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Rodrigues C, Bouchez V, Soares A, Trombert-Paolantoni S, Aït El Belghiti F, Cohen JF, Armatys N, Landier A, Blanchot T, Hervo M, Toubiana J, Brisse S. Resurgence of Bordetella pertussis, including one macrolide-resistant isolate, France, 2024. Euro Surveill 2024; 29:2400459. [PMID: 39092529 PMCID: PMC11295439 DOI: 10.2807/1560-7917.es.2024.29.31.2400459] [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: 07/15/2024] [Accepted: 07/31/2024] [Indexed: 08/04/2024] Open
Abstract
As other European countries, France is experiencing a resurgence of pertussis in 2024. Between 1 January and 31 May 2024, 5,616 (24.9%) positive Bordetella pertussis qPCR tests were identified, following a 3-year period of almost null incidence. Of 67 cultured and whole genome sequenced B. pertussis isolates, 66 produced pertactin and 56 produced FIM2, in contrast to pre-COVID-19 years. One isolate of genotype Bp-AgST4 was resistant to macrolides. Pertussis resurgence may favour isolates that produce FIM2 and pertactin.
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Affiliation(s)
- Carla Rodrigues
- These authors contributed equally to this work and share first authorship
- National Reference Center for Whooping Cough and other Bordetella infections, Institut Pasteur, Paris, France
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - Valérie Bouchez
- These authors contributed equally to this work and share first authorship
- National Reference Center for Whooping Cough and other Bordetella infections, Institut Pasteur, Paris, France
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | | | | | - Fatima Aït El Belghiti
- Santé publique France, Infectious Diseases Department, The French Public Health Agency, Saint-Maurice, France
| | - Jérémie F Cohen
- Centre for Research in Epidemiology and Statistics (Inserm UMR 1153), Université Paris Cité, Paris, France
- Department of General Paediatrics and Paediatric Infectious Diseases, Université Paris Cité, Hôpital Necker-Enfants Malades, APHP, Paris, France
| | - Nathalie Armatys
- National Reference Center for Whooping Cough and other Bordetella infections, Institut Pasteur, Paris, France
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - Annie Landier
- National Reference Center for Whooping Cough and other Bordetella infections, Institut Pasteur, Paris, France
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | | | | | - Julie Toubiana
- These authors co-supervised the work and share last authorship
- Department of General Paediatrics and Paediatric Infectious Diseases, Université Paris Cité, Hôpital Necker-Enfants Malades, APHP, Paris, France
- National Reference Center for Whooping Cough and other Bordetella infections, Institut Pasteur, Paris, France
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - Sylvain Brisse
- These authors co-supervised the work and share last authorship
- National Reference Center for Whooping Cough and other Bordetella infections, Institut Pasteur, Paris, France
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
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2
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Liao W, Wang X, Wang Y, Ma P, Chen K, Ge L, Yang X, Zeng S, Gao W, Zhang S, Wang H, Jia X, Luo T. Noncanonical mutations in ribosome nascent peptide exit tunnel confer clarithromycin resistance in Mycobacterium abscessus complex. Int J Antimicrob Agents 2024; 64:107223. [PMID: 38810940 DOI: 10.1016/j.ijantimicag.2024.107223] [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: 10/17/2023] [Revised: 05/04/2024] [Accepted: 05/20/2024] [Indexed: 05/31/2024]
Abstract
OBJECTIVES Mycobacterium abscessus is a non-tuberculous mycobacterial pathogen that causes pulmonary and skin infections globally. Clarithromycin plays a pivotal role in treating M. abscessus infections, with resistance often leading to treatment failure. While canonical mutations in the 23S rRNA residue 2270/2271 are recognized as the primary mechanism for acquired clarithromycin resistance, resistant isolates lacking these mutations have been widely reported. This study aims to identify new mechanisms of clarithromycin resistance in M. abscessus. METHODS We selected spontaneous resistant mutants derived from two parental strains characterized by erm(41) T28 and C28 sequevars, respectively. Whole-genome sequencing was performed on mutants lacking the 23S rRNA 2270/2271 mutations. Site-directed mutagenesis was used to confirm the resistance phenotypes of newly identified mutations. Bioinformatic analysis of publicly available genomes was conducted to evaluate the presence of these mutations in clinical isolates. The spatial localization of these mutations in the ribosome was analyzed to investigate potential mechanisms of resistance. RESULTS A total of 135 resistant mutants were selected from the parental strains. Sequencing of the 78 mutants lacking the 23S rRNA 2270/2271 mutations identified mutations within the peptidyl-transferase center and hairpin loops 35, 49, and 74 of the 23S rRNA. These noncanonical mutations were identified in 57 of 1875 genomes of clinical isolates. Thirteen representative mutations were introduced into the bacterial genome, and their contributions to macrolide resistance were confirmed. The newly identified mutations all localized at the entrance of the nascent peptide exit tunnel, potentially contributing to resistance by disrupting the macrolide binding pocket. CONCLUSION Several noncanonical 23S rRNA mutations conferring clarithromycin resistance were identified. These mutations enhance our understanding of macrolide resistance in M. abscessus and could serve as important markers for diagnosing clarithromycin resistance.
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Affiliation(s)
- Wei Liao
- Department of Pathogen Biology, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China; High Altitude Health Science Research Centre of Tibet University, Medical College of Tibet University, Lhasa, China
| | - Xinyan Wang
- Genomics Center of Core Facilities, West China Hospital, Sichuan University, Chengdu, China
| | - Yi Wang
- Department of Pathogen Biology, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Pengjiao Ma
- Department of Biochemistry and Molecular Biology, College of Basic Medical Science, Army Medical University, Chongqing, China
| | - Ken Chen
- Department of Pathogen Biology, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Liang Ge
- Department of Pathogen Biology, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Xiaoyan Yang
- Department of Pathogen Biology, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Shushu Zeng
- Department of Pathogen Biology, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Wenfeng Gao
- Sichuan Center for Disease Control and Prevention, Chengdu, China
| | - Shu Zhang
- Sichuan Center for Disease Control and Prevention, Chengdu, China
| | - Hongren Wang
- Department of Pathogen Biology, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Xu Jia
- Non-coding RNA and Drug Discovery Key Laboratory of Sichuan Province, Chengdu Medical College, Chengdu, China
| | - Tao Luo
- Department of Pathogen Biology, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China.
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3
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Xia X, Yang L, Ling Y, Yu J, Ding H. Emergence and Mechanism of Resistance of Tulathromycin Against Mycoplasma hyopneumoniae in a PK/PD Model and the Fitness Costs of 23S rRNA Mutants. Front Vet Sci 2022; 9:801800. [PMID: 35224081 PMCID: PMC8873822 DOI: 10.3389/fvets.2022.801800] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 01/17/2022] [Indexed: 12/02/2022] Open
Abstract
Macrolides are widely used in diseases caused by Mycoplasma spp. The new semi-synthetic macrolide antibiotic tulathromycin is currently in wide use for the treatment of respiratory diseases of livestock. The objective of this study was to evaluate the antibacterial effect of tulathromycin against Mycoplasma hyopneumoniae using an in vitro pharmacokinetic/pharmacodynamic (PK/PD) model to reveal mechanisms of antibiotic resistance and to evaluate the fitness of drug-resistant strains. In this study, high performance liquid chromatography-tandem mass spectrometry was used to determine drug concentrations for the in vitro model after dosing. The peak concentrations were in the range 0.3125–20 μg/mL (1 × MIC-64 × MIC). The ratio of the area under the concentration-time curve (AUC) over 72 h divided by the MIC (AUC72h/MIC) had the highest correlation with the antibacterial effect of tulathromycin against M. hyopneumoniae. Tulathromycin also showed concentration-dependent antimicrobial effects and promoted the emergence of drug-resistant bacteria after being cultured for 168 h and most were mutations in 23S rRNA at site A2058G (E.coli numbering) and only a single isolate was an A2058T (E.coli numbering) mutant. In the presence of reserpine, we determined the MIC of tulathromycin, tilmicosin, tiamulin and tylosin against these drug-resistant bacteria and the strains with efflux pump mechanisms were found among the strains resistant to tilmicosin. Gene expression analysis indicated that the ABC and MATE transporter efflux pump genes RS01935, RS02670, RS01115, RS01970, RS02395 and RS03540 (MATE family efflux transporter) were up-regulated in the three strains (P < 0.05 or P < 0.01). These investigations provide guidance for clinical administration of tulathromycin and elucidate the mechanism and fitness cost of drug resistance in M. hyopneumoniae.
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Yao W, Xu G, Bai B, Wang H, Deng M, Zheng J, Li D, Deng X, Liu X, Lin Z, Chen Z, Li G, Deng Q, Yu Z. In vitro-induced erythromycin resistance facilitates cross-resistance to the novel fluoroketolide, solithromycin, in Staphylococcus aureus. FEMS Microbiol Lett 2019; 365:4992303. [PMID: 29733362 DOI: 10.1093/femsle/fny116] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 05/02/2018] [Indexed: 12/31/2022] Open
Abstract
The aim of this study was to determine whether in vitro induced erythromycin resistance facilitates the cross-resistance to the novel fluoroketolide, solithromycin, in Staphylococcus aureus. Four strains of methicillin-susceptible S. aureus strains S2, S3, S5 and S7 were successfully induced to establish erythromycin-resistant strains by continuous in vitro culture with erythromycin. Mutations at drug binding sites were shown to increase the minimal inhibitory concentrations for ketolides, including telithromycin and the novel compound solithromycin, but did not increase for lincosamides, chloramphenicols or oxazolidinones. In S2-, S5- and S7-derived strains, L22 protein mutations occurred first, resulting in a low level of cross-resistance to ketolides (≤4 μg/mL). The L4 protein mutations were dependent on the L22 protein, resulting in high-level cross-resistance to ketolides (≥8 μg/mL). In S3-derived strains, high levels of cross-resistance occurred concurrently in the 23S rRNA domains II/V and the L22 protein. Hence, long-term exposure of erythromycin results in resistance to ketolides in S. aureus through drug binding site mutations. These results demonstrate that since erythromycin has been used clinically for a long time, it is necessary to carefully evaluate the rewards and risks when prescribing solithromycin for the treatment of infectious diseases.
