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Ochoa-Sánchez LE, Martínez JL, Gil-Gil T. Evolution of Resistance against Ciprofloxacin, Tobramycin, and Trimethoprim/Sulfamethoxazole in the Environmental Opportunistic Pathogen Stenotrophomonas maltophilia. Antibiotics (Basel) 2024; 13:330. [PMID: 38667006 PMCID: PMC11047544 DOI: 10.3390/antibiotics13040330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 03/27/2024] [Accepted: 04/02/2024] [Indexed: 04/29/2024] Open
Abstract
Stenotrophomonas maltophilia is an opportunistic pathogen that produces respiratory infections in immunosuppressed and cystic fibrosis patients. The therapeutic options to treat S. maltophilia infections are limited since it exhibits resistance to a wide variety of antibiotics such as β-lactams, aminoglycosides, tetracyclines, cephalosporins, macrolides, fluoroquinolones, or carbapenems. The antibiotic combination trimethoprim/sulfamethoxazole (SXT) is the treatment of choice to combat infections caused by S. maltophilia, while ceftazidime, ciprofloxacin, or tobramycin are used in most SXT-resistant infections. In the current study, experimental evolution and whole-genome sequencing (WGS) were used to examine the evolutionary trajectories of S. maltophilia towards resistance against tobramycin, ciprofloxacin, and SXT. The genetic changes underlying antibiotic resistance, as well as the evolutionary trajectories toward that resistance, were determined. Our results determine that genomic changes in the efflux pump regulatory genes smeT and soxR are essential to confer resistance to ciprofloxacin, and the mutation in the rplA gene is significant in the resistance to tobramycin. We identified mutations in folP and the efflux pump regulator smeRV as the basis of SXT resistance. Detailed and reliable knowledge of ciprofloxacin, tobramycin, and SXT resistance is essential for safe and effective use in clinical settings. Herein, we were able to prove once again the extraordinary ability that S. maltophilia has to acquire resistance and the importance of looking for alternatives to combat this resistance.
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Affiliation(s)
- Luz Edith Ochoa-Sánchez
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Darwin 3, 28049 Madrid, Spain;
| | - José Luis Martínez
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Darwin 3, 28049 Madrid, Spain;
| | - Teresa Gil-Gil
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Darwin 3, 28049 Madrid, Spain;
- Department of Biology, Emory University, Atlanta, GA 30322, USA
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2
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Rivetti S, Romano A, Mastrangelo S, Attinà G, Maurizi P, Ruggiero A. Aminoglycosides-Related Ototoxicity: Mechanisms, Risk Factors, and Prevention in Pediatric Patients. Pharmaceuticals (Basel) 2023; 16:1353. [PMID: 37895824 PMCID: PMC10610175 DOI: 10.3390/ph16101353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 09/17/2023] [Accepted: 09/21/2023] [Indexed: 10/29/2023] Open
Abstract
Aminoglycosides are broad-spectrum antibiotics largely used in children, but they have potential toxic side effects, including ototoxicity. Ototoxicity from aminoglycosides is permanent and is a consequence of its action on the inner ear cells via multiple mechanisms. Both uncontrollable risk factors and controllable risk factors are involved in the pathogenesis of aminoglycoside-related ototoxicity and, because of the irreversibility of ototoxicity, an important undertaking for preventing ototoxicity includes antibiotic stewardship to limit the use of aminoglycosides. Aminoglycosides are fundamental in the treatment of numerous infectious conditions at neonatal and pediatric age. In childhood, normal auditory function ensures adequate neurocognitive and social development. Hearing damage from aminoglycosides can therefore strongly affect the normal growth of the child. This review describes the molecular mechanisms of aminoglycoside-related ototoxicity and analyzes the risk factors and the potential otoprotective strategies in pediatric patients.
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Affiliation(s)
- Serena Rivetti
- Pediatric Oncology Unit, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy; (S.R.); (A.R.); (S.M.); (G.A.); (P.M.)
| | - Alberto Romano
- Pediatric Oncology Unit, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy; (S.R.); (A.R.); (S.M.); (G.A.); (P.M.)
| | - Stefano Mastrangelo
- Pediatric Oncology Unit, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy; (S.R.); (A.R.); (S.M.); (G.A.); (P.M.)
- Dipartimento di Scienze della Vita e Sanità Pubblica, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Giorgio Attinà
- Pediatric Oncology Unit, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy; (S.R.); (A.R.); (S.M.); (G.A.); (P.M.)
| | - Palma Maurizi
- Pediatric Oncology Unit, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy; (S.R.); (A.R.); (S.M.); (G.A.); (P.M.)
- Dipartimento di Scienze della Vita e Sanità Pubblica, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Antonio Ruggiero
- Pediatric Oncology Unit, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy; (S.R.); (A.R.); (S.M.); (G.A.); (P.M.)
- Dipartimento di Scienze della Vita e Sanità Pubblica, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
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3
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Ranjan N, Arya DP. Parallel G-quadruplex recognition by neomycin. Front Chem 2023; 11:1232514. [PMID: 37671393 PMCID: PMC10475565 DOI: 10.3389/fchem.2023.1232514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 07/25/2023] [Indexed: 09/07/2023] Open
Abstract
G-quadruplex-forming nucleic acids have evolved to have applications in biology, drug design, sensing, and nanotechnology, to name a few. Together with the structural understanding, several attempts have been made to discover and design new classes of chemical agents that target these structures in the hope of using them as future therapeutics. Here, we report the binding of aminoglycosides, in particular neomycin, to parallel G-quadruplexes that exist as G-quadruplex monomers, dimers, or compounds that have the propensity to form dimeric G-quadruplex structures. Using a combination of calorimetric and spectroscopic studies, we show that neomycin binds to the parallel G-quadruplex with affinities in the range of Ka ∼ 105-108 M-1, which depends on the base composition, ability to form dimeric G-quadruplex structures, salt, and pH of the buffer used. At pH 7.0, the binding of neomycin was found to be electrostatically driven potentially through the formation of ion pairs formed with the quadruplex. Lowering the pH resulted in neomycin's association constants in the range of Ka ∼ 106-107 M-1 in a salt dependent manner. Circular dichroism (CD) studies showed that neomycin's binding does not cause a change in the parallel conformation of the G-quadruplex, yet some binding-induced changes in the intensity of the CD signals were seen. A comparative binding study of neomycin and paromomycin using d(UG4T) showed paromomycin binding to be much weaker than neomycin, highlighting the importance of ring I in the recognition process. In toto, our results expanded the binding landscape of aminoglycosides where parallel G-quadruplexes have been discovered as one of the high-affinity sites. These results may offer a new understanding of some of the undesirable functions of aminoglycosides and help in the design of aminoglycoside-based G-quadruplex binders of high affinity.
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Affiliation(s)
| | - Dev P. Arya
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, SC, United States
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4
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Vila-Sanjurjo A, Mallo N, Atkins JF, Elson JL, Smith PM. Our current understanding of the toxicity of altered mito-ribosomal fidelity during mitochondrial protein synthesis: What can it tell us about human disease? Front Physiol 2023; 14:1082953. [PMID: 37457031 PMCID: PMC10349377 DOI: 10.3389/fphys.2023.1082953] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 02/28/2023] [Indexed: 07/18/2023] Open
Abstract
Altered mito-ribosomal fidelity is an important and insufficiently understood causative agent of mitochondrial dysfunction. Its pathogenic effects are particularly well-known in the case of mitochondrially induced deafness, due to the existence of the, so called, ototoxic variants at positions 847C (m.1494C) and 908A (m.1555A) of 12S mitochondrial (mt-) rRNA. It was shown long ago that the deleterious effects of these variants could remain dormant until an external stimulus triggered their pathogenicity. Yet, the link from the fidelity defect at the mito-ribosomal level to its phenotypic manifestation remained obscure. Recent work with fidelity-impaired mito-ribosomes, carrying error-prone and hyper-accurate mutations in mito-ribosomal proteins, have started to reveal the complexities of the phenotypic manifestation of mito-ribosomal fidelity defects, leading to a new understanding of mtDNA disease. While much needs to be done to arrive to a clear picture of how defects at the level of mito-ribosomal translation eventually result in the complex patterns of disease observed in patients, the current evidence indicates that altered mito-ribosome function, even at very low levels, may become highly pathogenic. The aims of this review are three-fold. First, we compare the molecular details associated with mito-ribosomal fidelity to those of general ribosomal fidelity. Second, we gather information on the cellular and organismal phenotypes associated with defective translational fidelity in order to provide the necessary grounds for an understanding of the phenotypic manifestation of defective mito-ribosomal fidelity. Finally, the results of recent experiments directly tackling mito-ribosomal fidelity are reviewed and future paths of investigation are discussed.
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Affiliation(s)
- Antón Vila-Sanjurjo
- Grupo GIBE, Departamento de Bioloxía e Centro de Investigacións Científicas Avanzadas (CICA), Universidade da Coruña (UDC), A Coruña, Spain
| | - Natalia Mallo
- Grupo GIBE, Departamento de Bioloxía e Centro de Investigacións Científicas Avanzadas (CICA), Universidade da Coruña (UDC), A Coruña, Spain
| | - John F Atkins
- Schools of Biochemistry and Microbiology, University College Cork, Cork, Ireland
| | - Joanna L Elson
- The Bioscience Institute, Newcastle University, Newcastle uponTyne, United Kingdom
- Human Metabolomics, North-West University, Potchefstroom, South Africa
| | - Paul M Smith
- Department of Paediatrics, Raigmore Hospital, Inverness, Scotland, United Kingdom
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5
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Chang Y, Sun W, Murchie AIH, Chen D. Genome-wide identification of Kanamycin B binding RNA in Escherichia coli. BMC Genomics 2023; 24:120. [PMID: 36927548 PMCID: PMC10018874 DOI: 10.1186/s12864-023-09234-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 03/07/2023] [Indexed: 03/18/2023] Open
Abstract
BACKGROUND The aminoglycosides are established antibiotics that inhibit bacterial protein synthesis by binding to ribosomal RNA. Additional non-antibiotic aminoglycoside cellular functions have also been identified through aminoglycoside interactions with cellular RNAs. The full extent, however, of genome-wide aminoglycoside RNA interactions in Escherichia coli has not been determined. Here, we report genome-wide identification and verification of the aminoglycoside Kanamycin B binding to Escherichia coli RNAs. Immobilized Kanamycin B beads in pull-down assays were used for transcriptome-profiling analysis (RNA-seq). RESULTS Over two hundred Kanamycin B binding RNAs were identified. Functional classification analysis of the RNA sequence related genes revealed a wide range of cellular functions. Small RNA fragments (ncRNA, tRNA and rRNA) or small mRNA was used to verify the binding with Kanamycin B in vitro. Kanamycin B and ibsC mRNA was analysed by chemical probing. CONCLUSIONS The results will provide biochemical evidence and understanding of potential extra-antibiotic cellular functions of aminoglycosides in Escherichia coli.
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Affiliation(s)
- Yaowen Chang
- Fudan University Pudong Medical Center, and Institute of Biomedical Sciences, Shanghai Medical College, Key Laboratory of Medical Epigenetics and Metabolism, Fudan University, 200032, Shanghai, China.,Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Wenxia Sun
- Fudan University Pudong Medical Center, and Institute of Biomedical Sciences, Shanghai Medical College, Key Laboratory of Medical Epigenetics and Metabolism, Fudan University, 200032, Shanghai, China.,Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Alastair I H Murchie
- Fudan University Pudong Medical Center, and Institute of Biomedical Sciences, Shanghai Medical College, Key Laboratory of Medical Epigenetics and Metabolism, Fudan University, 200032, Shanghai, China. .,Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China.
| | - Dongrong Chen
- Fudan University Pudong Medical Center, and Institute of Biomedical Sciences, Shanghai Medical College, Key Laboratory of Medical Epigenetics and Metabolism, Fudan University, 200032, Shanghai, China. .,Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China.
