51
|
Khade PK, Shi X, Joseph S. Steric complementarity in the decoding center is important for tRNA selection by the ribosome. J Mol Biol 2013; 425:3778-89. [PMID: 23542008 DOI: 10.1016/j.jmb.2013.02.038] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Revised: 02/23/2013] [Accepted: 02/27/2013] [Indexed: 11/27/2022]
Abstract
Accurate tRNA selection by the ribosome is essential for the synthesis of functional proteins. Previous structural studies indicated that the ribosome distinguishes between cognate and near-cognate tRNAs by monitoring the geometry of the codon-anticodon helix in the decoding center using the universally conserved 16S ribosomal RNA bases G530, A1492 and A1493. These bases form hydrogen bonds with the 2'-hydroxyl groups of the codon-anticodon helix, which are expected to be disrupted with a near-cognate codon-anticodon helix. However, a recent structural study showed that G530, A1492 and A1493 form hydrogen bonds in a manner identical with that of both cognate and near-cognate codon-anticodon helices. To understand how the ribosome discriminates between cognate and near-cognate tRNAs, we made 2'-deoxynucleotide and 2'-fluoro substituted mRNAs, which disrupt the hydrogen bonds between the A site codon and G530, A1492 and A1493. Our results show that multiple 2'-deoxynucleotide substitutions in the mRNA substantially inhibit tRNA selection, whereas multiple 2'-fluoro substitutions in the mRNA have only modest effects on tRNA selection. Furthermore, the miscoding antibiotics paromomycin and streptomycin rescue the defects in tRNA selection with the multiple 2'-deoxynucleotide substituted mRNA. These results suggest that steric complementarity in the decoding center is more important than the hydrogen bonds between the A site codon and G530, A1492 and A1493 for tRNA selection.
Collapse
Affiliation(s)
- Prashant K Khade
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0314, USA
| | | | | |
Collapse
|
52
|
Jia X, Zhang J, Sun W, He W, Jiang H, Chen D, Murchie AIH. Riboswitch control of aminoglycoside antibiotic resistance. Cell 2013; 152:68-81. [PMID: 23332747 DOI: 10.1016/j.cell.2012.12.019] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2012] [Revised: 06/04/2012] [Accepted: 12/13/2012] [Indexed: 12/23/2022]
Abstract
The majority of riboswitches are regulatory RNAs that regulate gene expression by binding small-molecule metabolites. Here we report the discovery of an aminoglycoside-binding riboswitch that is widely distributed among antibiotic-resistant bacterial pathogens. This riboswitch is present in the leader RNA of the resistance genes that encode the aminoglycoside acetyl transferase (AAC) and aminoglycoside adenyl transferase (AAD) enzymes that confer resistance to aminoglycoside antibiotics through modification of the drugs. We show that expression of the AAC and AAD resistance genes is regulated by aminoglycoside binding to a secondary structure in their 5' leader RNA. Reporter gene expression, direct measurements of drug RNA binding, chemical probing, and UV crosslinking combined with mutational analysis demonstrate that the leader RNA functions as an aminoglycoside-sensing riboswitch in which drug binding to the leader RNA leads to the induction of aminoglycosides antibiotic resistance.
Collapse
Affiliation(s)
- Xu Jia
- Key Laboratory of Molecular Medicine, the Ministry of Education, Department of Biochemistry and Molecular Biology, Fudan University Shanghai Medical College, Shanghai 200032, China
| | | | | | | | | | | | | |
Collapse
|
53
|
The impact of aminoglycosides on the dynamics of translation elongation. Cell Rep 2013; 3:497-508. [PMID: 23416053 DOI: 10.1016/j.celrep.2013.01.027] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2012] [Revised: 11/18/2012] [Accepted: 01/22/2013] [Indexed: 11/21/2022] Open
Abstract
Inferring antibiotic mechanisms on translation through static structures has been challenging, as biological systems are highly dynamic. Dynamic single-molecule methods are also limited to few simultaneously measurable parameters. We have circumvented these limitations with a multifaceted approach to investigate three structurally distinct aminoglycosides that bind to the aminoacyl-transfer RNA site (A site) in the prokaryotic 30S ribosomal subunit: apramycin, paromomycin, and gentamicin. Using several single-molecule fluorescence measurements combined with structural and biochemical techniques, we observed distinct changes to translational dynamics for each aminoglycoside. While all three drugs effectively inhibit translation elongation, their actions are structurally and mechanistically distinct. Apramycin does not displace A1492 and A1493 at the decoding center, as demonstrated by a solution nuclear magnetic resonance structure, causing only limited miscoding; instead, it primarily blocks translocation. Paromomycin and gentamicin, which displace A1492 and A1493, cause significant miscoding, block intersubunit rotation, and inhibit translocation. Our results show the power of combined dynamics, structural, and biochemical approaches to elucidate the complex mechanisms underlying translation and its inhibition.
Collapse
|
54
|
Ultrastructural cell wall characteristics of clinical gentamycin-resistant Staphylococcus aureus isolates. Med Mol Morphol 2013; 46:70-6. [PMID: 23338781 DOI: 10.1007/s00795-013-0009-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2012] [Accepted: 03/26/2012] [Indexed: 10/27/2022]
Abstract
The frequent use of gentamycin (GM) ointment for the treatment of skin infections has led to an increase in the number of GM-resistant clinical isolates of Staphylococcus aureus. We examined the ultrastructural characteristics of 14 clinical strains of S. aureus by transmission electron microscopy. Seven of these isolates were GM-resistant, and seven isolates were GM-sensitive. We found that the cell wall of GM-resistant strains (32.24 ± 5.99 nm) was significantly thicker than that of GM-sensitive strains (19.02 ± 2.72 nm). We genetically characterized these isolates by polymerase chain reaction, targeting the genes for three aminoglycoside-modifying enzymes, aac(6')-aph(2''), aph(3')-III, and ant(4')-I. All GM-resistant strains tested carried the gene encoding aac(6')-aph(2''). However, we were unable to establish a link between a specific gene and cell wall thickening, because one GM-resistant strain was also positive for aph(3')-III. We also demonstrated that a GM-resistant mutant strain, derived in vitro from a GM-sensitive S. aureus parent strain (209P), also exhibited a thickened cell wall. These results strongly suggest that a thickened cell wall is a common ultrastructural characteristic of GM-resistant S. aureus clinical strains.
Collapse
|
55
|
Novel nucleotide changes in mutational analysis of mitochondrial 12SrRNA gene in patients with nonsyndromic and aminoglycoside-induced hearing loss. Mol Biol Rep 2012; 40:2689-95. [PMID: 23242658 DOI: 10.1007/s11033-012-2355-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2012] [Accepted: 12/09/2012] [Indexed: 10/27/2022]
Abstract
Mitochondria have essential role in cellular energy metabolism and defects in their function lead to many metabolic diseases. Mitochondrial DNA (mtDNA) mutations have been associated with number diseases such as nonsyndromic and aminoglycoside-induced hearing loss. Mutational screening of entire 12SrRNA and tRNA (ser (UCN)) genes in 107 unrelated Iranian patients with amino glycoside-induced and nonsyndromic bilateral hearing loss by direct sequencing analysis method were performed. Twenty different homoplasmic sequence variants were identified; including fifteen common polymorphisms, two putatively pathogenic variants: m.921T>C and m.1005T>C, one 12SrRNA sequence variant m.739C>T and two nucleotides substitution; m.1245T>C and m.1545T>C. Deafness-associated mutation, m.1555A>G, was not found. In our patients we found the mutation 1005 was associated with R haplogroup. These finding show that m.1555A>G mutation is not important in our population. Nucleotide change, m.739C>T, previously reported with very low frequency. We suggested the variation of two nucleotides 1245 and 1545 that localized at conserved site of 12SrRNA may be new candidate for amino glycoside-induced and nonsyndromic hearing impairment associated mutations. However, aminoglycoside exposure is a risk factor for clinical phenotype appearance of these mutations.
