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A Structural Basis for Restricted Codon Recognition Mediated by 2-thiocytidine in tRNA Containing a Wobble Position Inosine. J Mol Biol 2020; 432:913-929. [PMID: 31945376 DOI: 10.1016/j.jmb.2019.12.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 11/25/2019] [Accepted: 12/05/2019] [Indexed: 11/20/2022]
Abstract
Three of six arginine codons (CGU, CGC, and CGA) are decoded by two Escherichia coli tRNAArg isoacceptors. The anticodon stem and loop (ASL) domains of tRNAArg1 and tRNAArg2 both contain inosine and 2-methyladenosine modifications at positions 34 (I34) and 37 (m2A37). tRNAArg1 is also modified from cytidine to 2-thiocytidine at position 32 (s2C32). The s2C32 modification is known to negate wobble codon recognition of the rare CGA codon by an unknown mechanism, while still allowing decoding of CGU and CGC. Substitution of s2C32 for C32 in the Saccharomyces cerevisiae tRNAIleIAU anticodon stem and loop domain (ASL) negates wobble decoding of its synonymous A-ending codon, suggesting that this function of s2C at position 32 is a generalizable property. X-ray crystal structures of variously modified ASLArg1ICG and ASLArg2ICG constructs bound to cognate and wobble codons on the ribosome revealed the disruption of a C32-A38 cross-loop interaction but failed to fully explain the means by which s2C32 restricts I34 wobbling. Computational studies revealed that the adoption of a spatially broad inosine-adenosine base pair at the wobble position of the codon cannot be maintained simultaneously with the canonical ASL U-turn motif. C32-A38 cross-loop interactions are required for stability of the anticodon/codon interaction in the ribosomal A-site.
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2
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Shigi N. Recent Advances in Our Understanding of the Biosynthesis of Sulfur Modifications in tRNAs. Front Microbiol 2018; 9:2679. [PMID: 30450093 PMCID: PMC6225789 DOI: 10.3389/fmicb.2018.02679] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Accepted: 10/19/2018] [Indexed: 12/30/2022] Open
Abstract
Sulfur is an essential element in all living organisms. In tRNA molecules, there are many sulfur-containing nucleosides, introduced post-transcriptionally, that function to ensure proper codon recognition or stabilization of tRNA structure, thereby enabling accurate and efficient translation. The biosynthesis of tRNA sulfur modifications involves unique sulfur trafficking systems that are closely related to cellular sulfur metabolism, and “modification enzymes” that incorporate sulfur atoms into tRNA. Herein, recent biochemical and structural characterization of the biosynthesis of sulfur modifications in tRNA is reviewed, with special emphasis on the reaction mechanisms of modification enzymes. It was recently revealed that TtuA/Ncs6-type 2-thiouridylases from thermophilic bacteria/archaea/eukaryotes are oxygen-sensitive iron-sulfur proteins that utilize a quite different mechanism from other 2-thiouridylase subtypes lacking iron-sulfur clusters such as bacterial MnmA. The various reaction mechanisms of RNA sulfurtransferases are also discussed, including tRNA methylthiotransferase MiaB (a radical S-adenosylmethionine-type iron-sulfur enzyme) and other sulfurtransferases involved in both primary and secondary sulfur-containing metabolites.
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Affiliation(s)
- Naoki Shigi
- Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
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3
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Torres AG, Wulff TF, Rodríguez-Escribà M, Camacho N, Ribas de Pouplana L. Detection of Inosine on Transfer RNAs without a Reverse Transcription Reaction. Biochemistry 2018; 57:5641-5647. [PMID: 30199619 DOI: 10.1021/acs.biochem.8b00718] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Inosine at the "wobble" position (I34) is one of the few essential posttranscriptional modifications in tRNAs (tRNAs). It results from the deamination of adenosine and occurs in bacteria on tRNAArgACG and in eukarya on six or seven additional tRNA substrates. Because inosine is structurally a guanosine analogue, reverse transcriptases recognize it as a guanosine. Most methods used to examine the presence of inosine rely on this phenomenon and detect the modified base as a change in the DNA sequence that results from the reverse transcription reaction. These methods, however, cannot always be applied to tRNAs because reverse transcription can be compromised by the presence of other posttranscriptional modifications. Here we present SL-ID (splinted ligation-based inosine detection), a reverse transcription-free method for detecting inosine based on an I34-dependent specific cleavage of tRNAs by endonuclease V, followed by a splinted ligation and polyacrylamide gel electrophoresis analysis. We show that the method can detect I34 on different tRNA substrates and can be applied to total RNA derived from different species, cell types, and tissues. Here we apply the method to solve previous controversies regarding the modification status of mammalian tRNAArgACG.