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Affiliation(s)
- Weiming Yao
- Department of Infectious Diseases and Shenzhen Key Lab for Endogenous Infection, Shenzhen Nanshan Hospital of Shenzhen University, No 89, Taoyuan Road, Nanshan District, Shenzhen 518052, China.,Quality Control Center of Hospital Infection Management of Shenzhen, No 89, Taoyuan Road, Nanshan District, Shenzhen 518052, China
| | - Guangjian Xu
- Department of Infectious Diseases and Shenzhen Key Lab for Endogenous Infection, Shenzhen Nanshan Hospital of Shenzhen University, No 89, Taoyuan Road, Nanshan District, Shenzhen 518052, China.,Quality Control Center of Hospital Infection Management of Shenzhen, No 89, Taoyuan Road, Nanshan District, Shenzhen 518052, China
| | - Bing Bai
- Department of Infectious Diseases and Shenzhen Key Lab for Endogenous Infection, Shenzhen Nanshan Hospital of Shenzhen University, No 89, Taoyuan Road, Nanshan District, Shenzhen 518052, China.,Quality Control Center of Hospital Infection Management of Shenzhen, No 89, Taoyuan Road, Nanshan District, Shenzhen 518052, China
| | - Hongyan Wang
- Department of Infectious Diseases and Shenzhen Key Lab for Endogenous Infection, Shenzhen Nanshan Hospital of Shenzhen University, No 89, Taoyuan Road, Nanshan District, Shenzhen 518052, China.,Quality Control Center of Hospital Infection Management of Shenzhen, No 89, Taoyuan Road, Nanshan District, Shenzhen 518052, China
| | - Minggui Deng
- Department of Infectious Diseases and Shenzhen Key Lab for Endogenous Infection, Shenzhen Nanshan Hospital of Shenzhen University, No 89, Taoyuan Road, Nanshan District, Shenzhen 518052, China.,Quality Control Center of Hospital Infection Management of Shenzhen, No 89, Taoyuan Road, Nanshan District, Shenzhen 518052, China
| | - Jinxin Zheng
- Department of Infectious Diseases and Shenzhen Key Lab for Endogenous Infection, Shenzhen Nanshan Hospital of Shenzhen University, No 89, Taoyuan Road, Nanshan District, Shenzhen 518052, China.,Quality Control Center of Hospital Infection Management of Shenzhen, No 89, Taoyuan Road, Nanshan District, Shenzhen 518052, China.,Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Science and Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, No 130, Dongan road, Xuhui District, Shanghai 200032, China
| | - Duoyun Li
- Department of Infectious Diseases and Shenzhen Key Lab for Endogenous Infection, Shenzhen Nanshan Hospital of Shenzhen University, No 89, Taoyuan Road, Nanshan District, Shenzhen 518052, China.,Quality Control Center of Hospital Infection Management of Shenzhen, No 89, Taoyuan Road, Nanshan District, Shenzhen 518052, China
| | - Xiangbin Deng
- Department of Infectious Diseases and Shenzhen Key Lab for Endogenous Infection, Shenzhen Nanshan Hospital of Shenzhen University, No 89, Taoyuan Road, Nanshan District, Shenzhen 518052, China.,Quality Control Center of Hospital Infection Management of Shenzhen, No 89, Taoyuan Road, Nanshan District, Shenzhen 518052, China
| | - Xiaojun Liu
- Department of Infectious Diseases and Shenzhen Key Lab for Endogenous Infection, Shenzhen Nanshan Hospital of Shenzhen University, No 89, Taoyuan Road, Nanshan District, Shenzhen 518052, China.,Quality Control Center of Hospital Infection Management of Shenzhen, No 89, Taoyuan Road, Nanshan District, Shenzhen 518052, China
| | - Zhiwei Lin
- Department of Infectious Diseases and Shenzhen Key Lab for Endogenous Infection, Shenzhen Nanshan Hospital of Shenzhen University, No 89, Taoyuan Road, Nanshan District, Shenzhen 518052, China.,Quality Control Center of Hospital Infection Management of Shenzhen, No 89, Taoyuan Road, Nanshan District, Shenzhen 518052, China.,Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Science and Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, No 130, Dongan road, Xuhui District, Shanghai 200032, China
| | - Zhong Chen
- Department of Infectious Diseases and Shenzhen Key Lab for Endogenous Infection, Shenzhen Nanshan Hospital of Shenzhen University, No 89, Taoyuan Road, Nanshan District, Shenzhen 518052, China.,Quality Control Center of Hospital Infection Management of Shenzhen, No 89, Taoyuan Road, Nanshan District, Shenzhen 518052, China
| | - Guiqiu Li
- Department of Infectious Diseases and Shenzhen Key Lab for Endogenous Infection, Shenzhen Nanshan Hospital of Shenzhen University, No 89, Taoyuan Road, Nanshan District, Shenzhen 518052, China.,Quality Control Center of Hospital Infection Management of Shenzhen, No 89, Taoyuan Road, Nanshan District, Shenzhen 518052, China
| | - Qiwen Deng
- Department of Infectious Diseases and Shenzhen Key Lab for Endogenous Infection, Shenzhen Nanshan Hospital of Shenzhen University, No 89, Taoyuan Road, Nanshan District, Shenzhen 518052, China.,Quality Control Center of Hospital Infection Management of Shenzhen, No 89, Taoyuan Road, Nanshan District, Shenzhen 518052, China
| | - Zhijian Yu
- Department of Infectious Diseases and Shenzhen Key Lab for Endogenous Infection, Shenzhen Nanshan Hospital of Shenzhen University, No 89, Taoyuan Road, Nanshan District, Shenzhen 518052, China.,Quality Control Center of Hospital Infection Management of Shenzhen, No 89, Taoyuan Road, Nanshan District, Shenzhen 518052, China
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5
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Dedkova LM, Hecht SM. Expanding the Scope of Protein Synthesis Using Modified Ribosomes. J Am Chem Soc 2019; 141:6430-6447. [PMID: 30901982 DOI: 10.1021/jacs.9b02109] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The ribosome produces all of the proteins and many of the peptides present in cells. As a macromolecular complex composed of both RNAs and proteins, it employs a constituent RNA to catalyze the formation of peptide bonds rapidly and with high fidelity. Thus, the ribosome can be argued to represent the key link between the RNA World, in which RNAs were the primary catalysts, and present biological systems in which protein catalysts predominate. In spite of the well-known phylogenetic conservation of rRNAs through evolutionary history, rRNAs can be altered readily when placed under suitable pressure, e.g. in the presence of antibiotics which bind to functionally critical regions of rRNAs. While the structures of rRNAs have been altered intentionally for decades to enable the study of their role(s) in the mechanism of peptide bond formation, it is remarkable that the purposeful alteration of rRNA structure to enable the elaboration of proteins and peptides containing noncanonical amino acids has occurred only recently. In this Perspective, we summarize the history of rRNA modifications, and demonstrate how the intentional modification of 23S rRNA in regions critical for peptide bond formation now enables the direct ribosomal incorporation of d-amino acids, β-amino acids, dipeptides and dipeptidomimetic analogues of the normal proteinogenic l-α-amino acids. While proteins containing metabolically important functional groups such as carbohydrates and phosphate groups are normally elaborated by the post-translational modification of nascent polypeptides, the use of modified ribosomes to produce such polymers directly is also discussed. Finally, we describe the elaboration of such modified proteins both in vitro and in bacterial cells, and suggest how such novel biomaterials may be exploited in future studies.
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Affiliation(s)
- Larisa M Dedkova
- Biodesign Center for BioEnergetics and School of Molecular Sciences , Arizona State University , Tempe , Arizona 85287 , United States
| | - Sidney M Hecht
- Biodesign Center for BioEnergetics and School of Molecular Sciences , Arizona State University , Tempe , Arizona 85287 , United States
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6
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Pereira RVV, Carroll LM, Lima S, Foditsch C, Siler JD, Bicalho RC, Warnick LD. Impacts of feeding preweaned calves milk containing drug residues on the functional profile of the fecal microbiota. Sci Rep 2018; 8:554. [PMID: 29323259 PMCID: PMC5764986 DOI: 10.1038/s41598-017-19021-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 12/20/2017] [Indexed: 11/30/2022] Open
Abstract
Feeding drug residue-containing milk to calves is common worldwide and no information is currently available on the impact on the functional profile of the fecal microbiota. Our objective was to characterize the functional profile of the fecal microbiota of preweaned dairy calves fed raw milk with residual concentrations of antimicrobials commonly found in waste milk from birth to weaning. Calves were assigned to a controlled feeding trial being fed milk with no drug residues or milk with antibiotic residues. Fecal samples collected from each calf once a week starting at birth, prior to the first feeding in the trial, until 6 weeks of age. Antibiotic residues resulted in a significant difference in relative abundance of microbial cell functions, especially with genes linked with stress response, regulation and cell signaling, and nitrogen metabolism. These changes could directly impacts selection and dissemination of virulence and antimicrobial. Our data also identified a strong association between age in weeks and abundance of Resistance to Antibiotics and Toxic Compounds. Findings from this study support the hypothesis that drug residues, even at very low concentrations, impact the gut microbiota of calves and result in changes in the functional profile of microbial populations.