Collapse
|
56
|
Kim H, Lee MK, Ko J, Park CJ, Kim M, Jeong Y, Hong S, Varani G, Choi BS. Aminoglycoside antibiotics bind to the influenza A virus RNA promoter. MOLECULAR BIOSYSTEMS 2012; 8:2857-9. [PMID: 22990985 DOI: 10.1039/c2mb25333j] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Aminoglycosides bind to the influenza A virus promoter (vRNA) at submicromolar concentration. The complex structure between the vRNA and neomycin illustrates that binding of neomycin causes a conformational change which would affect further transcription processes. Thus, aminoglycosides represent lead compounds for the discovery of antiviral therapeutics against influenza A virus.
Collapse
Affiliation(s)
- Henna Kim
- Department of Chemistry, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 305-701, Korea
| | | | | | | | | | | | | | | | | |
Collapse
|
57
|
Blaha GM, Polikanov YS, Steitz TA. Elements of ribosomal drug resistance and specificity. Curr Opin Struct Biol 2012; 22:750-8. [PMID: 22981944 DOI: 10.1016/j.sbi.2012.07.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Revised: 07/19/2012] [Accepted: 07/19/2012] [Indexed: 10/27/2022]
Abstract
The structures of ribosomes in complex with inhibitors of translation have not only shed light on the interactions of antibiotics with the ribosome but also on the underlying mechanisms by which they interfere with the ribosome function. Several recent papers [1(•),2(••),3,4] have correlated the available ribosome structures with the wealth of biochemical data [5(•)]. In this review we shall focus on the lessons learned for drug specificity rather than presenting a comprehensive survey of the known structures of ribosome complexes with antibiotics.
Collapse
Affiliation(s)
- Gregor M Blaha
- Department of Biochemistry, University of California, Riverside, CA 92521, USA
| | | | | |
Collapse
|
58
|
Wang L, Pulk A, Wasserman MR, Feldman MB, Altman RB, Cate JHD, Blanchard SC. Allosteric control of the ribosome by small-molecule antibiotics. Nat Struct Mol Biol 2012; 19:957-63. [PMID: 22902368 PMCID: PMC3645490 DOI: 10.1038/nsmb.2360] [Citation(s) in RCA: 103] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Accepted: 07/13/2012] [Indexed: 12/15/2022]
Abstract
Protein synthesis is targeted by numerous, chemically distinct antibiotics that bind and inhibit key functional centers of the ribosome. Using single-molecule imaging and X-ray crystallography, we show that the aminoglycoside neomycin blocks aminoacyl-transfer RNA (aa-tRNA) selection and translocation as well as ribosome recycling by binding to helix 69 (H69) of 23S ribosomal RNA within the large subunit of the Escherichia coli ribosome. There, neomycin prevents the remodeling of intersubunit bridges that normally accompanies the process of subunit rotation to stabilize a partially rotated ribosome configuration in which peptidyl (P)-site tRNA is constrained in a previously unidentified hybrid position. Direct measurements show that this neomycin-stabilized intermediate is incompatible with the translation factor binding that is required for distinct protein synthesis reactions. These findings reveal the functional importance of reversible intersubunit rotation to the translation mechanism and shed new light on the allosteric control of ribosome functions by small-molecule antibiotics.
Collapse
MESH Headings
- Anti-Bacterial Agents/chemistry
- Anti-Bacterial Agents/pharmacology
- Crystallography, X-Ray
- Escherichia coli/chemistry
- Escherichia coli/drug effects
- Escherichia coli/metabolism
- Escherichia coli Proteins/metabolism
- Models, Molecular
- Neomycin/chemistry
- Neomycin/pharmacology
- Protein Biosynthesis/drug effects
- RNA, Bacterial/chemistry
- RNA, Bacterial/metabolism
- RNA, Ribosomal/chemistry
- RNA, Ribosomal/metabolism
- RNA, Transfer, Amino Acyl/metabolism
- Ribosome Subunits, Large, Bacterial/chemistry
- Ribosome Subunits, Large, Bacterial/drug effects
- Ribosome Subunits, Large, Bacterial/metabolism
- Ribosome Subunits, Small, Bacterial/chemistry
- Ribosome Subunits, Small, Bacterial/drug effects
- Ribosome Subunits, Small, Bacterial/metabolism
Collapse
Affiliation(s)
- Leyi Wang
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York, USA
| | | | | | | | | | | | | |
Collapse
|
59
|
Fair RJ, Hensler ME, Thienphrapa W, Dam QN, Nizet V, Tor Y. Selectively guanidinylated aminoglycosides as antibiotics. ChemMedChem 2012; 7:1237-44. [PMID: 22639134 PMCID: PMC3383777 DOI: 10.1002/cmdc.201200150] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2012] [Indexed: 11/07/2022]
Abstract
The emergence of virulent, drug-resistant bacterial strains coupled with a minimal output of new pharmaceutical agents to combat them makes this a critical time for antibacterial research. Aminoglycosides are a well-studied, highly potent class of naturally occurring antibiotics with scaffolds amenable to modification, and therefore, they provide an excellent starting point for the development of semisynthetic, next-generation compounds. To explore the potential of this approach, we synthesized a small library of aminoglycoside derivatives selectively and minimally modified at one or two positions with a guanidine group replacing the corresponding amine or hydroxy functionality. Most guanidino-aminoglycosides showed increased affinity for the ribosomal decoding rRNA site, the cognate biological target of the natural products, when compared with their parent antibiotics, as measured by an in vitro fluorescence resonance energy transfer (FRET) A-site binding assay. Additionally, certain analogues showed improved minimum inhibitory concentration (MIC) values against resistant bacterial strains, including methicillin-resistant Staphylococcus aureus (MRSA). An amikacin derivative holds particular promise with activity greater than or equal to the parent antibiotic in the majority of bacterial strains tested.
Collapse
Affiliation(s)
- Richard J. Fair
- Department of Chemistry & Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093 (USA)
| | - Mary E. Hensler
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093 (USA)
| | - Wdee Thienphrapa
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093 (USA)
| | - Quang N. Dam
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093 (USA)
| | - Victor Nizet
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093 (USA)
| | - Yitzhak Tor
- Department of Chemistry & Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093 (USA)
| |
Collapse
|
60
|
Charles I, Davis E, Arya DP. Efficient stabilization of phosphodiester (PO), phosphorothioate (PS), and 2'-O-methoxy (2'-OMe) DNA·RNA hybrid duplexes by amino sugars. Biochemistry 2012; 51:5496-505. [PMID: 22639785 DOI: 10.1021/bi3004507] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Antisense strategies that target DNA·RNA hybrid structures offer potential for the development of new therapeutic drugs. The α-sarcin loop region of the 23S [corrected] rRNA domain has been shown to be a high value target for such strategies. Herein, aminoglycoside interaction with three RNA·DNA α-sarcin targeted duplexes (rR·dY, rR·S-dY, and rR·2'OMe-rY) have been investigated to determine the overall effect of aminoglycoside interaction on the stability, affinity, and conformation of these hybrid duplexes. To this end, UV thermal denaturation, circular dichroism spectroscopy, fluorescence intercalator displacement, and ITC as well as DSC calorimetry experiments were carried out. The results suggest the following. (1) Of all the aminoglycosides studied, neomycin confers the highest thermal stability on all three hybrid duplexes studied. (2) There is no appreciable difference in aminoglycoside-induced thermal stability between the unmodified rR·dY and phophorothioate modified rR·S-dY duplexes. (3) The rR·2'OMe-rY duplexes thermal stability is slightly less than the other two hybrids. (4) In all three duplexes, aminoglycoside-induced thermal stability decreased as the number of amino groups decreased. (5) CD scans revealed similar spectra for the rR·dY and rR·S-dY duplexes as well as a more pronounced A-form signal for the rR·2'OMe-rY duplex. (6) FID assays paralleled the CD results, yielding similar affinity values between the rR·dY and rR·S-dY duplexes and higher affinities with the rR·2'OMe-rY duplex. (7) The overall affinity trend between aminoglycosides and the three duplexes was determined to be neomycin > paromomycin > neamine > ribostamycin. (8) ITC K(a) values revealed similar binding constants for the rR·dY and rR·S-dY duplexes with rR·dY having a K(1) of (1.03 ± 0.58) × 10(7) M(-1) and K(2) of (1.13 ± 0.07) × 10(5) M(-1) while rR·S-dY produced a K(1) of (1.17 ± 0.54) × 10(7) M(-1) and K(2) of (1.27 ± 0.69) × 10(5) M(-1). (8) The rR·2'OMe-rY produced a slightly higher binding constant values with a K(1) of (1.25 ± 0.24) × 10(7) M(-1) and K(2) of (3.62 ± 0.18) × 10(5) M(-1). (9) The ΔT(m)-derived K(Tm) of 3.81 × 10(7) M(-1) for rR·S-dY was in relative agreement with the corresponding K(1) of 1.17 × 10(7) M(-1) derived constant from the fitted ITC. These results illustrate that the increased DNA·RNA hybrid duplex stability in the presence of aminoglycosides can help extend the roles of aminoglycosides in designing modified ODNs for targeting RNA.