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Affiliation(s)
- Adrian G Torres
- Institute for Research in Biomedicine (IRB Barcelona) , The Barcelona Institute of Science and Technology , Parc Científic de Barcelona, C/Baldiri Reixac 10 , 08028 Barcelona , Catalonia , Spain
| | - Thomas F Wulff
- Institute for Research in Biomedicine (IRB Barcelona) , The Barcelona Institute of Science and Technology , Parc Científic de Barcelona, C/Baldiri Reixac 10 , 08028 Barcelona , Catalonia , Spain
| | - Marta Rodríguez-Escribà
- Institute for Research in Biomedicine (IRB Barcelona) , The Barcelona Institute of Science and Technology , Parc Científic de Barcelona, C/Baldiri Reixac 10 , 08028 Barcelona , Catalonia , Spain
| | - Noelia Camacho
- Institute for Research in Biomedicine (IRB Barcelona) , The Barcelona Institute of Science and Technology , Parc Científic de Barcelona, C/Baldiri Reixac 10 , 08028 Barcelona , Catalonia , Spain
| | - Lluís Ribas de Pouplana
- Institute for Research in Biomedicine (IRB Barcelona) , The Barcelona Institute of Science and Technology , Parc Científic de Barcelona, C/Baldiri Reixac 10 , 08028 Barcelona , Catalonia , Spain.,Catalan Institution for Research and Advanced Studies (ICREA) , P/Lluis Companys 23 , 08010 Barcelona , Catalonia , Spain
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4
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Agris PF, Narendran A, Sarachan K, Väre VYP, Eruysal E. The Importance of Being Modified: The Role of RNA Modifications in Translational Fidelity. Enzymes 2017; 41:1-50. [PMID: 28601219 DOI: 10.1016/bs.enz.2017.03.005] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The posttranscriptional modifications of tRNA's anticodon stem and loop (ASL) domain represent a third level, a third code, to the accuracy and efficiency of translating mRNA codons into the correct amino acid sequence of proteins. Modifications of tRNA's ASL domain are enzymatically synthesized and site specifically located at the anticodon wobble position-34 and 3'-adjacent to the anticodon at position-37. Degeneracy of the 64 Universal Genetic Codes and the limitation in the number of tRNA species require some tRNAs to decode more than one codon. The specific modification chemistries and their impact on the tRNA's ASL structure and dynamics enable one tRNA to decode cognate and "wobble codons" or to expand recognition to synonymous codons, all the while maintaining the translational reading frame. Some modified nucleosides' chemistries prestructure tRNA to read the two codons of a specific amino acid that shares a twofold degenerate codon box, and other chemistries allow a different tRNA to respond to all four codons of a fourfold degenerate codon box. Thus, tRNA ASL modifications are critical and mutations in genes for the modification enzymes and tRNA, the consequences of which is a lack of modification, lead to mistranslation and human disease. By optimizing tRNA anticodon chemistries, structure, and dynamics in all organisms, modifications ensure translational fidelity of mRNA transcripts.
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Affiliation(s)
- Paul F Agris
- The RNA Institute, State University of New York, Albany, NY, United States.