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6
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Chang Y, Zhang X, Murchie AIH, Chen D. Transcriptome profiling in response to Kanamycin B reveals its wider non-antibiotic cellular function in Escherichia coli. Front Microbiol 2022; 13:937827. [DOI: 10.3389/fmicb.2022.937827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 11/10/2022] [Indexed: 12/03/2022] Open
Abstract
Aminoglycosides are not only antibiotics but also have wider and diverse non-antibiotic cellular functions. To elucidate the understanding of non-antibiotic cellular functions, here we report transcriptome-profiling analysis of Escherichia coli in the absence or presence of 0.5 and 1 μM of Kanamycin B, concentrations that are neither lethal nor inhibit growth, and identified the differentially expressed genes (DEGs) at two given concentrations of Kanamycin B. Functional classification of the DEGs revealed that they were mainly related to microbial metabolism including two-component systems, biofilm formation, oxidative phosphorylation and nitrogen metabolism in diverse environments. We further showed that Kanamycin B and other aminoglycosides can induce reporter gene expression through the 5′ UTR of napF gene or narK gene (both identified as DEG) and Kanamycin B can directly bind to the RNA. The results provide new insights into a better understanding of the wider aminoglycosides cellular function in E. coli rather than its known antibiotics function.
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7
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Bowling A, Eastman A, Merlo C, Lin G, West N, Patel S, Cutting G, Sharma N. Downstream Alternate Start Site Allows N-Terminal Nonsense Variants to Escape NMD and Results in Functional Recovery by Readthrough and Modulator Combination. J Pers Med 2022; 12:jpm12091448. [PMID: 36143233 PMCID: PMC9504986 DOI: 10.3390/jpm12091448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 08/26/2022] [Accepted: 08/31/2022] [Indexed: 11/23/2022] Open
Abstract
Genetic variants that introduce premature termination codons (PTCs) have remained difficult to therapeutically target due to lack of protein product. Nonsense mediated mRNA decay (NMD) targets PTC-bearing transcripts to reduce the potentially damaging effects of truncated proteins. Readthrough compounds have been tested on PTC-generating variants in attempt to permit translation through a premature stop. However, readthrough compounds have not proved efficacious in a clinical setting due to lack of stable mRNA. Here, we investigate N-terminal variants in the cystic fibrosis transmembrane conductance regulator (CFTR) gene, which have been shown to escape NMD, potentially through a mechanism of alternative translation initiation at downstream AUG codons. We hypothesized that N-terminal variants in CFTR that evade NMD will produce stable transcript, allowing CFTR function to be restored by a combination of readthrough and protein modulator therapy. We investigate this using two cell line models expressing CFTR-expression minigenes (EMG; HEK293s and CFBEs) and primary human nasal epithelial (NE) cells, and we test readthrough compounds G418 and ELX-02 in combination with CFTR protein modulators. HEK293 cells expressing the variants E60X and L88X generate CFTR-specific core glycosylated products that are consistent with downstream translation initiation. Mutation of downstream methionines at codons 150 and 152 does not result in changes in CFTR protein processing in cells expressing L88X-CFTR-EMG. However, mutation of methionine at 265 results in loss of detectable CFTR protein in cells expressing E60X, L88X, and Y122X CFTR-EMGs, indicating that downstream translation initiation is occurring at the AUG codon at position M265. In HEK293 stable cells harboring L88X, treatment with readthrough compounds alone allows for formation of full-length, but misfolded CFTR protein. Upon addition of protein modulators in combination with readthrough, we observe formation of mature, complex-glycosylated CFTR. In CFBE and NE cells, addition of readthrough ELX-02 and modulator therapy results in substantial recovery of CFTR function. Our work indicates that N-terminal variants generate stable CFTR transcript due to translation initiation at a downstream AUG codon. Thus, individuals with CF bearing 5′ nonsense variants that evade NMD are ideal candidates for treatment with clinically safe readthrough compounds and modulator therapy.
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Affiliation(s)
- Alyssa Bowling
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Alice Eastman
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Christian Merlo
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Johns Hopkins Hospital, Baltimore, MD 21205, USA
| | - Gabrielle Lin
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Natalie West
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Johns Hopkins Hospital, Baltimore, MD 21205, USA
| | - Shivani Patel
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Johns Hopkins Hospital, Baltimore, MD 21205, USA
| | - Garry Cutting
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Neeraj Sharma
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Correspondence:
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8
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Kim J, Hemachandran S, Cheng AG, Ricci AJ. Identifying targets to prevent aminoglycoside ototoxicity. Mol Cell Neurosci 2022; 120:103722. [PMID: 35341941 PMCID: PMC9177639 DOI: 10.1016/j.mcn.2022.103722] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 03/14/2022] [Accepted: 03/19/2022] [Indexed: 12/21/2022] Open
Abstract
Aminoglycosides are potent antibiotics that are commonly prescribed worldwide. Their use carries significant risks of ototoxicity by directly causing inner ear hair cell degeneration. Despite their ototoxic side effects, there are currently no approved antidotes. Here we review recent advances in our understanding of aminoglycoside ototoxicity, mechanisms of drug transport, and promising sites for intervention to prevent ototoxicity.
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Affiliation(s)
- Jinkyung Kim
- Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Sriram Hemachandran
- Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Alan G Cheng
- Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA.
| | - Anthony J Ricci
- Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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9
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Shi HQ, Ma Y, Wang YH, Fang F, Wu ZY. Current pulse signature of native kanamycin aptamer and its implication for molecular interactions on a single protein nanopore sensing interface. Biosens Bioelectron 2022; 201:113966. [PMID: 35016110 DOI: 10.1016/j.bios.2022.113966] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 12/30/2021] [Accepted: 01/03/2022] [Indexed: 11/02/2022]
Abstract
Due to the pore size limitation of single α-hemolysin (α-HL) nanopore sensing interface, ssDNA with secondary conformations can only pass through the nanopore after unzipping as linear ssDNA. For hairpin DNA, a tail with 15-50 bases was usually added to the stem terminal (5' or 3') to facilitate the capture rate and unzipping process, and the typical translocation signal behaves as a square wave with a short dip at the end of the pulse. In this work, the pulse signal of native kanamycin aptamer, a hairpin DNA without the added long tail, was investigated with the single nanopore sensing interface, and different current pulse pattern was observed. The pulse signal exhibited two precise current levels with significantly extended duration of the second, and both duration of the two levels correlate to the interaction of the aptamer to kanamycin. Moreover, the pulse signal not only reveals the selectivity of the aptamer to its target, but also sensitive to the loop sequence change of the aptamer. This work shows that a single nanopore sensing interface could be used as a unique alternative means for interaction investigation of hairpin DNA aptamer without labeling or adding the extra-long tail.
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Affiliation(s)
- Hui-Qing Shi
- Research Center for Analytical Sciences, Chemistry Department, College of Sciences, Northeastern University, Shenyang, 110819, China
| | - Yao Ma
- Research Center for Analytical Sciences, Chemistry Department, College of Sciences, Northeastern University, Shenyang, 110819, China
| | - Yu-Hang Wang
- Research Center for Analytical Sciences, Chemistry Department, College of Sciences, Northeastern University, Shenyang, 110819, China
| | - Fang Fang
- Research Center for Analytical Sciences, Chemistry Department, College of Sciences, Northeastern University, Shenyang, 110819, China
| | - Zhi-Yong Wu
- Research Center for Analytical Sciences, Chemistry Department, College of Sciences, Northeastern University, Shenyang, 110819, China.
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10
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Abstract
The spread of antibiotic resistance is turning many of the currently used antibiotics less effective against common infections. To address this public health challenge, it is critical to enhance our understanding of the mechanisms of action of these compounds. Aminoglycoside drugs bind the bacterial ribosome, and decades of results from in vitro biochemical and structural approaches suggest that these drugs disrupt protein synthesis by inhibiting the ribosome's translocation on the messenger RNA, as well as by inducing miscoding errors. So far, however, we have sparse information about the dynamic effects of these compounds on protein synthesis inside the cell. In the present study, we measured the effect of the aminoglycosides apramycin, gentamicin, and paromomycin on ongoing protein synthesis directly in live Escherichia coli cells by tracking the binding of dye-labeled transfer RNAs to ribosomes. Our results suggest that the drugs slow down translation elongation two- to fourfold in general, and the number of elongation cycles per initiation event seems to decrease to the same extent. Hence, our results imply that none of the drugs used in this study cause severe inhibition of translocation.
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11
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Zhang J, Liu G, Zhang X, Chang Y, Wang S, He W, Sun W, Chen D, Murchie AIH. Aminoglycoside riboswitch control of the expression of integron associated aminoglycoside resistance adenyltransferases. Virulence 2021; 11:1432-1442. [PMID: 33103573 PMCID: PMC7588185 DOI: 10.1080/21505594.2020.1836910] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Abstract
The proliferation of antibiotic resistance has its origins in horizontal gene transfer. The class 1 integrons mediate gene transfer by assimilating antibiotic-resistance genes through site-specific recombination. For the class 1 integrons the first assimilated gene normally encodes an aminoglycoside antibiotic resistance protein which is either an aminoglycoside acetyltransferase (AAC), nucleotidyltransferase - (ANT), or adenyl transferase (AAD). An aminoglycoside-sensing riboswitch RNA in the leader RNA of AAC/AAD that controls the expression of aminoglycoside resistance genes has been previously described. Here we explore the relationship between the recombinant products of integron recombination and a series of candidate riboswitch RNAs in the 5' UTR of aad (aminoglycoside adenyltransferases) genes. The RNA sequences from the 5' UTR of the aad genes from pathogenic strains that are the products of site-specific DNA recombination by class 1 integrons were investigated. Reporter assays, MicroScale Thermophoresis (MST) and covariance analysis revealed that a functional aminoglycoside-sensing riboswitch was selected at the DNA level through integron-mediated site-specific recombination. This study explains the close association between integron recombination and the aminoglycoside-sensing riboswitch RNA.
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Affiliation(s)
- Jun Zhang
- Key Laboratory of Medical Epigenetics and Metabolism, Fudan University Pudong Medical Center, Institutes of Biomedical Sciences, Fudan University , Shanghai, PR China.,Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University , Shanghai, PR China
| | - Getong Liu
- Key Laboratory of Medical Epigenetics and Metabolism, Fudan University Pudong Medical Center, Institutes of Biomedical Sciences, Fudan University , Shanghai, PR China.,Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University , Shanghai, PR China
| | - Xuhui Zhang
- Key Laboratory of Medical Epigenetics and Metabolism, Fudan University Pudong Medical Center, Institutes of Biomedical Sciences, Fudan University , Shanghai, PR China.,Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University , Shanghai, PR China
| | - Yaowen Chang
- Key Laboratory of Medical Epigenetics and Metabolism, Fudan University Pudong Medical Center, Institutes of Biomedical Sciences, Fudan University , Shanghai, PR China.,Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University , Shanghai, PR China
| | - Shasha Wang
- Key Laboratory of Medical Epigenetics and Metabolism, Fudan University Pudong Medical Center, Institutes of Biomedical Sciences, Fudan University , Shanghai, PR China.,Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University , Shanghai, PR China
| | - Weizhi He
- Key Laboratory of Medical Epigenetics and Metabolism, Fudan University Pudong Medical Center, Institutes of Biomedical Sciences, Fudan University , Shanghai, PR China.,Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University , Shanghai, PR China
| | - Wenxia Sun
- Key Laboratory of Medical Epigenetics and Metabolism, Fudan University Pudong Medical Center, Institutes of Biomedical Sciences, Fudan University , Shanghai, PR China.,Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University , Shanghai, PR China
| | - Dongrong Chen
- Key Laboratory of Medical Epigenetics and Metabolism, Fudan University Pudong Medical Center, Institutes of Biomedical Sciences, Fudan University , Shanghai, PR China.,Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University , Shanghai, PR China
| | - Alastair I H Murchie
- Key Laboratory of Medical Epigenetics and Metabolism, Fudan University Pudong Medical Center, Institutes of Biomedical Sciences, Fudan University , Shanghai, PR China.,Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University , Shanghai, PR China
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12
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Lade H, Kim JS. Bacterial Targets of Antibiotics in Methicillin-Resistant Staphylococcus aureus. Antibiotics (Basel) 2021; 10:398. [PMID: 33917043 PMCID: PMC8067735 DOI: 10.3390/antibiotics10040398] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/02/2021] [Accepted: 04/05/2021] [Indexed: 12/17/2022] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) is one of the most prevalent bacterial pathogens and continues to be a leading cause of morbidity and mortality worldwide. MRSA is a commensal bacterium in humans and is transmitted in both community and healthcare settings. Successful treatment remains a challenge, and a search for new targets of antibiotics is required to ensure that MRSA infections can be effectively treated in the future. Most antibiotics in clinical use selectively target one or more biochemical processes essential for S. aureus viability, e.g., cell wall synthesis, protein synthesis (translation), DNA replication, RNA synthesis (transcription), or metabolic processes, such as folic acid synthesis. In this review, we briefly describe the mechanism of action of antibiotics from different classes and discuss insights into the well-established primary targets in S. aureus. Further, several components of bacterial cellular processes, such as teichoic acid, aminoacyl-tRNA synthetases, the lipid II cycle, auxiliary factors of β-lactam resistance, two-component systems, and the accessory gene regulator quorum sensing system, are discussed as promising targets for novel antibiotics. A greater molecular understanding of the bacterial targets of antibiotics has the potential to reveal novel therapeutic strategies or identify agents against antibiotic-resistant pathogens.