Collapse
Affiliation(s)
- I Charles
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, South Carolina 29634, United States
| | | | | |
Collapse
|
61
|
Hariprasad G, Kumar M, Rani K, Kaur P, Srinivasan A. Aminoglycoside induced nephrotoxicity: molecular modeling studies of calreticulin-gentamicin complex. J Mol Model 2011; 18:2645-52. [DOI: 10.1007/s00894-011-1289-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2011] [Accepted: 10/20/2011] [Indexed: 12/11/2022]
|
62
|
Mechanisms of aminoglycoside ototoxicity and targets of hair cell protection. Int J Otolaryngol 2011; 2011:937861. [PMID: 22121370 PMCID: PMC3202092 DOI: 10.1155/2011/937861] [Citation(s) in RCA: 267] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2011] [Accepted: 08/18/2011] [Indexed: 01/14/2023] Open
Abstract
Aminoglycosides are commonly prescribed antibiotics with deleterious side effects to the inner ear. Due to their popular application as a result of their potent antimicrobial activities, many efforts have been undertaken to prevent aminoglycoside ototoxicity. Over the years, understanding of the antimicrobial as well as ototoxic mechanisms of aminoglycosides has increased. These mechanisms are reviewed in regard to established and potential future targets of hair cell protection.
Collapse
|
63
|
Galimand M, Schmitt E, Panvert M, Desmolaize B, Douthwaite S, Mechulam Y, Courvalin P. Intrinsic resistance to aminoglycosides in Enterococcus faecium is conferred by the 16S rRNA m5C1404-specific methyltransferase EfmM. RNA (NEW YORK, N.Y.) 2011; 17:251-262. [PMID: 21159796 PMCID: PMC3022275 DOI: 10.1261/rna.2233511] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2010] [Accepted: 11/04/2010] [Indexed: 05/29/2023]
Abstract
Aminoglycosides are ribosome-targeting antibiotics and a major drug group of choice in the treatment of serious enterococcal infections. Here we show that aminoglycoside resistance in Enterococcus faecium strain CIP 54-32 is conferred by the chromosomal gene efmM, encoding the E. faecium methyltransferase, as well as by the previously characterized aac(6')-Ii that encodes a 6'-N-aminoglycoside acetyltransferase. Inactivation of efmM in E. faecium increases susceptibility to the aminoglycosides kanamycin and tobramycin, and, conversely, expression of a recombinant version of efmM in Escherichia coli confers resistance to these drugs. The EfmM protein shows significant sequence similarity to E. coli RsmF (previously called YebU), which is a 5-methylcytidine (m⁵C) methyltransferase modifying 16S rRNA nucleotide C1407. The target for EfmM is shown by mass spectrometry to be a neighboring 16S rRNA nucleotide at C1404. EfmM uses the methyl group donor S-adenosyl-L-methionine to catalyze formation of m⁵C1404 on the 30S ribosomal subunit, whereas naked 16S rRNA and the 70S ribosome are not substrates. Addition of the 5-methyl to C1404 sterically hinders aminoglycoside binding. Crystallographic structure determination of EfmM at 2.28 Å resolution reveals an N-terminal domain connected to a central methyltransferase domain that is linked by a flexible lysine-rich region to two C-terminal subdomains. Mutagenesis of the methyltransferase domain established that two cysteines at specific tertiary locations are required for catalysis. The tertiary structure of EfmM is highly similar to that of RsmF, consistent with m⁵C formation at adjacent sites on the 30S subunit, while distinctive structural features account for the enzymes' respective specificities for nucleotides C1404 and C1407.
Collapse
Affiliation(s)
- Marc Galimand
- Unité des Agents Antibactériens, Institut Pasteur, F-75724 Paris Cedex 15, France.
| | | | | | | | | | | | | |
Collapse
|
64
|
McCoy LS, Xie Y, Tor Y. Antibiotics that target protein synthesis. WILEY INTERDISCIPLINARY REVIEWS-RNA 2010; 2:209-32. [DOI: 10.1002/wrna.60] [Citation(s) in RCA: 95] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
|
65
|
Guan MX. Mitochondrial 12S rRNA mutations associated with aminoglycoside ototoxicity. Mitochondrion 2010; 11:237-45. [PMID: 21047563 DOI: 10.1016/j.mito.2010.10.006] [Citation(s) in RCA: 105] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2010] [Revised: 08/31/2010] [Accepted: 10/19/2010] [Indexed: 11/18/2022]
Abstract
The mitochondrial 12S rRNA is a hot spot for mutations associated with both aminoglycoside-induced and nonsyndromic hearing loss. Of those, the homoplasmic 1555A>G and 1494C>T mutations at the highly conserved decoding region of the 12S rRNA have been associated with hearing loss worldwide. In particular, these two mutations account for a significant number of cases of aminoglycoside ototoxicity. The 1555A>G or 1494C>T mutation is expected to form a novel 1494C-G1555 or 1494U-A1555 base-pair at the highly conserved A-site of 12S rRNA. These transitions make the human mitochondrial ribosomes more bacteria-like and alter binding sites for aminoglycosides. As a result, the exposure to aminoglycosides can induce or worsen hearing loss in individuals carrying one of these mutations. Biochemical characterization demonstrated an impairment of mitochondrial protein synthesis and subsequent defects in respiration in cells carrying the A1555G or 1494C>T mutation. Furthermore, a wide range of severity, age-at-onset and penetrance of hearing loss was observed within and among families carrying these mutations. Nuclear modifier genes, mitochondrial haplotypes and aminoglycosides should modulate the phenotypic manifestation of the 12S rRNA 1555A>G and 1494C>T mutations. Therefore, these data provide valuable information and technology: (1) to predict which individuals are at risk for ototoxicity; (2) to improve the safety of aminoglycoside antibiotic therapy; and (3) eventually to decrease the incidence of hearing loss.
Collapse
Affiliation(s)
- Min-Xin Guan
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229-3039, USA.
| |
Collapse
|
66
|
Torres EM, Dephoure N, Panneerselvam A, Tucker CM, Whittaker CA, Gygi SP, Dunham MJ, Amon A. Identification of aneuploidy-tolerating mutations. Cell 2010; 143:71-83. [PMID: 20850176 DOI: 10.1016/j.cell.2010.08.038] [Citation(s) in RCA: 300] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2010] [Revised: 06/14/2010] [Accepted: 08/03/2010] [Indexed: 10/19/2022]
Abstract
Aneuploidy causes a proliferative disadvantage in all normal cells analyzed to date, yet this condition is associated with a disease characterized by unabated proliferative potential, cancer. The mechanisms that allow cancer cells to tolerate the adverse effects of aneuploidy are not known. To probe this question, we identified aneuploid yeast strains with improved proliferative abilities. Their molecular characterization revealed strain-specific genetic alterations as well as mutations shared between different aneuploid strains. Among the latter, a loss-of-function mutation in the gene encoding the deubiquitinating enzyme Ubp6 improves growth rates in four different aneuploid yeast strains by attenuating the changes in intracellular protein composition caused by aneuploidy. Our results demonstrate the existence of aneuploidy-tolerating mutations that improve the fitness of multiple different aneuploidies and highlight the importance of ubiquitin-proteasomal degradation in suppressing the adverse effects of aneuploidy.
