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Reconstruction of the rRNA Sequences of LUCA, with Bioinformatic Implication of the Local Similarities Shared by Them. BIOLOGY 2022; 11:biology11060837. [PMID: 35741358 PMCID: PMC9219793 DOI: 10.3390/biology11060837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 05/19/2022] [Accepted: 05/23/2022] [Indexed: 11/17/2022]
Abstract
The theory of the RNA world, especially with the catalytic capability of RNA, provides a reasonable framework explaining the evolution of molecular genetics system before the scenario of the central dogma. However, it remains a challenge to deduce the origin mechanism of rRNAs. Here we reconstructed the phylogenetic relationships of archaea and bacteria with bootstrap values of most nodes, especially the deep ones, higher than 90%. Based on the well-resolved tree, the full lengths of 16S, 5S, and 23S rRNA sequences of the last universal common ancestor (LUCA) were reconstructed for the first time. The potential similarities shared by the three ancestral rRNA sequences were further explored by searching for repeat short fragments in the level of purine–pyrimidine (RY) with certain lengths and arrangements. With the lengths ranging from 2 to 14, functional short fragments could be found in the three RNAs. As a representative, a set with a total of 75 short fragments of 11 nucleotides in length can recover all types of the known functional sites of ribosomes in a most concise manner. The 75 short fragments cluster around the functional center of the ribosome, among which 18 of them are highly conserved across five or six kingdoms and still contain all types of known functional sites except one. Alternatively, according to the strategy using the level of AUGC instead of RY, a similar pattern can be recovered. Such results indicate the local similarities shared by 16S, 5S, and 23S rRNAs and thus suggest a possible general mechanism in the formation of the LUCA rRNAs.
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Gładysz M, Andrałojć W, Czapik T, Gdaniec Z, Kierzek R. Thermodynamic and structural contributions of the 6-thioguanosine residue to helical properties of RNA. Sci Rep 2019; 9:4385. [PMID: 30867505 PMCID: PMC6416399 DOI: 10.1038/s41598-019-40715-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 02/21/2019] [Indexed: 12/21/2022] Open
Abstract
Thionucleotides, especially 4-thiouridine and 6-thioguanosine, are photosensitive molecules that photocrosslink to both proteins and nucleic acids, and this feature is a major reason for their application in various investigations. To get insight into the thermodynamic and structural contributions of 6-thioguanosine to the properties of RNA duplexes a systematic study was performed. In a series of RNA duplexes, selected guanosine residues located in G-C base pairs, mismatches (G-G, G-U, and G-A), or 5' and 3'-dangling ends were replaced with 6-thioguanosine. Generally, the presence of 6-thioguanosine diminishes the thermodynamic stability of RNA duplexes. This effect depends on its position within duplexes and the sequence of adjacent base pairs. However, when placed at a dangling end a 6-thioguanosine residue actually exerts a weak stabilizing effect. Furthermore, the structural effect of 6-thioguanosine substitution appears to be minimal based on NMR and Circular Dichroism (CD) data.
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Affiliation(s)
- Michał Gładysz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznan, Noskowskiego 12/14, Poland
| | - Witold Andrałojć
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznan, Noskowskiego 12/14, Poland
| | - Tomasz Czapik
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznan, Noskowskiego 12/14, Poland
| | - Zofia Gdaniec
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznan, Noskowskiego 12/14, Poland
| | - Ryszard Kierzek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznan, Noskowskiego 12/14, Poland.
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Graifer D, Karpova G. Photoactivatable RNA derivatives as tools for studying the structural and functional organization of complex cellular ribonucleoprotein machineries. RSC Adv 2013. [DOI: 10.1039/c2ra22095d] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
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Graifer D, Karpova G. Structural and functional topography of the human ribosome. Acta Biochim Biophys Sin (Shanghai) 2012; 44:281-99. [PMID: 22257731 DOI: 10.1093/abbs/gmr118] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
This review covers data on the structural organization of functional sites in the human ribosome, namely, the messenger RNA binding center, the binding site of the hepatitis C virus RNA internal ribosome entry site, and the peptidyl transferase center. The data summarized here have been obtained primarily by means of a site-directed cross-linking approach with application of the analogs of the respective ribosomal ligands bearing cross-linkers at the designed positions. These data are discussed taking into consideration available structural data on ribosomes from various kingdoms obtained with the use of cryo-electron microscopy, X-ray crystallography, and other approaches.
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Affiliation(s)
- Dmitri Graifer
- Laboratory of Ribosome Structure and Functions, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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Bulygin K, Baouz-Drahy S, Graifer D, Favre A, Karpova G. Sites of 18S rRNA contacting mRNA 3' and 5' of the P site codon in human ribosome: a cross-linking study with mRNAs carrying 4-thiouridines at specific positions. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2008; 1789:167-74. [PMID: 19118656 DOI: 10.1016/j.bbagrm.2008.12.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2008] [Revised: 11/27/2008] [Accepted: 12/02/2008] [Indexed: 10/21/2022]
Abstract
Long synthetic mRNAs were used to study the positioning of the E site codon, the 2nd and 3rd nucleotides of the A site bound codon and a nucleotide 3' of this codon with respect to the 18S rRNA in the human 80S ribosome. The mRNAs contained a GAC triplet coding for Asp and a single 4-thiouridine residue (s(4)U) upstream or downstream of the GAC codon. In the presence of tRNA(Asp), the GAC codon of the mRNAs was targeted to the ribosomal P site thus placing s(4)U in one of the following positions -3, -2, -1, +5, +6 or +7 with respect to the first nucleotide of the P site bound codon. It was found that mRNAs that bore s(4)U in positions +5 to +7 cross-linked to the 18S rRNA nucleotides C1696, C1698 and 1820-1825, the distribution of cross-links among these targets depending on the position of s(4)U. Cross-links of mRNAs containing s(4)U in positions -3 to -1 were found in the region 1699-1704 of the 18S rRNA. In the absence of tRNA, all mRNAs cross-linked only to C1696 and C1698. Absence of the cross-linked nucleotides C1696 and C1698 in the case of mRNAs containing s(4)U in positions -3 to -1 confirmed that tRNA(Asp) actually phased the mRNA on the ribosome.
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Affiliation(s)
- Konstantin Bulygin
- Institut Jacques Monod, Laboratoire de Photobiologie Moléculaire (CNRS-UMR 7033, BioMoCeTi) Universités Paris 6 et Paris 13, 75251 Paris Cedex 05, France
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Graifer D, Molotkov M, Styazhkina V, Demeshkina N, Bulygin K, Eremina A, Ivanov A, Laletina E, Ven'yaminova A, Karpova G. Variable and conserved elements of human ribosomes surrounding the mRNA at the decoding and upstream sites. Nucleic Acids Res 2004; 32:3282-93. [PMID: 15208366 PMCID: PMC443533 DOI: 10.1093/nar/gkh657] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2004] [Revised: 05/20/2004] [Accepted: 06/01/2004] [Indexed: 11/12/2022] Open
Abstract
This study is centred upon an important biological problem concerning the structural organization of mammalian ribosomes that cannot be studied by X-ray analysis because 80S ribosome crystals are still unavailable. Here, positioning of the mRNA on 80S ribosomes was studied using mRNA analogues containing the perfluorophenylazide cross-linker on either the guanosine or an uridine residue. The modified nucleotides were directed to positions from -9 to +6 with respect to the first nucleotide of the P site bound codon by a tRNA cognate to the triplet targeted to the P site. Upon mild UV-irradiation, the modified nucleotides at positions +4 to +6 cross-linked to protein S15 and 18S rRNA nucleotides A1823-A1825. In addition, modified guanosines in positions +5 and +6 also cross-linked to G626, and in position +1 to G1702. Cross-linking from the upstream positions was mainly to protein S26 that has no prokaryotic homologues. These findings indicate that the tail of mammalian S15 comes closer to the decoding site than that of its prokaryotic homologue S19, and that the environments of the upstream part of mRNA on 80S and 70S ribosomes differ. On the other hand, the results confirm the widely accepted idea regarding the conserved nature of the decoding site of the small subunit rRNA.