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Affiliation(s)
| | - Laura M Carroll
- Department of Food Science, Cornell University, Ithaca, New York, USA
| | - Svetlana Lima
- College of Veterinary Medicine, University of California Davis, Davis, CA, USA
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, United States of America
| | - Carla Foditsch
- College of Veterinary Medicine, University of California Davis, Davis, CA, USA
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, United States of America
| | - Julie D Siler
- College of Veterinary Medicine, University of California Davis, Davis, CA, USA
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, United States of America
| | - Rodrigo Carvalho Bicalho
- College of Veterinary Medicine, University of California Davis, Davis, CA, USA
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, United States of America
| | - Lorin D Warnick
- College of Veterinary Medicine, University of California Davis, Davis, CA, USA
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, United States of America
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7
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Mycobacterium smegmatis PafBC is involved in regulation of DNA damage response. Sci Rep 2017; 7:13987. [PMID: 29070902 PMCID: PMC5656591 DOI: 10.1038/s41598-017-14410-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 10/11/2017] [Indexed: 01/08/2023] Open
Abstract
Two genes, pafB and pafC, are organized in an operon with the Pup-ligase gene pafA, which is part of the Pup-proteasome system (PPS) present in mycobacteria and other actinobacteria. The PPS is crucial for Mycobacterium tuberculosis resistance towards reactive nitrogen intermediates (RNI). However, pafB and pafC apparently play only a minor role in RNI resistance. To characterize their function, we generated a pafBC deletion in Mycobacterium smegmatis (Msm). Proteome analysis of the mutant strain revealed decreased cellular levels of various proteins involved in DNA damage repair, including recombinase A (RecA). In agreement with this finding, Msm ΔpafBC displayed increased sensitivity to DNA damaging agents. In mycobacteria two pathways regulate DNA repair genes: the LexA/RecA-dependent SOS response and a predominant pathway that controls gene expression via a LexA/RecA-independent promoter, termed P1. PafB and PafC feature winged helix-turn-helix DNA binding motifs and we demonstrate that together they form a stable heterodimer in vitro, implying a function as a heterodimeric transcriptional regulator. Indeed, P1-driven transcription of recA was decreased in Msm ΔpafBC under standard conditions and induction of recA expression upon DNA damage was strongly impaired. Taken together, our data indicate an important regulatory function of PafBC in the mycobacterial DNA damage response.
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8
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Dinos GP. The macrolide antibiotic renaissance. Br J Pharmacol 2017; 174:2967-2983. [PMID: 28664582 DOI: 10.1111/bph.13936] [Citation(s) in RCA: 217] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 05/29/2017] [Accepted: 06/20/2017] [Indexed: 12/19/2022] Open
Abstract
Macrolides represent a large family of protein synthesis inhibitors of great clinical interest due to their applicability to human medicine. Macrolides are composed of a macrocyclic lactone of different ring sizes, to which one or more deoxy-sugar or amino sugar residues are attached. Macrolides act as antibiotics by binding to bacterial 50S ribosomal subunit and interfering with protein synthesis. The high affinity of macrolides for bacterial ribosomes, together with the highly conserved structure of ribosomes across virtually all of the bacterial species, is consistent with their broad-spectrum activity. Since the discovery of the progenitor macrolide, erythromycin, in 1950, many derivatives have been synthesised, leading to compounds with better bioavailability and acid stability and improved pharmacokinetics. These efforts led to the second generation of macrolides, including well-known members such as azithromycin and clarithromycin. Subsequently, in order to address increasing antibiotic resistance, a third generation of macrolides displaying improved activity against many macrolide resistant strains was developed. However, these improvements were accompanied with serious side effects, leading to disappointment and causing many researchers to stop working on macrolide derivatives, assuming that this procedure had reached the end. In contrast, a recent published breakthrough introduced a new chemical platform for synthesis and discovery of a wide range of diverse macrolide antibiotics. This chemical synthesis revolution, in combination with reduction in the side effects, namely, 'Ketek effects', has led to a macrolide renaissance, increasing the hope for novel and safe therapeutic agents to combat serious human infectious diseases.
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Affiliation(s)
- George P Dinos
- Department of Biochemistry, School of Medicine, University of Patras, Patras, Greece
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9
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New Real-Time PCR Assays for Detection of Inducible and Acquired Clarithromycin Resistance in the Mycobacterium abscessus Group. J Clin Microbiol 2015; 53:3430-7. [PMID: 26269619 DOI: 10.1128/jcm.01714-15] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 08/01/2015] [Indexed: 11/20/2022] Open
Abstract
Members of the Mycobacterium abscessus group (MAG) cause lung, soft tissue, and disseminated infections. The oral macrolides clarithromycin and azithromycin are commonly used for treatment. MAG can display clarithromycin resistance through the inducible erm(41) gene or via acquired mutations in the rrl (23S rRNA) gene. Strains harboring a truncation or a T28C substitution in erm(41) lose the inducible resistance trait. Phenotypic detection of clarithromycin resistance requires extended incubation (14 days), highlighting the need for faster methods to detect resistance. Two real-time PCR-based assays were developed to assess inducible and acquired clarithromycin resistance and tested on a total of 90 clinical and reference strains. A SYBR green assay was designed to distinguish between a full-length and truncated erm(41) gene by temperature shift in melting curve analysis. Single nucleotide polymorphism (SNP) allele discrimination assays were developed to distinguish T or C at position 28 of erm(41) and 23S rRNA rrl gene mutations at position 2058 and/or 2059. Truncated and full-size erm(41) genes were detected in 21/90 and 69/90 strains, respectively, with 64/69 displaying T at nucleotide position 28 and 5/69 containing C at that position. Fifteen isolates showed rrl mutations conferring clarithromycin resistance, including A2058G (11 isolates), A2058C (3 isolates), and A2059G (1 isolate). Targeted sequencing and phenotypic assessment of resistance concurred with molecular assay results. Interestingly, we also noted cooccurring strains harboring an active erm(41), inactive erm(41), and/or acquired mutational resistance, as well as slowly growing MAG strains and also strains displaying an inducible resistance phenotype within 5 days, long before the recommended 14-day extended incubation.
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10
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Hughes D. Selection and evolution of resistance to antimicrobial drugs. IUBMB Life 2014; 66:521-9. [PMID: 24933583 DOI: 10.1002/iub.1278] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2014] [Accepted: 05/21/2014] [Indexed: 01/22/2023]
Abstract
The overuse and misuse of antibiotics over many years has selected a high frequency of resistance among medically important bacterial pathogens. The evolution of resistance is complex, frequently involving multiple genetic alterations that minimize biological fitness costs and/or increase the resistance level. Resistance is selected at very low drug concentrations, such as found widely distributed in the environment, and this selects for resistant mutants with a high fitness. Once resistance with high fitness is established in a community it is very difficult to reduce its frequency. Addressing the problem of resistance is essential if we are to ensure a future where we can continue to enjoy effective medical control of bacterial infections. This will require several actions including the discovery and development of novel antibiotics, the creation of a continuous pipeline of drug discovery, and the implementation of effective global antibiotic stewardship to reduce the misuse of antibiotics and their release into the environment.
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Affiliation(s)
- Diarmaid Hughes
- Department of Medical Biochemistry and Microbiology, Biomedical Center, Uppsala University, Uppsala, Sweden
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11
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Nie W, Duan H, Huang H, Lu Y, Bi D, Chu N. Species identification of Mycobacterium abscessus subsp. abscessus and Mycobacterium abscessus subsp. bolletii using rpoB and hsp65, and susceptibility testing to eight antibiotics. Int J Infect Dis 2014; 25:170-4. [PMID: 24932856 DOI: 10.1016/j.ijid.2014.02.014] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Revised: 01/27/2014] [Accepted: 02/13/2014] [Indexed: 10/25/2022] Open
Abstract
OBJECTIVES To separate Mycobacterium abscessus subsp. bolletii from Mycobacterium abscessus subsp. abscessus using species identification, and to investigate the in vitro activity of amikacin, cefoxitin, imipenem, levofloxacin, moxifloxacin, clarithromycin, azithromycin, and linezolid against Mycobacterium abscessus. METHODS Seventy M. abscessus isolates, previously identified by 16S rRNA sequencing, were further identified by comparative sequence analysis of rpoB and hsp65. Drug susceptibility testing was conducted using the microplate Alamar Blue assay in accordance with Clinical and Laboratory Standards Institute (CLSI) guidelines and interpreted using CLSI breakpoints. RESULTS Of the 70 strains, 45 (64%) were M. abscessus subsp. abscessus and 25 (36%) were M. abscessus subsp. bolletii. The majority of M. abscessus isolates were susceptible to azithromycin, amikacin, linezolid, and imipenem (M. abscessus subsp. abscessus: 93%, 98%, 93%, and 73%, respectively; M. abscessus subsp. bolletii: 96%, 96%, 80%, and 68%, respectively). Approximately half of the M. abscessus isolates were moderately susceptible to cefoxitin and moxifloxacin (M. abscessus subsp. abscessus 53% and 49%; M. abscessus subsp. bolletii 72% and 68%). Nearly all the M. abscessus isolates were resistant to levofloxacin (M. abscessus subsp. abscessus 96%, M. abscessus subsp. bolletii 100%). Inducible clarithromycin resistance was found in M. abscessus. After 14 days of incubation, 83% M. abscessus subsp. abscessus and 36% M. abscessus subsp. bolletii were resistant to clarithromycin. CONCLUSIONS Using rpoB and hsp65, M. abscessus subsp. bolletii could be distinguished from M. abscessus subsp. abscessus. Amikacin and azithromycin showed excellent activity against M. abscessus in vitro. Imipenem, linezolid, cefoxitin, and moxifloxacin also showed good activity. Levofloxacin was inactive against M. abscessus. Although clarithromycin showed excellent activity against M. abscessus on day 3, inducible resistance occurred, and after 14 days clarithromycin showed little activity against M. abscessus subsp. abscessus, but still had good activity against M. abscessus subsp. bolletii.
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Affiliation(s)
- Wenjuan Nie
- Department of Tuberculosis, Beijing Chest Hospital, Capital Medical University, Tongzhou District, Beijing, PR China
| | - Hongfei Duan
- Department of Tuberculosis, Beijing Chest Hospital, Capital Medical University, Tongzhou District, Beijing, PR China
| | - Hairong Huang
- Reference Laboratory, Beijing Chest Hospital, Capital Medical University, Tongzhou District, Beijing, PR China
| | - Yu Lu
- Department of Pharmacology, Beijing Chest Hospital, Capital Medical University, Tongzhou District, Beijing, PR China
| | - Dapeng Bi
- Department of Internal Medicine, The Second People's Hospital of Jinan, Huaiyin District, Jinan City, Shandong Province, PR China
| | - Naihui Chu
- Department of Tuberculosis, Beijing Chest Hospital, Capital Medical University, Tongzhou District, Beijing, PR China.
