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Nessar R, Reyrat JM, Murray A, Gicquel B. Genetic analysis of new 16S rRNA mutations conferring aminoglycoside resistance in Mycobacterium abscessus. J Antimicrob Chemother 2011; 66:1719-24. [PMID: 21652621 DOI: 10.1093/jac/dkr209] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES We studied the development and fitness cost of 2-deoxystreptamine aminoglycoside resistance of Mycobacterium abscessus. METHODS Spontaneous 2-deoxystreptamine aminoglycoside-resistant mutants were selected and the frequency of their appearance was determined. The 3' part of the rrs gene was sequenced to characterize mutations. Additionally, we determined the MICs of aminoglycoside drugs for the different mutants obtained. The dominance/recessivity traits of the different mutations were examined and we explored the potential cost conferred by the mutations selected in vitro on the fitness of these isolates compared with the wild-type strain. RESULTS The in vitro mutation rate for 2-deoxystreptamine aminoglycoside resistance was ∼10(-7) mutations/cell division. In addition to the known rrs A→G substitution at position 1408 (Escherichia coli numbering), which confers kanamycin resistance (Kan(R)), three new substitutions in rrs were identified in M. abscessus Kan(R) mutants, i.e. T→A at 1406, C→T at 1409 and G→T at 1491. Heterodiploids carrying genomic mutations T→A at 1406 and A→G at 1408 with the wild-type rrs gene carried by the pNBV1 vector showed a resistant phenotype. In contrast, heterodiploids carrying genomic mutations C→T at 1409 and G→T at 1491 with the wild-type rrs gene carried by the pNBV1 vector had a susceptible phenotype. No burden on fitness was observed for the different mutations. CONCLUSION Mutations in the rrs gene that confer high-level 2-deoxystreptamine aminoglycoside resistance on M. abscessus differ in their dominance/recessivity traits and have no biological cost under our experimental conditions.
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Affiliation(s)
- Rachid Nessar
- Université Paris Descartes, Faculté de Médecine Paris Descartes, F-75730 Paris Cedex 15, France.
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52
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Biswas S, Rolain JM. Bartonella infection: treatment and drug resistance. Future Microbiol 2011; 5:1719-31. [PMID: 21133691 DOI: 10.2217/fmb.10.133] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Bartonella species, which belong to the α-2 subgroup of Proteobacteria, are fastidious Gram-negative bacteria that are highly adapted to their mammalian host reservoirs. Bartonella species are responsible for different clinical conditions affecting humans, including Carrion's disease, cat scratch disease, trench fever, bacillary angiomatosis, endocarditis and peliosis hepatis. While some of these diseases can resolve spontaneously without treatment, in other cases, the disease is fatal without antibiotic treatment. In this article, we discuss the antibiotic susceptibility patterns of Bartonella species, detected using several methods. We also provide an overview of Bartonella infection in humans and animals and discuss the antibiotic treatment recommendations for the different infections, treatment failure and the molecular mechanism of antibiotic resistance in these bacteria.
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Affiliation(s)
- Silpak Biswas
- CNRS-IRD, UMR 6236, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Faculté de Médecine et de Pharmacie, Université de la Méditerranée, 27 boulevard Jean-Moulin, Marseille cedex 05, France
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53
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Lamichhane TN, Abeydeera ND, Duc ACE, Cunningham PR, Chow CS. Selection of peptides targeting helix 31 of bacterial 16S ribosomal RNA by screening M13 phage-display libraries. Molecules 2011; 16:1211-39. [PMID: 21278676 PMCID: PMC6259748 DOI: 10.3390/molecules16021211] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2011] [Revised: 01/24/2011] [Accepted: 01/25/2011] [Indexed: 01/13/2023] Open
Abstract
Ribosomal RNA is the catalytic portion of ribosomes, and undergoes a variety of conformational changes during translation. Structural changes in ribosomal RNA can be facilitated by the presence of modified nucleotides. Helix 31 of bacterial 16S ribosomal RNA harbors two modified nucleotides, m²G966 and m⁵C967, that are highly conserved among bacteria, though the degree and nature of the modifications in this region are different in eukaryotes. Contacts between helix 31 and the P-site tRNA, initiation factors, and ribosomal proteins highlight the importance of this region in translation. In this work, a heptapeptide M13 phage-display library was screened for ligands that target the wild-type, naturally modified bacterial helix 31. Several peptides, including TYLPWPA, CVRPFAL, TLWDLIP, FVRPFPL, ATPLWLK, and DIRTQRE, were found to be prevalent after several rounds of screening. Several of the peptides exhibited moderate affinity (in the high nM to low µM range) to modified helix 31 in biophysical assays, including surface plasmon resonance (SPR), and were also shown to bind 30S ribosomal subunits. These peptides also inhibited protein synthesis in cell-free translation assays.
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Affiliation(s)
- Tek N. Lamichhane
- Department of Chemistry, Wayne State University, Detroit, MI 48202, USA
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, USA
| | | | | | - Philip R. Cunningham
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, USA
| | - Christine S. Chow
- Department of Chemistry, Wayne State University, Detroit, MI 48202, USA
- Author to whom correspondence should be addressed; E-Mail: ; Tel: +1-313-577-2594; Fax: +1-313-577-8822
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54
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Husain N, Obranic S, Koscinski L, Seetharaman J, Babic F, Bujnicki JM, Maravic-Vlahovicek G, Sivaraman J. Structural basis for the methylation of A1408 in 16S rRNA by a panaminoglycoside resistance methyltransferase NpmA from a clinical isolate and analysis of the NpmA interactions with the 30S ribosomal subunit. Nucleic Acids Res 2010; 39:1903-18. [PMID: 21062819 PMCID: PMC3061052 DOI: 10.1093/nar/gkq1033] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
NpmA, a methyltransferase that confers resistance to aminoglycosides was identified in an Escherichia coli clinical isolate. It belongs to the kanamycin–apramycin methyltransferase (Kam) family and specifically methylates the 16S rRNA at the N1 position of A1408. We determined the structures of apo-NpmA and its complexes with S-adenosylmethionine (AdoMet) and S-adenosylhomocysteine (AdoHcy) at 2.4, 2.7 and 1.68 Å, respectively. We generated a number of NpmA variants with alanine substitutions and studied their ability to bind the cofactor, to methylate A1408 in the 30S subunit, and to confer resistance to kanamycin in vivo. Residues D30, W107 and W197 were found to be essential. We have also analyzed the interactions between NpmA and the 30S subunit by footprinting experiments and computational docking. Helices 24, 42 and 44 were found to be the main NpmA-binding site. Both experimental and theoretical analyses suggest that NpmA flips out the target nucleotide A1408 to carry out the methylation. NpmA is plasmid-encoded and can be transferred between pathogenic bacteria; therefore it poses a threat to the successful use of aminoglycosides in clinical practice. The results presented here will assist in the development of specific NpmA inhibitors that could restore the potential of aminoglycoside antibiotics.
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Affiliation(s)
- Nilofer Husain
- Department of Biological Sciences, 14 Science drive 4, National University of Singapore, Singapore
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55
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Kalapala SK, Hobbie SN, Böttger EC, Shcherbakov D. Mutation K42R in ribosomal protein S12 does not affect susceptibility of Mycobacterium smegmatis 16S rRNA A-site mutants to 2-deoxystreptamines. PLoS One 2010; 5:e11960. [PMID: 20700526 PMCID: PMC2916820 DOI: 10.1371/journal.pone.0011960] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2010] [Accepted: 06/05/2010] [Indexed: 11/18/2022] Open
Abstract
Recent studies have suggested that ribosomal protein S12 modulates 16S rRNA function and susceptibility to 2-deoxystreptamine aminoglycosides. To study whether the non-restrictive K42R mutation in RpsL affects 2-deoxystreptamine susceptibility in Mycobacterium smegmatis, we studied the drug susceptibility pattern of various mutants with genetic alterations in the 16S rRNA decoding A-site in the context of wild-type and mutant protein S12. RpsL K42R substitution was found not to affect the drug resistance pattern associated with mutational alterations in 16S rRNA H44.
