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Cooper HB, Krause KL, Gardner PP. Finding priority bacterial ribosomes for future structural and antimicrobial research based upon global RNA and protein sequence analysis. PeerJ 2023; 11:e14969. [PMID: 36974140 PMCID: PMC10039652 DOI: 10.7717/peerj.14969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 02/07/2023] [Indexed: 03/29/2023] Open
Abstract
Ribosome-targeting antibiotics comprise over half of antibiotics used in medicine, but our fundamental knowledge of their binding sites is derived primarily from ribosome structures of non-pathogenic species. These include Thermus thermophilus, Deinococcus radiodurans and the archaean Haloarcula marismortui, as well as the commensal and sometimes pathogenic organism, Escherichia coli. Advancements in electron cryomicroscopy have allowed for the determination of more ribosome structures from pathogenic bacteria, with each study highlighting species-specific differences that had not been observed in the non-pathogenic structures. These observed differences suggest that more novel ribosome structures, particularly from pathogens, are required for a more accurate understanding of the level of diversity of the entire bacterial ribosome, with the potential of leading to innovative advancements in antibiotic research. In this study, high accuracy covariance and hidden Markov models were used to annotate ribosomal RNA and protein sequences respectively from genomic sequence, allowing us to determine the underlying ribosomal sequence diversity using phylogenetic methods. This analysis provided evidence that the current non-pathogenic ribosome structures are not sufficient representatives of some pathogenic bacteria, such as Campylobacter pylori, or of whole phyla such as Bacteroidota (Bacteroidetes).
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Affiliation(s)
- Helena B. Cooper
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Kurt L. Krause
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Paul P. Gardner
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
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Golparian D, Unemo M. Antimicrobial resistance prediction in Neisseria gonorrhoeae: Current status and future prospects. Expert Rev Mol Diagn 2021; 22:29-48. [PMID: 34872437 DOI: 10.1080/14737159.2022.2015329] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
INTRODUCTION Several nucleic acid amplification tests (NAATs), mostly real-time PCRs, to detect antimicrobial resistance (AMR) determinants and predict AMR in Neisseria gonorrhoeae are promising, and some may be ready to apply at the point-of-care (POC), but important limitations remain with most NAATs. Next-generation sequencing (NGS) can overcome many of these limitations.Areas covered: Recent advances, with main focus on publications since 2017, in the development and use of NAATs and NGS to predict gonococcal AMR for surveillance and clinical use, and pros and cons of these tests as well as future perspectives for appropriate use of molecular AMR prediction for N. gonorrhoeae.Expert Commentary: NAATs and/or NGS for AMR prediction should supplement culture-based AMR surveillance, which will remain because it detects also AMR due to unknown AMR determinants, and translation into POC tests is imperative for the end-goal of individualized treatment, sparing ceftriaxone±azithromycin. Several challenges for direct testing of clinical, especially pharyngeal, specimens and for accurate prediction of cephalosporins and azithromycin resistance, especially using NAATs, remain. The choice of AMR prediction assay needs to carefully consider the intended use of the assay; limitations intrinsic to the AMR prediction technology, algorithms and specific to chosen methodology; specimen types analyzed; and cost-effectiveness.
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Affiliation(s)
- Daniel Golparian
- WHO Collaborating Centre for Gonorrhoea and other STIs, National Reference Laboratory for STIs, Department of Laboratory Medicine, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Magnus Unemo
- WHO Collaborating Centre for Gonorrhoea and other STIs, National Reference Laboratory for STIs, Department of Laboratory Medicine, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
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DeTar RA, Barahimipour R, Manavski N, Schwenkert S, Höhner R, Bölter B, Inaba T, Meurer J, Zoschke R, Kunz HH. Loss of inner-envelope K+/H+ exchangers impairs plastid rRNA maturation and gene expression. THE PLANT CELL 2021; 33:2479-2505. [PMID: 34235544 PMCID: PMC8364240 DOI: 10.1093/plcell/koab123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 04/30/2021] [Indexed: 05/08/2023]
Abstract
The inner-envelope K+ EFFLUX ANTIPORTERS (KEA) 1 and 2 are critical for chloroplast development, ion homeostasis, and photosynthesis. However, the mechanisms by which changes in ion flux across the envelope affect organelle biogenesis remained elusive. Chloroplast development requires intricate coordination between the nuclear genome and the plastome. Many mutants compromised in plastid gene expression (PGE) display a virescent phenotype, that is delayed greening. The phenotypic appearance of Arabidopsis thaliana kea1 kea2 double mutants fulfills this criterion, yet a link to PGE has not been explored. Here, we show that a simultaneous loss of KEA1 and KEA2 results in maturation defects of the plastid ribosomal RNAs. This may be caused by secondary structure changes of rRNA transcripts and concomitant reduced binding of RNA-processing proteins, which we documented in the presence of skewed ion homeostasis in kea1 kea2. Consequently, protein synthesis and steady-state levels of plastome-encoded proteins remain low in mutants. Disturbance in PGE and other signs of plastid malfunction activate GENOMES UNCOUPLED 1-dependent retrograde signaling in kea1 kea2, resulting in a dramatic downregulation of GOLDEN2-LIKE transcription factors to halt expression of photosynthesis-associated nuclear-encoded genes (PhANGs). PhANG suppression delays the development of fully photosynthesizing kea1 kea2 chloroplasts, probably to avoid progressing photo-oxidative damage. Overall, our results reveal that KEA1/KEA2 function impacts plastid development via effects on RNA-metabolism and PGE.
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Affiliation(s)
- Rachael Ann DeTar
- Plant Physiology, School of Biological Sciences, Washington State University, PO Box 644236, Pullman, WA 99164-4236, USA
| | - Rouhollah Barahimipour
- Max Planck Institute of Molecular Plant Physiology, Wissenschaftspark Golm, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Nikolay Manavski
- Plant Sciences, Department I, LMU Munich, Großhaderner Str. 2-4, 82152 Planegg-Martinsried, Germany
| | - Serena Schwenkert
- Plant Sciences, Department I, LMU Munich, Großhaderner Str. 2-4, 82152 Planegg-Martinsried, Germany
| | - Ricarda Höhner
- Plant Physiology, School of Biological Sciences, Washington State University, PO Box 644236, Pullman, WA 99164-4236, USA
| | - Bettina Bölter
- Plant Sciences, Department I, LMU Munich, Großhaderner Str. 2-4, 82152 Planegg-Martinsried, Germany
| | - Takehito Inaba
- Department of Agricultural and Environmental Sciences, Faculty of Agriculture, University of Miyazaki, Miyazaki 889-2192, Japan
| | - Jörg Meurer
- Plant Sciences, Department I, LMU Munich, Großhaderner Str. 2-4, 82152 Planegg-Martinsried, Germany
| | - Reimo Zoschke
- Max Planck Institute of Molecular Plant Physiology, Wissenschaftspark Golm, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Hans-Henning Kunz
- Plant Physiology, School of Biological Sciences, Washington State University, PO Box 644236, Pullman, WA 99164-4236, USA
- Plant Sciences, Department I, LMU Munich, Großhaderner Str. 2-4, 82152 Planegg-Martinsried, Germany
- Author for correspondence:
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Sengupta A, Rice GM, Weeks KM. Single-molecule correlated chemical probing reveals large-scale structural communication in the ribosome and the mechanism of the antibiotic spectinomycin in living cells. PLoS Biol 2019; 17:e3000393. [PMID: 31487286 PMCID: PMC6748448 DOI: 10.1371/journal.pbio.3000393] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 09/17/2019] [Accepted: 08/14/2019] [Indexed: 11/18/2022] Open
Abstract
The ribosome moves between distinct structural states and is organized into multiple functional domains. Here, we examined hundreds of occurrences of pairwise through-space communication between nucleotides in the ribosome small subunit RNA using RNA interaction groups analyzed by mutational profiling (RING-MaP) single-molecule correlated chemical probing in bacterial cells. RING-MaP revealed four structural communities in the small subunit RNA, each distinct from the organization defined by the RNA secondary structure. The head domain contains 2 structural communities: the outer-head contains the pivot for head swiveling, and an inner-head community is structurally integrated with helix 44 and spans the entire ribosome intersubunit interface. In-cell binding by the antibiotic spectinomycin (Spc) barely perturbs its local binding pocket as revealed by the per-nucleotide chemical probing signal. In contrast, Spc binding overstabilizes long-range RNA–RNA contacts that extend 95 Å across the ribosome that connect the pivot for head swiveling with the axis of intersubunit rotation. The two major motions of the small subunit—head swiveling and intersubunit rotation—are thus coordinated via long-range RNA structural communication, which is specifically modulated by Spc. Single-molecule correlated chemical probing reveals trans-domain structural communication and rationalizes the profound functional effects of binding by a low–molecular-mass antibiotic to the megadalton ribosome. Single molecule chemical probing of pair-wise interactions across the ribosome in living cells redefines the domains of the small subunit of the ribosome and reveals that the antibiotic spectinomycin disrupts ribosome function by over-stabilizing interactions that span nearly 100 Å.