| | - Amithi Narendran
- The RNA Institute, State University of New York, Albany, NY, United States
| | - Kathryn Sarachan
- The RNA Institute, State University of New York, Albany, NY, United States
| | - Ville Y P Väre
- The RNA Institute, State University of New York, Albany, NY, United States
| | - Emily Eruysal
- The RNA Institute, State University of New York, Albany, NY, United States
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5
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Igloi GL, Aldinger CA. Where have all the inosines gone? Conflicting evidence for A-to-I editing of the anticodon of higher eukaryotic tRNAACGArg questions the dogma of a universal wobble-mediated decoding of CGN codons. IUBMB Life 2016; 68:419-22. [DOI: 10.1002/iub.1497] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 03/05/2016] [Indexed: 11/06/2022]
Affiliation(s)
- Gabor L. Igloi
- Institut für Biologie III, Universität Freiburg; Freiburg Germany
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6
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Cantara WA, Bilbille Y, Kim J, Kaiser R, Leszczyńska G, Malkiewicz A, Agris PF. Modifications Modulate Anticodon Loop Dynamics and Codon Recognition of E. coli tRNAArg1,2. J Mol Biol 2012; 416:579-97. [DOI: 10.1016/j.jmb.2011.12.054] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2011] [Revised: 12/13/2011] [Accepted: 12/27/2011] [Indexed: 10/14/2022]
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7
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Smith WS, Nawrot B, Malkiewicz A, Agris PF. RNA Modified Uridines VI: Conformations of 3-[3-(S)-Amino-3-Carboxypropyl]Uridine (acp3U) from tRNA and 1-Methyl-3-[3-(S)-Amino-3-Carboxypropyl]Pseudouridine (m1acp3Ψ) from rRNA. ACTA ACUST UNITED AC 1992. [DOI: 10.1080/07328319208017815] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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8
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Abstract
Codon usage is compared between four classes of species, with an emphasis on characterization of low-usage codons. The classes of species analyzed include the bacterium Escherichia coli (ECO), the yeast Saccharomyces cerevisiae (YSC), the fruit fly Drosophila melanogaster (DRO), and several species of primates (PRI) (taken as a group; includes eleven species for which nucleotide sequence data have been reported to GenBank, however, greater than 90% of the sequences were from Homo sapiens). The number of protein-coding sequences analyzed were 968 for ECO, 484 for YSC, 244 for DRO, and 1518 for PRI. Three methods have been used to determine low-usage codons in these species. The first and most common way of assessing codon usage is by summing the number of time codons appear in reading frames of the genome in question. The second way is to examine the distribution of usage in different genes by scoring the number of protein reading frames in which a particular codon does not appear. The third way starts with a similar notion, but instead considers combinations of codons that are missing from the maximum number of genes. These three methods give very similar results. Each species has a unique combination of eight least-used codons, but all species contain the arginine codons, CGA and CGG. The agreement between YSC and PRI is particularly striking as they share six low-usage codons. All six carry the dinucleotide sequence, CG. The eight least-used codons in PRI include all codons that contain the CG dinucleotide sequence. Low-usage codons are clearly avoided in genes encoding abundant proteins for ECO, YSC DRO. In all species, proteins containing a high percentage of low-usage codons could be characterized as cases where an excess of the protein could be detrimental. Low codon usage is relatively insensitive to gross base composition. However, dinucleotide usage can sometimes influence codon usage. This is particularly notable in the case of CG dinucleotides in PRI.
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Affiliation(s)
- S P Zhang
- Fairchild Center for Biological Sciences, Columbia University, New York, NY 10027
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9
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Zhang SP, Zubay G. The Peculiar Nature of Codon Usage in Primates. GENETIC ENGINEERING 1991; 13:73-113. [PMID: 1370052 DOI: 10.1007/978-1-4615-3760-1_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- S P Zhang
- Fairchild Center for Biological Sciences, Columbia University, New York, NY 10027
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10
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Normanly J, Kleina LG, Masson JM, Abelson J, Miller JH. Construction of Escherichia coli amber suppressor tRNA genes. III. Determination of tRNA specificity. J Mol Biol 1990; 213:719-26. [PMID: 2141650 DOI: 10.1016/s0022-2836(05)80258-x] [Citation(s) in RCA: 123] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Using synthetic oligonucleotides, we have constructed a collection of Escherichia coli amber suppressor tRNA genes. In order to determine their specificities, these tRNAs were each used to suppress an amber (UAG) nonsense mutation in the E. coli dihydrofolate reductase gene fol. The mutant proteins were purified and subjected to N-terminal sequence analysis to determine which amino acid had been inserted by the suppressor tRNAs at the position of the amber codon. The suppressors can be classified into three groups on the basis of the protein sequence information. Class I suppressors, tRNA(CUAAla2), tRNA(CUAGly1), tRNA(CUAHisA), tRNA(CUALys) and tRNA(CUAProH), inserted the predicted amino acid. The class II suppressors, tRNA(CUAGluA), tRNA(CUAGly2) and tRNA(CUAIle1) were either partially or predominantly mischarged by the glutamine aminoacyl tRNA synthetase. The class III suppressors, tRNA(CUAArg), tRNA(CUAAspM), tRNA(CUAIle2), tRNA(CUAThr2), tRNA(CUAMet(m)) and tRNA(CUAVal) inserted predominantly lysine.