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MESH Headings
- Bacterial Proteins/chemistry
- Bacterial Proteins/genetics
- Bacterial Proteins/metabolism
- Base Sequence
- Binding Sites
- Hexosamines/pharmacology
- Microbial Sensitivity Tests
- Models, Molecular
- Mutation
- Mycobacterium smegmatis/cytology
- Mycobacterium smegmatis/drug effects
- Mycobacterium smegmatis/genetics
- Protein Conformation
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 16S/metabolism
- Ribosomal Proteins/chemistry
- Ribosomal Proteins/genetics
- Ribosomal Proteins/metabolism
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Affiliation(s)
- Sarath K. Kalapala
- Institut für Medizinische Mikrobiologie, Universität Zürich, Zürich, Switzerland
| | - Sven N. Hobbie
- Institut für Medizinische Mikrobiologie, Universität Zürich, Zürich, Switzerland
- Singapore-MIT Alliance for Research and Technology (SMART), Centre for Life Sciences, Singapore, Singapore
| | - Erik C. Böttger
- Institut für Medizinische Mikrobiologie, Universität Zürich, Zürich, Switzerland
| | - Dmitry Shcherbakov
- Institut für Medizinische Mikrobiologie, Universität Zürich, Zürich, Switzerland
- * E-mail:
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56
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Matt T, Akbergenov R, Shcherbakov D, Böttger EC. The Ribosomal A-site: Decoding, Drug Target, and Disease. Isr J Chem 2010. [DOI: 10.1002/ijch.201000003] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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57
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Shcherbakov D, Akbergenov R, Matt T, Sander P, Andersson DI, Böttger EC. Directed mutagenesis of Mycobacterium smegmatis 16S rRNA to reconstruct the in vivo evolution of aminoglycoside resistance in Mycobacterium tuberculosis. Mol Microbiol 2010; 77:830-40. [DOI: 10.1111/j.1365-2958.2010.07218.x] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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58
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Houghton JL, Green KD, Chen W, Garneau-Tsodikova S. The future of aminoglycosides: the end or renaissance? Chembiochem 2010; 11:880-902. [PMID: 20397253 DOI: 10.1002/cbic.200900779] [Citation(s) in RCA: 146] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2009] [Indexed: 11/05/2022]
Abstract
Although aminoglycosides have been used as antibacterials for decades, their use has been hindered by their inherent toxicity and the resistance that has emerged to these compounds. It seems that such issues have relegated a formerly front-line class of antimicrobials to the proverbial back shelf. However, recent advances have demonstrated that novel aminoglycosides have a potential to overcome resistance as well as to be used to treat HIV-1 and even human genetic disorders, with abrogated toxicity. It is not the end for aminoglycosides, but rather, the challenges faced by researchers have led to ingenuity and a change in how we view this class of compounds, a renaissance.
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Affiliation(s)
- Jacob L Houghton
- Department of Medicinal Chemistry in the College of Pharmacy, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI 48109, USA
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59
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Sherer EC. Antibiotics Targeting the Ribosome: Structure-Based Design and the Nobel Prize. ACTA ACUST UNITED AC 2010. [DOI: 10.1016/s1574-1400(10)06009-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
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60
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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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61
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Li M, Duc ACE, Klosi E, Pattabiraman S, Spaller MR, Chow CS. Selection of peptides that target the aminoacyl-tRNA site of bacterial 16S ribosomal RNA. Biochemistry 2009; 48:8299-311. [PMID: 19645415 DOI: 10.1021/bi900982t] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
For almost five decades, antibiotics have been used successfully to control infectious diseases caused by bacterial pathogens. More recently, however, two-thirds of bacterial pathogens exhibit resistance and are continually evolving new resistance mechanisms against almost every clinically used antibiotic. Novel efforts are required for the development of new drugs or drug leads to combat these infectious diseases. A number of antibiotics target the bacterial aminoacyl-tRNA site (A site) of 16S rRNA (rRNA). Mutations in the A-site region are known to cause antibiotic resistance. In this study, a bacterial (Escherichia coli) A-site rRNA model was chosen as a target to screen for peptide binders. Two heptapeptides, HPVHHYQ and LPLTPLP, were selected through M13 phage display. Both peptides display selective binding to the A-site 16S rRNA with on-bead fluorescence assays. Dissociation constants (Kd's) of the amidated peptide HPVHHYQ-NH2 to various A-site RNA constructs were determined by using enzymatic footprinting, electrospray ionization mass spectrometry (ESI-MS), and isothermal titration calorimetry (ITC) under a variety of buffer and solution conditions. HPVHHYQ-NH2 exhibits moderate affinity for the A-site RNA, with an average Kd value of 16 microM. In addition, enzymatic footprinting assays and competition ESI-MS with a known A-site binder (paromomycin) revealed that peptide binding occurs near the asymmetric bulge at positions U1495 and G1494 and leads to increased exposure of residues A1492 and A1493.
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Affiliation(s)
- Mei Li
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
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62
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The uracil DNA glycosylase UdgB of Mycobacterium smegmatis protects the organism from the mutagenic effects of cytosine and adenine deamination. J Bacteriol 2009; 191:6312-9. [PMID: 19684133 DOI: 10.1128/jb.00613-09] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Spontaneous hydrolytic deamination of DNA bases represents a considerable mutagenic threat to all organisms, particularly those living in extreme habitats. Cytosine is readily deaminated to uracil, which base pairs with adenine during replication, and most organisms encode at least one uracil DNA glycosylase (UDG) that removes this aberrant base from DNA with high efficiency. Adenine deaminates to hypoxanthine approximately 10-fold less efficiently, and its removal from DNA in vivo has to date been reported to be mediated solely by alkyladenine DNA glycosylase. We previously showed that UdgB from Pyrobaculum aerophilum, a hyperthermophilic crenarchaeon, can excise hypoxanthine from oligonucleotide substrates, but as this organism is not amenable to genetic manipulation, we were unable to ascertain that the enzyme also has this role in vivo. In the present study, we show that UdgB from Mycobacterium smegmatis protects this organism against mutagenesis associated with deamination of both cytosine and adenine. Together with Ung-type uracil glycosylase, M. smegmatis UdgB also helps attenuate the cytotoxicity of the antimicrobial agent 5-fluorouracil.
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63
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64
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Setny P, Trylska J. Search for novel aminoglycosides by combining fragment-based virtual screening and 3D-QSAR scoring. J Chem Inf Model 2009; 49:390-400. [PMID: 19434840 DOI: 10.1021/ci800361a] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Aminoglycosides are antibiotics targeting the 16S RNA A site of the bacterial ribosome. There have been many efforts directed toward design of their synthetic derivatives, however with only few successes. As RNA binders, aminoglycosides are also a difficult target for computational drug design, since most of the existing methods were developed for protein ligands. Here, we present an approach that allows for evading the problems related to still poorly developed RNA docking and scoring algorithms. It is aimed at identification of new molecular scaffolds potentially binding to the A site. The considered molecules are based on the neamine core, which is common for all aminoglycosides and provides specificity toward the binding site, linked with diverse molecular fragments via its O5 or O6 oxygen atom. Suitable fragments are selected with the use of 3D searches of molecular fragments library against two distinct pharmacophores designed on the basis of available structural data for aminoglycoside-RNA complexes. The compounds resulting from fragments assembly with neamine are then scored with a 3D-QSAR model developed using the biological data for known aminoglycoside derivatives. Twenty-one new potential ligands are obtained, four of which have predicted activities comparable to less potent aminoglycoside antibiotics.
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Affiliation(s)
- Piotr Setny
- Interdisciplinary Centre for Mathematical and Computational Modelling and Faculty of Physics, University of Warsaw, Warsaw 02-089, Poland.
