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Zhao Y, Patel N, Sun P, Faulds K, Graham D, Liu J. Light-up split aptamers: binding thermodynamics and kinetics for sensing. Analyst 2023; 148:5612-5618. [PMID: 37819248 DOI: 10.1039/d3an01368e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
Due to their programmable structures, many aptamers can be readily split into two halves while still retaining their target binding function. While split aptamers are prevalent in the biosensor field, fundamental studies of their binding are still lacking. In this work, we took advantage of the fluorescence enhancement property of a new aptamer named OTC5 that can bind to tetracycline antibiotics to compare various split aptamers with the full-length aptamer. The split aptamers were designed to have different stem lengths. Longer stem length aptamers showed similar dissociation constants (Kd) to the full-length aptamer, while a shorter stem construct showed an 85-fold increase in Kd. Temperature-dependent fluorescence measurements confirmed the lower thermostability of split aptamers. Isothermal titration calorimetry indicated that split aptamer binding can release more heat but have an even larger entropy loss. Finally, a colorimetric biosensor using gold nanoparticles was designed by pre-assembling two thiolated aptamer halves, which can then link gold nanoparticles to give a red-to-blue color change.
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Affiliation(s)
- Yichen Zhao
- Department of Chemistry, Waterloo Institute for Nanotechnology, Waterloo, Ontario, N2L 3G1, Canada.
| | - Nikesh Patel
- Department of Chemistry, Waterloo Institute for Nanotechnology, Waterloo, Ontario, N2L 3G1, Canada.
- Department of Pure and Applied Chemistry, Technology and Innovation Center, University of Strathclyde, 99 George Street, Glasgow G1 1RD, UK.
| | - Peihuan Sun
- Department of Chemistry, Waterloo Institute for Nanotechnology, Waterloo, Ontario, N2L 3G1, Canada.
| | - Karen Faulds
- Department of Pure and Applied Chemistry, Technology and Innovation Center, University of Strathclyde, 99 George Street, Glasgow G1 1RD, UK.
| | - Duncan Graham
- Department of Pure and Applied Chemistry, Technology and Innovation Center, University of Strathclyde, 99 George Street, Glasgow G1 1RD, UK.
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, Waterloo, Ontario, N2L 3G1, Canada.
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2
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Doxycycline-Induced Changes in Circulating MMP or TIMP2 Levels Are Not Associated with Skeletal-Related Event-Free or Overall Survival in Patients with Bone Metastases from Breast Cancer. Cancers (Basel) 2023; 15:cancers15030571. [PMID: 36765529 PMCID: PMC9913061 DOI: 10.3390/cancers15030571] [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: 12/08/2022] [Revised: 01/10/2023] [Accepted: 01/13/2023] [Indexed: 01/20/2023] Open
Abstract
Doxycycline is often used as a promoter of inducible gene expression in preclinical models; however, it can also have direct effects on tumor growth and survival. This is due in part to its ability to inhibit cell invasion and regulate matrix metalloproteinase (MMP) expression. Given that doxycycline is also osteotropic, a clinical study to assess its effects on modulation of tumor progression or prevention of skeletal-related events (SRE) in patients with bone metastases from breast cancer (the Achilles trial) was undertaken. Patients received 100 mg of oral doxycycline twice daily for 12 weeks, with serum obtained at baseline and 4, 8 and 12 weeks post-initiation of doxycycline treatment. Exploratory analysis of the effects of doxycycline on circulating levels of MMP or tissue inhibitor of matrix metalloproteinase 2 (TIMP2) was performed in enrolled patients. Statistically significant associations were observed between MMP2, MMP9 and TIMP2 at baseline with significant associations maintained between absolute levels and changes in levels of MMP2 and TIMP2 at weeks 4-12 post initiation of doxycycline. Treatment with doxycycline generally resulted in decreases in MMP2 and MMP9 levels with concurrent upregulation of TIMP2 at 12 weeks post-initiation of doxycycline treatment. Despite this, we observed no association with the levels of any of these factors with either SRE-free or overall survival in this patient cohort. In summary, despite observing hypothesized effects of doxycycline administration on surrogate markers of its anti-tumor activity, measures of circulating levels of these biomarkers were not prognostic in this patient population.
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3
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Hossain F, Billah MM, Yamazaki M. Single-Cell Analysis of the Antimicrobial and Bactericidal Activities of the Antimicrobial Peptide Magainin 2. Microbiol Spectr 2022; 10:e0011422. [PMID: 35863040 PMCID: PMC9431230 DOI: 10.1128/spectrum.00114-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 06/28/2022] [Indexed: 11/20/2022] Open
Abstract
Antimicrobial peptides (AMPs) inhibit the proliferation of or kill bacterial cells. To measure these activities, several methods have been used, which provide only the average value of many cells. Here, we report the development of a method to examine the antimicrobial and bactericidal activities of AMPs at the single-cell level (i.e., single-cell analysis) and apply this strategy to examine the interaction of an AMP, magainin 2 (Mag), with Escherichia coli cells. Using this method, we monitored the proliferation of single cells on agar in a microchamber and measured the distribution of the number of cells in each microcolony using optical microscopy. For method A, we incubated cells in the presence of various concentrations of AMPs for 3 h. The fraction of microcolonies containing only a single cell, Psingle, increased with the Mag concentration and reached 1 at a specific concentration, which corresponded to the MIC. For method B, after the interaction of a cell suspension with an AMP for a specific time, an aliquot was diluted to stop the interaction, and the proliferation of single cells then was monitored after a 3-h incubation; this method permits the definition of Psingle(t), the fraction of dead cells after the interaction. For the interaction of Mag with E. coli cells, Psingle(t) increased with the interaction time, reaching ~1 at 10 and 20 min for 25 and 13 μM Mag, respectively. Thus, these results indicate that a short interaction time between Mag and E. coli cells is sufficient to induce bacterial cell death. IMPORTANCE To elucidate the activity of antimicrobial peptides (AMPs) against bacterial cells, it is important to estimate the interaction time that is sufficient to induce cell death. We have developed a method to examine the antimicrobial and bactericidal activities of AMPs at the single-cell level (i.e., single-cell analysis). Using this method, we monitored the proliferation of single cells on agar in a microchamber and measured the distribution of the number of cells in each microcolony using optical microscopy. We found that during the interaction of magainin 2 (Mag) with E. coli cells, the fraction of dead cells, Psingle(t), increased with the interaction time, rapidly reaching 1 (e.g., 10 min for 25 μM Mag). This result indicates that Mag induces cell death after a short time of interaction.
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Affiliation(s)
- Farzana Hossain
- Nanomaterials Research Division, Research Institute of Electronics, Shizuoka University, Shizuoka, Japan
| | - Md Masum Billah
- Integrated Bioscience Section, Graduate School of Science and Technology, Shizuoka University, Shizuoka, Japan
| | - Masahito Yamazaki
- Nanomaterials Research Division, Research Institute of Electronics, Shizuoka University, Shizuoka, Japan
- Integrated Bioscience Section, Graduate School of Science and Technology, Shizuoka University, Shizuoka, Japan
- Department of Physics, Faculty of Science, Shizuoka University, Shizuoka, Japan
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4
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Challenges and current status of computational methods for docking small molecules to nucleic acids. Eur J Med Chem 2019; 168:414-425. [PMID: 30831409 DOI: 10.1016/j.ejmech.2019.02.046] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 02/12/2019] [Accepted: 02/12/2019] [Indexed: 01/29/2023]
Abstract
Since the development of the first docking program in 1982, the use of docking-based in silico screening for potentially bioactive molecule discovery has become a common strategy in academia and pharmaceutical industry. Up until recently, application of docking programs has largely focused on drugs binding to proteins. However, with the discovery of promising drug targets in nucleic acids, including RNA riboswitches, DNA G-quadruplexes, and extended repeats in RNA, there has been greater interests in developing drugs for nucleic acids. However, due to major biochemical and physical differences in charges, binding pockets, and solvation, existing docking programs, developed for proteins, face difficulties when adopted directly for nucleic acids. In this review, we cover the current field of in silico docking to nucleic acids, available programs, as well as challenges faced in the field.
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5
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Doxycycline inhibits pre-rRNA processing and mature rRNA formation in E. coli. J Antibiot (Tokyo) 2019; 72:225-236. [PMID: 30737453 DOI: 10.1038/s41429-019-0149-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 01/11/2019] [Accepted: 01/22/2019] [Indexed: 01/06/2023]
Abstract
In bacteria, RNase III cleaves the initial long primary ribosomal RNA transcripts/precursors (pre-rRNAs), thereby releasing the pre-16S and pre-23S rRNAs for maturation. This cleavage is specified by the double-stranded secondary structures flanking the mature rRNAs, and not necessarily by the nucleotide sequences. Inhibition of this cleavage would lead to a build-up of pre-rRNA molecules. Doxycycline has earlier been shown to bind synthetic double-stranded RNAs and inhibit their cleavage by RNase III. Since bacterial rRNA processing is primarily dependent on RNase III cleavage (which is inhibited by doxycycline), doxycycline could therefore inhibit the normal processing of bacterial rRNA. In this study, the effect of doxycycline on bacterial rRNA processing was investigated by analyzing the amounts of various rRNAs in growing Escherichia coli cells treated with doxycycline. The results showed a doxycycline dose-dependent decrease in mature 16S and 23S rRNAs, concurrent with an accumulation of the initial rRNA transcripts and long precursors. Morphologically, treated cells were elongated at low drug concentrations, while nucleoid degeneration indicative of cell death occurred at higher drug concentrations. These observations suggest that doxycycline inhibits the cleavage and processing of bacterial rRNA transcripts/precursors, leading to impaired formation of mature rRNAs, and the consequent inhibition of protein synthesis for which the tetracycline group of antibiotics are renowned. Since rRNA structure and processing pathway is conserved among bacterial species, this mechanism may account for the broad spectrum of antibiotic activity and selective microbial protein synthesis inhibition of doxycycline and the tetracyclines.
