1
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Smith PM, Elson JL, Greaves LC, Wortmann SB, Rodenburg RJT, Lightowlers RN, Chrzanowska-Lightowlers ZMA, Taylor RW, Vila-Sanjurjo A. The role of the mitochondrial ribosome in human disease: searching for mutations in 12S mitochondrial rRNA with high disruptive potential. Hum Mol Genet 2013; 23:949-67. [PMID: 24092330 PMCID: PMC3900107 DOI: 10.1093/hmg/ddt490] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Mutations of mitochondrial DNA are linked to many human diseases. Despite the identification of a large number of variants in the mitochondrially encoded rRNA (mt-rRNA) genes, the evidence supporting their pathogenicity is, at best, circumstantial. Establishing the pathogenicity of these variations is of major diagnostic importance. Here, we aim to estimate the disruptive effect of mt-rRNA variations on the function of the mitochondrial ribosome. In the absence of direct biochemical methods to study the effect of mt-rRNA variations, we relied on the universal conservation of the rRNA fold to infer their disruptive potential. Our method, named heterologous inferential analysis or HIA, combines conservational information with functional and structural data obtained from heterologous ribosomal sources. Thus, HIA's predictive power is superior to the traditional reliance on simple conservation indexes. By using HIA, we have been able to evaluate the disruptive potential for a subset of uncharacterized 12S mt-rRNA variations. Our analysis revealed the existence of variations in the rRNA component of the human mitoribosome with different degrees of disruptive power. In cases where sufficient information regarding the genetic and pathological manifestation of the mitochondrial phenotype is available, HIA data can be used to predict the pathogenicity of mt-rRNA mutations. In other cases, HIA analysis will allow the prioritization of variants for additional investigation. Eventually, HIA-inspired analysis of potentially pathogenic mt-rRNA variations, in the context of a scoring system specifically designed for these variants, could lead to a powerful diagnostic tool.
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Affiliation(s)
- Paul M Smith
- Institute of Medical Sciences, Ninewells Hospital and Medical School, Dundee University, Dundee DD1 9SY, Scotland, UK
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2
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Spano MN, Walter NG. Solution structure of an alternate conformation of helix27 from Escherichia coli16S rRNA. Biopolymers 2011; 95:653-68. [PMID: 21442607 DOI: 10.1002/bip.21626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2010] [Revised: 03/08/2011] [Accepted: 03/09/2011] [Indexed: 11/09/2022]
Abstract
Helix (H)27 of 16S ribosomal (r)RNA from Escherichia coli was dubbed the "switch helix" when mutagenesis suggested that two alternative base pair registers may have distinct functional roles in the bacterial ribosome. Although more recent genetic analyses suggest that H27 conformational switching is not required for translation, previous solution studies demonstrated that the isolated E. coli H27 can dynamically convert between the 885 and 888 conformations. Here, we have solved the nuclear magnetic resonance solution structure of a locked 888 conformation. NOE and residual dipolar coupling restraints reveal an architecture that markedly differs from that of the 885 conformation found in crystal structures of the bacterial ribosome. In place of the loop E motif that characterizes the 885 conformer and that the 888 conformer cannot adopt, we find evidence for an asymmetrical A-rich internal loop stabilized by stacking interactions among the unpaired A's. Comparison of the isolated H27 888 solution structure with the 885 crystal structure within the context of the ribosome suggests a difference in overall length of H27 that presents one plausible reason for the absence of H27 conformational switching within the sterically confining ribosome.
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3
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McClory SP, Leisring JM, Qin D, Fredrick K. Missense suppressor mutations in 16S rRNA reveal the importance of helices h8 and h14 in aminoacyl-tRNA selection. RNA (NEW YORK, N.Y.) 2010; 16:1925-34. [PMID: 20699303 PMCID: PMC2941101 DOI: 10.1261/rna.2228510] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
The molecular basis of the induced-fit mechanism that determines the fidelity of protein synthesis remains unclear. Here, we isolated mutations in 16S rRNA that increase the rate of miscoding and stop codon read-through. Many of the mutations clustered along interfaces between the 30S shoulder domain and other parts of the ribosome, strongly implicating shoulder movement in the induced-fit mechanism of decoding. The largest subset of mutations mapped to helices h8 and h14. These helices interact with each other and with the 50S subunit to form bridge B8. Previous cryo-EM studies revealed a contact between h14 and the switch 1 motif of EF-Tu, raising the possibility that h14 plays a direct role in GTPase activation. To investigate this possibility, we constructed both deletions and insertions in h14. While ribosomes harboring a 2-base-pair (bp) insertion in h14 were completely inactive in vivo, those containing a 2-bp deletion retained activity but were error prone. In vitro, the truncation of h14 accelerated GTP hydrolysis for EF-Tu bearing near-cognate aminoacyl-tRNA, an effect that can largely account for the observed miscoding in vivo. These data show that h14 does not help activate EF-Tu but instead negatively controls GTP hydrolysis by the factor. We propose that bridge B8 normally acts to counter inward rotation of the shoulder domain; hence, mutations in h8 and h14 that compromise this bridge decrease the stringency of aminoacyl-tRNA selection.