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65
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Islam S, Oh H, Jalal S, Karpati F, Ciofu O, Høiby N, Wretlind B. Chromosomal mechanisms of aminoglycoside resistance in Pseudomonas aeruginosa isolates from cystic fibrosis patients. Clin Microbiol Infect 2009; 15:60-6. [DOI: 10.1111/j.1469-0691.2008.02097.x] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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66
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A novel insertion mutation in Streptomyces coelicolor ribosomal S12 protein results in paromomycin resistance and antibiotic overproduction. Antimicrob Agents Chemother 2008; 53:1019-26. [PMID: 19104019 DOI: 10.1128/aac.00388-08] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We identified a novel paromomycin resistance-associated mutation in rpsL, caused by the insertion of a glycine residue at position 92, in Streptomyces coelicolor ribosomal protein S12. This insertion mutation (GI92) resulted in a 20-fold increase in the paromomycin resistance level. In combination with another S12 mutation, K88E, the GI92 mutation markedly enhanced the production of the blue-colored polyketide antibiotic actinorhodin and the red-colored antibiotic undecylprodigiosin. The gene replacement experiments demonstrated that the K88E-GI92 double mutation in the rpsL gene was responsible for the marked enhancement of antibiotic production observed. Ribosomes with the K88E-GI92 double mutation were characterized by error restrictiveness (i.e., hyperaccuracy). Using a cell-free translation system, we found that mutant ribosomes harboring the K88E-GI92 double mutation but not ribosomes harboring the GI92 mutation alone displayed sixfold greater translation activity relative to that of the wild-type ribosomes at late growth phase. This resulted in the overproduction of actinorhodin, caused by the transcriptional activation of the pathway-specific regulatory gene actII-orf4, possibly due to the increased translation of transcripts encoding activators of actII-orf4. The mutant with the K88E-GI92 double mutation accumulated a high level of ribosome recycling factor at late stationary phase, underlying the high level of protein synthesis activity observed.
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67
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Genetic analysis of interactions with eukaryotic rRNA identify the mitoribosome as target in aminoglycoside ototoxicity. Proc Natl Acad Sci U S A 2008; 105:20888-93. [PMID: 19104050 DOI: 10.1073/pnas.0811258106] [Citation(s) in RCA: 138] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Aminoglycoside ototoxicity has been related to a surprisingly large number of cellular structures and metabolic pathways. The finding that patients with mutations in mitochondrial rRNA are hypersusceptible to aminoglycoside-induced hearing loss has indicated a possible role for mitochondrial protein synthesis. To study the molecular interaction of aminoglycosides with eukaryotic ribosomes, we made use of the observation that the drug binding site is a distinct domain defined by the small subunit rRNA, and investigated drug susceptibility of bacterial hybrid ribosomes carrying various alleles of the eukaryotic decoding site. Compared to hybrid ribosomes with the A site of human cytosolic ribosomes, susceptibility of mitochondrial hybrid ribosomes to various aminoglycosides correlated with the relative cochleotoxicity of these drugs. Sequence alterations that correspond to the mitochondrial deafness mutations A1555G and C1494T increased drug-binding and rendered the ribosomal decoding site hypersusceptible to aminoglycoside-induced mistranslation and inhibition of protein synthesis. Our results provide experimental support for aminoglycoside-induced dysfunction of the mitochondrial ribosome. We propose a pathogenic mechanism in which interference of aminoglycosides with mitochondrial protein synthesis exacerbates the drugs' cochlear toxicity, playing a key role in sporadic dose-dependent and genetically inherited, aminoglycoside-induced deafness.
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68
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Bruell CM, Eichholz C, Kubarenko A, Post V, Katunin VI, Hobbie SN, Rodnina MV, Böttger EC. Conservation of bacterial protein synthesis machinery: initiation and elongation in Mycobacterium smegmatis. Biochemistry 2008; 47:8828-39. [PMID: 18672904 DOI: 10.1021/bi800527k] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Most of our understanding of ribosome function is based on experiments utilizing translational components from Escherichia coli. It is not clear to which extent the details of translation mechanisms derived from this single organism are true for all bacteria. Here we investigate translation factor-dependent reactions of initiation and elongation in a reconstituted translation system from a Gram-positive bacterium Mycobacterium smegmatis. This organism was chosen because mutations in rRNA have very different phenotypes in E. coli and M. smegmatis, and the docking site for translational GTPases, the L12 stalk, is extended in the ribosomes from M. smegmatis compared to E. coli. M. smegmatis genes coding for IF1, IF2, IF3, EF-G, and EF-Tu were identified by sequence alignments; the respective recombinant proteins were prepared and studied in a variety of biochemical and biophysical assays with M. smegmatis ribosomes. We found that the activities of initiation and elongation factors and the rates of elemental reactions of initiation and elongation of protein synthesis are remarkably similar with M. smegmatis and E. coli components. The data suggest a very high degree of conservation of basic translation mechanisms, probably due to coevolution of the ribosome components and translation factors. This work establishes the reconstituted translation system from individual purified M. smegmatis components as an alternative to that from E. coli to study the mechanisms of translation and to test the action of antibiotics against Gram-positive bacteria.
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69
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Pathak R, Perez-Fernandez D, Nandurdikar R, Kalapala S, Böttger E, Vasella A. Synthesis and Evaluation of Paromomycin Derivatives Modified at C(4′). Helv Chim Acta 2008. [DOI: 10.1002/hlca.200890167] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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70
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Kimura T, Takagi K, Hirata Y, Hase Y, Muto A, Himeno H. Ribosome-small-subunit-dependent GTPase interacts with tRNA-binding sites on the ribosome. J Mol Biol 2008; 381:467-77. [PMID: 18588897 DOI: 10.1016/j.jmb.2008.06.023] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2008] [Revised: 06/03/2008] [Accepted: 06/07/2008] [Indexed: 10/21/2022]
Abstract
RsgA (ribosome-small-subunit-dependent GTPase A, also known as YjeQ) is a unique GTPase in that guanosine triphosphate hydrolytic activity is activated by the small subunit of the ribosome. Disruption of the gene for RsgA from the genome affects the growth of cells, the subunit association of the ribosome, and the maturation of 16S rRNA. To study the interaction of Escherichia coli RsgA with the ribosome, chemical modifications using dimethylsulfate and kethoxal were performed on the small subunit in the presence or in the absence of RsgA. The chemical reactivities at G530, A790, G925, G926, G966, C1054, G1339, G1405, A1413, and A1493 in 16S rRNA were reduced, while those at A532, A923, G1392, A1408, A1468, and A1483 were enhanced, by the addition of RsgA, together with 5'-guanylylimidodiphosphate. Among them, the chemical reactivities at A532, A790, A923, G925, G926, C1054, G1392, A1413, A1468, A1483, and A1493 were not changed when RsgA was added together with GDP. These results indicate that the binding of RsgA induces conformational changes around the A site, P site, and helix 44, and that guanosine triphosphate hydrolysis induces partial conformational restoration, especially in the head, to dissociate RsgA from the small subunit. RsgA has the capacity to coexist with mRNA in the ribosome while it promotes dissociation of tRNA from the ribosome.
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Affiliation(s)
- Takatsugu Kimura
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Aomori 036-8561, Japan
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71
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Tselika S, Konstantinidis T, Synetos D. Two nucleotide substitutions in the A-site of yeast 18S rRNA affect translation and differentiate the interaction of ribosomes with aminoglycoside antibiotics. Biochimie 2008; 90:908-17. [DOI: 10.1016/j.biochi.2008.02.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2007] [Accepted: 02/12/2008] [Indexed: 11/27/2022]
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72
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Zhou Y, Chow C, Murphy DE, Sun Z, Bertolini T, Froelich JM, Webber SE, Hermann T, Wall D. Antibacterial activity in serum of the 3,5-diamino-piperidine translation inhibitors. Bioorg Med Chem Lett 2008; 18:3369-75. [PMID: 18440814 DOI: 10.1016/j.bmcl.2008.04.023] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2008] [Revised: 04/09/2008] [Accepted: 04/10/2008] [Indexed: 10/22/2022]
Abstract
Translation inhibitors of the 3,5-diamino-piperidine series act as aminoglycoside mimetics that inhibit bacterial growth. Here we show antibacterial SAR in the presence and absence of serum with a particular focus toward Pseudomonas aeruginosa.
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Affiliation(s)
- Yuefen Zhou
- Anadys Pharmaceuticals, Inc., San Diego, USA
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73
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Kondo J, Westhof E. The bacterial and mitochondrial ribosomal A-site molecular switches possess different conformational substates. Nucleic Acids Res 2008; 36:2654-66. [PMID: 18346970 PMCID: PMC2377432 DOI: 10.1093/nar/gkn112] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The A site of the small ribosomal subunit participates in the fidelity of decoding by switching between two states, a resting ‘off’ state and an active decoding ‘on’ state. Eight crystal structures of RNA duplexes containing two minimal decoding A sites of the Homo sapiens mitochondrial wild-type, the A1555G mutant or bacteria have been solved. The resting ‘off’ state of the mitochondrial wild-type A site is surprisingly different from that of the bacterial A site. The mitochondrial A1555G mutant has two types of the ‘off’ states; one is similar to the mitochondrial wild-type ‘off’ state and the other is similar to the bacterial ‘off’ state. Our present results indicate that the dynamics of the A site in bacteria and mitochondria are different, a property probably related to the small number of tRNAs used for decoding in mitochondria. Based on these structures, we propose a hypothesis for the molecular mechanism of non-syndromic hearing loss due to the mitochondrial A1555G mutation.