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Affiliation(s)
- Arnab Sengupta
- Department of Chemistry, University of North Carolina Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Greggory M. Rice
- Department of Chemistry, University of North Carolina Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Kevin M. Weeks
- Department of Chemistry, University of North Carolina Chapel Hill, Chapel Hill, North Carolina, United States of America
- * E-mail:
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5
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Abstract
Members of the highly heterogeneous family Pasteurellaceae cause a wide variety of diseases in humans and animals. Antimicrobial agents are the most powerful tools to control such infections. However, the acquisition of resistance genes, as well as the development of resistance-mediating mutations, significantly reduces the efficacy of the antimicrobial agents. This article gives a brief description of the role of selected members of the family Pasteurellaceae in animal infections and of the most recent data on the susceptibility status of such members. Moreover, a review of the current knowledge of the genetic basis of resistance to antimicrobial agents is included, with particular reference to resistance to tetracyclines, β-lactam antibiotics, aminoglycosides/aminocyclitols, folate pathway inhibitors, macrolides, lincosamides, phenicols, and quinolones. This article focusses on the genera of veterinary importance for which sufficient data on antimicrobial susceptibility and the detection of resistance genes are currently available (Pasteurella, Mannheimia, Actinobacillus, Haemophilus, and Histophilus). Additionally, the role of plasmids, transposons, and integrative and conjugative elements in the spread of the resistance genes within and beyond the aforementioned genera is highlighted to provide insight into horizontal dissemination, coselection, and persistence of antimicrobial resistance genes. The article discusses the acquisition of diverse resistance genes by the selected Pasteurellaceae members from other Gram-negative or maybe even Gram-positive bacteria. Although the susceptibility status of these members still looks rather favorable, monitoring of their antimicrobial susceptibility is required for early detection of changes in the susceptibility status and the newly acquired/developed resistance mechanisms.
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6
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Zankari E, Allesøe R, Joensen KG, Cavaco LM, Lund O, Aarestrup FM. PointFinder: a novel web tool for WGS-based detection of antimicrobial resistance associated with chromosomal point mutations in bacterial pathogens. J Antimicrob Chemother 2018; 72:2764-2768. [PMID: 29091202 PMCID: PMC5890747 DOI: 10.1093/jac/dkx217] [Citation(s) in RCA: 458] [Impact Index Per Article: 76.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 06/07/2017] [Indexed: 11/23/2022] Open
Abstract
Background Antibiotic resistance is a major health problem, as drugs that were once highly effective no longer cure bacterial infections. WGS has previously been shown to be an alternative method for detecting horizontally acquired antimicrobial resistance genes. However, suitable bioinformatics methods that can provide easily interpretable, accurate and fast results for antimicrobial resistance associated with chromosomal point mutations are still lacking. Methods Phenotypic antimicrobial susceptibility tests were performed on 150 isolates covering three different bacterial species: Salmonella enterica, Escherichia coli and Campylobacter jejuni. The web-server ResFinder-2.1 was used to identify acquired antimicrobial resistance genes and two methods, the novel PointFinder (using BLAST) and an in-house method (mapping of raw WGS reads), were used to identify chromosomal point mutations. Results were compared with phenotypic antimicrobial susceptibility testing results. Results A total of 685 different phenotypic tests associated with chromosomal resistance to quinolones, polymyxin, rifampicin, macrolides and tetracyclines resulted in 98.4% concordance. Eleven cases of disagreement between tested and predicted susceptibility were observed: two C. jejuni isolates with phenotypic fluoroquinolone resistance and two with phenotypic erythromycin resistance and five colistin-susceptible E. coli isolates with a detected pmrB V161G mutation when assembled with Velvet, but not when using SPAdes or when mapping the reads. Conclusions PointFinder proved, with high concordance between phenotypic and predicted antimicrobial susceptibility, to be a user-friendly web tool for detection of chromosomal point mutations associated with antimicrobial resistance.
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Affiliation(s)
- Ea Zankari
- National Food Institute, Technical University of Denmark, 2800 Kgs Lyngby, Denmark.,Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, 2800 Kgs Lyngby, Denmark
| | - Rosa Allesøe
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, 2800 Kgs Lyngby, Denmark
| | - Katrine G Joensen
- Department of Microbiology and Infection Control, Statens Serum Institut, Copenhagen, Denmark
| | - Lina M Cavaco
- National Food Institute, Technical University of Denmark, 2800 Kgs Lyngby, Denmark
| | - Ole Lund
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, 2800 Kgs Lyngby, Denmark
| | - Frank M Aarestrup
- National Food Institute, Technical University of Denmark, 2800 Kgs Lyngby, Denmark
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7
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Functional metagenomic approach to identify overlooked antibiotic resistance mutations in bacterial rRNA. Sci Rep 2018; 8:5179. [PMID: 29615654 PMCID: PMC5882664 DOI: 10.1038/s41598-018-23474-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 03/13/2018] [Indexed: 12/14/2022] Open
Abstract
Our knowledge as to how bacteria acquire antibiotic resistance is still fragmented, especially for the ribosome-targeting drugs. In this study, with the aim of finding novel mechanisms that render bacteria resistant to the ribosome-targeting antibiotics, we developed a general method to systematically screen for antibiotic resistant 16 S ribosomal RNAs (rRNAs), which are the major target for multiple antibiotics (e.g. spectinomycin, tetracycline, and aminoglycosides), and identify point mutations therein. We used Escherichia coli ∆7, a null mutant of the rrn (ribosomal RNA) operons, as a surrogate host organism to construct a metagenomic library of 16 S rRNA genes from the natural (non-clinical) environment. The library was screened for spectinomycin resistance to obtain four resistant 16 S rRNA genes from non-E. coli bacterial species. Bioinformatic analysis and site-directed mutagenesis identified three novel mutations - U1183C (the first mutation discovered in a region other than helix 34), and C1063U and U1189C in helix 34 - as well as three well-described mutations (C1066U, C1192G, and G1193A). These results strongly suggest that uncharacterized antibiotic resistance mutations still exist, even for traditional antibiotics.
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8
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The Loop 2 Region of Ribosomal Protein uS5 Influences Spectinomycin Sensitivity, Translational Fidelity, and Ribosome Biogenesis. Antimicrob Agents Chemother 2017; 61:AAC.01186-16. [PMID: 27855073 DOI: 10.1128/aac.01186-16] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 11/07/2016] [Indexed: 12/24/2022] Open
Abstract
Ribosomal protein uS5 is an essential component of the small ribosomal subunit that is involved in subunit assembly, maintenance of translational fidelity, and the ribosome's response to the antibiotic spectinomycin. While many of the characterized uS5 mutations that affect decoding map to its interface with uS4, more recent work has shown that residues distant from the uS4-uS5 interface can also affect the decoding process. We targeted one such interface-remote area, the loop 2 region (residues 20 to 31), for mutagenesis in Escherichia. coli and generated 21 unique mutants. A majority of the loop 2 alterations confer resistance to spectinomycin and affect the fidelity of translation. However, only a minority show altered rRNA processing or ribosome biogenesis defects.
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9
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Abstract
During ribosomal translocation, a process central to the elongation phase of protein synthesis, movement of mRNA and tRNAs requires large-scale rotation of the head domain of the small (30S) subunit of the ribosome. It has generally been accepted that the head rotates by pivoting around the neck helix (h28) of 16S rRNA, its sole covalent connection to the body domain. Surprisingly, we observe that the calculated axis of rotation does not coincide with the neck. Instead, comparative structure analysis across 55 ribosome structures shows that 30S head movement results from flexing at two hinge points lying within conserved elements of 16S rRNA. Hinge 1, although located within the neck, moves by straightening of the kinked helix h28 at the point of contact with the mRNA. Hinge 2 lies within a three-way helix junction that extends to the body through a second, noncovalent connection; its movement results from flexing between helices h34 and h35 in a plane orthogonal to the movement of hinge 1. Concerted movement at these two hinges accounts for the observed magnitudes of head rotation. Our findings also explain the mode of action of spectinomycin, an antibiotic that blocks translocation by binding to hinge 2.