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MESH Headings
- Binding Sites/genetics
- Codon, Nonsense
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Kinetics
- Models, Molecular
- Mutation, Missense
- Nucleic Acid Conformation
- Protein Biosynthesis
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 16S/metabolism
- RNA, Transfer, Amino Acyl/metabolism
- Ribosomes/genetics
- Ribosomes/metabolism
- Suppression, Genetic
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Affiliation(s)
- Sean P McClory
- Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio 43210, USA
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4
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Sequence-specific bacterial growth inhibition by peptide nucleic acid targeted to the mRNA binding site of 16S rRNA. Appl Microbiol Biotechnol 2009; 84:1161-8. [PMID: 19578844 DOI: 10.1007/s00253-009-2099-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2009] [Revised: 06/11/2009] [Accepted: 06/16/2009] [Indexed: 12/22/2022]
Abstract
Peptide nucleic acid (PNA) targeted to the functional domains of 23S rRNA can inhibit translation and cell growth. However, effective inhibition of translation and cell growth using 16S rRNA-targeted PNA has still not been achieved. Here, we report that PNA targeted to the functional site of 16S rRNA could inhibit both gene expression in vitro and bacterial growth in pure culture with sequence specificity. We used 10-mer PNAs conjugated with a cell-penetrating peptide, which targeted the mRNA binding site at the 3' end of 16S rRNA. Using 0.6 microM of the peptide-PNAs, cell-free ss-galactosidase production decreased by 50%, whereas peptide-PNAs with one or two mismatches to the target sequence showed much weaker inhibition effects. To determine the growth inhibition and bactericidal effects of the peptide-PNA conjugate, we performed OD measurement and viable cell counting. We observed dose- and sequence-dependent inhibition of cell growth and bactericidal effects. These growth inhibitory effects are observed both in the Gram-negative bacterium of Escherichia coli and the Gram-positive bacteria Bacillus subtilis and Corynebacterium efficiens, although inhibitory concentrations were different for each bacterial species. These results present possibilities for 16S rRNA sequence-based specific bacterial growth inhibition using a peptide-PNA conjugate.
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5
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Yassin A, Mankin AS. Potential New Antibiotic Sites in the Ribosome Revealed by Deleterious Mutations in RNA of the Large Ribosomal Subunit. J Biol Chem 2007; 282:24329-42. [PMID: 17591769 DOI: 10.1074/jbc.m703106200] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The ribosome is the main target for antibiotics that inhibit protein biosynthesis. Despite the chemical diversity of the known antibiotics that affect functions of the large ribosomal subunit, these drugs act on only a few sites corresponding to some of the known functional centers. We have used a genetic approach for identifying structurally and functionally critical sites in the ribosome that can be used as new antibiotic targets. By using randomly mutagenized rRNA genes, we mapped rRNA sites where nucleotide alterations impair the ribosome function or assembly and lead to a deleterious phenotype. A total of 77 single-point deleterious mutations were mapped in 23 S rRNA and ranked according to the severity of their deleterious phenotypes. Many of the mutations mapped to familiar functional sites that are targeted by known antibiotics. However, a number of mutations were located in previously unexplored regions. The distribution of the mutations in the spatial structure of the ribosome showed a strong bias, with the strongly deleterious mutations being mainly localized at the interface of the large subunit and the mild ones on the solvent side. Five sites where deleterious mutations tend to cluster within discrete rRNA elements were identified as potential new antibiotic targets. One of the sites, the conserved segment of helix 38, was studied in more detail. Although the ability of the mutant 50 S subunits to associate with 30 S subunits was impaired, the lethal effect of mutations in this rRNA element was unrelated to its function as an intersubunit bridge. Instead, mutations in this region had a profound deleterious effect on the ribosome assembly.