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Affiliation(s)
- Jiro Kondo
- Architecture et Réactivité de l'ARN, Université Louis Pasteur, Institut de Biologie Moléculaire et Cellulaire, CNRS, 15 rue René Descartes, 67084 Strasbourg, France
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74
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Fan-Minogue H, Bedwell DM. Eukaryotic ribosomal RNA determinants of aminoglycoside resistance and their role in translational fidelity. RNA (NEW YORK, N.Y.) 2008; 14:148-57. [PMID: 18003936 PMCID: PMC2151042 DOI: 10.1261/rna.805208] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Recent studies of prokaryotic ribosomes have dramatically increased our knowledge of ribosomal RNA (rRNA) structure, functional centers, and their interactions with antibiotics. However, much less is known about how rRNA function differs between prokaryotic and eukaryotic ribosomes. The core decoding sites are identical in yeast and human 18S rRNAs, suggesting that insights obtained in studies with yeast rRNA mutants can provide information about ribosome function in both species. In this study, we examined the importance of key nucleotides of the 18S rRNA decoding site on ribosome function and aminoglycoside susceptibility in Saccharomyces cerevisiae cells expressing homogeneous populations of mutant ribosomes. We found that residues G577, A1755, and A1756 (corresponding to Escherichia coli residues G530, A1492, and A1493, respectively) are essential for cell viability. We also found that residue G1645 (A1408 in E. coli) and A1754 (G1491 in E. coli) both make significant and distinct contributions to aminoglycoside resistance. Furthermore, we found that mutations at these residues do not alter the basal level of translational accuracy, but influence both paromomycin-induced misreading of sense codons and readthrough of stop codons. This study represents the most comprehensive mutational analysis of the eukaryotic decoding site to date, and suggests that many fundamental features of decoding site function are conserved between prokaryotes and eukaryotes.
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Affiliation(s)
- Hua Fan-Minogue
- Department of Cell Biology, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
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75
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Kondo J, Pachamuthu K, François B, Szychowski J, Hanessian S, Westhof E. Crystal Structure of the Bacterial Ribosomal Decoding Site Complexed with a Synthetic Doubly Functionalized Paromomycin Derivative: a New Specific Binding Mode to an A-Minor Motif Enhances in vitro Antibacterial Activity. ChemMedChem 2007; 2:1631-8. [PMID: 17722211 DOI: 10.1002/cmdc.200700113] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The crystal structure of the complex between oligonucleotide containing the bacterial ribosomal decoding site (A site) and the synthetic paromomycin analogue 1, which contains the gamma-amino-alpha-hydroxybutyryl (L-haba) group at position N1 of ring II (2-DOS ring), and an ether chain with an O-phenethylaminoethyl group at position C2'' of ring III, is reported. Interestingly, next to the paromomycin analogue 1 specifically bound to the A site, a second molecule of 1 with a different conformation is observed at the crystal packing interface which mimics the A-minor interaction between two bulged-out adenines from the A site and the codon-anticodon stem of the mRNA-tRNA complex. Improved antibacterial activity supports the conclusion that analogue 1 might affect protein synthesis on the ribosome in two different ways: 1) specific binding to the A site forces maintenance of the "on" state with two bulged out adenines, and 2) a new binding mode of 1 to an A-minor motif which stabilizes complex formation between the ribosome and the mRNA-tRNA complex regardless of whether the codon-anticodon stem is of the cognate or near-cognate type.
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Affiliation(s)
- Jiro Kondo
- Architecture et Réactivité de l'ARN, Université Louis Pasteur, Institut de Biologie Moléculaire et Cellulaire, CNRS, 15 rue René Descartes, 67084 Strasbourg, France
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76
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Hainrichson M, Nudelman I, Baasov T. Designer aminoglycosides: the race to develop improved antibiotics and compounds for the treatment of human genetic diseases. Org Biomol Chem 2007; 6:227-39. [PMID: 18174989 DOI: 10.1039/b712690p] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Aminoglycosides are highly potent, broad-spectrum antibiotics that exert their bactericidal therapeutic effect by selectively binding to the decoding aminoacyl site (A-site) of the bacterial 16 S rRNA, thereby interfering with translational fidelity during protein synthesis. The appearance of bacterial strains resistant to these drugs, as well as their relative toxicity, have inspired extensive searches towards the goal of obtaining novel molecular designs with improved antibacterial activity and reduced toxicity. In the last few years, a new, aminoglycoside dependent therapeutic approach for the treatment of certain human genetic diseases has been identified. These treatments rely on the ability of certain aminoglycosides to induce mammalian ribosomes to readthrough premature stop codon mutations. This new and challenging task has introduced fresh research avenues in the field of aminoglycoside research. Recent observations and current challenges in the design of aminoglycosides with improved antibacterial activity and the treatment of human genetic diseases are discussed.
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Affiliation(s)
- Mariana Hainrichson
- The Edith and Joseph Fischer Enzyme Inhibitors Laboratory, Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa 32000, Israel
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77
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Wachino JI, Shibayama K, Kurokawa H, Kimura K, Yamane K, Suzuki S, Shibata N, Ike Y, Arakawa Y. Novel plasmid-mediated 16S rRNA m1A1408 methyltransferase, NpmA, found in a clinically isolated Escherichia coli strain resistant to structurally diverse aminoglycosides. Antimicrob Agents Chemother 2007; 51:4401-9. [PMID: 17875999 PMCID: PMC2168023 DOI: 10.1128/aac.00926-07] [Citation(s) in RCA: 127] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We have isolated a multiple-aminoglycoside-resistant Escherichia coli strain, strain ARS3, and have been the first to identify a novel plasmid-mediated 16S rRNA methyltransferase, NpmA. This new enzyme shared a relatively low level of identity (30%) to the chromosomally encoded 16S rRNA methyltransferase (KamA) of Streptomyces tenjimariensis, an actinomycete aminoglycoside producer. The introduction of a recombinant plasmid carrying npmA could confer on E. coli consistent resistance to both 4,6-disubstituted 2-deoxystreptamines, such as amikacin and gentamicin, and 4,5-disubstituted 2-deoxystreptamines, including neomycin and ribostamycin. The histidine-tagged NpmA elucidated methyltransferase activity against 30S ribosomal subunits but not against 50S subunits and the naked 16S rRNA molecule in vitro. We further confirmed that NpmA is an adenine N-1 methyltransferase specific for the A1408 position at the A site of 16S rRNA. Drug footprinting data indicated that binding of aminoglycosides to the target site was apparently interrupted by methylation at the A1408 position. These observations demonstrate that NpmA is a novel plasmid-mediated 16S rRNA methyltransferase that provides a panaminoglycoside-resistant nature through interference with the binding of aminoglycosides toward the A site of 16S rRNA through N-1 methylation at position A1408.
