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The Mitochondrial tRNA Ser(UCN) Gene: A Novel m.7484A>G Mutation Associated with Mitochondrial Encephalomyopathy and Literature Review. Life (Basel) 2023; 13:life13020554. [PMID: 36836911 PMCID: PMC9963529 DOI: 10.3390/life13020554] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 01/26/2023] [Accepted: 02/14/2023] [Indexed: 02/18/2023] Open
Abstract
Mitochondrial tRNASer(UCN) is considered a hot-spot for non-syndromic and aminoglycoside-induced hearing loss. However, many patients have been described with more extensive neurological diseases, mainly including epilepsy, myoclonus, ataxia, and myopathy. We describe a novel homoplasmic m.7484A>G mutation in the tRNASer(UCN) gene affecting the third base of the anticodon triplet in a girl with profound intellectual disability, spastic tetraplegia, sensorineural hearing loss, a clinical history of epilepsia partialis continua and vomiting, typical of MELAS syndrome, leading to a myoclonic epilepticus status, and myopathy with severe COX deficiency at muscle biopsy. The mutation was also found in the homoplasmic condition in the mother who presented with mild cognitive deficit, cerebellar ataxia, myoclonic epilepsy, sensorineural hearing loss and myopathy with COX deficient ragged-red fibers consistent with MERRF syndrome. This is the first anticodon mutation in the tRNASer(UCN) and the second homoplasmic mutation in the anticodon triplet reported to date.
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2
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Ramakrishnan C, Nagarajan R, Sekijima M, Michael Gromiha M. Molecular dynamics simulations of cognate and non-cognate AspRS-tRNA Asp complexes. J Biomol Struct Dyn 2020; 39:493-501. [PMID: 31900102 DOI: 10.1080/07391102.2019.1711188] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Aspartyl tRNA synthetase (AspRS), one of the 20 aminoacyl-tRNA synthetases, plays an important role in protein synthesis by catalyzing the aminoacylation reaction and synthesises Aspartyl-tRNA (tRNAAsp). A typical three-dimensional structure of AspRS comprises three distinct domains for the recognition of cognate tRNA and catalysis, namely, anti-codon binding domain/N-terminal domain, hinge domain and catalytic domain through their interactions with anti-codon loop, D-stem and acceptor arm of cognate tRNA, respectively. In this work, we have studied the structural characteristics of each domain of AspRS to understand the recognition mechanism of tRNAAsp using molecular dynamics simulations. The dynamics of AspRS-tRNAAsp complexes from E.coli (cognate and non-cognate), S.cerevisiae (cognate) and T.thermophilus (non-cognate) were compared to understand the differences in recognition of cognate and non-cognate tRNAs. Our results explain that the conformational changes associated with the recognition of tRNA occur only in the cognate complexes. Among the cognate complexes, the conformational changes in yeast AspRS are highly controlled during tRNAAsp recognition than that of in the E. coli AspRS. Moreover, the functional motions required for the tRNA recognition are observed only in the cognate complexes, and the conformational changes in AspRS and their recognition of tRNAAsp are organism specific.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- C Ramakrishnan
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, India
| | - R Nagarajan
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, India
| | - M Sekijima
- Advanced Computational Drug Discovery Unit, Tokyo Institute of Technology, Yokohama, Japan
| | - M Michael Gromiha
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, India.,Advanced Computational Drug Discovery Unit, Tokyo Tech World Research Hub Initiative (WRHI), Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
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3
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Jakubowski H. Homocysteine Editing, Thioester Chemistry, Coenzyme A, and the Origin of Coded Peptide Synthesis †. Life (Basel) 2017; 7:life7010006. [PMID: 28208756 PMCID: PMC5370406 DOI: 10.3390/life7010006] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 02/03/2017] [Indexed: 12/22/2022] Open
Abstract
Aminoacyl-tRNA synthetases (AARSs) have evolved “quality control” mechanisms which prevent tRNA aminoacylation with non-protein amino acids, such as homocysteine, homoserine, and ornithine, and thus their access to the Genetic Code. Of the ten AARSs that possess editing function, five edit homocysteine: Class I MetRS, ValRS, IleRS, LeuRS, and Class II LysRS. Studies of their editing function reveal that catalytic modules of these AARSs have a thiol-binding site that confers the ability to catalyze the aminoacylation of coenzyme A, pantetheine, and other thiols. Other AARSs also catalyze aminoacyl-thioester synthesis. Amino acid selectivity of AARSs in the aminoacyl thioesters formation reaction is relaxed, characteristic of primitive amino acid activation systems that may have originated in the Thioester World. With homocysteine and cysteine as thiol substrates, AARSs support peptide bond synthesis. Evolutionary origin of these activities is revealed by genomic comparisons, which show that AARSs are structurally related to proteins involved in coenzyme A/sulfur metabolism and non-coded peptide bond synthesis. These findings suggest that the extant AARSs descended from ancestral forms that were involved in non-coded Thioester-dependent peptide synthesis, functionally similar to the present-day non-ribosomal peptide synthetases.
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Affiliation(s)
- Hieronim Jakubowski
- Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, NJ 07103, USA.
- Department of Biochemistry and Biotechnology, University of Life Sciences, Poznan 60-632, Poland.
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Dyubankova N, Sochacka E, Kraszewska K, Nawrot B, Herdewijn P, Lescrinier E. Contribution of dihydrouridine in folding of the D-arm in tRNA. Org Biomol Chem 2015; 13:4960-6. [PMID: 25815904 DOI: 10.1039/c5ob00164a] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Posttranscriptional modifications of transfer RNAs (tRNAs) are proven to be critical for all core aspects of tRNA function. While the majority of tRNA modifications were discovered in the 1970s, their contribution in tRNA folding, stability, and decoding often remains elusive. In this work an NMR study was performed to obtain more insight in the role of the dihydrouridine (D) modification in the D-arm of tRNAi(Met) from S. pombe. While the unmodified oligonucleotide adopted several undefined conformations that interconvert in solution, the presence of a D nucleoside triggered folding into a hairpin with a stable stem and flexible loop region. Apparently the D modification is required in the studied sequence to fold into a stable hairpin. Therefore we conclude that D contributes to the correct folding and stability of D-arm in tRNA. In contrast to what is generally assumed for nucleic acids, the sharp 'imino' signal for the D nucleobase at 10 ppm in 90% H2O is not indicative for the presence of a stable hydrogen bond. The strong increase in pKa upon loss of the aromatic character in the modified nucleobase slows down the exchange of its 'imino' proton significantly, allowing its observation even in an isolated D nucleoside in 90% H2O in acidic to neutral conditions.
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Affiliation(s)
- N Dyubankova
- Medicinal Chemistry, Department of Pharmaceutical Sciences, Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium.
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5
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Wang SH, You ZY, Ye LP, Che J, Qian Q, Nanjo Y, Komatsu S, Zhong BX. Quantitative Proteomic and Transcriptomic Analyses of Molecular Mechanisms Associated with Low Silk Production in Silkworm Bombyx mori. J Proteome Res 2014; 13:735-51. [DOI: 10.1021/pr4008333] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Shao-hua Wang
- College
of Animal Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, P.R. China
| | - Zheng-ying You
- College
of Animal Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, P.R. China
| | - Lu-peng Ye
- College
of Animal Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, P.R. China
| | - Jiaqian Che
- College
of Animal Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, P.R. China
| | - Qiujie Qian
- College
of Animal Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, P.R. China
| | - Yohei Nanjo
- National
Institute of Crop Science, NARO, Kannondai 2-1-18, Tsukuba 305-8518, Japan
| | - Setsuko Komatsu
- National
Institute of Crop Science, NARO, Kannondai 2-1-18, Tsukuba 305-8518, Japan
| | - Bo-xiong Zhong
- College
of Animal Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, P.R. China
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6
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Jones TE, Ribas de Pouplana L, Alexander RW. Evidence for late resolution of the aux codon box in evolution. J Biol Chem 2013; 288:19625-32. [PMID: 23696642 DOI: 10.1074/jbc.m112.449249] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Recognition strategies for tRNA aminoacylation are ancient and highly conserved, having been selected very early in the evolution of the genetic code. In most cases, the trinucleotide anticodons of tRNA are important identity determinants for aminoacylation by cognate aminoacyl-tRNA synthetases. However, a degree of ambiguity exists in the recognition of certain tRNA(Ile) isoacceptors that are initially transcribed with the methionine-specifying CAU anticodon. In most organisms, the C34 wobble position in these tRNA(Ile) precursors is rapidly modified to lysidine to prevent recognition by methionyl-tRNA synthetase (MRS) and production of a chimeric Met-tRNA(Ile) that would compromise translational fidelity. In certain bacteria, however, lysidine modification is not required for MRS rejection, indicating that this recognition strategy is not universally conserved and may be relatively recent. To explore the actual distribution of lysidine-dependent tRNA(Ile) rejection by MRS, we have investigated the ability of bacterial MRSs from different clades to differentiate cognate tRNACAU(Met) from near-cognate tRNACAU(Ile). Discrimination abilities vary greatly and appear unrelated to phylogenetic or structural features of the enzymes or sequence determinants of the tRNA. Our data indicate that tRNA(Ile) identity elements were established late and independently in different bacterial groups. We propose that the observed variation in MRS discrimination ability reflects differences in the evolution of genetic code machineries of emerging bacterial clades.