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6
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GC K, To D, Jayalath K, Abeysirigunawardena S. Discovery of a novel small molecular peptide that disrupts helix 34 of bacterial ribosomal RNA. RSC Adv 2019; 9:40268-40276. [PMID: 35542650 PMCID: PMC9076165 DOI: 10.1039/c9ra07812f] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 11/25/2019] [Indexed: 12/14/2022] Open
Abstract
Despite the advances in modern medicine, antibiotic resistance is a persistent and growing threat to the world. Thus, the discovery and development of novel antibiotics have become crucial to combat multi-drug resistant pathogens. The goal of our research is to discover a small molecular peptide that can disrupt the synthesis of new ribosomes. Using the phage display technique, we have discovered a 7-mer peptide that binds to the second strand of 16S h34 RNA with a dissociation constant in the low micromolar range. Binding of the peptide alters RNA structure and inhibits the binding of the ribosomal RNA small subunit methyltransferase C (RsmC) enzyme that methylates the exocyclic amine of G1207. The addition of this peptide also increases the lag phase of bacterial growth. Introduction of chemical modifications to increase the binding affinity of the peptide to RNA, its uptake and stability can further improve the efficacy of the peptide as an antibiotic agent against pathogenic bacteria. Discovery of a novel heptapeptide that disrupts RNA–RNA and RNA–protein interactions in bacterial ribosome.![]()
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Affiliation(s)
- Keshav GC
- Department of Chemistry and Biochemistry
- Kent State University
- Kent
- USA
| | - Davidnhan To
- Department of Chemistry and Biochemistry
- Kent State University
- Kent
- USA
| | - Kumudie Jayalath
- Department of Chemistry and Biochemistry
- Kent State University
- Kent
- USA
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7
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Abstract
Antibiotics have been used for the management of relatively few bacterial plant diseases and are largely restricted to high-value fruit crops because of the expense involved. Antibiotic resistance in plant-pathogenic bacteria has become a problem in pathosystems where these antibiotics have been used for many years. Where the genetic basis for resistance has been examined, antibiotic resistance in plant pathogens has most often evolved through the acquisition of a resistance determinant via horizontal gene transfer. For example, the strAB streptomycin-resistance genes occur in Erwinia amylovora, Pseudomonas syringae, and Xanthomonas campestris, and these genes have presumably been acquired from nonpathogenic epiphytic bacteria colocated on plant hosts under antibiotic selection. We currently lack knowledge of the effect of the microbiome of commensal organisms on the potential of plant pathogens to evolve antibiotic resistance. Such knowledge is critical to the development of robust resistance management strategies to ensure the safe and effective continued use of antibiotics in the management of critically important diseases.
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Affiliation(s)
- George W Sundin
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, Michigan 48824, USA;
| | - Nian Wang
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, Florida 33850, USA
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8
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Tereshchenkov AG, Shishkina AV, Karpenko VV, Chertkov VA, Konevega AL, Kasatsky PS, Bogdanov AA, Sumbatyan NV. New Fluorescent Macrolide Derivatives for Studying Interactions of Antibiotics and Their Analogs with the Ribosomal Exit Tunnel. BIOCHEMISTRY (MOSCOW) 2017; 81:1163-1172. [PMID: 27908240 DOI: 10.1134/s0006297916100138] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Novel fluorescent derivatives of macrolide antibiotics related to tylosin bearing rhodamine, fluorescein, Alexa Fluor 488, BODIPY FL, and nitrobenzoxadiazole (NBD) residues were synthesized. The formation of complexes of these compounds with 70S E. coli ribosomes was studied by measuring the fluorescence polarization depending on the ribosome amount at constant concentration of the fluorescent substance. With the synthesized fluorescent tylosin derivatives, the dissociation constants for ribosome complexes with several known antibiotics and macrolide analogs previously obtained were determined. It was found that the fluorescent tylosin derivatives containing BODIPY FL and NBD groups could be used to screen the binding of novel antibiotics to bacterial ribosomes in the macrolide-binding site.
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Affiliation(s)
- A G Tereshchenkov
- Lomonosov Moscow State University, Faculty of Chemistry, Moscow, 119991, Russia.
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Heidrich CG, Mitova S, Schedlbauer A, Connell SR, Fucini P, Steenbergen JN, Berens C. The Novel Aminomethylcycline Omadacycline Has High Specificity for the Primary Tetracycline-Binding Site on the Bacterial Ribosome. Antibiotics (Basel) 2016; 5:antibiotics5040032. [PMID: 27669321 PMCID: PMC5187513 DOI: 10.3390/antibiotics5040032] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2016] [Revised: 09/01/2016] [Accepted: 09/12/2016] [Indexed: 01/02/2023] Open
Abstract
Omadacycline is an aminomethylcycline antibiotic with potent activity against many Gram-positive and Gram-negative pathogens, including strains carrying the major efflux and ribosome protection resistance determinants. This makes it a promising candidate for therapy of severe infectious diseases. Omadacycline inhibits bacterial protein biosynthesis and competes with tetracycline for binding to the ribosome. Its interactions with the 70S ribosome were, therefore, analyzed in great detail and compared with tigecycline and tetracycline. All three antibiotics are inhibited by mutations in the 16S rRNA that mediate resistance to tetracycline in Brachyspira hyodysenteriae, Helicobacter pylori, Mycoplasma hominis, and Propionibacterium acnes. Chemical probing with dimethyl sulfate and Fenton cleavage with iron(II)-complexes of the tetracycline derivatives revealed that each antibiotic interacts in an idiosyncratic manner with the ribosome. X-ray crystallography had previously revealed one primary binding site for tetracycline on the ribosome and up to five secondary sites. All tetracyclines analyzed here interact with the primary site and tetracycline also with two secondary sites. In addition, each derivative displays a unique set of non-specific interactions with the 16S rRNA.
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Affiliation(s)
- Corina G Heidrich
- Microbiology, Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91058 Erlangen, Germany.
| | - Sanya Mitova
- Microbiology, Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91058 Erlangen, Germany.
| | | | - Sean R Connell
- Structural Biology Unit, CIC bioGUNE, 48160 Derio, Bizkaia, Spain.
- IKERBASQUE, Basque Foundation for Science, 48013 Bilbao, Spain.
| | - Paola Fucini
- Structural Biology Unit, CIC bioGUNE, 48160 Derio, Bizkaia, Spain.
- IKERBASQUE, Basque Foundation for Science, 48013 Bilbao, Spain.
| | | | - Christian Berens
- Microbiology, Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91058 Erlangen, Germany.
- Institute of Molecular Pathogenesis, Friedrich-Loeffler-Institut, 07743 Jena, Germany.
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10
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rRNA Binding Sites and the Molecular Mechanism of Action of the Tetracyclines. Antimicrob Agents Chemother 2016; 60:4433-41. [PMID: 27246781 DOI: 10.1128/aac.00594-16] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The tetracycline antibiotics are known to be effective in the treatment of both infectious and noninfectious disease conditions. The 16S rRNA binding mechanism currently held for the antibacterial action of the tetracyclines does not explain their activity against viruses, protozoa that lack mitochondria, and noninfectious conditions. Also, the mechanism by which the tetracyclines selectively inhibit microbial protein synthesis against host eukaryotic protein synthesis despite conservation of ribosome structure and functions is still questionable. Many studies have investigated the binding of the tetracyclines to the 16S rRNA using the small ribosomal subunit of different bacterial species, but there seems to be no agreement between various reports on the exact binding site on the 16S rRNA. The wide range of activity of the tetracyclines against a broad spectrum of bacterial pathogens, viruses, protozoa, and helminths, as well as noninfectious conditions, indicates a more generalized effect on RNA. In the light of recent evidence that the tetracyclines bind to various synthetic double-stranded RNAs (dsRNAs) of random base sequences, suggesting that the double-stranded structures may play a more important role in the binding of the tetracyclines to RNA than the specific base pairs, as earlier speculated, it is imperative to consider possible alternative binding modes or sites that could help explain the mechanisms of action of the tetracyclines against various pathogens and disease conditions.