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Affiliation(s)
- Dmitri Graifer
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentieva, 8, Novosibirsk, 630090, Russia
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Sergiev P, Leonov A, Dokudovskaya S, Shpanchenko O, Dontsova O, Bogdanov A, Rinke-Appel J, Mueller F, Osswald M, von Knoblauch K, Brimacombe R. Correlating the X-ray structures for halo- and thermophilic ribosomal subunits with biochemical data for the Escherichia coli ribosome. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2003; 66:87-100. [PMID: 12762011 DOI: 10.1101/sqb.2001.66.87] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- P Sergiev
- Department of Chemistry of Natural Compounds and Belozersky Institute, Moscow State University, Moscow 119899, Russia
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Demeshkina N, Laletina E, Meschaninova M, Ven'yaminova A, Graifer D, Karpova G. Positioning of mRNA codons with respect to 18S rRNA at the P and E sites of human ribosome. BIOCHIMICA ET BIOPHYSICA ACTA 2003; 1627:39-46. [PMID: 12759190 DOI: 10.1016/s0167-4781(03)00072-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Positioning of each nucleotide of the E site and the P site bound codons with respect to the 18S rRNA on the human ribosome was studied by cross-linking with mRNA analogs, derivatives of the hexaribonucleotide UUUGUU (comprising Phe and Val codons) that carried a perfluorophenylazide group on the second or the third uracil, and a derivative of the dodecaribonucleotide UUAGUAUUUAUU with a similar group on the guanine residue. The location of the modified nucleotides at any mRNA position from -3 to +3 (position +1 corresponds to the 5' nucleotide of the P site bound codon) was adjusted by the cognate tRNAs. A modified uridine at positions from -1 to +3 cross-linked to nucleotide G1207 of the 18S rRNA, and to nucleotide G961 when it was in position -2. A modified guanosine cross-linked to nucleotide G1207 if it was in position -3 of the mRNA. These data indicate that nucleotide G961 of the 18S rRNA is close only to mRNA positions -3 and -2, while G1207 is in the vicinity of positions from -3 to +3. The latter suggests that there is a sharp turn between the P and E site bound codons that brings nucleotide G1207 of the 18S rRNA close to each nucleotide of these codons. This correlates well with X-ray crystallographic data on bacterial ribosomes, indicating existence of a sharp turn between the P site and E site bound codons near a conserved nucleotide G926 of the 16S rRNA (corresponding to G1207 in 18S rRNA) close to helix 23b containing the conserved nucleotide 693 of the 16S rRNA (corresponding exactly to G961 of the 18S rRNA).
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Affiliation(s)
- Natalia Demeshkina
- Laboratory of Ribosomal Structure and Function, and Group of Oligoribonucleotide Chemistry, Novosibirsk Institute of Bioorganic Chemistry, Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentieva, 8, 630090, Novosibirsk, Russia
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Sloma MS, Nygård O. Possible interaction sites of mRNA, tRNA, translation factors and the nascent peptide in 5S, 5.8S and 28S rRNA in in vivo assembled eukaryotic ribosomal complexes. BIOCHIMICA ET BIOPHYSICA ACTA 2001; 1521:30-8. [PMID: 11690633 DOI: 10.1016/s0167-4781(01)00286-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
We have investigated possible interaction sites for mRNA, tRNA, translation factors and the nascent peptide on 5S, 5.8S and 28S rRNA in in vivo assembled translational active mouse ribosomes by comparing the chemical footprinting patterns derived from native polysomes, salt-washed polysomes (mainly lacking translational factors) and salt-washed runoff ribosomes (lacking mRNA, tRNA and translational factors). Several ligand-induced footprints were observed in 28S rRNA while no reactivity changes were seen in 5S and 5.8S rRNA. Footprints derived from mRNA, tRNA and/or the nascent peptide chain were observed in domain I of 28S rRNA (hairpin 23), in domain II (helix 37/38 and helices 42 and 43 and in the eukaryotic expansion segment 15), in domain IV (helices 67 and 74) and in domain V (helices 94 and 96 and in the peptidyl transferase ring). Some of the protected sites were homologous to sites previously suggested to be involved in mRNA, tRNA and/or peptide binding in in vitro assembled prokaryotic complexes. Additional footprints were located in regions that have not previously been found involved in ligand binding. Part of these sites could derive from the nascent peptide in the exit channel of the ribosome.
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MESH Headings
- Animals
- Binding Sites
- CME-Carbodiimide/analogs & derivatives
- Eukaryotic Cells/chemistry
- Eukaryotic Cells/metabolism
- Ligands
- Liver/chemistry
- Liver/metabolism
- Mice
- Peptide Initiation Factors/chemistry
- Polyribosomes/chemistry
- Polyribosomes/metabolism
- Protein Structure, Secondary
- Protein Structure, Tertiary
- RNA, Messenger/chemistry
- RNA, Ribosomal, 28S/chemistry
- RNA, Ribosomal, 5.8S/chemistry
- RNA, Ribosomal, 5S/chemistry
- RNA, Transfer/chemistry
- Sulfuric Acid Esters
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Affiliation(s)
- M S Sloma
- Natural Science Section, Södertörns högskola, Huddinge, Sweden
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Abstract
Using X-ray crystallography, we have directly observed the path of mRNA in the 70S ribosome in Fourier difference maps at 7 A resolution. About 30 nucleotides of the mRNA are wrapped in a groove that encircles the neck of the 30S subunit. The Shine-Dalgarno helix is bound in a large cleft between the head and the back of the platform. At the interface, only about eight nucleotides (-1 to +7), centered on the junction between the A and P codons, are exposed, and bond almost exclusively to 16S rRNA. The mRNA enters the ribosome around position +13 to +15, the location of downstream pseudoknots that stimulate -1 translational frame shifting.