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Affiliation(s)
| | - Jae-Seok Kim
- Department of Laboratory Medicine, Kangdong Sacred Heart Hospital, Hallym University College of Medicine, Seoul 05355, Korea;
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13
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Cardenas G, Menger MFSJ, Ramos-Berdullas N, Sánchez-Murcia PA. Deciphering the Chemical Basis of Fluorescence of a Selenium-Labeled Uracil Probe when Bound at the Bacterial Ribosomal A-Site. Chemistry 2021; 27:4927-4931. [PMID: 33368691 DOI: 10.1002/chem.202004818] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Indexed: 12/23/2022]
Abstract
We unveil in this work the main factors that govern the turn-on/off fluorescence of a Se-modified uracil probe at the ribosomal RNA A-site. Whereas the constraint into an "in-plane" conformation of the two rings of the fluorophore is the main driver for the observed turn-on fluorescence emission in the presence of the antibiotic paromomycin, the electrostatics of the environment plays a minor role during the emission process. Our computational strategy clearly indicates that, in the absence of paromomycin, the probe prefers conformations that show a dark S1 electronic state with participation of nπ* electronic transition contributions between the selenium atom and the π-system of the uracil moiety.
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Affiliation(s)
- Gustavo Cardenas
- Chemistry Department, Universidad Autónoma de Madrid, Calle Francisco Tomás y Valiente 7, 28049, Madrid, Spain
| | - Maximilian F S J Menger
- Zernike Institute for Advanced Materials, Faculty of Science and Engineering, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Nicolás Ramos-Berdullas
- Department of Physical Chemistry, University of Vigo, Lagoas Marcosende s/n, 36310, Vigo, Spain
| | - Pedro A Sánchez-Murcia
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, 1090, Vienna, Austria.,Present address: Division of Physiological Chemistry, Otto-Loewi Research Center, Medical University of Graz, Neue Stiftingstalstraße 6/III, 8010, Graz, Austria
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14
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Godeshala S, Miryala B, Dutta S, Christensen MD, Nandi P, Chiu PL, Rege K. A library of aminoglycoside-derived lipopolymer nanoparticles for delivery of small molecules and nucleic acids. J Mater Chem B 2020; 8:8558-8572. [PMID: 32830211 DOI: 10.1039/d0tb00924e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Simultaneous delivery of small molecules and nucleic acids using a single vehicle can lead to novel combination treatments and multifunctional carriers for a variety of diseases. In this study, we report a novel library of aminoglycoside-derived lipopolymers nanoparticles (LPNs) for the simultaneous delivery of different molecular cargoes including nucleic acids and small-molecules. The LPN library was screened for transgene expression efficacy following delivery of plasmid DNA, and lead LPNs that showed high transgene expression efficacies were characterized using hydrodynamic size, zeta potential, 1H NMR and FT-IR spectroscopy, and transmission electron microscopy. LPNs demonstrated significantly higher efficacies for transgene expression than 25 kDa polyethyleneamine (PEI) and lipofectamine, including in presence of serum. Self-assembly of these cationic lipopolymers into nanoparticles also facilitated the delivery of small molecule drugs (e.g. doxorubicin) to cancer cells. LPNs were also employed for the simultaneous delivery of the small-molecule histone deacetylase (HDAC) inhibitor AR-42 together with plasmid DNA to cancer cells as a combination treatment approach for enhancing transgene expression. Taken together, our results indicate that aminoglycoside-derived LPNs are attractive vehicles for simultaneous delivery of imaging agents or chemotherapeutic drugs together with nucleic acids for different applications in medicine and biotechnology.
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Affiliation(s)
- Sudhakar Godeshala
- Chemical Engineering, Arizona State University, 501 E. Tyler Mall, ECG 303, Tempe, AZ 85287-6106, USA.
| | - Bhavani Miryala
- Chemical Engineering, Arizona State University, 501 E. Tyler Mall, ECG 303, Tempe, AZ 85287-6106, USA.
| | - Subhadeep Dutta
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-6106, USA
| | - Matthew D Christensen
- Chemical Engineering, Arizona State University, 501 E. Tyler Mall, ECG 303, Tempe, AZ 85287-6106, USA.
| | - Purbasha Nandi
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-6106, USA
| | - Po-Lin Chiu
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-6106, USA
| | - Kaushal Rege
- Chemical Engineering, Arizona State University, 501 E. Tyler Mall, ECG 303, Tempe, AZ 85287-6106, USA.
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15
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Callahan BP, Ciulla DA, Wagner AG, Xu Z, Zhang X. Specificity Distorted: Chemical Induction of Biological Paracatalysis. Biochemistry 2020; 59:3517-3522. [PMID: 32931253 DOI: 10.1021/acs.biochem.0c00643] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
We define paracatalysis as the acceleration of a reaction that appears abnormal or nonphysiological. With the high specificity of enzymes, side reactivity of this kind is typically negligible. However, enzyme paracatalysis can be amplified to levels that are biologically significant through interactions with a special class of small molecule "antagonist", here termed a paracatalytic inducer. Compounds with this unusual mode of action tend to be natural products, identified by chance through phenotypic screens. In this Perspective, we suggest two general types of paracatalytic inducer. The first type promotes substrate ambiguity, where the enzyme's ground state selectivity is compromised, enabling the transformation of non-native substrates. The second type involves transition state ambiguity, where the paracatalytic inducer changes the enzyme's interactions with the activated substrate, giving rise to non-native bond making. Although they are unusual, small molecules that induce paracatalysis have established value as hypothesis-generating probes and a few substances, i.e., aspirin and the aminoglycosides, have proven to be translatable as medicines.
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Affiliation(s)
- Brian P Callahan
- Department of Chemistry, Binghamton University, the State University of New York, 4400 Vestal Parkway East, Binghamton, New York 13902, United States
| | - Daniel A Ciulla
- Department of Chemistry, Binghamton University, the State University of New York, 4400 Vestal Parkway East, Binghamton, New York 13902, United States
| | - Andrew G Wagner
- Department of Chemistry, Binghamton University, the State University of New York, 4400 Vestal Parkway East, Binghamton, New York 13902, United States
| | - Zihan Xu
- Department of Chemistry, Binghamton University, the State University of New York, 4400 Vestal Parkway East, Binghamton, New York 13902, United States
| | - Xiaoyu Zhang
- Department of Chemistry, Binghamton University, the State University of New York, 4400 Vestal Parkway East, Binghamton, New York 13902, United States
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16
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Zhang J, Liu G, Sun W, Chen D, Murchie AIH. Aminoglycoside antibiotics can inhibit or activate twister ribozyme cleavage. FEBS J 2020; 288:1586-1598. [PMID: 32790122 DOI: 10.1111/febs.15517] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 07/19/2020] [Accepted: 08/10/2020] [Indexed: 12/11/2022]
Abstract
Interactions between aminoglycoside antibiotics and the twister ribozyme were investigated in this study. An initial screen of 17 RNA-binding antibiotics showed that a number of aminoglycosides inhibit the ribozyme, while a subset of aminoglycosides enhances twister cleavage. Initial kinetic analysis of the twister ribozyme showed a sevenfold inhibition of ribozyme cleavage by paromomycin and a fivefold enhancement of cleavage by sisomicin. Direct binding between the twister ribozyme RNA and paromomycin or sisomicin was measured by microscale thermophoresis. Selective 2'-hydroxyl acylation analysed by primer extension shows that both paromomycin and sisomicin induce distinctive tertiary structure changes to the twister ribozyme. Published crystal structures and mechanistic analysis of the twister ribozyme have deduced a nucleobase-mediated general acid-base catalytic mechanism, in which a conserved guanine plays a key role. Here, we show that paromomycin binding induces a structural transition to the twister ribozyme such that a highly conserved guanine in the active site becomes displaced, leading to inhibition of cleavage. In contrast, sisomicin binding appears to change interactions between P3 and L2, inducing allosteric changes to the active site that enhance twister RNA cleavage. Therefore, we show that small-molecule binding can modulate twister ribozyme activity. These results suggest that aminoglycosides may be used as molecular tools to study this widely distributed ribozyme.
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Affiliation(s)
- Jun Zhang
- Fudan University Pudong Medical Center, and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China.,Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Getong Liu
- Fudan University Pudong Medical Center, and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China.,Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Wenxia Sun
- Fudan University Pudong Medical Center, and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China.,Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Dongrong Chen
- Fudan University Pudong Medical Center, and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China.,Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Alastair I H Murchie
- Fudan University Pudong Medical Center, and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China.,Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University, Shanghai, China
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17
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Wang N, Liu X, Li J, Zhang Q, Li X, An Q, Ye X, Zhao Z, Cai L, Han Y, Zhao M, Wenjun W. Antibacterial mechanism of the synergistic combination between streptomycin and alcohol extracts from the Chimonanthus salicifolius S. Y. Hu. leaves. JOURNAL OF ETHNOPHARMACOLOGY 2020; 250:112467. [PMID: 31837412 DOI: 10.1016/j.jep.2019.112467] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 12/07/2019] [Accepted: 12/07/2019] [Indexed: 06/10/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Chimonanthus salicifolius S. Y. Hu. Is a unique traditional medicinal plant in ancient China, and it can eliminate turbid pathogens with aromatics, clear heat, detoxify, prevent colds and influenza, Xinhua Compendium of Materia Medica records that. AIM OF THE STUDY In previous study, we investigated the regulation of ethanol extracts (EEs) from C. salicifolius S. Y. Hu. leaves on three common antibiotics (chloramphenicol, streptomycin, imipenem) by the checkerboard method. The combination exhibited the best synergy among all combinations, which were composed of streptomycin and 50% EE (SE) from the C. salicifolius S. Y. Hu. leaves. The aim of this study was to investigate the antibacterial mechanism of the SE against Escherichia coli (E. coli, G-) and Staphylococcus aureus (S. aureus, G+). MATERIALS AND METHODS The antibacterial mechanism of the SE was explored by the time-kill test, the phosphorus metabolism, cell membrane integrity assays, the SDS-PAGE, the SEM and TEM observation. RESULTS The time-kill test illustrated that the SE was bacteriostatic with a time-dependent relationship, not sterilization. The phosphorus metabolism indicated that the SE lowered phosphorus consumption. The cell membrane integrity assays demonstrated that the cell membrane was damaged, with the nucleic acid flowing out. The SDS-PAGE analysis found that the SE inhibited the synthesis of the total protein. The SEM and TEM results revealed that the surface and internal ultrastructure of bacteria were damaged. The surface of the bacteria was shriveled and deformed, and the internal structure of the cells was also mutilated. CONCLUSIONS The SE damaged the cell membrane, with the cytoplasm flowing out, disturbed the synthesis of total protein and phosphorus metabolism, and ultimately killed the bacteria.