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11
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Colton B, McConeghy KW, Schreckenberger PC, Danziger LH. I.V. minocycline revisited for infections caused by multidrug-resistant organisms. Am J Health Syst Pharm 2016; 73:279-85. [DOI: 10.2146/ajhp150290] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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12
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Interaction of the tetracyclines with double-stranded RNAs of random base sequence: new perspectives on the target and mechanism of action. J Antibiot (Tokyo) 2016; 69:622-30. [PMID: 26786504 DOI: 10.1038/ja.2015.145] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Revised: 11/02/2015] [Accepted: 12/08/2015] [Indexed: 02/07/2023]
Abstract
The 16S rRNA binding mechanism proposed for the antibacterial action of the tetracyclines does not explain their mechanism of action against non-bacterial pathogens. In addition, several contradictory base pairs have been proposed as their binding sites on the 16S rRNA. This study investigated the binding of minocycline and doxycycline to short double-stranded RNAs (dsRNAs) of random base sequences. These tetracyclines caused a dose-dependent decrease in the fluorescence intensities of 6-carboxyfluorescein (FAM)-labelled dsRNA and ethidium bromide (EtBr)-stained dsRNA, indicating that both drugs bind to dsRNA of random base sequence in a manner that is competitive with the binding of EtBr and other nucleic acid ligands often used as stains. This effect was observable in the presence of Mg(2+). The binding of the tetracyclines to dsRNA changed features of the fluorescence emission spectra of the drugs and the CD spectra of the RNA, and inhibited RNase III cleavage of the dsRNA. These results indicate that the double-stranded structures of RNAs may have a more important role in their interaction with the tetracyclines than the specific base pairs, which had hitherto been the subject of much investigation. Given the diverse functions of cellular RNAs, the binding of the tetracyclines to their double-stranded helixes may alter the normal processing and functioning of the various biological processes they regulate. This could help to explain the wide range of action of the tetracyclines against various pathogens and disease conditions.
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13
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Hong W, Zeng J, Xie J. Antibiotic drugs targeting bacterial RNAs. Acta Pharm Sin B 2014; 4:258-65. [PMID: 26579393 PMCID: PMC4629089 DOI: 10.1016/j.apsb.2014.06.012] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Revised: 06/04/2014] [Accepted: 06/20/2014] [Indexed: 10/26/2022] Open
Abstract
RNAs have diverse structures that include bulges and internal loops able to form tertiary contacts or serve as ligand binding sites. The recent increase in structural and functional information related to RNAs has put them in the limelight as a drug target for small molecule therapy. In addition, the recognition of the marked difference between prokaryotic and eukaryotic rRNA has led to the development of antibiotics that specifically target bacterial rRNA, reduce protein translation and thereby inhibit bacterial growth. To facilitate the development of new antibiotics targeting RNA, we here review the literature concerning such antibiotics, mRNA, riboswitch and tRNA and the key methodologies used for their screening.
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Affiliation(s)
| | | | - Jianping Xie
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Ministry of Education Eco-Environment of the Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Chongqing 400715, China
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14
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Boonkong W, Petsom A, Thongchul N. Rapidly stopping hemorrhage by enhancing blood clotting at an opened wound using chitosan/polylactic acid/polycaprolactone wound dressing device. JOURNAL OF MATERIALS SCIENCE. MATERIALS IN MEDICINE 2013; 24:1581-1593. [PMID: 23612939 DOI: 10.1007/s10856-013-4864-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Accepted: 01/18/2013] [Indexed: 06/02/2023]
Abstract
Doxycycline and monosodium glutamate (MSG) loaded chitosan (CHI)/polylactic acid (PLA)/polycaprolactone (PCL) blend film was studied as a model device to deliver drug to targeted human organ which in this case was the skin with opened wound. The CHI/PLA/PCL blend film containing 60 % CHI, 28 % PLA, and 12 % PCL exhibited the good properties for making the dressing device. It was observed that doxycycline/MSG loaded CHI/PLA/PCL blend film could rapidly deliver both doxycycline and MSG at the high release percentage approaching 100 % loaded. MSG accelerated blood clotting and fibrin formation; thus, it exhibited the good hemostatic activity. The antibacterial activity of doxycycline loaded CHI/PLA/PCL blend film against Staphylococcus aureus and Escherichia coli as model bacteria was investigated. Doxycycline release played the crucial role in bacterial inhibition as observed from the lowest bacterial cell dry weight observed when compared with the control bacterial culture or the bacterial cultures with the presence of other films studied.
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Affiliation(s)
- Wasinee Boonkong
- Program in Petrochemistry and Polymer Science, Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
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15
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Target- and resistance-based mechanistic studies with TP-434, a novel fluorocycline antibiotic. Antimicrob Agents Chemother 2012; 56:2559-64. [PMID: 22354310 DOI: 10.1128/aac.06187-11] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
TP-434 is a novel, broad-spectrum fluorocycline antibiotic with activity against bacteria expressing major antibiotic resistance mechanisms, including tetracycline-specific efflux and ribosomal protection. The mechanism of action of TP-434 was assessed using both cell-based and in vitro assays. In Escherichia coli cells expressing recombinant tetracycline resistance genes, the MIC of TP-434 (0.063 μg/ml) was unaffected by tet(M), tet(K), and tet(B) and increased to 0.25 and 4 μg/ml in the presence of tet(A) and tet(X), respectively. Tetracycline, in contrast, was significantly less potent (MIC ≥ 128 μg/ml) against E. coli cells when any of these resistance mechanisms were present. TP-434 showed potent inhibition in E. coli in vitro transcription/translation (50% inhibitory concentration [IC(50)] = 0.29 ± 0.09 μg/ml) and [(3)H]tetracycline ribosome-binding competition (IC(50) = 0.22 ± 0.07 μM) assays. The antibacterial potencies of TP-434 and all other tetracycline class antibiotics tested were reduced by 4- to 16-fold, compared to that of the wild-type control strain, against Propionibacterium acnes strains carrying a 16S rRNA mutation, G1058C, a modification that changes the conformation of the primary binding site of tetracycline in the ribosome. Taken together, the findings support the idea that TP-434, like other tetracyclines, binds the ribosome and inhibits protein synthesis and that this activity is largely unaffected by the common tetracycline resistance mechanisms.
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16
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Bishburg E, Bishburg K. Minocycline--an old drug for a new century: emphasis on methicillin-resistant Staphylococcus aureus (MRSA) and Acinetobacter baumannii. Int J Antimicrob Agents 2009; 34:395-401. [PMID: 19665876 DOI: 10.1016/j.ijantimicag.2009.06.021] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2009] [Revised: 06/04/2009] [Accepted: 06/23/2009] [Indexed: 10/20/2022]
Abstract
The epidemiology of nosocomial and community-acquired infections has changed in recent years. Methicillin-resistant Staphylococcus aureus (MRSA), especially community-associated MRSA (CA-MRSA), has emerged as a gram-positive organism with an increasing impact in clinical practice. Infections with Acinetobacter baumannii have become a major cause of morbidity and mortality. Minocycline has significant in vitro activity against MRSA and A. baumannii that is comparable with agents currently used against these organisms. The absence of an intravenous (i.v.) minocycline formulation in recent years has limited its use in seriously ill patients infected with these organisms. However, minocycline i.v. has recently been reintroduced to the US market. The objective of this study was to review available information on the chemistry, mechanism of action, in vitro activity, resistance mechanisms, pharmacokinetics, tolerability and efficacy of minocycline against MRSA and A. baumannii. This article provides suggestions for future studies and potential uses of minocycline and is designed to trigger interest in systematic clinical evaluation of minocycline for patients infected with these organisms. In conclusion, minocycline is an old drug that has the potential to become an important part of the armamentarium against emerging infections such as CA-MRSA and A. baumannii. Owing to its promising profile against these clinically important pathogens as well as excellent pharmacokinetic properties, minocycline merits evaluation in serious infections.
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Affiliation(s)
- Eliahu Bishburg
- Division of Infectious Diseases, Beth Israel Medical Center, 201 Lyons Avenue G3, Newark, NJ 07112, USA.
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17
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Multinormal in vitro distribution model suitable for the distribution of Plasmodium falciparum chemosusceptibility to doxycycline. Antimicrob Agents Chemother 2008; 53:688-95. [PMID: 19047651 DOI: 10.1128/aac.00546-08] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The distribution and range of 50% inhibitory concentrations (IC(50)s) of doxycycline were determined for 747 isolates obtained between 1997 and 2006 from patients living in Senegal, Republic of the Congo, and Gabon and patients hospitalized in France for imported malaria. The statistical analysis was designed to answer the specific question of whether Plasmodium falciparum has different phenotypes of susceptibility to doxycycline. A triple normal distribution was fitted to the data using a Bayesian mixture modeling approach. The IC(50) geometric mean ranged from 6.2 microM to 11.1 microM according to the geographical origin, with a mean of 9.3 microM for all 747 parasites. The values for all 747 isolates were classified into three components: component A, with an IC(50) mean of 4.9 microM (+/-2.1 microM [standard deviation]); component B, with an IC(50) mean of 7.7 microM (+/-1.2 microM); and component C, with an IC(50) mean of 17.9 microM (+/-1.4 microM). According to the origin of the P. falciparum isolates, the triple normal distribution was found in each subgroup. However, the proportion of isolates predicted to belong to component B was most important in isolates from Gabon and Congo and in isolates imported from Africa (from 46 to 56%). In Senegal, 55% of the P. falciparum isolates were predicted to be classified as component C. The cutoff of reduced susceptibility to doxycycline in vitro was estimated to be 35 microM.