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Affiliation(s)
- J Normanly
- Department of Biology, California Institute of Technology, Pasadena 91125
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11
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Kleina LG, Masson JM, Normanly J, Abelson J, Miller JH. Construction of Escherichia coli amber suppressor tRNA genes. II. Synthesis of additional tRNA genes and improvement of suppressor efficiency. J Mol Biol 1990; 213:705-17. [PMID: 2193162 DOI: 10.1016/s0022-2836(05)80257-8] [Citation(s) in RCA: 121] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Using synthetic oligonucleotides, we have constructed 17 tRNA suppressor genes from Escherichia coli representing 13 species of tRNA. We have measured the levels of in vivo suppression resulting from introducing each tRNA gene into E. coli via a plasmid vector. The suppressors function at varying efficiencies. Some synthetic suppressors fail to yield detectable levels of suppression, whereas others insert amino acids with greater than 70% efficiency. Results reported in the accompanying paper demonstrate that some of these suppressors insert the original cognate amino acid, whereas others do not. We have altered some of the synthetic tRNA genes in order to improve the suppressor efficiency of the resulting tRNAs. Both tRNA(CUAHis) and tRNA(CUAGlu) were altered by single base changes, which generated -A-A- following the anticodon, resulting in a markedly improved efficiency of suppression. The tRNA(CUAPro) was inactive, but a hybrid suppressor tRNA consisting of the tRNA(CUAPhe) anticodon stem and loop together with the remainder of the tRNA(Pro) proved highly efficient at suppressing nonsense codons. Protein chemistry results reported in the accompanying paper show that the altered tRNA(CUAHis) and the hybrid tRNA(CUAPro) insert only histidine and proline, respectively, whereas the altered tRNA(CUAGlu) inserts principally glutamic acid but some glutamine. Also, a strain deficient in release factor I was employed to increase the efficiency of weak nonsense suppressors.
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MESH Headings
- Anticodon
- Base Sequence
- Cloning, Molecular
- Escherichia coli/genetics
- Genes, Bacterial
- Molecular Sequence Data
- Nucleic Acid Conformation
- Plasmids
- RNA, Transfer/genetics
- RNA, Transfer, Glu/genetics
- RNA, Transfer, His/genetics
- RNA, Transfer, Pro/genetics
- Suppression, Genetic
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Affiliation(s)
- L G Kleina
- Department of Biology, University of California, Los Angeles 90024
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12
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McClain WH, Foss K. Changing the acceptor identity of a transfer RNA by altering nucleotides in a "variable pocket". Science 1988; 241:1804-7. [PMID: 2459773 DOI: 10.1126/science.2459773] [Citation(s) in RCA: 111] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The specificity of tRNA(Arg) (arginine transfer RNA) for aminoacylation (its acceptor identity) were first identified by computer analysis and then examined with amber suppressor tRNAs in Escherichia coli. On replacing two nucleotides in tRNA(Phe) (phenylalanine transfer RNA) with the corresponding nucleotides from tRNA(Arg), the acceptor identity of the resulting tRNA was changed to that of tRNA(Arg). The nucleotides used in the identity transformation occupy a "variable pocket" structure on the surface of the tRNA molecule where two single-stranded loop segments interact. The middle nucleotide in the anticodon also probably contributes to the interaction, since an amber suppressor of tRNA(Arg) had an acceptor identity for lysine as well as arginine.
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Affiliation(s)
- W H McClain
- Department of Bacteriology, University of Wisconsin, Madison 53706
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13
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McClain WH, Foss K. Changing the identity of a tRNA by introducing a G-U wobble pair near the 3' acceptor end. Science 1988; 240:793-6. [PMID: 2452483 DOI: 10.1126/science.2452483] [Citation(s) in RCA: 296] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Although the genetic code for protein was established in the 1960's, the basis for amino acid identity of transfer RNA (tRNA) has remained unknown. To investigate the identity of a tRNA, the nucleotides at three computer-identified positions in tRNAPhe (phenylalanine tRNA) were replaced with the corresponding nucleotides from tRNAAla (alanine tRNA). The identity of the resulting tRNA, when examined as an amber suppressor in Escherichia coli, was that of tRNAAla.
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MESH Headings
- Alanine/genetics
- Amino Acids/genetics
- Base Composition
- Base Sequence
- Escherichia coli/genetics
- Guanosine
- Mutation
- Phenylalanine/genetics
- RNA, Bacterial/genetics
- RNA, Transfer/genetics
- RNA, Transfer, Ala/genetics
- RNA, Transfer, Gly/genetics
- RNA, Transfer, Lys/genetics
- RNA, Transfer, Phe/genetics
- Suppression, Genetic
- Uridine
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Affiliation(s)
- W H McClain
- Department of Bacteriology, University of Wisconsin, Madison 53706
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14
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Yavachev L, Ivanov I. What does the homology between E. coli tRNAs and RNAs controlling ColE1 plasmid replication mean? J Theor Biol 1988; 131:235-41. [PMID: 2457135 DOI: 10.1016/s0022-5193(88)80240-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Nucleotide sequences of E. coli tRNAs and RNA I or RNA II (controlling replication of ColE1 plasmids) were compared using the computer. The homology between some of these molecules is over 60%. The distribution of homologous nucleotides among the functional elements (stems and loops) of either RNA I or RNA II and the tRNAs molecules was studied. It was found that the homologous domains are located mainly in the loop regions of RNA I or RNA II. A consensus sequence, the nonanucleotide AGUUGGUAG, was discovered in loop II of RNA I and in the dihydrouridylic loop of tRNAs showing homology with RNA I. Based on this observation, a hypothesis was drawn for a possible role of the tRNAs in the regulation of plasmid DNA replication.