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10
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Smith PM, Elson JL, Greaves LC, Wortmann SB, Rodenburg RJT, Lightowlers RN, Chrzanowska-Lightowlers ZMA, Taylor RW, Vila-Sanjurjo A. The role of the mitochondrial ribosome in human disease: searching for mutations in 12S mitochondrial rRNA with high disruptive potential. Hum Mol Genet 2013; 23:949-67. [PMID: 24092330 PMCID: PMC3900107 DOI: 10.1093/hmg/ddt490] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Mutations of mitochondrial DNA are linked to many human diseases. Despite the identification of a large number of variants in the mitochondrially encoded rRNA (mt-rRNA) genes, the evidence supporting their pathogenicity is, at best, circumstantial. Establishing the pathogenicity of these variations is of major diagnostic importance. Here, we aim to estimate the disruptive effect of mt-rRNA variations on the function of the mitochondrial ribosome. In the absence of direct biochemical methods to study the effect of mt-rRNA variations, we relied on the universal conservation of the rRNA fold to infer their disruptive potential. Our method, named heterologous inferential analysis or HIA, combines conservational information with functional and structural data obtained from heterologous ribosomal sources. Thus, HIA's predictive power is superior to the traditional reliance on simple conservation indexes. By using HIA, we have been able to evaluate the disruptive potential for a subset of uncharacterized 12S mt-rRNA variations. Our analysis revealed the existence of variations in the rRNA component of the human mitoribosome with different degrees of disruptive power. In cases where sufficient information regarding the genetic and pathological manifestation of the mitochondrial phenotype is available, HIA data can be used to predict the pathogenicity of mt-rRNA mutations. In other cases, HIA analysis will allow the prioritization of variants for additional investigation. Eventually, HIA-inspired analysis of potentially pathogenic mt-rRNA variations, in the context of a scoring system specifically designed for these variants, could lead to a powerful diagnostic tool.
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Affiliation(s)
- Paul M Smith
- Institute of Medical Sciences, Ninewells Hospital and Medical School, Dundee University, Dundee DD1 9SY, Scotland, UK
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11
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Ilina EN, Malakhova MV, Bodoev IN, Oparina NY, Filimonova AV, Govorun VM. Mutation in ribosomal protein S5 leads to spectinomycin resistance in Neisseria gonorrhoeae. Front Microbiol 2013; 4:186. [PMID: 23847609 PMCID: PMC3706878 DOI: 10.3389/fmicb.2013.00186] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Accepted: 06/19/2013] [Indexed: 11/15/2022] Open
Abstract
Spectinomycin remains a useful reserve option for therapy of gonorrhea. The emergence of multidrug-resistant Neisseria gonorrhoeae strains with decreased susceptibility to cefixime and to ceftriaxone makes it the only medicine still effective for treatment of gonorrhea infection in analogous cases. However, adoption of spectinomycin as a routinely used drug of choice was soon followed by reports of spectinomycin resistance. The main molecular mechanism of spectinomycin resistance in N. gonorrhoeae was C1192T substitution in 16S rRNA genes. Here we reported a Thr-24→Pro mutation in ribosomal protein S5 (RPS5) found in spectinomycin resistant clinical N. gonorrhoeae strain, which carried no changes in 16S rRNA. In a series of experiments, the transfer of rpsE gene allele encoding the mutant RPS5 to the recipient N. gonorrhoeae strains was analyzed. The relatively high rate of transformation [ca. 10−5 colony-forming units (CFUs)] indicates the possibility of spread of spectinonycin resistance within gonococcal population due to the horizontal gene transfer (HGT).
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Affiliation(s)
- Elena N Ilina
- Research Institute of Physico-Chemical Medicine Moscow, Russia
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12
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Neisseria gonorrhoeae strain with high-level resistance to spectinomycin due to a novel resistance mechanism (mutated ribosomal protein S5) verified in Norway. Antimicrob Agents Chemother 2012. [PMID: 23183436 DOI: 10.1128/aac.01775-12] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Gonorrhea may become untreatable, and new treatment options are essential. Verified resistance to spectinomycin is exceedingly rare. However, we describe a high-level spectinomycin-resistant (MIC, >1,024 μg/ml) Neisseria gonorrhoeae strain from Norway with a novel resistance mechanism. The resistance determinant was a deletion of codon 27 (valine) and a K28E alteration in the ribosomal protein 5S. The traditional spectinomycin resistance gene (16S rRNA) was wild type. Despite this exceedingly rare finding, spectinomycin available for treatment of ceftriaxone-resistant urogenital gonorrhea would be very valuable.
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13
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Filipenko EA, Sidorchuk YV, Titov II, Maltsev VP, Deineko EV. Spontaneous spectinomycin resistance mutations detected after biolistic transformation of Daucus carota L. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2011; 17:79-86. [PMID: 23572997 PMCID: PMC3550566 DOI: 10.1007/s12298-011-0051-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Spectinomycin resistant mutant carrot (Daucus carota L.) callus lines detected in the experiments on biolistic transformation of plastome were analyzed. It has been found that this antibiotic resistance is determined by point nucleotide substitutions at two distinct sites of the chloroplast gene rrn16, coding for 16S rRNA, namely, G1012T, G1012C, and A1138G. The detected mutations are localized to the 16S rRNA region forming helix h34, which contains spectinomycin binding site, and lead to its destabilization by several kilocalories per mole. Comparative analysis of rrn16 gene sequences has demonstrated conservation of the positions of the nucleotide substitutions determining this antibiotic resistance in carrot (D. carota L.), tobacco (Nicotiana tabacum L.), and bladder pod (Lesquerella fendleri L.), as well as in Escherichia coli.
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Affiliation(s)
- Elena A. Filipenko
- />Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, pr. Lavrentieva 10, Novosibirsk, 630090 Russia
| | - Yuri V. Sidorchuk
- />Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, pr. Lavrentieva 10, Novosibirsk, 630090 Russia
| | - Igor I. Titov
- />Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, pr. Lavrentieva 10, Novosibirsk, 630090 Russia
| | - Valery P. Maltsev
- />Institute of Chemical Kinetics and Combustion, Siberian Branch, Russian Academy of Sciences, Institutskaya 3, Novosibirsk, 630090 Russia
| | - Elena V. Deineko
- />Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, pr. Lavrentieva 10, Novosibirsk, 630090 Russia
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14
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Aitken CE, Puglisi JD. Following the intersubunit conformation of the ribosome during translation in real time. Nat Struct Mol Biol 2010; 17:793-800. [PMID: 20562856 PMCID: PMC4459212 DOI: 10.1038/nsmb.1828] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2010] [Accepted: 04/08/2010] [Indexed: 11/09/2022]
Abstract
We report the direct observation of conformational rearrangements of the ribosome during multiple rounds of elongation. Using single-molecule fluorescence resonance energy transfer, we monitored the intersubunit conformation of the ribosome in real time as it proceeds from codon to codon. During each elongation cycle, the ribosome unlocks upon peptide bond formation, then reverts to the locked state upon translocation onto the next codon. Our data reveal both the specific and cumulative effects of antibiotics on individual steps of translation and uncover the processivity of the ribosome as it elongates. Our approach interrogates the precise molecular events occurring at each codon of the mRNA within the full context of ongoing translation.
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15
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Abstract
Protein synthesis is one of the major targets in the cell for antibiotics. This review endeavors to provide a comprehensive "post-ribosome structure" A-Z of the huge diversity of antibiotics that target the bacterial translation apparatus, with an emphasis on correlating the vast wealth of biochemical data with more recently available ribosome structures, in order to understand function. The binding site, mechanism of action, and modes of resistance for 26 different classes of protein synthesis inhibitors are presented, ranging from ABT-773 to Zyvox. In addition to improving our understanding of the process of translation, insight into the mechanism of action of antibiotics is essential to the development of novel and more effective antimicrobial agents to combat emerging bacterial resistance to many clinically-relevant drugs.
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Affiliation(s)
- Daniel N Wilson
- Gene Center and Department of Chemistry and Biochemistry, University of Munich, LMU, Munich, Germany.