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Affiliation(s)
- Ning Wang
- Key Lab for Natural Products and Functional Foods of Jiangxi Province, College of Food Science and Engineering, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Xin Liu
- Key Lab for Natural Products and Functional Foods of Jiangxi Province, College of Food Science and Engineering, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Jingen Li
- Key Lab for Natural Products and Functional Foods of Jiangxi Province, College of Food Science and Engineering, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Qingfeng Zhang
- Key Lab for Natural Products and Functional Foods of Jiangxi Province, College of Food Science and Engineering, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Xiang Li
- Key Lab for Natural Products and Functional Foods of Jiangxi Province, College of Food Science and Engineering, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Qi An
- Key Lab for Natural Products and Functional Foods of Jiangxi Province, College of Food Science and Engineering, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Ximei Ye
- Key Lab for Natural Products and Functional Foods of Jiangxi Province, College of Food Science and Engineering, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Zitong Zhao
- Key Lab for Natural Products and Functional Foods of Jiangxi Province, College of Food Science and Engineering, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Lei Cai
- Key Lab for Natural Products and Functional Foods of Jiangxi Province, College of Food Science and Engineering, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Yi Han
- Key Lab for Natural Products and Functional Foods of Jiangxi Province, College of Food Science and Engineering, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Meng Zhao
- Key Lab for Natural Products and Functional Foods of Jiangxi Province, College of Food Science and Engineering, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Wang Wenjun
- Key Lab for Natural Products and Functional Foods of Jiangxi Province, College of Food Science and Engineering, Jiangxi Agricultural University, Nanchang, 330045, China.
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Wangen JR, Green R. Stop codon context influences genome-wide stimulation of termination codon readthrough by aminoglycosides. eLife 2020; 9:52611. [PMID: 31971508 PMCID: PMC7089771 DOI: 10.7554/elife.52611] [Citation(s) in RCA: 117] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 01/22/2020] [Indexed: 12/14/2022] Open
Abstract
Stop codon readthrough (SCR) occurs when the ribosome miscodes at a stop codon. Such readthrough events can be therapeutically desirable when a premature termination codon (PTC) is found in a critical gene. To study SCR in vivo in a genome-wide manner, we treated mammalian cells with aminoglycosides and performed ribosome profiling. We find that in addition to stimulating readthrough of PTCs, aminoglycosides stimulate readthrough of normal termination codons (NTCs) genome-wide. Stop codon identity, the nucleotide following the stop codon, and the surrounding mRNA sequence context all influence the likelihood of SCR. In comparison to NTCs, downstream stop codons in 3′UTRs are recognized less efficiently by ribosomes, suggesting that targeting of critical stop codons for readthrough may be achievable without general disruption of translation termination. Finally, we find that G418-induced miscoding alters gene expression with substantial effects on translation of histone genes, selenoprotein genes, and S-adenosylmethionine decarboxylase (AMD1). Many genes provide a set of instructions needed to build a protein, which are read by structures called ribosomes through a process called translation. The genetic information contains a short, coded instruction called a stop codon which marks the end of the protein. When a ribosome finds a stop codon it should stop building and release the protein it has made. Ribosomes do not always stop at stop codons. Certain chemicals can actually prevent ribosomes from detecting stop codons correctly, and aminoglycosides are drugs that have exactly this effect. Aminoglycosides can be used as antibiotics at low doses because they interfere with ribosomes in bacteria, but at higher doses they can also prevent ribosomes from detecting stop codons in human cells. When ribosomes do not stop at a stop codon this is called readthrough. There are different types of stop codons and some are naturally more effective at stopping ribosomes than others. Wangen and Green have now examined the effect of an aminoglycoside called G418 on ribosomes in human cells grown in the laboratory. The results showed how ribosomes interacted with genetic information and revealed that certain stop codons are more affected by G418 than others. The stop codon and other genetic sequences around it affect the likelihood of readthrough. Wangen and Green also showed that sequences that encourage translation to stop are more common in the area around stop codons. These findings highlight an evolutionary pressure driving more genes to develop strong stop codons that resist readthrough. Despite this, some are still more affected by drugs like G418 than others. Some genetic conditions, like cystic fibrosis, result from incorrect stop codons in genes. Drugs that promote readthrough specifically in these genes could be useful new treatments.
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Affiliation(s)
- Jamie R Wangen
- Department of Molecular Biology and Genetics, Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Rachel Green
- Department of Molecular Biology and Genetics, Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, United States
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19
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Xu M, Xue H, Li X, Zhao Y, Lin L, Yang L, Zheng G. Chemical composition, antibacterial properties, and mechanism of Smilax china L. polyphenols. Appl Microbiol Biotechnol 2019; 103:9013-9022. [DOI: 10.1007/s00253-019-10100-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 08/08/2019] [Accepted: 08/26/2019] [Indexed: 10/25/2022]
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20
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Amphiphilic nebramine-based hybrids Rescue legacy antibiotics from intrinsic resistance in multidrug-resistant Gram-negative bacilli. Eur J Med Chem 2019; 175:187-200. [DOI: 10.1016/j.ejmech.2019.05.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 04/24/2019] [Accepted: 05/01/2019] [Indexed: 12/15/2022]
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21
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Integron-Derived Aminoglycoside-Sensing Riboswitches Control Aminoglycoside Acetyltransferase Resistance Gene Expression. Antimicrob Agents Chemother 2019; 63:AAC.00236-19. [PMID: 30936094 DOI: 10.1128/aac.00236-19] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 03/24/2019] [Indexed: 02/06/2023] Open
Abstract
Class 1 integrons accumulate antibiotic resistance genes by site-specific recombination at aatI-1 sites. Captured genes are transcribed from a promoter located within the integron; for class 1 integrons, the first gene to be transcribed and translated normally encodes an aminoglycoside antibiotic resistance protein (either an acetyltransferase [AAC] or adenyltransferase [AAD]). The leader RNA from the Pseudomonas fluorescens class 1 integron contains an aminoglycoside-sensing riboswitch RNA that controls the expression of the downstream aminoglycoside resistance gene. Here, we explore the relationship between integron-dependent DNA recombination and potential aminoglycoside-sensing riboswitch products of recombination derived from a series of aminoglycoside-resistant clinical strains. Sequence analysis of the clinical strains identified a series of sequence variants that were associated with class I integron-derived aminoglycoside-resistant (both aac and aad) recombinants. For the aac recombinants, representative sequences showed up to 6-fold aminoglycoside-dependent regulation of reporter gene expression. Microscale thermophoresis (MST) confirmed RNA binding. Covariance analysis generated a secondary-structure model for the RNA that is an independent verification of previous models that were derived from mutagenesis and chemical probing data and that was similar to that of the P. fluorescens riboswitch RNA. The aminoglycosides were among the first antibiotics to be used clinically, and the data suggest that in an aminoglycoside-rich environment, functional riboswitch recombinants were selected during integron-mediated recombination to regulate aminoglycoside resistance. The incorporation of a functional aminoglycoside-sensing riboswitch by integron recombination confers a selective advantage for the expression of resistance genes of diverse origins.
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22
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Wang N, Chen H, Xiong L, Liu X, Li X, An Q, Ye X, Wang W. Phytochemical profile of ethanolic extracts of Chimonanthus salicifolius S. Y. Hu. leaves and its antimicrobial and antibiotic-mediating activity. INDUSTRIAL CROPS AND PRODUCTS 2018. [DOI: 10.1016/j.indcrop.2018.09.021] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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23
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Basabe-Burgos O, Zebialowicz J, Stichtenoth G, Curstedt T, Bergman P, Johansson J, Rising A. Natural Derived Surfactant Preparation As a Carrier of Polymyxin E for Treatment of Pseudomonas aeruginosa Pneumonia in a Near-Term Rabbit Model. J Aerosol Med Pulm Drug Deliv 2018; 32:110-118. [PMID: 30339061 DOI: 10.1089/jamp.2018.1468] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Pulmonary surfactant spreads rapidly over the airway epithelium, a property that could be harnessed to transport drugs into the lungs. For efficient drug delivery, an interaction between pulmonary surfactant and the drug to be administered is likely needed. On the other hand, the interaction should not compromise the activity of surfactant or the drug once delivered in vivo. The antibiotics gentamicin (an aminoglycoside) and polymyxin E represent drugs that could benefit from being delivered directly to the lung, thereby increasing local concentrations and reducing systemic side effects. Our aim was to study how the animal-derived surfactant poractant alfa (Curosurf®) affects the activities of polymyxin E and gentamicin against Pseudomonas aeruginosa. METHODS In vitro antimicrobial assays and a neonatal near-term rabbit model were used to evaluate the combinations of antibiotics and surfactant against Pseudomonas aeruginosa. RESULTS The bactericidal activity of polymyxin E, but not of gentamicin, against P. aeruginosa was partly reduced in vitro in the presence of poractant alfa. In contrast, in the rabbit model of P. aeruginosa pneumonia, polymyxin E administrated together with surfactant was superior in lowering the bacterial load in the lungs compared to polymyxin E alone, without affecting plethysmographically recorded lung compliance. CONCLUSIONS The results suggest that polymyxin E interacts with poractant alfa, which reduces the antibacterial effect in vitro. However, when polymyxin E mixed with surfactant is used in the in vivo pneumonia model, increased bactericidal effect was observed. This may be due to a more efficient spreading mediated by interactions between polymyxin E and surfactant. These results warrant further studies of surfactant preparations for drug delivery against lung infections.
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Affiliation(s)
- Oihana Basabe-Burgos
- 1 Division for Neurogeriatrics, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet , Huddinge, Sweden
| | - Jakub Zebialowicz
- 1 Division for Neurogeriatrics, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet , Huddinge, Sweden
| | - Guido Stichtenoth
- 2 Department of Pediatrics, University of Lübeck , Lübeck, Germany .,3 Department of Molecular Medicine and Surgery, Karolinska Institutet, Karolinska University Hospital , Stockholm, Sweden
| | - Tore Curstedt
- 3 Department of Molecular Medicine and Surgery, Karolinska Institutet, Karolinska University Hospital , Stockholm, Sweden
| | - Peter Bergman
- 4 Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Karolinska University Hospital , Stockholm, Sweden
| | - Jan Johansson
- 1 Division for Neurogeriatrics, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet , Huddinge, Sweden
| | - Anna Rising
- 1 Division for Neurogeriatrics, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet , Huddinge, Sweden .,5 Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences , Uppsala, Sweden
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24
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Abd-Elhamid TH, Elgamal DA, Ali SS, Ali FEM, Hassanein EHM, El-Shoura EAM, Hemeida RAM. Reno-protective effects of ursodeoxycholic acid against gentamicin-induced nephrotoxicity through modulation of NF-κB, eNOS and caspase-3 expressions. Cell Tissue Res 2018; 374:367-387. [PMID: 30078101 DOI: 10.1007/s00441-018-2886-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Accepted: 07/04/2018] [Indexed: 12/13/2022]
Abstract
Gentamicin (GNT) is a potent aminoglycoside antibiotic widely used to treat life-threatening bacterial infections. We aim to investigate the potential protective effect of ursodeoxycholic acid (UDCA) against GNT-induced nephrotoxicity. In this study, 24 male Wistar rats were used and randomly divided into four groups of six animals each. Control group received 0.5% carboxymethyl cellulose orally for 15 days, GNT group received GNT 100 mg/kg/day i.p. for 8 days, UDCA group received UDCA orally for 15 consecutive days at a dose of 60 mg/kg/day suspended in 0.5% carboxymethyl cellulose and UDCA-pretreated group received UDCA orally for 7 days then co-administered with GNT i.p. for 8 days at the same fore-mentioned doses. Serum levels of kidney function parameters (urea, creatinine, uric acid and albumin) were measured. Renal tissues were used to evaluate oxidative stress markers; malonaldehyde (MDA), reduced glutathione (GSH) and the anti-oxidant enzyme superoxide dismutase (SOD) activities and nuclear factor kappa light-chain enhancer of activated B cells (NF-κB) and kidney injury molecule-1 (KIM-1) mRNA levels. Immunohistochemical expression of endothelial nitric oxide synthase (eNOS) and caspase-3 and histological and ultrastructural examination were performed. Treatment with GNT increased the serum levels of renal function parameters and renal MDA, NF-κB and KIM-1 mRNA levels, while it decreased GSH and SOD activities. Marked immunohistochemical expression of caspase-3 was observed after GNT administration while it decreased eNOS expression. Histological and ultrastructural alterations were also evident in renal corpuscles and tubules. In contrast, pretreatment with UDCA reversed changes caused by GNT administration. These results suggest that UDCA ameliorates GNT-induced kidney injury via inhibition of oxidative stress, inflammation and apoptosis.