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Affiliation(s)
- Aymen Yassin
- Center for Pharmaceutical Biotechnology, University of Illinois, Chicago, Illinois 60607, USA
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6
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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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7
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O'connor M. Interaction between the ribosomal subunits: 16S rRNA suppressors of the lethal DeltaA1916 mutation in the 23S rRNA of Escherichia coli. Mol Genet Genomics 2007; 278:307-15. [PMID: 17564727 DOI: 10.1007/s00438-007-0252-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2007] [Accepted: 05/17/2007] [Indexed: 11/29/2022]
Abstract
A1916 in 23S rRNA is located in one of the major intersubunit bridges of the 70S ribosome. Deletion of A1916 disrupts the intersubunit bridge B2a, promotes misreading of the genetic code and is lethal. In a genetic selection for suppressor mutations, two base substitutions in 16S rRNA were recovered that restored viability and also allowed expression of DeltaA1916-associated capreomycin resistance. These mutations were G1048A in helix 34 and U1471C in helix 44. Restoration of function is incomplete, however, and the double mutants are slow-growing, defective in subunit association and support high levels of translational errors. In contrast, none of these parameters is affected by the single 16S suppressor mutations. U1471C likely affects another intersubunit contact, bridge B6, suggesting that interactions between different bridges and cross-talk between subunits contributes to ribosomal function.
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MESH Headings
- Capreomycin/pharmacology
- Drug Resistance, Bacterial/genetics
- Escherichia coli/drug effects
- Escherichia coli/genetics
- Genes, Bacterial
- Genes, Lethal
- Macromolecular Substances
- Models, Molecular
- Mutation
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 23S/chemistry
- RNA, Ribosomal, 23S/genetics
- Ribosomes/chemistry
- Ribosomes/genetics
- Suppression, Genetic
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Affiliation(s)
- Michael O'connor
- School of Biological Sciences, University of Missouri-Kansas City, 5007 Rockhill Rd., Kansas City, MO 64110, USA.
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8
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Vila-Sanjurjo A, Lu Y, Aragonez JL, Starkweather RE, Sasikumar M, O'Connor M. Modulation of 16S rRNA function by ribosomal protein S12. ACTA ACUST UNITED AC 2007; 1769:462-71. [PMID: 17512991 DOI: 10.1016/j.bbaexp.2007.04.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2006] [Revised: 03/20/2007] [Accepted: 04/09/2007] [Indexed: 11/22/2022]
Abstract
Ribosomal protein S12 is a critical component of the decoding center of the 30S ribosomal subunit and is involved in both tRNA selection and the response to streptomycin. We have investigated the interplay between S12 and some of the surrounding 16S rRNA residues by examining the phenotypes of double-mutant ribosomes in strains of Escherichia coli carrying deletions in all chromosomal rrn operons and expressing total rRNA from a single plasmid-borne rrn operon. We show that the combination of S12 and otherwise benign mutations at positions C1409-G1491 in 16S rRNA severely compromises cell growth while the level and range of aminoglycoside resistances conferred by the G1491U/C substitutions is markedly increased by a mutant S12 protein. The G1491U/C mutations in addition confer resistance to the unrelated antibiotic, capreomycin. S12 also interacts with the 912 region of 16S rRNA. Genetic selection of suppressors of streptomycin dependence caused by mutations at proline 90 in S12 yielded a C912U substitution in 16S rRNA. The C912U mutation on its own confers resistance to streptomycin and restricts miscoding, properties that distinguish it from a majority of the previously described error-promoting ram mutants that also reverse streptomycin dependence.
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Affiliation(s)
- Anton Vila-Sanjurjo
- Berkeley Center for Synthetic Biology, University of California, Berkeley, 717 Potter St., Berkeley, CA 94720-3224, USA
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9
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Gagnon MG, Mukhopadhyay A, Steinberg SV. Close Packing of Helices 3 and 12 of 16 S rRNA Is Required for the Normal Ribosome Function. J Biol Chem 2006; 281:39349-57. [PMID: 17060325 DOI: 10.1074/jbc.m607725200] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The along-groove packing motif is a quasi-reciprocal arrangement of two RNA double helices in which a backbone of each helix is closely packed within the minor groove of the other helix. At the center of the inter-helix contact, a GU base pair in one helix packs against a Watson-Crick base pair in the other helix. Here, based on in vivo selection from a combinatorial gene library of 16 S rRNA and on functional characterization of the selected clones, we demonstrate that the normal ribosome performance requires that helices 3 and 12 be closely packed. In some clones the Watson-Crick and GU base pairs exchange in their positions between the two helices, which affects neither the quality of the helix packing, nor the ribosome function. On the other hand, perturbations in the close packing usually lead to a substantial drop in the ribosome activity. The functionality of the clones containing such perturbations may depend on the presence of particular elements in the vicinity of the area of contact between helices 3 and 12. Such cases do not exist in natural 16 S rRNA, and their selection enriches our knowledge of the constraints imposed on the structure of ribosomal RNA in functional ribosomes.