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18
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Biswas S, Raoult D, Rolain JM. A bioinformatic approach to understanding antibiotic resistance in intracellular bacteria through whole genome analysis. Int J Antimicrob Agents 2008; 32:207-20. [PMID: 18619818 DOI: 10.1016/j.ijantimicag.2008.03.017] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2008] [Accepted: 03/19/2008] [Indexed: 12/17/2022]
Abstract
Intracellular bacteria survive within eukaryotic host cells and are difficult to kill with certain antibiotics. As a result, antibiotic resistance in intracellular bacteria is becoming commonplace in healthcare institutions. Owing to the lack of methods available for transforming these bacteria, we evaluated the mechanisms of resistance using molecular methods and in silico genome analysis. The objective of this review was to understand the molecular mechanisms of antibiotic resistance through in silico comparisons of the genomes of obligate and facultative intracellular bacteria. The available data on in vitro mutants reported for intracellular bacteria were also reviewed. These genomic data were analysed to find natural mutations in known target genes involved in antibiotic resistance and to look for the presence or absence of different resistance determinants. Our analysis revealed the presence of tetracycline resistance protein (Tet) in Bartonella quintana, Francisella tularensis and Brucella ovis; moreover, most of the Francisella strains possessed the blaA gene, AmpG protein and metallo-beta-lactamase family protein. The presence or absence of folP (dihydropteroate synthase) and folA (dihydrofolate reductase) genes in the genome could explain natural resistance to co-trimoxazole. Finally, multiple genes encoding different efflux pumps were studied. This in silico approach was an effective method for understanding the mechanisms of antibiotic resistance in intracellular bacteria. The whole genome sequence analysis will help to predict several important phenotypic characteristics, in particular resistance to different antibiotics. In the future, stable mutants should be obtained through transformation methods in order to demonstrate experimentally the determinants of resistance in intracellular bacteria.
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Affiliation(s)
- Silpak Biswas
- URMITE UMR 6236, CNRS IRD, Faculté de Médecine et de Pharmacie, Université de la Méditerranée, 27 Bd Jean Moulin, 13385 Marseille Cedex 05, France
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19
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Sidhu ABS, Sun Q, Nkrumah LJ, Dunne MW, Sacchettini JC, Fidock DA. In vitro efficacy, resistance selection, and structural modeling studies implicate the malarial parasite apicoplast as the target of azithromycin. J Biol Chem 2006; 282:2494-504. [PMID: 17110371 DOI: 10.1074/jbc.m608615200] [Citation(s) in RCA: 119] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Azithromycin (AZ), a broad-spectrum antibacterial macrolide that inhibits protein synthesis, also manifests reasonable efficacy as an antimalarial. Its mode of action against malarial parasites, however, has remained undefined. Our in vitro investigations with the human malarial parasite Plasmodium falciparum document a remarkable increase in AZ potency when exposure is prolonged from one to two generations of intraerythrocytic growth, with AZ producing 50% inhibition of parasite growth at concentrations in the mid to low nanomolar range. In our culture-adapted lines, AZ displayed no synergy with chloroquine (CQ), amodiaquine, or artesunate. AZ activity was also unaffected by mutations in the pfcrt (P. falciparum chloroquine resistance transporter) or pfmdr1 (P. falciparum multidrug resistance-1) drug resistance loci, as determined using transgenic lines. We have selected mutant, AZ-resistant 7G8 and Dd2 parasite lines. In the AZ-resistant 7G8 line, the bacterial-like apicoplast large subunit ribosomal RNA harbored a U438C mutation in domain I. Both AZ-resistant lines revealed a G76V mutation in a conserved region of the apicoplast-encoded P. falciparum ribosomal protein L4 (PfRpl4). This protein is predicted to associate with the nuclear genome-encoded P. falciparum ribosomal protein L22 (PfRpl22) and the large subunit rRNA to form the 50 S ribosome polypeptide exit tunnel that can be occupied by AZ. The PfRpl22 sequence remained unchanged. Molecular modeling of mutant PfRpl4 with AZ suggests an altered orientation of the L75 side chain that could preclude AZ binding. These data imply that AZ acts on the apicoplast bacterial-like translation machinery and identify Pfrpl4 as a potential marker of resistance.
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Affiliation(s)
- Amar Bir Singh Sidhu
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
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20
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Wu JY, Kim JJ, Reddy R, Wang WM, Graham DY, Kwon DH. Tetracycline-resistant clinical Helicobacter pylori isolates with and without mutations in 16S rRNA-encoding genes. Antimicrob Agents Chemother 2005; 49:578-83. [PMID: 15673736 PMCID: PMC547221 DOI: 10.1128/aac.49.2.578-583.2005] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Tetracycline-resistant Helicobacter pylori strains have been increasingly reported worldwide. However, only a small number of tetracycline-resistant strains have been studied with regard to possible mechanisms of resistance and those studies have focused on mutations in the tetracycline binding sites of 16S rRNA-encoding genes. We here report studies of 41 tetracycline-resistant H. pylori strains (tetracycline MICs, 4 to 32 microg/ml) from North America (n = 12) and from East Asia (n = 29). DNA sequence analyses of 16S rRNA-encoding genes revealed that 22 (54%) of the resistant isolates carried one of five different single-nucleotide substitutions (CGA, GGA, TGA, AGC, or AGT) at the putative tetracycline binding site (AGA(965-967)). Single-nucleotide substitutions were associated with reduced ribosomal binding and with slightly increased tetracycline MICs (1 to 2 microg/ml). The 19 tetracycline-resistant isolates with no detectable mutations in the tetracycline binding site had normal tetracycline-ribosome binding. All tetracycline-resistant isolates, including those with and those without mutations in the tetracycline binding site, showed decreased accumulation of tetracycline. These results suggest that tetracycline resistance is multifactorial, involving alterations both in ribosomal binding and in membrane permeability.
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Affiliation(s)
- Jeng Yih Wu
- Veterans Affairs Medical Center and Department of Medicine, Baylor College of Medicine, Houston, Texas, USA
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21
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Kasai K, Kanno T, Endo Y, Wakasa K, Tozawa Y. Guanosine tetra- and pentaphosphate synthase activity in chloroplasts of a higher plant: association with 70S ribosomes and inhibition by tetracycline. Nucleic Acids Res 2004; 32:5732-41. [PMID: 15507686 PMCID: PMC528801 DOI: 10.1093/nar/gkh916] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2004] [Revised: 08/17/2004] [Accepted: 10/11/2004] [Indexed: 11/14/2022] Open
Abstract
Chloroplasts possess bacterial-type systems for transcription and translation. On the basis of the identification of a Chlamydomonas reinhardtii gene encoding a RelA-SpoT homolog (RSH) that catalyzes the synthesis of guanosine tetra- or pentaphosphate [(p)ppGpp], we have previously suggested the operation of stringent control in the chloroplast genetic system. Although RSH genes have also been identified in several higher plants, the activities of the encoded enzymes and their mode of action in chloroplasts have remained uncharacterized. We have now characterized the intrinsic (p)ppGpp synthase activity of chloroplast extracts prepared from pea (Pisum sativum). Fractionation by ultracentrifugation suggested that the (p)ppGpp synthase activity of a translationally active chloroplast stromal extract was associated with 70S ribosomes. Furthermore, this enzymatic activity was inhibited by tetracycline, as was the peptide elongation activity of the extract. Structural comparisons between rRNA molecules of Escherichia coli and pea chloroplasts revealed the conservation of putative tetracycline-binding sites. These observations demonstrate the presence of a ribosome-associated (p)ppGpp synthase activity in the chloroplasts of a higher plant, further implicating (p)ppGpp in a genetic system of chloroplasts similar to that operative in bacteria.
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Affiliation(s)
- Koji Kasai
- JST/CREST, Bunkyo-cho 3, Matsuyama, Ehime 890-8577, Japan
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22
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Anokhina MM, Barta A, Nierhaus KH, Spiridonova VA, Kopylov AM. Mapping of the second tetracycline binding site on the ribosomal small subunit of E.coli. Nucleic Acids Res 2004; 32:2594-7. [PMID: 15141029 PMCID: PMC419471 DOI: 10.1093/nar/gkh583] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2004] [Revised: 03/22/2004] [Accepted: 04/14/2004] [Indexed: 11/13/2022] Open
Abstract
Tetracycline blocks stable binding of aminoacyl-tRNA to the bacterial ribosomal A-site. Various tetracycline binding sites have been identified in crystals of the 30S ribosomal small subunit of Thermus thermophilus. Here we describe a direct photo- affinity modification of the ribosomal small subunits of Escherichia coli with 7-[3H]-tetracycline. To select for specific interactions, an excess of the 30S subunits over tetracycline has been used. Primer extension analysis of the 16S rRNA revealed two sites of the modifications: C936 and C948. Considering available data on tetracycline interactions with the prokaryotic 30S subunits, including the presented data (E.coli), X-ray data (T.thermophilus) and genetic data (Helicobacter pylori, E.coli), a second high affinity tetracycline binding site is proposed within the 3'-major domain of the 16S rRNA, in addition to the A-site related tetracycline binding site.