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MESH Headings
- Bacteriophage T4/genetics
- Base Pairing
- Base Sequence
- Binding Sites
- Codon/genetics
- Crystallography, X-Ray
- DNA-Binding Proteins/genetics
- Escherichia coli/genetics
- Fourier Analysis
- Frameshifting, Ribosomal
- Models, Molecular
- Molecular Sequence Data
- Nucleic Acid Conformation
- Protein Binding
- Protein Conformation
- Protein Subunits
- RNA, Messenger/chemistry
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 16S/metabolism
- Ribosomes/chemistry
- Ribosomes/genetics
- Ribosomes/metabolism
- Thermus thermophilus/chemistry
- Viral Proteins/genetics
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Affiliation(s)
- G Z Yusupova
- Center for Molecular Biology of RNA, Sinsheimer Laboratories, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
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Pioletti M, Schlünzen F, Harms J, Zarivach R, Glühmann M, Avila H, Bashan A, Bartels H, Auerbach T, Jacobi C, Hartsch T, Yonath A, Franceschi F. Crystal structures of complexes of the small ribosomal subunit with tetracycline, edeine and IF3. EMBO J 2001; 20:1829-39. [PMID: 11296217 PMCID: PMC125237 DOI: 10.1093/emboj/20.8.1829] [Citation(s) in RCA: 362] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The small ribosomal subunit is responsible for the decoding of genetic information and plays a key role in the initiation of protein synthesis. We analyzed by X-ray crystallography the structures of three different complexes of the small ribosomal subunit of Thermus thermophilus with the A-site inhibitor tetracycline, the universal initiation inhibitor edeine and the C-terminal domain of the translation initiation factor IF3. The crystal structure analysis of the complex with tetracycline revealed the functionally important site responsible for the blockage of the A-site. Five additional tetracycline sites resolve most of the controversial biochemical data on the location of tetracycline. The interaction of edeine with the small subunit indicates its role in inhibiting initiation and shows its involvement with P-site tRNA. The location of the C-terminal domain of IF3, at the solvent side of the platform, sheds light on the formation of the initiation complex, and implies that the anti-association activity of IF3 is due to its influence on the conformational dynamics of the small ribosomal subunit.
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Affiliation(s)
- Marta Pioletti
- Max-Planck-Institut für Molekulare Genetik, Ihnestrasse 73, 14195 Berlin, FB Biologie, Chemie, Pharmazie, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Max-Planck-Research Unit for Ribosomal Structure, Notkestrasse 85, 22603 Hamburg, Göttingen Genomics Laboratory, Georg-August Universität, Griesebacherstrasse 8, 37077 Göttingen, Germany, Department of Structural Biology, Weizmann Institute, 76100 Rehovot, Israel and Centro de Investigaciones Biomédicas, Universidad de Carabobo, Las Delicias, Maracay, Venezuela Corresponding author e-mail:
M.Pioletti, F.Schlünzen and J.Harms contributed equally to this work
| | - Frank Schlünzen
- Max-Planck-Institut für Molekulare Genetik, Ihnestrasse 73, 14195 Berlin, FB Biologie, Chemie, Pharmazie, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Max-Planck-Research Unit for Ribosomal Structure, Notkestrasse 85, 22603 Hamburg, Göttingen Genomics Laboratory, Georg-August Universität, Griesebacherstrasse 8, 37077 Göttingen, Germany, Department of Structural Biology, Weizmann Institute, 76100 Rehovot, Israel and Centro de Investigaciones Biomédicas, Universidad de Carabobo, Las Delicias, Maracay, Venezuela Corresponding author e-mail:
M.Pioletti, F.Schlünzen and J.Harms contributed equally to this work
| | - Jörg Harms
- Max-Planck-Institut für Molekulare Genetik, Ihnestrasse 73, 14195 Berlin, FB Biologie, Chemie, Pharmazie, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Max-Planck-Research Unit for Ribosomal Structure, Notkestrasse 85, 22603 Hamburg, Göttingen Genomics Laboratory, Georg-August Universität, Griesebacherstrasse 8, 37077 Göttingen, Germany, Department of Structural Biology, Weizmann Institute, 76100 Rehovot, Israel and Centro de Investigaciones Biomédicas, Universidad de Carabobo, Las Delicias, Maracay, Venezuela Corresponding author e-mail:
M.Pioletti, F.Schlünzen and J.Harms contributed equally to this work
| | - Raz Zarivach
- Max-Planck-Institut für Molekulare Genetik, Ihnestrasse 73, 14195 Berlin, FB Biologie, Chemie, Pharmazie, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Max-Planck-Research Unit for Ribosomal Structure, Notkestrasse 85, 22603 Hamburg, Göttingen Genomics Laboratory, Georg-August Universität, Griesebacherstrasse 8, 37077 Göttingen, Germany, Department of Structural Biology, Weizmann Institute, 76100 Rehovot, Israel and Centro de Investigaciones Biomédicas, Universidad de Carabobo, Las Delicias, Maracay, Venezuela Corresponding author e-mail:
M.Pioletti, F.Schlünzen and J.Harms contributed equally to this work
| | - Marco Glühmann
- Max-Planck-Institut für Molekulare Genetik, Ihnestrasse 73, 14195 Berlin, FB Biologie, Chemie, Pharmazie, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Max-Planck-Research Unit for Ribosomal Structure, Notkestrasse 85, 22603 Hamburg, Göttingen Genomics Laboratory, Georg-August Universität, Griesebacherstrasse 8, 37077 Göttingen, Germany, Department of Structural Biology, Weizmann Institute, 76100 Rehovot, Israel and Centro de Investigaciones Biomédicas, Universidad de Carabobo, Las Delicias, Maracay, Venezuela Corresponding author e-mail:
M.Pioletti, F.Schlünzen and J.Harms contributed equally to this work
| | - Horacio Avila
- Max-Planck-Institut für Molekulare Genetik, Ihnestrasse 73, 14195 Berlin, FB Biologie, Chemie, Pharmazie, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Max-Planck-Research Unit for Ribosomal Structure, Notkestrasse 85, 22603 Hamburg, Göttingen Genomics Laboratory, Georg-August Universität, Griesebacherstrasse 8, 37077 Göttingen, Germany, Department of Structural Biology, Weizmann Institute, 76100 Rehovot, Israel and Centro de Investigaciones Biomédicas, Universidad de Carabobo, Las Delicias, Maracay, Venezuela Corresponding author e-mail:
M.Pioletti, F.Schlünzen and J.Harms contributed equally to this work
| | - Anat Bashan
- Max-Planck-Institut für Molekulare Genetik, Ihnestrasse 73, 14195 Berlin, FB Biologie, Chemie, Pharmazie, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Max-Planck-Research Unit for Ribosomal Structure, Notkestrasse 85, 22603 Hamburg, Göttingen Genomics Laboratory, Georg-August Universität, Griesebacherstrasse 8, 37077 Göttingen, Germany, Department of Structural Biology, Weizmann Institute, 76100 Rehovot, Israel and Centro de Investigaciones Biomédicas, Universidad de Carabobo, Las Delicias, Maracay, Venezuela Corresponding author e-mail:
M.Pioletti, F.Schlünzen and J.Harms contributed equally to this work
| | - Heike Bartels