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Gupta P, Sothiselvam S, Vázquez-Laslop N, Mankin AS. Deregulation of translation due to post-transcriptional modification of rRNA explains why erm genes are inducible. Nat Commun 2013; 4:1984. [PMID: 23749080 DOI: 10.1038/ncomms2984] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Accepted: 05/07/2013] [Indexed: 01/28/2023] Open
Abstract
A key mechanism of bacterial resistance to macrolide antibiotics is the dimethylation of a nucleotide in the large ribosomal subunit by erythromycin resistance methyltransferases. The majority of erm genes are expressed only when the antibiotic is present and the erythromycin resistance methyltransferase activity is critical for the survival of bacteria. Although these genes were among the first discovered inducible resistance genes, the molecular basis for their inducibility has remained unknown. Here we show that erythromycin resistance methyltransferase expression reduces cell fitness. Modification of the nucleotide in the ribosomal tunnel skews the cellular proteome by deregulating the expression of a set of proteins. We further demonstrate that aberrant translation of specific proteins results from abnormal interactions of the nascent peptide with the erythromycin resistance methyltransferase-modified ribosomal tunnel. Our findings provide a plausible explanation why erm genes have evolved to be inducible and underscore the importance of nascent peptide recognition by the ribosome for generating a balanced cellular proteome.
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Affiliation(s)
- Pulkit Gupta
- Center for Pharmaceutical Biotechnology, University of Illinois at Chicago, 900 S. Ashland Avenue, Chicago, IL 60607, USA
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13
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He X, Zhu X, Wang X, Wang W, Dai Y, Yan Q. Nuclear modifier MTO2 modulates the aminoglycoside-sensitivity of mitochondrial 15S rRNA C1477G mutation in Saccharomyces cerevisiae. PLoS One 2013; 8:e81490. [PMID: 24339937 PMCID: PMC3858254 DOI: 10.1371/journal.pone.0081490] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Accepted: 10/14/2013] [Indexed: 12/23/2022] Open
Abstract
The phenotypic manifestations of mitochondrial DNA (mtDNA) mutations are modulated by mitochondrial DNA haplotypes, nuclear modifier genes and environmental factors. The yeast mitochondrial 15S rRNA C1477G (PR or PR454) mutation corresponds to the human 12S rRNA C1494T and A1555G mutations, which are well known as primary factors for aminoglycoside-induced nonsyndromic deafness. Here we report that the deletion of the nuclear modifier gene MTO2 suppressed the aminoglycoside-sensitivity of mitochondrial 15S rRNA C1477G mutation in Saccharomyces cerevisiae. First, the strain with a single mtDNA C1477G mutation exhibited hypersensitivity to neomycin. Functional assays indicated that the steady-state transcription level of mitochondrial DNA, the mitochondrial respiratory rate, and the membrane potential decreased significantly after neomycin treatment. The impaired mitochondria could not produce sufficient energy to maintain cell viability. Second, when the mto2 null and the mitochondrial C1477G mutations co-existed (mto2(PR)), the oxygen consumption rate in the double mutant decreased markedly compared to that of the control strains (MTO2(PS), mto2(PS) and MTO2(PR)). The expression levels of the key glycolytic genes HXK2, PFK1 and PYK1 in the mto2(PR) strain were stimulated by neomycin and up-regulated by 89%, 112% and 55%, respectively. The enhanced glycolysis compensated for the respiratory energy deficits, and could be inhibited by the glycolytic enzyme inhibitor. Our findings in yeast will provide a new insight into the pathogenesis of human deafness.
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Affiliation(s)
- Xiangyu He
- College of Life Science, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xiaoyu Zhu
- College of Life Science, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xuexiang Wang
- College of Life Science, Zhejiang University, Hangzhou, Zhejiang, China
| | - Wei Wang
- College of Life Science, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yu Dai
- College of Life Science, Zhejiang University, Hangzhou, Zhejiang, China
| | - Qingfeng Yan
- College of Life Science, Zhejiang University, Hangzhou, Zhejiang, China
- * E-mail:
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14
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Maurer FP, Rüegger V, Ritter C, Bloemberg GV, Böttger EC. Acquisition of clarithromycin resistance mutations in the 23S rRNA gene of Mycobacterium abscessus in the presence of inducible erm(41). J Antimicrob Chemother 2012; 67:2606-11. [PMID: 22833642 DOI: 10.1093/jac/dks279] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES Antibiotic therapy of pulmonary Mycobacterium abscessus infection is based on a combination treatment including clarithromycin. Recent data demonstrated that M. abscessus may carry a chromosomal, inducible erm gene coding for the ribosomal methylase Erm(41). The purpose of this study was to investigate whether in patients with chronic M. abscessus infection undergoing clarithromycin therapy, M. abscessus acquires clarithromycin resistance mutations in the rrl gene in addition to the presence of an inducible Erm(41) methylase. METHODS We determined clarithromycin MICs, erm(41) and rrl sequences for 29 clinical M. abscessus subsp. abscessus isolates of five different patients. The isolates were obtained between 2007 and 2011 covering a longitudinal observation period of 2-4 years for the individual patients. RESULTS In three out of five patients with an initial rrl wild-type isolate, follow-up isolates demonstrated acquisition of resistance mutations in the rrl gene in addition to the presence of an inducible Erm methylase. CONCLUSIONS Our results show that in M. abscessus, clarithromycin resistance mutations in the 23S rRNA peptidyltransferase region provide an additional selective advantage independent of a functional erm(41) gene.
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Affiliation(s)
- Florian P Maurer
- Institut für Medizinische Mikrobiologie, Nationales Zentrum für Mykobakterien, Universität Zürich, 8006 Zürich, Switzerland.
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15
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Oldenburg M, Krüger A, Ferstl R, Kaufmann A, Nees G, Sigmund A, Bathke B, Lauterbach H, Suter M, Dreher S, Koedel U, Akira S, Kawai T, Buer J, Wagner H, Bauer S, Hochrein H, Kirschning CJ. TLR13 recognizes bacterial 23S rRNA devoid of erythromycin resistance-forming modification. Science 2012; 337:1111-5. [PMID: 22821982 DOI: 10.1126/science.1220363] [Citation(s) in RCA: 296] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Host protection from infection relies on the recognition of pathogens by innate pattern-recognition receptors such as Toll-like receptors (TLRs). Here, we show that the orphan receptor TLR13 in mice recognizes a conserved 23S ribosomal RNA (rRNA) sequence that is the binding site of macrolide, lincosamide, and streptogramin group (MLS) antibiotics (including erythromycin) in bacteria. Notably, 23S rRNA from clinical isolates of erythromycin-resistant Staphylococcus aureus and synthetic oligoribonucleotides carrying methylated adenosine or a guanosine mimicking a MLS resistance-causing modification failed to stimulate TLR13. Thus, our results reveal both a natural TLR13 ligand and specific mechanisms of antibiotic resistance as potent bacterial immune evasion strategy, avoiding recognition via TLR13.
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Affiliation(s)
- Marina Oldenburg
- Institute of Medical Microbiology, University of Duisburg-Essen, Essen, Germany
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16
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Kostopoulou ON, Petropoulos AD, Dinos GP, Choli-Papadopoulou T, Kalpaxis DL. Investigating the entire course of telithromycin binding to Escherichia coli ribosomes. Nucleic Acids Res 2012; 40:5078-87. [PMID: 22362747 PMCID: PMC3367204 DOI: 10.1093/nar/gks174] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Applying kinetics and footprinting analysis, we show that telithromycin, a ketolide antibiotic, binds to Escherichia coli ribosomes in a two-step process. During the first, rapidly equilibrated step, telithromycin binds to a low-affinity site (KT = 500 nM), in which the lactone ring is positioned at the upper portion of the peptide exit tunnel, while the alkyl–aryl side chain of the drug inserts a groove formed by nucleotides A789 and U790 of 23S rRNA. During the second step, telithromycin shifts slowly to a high-affinity site (KT* = 8.33 nM), in which the lactone ring remains essentially at the same position, while the side chain interacts with the base pair U2609:A752 and the extended loop of protein L22. Consistently, mutations perturbing either the base pair U2609:A752 or the L22-loop hinder shifting of telithromycin to the final position, without affecting the initial step of binding. In contrast, mutation Lys63Glu in protein L4 placed on the opposite side of the tunnel, exerts only a minor effect on telithromycin binding. Polyamines disfavor both sequential steps of binding. Our data correlate well with recent crystallographic data and rationalize the changes in the accessibility of ribosomes to telithromycin in response to ribosomal mutations and ionic changes.
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Affiliation(s)
- Ourania N Kostopoulou
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece
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17
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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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18
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Dedkova LM, Fahmi NE, Paul R, del Rosario M, Zhang L, Chen S, Feder G, Hecht SM. β-Puromycin Selection of Modified Ribosomes for in Vitro Incorporation of β-Amino Acids. Biochemistry 2011; 51:401-15. [DOI: 10.1021/bi2016124] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Larisa M. Dedkova
- Center for BioEnergetics, Biodesign
Institute and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United
States
| | - Nour Eddine Fahmi
- Center for BioEnergetics, Biodesign
Institute and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United
States
| | - Rakesh Paul
- Center for BioEnergetics, Biodesign
Institute and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United
States
| | - Melissa del Rosario
- Center for BioEnergetics, Biodesign
Institute and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United
States
| | - Liqiang Zhang
- Center for BioEnergetics, Biodesign
Institute and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United
States
| | - Shengxi Chen
- Center for BioEnergetics, Biodesign
Institute and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United
States
| | - Glen Feder
- Center for BioEnergetics, Biodesign
Institute and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United
States
| | - Sidney M. Hecht
- Center for BioEnergetics, Biodesign
Institute and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United
States
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Phylogenetic sequence variations in bacterial rRNA affect species-specific susceptibility to drugs targeting protein synthesis. Antimicrob Agents Chemother 2011; 55:4096-102. [PMID: 21730122 DOI: 10.1128/aac.01398-10] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Antibiotics targeting the bacterial ribosome typically bind to highly conserved rRNA regions with only minor phylogenetic sequence variations. It is unclear whether these sequence variations affect antibiotic susceptibility or resistance development. To address this question, we have investigated the drug binding pockets of aminoglycosides and macrolides/ketolides. The binding site of aminoglycosides is located within helix 44 of the 16S rRNA (A site); macrolides/ketolides bind to domain V of the 23S rRNA (peptidyltransferase center). We have used mutagenesis of rRNA sequences in Mycobacterium smegmatis ribosomes to reconstruct the different bacterial drug binding sites and to study the effects of rRNA sequence variations on drug activity. Our results provide a rationale for differences in species-specific drug susceptibility patterns and species-specific resistance phenotypes associated with mutational alterations in the drug binding pocket.