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Affiliation(s)
- Maria M Anokhina
- Department of Chemistry, Moscow State University, 119992 Moscow, Russian Federation
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23
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Connell SR, Tracz DM, Nierhaus KH, Taylor DE. Ribosomal protection proteins and their mechanism of tetracycline resistance. Antimicrob Agents Chemother 2004; 47:3675-81. [PMID: 14638464 PMCID: PMC296194 DOI: 10.1128/aac.47.12.3675-3681.2003] [Citation(s) in RCA: 238] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Sean R Connell
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
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24
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Abstract
Although most antibiotics do not need metal ions for their biological activities, there are a number of antibiotics that require metal ions to function properly, such as bleomycin (BLM), streptonigrin (SN), and bacitracin. The coordinated metal ions in these antibiotics play an important role in maintaining proper structure and/or function of these antibiotics. Removal of the metal ions from these antibiotics can cause changes in structure and/or function of these antibiotics. Similar to the case of "metalloproteins," these antibiotics are dubbed "metalloantibiotics" which are the title subjects of this review. Metalloantibiotics can interact with several different kinds of biomolecules, including DNA, RNA, proteins, receptors, and lipids, rendering their unique and specific bioactivities. In addition to the microbial-originated metalloantibiotics, many metalloantibiotic derivatives and metal complexes of synthetic ligands also show antibacterial, antiviral, and anti-neoplastic activities which are also briefly discussed to provide a broad sense of the term "metalloantibiotics."
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Affiliation(s)
- Li-June Ming
- Department of Chemistry and Institute for Biomolecular Science, University of South Florida, Tampa, Florida 33620-5250, USA.
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25
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Trieber CA, Taylor DE. Mutations in the 16S rRNA genes of Helicobacter pylori mediate resistance to tetracycline. J Bacteriol 2002; 184:2131-40. [PMID: 11914344 PMCID: PMC134973 DOI: 10.1128/jb.184.8.2131-2140.2002] [Citation(s) in RCA: 102] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2001] [Accepted: 01/24/2002] [Indexed: 12/11/2022] Open
Abstract
Low-cost and rescue treatments for Helicobacter pylori infections involve combinations of several drugs including tetracycline. Resistance to tetracycline has recently emerged in H. pylori. The 16S rRNA gene sequences of two tetracycline-resistant clinical isolates (MIC = 64 microg/ml) were determined and compared to the consensus H. pylori 16S rRNA sequence. One isolate had four nucleotide substitutions, and the other had four substitutions and two deletions. Natural transformation with the 16S rRNA genes from the resistant organisms conferred tetracycline resistance on susceptible strains. 16S rRNA genes containing the individual mutations were constructed and tested for the ability to confer resistance. Only the 16S rRNA gene containing the triple mutation, AGA965-967TTC, was able to confer tetracycline resistance on H. pylori 26695. The MICs of tetracycline for the transformed strains were equivalent to those for the original clinical isolates. The two original isolates were also metronidazole resistant, but this trait was not linked to the tetracycline resistance phenotype. Serial passage of several H. pylori strains on increasing concentrations of tetracycline yielded mutants with only a very modest increase in tetracycline resistance to a MIC of 4 to 8 microg/ml. These mutants all had a deletion of G942 in the 16S rRNA genes. The mutations in the 16S rRNA are clearly responsible for tetracycline resistance in H. pylori.
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Affiliation(s)
- Catharine A Trieber
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta, Canada
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26
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Camps M, Arrizabalaga G, Boothroyd J. An rRNA mutation identifies the apicoplast as the target for clindamycin in Toxoplasma gondii. Mol Microbiol 2002; 43:1309-18. [PMID: 11918815 DOI: 10.1046/j.1365-2958.2002.02825.x] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Toxoplasma gondii is a protozoan sensitive to several inhibitors of prokaryotic translation (e.g. clindamycin, macrolides and tetracyclines). A priori, two prokaryotic-like organelles, the 'apicoplast' (a non-photosynthetic plastid) and the mitochondrion, are likely targets for these drugs. Without using overt mutagenesis, we selected two independent clones (ClnR-4 and ClnR-21) with strong and stable clindamycin resistance. Several lines with substantial but lower levels of resistance were also isolated with (XR-46) or without (ClnR-23) overt mutagenesis. The ClnR-4 and ClnR-21 mutants uniquely possess a G-->U point mutation at position 1857 of the apicoplast large-subunit rRNA, whereas no mutation was identified in this region for ClnR-23 or XR-46. Position 1857 corresponds to position 2061 in Escherichia coli where it is predicted to bind clindamycin. The mutation is present in all the apicoplast rDNA copies (an estimated 12 per organelle), indicative of a strong selective advantage in the presence of clindamycin. In the absence of drug, however, such a mutation is unlikely to be neutral, as the G is a critical contributor to the transpeptidation reaction and absolutely conserved in all kingdoms. This may explain why ClnR-4 shows a slight growth defect in vitro. These mutants provide direct genetic evidence that apicoplast translation is the target for clindamycin in Toxoplasma. Further, their sensitivity profiles to other antibiotics specific for the large ribosomal subunit (macrolides and chloramphenicol) and, intriguingly, the small subunit (doxycycline) argue that these drugs also target the apicoplast ribosome.
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Affiliation(s)
- Manel Camps
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305-5124, USA
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27
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Hertweck M, Hiller R, Mueller MW. Inhibition of nuclear pre-mRNA splicing by antibiotics in vitro. EUROPEAN JOURNAL OF BIOCHEMISTRY 2002; 269:175-83. [PMID: 11784311 DOI: 10.1046/j.0014-2956.2001.02636.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
A number of antibiotics have been reported to disturb the decoding process in prokaryotic translation and to inhibit the function of various natural ribozymes. We investigated the effect of several antibiotics on in vitro splicing of a eukaryotic nuclear pre-mRNA (beta-globin). Of the eight antibiotics studied, erythromycin, Cl-tetracycline and streptomycin were identified as splicing inhibitors in nuclear HeLa cell extract. The K(i) values were 160, 180 and 230 microm, respectively. Cl-tetracycline-mediated and streptomycin-mediated splicing inhibition were in the molar inhibition range for hammerhead and human hepatitis delta virus ribozyme self-cleavage (tetracycline), of group-I intron self-splicing (streptomycin) and inhibition of RNase P cleavage by some aminoglycosides. Cl-tetracycline and the aminocyclitol glycoside streptomycin were found to have an indirect effect on splicing by unspecific binding to the pre-mRNA, suggesting that the inhibition is the result of disturbance of the correct folding of the pre-mRNA into the splicing-compatible tertiary structure by the charged groups of these antibiotics. The macrolide, erythromycin, the strongest inhibitor, had only a slight effect on formation of the presplicing complexes A and B, but almost completely inhibited formation of the splicing-active C complex by binding to nuclear extract component(s). This results in direct inhibition of the second step of pre-mRNA splicing. To our knowledge, this is the first report on specific inhibition of nuclear splicing by an antibiotic. The functional groups involved in the interaction of erythromycin with snRNAs and/or splicing factors require further investigation.
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Affiliation(s)
- Maren Hertweck
- Vienna BioCenter, Institute of Microbiology and Genetics, Vienna, Austria
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28
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Chopra I, Roberts M. Tetracycline antibiotics: mode of action, applications, molecular biology, and epidemiology of bacterial resistance. Microbiol Mol Biol Rev 2001; 65:232-60 ; second page, table of contents. [PMID: 11381101 PMCID: PMC99026 DOI: 10.1128/mmbr.65.2.232-260.2001] [Citation(s) in RCA: 2451] [Impact Index Per Article: 106.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Tetracyclines were discovered in the 1940s and exhibited activity against a wide range of microorganisms including gram-positive and gram-negative bacteria, chlamydiae, mycoplasmas, rickettsiae, and protozoan parasites. They are inexpensive antibiotics, which have been used extensively in the prophlylaxis and therapy of human and animal infections and also at subtherapeutic levels in animal feed as growth promoters. The first tetracycline-resistant bacterium, Shigella dysenteriae, was isolated in 1953. Tetracycline resistance now occurs in an increasing number of pathogenic, opportunistic, and commensal bacteria. The presence of tetracycline-resistant pathogens limits the use of these agents in treatment of disease. Tetracycline resistance is often due to the acquisition of new genes, which code for energy-dependent efflux of tetracyclines or for a protein that protects bacterial ribosomes from the action of tetracyclines. Many of these genes are associated with mobile plasmids or transposons and can be distinguished from each other using molecular methods including DNA-DNA hybridization with oligonucleotide probes and DNA sequencing. A limited number of bacteria acquire resistance by mutations, which alter the permeability of the outer membrane porins and/or lipopolysaccharides in the outer membrane, change the regulation of innate efflux systems, or alter the 16S rRNA. New tetracycline derivatives are being examined, although their role in treatment is not clear. Changing the use of tetracyclines in human and animal health as well as in food production is needed if we are to continue to use this class of broad-spectrum antimicrobials through the present century.