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Affiliation(s)
- L Yavachev
- Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia
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15
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Baumann U, Fischer W, Sprinzl M. Analysis of modification-dependent structural alterations in the anticodon loop of Escherichia coli tRNAArg and their effects on the translation of MS2 RNA. EUROPEAN JOURNAL OF BIOCHEMISTRY 1985; 152:645-9. [PMID: 2996897 DOI: 10.1111/j.1432-1033.1985.tb09243.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The conformation of the anticodon loop of Escherichia coli tRNAArg was investigated. It is shown that the structure of the anticodon loop is influenced by the base composition of the anticodon stem, and the natural modification of the nucleoside residue 32 in the anticodon loop. The structural effects detected by analysis of the accessibility of the anticodon loop to nuclease S1 could be correlated with the ability of different Arg-tRNAArg species to suppress frame-shifting during translation of MS2 RNA.
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16
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Hellmund D, Metzlaff M, Serfling E. A transfer RNAArg gene of Pelargonium chloroplasts, but not a 5S RNA gene, is efficiently transcribed after injection into Xenopus oocyte nuclei. Nucleic Acids Res 1984; 12:8253-68. [PMID: 6209611 PMCID: PMC320309 DOI: 10.1093/nar/12.21.8253] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
We present the primary structure of a chloroplast tRNAArgACG gene of the plant, Pelargonium zonale, and its faithful expression in Xenopus oocyte nuclei. This tRNAArg gene is located 250 bp downstream of a 5S RNA gene within a cloned 5kb long ribosomal DNA segment (Fig. 1). The Pelargonium tRNAArg gene shares 97% and 86% sequence homology with tRNAArgACG genes of Spirodela oligorhiza and Euglena gracilis chloroplasts, respectively, and also extensive homology (70%) with the corresponding gene of E. coli. It lacks an intervening sequence and, like eukaryotic tRNA genes, does not code for the 3' terminal CCA nucleotides. Moreover, the chloroplast tRNAArg gene carries all the sequence elements essential for transcription by vertebrate RNA polymerase III since it is efficiently expressed in Xenopus oocyte nuclei, even in the presence of 1 microgram/ml alpha-amanitin. In Xenopus oocyte nuclei, no transcripts of the chloroplast 5S RNA gene were detected.
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17
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Keus RJ, Stam NJ, Zwiers T, de Heij HT, Groot GS. The nucleotide sequences of the genes coding for tRNAArgUCU, tRNAArgACG and tRNAAsnGUU on Spirodela oligorhiza chloroplast DNA. Nucleic Acids Res 1984; 12:5639-46. [PMID: 6462915 PMCID: PMC320020 DOI: 10.1093/nar/12.14.5639] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The nucleotide sequences of the genes coding for tRNAArgUCU, tRNAArgACG and tRNAAsnGUU on chloroplast DNA of Spirodela oligorhiza have been determined. All three genes are expressed. 5' Proximal to these genes sequences are found homologous to prokaryotic promoter sequences, which might be involved as transcriptional start motifs.
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18
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Dirheimer G. Chemical nature, properties, location, and physiological and pathological variations of modified nucleosides in tRNAs. Recent Results Cancer Res 1983; 84:15-46. [PMID: 6342070 DOI: 10.1007/978-3-642-81947-6_2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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19
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Ikemura T. Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes. J Mol Biol 1981; 146:1-21. [PMID: 6167728 DOI: 10.1016/0022-2836(81)90363-6] [Citation(s) in RCA: 629] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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20
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Abstract
Escherichia coli tRNAArg was digested with ribonuclease T1 under restrictive conditions in order to dissect a minimum number of diester bonds. The number of diester bonds cleaved and their locations were determined by phosphorylation of the newly formed 5' hydroxyl groups with [32P] ATP and polynucleotide kinase. There was complete loss of aminoacylation of tRNAARg when two diester bonds were cleaved at the anticodon. However, this material retained the specific properties of synthetase recognition. Two fragments were derived by further digestion of this tRNA. One 19 nucleotide-long fragment derived from the 3' end of tRNAArg and another 18 nucleotide-long fragment derived from the 5' end of the molecule were required to maintain the properties of the specific recognition by the arginyl tRNA synthetase in the absence of the rest of the structure including the anticodon.