- Max-Planck-Institut für Molekulare Genetik, Ihnestrasse 73, 14195 Berlin, FB Biologie, Chemie, Pharmazie, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Max-Planck-Research Unit for Ribosomal Structure, Notkestrasse 85, 22603 Hamburg, Göttingen Genomics Laboratory, Georg-August Universität, Griesebacherstrasse 8, 37077 Göttingen, Germany, Department of Structural Biology, Weizmann Institute, 76100 Rehovot, Israel and Centro de Investigaciones Biomédicas, Universidad de Carabobo, Las Delicias, Maracay, Venezuela Corresponding author e-mail:
M.Pioletti, F.Schlünzen and J.Harms contributed equally to this work
| | - Tamar Auerbach
- Max-Planck-Institut für Molekulare Genetik, Ihnestrasse 73, 14195 Berlin, FB Biologie, Chemie, Pharmazie, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Max-Planck-Research Unit for Ribosomal Structure, Notkestrasse 85, 22603 Hamburg, Göttingen Genomics Laboratory, Georg-August Universität, Griesebacherstrasse 8, 37077 Göttingen, Germany, Department of Structural Biology, Weizmann Institute, 76100 Rehovot, Israel and Centro de Investigaciones Biomédicas, Universidad de Carabobo, Las Delicias, Maracay, Venezuela Corresponding author e-mail:
M.Pioletti, F.Schlünzen and J.Harms contributed equally to this work
| | - Carsten Jacobi
- Max-Planck-Institut für Molekulare Genetik, Ihnestrasse 73, 14195 Berlin, FB Biologie, Chemie, Pharmazie, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Max-Planck-Research Unit for Ribosomal Structure, Notkestrasse 85, 22603 Hamburg, Göttingen Genomics Laboratory, Georg-August Universität, Griesebacherstrasse 8, 37077 Göttingen, Germany, Department of Structural Biology, Weizmann Institute, 76100 Rehovot, Israel and Centro de Investigaciones Biomédicas, Universidad de Carabobo, Las Delicias, Maracay, Venezuela Corresponding author e-mail:
M.Pioletti, F.Schlünzen and J.Harms contributed equally to this work
| | - Thomas Hartsch
- Max-Planck-Institut für Molekulare Genetik, Ihnestrasse 73, 14195 Berlin, FB Biologie, Chemie, Pharmazie, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Max-Planck-Research Unit for Ribosomal Structure, Notkestrasse 85, 22603 Hamburg, Göttingen Genomics Laboratory, Georg-August Universität, Griesebacherstrasse 8, 37077 Göttingen, Germany, Department of Structural Biology, Weizmann Institute, 76100 Rehovot, Israel and Centro de Investigaciones Biomédicas, Universidad de Carabobo, Las Delicias, Maracay, Venezuela Corresponding author e-mail:
M.Pioletti, F.Schlünzen and J.Harms contributed equally to this work
| | - Ada Yonath
- Max-Planck-Institut für Molekulare Genetik, Ihnestrasse 73, 14195 Berlin, FB Biologie, Chemie, Pharmazie, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Max-Planck-Research Unit for Ribosomal Structure, Notkestrasse 85, 22603 Hamburg, Göttingen Genomics Laboratory, Georg-August Universität, Griesebacherstrasse 8, 37077 Göttingen, Germany, Department of Structural Biology, Weizmann Institute, 76100 Rehovot, Israel and Centro de Investigaciones Biomédicas, Universidad de Carabobo, Las Delicias, Maracay, Venezuela Corresponding author e-mail:
M.Pioletti, F.Schlünzen and J.Harms contributed equally to this work
| | - François Franceschi
- Max-Planck-Institut für Molekulare Genetik, Ihnestrasse 73, 14195 Berlin, FB Biologie, Chemie, Pharmazie, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Max-Planck-Research Unit for Ribosomal Structure, Notkestrasse 85, 22603 Hamburg, Göttingen Genomics Laboratory, Georg-August Universität, Griesebacherstrasse 8, 37077 Göttingen, Germany, Department of Structural Biology, Weizmann Institute, 76100 Rehovot, Israel and Centro de Investigaciones Biomédicas, Universidad de Carabobo, Las Delicias, Maracay, Venezuela Corresponding author e-mail:
M.Pioletti, F.Schlünzen and J.Harms contributed equally to this work
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Abstract
Chemical cleavage is developing into a powerful tool for analysis and characterization of nucleic acids. Phenanthroline-Cu(II) cleavage has been used extensively for studies of DNA for the last two decades, but recently has been applied to structural studies of RNA as well. This approach has been used to study the structure and structural changes occurring in ribosomal RNA within the ribosomes. In this article we discuss the mechanism by which phenanthroline cleaves, the applications possible using this approach, and the results that can be obtained. Protocols for use of phenanthroline are outlined as well.
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Affiliation(s)
- G W Muth
- Division of Biological Sciences and Department of Chemistry, University of Montana, Missoula, Montana 59812, USA
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14
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Metzler DE, Metzler CM, Sauke DJ. Ribosomes and the Synthesis of Proteins. Biochemistry 2001. [DOI: 10.1016/b978-012492543-4/50032-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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15
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Shapkina TG, Dolan MA, Babin P, Wollenzien P. Initiation factor 3-induced structural changes in the 30 S ribosomal subunit and in complexes containing tRNA(f)(Met) and mRNA. J Mol Biol 2000; 299:615-28. [PMID: 10835272 DOI: 10.1006/jmbi.2000.3774] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Initiation factor 3 (IF3) acts to switch the decoding preference of the small ribosomal subunit from elongator to initiator tRNA. The effects of IF3 on the 30 S ribosomal subunit and on the 30 S.mRNA. tRNA(f)(Met) complex were determined by UV-induced RNA crosslinking. Three intramolecular crosslinks in the 16 S rRNA (of the 14 that were monitored by gel electrophoresis) are affected by IF3. These are the crosslinks between C1402 and C1501 within the decoding region, between C967xC1400 joining the end loop of a helix of 16 S rRNA domain III and the decoding region, and between U793 and G1517 joining the 790 end loop of 16 S rRNA domain II and the end loop of the terminal helix. These changes occur even in the 30 S.IF3 complex, indicating they are not mediated through tRNA(f)(Met) or mRNA. UV-induced crosslinks occur between 16 S rRNA position C1400 and tRNA(f)(Met) position U34, in tRNA(f)(Met) the nucleotide adjacent to the 5' anticodon nucleotide, and between 16 S rRNA position C1397 and the mRNA at positions +9 and +10 (where A of the initiator AUG codon is +1). The presence of IF3 reduces both of these crosslinks by twofold and fourfold, respectively. The binding site for IF3 involves the 790 region, some other parts of the 16 S rRNA domain II and the terminal stem/loop region. These are located in the front bottom part of the platform structure in the 30 S subunit, a short distance from the decoding region. The changes that occur in the decoding region, even in the absence of mRNA and tRNA, may be induced by IF3 from a short distance or could be caused by the second IF3 structural domain.