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16
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Abstract
Antibiotic resistance is a fundamental aspect of microbiology, but it is also a phenomenon of vital importance in the treatment of diseases caused by pathogenic microorganisms. A resistance mechanism can involve an inherent trait or the acquisition of a new characteristic through either mutation or horizontal gene transfer. The natural susceptibilities of bacteria to a certain drug vary significantly from one species of bacteria to another and even from one strain to another. Once inside the cell, most antibiotics affect all bacteria similarly. The ribosome is a major site of antibiotic action and is targeted by a large and chemically diverse group of antibiotics. A number of these antibiotics have important applications in human and veterinary medicine in the treatment of bacterial infections. The antibiotic binding sites are clustered at functional centers of the ribosome, such as the decoding center, the peptidyl transferase center, the GTPase center, the peptide exit tunnel, and the subunit interface spanning both subunits on the ribosome. Upon binding, the drugs interfere with the positioning and movement of substrates, products, and ribosomal components that are essential for protein synthesis. Ribosomal antibiotic resistance is due to the alteration of the antibiotic binding sites through either mutation or methylation. Our knowledge of antibiotic resistance mechanisms has increased, in particular due to the elucidation of the detailed structures of antibiotic-ribosome complexes and the components of the efflux systems. A number of mutations and methyltransferases conferring antibiotic resistance have been characterized. These developments are important for understanding and approaching the problems associated with antibiotic resistance, including design of antimicrobials that are impervious to known bacterial resistance mechanisms.
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17
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Borovinskaya MA, Shoji S, Holton JM, Fredrick K, Cate JHD. A steric block in translation caused by the antibiotic spectinomycin. ACS Chem Biol 2007; 2:545-552. [PMID: 17696316 PMCID: PMC4624401 DOI: 10.1021/cb700100n] [Citation(s) in RCA: 104] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The widely used antibiotic spectinomycin inhibits bacterial protein synthesis by blocking translocation of messenger RNA and transfer RNAs on the ribosome. Here, we show that in crystals of the Escherichia coli 70S ribosome spectinomycin binding traps a distinct swiveling state of the head domain of the small ribosomal subunit. Spectinomycin also alters the rate and completeness of reverse translocation in vitro. These structural and biochemical data indicate that in solution spectinomycin sterically blocks swiveling of the head domain of the small ribosomal subunit and thereby disrupts the translocation cycle.
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Affiliation(s)
- Maria A. Borovinskaya
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Shinichiro Shoji
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210
| | - James M. Holton
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
- Department of Biochemistry and Biophysics, University of California, San Francisco, California 94158
| | - Kurt Fredrick
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210
- Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio 43210
| | - Jamie H. D. Cate
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
- Department of Chemistry, University of California, Berkeley, California 94720
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720
- Corresponding author,
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18
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Pan D, Kirillov SV, Cooperman BS. Kinetically competent intermediates in the translocation step of protein synthesis. Mol Cell 2007; 25:519-29. [PMID: 17317625 PMCID: PMC1995019 DOI: 10.1016/j.molcel.2007.01.014] [Citation(s) in RCA: 148] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2006] [Revised: 12/17/2006] [Accepted: 01/11/2007] [Indexed: 10/23/2022]
Abstract
Translocation requires large-scale movements of ribosome-bound tRNAs. Using tRNAs that are proflavin labeled and single-turnover rapid kinetics assays, we identify one or possibly two kinetically competent intermediates in translocation. EF-G.GTP binding to the pretranslocation (PRE) complex and GTP hydrolysis are rapidly followed by formation of the securely identified intermediate complex (INT), which is more slowly converted to the posttranslocation (POST) complex. Peptidyl tRNA within the INT complex occupies a hybrid site, which has a puromycin reactivity intermediate between those of the PRE and POST complexes. Thiostrepton and viomycin inhibit INT formation, whereas spectinomycin selectively inhibits INT disappearance. The effects of other translocation modulators suggest that EF-G-dependent GTP hydrolysis is more important for INT complex formation than for INT complex conversion to POST complex and that subtle changes in tRNA structure influence coupling of tRNA movement to EF-G.GTP-induced conformational changes.
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Affiliation(s)
- Dongli Pan
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, USA 19104-6323
| | - Stanislav V. Kirillov
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, USA 19104-6323
- Petersburg Nuclear Physics Institute RAS, 188300 Gatchina, Russia
| | - Barry S. Cooperman
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, USA 19104-6323
- *Correspondence: , 215-898-6330
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19
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Kehrenberg C, Schwarz S. Mutations in 16S rRNA and ribosomal protein S5 associated with high-level spectinomycin resistance in Pasteurella multocida. Antimicrob Agents Chemother 2007; 51:2244-6. [PMID: 17371823 PMCID: PMC1891365 DOI: 10.1128/aac.00229-07] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pasteurella multocida isolates with high-level spectinomycin resistance in which no adenyltransferase genes could be demonstrated exhibited a C1192G transversion in the 16S rRNA of all six or five of the six rRNA operons and/or two different types of 3-bp deletions in the rpsE gene that codes for the ribosomal protein S5.
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Affiliation(s)
- Corinna Kehrenberg
- Institut für Tierzucht, Bundesforschungsanstalt für Landwirtschaft (FAL), Höltystr. 10, 31535 Neustadt-Mariensee, Germany
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20
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Kirthi N, Roy-Chaudhuri B, Kelley T, Culver GM. A novel single amino acid change in small subunit ribosomal protein S5 has profound effects on translational fidelity. RNA (NEW YORK, N.Y.) 2006; 12:2080-91. [PMID: 17053085 PMCID: PMC1664723 DOI: 10.1261/rna.302006] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2006] [Accepted: 09/22/2006] [Indexed: 05/03/2023]
Abstract
S5 is a small subunit ribosomal protein (r-protein) linked to the functional center of the 30S ribosomal subunit. In this study we have identified a unique amino acid mutation in Escherichia coli S5 that produces spectinomycin-resistance and cold sensitivity. This mutation significantly alters cell growth, folding of 16S ribosomal RNA, and translational fidelity. While translation initiation is not affected, both +1 and -1 frameshifting and nonsense suppression are greatly enhanced in the mutant strain. Interestingly, this S5 ribosome ambiguity-like mutation is spatially remote from previously identified S5 ribosome ambiguity (ram) mutations. This suggests that the mechanism responsible for ram phenotypes in the novel mutant strain is possibly distinct from those proposed for other known S5 (and S4) ram mutants. This study highlights the importance of S5 in ribosome function and cell physiology, and suggests that translational fidelity can be regulated in multiple ways.
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Affiliation(s)
- Narayanaswamy Kirthi
- Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa 50011, USA
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21
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Skorski P, Leroy P, Fayet O, Dreyfus M, Hermann-Le Denmat S. The highly efficient translation initiation region from the Escherichia coli rpsA gene lacks a shine-dalgarno element. J Bacteriol 2006; 188:6277-85. [PMID: 16923895 PMCID: PMC1595398 DOI: 10.1128/jb.00591-06] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The translational initiation region (TIR) of the Escherichia coli rpsA gene, which encodes ribosomal protein S1, shows a number of unusual features. It extends far upstream (to position -91) of the initiator AUG, it lacks a canonical Shine-Dalgarno sequence (SD) element, and it can fold into three successive hairpins (I, II, and III) that are essential for high translational activity. Two conserved GGA trinucleotides, present in the loops of hairpins I and II, have been proposed to form a discontinuous SD. Here, we have tested this hypothesis with the "specialized ribosome" approach. Depending upon the constructs used, translation initiation was decreased three- to sevenfold upon changing the conserved GGA to CCU. However, although chemical probing showed that the mutated trinucleotides were accessible, no restoration was observed when the ribosome anti-SD was symmetrically changed from CCUCC to GGAGG. When the same change was introduced in the SD from a conventional TIR as a control, activity was stimulated. This result suggests that the GGA trinucleotides do not form a discontinuous SD. Others hypotheses that may account for their role are discussed. Curiously, we also find that, when expressed at moderate level (30 to 40% of total ribosomes), specialized ribosomes are only twofold disadvantaged over normal ribosomes for the translation of bulk cellular mRNAs. These findings suggest that, under these conditions, the SD-anti-SD interaction plays a significant but not essential role for the synthesis of bulk cellular proteins.