Collapse
Affiliation(s)
- Eduardo M Torres
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | | | | | | | | | | | | |
Collapse
|
67
|
Scheunemann AE, Graham WD, Vendeix FAP, Agris PF. Binding of aminoglycoside antibiotics to helix 69 of 23S rRNA. Nucleic Acids Res 2010; 38:3094-105. [PMID: 20110260 PMCID: PMC2875026 DOI: 10.1093/nar/gkp1253] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Aminoglycosides antibiotics negate dissociation and recycling of the bacterial ribosome’s subunits by binding to Helix 69 (H69) of 23S rRNA. The differential binding of various aminoglycosides to the chemically synthesized terminal domains of the Escherichia coli and human H69 has been characterized using spectroscopy, calorimetry and NMR. The unmodified E. coli H69 hairpin exhibited a significantly higher affinity for neomycin B and tobramycin than for paromomycin (Kds = 0.3 ± 0.1, 0.2 ± 0.2 and 5.4 ± 1.1 µM, respectively). The binding of streptomycin was too weak to assess. In contrast to the E. coli H69, the human 28S rRNA H69 had a considerable decrease in affinity for the antibiotics, an important validation of the bacterial target. The three conserved pseudouridine modifications (Ψ1911, Ψ1915, Ψ1917) occurring in the loop of the E. coli H69 affected the dissociation constant, but not the stoichiometry for the binding of paromomycin (Kd = 2.6 ± 0.1 µM). G1906 and G1921, observed by NMR spectrometry, figured predominantly in the aminoglycoside binding to H69. The higher affinity of the E. coli H69 for neomycin B and tobramycin, as compared to paromomycin and streptomycin, indicates differences in the efficacy of the aminoglycosides.
Collapse
Affiliation(s)
- Ann E Scheunemann
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695-7622, USA
| | | | | | | |
Collapse
|
68
|
Aminoglycoside activity observed on single pre-translocation ribosome complexes. Nat Chem Biol 2009; 6:54-62. [PMID: 19946275 DOI: 10.1038/nchembio.274] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2009] [Accepted: 10/06/2009] [Indexed: 11/08/2022]
Abstract
Aminoglycoside-class antibiotics bind directly to ribosomal RNA, imparting pleiotropic effects on ribosome function. Despite in-depth structural investigations of aminoglycoside-RNA oligonucleotide and aminoglycoside-ribosome interactions, mechanisms explaining the unique ribosome inhibition profiles of chemically similar aminoglycosides remain elusive. Here, using single-molecule fluorescence resonance energy transfer (smFRET) methods, we show that high-affinity aminoglycoside binding to the conserved decoding site region of the functional pre-translocation ribosome complex specifically remodels the nature of intrinsic dynamic processes within the particle. The extents of these effects, which are distinct for each member of the aminoglycoside class, strongly correlate with their inhibition of EF-G-catalyzed translocation. Neomycin, a 4,5-linked aminoglycoside, binds with lower affinity to one or more secondary binding sites, mediating distinct structural and dynamic perturbations that further enhance translocation inhibition. These new insights help explain why closely related aminoglycosides elicit pleiotropic translation activities and demonstrate the potential utility of smFRET as a tool for dissecting the mechanisms of antibiotic action.
Collapse
|
69
|
Qian Y, Guan MX. Interaction of aminoglycosides with human mitochondrial 12S rRNA carrying the deafness-associated mutation. Antimicrob Agents Chemother 2009; 53:4612-8. [PMID: 19687236 PMCID: PMC2772318 DOI: 10.1128/aac.00965-08] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2008] [Revised: 11/12/2008] [Accepted: 08/12/2009] [Indexed: 11/20/2022] Open
Abstract
The mitochondrial 12S rRNA A1555G mutation is one of the important causes of aminoglycoside-induced and nonsyndromic hearing loss. Here we employed an RNA-directed chemical-modification approach to understanding the pathogenesis of aminoglycoside-induced hearing loss. The patterns of chemical modification of RNA oligonucleotides carrying the A1555G mutation by dimethyl sulfate (DMS) were distinct from those of the RNA oligonucleotides carrying wild-type sequence in the presence of aminoglycosides. In the RNA analogue carrying the A1555G mutation, reduced reactivity to DMS occurred in base G1555 as well as in bases C1556 and A1553 in the presence of paromomycin, neomycin, gentamicin, kanamycin, tobramycin, or streptomycin. In particular, base G1555 exhibited marked but similar levels of protection in the presence of 0.1 microM to 100 microM neomycin, gentamicin, or kanamycin. In contrast, the levels of protection in base G1555 appeared to be correlated with the concentration of paromycin, tobramycin, or streptomycin. Furthermore, increasing reactivities to DMS in the presence of these aminoglycosides were observed for bases A1492, C1493, C1494, and A1557 in the RNA analogue carrying the A1555G mutation. These data suggested that the A1555G mutation altered the binding properties of aminoglycosides at the A site of 12S rRNA and led to local conformational changes in 12S rRNA carrying the A1555G mutation. The interaction between aminoglycosides and 12S rRNA carrying the A1555G mutation provides new insight into the pathogenesis of aminoglycoside ototoxicity.
Collapse
Affiliation(s)
- Yaping Qian
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Min-Xin Guan
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio
| |
Collapse
|
70
|
|
71
|
|
72
|
Zietse R, Zoutendijk R, Hoorn EJ. Fluid, electrolyte and acid–base disorders associated with antibiotic therapy. Nat Rev Nephrol 2009; 5:193-202. [DOI: 10.1038/nrneph.2009.17] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
73
|
Schmitt E, Galimand M, Panvert M, Courvalin P, Mechulam Y. Structural bases for 16 S rRNA methylation catalyzed by ArmA and RmtB methyltransferases. J Mol Biol 2009; 388:570-82. [PMID: 19303884 DOI: 10.1016/j.jmb.2009.03.034] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2009] [Revised: 03/04/2009] [Accepted: 03/13/2009] [Indexed: 10/21/2022]
Abstract
Aminoglycosides are used extensively for the treatment of severe infections due to Gram-negative bacteria. However, certain species have become highly resistant after acquisition of genes for methyltransferases which catalyze post-transcriptional methylation of N7-G1405 in 16 S rRNA of 30 S ribosomal subunits. Inactivation of this enzymatic activity is therefore an important challenge for development of an effective therapy. The present work describes the crystallographic structures of methyltransferases RmtB and ArmA from clinical isolates. Together with biochemical experiments, the 3D structures indicate that the N-terminal domain specific for this family of methyltransferases is required for enzymatic activity. Site-directed mutagenesis has enabled important residues for catalysis and RNA binding to be identified. These high-resolution structures should underpin the design of potential inhibitors of these enzymes, which could be used to restore the activity of aminoglycosides against resistant pathogens.
Collapse
Affiliation(s)
- Emmanuelle Schmitt
- Laboratoire de Biochimie, Ecole Polytechnique, Centre National de la Recherche Scientifique, Palaiseau Cedex, France.
| | | | | | | | | |
Collapse
|
74
|
Abstract
The faithful and rapid translation of genetic information into peptide sequences is an indispensable property of the ribosome. The mechanistic understanding of strategies used by the ribosome to achieve both speed and fidelity during translation results from nearly a half century of biochemical and structural studies. Emerging from these studies is the common theme that the ribosome uses local as well as remote conformational switches to govern induced-fit mechanisms that ensure accuracy in codon recognition during both tRNA selection and translation termination.
Collapse
|
75
|
Shoji S, Walker SE, Fredrick K. Ribosomal translocation: one step closer to the molecular mechanism. ACS Chem Biol 2009; 4:93-107. [PMID: 19173642 DOI: 10.1021/cb8002946] [Citation(s) in RCA: 98] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Protein synthesis occurs in ribosomes, the targets of numerous antibiotics. How these large and complex machines read and move along mRNA have proven to be challenging questions. In this Review, we focus on translocation, the last step of the elongation cycle in which movement of tRNA and mRNA is catalyzed by elongation factor G. Translocation entails large-scale movements of the tRNAs and conformational changes in the ribosome that require numerous tertiary contacts to be disrupted and reformed. We highlight recent progress toward elucidating the molecular basis of translocation and how various antibiotics influence tRNA-mRNA movement.
