1
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Westhof E, Yusupov M, Yusupova G. Recognition of Watson-Crick base pairs: constraints and limits due to geometric selection and tautomerism. F1000PRIME REPORTS 2014; 6:19. [PMID: 24765524 PMCID: PMC3974571 DOI: 10.12703/p6-19] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The natural bases of nucleic acids have a strong preference for one tautomer form, guaranteeing fidelity in their hydrogen bonding potential. However, base pairs observed in recent crystal structures of polymerases and ribosomes are best explained by an alternative base tautomer, leading to the formation of base pairs with Watson-Crick-like geometries. These observations set limits to geometric selection in molecular recognition of complementary Watson-Crick pairs for fidelity in replication and translation processes.
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Affiliation(s)
- Eric Westhof
- Architecture et Réactivité de l’ARN, Université de Strasbourg, Institut de Biologie Moléculaire et CellulaireCNRS, 15 rue René Descartes, F-67084 Strasbourg CedexFrance
| | - Marat Yusupov
- Département de Biologie et de Génomique Structurales, Institut de Génétique et de Biologie Moléculaire et CellulaireCNRS, INSERM, Université de Strasbourg, F-67400 IllkirchFrance
| | - Gulnara Yusupova
- Département de Biologie et de Génomique Structurales, Institut de Génétique et de Biologie Moléculaire et CellulaireCNRS, INSERM, Université de Strasbourg, F-67400 IllkirchFrance
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2
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Das G, Lyngdoh RHD. Configuration of wobble base pairs having pyrimidines as anticodon wobble bases: significance for codon degeneracy. J Biomol Struct Dyn 2013; 32:1500-20. [PMID: 23968386 DOI: 10.1080/07391102.2013.824822] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Degeneracy of the genetic code was attributed by Crick to imprecise hydrogen-bonded base-pairing at the wobble position during codon-anticodon pairing. The Crick wobble rules define but do not explain the RNA base pair combinations allowed at this position. We select six pyrimidine bases functioning as anticodon wobble bases (AWBs) to study their H-bonded pairing properties with the four major RNA bases using density functional theory at the B3LYP/6-31G(d,p) level. This is done to assess the extent to which the configuration of a solitary RNA wobble base pair may in itself determine specificity and degeneracy of the genetic code by allowing or disallowing the given base pair during codon-anticodon pairing. Calculated values of select configuration markers for the base pairs screen well between allowed and disallowed base pairs for most cases examined here, where the base pair width emerges as an important factor. A few allowed wobble pairs invoke the involvement of RNA nucleoside conformation, as well as involvement of the exocyclic substituent in H-bonding. This study, however, cannot explain the disallowed status of the Ura⋯Gua wobble pair on the basis of configuration alone. Explanation of the allowed status of the V⋯Ura pair requires further study on the mediatory role of water molecules. Apart from these two cases, these computational results are sufficient, on the basis of base pair configuration alone, to account for the specificity and degeneracy of the genetic code for all known cases of codon-anticodon pairing which involve the pyrimidine AWBs studied here.
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Affiliation(s)
- Gunajyoti Das
- a Department of Chemistry , North-Eastern Hill University , Shillong , 793022 , India
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3
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Khade PK, Shi X, Joseph S. Steric complementarity in the decoding center is important for tRNA selection by the ribosome. J Mol Biol 2013; 425:3778-89. [PMID: 23542008 DOI: 10.1016/j.jmb.2013.02.038] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Revised: 02/23/2013] [Accepted: 02/27/2013] [Indexed: 11/27/2022]
Abstract
Accurate tRNA selection by the ribosome is essential for the synthesis of functional proteins. Previous structural studies indicated that the ribosome distinguishes between cognate and near-cognate tRNAs by monitoring the geometry of the codon-anticodon helix in the decoding center using the universally conserved 16S ribosomal RNA bases G530, A1492 and A1493. These bases form hydrogen bonds with the 2'-hydroxyl groups of the codon-anticodon helix, which are expected to be disrupted with a near-cognate codon-anticodon helix. However, a recent structural study showed that G530, A1492 and A1493 form hydrogen bonds in a manner identical with that of both cognate and near-cognate codon-anticodon helices. To understand how the ribosome discriminates between cognate and near-cognate tRNAs, we made 2'-deoxynucleotide and 2'-fluoro substituted mRNAs, which disrupt the hydrogen bonds between the A site codon and G530, A1492 and A1493. Our results show that multiple 2'-deoxynucleotide substitutions in the mRNA substantially inhibit tRNA selection, whereas multiple 2'-fluoro substitutions in the mRNA have only modest effects on tRNA selection. Furthermore, the miscoding antibiotics paromomycin and streptomycin rescue the defects in tRNA selection with the multiple 2'-deoxynucleotide substituted mRNA. These results suggest that steric complementarity in the decoding center is more important than the hydrogen bonds between the A site codon and G530, A1492 and A1493 for tRNA selection.