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Affiliation(s)
- Thomas E Jones
- Department of Chemistry, Wake Forest University, Winston-Salem, North Carolina 27109-7486, USA
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7
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Abstract
MOTIVATION The standard genetic code translates 61 codons into 20 amino acids using fewer than 61 transfer RNAs (tRNAs). This is possible because of the tRNA's ability to 'wobble' at the third base to decode more than one codon. Although the anticodon-codon mapping of tRNA to mRNA is a prerequisite for certain codon usage indices and can contribute to the understanding of the evolution of alternative genetic codes, it is usually not determined experimentally because such assays are prohibitively expensive and elaborate. Instead, the codon reading is approximated from theoretical inferences of nucleotide binding, the wobble rules. Unfortunately, these rules fail to capture all of the nuances of codon reading. This study addresses the codon reading properties of tRNAs and their evolutionary impact on codon usage bias. RESULTS Using three different computational methods, the signal of tRNA decoding in codon usage bias is identified. The predictions by the methods generally agree with each other and compare well with experimental evidence of codon reading. This analysis suggests a revised codon reading for cytosolic tRNA in the yeast genome (Saccharomyces cerevisiae) that is more accurate than the common assignment by wobble rules. The results confirm the earlier observation that the wobble rules are not sufficient for a complete description of codon reading, because they depend on genome-specific factors. The computational methods presented here are applicable to any fully sequenced genome. AVAILABILITY By request from the author. CONTACT alexander.roth@isb-sib.ch.
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Affiliation(s)
- Alexander C Roth
- Swiss Institute of Bioinformatics, and Department of Computer Science, ETH Zurich, 8092 Zurich, Switzerland.
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8
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Jakubowski H. Quality control in tRNA charging. WILEY INTERDISCIPLINARY REVIEWS-RNA 2011; 3:295-310. [PMID: 22095844 DOI: 10.1002/wrna.122] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Faithful translation of the genetic code during protein synthesis is fundamental to the growth, development, and function of living organisms. Aminoacyl-tRNA synthetases (AARSs), which define the genetic code by correctly pairing amino acids with their cognate tRNAs, are responsible for 'quality control' in the flow of information from a gene to a protein. When differences in binding energies of amino acids to an AARS are inadequate, editing is used to achieve high selectivity. Editing occurs at the synthetic active site by hydrolysis of noncognate aminoacyl-adenylates (pretransfer editing) and at a dedicated editing site located in a separate domain by deacylation of mischarged aminoacyl-tRNA (posttransfer editing). Access of nonprotein amino acids, such as homocysteine or ornithine, to the genetic code is prevented by the editing function of AARSs, which functionally partitions amino acids present in living cells into protein and nonprotein amino acids. Continuous editing is part of the tRNA aminoacylation process in living organisms from bacteria to human beings. Preventing mistranslation by the clearance of misactivated amino acids is crucial to cellular homeostasis and has a role in etiology of disease. Although there is a strong selective pressure to minimize mistranslation, some organisms possess error-prone AARSs that cause mistranslation. Elevated levels of mistranslation and the synthesis of statistical proteins can be beneficial for pathogens by increasing phenotypic variation essential for the evasion of host defenses.
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Affiliation(s)
- Hieronim Jakubowski
- Department of Microbiology and Molecular Genetics, UMDNJ-New Jersey Medical School, International Center for Public Health, Newark, NJ, USA.
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9
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Kramer EB, Vallabhaneni H, Mayer LM, Farabaugh PJ. A comprehensive analysis of translational missense errors in the yeast Saccharomyces cerevisiae. RNA (NEW YORK, N.Y.) 2010; 16:1797-808. [PMID: 20651030 PMCID: PMC2924539 DOI: 10.1261/rna.2201210] [Citation(s) in RCA: 95] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
The process of protein synthesis must be sufficiently rapid and sufficiently accurate to support continued cellular growth. Failure in speed or accuracy can have dire consequences, including disease in humans. Most estimates of the accuracy come from studies of bacterial systems, principally Escherichia coli, and have involved incomplete analysis of possible errors. We recently used a highly quantitative system to measure the frequency of all types of misreading errors by a single tRNA in E. coli. That study found a wide variation in error frequencies among codons; a major factor causing that variation is competition between the correct (cognate) and incorrect (near-cognate) aminoacyl-tRNAs for the mutant codon. Here we extend that analysis to measure the frequency of missense errors by two tRNAs in a eukaryote, the yeast Saccharomyces cerevisiae. The data show that in yeast errors vary by codon from a low of 4 x 10(-5) to a high of 6.9 x 10(-4) per codon and that error frequency is in general about threefold lower than in E. coli, which may suggest that yeast has additional mechanisms that reduce missense errors. Error rate again is strongly influenced by tRNA competition. Surprisingly, missense errors involving wobble position mispairing were much less frequent in S. cerevisiae than in E. coli. Furthermore, the error-inducing aminoglycoside antibiotic, paromomycin, which stimulates errors on all error-prone codons in E. coli, has a more codon-specific effect in yeast.
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Affiliation(s)
- Emily B Kramer
- Program in Molecular and Cell Biology, Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, Maryland 21250, USA
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10
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Schrader JM, Chapman SJ, Uhlenbeck OC. Understanding the sequence specificity of tRNA binding to elongation factor Tu using tRNA mutagenesis. J Mol Biol 2009; 386:1255-64. [PMID: 19452597 DOI: 10.1016/j.jmb.2009.01.021] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Measuring the binding affinities of 42 single-base-pair mutants in the acceptor and T Psi C stems of Saccharomyces cerevisiae tRNA Phe to Thermus thermophilus elongation factor Tu (EF-Tu) revealed that much of the specificity for tRNA occurs at the 49-65, 50-64, and 51-63 base pairs. Introducing the same mutations at the three positions into Escherichia coli tRNA CAG Leu resulted in similar changes in binding affinity. Swapping the three pairs from several E. coli tRNAs into yeast tRNA Phe resulted in chimeras with EF-Tu binding affinities similar to those for the donor tRNA. Finally, analysis of double- and triple-base-pair mutants of tRNA Phe showed that the thermodynamic contributions at the three sites are additive, permitting reasonably accurate prediction of the EF-Tu binding affinity for all E. coli tRNAs. Thus, it appears that the thermodynamic contributions of three base pairs in the T Psi C stem primarily account for tRNA binding specificity to EF-Tu.
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Affiliation(s)
- Jared M Schrader
- Department of Biochemistry, Molecular Biology, and Cell Biology, Northwestern University, 2205 Tech Drive, Hogan 2-100, Evanston, IL 60208, USA
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11
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Carullo M, Xia X. An extensive study of mutation and selection on the wobble nucleotide in tRNA anticodons in fungal mitochondrial genomes. J Mol Evol 2008; 66:484-93. [PMID: 18401633 DOI: 10.1007/s00239-008-9102-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2007] [Revised: 03/05/2008] [Accepted: 03/19/2008] [Indexed: 10/22/2022]
Abstract
Two alternative hypotheses aim to predict the wobble nucleotide of tRNA anticodons in mitochondrion. The codon-anticodon adaptation hypothesis predicts that the wobble nucleotide of tRNA anticodon should evolve toward maximizing the Watson-Crick base pairing with the most frequently used codon within each synonymous codon family. In contrast, the wobble versatility hypothesis argues that the nucleotide at the wobble site should be occupied by a nucleotide most versatile in wobble pairing, i.e., the wobble site of the tRNA anticodon should be G for NNY codon families and U for NNR and NNN codon families (where Y stands for C or U, R for A or G, and N for any nucleotide). We examined codon usage and anticodon wobble sites in 36 fungal genomes to evaluate these two alternative hypotheses and identify exceptional cases that deserve new explanations. While the wobble versatility hypothesis is generally supported, there are interesting exceptions involving tRNA(Arg) translating the CGN codon family, tRNA(Trp) translating the UGR codon family, and tRNA(Met) translating the AUR codon family. Our results suggest that the potential to suppress stop codons, the historical inertia, and the conflict between translation initiation and elongation can all contribute to determining the wobble nucleotide of tRNA anticodons.
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Affiliation(s)
- Malisa Carullo
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
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12
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Eshete M, Marchbank MT, Deutscher SL, Sproat B, Leszczynska G, Malkiewicz A, Agris PF. Specificity of Phage Display Selected Peptides for Modified Anticodon Stem and Loop Domains of tRNA. Protein J 2007; 26:61-73. [PMID: 17237992 DOI: 10.1007/s10930-006-9046-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Protein recognition of RNA has been studied using Peptide Phage Display Libraries, but in the absence of RNA modifications. Peptides from two libraries, selected for binding the modified anticodon stem and loop (ASL) of human tRNA(LyS3) having 2-thiouridine (s(2)U34) and pseudouridine (psi39), bound the modified human ASL(Lys3)(s(2)U34;psi39) preferentially and had significant homology with RNA binding proteins. Selected peptides were narrowed to a manageable number using a less sensitive, but inexpensive assay before conducting intensive characterization. The affinity and specificity of the best binding peptide (with an N-terminal fluorescein) were characterized by fluorescence spectrophotometry. The peptide exhibited the highest binding affinity for ASL(LYS3)(s(2)U34; psi39), followed by the hypermodified ASL(Lys3) (mcm(5)s(2) U34; ms(2)t(6)A37) and the unmodified ASL(Lys3), but bound poorly to singly modified ASL(Lys3) constructs (psi39, ms(2)t(6)A37, s(2)34), ASL(Lys1,2) (t(6)A37) and Escherichia coli ASL(Glu) (s(2)U34). Thus, RNA modifications are potentially important recognition elements for proteins and can be targets for selective recognition by peptides.
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Affiliation(s)
- Matthewos Eshete
- Department of Molecular and Structural Biochemistry, North Carolina State University, 128 Polk Hall, Campus Box 7622, Raleigh, NC, 27695-7622, USA
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13
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Kramer EB, Farabaugh PJ. The frequency of translational misreading errors in E. coli is largely determined by tRNA competition. RNA (NEW YORK, N.Y.) 2007; 13:87-96. [PMID: 17095544 PMCID: PMC1705757 DOI: 10.1261/rna.294907] [Citation(s) in RCA: 344] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Estimates of missense error rates (misreading) during protein synthesis vary from 10(-3) to 10(-4) per codon. The experiments reporting these rates have measured several distinct errors using several methods and reporter systems. Variation in reported rates may reflect real differences in rates among the errors tested or in sensitivity of the reporter systems. To develop a more accurate understanding of the range of error rates, we developed a system to quantify the frequency of every possible misreading error at a defined codon in Escherichia coli. This system uses an essential lysine in the active site of firefly luciferase. Mutations in Lys529 result in up to a 1600-fold reduction in activity, but the phenotype varies with amino acid. We hypothesized that residual activity of some of the mutant genes might result from misreading of the mutant codons by tRNA(Lys) (UUUU), the cognate tRNA for the lysine codons, AAA and AAG. Our data validate this hypothesis and reveal details about relative missense error rates of near-cognate codons. The error rates in E. coli do, in fact, vary widely. One source of variation is the effect of competition by cognate tRNAs for the mutant codons; higher error frequencies result from lower competition from low-abundance tRNAs. We also used the system to study the effect of ribosomal protein mutations known to affect error rates and the effect of error-inducing antibiotics, finding that they affect misreading on only a subset of near-cognate codons and that their effect may be less general than previously thought.