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MESH Headings
- Alkalies/metabolism
- Anticodon/genetics
- Bacterial Proteins/chemistry
- Bacterial Proteins/metabolism
- Base Sequence
- Binding Sites/radiation effects
- Escherichia coli/chemistry
- Escherichia coli/genetics
- Hydrolysis
- Models, Molecular
- Nucleic Acid Conformation
- Peptide Initiation Factors/chemistry
- Peptide Initiation Factors/metabolism
- Prokaryotic Initiation Factor-3
- Protein Binding/radiation effects
- Protein Structure, Tertiary
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 16S/metabolism
- RNA, Transfer, Met/genetics
- RNA, Transfer, Met/metabolism
- RNA-Binding Proteins/chemistry
- RNA-Binding Proteins/metabolism
- Ribosomal Proteins/chemistry
- Ribosomal Proteins/metabolism
- Ribosomes/chemistry
- Ribosomes/genetics
- Ribosomes/metabolism
- Transcription, Genetic/genetics
- Ultraviolet Rays
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Affiliation(s)
- T G Shapkina
- Department of Biochemistry, North Carolina State University, Raleigh, NC, Box 7622, USA
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16
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Environment of the 5′-terminal nucleotide of the mRNA codon at the P and E sites of human ribosome: Crosslinking with pUUUGUU derivatives bearing a photoactivatable group at an uracil residue or 5′-phosphate. Mol Biol 2000. [DOI: 10.1007/bf02759645] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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17
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Wang R, Alexander RW, VanLoock M, Vladimirov S, Bukhtiyarov Y, Harvey SC, Cooperman BS. Three-dimensional placement of the conserved 530 loop of 16 S rRNA and of its neighboring components in the 30 S subunit. J Mol Biol 1999; 286:521-40. [PMID: 9973568 DOI: 10.1006/jmbi.1998.2493] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Nucleotides 518-533 form a loop in ribosomal 30 S subunits that is almost universally conserved. Both biochemical and genetic evidence clearly implicate the 530 loop in ribosomal function, with respect both to the accuracy control mechanism and to tRNA binding. Here, building on earlier work, we identify proteins and nucleotides (or limited sequences) site-specifically photolabeled by radioactive photolabile oligoDNA probes targeted toward the 530 loop of 30 S subunits. The probes we employ are complementary to 16 S rRNA nucleotides 517-527, and have aryl azides attached to nucleotides complementary to nucleotides 518, 522, and 525-527, positioning the photogenerated nitrene a maximum of 19-26 A from the complemented rRNA base. The crosslinks obtained are used as constraints to revise an earlier model of 30 S structure, using the YAMMP molecular modeling package, and to place the 530 loop region within that structure.
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MESH Headings
- Cross-Linking Reagents/radiation effects
- DNA, Complementary/metabolism
- Escherichia coli/chemistry
- Escherichia coli/ultrastructure
- Models, Molecular
- Nucleic Acid Conformation
- Photoaffinity Labels/radiation effects
- RNA, Bacterial/chemistry
- RNA, Bacterial/radiation effects
- RNA, Messenger/chemistry
- RNA, Messenger/radiation effects
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/radiation effects
- Ribosomal Proteins/chemistry
- Ribosomal Proteins/radiation effects
- Ribosomes/chemistry
- Ribosomes/metabolism
- Ribosomes/ultrastructure
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Affiliation(s)
- R Wang
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA
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18
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Hu MC, Tranque P, Edelman GM, Mauro VP. rRNA-complementarity in the 5' untranslated region of mRNA specifying the Gtx homeodomain protein: evidence that base- pairing to 18S rRNA affects translational efficiency. Proc Natl Acad Sci U S A 1999; 96:1339-44. [PMID: 9990025 PMCID: PMC15464 DOI: 10.1073/pnas.96.4.1339] [Citation(s) in RCA: 68] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Numerous eukaryotic mRNAs contain sequences complementary to segments of the 18S and 28S rRNAs. Previous studies raised the possibility that these complementarities might allow mRNA-rRNA interactions and affect rates of translation. In the present study, we investigated the mRNA encoding the mouse Gtx homeodomain protein. This mRNA contains within its 5' untranslated region (UTR) a segment that is complementary to two regions of the 18S rRNA, located at nucleotides 701-741 and 1104-1136. A Gtx RNA probe containing this complementarity could be photochemically cross-linked to ribosomal subunits through a linkage to 18S rRNA but not to 28S rRNA. Oligonucleotide-directed RNase H digestion of the rRNA and a reverse transcription analysis localized the cross-linked probe to the complementary segment of 18S rRNA at nucleotides 1104-1136 but not at nucleotides 701-741. To determine whether complementarity in the Gtx mRNA affected translation, a mutational analysis was performed with a Gtx-luciferase fusion construct and four related constructs with altered complementarity to the 18S rRNA. These constructs were examined for their ability to be translated in cell-free lysates prepared from P19 embryonal carcinoma and C6 glioma cell lines and after cellular transfection into these same cell lines. In both cell-free translation and transfection studies, the rate of translation decreased more than 9-fold as the degree of complementarity to nucleotides 1104-1136 of the 18S rRNA increased. We hypothesize that segments complementary to rRNA, such as those contained within the Gtx mRNA, form a category of cis-acting regulatory elements in mRNAs that affect translation by base pairing to rRNA within ribosomes.
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MESH Headings
- Animals
- Base Pairing
- Base Sequence
- Binding Sites
- Cell Line
- Cell-Free System
- Homeodomain Proteins/biosynthesis
- Homeodomain Proteins/genetics
- Luciferases/genetics
- Mice
- Molecular Sequence Data
- Protein Biosynthesis
- RNA Probes
- RNA, Messenger/chemistry
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Ribosomal, 18S/chemistry
- RNA, Ribosomal, 18S/genetics
- RNA, Ribosomal, 18S/metabolism
- Recombinant Fusion Proteins/biosynthesis
- Ribonuclease H
- Ribosomes/metabolism
- Sequence Alignment
- Sequence Homology, Amino Acid
- Transcription Factors/biosynthesis
- Transcription Factors/genetics
- Transcription, Genetic
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Affiliation(s)
- M C Hu
- Department of Neurobiology, The Scripps Research Institute and The Skaggs Institute for Chemical Biology, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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19
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Tranque P, Hu MC, Edelman GM, Mauro VP. rRNA complementarity within mRNAs: a possible basis for mRNA-ribosome interactions and translational control. Proc Natl Acad Sci U S A 1998; 95:12238-43. [PMID: 9770470 PMCID: PMC22815 DOI: 10.1073/pnas.95.21.12238] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Our recent demonstration that many eukaryotic mRNAs contain sequences complementary to rRNA led to the hypothesis that these sequences might mediate specific interactions between mRNAs and ribosomes and thereby affect translation. In the present experiments, the ability of complementary sequences to bind to rRNA was investigated by using photochemical cross-linking. RNA probes with perfect complementarity to 18S or 28S rRNA were shown to cross-link specifically to the corresponding rRNA within intact ribosomal subunits. Similar results were obtained by using probes based on natural mRNA sequences with varying degrees of complementarity to the 18S rRNA. RNase H cleavage localized four such probes to complementary regions of the 18S rRNA. The effects of complementarity on translation were assessed by using the mRNA encoding ribosomal protein S15. This mRNA contains a sequence within its coding region that is complementary to the 18S rRNA at 20 of 22 nucleotides. RNA from an S15-luciferase fusion construct was translated in a cell-free lysate and compared with the translation of four related constructs that were mutated to decrease complementarity to the 18S rRNA. These mutations did not alter the amino acid sequence or the codon bias. A correlation between complementarity and translation was observed; constructs with less complementarity increased the amount of translation up to 54%. These findings raised the possibility that direct base-pairing of particular mRNAs to rRNAs within ribosomes may function as a mechanism of translational control.
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Affiliation(s)
- P Tranque
- Department of Neurobiology, The Scripps Research Institute and The Skaggs Institute for Chemical Biology, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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20
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Matassova NB, Venjaminova AG, Karpova GG. Nucleotides of 18S rRNA surrounding mRNA at the decoding site of translating human ribosome as revealed from the cross-linking data. BIOCHIMICA ET BIOPHYSICA ACTA 1998; 1397:231-9. [PMID: 9565692 DOI: 10.1016/s0167-4781(98)00015-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
mRNA analogs, 4-(N-2-chloroethyl-N-methylamino)benzylmethyl-[5'-32P]-phosphamide derivatives of oligoribonucleotides pAUGUn (n=0, 3 or 6), were used for affinity labelling of human 80S ribosomes in complexes with codon-anticodon interaction at the P-site. These complexes were obtained in the presence of fractionated lysate from rabbit reticulocytes deprived of endogenous ribosomes and mRNAs. In all cases, 40S subunits were labelled preferentially. Within the subunits, both ribosomal proteins and 18S rRNA were modified. Ribosomal proteins cross-linked to pAUGUn derivatives were identified earlier. In this paper, nucleotides G-1010, G-1029, G-1033, G-1051, G-1054 and G-1059 of 18S rRNA cross-linked to both pAUG and pAUGU3 derivatives were identified by reverse transcription analysis.