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Affiliation(s)
- Prashant K Khade
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0314, USA
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4
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Vallabhaneni H, Farabaugh PJ. Accuracy modulating mutations of the ribosomal protein S4-S5 interface do not necessarily destabilize the rps4-rps5 protein-protein interaction. RNA (NEW YORK, N.Y.) 2009; 15:1100-9. [PMID: 19386726 PMCID: PMC2685513 DOI: 10.1261/rna.1530509] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2008] [Accepted: 02/24/2009] [Indexed: 05/24/2023]
Abstract
During the process of translation, an aminoacyl tRNA is selected in the A site of the decoding center of the small subunit based on the correct codon-anticodon base pairing. Though selection is usually accurate, mutations in the ribosomal RNA and proteins and the presence of some antibiotics like streptomycin alter translational accuracy. Recent crystallographic structures of the ribosome suggest that cognate tRNAs induce a "closed conformation" of the small subunit that stabilizes the codon-anticodon interactions at the A site. During formation of the closed conformation, the protein interface between rpS4 and rpS5 is broken while new contacts form with rpS12. Mutations in rpS12 confer streptomycin resistance or dependence and show a hyperaccurate phenotype. Mutations reversing streptomycin dependence affect rpS4 and rpS5. The canonical rpS4 and rpS5 streptomycin independent mutations increase translational errors and were called ribosomal ambiguity mutations (ram). The mutations in these proteins are proposed to affect formation of the closed complex by breaking the rpS4-rpS5 interface, which reduces the cost of domain closure and thus increases translational errors. We used a yeast two-hybrid system to study the interactions between the small subunit ribosomal proteins rpS4 and rpS5 and to test the effect of ram mutations on the stability of the interface. We found no correlation between ram phenotype and disruption of the interface.
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Affiliation(s)
- Haritha Vallabhaneni
- Program in Molecular and Cell Biology, Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, Maryland 21250, USA
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5
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Das G, Lyngdoh RD. Can configuration of solitary wobble base pairs determine the specificity and degeneracy of the genetic code? Clues from molecular orbital modelling studies. ACTA ACUST UNITED AC 2008. [DOI: 10.1016/j.theochem.2007.11.027] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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6
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Almlöf M, Andér M, Aqvist J. Energetics of codon-anticodon recognition on the small ribosomal subunit. Biochemistry 2007; 46:200-9. [PMID: 17198390 DOI: 10.1021/bi061713i] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Recent crystal structures of the small ribosomal subunit have made it possible to examine the detailed energetics of codon recognition on the ribosome by computational methods. The binding of cognate and near-cognate anticodon stem loops to the ribosome decoding center, with mRNA containing the Phe UUU and UUC codons, are analyzed here using explicit solvent molecular dynamics simulations together with the linear interaction energy (LIE) method. The calculated binding free energies are in excellent agreement with experimental binding constants and reproduce the relative effects of mismatches in the first and second codon position versus a mismatch at the wobble position. The simulations further predict that the Leu2 anticodon stem loop is about 10 times more stable than the Ser stem loop in complex with the Phe UUU codon. It is also found that the ribosome significantly enhances the intrinsic stability differences of codon-anticodon complexes in aqueous solution. Structural analysis of the simulations confirms the previously suggested importance of the universally conserved nucleotides A1492, A1493, and G530 in the decoding process.