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Affiliation(s)
- Matthieu G Gagnon
- Département de Biochimie, Université de Montréal, Montréal, Quebec H3C 3J7, Canada
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10
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Skorski P, Leroy P, Fayet O, Dreyfus M, Hermann-Le Denmat S. The highly efficient translation initiation region from the Escherichia coli rpsA gene lacks a shine-dalgarno element. J Bacteriol 2006; 188:6277-85. [PMID: 16923895 PMCID: PMC1595398 DOI: 10.1128/jb.00591-06] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The translational initiation region (TIR) of the Escherichia coli rpsA gene, which encodes ribosomal protein S1, shows a number of unusual features. It extends far upstream (to position -91) of the initiator AUG, it lacks a canonical Shine-Dalgarno sequence (SD) element, and it can fold into three successive hairpins (I, II, and III) that are essential for high translational activity. Two conserved GGA trinucleotides, present in the loops of hairpins I and II, have been proposed to form a discontinuous SD. Here, we have tested this hypothesis with the "specialized ribosome" approach. Depending upon the constructs used, translation initiation was decreased three- to sevenfold upon changing the conserved GGA to CCU. However, although chemical probing showed that the mutated trinucleotides were accessible, no restoration was observed when the ribosome anti-SD was symmetrically changed from CCUCC to GGAGG. When the same change was introduced in the SD from a conventional TIR as a control, activity was stimulated. This result suggests that the GGA trinucleotides do not form a discontinuous SD. Others hypotheses that may account for their role are discussed. Curiously, we also find that, when expressed at moderate level (30 to 40% of total ribosomes), specialized ribosomes are only twofold disadvantaged over normal ribosomes for the translation of bulk cellular mRNAs. These findings suggest that, under these conditions, the SD-anti-SD interaction plays a significant but not essential role for the synthesis of bulk cellular proteins.
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Affiliation(s)
- Patricia Skorski
- Laboratoire de Génétique Moléculaire, Ecole Normale Supérieure-CNRS UMR 8541, 46 rue d'Ulm, 75230 Paris Cedex 05, France
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11
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Kiparisov SV, Sergiev PV, Bogdanov AA, Dontsova OA. Structural changes in the ribosome during the elongation cycle. Mol Biol 2006. [DOI: 10.1134/s0026893306050013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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12
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Kubarenko A, Sergiev P, Wintermeyer W, Dontsova O, Rodnina MV. Involvement of helix 34 of 16 S rRNA in decoding and translocation on the ribosome. J Biol Chem 2006; 281:35235-44. [PMID: 16990269 DOI: 10.1074/jbc.m608060200] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Helix 34 of 16 S rRNA is located in the head of the 30 S ribosomal subunit close to the decoding center and has been invoked in a number of ribosome functions. In the present work, we have studied the effects of mutations in helix 34 both in vivo and in vitro. Several nucleotides in helix 34 that are either highly conserved or form important tertiary contacts in 16 S rRNA (U961, C1109, A1191, and A1201) were mutated, and the mutant ribosomes were expressed in the Escherichia coli MC250 Delta7 strain that lacks all seven chromosomal rRNA operons. Mutations at positions A1191 and U961 reduced the efficiency of subunit association and resulted in structural rearrangements in helix 27 (position 908) and helix 31 (position 974) of 16 S rRNA. All mutants exhibited increased levels of frameshifting and nonsense readthrough. The effects on frameshifting were specific in that -1 frameshifting was enhanced with mutant A1191G and +1 frameshifting with the other mutants. Mutations of A1191 moderately (approximately 2-fold) inhibited tRNA translocation. No significant effects were found on efficiency and rate of initiation, misreading of sense codons, or binding of tRNA to the E site. The data indicate that helix 34 is involved in controlling the maintenance of the reading frame and in tRNA translocation.