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20
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Li BB, Wu CM, Wang Y, Shen JZ. Single and dual mutations at positions 2058, 2503 and 2504 of 23S rRNA and their relationship to resistance to antibiotics that target the large ribosomal subunit. J Antimicrob Chemother 2011; 66:1983-6. [PMID: 21700630 DOI: 10.1093/jac/dkr268] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES To study mutations at positions A2058, A2503 and U2504 (Escherichia coli numbering) of 23S rRNA and their relationship to resistance to antibiotics that target the large ribosomal subunit. METHODS Single and dual mutations at positions 2058, 2503 and 2504 of 23S rRNA were introduced into a Mycobacterium smegmatis strain with a single functional rRNA operon. MICs of macrolide, pleuromutilin, phenicol, lincosamide and oxazolidinone antibiotics were determined for the engineered mutants. The doubling times of the mutant strains were measured to investigate how the introduced mutations affected growth rate. RESULTS Single mutations A2058G, A2503U and U2504G and double mutations A2058G-A2503U and A2058G-U2504G were successfully introduced. The A2058G mutation resulted in various levels of resistance to macrolides and clindamycin. The A2503U and U2504G mutations conferred resistance to valnemulin, chloramphenicol, florfenicol and linezolid. In addition, the A2503U mutant showed reduced susceptibility to the 16-membered macrolides tylosin, spiramycin and josamycin, and the U2504G mutant exhibited decreased susceptibility to spiramycin and josamycin. Moreover, the dual mutations A2058G-A2503U and A2058G-U2504G had co-effects on resistance to 16-membered macrolides. CONCLUSIONS 23S rRNA mutations A2058G, A2503U and U2504G play key roles in resistance to clinically useful antibiotics that target the large ribosomal subunit. Furthermore, the double mutations A2058G-A2503U and A2058G-U2504G have combined effects on resistance to 16-membered macrolides.
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Affiliation(s)
- Bei-Bei Li
- Key Laboratory of Development and Evaluation of the Chemical and Herbal Drugs for Animal Use, Department of Veterinary Pharmacology and Toxicology, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
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Trends towards lower antimicrobial susceptibility and characterization of acquired resistance among clinical isolates of Brachyspira hyodysenteriae in Spain. Antimicrob Agents Chemother 2011; 55:3330-7. [PMID: 21555771 DOI: 10.1128/aac.01749-10] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The antimicrobial susceptibility of clinical isolates of Brachyspira hyodysenteriae in Spain was monitored, and the underlying molecular mechanisms of resistance were investigated. MICs of tylosin, tiamulin, valnemulin, lincomycin, and tylvalosin were determined for 87 B. hyodysenteriae isolates recovered from 2008 to 2009 by broth dilution. Domain V of the 23S rRNA gene and the ribosomal protein L3 gene were sequenced in 20 isolates for which the tiamulin MIC was ≥ 4 μg/ml, presenting decreased susceptibility, and in 18 tiamulin-susceptible isolates (MIC ≤ 0.125 μg/ml), and all isolates were typed by multiple-locus variable-number tandem repeats analysis. A comparison with antimicrobial susceptibility data from 2000 to 2007 showed an increase in pleuromutilin resistance over time, doubling the number of isolates with decreased susceptibility to tiamulin. No alteration in susceptibility was detected for lincomycin, and the MIC of tylosin remained high (MIC(50) > 128 μg/ml). The decreased susceptibility to tylosin and lincomycin can be explained by mutations at position A2058 of the 23S rRNA gene (Escherichia coli numbering). A2058T was the predominant mutation, but A2058G also was found together with a change of the neighboring base pair at positions 2057 to 2611. The role of additional point mutations in the vicinity of the peptidyl transferase center and mutations in the L3 at amino acids 148 and 149 and their possible involvement in antimicrobial susceptibility are considered. An association between G2032A and high levels of tiamulin and lincomycin MICs was found, suggesting an increasing importance of this mutation in antimicrobial resistance of clinical isolates of B. hyodysenteriae.
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The origin of a derived superkingdom: how a gram-positive bacterium crossed the desert to become an archaeon. Biol Direct 2011; 6:16. [PMID: 21356104 PMCID: PMC3056875 DOI: 10.1186/1745-6150-6-16] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2010] [Accepted: 02/28/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The tree of life is usually rooted between archaea and bacteria. We have previously presented three arguments that support placing the root of the tree of life in bacteria. The data have been dismissed because those who support the canonical rooting between the prokaryotic superkingdoms cannot imagine how the vast divide between the prokaryotic superkingdoms could be crossed. RESULTS We review the evidence that archaea are derived, as well as their biggest differences with bacteria. We argue that using novel data the gap between the superkingdoms is not insurmountable. We consider whether archaea are holophyletic or paraphyletic; essential to understanding their origin. Finally, we review several hypotheses on the origins of archaea and, where possible, evaluate each hypothesis using bioinformatics tools. As a result we argue for a firmicute ancestry for archaea over proposals for an actinobacterial ancestry. CONCLUSION We believe a synthesis of the hypotheses of Lake, Gupta, and Cavalier-Smith is possible where a combination of antibiotic warfare and viral endosymbiosis in the bacilli led to dramatic changes in a bacterium that resulted in the birth of archaea and eukaryotes. REVIEWERS This article was reviewed by Patrick Forterre, Eugene Koonin, and Gáspár Jékely.
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Inagaki T, Yagi T, Ichikawa K, Nakagawa T, Moriyama M, Uchiya KI, Nikai T, Ogawa K. Evaluation of a rapid detection method of clarithromycin resistance genes in Mycobacterium avium complex isolates. J Antimicrob Chemother 2011; 66:722-9. [DOI: 10.1093/jac/dkq536] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Bogdanov AA, Sumbatyan NV, Shishkina AV, Karpenko VV, Korshunova GA. Ribosomal tunnel and translation regulation. BIOCHEMISTRY (MOSCOW) 2011; 75:1501-16. [DOI: 10.1134/s0006297910130018] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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Zhu H, Wang HP, Jiang Y, Hou SP, Liu YJ, Liu QZ. Mutations in 23S rRNA and ribosomal protein L4 account for resistance in Chlamydia trachomatis strains selected in vitro by macrolide passage. Andrologia 2010; 42:274-80. [DOI: 10.1111/j.1439-0272.2009.01019.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Yonath A. Winterschlafende Bären, Antibiotika und die Evolution des Ribosoms (Nobel-Aufsatz). Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201001297] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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27
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Yonath A. Hibernating Bears, Antibiotics, and the Evolving Ribosome (Nobel Lecture). Angew Chem Int Ed Engl 2010; 49:4341-54. [DOI: 10.1002/anie.201001297] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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28
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The structure of ribosome-lankacidin complex reveals ribosomal sites for synergistic antibiotics. Proc Natl Acad Sci U S A 2010; 107:1983-8. [PMID: 20080686 PMCID: PMC2804743 DOI: 10.1073/pnas.0914100107] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Crystallographic analysis revealed that the 17-member polyketide antibiotic lankacidin produced by Streptomyces rochei binds at the peptidyl transferase center of the eubacterial large ribosomal subunit. Biochemical and functional studies verified this finding and showed interference with peptide bond formation. Chemical probing indicated that the macrolide lankamycin, a second antibiotic produced by the same species, binds at a neighboring site, at the ribosome exit tunnel. These two antibiotics can bind to the ribosome simultaneously and display synergy in inhibiting bacterial growth. The binding site of lankacidin and lankamycin partially overlap with the binding site of another pair of synergistic antibiotics, the streptogramins. Thus, at least two pairs of structurally dissimilar compounds have been selected in the course of evolution to act synergistically by targeting neighboring sites in the ribosome. These results underscore the importance of the corresponding ribosomal sites for development of clinically relevant synergistic antibiotics and demonstrate the utility of structural analysis for providing new directions for drug discovery.
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Imkamp F, Rosenberger T, Striebel F, Keller PM, Amstutz B, Sander P, Weber-Ban E. Deletion of dop in Mycobacterium smegmatis abolishes pupylation of protein substrates in vivo. Mol Microbiol 2009; 75:744-54. [PMID: 20025664 DOI: 10.1111/j.1365-2958.2009.07013.x] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Proteasome-bearing bacteria make use of a ubiquitin-like modification pathway to target proteins for proteasomal turnover. In a process termed pupylation, proteasomal substrates are covalently modified with the small protein Pup that serves as a degradation signal. Pup is attached to substrate proteins by action of PafA. Prior to its attachment, Pup needs to undergo deamidation at its C-terminal residue, converting glutamine to glutamate. This step is catalysed in vitro by Dop. In order to characterize Dop activity in vivo, we generated a dop deletion mutant in Mycobacterium smegmatis. In the Deltadop strain, pupylation is severely impaired and the steady-state levels of two known proteasomal substrates are drastically increased. Pupylation can be re-established by complementing the mutant with either DopWt or a Pup variant carrying a glutamate at its ultimate C-terminal position (PupGGE). Our data show that Pup is deamidated by Dop in vivo and that likely Dop alone is responsible for this activity. Furthermore, we demonstrate that a putative N-terminal ATP-binding motif is crucial for catalysis, as a single point mutation (E10A) in this motif abolishes Dop activity both in vivo and in vitro.