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Affiliation(s)
- Tarek Hamdy Abd-Elhamid
- Department of Histology and Cell Biology, Faculty of Medicine, Assiut University, Assiut, Egypt.
| | - Dalia A Elgamal
- Department of Histology and Cell Biology, Faculty of Medicine, Assiut University, Assiut, Egypt
| | - Safaa S Ali
- Department of Histology and Cell Biology, Faculty of Medicine, Assiut University, Assiut, Egypt
| | - Fares E M Ali
- Department of Pharmacology, Faculty of Pharmacy, Al-Azhar University, Assiut, Egypt
| | - Emad H M Hassanein
- Department of Pharmacology, Faculty of Pharmacy, Al-Azhar University, Assiut, Egypt
| | - Ehab A M El-Shoura
- Department of Pharmacology, Faculty of Pharmacy, Al-Azhar University, Assiut, Egypt
| | - Ramadan A M Hemeida
- Department of Pharmacology, Faculty of Pharmacy, Al-Azhar University, Assiut, Egypt
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Zhu Y, Li W, Tan S, Chen T. Label-Free and Simple G-quadruplex-based Turn-Off Fluorescence Assay for the Detection of Kanamycin. ANAL LETT 2018. [DOI: 10.1080/00032719.2017.1387136] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Yuqing Zhu
- School of Chemistry and Biological Engineering, Changsha University of Science and Technology, Changsha, China
| | - Wei Li
- School of Chemistry and Biological Engineering, Changsha University of Science and Technology, Changsha, China
| | - Shuzhen Tan
- School of Chemistry and Biological Engineering, Changsha University of Science and Technology, Changsha, China
| | - Tianxiao Chen
- School of Chemistry and Biological Engineering, Changsha University of Science and Technology, Changsha, China
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26
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Zhang Y, Wang L, Xu X, Li F, Wu Q. Combined systems of different antibiotics with nano-CuO against Escherichia coli and the mechanisms involved. Nanomedicine (Lond) 2018; 13:339-351. [DOI: 10.2217/nnm-2017-0290] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Aim: The combined efficacy of CuO nanoparticles (NPs) with 22 kinds of antibiotics against Escherichia coli was systematic studied, and CuO with cephalexin synergistic system was screened out. Methods: Antimicrobial susceptibility test included disk diffusion test, checkerboard method and time-kill assay. The interactions of CuO NPs and antibiotics were analyzed by x-ray photoelectron spectroscopy, Fourier transform infrared spectra and Zeta. The interactions between bacteria and antibacterial agents were studied by surface plasmon resonance sensor for the first time. Results & Conclusion: Synergistic effect (1+1>2) was observed when CuO NPs combined with cephalexin against E. coli. The concentrated cephalexin molecules interacted more strongly with the E. coli cells to make cell wall become loose. Then, CuO NPs were more easily to damage and penetrate cells. Besides, the presence of antibiotics did not enhance Cu2+ release, Cu2+ uptake and reactive oxygen species generation. But the presence of cephalexin greatly enhanced cell permeability in comparison to others.
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Affiliation(s)
- Yahui Zhang
- School of Chemical Science and Engineering, Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University, Shanghai 200092, PR China
| | - Lin Wang
- Department of Ophthalmology, Anhui Provincial Hospital, Hefei 230001, PR China
| | - Xiang Xu
- School of Chemical Science and Engineering, Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University, Shanghai 200092, PR China
| | - Fang Li
- Department of Gynaecology, First Maternity and Infant Hospital Affiliated to Tongji University, Shanghai 200040, PR China
| | - Qingsheng Wu
- School of Chemical Science and Engineering, Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University, Shanghai 200092, PR China
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Mutations in Gene fusA1 as a Novel Mechanism of Aminoglycoside Resistance in Clinical Strains of Pseudomonas aeruginosa. Antimicrob Agents Chemother 2018; 62:AAC.01835-17. [PMID: 29133559 DOI: 10.1128/aac.01835-17] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 11/05/2017] [Indexed: 01/03/2023] Open
Abstract
Resistance of clinical strains of Pseudomonas aeruginosa to aminoglycosides can result from production of transferable aminoglycoside-modifying enzymes, of 16S rRNA methylases, and/or mutational derepression of intrinsic multidrug efflux pump MexXY(OprM). We report here the characterization of a new type of mutant that is 4- to 8-fold more resistant to 2-deoxystreptamine derivatives (e.g., gentamicin, amikacin, and tobramycin) than the wild-type strain PAO1. The genetic alterations of three in vitro mutants were mapped on fusA1 and found to result in single amino acid substitutions in domains II, III, and V of elongation factor G (EF-G1A), a key component of translational machinery. Transfer of the mutated fusA1 alleles into PAO1 reproduced the resistance phenotype. Interestingly, fusA1 mutants with other amino acid changes in domains G, IV, and V of EF-G1A were identified among clinical strains with decreased susceptibility to aminoglycosides. Allelic-exchange experiments confirmed the relevance of these latter mutations and of three other previously reported alterations located in domains G and IV. Pump MexXY(OprM) partly contributed to the resistance conferred by the mutated EF-G1A variants and had additive effects on aminoglycoside MICs when mutationally upregulated. Altogether, our data demonstrate that cystic fibrosis (CF) and non-CF strains of P. aeruginosa can acquire a therapeutically significant resistance to important aminoglycosides via a new mechanism involving mutations in elongation factor EF-G1A.
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John T, Thomas T, Abel B, Wood BR, Chalmers DK, Martin LL. How kanamycin A interacts with bacterial and mammalian mimetic membranes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:2242-2252. [DOI: 10.1016/j.bbamem.2017.08.016] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2017] [Revised: 08/09/2017] [Accepted: 08/23/2017] [Indexed: 01/11/2023]
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Jiang M, Karasawa T, Steyger PS. Aminoglycoside-Induced Cochleotoxicity: A Review. Front Cell Neurosci 2017; 11:308. [PMID: 29062271 PMCID: PMC5640705 DOI: 10.3389/fncel.2017.00308] [Citation(s) in RCA: 171] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 09/15/2017] [Indexed: 12/20/2022] Open
Abstract
Aminoglycoside antibiotics are used as prophylaxis, or urgent treatment, for many life-threatening bacterial infections, including tuberculosis, sepsis, respiratory infections in cystic fibrosis, complex urinary tract infections and endocarditis. Although aminoglycosides are clinically-essential antibiotics, the mechanisms underlying their selective toxicity to the kidney and inner ear continue to be unraveled despite more than 70 years of investigation. The following mechanisms each contribute to aminoglycoside-induced toxicity after systemic administration: (1) drug trafficking across endothelial and epithelial barrier layers; (2) sensory cell uptake of these drugs; and (3) disruption of intracellular physiological pathways. Specific factors can increase the risk of drug-induced toxicity, including sustained exposure to higher levels of ambient sound, and selected therapeutic agents such as loop diuretics and glycopeptides. Serious bacterial infections (requiring life-saving aminoglycoside treatment) induce systemic inflammatory responses that also potentiate the degree of ototoxicity and permanent hearing loss. We discuss prospective clinical strategies to protect auditory and vestibular function from aminoglycoside ototoxicity, including reduced cochlear or sensory cell uptake of aminoglycosides, and otoprotection by ameliorating intracellular cytotoxicity.
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Affiliation(s)
- Meiyan Jiang
- Oregon Hearing Research Center, Oregon Health & Science University, Portland, OR, United States
| | - Takatoshi Karasawa
- Oregon Hearing Research Center, Oregon Health & Science University, Portland, OR, United States
| | - Peter S Steyger
- Oregon Hearing Research Center, Oregon Health & Science University, Portland, OR, United States.,National Center for Rehabilitative Auditory Research, Portland VA Medical Center (VHA), Portland, OR, United States
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30
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Miscoding-induced stalling of substrate translocation on the bacterial ribosome. Proc Natl Acad Sci U S A 2017; 114:E8603-E8610. [PMID: 28973849 DOI: 10.1073/pnas.1707539114] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Directional transit of the ribosome along the messenger RNA (mRNA) template is a key determinant of the rate and processivity of protein synthesis. Imaging of the multistep translocation mechanism using single-molecule FRET has led to the hypothesis that substrate movements relative to the ribosome resolve through relatively long-lived late intermediates wherein peptidyl-tRNA enters the P site of the small ribosomal subunit via reversible, swivel-like motions of the small subunit head domain within the elongation factor G (GDP)-bound ribosome complex. Consistent with translocation being rate-limited by recognition and productive engagement of peptidyl-tRNA within the P site, we now show that base-pairing mismatches between the peptidyl-tRNA anticodon and the mRNA codon dramatically delay this rate-limiting, intramolecular process. This unexpected relationship between aminoacyl-tRNA decoding and translocation suggests that miscoding antibiotics may impact protein synthesis by impairing the recognition of peptidyl-tRNA in the small subunit P site during EF-G-catalyzed translocation. Strikingly, we show that elongation factor P (EF-P), traditionally known to alleviate ribosome stalling at polyproline motifs, can efficiently rescue translocation defects arising from miscoding. These findings help reveal the nature and origin of the rate-limiting steps in substrate translocation on the bacterial ribosome and indicate that EF-P can aid in resuming translation elongation stalled by miscoding errors.
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31
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Degtyareva NN, Gong C, Story S, Levinson NS, Oyelere AK, Green KD, Garneau-Tsodikova S, Arya DP. Antimicrobial Activity, AME Resistance, and A-Site Binding Studies of Anthraquinone-Neomycin Conjugates. ACS Infect Dis 2017; 3:206-215. [PMID: 28103015 PMCID: PMC5971063 DOI: 10.1021/acsinfecdis.6b00176] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The antibacterial effects of aminoglycosides are based on their association with the A-site of bacterial rRNA and interference with the translational process in the bacterial cell, causing cell death. The clinical use of aminoglycosides is complicated by resistance and side effects, some of which arise from their interactions with the human mitochondrial 12S rRNA and its deafness-associated mutations, C1494U and A1555G. We report a rapid assay that allows screening of aminoglycoside compounds to these classes of rRNAs. These screening tools are important to find antibiotics that selectively bind to the bacterial A-site rather than human, mitochondrial A-sites and its mutant homologues. Herein, we report our preliminary work on the optimization of this screen using 12 anthraquinone-neomycin (AMA-NEO) conjugates against molecular constructs representing five A-site homologues, Escherichia coli, human cytosolic, mitochondrial, C1494U, and A1555G, using a fluorescent displacement screening assay. These conjugates were also tested for inhibition of protein synthesis, antibacterial activity against 14 clinically relevant bacterial strains, and the effect on enzymes that inactivate aminoglycosides. The AMA-NEO conjugates demonstrated significantly improved resistance against aminoglycoside-modifying enzymes (AMEs), as compared with NEO. Several compounds exhibited significantly greater inhibition of prokaryotic protein synthesis as compared to NEO and were extremely poor inhibitors of eukaryotic translation. There was significant variation in antibacterial activity and MIC of selected compounds between bacterial strains, with Escherichia coli, Enteroccocus faecalis, Citrobacter freundii, Shigella flexneri, Serratia marcescens, Proteus mirabilis, Enterobacter cloacae, Staphylococcus epidermidis, and Listeria monocytogenes exhibiting moderate to high sensitivity (50-100% growth inhibition) whereas Acinetobacter baumannii, Pseudomonas aeruginosa, Klebsiellla pneumoniae, and MRSA strains expressed low sensitivity, as compared to the parent aminoglycoside NEO.