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Affiliation(s)
- N B Matassova
- Laboratory of Ribosomal Structure and Functions, Novosibirsk Institute of Bioorganic Chemistry, Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentieva, 8, 630090, Novosibirsk, Russian Federation
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21
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Favre A, Saintomé C, Fourrey JL, Clivio P, Laugâa P. Thionucleobases as intrinsic photoaffinity probes of nucleic acid structure and nucleic acid-protein interactions. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 1998; 42:109-24. [PMID: 9540218 DOI: 10.1016/s1011-1344(97)00116-4] [Citation(s) in RCA: 153] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
In the past few years thionucleobases have been extensively used as intrinsic photolabels to probe the structure in solution of folded RNA molecules and to identify contacts within nucleic acids and/or between nucleic acids and proteins, in complex nucleoprotein assemblies. These thio residues such as 4-thiouracil found in E. coli tRNA and its non-natural congeners 4-thiothymine, 6-thioguanine and 6-mercaptopurine absorb light at wavelengths longer than 320 nm and, thus, can be selectively photoactivated. Synthetic or enzymatic procedures have been established, allowing the random or site-specific incorporation of thionucleotide(s) within a RNA (DNA) chain which, in most cases, retains unaltered structural and biological properties. Owing to the high photoreactivity of their triplet state (intersystem yield close to unity), 4-thiouracil and 4-thiothymine derivatives exhibit a high photocrosslinking ability towards pyrimidines (particularly thymine) but also purines. From the nature of the photoproducts obtained in base or nucleotide mixtures and in dinucleotides, the main photochemical pathway was identified as a (2 + 2) photoaddition of the excited C-S bond onto the 5, 6 double bond of pyrimidines yielding thietane intermediates whose structure could be characterized. Depending on the mutual orientation of these bonds in the thietanes, their subsequent dark rearrangement yielded, respectively, either the 5-4 or 6-4 bipyrimidine photoadduct. A similar mechanism appears to be involved in the formation of the unique photoadduct formed between 4-thiothymidine and adenosine. The higher reactivity of thymine derived acceptors can be explained by an additional pathway which involves hydrogen abstraction from the thymine methyl group, followed by radical recombination, leading to methylene linked bipyrimidines. The high photocrosslinking potential of thionucleosides inserted in nucleic acid chains has been used to probe RNA-RNA contacts within the ribosome permitting, in particular, the elucidation of the path of mRNA throughout the small ribosomal subunit. Functional interactions between the mRNA spliced sites and U RNAs could be detected within the spliceosome. Analysis of the photocrosslinks obtained within small endonucleolytic ribozymes in solution led to a tertiary folded pseudo-knot structure for the HDV ribozyme and allowed the construction of a Y form of a hammerhead ribozyme, which revealed to be in close agreement with the structure observed in crystals. Thionucleosides incorporated in nucleic acids crosslink efficiently amino-acid residues of proteins in contact with them. Despite the fact that little is known about the nature of the photoadducts formed, this approach has been extensively used to identify protein components interacting at a defined nucleic acid site and applied to various systems (replisome, spliceosome, transcription complexes and ribosomes).
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Affiliation(s)
- A Favre
- Institut Jacques Monod, CNRS-Université Paris VII, France
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22
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Bucklin DJ, van Waes MA, Bullard JM, Hill WE. Cleavage of 16S rRNA within the ribosome by mRNA modified in the A-site codon with phenanthroline-Cu(II). Biochemistry 1997; 36:7951-7. [PMID: 9201941 DOI: 10.1021/bi9624954] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Cleavage of 16S rRNA was obtained through mRNA modified at position +5 with the chemical cleavage agent 1,10-o-phenanthroline. In the presence of Cu2+, and after addition of reducing agent to the modified mRNA-70S complex, cleavage of proximal nucleotides within the 16S rRNA occurred. Primer extension analysis of 16S rRNA fragments revealed that nucleotides 528-532, 1196, and 1396-1397 were cleaved. Nucleotides 1053-1055 were also cleaved but did not show the same level of specificity as the former. These results provide evidence that at some point in the translation process these regions are all within 15 A of position +5, the A-site codon, on the mRNA.
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Affiliation(s)
- D J Bucklin
- Division of Biological Sciences, University of Montana, Missoula, Montana 59812, USA
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23
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Graifer DM, Malygin AA, Matasova NB, Mundus DA, Zenkova MA, Karpova GG. Studying functional significance of the sequence 980-1061 in the central domain of human 18S rRNA using complementary DNA probes. BIOCHIMICA ET BIOPHYSICA ACTA 1997; 1350:335-44. [PMID: 9061030 DOI: 10.1016/s0167-4781(96)00176-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Region 980-1061 in human 18S rRNA has been chosen on the basis of our previous results, indicating that cross-linking sites of the alkylating mRNA analogs are located within this region. In the present study, we have used 10 DNA 15-mers complementary to various overlapping sequences within the 18S rRNA positions 980-1061. Their abilities to bind selectively to the target rRNA sequences were proved by hydrolysis of 18S rRNA within heteroduplexes with the corresponding probes by RNase H. Four sequences (980-994, 987-1001, 1025-1039 and 1032-1046) were found to be well accessible for binding of the respective cDNA probes within 40S subunits. None of the oligomers inhibited tRNA(Phe)-dependent binding of oligo(U) messenger to 40S subunits and binding of Met-tRNA(imet) to 40S subunits in the presence of eIF-2 and nonhydrolysable GTP analog. Nevertheless, two probes (complementary to the 18S rRNA sequences 987-1001 and 1025-1039) being covalently attached to 40S subunits, inhibited translation of poly(U) by human 80S ribosomes in a cell-free system. The same oligomers revealed the most pronounced inhibitory action on the binding of messenger trinucleotide in the complex pAUG.40S.Met-tRNA(imet).eIF-2.GTP. Results of these functional assays demonstrate the importance of the 18S rRNA sequences 987-1001 and 1025-1039 for translation process on human ribosomes, most probably at the initiation step.
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Affiliation(s)
- D M Graifer
- Laboratory of Ribosomal Structure and Function, Novosibirsk Institute of Bioorganic Chemistry, Siberian Branch of the Russian Academy of Sciences, Russia
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24
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Abstract
The ribosome is a large multifunctional complex composed of both RNA and proteins. Biophysical methods are yielding low-resolution structures of the overall architecture of ribosomes, and high-resolution structures of individual proteins and segments of rRNA. Accumulating evidence suggests that the ribosomal RNAs play central roles in the critical ribosomal functions of tRNA selection and binding, translocation, and peptidyl transferase. Biochemical and genetic approaches have identified specific functional interactions involving conserved nucleotides in 16S and 23S rRNA. The results obtained by these quite different approaches have begun to converge and promise to yield an unprecedented view of the mechanism of translation in the coming years.