Collapse
Affiliation(s)
| | | | - Kurt Fredrick
- Department of Microbiology
- Center for RNA Biology
- Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio 43210
| |
Collapse
|
76
|
Bindu LH, Reddy PP. Genetics of aminoglycoside-induced and prelingual non-syndromic mitochondrial hearing impairment: a review. Int J Audiol 2009; 47:702-7. [PMID: 19031229 DOI: 10.1080/14992020802215862] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Pathogenic mitochondrial DNA mutations are most often implicated in inherited and acquired hearing impairment. The current review mainly focuses on the 12S rRNA mitochondrial gene mutations associated with non-syndromic deafness without or after aminoglycosides exposure. Aminoglycoside-induced and nonsyndromic deafness has been shown to have a genetic susceptibility and the pathogenic mitochondrial 12S rRNA A1555G mutation was identified as the primary factor underlying the hearing loss in many familial as well as in genetically unrelated cases, particularly in Asian populations where aminoglycoside antibiotics are commonly used even for minor infections. Many families were shown to transmit the aminoglycoside ototoxicity through matrilineal inheritance and the A1555G mutation in the 12S rRNA gene was frequently identified. The aminoglycoside antibiotics are believed to target the mitochondrial ribosome in the cochlea resulting in abnormal RNA processing or decreased efficiency of translation thereby leading to irreversible auditory dysfunction. Such cases may have a genetic predisposition to aminoglycoside ototoxicity following autosomal dominant, autosomal recessive, X-linked, or mitochondrial pattern of inheritance.
Collapse
Affiliation(s)
- L Hema Bindu
- Department of Environmental Toxicology, Institute of Genetics and Hospital for Genetic Diseases, Osmania University, Hyderabad, India
| | | |
Collapse
|
77
|
Belousoff MJ, Graham B, Spiccia L, Tor Y. Cleavage of RNA oligonucleotides by aminoglycosides. Org Biomol Chem 2008; 7:30-3. [PMID: 19081939 DOI: 10.1039/b813252f] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A number of aminoglycoside antibiotics, and in particular neomycin B, are demonstrated to promote strand cleavage of RNA oligonucleotides (minimised HIV-1 TAR element and prokaryotic ribosomal A-site), by binding and causing sufficient distortion to the RNA backbone to render it more susceptible to intramolecular transesterification.
Collapse
|
78
|
Kren V, Rezanka T. Sweet antibiotics - the role of glycosidic residues in antibiotic and antitumor activity and their randomization. FEMS Microbiol Rev 2008; 32:858-89. [PMID: 18647177 DOI: 10.1111/j.1574-6976.2008.00124.x] [Citation(s) in RCA: 141] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
A large number of antibiotics are glycosides. In numerous cases the glycosidic residues are crucial to their activity; sometimes, glycosylation only improves their pharmacokinetic parameters. Recent developments in molecular glycobiology have improved our understanding of aglycone vs. glycoside activities and made it possible to develop new, more active or more effective glycodrugs based on these findings - a very illustrative recent example is vancomycin. The majority of attention has been devoted to glycosidic antibiotics including their past, present, and probably future position in antimicrobial therapy. The role of the glycosidic residue in the biological activity of glycosidic antibiotics, and the attendant targeting and antibiotic selectivity mediated by glycone and aglycone in antibiotics some antitumor agents is discussed here in detail. Chemical and enzymatic modifications of aglycones in antibiotics, including their synthesis, are demonstrated on various examples, with particular emphasis on the role of specific and mutant glycosyltransferases and glycorandomization in the preparation of these compounds. The last section of this review describes and explains the interactions of the glycone moiety of the antibiotics with DNA and especially the design and structure-activity relationship of glycosidic antibiotics, including their classification based on their aglycone and glycosidic moiety. The new enzymatic methodology 'glycorandomization' enabled the preparation of glycoside libraries and opened up new ways to prepare optimized or entirely novel glycoside antibiotics.
Collapse
Affiliation(s)
- Vladimír Kren
- Centre of Biocatalysis and Biotransformation, Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic.
| | | |
Collapse
|
79
|
Liu >X, Angeli S, Ouyang X, Liu W, Ke X, Liu Y, Liu S, Du L, Deng X, Yuan H, Yan D. Audiological and genetic features of the mtDNA mutations. Acta Otolaryngol 2008; 128:732-8. [PMID: 18568513 DOI: 10.1080/00016480701719011] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
CONCLUSIONS Significant difference in the incidence of mitochondrial DNA (mtDNA) mutations was found between the Chinese and USA populations. The identification of the mtDNA A1555G mutation in a large proportion of Chinese probands with nonsyndromic sensorineural hearing loss (NSHL) provides a molecular explanation for the high prevalence of aminoglycoside-induced deafness in China. OBJECTIVE The aim was to characterize the audiological and genetic features of NSHL due to mutations in mtDNA. SUBJECTS AND METHODS The mtDNA and audiogram analyses were performed in 498 NSHL patients (290 from China and 208 from the USA) with and without history of aminoglycoside exposure. A PCR and restriction enzyme digestion protocol was used for mutational screening and the European Workshop on Genetic Hearing Loss criteria were applied for audiological classification. RESULTS All Chinese probands (15.5%) with mtDNA mutation were found to carry the homoplasmic mtDNA A1555G mutation, whereas four probands (1.9%) from the USA were found to carry the mtDNA A1555G and two (1%) had mtDNA G7444A. Approximately 63% of the probands with mtDNA mutations had post-lingual hearing loss and 56.8% of them had a medical history of exposure to aminoglycosides. Hearing losses are bilateral, sensorineural, and symmetric. The main audiogram shapes found were sloping.
Collapse
|
80
|
Balenci D, Bernardi F, Cellai L, D'Amelio N, Gaggelli E, Gaggelli N, Molteni E, Valensin G. Effect of Cu(II) on the complex between kanamycin A and the bacterial ribosomal A site. Chembiochem 2008; 9:114-23. [PMID: 18058790 DOI: 10.1002/cbic.200700387] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The solution structure of kanamycin A interacting with a ribosomal A-site fragment was solved by transferred-NOE techniques and found to agree with the structure of the complex observed in the crystal. Despite the fast exchange conditions found for the interaction, the bound form was identified by NOESY spectroscopy. At 600 MHz, NOE effects are only observed for the RNA-associated antibiotic. Dissociation constants were measured by NMR spectroscopy for two sites of interaction (K(d1)=150+/-40 microM; K(d2)=360+/-50 microM). Furthermore, the effects of the Cu(II) ion on the antibiotic, on the RNA fragment that mimics the bacterial ribosomal A site, and on the complex formed between these two entities were analyzed. The study led to the proposal of a model that localizes the copper ion within the kanamycin-RNA complex.
Collapse
Affiliation(s)
- Duccio Balenci
- Department of Chemistry, University of Siena, Via A. Moro, 53100 Siena, Italy
| | | | | | | | | | | | | | | |
Collapse
|
81
|
Barbault F, Ren B, Rebehmed J, Teixeira C, Luo Y, Smila-Castro O, Maurel F, Fan B, Zhang L, Zhang L. Flexible computational docking studies of new aminoglycosides targeting RNA 16S bacterial ribosome site. Eur J Med Chem 2007; 43:1648-56. [PMID: 18096272 DOI: 10.1016/j.ejmech.2007.10.022] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2007] [Revised: 10/08/2007] [Accepted: 10/11/2007] [Indexed: 10/22/2022]
Abstract
Ribonucleic acids (RNAs) have only recently been viewed as a target for small-molecules drug discovery. Aminoglycoside compounds are antibiotics which bind the ribosomal A site (16S fragment) and cause misreading of the bacterial genetic code and inhibit translocation. In this work, a complete molecular modeling study is done for 16 newly derived aminoglycoside compounds where diverse nucleoside fragments are linked. Docking calculations are applied to 16S RNA target and a weak linear correlation, between experimental and calculated data, is obtained. However, one particularity of RNA is its high flexibility. To mimic this behavior, all docking calculations are followed by small molecular dynamic simulations. This last computational step improves significantly the correlation with experimental data and allowed us to establish structure-activity relationships. The overall results showed that the consideration of the RNA dynamic behavior is of great interest.