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Affiliation(s)
- Andrew Kubarenko
- Institute of Physical Biochemistry, University of Witten/Herdecke, 58448 Witten, Germany
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13
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Criswell D, Tobiason VL, Lodmell JS, Samuels DS. Mutations conferring aminoglycoside and spectinomycin resistance in Borrelia burgdorferi. Antimicrob Agents Chemother 2006; 50:445-52. [PMID: 16436695 PMCID: PMC1366916 DOI: 10.1128/aac.50.2.445-452.2006] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
We have isolated and characterized in vitro mutants of the Lyme disease agent Borrelia burgdorferi that are resistant to spectinomycin, kanamycin, gentamicin, or streptomycin, antibiotics that target the small subunit of the ribosome. 16S rRNA mutations A1185G and C1186U, homologous to Escherichia coli nucleotides A1191 and C1192, conferred >2,200-fold and 1,300-fold resistance to spectinomycin, respectively. A 16S rRNA A1402G mutation, homologous to E. coli A1408, conferred >90-fold resistance to kanamycin and >240-fold resistance to gentamicin. Two mutations were identified in the gene for ribosomal protein S12, at a site homologous to E. coli residue Lys-87, in mutants selected in streptomycin. Substitutions at codon 88, K88R and K88E, conferred 7-fold resistance and 10-fold resistance, respectively, to streptomycin on B. burgdorferi. The 16S rRNA A1185G and C1186U mutations, associated with spectinomycin resistance, appeared in a population of B. burgdorferi parental strain B31 at a high frequency of 6 x 10(-6). These spectinomycin-resistant mutants successfully competed with the wild-type strain during 100 generations of coculture in vitro. The aminoglycoside-resistant mutants appeared at a frequency of 3 x 10(-9) to 1 x10(-7) in a population and were unable to compete with wild-type strain B31 after 100 generations. This is the first description of mutations in the B. burgdorferi ribosome that confer resistance to antibiotics. These results have implications for the evolution of antibiotic resistance, because the 16S rRNA mutations conferring spectinomycin resistance have no significant fitness cost in vitro, and for the development of new selectable markers.
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Affiliation(s)
- Daniel Criswell
- Division of Biological Sciences, The University of Montana, Missoula, MT 59812-4824, USA
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14
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Yassin A, Fredrick K, Mankin AS. Deleterious mutations in small subunit ribosomal RNA identify functional sites and potential targets for antibiotics. Proc Natl Acad Sci U S A 2005; 102:16620-5. [PMID: 16269538 PMCID: PMC1283848 DOI: 10.1073/pnas.0508444102] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Many clinically useful antibiotics interfere with protein synthesis in bacterial pathogens by inhibiting ribosome function. The sites of action of known drugs are limited in number, are composed primarily of ribosomal RNA (rRNA), and coincide with functionally critical centers of the ribosome. Nucleotide alterations within such sites are often deleterious. To identify functional sites and potential sites of antibiotic action in the ribosome, we prepared a random mutant library of rRNA genes and selected dominant mutations in 16S rRNA that interfere with cell growth. Fifty-three 16S rRNA positions were identified whose mutation inhibits protein synthesis. Mutations were ranked according to the severity of the phenotype, and the detrimental effect of several mutations on translation was verified in a specialized ribosome system. Analysis of the polysome profiles of mutants suggests that the majority of the mutations directly interfered with ribosome function, whereas a smaller fraction of mutations affected assembly of the small ribosomal subunit. Twelve of the identified mutations mapped to sites targeted by known antibiotics, confirming that deleterious mutations can be used to identify antibiotic targets. About half of the mutations coincided with known functional sites in the ribosome, whereas the rest of the mutations affected ribosomal sites with less clear functional significance. Four clusters of deleterious mutations in otherwise unremarkable ribosomal sites were identified, suggesting their functional importance and potential as antibiotic targets.
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Affiliation(s)
- Aymen Yassin
- Center for Pharmaceutical Biotechnology, University of Illinois at Chicago, IL 60607, USA
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15
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Lambert MN, Hoerter JAH, Pereira MJB, Walter NG. Solution probing of metal ion binding by helix 27 from Escherichia coli 16S rRNA. RNA (NEW YORK, N.Y.) 2005; 11:1688-700. [PMID: 16244134 PMCID: PMC1370855 DOI: 10.1261/rna.2940705] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Helix (H)27 from Escherichia coli 16S ribosomal (r)RNA is centrally located within the small (30S) ribosomal subunit, immediately adjacent to the decoding center. Bacterial 30S subunit crystal structures depicting Mg(2+) binding sites resolve two magnesium ions within the vicinity of H27: one in the major groove of the G886-U911 wobble pair, and one within the GCAA tetraloop. Binding of such metal cations is generally thought to be crucial for RNA folding and function. To ask how metal ion-RNA interactions in crystals compare with those in solution, we have characterized, using solution NMR spectroscopy, Tb(3+) footprinting and time-resolved fluorescence resonance energy transfer (tr-FRET), location, and modes of metal ion binding in an isolated H27. NMR and Tb(3+) footprinting data indicate that solution secondary structure and Mg(2+) binding are generally consistent with the ribosomal crystal structures. However, our analyses also suggest that H27 is dynamic in solution and that metal ions localize within the narrow major groove formed by the juxtaposition of the loop E motif with the tandem G894-U905 and G895-U904 wobble pairs. In addition, tr-FRET studies provide evidence that Mg(2+) uptake by the H27 construct results in a global lengthening of the helix. We propose that only a subset of H27-metal ion interactions has been captured in the crystal structures of the 30S ribosomal subunit, and that small-scale structural dynamics afforded by solution conditions may contribute to these differences. Our studies thus highlight an example for differences between RNA-metal ion interactions observed in solution and in crystals.