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Affiliation(s)
- R Green
- Center for Molecular Biology of RNA, Sinsheimer Laboratories, University of California, Santa Cruz 95064, USA
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25
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Van Ryk DI, Dahlberg AE. Structural changes in the 530 loop of Escherichia coli 16S rRNA in mutants with impaired translational fidelity. Nucleic Acids Res 1995; 23:3563-70. [PMID: 7567470 PMCID: PMC307238 DOI: 10.1093/nar/23.17.3563] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The higher order structure of the functionally important 530 loop in Escherichia coli 16S rRNA was studied in mutants with single base changes at position 517, which significantly impair translational fidelity. The 530 loop has been proposed to interact with the EF-Tu-GTP-aatRNA ternary complex during decoding. The reactivity at G530, U531 and A532 to the chemical probes kethoxal, CMCT and DMS respectively was increased in the mutant 16S rRNA compared with the wild-type, suggesting a more open 530 loop structure in the mutant ribosomes. This was supported by oligonucleotide binding experiments in which probes complementary to positions 520-526 and 527-533, but not control probes, showed increased binding to the 517C mutant 70S ribosomes compared with the non-mutant control. Furthermore, enzymatic digestion of 70S ribosomes with RNase T1, specific for single-stranded RNA, substantially cleaved both wild-type and mutant rRNAs between G524 and C525, two of the nucleotides involved in the 530 loop pseudoknot. This site was also cleaved in the 517C mutant, but not wild-type rRNA, by RNase V1. Such a result is still consistent with a more open 530 loop structure in the mutant ribosomes, since RNase V1 can cut at appropriately stacked single-stranded regions of RNA. Together these data indicate that the 517C mutant rRNA has a rather extensively unfolded 530 loop structure. Less extensive structural changes were found in mutants 517A and 517U, which caused less misreading. A correlation between the structural changes in the 530 loop and impaired translational accuracy is proposed.
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Affiliation(s)
- D I Van Ryk
- Department of Molecular and Cellular Biology and Biochemistry, Brown University, Providence, RI 02912, USA
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26
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27
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Juzumiene DI, Shapkina TG, Wollenzien P. Distribution of cross-links between mRNA analogues and 16 S rRNA in Escherichia coli 70 S ribosomes made under equilibrium conditions and their response to tRNA binding. J Biol Chem 1995; 270:12794-800. [PMID: 7759534 DOI: 10.1074/jbc.270.21.12794] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The interaction between mRNA and Escherichia coli ribosomes has been studied by photochemical cross-linking using mRNA analogues that contain 4-thiouridine (s4U) or s4U modified with azidophenylacyl bromide (APAB), either two nucleotides upstream or eight nucleotides downstream from the nucleotide sequence ACC, the codon for tRNA(Thr). The sequences of the mRNA analogues were described earlier (Stade, K., Rinke-Appel, J., and Brimacombe, R. (1989) Nucleic Acids Res. 17, 9889-9908; Rinke-Appel, J., Stade, K., and Brimacombe, R. (1991) EMBO J. 10, 2195-2202). Under equilibrium conditions, both of these mRNA analogues bind and cross-link to 70 S ribosomes without the presence of tRNA(Thr); however, there are significant increases both in binding and particularly in cross-linking in the presence of the tRNA(Thr). Four regions contain cross-linking sites that increase in the presence of tRNA, C1395, A532, A1196 (and minor sites around these three positions), and C1533/U1532. Three other cross-linking sites, U723, A845, and U1381, show very little change in extent of cross-linking when tRNA is present. A conformational change in the 30 S subunit allowing additional accessibility to the 16 S rRNA by the mRNA analogues upon tRNA binding best explains the behavior of the tRNA-dependent and tRNA-independent mRNA-16 S rRNA cross-linking sites.
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Affiliation(s)
- D I Juzumiene
- Department of Biochemistry, North Carolina State University, Raleigh 27695, USA
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28
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Malygin AA, Graifer DM, Bulygin KN, Zenkova MA, Yamkovoy VI, Stahl J, Karpova GG. Arrangement of mRNA at the decoding site of human ribosomes. 18S rRNA nucleotides and ribosomal proteins cross-linked to oligouridylate derivatives with alkylating groups at either the 3' or the 5' termini. EUROPEAN JOURNAL OF BIOCHEMISTRY 1994; 226:715-23. [PMID: 8001589 DOI: 10.1111/j.1432-1033.1994.tb20100.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Affinity labeling of human placental 80S ribosomes with mRNA analogs of up to 12 uridyl residues, i.e. alkylating derivatives of oligouridylates bearing either 4-(N-2-chloroethyl-N-methylamino)benzylmethylphosphamide group at the 5'-termini or 2',3'-O-[4-(N-2-chloroethyl-N-methylamino)]benzylidene residue attached to the 3'-termini, in the presence of cognate Phe-tRNA(Phe) has been investigated. All the mRNA analogs modified only the 40S subunit. The fraction of 18S rRNA modified by the mRNA analogs with the alkylating group at the 5'-end decreased dramatically with extension of the reagent oligouridylate moiety. Nucleotides of 18S rRNA alkylated with the mRNA analogs were determined using a reverse transcription technique. For the mRNA analogs with the alkylating groups at the 3'-termini, G1702 and G1763/G1764 were identified as the cross-linking sites. The intensities of the bands corresponding to reverse transcriptase stops depended on the length of the reagent oligouridylate moieties. Cross-linking sites of the mRNA analogs with the alkylating group at the 5'-termini on 18S rRNA were A1023, C1026, C1057 and A1058 for the (pU)3 and (pU)4 derivatives and a single nucleotide C1057 for the (pU)6 one. Ribosomal protein S26 was found as the main target of modification with the same derivatives of (pU)6 and (pU)12.
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Affiliation(s)
- A A Malygin
- Laboratory of Ribosomal Structure and Functions, Novosibirsk Institute of Bioorganic Chemistry, Siberian Division, Russian Academy of Sciences
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29
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Graifer DM, Juzumiene DI, Karpova GG, Wollenzien P. mRNA binding track in the human 80S ribosome for mRNA analogues randomly substituted with 4-thiouridine residues. Biochemistry 1994; 33:6201-6. [PMID: 7514889 DOI: 10.1021/bi00186a020] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The interaction between mRNA and 18S rRNA in human 80S ribosomes has been studied using synthetic mRNA analogues randomly substituted with 4-thiouridine, which can be photoactivated for cross-linking. Two mRNA analogues with different sequences have been used for complex formation with ribosomes without or with the presence of a cognate tRNA. Cross-linked 18S rRNA nucleotides were identified by reverse transcription analysis. The base U630 in 18S rRNA was the main target of cross-linking for both of the mRNA analogues studied, and three minor sites of cross-linking, A1060, U1046, and U966, were also identified. Thus, in the case of human 80S ribosomes, the set of nucleotide residues cross-linked to the mRNA analogues is significantly smaller than the twelve sites seen for Escherichia coli with these same two mRNA analogues [Bhangu, R., & Wollenzien, P. (1992) Biochemistry 31, 5937-5944]. The residue U630 is within a highly conserved region corresponding to the 530 loop region of eubacterial 16S rRNA; the cross-link to this site indicates that it plays a key role in interacting with mRNA on 80S ribosomes independently of the presence of a cognate tRNA at the P site.