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Affiliation(s)
- Patricia Skorski
- Laboratoire de Génétique Moléculaire, Ecole Normale Supérieure-CNRS UMR 8541, 46 rue d'Ulm, 75230 Paris Cedex 05, France
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22
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Kubarenko A, Sergiev P, Wintermeyer W, Dontsova O, Rodnina MV. Involvement of helix 34 of 16 S rRNA in decoding and translocation on the ribosome. J Biol Chem 2006; 281:35235-44. [PMID: 16990269 DOI: 10.1074/jbc.m608060200] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Helix 34 of 16 S rRNA is located in the head of the 30 S ribosomal subunit close to the decoding center and has been invoked in a number of ribosome functions. In the present work, we have studied the effects of mutations in helix 34 both in vivo and in vitro. Several nucleotides in helix 34 that are either highly conserved or form important tertiary contacts in 16 S rRNA (U961, C1109, A1191, and A1201) were mutated, and the mutant ribosomes were expressed in the Escherichia coli MC250 Delta7 strain that lacks all seven chromosomal rRNA operons. Mutations at positions A1191 and U961 reduced the efficiency of subunit association and resulted in structural rearrangements in helix 27 (position 908) and helix 31 (position 974) of 16 S rRNA. All mutants exhibited increased levels of frameshifting and nonsense readthrough. The effects on frameshifting were specific in that -1 frameshifting was enhanced with mutant A1191G and +1 frameshifting with the other mutants. Mutations of A1191 moderately (approximately 2-fold) inhibited tRNA translocation. No significant effects were found on efficiency and rate of initiation, misreading of sense codons, or binding of tRNA to the E site. The data indicate that helix 34 is involved in controlling the maintenance of the reading frame and in tRNA translocation.
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Affiliation(s)
- Andrew Kubarenko
- Institute of Physical Biochemistry, University of Witten/Herdecke, 58448 Witten, Germany
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23
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Okumura S, Sawada M, Park YW, Hayashi T, Shimamura M, Takase H, Tomizawa KI. Transformation of poplar (Populus alba) plastids and expression of foreign proteins in tree chloroplasts. Transgenic Res 2006; 15:637-46. [PMID: 16952016 DOI: 10.1007/s11248-006-9009-3] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2006] [Accepted: 04/30/2006] [Indexed: 11/28/2022]
Abstract
Plastid transformation offers several unique advantages compared with nuclear genome transformation, such as high level of transgene expression within plastids, expressing multiple transgenes as operons, lack of position effect due to site-specific transgene integration, and reducing risks of gene flow via pollen due to maternal inheritance of the plastid genome. Plastid transformation has been applied to several herbal species, but as yet there are no applications to tree species. We report here the first successful plastid transformation in a tree species, Populus alba. A vector for plastid transformation of poplar (Populus alba) was constructed, which carried the spectinomycin resistance gene and the green fluorescence protein gene as marker genes. In the regenerated shoots, the site-specific integration of foreign genes and the establishment of a high homoplastomic state were confirmed. Immunoblot analysis and histological observations corroborated the accumulation of green fluorescence protein in chloroplasts. The establishment of a plastid transformation system in poplar provides a novel tool for tree biotechnology.
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Affiliation(s)
- Satoru Okumura
- Plant Research Group, Research Institute of Innovative Technology for the Earth (RITE), 9-2 Kizugawadai, Soraku-gun, Kyoto 619-0292, Japan
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24
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Liang FS, Greenberg WA, Hammond JA, Hoffmann J, Head SR, Wong CH. Evaluation of RNA-binding specificity of aminoglycosides with DNA microarrays. Proc Natl Acad Sci U S A 2006; 103:12311-6. [PMID: 16891415 PMCID: PMC1567877 DOI: 10.1073/pnas.0605264103] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We have developed methods for using DNA array technology to probe the entire transcriptome to determine the RNA-binding specificity of ligands. Two methods were investigated. In the first method, the RNA-binding aminoglycoside antibiotic tobramycin was covalently linked to magnetic beads. The beads were bound to human liver mRNA and washed, and specifically bound RNA was eluted, amplified, and analyzed with DNA array technology. A small number of genes were found to bind specifically to the tobramycin beads. In the second method, the aminoglycoside ligand was added directly to the array hybridization reaction, and the signal was compared with a control experiment in the absence of ligand. The aminoglycosides were found to interfere with a small percentage of all hybridization events. These methods differ from traditional DNA array experiments in that the readout is a direct measure of the interaction between mRNA and a ligand, rather than an indirect measure of effect on expression. We expect that the results will lead to the discovery of new aminoglycoside-binding RNA motifs and may also have relevance toward understanding and overcoming the side effects observed with these antibiotics in the clinic.
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Affiliation(s)
- Fu-Sen Liang
- *Department of Chemistry and The Skaggs Institute for Chemical Biology and
| | | | - Jennifer A. Hammond
- Array Core Facility, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037
| | - Julia Hoffmann
- Array Core Facility, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037
| | - Steven R. Head
- Array Core Facility, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037
| | - Chi-Huey Wong
- *Department of Chemistry and The Skaggs Institute for Chemical Biology and
- To whom correspondence should be addressed. E-mail:
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25
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Criswell D, Tobiason VL, Lodmell JS, Samuels DS. Mutations conferring aminoglycoside and spectinomycin resistance in Borrelia burgdorferi. Antimicrob Agents Chemother 2006; 50:445-52. [PMID: 16436695 PMCID: PMC1366916 DOI: 10.1128/aac.50.2.445-452.2006] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
We have isolated and characterized in vitro mutants of the Lyme disease agent Borrelia burgdorferi that are resistant to spectinomycin, kanamycin, gentamicin, or streptomycin, antibiotics that target the small subunit of the ribosome. 16S rRNA mutations A1185G and C1186U, homologous to Escherichia coli nucleotides A1191 and C1192, conferred >2,200-fold and 1,300-fold resistance to spectinomycin, respectively. A 16S rRNA A1402G mutation, homologous to E. coli A1408, conferred >90-fold resistance to kanamycin and >240-fold resistance to gentamicin. Two mutations were identified in the gene for ribosomal protein S12, at a site homologous to E. coli residue Lys-87, in mutants selected in streptomycin. Substitutions at codon 88, K88R and K88E, conferred 7-fold resistance and 10-fold resistance, respectively, to streptomycin on B. burgdorferi. The 16S rRNA A1185G and C1186U mutations, associated with spectinomycin resistance, appeared in a population of B. burgdorferi parental strain B31 at a high frequency of 6 x 10(-6). These spectinomycin-resistant mutants successfully competed with the wild-type strain during 100 generations of coculture in vitro. The aminoglycoside-resistant mutants appeared at a frequency of 3 x 10(-9) to 1 x10(-7) in a population and were unable to compete with wild-type strain B31 after 100 generations. This is the first description of mutations in the B. burgdorferi ribosome that confer resistance to antibiotics. These results have implications for the evolution of antibiotic resistance, because the 16S rRNA mutations conferring spectinomycin resistance have no significant fitness cost in vitro, and for the development of new selectable markers.
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Affiliation(s)
- Daniel Criswell
- Division of Biological Sciences, The University of Montana, Missoula, MT 59812-4824, USA
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26
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Binet R, Maurelli AT. Fitness cost due to mutations in the 16S rRNA associated with spectinomycin resistance in Chlamydia psittaci 6BC. Antimicrob Agents Chemother 2006; 49:4455-64. [PMID: 16251283 PMCID: PMC1280162 DOI: 10.1128/aac.49.11.4455-4464.2005] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
The fitness cost of a resistance determinant is the primary parameter that determines its frequency in vivo. As a model for analysis of the impact of drug resistance mutations on the intracellular life cycle of Chlamydia spp., we studied the growth of four genetically defined spectinomycin-resistant (Spc(r)) clonal variants of Chlamydia psittaci 6BC isolated in the plaque assay. The development of each variant was monitored over 46 h postinfection in the absence of drug, either in pure culture or in 1:1 competition with the parent strain. Spc(r) mutations in the 16S rRNA gene at positions 1191 and 1193 were associated with a marked impairment of C.psittaci biological fitness, and the bacteria were severely out-competed by the wild-type parent. In contrast, mutations at position 1192 had minor effects on the bacterial life cycle, allowing the resistant isolates to compete more efficiently with the wild-type strain. Thus, mutations with a wide range of fitness costs can be selected in the plaque assay, providing a new strategy for prediction and monitoring of the emergence of antibiotic resistance in chlamydiae. So far, drug resistance has not been a serious threat for the treatment of chlamydial infections. Tetracycline is an effective antichlamydial drug that targets 16S rRNA. Attempts to isolate spontaneous tetracycline-resistant mutants of C. psittaci 6BC revealed a frequency <3 x 10(-9). We suggest that the rarity of genotypic antibiotic resistance among chlamydial clinical isolates reflects the deleterious effects of such mutations on the fitness of these obligate intracellular bacteria in the host.