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Affiliation(s)
- Frank Imkamp
- ETH Zurich, Institute of Molecular Biology & Biophysics, Zurich, Switzerland
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Kempf I, Zeitouni S. [The cost of antibiotic resistance: analysis and consequences]. ACTA ACUST UNITED AC 2009; 60:e9-14. [PMID: 19942376 DOI: 10.1016/j.patbio.2009.10.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2009] [Accepted: 10/27/2009] [Indexed: 11/16/2022]
Abstract
Antimicrobial resistance, either by mutation or acquisition of resistance determinants harbored by mobile genetic elements, may confer a biological cost for the bacteria. This biological cost can be evaluated by comparing the resistant mutant to the wild susceptible strain, in the absence of antibiotic selection. This fitness cost can affect the growth rate in vitro or the survival in the host or in the environment or the virulence capacity. Various studies have evidenced this cost, either in vitro or in vivo, in different analysis models. However, bacteria can evolve and adapt to reduce this cost, by compensatory mutations or fine regulation of resistance expression. This compensatory evolution allows resistant bacteria to persist even in the absence of antibiotic selection pressure.
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Affiliation(s)
- I Kempf
- Unite´ mycoplasmologie-bacteriologie, Zoopole-les-Croix, 22440 Ploufragan, France.
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31
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Wekselman I, Davidovich C, Agmon I, Zimmerman E, Rozenberg H, Bashan A, Berisio R, Yonath A. Ribosome's mode of function: myths, facts and recent results. J Pept Sci 2009; 15:122-30. [DOI: 10.1002/psc.1077] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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32
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Fulle S, Gohlke H. Statics of the ribosomal exit tunnel: implications for cotranslational peptide folding, elongation regulation, and antibiotics binding. J Mol Biol 2009; 387:502-17. [PMID: 19356596 DOI: 10.1016/j.jmb.2009.01.037] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2008] [Revised: 01/18/2009] [Accepted: 01/21/2009] [Indexed: 10/21/2022]
Abstract
A sophisticated interplay between the static properties of the ribosomal exit tunnel and its functional role in cotranslational processes is revealed by constraint counting on topological network representations of large ribosomal subunits from four different organisms. As for the global flexibility characteristics of the subunit, the results demonstrate a conserved stable structural environment of the tunnel. The findings render unlikely that deformations of the tunnel move peptides down the tunnel in an active manner. Furthermore, the stable environment rules out that the tunnel can adapt widely so as to allow tertiary folding of nascent chains. Nevertheless, there are local zones of flexible nucleotides within the tunnel, between the peptidyl transferase center and the tunnel constriction, and at the tunnel exit. These flexible zones strikingly agree with previously identified folding zones. As for cotranslational elongation regulation, flexible residues in the beta-hairpin of the ribosomal L22 protein were verified, as suggested previously based on structural results. These results support the hypothesis that L22 can undergo conformational changes that regulate the tunnel voyage of nascent polypeptides. Furthermore, rRNA elements, for which conformational changes have been observed upon interaction of the tunnel wall with a nascent SecM peptide, are less strongly coupled to the subunit core. Sequences of coupled rigid clusters are identified between the tunnel and some of these elements, suggesting signal transmission by a domino-like mechanical coupling. Finally, differences in the flexibility of the glycosidic bonds of bases that form antibiotics-binding crevices within the peptidyl transferase center and the tunnel region are revealed for ribosomal structures from different kingdoms. In order to explain antibiotics selectivity, action, and resistance, according to these results, differences in the degrees of freedom of the binding regions may need to be considered.
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Affiliation(s)
- Simone Fulle
- Department of Biological Sciences, Molecular Bioinformatics Group, Goethe University, Frankfurt, Germany
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33
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Ribosome: an Ancient Cellular Nano-Machine for Genetic Code Translation. NATO SCIENCE FOR PEACE AND SECURITY SERIES B: PHYSICS AND BIOPHYSICS 2009. [DOI: 10.1007/978-90-481-2368-1_8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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34
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Genetic analysis of interactions with eukaryotic rRNA identify the mitoribosome as target in aminoglycoside ototoxicity. Proc Natl Acad Sci U S A 2008; 105:20888-93. [PMID: 19104050 DOI: 10.1073/pnas.0811258106] [Citation(s) in RCA: 138] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Aminoglycoside ototoxicity has been related to a surprisingly large number of cellular structures and metabolic pathways. The finding that patients with mutations in mitochondrial rRNA are hypersusceptible to aminoglycoside-induced hearing loss has indicated a possible role for mitochondrial protein synthesis. To study the molecular interaction of aminoglycosides with eukaryotic ribosomes, we made use of the observation that the drug binding site is a distinct domain defined by the small subunit rRNA, and investigated drug susceptibility of bacterial hybrid ribosomes carrying various alleles of the eukaryotic decoding site. Compared to hybrid ribosomes with the A site of human cytosolic ribosomes, susceptibility of mitochondrial hybrid ribosomes to various aminoglycosides correlated with the relative cochleotoxicity of these drugs. Sequence alterations that correspond to the mitochondrial deafness mutations A1555G and C1494T increased drug-binding and rendered the ribosomal decoding site hypersusceptible to aminoglycoside-induced mistranslation and inhibition of protein synthesis. Our results provide experimental support for aminoglycoside-induced dysfunction of the mitochondrial ribosome. We propose a pathogenic mechanism in which interference of aminoglycosides with mitochondrial protein synthesis exacerbates the drugs' cochlear toxicity, playing a key role in sporadic dose-dependent and genetically inherited, aminoglycoside-induced deafness.
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35
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Petropoulos AD, Kouvela EC, Starosta AL, Wilson DN, Dinos GP, Kalpaxis DL. Time-resolved binding of azithromycin to Escherichia coli ribosomes. J Mol Biol 2008; 385:1179-92. [PMID: 19071138 DOI: 10.1016/j.jmb.2008.11.042] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2008] [Revised: 11/13/2008] [Accepted: 11/18/2008] [Indexed: 11/19/2022]
Abstract
Azithromycin is a semisynthetic derivative of erythromycin that inhibits bacterial protein synthesis by binding within the peptide exit tunnel of the 50S ribosomal subunit. Nevertheless, there is still debate over what localization is primarily responsible for azithromycin binding and as to how many molecules of the drug actually bind per ribosome. In the present study, kinetic methods and footprinting analysis are coupled together to provide time-resolved details of the azithromycin binding process. It is shown that azithromycin binds to Escherichia coli ribosomes in a two-step process: The first-step involves recognition of azithromycin by the ribosomal machinery and places the drug in a low-affinity site located in the upper part of the exit tunnel. The second step corresponds to the slow formation of a final complex that is both much tighter and more potent in hindering the progression of the nascent peptide through the exit tunnel. Substitution of uracil by cytosine at nucleoside 2609 of 23S rRNA, a base implicated in the high-affinity site, facilitates the shift of azithromycin to this site. In contrast, mutation U754A hardly affects the binding process. Binding of azithromycin to both sites is hindered by high concentrations of Mg(2+) ions. Unlike Mg(2+) ions, polyamines do not significantly affect drug binding to the low-affinity site but attenuate the formation of the final complex. The low- and high-affinity sites of azithromycin binding are mutually exclusive, which means that one molecule of the drug binds per E. coli ribosome at a time. In contrast, kinetic and binding data indicate that in Deinococcus radiodurans, two molecules of azithromycin bind cooperatively to the ribosome. This finding confirms previous crystallographic results and supports the notion that species-specific structural differences may primarily account for the apparent discrepancies between the antibiotic binding modes obtained for different organisms.
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36
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Mankin AS. Macrolide myths. Curr Opin Microbiol 2008; 11:414-21. [PMID: 18804176 DOI: 10.1016/j.mib.2008.08.003] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2008] [Revised: 08/11/2008] [Accepted: 08/22/2008] [Indexed: 10/21/2022]
Abstract
In spite of decades of research, our knowledge of the mode of interaction of macrolide antibiotics with their ribosomal target and of the mechanism of action of these drugs remain fragmentary. Experimental facts obtained over the past several years question some of the concepts that were viewed as a 'common knowledge'. This review focuses on certain aspects of binding and action of macrolides that may need re-evaluation in view of the new findings.
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Affiliation(s)
- Alexander S Mankin
- Center for Pharmaceutical Biotechnology-m/c 870, University of Illinois at Chicago, 900 S. Ashland Avenue, Room 3052, Chicago, IL 60607, USA.
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37
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Bruell CM, Eichholz C, Kubarenko A, Post V, Katunin VI, Hobbie SN, Rodnina MV, Böttger EC. Conservation of bacterial protein synthesis machinery: initiation and elongation in Mycobacterium smegmatis. Biochemistry 2008; 47:8828-39. [PMID: 18672904 DOI: 10.1021/bi800527k] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Most of our understanding of ribosome function is based on experiments utilizing translational components from Escherichia coli. It is not clear to which extent the details of translation mechanisms derived from this single organism are true for all bacteria. Here we investigate translation factor-dependent reactions of initiation and elongation in a reconstituted translation system from a Gram-positive bacterium Mycobacterium smegmatis. This organism was chosen because mutations in rRNA have very different phenotypes in E. coli and M. smegmatis, and the docking site for translational GTPases, the L12 stalk, is extended in the ribosomes from M. smegmatis compared to E. coli. M. smegmatis genes coding for IF1, IF2, IF3, EF-G, and EF-Tu were identified by sequence alignments; the respective recombinant proteins were prepared and studied in a variety of biochemical and biophysical assays with M. smegmatis ribosomes. We found that the activities of initiation and elongation factors and the rates of elemental reactions of initiation and elongation of protein synthesis are remarkably similar with M. smegmatis and E. coli components. The data suggest a very high degree of conservation of basic translation mechanisms, probably due to coevolution of the ribosome components and translation factors. This work establishes the reconstituted translation system from individual purified M. smegmatis components as an alternative to that from E. coli to study the mechanisms of translation and to test the action of antibiotics against Gram-positive bacteria.
