight into the mechanism of action of antibiotics is essential to the development of novel and more effective antimicrobial agents to combat emerging bacterial resistance to many clinically-relevant drugs.
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Affiliation(s)
- Daniel N Wilson
- Gene Center and Department of Chemistry and Biochemistry, University of Munich, LMU, Munich, Germany.
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Kurkcuoglu O, Kurkcuoglu Z, Doruker P, Jernigan RL. Collective dynamics of the ribosomal tunnel revealed by elastic network modeling. Proteins 2009; 75:837-45. [PMID: 19004020 DOI: 10.1002/prot.22292] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The collective dynamics of the nascent polypeptide exit tunnel are investigated with the computationally efficient elastic network model using normal mode analysis. The calculated normal modes are considered individually and in linear combinations with different coefficients mimicking the phase angles between modes, in order to follow the mechanistic motions of tunnel wall residues. The low frequency fluctuations indicate three distinct regions along the tunnel-the entrance, the neck, and the exit-each having distinctly different domain motions. Generally, the lining of the entrance region moves in the exit direction, with the exit region having significantly larger motions, but in a perpendicular direction, whereas the confined neck region has rotational motions. Especially the universally conserved extensions of ribosomal proteins L4 and L22 located at the narrowest and mechanistically strategic region of tunnel undergo generally anti- or non-correlated motions, which may have an important role in nascent polypeptide gating mechanism. These motions appear to be sufficiently robust so as to be unaffected by the presence of a peptide chain in the tunnel.
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Affiliation(s)
- Ozge Kurkcuoglu
- Department of Chemical Engineering and Polymer Research Center, Bogazici University, 34342 Bebek, Istanbul, Turkey
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Concurrent titration and determination of antibiotic resistance in ureaplasma species with identification of novel point mutations in genes associated with resistance. Antimicrob Agents Chemother 2009; 53:2020-7. [PMID: 19273669 PMCID: PMC2681543 DOI: 10.1128/aac.01349-08] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Antibiotic resistance determination of Ureaplasma spp. (Ureaplasma parvum and Ureaplasma urealyticum) usually requires predetermination of bacterial titer, followed by antibiotic interrogation using a set bacterial input. This 96-well method allows simultaneous quantification of bacteria in the presence and absence of antibiotics. A method for determining precise MICs and a method for screening against multiple antibiotics using breakpoint thresholds are detailed. Of the 61 Ureaplasma-positive clinical isolates screened, one (1.6%) was resistant to erythromycin (MIC, >64 mg/liter) and clarithromycin (MIC, 4 mg/liter), one to ciprofloxacin (1.6%), and one to tetracycline/doxycycline (1.6%). Five isolates were also consistently found to have an elevated MIC of 8 mg/liter for erythromycin, but this may not represent true antibiotic resistance, as no mutations were found in the 23S rRNA operons or ribosome-associated L4 and L22 proteins for these strains. However, two amino acids (R66Q67) were deleted from the L4 protein of the erythromycin-/clarithromycin-resistant strain. The tetM genetic element was detected in the tetracycline-resistant clinical isolate as well as in the positive control Vancouver strain serotype 9. The tetM gene was also found in a fully tetracycline-susceptible Ureaplasma clinical isolate, and no mutations were found in the coding region that would explain its failure to mediate tetracycline resistance. An amino acid substitution (D82N) was found in the ParC subunit of the ciprofloxacin-resistant isolate, adjacent to the S83L mutation reported by other investigators in many ciprofloxacin-resistant Ureaplasma isolates. It is now possible to detect antibiotic resistance in Ureaplasma within 48 h of positive culture without prior knowledge of bacterial load, identifying them for further molecular analysis.
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Lovmar M, Nilsson K, Lukk E, Vimberg V, Tenson T, Ehrenberg M. Erythromycin resistance by L4/L22 mutations and resistance masking by drug efflux pump deficiency. EMBO J 2009; 28:736-44. [PMID: 19197244 DOI: 10.1038/emboj.2009.17] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2008] [Accepted: 01/08/2009] [Indexed: 12/28/2022] Open
Abstract
We characterized the effects of classical erythromycin resistance mutations in ribosomal proteins L4 and L22 of the large ribosomal subunit on the kinetics of erythromycin binding. Our data are consistent with a mechanism in which the macrolide erythromycin enters and exits the ribosome through the nascent peptide exit tunnel, and suggest that these mutations both impair passive transport through the tunnel and distort the erythromycin-binding site. The growth-inhibitory action of erythromycin was characterized for bacterial populations with wild-type and L22-mutated ribosomes in drug efflux pump deficient and proficient backgrounds. The L22 mutation conferred reduced erythromycin susceptibility in the drug efflux pump proficient, but not deficient, background. This 'masking' of drug resistance by pump deficiency was reproduced by modelling with input data from our biochemical experiments. We discuss the general principles behind the phenomenon of drug resistance 'masking', and highlight its potential importance for slowing down the evolution of drug resistance among pathogens.