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Affiliation(s)
- Rachel Binet
- Department of Microbiology and Immunology, F. Edward Hébert School of Medicine, Uniformed Services University of the Health Sciences, 4301 Jones Bridge Road, Bethesda, Maryland 20814-4799, USA
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27
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Affiliation(s)
- Bert Willis
- Department of Chemistry, Clemson University, Clemson, SC 29634, USA
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28
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Binet R, Maurelli AT. Frequency of spontaneous mutations that confer antibiotic resistance in Chlamydia spp. Antimicrob Agents Chemother 2005; 49:2865-73. [PMID: 15980362 PMCID: PMC1168699 DOI: 10.1128/aac.49.7.2865-2873.2005] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Mutations in rRNA genes (rrn) that confer resistance to ribosomal inhibitors are typically recessive or weakly codominant and have been mostly reported for clinical strains of pathogens possessing only one or two rrn operons, such as Helicobacter pylori and Mycobacterium spp. An analysis of the genome sequences of several members of the Chlamydiaceae revealed that these obligate intracellular bacteria harbor only one or two sets of rRNA genes. To study the contribution of rRNA mutations to the emergence of drug resistance in the Chlamydiaceae, we used the sensitivities of Chlamydia trachomatis L2 (two rrn operons) and Chlamydophila psittaci 6BC (one rrn operon) to the aminoglycoside spectinomycin as a model. Confluent cell monolayers were infected in a plaque assay with about 10(8) wild-type infectious particles and then treated with the antibiotic. After a 2-week incubation time, plaques formed by spontaneous spectinomycin-resistant (Spc(r)) mutants appeared with a frequency of 5 x 10(-5) for C. psittaci 6BC. No Spc(r) mutants were isolated for C. trachomatis L2, although the frequencies of rifampin resistance were in the same range for both strains (i.e., 10(-7)). The risk of emergence of Chlamydia strains resistant to tetracyclines and macrolides, the ribosomal drugs currently used to treat chlamydial infections, is discussed.
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Affiliation(s)
- Rachel Binet
- Department of Microbiology and Immunology, F. Edward Hébert School of Medicine, Uniformed Services University of the Health Sciences, 4301 Jones Bridge Road, Bethesda, Maryland 20814-4799,USA
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29
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Affiliation(s)
- Sophie Magnet
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, USA
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30
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He X, Miao V, Baltz RH. Spectinomycin Resistance in rpsE Mutants is Recessive in Streptomyces roseosporus. J Antibiot (Tokyo) 2005; 58:284-8. [PMID: 15981417 DOI: 10.1038/ja.2005.35] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Eight spontaneous mutants of Streptomyces roseosporus resistant to spectinomycin (SpcR) were mapped to distinct transversions or deletions in the rpsE gene. Most of the mutations were strongly recessive to the wild type SpcS allele. This suggests that some SpcR alleles of rpsE may be useful in a spectinomycin based counter-selection system.
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Affiliation(s)
- Xiaowei He
- Cubist Pharmaceuticals, Inc., Lexington, MA 02421, USA
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31
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Peske F, Savelsbergh A, Katunin VI, Rodnina MV, Wintermeyer W. Conformational changes of the small ribosomal subunit during elongation factor G-dependent tRNA-mRNA translocation. J Mol Biol 2004; 343:1183-94. [PMID: 15491605 DOI: 10.1016/j.jmb.2004.08.097] [Citation(s) in RCA: 136] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2004] [Revised: 08/29/2004] [Accepted: 08/30/2004] [Indexed: 10/26/2022]
Abstract
Translocation, a coordinated movement of two tRNAs together with mRNA on the ribosome, is catalyzed by elongation factor G (EF-G). The reaction is accompanied by conformational rearrangements of the ribosome that are, as yet, not well characterized. Here, we analyze those rearrangements by restricting the conformational flexibility of the ribosome by antibiotics binding to specific sites of the ribosome. Paromomycin (Par), viomycin (Vio), spectinomycin (Spc), and hygromycin B (HygB) inhibited the tRNA-mRNA movement, while the other partial reactions of translocation, including the unlocking rearrangement of the ribosome that precedes tRNA-mRNA movement, were not affected. The functional cycle of EF-G, i.e. binding of EF-G.GTP to the ribosome, GTP hydrolysis, Pi release, and dissociation of EF-G.GDP from the ribosome, was not affected either, indicating that EF-G turnover is not coupled directly to tRNA-mRNA movement. The inhibition of translocation by Par and Vio is attributed to the stabilization of tRNA binding in the A site, whereas Spc and HygB had a direct inhibitory effect on tRNA-mRNA movement. Streptomycin (Str) had essentially no effect on translocation, although it caused a large increase in tRNA affinity to the A site. These results suggest that conformational changes in the vicinity of the decoding region at the binding sites of Spc and HygB are important for tRNA-mRNA movement, whereas Str seems to stabilize a conformation of the ribosome that is prone to rapid translocation, thereby compensating the effect on tRNA affinity.
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Affiliation(s)
- Frank Peske
- Institute of Molecular Biology, University of Witten/Herdecke, 58448 Witten, Germany
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32
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Brodersen DE, Carter AP, Clemons WM, Morgan-Warren RJ, Murphy FV, Ogle JM, Tarry MJ, Wimberly BT, Ramakrishnan V. Atomic structures of the 30S subunit and its complexes with ligands and antibiotics. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2003; 66:17-32. [PMID: 12762005 DOI: 10.1101/sqb.2001.66.17] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- D E Brodersen
- MRC Laboratory of Molecular Biology, Cambridge CB2 2QH, United Kingdom
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33
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Matassova AB, Rodnina MV, Wintermeyer W. Elongation factor G-induced structural change in helix 34 of 16S rRNA related to translocation on the ribosome. RNA (NEW YORK, N.Y.) 2001; 7:1879-1885. [PMID: 11780642 PMCID: PMC1370225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
During the translocation step of the elongation cycle, two tRNAs together with the mRNA move synchronously and rapidly on the ribosome. The movement is catalyzed by the binding of elongation factor G (EF-G) and driven by GTP hydrolysis. Here we study structural changes of the ribosome related to EF-G binding and translocation by monitoring the accessibility of ribosomal RNA (rRNA) for chemical modification by dimethyl sulfate or cleavage by hydroxyl radicals generated by Fe(II)-EDTA. In the state of the ribosome that is formed upon binding of EF-G but before the movement of the tRNAs takes place, residues 1054,1196, and 1201 in helix 34 in 16S rRNA are strongly protected. The protections depend on EF-G binding, but do not require GTP hydrolysis, and are lost upon translocation. Mutants of EF-G, which are active in ribosome binding and GTP hydrolysis but impaired in translocation, do not bring about the protections. According to cryo-electron microscopy (Stark et al., Cell, 2000, 100:301-309), there is no contact of EF-G with the protected residues of helix 34 in the pretranslocation state, suggesting that the observed protections are due to an induced conformational change. Thus, the present results indicate that EF-G binding to the pretranslocation ribosome induces a structural change of the head of the 30S subunit that is essential for subsequent tRNA-mRNA movement in translocation.
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Affiliation(s)
- A B Matassova
- Institute of Molecular Biology. University of Witten/Herdecke, Germany
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34
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35
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36
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Stoilova-Disheva M, Peltekova V, Lyutzkanova D. Isolation and Preliminary Charactrization of Strptomyces Flavopersicus Mutants Blocked in Spectinomycin Biosynthesis. BIOTECHNOL BIOTEC EQ 2001. [DOI: 10.1080/13102818.2001.10819126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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37
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Carter AP, Clemons WM, Brodersen DE, Morgan-Warren RJ, Wimberly BT, Ramakrishnan V. Functional insights from the structure of the 30S ribosomal subunit and its interactions with antibiotics. Nature 2000; 407:340-8. [PMID: 11014183 DOI: 10.1038/35030019] [Citation(s) in RCA: 1129] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The 30S ribosomal subunit has two primary functions in protein synthesis. It discriminates against aminoacyl transfer RNAs that do not match the codon of messenger RNA, thereby ensuring accuracy in translation of the genetic message in a process called decoding. Also, it works with the 50S subunit to move the tRNAs and associated mRNA by precisely one codon, in a process called translocation. Here we describe the functional implications of the high-resolution 30S crystal structure presented in the accompanying paper, and infer details of the interactions between the 30S subunit and its tRNA and mRNA ligands. We also describe the crystal structure of the 30S subunit complexed with the antibiotics paromomycin, streptomycin and spectinomycin, which interfere with decoding and translocation. This work reveals the structural basis for the action of these antibiotics, and leads to a model for the role of the universally conserved 16S RNA residues A1492 and A1493 in the decoding process.