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16
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Huggins W, Ghosh SK, Nanda K, Wollenzien P. Internucleotide movements during formation of 16 S rRNA-rRNA photocrosslinks and their connection to the 30 S subunit conformational dynamics. J Mol Biol 2005; 354:358-74. [PMID: 16242153 DOI: 10.1016/j.jmb.2005.09.060] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2005] [Revised: 09/14/2005] [Accepted: 09/19/2005] [Indexed: 10/25/2022]
Abstract
UV light-induced RNA photocrosslinks are formed at a limited number of specific sites in the Escherichia coli and in other eubacterial 16 S rRNAs. To determine if unusually favorable internucleotide geometries could explain the restricted crosslinking patterns, parameters describing the internucleotide geometries were calculated from the Thermus thermophilus 30 S subunit X-ray structure and compared to crosslinking frequencies. Significant structural adjustments between the nucleotide pairs usually are needed for crosslinking. Correlations between the crosslinking frequencies and the geometrical parameters indicate that nucleotide pairs closer to the orientation needed for photoreaction have higher crosslinking frequencies. These data are consistent with transient conformational changes during crosslink formation in which the arrangements needed for photochemical reaction are attained during the electronic excitation times. The average structural rearrangement for UVA-4-thiouridine (s4U)-induced crosslinking is larger than that for UVB or UVC-induced crosslinking; this is associated with the longer excitation time for s4U and is also consistent with transient conformational changes. The geometrical parameters do not completely predict the crosslinking frequencies, implicating other aspects of the tertiary structure or conformational flexibility in determining the frequencies and the locations of the crosslinking sites. The majority of the UVB/C and UVA-s4U-induced crosslinks are located in four regions in the 30 S subunit, within or at the ends of RNA helix 34, in the tRNA P-site, in the distal end of helix 28 and in the helix 19/helix 27 region. These regions are implicated in different aspects of tRNA accommodation, translocation and in the termination reaction. These results show that photocrosslinking is an indicator for sites where there is internucleotide conformational flexibility and these sites are largely restricted to parts of the 30 S subunit associated with ribosome function.
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MESH Headings
- Base Pairing
- Base Sequence
- Binding Sites
- Cross-Linking Reagents
- Escherichia coli/chemistry
- Escherichia coli/genetics
- Escherichia coli/radiation effects
- Models, Molecular
- Molecular Sequence Data
- Nucleic Acid Conformation/radiation effects
- Nucleotides/chemistry
- Nucleotides/metabolism
- Nucleotides/radiation effects
- Photochemistry
- Protein Conformation/radiation effects
- Protein Subunits
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/radiation effects
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/metabolism
- RNA, Ribosomal, 16S/radiation effects
- RNA, Transfer/chemistry
- RNA, Transfer/genetics
- RNA, Transfer/metabolism
- Ribosomal Proteins/chemistry
- Ribosomal Proteins/genetics
- Ribosomal Proteins/metabolism
- Ribosomes/chemistry
- Ribosomes/metabolism
- Ribosomes/radiation effects
- Ultraviolet Rays
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Affiliation(s)
- Wayne Huggins
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695-7622, USA
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17
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Abstract
The underlying basis for the accuracy of protein synthesis has been the subject of over four decades of investigation. Recent biochemical and structural data make it possible to understand at least in outline the structural basis for tRNA selection, in which codon recognition by cognate tRNA results in the hydrolysis of GTP by EF-Tu over 75 A away. The ribosome recognizes the geometry of codon-anticodon base pairing at the first two positions but monitors the third, or wobble position, less stringently. Part of the additional binding energy of cognate tRNA is used to induce conformational changes in the ribosome that stabilize a transition state for GTP hydrolysis by EF-Tu and subsequently result in accelerated accommodation of tRNA into the peptidyl transferase center. The transition state for GTP hydrolysis is characterized, among other things, by a distorted tRNA. This picture explains a large body of data on the effect of antibiotics and mutations on translational fidelity. However, many fundamental questions remain, such as the mechanism of activation of GTP hydrolysis by EF-Tu, and the relationship between decoding and frameshifting.
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Affiliation(s)
- James M Ogle
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 2QH, United Kingdom.