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Affiliation(s)
- Martin Almlöf
- Department of Cell and Molecular Biology, Uppsala University Biomedical Center, Box 596, SE-751 24 Uppsala, Sweden
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7
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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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8
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Agris PF. Decoding the genome: a modified view. Nucleic Acids Res 2004; 32:223-38. [PMID: 14715921 PMCID: PMC384350 DOI: 10.1093/nar/gkh185] [Citation(s) in RCA: 266] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2003] [Revised: 12/02/2003] [Accepted: 12/02/2003] [Indexed: 11/12/2022] Open
Abstract
Transfer RNA's role in decoding the genome is critical to the accuracy and efficiency of protein synthesis. Though modified nucleosides were identified in RNA 50 years ago, only recently has their importance to tRNA's ability to decode cognate and wobble codons become apparent. RNA modifications are ubiquitous. To date, some 100 different posttranslational modifications have been identified. Modifications of tRNA are the most extensively investigated; however, many other RNAs have modified nucleosides. The modifications that occur at the first, or wobble position, of tRNA's anticodon and those 3'-adjacent to the anticodon are of particular interest. The tRNAs most affected by individual and combinations of modifications respond to codons in mixed codon boxes where distinction of the third codon base is important for discriminating between the correct cognate or wobble codons and the incorrect near-cognate codons (e.g. AAA/G for lysine versus AAU/C asparagine). In contrast, other modifications expand wobble codon recognition, such as U*U base pairing, for tRNAs that respond to multiple codons of a 4-fold degenerate codon box (e.g. GUU/A/C/G for valine). Whether restricting codon recognition, expanding wobble, enabling translocation, or maintaining the messenger RNA, reading frame modifications appear to reduce anticodon loop dynamics to that accepted by the ribosome. Therefore, we suggest that anticodon stem and loop domain nucleoside modifications allow a limited number of tRNAs to accurately and efficiently decode the 61 amino acid codons by selectively restricting some anticodon-codon interactions and expanding others.
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Affiliation(s)
- Paul F Agris
- Department of Molecular and Structural Biochemistry, 128 Polk Hall, Campus Box 7622, North Carolina State University, Raleigh, NC 27695-7622, USA.
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9
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Brodersen DE, Carter AP, Clemons WM, Morgan-Warren RJ, Murphy FV, Ogle JM, Tarry MJ, Wimberly BT, Ramakrishnan V. Atomic structures of the 30S subunit and its complexes with ligands and antibiotics. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2003; 66:17-32. [PMID: 12762005 DOI: 10.1101/sqb.2001.66.17] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- D E Brodersen
- MRC Laboratory of Molecular Biology, Cambridge CB2 2QH, United Kingdom
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10
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Ogle JM, Carter AP, Ramakrishnan V. Insights into the decoding mechanism from recent ribosome structures. Trends Biochem Sci 2003; 28:259-66. [PMID: 12765838 DOI: 10.1016/s0968-0004(03)00066-5] [Citation(s) in RCA: 289] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
During the decoding process, tRNA selection by the ribosome is far more accurate than expected from codon-anticodon pairing. Antibiotics such as streptomycin and paromomycin have long been known to increase the error rate of translation, and many mutations that increase or lower accuracy have been characterized. Recent crystal structures show that the specific recognition of base-pairing geometry leads to a closure of the domains of the small subunit around cognate tRNA. This domain closure is likely to trigger subsequent steps in tRNA selection. Many antibiotics and mutations act by making the domain closure more or less favourable. In conjunction with recent cryoelectron microscopy structures of the ribosome, a comprehensive structural understanding of the decoding process is beginning to emerge.
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Affiliation(s)
- James M Ogle
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK
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11
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Rodnina MV, Wintermeyer W. Fidelity of aminoacyl-tRNA selection on the ribosome: kinetic and structural mechanisms. Annu Rev Biochem 2002; 70:415-35. [PMID: 11395413 DOI: 10.1146/annurev.biochem.70.1.415] [Citation(s) in RCA: 231] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The ribosome discriminates between correct and incorrect aminoacyl-tRNAs (aa-tRNAs), or their complexes with elongation factor Tu (EF-Tu) and GTP, according to the match between anticodon and mRNA codon in the A site. Selection takes place at two stages, prior to GTP hydrolysis (initial selection) and after GTP hydrolysis but before peptide bond formation (proofreading). In part, discrimination results from different rejection rates that are due to different stabilities of the respective codon-anticodon complexes. An important additional contribution is provided by induced fit, in that only correct codon recognition leads to acceleration of rate-limiting rearrangements that precede chemical steps. Recent elucidation of ribosome structures and mutational analyses suggest which residues of the decoding center may be involved in signaling formation of the correct codon-anticodon duplex to the functional centers of the ribosome. In utilizing induced fit for substrate discrimination, the ribosome resembles other nucleic acid-programmed polymerases.