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MESH Headings
- Anti-Bacterial Agents/chemistry
- Anti-Bacterial Agents/pharmacology
- Binding Sites
- Crystallography, X-Ray
- Genetic Code
- Macromolecular Substances
- Models, Molecular
- Molecular Mimicry
- Nucleic Acid Conformation
- Paromomycin/chemistry
- Paromomycin/pharmacology
- Protein Conformation
- RNA, Bacterial/chemistry
- RNA, Bacterial/physiology
- RNA, Messenger/metabolism
- RNA, Ribosomal/chemistry
- RNA, Ribosomal/physiology
- RNA, Ribosomal, 16S/chemistry
- RNA, Transfer/metabolism
- Ribosomal Proteins/chemistry
- Ribosomal Proteins/physiology
- Ribosomes/chemistry
- Ribosomes/drug effects
- Ribosomes/metabolism
- Spectinomycin/chemistry
- Spectinomycin/pharmacology
- Streptomycin/chemistry
- Streptomycin/pharmacology
- Structure-Activity Relationship
- Thermus thermophilus
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Affiliation(s)
- A P Carter
- MRC Laboratory of Molecular Biology, Cambridge, UK
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38
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Galimand M, Gerbaud G, Courvalin P. Spectinomycin resistance in Neisseria spp. due to mutations in 16S rRNA. Antimicrob Agents Chemother 2000; 44:1365-6. [PMID: 10770780 PMCID: PMC89873 DOI: 10.1128/aac.44.5.1365-1366.2000] [Citation(s) in RCA: 69] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Spectinomycin resistance in clinical isolates of Neisseria meningitidis and Neisseria gonorrhoeae was found to be due to mutations G1064C and C1192U (Escherichia coli numbering) in 16S rRNA genes, respectively.
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Affiliation(s)
- M Galimand
- Unité des Agents Antibactériens, Institut Pasteur, 75724 Paris Cedex 15, France.
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39
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Stark H, Rodnina MV, Wieden HJ, van Heel M, Wintermeyer W. Large-scale movement of elongation factor G and extensive conformational change of the ribosome during translocation. Cell 2000; 100:301-9. [PMID: 10676812 DOI: 10.1016/s0092-8674(00)80666-2] [Citation(s) in RCA: 216] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Elongation factor (EF) G promotes tRNA translocation on the ribosome. We present three-dimensional reconstructions, obtained by cryo-electron microscopy, of EF-G-ribosome complexes before and after translocation. In the pretranslocation state, domain 1 of EF-G interacts with the L7/12 stalk on the 50S subunit, while domain 4 contacts the shoulder of the 30S subunit in the region where protein S4 is located. During translocation, EF-G experiences an extensive reorientation, such that, after translocation, domain 4 reaches into the decoding center. The factor assumes different conformations before and after translocation. The structure of the ribosome is changed substantially in the pretranslocation state, in particular at the head-to-body junction in the 30S subunit, suggesting a possible mechanism of translocation.
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Affiliation(s)
- H Stark
- Imperial College of Science Medicine and Technology, Department of Biochemistry, London, United Kingdom
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40
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Rodnina MV, Savelsbergh A, Wintermeyer W. Dynamics of translation on the ribosome: molecular mechanics of translocation. FEMS Microbiol Rev 1999; 23:317-33. [PMID: 10371036 DOI: 10.1111/j.1574-6976.1999.tb00402.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The translocation step of protein elongation entails a large-scale rearrangement of the tRNA-mRNA-ribosome complex. Recent years have seen major advances in unraveling the mechanism of the process on the molecular level. A number of intermediate states have been defined and, in part, characterized structurally. The article reviews the recent evidence that suggests a dynamic role of the ribosome and its ligands during translocation. The focus is on dynamic aspects of tRNA movement and on the role of elongation factor G and GTP hydrolysis in translocation catalysis. The significance of structural changes of the ribosome induced by elongation factor G as well the role of ribosomal RNA are addressed. A functional model of elongation factor G as a motor protein driven by GTP hydrolysis is discussed.
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Affiliation(s)
- M V Rodnina
- Institute of Molecular Biology, University of Witten/Herdecke, Germany
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41
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Fewell SW, Woolford JL. Ribosomal protein S14 of Saccharomyces cerevisiae regulates its expression by binding to RPS14B pre-mRNA and to 18S rRNA. Mol Cell Biol 1999; 19:826-34. [PMID: 9858605 PMCID: PMC83939 DOI: 10.1128/mcb.19.1.826] [Citation(s) in RCA: 111] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/1998] [Accepted: 09/24/1998] [Indexed: 11/20/2022] Open
Abstract
Production of ribosomal protein S14 in Saccharomyces cerevisiae is coordinated with the rate of ribosome assembly by a feedback mechanism that represses expression of RPS14B. Three-hybrid assays in vivo and filter binding assays in vitro demonstrate that rpS14 directly binds to an RNA stem-loop structure in RPS14B pre-mRNA that is necessary for RPS14B regulation. Moreover, rpS14 binds to a conserved helix in 18S rRNA with approximately five- to sixfold-greater affinity. These results support the model that RPS14B regulation is mediated by direct binding of rpS14 either to its pre-mRNA or to rRNA. Investigation of these interactions with the three-hybrid system reveals two regions of rpS14 that are involved in RNA recognition. D52G and E55G mutations in rpS14 alter the specificity of rpS14 for RNA, as indicated by increased affinity for RPS14B RNA but reduced affinity for the rRNA target. Deletion of the C terminus of rpS14, where multiple antibiotic resistance mutations map, prevents binding of rpS14 to RNA and production of functional 40S subunits. The emetine-resistant protein, rpS14-EmRR, which contains two mutations near the C terminus of rpS14, does not bind either RNA target in the three-hybrid or in vitro assays. This is the first direct demonstration that an antibiotic resistance mutation alters binding of an r protein to rRNA and is consistent with the hypothesis that antibiotic resistance mutations can result from local alterations in rRNA structure.
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Affiliation(s)
- S W Fewell
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
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42
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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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43
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Guyot A, Jarrett B, Sanvee L, Dore D. Antimicrobial resistance of Neisseria gonorrhoeae in Liberia. Trans R Soc Trop Med Hyg 1998; 92:670-4. [PMID: 10326119 DOI: 10.1016/s0035-9203(98)90808-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The prevalence and molecular characteristics of penicillinase-producing Neisseria gonorrhoeae (PPNG) and tetracycline-resistant N. gonorrhoeae (TRNG) were determined in 10 clinics in Monrovia, Liberia, to assess the likely effectiveness of the current standard treatment with penicillin or tetracycline. One hundred gonococcal strains were isolated from 146 urethral swabs and 261 cervical swabs and screened for susceptibility to ceftriaxone, penicillin, spectinomycin and tetracycline by the disk diffusion method; 83% were resistant to penicillin and 63% to tetracycline. Twenty-one strains from 18 men and 3 women with uncomplicated gonorrhoea were subjected to more detailed characterization. These 21 strains belonged to 5 auxotype/serovar classes; 86% were PPNG/TRNG. Three PPNG harboured the 4.4 MDa penicillinase plasmid and 16 the 3.2 MDa plasmid. All TRNG harboured the 25.2 MDa plasmid and their MICs for tetracycline were > 32 mg/L. They gave a PCR product which, according to its restriction pattern, corresponded to the American type tetM gene. By the agar dilution method, all strains exhibited intermediate resistance to sulphamethoxazole-trimethoprim (19:1) (co-trimoxazole) with MICs of 8-32 mg/L. All strains were susceptible to spectinomycin and ciprofloxacin. The MICs for gentamicin were 4-8 mg/L. The use of effective and affordable antimicrobial chemotherapy with either 500 mg ciprofloxacin or a single dose of gentamicin is discussed, with consideration of molecular biological, pharmacological and public health aspects.
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Affiliation(s)
- A Guyot
- St Joseph's Catholic Hospital, Sinkor, Monrovia, Liberia.