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Affiliation(s)
- Emily B Kramer
- Department of Biological Sciences and Program in Molecular and Cell Biology, University of Maryland, Baltimore, Maryland 21250, USA
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Arnold S, Siemann-Herzberg M, Schmid J, Reuss M. Model-based inference of gene expression dynamics from sequence information. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2005; 100:89-179. [PMID: 16270657 DOI: 10.1007/b136414] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
A dynamic model of prokaryotic gene expression is developed that makes considerable use of gene sequence information. The main contribution arises from the fact that the combined gene expression model allows us to access the impact of altering a nucleotide sequence on the dynamics of gene expression rates mechanistically. The high level of detail of the mathematical model is considered as an important step towards bringing together the tremendous amount of biological in-depth knowledge that has been accumulated at the molecular level, using a systems level analysis (in the sense of a bottom-up, inductive approach). This enables to the model to provide highly detailed insights into the various steps of the protein expression process and it allows us to access possible targets for model-based design. Taken as a whole, the mathematical gene expression model presented in this study provides a comprehensive framework for a thorough analysis of sequence-related effects on the stages of mRNA synthesis, mRNA degradation and ribosomal translation, as well as their nonlinear interconnectedness. Therefore, it may be useful in the rational design of recombinant bacterial protein synthesis systems, the modulation of enzyme activities in pathway design, in vitro protein biosynthesis, and RNA-based vaccination.
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Affiliation(s)
- Sabine Arnold
- Biotechnology R&D, DSM Nutritional Products Ltd., Bldg. 203/113A, 4002 Basel, Switzerland
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15
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McDaneld TG, Hancock DL, Moody DE. Altered mRNA abundance of ASB15 and four other genes in skeletal muscle following administration of beta-adrenergic receptor agonists. Physiol Genomics 2004; 16:275-83. [PMID: 14645738 DOI: 10.1152/physiolgenomics.00127.2003] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Beta-adrenergic receptor agonists (BA) stimulate skeletal muscle growth. However, downstream signaling pathways that facilitate this effect remain poorly defined. Objectives of this study were to identify genes differentially expressed after administration of a novel BA and to evaluate the expression of one of those genes in additional models of skeletal muscle growth. Differentially expressed gene fragments were identified through differential display of skeletal muscle biopsies from five steers 24 h after administration of the BA. Five gene fragments designated DD53, DD143, DD163, DD209, and DD214 were identified. Tissue distribution of these genes was evaluated by RT-PCR. While DD53, DD163, DD209, and DD214 were expressed across tissues, DD143 mRNA expression was most abundant in skeletal muscle. DD143, later identified as bovine ASB15, was evaluated in rats following administration of anabolic compounds. Thirteen 7-wk-old female rats were randomly assigned to each of four treatment groups including: control, clenbuterol, trenbolone acetate (TBA), and growth hormone (GH). Changes in rat Asb-15 mRNA were measured at 30 min, 12 h, and 24 h following intraperitoneal injections of each compound. Clenbuterol treatment decreased Asb-15 mRNA in skeletal muscle at 12 and 24 h (P < 0.01) and also decreased mRNA in lung at 12 h (P < 0.05). TBA and GH treatments did not alter Asb-15 mRNA in any of the tissues evaluated (P > 0.10). These results are the first to associate an Asb gene family member with muscle growth or BA administration and suggest a potential role for ASB15 in beta-agonist-induced skeletal muscle hypertrophy.
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Affiliation(s)
- Tara G McDaneld
- Department of Animal Sciences, Purdue University, West Lafayette 47907-2054, USA
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16
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Shimada N, Suzuki T, Watanabe K. Dual mode recognition of two isoacceptor tRNAs by mammalian mitochondrial seryl-tRNA synthetase. J Biol Chem 2001; 276:46770-8. [PMID: 11577083 DOI: 10.1074/jbc.m105150200] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Animal mitochondrial translation systems contain two serine tRNAs, corresponding to the codons AGY (Y = U and C) and UCN (N = U, C, A, and G), each possessing an unusual secondary structure; tRNA(GCU)(Ser) (for AGY) lacks the entire D arm, whereas tRNA(UGA)(Ser) (for UCN) has an unusual cloverleaf configuration. We previously demonstrated that a single bovine mitochondrial seryl-tRNA synthetase (mt SerRS) recognizes these topologically distinct isoacceptors having no common sequence or structure. Recombinant mt SerRS clearly footprinted at the TPsiC loop of each isoacceptor, and kinetic studies revealed that mt SerRS specifically recognized the TPsiC loop sequence in each isoacceptor. However, in the case of tRNA(UGA)(Ser), TPsiC loop-D loop interaction was further required for recognition, suggesting that mt SerRS recognizes the two substrates by distinct mechanisms. mt SerRS could slightly but significantly misacylate mitochondrial tRNA(Gln), which has the same TPsiC loop sequence as tRNA(UGA)(Ser), implying that the fidelity of mitochondrial translation is maintained by kinetic discrimination of tRNAs in the network of aminoacyl-tRNA synthetases.
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Affiliation(s)
- N Shimada
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
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17
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Alexander RW, Schimmel P. Domain-domain communication in aminoacyl-tRNA synthetases. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 2001; 69:317-49. [PMID: 11550797 DOI: 10.1016/s0079-6603(01)69050-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
Abstract
Aminoacyl-tRNA synthetases are modular proteins, with domains that have distinct roles in the aminoacylation reaction. The catalytic core is responsible for aminoacyl adenylate formation and transfer of the amino acid to the 3' end of the bound transfer RNA (tRNA). Appended and inserted domains contact portions of the tRNA outside the acceptor site and contribute to the efficiency and specificity of aminoacylation. Some aminoacyl-tRNA synthetases also have distinct editing activities that are localized to unique domains. Efficient aminoacylation and editing require communication between RNA-binding and catalytic domains, and can be considered as a signal transduction system. Here, evidence for domain-domain communication in aminoacyl-tRNA synthetases is summarized, together with insights from structural analysis.
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Affiliation(s)
- R W Alexander
- Department of Chemistry, Wake Forest University, Winston-Salem, North Carolina 27109, USA
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18
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Yokogawa T, Shimada N, Takeuchi N, Benkowski L, Suzuki T, Omori A, Ueda T, Nishikawa K, Spremulli LL, Watanabe K. Characterization and tRNA recognition of mammalian mitochondrial seryl-tRNA synthetase. J Biol Chem 2000; 275:19913-20. [PMID: 10764807 DOI: 10.1074/jbc.m908473199] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Animal mitochondrial protein synthesis systems contain two serine tRNAs (tRNAs(Ser)) corresponding to the codons AGY and UCN, each possessing an unusual secondary structure; the former lacks the entire D arm, and the latter has a slightly different cloverleaf structure. To elucidate whether these two tRNAs(Ser) can be recognized by the single animal mitochondrial seryl-tRNA synthetase (mt SerRS), we purified mt SerRS from bovine liver 2400-fold and showed that it can aminoacylate both of them. Specific interaction between mt SerRS and either of the tRNAs(Ser) was also observed in a gel retardation assay. cDNA cloning of bovine mt SerRS revealed that the deduced amino acid sequence of the enzyme contains 518 amino acid residues. The cDNAs of human and mouse mt SerRS were obtained by reverse transcription-polymerase chain reaction and expressed sequence tag data base searches. Elaborate inspection of primary sequences of mammalian mt SerRSs revealed diversity in the N-terminal domain responsible for tRNA recognition, indicating that the recognition mechanism of mammalian mt SerRS differs considerably from that of its prokaryotic counterpart. In addition, the human mt SerRS gene was found to be located on chromosome 19q13.1, to which the autosomal deafness locus DFNA4 is mapped.
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Affiliation(s)
- T Yokogawa
- Department of Biomolecular Science, Faculty of Engineering, Gifu University, 1-1 Yanagito, Gifu 501-1193, Japan
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19
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Abstract
The aminoacyl-tRNA synthetases are an ancient group of enzymes that catalyze the covalent attachment of an amino acid to its cognate transfer RNA. The question of specificity, that is, how each synthetase selects the correct individual or isoacceptor set of tRNAs for each amino acid, has been referred to as the second genetic code. A wealth of structural, biochemical, and genetic data on this subject has accumulated over the past 40 years. Although there are now crystal structures of sixteen of the twenty synthetases from various species, there are only a few high resolution structures of synthetases complexed with cognate tRNAs. Here we review briefly the structural information available for synthetases, and focus on the structural features of tRNA that may be used for recognition. Finally, we explore in detail the insights into specific recognition gained from classical and atomic group mutagenesis experiments performed with tRNAs, tRNA fragments, and small RNAs mimicking portions of tRNAs.
