1
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Cavallin I, Bartosovic M, Skalicky T, Rengaraj P, Demko M, Schmidt-Dengler MC, Drino A, Helm M, Vanacova S. HITS-CLIP analysis of human ALKBH8 reveals interactions with fully processed substrate tRNAs and with specific noncoding RNAs. RNA (NEW YORK, N.Y.) 2022; 28:1568-1581. [PMID: 36192131 PMCID: PMC9670814 DOI: 10.1261/rna.079421.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 09/09/2022] [Indexed: 06/16/2023]
Abstract
Transfer RNAs acquire a large plethora of chemical modifications. Among those, modifications of the anticodon loop play important roles in translational fidelity and tRNA stability. Four human wobble U-containing tRNAs obtain 5-methoxycarbonylmethyluridine (mcm5U34) or 5-methoxycarbonylmethyl-2-thiouridine (mcm5s2U34), which play a role in decoding. This mark involves a cascade of enzymatic activities. The last step is mediated by alkylation repair homolog 8 (ALKBH8). In this study, we performed a transcriptome-wide analysis of the repertoire of ALKBH8 RNA targets. Using a combination of HITS-CLIP and RIP-seq analyses, we uncover ALKBH8-bound RNAs. We show that ALKBH8 targets fully processed and CCA modified tRNAs. Our analyses uncovered the previously known set of wobble U-containing tRNAs. In addition, both our approaches revealed ALKBH8 binding to several other types of noncoding RNAs, in particular C/D box snoRNAs.
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Affiliation(s)
- Ivana Cavallin
- Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic
| | - Marek Bartosovic
- Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic
| | - Tomas Skalicky
- Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 370 05 České Budějovice, Czech Republic
| | - Praveenkumar Rengaraj
- Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic
| | - Martin Demko
- Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic
| | | | - Aleksej Drino
- Medical University of Vienna, Center for Anatomy and Cell Biology, 1090 Vienna, Austria
| | - Mark Helm
- Johannes Gutenberg-Universität Mainz, Institute of Pharmaceutical and Biomedical Science (IPBS), D-55128 Mainz, Germany
| | - Stepanka Vanacova
- Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic
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2
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Johansson MJO, Xu F, Byström AS. Elongator-a tRNA modifying complex that promotes efficient translational decoding. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2017; 1861:401-408. [PMID: 29170010 DOI: 10.1016/j.bbagrm.2017.11.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 11/19/2017] [Indexed: 12/22/2022]
Abstract
Naturally occurring modifications of the nucleosides in the anticodon region of tRNAs influence their translational decoding properties. Uridines present at the wobble position in eukaryotic cytoplasmic tRNAs often contain a 5-carbamoylmethyl (ncm(5)) or 5-methoxycarbonylmethyl (mcm(5)) side-chain and sometimes also a 2-thio or 2'-O-methyl group. The first step in the formation of the ncm(5) and mcm(5) side-chains requires the conserved six-subunit Elongator complex. Although Elongator has been implicated in several different cellular processes, accumulating evidence suggests that its primary, and possibly only, cellular function is to promote modification of tRNAs. In this review, we discuss the biosynthesis and function of modified wobble uridines in eukaryotic cytoplasmic tRNAs, focusing on the in vivo role of Elongator-dependent modifications in Saccharomyces cerevisiae. This article is part of a Special Issue entitled: SI: Regulation of tRNA synthesis and modification in physiological conditions and disease edited by Dr. Boguta Magdalena.
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Affiliation(s)
| | - Fu Xu
- Department of Molecular Biology, Umeå University, 901 87 Umeå, Sweden
| | - Anders S Byström
- Department of Molecular Biology, Umeå University, 901 87 Umeå, Sweden.
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3
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Xu H, Bygdell J, Wingsle G, Byström AS. Yeast Elongator protein Elp1p does not undergo proteolytic processing in exponentially growing cells. Microbiologyopen 2015; 4:867-78. [PMID: 26407534 PMCID: PMC4694139 DOI: 10.1002/mbo3.285] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Revised: 07/27/2015] [Accepted: 07/30/2015] [Indexed: 01/09/2023] Open
Abstract
In eukaryotic organisms, Elongator is a six-subunit protein complex required for the formation of 5-carbamoylmethyl (ncm(5) ) and 5-methylcarboxymethyl (mcm(5) ) side chains on uridines present at the wobble position (U34 ) of tRNA. The open reading frame encoding the largest Elongator subunit Elp1p has two in-frame 5' AUG methionine codons separated by 48 nucleotides. Here, we show that the second AUG acts as the start codon of translation. Furthermore, Elp1p was previously shown to exist in two major forms of which one was generated by proteolysis of full-length Elp1p and this proteolytic cleavage was suggested to regulate Elongator complex activity. In this study, we found that the vacuolar protease Prb1p was responsible for the cleavage of Elp1p. The cleavage occurs between residues 203 (Lys) and 204 (Ala) as shown by amine reactive Tandem Mass Tag followed by LC-MS/MS (liquid chromatography mass spectrometry) analysis. However, using a modified protein extraction procedure, including trichloroacetic acid, only full-length Elp1p was observed, showing that truncation of Elp1p is an artifact occurring during protein extraction. Consequently, our results indicate that N-terminal truncation of Elp1p is not likely to regulate Elongator complex activity.