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Affiliation(s)
| | - Changjun Gong
- Department of Chemistry, Clemson University, Clemson, South Carolina 29634, United States
| | - Sandra Story
- NUBAD, LLC, Greenville, South Carolina 29605, United States
| | - Nathanael S. Levinson
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
| | - Adegboyega K. Oyelere
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
| | - Keith D. Green
- College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536-0596, United States
| | | | - Dev P. Arya
- NUBAD, LLC, Greenville, South Carolina 29605, United States
- Department of Chemistry, Clemson University, Clemson, South Carolina 29634, United States
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32
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Gao Z, Chen Y, Guan MX. Mitochondrial DNA mutations associated with aminoglycoside induced ototoxicity. J Otol 2017; 12:1-8. [PMID: 29937831 PMCID: PMC6011804 DOI: 10.1016/j.joto.2017.02.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 02/07/2017] [Accepted: 02/08/2017] [Indexed: 11/25/2022] Open
Abstract
Aminoglycosides (AmAn) are widely used for their great efficiency against gram-negative bacterial infections. However, they can also induce ototoxic hearing loss, which has affected millions of people around the world. As previously reported, individuals bearing mitochondrial DNA mutations in the 12S rRNA gene, such as m.1555A>G and m.1494C>T, are more prone to AmAn-induced ototoxicity. These mutations cause human mitochondrial ribosomes to more closely resemble bacterial ribosomes and enable a stronger aminoglycoside interaction. Consequently, exposure to AmAn can induce or worsen hearing loss in these individuals. Furthermore, a wide range of severity and penetrance of hearing loss was observed among families carrying these mutations. Studies have revealed that these mitochondria mutations are the primary molecular mechanism of genetic susceptibility to AmAn ototoxicity, though nuclear modifier genes and mitochondrial haplotypes are known to modulate the phenotypic manifestation.
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Affiliation(s)
- Zewen Gao
- Division of Clinical Genetics and Genomics, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China.,Institute of Genetics, Zhejiang University and Department of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Ye Chen
- Division of Clinical Genetics and Genomics, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China.,Institute of Genetics, Zhejiang University and Department of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Min-Xin Guan
- Division of Clinical Genetics and Genomics, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China.,Institute of Genetics, Zhejiang University and Department of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
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33
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Colameco S, Elliot MA. Non-coding RNAs as antibiotic targets. Biochem Pharmacol 2016; 133:29-42. [PMID: 28012959 DOI: 10.1016/j.bcp.2016.12.015] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 12/12/2016] [Indexed: 02/07/2023]
Abstract
Antibiotics inhibit a wide range of essential processes in the bacterial cell, including replication, transcription, translation and cell wall synthesis. In many instances, these antibiotics exert their effects through association with non-coding RNAs. This review highlights many classical antibiotic targets (e.g. rRNAs and the ribosome), explores a number of emerging targets (e.g. tRNAs, RNase P, riboswitches and small RNAs), and discusses the future directions and challenges associated with non-coding RNAs as antibiotic targets.
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Affiliation(s)
- Savannah Colameco
- Department of Biology and Institute for Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada
| | - Marie A Elliot
- Department of Biology and Institute for Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada.
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34
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Hailey DW, Esterberg R, Linbo TH, Rubel EW, Raible DW. Fluorescent aminoglycosides reveal intracellular trafficking routes in mechanosensory hair cells. J Clin Invest 2016; 127:472-486. [PMID: 27991862 DOI: 10.1172/jci85052] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 11/03/2016] [Indexed: 11/17/2022] Open
Abstract
Aminoglycosides (AGs) are broad-spectrum antibiotics that are associated with kidney damage, balance disorders, and permanent hearing loss. This damage occurs primarily by killing of proximal tubule kidney cells and mechanosensory hair cells, though the mechanisms underlying cell death are not clear. Imaging molecules of interest in living cells can elucidate how molecules enter cells, traverse intracellular compartments, and interact with sites of activity. Here, we have imaged fluorescently labeled AGs in live zebrafish mechanosensory hair cells. We determined that AGs enter hair cells via both nonendocytic and endocytic pathways. Both routes deliver AGs from the extracellular space to lysosomes, and structural differences between AGs alter the efficiency of this delivery. AGs with slower delivery to lysosomes were immediately toxic to hair cells, and impeding lysosome delivery increased AG-induced death. Therefore, pro-death cascades induced at early time points of AG exposure do not appear to derive from the lysosome. Our findings help clarify how AGs induce hair cell death and reveal properties that predict toxicity. Establishing signatures for AG toxicity may enable more efficient evaluation of AG treatment paradigms and structural modifications to reduce hair cell damage. Further, this work demonstrates how following fluorescently labeled drugs at high resolution in living cells can reveal important details about how drugs of interest behave.
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35
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Hamilton KS, Gopal KV, Moore EJ, Gross GW. Pharmacological response sensitization in nerve cell networks exposed to the antibiotic gentamicin. Eur J Pharmacol 2016; 794:92-99. [PMID: 27864104 DOI: 10.1016/j.ejphar.2016.11.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Revised: 11/08/2016] [Accepted: 11/09/2016] [Indexed: 11/26/2022]
Abstract
Gentamicin is an aminoglycoside antibiotic that is used in clinical, organismic, and agricultural applications to combat gram-negative, aerobic bacteria. The clinical use of gentamicin is widely linked to various toxicities, but there is a void in our knowledge about the neuromodulatory or neurotoxicity effects of gentamicin. This investigation explored the electrophysiologic effects of gentamicin on GABAergic pharmacological profiles in spontaneously active neuronal networks in vitro derived from auditory cortices of E16 mouse embryos and grown on microelectrode arrays. Using the GABAA agonist muscimol as the test substance, responses from networks to dose titrations of muscimol were compared in the presence and absence of 100µM gentamicin (the recommended concentration for cell culture conditions). Spike-rate based EC50 values were generated using sigmoidal fit concentration response curves (CRCs). Exposure to 100µM gentamicin exhibited a muscimol EC50±S.E.M. of 80±6nM (n=10). The EC50 value obtained in the absence of gentamicin was 124±11nM (n=10). The 35% increase in potency suggests network sensitization to muscimol in the presence of gentamicin. Action potential (AP) waveform analyses of neurons exposed to gentamicin demonstrated a concentration-dependent decrease in AP amplitudes (extracellular recordings), possibly reflecting gentamicin effects on voltage-gated ion channels. These in vitro results reveal alteration of pharmacological responses by antibiotics that could have significant influence on the behavior and performance of animals.
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Affiliation(s)
- Kevin S Hamilton
- Department of Audiology & Speech-Language Pathology, University of North Texas, 1155 Union Circle #305010, Denton, TX 76203, USA; Center for Network Neuroscience, University of North Texas, 1155 Union Circle #305010, Denton, TX 76203, USA.
| | - Kamakshi V Gopal
- Department of Audiology & Speech-Language Pathology, University of North Texas, 1155 Union Circle #305010, Denton, TX 76203, USA; Center for Network Neuroscience, University of North Texas, 1155 Union Circle #305010, Denton, TX 76203, USA.
| | - Ernest J Moore
- Department of Audiology & Speech-Language Pathology, University of North Texas, 1155 Union Circle #305010, Denton, TX 76203, USA; Center for Network Neuroscience, University of North Texas, 1155 Union Circle #305010, Denton, TX 76203, USA.
| | - Guenter W Gross
- Dept. of Biological Sciences, University of North Texas, 1155 Union Circle #305010, Denton, TX 76203, USA; Center for Network Neuroscience, University of North Texas, 1155 Union Circle #305010, Denton, TX 76203, USA.
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36
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Godeshala S, Nitiyanandan R, Thompson B, Goklany S, Nielsen DR, Rege K. Folate receptor-targeted aminoglycoside-derived polymers for transgene expression in cancer cells. Bioeng Transl Med 2016; 1:220-231. [PMID: 29313013 PMCID: PMC5675079 DOI: 10.1002/btm2.10038] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Revised: 09/02/2016] [Accepted: 09/13/2016] [Indexed: 12/25/2022] Open
Abstract
Targeted delivery of anticancer therapeutics can potentially overcome the limitations associated with current chemotherapeutic regimens. Folate receptors are overexpressed in several cancers, including ovarian, triple-negative breast and bladder cancers, making them attractive for targeted delivery of nucleic acid therapeutics to these tumors. This work describes the synthesis, characterization and evaluation of folic acid-conjugated, aminoglycoside-derived polymers for targeted delivery of transgenes to breast and bladder cancer cell lines. Transgene expression was significantly higher with FA-conjugated aminoglycoside-derived polymers than with Lipofectamine, and these polymers demonstrated minimal cytotoxicty. Competitive inhibition using free folic acid significantly reduced transgene expression efficacy of folate-targeted polymers, suggesting a role for folate receptor-mediated uptake. High efficacy FA-targeted polymers were employed to deliver a plasmid expressing the TRAIL protein, which induced death in cancer cells. These results indicate that FA-conjugated aminoglycoside-derived polymers are promising for targeted delivery of nucleic acids to cancer cells that overexpress folate receptors.
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Affiliation(s)
| | | | - Brian Thompson
- Chemical EngineeringArizona State UniversityTempeAZ85287
| | - Sheba Goklany
- Chemical EngineeringArizona State UniversityTempeAZ85287
| | | | - Kaushal Rege
- Chemical EngineeringArizona State UniversityTempeAZ85287
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Mok WWK, Park JO, Rabinowitz JD, Brynildsen MP. RNA Futile Cycling in Model Persisters Derived from MazF Accumulation. mBio 2015; 6:e01588-15. [PMID: 26578677 PMCID: PMC4659464 DOI: 10.1128/mbio.01588-15] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 10/19/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Metabolism plays an important role in the persister phenotype, as evidenced by the number of strategies that perturb metabolism to sabotage this troublesome subpopulation. However, the absence of techniques to isolate high-purity populations of native persisters has precluded direct measurement of persister metabolism. To address this technical challenge, we studied Escherichia coli populations whose growth had been inhibited by the accumulation of the MazF toxin, which catalyzes RNA cleavage, as a model system for persistence. Using chromosomally integrated, orthogonally inducible promoters to express MazF and its antitoxin MazE, bacterial populations that were almost entirely tolerant to fluoroquinolone and β-lactam antibiotics were obtained upon MazF accumulation, and these were subjected to direct metabolic measurements. While MazF model persisters were nonreplicative, they maintained substantial oxygen and glucose consumption. Metabolomic analysis revealed accumulation of all four ribonucleotide monophosphates (NMPs). These results are consistent with a MazF-catalyzed RNA futile cycle, where the energy derived from catabolism is dissipated through continuous transcription and MazF-mediated RNA degradation. When transcription was inhibited, oxygen consumption and glucose uptake decreased, and nucleotide triphosphates (NTPs) and NTP/NMP ratios increased. Interestingly, the MazF-inhibited cells were sensitive to aminoglycosides, and this sensitivity was blocked by inhibition of transcription. Thus, in MazF model persisters, futile cycles of RNA synthesis and degradation result in both significant metabolic demands and aminoglycoside sensitivity. IMPORTANCE Metabolism plays a critical role in controlling each stage of bacterial persistence (shutdown, stasis, and reawakening). In this work, we generated an E. coli strain in which the MazE antitoxin and MazF toxin were artificially and independently inducible, and we used this strain to generate model persisters and study their metabolism. We found that even though growth of the model persisters was inhibited, they remained highly metabolically active. We further uncovered a futile cycle driven by continued transcription and MazF-mediated transcript degradation that dissipated the energy derived from carbon catabolism. Interestingly, the existence of this futile cycle acted as an Achilles' heel for MazF model persisters, rendering them vulnerable to killing by aminoglycosides.