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Affiliation(s)
- P J Beuning
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
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20
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Eriani G, Gangloff J. Yeast aspartyl-tRNA synthetase residues interacting with tRNA(Asp) identity bases connectively contribute to tRNA(Asp) binding in the ground and transition-state complex and discriminate against non-cognate tRNAs. J Mol Biol 1999; 291:761-73. [PMID: 10452887 DOI: 10.1006/jmbi.1999.3012] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Crystallographic studies of the aspartyl-tRNA synthetase-tRNA(Asp)complex from yeast identified on the enzyme a number of residues potentially able to interact with tRNA(Asp). Alanine replacement of these residues (thought to disrupt the interactions) was used in the present study to evaluate their importance in tRNA(Asp)recognition and acylation. The results showed that contacts with the acceptor A of tRNA(Asp)by amino acid residues interacting through their side-chain occur only in the acylation transition state, whereas those located near the G73 discriminator base occur also during initial binding of tRNA(Asp). Interactions with the anticodon bases provide the largest free energy contribution to stability of the enzyme-tRNA complex in its ground state. These contacts also favour catalysis, by acting connectively with each other and with those of G73, as shown by multiple mutant analysis. This implies structural communication transmitting the anticodon recognition signal to the distally located acylation site. This signal might be conveyed via tRNA(Asp)as suggested by the observed conformational change of this molecule upon interaction with AspRS. From binding free energy values corresponding to the different AspRS-tRNA(Asp)interaction domains, it might be concluded that upon complex formation, the anticodon interacts first. Finally, acylation efficiencies of AspRS mutants in the presence of pure tRNA(Asp)and non-fractionated tRNAs indicate that residues involved in the binding of identity bases also discriminate against non-cognate tRNAs.
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MESH Headings
- Acylation
- Anticodon/chemistry
- Anticodon/genetics
- Anticodon/metabolism
- Aspartate-tRNA Ligase/chemistry
- Aspartate-tRNA Ligase/genetics
- Aspartate-tRNA Ligase/metabolism
- Binding Sites
- Cell Division/genetics
- Crystallography, X-Ray
- Macromolecular Substances
- Models, Molecular
- Mutagenesis, Site-Directed
- Mutation
- Nucleic Acid Conformation
- Phosphates/chemistry
- Protein Conformation
- RNA, Fungal/chemistry
- RNA, Fungal/genetics
- RNA, Fungal/metabolism
- RNA, Transfer, Asp/chemistry
- RNA, Transfer, Asp/genetics
- RNA, Transfer, Asp/metabolism
- Ribose/chemistry
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae/growth & development
- Saccharomyces cerevisiae/metabolism
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Affiliation(s)
- G Eriani
- UPR 9002 SMBMR du CNRS, Institut de Biologie Moléculaire et Cellulaire, 15, rue René Descartes, Strasbourg, 67084, France
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21
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Abstract
The highly specific interaction of each aminoacyl-tRNA synthetase and its substrate tRNAs constitutes an intriguing problem in protein-RNA recognition. All tRNAs have the same overall three-dimensional structure in order to fit interchangeably into the translational apparatus. Thus, the recognition by aminoacyl-tRNA synthetase must be more or less limited to discrimination between bases at specific positions within the tRNA. The hypermodified nucleotide 5-methylaminomethyl-2-thiouridine (mnm5s2U) present at the wobble position of bacterial tRNAs specific for glutamic acid, lysine and possibly glutamine has been shown to be important in the recognition of these tRNAs by their synthetases in vitro. Here, we have determined the aminoacylation level in vivo of tRNAGlu, tRNALys, and tRNA1GIn in Escherichia coli strains containing undermodified derivatives of mnm5s2U34. Lack of the 5-methylaminomethyl group did not reduce charging levels for any of the three tRNAs. Lack of the s2U34 modification caused a 40% reduction in the charging level of tRNAGlu. Charging of tRNALys and tRNA1Gln were less affected. There was no compensating regulation of expression of glutamyl-tRNA synthetase because the relative synthesis rate was the same in the wild-type and mutant strains. These results indicate that the mnm5U34 modification is not an important recognition element in vivo for the glutamyl-tRNA synthetase. In contrast, lack of the s2U34 modification reduced the efficiency of charging by at least 40%. This is the minimal estimate because the turn-over rate of Glu-tRNAGlu was also reduced in the absence of the 2-thio group. Lack of either modification did not affect mischarging or mistranslation.
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Affiliation(s)
- M K Krüger
- Department of Molecular Cell Biology, University of Copenhagen, Denmark
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22
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Affiliation(s)
- Paul Schimmel
- The Skaggs Institute for Chemical BiologyThe Scripps Research InstituteBeckman Center La Jolla California 92037 USA
| | - Jianshi Tao
- Cubist Pharmaceuticals Inc. Cambridge Massachusetts 02139 USA
| | - Jason Hill
- Cubist Pharmaceuticals Inc. Cambridge Massachusetts 02139 USA
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23
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Giegé R, Sissler M, Florentz C. Universal rules and idiosyncratic features in tRNA identity. Nucleic Acids Res 1998; 26:5017-35. [PMID: 9801296 PMCID: PMC147952 DOI: 10.1093/nar/26.22.5017] [Citation(s) in RCA: 599] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Correct expression of the genetic code at translation is directly correlated with tRNA identity. This survey describes the molecular signals in tRNAs that trigger specific aminoacylations. For most tRNAs, determinants are located at the two distal extremities: the anticodon loop and the amino acid accepting stem. In a few tRNAs, however, major identity signals are found in the core of the molecule. Identity elements have different strengths, often depend more on k cat effects than on K m effects and exhibit additive, cooperative or anti-cooperative interplay. Most determinants are in direct contact with cognate synthetases, and chemical groups on bases or ribose moieties that make functional interactions have been identified in several systems. Major determinants are conserved in evolution; however, the mechanisms by which they are expressed are species dependent. Recent studies show that alternate identity sets can be recognized by a single synthetase, and emphasize the importance of tRNA architecture and anti-determinants preventing false recognition. Identity rules apply to tRNA-like molecules and to minimalist tRNAs. Knowledge of these rules allows the manipulation of identity elements and engineering of tRNAs with switched, altered or multiple specificities.
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MESH Headings
- Amino Acyl-tRNA Synthetases/metabolism
- Evolution, Molecular
- Genetic Code
- Humans
- Kinetics
- Models, Molecular
- Nucleic Acid Conformation
- Protein Biosynthesis
- RNA, Transfer/chemistry
- RNA, Transfer/genetics
- RNA, Transfer/metabolism
- RNA, Transfer, Amino Acyl/chemistry
- RNA, Transfer, Amino Acyl/genetics
- RNA, Transfer, Amino Acyl/metabolism
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Affiliation(s)
- R Giegé
- Unité Propre de Recherche 9002, 'Structure des Macromolécules Biologiques et Mécanismes de Reconnaissance', Scientifique, 15 rue René Descartes, F-67084, Strasbourg Cedex, France.
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24
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Heckl M, Busch K, Gross HJ. Minimal tRNA(Ser) and tRNA(Sec) substrates for human seryl-tRNA synthetase: contribution of tRNA domains to serylation and tertiary structure. FEBS Lett 1998; 427:315-9. [PMID: 9637248 DOI: 10.1016/s0014-5793(98)00435-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The recognition process of tRNA(Ser) and tRNA(Sec) by human seryl-tRNA synthetase (SerRS) was studied using T7 transcripts representing defined regions of human tRNA(Ser) or tRNA(Sec) and the influence of the tRNA elements on serylation and tertiary structure was elucidated. The anticodon arms of both tRNAs showed no contribution to serylation in contrast to the acceptor stems and the long extra arms. D and T arms were only involved in formation of the L-shaped tRNA structure, not in the recognition process between tRNAs and SerRS. This is the first report of microhelices adapted from human tRNAs being aminoacylated by their homologous synthetase.
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Affiliation(s)
- M Heckl
- Institut für Biochemie, Bayerische Julius-Maximilians-Universität, Biozentrum, Würzburg, Germany
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25
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Felden B, Florentz C, Westhof E, Giegé R. Transfer RNA identity rules and conformation of the tyrosine tRNA-like domain of BMV RNA imply additional charging by histidine and valine. Biochem Biophys Res Commun 1998; 243:426-34. [PMID: 9480825 DOI: 10.1006/bbrc.1997.7753] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
This paper reports the first example of a triple aminoacylation specificity of a viral tRNA-like domain. These findings were based on structural studies on the brome mosaic virus (BMV) tRNA-like domain (Felden et al., 1994, J. Mol. Biol. 235, 508-531) together with knowledge on tRNA aminoacylation identity rules suggesting potential histidinylation and valylation capacities of the viral RNA in addition to its already known tyrosylation ability. Here, both predictions are demonstrated by in vitro aminoacylation assays. Kinetic parameters of histidinylation and valylation of BMV tRNA-like structure have been determined and compared to those of the corresponding tRNA transcripts and to the tyrosylation capacity of the molecule. The influence of experimental conditions on aminoacylation reactions was also studied. The novel aminoacylation capacities of BMV tRNA-like domain support its already reported three-dimensional fold and illustrate the predictive potential of modeling data. Biological necessity of specific or non specific aminoacylation will be discussed.
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MESH Headings
- Base Sequence
- Bromovirus/chemistry
- Kinetics
- Models, Molecular
- Molecular Sequence Data
- Nucleic Acid Conformation
- RNA, Fungal/chemistry
- RNA, Transfer/chemistry
- RNA, Transfer/metabolism
- RNA, Transfer, His/chemistry
- RNA, Transfer, Tyr/chemistry
- RNA, Transfer, Val/chemistry
- RNA, Viral/chemistry
- Substrate Specificity
- Transcription, Genetic/genetics
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Affiliation(s)
- B Felden
- Institut de Biologie Moléculaire et Cellulaire du Centre National de la Recherche Scientifique, Strasbourg, France.