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21
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Keith G, Dirheimer G. Reinvestigation of the primary structure of brewer's yeast tRNA 3 Arg. Biochem Biophys Res Commun 1980; 92:116-9. [PMID: 6986864 DOI: 10.1016/0006-291x(80)91527-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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22
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Taylor MJ, Gantt R. Partial purification and characterization of a ribonucleic acid N2-guanine methyltransferase associated with avian myeloblastosis virus. Biochemistry 1979; 18:5253-8. [PMID: 227452 DOI: 10.1021/bi00590a033] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A nucleic acid methylase, N2-guanine ribonucleic acid (RNA) methyltransferase, which is associated with type C RNA tumor viruses, has been purified from avian myeloblastosis virions by gel filtration on Sephadex G-200, followed by chromatography on hydroxylapatite. The molecular weight estimated by gel filtration is 220 000, and the methylase activity has a pH optimum of 7.6--7.9. Magnesium and ammonium ions both stimulate activity 1.5-fold at 9.5 mM and 0.36 M, respectively, but apparently neither is essential for activity. Both daunomycin and adriamycin, antineoplastic drugs, also increase activity 1.5-fold at 1 mM. The enzyme was purified 120-fold from the virions and the activity is partially stabilized by dithiothretiol, but large losses were sustained during 24-h dialysis. The purified enzyme retains 75% of its activity on storage at -25 degrees C for 2 months in buffer containing 50% glycerol. Escherichia coli tRNAPhe and tRNAVal are preferred substrates with methylation occurring at position 10 of E. coli tRNAPhe.
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23
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Hansske F, Seela F, Watanabe K, Cramer F. Modification of the rare nucleoside X in Escherichia coli tRNAs with antigenic determining, photolabile, and paramagnetic residues. Methods Enzymol 1979; 59:166-71. [PMID: 86934 DOI: 10.1016/0076-6879(79)59078-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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24
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Shugart L, Chastain B. m7guanosine in tRNA of Escherichia coli. THE INTERNATIONAL JOURNAL OF BIOCHEMISTRY 1979; 10:155-7. [PMID: 372029 DOI: 10.1016/0020-711x(79)90110-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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25
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Goddard JP. The structures and functions of transfer RNA. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 1978. [DOI: 10.1016/0079-6107(78)90021-4] [Citation(s) in RCA: 57] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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26
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Bloch JC, Garel JP. Influence of modified nucleosides in E. coli transfer ribonucleic acids on chromatographic mobilities of transfer RNA. J Chromatogr A 1977; 137:93-109. [PMID: 330553 DOI: 10.1016/s0021-9673(00)89244-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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27
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Reid BR, Ribeiro NS, McCollum L, Abbate J, Hurd RE. High-resolution nuclear magnetic resonance determination of transfer RNA tertiary base pairs in solution. 1. Species containing a small variable loop. Biochemistry 1977; 16:2086-94. [PMID: 324514 DOI: 10.1021/bi00629a006] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Eight class I tRNA species have been purified to homogeneity and their proton nuclear magnetic resonance (NMR) spectra in the low-field region (-11 to -15 ppm) have been studied at 360 MHz. The low-field spectra contain only one low-field resonance from each base pair (the ring NH hydrogen bond) and hence directly monitor the number of long-lived secondary and tertiary base pairs in solution. The tRNA species were chosen on the basis of their sequence homology with yeast phenylalanine tRNA in the regions which form tertiary base pairs in the crystal structure of this tRNA. All of the spectra show 26 or 27 low-field resonances approximately 7 of which are derived from tertiary base pairs. These results are contrary to previous claims that the NMR spectra indicate the presence of resonances from secondary base pairs only, as well as more recent claims of only 1-3 tertiary resonances, but are in good agreement with the number of tertiary base pairs expected in solution based on the crystal structure. The tertiary base pair resonances are stable up to at least 46 degrees C. Removal of magnesium ions causes structural changes in the tRNA but does not result in the loss of any secondary or tertiary base pairs.