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Affiliation(s)
- Wendy W K Mok
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey, USA
| | - Junyoung O Park
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey, USA Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, USA
| | - Joshua D Rabinowitz
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, USA Department of Chemistry, Princeton University, Princeton, New Jersey, USA
| | - Mark P Brynildsen
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey, USA
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38
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Hong S, Harris KA, Fanning KD, Sarachan KL, Frohlich KM, Agris PF. Evidence That Antibiotics Bind to Human Mitochondrial Ribosomal RNA Has Implications for Aminoglycoside Toxicity. J Biol Chem 2015; 290:19273-86. [PMID: 26060252 DOI: 10.1074/jbc.m115.655092] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Indexed: 12/11/2022] Open
Abstract
Aminoglycosides are a well known antibiotic family used to treat bacterial infections in humans and animals, but which can be toxic. By binding to the decoding site of helix44 of the small subunit RNA of the bacterial ribosome, the aminoglycoside antibiotics inhibit protein synthesis, cause misreading, or obstruct peptidyl-tRNA translocation. Although aminoglycosides bind helix69 of the bacterial large subunit RNA as well, little is known about their interaction with the homologous human helix69. To probe the role this binding event plays in toxicity, changes to thermal stability, base stacking, and conformation upon aminoglycoside binding to the human cytoplasmic helix69 were compared with those of the human mitochondrial and Escherichia coli helix69. Surprisingly, binding of gentamicin and kanamycin A to the chemically synthesized terminal hairpins of the human cytoplasmic, human mitochondrial, and E. coli helix69 revealed similar dissociation constants (1.3-1.7 and 4.0-5.4 μM, respectively). In addition, aminoglycoside binding enhanced conformational stability of the human mitochondrial helix69 by increasing base stacking. Proton one-dimensional and two-dimensional NMR suggested significant and specific conformational changes of human mitochondrial and E. coli helix69 upon aminoglycoside binding, as compared with human cytoplasmic helix69. The conformational changes and similar aminoglycoside binding affinities observed for human mitochondrial helix69 and E. coli helix69, as well as the increase in structural stability shown for the former, suggest that this binding event is important to understanding aminoglycoside toxicity.
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Affiliation(s)
- Seoyeon Hong
- From The RNA Institute and the Department of Biological Sciences, University at Albany, Albany, New York 12222
| | - Kimberly A Harris
- From The RNA Institute and the Department of Biological Sciences, University at Albany, Albany, New York 12222
| | - Kathryn D Fanning
- From The RNA Institute and the Department of Biological Sciences, University at Albany, Albany, New York 12222
| | - Kathryn L Sarachan
- From The RNA Institute and the Department of Biological Sciences, University at Albany, Albany, New York 12222
| | - Kyla M Frohlich
- From The RNA Institute and the Department of Biological Sciences, University at Albany, Albany, New York 12222
| | - Paul F Agris
- From The RNA Institute and the Department of Biological Sciences, University at Albany, Albany, New York 12222
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39
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De Silva D, Tu YT, Amunts A, Fontanesi F, Barrientos A. Mitochondrial ribosome assembly in health and disease. Cell Cycle 2015; 14:2226-50. [PMID: 26030272 DOI: 10.1080/15384101.2015.1053672] [Citation(s) in RCA: 130] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The ribosome is a structurally and functionally conserved macromolecular machine universally responsible for catalyzing protein synthesis. Within eukaryotic cells, mitochondria contain their own ribosomes (mitoribosomes), which synthesize a handful of proteins, all essential for the biogenesis of the oxidative phosphorylation system. High-resolution cryo-EM structures of the yeast, porcine and human mitoribosomal subunits and of the entire human mitoribosome have uncovered a wealth of new information to illustrate their evolutionary divergence from their bacterial ancestors and their adaptation to synthesis of highly hydrophobic membrane proteins. With such structural data becoming available, one of the most important remaining questions is that of the mitoribosome assembly pathway and factors involved. The regulation of mitoribosome biogenesis is paramount to mitochondrial respiration, and thus to cell viability, growth and differentiation. Moreover, mutations affecting the rRNA and protein components produce severe human mitochondrial disorders. Despite its biological and biomedical significance, knowledge on mitoribosome biogenesis and its deviations from the much-studied bacterial ribosome assembly processes is scarce, especially the order of rRNA processing and assembly events and the regulatory factors required to achieve fully functional particles. This article focuses on summarizing the current available information on mitoribosome assembly pathway, factors that form the mitoribosome assembly machinery, and the effect of defective mitoribosome assembly on human health.
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Affiliation(s)
- Dasmanthie De Silva
- a Department of Biochemistry and Molecular Biology ; University of Miami Miller School of Medicine ; Miami , FL USA
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An aptamer-based signal-on bio-assay for sensitive and selective detection of Kanamycin A by using gold nanoparticles. Talanta 2015; 139:226-32. [PMID: 25882430 DOI: 10.1016/j.talanta.2015.02.036] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Revised: 02/10/2015] [Accepted: 02/19/2015] [Indexed: 11/20/2022]
Abstract
In this study, a simple and sensitive aptamer-based fluorescence method for the detection of Kanamycin A by using gold nanoparticles (AuNPs) has been developed. In this assay, AuNPs were utilized as DNA nanocarrier as well as efficient fluorescence quencher. In the absence of Kanamycin A, dye-labeled aptamer could be adsorbed onto the surface of AuNPs and the fluorescence signal was quenched. In the presence of Kanamycin A, the specific binding between dye-labeled aptamer and its target induced the formation of rigid structure, which led to dye-labeled aptamer releasing from the surface of AuNPs and the fluorescence intensity was recovered consequently. Under optimum conditions, calibration modeling showed that the analytical linear range covered from 0.8nM to 350nM and the detection limit of 0.3nM was realized successfully. This proposed bio-assay also showed high selectivity over other antibiotics. Meanwhile, this strategy was further used to determine the concentrations of Kanamycin A in milk sample with satisfying results.
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41
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Mogre A, Sengupta T, Veetil RT, Ravi P, Seshasayee ASN. Genomic analysis reveals distinct concentration-dependent evolutionary trajectories for antibiotic resistance in Escherichia coli. DNA Res 2014; 21:711-26. [PMID: 25281544 PMCID: PMC4263303 DOI: 10.1093/dnares/dsu032] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Evolution of bacteria under sublethal concentrations of antibiotics represents a trade-off between growth and resistance to the antibiotic. To understand this trade-off, we performed in vitro evolution of laboratory Escherichia coli under sublethal concentrations of the aminoglycoside kanamycin over short time durations. We report that fixation of less costly kanamycin-resistant mutants occurred earlier in populations growing at lower sublethal concentration of the antibiotic, compared with those growing at higher sublethal concentrations; in the latter, resistant mutants with a significant growth defect persisted longer. Using deep sequencing, we identified kanamycin resistance-conferring mutations, which were costly or not in terms of growth in the absence of the antibiotic. Multiple mutations in the C-terminal end of domain IV of the translation elongation factor EF-G provided low-cost resistance to kanamycin. Despite targeting the same or adjacent residues of the protein, these mutants differed from each other in the levels of resistance they provided. Analysis of one of these mutations showed that it has little defect in growth or in synthesis of green fluorescent protein (GFP) from an inducible plasmid in the absence of the antibiotic. A second class of mutations, recovered only during evolution in higher sublethal concentrations of the antibiotic, deleted the C-terminal end of the ATP synthase shaft. This mutation confers basal-level resistance to kanamycin while showing a strong growth defect in the absence of the antibiotic. In conclusion, the early dynamics of the development of resistance to an aminoglycoside antibiotic is dependent on the levels of stress (concentration) imposed by the antibiotic, with the evolution of less costly variants only a matter of time.
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Affiliation(s)
- Aalap Mogre
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK, Bellary Road, Bangalore, Karnataka 560065, India
| | - Titas Sengupta
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK, Bellary Road, Bangalore, Karnataka 560065, India
| | - Reshma T Veetil
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK, Bellary Road, Bangalore, Karnataka 560065, India
| | - Preethi Ravi
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK, Bellary Road, Bangalore, Karnataka 560065, India
| | - Aswin Sai Narain Seshasayee
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK, Bellary Road, Bangalore, Karnataka 560065, India
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42
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Wang Z, Zhang L, Wang J, Wei D, Shi B, Shan A. Synergistic interaction of PMAP-36 and PRW4 with aminoglycoside antibiotics and their antibacterial mechanism. World J Microbiol Biotechnol 2014; 30:3121-8. [DOI: 10.1007/s11274-014-1739-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Accepted: 09/10/2014] [Indexed: 10/24/2022]
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Wu W, Lesnik KL, Xu S, Wang L, Liu H. Impact of tobramycin on the performance of microbial fuel cell. Microb Cell Fact 2014; 13:91. [PMID: 24993129 PMCID: PMC4094288 DOI: 10.1186/s12934-014-0091-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Accepted: 06/15/2014] [Indexed: 11/12/2022] Open
Abstract
Background The release of antibiotics into aquatic environments has made the treatment of wastewater containing antibiotics a world-wide public health problem. The ability of microbial fuel cells (MFCs) to harvest electricity from organic waste and renewable biomass is attracting increased interest in wastewater treatment. In this paper we investigated the bioelectrochemical response of an electroactive mixed-culture biofilm in MFC to different tobramycin concentrations. Results The electroactive biofilms showed a high degree of robustness against tobramycin at the level of μg/L. The current generation responses of the biofilms were affected by the presence of tobramycin. The inhibition ratio of the MFC increased exponentially with the tobramycin concentrations in the range of 0.1-1.9 g/L. The bacterial communities of the biofilms vary with the concentrations of tobramycin, the equilibrium of which is critical for the stability of electroactive biofilms based-MFC. Conclusions Experimental results demonstrate that the electroactive biofilm-based MFC is robust against antibiotics at the level of μg/L, but sensitive to changes in antibiotic concentration at the level of g/L. These results could provide significant information about the effects of antibiotics on the performance MFC as a waste-treatment technology.
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Chen D, Murchie AIH. An aminoglycoside sensing riboswitch controls the expression of aminoglycoside resistance acetyltransferase and adenyltransferases. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:951-8. [PMID: 24631585 DOI: 10.1016/j.bbagrm.2014.02.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Revised: 02/13/2014] [Accepted: 02/25/2014] [Indexed: 11/27/2022]
Abstract
The emergence of antibiotic resistance in human pathogens is an increasing threat to public health. The fundamental mechanisms that control the high levels of expression of antibiotic resistance genes are not yet completely understood. The aminoglycosides are one of the earliest classes of antibiotics that were introduced in the 1940s. In the clinic aminoglycoside resistance is conferred most commonly through enzymatic modification of the drug although resistance through enzymatic modification of the target rRNA through methylation or the overexpression of efflux pumps is also appearing. An aminoglycoside sensing riboswitch has been identified that controls expression of the aminoglycoside resistance genes that encode the aminoglycoside acetyltransferase (AAC) and aminoglycoside nucleotidyltransferase (ANT) (adenyltransferase (AAD)) enzymes. AAC and ANT cause resistance to aminoglycoside antibiotics through modification of the drugs. Expression of the AAC and ANT resistance genes is regulated by aminoglycoside binding to the 5' leader RNA of the aac/aad genes. The aminoglycoside sensing RNA is also associated with the integron cassette system that captures antibiotic resistance genes. Specific aminoglycoside binding to the leader RNA induces a structural transition in the leader RNA, and consequently induction of resistance protein expression. Reporter gene expression, direct measurements of drug RNA binding, chemical probing and UV cross-linking combined with mutational analysis demonstrated that the leader RNA functioned as an aminoglycoside sensing riboswitch in which drug binding to the leader RNA leads to the induction of aminoglycoside antibiotic resistance. This article is part of a Special Issue entitled: Riboswitches.
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Affiliation(s)
- Dongrong Chen
- Key Laboratory of Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, Fudan University Shanghai Medical College, Shanghai 200032, PR China; Institutes of Biomedical Sciences, Fudan University Shanghai Medical College, Shanghai 200032, PR China.
| | - Alastair I H Murchie
- Key Laboratory of Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, Fudan University Shanghai Medical College, Shanghai 200032, PR China; Institutes of Biomedical Sciences, Fudan University Shanghai Medical College, Shanghai 200032, PR China; School of Pharmacy, Fudan University, Zhang Heng Road 826, Pudong 201203, Shanghai, PR China.