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26
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Norcum MT, Warrington JA. Structural analysis of the multienzyme aminoacyl-tRNA synthetase complex: a three-domain model based on reversible chemical crosslinking. Protein Sci 1998; 7:79-87. [PMID: 9514262 PMCID: PMC2143804 DOI: 10.1002/pro.5560070108] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
A subset of eukaryotic aminoacyl-tRNA synthetases (a-RS) are contained in a multienzyme complex for which little structural detail is known. Three reversible chemical crosslinking reagents have been used to investigate the arrangement of polypeptides within this particle as isolated from rabbit reticulocytes. Identification of the crosslinked protein pairs was accomplished by two-dimensional SDS diagonal gel electrophoresis. Seventeen neighboring protein pairs have been identified. Eight are seen with at least two reagents: K-RS:p38, D-RS:K-RS, R-RS dimer, K-RS dimer, K-RS:Q-RS, E/P-RS:K-RS, E/P-RS:I-RS, and Q-RS with one of the nonsynthetase proteins. Nine more are observed with one reagent: D-RS dimer, R-RS:p43, D-RS:Q-RS, D-RS:M-RS, K-RS:L-RS, I-RS:R-RS, D-RS:E/P-RS, I-RS:Q-RS, I-RS:L-RS. One trimeric association is seen: E/P-RS:I-RS:L-RS. The observed neighboring protein pairs suggest that the polypeptides within the aminoacyl-tRNA synthetase complex are distributed in three structural domains of similar mass. These can be arranged in a U-shaped particle in which each "arm" is considered a domain and the third forms the "base" of the structure. The arms have been termed domain I (D-RS, M-RS, Q-RS) and domain II (K-RS, R-RS), with domain III (E/P-RS, I-RS, L-RS) assigned to the base. The smaller proteins (p38, p43) may bridge the domains. This proposed spatial relationship of these domains, as well as their compositions, are consistent with earlier studies. Thus, this study provides an initial three-dimensional working model of the arrangement of polypeptides within the multienzyme aminoacyl-tRNA synthetase complex.
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Affiliation(s)
- M T Norcum
- Department of Biochemistry, University of Mississippi Medical Center, Jackson 39216-4505, USA.
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27
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Becker HF, Motorin Y, Sissler M, Florentz C, Grosjean H. Major identity determinants for enzymatic formation of ribothymidine and pseudouridine in the T psi-loop of yeast tRNAs. J Mol Biol 1997; 274:505-18. [PMID: 9417931 DOI: 10.1006/jmbi.1997.1417] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Almost all transfer RNA molecules sequenced so far contain two universal modified nucleosides at positions 54 and 55, respectively: ribothymidine (T54) and pseudouridine (psi 55). To identify the tRNA elements recognized by tRNA:m5uridine-54 methyltransferase and tRNA:pseudouridine-55 synthase from the yeast Saccharomyces cerevisiae, a set of 43 yeast tRNA(Asp) mutants were used. Some variants contained point mutations, while the others included progressive reductions in size down to a tRNA minisubstrate consisting of the T psi-loop with only one G.C base-pair as stem (9-mer). All substrates (full-sized tRNA(Asp) and various minihelices) were produced in vitro by T7 transcription and tested using yeast extract (S100) as a source of enzymatic activities and S-adenosyl-L-methionine as a methyl donor. The results indicate that the minimal substrate for enzymatic formation of psi 55 is a stem/loop structure with only four G.C base-pairs in the stem, while a longer stem is required for efficient T54 formation. None of the conserved nucleotides (G53, C56, A58 and C61) and U54 for psi 55 or U55 for T54 formation can be replaced by any of the other three canonical nucleotides. Yeast tRNA:m5uridine-54 methyltransferase additionally requires the presence of a pyrimidine-60 in the loop. Interestingly, in a tRNA(Asp) variant in which the T psi-loop was permuted with the anticodon-loop, the new U32 and U33 residues derived from the T psi-loop were quantitatively converted to T32 and psi 33, respectively. Structural mapping of this variant with ethylnitrosourea confirmed that the intrinsic characteristic structure of the T psi-loop was conserved upon permutation and that the displaced anticodon-loop did not acquire a T psi-loop structure. These results demonstrate that a local conformation rather than the exact location of the U-U sequence within the tRNA architecture is the important identity determinant for recognition by yeast tRNA:m5uridine-54 methyltransferase and tRNA:pseudouridine-55 synthase.
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Affiliation(s)
- H F Becker
- Laboratoire d'Enzymologie et Biochimie Structurales du CNRS, Gif-sur-Yvette, France
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28
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Liu DR, Magliery TJ, Schultz PG. Characterization of an 'orthogonal' suppressor tRNA derived from E. coli tRNA2(Gln). CHEMISTRY & BIOLOGY 1997; 4:685-91. [PMID: 9331409 DOI: 10.1016/s1074-5521(97)90224-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
BACKGROUND In an effort to expand further our ability to manipulate protein structure, we have completed the first step towards a general method that allows the site-specific incorporation of unnatural amino acids into proteins in vivo. Our approach involves the construction of an 'orthogonal' suppressor tRNA that is uniquely acylated in vivo, by an engineered aminoacyl-tRNA synthetase, with the desired unnatural amino acid. The Escherichia coli tRNA2(Gln)-glutaminyl-tRNA synthetase (GlnRS) pair provides a biochemically and structurally well-characterized starting point for developing this methodology. To generate the orthogonal tRNA, mutations were introduced into the acceptor stem, D-loop/stem, and anticodon loop of tRNA2(Gln). We report here the characterization of the properties of the resulting tRNAs and their suitability to severe as an orthogonal suppressor. Our efforts to generate an engineered synthetase are described elsewhere. RESULTS Mutant tRNAs were generated by runoff transcription and assayed for their ability to be aminoacylated by purified E. coli GlnRS and to suppress an amber codon in an in vitro transcription/translation reaction. One tRNA bearing eight mutations satisfies the minimal requirements for the delivery of an unnatural amino acid: it is not acylated by any endogenous E. coli aminoacyl-tRNA synthetase, including GlnRS, yet functions efficiently during protein translation. Mutations in the acceptor stem and D-loop/stem, when introduced in combination, had very different effects on the properties of the resulting tRNAs compared with the effects of the individual mutations. CONCLUSIONS Mutations at sites within tRNA2(Gln) separated by 23-31 A interact strongly with each other, often in a nonadditive fashion, to modulate both aminoacylation activities and translational efficiencies. The observed correlation between the effects of mutations at very distinct regions of the GlnRS-tRNA and possibly the ribosomal/tRNA complexes may contribute in part to the fidelity of protein biosynthesis.
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Affiliation(s)
- D R Liu
- Howard Hughes Medical Institute, Department of Chemistry, University of California, Berkeley 94720, USA.
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29
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Abstract
Recognition of tRNAs by aminoacyl tRNA synthetases establishes the connection between amino acids and anticodon triplets of the genetic code. Although anticodons and nucleotides adjacent to the amino acid attachment site are generally important, the tertiary structural framework of tRNAs has recently been implicated to have a role in tRNA recognition. A G15:G48 tertiary hydrogen base pair of E. coli tRNA(Cys) is important for recognition of the tRNA by cysteine tRNA synthetase. This base pair is proposed to consist of N2:N3, rather than N1:O6, hydrogen bonds. The reproduction of the hydrogen pairing scheme of tRNA(Gly). This reproduction required an A13:A22 mismatch in the dihyrouridine stem. To determine if A13:A22 is a determinant of the structural features of G15:G48, we investigated the A15:U48 and A15:A48 variants of tRNA(Gly) which harbored specific substitutions of A13:A22. We show here that introduction of A13:A22 to both tRNA frameworks confers structural features similar to those of G15:G48 in E. coli tRNA(Cys). These structural features are accompanied by efficient recognition of both tRNAs by cysteine tRNA synthetase. Substitution of A13:A22 with U13:A22 alters the structural features at 15:48 and impairs tRNA recognition. The dependence on A13:22 for tRNA recognition has a distinct similarity to that of E. coli tRNA(Cys) and to that of the G15:G48 variant of tRNA(Gly). The results have implications for the design and manipulation of RNA structural elements as the basis for tRNA recognition.
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Affiliation(s)
- C S Hamann
- Department of Biochemistry and Molecular Pharmacology, Thomas Jefferson University, Philadelphia, PA 19107, USA
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30
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Hale SP, Auld DS, Schmidt E, Schimmel P. Discrete determinants in transfer RNA for editing and aminoacylation. Science 1997; 276:1250-2. [PMID: 9157882 DOI: 10.1126/science.276.5316.1250] [Citation(s) in RCA: 75] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
During translation errors of aminoacylation are corrected in editing reactions which ensure that an amino acid is stably attached to its corresponding transfer RNA (tRNA). Previous studies have not shown whether the tRNA nucleotides needed for effecting translational editing are the same as or distinct from those required for aminoacylation, but several considerations have suggested that they are the same. Here, designed tRNAs that are highly active for aminoacylation but are not active in translational editing are presented. The editing reaction can be controlled by manipulation of nucleotides at the corner of the L-shaped tRNA. In contrast, these manipulations do not affect aminoacylation. These results demonstrate the segregation of nucleotide determinants for the editing and aminoacylation functions of tRNA.
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MESH Headings
- Acetylation
- Base Sequence
- Binding Sites
- Cloning, Molecular
- Escherichia coli
- Molecular Sequence Data
- Nucleic Acid Conformation
- RNA Editing
- RNA, Transfer/metabolism
- RNA, Transfer, Ile/chemistry
- RNA, Transfer, Ile/metabolism
- RNA, Transfer, Val/chemistry
- RNA, Transfer, Val/metabolism
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Affiliation(s)
- S P Hale
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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31
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Himeno H, Yoshida S, Soma A, Nishikawa K. Only one nucleotide insertion to the long variable arm confers an efficient serine acceptor activity upon Saccharomyces cerevisiae tRNA(Leu) in vitro. J Mol Biol 1997; 268:704-11. [PMID: 9175855 DOI: 10.1006/jmbi.1997.0991] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Several tRNA species have a long variable arm composed of over ten nucleotides, which are relevant to those specific to serine, leucine and tyrosine in prokaryotes, while there are only serine and leucine-specific tRNAs in eukaryotes. To clarify the evolutionary aspects of the identity determination mechanism of these tRNAs, the tRNA(Ser) recognition in Saccharomyces cerevisiae was studied. Unmodified tRNA(Leu) transcript had serylation ability of low efficiency, but native tRNA(Leu) did not, indicating that some modification of tRNA(Leu) serves as a negative identity determinant for seryl-tRNA synthetase. Changing the discriminator base did not seriously affect the serine accepting efficiency. The tRNA(Leu) transcript possessing the variable arm of tRNA(Ser) was efficiently aminoacylated with serine. Eventually, it was found that only one nucleotide insertion to the variable arm of tRNA(Leu) was sufficient to confer an efficient serine accepting activity. The mode of serine tRNA recognition is similar to that in Escherichia coli in that the end of the long variable arm, but not the anticodon or discriminator base, is important. However, S. cerevisiae seryl-tRNA synthetase adopts a substantially different mechanism for rejection of tRNA(Leu) from that of its E. coli counterpart.