Collapse
Affiliation(s)
- Florent Barbault
- ITODYS, Université Paris Diderot, CNRS UMR 7086, 1 rue Guy de la Brosse, 75005 Paris, France.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
82
|
Périchon B, Courvalin P, Galimand M. Transferable resistance to aminoglycosides by methylation of G1405 in 16S rRNA and to hydrophilic fluoroquinolones by QepA-mediated efflux in Escherichia coli. Antimicrob Agents Chemother 2007; 51:2464-9. [PMID: 17470656 PMCID: PMC1913276 DOI: 10.1128/aac.00143-07] [Citation(s) in RCA: 180] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Plasmid pIP1206 was detected in Escherichia coli strain 1540 during the screening of clinical isolates of Enterobacteriaceae for high-level resistance to aminoglycosides. The sequence of this IncFI conjugative plasmid of ca. 100 kb was partially determined. pIP1206 carried the rmtB gene for a ribosome methyltransferase that was shown to modify the N7 position of nucleotide G1405, located in the A site of 16S rRNA. It also contained the qepA (quinolone efflux pump) gene that encodes a 14-transmembrane-segment putative efflux pump belonging to the major facilitator superfamily of proton-dependent transporters. Disruption of membrane proton potential by the efflux pump inhibitor carbonyl cyanide m-chlorophenylhydrazone in a transconjugant harboring the qepA gene resulted in elevation of norfloxacin accumulation. The transporter conferred resistance to the hydrophilic quinolones norfloxacin and ciprofloxacin.
Collapse
Affiliation(s)
- Bruno Périchon
- Unité des Agents Antibactériens, Institut Pasteur, 75724 Paris Cedex 15, France
| | | | | |
Collapse
|
83
|
Charles I, Xi H, Arya DP. Sequence-specific targeting of RNA with an oligonucleotide-neomycin conjugate. Bioconjug Chem 2007; 18:160-9. [PMID: 17226969 DOI: 10.1021/bc060249r] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The synthesis of neomycin covalently attached at the C5-position of 2'-deoxyuridine is reported. The synthesis outlined allows for incorporation of an aminoglycoside (neomycin) at any given site in an oligonucleotide (ODN) where a thymidine (or uridine) is present. Incorporation of this modified base into an oligonucleotide, which is complementary to a seven-bases-long alpha-sarcin loop RNA sequence, leads to enhanced duplex hybridization. The increase in Tm for this duplex (DeltaTm = 6 degrees C) suggests a favorable interaction of neomycin within the duplex groove. CD spectroscopy shows that the modified duplex adopts an A-type confirmation. ITC measurements indicate the additive effects of ODN and neomycin binding to the RNA target (Ka = 4.5 x 107 M-1). The enhanced stability of the hybrid duplex from this neomycin-ODN conjugate originates primarily from the enthalpic contribution of neomycin {DeltaDeltaHobs = -7.21 kcal/mol (DeltaHneomycin conjugated - DeltaH nonconjugated)} binding to the hybrid duplex. The short linker length allows for selective stabilization of the hybrid duplex over the hybrid triplex. The results described here open up new avenues in the design and synthesis of nucleo-aminoglycoside-conjugates (N-Ag-C) where the inclusion of any number of aminoglycoside (neomycin) molecules per oligonucleotide can be accomplished.
Collapse
Affiliation(s)
- Irudayasamy Charles
- Laboratories of Medicinal Chemistry, Clemson University, Clemson, South Carolina 29634, USA
| | | | | |
Collapse
|
84
|
Affiliation(s)
- Stephen Hanessian
- Department of Chemistry, Université de Montréal, C.P. 6128, Succursale Centre-Ville, Montréal, QC, H3C3J7, Canada.
| |
Collapse
|
85
|
|
86
|
Xin L, Pu D, Deliang H, Huijun Y, Weiming L, Fei Y, Xin Z, Dongyang K, Juyang C, Weiyan Y, Dongyi H, Zhengce J, Minxin G. Mitochondrial DNA A1555G mutation screening using a testing kit method and its significance in preventing aminoglycoside-related hearing loss. J Otol 2006. [DOI: 10.1016/s1672-2930(06)50011-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
|
87
|
Dai P, Liu X, Han D, Qian Y, Huang D, Yuan H, Li W, Yu F, Zhang R, Lin H, He Y, Yu Y, Sun Q, Qin H, Li R, Zhang X, Kang D, Cao J, Young WY, Guan MX. Extremely low penetrance of deafness associated with the mitochondrial 12S rRNA mutation in 16 Chinese families: Implication for early detection and prevention of deafness. Biochem Biophys Res Commun 2006; 340:194-9. [PMID: 16375862 DOI: 10.1016/j.bbrc.2005.11.156] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2005] [Accepted: 11/23/2005] [Indexed: 11/21/2022]
Abstract
Mutations in mitochondrial DNA (mtDNA) have been found to be associated with sensorineural hearing loss. We report here the clinical, genetic, and molecular characterization of 16 Chinese pedigrees (a total of 246 matrilineal relatives) with aminoglycoside-induced impairment. Clinical evaluation revealed the variable phenotype of hearing impairment including audiometric configuration in these subjects, although these subjects share some common features: being bilateral and sensorineural hearing impairment. Strikingly, these Chinese pedigrees exhibited extremely low penetrance of hearing loss, ranging from 4% to 18%, with an average of 8%. In particular, nineteen of 246 matrilineal relatives in these pedigrees had aminoglycoside-induced hearing loss. Mutational analysis of the mtDNA in these pedigrees showed the presence of homoplasmic 12S rRNA A1555G mutation, which has been associated with hearing impairment in many families worldwide. The extremely low penetrance of hearing loss in these Chinese families carrying the A1555G mutation strongly supports the notion that the A1555G mutation itself is not sufficient to produce the clinical phenotype. Children carrying the A1555G mutation are susceptible to the exposure of aminoglycosides, thereby inducing or worsening hearing impairment, as in the case of these Chinese families. Using those genetic and molecular approaches, we are able to diagnose whether children carry the ototoxic mtDNA mutation. Therefore, these data have been providing valuable information and technology to predict which individuals are at risk for ototoxicity, to improve the safety of aminoglycoside therapy, and eventually to decrease the incidence of deafness.
Collapse
Affiliation(s)
- Pu Dai
- Department of Otolaryngology, Chinese PLA General Hospital, Beijing, China
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
88
|
Fahlman RP, Olejniczak M, Uhlenbeck OC. Quantitative analysis of deoxynucleotide substitutions in the codon-anticodon helix. J Mol Biol 2005; 355:887-92. [PMID: 16343529 DOI: 10.1016/j.jmb.2005.11.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2005] [Revised: 11/01/2005] [Accepted: 11/03/2005] [Indexed: 10/25/2022]
Abstract
The role of 2' hydroxyl groups in the codon-anticodon helix was evaluated by introducing single deoxynucleotides into each of the six positions in the helix and measuring the affinity of tRNA to either the A site or the P site of Escherichia coli 70S ribosomes. In perfect agreement with the X-ray structure of the Thermus thermophilus 30S subunit, A site binding was weaker in five of the six positions but P site binding was unaffected. Since the addition of paromomycin restores A site binding, it appears that the deoxynucleotide substituted complexes are impaired in their ability to promote the ribosomal conformational change that accompanies tRNA binding.