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45
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Potta T, Zhen Z, Grandhi TSP, Christensen MD, Ramos J, Breneman CM, Rege K. Discovery of antibiotics-derived polymers for gene delivery using combinatorial synthesis and cheminformatics modeling. Biomaterials 2013; 35:1977-88. [PMID: 24331709 DOI: 10.1016/j.biomaterials.2013.10.069] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Accepted: 10/27/2013] [Indexed: 01/06/2023]
Abstract
We describe the combinatorial synthesis and cheminformatics modeling of aminoglycoside antibiotics-derived polymers for transgene delivery and expression. Fifty-six polymers were synthesized by polymerizing aminoglycosides with diglycidyl ether cross-linkers. Parallel screening resulted in identification of several lead polymers that resulted in high transgene expression levels in cells. The role of polymer physicochemical properties in determining efficacy of transgene expression was investigated using Quantitative Structure-Activity Relationship (QSAR) cheminformatics models based on Support Vector Regression (SVR) and 'building block' polymer structures. The QSAR model exhibited high predictive ability, and investigation of descriptors in the model, using molecular visualization and correlation plots, indicated that physicochemical attributes related to both, aminoglycosides and diglycidyl ethers facilitated transgene expression. This work synergistically combines combinatorial synthesis and parallel screening with cheminformatics-based QSAR models for discovery and physicochemical elucidation of effective antibiotics-derived polymers for transgene delivery in medicine and biotechnology.
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Affiliation(s)
- Thrimoorthy Potta
- Chemical Engineering, Arizona State University, Tempe, AZ 85287-6106, USA
| | - Zhuo Zhen
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | | | | | - James Ramos
- Harrington Biomedical Engineering, Arizona State University, Tempe, AZ 85287, USA
| | - Curt M Breneman
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Kaushal Rege
- Chemical Engineering, Arizona State University, Tempe, AZ 85287-6106, USA; Harrington Biomedical Engineering, Arizona State University, Tempe, AZ 85287, USA.
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Banerjee D, Banerjee A, Mookherjee S, Vishal M, Mukhopadhyay A, Sen A, Basu A, Ray K. Mitochondrial genome analysis of primary open angle glaucoma patients. PLoS One 2013; 8:e70760. [PMID: 23940637 PMCID: PMC3733777 DOI: 10.1371/journal.pone.0070760] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Accepted: 06/23/2013] [Indexed: 12/24/2022] Open
Abstract
Primary open angle glaucoma (POAG) is a multi-factorial optic disc neuropathy characterized by accelerating damage of the retinal ganglion cells and atrophy of the optic nerve head. The vulnerability of the optic nerve damage leading to POAG has been postulated to result from oxidative stress and mitochondrial dysfunction. In this study, we investigated the possible involvement of the mitochondrial genomic variants in 101 patients and 71 controls by direct sequencing of the entire mitochondrial genome. The number of variable positions in the mtDNA with respect to the revised Cambridge Reference Sequence (rCRS), have been designated "Segregating Sites". The segregating sites present only in the patients or controls have been designated "Unique Segregating Sites (USS)". The population mutation rate (θ = 4Neμ) as estimated by Watterson's θ (θw), considering only the USS, was significantly higher among the patients (p = 9.8 × 10(-15)) compared to controls. The difference in θw and the number of USS were more pronounced when restricted to the coding region (p<1.31 × 10(-21) and p = 0.006607, respectively). Further analysis of the region revealed non-synonymous variations were significantly higher in Complex I among the patients (p = 0.0053). Similar trends were retained when USS was considered only within complex I (frequency 0.49 vs 0.31 with p<0.0001 and mutation rate p-value <1.49×10(-43)) and ND5 within its gene cluster (frequency 0.47 vs 0.23 with p<0.0001 and mutation rate p-value <4.42×10(-47)). ND5 is involved in the proton pumping mechanism. Incidentally, glaucomatous trabecular meshwork cells have been reported to be more sensitive to inhibition of complex I activity. Thus mutations in ND5, expected to inhibit complex I activity, could lead to generation of oxidative stress and favor glaucomatous condition.
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Affiliation(s)
- Deblina Banerjee
- Molecular & Human Genetics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Antara Banerjee
- Molecular & Human Genetics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Suddhasil Mookherjee
- Molecular & Human Genetics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Mansi Vishal
- Molecular & Human Genetics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | | | | | - Analabha Basu
- National Institute of Biomedical Genomics, Kalyani, India
| | - Kunal Ray
- Molecular & Human Genetics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
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47
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Gutierrez B, Douthwaite S, Gonzalez-Zorn B. Indigenous and acquired modifications in the aminoglycoside binding sites of Pseudomonas aeruginosa rRNAs. RNA Biol 2013; 10:1324-32. [PMID: 23948732 PMCID: PMC3817154 DOI: 10.4161/rna.25984] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Revised: 07/26/2013] [Accepted: 07/31/2013] [Indexed: 01/23/2023] Open
Abstract
Aminoglycoside antibiotics remain the drugs of choice for treatment of Pseudomonas aeruginosa infections, particularly for respiratory complications in cystic-fibrosis patients. Previous studies on other bacteria have shown that aminoglycosides have their primary target within the decoding region of 16S rRNA helix 44 with a secondary target in 23S rRNA helix 69. Here, we have mapped P. aeruginosa rRNAs using MALDI mass spectrometry and reverse transcriptase primer extension to identify nucleotide modifications that could influence aminoglycoside interactions. Helices 44 and 45 contain indigenous (housekeeping) modifications at m (4)Cm1402, m (3)U1498, m (2)G1516, m (6) 2A1518, and m (6) 2A1519; helix 69 is modified at m (3)Ψ1915, with m (5)U1939 and m (5)C1962 modification in adjacent sequences. All modifications were close to stoichiometric, with the exception of m (3)Ψ1915, where about 80% of rRNA molecules were methylated. The modification status of a virulent clinical strain expressing the acquired methyltransferase RmtD was altered in two important respects: RmtD stoichiometrically modified m (7)G1405 conferring high resistance to the aminoglycoside tobramycin and, in doing so, impeded one of the methylation reactions at C1402. Mapping the nucleotide methylations in P. aeruginosa rRNAs is an essential step toward understanding the architecture of the aminoglycoside binding sites and the rational design of improved drugs against this bacterial pathogen.
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MESH Headings
- Aminoglycosides/chemistry
- Aminoglycosides/genetics
- Aminoglycosides/metabolism
- Bacterial Proteins/genetics
- Bacterial Proteins/metabolism
- Binding Sites
- Circular Dichroism
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Escherichia coli Proteins/chemistry
- Escherichia coli Proteins/genetics
- Escherichia coli Proteins/metabolism
- Methylation
- Methyltransferases/chemistry
- Methyltransferases/genetics
- Methyltransferases/metabolism
- Models, Molecular
- Nucleic Acid Conformation
- Protein Structure, Tertiary
- Pseudomonas aeruginosa/genetics
- Pseudomonas aeruginosa/metabolism
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 16S/metabolism
- RNA, Ribosomal, 23S/chemistry
- RNA, Ribosomal, 23S/genetics
- RNA, Ribosomal, 23S/metabolism
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
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Affiliation(s)
- Belen Gutierrez
- Departamento de Sanidad Animal; Facultad de Veterinaria; Universidad Complutense de Madrid; Madrid, Spain
- Centro de Vigilancia Sanitaria Veterinaria (VISAVET); Universidad Complutense de Madrid; Madrid, Spain
| | - Stephen Douthwaite
- Department of Biochemistry & Molecular Biology; University of Southern Denmark; Odense, Denmark
| | - Bruno Gonzalez-Zorn
- Departamento de Sanidad Animal; Facultad de Veterinaria; Universidad Complutense de Madrid; Madrid, Spain
- Centro de Vigilancia Sanitaria Veterinaria (VISAVET); Universidad Complutense de Madrid; Madrid, Spain
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48
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He W, Zhang X, Zhang J, Jia X, Zhang J, Sun W, Jiang H, Chen D, Murchie AIH. Riboswitch control of induction of aminoglycoside resistance acetyl and adenyl-transferases. RNA Biol 2013; 10:1266-73. [PMID: 23880830 DOI: 10.4161/rna.25757] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The acquisition of antibiotic resistance by human pathogens poses a significant threat to public health. The mechanisms that control the proliferation and expression of antibiotic resistance genes are not yet completely understood. The aminoglycosides are a historically important class of antibiotics that were introduced in the 1940s. Aminoglycoside resistance is conferred most commonly through enzymatic modification of the drug or enzymatic modification of the target rRNA through methylation or through the overexpression of efflux pumps. In our recent paper, we reported that expression of the aminoglycoside resistance genes encoding the aminoglycoside acetyl transferase (AAC) and aminoglycoside adenyl transferase (AAD) enzymes was controlled by an aminoglycoside-sensing riboswitch RNA. This riboswitch is embedded in the leader RNA of the aac/aad genes and is associated with the integron cassette system. The leader RNA can sense and bind specific aminoglycosides such that the binding causes a structural transition in the leader RNA, which leads to the induction of aminoglycoside antibiotic resistance. Specific aminoglycosides induce reporter gene expression mediated by the leader RNA. Aminoglycoside RNA binding was measured directly and, aminoglycoside-induced changes in RNA structure monitored by chemical probing. UV cross-linking and mutational analysis identified potential aminoglycoside binding sites on the RNA.
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Affiliation(s)
- Weizhi He
- Key Laboratory of Molecular Medicine; the Ministry of Education; Department of Biochemistry and Molecular Biology; Fudan University Shanghai Medical College; Shanghai, PR China; Institutes of Biomedical Sciences; Fudan University Shanghai Medical College; Shanghai, PR China; School of Pharmacy; Fudan University; Pudong, Shanghai, China
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Demirci H, Murphy F, Murphy E, Gregory ST, Dahlberg AE, Jogl G. A structural basis for streptomycin-induced misreading of the genetic code. Nat Commun 2013; 4:1355. [PMID: 23322043 PMCID: PMC3552334 DOI: 10.1038/ncomms2346] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Accepted: 11/30/2012] [Indexed: 11/09/2022] Open
Abstract
During protein synthesis, the ribosome selects aminoacyl-tRNAs with anticodons matching the mRNA codon present in the A-site of the small ribosomal subunit. The aminoglycoside antibiotic streptomycin disrupts decoding by binding close to the site of codon recognition. Here we use X-ray crystallography to define the impact of streptomycin on the decoding site of the Thermus thermophilus 30S ribosomal subunit in complexes with cognate or near-cognate anticodon stem-loop analogs (ASLs) and mRNA. Our crystal structures display a significant local distortion of 16S rRNA induced by streptomycin, including the crucial bases A1492 and A1493 that participate directly in codon recognition. Consistent with kinetic data, we observe that streptomycin stabilizes the near-cognate ASL complex, while destabilizing the cognate ASL complex. These data reveal how streptomycin disrupts the recognition of cognate ASLs and yet improves recognition of a near-cognate ASL.
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Affiliation(s)
- Hasan Demirci
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island 02912, USA
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50
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Ding Y, Leng J, Fan F, Xia B, Xu P. The role of mitochondrial DNA mutations in hearing loss. Biochem Genet 2013; 51:588-602. [PMID: 23605717 DOI: 10.1007/s10528-013-9589-6] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2012] [Accepted: 10/10/2012] [Indexed: 11/29/2022]
Abstract
Mutations in mitochondrial DNA (mtDNA) are one of the most important causes of hearing loss. Of these, the homoplasmic A1555G and C1494T mutations at the highly conserved decoding site of the 12S rRNA gene are well documented as being associated with either aminoglycoside-induced or nonsyndromic hearing loss in many families worldwide. Moreover, five mutations associated with nonsyndromic hearing loss have been identified in the tRNA(Ser(UCN)) gene: A7445G, 7472insC, T7505C, T7510C, and T7511C. Other mtDNA mutations associated with deafness are mainly located in tRNA and protein-coding genes. Failures in mitochondrial tRNA metabolism or protein synthesis were observed from cybrid cells harboring these primary mutations, thereby causing the mitochondrial dysfunctions responsible for deafness. This review article provides a detailed summary of mtDNA mutations that have been reported in deafness and further discusses the molecular mechanisms of these mtDNA mutations in deafness expression.
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Affiliation(s)
- Yu Ding
- Central Laboratory, Hangzhou First People's Hospital, Nanjing Medical University, Huansha Road, Hangzhou, China.
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