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MESH Headings
- Base Sequence
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Evolution, Molecular
- Kinetics
- Molecular Sequence Data
- Mutagenesis, Insertional
- Nucleic Acid Conformation
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Fungal/chemistry
- RNA, Fungal/genetics
- RNA, Fungal/metabolism
- RNA, Transfer, Leu/chemistry
- RNA, Transfer, Leu/genetics
- RNA, Transfer, Leu/metabolism
- RNA, Transfer, Ser/chemistry
- RNA, Transfer, Ser/genetics
- RNA, Transfer, Ser/metabolism
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae/metabolism
- Serine/metabolism
- Serine-tRNA Ligase/metabolism
- Species Specificity
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Affiliation(s)
- H Himeno
- Department of Biology, Faculty of Science, Hirosaki University, Japan
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32
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Qian Q, Björk GR. Structural requirements for the formation of 1-methylguanosine in vivo in tRNA(Pro)GGG of Salmonella typhimurium. J Mol Biol 1997; 266:283-96. [PMID: 9047363 DOI: 10.1006/jmbi.1996.0789] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Maturation of tRNA and rRNA and the assembly of the ribosome in all organisms occurs in vivo in a complex pathway in which various proteins such as endo- and exonucleases, tRNA and rRNA modifying enzymes and ribosomal proteins, act concomitantly and temporarily during the maturation process. One class of RNA binding proteins are the tRNA modifying enzymes, which catalyse the formation of various modified nucleosides present in tRNA. Here we analyse the consequences of various alterations in a tRNA on the formation of modified nucleosides in the tRNA and the aminoacylation of it under true in vivo conditions, i.e. in a cell with normal amounts of the tRNA substrate and the tRNA binding protein. We have devised a selection method to obtain mutants of tRNA(Pro)GGG in Salmonella typhimurium that may no longer be a substrate inl vivo for the tRNA(m1G37)methyltransferase. These mutant tRNAs were purified from cells in balanced growth by a solid phase hybridisation technique and the presence of 1-methylguanosine (m1G) in position 37 next to the anticodon was monitored. Of 13 different mutant tRNA(Pro)GGG species analysed, eight of them had a drastically reduced level of m1G. Some of these mutant tRNA species had alterations far from the nucleotide G37 modified by the enzyme; e.g. base-pair disruptions in the first, fourth and eighth (last) base-pair of the acceptor stem, in the D-stem, and in the top of the anticodon stem. The structure of all the mutant tRNA(Pro)GGG species must deviate from the wild-type form, since they all induced +1 frameshifting. Still, tRNA(Pro)GGG from five of the mutants had normal levels of m1G. Thus, only a subset of mutations, all inducing an altered tRNA structure, resulted in m1G deficiency. However, those alterations in tRNA(Pro)GGG, which influenced the tRNA(m1G37)methyltransferase activity, did not affect in vivo the formation of four other modified nucleosides and the aminoacylation of tRNA(Pro)GGG, demonstrating the extreme dependence of the tRNA(m1G37)methyltransferase on an almost perfect three-dimensional structure of the tRNA. We discuss that the conformation of the anticodon loop may be a major determining element for the formation of m1G37 in vivo.
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MESH Headings
- Base Sequence
- DNA, Bacterial/genetics
- Frameshift Mutation
- Guanosine/analogs & derivatives
- Guanosine/genetics
- In Situ Hybridization/methods
- Models, Molecular
- Molecular Sequence Data
- Mutation
- RNA Precursors/genetics
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Transfer, Pro/chemistry
- RNA, Transfer, Pro/genetics
- RNA, Transfer, Pro/metabolism
- Salmonella typhimurium/genetics
- Structure-Activity Relationship
- Substrate Specificity
- Suppression, Genetic
- tRNA Methyltransferases/genetics
- tRNA Methyltransferases/metabolism
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Affiliation(s)
- Q Qian
- Department of Microbiology, Umeå University, Sweden
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33
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Kitabatake M, Ibba M, Hong KW, Söll D, Inokuchi H. Genetic analysis of functional connectivity between substrate recognition domains of Escherichia coli glutaminyl-tRNA synthetase. MOLECULAR & GENERAL GENETICS : MGG 1996; 252:717-22. [PMID: 8917315 DOI: 10.1007/bf02173978] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
It has previously been shown that the single mutation E222K in glutaminyl-tRNA synthetase (GlnRS) confers a temperature-sensitive phenotype on Escherichia coli. Here we report the isolation of a pseudorevertant of this mutation, E222K/C171G, which was subsequently employed to investigate the role of these residues in substrate discrimination. The three-dimensional structure of the tRNA(Gln): GlnRS: ATP ternary complex revealed that both E222 and C171 are close to regions of the protein involved in interactions with both the acceptor stem and the 3' end of tRNA(Gln). The potential involvement of E222 and C171 in these interactions was confirmed by the observation that GlnRS-E222K was able to mischarge supF tRNA(Tyr) considerably more efficiently than the wild-type enzyme, whereas GlnRS-E222K/C171G could not. These differences in substrate specificity also extended to anticodon recognition, with the double mutant able to distinguish supE tRNA(CUA)(Gln) from tRNA2(Gln) considerably more efficiently than GlnRS E222K. Furthermore, GlnRS-E222K was found to have a 15-fold higher K(m) for glutamine than the wild-type enzyme, whereas the double mutant only showed a 7-fold increase. These results indicate that the C171G mutation improves both substrate discrimination and recognition at three domains in GlnRS-E222K, confirming recent proposals that there are extensive interactions between the active site and regions of the enzyme involved in tRNA binding.
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Affiliation(s)
- M Kitabatake
- Department of Biophysics, Faculty of Science, Kyoto University, Japan
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34
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Felden B, Florentz C, Westhof E, Giegé R. Usefulness of functional and structural solution data for the modeling of tRNA-like structures. PHARMACEUTICA ACTA HELVETIAE 1996; 71:3-9. [PMID: 8786997 DOI: 10.1016/0031-6865(95)00044-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Structures of large RNAs are not easily solved by X-ray crystallography or by NMR spectroscopy. This paper reviews the alternate methodology based on enzymatic and chemical mapping data collected on RNAs combined with graphical modeling for the construction of three-dimensional models. The different steps that lead to the establishment of the models are critically discussed. It is shown how the correctness of an RNA model can be strengthened by establishing correlations between the structure and the functionality of the molecule and its variants. Finally, the predictive potential of a model is discussed The approach is illustrated by results obtained on plant viral tRNA-like structures, and particularly on that of brome mosaic virus (BMV) RNA.
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Affiliation(s)
- B Felden
- Unité Propre de Recherche n. 9002 du CNRS Structure des Macromolécules Biologiques et Mécanismes de Reconnaissance, Centre National de la Recherche Scientifique, Strasbourg, France.
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35
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Breitschopf K, Gross HJ. The discriminator bases G73 in human tRNA(Ser) and A73 in tRNA(Leu) have significantly different roles in the recognition of aminoacyl-tRNA synthetases. Nucleic Acids Res 1996; 24:405-10. [PMID: 8602350 PMCID: PMC145663 DOI: 10.1093/nar/24.3.405] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The recognition of human tRNA(Leu) or tRNA(Ser) by cognate aminoacyl- tRNA synthetases has distinct requirements. Only one base change (A73-->G) in tRNA(Leu) is required to generate an efficient serine acceptor in vitro, whereas several changes in three structural domains (the acceptor stem, DHU loop and long extra arm) of tRNA(Ser) are necessary in order to produce a leucine acceptor. Hence, the molecular basis for the discrimination between human tRNA(Ser) and tRNA(Leu) by the seryl-tRNA synthetase depends almost exclusively on a highly specific recognition of the discriminator base G73. In order to elucidate the specific role of the functional groups of this base in discrimination, tRNA(Ser) constructs were made which contain the artificial base analogues 2-aminopurine riboside or inosine at the discriminator position 73. Aminoacylation of these constructs by a HeLa S100 extract showed that molecules with 2-aminopurine riboside, but not with inosine, in position 73 could be serylated at low efficiency. However, the 2-aminopurine riboside and the inosine derivatives of tRNA(Ser) were equally efficient competitive inhibitors of serylation, whereas tRNAs(Ser) with any other natural base at position 73 did not competitively inhibit serylation of tRNA(Ser). This was in contrast to leucylation of tRNA(Leu), where tRNA(Leu) transcripts with any other nucleotide in the discriminator position acted as strong competitive inhibitors. These results suggest that the discriminator bases in human tRNA(Ser) and tRNA(Leu) play completely different roles in recognition of the tRNAs by their cognate aminoacyl-tRNA synthetases.