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MESH Headings
- Amino Acid Sequence
- Aminoglycosides/chemistry
- Aminoglycosides/pharmacology
- Anti-Bacterial Agents/chemistry
- Anti-Bacterial Agents/pharmacology
- Chromatography, High Pressure Liquid
- Drug Resistance, Bacterial/genetics
- Escherichia coli/drug effects
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Escherichia coli Proteins/chemistry
- Escherichia coli Proteins/genetics
- Escherichia coli Proteins/metabolism
- Methyltransferases/chemistry
- Methyltransferases/genetics
- Methyltransferases/metabolism
- Microbial Sensitivity Tests
- Models, Molecular
- Molecular Sequence Data
- Plasmids/genetics
- Protein Binding
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/metabolism
- Ribosome Subunits, Small/chemistry
- Ribosome Subunits, Small/metabolism
- Sequence Homology, Amino Acid
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Affiliation(s)
- Jun-ichi Wachino
- Department of Bacterial Pathogenesis and Infection Control, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashi-Murayama, Tokyo 208-0011, Japan
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78
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Hobbie SN, Kalapala SK, Akshay S, Bruell C, Schmidt S, Dabow S, Vasella A, Sander P, Böttger EC. Engineering the rRNA decoding site of eukaryotic cytosolic ribosomes in bacteria. Nucleic Acids Res 2007; 35:6086-93. [PMID: 17766247 PMCID: PMC2094070 DOI: 10.1093/nar/gkm658] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Structural and genetic studies on prokaryotic ribosomes have provided important insights into fundamental aspects of protein synthesis and translational control and its interaction with ribosomal drugs. Comparable mechanistic studies in eukaryotes are mainly hampered by the absence of both high-resolution crystal structures and efficient genetic models. To study the interaction of aminoglycoside antibiotics with selected eukaryotic ribosomes, we replaced the bacterial drug binding site in 16S rRNA with its eukaryotic counterpart, resulting in bacterial hybrid ribosomes with a fully functional eukaryotic rRNA decoding site. Cell-free translation assays demonstrated that hybrid ribosomes carrying the rRNA decoding site of higher eukaryotes show pronounced resistance to aminoglycoside antibiotics, equivalent to that of rabbit reticulocyte ribosomes, while the decoding sites of parasitic protozoa show distinctive drug susceptibility. Our findings suggest that phylogenetically variable components of the ribosome, other than the rRNA-binding site, do not affect aminoglycoside susceptibility of the protein-synthesis machinery. The activities of the hybrid ribosomes indicate that helix 44 of the rRNA decoding site behaves as an autonomous domain, which can be exchanged between ribosomes of different phylogenetic domains for study of function.
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Affiliation(s)
- Sven N Hobbie
- Institut für Medizinische Mikrobiologie, Universität Zürich and Laboratorium für Organische Chemie, ETH Zürich, Switzerland.
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79
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Abstract
The ribosome is responsible for protein synthesis, the translation of the genetic code, in all living organisms. Ribosomes are composed of RNA (ribosomal RNA) and protein (ribosomal protein). Soluble protein factors bind to the ribosome and facilitate different phases of translation. Genetic approaches have proved useful for the identification and characterization of the structural and functional roles of specific nucleotides in ribosomal RNA and of specific amino acids in ribosomal proteins and in ribosomal factors. This chapter summarizes examples of mutations identified in ribosomal RNA, ribosomal proteins, and ribosomal factors.
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MESH Headings
- Animals
- Base Sequence
- DNA Mutational Analysis
- Humans
- Mutation
- Nucleic Acid Conformation
- Peptide Elongation Factors/genetics
- Peptide Initiation Factors/genetics
- Peptide Termination Factors/genetics
- Protein Subunits/genetics
- RNA, Ribosomal, 16S/analysis
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/physiology
- RNA, Ribosomal, 23S/analysis
- RNA, Ribosomal, 23S/chemistry
- RNA, Ribosomal, 23S/physiology
- Ribosomal Proteins/genetics
- Ribosomes/genetics
- Sequence Analysis, RNA
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Affiliation(s)
- Kathleen L Triman
- Department of Biology, Franklin and Marshall College, Lancaster, PA 17604, USA
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80
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Hanessian S, Szychowski J, Adhikari SS, Vasquez G, Kandasamy P, Swayze EE, Migawa MT, Ranken R, François B, Wirmer-Bartoschek J, Kondo J, Westhof E. Structure-based design, synthesis, and A-site rRNA cocrystal complexes of functionally novel aminoglycoside antibiotics: C2" ether analogues of paromomycin. J Med Chem 2007; 50:2352-69. [PMID: 17458946 DOI: 10.1021/jm061200+] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A series of 2"-O-substituted ether analogues of paromomycin were prepared based on new site-selective functionalizations. X-ray cocrystal complexes of several such analogues revealed a new mode of binding in the A-site rRNA, whereby rings I and II adopted the familiar orientation and position previously observed with paromomycin, but rings III and IV were oriented differently. With few exceptions, all of the new analogues showed potent inhibitory activity equal or better than paromomycin against a sensitive strain of S. aureus. Single digit microM MIC values were obtained against E. coli, with some of the ether appendages containing polar or basic end groups. Two analogues showed excellent survival rate in a mouse septicemia protection assay. Preliminary histopathological analysis of the kidney showed no overt signs of toxicity, while controls with neomycin and kanamycin were toxic at lower doses.
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Affiliation(s)
- Stephen Hanessian
- Department of Chemistry, Université de Montréal, C. P. 6128, Succ. Centre-Ville, Montréal, P. Q., Canada.
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81
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Zhou Y, Gregor VE, Ayida BK, Winters GC, Sun Z, Murphy D, Haley G, Bailey D, Froelich JM, Fish S, Webber SE, Hermann T, Wall D. Synthesis and SAR of 3,5-diamino-piperidine derivatives: novel antibacterial translation inhibitors as aminoglycoside mimetics. Bioorg Med Chem Lett 2007; 17:1206-10. [PMID: 17188860 PMCID: PMC1858661 DOI: 10.1016/j.bmcl.2006.12.024] [Citation(s) in RCA: 105] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2006] [Revised: 12/05/2006] [Accepted: 12/07/2006] [Indexed: 11/16/2022]
Abstract
Aminoglycoside antibiotics target an internal RNA loop within the bacterial ribosomal decoding site. Here, we describe the synthesis and SAR of novel 3,5-diamino-piperidine derivatives as aminoglycoside mimetics, and show they act as inhibitors of bacterial translation and growth.
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Affiliation(s)
- Yuefen Zhou
- Anadys Pharmaceuticals, Inc., San Diego, USA
| | | | | | | | | | | | - Greg Haley
- Anadys Pharmaceuticals, Inc., San Diego, USA
| | | | | | - Sarah Fish
- Anadys Pharmaceuticals, Inc., San Diego, USA
| | | | | | - Daniel Wall
- Anadys Pharmaceuticals, Inc., San Diego, USA
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82
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Ironmonger A, Whittaker B, Baron AJ, Clique B, Adams CJ, Ashcroft AE, Stockley PG, Nelson A. Scanning conformational space with a library of stereo- and regiochemically diverse aminoglycoside derivatives: the discovery of new ligands for RNA hairpin sequences. Org Biomol Chem 2007; 5:1081-6. [PMID: 17377661 PMCID: PMC7612281 DOI: 10.1039/b618683a] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A library of stereo- and regiochemically diverse aminoglycoside derivatives was screened at 1 microM using surface plasmon resonance (SPR) against RNA hairpin models of the bacterial A-site, and the HIV viral TAR and RRE sequences. In order to double the stereochemical diversity of the library, the compounds were screened against both enantiomers of each of these sequences. Remarkably, this initial screen suggested that the same four aminoglycoside derivatives bound most tightly to all three of the RNAs, suggesting that these compounds were good RNA binders which, nonetheless, discriminated poorly between the RNA sequences. The interactions between selected isomeric aminoglycoside derivatives and the RNA hairpins were then studied in more detail using an SPR assay. Three isomeric tight-binding aminoglycoside derivatives, which had been identified from the initial screen, were found to bind more tightly to the RNA hairpins (with K(D) values in the range 0.23 to 4.7 microM) than a fourth isomeric derivative (which had K(D) values in the range 6.0 to 30 microM). The magnitude of the tightest RNA-aminoglycoside interactions stemmed, in large part, from remarkably slow dissociation of the aminoglycosides from the RNA targets. The three tight-binding aminoglycoside derivatives were found, however, to discriminate rather poorly between alternative RNA sequences with, at best, around a twenty-fold difference in affinity for alternative RNA hairpin sequences. Within the aminoglycoside derivative library studied, high affinity for an RNA target was not accompanied by good discrimination between alternative RNA sequences.