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Affiliation(s)
- I Chopra
- Antimicrobial Research Centre and Division of Microbiology, School of Biochemistry & Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
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29
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Chopra I, Roberts M. Tetracycline antibiotics: mode of action, applications, molecular biology, and epidemiology of bacterial resistance. Microbiol Mol Biol Rev 2001. [PMID: 11381101 DOI: 10.1016/s0022-3093(98)00783-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2023] Open
Abstract
Tetracyclines were discovered in the 1940s and exhibited activity against a wide range of microorganisms including gram-positive and gram-negative bacteria, chlamydiae, mycoplasmas, rickettsiae, and protozoan parasites. They are inexpensive antibiotics, which have been used extensively in the prophlylaxis and therapy of human and animal infections and also at subtherapeutic levels in animal feed as growth promoters. The first tetracycline-resistant bacterium, Shigella dysenteriae, was isolated in 1953. Tetracycline resistance now occurs in an increasing number of pathogenic, opportunistic, and commensal bacteria. The presence of tetracycline-resistant pathogens limits the use of these agents in treatment of disease. Tetracycline resistance is often due to the acquisition of new genes, which code for energy-dependent efflux of tetracyclines or for a protein that protects bacterial ribosomes from the action of tetracyclines. Many of these genes are associated with mobile plasmids or transposons and can be distinguished from each other using molecular methods including DNA-DNA hybridization with oligonucleotide probes and DNA sequencing. A limited number of bacteria acquire resistance by mutations, which alter the permeability of the outer membrane porins and/or lipopolysaccharides in the outer membrane, change the regulation of innate efflux systems, or alter the 16S rRNA. New tetracycline derivatives are being examined, although their role in treatment is not clear. Changing the use of tetracyclines in human and animal health as well as in food production is needed if we are to continue to use this class of broad-spectrum antimicrobials through the present century.
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Affiliation(s)
- I Chopra
- Antimicrobial Research Centre and Division of Microbiology, School of Biochemistry & Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
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30
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Spahn CM, Blaha G, Agrawal RK, Penczek P, Grassucci RA, Trieber CA, Connell SR, Taylor DE, Nierhaus KH, Frank J. Localization of the ribosomal protection protein Tet(O) on the ribosome and the mechanism of tetracycline resistance. Mol Cell 2001; 7:1037-45. [PMID: 11389850 DOI: 10.1016/s1097-2765(01)00238-6] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Tet(O) belongs to a class of ribosomal protection proteins that mediate tetracycline resistance. It is a G protein that shows significant sequence similarity to elongation factor EF-G. Here we present a cryo-electron microscopic reconstruction, at 16 A resolution, of its complex with the E. coli 70S ribosome. Tet(O) was bound in the presence of a noncleavable GTP analog to programmed ribosomal complexes carrying fMet-tRNA in the P site. Tet(O) is directly visible as a mass close to the A-site region, similar in shape and binding position to EF-G. However, there are important differences. One of them is the different location of the tip of domain IV, which in the Tet(O) case, does not overlap with the ribosomal A site but is directly adjacent to the primary tetracycline binding site. Our findings give insights into the mechanism of tetracycline resistance.
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Affiliation(s)
- C M Spahn
- Howard Hughes Medical Institute, Health Research Inc. at the Wadsworth Center, Empire State Plaza, Albany, NY 12201, USA
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31
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Pioletti M, Schlünzen F, Harms J, Zarivach R, Glühmann M, Avila H, Bashan A, Bartels H, Auerbach T, Jacobi C, Hartsch T, Yonath A, Franceschi F. Crystal structures of complexes of the small ribosomal subunit with tetracycline, edeine and IF3. EMBO J 2001; 20:1829-39. [PMID: 11296217 PMCID: PMC125237 DOI: 10.1093/emboj/20.8.1829] [Citation(s) in RCA: 362] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The small ribosomal subunit is responsible for the decoding of genetic information and plays a key role in the initiation of protein synthesis. We analyzed by X-ray crystallography the structures of three different complexes of the small ribosomal subunit of Thermus thermophilus with the A-site inhibitor tetracycline, the universal initiation inhibitor edeine and the C-terminal domain of the translation initiation factor IF3. The crystal structure analysis of the complex with tetracycline revealed the functionally important site responsible for the blockage of the A-site. Five additional tetracycline sites resolve most of the controversial biochemical data on the location of tetracycline. The interaction of edeine with the small subunit indicates its role in inhibiting initiation and shows its involvement with P-site tRNA. The location of the C-terminal domain of IF3, at the solvent side of the platform, sheds light on the formation of the initiation complex, and implies that the anti-association activity of IF3 is due to its influence on the conformational dynamics of the small ribosomal subunit.
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Affiliation(s)
- Marta Pioletti
- Max-Planck-Institut für Molekulare Genetik, Ihnestrasse 73, 14195 Berlin, FB Biologie, Chemie, Pharmazie, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Max-Planck-Research Unit for Ribosomal Structure, Notkestrasse 85, 22603 Hamburg, Göttingen Genomics Laboratory, Georg-August Universität, Griesebacherstrasse 8, 37077 Göttingen, Germany, Department of Structural Biology, Weizmann Institute, 76100 Rehovot, Israel and Centro de Investigaciones Biomédicas, Universidad de Carabobo, Las Delicias, Maracay, Venezuela Corresponding author e-mail:
M.Pioletti, F.Schlünzen and J.Harms contributed equally to this work
| | - Frank Schlünzen
- Max-Planck-Institut für Molekulare Genetik, Ihnestrasse 73, 14195 Berlin, FB Biologie, Chemie, Pharmazie, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Max-Planck-Research Unit for Ribosomal Structure, Notkestrasse 85, 22603 Hamburg, Göttingen Genomics Laboratory, Georg-August Universität, Griesebacherstrasse 8, 37077 Göttingen, Germany, Department of Structural Biology, Weizmann Institute, 76100 Rehovot, Israel and Centro de Investigaciones Biomédicas, Universidad de Carabobo, Las Delicias, Maracay, Venezuela Corresponding author e-mail:
M.Pioletti, F.Schlünzen and J.Harms contributed equally to this work
| | - Jörg Harms
- Max-Planck-Institut für Molekulare Genetik, Ihnestrasse 73, 14195 Berlin, FB Biologie, Chemie, Pharmazie, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Max-Planck-Research Unit for Ribosomal Structure, Notkestrasse 85, 22603 Hamburg, Göttingen Genomics Laboratory, Georg-August Universität, Griesebacherstrasse 8, 37077 Göttingen, Germany, Department of Structural Biology, Weizmann Institute, 76100 Rehovot, Israel and Centro de Investigaciones Biomédicas, Universidad de Carabobo, Las Delicias, Maracay, Venezuela Corresponding author e-mail:
M.Pioletti, F.Schlünzen and J.Harms contributed equally to this work
| | - Raz Zarivach
- Max-Planck-Institut für Molekulare Genetik, Ihnestrasse 73, 14195 Berlin, FB Biologie, Chemie, Pharmazie, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Max-Planck-Research Unit for Ribosomal Structure, Notkestrasse 85, 22603 Hamburg, Göttingen Genomics Laboratory, Georg-August Universität, Griesebacherstrasse 8, 37077 Göttingen, Germany, Department of Structural Biology, Weizmann Institute, 76100 Rehovot, Israel and Centro de Investigaciones Biomédicas, Universidad de Carabobo, Las Delicias, Maracay, Venezuela Corresponding author e-mail:
M.Pioletti, F.Schlünzen and J.Harms contributed equally to this work
| | - Marco Glühmann
- Max-Planck-Institut für Molekulare Genetik, Ihnestrasse 73, 14195 Berlin, FB Biologie, Chemie, Pharmazie, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Max-Planck-Research Unit for Ribosomal Structure, Notkestrasse 85, 22603 Hamburg, Göttingen Genomics Laboratory, Georg-August Universität, Griesebacherstrasse 8, 37077 Göttingen, Germany, Department of Structural Biology, Weizmann Institute, 76100 Rehovot, Israel and Centro de Investigaciones Biomédicas, Universidad de Carabobo, Las Delicias, Maracay, Venezuela Corresponding author e-mail:
M.Pioletti, F.Schlünzen and J.Harms contributed equally to this work
| | - Horacio Avila
- Max-Planck-Institut für Molekulare Genetik, Ihnestrasse 73, 14195 Berlin, FB Biologie, Chemie, Pharmazie, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Max-Planck-Research Unit for Ribosomal Structure, Notkestrasse 85, 22603 Hamburg, Göttingen Genomics Laboratory, Georg-August Universität, Griesebacherstrasse 8, 37077 Göttingen, Germany, Department of Structural Biology, Weizmann Institute, 76100 Rehovot, Israel and Centro de Investigaciones Biomédicas, Universidad de Carabobo, Las Delicias, Maracay, Venezuela Corresponding author e-mail:
M.Pioletti, F.Schlünzen and J.Harms contributed equally to this work
| | - Anat Bashan