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Affiliation(s)
- K Breitschopf
- Institut für Biochemie, Bayerische Julius- Maximillians-Universität, D-97074 Würzburg, Germany
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36
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Abstract
Structure/function relationships accounting for specific tRNA charging by class II aspartyl-tRNA synthetases from Saccharomyces cerevisiae, Escherichia coli and Thermus thermophilus are reviewed. Effects directly linked to tRNA features are emphasized and aspects about synthetase contribution in expression of tRNA(Asp) identity are also covered. Major identity nucleotides conferring aspartate specificity to yeast, E coli and T thermophilus tRNAs comprise G34, U35, C36, C38 and G73, a set of nucleotides conserved in tRNA(Asp) molecules of other biological origin. Aspartate specificity can be enhanced by negative discrimination preventing, eg mischarging of native yeast tRNA(Asp by yeast arginyl-tRNA synthetase. In the yeast system crystallography shows that identity nucleotides are in contact with identity amino acids located in the catalytic and anticodon binding domains of the synthetase. Specificity of RNA/protein interaction involves a conformational change of the tRNA that optimizes the H-bonding potential of the identity signals on both partners of the complex. Mutation of identity nucleotides leads to decreased aspartylation efficiencies accompanied by a loss of specific H-bonds and an altered adaptation of tRNA on the synthetase. Species-specific characteristics of aspartate systems are the number, location and nature of minor identity signals. These features and the structural variations in aspartate tRNAs and synthetases are correlated with mechanistic differences in the aminoacylation reactions catalyzed by the various aspartyl-tRNA synthetases. The reality of the aspartate identity set is verified by its functional expression in a variety of RNA frameworks. Inversely a number of identities can be expressed within a tRNA(Asp) framework. From this emerged the concept of the RNA structural frameworks underlying expression of identities which is illustrated with data obtained with engineered tRNAs. Efficient aspartylation of minihelices is explained by the primordial role of G73. From this and other considerations it is suggested that aspartate identity appeared early in the history of tRNA aminoacylation systems.
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Affiliation(s)
- R Giegé
- Unité Structure des Macromolécules Biologioues et Mécanismes de Reconnaissance, Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg, France
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37
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Senger B, Fasiolo F. Yeast tRNA(Met) recognition by methionyl-tRNA synthetase requires determinants from the primary, secondary and tertiary structure: a review. Biochimie 1996; 78:597-604. [PMID: 8955903 DOI: 10.1016/s0300-9084(96)80006-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The primordial role of the CAU anticodon in methionine identity of the tRNA has been established by others nearly a decade ago in Escherichia coli and yeast tRNA(Met). We show here that the CAU triplet alone is unable to confer methionine acceptance to a tRNA. This requires the contribution of the discriminatory base A73 and the non-anticodon bases of the anticodon loop. To better understand the functional communication between the anticodon and the active site, we analysed the binding and aminoacylation of tRNA(Met) based anticodon and acceptor-stem minihelices and of tRNA(Met) chimeras where the central core region of yeast tRNA(Met) is replaced by that of unusual mitochondrial forms lacking either a D-stem or a T-stem. These studies suggest that the high selectivity of the anticodon bases in tRNA(Met) implies the L-conformation of the tRNA and the presence of a D-stem. The importance of a L-structure for recognition of tRNA(Met) was also deduced from mutations of tertiary interactions known to play a general role in tRNA(Met) folding.
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Affiliation(s)
- B Senger
- CNRS, UPR 9002, Structure des Macromolécules Biologiques et Mécanismes de Reconnaissance, Institut de Biologie Moléculaire et Cellulaire, Strasbourg, France
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38
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Tateno M, Nureki O, Sekine S, Kaneda K, Go M, Yokoyama S. A three-dimensional structure model of the complex of glutamyl-tRNA synthetase and its cognate tRNA. FEBS Lett 1995; 377:77-81. [PMID: 8543024 DOI: 10.1016/0014-5793(95)01295-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
A docking model of glutamyl-tRNA synthetase (GluRS) and tRNAGlu was constructed, on the basis of the distinguished similarity between the X-ray crystallographic three-dimensional structures of the N-terminal halves of the Thermus thermophilus GluRS in the free state and the Escherichia coli glutaminyl-tRNA synthetase in a complex with tRNAGln. The modeled structure is energetically favorable and is also well consistent with the results of site-directed mutagenesis studies. The model indicates that the GluRS-specific insertions 2 and 3 fit and bind to the acceptor stem and the D arm, respectively, of the cognate tRNA without affecting other contacts. In particular, insertion 3 strongly interacts with the two D-stem base pairs that are essential for the tRNA-GluRS recognition.
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Affiliation(s)
- M Tateno
- Department of Biophysics and Biochemistry, School of Science, University of Tokyo, Japan
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39
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Yap LP, Stehlin C, Musier-Forsyth K. Use of semi-synthetic transfer RNAs to probe molecular recognition by Escherichia coli proline-tRNA synthetase. CHEMISTRY & BIOLOGY 1995; 2:661-6. [PMID: 9383472 DOI: 10.1016/1074-5521(95)90029-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
BACKGROUND The attachment of specific amino acids to the 3'-end of cognate transfer of RNAs (tRNAs) is catalyzed by a class of enzymes known as aminoacyl-tRNA synthetases (aaRS). We have previously demonstrated that Escherichia coli proline-tRNA synthetase (ProRS) can aminoacylate semi-synthetic tRNAs prepared by annealing two RNA oligonucleotides. We set out to examine the factors that are important in selective recognition of tRNAPro by ProRS, using semi-synthetic tRNAs and full-length tRNA transcripts. RESULTS Deletion of nucleotides A58, A59, and U60 in the T psi C-loop of semi-synthetic tRNAs has no adverse effect on aminoacylation. Nucleotide deletions that extend into the T psi stem, particularly beyond C61, significantly reduce the efficiency of aminoacylation, however. Site-directed mutagenesis of full-length tRNAPro transcripts shows that, although there is no strict sequence requirement at base pair 52.62 in the T psi C stem, helix destabilizing purine-purine mismatches at this position result in decreased aminoacylation activity. Moreover, aminoacylation is severely affected when a DNA-RNA hybrid helix is incorporated into the acceptor-T psi C stem domain. CONCLUSIONS At least three nucleotides in the T psi C-loop are dispensable for aminoacylation of E. coli tRNAPro. These results, combined with previous data, demonstrate that four out of five of the so-called 'variable pocket' nucleotides are not important for recognition of tRNAPro by E. coli ProRS. ProRS is also sensitive to changes that are likely to alter the helical conformation in the T psi C stem.
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Affiliation(s)
- L P Yap
- Department of Chemistry, University of Minnesota, Minneapolis 55455, USA
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40
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Liu H, Kessler J, Peterson R, Musier-Forsyth K. Evidence for class-specific discrimination of a semiconserved base pair by tRNA synthetases. Biochemistry 1995; 34:9795-800. [PMID: 7542924 DOI: 10.1021/bi00030a017] [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: 01/25/2023]
Abstract
Aminoacyl-tRNA synthetases have been divided into two classes based on the existence of two structurally distinct active sites. To date, few class-specific tRNA recognition features have been elucidated. High-resolution X-ray structures of representative class I and class II synthetases complexed to cognate tRNA substrates have been solved. In these structures, the class I enzyme approaches the end of the tRNA acceptor stem from the minor-groove side, while the class II synthetase approaches its cognate tRNA from the major-groove side. This distinction is reflected in the different initial sites (2'- or 3'-OH) of amino acid attachment. The role that the semiconserved G1.C72 terminal base pair plays in the aminoacylation of Escherichia coli tRNAs is probed in this in vitro study. We show here that class II alanyl-, prolyl-, and histidyl-tRNA synthetases are sensitive to changes at position 1 x 72. Previous work on class I synthetases and new data presented here with the valine-specific enzyme indicate that class I enzymes show little sensitivity to replacements of G1.C72. This work provides new evidence for class-specific differences in tRNA acceptor stem interactions that appear to be reflected not only in the initial site of aminoacylation but also in the mode of synthetase interaction with the semiconserved G1.C72 base pair proximal to the amino acid attachment site.
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MESH Headings
- Alanine-tRNA Ligase/chemistry
- Alanine-tRNA Ligase/classification
- Alanine-tRNA Ligase/metabolism
- Base Composition
- Base Sequence
- Binding Sites
- Conserved Sequence
- Crystallography, X-Ray
- Escherichia coli/enzymology
- Molecular Sequence Data
- Nucleic Acid Conformation
- RNA, Bacterial/chemistry
- RNA, Transfer/chemistry
- RNA, Transfer/metabolism
- RNA, Transfer, Ala/chemistry
- RNA, Transfer, Ala/metabolism
- RNA, Transfer, Pro/chemistry
- RNA, Transfer, Pro/metabolism
- RNA, Transfer, Val/chemistry
- RNA, Transfer, Val/metabolism
- Structure-Activity Relationship
- Substrate Specificity
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Affiliation(s)
- H Liu
- Department of Chemistry, University of Minnesota, Minneapolis 55455, USA
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41
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Affiliation(s)
- P Schimmel
- Department of Biology, Massachusetts Institute of Technology, Cambridge 02139, USA
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42
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Mechulam Y, Meinnel T, Blanquet S. A family of RNA-binding enzymes. the aminoacyl-tRNA synthetases. Subcell Biochem 1995; 24:323-376. [PMID: 7900181 DOI: 10.1007/978-1-4899-1727-0_11] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Affiliation(s)
- Y Mechulam
- Laboratoire de Biochimie, CNRS n. 240, Ecole Polytechnique, Palaiseau, France
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43
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Carneiro VT, Dietrich A, Maréchal-Drouard L, Cosset A, Pelletier G, Small I. Characterization of some major identity elements in plant alanine and phenylalanine transfer RNAs. PLANT MOLECULAR BIOLOGY 1994; 26:1843-53. [PMID: 7532029 DOI: 10.1007/bf00019497] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Alanine and phenylalanine tRNA sequences were amplified by PCR from Arabidopsis thaliana nuclear DNA using degenerate oligonucleotides which introduced specific mutations into the acceptor stem. The aminoacylation of T7 RNA polymerase transcripts of these sequences was investigated in vitro using partially purified bean alanyl- or phenylalanyl-tRNA synthetase. In parallel, the in vivo activity of amber suppressor derivatives of these tRNAs was investigated in transient expression assays in tobacco protoplasts using a beta-glucuronidase (GUS) reporter gene containing a premature amber stop codon. The results show that mutation of the G3:U70 base pair to G3:C70 blocks aminoacylation of plant alanine tRNA, whilst conversion of the G3:C70 pair normally found in plant tRNA(Phe) to G3:U70 enables the mutated tRNA(Phe) to be a good substrate for alanyl-tRNA synthetase and impairs its aminoacylation with phenylalanine. In addition, the amber suppressor derivative of wild-type tRNA(Phe) showed very little suppressor activity in vivo, and was poorly aminoacylated with phenylalanine in vitro, suggesting that the anticodon is a major identity determinant for tRNA(Phe) in plant cells.