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28
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Murao K, Hasegawa T, Ishikura H. 5-methoxyuridine: a new minor constituent located in the first position of the anticodon of tRNAAla, tRNAThr, and tRNAVal from Bacillus subtilis. Nucleic Acids Res 1976; 3:2851-60. [PMID: 825836 PMCID: PMC343132 DOI: 10.1093/nar/3.10.2851] [Citation(s) in RCA: 39] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The sequences of the anticodon of tRNAAla, tRNAThr, and tRNAVal from Bacillus subtilis W 168 were N-G-C, N-G-U, and N-A-C, respectively. A new minor constituent, N, occupied the first position of the anticodon of each tRNA. N was indentified as 5-methoxyuridine (mo5U, Figure 1) by comparison of its UV absorption spectra, Rf values in thin-layer chromatography using several solvent systems and mass spectra with those of chemically synthesized specimen.
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30
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Abstract
tRNA Arg II of E. coli has 77 nucleotides. There are eight minor nucleotides including inosine and 2-methyladenosine. Except for a few differences, the structure of tRNA Arg II is very similar to the structure of tRNA Arg I reported by Murao et al.3. The major difference is in the size of dihydrouridine loop. tRNA Arg II does not contain 2-thiocytosine. The unidentified nucleoside X seems to be a different modification other than nucleoside N reported to be present in tRNA Arg I.
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31
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Chakraburtty K. Effect of sodium bisulfite modification on the arginine acceptance of E. coli tRNA Arg. Nucleic Acids Res 1975; 2:1793-804. [PMID: 1103086 PMCID: PMC343547 DOI: 10.1093/nar/2.10.1793] [Citation(s) in RCA: 40] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Escherichia coli tRNA Arg was treated with sodium bisulfite to convert exposed cytosine residues to uracil. This treatment resulted in the loss of amino acid acceptance of the tRNA Arg with pseudo first-order reaction kinetics. The active and inactive molecules were separated after about 60e active and inactive molecules were separated after about 60 percent inactivation and analyzed for U in various positions by finger-printing of the oligonucleotides produced by nucleases. The results show that C to U base transitions in the dihydrouridine loop and in the CCA terminus have no effect on the aminoacylation of this tRNA. Deamination of a cytosine residue at the second position of the anticodon resulted in the loss of amino acid acceptor activity of arginine transfer RNA.
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32
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Kuntzel B, Weissenbach J, Dirheimer G. [Primary structure of tRNA Arg/III of brewer's yeast. 2-Partial hydrolysis of tRNA Arg/III by pancreatic and T1 ribonucleases and determination of their complete primary structure]. Biochimie 1974; 56:1069-87. [PMID: 4614865 DOI: 10.1016/s0300-9084(74)80096-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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33
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Hilbers CW, Shulman RG. Assignment of the hydrogen bonded proton resonances in (Escherichia coli) tRNAGlu by sequential melting. Proc Natl Acad Sci U S A 1974; 71:3239-42. [PMID: 4606251 PMCID: PMC388659 DOI: 10.1073/pnas.71.8.3239] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The 300 MHz nuclear magnetic resonance peaks from the hydrogen bonded protons in (Escherichia coli) tRNA(Glu) in Mg(++) solutions have been measured at temperatures between 25 degrees and 74 degrees . Between 25 degrees and 49 degrees four resonances broaden, three of which are assigned to the hU arm and one to a G.C pair of the tertiary structure. By 64 degrees these four resonances have disappeared and the nuclear magnetic resonance spectrum is fitted very well by a computer simulation based upon resonances from the acceptor, T-Psi-C, and anticodon arms. At 66 degrees the resonances from the T-Psi-C arm are lost and at 74 degrees only those from the anticodon are left. All 20 resonances expected from the cloverleaf model have been assigned by comparing the calculated positions of resonances in a particular arm with the stepwise loss of intensity with temperature. The root mean square error between calculated and observed positions is 0.17 ppm. Resonances at the end of helical regions which are sensitive to stacking beyond the helix allow us to conclude that the acceptor arm is stacked upon the T-Psi-C in a regular helix and that G [unk]73 is stacked upon base pair [unk]1-72 but the hU and anticodon arms are not stacked in a regular helix upon the intervening base A [unk]27.