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Affiliation(s)
- M V Rodnina
- Institute of Physical Biochemistry, University of Witten/Herdecke, 58448 Witten, Germany.
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12
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Abstract
The publication of crystal structures of the 50S and 30S ribosomal subunits and the intact 70S ribosome is revolutionizing our understanding of protein synthesis. This review is an attempt to correlate the structures with biochemical and genetic data to identify the gaps and limits in our current knowledge of the mechanisms involved in translation.
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Affiliation(s)
- V Ramakrishnan
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, United Kingdom.
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13
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Ogle JM, Brodersen DE, Clemons WM, Tarry MJ, Carter AP, Ramakrishnan V. Recognition of cognate transfer RNA by the 30S ribosomal subunit. Science 2001; 292:897-902. [PMID: 11340196 DOI: 10.1126/science.1060612] [Citation(s) in RCA: 865] [Impact Index Per Article: 37.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Crystal structures of the 30S ribosomal subunit in complex with messenger RNA and cognate transfer RNA in the A site, both in the presence and absence of the antibiotic paromomycin, have been solved at between 3.1 and 3.3 angstroms resolution. Cognate transfer RNA (tRNA) binding induces global domain movements of the 30S subunit and changes in the conformation of the universally conserved and essential bases A1492, A1493, and G530 of 16S RNA. These bases interact intimately with the minor groove of the first two base pairs between the codon and anticodon, thus sensing Watson-Crick base-pairing geometry and discriminating against near-cognate tRNA. The third, or "wobble," position of the codon is free to accommodate certain noncanonical base pairs. By partially inducing these structural changes, paromomycin facilitates binding of near-cognate tRNAs.
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MESH Headings
- Anti-Bacterial Agents/metabolism
- Anti-Bacterial Agents/pharmacology
- Anticodon/chemistry
- Anticodon/metabolism
- Base Pairing
- Binding Sites
- Codon/chemistry
- Codon/metabolism
- Crystallography, X-Ray
- Guanosine Triphosphate/metabolism
- Hydrogen Bonding
- Models, Molecular
- Nucleic Acid Conformation
- Paromomycin/metabolism
- Paromomycin/pharmacology
- Peptide Chain Elongation, Translational
- Peptide Elongation Factor Tu/metabolism
- Protein Biosynthesis
- RNA, Bacterial/chemistry
- RNA, Bacterial/metabolism
- RNA, Messenger/chemistry
- RNA, Messenger/metabolism
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/metabolism
- RNA, Transfer/chemistry
- RNA, Transfer/metabolism
- RNA, Transfer, Amino Acid-Specific/chemistry
- RNA, Transfer, Amino Acid-Specific/metabolism
- RNA, Transfer, Phe/chemistry
- RNA, Transfer, Phe/metabolism
- Ribosomes/chemistry
- Ribosomes/metabolism
- Ribosomes/ultrastructure
- Thermodynamics
- Thermus thermophilus/chemistry
- Thermus thermophilus/metabolism
- Thermus thermophilus/ultrastructure
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Affiliation(s)
- J M Ogle
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK
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14
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Burkhardt N, Jünemann R, Spahn CM, Nierhaus KH. Ribosomal tRNA binding sites: three-site models of translation. Crit Rev Biochem Mol Biol 1998; 33:95-149. [PMID: 9598294 DOI: 10.1080/10409239891204189] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The first models of translation described protein synthesis in terms of two operationally defined tRNA binding sites, the P-site for the donor substrate, the peptidyl-tRNA, and the A-site for the acceptor substrates, the aminoacyl-tRNAs. The discovery and analysis of the third tRNA binding site, the E-site specific for deacylated tRNAs, resulted in the allosteric three-site model, the two major features of which are (1) the reciprocal relationship of A-site and E-site occupation, and (2) simultaneous codon-anticodon interactions of both tRNAs present at the elongating ribosome. However, structural studies do not support the three operationally defined sites in a simple fashion as three topographically fixed entities, thus leading to new concepts of tRNA binding and movement: (1) the hybrid-site model describes the tRNAs' movement through the ribosome in terms of changing binding sites on the 30S and 50S subunits in an alternating fashion. The tRNAs thereby pass through hybrid binding states. (2) The alpha-epsilon model introduces the concept of a movable tRNA-binding domain comprising two binding sites, termed alpha and epsilon. The translocation movement is seen as a result of a conformational change of the ribosome rather than as a diffusion process between fixed binding sites. The alpha-epsilon model reconciles most of the experimental data currently available.