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MESH Headings
- Alanine-tRNA Ligase/metabolism
- Anticodon
- Arabidopsis/genetics
- Base Composition
- Base Sequence
- Brassica/genetics
- Cloning, Molecular
- Genes, Reporter
- Glucuronidase/biosynthesis
- Glucuronidase/genetics
- Molecular Sequence Data
- Phenylalanine-tRNA Ligase/metabolism
- Plants/genetics
- Plants, Toxic
- Polymerase Chain Reaction
- Protoplasts
- RNA/biosynthesis
- RNA, Transfer, Ala/genetics
- RNA, Transfer, Ala/metabolism
- RNA, Transfer, Phe/genetics
- RNA, Transfer, Phe/metabolism
- Sequence Analysis, DNA
- Solanum tuberosum/genetics
- Substrate Specificity
- Suppression, Genetic
- Nicotiana/genetics
- Transcription, Genetic
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Affiliation(s)
- V T Carneiro
- Station de Génétique et d'Amélioration des Plantes, INRA, Centre de Versailles, France
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44
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Jakubowski H. Energy cost of translational proofreading in vivo. The aminoacylation of transfer RNA in Escherichia coli. Ann N Y Acad Sci 1994; 745:4-20. [PMID: 7530434 DOI: 10.1111/j.1749-6632.1994.tb44360.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
In many cases, the intrinsic binding energies of amino acids to aminoacyl-tRNA synthetases are inadequate to give the required accuracy of translation. This has necessitated the evolution of a second determinant of specificity, proofreading, or editing mechanisms that involve the expenditure of energy to remove errors. Studies of an error-editing function of bacterial methionyl-tRNA synthetase have led to the discovery of a distinct chemical mechanism of editing and to molecular dissection of the dual synthetic-editing function of the active site of the synthetase. Studies have also established the importance of proofreading in living cells and allowed direct measurements of energy costs associated with editing in vivo. An unexpected outcome of these studies was a discovery of functional and structural similarities between methionyl-tRNA synthetase and S-adenosylmethionine synthetase, suggesting an evolutionary relationship between the two proteins. The mechanism of editing involves a nucleophilic attack of a sulfur atom on the side chain of homocysteine in homocysteinyl adenylate on its carbonyl carbon, yielding homocysteine thiolactone. The model of the active site of methionyl-tRNA synthetase derived from structure-function studies explains how the active site partitions amino acids between synthetic and editing pathways. Hydrophobic and hydrogen bonding interactions of active site residues Trp305 and Tyr15 with the side chain of methionine prevent the cognate amino acid from entering the editing pathway. These interactions are missing in the case of the smaller side chain of the noncognate homocysteine, which therefore enters the editing pathway. Homocysteine thiolactone is formed as a result of editing of homocysteine by methionyl-tRNA synthetase in bacteria, yeast, and some cultured mammalian cells. In mammalian cells, enhanced synthesis of homocysteine thiolactone, is, thus far, associated with oncogenic transformation. In E. coli, most of the energy cost of proofreading by methionyl-tRNA synthetase is due to editing of the incorrect product, homocysteinyl adenylate.
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Affiliation(s)
- H Jakubowski
- Department of Microbiology and Molecular Genetics, University of Medicine and Dentistry, New Jersey Medical School, Newark 07103
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45
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Abstract
Recent reports suggest that the ribosome retains considerable peptidyl transferase activity even when much of the protein of the ribosome is removed and further suggests that rRNA may be the peptidyl transferase. The work here suggests that the AMP residue at the 3' terminus of each tRNA has some catalytic activity both in the esterification reaction and in forming a pseudopeptide, AcGly, and further suggests that whatever peptidyl transferase is, it finds a cooperative substrate in the aminoacyl-AMP at the 3' terminus of tRNA.
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Affiliation(s)
- N S Wickramasinghe
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham 35294
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46
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Abstract
Peptidyl transfer is a key step in the process of protein biosynthesis. To examine the role of the universal CCA terminal sequence of tRNA in the process of peptidyl transfer, various mutant transcripts of Escherichia coli valine tRNA were constructed. Peptidyl transferase activity, monitored by the 'fragment reaction' with a slight modification, was decreased by mutation at any one base of CCA. The effect of mutation was moderate in the UCA, CUA and CCG mutants. Replacement of A76 by a pyrimidine nucleotide, or replacement of either C74 or C75 by a purine nucleotide caused a marked decrease in the activity. These findings suggested that the universal CCA terminus of tRNA makes a functional interaction with ribosomal RNA by base-pairing.
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Affiliation(s)
- K Tamura
- Biophysical Chemistry Laboratory, Institute of Physical and Chemical Research (RIKEN), Saitama, Japan
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47
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Kim S, Ribas de Pouplana L, Schimmel P. An RNA binding site in a tRNA synthetase with a reduced set of amino acids. Biochemistry 1994; 33:11040-5. [PMID: 7522052 DOI: 10.1021/bi00202a025] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
A 30 amino acid helix-loop of known structure on the surface of the C-terminal domain of the class I Escherichia coli methionine tRNA synthetase is essential for methionine tRNA anticodon discrimination. Replacing this 30 amino acid peptide with a previously described sequence containing residues from the wild-type protein imbedded in a sequence matrix of mostly alanines and serines, we used a combinatorial mutagenesis and selection strategy to define residual wild-type residues that are not replaceable with alanine or serine, because they are needed for specific recognition of methionine tRNA. Four were identified, of which three have functional side chains (Asn, Arg, Lys). These four and a fifth (Trp) that was previously identified are located at the end of the helix and within the loop, lie on the same side of the structure, and span a distance of about 20 A. We conclude that, within the alanine, serine sequence matrix, only a few non-alanine, non-serine residues in the specificity-determining part of the structure are essential.
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Affiliation(s)
- S Kim
- Department of Biology, Massachusetts Institute of Technology, Cambridge 02139
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48
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Pütz J, Florentz C, Benseler F, Giegé R. A single methyl group prevents the mischarging of a tRNA. NATURE STRUCTURAL BIOLOGY 1994; 1:580-2. [PMID: 7634096 DOI: 10.1038/nsb0994-580] [Citation(s) in RCA: 98] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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49
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Frugier M, Söll D, Giegé R, Florentz C. Identity switches between tRNAs aminoacylated by class I glutaminyl- and class II aspartyl-tRNA synthetases. Biochemistry 1994; 33:9912-21. [PMID: 8060999 DOI: 10.1021/bi00199a013] [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: 01/28/2023]
Abstract
High-resolution X-ray structures for the tRNA/aminoacyl-tRNA synthetase complexes between Escherichia coli tRNAGln/GlnRS and yeast tRNAAsp/AspRS have been determined. Positive identity nucleotides that direct aminoacylation specificity have been defined in both cases; E. coli tRNAGln identity is governed by 10 elements scattered in the tRNA structure, while specific aminoacylation of yeast tRNAAsp is dependent on 5 positions. Both identity sets are partially overlapping and share 3 nucleotides. Interestingly, the two enzymes belong to two different classes described for aminoacyl-tRNA synthetases. The class I glutaminyl-tRNA synthetase and the class II aspartyl-tRNA synthetase recognize their cognate tRNA from opposite sides. Mutants derived from glutamine and aspartate tRNAs have been created by progressively introducing identity elements from one tRNA into the other one. Glutaminylation and aspartylation assays of the transplanted tRNAs show that identity nucleotides from a tRNA originally aminoacylated by a synthetase from one class are still recognized if they are presented to the enzyme in a structural framework corresponding to a tRNA aminoacylated by a synthetase belonging to the other class. The simple transplantation of the glutamine identity set into tRNAAsp is sufficient to obtain glutaminylatable tRNA, but additional subtle features seem to be important for the complete conversion of tRNAGln in an aspartylatable substrate. This study defines C38 in yeast tRNAAsp as a new identity nucleotide for aspartylation. We show also in this paper that, during the complex formation, aminoacyl-tRNA synthetases are at least partially responsible for conformational changes which involve structural constraints in tRNA molecules.
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Affiliation(s)
- M Frugier
- Unité Propre de Recherche Structure des Macromolécules Biologiques et Mécanismes de Reconnaissance, Institut de Biologie Moléculaire et Cellulaire du Centre National de la Recherche Scientifique, Strasbourg, France
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Binder S, Marchfelder A, Brennicke A. RNA editing of tRNA(Phe) and tRNA(Cys) in mitochondria of Oenothera berteriana is initiated in precursor molecules. MOLECULAR & GENERAL GENETICS : MGG 1994; 244:67-74. [PMID: 8041363 DOI: 10.1007/bf00280188] [Citation(s) in RCA: 70] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
We have analyzed the role of RNA editing in the correction of mismatched base pairs in tRNA secondary structures in mitochondria of the flowering plant Oenothera berteriana. Comparison of genomic and cDNA sequences from unprocessed primary transcripts of the newly characterized genes for tRNA(Cys), tRNA(Asn) and tRNA(Ile) and the previously described gene for tRNA(Phe) revealed single nucleotide discrepancies in the tRNA(Cys) and tRNA(Phe) sequences. While the change in the anticodon stem of tRNA(Cys) alters a C-T to a T-T mismatch, the nucleotide transition in the tRNA(Phe) restores a conventional T-A Watson-Crick base pair, replacing a C-A mismatch in the acceptor stem. Since both nucleotide alterations are conversions from genomic cytidines to thymidines in the cDNA (uridines in the tRNAs), they are attributed to RNA editing, which is observed in nearly all mRNAs from plant mitochondria.
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Affiliation(s)
- S Binder
- Institut für Genbiologische Forschung, Berlin, Germany
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