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34
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Friedman S, Li HJ, Nakanishi K, Van Lear G. 3-(3-amino-3-carboxy-n-propyl)uridine. The structure of the nucleoside in Escherichia coli transfer ribonucleic acid that reacts with phenoxyacetoxysuccinimide. Biochemistry 1974; 13:2932-7. [PMID: 4601538 DOI: 10.1021/bi00711a024] [Citation(s) in RCA: 42] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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35
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Seno T, Agris PF, Söll D. Involvement of the anticodon region of Escherichia coli tRNAGln and tRNAGlu in the specific interaction with cognate aminoacyl-tRNA synthetase. Alteration of the 2-thiouridine derivatives located in the anticodon of the tRNAs by BrCN or sulfur deprivation. BIOCHIMICA ET BIOPHYSICA ACTA 1974; 349:328-38. [PMID: 4366808 DOI: 10.1016/0005-2787(74)90120-8] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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36
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Nauheimer U, Hedgcoth C. Activation of several tRNAs of Escherichia coli by the phenoxyacetyl derivative of N-hydroxysuccinimide. Arch Biochem Biophys 1974; 160:631-42. [PMID: 4598621 DOI: 10.1016/0003-9861(74)90440-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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37
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Harada F, Nishimura S. Purification and characterization of AUA specific isoleucine transfer ribonucleic acid from Escherichia coli B. Biochemistry 1974; 13:300-7. [PMID: 4589307 DOI: 10.1021/bi00699a011] [Citation(s) in RCA: 79] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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38
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Inouye H, Fuchs S, Sela M, Littauer UZ. Detection of Inosine-containing Transfer Ribonucleic Acid Species by Affinity Chromatography on Columns of Anti-Inosine Antibodies. J Biol Chem 1973. [DOI: 10.1016/s0021-9258(19)43202-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
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39
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Thomas GJ, Chen MC, Hartman KA. Raman studies of nucleic acids. X. Conformational structures of Escherichia coli transfer RNAs in aqueous solution. BIOCHIMICA ET BIOPHYSICA ACTA 1973; 324:37-49. [PMID: 4584698 DOI: 10.1016/0005-2787(73)90248-7] [Citation(s) in RCA: 44] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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40
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41
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Shulman RG, Hilbers CW. Ring-current shifts in the 300 MHz nuclear magnetic resonance spectra of six purified transfer RNA molecules. J Mol Biol 1973; 78:57-69. [PMID: 4581295 DOI: 10.1016/0022-2836(73)90428-2] [Citation(s) in RCA: 73] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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42
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Unger FM, Takemura S. A comparison between inosine- and guanosine-containing anticodons in ribosome-free codon-anticodon binding. Biochem Biophys Res Commun 1973; 52:1141-7. [PMID: 4577824 DOI: 10.1016/0006-291x(73)90619-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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43
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Singhal RP, Cohn WE. Cation-exclusion chromatography on anion exchangers: application to nucleic acid components and comparison with anion-exchange chromatography. Biochemistry 1973; 12:1532-7. [PMID: 4573198 DOI: 10.1021/bi00732a010] [Citation(s) in RCA: 52] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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44
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Mullins DW, Lacey JC, Hearn RA. 5S rRNA and t RNA: evidence for a common evolutionary origin. NATURE: NEW BIOLOGY 1973; 242:80-2. [PMID: 4572533 DOI: 10.1038/newbio242080a0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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45
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Affiliation(s)
- Y Yamada
- Biology Division, National Cancer Center Research Institute, Tsukiji, Chuo-ku, Tokyo, Japan
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46
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Weissenbach J, Martin R, Dirheimer G. Nucleotide sequence of tRNA(Arg)(II) from brewer's yeast. FEBS Lett 1972; 28:353-355. [PMID: 11946894 DOI: 10.1016/0014-5793(72)80748-8] [Citation(s) in RCA: 53] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- J Weissenbach
- Laboratoire de Toxicologie et de Biologie moléculaires, U.E.R. de Sciences pharmaceutiques, Université Louis Pasteur, 67083, Strasbourg, France
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47
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Abstract
We determined the nature of the fourth nucleotide from the 3'-end of several Escherichia coli tRNAs, and tabulated these results with the same data for all known tRNA sequences. We find a striking constancy of the fourth nucleotide in tRNAs specific for a given amino acid. Furthermore, tRNAs specific for chemically related amino acids are very likely to have the same nucleotide at the fourth position. One possible explanation for these regularities is the "discriminator" hypothesis: The code by which tRNA is recognized by its cognate aminoacyl-tRNA synthetase is logically hierarchical, with the fourth nucleotide serving as a primary "discriminator" site to subdivide the tRNAs into groups for recognition purposes. Each such group could have its own recognition code, or could be further subdivided by a secondary discriminator site. According to this hypothesis, chemically similar amino acids have the same discriminator nucleotide because they evolved from a single set of related amino acids indistinguishable to a primitive system. There are other possible explanations for the observed regularities at the fourth nucleotide. For example, it is conceivable that the position is used for a direct physical interaction with the amino acid in the charging process, and chemically similar amino acids naturally select the same nucleotide. Further experiments can be expected to clarify this question.
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