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Affiliation(s)
- Alan Ironmonger
- School of Chemistry, University of Leeds, Leeds, UK LS2 9JT
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK LS2 9JT
| | - Benjamin Whittaker
- School of Chemistry, University of Leeds, Leeds, UK LS2 9JT
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK LS2 9JT
| | - Andrew J. Baron
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK LS2 9JT
| | - Blandine Clique
- School of Chemistry, University of Leeds, Leeds, UK LS2 9JT
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK LS2 9JT
| | - Chris J. Adams
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK LS2 9JT
| | - Alison E. Ashcroft
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK LS2 9JT
| | - Peter G. Stockley
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK LS2 9JT
| | - Adam Nelson
- School of Chemistry, University of Leeds, Leeds, UK LS2 9JT
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK LS2 9JT
- Corresponding author:
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83
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Tam VK, Kwong D, Tor Y. Fluorescent HIV-1 Dimerization Initiation Site: design, properties, and use for ligand discovery. J Am Chem Soc 2007; 129:3257-66. [PMID: 17319662 PMCID: PMC2525870 DOI: 10.1021/ja0675797] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The HIV-1 Dimerization Initiation Site (DIS) is an intriguing, yet underutilized, viral RNA target for potential antiretroviral therapy. To study the recognition features of this target and to provide a quantitative, rapid, and real-time tool for the discovery of new binders, a fluorescence-based assay has been constructed. It relies on strategic incorporation of 2-aminopurine, an isosteric fluorescent adenosine analogue, into short hairpin RNA constructs. These oligomers self-associate to form a kissing loop that thermally rearranges into a more stable extended duplex, thereby mimicking the association and structural features of the native RNA sequence. We demonstrate the ability of two fluorescent DIS constructs, DIS272(2AP) and DIS273(2AP), to report the binding of known DIS binders via changes in their emission intensity. Binding of aminoglycosides such as paromomycin to DIS272(2AP) results in significant fluorescence enhancement, while ligand binding to DIS273(2AP) results in fluorescence quenching. These observations are rationalized by comparison to the sequence-analogous bacterial A-site, where the relative emission of the fluorescent probe is dependent on the placement of the flexible purine residues inside or outside the helical domain. Analysis of binding isotherms generated using DIS272(2AP) yields submicromolar EC50 values for paromomycin (0.5 +/- 0.2 microM) and neomycin B (0.6 +/- 0.2 microM). Other neomycin-family aminoglycosides are less potent binders with neamine, the core pharmacophore, displaying the lowest affinity of 21 +/- 1 microM. Screening of additional aminoglycosides and their derivatives led to the discovery of new, previously unreported, aminoglycoside binders of the HIV DIS RNA, among them butirosin A (5.5 +/- 0.6 microM) and apramycin (7.6 +/- 1.0 microM). A conformationally constrained neomycin B analogue displays a rather high affinity to the DIS (1.9 +/- 0.2 microM). Among a series of nucleobase aminoglycoside conjugates, only the uracil derivatives display a measurable affinity using this assay with EC50 values in the 2 microM range. In addition, similarity between the solution behavior of HIV-1 DIS and the bacterial decoding A-site has been observed, particularly with respect to the intra- and extra-helical residence of the conformationally flexible A residues within the bulge. Taken together, the observations reported here shed light on the solution behavior of this important RNA target and are likely to facilitate the design of new DIS selective ligands as potential antiretroviral agents.
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84
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Kudyba I, Fernandez DP, Böttger EC, Vasella A. Synthesis of paromomycin derivatives modified at C(5″) to selectively target bacterial rRNA. Carbohydr Res 2007; 342:499-519. [PMID: 17049499 DOI: 10.1016/j.carres.2006.09.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2006] [Revised: 09/18/2006] [Accepted: 09/18/2006] [Indexed: 10/24/2022]
Abstract
The furanosyl moiety (ring III) of C(6')-deoxyparomomycin and paromomycin was modified in search of aminoglycoside antibiotics with altered selectivity. The key intermediates were the N-Boc-protected derivative of C(6')-deoxyparomomycin and the benzylidene-protected paromomycin. Their H(2)C(5'')-OH group was oxidised with trichlorocyanuric acid or [bis(acetoxy)iodo]benzene in the presence of catalytic amounts of TEMPO to yield the corresponding aldehydes and acids, which were transformed into the protected alkoxy imines, amides and the amine. Standard deprotection gave the title compounds derived from C(6')-deoxyparomomycin and derived from paromomycin that proved less active than paromomycin and its C(6')-deoxy analogue.
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Affiliation(s)
- Iwona Kudyba
- Laboratorium für Organische Chemie, ETH Zürich, HCI, CH-8093 Zürich, Switzerland
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85
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Hanessian S, Adhikari S, Szychowski J, Pachamuthu K, Wang X, Migawa MT, Griffey RH, Swayze EE. Probing the ribosomal RNA A-site with functionally diverse analogues of paromomycin—synthesis of ring I mimetics. Tetrahedron 2007. [DOI: 10.1016/j.tet.2006.10.079] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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86
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Yang G, Trylska J, Tor Y, McCammon JA. Binding of aminoglycosidic antibiotics to the oligonucleotide A-site model and 30S ribosomal subunit: Poisson-Boltzmann model, thermal denaturation, and fluorescence studies. J Med Chem 2006; 49:5478-90. [PMID: 16942021 DOI: 10.1021/jm060288o] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The binding of paromomycin and similar antibiotics to the oligonucleotide A-site model and the small (30S) ribosomal subunit has been studied using continuum electrostatics methods. Crystallographic information from complexes of paromomycin, tobramycin, and Geneticin bound to an A-site oligonucleotide, and paromomycin and streptomycin complexed to the 30S subunit was used as a foundation to develop structures of similar antibiotics in the same ribosomal binding site. Relative binding free energies were calculated by combining the electrostatic contribution, which was obtained by solving the Poisson-Boltzmann equation, with a surface-area-dependent apolar term and contributions from conformational changes. These computed results showed good correlation with the experimental data resulting from fluorescence binding assays and thermal denaturation studies, demonstrating the ability of the Poisson-Boltzmann model to provide insight into the electrostatic mechanisms for aminoglycoside binding and direction for designing more effective antibiotics.
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Affiliation(s)
- Grace Yang
- Department of Chemistry and Biochemistry, University of California-San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA
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87
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Han Q, Zhao Q, Fish S, Simonsen KB, Vourloumis D, Froelich JM, Wall D, Hermann T. Molecular recognition by glycoside pseudo base pairs and triples in an apramycin-RNA complex. Angew Chem Int Ed Engl 2006; 44:2694-2700. [PMID: 15849690 DOI: 10.1002/anie.200500028] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Qing Han
- Department of Structural Chemistry, Anadys Pharmaceuticals, Inc. 3115 Merryfield Row, San Diego, CA 92121, USA, Fax: (+1) 858-527-1539
| | - Qiang Zhao
- Department of Structural Chemistry, Anadys Pharmaceuticals, Inc. 3115 Merryfield Row, San Diego, CA 92121, USA, Fax: (+1) 858-527-1539
| | - Sarah Fish
- Department of Structural Chemistry, Anadys Pharmaceuticals, Inc. 3115 Merryfield Row, San Diego, CA 92121, USA, Fax: (+1) 858-527-1539
| | - Klaus B Simonsen
- Department of Medicinal Chemistry, Anadys Pharmaceuticals, Inc., USA
- Current address: H. Lundbeck A/S, Copenhagen Valby, Denmark
| | | | | | - Daniel Wall
- Department of Microbiology, Anadys Pharmaceuticals, Inc., USA
| | - Thomas Hermann
- Department of Structural Chemistry, Anadys Pharmaceuticals, Inc. 3115 Merryfield Row, San Diego, CA 92121, USA, Fax: (+1) 858-527-1539
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88
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Hobbie SN, Pfister P, Bruell C, Sander P, François B, Westhof E, Böttger EC. Binding of neomycin-class aminoglycoside antibiotics to mutant ribosomes with alterations in the A site of 16S rRNA. Antimicrob Agents Chemother 2006; 50:1489-96. [PMID: 16569869 PMCID: PMC1426975 DOI: 10.1128/aac.50.4.1489-1496.2006] [Citation(s) in RCA: 53] [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
Aminoglycoside antibiotics that bind to the aminoacyl-tRNA site (A site) of the ribosome are composed of a common neamine core in which a glycopyranosyl ring is attached to position 4 of a 2-deoxystreptamine moiety. The core is further substituted by one (ribostamycin), two (neomycin and paromomycin), or three (lividomycin A) additional sugars attached to position 5 of the 2-deoxystreptamine. To study the role of rings III, IV, and V in aminoglycoside binding, we used isogenic Mycobacterium smegmatis DeltarrnB mutants carrying homogeneous populations of mutant ribosomes with alterations in the 16S rRNA A site. MICs were determined to investigate drug-ribosome interactions, and the results were compared with that of the previously published crystal structure of paromomycin bound to the ribosomal A site. Our analysis demonstrates that the stacking interaction between ring I and G1491 is largely sequence independent, that rings III and IV each increase the strength of drug binding to the ribosome, that ring IV of the 6'-NH3+ aminoglycosides compensates for loss of interactions between ring II and U1495 and between ring III and G1491, that the aminoglycosides rely on pseudo-base pairing between ring I and A1408 for binding independently of the number of sugar rings attached to the neamine core, that addition of ring V to the 6'-OH 4,5-aminoglycoside paromomycin does not alter the mode of binding, and that alteration of the U1406.U1495 wobble base pair to the Watson-Crick interaction pair 1406C-1495G yields ribosomal drug susceptibilities to 4,5-aminoglycosides comparable to those seen with the wild-type A site.