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38
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Novel mutation in 23S rRNA that confers low-level resistance to clarithromycin in Helicobacter pylori. Antimicrob Agents Chemother 2008; 52:3465-6. [PMID: 18606842 DOI: 10.1128/aac.00445-08] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
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39
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Bashan A, Yonath A. Correlating ribosome function with high-resolution structures. Trends Microbiol 2008; 16:326-35. [PMID: 18547810 DOI: 10.1016/j.tim.2008.05.001] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2007] [Revised: 05/03/2008] [Accepted: 05/07/2008] [Indexed: 10/22/2022]
Abstract
Ribosome research has undergone astonishing progress in recent years. Crystal structures have shed light on the functional properties of the translation machinery and revealed how the striking architecture of the ribosome is ingeniously designed as the framework for its unique capabilities: precise decoding, substrate-mediated peptide-bond formation and efficient polymerase activity. New findings include the two concerted elements of tRNA translocation: sideways shift and a ribosomal-navigated rotatory motion; the dynamics of the nascent-chain exit tunnel and the shelter formed by the ribosome-bound trigger-factor, which acts as a chaperone to prevent nascent-chain aggregation and misfolding. The availability of these structures has also illuminated the action, selectivity, resistance and synergism of antibiotics that target ribosomes.
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Affiliation(s)
- Anat Bashan
- Department of Structural Biology, Weizmann Institute, Rehovot, 76100, Israel
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40
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Ashby CR, Jodlowski TZ, Sym D. Medications for Extensively Drug-Resistant Tuberculosis: Back to the Future? J Pharm Technol 2008. [DOI: 10.1177/875512250802400205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Objective: To reexamine the existing medications for the potential treatment of extensively drug-resistant tuberculosis (XDR-TB), based on susceptibility data, and to identify potential future medications from the literature. Data Sources: Relevant information was identified through a search of MEDLINE (1966–November 2007), PubMed (1955–November 2007), American Search Premier (1975–November 2007), International Pharmaceutical Abstracts (1960–November 2007), Science Citation Index Expanded (1996–November 2007), Cochrane Databases (publications archived until November 2007), and various tertiary sources as listed in the references, using the terms extensively drug-resistant tuberculosis (XDR-TB), ethambutol, pyrazinamide, para-aminosalicylic acid, cycloserine, linezolid, diarylquinoline, nitroimidazopyran, fluoroquinolones, β-lactams, new treatments, and ethionamide alone or in combination regimens. Study Selection and Data Extraction: After identification of the relevant information, the data presented in this article were selected based on clinical relevance and value of information. Data Synthesis: Based on susceptibility data, pyrazinamide, ethambutol, para-aminosalicylic acid, cycloserine, and ethionamide may be used for the treatment of tuberculosis. However, due to the emergence of XDR-TB, many of these agents are no longer successful treatment regimens. We have found limited data supporting potential future use of β-lactams, clarithromycin, and linezolid in resistant TB infections. TMC207, nitroimidazopyran, and SQ109 compounds may also prove to be viable options in the near future for treatment of tuberculosis, especially in cases with resistance to mainstay medications. Conclusions: Extensively resistant tuberculosis appears to be a potentially catastrophic disease if allowed to spread. Due to its resistance profile, very few potentially effective agents are available, calling attention to this growing problem.
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Affiliation(s)
- Charles R Ashby
- CHARLES R ASHBY JR PhD, Professor, St. John's University College of Pharmacy and Allied Health Professions, Queens, NY
| | - Tomasz Z Jodlowski
- TOMASZ Z JODLOWSKI PharmD BCPS, Assistant Clinical Professor, St. John's University College of Pharmacy and Allied Health Professions, Queens, NY; Infectious Diseases Clinical Pharmacist, Beth Israel Medical Center, New York, NY
| | - Donna Sym
- DONNA SYM BS PharmD, Assistant Clinical Professor, St. John's University College of Pharmacy and Allied Health Professions; Clinical Preceptor, North Shore University Hospital, Manhasset, NY
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41
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Bommakanti AS, Lindahl L, Zengel JM. Mutation from guanine to adenine in 25S rRNA at the position equivalent to E. coli A2058 does not confer erythromycin sensitivity in Sacchromyces cerevisae. RNA (NEW YORK, N.Y.) 2008; 14:460-464. [PMID: 18218702 PMCID: PMC2248265 DOI: 10.1261/rna.786408] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2007] [Accepted: 11/27/2007] [Indexed: 05/25/2023]
Abstract
The macrolide erythromycin binds to the large subunit of the prokaryotic ribosome near the peptidyltransferase center (PTC) and inhibits elongation of new peptide chains beyond a few amino acids. Nucleotides A2058 and A2059 (E. coli numbering) in 23S rRNA play a crucial role in the binding of erythromycin, and mutation of nucleotide A2058 confers erythromycin resistance in both gram-positive and gram-negative bacteria. There are high levels of sequence and structural similarity in the PTC of prokaryotic and eukaryotic ribosomes. However, eukaryotic ribosomes are resistant to erythromycin and the presence of a G at the position equivalent to E. coli nucleotide A2058 is believed to be the reason. To test this hypothesis, we introduced a G to A mutation at this position of the yeast Saccharomyces cerevisiae 25S rRNA and analyzed sensitivity toward erythromycin. Neither growth studies nor erythromycin binding assays on mutated yeast ribosomes indicated any erythromycin sensitivity in mutated yeast strains. These results suggest that the identity of nucleotide 2058 is not the only determinant responsible for the difference in erythromycin sensitivity between yeast and prokaryotes.
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MESH Headings
- Base Sequence
- DNA Primers/genetics
- Drug Resistance, Fungal/genetics
- Erythromycin/metabolism
- Erythromycin/pharmacology
- Escherichia coli/drug effects
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Genes, Bacterial
- Genes, Fungal
- Molecular Sequence Data
- Mutagenesis, Site-Directed
- Nucleic Acid Conformation
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Fungal/chemistry
- RNA, Fungal/genetics
- RNA, Fungal/metabolism
- RNA, Ribosomal/chemistry
- RNA, Ribosomal/genetics
- RNA, Ribosomal/metabolism
- Ribosomes/metabolism
- Saccharomyces cerevisiae/drug effects
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae/metabolism
- Species Specificity
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Affiliation(s)
- Ananth S Bommakanti
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, Maryland 21250, USA
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42
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Fan-Minogue H, Bedwell DM. Eukaryotic ribosomal RNA determinants of aminoglycoside resistance and their role in translational fidelity. RNA (NEW YORK, N.Y.) 2008; 14:148-57. [PMID: 18003936 PMCID: PMC2151042 DOI: 10.1261/rna.805208] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Recent studies of prokaryotic ribosomes have dramatically increased our knowledge of ribosomal RNA (rRNA) structure, functional centers, and their interactions with antibiotics. However, much less is known about how rRNA function differs between prokaryotic and eukaryotic ribosomes. The core decoding sites are identical in yeast and human 18S rRNAs, suggesting that insights obtained in studies with yeast rRNA mutants can provide information about ribosome function in both species. In this study, we examined the importance of key nucleotides of the 18S rRNA decoding site on ribosome function and aminoglycoside susceptibility in Saccharomyces cerevisiae cells expressing homogeneous populations of mutant ribosomes. We found that residues G577, A1755, and A1756 (corresponding to Escherichia coli residues G530, A1492, and A1493, respectively) are essential for cell viability. We also found that residue G1645 (A1408 in E. coli) and A1754 (G1491 in E. coli) both make significant and distinct contributions to aminoglycoside resistance. Furthermore, we found that mutations at these residues do not alter the basal level of translational accuracy, but influence both paromomycin-induced misreading of sense codons and readthrough of stop codons. This study represents the most comprehensive mutational analysis of the eukaryotic decoding site to date, and suggests that many fundamental features of decoding site function are conserved between prokaryotes and eukaryotes.
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Affiliation(s)
- Hua Fan-Minogue
- Department of Cell Biology, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
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43
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Petropoulos AD, Kouvela EC, Dinos GP, Kalpaxis DL. Stepwise binding of tylosin and erythromycin to Escherichia coli ribosomes, characterized by kinetic and footprinting analysis. J Biol Chem 2007; 283:4756-65. [PMID: 18079110 DOI: 10.1074/jbc.m708371200] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Erythromycin and tylosin are 14- and 16-membered lactone ring macrolides, respectively. The current work shows by means of kinetic and chemical footprinting analysis that both antibiotics bind to Escherichia coli ribosomes in a two-step process. The first step established rapidly, involves a low-affinity binding site placed at the entrance of the exit tunnel in the large ribosomal subunit, where macrolides bind primarily through their hydrophobic portions. Subsequently, slow conformational changes mediated by the antibiotic hydrophilic portion push the drugs deeper into the tunnel, in a high-affinity site. Compared with erythromycin, tylosin shifts to the high-affinity site more rapidly, due to the interaction of the mycinose sugar of the drug with the loop of H35 in domain II of 23 S rRNA. Consistently, mutations of nucleosides U2609 and U754 implicated in the high-affinity site reduce the shift of tylosin to this site and destabilize, respectively, the final drug-ribosome complex. The weak interaction between tylosin and the ribosome is Mg2+ independent, unlike the tight binding. In contrast, both interactions between erythromycin and the ribosome are reduced by increasing concentrations of Mg2+ ions. Polyamines attenuate erythromycin affinity for the ribosome at both sequential steps of binding. In contrast, polyamines facilitate the initial binding of tylosin, but exert a detrimental, more pronounced, effect on the drug accommodation at its final position. Our results emphasize the role of the particular interactions that side chains of tylosin and erythromycin establish with 23 S rRNA, which govern the exact binding process of each drug and its response to the ionic environment.
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44
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Binet R, Maurelli AT. Frequency of development and associated physiological cost of azithromycin resistance in Chlamydia psittaci 6BC and C. trachomatis L2. Antimicrob Agents Chemother 2007; 51:4267-75. [PMID: 17908942 PMCID: PMC2167982 DOI: 10.1128/aac.00962-07] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Azithromycin is a major drug used in the treatment and prophylaxis of chlamydial infections. Spontaneous azithromycin-resistant mutants of Chlamydia psittaci 6BC were isolated in vitro in the plaque assay at a frequency of about 10(-8). Isogenic clonal variants with A(2058)C, A(2059)G, or A(2059)C mutations in the unique 23S rRNA gene (Escherichia coli numbering system) displayed MICs for multiple macrolides (i.e., azithromycin, erythromycin, josamycin, and spiramycin) at least 100 times higher than those of the parent strain and were also more resistant to the lincosamide clindamycin. Chlamydia trachomatis L2 variants with a Gln-to-Lys substitution in ribosomal protein L4 at position 66 (E. coli numbering system), conferring an eightfold decrease in azithromycin and erythromycin sensitivities and a fourfold decrease in josamycin and spiramycin sensitivities, were isolated following serial passage in subinhibitory concentrations of azithromycin. Each mutation was stably maintained in the absence of selection but severely affected chlamydial infectivity, as determined by monitoring the development of each isolate over 46 h in the absence of selection, in pure culture or in 1:1 competition with the isogenic parent. Data in this study support the hypothesis that the mechanisms which confer high-level macrolide resistance in chlamydiae carry a prohibitive physiological cost and may thus limit the emergence of highly resistant clones of these important pathogens in vivo.