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MESH Headings
- Allosteric Site/genetics
- Animals
- Base Sequence
- Escherichia coli
- Humans
- Models, Biological
- Models, Molecular
- Molecular Sequence Data
- Peptide Chain Elongation, Translational/genetics
- Protein Biosynthesis
- RNA, Transfer, Amino Acid-Specific/chemistry
- RNA, Transfer, Amino Acid-Specific/genetics
- RNA, Transfer, Amino Acid-Specific/metabolism
- RNA, Transfer, Amino Acyl/chemistry
- RNA, Transfer, Amino Acyl/genetics
- RNA, Transfer, Amino Acyl/metabolism
- Ribosomes/chemistry
- Ribosomes/genetics
- Ribosomes/metabolism
- Structure-Activity Relationship
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Affiliation(s)
- N Burkhardt
- Max-Planck-Institut für Molekulare Genetik, Berlin, Germany
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15
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Potapov AP, Triana-Alonso FJ, Nierhaus KH. Ribosomal decoding processes at codons in the A or P sites depend differently on 2'-OH groups. J Biol Chem 1995; 270:17680-4. [PMID: 7629066 DOI: 10.1074/jbc.270.30.17680] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The importance of 2'-OH groups of codons for binding of cognate tRNAs to ribosomal P and A sites was analyzed applying the following strategy. An mRNA of 41 nucleotides was synthesized with the structure C16-GAA-UUC-GUC-C16 coding for glutamic acid (E), phenylalanine (F) and valine (V), respectively, in the middle (EFV-mRNA). A second template, the E(dF)V-mRNA, was identical except that it carried a deoxyribo-codon-dUdUdC- for phenylalanine. tRNA binding to the P site is totally insensitive to the presence or absence of the 2'-OH group of the P-site codon, and tRNA binding to the P site is also not affected if the A-site codon lacks the 2'-OH groups. However, binding is impaired if the deoxy-codon is present at the E site. In sharp contrast, the A-site binding of Ac-aminoacyl-tRNA was severely reduced in the presence of the deoxy-codon at the A site as well as at the P site. The results demonstrate that the correctness of base pairing is also "sensed" via a correct sugar structure of the codon, e.g. positioning of the sugar pucker (2'-OH), during the decoding process at the A site (elongation) but not during the decoding at the P site (initiation).
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Affiliation(s)
- A P Potapov
- Max-Planck-Institut für Molekulare Genetik, AG Ribosomen, Berlin, Federal Republic of Germany
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16
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Nierhaus KH. Solution of the ribosome riddle: how the ribosome selects the correct aminoacyl-tRNA out of 41 similar contestants. Mol Microbiol 1993; 9:661-9. [PMID: 7694034 DOI: 10.1111/j.1365-2958.1993.tb01726.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Three tRNA binding sites, the A, P and E sites, have been demonstrated on ribosomes of bacterial, archaebacterial and eukaryotic origin. In all these cases the first and the third site, the A and the E site, are allosterically coupled in the sense of a negative co-operativity. Therefore, the allosteric three-site model seems to be a generally valid description of the ribosomal elongation phase, where in a cycle of reactions the nascent peptide chain is prolonged by one amino acid. The molecular concept of the allosteric three-site model explains the astonishing ability of the ribosome to select the correct substrate out of a large number of very similar substrates, and it provides a framework within which the mechanisms of the elongation factors could be understood.