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Affiliation(s)
- Sven N Hobbie
- Institut für Medizinische Mikrobiologie, Universität Zürich, Gloriastr. 30/32, CH-8006 Zürich, Switzerland.
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89
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Böttger EC. The ribosome as a drug target. Trends Biotechnol 2006; 24:145-7. [PMID: 16490268 DOI: 10.1016/j.tibtech.2006.02.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2005] [Revised: 01/30/2006] [Accepted: 02/10/2006] [Indexed: 11/26/2022]
Abstract
The elucidation of the crystal structure of the ribosome and its subunits has dramatically increased our understanding of this organelle and the molecular interactions that determine its functional capabilities. Two recent publications, one on the structure of the bacterial ribosome at 3.5A resolution and one on the identification of functionally relevant sites within the small subunit rRNA, illustrate the importance of interdisciplinary approaches in exploiting the ribosome as a drug target.
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Affiliation(s)
- Erik C Böttger
- Institut für Medizinische Mikrobiologie, Universität Zürich, Gloriastrasse 30/32, CH-8006, Switzerland.
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90
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Hobbie SN, Pfister P, Brüll C, Westhof E, Böttger EC. Analysis of the contribution of individual substituents in 4,6-aminoglycoside-ribosome interaction. Antimicrob Agents Chemother 2006; 49:5112-8. [PMID: 16304180 PMCID: PMC1315939 DOI: 10.1128/aac.49.12.5112-5118.2005] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The 4,6-disubstituted 2-deoxystreptamines interfere with protein biosynthesis by specifically targeting the ribosomal A site. These drugs show subtle variations in the chemical groups of rings I, II, and III. In the present study we used site-directed mutagenesis to generate mutant strains of Mycobacterium smegmatis mc(2)155 SMR5 DeltarrnB with mutations in its single rRNA allele, rrnA. This genetic procedure gives rise to strains carrying homogeneous populations of mutant ribosomes and was used to study the contribution of individual chemical substituents to the binding of 4,6-disubstituted aminoglycosides. X-ray crystal structures of geneticin and tobramycin complexed to oligonucleotides containing the minimal bacterial ribosomal A site were used for interpretation of MICs determined for a panel of 4,6-aminoglycosides, including tobramycin, kanamycin A, kanamycin B, amikacin, gentamicin, and geneticin. Surprisingly, the considerable differences present within ring III did not seem to alter the interaction of the drug with the ribosome, as determined by site-directed mutagenesis of the A site. In contrast, subtle variations in ring I significantly influenced binding: (i) a 4'-hydroxyl moiety participates in the proper drug target interaction; and (ii) a 2'-amino group contributes an additional positive charge to ring I, making the drug less susceptible to any kind of sequence alteration within the decoding site, most notably, to conformational changes induced by transversion of U1495 to 1495A. The 4-amino-2-hydroxyl-1-oxobutyl extension at position 1 of ring II of amikacin provides an additional anchor and renders amikacin less dependent on the structural conformation of nucleotide U1406 compared to the dependencies of other kanamycins. Overall, the set of interactions forming the complex between drug substituents and nucleotides of the A site constitutes a network in which the interactions can partly compensate for each other when they are disrupted.
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Affiliation(s)
- Sven N Hobbie
- Institut für Medizinische Mikrobiologie, Universität Zürich, Gloriastr. 30/32, CH-8006 Zürich, Switzerland
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91
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Abstract
Crystal structures of complexes between ribosomal particles and antibiotics have pinned down very precisely the discrete binding sites of several classes of antibiotics inhibiting protein synthesis. The crystal structures of complexes between various antibiotics and ribosomal particles show definitively that ribosomal RNAs (rRNAs), rather than ribosomal proteins, are overwhelmingly targeted. The antibiotics are found at messenger RNA or transfer RNA binding sites and, most importantly, at pivot locations that are key for the structural rearrangements during the molecular mechanical steps in initiation, elongation, or termination of protein synthesis. We focus here on the 30S particle. Structurally, the antibiotics interact in many ways with RNA: (i) only with the phosphate groups (streptomycin); (ii) mainly with bases (hygromycin, spectinomycin); (iii) with a mixture of both (paromomycin, Geneticin); (iv) via magnesium ions (tetracycline) or a protein side chain (streptomycin). The antibiotics can mimic base stacking (pactamycin) or form pseudo-base pairing interactions with ribosomal bases (paromomycin and related aminoglycosides). Resistance strategies (mutations or methylations in rRNA or enzymatic modifications of the antibiotics) can generally be understood on the basis of the intermolecular contacts made between the antibiotics and rRNA residues in the crystal structures. In humans, toxicity of ribosomal antibiotics is most likely due, at least in part, to the sensitivity of mitochondrial ribosomes, since mitochondria evolved from a bacterial ancestor. Antibiotic families (e.g., aminoglycosides) form a set of invariant H-bonds to defined rRNA residues. When such residues are conserved in bacteria, but not in eukaryotes, resistance of eukaryotic ribosomes is observed. The structural knowledge, together with comparative genomic analysis, should allow for the development of new broad-spectrum antibiotics with higher selectivity toward bacterial ribosomes and less toxicity on eukaryotic cytoplasmic and mitochondrial ribosomes.
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Affiliation(s)
- Julia Wirmer
- Biologie Moléculaire et Cellulaire du CNRS, Université Louis Pasteur, Strasbourg, France
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92
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Ennifar E, Paillart JC, Bodlenner A, Walter P, Weibel JM, Aubertin AM, Pale P, Dumas P, Marquet R. Targeting the dimerization initiation site of HIV-1 RNA with aminoglycosides: from crystal to cell. Nucleic Acids Res 2006; 34:2328-39. [PMID: 16679451 PMCID: PMC1458285 DOI: 10.1093/nar/gkl317] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The kissing-loop complex that initiates dimerization of genomic RNA is crucial for Human Immunodeficiency Virus Type 1 (HIV-1) replication. We showed that owing to its strong similitude with the bacterial ribosomal A site it can be targeted by aminoglycosides. Here, we present its crystal structure in complex with neamine, ribostamycin, neomycin and lividomycin. These structures explain the specificity for 4,5-disubstituted 2-deoxystreptamine (DOS) derivatives and for subtype A and subtype F kissing-loop complexes, and provide a strong basis for rational drug design. As a consequence of the different topologies of the kissing-loop complex and the A site, these aminoglycosides establish more contacts with HIV-1 RNA than with 16S RNA. Together with biochemical experiments, they showed that while rings I, II and III confer binding specificity, rings IV and V are important for affinity. Binding of neomycin, paromomycin and lividomycin strongly stabilized the kissing-loop complex by bridging the two HIV-1 RNA molecules. Furthermore, in situ footprinting showed that the dimerization initiation site (DIS) of HIV-1 genomic RNA could be targeted by these aminoglycosides in infected cells and virions, demonstrating its accessibility.