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Affiliation(s)
- Rachel Binet
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, 4301 Jones Bridge Road, Bethesda, MD 20814-4799, USA
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45
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Hobbie SN, Kalapala SK, Akshay S, Bruell C, Schmidt S, Dabow S, Vasella A, Sander P, Böttger EC. Engineering the rRNA decoding site of eukaryotic cytosolic ribosomes in bacteria. Nucleic Acids Res 2007; 35:6086-93. [PMID: 17766247 PMCID: PMC2094070 DOI: 10.1093/nar/gkm658] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Structural and genetic studies on prokaryotic ribosomes have provided important insights into fundamental aspects of protein synthesis and translational control and its interaction with ribosomal drugs. Comparable mechanistic studies in eukaryotes are mainly hampered by the absence of both high-resolution crystal structures and efficient genetic models. To study the interaction of aminoglycoside antibiotics with selected eukaryotic ribosomes, we replaced the bacterial drug binding site in 16S rRNA with its eukaryotic counterpart, resulting in bacterial hybrid ribosomes with a fully functional eukaryotic rRNA decoding site. Cell-free translation assays demonstrated that hybrid ribosomes carrying the rRNA decoding site of higher eukaryotes show pronounced resistance to aminoglycoside antibiotics, equivalent to that of rabbit reticulocyte ribosomes, while the decoding sites of parasitic protozoa show distinctive drug susceptibility. Our findings suggest that phylogenetically variable components of the ribosome, other than the rRNA-binding site, do not affect aminoglycoside susceptibility of the protein-synthesis machinery. The activities of the hybrid ribosomes indicate that helix 44 of the rRNA decoding site behaves as an autonomous domain, which can be exchanged between ribosomes of different phylogenetic domains for study of function.
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Affiliation(s)
- Sven N Hobbie
- Institut für Medizinische Mikrobiologie, Universität Zürich and Laboratorium für Organische Chemie, ETH Zürich, Switzerland.
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46
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Abstract
The ribosome is responsible for protein synthesis, the translation of the genetic code, in all living organisms. Ribosomes are composed of RNA (ribosomal RNA) and protein (ribosomal protein). Soluble protein factors bind to the ribosome and facilitate different phases of translation. Genetic approaches have proved useful for the identification and characterization of the structural and functional roles of specific nucleotides in ribosomal RNA and of specific amino acids in ribosomal proteins and in ribosomal factors. This chapter summarizes examples of mutations identified in ribosomal RNA, ribosomal proteins, and ribosomal factors.
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MESH Headings
- Animals
- Base Sequence
- DNA Mutational Analysis
- Humans
- Mutation
- Nucleic Acid Conformation
- Peptide Elongation Factors/genetics
- Peptide Initiation Factors/genetics
- Peptide Termination Factors/genetics
- Protein Subunits/genetics
- RNA, Ribosomal, 16S/analysis
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/physiology
- RNA, Ribosomal, 23S/analysis
- RNA, Ribosomal, 23S/chemistry
- RNA, Ribosomal, 23S/physiology
- Ribosomal Proteins/genetics
- Ribosomes/genetics
- Sequence Analysis, RNA
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Affiliation(s)
- Kathleen L Triman
- Department of Biology, Franklin and Marshall College, Lancaster, PA 17604, USA
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47
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Montero CI, Johnson MR, Chou CJ, Conners SB, Geouge SG, Tachdjian S, Nichols JD, Kelly RM. Responses of wild-type and resistant strains of the hyperthermophilic bacterium Thermotoga maritima to chloramphenicol challenge. Appl Environ Microbiol 2007; 73:5058-65. [PMID: 17557852 PMCID: PMC1951032 DOI: 10.1128/aem.00453-07] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Transcriptomes and growth physiologies of the hyperthermophile Thermotoga maritima and an antibiotic-resistant spontaneous mutant were compared prior to and following exposure to chloramphenicol. While the wild-type response was similar to that of mesophilic bacteria, reduced susceptibility of the mutant was attributed to five mutations in 23S rRNA and phenotypic preconditioning to chloramphenicol.
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Affiliation(s)
- Clemente I Montero
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695-7905, USA
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48
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Biswas S, Raoult D, Rolain JM. Molecular mechanisms of resistance to antibiotics in Bartonella bacilliformis. J Antimicrob Chemother 2007; 59:1065-70. [PMID: 17449882 DOI: 10.1093/jac/dkm105] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
OBJECTIVES Bartonella bacilliformis is the aetiological agent of Carrion's disease. Although ciprofloxacin, rifampicin and erythromycin have been successfully used in the treatment of the disease, failures and relapses have been reported. The objective of our study was to select in vitro mutants resistant to antibiotics in order to determine the frequency of mutations and to characterize the mechanism of resistance at the molecular level. METHODS Antibiotic-resistant mutants were selected by serial passages of bacteria on blood agar plates containing antibiotics. Candidate genes involved in resistance were amplified and sequenced and compared in order to look at mutations associated with antibiotic resistance. RESULTS Ciprofloxacin-, rifampicin- and erythromycin-resistant mutants were obtained after five, three and four passages, respectively. Conversely, no mutant was obtained with either gentamicin or doxycycline even after 16 passages. The ciprofloxacin mutant contained an amino acid change at position 87 (Asp --> Asn) in its quinolone resistance-determining region of the DNA gyrase protein, whereas the rifampicin-resistant strain had an amino acid change at position 531 (Ser --> Phe) in the rifampicin resistance-determining region of the rpoB gene. Similarly, the erythromycin-resistant mutant showed an A2058G mutation in the 23S rRNA gene. CONCLUSIONS According with the current knowledge on the treatment of human bartonellosis, we believe that doxycycline in association with gentamicin may be the preferred regimen for the treatment of the acute and eruptive stages of Carrion's disease, but clinical trials are warranted to support our findings.
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Affiliation(s)
- Silpak Biswas
- Unité des Rickettsies, CNRS UMR 6020, IFR 48, Faculté de Médecine et de Pharmacie, Université de la Méditerranée, 27 Bd Jean Moulin, 13385 Marseille Cedex 05, France
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49
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Pyetan E, Baram D, Auerbach-Nevo T, Yonath A. Chemical parameters influencing fine-tuning in the binding of macrolide antibiotics to the ribosomal tunnel. PURE APPL CHEM 2007. [DOI: 10.1351/pac200779060955] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
In comparison to existing structural, biochemical, and therapeutical data, the crystal structures of large ribosomal subunit from the eubacterial pathogen model Deinococcus radiodurans in complex with the 14-membered macrolides erythromycylamine, RU69874, and the 16-membered macrolide josamycin, highlighted the similarities and differences in macrolides binding to the ribosomal tunnel. The three compounds occupy the macrolide binding pocket with their desosamine or mycaminose aminosugar, the C4-C7 edge of the macrolactone ring and the cladinose sugar sharing similar positions and orientations, although the latter, known to be unnecessary for antibiotic activity, displays fewer contacts. The macrolactone ring displays altogether few contacts with the ribosome and can, therefore, tilt in order to optimize its interaction with the 23S rRNA. In addition to their contacts with nucleotides of domain V of the 23S RNA, erythromycylamine and RU69874 interact with domain II nucleotide U790, and RU69874 also reaches van der Waals distance from A752, in a fashion similar to that observed for the ketolides telithromycin and cethromycin. The variability in the sequences and consequently the diversity of the conformations of macrolide binding pockets in various bacterial species can explain the drug's altered level of effectiveness on different organisms and is thus an important factor in structure-based drug design.
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Affiliation(s)
- Erez Pyetan
- 1Department of Structural Biology, the Weizmann Institute of Science, 76100 Rehovot, Israel
| | - David Baram
- 1Department of Structural Biology, the Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Tamar Auerbach-Nevo
- 1Department of Structural Biology, the Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Ada Yonath
- 1Department of Structural Biology, the Weizmann Institute of Science, 76100 Rehovot, Israel
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Robinson DA, Sutcliffe JA, Tewodros W, Manoharan A, Bessen DE. Evolution and global dissemination of macrolide-resistant group A streptococci. Antimicrob Agents Chemother 2006; 50:2903-11. [PMID: 16940080 PMCID: PMC1563541 DOI: 10.1128/aac.00325-06] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Macrolide-resistant group A streptococci (MRGAS) have been recovered from many countries worldwide. However, the strain typing information that is available has been insufficient for estimating the total number of macrolide-resistant clones, their geographic distributions, and their evolutionary relationships. In this study, sequence-based strain typing was used to characterize 212 MRGAS isolates from 34 countries. Evaluation of clonal complexes, emm type, and resistance gene content [erm(A), erm(B), mef(A), and undefined] indicate that macrolide resistance was acquired by GAS organisms via > or independent genetic events. In contrast to other collections of mostly susceptible GAS, genetic diversification of MRGAS clones has occurred primarily by mutation rather than by recombination. Twenty-two MRGAS clonal complexes were recovered from more than one continent; intercontinental strains represent nearly 80% of the MRGAS isolates under study. The findings suggest that horizontal transfer of macrolide resistance genes to numerous genetic backgrounds and global dissemination of resistant clones and their descendants are both major components of the present-day macrolide resistance problem found within this species.
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Affiliation(s)
- D Ashley Robinson
- Department of Microbiology and Immunology, New York Medical College, Valhalla, NY 10595, USA
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