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18
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Bélanger F, Théberge-Julien G, Cunningham PR, Brakier-Gingras L. A functional relationship between helix 1 and the 900 tetraloop of 16S ribosomal RNA within the bacterial ribosome. RNA (NEW YORK, N.Y.) 2005; 11:906-13. [PMID: 15872184 PMCID: PMC1370775 DOI: 10.1261/rna.2160405] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
The conserved 900 tetraloop that caps helix 27 of 16S ribosomal RNA (rRNA) interacts with helix 24 of 16S rRNA and also with helix 67 of 23S rRNA, forming the intersubunit bridge B2c, proximal to the decoding center. In previous studies, we investigated how the interaction between the 900 tetraloop and helix 24 participates in subunit association and translational fidelity. In the present study, we investigated whether the 900 tetraloop is involved in other undetected interactions with different regions of the Escherichia coli 16S rRNA. Using a genetic complementation approach, we selected mutations in 16S rRNA that compensate for a 900 tetraloop mutation, A900G, which severely impairs subunit association and translational fidelity. Mutations were randomly introduced in 16S rRNA, using either a mutagenic XL1-Red E. coli strain or an error-prone PCR strategy. Gain-offunction mutations were selected in vivo with a specialized ribosome system. Two mutations, the deletion of U12 and the U12C substitution, were thus independently selected in helix 1 of 16S rRNA. This helix is located in the vicinity of helix 27, but does not directly contact the 900 tetraloop in the crystal structures of the ribosome. Both mutations correct the subunit association and translational fidelity defects caused by the A900G mutation, revealing an unanticipated functional interaction between these two regions of 16S rRNA.
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MESH Headings
- Base Sequence
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Molecular Sequence Data
- Mutation
- Nucleic Acid Conformation
- Peptide Chain Initiation, Translational/genetics
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 16S/metabolism
- Ribosomes/metabolism
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19
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Hoerter JAH, Lambert MN, Pereira MJB, Walter NG. Dynamics inherent in helix 27 from Escherichia coli 16S ribosomal RNA. Biochemistry 2005; 43:14624-36. [PMID: 15544333 DOI: 10.1021/bi048533y] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The original interpretation of a series of genetic studies suggested that the highly conserved Escherichia coli 16S ribosomal RNA helix 27 (H27) adopts two alternative secondary structure motifs, the 885 and 888 conformations, during each cycle of amino acid incorporation. Recent crystallographic and genetic evidence has called this hypothesis into question. To ask whether a slippery sequence such as that of H27 may harbor inherent conformational dynamics, we have designed a series of model RNAs based on E. coli H27 for in vitro physicochemical studies. One-dimensional (1)H NMR spectroscopy demonstrates that both the 885 and 888 conformations are occupied to approximately the same extent (f(888) = 0.427 +/- 0.04) in the native H27 sequence at low pH (6.4) and low ionic strength (50 mM NaCl). UV irradiation assays conducted under conditions analogous to those used for assays of ribosomal function (pH 7.5 and 20 mM MgCl(2)) suggest that nucleotides 892 and 905, which are too far apart in the known 885 crystal structures, can approach each other closely enough to form an efficient cross-link. The use of a fluorescence resonance energy transfer (FRET)-labeled RNA together with a partially complementary DNA oligonucleotide that induces a shift to the 888 conformation shows that H27 interchanges between the 885 and 888 conformations on the millisecond time scale, with an equilibrium constant of 0.33 +/-0.12. FRET assays also show that tetracycline interferes with the induced shift to the 888 conformation, a finding that is consistent with crystallographic localization of tetracycline bound to the 885 conformation of H27 in the 30S ribosomal subunit. Taken together, our data demonstrate the innate tendency of an isolated H27 to exist in a dynamic equilibrium between the 885 and 888 conformations. This begs the question of how these inherent structural dynamics are suppressed within the context of the ribosome.
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Affiliation(s)
- John A H Hoerter
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, USA
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20
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Hennelly SP, Antoun A, Ehrenberg M, Gualerzi CO, Knight W, Lodmell JS, Hill WE. A time-resolved investigation of ribosomal subunit association. J Mol Biol 2005; 346:1243-58. [PMID: 15713478 DOI: 10.1016/j.jmb.2004.12.054] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2004] [Revised: 12/23/2004] [Accepted: 12/29/2004] [Indexed: 11/19/2022]
Abstract
The notion that the ribosome is dynamic has been supported by various biochemical techniques, as well as by differences observed in high-resolution structures of ribosomal complexes frozen in various functional states. Yet, the mechanisms and extent of rRNA dynamics are still largely unknown. We have used a novel, fast chemical-modification technique to provide time-resolved details of 16 S rRNA structural changes that occur as bridges are formed between the ribosomal subunits as they associate. Association of different 16 S rRNA regions was found to be a sequential, multi-step process involving conformational rearrangements within the 30 S subunit. Our results suggest that key regions of 16 S rRNA, necessary for decoding and tRNA A-site binding, are structurally altered in a time-dependent manner by association with the 50 S ribosomal subunits.