- Max-Planck-Institut für Molekulare Genetik, Ihnestrasse 73, 14195 Berlin, FB Biologie, Chemie, Pharmazie, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Max-Planck-Research Unit for Ribosomal Structure, Notkestrasse 85, 22603 Hamburg, Göttingen Genomics Laboratory, Georg-August Universität, Griesebacherstrasse 8, 37077 Göttingen, Germany, Department of Structural Biology, Weizmann Institute, 76100 Rehovot, Israel and Centro de Investigaciones Biomédicas, Universidad de Carabobo, Las Delicias, Maracay, Venezuela Corresponding author e-mail:
M.Pioletti, F.Schlünzen and J.Harms contributed equally to this work
| | - Heike Bartels
- Max-Planck-Institut für Molekulare Genetik, Ihnestrasse 73, 14195 Berlin, FB Biologie, Chemie, Pharmazie, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Max-Planck-Research Unit for Ribosomal Structure, Notkestrasse 85, 22603 Hamburg, Göttingen Genomics Laboratory, Georg-August Universität, Griesebacherstrasse 8, 37077 Göttingen, Germany, Department of Structural Biology, Weizmann Institute, 76100 Rehovot, Israel and Centro de Investigaciones Biomédicas, Universidad de Carabobo, Las Delicias, Maracay, Venezuela Corresponding author e-mail:
M.Pioletti, F.Schlünzen and J.Harms contributed equally to this work
| | - Tamar Auerbach
- Max-Planck-Institut für Molekulare Genetik, Ihnestrasse 73, 14195 Berlin, FB Biologie, Chemie, Pharmazie, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Max-Planck-Research Unit for Ribosomal Structure, Notkestrasse 85, 22603 Hamburg, Göttingen Genomics Laboratory, Georg-August Universität, Griesebacherstrasse 8, 37077 Göttingen, Germany, Department of Structural Biology, Weizmann Institute, 76100 Rehovot, Israel and Centro de Investigaciones Biomédicas, Universidad de Carabobo, Las Delicias, Maracay, Venezuela Corresponding author e-mail:
M.Pioletti, F.Schlünzen and J.Harms contributed equally to this work
| | - Carsten Jacobi
- Max-Planck-Institut für Molekulare Genetik, Ihnestrasse 73, 14195 Berlin, FB Biologie, Chemie, Pharmazie, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Max-Planck-Research Unit for Ribosomal Structure, Notkestrasse 85, 22603 Hamburg, Göttingen Genomics Laboratory, Georg-August Universität, Griesebacherstrasse 8, 37077 Göttingen, Germany, Department of Structural Biology, Weizmann Institute, 76100 Rehovot, Israel and Centro de Investigaciones Biomédicas, Universidad de Carabobo, Las Delicias, Maracay, Venezuela Corresponding author e-mail:
M.Pioletti, F.Schlünzen and J.Harms contributed equally to this work
| | - Thomas Hartsch
- Max-Planck-Institut für Molekulare Genetik, Ihnestrasse 73, 14195 Berlin, FB Biologie, Chemie, Pharmazie, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Max-Planck-Research Unit for Ribosomal Structure, Notkestrasse 85, 22603 Hamburg, Göttingen Genomics Laboratory, Georg-August Universität, Griesebacherstrasse 8, 37077 Göttingen, Germany, Department of Structural Biology, Weizmann Institute, 76100 Rehovot, Israel and Centro de Investigaciones Biomédicas, Universidad de Carabobo, Las Delicias, Maracay, Venezuela Corresponding author e-mail:
M.Pioletti, F.Schlünzen and J.Harms contributed equally to this work
| | - Ada Yonath
- Max-Planck-Institut für Molekulare Genetik, Ihnestrasse 73, 14195 Berlin, FB Biologie, Chemie, Pharmazie, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Max-Planck-Research Unit for Ribosomal Structure, Notkestrasse 85, 22603 Hamburg, Göttingen Genomics Laboratory, Georg-August Universität, Griesebacherstrasse 8, 37077 Göttingen, Germany, Department of Structural Biology, Weizmann Institute, 76100 Rehovot, Israel and Centro de Investigaciones Biomédicas, Universidad de Carabobo, Las Delicias, Maracay, Venezuela Corresponding author e-mail:
M.Pioletti, F.Schlünzen and J.Harms contributed equally to this work
| | - François Franceschi
- Max-Planck-Institut für Molekulare Genetik, Ihnestrasse 73, 14195 Berlin, FB Biologie, Chemie, Pharmazie, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Max-Planck-Research Unit for Ribosomal Structure, Notkestrasse 85, 22603 Hamburg, Göttingen Genomics Laboratory, Georg-August Universität, Griesebacherstrasse 8, 37077 Göttingen, Germany, Department of Structural Biology, Weizmann Institute, 76100 Rehovot, Israel and Centro de Investigaciones Biomédicas, Universidad de Carabobo, Las Delicias, Maracay, Venezuela Corresponding author e-mail:
M.Pioletti, F.Schlünzen and J.Harms contributed equally to this work
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McFadden DC, Camps M, Boothroyd JC. Resistance as a tool in the study of old and new drug targets in Toxoplasma. Drug Resist Updat 2001; 4:79-84. [PMID: 11512524 DOI: 10.1054/drup.2001.0184] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Drug resistance generated in vitro in the protozoan parasite Toxoplasma gondii is described. We focus on drugs that are in use in patients, that show some promise for such use, or that represent lead compounds for further development. No instance has yet been reported where resistance to any of these drugs has arisen in a patient or in the field although different strains do show varying degrees of sensitivity. For many of these drugs, however, resistant lines have been generated in the laboratory and these have proven very useful for elucidating a given drug's target. These targets range from metabolic pathways in the cytosol to organellar functions encoded in the mitochondrion or plastid. Such information makes predictions about how fast resistance will arise in the field but more importantly, it helps identify targets that are crucial to the parasite and predicts which combinations of drugs should act synergistically.
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Affiliation(s)
- D C McFadden
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305-5412, USA
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33
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Morosyuk SV, SantaLucia J, Cunningham PR. Structure and function of the conserved 690 hairpin in Escherichia coli 16 S ribosomal RNA. III. Functional analysis of the 690 loop. J Mol Biol 2001; 307:213-28. [PMID: 11243815 DOI: 10.1006/jmbi.2000.4432] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
An instant-evolution experiment was performed on the eight nucleotides comprising the loop region of the 690 hairpin in Escherichia coli 16 S ribosomal RNA. Positions 690 to 697 were randomly mutated and 101 unique functional mutants were isolated, sequenced and analyzed for function in vivo. Non-random nucleotide distributions were observed at each of the mutated positions except 693 and 694. Nucleotide identity significantly affected ribosome function at positions 690, 695, 696 and 697. Pyrimidines were absent at position 696 in the instant-evolution pool as were C at position 691 and G at position 697. A highly significant covariation was observed between nucleotides 690 and 697. No functional double mutants at positions 691 and 696 were obtained from the instant-evolution pool. In our NMR structure of the 690 loop, both the G690.U697 and G691.A696 form sheared hydrogen-bonded mismatches. To further examine the functional constraints between these paired nucleotides, one set of site-directed mutations was constructed at positions 690:697 and another set was constructed at positions 691:696. Functional analysis of the site-directed mutants is consistent with our instant-evolution findings and revealed constraints on the placement of specific functional groups observed in the NMR structure. Ten instant-evolution mutants were isolated that are more functional than the wild-type. Hyperactivity in these mutants correlates with a single mutation at position 693.
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MESH Headings
- Base Pair Mismatch/physiology
- Conserved Sequence
- Escherichia coli/chemistry
- Escherichia coli/genetics
- Escherichia coli/physiology
- Evolution, Molecular
- Magnetic Resonance Spectroscopy
- Models, Molecular
- Mutagenesis, Site-Directed
- Nucleic Acid Conformation
- Phylogeny
- Protons
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/classification
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 16S/physiology
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Affiliation(s)
- S V Morosyuk
- Department of Chemistry, Wayne State University, Detroit, MI 48202, USA
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34
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Morosyuk SV, Cunningham PR, SantaLucia J. Structure and function of the conserved 690 hairpin in Escherichia coli 16 S ribosomal RNA. II. NMR solution structure. J Mol Biol 2001; 307:197-211. [PMID: 11243814 DOI: 10.1006/jmbi.2000.4431] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The solution structure of the conserved 690 hairpin from Escherichia coli 16 S rRNA was determined by NMR spectroscopy. The 690 loop is located at the surface of the 30 S subunit in the platform region and has been implicated in interactions with P-site bound tRNA, E-site mRNA, S11 binding, IF3 binding, and in RNA-RNA interactions with the 790 loop of 16 S rRNA and domain IV of 23 S rRNA. The structure reveals a novel sheared type G690.U697 base-pair with a single hydrogen bond from the G690 amino to U697-04. G691 and A696 also form a sheared pair and U692 forms a U-turn with an H-bond to the A695 non-bridging phosphate oxygen. The sheared pairs and U-turn result in the continuous single-stranded stacking of five residues from 6693 to U697 with their Watson-Crick functional groups exposed in the minor groove. The overall fold of the 690 hairpin is similar to the anticodon loop of tRNA. The structure provides an explanation for chemical protection patterns in the loop upon interaction with tRNA, the 50 S subunit, and S11. In vivo genetic studies demonstrate the functional importance of the motifs observed in the solution structure of the 690 hairpin.