Collapse
Affiliation(s)
- Richard P Fahlman
- Department of Biochemistry, Molecular Biology, Cell Biology, Northwestern University, Evanston, IL 60208, USA
| | | | | |
Collapse
|
89
|
Galimand M, Sabtcheva S, Courvalin P, Lambert T. Worldwide disseminated armA aminoglycoside resistance methylase gene is borne by composite transposon Tn1548. Antimicrob Agents Chemother 2005; 49:2949-53. [PMID: 15980373 PMCID: PMC1168633 DOI: 10.1128/aac.49.7.2949-2953.2005] [Citation(s) in RCA: 155] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The armA (aminoglycoside resistance methylase) gene, which confers resistance to 4,6-disubstituted deoxystreptamines and fortimicin, was initially found in Klebsiella pneumoniae BM4536 on IncL/M plasmid pIP1204 of ca. 90 kb which also encodes the extended-spectrum beta-lactamase CTX-M-3. Thirty-four enterobacteria from various countries that were likely to produce a CTX-M enzyme since they were more resistant to cefotaxime than to ceftazidime were studied. The armA gene was detected in 12 clinical isolates of Citrobacter freundii, Enterobacter cloacae, Escherichia coli, K. pneumoniae, Salmonella enterica, and Shigella flexneri, in which it was always associated with bla(CTX-M-3) on an IncL/M plasmid. Conjugation, analysis of DNA sequences, PCR mapping, and plasmid conduction experiments indicated that the armA gene was part of composite transposon Tn1548 together with genes ant3"9, sul1, and dfrXII, which are responsible for resistance to streptomycin-spectinomycin, sulfonamides, and trimethoprim, respectively. The 16.6-kb genetic element was flanked by two copies of IS6 and migrated by replicative transposition. This observation accounts for the presence of armA on self-transferable plasmids of various incompatibility groups and its worldwide dissemination. It thus appears that posttranscriptional modification of 16S rRNA confers high-level resistance to all the clinically available aminoglycosides except streptomycin in gram-negative human and animal pathogens.
Collapse
Affiliation(s)
- M Galimand
- Unité des Agents Antibactériens, Institut Pasteur, 25, rue du Docteur Roux, 75724 Paris Cedex 15, France.
| | | | | | | |
Collapse
|
90
|
Li Z, Li R, Chen J, Liao Z, Zhu Y, Qian Y, Xiong S, Heman-Ackah S, Wu J, Choo DI, Guan MX. Mutational analysis of the mitochondrial 12S rRNA gene in Chinese pediatric subjects with aminoglycoside-induced and non-syndromic hearing loss. Hum Genet 2005; 117:9-15. [PMID: 15841390 PMCID: PMC1484504 DOI: 10.1007/s00439-005-1276-1] [Citation(s) in RCA: 132] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2004] [Accepted: 01/12/2005] [Indexed: 11/27/2022]
Abstract
Mutations in mitochondrial DNA (mtDNA) have been found to be associated with sensorineural hearing loss. We report here a systematic mutational screening of the mitochondrial 12S rRNA gene in 128 Chinese pediatric subjects with sporadic aminoglycoside-induced and non-syndromic hearing loss. We show that aminoglycoside ototoxicity accounts for 48% of cases of hearing loss in this Chinese pediatric population. Of the known deafness-associated mutations in this gene, the incidence of the A1555G mutation is approximately 13% and approximately 2.9% in this Chinese pediatric population with aminoglycoside-induced and non-syndromic hearing loss, respectively. Furthermore, mutations at position 961 in the 12S rRNA gene account for approximately 1.7% and 4.4% of cases of aminoglycoside-induced and non-syndromic hearing loss in this Chinese clinical population, respectively. The T1095C mutation has been identified in one maternally inherited family with aminoglycoside-induced and non-syndromic hearing loss. However, the C1494T mutation was not detected in this clinical population. In addition, three variants, A827G, T1005C and A1116G, in the 12S rRNA gene, localized at highly conserved sites, may play a role in the pathogenesis of aminoglycoside ototoxicity. These data strongly suggest that the mitochondrial 12S rRNA is a hot-spot for deafness-associated mutations in the Chinese population.
Collapse
Affiliation(s)
- Zhiyuan Li
- Department of Otolaryngology, The First Affiliated Hospital and Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical College, Wenzhou, Zhejiang, China
| | - Ronghua Li
- Division and Program in Human Genetics, Cincinnati Children’s Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229-3039, USA
| | - Jianfu Chen
- Department of Otolaryngology, The First Affiliated Hospital and Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical College, Wenzhou, Zhejiang, China
| | - Zhisu Liao
- Department of Otolaryngology, The First Affiliated Hospital and Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical College, Wenzhou, Zhejiang, China
| | - Yi Zhu
- Department of Otolaryngology, The First Affiliated Hospital and Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical College, Wenzhou, Zhejiang, China
| | - Yaping Qian
- Division and Program in Human Genetics, Cincinnati Children’s Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229-3039, USA
| | - Sudao Xiong
- Department of Otolaryngology, The First Affiliated Hospital and Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical College, Wenzhou, Zhejiang, China
| | - Selena Heman-Ackah
- Division and Program in Human Genetics, Cincinnati Children’s Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229-3039, USA
| | - Jianbo Wu
- Department of Otolaryngology, The First Affiliated Hospital and Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical College, Wenzhou, Zhejiang, China
| | - Daniel I. Choo
- Center for Hearing and Deafness Research, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Min-Xin Guan
- Division and Program in Human Genetics, Cincinnati Children’s Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229-3039, USA
- Center for Hearing and Deafness Research, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
- Zhejiang Provincial Key Laboratory of Medical Genetics, School of Life Sciences, Wenzhou Medical College, Wenzhou, Zhejiang, China
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
- E-mail: Tel.: +1-513-636-3337 Fax: +1-513-636-3486
| |
Collapse
|
91
|
Znosko BM, Kennedy SD, Wille PC, Krugh TR, Turner DH. Structural features and thermodynamics of the J4/5 loop from the Candida albicans and Candida dubliniensis group I introns. Biochemistry 2005; 43:15822-37. [PMID: 15595837 DOI: 10.1021/bi049256y] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The J4/5 loop of group I introns has tertiary interactions with the P1 helix that position the P1 substrate for the self-splicing reaction. The J4/5 loop of Candida albicans and Candida dubliniensis, 5'GAAGG3'/3'UAAUU5', potentially contains two A.A pairs flanked by one G.U pair on one side and two G.U pairs on the other side. Results from optical melting, nuclear magnetic resonance spectroscopy, and functional group substitution experiments with a mimic of the C. albicans and C. dubliniensis J4/5 loop are consistent with the adenosines forming tandem sheared A.A pairs with a cross-strand stack and only the G.U pair not adjacent to an A.A pair forming a static wobble G.U pair. The two G.U pairs adjacent to the tandem A.A pairs are likely in a dynamic equilibrium between multiple conformations. Although Co(NH(3))(6)(3+) stabilizes the loop by several kilocalories per mole at 37 degrees C, addition of Mg(2+) or Co(NH(3))(6)(3+) has no effect on the structure of the loop. The tandem G.U pairs provide a pocket of negative charge for Co(NH(3))(6)(3+) to bind. The results contribute to understanding the structure and dynamics of purine-rich internal loops and potential G.U pairs adjacent to internal loops.
Collapse
Affiliation(s)
- Brent M Znosko
- Department of Chemistry, School of Medicine and Dentistry, University of Rochester, Rochester, New York 14642, USA
| | | | | | | | | |
Collapse
|
92
|
Abstract
Ototoxicity is the major irreversible toxicity of aminoglycosides, and it occurs both in a dose-dependent and idiosyncratic fashion. The idiosyncratic pathway is presumably due to genetic predispositions, and an inherited mutation in the mitochondrial 12S ribosomal RNA gene that predisposes carriers to aminoglycoside ototoxicity was identified in 1993. Up to a third of patients with aminoglycoside ototoxicity carry this mutation. Two other mutations in the same mitochondrial gene affect a small minority of additional patients. Thus, the prevention of aminoglycoside-induced ototoxicity through family history and molecular diagnosis is possible in many cases. It is the challenge of genomic medicine to translate this more than a decade-old knowledge into clinical practice.