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44
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Piepersberg W. Molecular Biology, Biochemistry and Fermentation of Aminoglycoside Antibiotics. DRUGS AND THE PHARMACEUTICAL SCIENCES 1997. [DOI: 10.1201/b14856-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
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45
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Lyutzkanova D, Distler J, Altenbuchner J. A spectinomycin resistance determinant from the spectinomycin producer Streptomyces flavopersicus. MICROBIOLOGY (READING, ENGLAND) 1997; 143 ( Pt 7):2135-2143. [PMID: 9245803 DOI: 10.1099/00221287-143-7-2135] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The spectinomycin (sp) resistance determinant from Streptomyces flavopersicus was cloned into Streptomyces lividans using the plasmid vector pIJ699. A plasmid, pDGL15, with a 3.65 kb insert from S. flavopersicus conferring resistance to Sp was isolated. DNA sequence analysis of the 3651 1 bp DNA insert revealed four open reading frames (ORFs). The amino acid sequence deduced from one ORF (SpcN) showed a high degree of similarity to an aminoglycoside phosphotransferase (StrN) and from a second one (SpcR) to a regulatory protein (StrR) of the streptomycin biosynthesis gene cluster from S. griseus. The two other ORFs were incomplete and the deduced amino acid sequences showed similarities to an amidinotransferase encoded in the streptomycin biosynthesis gene cluster of S. griseus and to the transposase of IS112, respectively. Expression of the spcN gene in E. coli under the control of tac promoter conferred Sp resistance to the cells. An enzymic assay confirmed that the gene product of spcN is an ATP-dependent aminoglycoside phosphotransferase which phosphorylates Sp and actinamine, the aminocyclitol moiety of Sp.
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Affiliation(s)
- Dimitrina Lyutzkanova
- Institut für Industrielle Genetik, Universität Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Jurgen Distler
- FB9-Mikrobiologie, Bergische Universität-GH, 42097 Wuppertal, Germany
| | - Josef Altenbuchner
- Institut für Industrielle Genetik, Universität Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
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46
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Thom G, Prescott CD. The selection in vivo and characterization of an RNA recognition motif for spectinomycin. Bioorg Med Chem 1997; 5:1081-6. [PMID: 9222501 DOI: 10.1016/s0968-0896(97)00060-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Ribonucleoprotein (RNP) complexes participate in almost all macromolecular processes, including RNA processing, protein synthesis, and the signal recognition of proteins targeted for export. An understanding of these processes requires detailed knowledge of interactions at the molecular level, which has evidently been difficult due to the size and complexity of the particles. Fragmentation of large RNP complexes into functional subdomains is proven to be a successful in vitro strategy to probe ligand interactions at the molecular level. We reasoned that RNA molecules expressed in vivo may fold in such a manner as to mimic a drug binding site present on the intact ribosome. If expressed at sufficient levels, the RNA would sequester the antibiotic thereby permitting the continued function of the ribosome and consequently allow the cell to survive in the presence of the drug. Evidence is presented here in support of this RNA fragment-rescue concept following the selection and characterization of RNA fragments that confer resistance to the antibiotic spectinomycin.
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Affiliation(s)
- G Thom
- SmithKline Beecham Pharmaceuticals, Department of Molecular Recognition, Collegeville, PA 19426-0989, USA
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47
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Pagel FT, Zhao SQ, Hijazi KA, Murgola EJ. Phenotypic heterogeneity of mutational changes at a conserved nucleotide in 16 S ribosomal RNA. J Mol Biol 1997; 267:1113-23. [PMID: 9150400 DOI: 10.1006/jmbi.1997.0943] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
RNA sites that contain unpaired or mismatched nucleotides can be interaction sites for other macromolecules. C1054, a virtually universally conserved nucleotide in the 16 S (small subunit) ribosomal RNA of Escherichia coli, is part of a highly conserved bulge in helix 34, which has been located at the decoding site of the ribosome. This helix has been implicated in several translational events, including peptide chain termination and decoding accuracy. Here, we observed interesting differences in phenotype associated with the three base substitutions at, and the deletion of, nucleotide C1054. The phenotypes examined include suppression of nonsense codons on different media and at different temperatures, lethality conditioned by temperature and level of expression of the mutant rRNA, ribosome profiles upon centrifugation through sucrose density gradients, association of mutant 30 S subunits with 50 S subunits, and effects on the action of tRNA suppressor mutants. Some of our findings contradict previously reported properties of individual mutants. Particularly notable is our finding that the first reported 16 S rRNA suppressor of UGA mutations was not a C1054 deletion but rather the base substitution C1054A. After constructing deltaC1054 by site-directed mutagenesis, we observed, among other differences, that it does not suppress any of the trpA mutations previously reported to be suppressed by the original UGA suppressor. In general, our results are consistent with the suggestion that the termination codon readthrough effects of mutations at nucleotide 1054 are the result of defects in peptide chain termination rather than of decreases in general translational accuracy. The phenotypic heterogeneity associated with different mutations at this one nucleotide position may be related to the mechanisms of involvement of this nucleotide, the two-nucleotide bulge, and/or helix 34 in particular translational events. In particular, previous indications from other laboratories of conformational changes associated with this region are consistent with differential effects of 1054 mutations on RNA-RNA or RNA-protein interactions. Finally, the association of a variety of phenotypes with different changes at the same nucleotide may eventually shed light on speculations about the coevolution of parts of ribosomal RNA with other translational macromolecules.
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Affiliation(s)
- F T Pagel
- Department of Molecular Genetics, The University of Texas M.D. Anderson Cancer Center, Houston 77030, USA
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48
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Spahn CM, Prescott CD. Throwing a spanner in the works: antibiotics and the translation apparatus. J Mol Med (Berl) 1996; 74:423-39. [PMID: 8872856 DOI: 10.1007/bf00217518] [Citation(s) in RCA: 141] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The protein synthetic machinery is essential to all living cells and is one of the major targets for antibiotics. Knowledge of the structure and function of the ribosome and its associated factors is key to understanding the mechanism of drug action. Conversely, drugs have been used as tools to probe the translation cycle, thus providing a means to further our understanding of the steps that lead to protein synthesis. Our current understanding as to how antibiotics disrupt this process is reviewed here, with particular emphasis on the prokaryotic elongation cycle and those drugs that interact with ribosomal RNAs.
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Affiliation(s)
- C M Spahn
- Max Planck Institut für Molekulare Genetik, AG Ribosomen, Berlin, Germany
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49
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Abstract
The 16S ribosomal RNA mutation database (16SMDB) provides a list of mutated positions in 16S ribosomal RNA from Escherichia coli and the identity of each alteration. Information provided for each mutation includes: (i) a brief description of the phenotype(s) associated with each mutation; (ii) whether a mutant phenotype has been detected by in vivo or in vitro methods; (iii) relevant literature citations. The database is available via ftp and on the World Wide Web.
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Affiliation(s)
- K L Triman
- Department of Biology, Franklin and Marshall College, Lancaster, PA 17604, USA
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50
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Abstract
Bradyrhizobium japonicum contains only a single rRNA (rrn) gene region, despite its comparatively large genome size of 8,700 kb. The nucleotide sequence revealed an organization of rRNA and tRNA genes that is frequently found in bacteria: 5'-rrs (16S rRNA)-ileT (tRNA(Ile))-alaT (tRNA(Ala))-rrl (23S rRNA)-rrf (5S rRNA)-3'. The 5' end of the primary transcript, one of the 16S rRNA processing sites, and the 5' end of the mature 16S rRNA were determined by primer extension. DNA hybridization experiments showed that the slowly growing Bradyrhizobium strains generally have only a single copy of the 16S rRNA gene, whereas the faster-growing Rhizobium species contain three rrs copies.
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MESH Headings
- Base Sequence
- Cloning, Molecular
- DNA, Ribosomal/genetics
- Gene Dosage
- Gene Expression
- Genes, Bacterial/genetics
- Genome, Bacterial
- Molecular Sequence Data
- RNA, Ribosomal/genetics
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 23S/genetics
- RNA, Ribosomal, 5S/genetics
- RNA, Transfer, Ala/genetics
- RNA, Transfer, Ile/genetics
- Restriction Mapping
- Rhizobiaceae/genetics
- Sequence Analysis, DNA
- Transcription, Genetic
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Affiliation(s)
- C Kündig
- Mikrobiologisches Institut, Eidgenössische Technische Hochschule, ETH-Zentrum, Zürich, Switzerland
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