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MESH Headings
- Allosteric Regulation
- Anticodon
- Bacterial Proteins/metabolism
- Base Sequence
- Binding Sites
- Codon
- Guanosine Triphosphate/metabolism
- Models, Biological
- Molecular Sequence Data
- Nucleic Acid Conformation
- Peptide Chain Elongation, Translational
- Peptide Elongation Factors/metabolism
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Transfer, Amino Acyl/chemistry
- RNA, Transfer, Amino Acyl/genetics
- RNA, Transfer, Amino Acyl/metabolism
- Ribosomes/physiology
- Substrate Specificity
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Affiliation(s)
- K H Nierhaus
- Max-Planck-Institut für Molekulare Genetik, Berlin, Germany
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17
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Potapov AP, Ovcharenko GV, Soldatkin KO, Shul'ga NI, Soldatkin AP, el'skaya AV. Cell-free translation systems from different eukaryotes differ in their sensitivity to a template sugar-phosphate backbone. Biochimie 1992; 74:435-41. [PMID: 1637868 DOI: 10.1016/0300-9084(92)90083-q] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
To study the role of a messenger sugar-phosphate backbone in the ribosomal decoding process, poly(U) and poly(dT) template activity in different eukaryotic systems has been compared. 80S ribosomes from Saccharomyces cerevisiae appeared to be able to translate poly(dT) both in the presence and in the absence of elongation factors, contrary to poly(U). However, ribosomes from higher eukaryotes (wheat germ, rabbit liver) are completely inefficient in poly(dT) translation. Moreover, rabbit liver ribosomes fail to bind effectively phenylalanyl-tRNA in the presence of poly(dT) although the polynucleotide seems to interact with the ribosomal decoding center. It is also of particular interest that hybrid ribosomes formed from the yeast and rabbit liver subunits can translate poly(dT) only when the large ribosomal subunit from yeast is used.
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Affiliation(s)
- A P Potapov
- Institute of Molecular Biology and Genetics, Ukrainian Academy of Sciences, Kiev
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18
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Koval'chuke O, Potapov AP, el'skaya AV. Interaction of yeast tRNA(Phe) anticodon arm with 40S ribosomal subunit of rabbit liver. Biochimie 1992; 74:443-6. [PMID: 1637869 DOI: 10.1016/0300-9084(92)90084-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The 15-nucleotide analog of yeast tRNA(Phe) anticodon arm binds cooperatively to two sites of poly(U) programmed 40S ribosome like intact tRNA(Phe). The cooperativity coefficients appeared to be about 4 for tRNA(Phe) and 50 for its anticodon arm. Anticodon arm contributes the majority of free energy of tRNA binding to a programmed 40S ribosomal subunit. The correct codon-anticodon pairing seems to play the key role in the cooperativity origin. Contrary to the anticodon arm template independent binding of the whole tRNA to the small ribosomal subunit is revealed.
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Affiliation(s)
- O Koval'chuke
- Institute of Molecular Biology and Genetics, Kiev, Ukraine
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19
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Soldatkin KO, Koval'chuke O, Potapov AP, El'skaya AV. A codon sugar structure strongly influences tRNA binding to programmed ribosomes. BIOCHIMICA ET BIOPHYSICA ACTA 1992; 1130:38-40. [PMID: 1543747 DOI: 10.1016/0167-4781(92)90458-c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
To study the role of a codon sugar-phosphate backbone in aminoacyl-tRNA selection on the ribosome a comparison of tRNA(Phe) affinity for pdTpdTpdT and prUprUprU in solution, and for correspondingly programmed 30S ribosomal subunits has been performed. In solution the tRNA(Phe) affinity for pdTpdTpdT appeared to be even slightly higher than for prUprUprU, whereas deoxyribocodon was significantly less efficient in the stimulation of Phe-tRNA(Phe) binding to the 30S ribosomal subunit. Some difference in neomycin action in both systems was revealed.