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Affiliation(s)
- Eric Ennifar
- UPR 9002 du CNRS conventionnée à l'Université Louis Pasteur, IBMC15 rue René Descartes, 67084, Strasbourg cedex, France
| | - Jean-Christophe Paillart
- UPR 9002 du CNRS conventionnée à l'Université Louis Pasteur, IBMC15 rue René Descartes, 67084, Strasbourg cedex, France
| | - Anne Bodlenner
- UMR 7123 CNRS—Université Louis Pasteur, Institut Le Bel4 rue Blaise Pascal, BP 1032/F, 67070, Strasbourg cedex, France
| | - Philippe Walter
- UPR 9002 du CNRS conventionnée à l'Université Louis Pasteur, IBMC15 rue René Descartes, 67084, Strasbourg cedex, France
| | - Jean-Marc Weibel
- UMR 7123 CNRS—Université Louis Pasteur, Institut Le Bel4 rue Blaise Pascal, BP 1032/F, 67070, Strasbourg cedex, France
| | - Anne-Marie Aubertin
- UMR 544 INSERM—Université Louis Pasteur, Institut de Virologie3 rue Koberlé, 67000 Strasbourg, France
| | - Patrick Pale
- UMR 7123 CNRS—Université Louis Pasteur, Institut Le Bel4 rue Blaise Pascal, BP 1032/F, 67070, Strasbourg cedex, France
| | - Philippe Dumas
- UPR 9002 du CNRS conventionnée à l'Université Louis Pasteur, IBMC15 rue René Descartes, 67084, Strasbourg cedex, France
- To whom correspondence should be addressed. Tel: +33388417002; Fax: +33388602218;
| | - Roland Marquet
- UPR 9002 du CNRS conventionnée à l'Université Louis Pasteur, IBMC15 rue René Descartes, 67084, Strasbourg cedex, France
- Correspondence may also be addressed to Roland Marquet. Tel: +33388417054; Fax: +33388602218;
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93
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94
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Pathak R, Böttger E, Vasella A. Design and Synthesis of Aminoglycoside Antibiotics to Selectively Target 16S Ribosomal RNA Position 1408. Helv Chim Acta 2005. [DOI: 10.1002/hlca.200590240] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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95
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François B, Szychowski J, Adhikari SS, Pachamuthu K, Swayze EE, Griffey RH, Migawa MT, Westhof E, Hanessian S. Antibacterial aminoglycosides with a modified mode of binding to the ribosomal-RNA decoding site. Angew Chem Int Ed Engl 2005; 43:6735-8. [PMID: 15593140 DOI: 10.1002/anie.200462092] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Boris François
- Institut de biologie moléculaire et cellulaire UPR9002 CNRS, Université Louis Pasteur, 15 rue René Descartes, 67084 Strasbourg Cedex, France
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96
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François B, Russell RJM, Murray JB, Aboul-ela F, Masquida B, Vicens Q, Westhof E. Crystal structures of complexes between aminoglycosides and decoding A site oligonucleotides: role of the number of rings and positive charges in the specific binding leading to miscoding. Nucleic Acids Res 2005; 33:5677-90. [PMID: 16214802 PMCID: PMC1251667 DOI: 10.1093/nar/gki862] [Citation(s) in RCA: 280] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2005] [Revised: 09/07/2005] [Accepted: 09/07/2005] [Indexed: 01/07/2023] Open
Abstract
The crystal structures of six complexes between aminoglycoside antibiotics (neamine, gentamicin C1A, kanamycin A, ribostamycin, lividomycin A and neomycin B) and oligonucleotides containing the decoding A site of bacterial ribosomes are reported at resolutions between 2.2 and 3.0 A. Although the number of contacts between the RNA and the aminoglycosides varies between 20 and 31, up to eight direct hydrogen bonds between rings I and II of the neamine moiety are conserved in the observed complexes. The puckered sugar ring I is inserted into the A site helix by stacking against G1491 and forms a pseudo base pair with two H-bonds to the Watson-Crick sites of the universally conserved A1408. This central interaction helps to maintain A1492 and A1493 in a bulged-out conformation. All these structures of the minimal A site RNA complexed to various aminoglycosides display crystal packings with intermolecular contacts between the bulging A1492 and A1493 and the shallow/minor groove of Watson-Crick pairs in a neighbouring helix. In one crystal, one empty A site is observed. In two crystals, two aminoglycosides are bound to the same A site with one bound specifically and the other bound in various ways in the deep/major groove at the edge of the A sites.
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Affiliation(s)
- Boris François
- Institut de biologie moléculaire et cellulaire du CNRS, UPR9002 ‘Architecture et Réactivité de l'ARN’, Université Louis PasteurF-67084 Strasbourg, France
- Vernalis (R&D)Granta Park, Cambridge, CB1 6GB, UK
| | | | | | | | - Benoît Masquida
- Institut de biologie moléculaire et cellulaire du CNRS, UPR9002 ‘Architecture et Réactivité de l'ARN’, Université Louis PasteurF-67084 Strasbourg, France
- Vernalis (R&D)Granta Park, Cambridge, CB1 6GB, UK
| | - Quentin Vicens
- Institut de biologie moléculaire et cellulaire du CNRS, UPR9002 ‘Architecture et Réactivité de l'ARN’, Université Louis PasteurF-67084 Strasbourg, France
- Vernalis (R&D)Granta Park, Cambridge, CB1 6GB, UK
| | - Eric Westhof
- To whom correspondence should be addressed. Tel: +33388417046; Fax: +33388601822;
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97
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Beringer M, Bruell C, Xiong L, Pfister P, Bieling P, Katunin VI, Mankin AS, Böttger EC, Rodnina MV. Essential mechanisms in the catalysis of peptide bond formation on the ribosome. J Biol Chem 2005; 280:36065-72. [PMID: 16129670 DOI: 10.1074/jbc.m507961200] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Peptide bond formation is the main catalytic function of the ribosome. The mechanism of catalysis is presumed to be highly conserved in all organisms. We tested the conservation by comparing mechanistic features of the peptidyl transfer reaction on ribosomes from Escherichia coli and the Gram-positive bacterium Mycobacterium smegmatis. In both cases, the major contribution to catalysis was the lowering of the activation entropy. The rate of peptide bond formation was pH independent with the natural substrate, amino-acyl-tRNA, but was slowed down 200-fold with decreasing pH when puromycin was used as a substrate analog. Mutation of the conserved base A2451 of 23 S rRNA to U did not abolish the pH dependence of the reaction with puromycin in M. smegmatis, suggesting that A2451 did not confer the pH dependence. However, the A2451U mutation alters the structure of the peptidyl transferase center and changes the pattern of pH-dependent rearrangements, as probed by chemical modification of 23 S rRNA. A2451 seems to function as a pivot point in ordering the structure of the peptidyl transferase center rather than taking part in chemical catalysis.
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Affiliation(s)
- Malte Beringer
- Institute of Physical Biochemistry, University of Witten/Herdecke, Stockumer Strasse 10, 58448 Witten, Germany
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98
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Hermann T. Drugs targeting the ribosome. Curr Opin Struct Biol 2005; 15:355-66. [PMID: 15919197 DOI: 10.1016/j.sbi.2005.05.001] [Citation(s) in RCA: 144] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2005] [Revised: 01/31/2005] [Accepted: 05/04/2005] [Indexed: 11/30/2022]
Abstract
Several classes of clinically important antibiotics target the bacterial ribosome, where they interfere with microbial protein synthesis. Structural studies of the interaction of antibiotics with the ribosome have revealed that these small molecules recognize predominantly the rRNA components. Over the past two years, three-dimensional structures of ribosome-antibiotic complexes have been determined, providing a detailed picture of the binding sites and mechanism of action of antibacterials, including 'blockbuster' drugs such as the macrolides. Structure-based approaches have come to fruition that comprise the design and crystal structure analysis of novel semi-synthetic antibiotics that target the ribosome decoding site.
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Affiliation(s)
- Thomas Hermann
- Department of Structural Chemistry, Anadys Pharmaceuticals Inc, 3115 Merryfield Row, San Diego, CA 92121, USA.
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99
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Busscher GF, Rutjes FPJT, van Delft FL. 2-Deoxystreptamine: central scaffold of aminoglycoside antibiotics. Chem Rev 2005; 105:775-91. [PMID: 15755076 DOI: 10.1021/cr0404085] [Citation(s) in RCA: 119] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Guuske F Busscher
- IMM Organic Chemistry, Radboud University Nijmegen, Toernooiveld 1, 6525 ED Nijmegen, The Netherlands
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100
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Han Q, Zhao Q, Fish S, Simonsen KB, Vourloumis D, Froelich JM, Wall D, Hermann T. Molecular Recognition by Glycoside Pseudo Base Pairs and Triples in an Apramycin-RNA Complex. Angew Chem Int Ed Engl 2005. [DOI: 10.1002/ange.200500028] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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