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Affiliation(s)
- D M Graifer
- Department of Biochemistry, North Carolina State University, Raleigh 27695
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30
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Stade K, Riens S, Bochkariov D, Brimacombe R. Contacts between the growing peptide chain and the 23S RNA in the 50S ribosomal subunit. Nucleic Acids Res 1994; 22:1394-9. [PMID: 8190630 PMCID: PMC307996 DOI: 10.1093/nar/22.8.1394] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Peptides of defined length carrying a diazirine photoaffinity label attached either to the alpha-NH2 group of the N-terminal methionine residue, or to the epsilon-NH2 group of an immediately adjacent lysine residue, were prepared in situ on Escherichia coli ribosomes in the presence of a synthetic mRNA analogue. Peptide growth was stopped simply by withholding the aminoacyl-tRNA cognate to an appropriate downstream codon. After photo-activation at 350 nm the sites of cross-linking to ribosomal RNA were determined by our standard procedures; the C-terminal amino acid of each peptide was labelled with tritium, in order to confirm whether the individual cross-linked complexes contained the expected 'full-length' peptide, as opposed to shorter products. The shortest peptides became cross-linked to sites within the 'peptidyl transferase ring' of the 23S RNA, namely to positions 2062, 2506, 2585 and 2609. However, already when the peptide was three or four residues long, a new cross-link was observed several hundred nucleotides away in another secondary structural domain; this site, at position 1781, lies within one of several RNA regions which have been implicated in other studies as being located close to the peptidyl transferase ring. Further application of this approach, combined with model-building studies, should enable the path of the nascent peptide through the large ribosomal subunit to be definitively mapped.
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Affiliation(s)
- K Stade
- Max-Planck-Institut für Molekulare Genetik, Abteilung Wittmann, Berlin, Germany
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31
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Koo J, Spremulli L. Analysis of the translational initiation region on the Euglena gracilis chloroplast ribulose-bisphosphate carboxylase/oxygenase (rbcL) messenger RNA. J Biol Chem 1994. [DOI: 10.1016/s0021-9258(17)37313-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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32
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Ringquist S, MacDonald M, Gibson T, Gold L. Nature of the ribosomal mRNA track: analysis of ribosome-binding sites containing different sequences and secondary structures. Biochemistry 1993; 32:10254-62. [PMID: 7691171 DOI: 10.1021/bi00089a048] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The ribosomal mRNA track was investigated by toeprinting 30S ribosomes, in the presence or absence of tRNA, using a variety of different ribosome-binding sites. We found that: (1) the ribosome, by itself, recognizes the mRNA translational initiation site; (2) the ribosomal mRNA track makes extensive contact with mRNA independent of tRNA and the start codon; (3) ribosome-mRNA complexes are less stable than complexes containing tRNA; and (4) toeprinting can be used to analyze the contour of the ribosomal mRNA track, yielding information on its "height" as well as its "length" dimension. Examination of several ribosome-binding sites, including those containing very stable secondary structure, indicated that the "height" of the mRNA track is quite roomy, while the nucleotide distance between the site of Shine-Dalgarno annealing, the P site, and the 3'-edge of the mRNA track is fixed. The data suggest a mechanism for tethering regulatory elements to the ribosome during translation.
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Affiliation(s)
- S Ringquist
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder 80309
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33
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Rinke-Appel J, Jünke N, Brimacombe R, Dukudovskaya S, Dontsova O, Bogdanov A. Site-directed cross-linking of mRNA analogues to 16S ribosomal RNA; a complete scan of cross-links from all positions between '+1' and '+16' on the mRNA, downstream from the decoding site. Nucleic Acids Res 1993; 21:2853-9. [PMID: 8392709 PMCID: PMC309668 DOI: 10.1093/nar/21.12.2853] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
mRNA analogues containing 4-thiouridine residues at selected sites were used to extend our analysis of photo-induced cross-links between mRNA and 16S RNA to cover the entire downstream range between positions +1 and +16 on the mRNA (position +1 is the 5'-base of the P-site codon). No tRNA-dependent cross-links were observed from positions +1, +2, +3 or +5. Position +4 on the mRNA was cross-linked in a tRNA-dependent manner to 16S RNA at a site between nucleotides ca 1402-1415 (most probably to the modified residue 1402), and this was absolutely specific for the +4 position. Similarly, the previously observed cross-link to nucleotide 1052 was absolutely specific for the +6 position. The previously observed cross-links from +7 to nucleotide 1395 and from +11 to 532 were however seen to a lesser extent with certain types of mRNA sequence from neighbouring positions (+6 to +10, and +10 to +13, respectively); no tRNA-dependent cross-links to other sites on 16S RNA were found from these positions, and no cross-linking was seen from positions +14 to +16. In each case the effect of a second cognate tRNA (at the ribosomal A-site) on the level of cross-linking was studied, and the specificity of each cross-link was confirmed by translocation experiments with elongation factor G, using appropriate mRNA analogues.
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MESH Headings
- Base Sequence
- Binding Sites
- Cross-Linking Reagents
- Molecular Sequence Data
- Peptide Elongation Factor G
- Peptide Elongation Factors/pharmacology
- Photochemistry
- RNA, Messenger/chemistry
- RNA, Messenger/metabolism
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/metabolism
- RNA, Transfer, Met/pharmacology
- RNA, Transfer, Tyr/pharmacology
- Ribonuclease H/metabolism
- Thiouridine/chemistry
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Affiliation(s)
- J Rinke-Appel
- Max-Planck-Institut für Molekulare Genetik, Abteilung Wittmann, Berlin, Germany
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34
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Brown CM, McCaughan KK, Tate WP. Two regions of the Escherichia coli 16S ribosomal RNA are important for decoding stop signals in polypeptide chain termination. Nucleic Acids Res 1993; 21:2109-15. [PMID: 8502551 PMCID: PMC309472 DOI: 10.1093/nar/21.9.2109] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Two regions of the 16S rRNA, helix 34, and the aminoacyl site component of the decoding site at the base of helix 44, have been implicated in decoding of translational stop signals during the termination of protein synthesis. Antibiotics specific for these regions have been tested to see how they discriminate the decoding of UAA, UAG, and UGA by the two polypeptide chain release factors (RF-1 and RF-2). Spectinomycin, which interacts with helix 34, stimulated RF-1 dependent binding to the ribosome and termination. It also stimulated UGA dependent RF-2 termination at micromolar concentrations but inhibited UGA dependent RF-2 binding at higher concentrations. Alterations at position C1192 of helix 34, known to confer spectinomycin resistance, reduced the binding of f[3H]Met-tRNA to the peptidyl-tRNA site. They also impaired termination in vitro, with both factors and all three stop codons, although the effect was greater with RF-2 mediated reactions. These alterations had previously been shown to inhibit EF-G mediated translocation. As perturbations in helix 34 effect both termination and elongation reactions, these results indicate that helix 34 is close to the decoding site on the bacterial ribosome. Several antibiotics, hygromycin, neomycin and tetracycline, specific for the aminoacyl site, were shown to inhibit the binding and function of both RFs in termination with all three stop codons in vitro. These studies indicate that decoding of all stop signals is likely to occur at a similar site on the ribosome to the decoding of sense codons, the aminoacyl site, and are consistent with a location for helix 34 near this site.
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Affiliation(s)
- C M Brown
- Biochemistry Department, University of Otago, Dunedin, New Zealand
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