Collapse
Affiliation(s)
- Nathan Fischel-Ghodsian
- Cedars-Sinai Medical Center, Department of Pediatrics, Suite 1165WT, 8700 Beverly Blvd., Los Angeles, CA 90048, USA.
| |
Collapse
|
93
|
Pfister P, Hobbie S, Brüll C, Corti N, Vasella A, Westhof E, Böttger EC. Mutagenesis of 16S rRNA C1409-G1491 base-pair differentiates between 6'OH and 6'NH3+ aminoglycosides. J Mol Biol 2004; 346:467-75. [PMID: 15670597 DOI: 10.1016/j.jmb.2004.11.073] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2004] [Revised: 11/24/2004] [Accepted: 11/24/2004] [Indexed: 11/18/2022]
Abstract
Using a single rRNA allelic Gram-positive model system, we systematically mutagenized 16S rRNA positions 1409 and 1491 to probe the functional relevance of structural interactions between aminoglycoside antibiotics and the A-site rRNA that were suggested by X-ray crystallography. At the structural level, the interaction of the 2-deoxystreptamine aminoglycosides with the rRNA base-pair C1409-G1491 has been suggested to involve the following features: (i) ring I of the disubstituted 2-deoxystreptamines stacks upon G1491 and H-bonds to the Watson-Crick edge of A1408; (ii) ring III of the 4,5-disubstituted aminoglycosides shows hydrogen bonding to G1491. However, we found that mutants with altered 16S rRNA bases 1409 and 1491 discriminated poorly between 4,5-disubstituted and 4,6-disubstituted 2-deoxystreptamines, but differentially affected aminoglycosides with a hydroxyl group versus an ammonium group at position 6' of ring I, e.g. G1491U conferred high-level drug resistance to paromomycin and geneticin, but not to neomycin, tobramycin or gentamicin.
Collapse
Affiliation(s)
- P Pfister
- Institut für Medizinische Mikrobiologie, Universität Zürich, Gloriastr. 30/32, CH-8028 Zürich, Switzerland
| | | | | | | | | | | | | |
Collapse
|
94
|
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.
Collapse
Affiliation(s)
- Frank Peske
- Institute of Molecular Biology, University of Witten/Herdecke, 58448 Witten, Germany
| | | | | | | | | |
Collapse
|
95
|
Inoue Y, Shiraishi A, Hada T, Hirose K, Hamashima H, Shimada J. The antibacterial effects of terpene alcohols on Staphylococcus aureus and their mode of action. FEMS Microbiol Lett 2004. [DOI: 10.1111/j.1574-6968.2004.tb09714.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
|
96
|
Yao S, Sgarbi PWM, Marby KA, Rabuka D, O'Hare SM, Cheng ML, Bairi M, Hu C, Hwang SB, Hwang CK, Ichikawa Y, Sears P, Sucheck SJ. Glyco-optimization of aminoglycosides: new aminoglycosides as novel anti-infective agents. Bioorg Med Chem Lett 2004; 14:3733-8. [PMID: 15203152 DOI: 10.1016/j.bmcl.2004.05.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2004] [Accepted: 05/03/2004] [Indexed: 10/26/2022]
Abstract
Glyco-optimization (OPopS) of aminoglycosides has been performed by replacing the existing sugar moiety with a variety of sugar derivatives. Glycosylation of the 6-position of nebramine provided a library of novel 4,6-linked aminoglycosides (AMGs). Among them, compounds 8b,g,i,l, and 8u with 2"-amino, 2",3"-diamino, 2",4"-diamino, 3",4"-diamino, 3"-amino groups, respectively, showed significant antimicrobial activity against Gram-(+) and -(-) bacteria. Several were particularly potent against Pseudomonus aeruginosa with MICs in the 1-2 microg/mL range.
Collapse
Affiliation(s)
- Sulan Yao
- Department of Chemistry, Optimer Pharmaceuticals, Inc., 10110 Sorrento Valley Road, Suite C, San Diego, CA 92121, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
97
|
Abstract
Mutations in the mitochondrial DNA (mtDNA) have been shown to be one important cause of deafness. In particular, mutations in the mtDNA have been associated with both syndromic and nonsyndromic forms of sensori-neural hearing loss. The deafness-linked mutations often occur in the mitochondrial 12S rRNA gene and in tRNA genes. Mutations in the 12S rRNA gene account for most of the cases of aminoglycoside ototoxicity. The other hot spot for mutations associated with hearing impairment is the tRNA(Ser(UCN)) gene, as five deafness-linked mutations have been identified in this gene. Nonsyndromic deafness-linked mtDNA mutations are often homoplasmic or at high levels of heteroplasmy, indicating a high threshold for pathogenicity. Phenotypic expression of these mtDNA mutations requires the contribution of other factors such as nuclear modifier gene(s), environmental factor(s), or mitochondrial haplotype(s).
Collapse
Affiliation(s)
- Min-Xin Guan
- Cincinnati Children's Hospital Medical Center, and Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio 45229, USA.
| |
Collapse
|
98
|
|
99
|
Qazi SNA, Harrison SE, Self T, Williams P, Hill PJ. Real-time monitoring of intracellular Staphylococcus aureus replication. J Bacteriol 2004; 186:1065-77. [PMID: 14762001 PMCID: PMC344210 DOI: 10.1128/jb.186.4.1065-1077.2004] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A high-throughput system to rapidly assess the intracellular replication of Staphylococcus aureus has been developed utilizing S. aureus transformed with a dual gfp-luxABCDE reporter operon under the control of a growth-dependent promoter. Replication of tagged bacteria internalized into bovine mammary epithelial cells (MAC-T) could be measured by monitoring fluorescence and bioluminescence from the reporter operon following removal of extracellular bacteria from the plates. Bacterial replication inside cells was confirmed by a novel ex vivo time-lapse confocal microscopic method. This assay of bacterial replication was used to evaluate the efficacy of antibiotics which are commonly used to treat staphylococcal infections. Not all antibiotics tested were able to prevent intracellular replication of S. aureus and some were ineffective at preventing replication of intracellular bacteria at concentrations above the MIC determined for bacteria in broth culture. Comparison of the fluorescence and bioluminescence signals from the bacteria enabled effects on protein synthesis and metabolism to be discriminated and gave information on the entry of compounds into the eukaryotic cell, even if bacterial replication was not prevented. Elevated resistance of S. aureus to antibiotics inside host cells increases the likelihood of selecting S. aureus strains which are resistant to commonly used antimicrobial agents within the intracellular niche. The approach presented directly assesses intracellular efficacy of antibiotics and provides an evidence-based approach to antibiotic selection for prescribing physicians and medical microbiologists.
Collapse
Affiliation(s)
- S N A Qazi
- Institute of Infection, Immunity, and Inflammation. Institute of Cell Signalling, Queens Medical Centre, University of Nottingham, Nottingham NG7 2UH, United Kingdom
| | | | | | | | | |
Collapse
|
100
|
D'Amelio N, Gaggelli E, Gaggelli N, Molteni E, Baratto MC, Valensin G, Jezowska-Bojczuk M, Szczepanik W. NMR and EPR structural delineation of copper(ii) complexes formed by kanamycin A in water. Dalton Trans 2004:363-8. [PMID: 15252540 DOI: 10.1039/b313060f] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The complexes formed by kanamycin A at three different pH values (5.5, 7.4 and 12.0) were investigated by NMR and EPR spectroscopy. Paramagnetic relaxation contributions to proton relaxation rates were measured using a combination of the TOCSY sequence with the inversion recovery experiment in order to gain signal resolution in the bulk region. Measured contributions were converted into distances and used for structural determination by restrained simulated annealing where all possible chair and boat conformations of the rings were taken into account. The interaction of the Cu(II) ion with the nitrogen of the C ring is apparent at all pH values. At higher pH also the amino group of ring A starts to be involved in the metal coordination sphere. This is accompanied by a switch in conformation of ring C. Structures are consistent with the involvement in the coordination sphere either of the 2' or 4' hydroxyl oxygens at pH 5.5 and the 5 and the 6' hydroxyl oxygens (or the ring oxygen) at pH 12.0.
Collapse
Affiliation(s)
- Nicola D'Amelio
- Department of Chemistry and the NMR Center, University of Siena, Via A.Moro 2, Siena 53100, Italy
| | | | | | | | | | | | | | | |
Collapse
|