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Affiliation(s)
- S V Morosyuk
- Department of Chemistry, Wayne State University, Detroit, MI 48202, USA
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35
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Brodersen DE, Clemons WM, Carter AP, Morgan-Warren RJ, Wimberly BT, Ramakrishnan V. The structural basis for the action of the antibiotics tetracycline, pactamycin, and hygromycin B on the 30S ribosomal subunit. Cell 2000; 103:1143-54. [PMID: 11163189 DOI: 10.1016/s0092-8674(00)00216-6] [Citation(s) in RCA: 604] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
We have used the recently determined atomic structure of the 30S ribosomal subunit to determine the structures of its complexes with the antibiotics tetracycline, pactamycin, and hygromycin B. The antibiotics bind to discrete sites on the 30S subunit in a manner consistent with much but not all biochemical data. For each of these antibiotics, interactions with the 30S subunit suggest a mechanism for its effects on ribosome function.
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Affiliation(s)
- D E Brodersen
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, United Kingdom
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36
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Beliakova MM, Anokhina MM, Spiridonov VA, Dobrov EN, Egorov TA, Wittmann-Liebold B, Orth P, Saenger W, Kopylov AM. A direct photo-activated affinity modification of tetracycline transcription repressor protein TetR(D) with tetracycline(1). FEBS Lett 2000; 477:263-7. [PMID: 10908732 DOI: 10.1016/s0014-5793(00)01728-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Results of a first successful application of a direct photo-induced affinity modification of Tet repressor (TetR(D)) protein with tetracycline within a complex of known three-dimensional structure are described. The conditions of the modification have provided suitable yields of the modified complex and allowed characterization of the modified segments of the protein. The potential of tetracycline as a fine modifying reagent was established. In the complex of TetR(D) protein with tetracycline, the antibiotic modifies at least two segments, Ile59-Glu73 and Ala173-Glu183, which form a binding tunnel for the drug according to the X-ray analysis. These data open possibilities for the use of different tetracycline targets for structural studies in solution.
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Affiliation(s)
- M M Beliakova
- Department of Chemistry, Moscow State University, 119899 Moscow, Russia
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37
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Morosyuk SV, Lee K, SantaLucia J, Cunningham PR. Structure and function of the conserved 690 hairpin in Escherichia coli 16 S ribosomal RNA: analysis of the stem nucleotides. J Mol Biol 2000; 300:113-26. [PMID: 10864503 DOI: 10.1006/jmbi.2000.3852] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Nucleotides 680 to 710 of Escherichia coli 16 S rRNA form a distinct structural domain required for ribosome function. The goal of this study was to determine the functional significance of pairing interactions in the 690 region. Two different secondary structures were proposed for this hairpin, based on phylogenetic and chemical modification studies. To study the effect of pairing interactions in the 690 hairpin on ribosome function and to determine which of the proposed secondary structures is biologically significant, we performed an instant-evolution experiment in which the nine nucleotides that form the proposed base-pairs and dangling ends of the 690 stem were randomly mutated, and functional mutant combinations were selected. A total of 96 unique functional mutants were isolated, assayed in vivo, and sequenced. Analysis of these data revealed extensive base-pairing and stacking interactions among the mutated nucleotides. Formation of either a Watson-Crick base-pair or G.U pair between positions 688 and 699 is absolutely required for ribosome function. We also performed NMR studies of a 31-nucleotide RNA which indicate the formation of a functionally important base-pair between nucleotides 688 and 699. Formation of a second base-pair between positions 689 and 698, however, is not essential for ribosome function, but the level of ribosome function correlates with the predicted thermodynamic stability of the nucleotide pairs in these positions. The universally conserved positions G690 and U697 are generally portrayed as forming a G.U mismatch. Our data show co-variation between these positions, but do not support the hypothesis that the G690:U697 pair forms a wobble structure. NMR studies of model 14-nt and 31-nt RNAs support these findings and show that G690 and U697 are involved in unusual stacking interactions but do not form a wobble pair. Preliminary NMR structural analysis reveals that the loop portion of the 690 hairpin folds into a highly structured and novel conformation.
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Affiliation(s)
- S V Morosyuk
- Department of Chemistry Sciences, Wayne State University, Detroit, MI, 48202, USA
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38
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Noah JW, Dolan MA, Babin P, Wollenzien P. Effects of tetracycline and spectinomycin on the tertiary structure of ribosomal RNA in the Escherichia coli 30 S ribosomal subunit. J Biol Chem 1999; 274:16576-81. [PMID: 10347223 DOI: 10.1074/jbc.274.23.16576] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Structural analysis of the 16 S rRNA in the 30 S subunit and 70 S ribosome in the presence of ribosome-specific antibiotics was performed to determine whether they produced rRNA structural changes that might provide further insight to their action. An UV cross-linking procedure that determines the pattern and frequency of intramolecular 16 S RNA cross-links was used to detect differences reflecting structural changes. Tetracycline and spectinomycin have specific effects detected by this assay. The presence of tetracycline inhibits the cross-link C967xC1400 completely, increases the frequency of cross-link C1402x1501 twofold, and decreases the cross-link G894xU244 by one-half without affecting other cross-links. Spectinomycin reduces the frequency of the cross-link C934xU1345 by 60% without affecting cross-linking at other sites. The structural changes occur at concentrations at which the antibiotics exert their inhibitory effects. For spectinomycin, the apparent binding site and the affected cross-linking site are distant in the secondary structure but are close in tertiary structure in several recent models, indicating a localized effect. For tetracycline, the apparent binding sites are significantly separated in both the secondary and the three-dimensional structures, suggesting a more regional effect.
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MESH Headings
- Anti-Bacterial Agents/pharmacology
- Base Sequence
- Electrophoresis, Polyacrylamide Gel
- Escherichia coli/drug effects
- Escherichia coli/genetics
- Escherichia coli/radiation effects
- Models, Molecular
- Molecular Sequence Data
- Nucleic Acid Conformation
- RNA, Bacterial/drug effects
- RNA, Bacterial/metabolism
- RNA, Bacterial/radiation effects
- RNA, Ribosomal, 16S/drug effects
- RNA, Ribosomal, 16S/radiation effects
- RNA, Ribosomal, 16S/ultrastructure
- Ribosomes/radiation effects
- Ribosomes/ultrastructure
- Spectinomycin/pharmacology
- Tetracycline/pharmacology
- Ultraviolet Rays
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Affiliation(s)
- J W Noah
- Department of Biochemistry, North Carolina State University, Raleigh, North Carolina 27695-7622, USA
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39
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Montpetit A, Payant C, Nolan JM, Brakier-Gingras L. Analysis of the conformation of the 3' major domain of Escherichia coli16S ribosomal RNA using site-directed photoaffinity crosslinking. RNA (NEW YORK, N.Y.) 1998; 4:1455-1466. [PMID: 9814765 PMCID: PMC1369717 DOI: 10.1017/s1355838298981079] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The 3' major domain of Escherichia coli 16S rRNA, which occupies the head of the small ribosomal subunit, is involved in several functions of the ribosome. We have used a site-specific crosslinking procedure to gain further insights into the higher-order structure of this domain. Circularly permuted RNAs were used to introduce an azidophenacyl group at specific positions within the 3' major domain. Crosslinks were generated in a high-ionic strength buffer that has been used for ribosome reconstitution studies and so enables the RNA to adopt a structure recognized by ribosomal proteins. The crosslinking sites were identified by primer extension and confirmed by assessing the mobility of the crosslinked RNA lariats in denaturing polyacrylamide gels. Eight crosslinks were characterized. Among them, one crosslink demonstrates that helix 28 is proximal to the top of helix 34, and two others show that the 1337 region, located in an internal loop at the junction of helices 29, 30, 41, and 42, is proximal to the center of helix 30 and to a segment connecting helix 28 to helix 29. These relationships of vicinity have previously been observed in native 30S subunits, which suggests that the free domain adopts a conformation similar to that within the 30S subunit. Furthermore, crosslinks were obtained in helix 34, which suggest that the upper and lower portions of this helix are in close proximity.
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Affiliation(s)
- A Montpetit
- Département de Biochimie, Université de Montréal, Québec, Canada
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40
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Ross JI, Eady EA, Cove JH, Cunliffe WJ. 16S rRNA mutation associated with tetracycline resistance in a gram-positive bacterium. Antimicrob Agents Chemother 1998; 42:1702-5. [PMID: 9661007 PMCID: PMC105669 DOI: 10.1128/aac.42.7.1702] [Citation(s) in RCA: 134] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
A genetic basis for tetracycline resistance in cutaneous propionibacteria was suggested by comparing the nucleotide sequences of the 16S rRNA genes from 16 susceptible and 21 resistant clinical isolates and 6 laboratory-selected tetracycline-resistant mutants of a susceptible strain. Fifteen clinical isolates resistant to tetracycline were found to have cytosine instead of guanine at a position cognate with Escherichia coli 16S rRNA base 1058 in a region important for peptide chain termination and translational accuracy known as helix 34. Cytosine at base 1058 was not detected in the laboratory mutants or the tetracycline-susceptible strains. The apparent mutation was recreated by site-directed mutagenesis in the cloned E. coli ribosomal operon, rrnB, encoded by pKK3535.E. coli strains carrying the mutant plasmid were more resistant to tetracycline than those carrying the wild-type plasmid both in MIC determinations and when grown in tetracycline-containing liquid medium. These data are consistent with a role for the single 16S rRNA base mutation in clinical tetracycline resistance in cutaneous propionibacteria.
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Affiliation(s)
- J I Ross
- Department of Microbiology, University of Leeds, United Kingdom.
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