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MESH Headings
- Base Pairing
- Binding Sites
- Crystallography, X-Ray
- Escherichia coli/chemistry
- Escherichia coli/metabolism
- Models, Molecular
- Nucleic Acid Conformation
- Protein Conformation
- RNA, Bacterial/chemistry
- RNA, Bacterial/metabolism
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/metabolism
- RNA, Transfer/chemistry
- RNA, Transfer/metabolism
- Ribosomes/metabolism
- Time Factors
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Affiliation(s)
- Scott P Hennelly
- Division of Biological Sciences, The University of Montana, Missoula, MT 59812, USA
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21
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Novotny GW, Jakobsen L, Andersen NM, Poehlsgaard J, Douthwaite S. Ketolide antimicrobial activity persists after disruption of interactions with domain II of 23S rRNA. Antimicrob Agents Chemother 2004; 48:3677-83. [PMID: 15388419 PMCID: PMC521900 DOI: 10.1128/aac.48.10.3677-3683.2004] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Ketolides are the latest derivatives developed from the macrolide erythromycin to improve antimicrobial activity. All macrolides and ketolides bind to the 50S ribosomal subunit, where they come into contact with adenosine 2058 (A2058) within domain V of the 23S rRNA and block protein synthesis. An additional interaction at nucleotide A752 in the rRNA domain II is made via the synthetic carbamate-alkyl-aryl substituent in the ketolides HMR3647 (telithromycin) and HMR3004, and this interaction contributes to their improved activities. Only a few macrolides, including tylosin, come into contact with domain II of the rRNA and do so via interactions with nucleotides G748 and A752. We have disrupted these macrolide-ketolide interaction sites in the rRNA to assess their relative importance for binding. Base substitutions at A752 were shown to confer low levels of resistance to telithromycin but not to HMR3004, while deletion of A752 confers low levels of resistance to both ketolides. Mutations at position 748 confer no resistance. Substitution of guanine at A2058 gives rise to the MLS(B) (macrolide, lincosamide, and streptogramin B) phenotype, which confers resistance to all the drugs. However, resistance to ketolides was abolished when the mutation at position 2058 was combined with a mutation in domain II of the same rRNA. In contrast, the same dual mutations in rRNAs conferred enhanced resistance to tylosin. Our results show that the domain II interactions of telithromycin and HMR3004 differ from each other and from those of tylosin. The data provide no indication that mutations within domain II, either alone or in combination with an A2058 mutation, can confer significant levels of telithromycin resistance.
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Affiliation(s)
- Guy W Novotny
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark
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22
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Bélanger F, Gagnon MG, Steinberg SV, Cunningham PR, Brakier-Gingras L. Study of the Functional Interaction of the 900 Tetraloop of 16S Ribosomal RNA with Helix 24 within the Bacterial Ribosome. J Mol Biol 2004; 338:683-93. [PMID: 15099737 DOI: 10.1016/j.jmb.2004.03.024] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2003] [Revised: 03/08/2004] [Accepted: 03/10/2004] [Indexed: 10/26/2022]
Abstract
The 900 tetraloop that caps helix 27 of 16S ribosomal RNA (rRNA) is amongst the most conserved regions of rRNA. This tetraloop forms a GNRA motif that docks into the minor groove of three base-pairs at the bottom of helix 24 of 16S rRNA in the 30S subunit. Both the tetraloop and its receptor in helix 24 contact the 23S rRNA, forming the intersubunit bridge B2c. Here, we investigated the interaction between the 900 tetraloop and its receptor by genetic complementation. We used a specialized ribosome system in combination with an in vivo instant evolution approach to select mutations in helix 24 compensating for a mutation in the 900 tetraloop (A900G) that severely decreases ribosomal activity, impairing subunit association and translational fidelity. We selected two mutants where the G769-C810 base-pair of helix 24 was substituted with either U-A or C x A. When these mutations in helix 24 were investigated in the context of a wild-type 900 tetraloop, the C x A but not the U-A mutation severely impaired ribosome activity, interfering with subunit association and decreasing translational fidelity. In the presence of the A900G mutation, both mutations in helix 24 increased the ribosome activity to the same extent. Subunit association and translational fidelity were increased to the same level. Computer modeling was used to analyze the effect of the mutations in helix 24 on the interaction between the tetraloop and its receptor. This study demonstrates the functional importance of the interaction between the 900 tetraloop and helix 24.
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Affiliation(s)
- François Bélanger
- Département de Biochimie, Université de Montréal, Montréal, Qué., Canada H3T 1J4
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