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Affiliation(s)
- Martin Lovmar
- Department of Cell and Molecular Biology, Molecular Biology Program, Uppsala University, Uppsala, Sweden
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Diner EJ, Hayes CS. Recombineering reveals a diverse collection of ribosomal proteins L4 and L22 that confer resistance to macrolide antibiotics. J Mol Biol 2009; 386:300-15. [PMID: 19150357 DOI: 10.1016/j.jmb.2008.12.064] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2008] [Revised: 12/18/2008] [Accepted: 12/20/2008] [Indexed: 11/19/2022]
Abstract
Mutations in ribosomal proteins L4 and L22 confer resistance to erythromycin and other macrolide antibiotics in a variety of bacteria. L4 and L22 have elongated loops whose tips converge in the peptide exit tunnel near the macrolide-binding site, and resistance mutations typically affect residues within these loops. Here, we used bacteriophage lambda Red-mediated recombination, or "recombineering," to uncover new L4 and L22 alleles that confer macrolide resistance in Escherichia coli. We randomized residues at the tips of the L4 and L22 loops using recombineered oligonucleotide libraries and selected the mutagenized cells for erythromycin-resistant mutants. These experiments led to the identification of 341 resistance mutations encoding 278 unique L4 and L22 proteins-the overwhelming majority of which are novel. Many resistance mutations were complex, involving multiple missense mutations, in-frame deletions, and insertions. Transfer of L4 and L22 mutations into wild-type cells by phage P1-mediated transduction demonstrated that each allele was sufficient to confer macrolide resistance. Although L4 and L22 mutants are typically resistant to most macrolides, selections carried out on different antibiotics revealed macrolide-specific resistance mutations. L22 Lys90Trp is one such allele that confers resistance to erythromycin but not to tylosin and spiramycin. Purified L22 Lys90Trp ribosomes show reduced erythromycin binding but have the same affinity for tylosin as wild-type ribosomes. Moreover, dimethyl sulfate methylation protection assays demonstrated that L22 Lys90Trp ribosomes bind tylosin more readily than erythromycin in vivo. This work underscores the exceptional functional plasticity of the L4 and L22 proteins and highlights the utility of Red-mediated recombination in targeted genetic selections.
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Affiliation(s)
- Elie J Diner
- University of California, Santa Barbara, 93106-9610, USA
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Revisiting the mechanism of macrolide-antibiotic resistance mediated by ribosomal protein L22. Proc Natl Acad Sci U S A 2008; 105:18261-6. [PMID: 19015512 DOI: 10.1073/pnas.0810357105] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bacterial antibiotic resistance can occur by many mechanisms. An intriguing class of mutants is resistant to macrolide antibiotics even though these drugs still bind to their targets. For example, a 3-residue deletion (DeltaMKR) in ribosomal protein L22 distorts a loop that forms a constriction in the ribosome exit tunnel, apparently allowing nascent-chain egress and translation in the presence of bound macrolides. Here, however, we demonstrate that DeltaMKR and wild-type ribosomes show comparable macrolide sensitivity in vitro. In Escherichia coli, we find that this mutation reduces antibiotic occupancy of the target site on ribosomes in a manner largely dependent on the AcrAB-TolC efflux system. We propose a model for antibiotic resistance in which DeltaMKR ribosomes alter the translation of specific proteins, possibly via changes in programmed stalling, and modify the cell envelope in a manner that lowers steady-state macrolide levels.
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Effects on translation pausing of alterations in protein and RNA components of the ribosome exit tunnel. J Bacteriol 2008; 190:5862-9. [PMID: 18586934 DOI: 10.1128/jb.00632-08] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Amino acids are polymerized into peptides in the peptidyl transferase center of the ribosome. The nascent peptides then pass through the exit tunnel before they reach the extraribosomal environment. A number of nascent peptides interact with the exit tunnel and stall elongation at specific sites within their peptide chain. Several mutational changes in RNA and protein components of the ribosome have previously been shown to interfere with pausing. These changes are localized in the narrowest region of the tunnel, near a constriction formed by ribosomal proteins L4 and L22. To expand our knowledge about peptide-induced pausing, we performed a comparative study of pausing induced by two peptides, SecM and a short peptide, Crb(CmlA), that requires chloramphenicol as a coinducer of pausing. We analyzed the effects of 15 mutational changes in L4 and L22, as well as the effects of methylating nucleotide A2058 of 23S rRNA, a nucleotide previously implicated in pausing and located close to the L4-L22 constriction. Our results show that methylation of A2058 and most mutational changes in L4 and L22 have differential effects on pausing in response to Crb(CmlA) and SecM. Only one change, a 6-amino-acid insertion after amino acid 72 in L4, affects pausing in both peptides. We conclude that the two peptides interact with different regions of the exit tunnel. Our results suggest that either the two peptides use different mechanisms of pausing or they interact differently but induce similar inhibitory conformational changes in functionally important regions of the ribosome.
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