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Affiliation(s)
- K O Soldatkin
- Institute of Molecular Biology and Genetics, Kiev, Ukraine
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Koval'chuke OV, Potapov AP, El'skaya AV, Potapov VK, Krinetskaya NF, Dolinnaya NG, Shabarova ZA. Interaction of ribo- and deoxyriboanalogs of yeast tRNA(Phe) anticodon arm with programmed small ribosomal subunits of Escherichia coli and rabbit liver. Nucleic Acids Res 1991; 19:4199-201. [PMID: 1870974 PMCID: PMC328562 DOI: 10.1093/nar/19.15.4199] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
A synthetic ribooligonucleotide, r(CCAGACUGm-AAGAUCUGG), corresponding to the unmodified yeast tRNA(Phe) anticodon arm is shown to bind to poly(U) programmed small ribosomal subunits of both E. coli and rabbit liver with affinity two order less than that of a natural anticodon arm. Its deoxyriboanalogs d(CCAGACTGAAGATCTGG) and d(CCAGA)r(CUGm-AAGA)d(TCTGG), are used to study the influence of sugar-phosphate modification on the interaction of tRNA with programmed small ribosomal subunits. The deoxyribooligonucleotide is shown to adopt a hairpin structure. Nevertheless, as well as oligonucleotide with deoxyriboses in stem region, it is not able to bind to 30S or 40S ribosomal subunits in the presence of ribo-(poly(U] or deoxyribo-(poly (dT) template. The deoxyribooligonucleotide also has no inhibitory effect on tRNA(Phe) binding to 30S ribosomes at 10-fold excess over tRNA. Neomycin does not influence binding of tRNA anticodon arm analogs used. Complete tRNA molecule and natural modifications of anticodon arm are considered to stabilize the arm structure needed for its interaction with a programmed ribosome.
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21
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Potapov AP, Groisman IS, El'skaya AV. Correlation between poly(U) misreading and poly(dT) translation efficiency in E coli cell-free systems. Biochimie 1990; 72:345-9. [PMID: 2119818 DOI: 10.1016/0300-9084(90)90030-k] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
A positive correlation between poly(U) misreading and efficiency of poly(dT) translation has been revealed in cell-free systems from wild-type E coli and streptomycin--resistant mutants with altered ribosomal protein S12. Different factors promoting misreading of poly(U) such as aminoglycoside antibiotics and Mg2+ ions also stimulate poly(dT) translation. The effect of the antibiotics on poly(U) translation efficiency and misreading as well as on poly(dT) decoding is characterised by the same order: neomycin greater than kanamycin greater than streptomycin. S12 mutants ribosomes are less erroneous in poly(U) translation and less efficient in poly(dT) decoding. The data obtained are in good agreement with the hypothesis of stereospecific stabilization of codon-anticodon complexes by the ribosome decoding centre.
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Affiliation(s)
- A P Potapov
- Institute of Molecular Biology and Genetics, Ukrainian SSR Academy of Sciences, Kiev
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22
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Potapov AP, Soldatkin KA, Soldatkin AP, El'skaya AV. The role of a template sugar-phosphate backbone in the ribosomal decoding mechanism. Comparative study of poly(U) and poly(dT) template activity. J Mol Biol 1988; 203:885-93. [PMID: 2463369 DOI: 10.1016/0022-2836(88)90114-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
To study the role of a template sugar-phosphate backbone in the ribosomal decoding process, poly(U), poly(dT) and poly(dU)-directed cell-free amino acid incorporation was investigated under the influence of neomycin and high concentrations of Mg2+. The specificity of a factor-dependent translation system of Escherichia coli was shown to change according to the principle: "either ribo- or deoxyribopolynucleotide messenger". Poly(dT) is shown to be effectively translated in the absence of elongation factors, both at low (2 degrees C) and high (37 degrees C) temperature. Neomycin inhibits factor-free poly(dT) translation. Little or no poly(U) translation is observed in this system. A chromatographic analysis of the oligophenylalanine residues synthesized seems to show that translocation is the main step responsible for ribosome specificity to the ribo- or deoxyribopolynucleotide template in both factor-dependent and factor-free translation systems.
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Affiliation(s)
- A P Potapov
- Institute of Molecular Biology and Genetics, Ukrainian SSR Academy of Sciences, Kiev, U.S.S.R
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