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Affiliation(s)
- Hao Xu
- Department of Molecular Biology, Umeå University, 901 87, Umeå, Sweden
| | - Joakim Bygdell
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, 901 87, Umeå, Sweden
| | - Gunnar Wingsle
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, 901 87, Umeå, Sweden
| | - Anders S Byström
- Department of Molecular Biology, Umeå University, 901 87, Umeå, Sweden
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4
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Tükenmez H, Xu H, Esberg A, Byström AS. The role of wobble uridine modifications in +1 translational frameshifting in eukaryotes. Nucleic Acids Res 2015; 43:9489-99. [PMID: 26283182 PMCID: PMC4627075 DOI: 10.1093/nar/gkv832] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 08/06/2015] [Indexed: 12/31/2022] Open
Abstract
In Saccharomyces cerevisiae, 11 out of 42 tRNA species contain 5-methoxycarbonylmethyl-2-thiouridine (mcm(5)s(2)U), 5-methoxycarbonylmethyluridine (mcm(5)U), 5-carbamoylmethyluridine (ncm(5)U) or 5-carbamoylmethyl-2'-O-methyluridine (ncm(5)Um) nucleosides in the anticodon at the wobble position (U34). Earlier we showed that mutants unable to form the side chain at position 5 (ncm(5) or mcm(5)) or lacking sulphur at position 2 (s(2)) of U34 result in pleiotropic phenotypes, which are all suppressed by overexpression of hypomodified tRNAs. This observation suggests that the observed phenotypes are due to inefficient reading of cognate codons or an increased frameshifting. The latter may be caused by a ternary complex (aminoacyl-tRNA*eEF1A*GTP) with a modification deficient tRNA inefficiently being accepted to the ribosomal A-site and thereby allowing an increased peptidyl-tRNA slippage and thus a frameshift error. In this study, we have investigated the role of wobble uridine modifications in reading frame maintenance, using either the Renilla/Firefly luciferase bicistronic reporter system or a modified Ty1 frameshifting site in a HIS4A::lacZ reporter system. We here show that the presence of mcm(5) and s(2) side groups at wobble uridines are important for reading frame maintenance and thus the aforementioned mutant phenotypes might partly be due to frameshift errors.
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Affiliation(s)
- Hasan Tükenmez
- Department of Molecular Biology, Umeå University, Umeå, 901 87, Sweden
| | - Hao Xu
- Department of Molecular Biology, Umeå University, Umeå, 901 87, Sweden
| | - Anders Esberg
- Department of Odontology/Cariology, Umeå University, Umeå, 901 87, Sweden
| | - Anders S Byström
- Department of Molecular Biology, Umeå University, Umeå, 901 87, Sweden
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5
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Huang B, Johansson MJO, Byström AS. An early step in wobble uridine tRNA modification requires the Elongator complex. RNA (NEW YORK, N.Y.) 2005; 11:424-36. [PMID: 15769872 PMCID: PMC1370732 DOI: 10.1261/rna.7247705] [Citation(s) in RCA: 346] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2004] [Accepted: 01/06/2005] [Indexed: 05/17/2023]
Abstract
Elongator has been reported to be a histone acetyltransferase complex involved in elongation of RNA polymerase II transcription. In Saccharomyces cerevisiae, mutations in any of the six Elongator protein subunit (ELP1-ELP6) genes or the three killer toxin insensitivity (KTI11-KTI13) genes cause similar pleiotropic phenotypes. By analyzing modified nucleosides in individual tRNA species, we show that the ELP1-ELP6 and KTI11-KTI13 genes are all required for an early step in synthesis of 5-methoxycarbonylmethyl (mcm5) and 5-carbamoylmethyl (ncm5) groups present on uridines at the wobble position in tRNA. Transfer RNA immunoprecipitation experiments showed that the Elp1 and Elp3 proteins specifically coprecipitate a tRNA susceptible to formation of an mcm5 side chain, indicating a direct role of Elongator in tRNA modification. The presence of mcm5U, ncm5U, or derivatives thereof at the wobble position is required for accurate and efficient translation, suggesting that the phenotypes of elp1-elp6 and kti11-kti13 mutants could be caused by a translational defect. Accordingly, a deletion of any ELP1-ELP6 or KTI11-KTI13 gene prevents an ochre suppressor tRNA that normally contains mcm5U from reading ochre stop codons.
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Affiliation(s)
- Bo Huang
- Department of Molecular Biology, Umeå University, 901 87 Umeå, Sweden
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6
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Transfer RNA modifications and modifying enzymes in Saccharomyces cerevisiae. FINE-TUNING OF RNA FUNCTIONS BY MODIFICATION AND EDITING 2005. [DOI: 10.1007/b105814] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
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7
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Johansson MJO, Byström AS. The Saccharomyces cerevisiae TAN1 gene is required for N4-acetylcytidine formation in tRNA. RNA (NEW YORK, N.Y.) 2004; 10:712-9. [PMID: 15037780 PMCID: PMC1370561 DOI: 10.1261/rna.5198204] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
The biogenesis of transfer RNA is a process that requires many different factors. In this study, we describe a genetic screen aimed to identify gene products participating in this process. By screening for mutations lethal in combination with a sup61-T47:2C allele, coding for a mutant form of, the nonessential TAN1 gene was identified. We show that the TAN1 gene product is required for formation of the modified nucleoside N(4)-acetylcytidine (ac(4)C) in tRNA. In Saccharomyces cerevisiae, ac(4)C is present at position 12 in tRNAs specific for leucine and serine as well as in 18S ribosomal RNA. Analysis of RNA isolated from a tan1-null mutant revealed that ac(4)C was absent in tRNA, but not rRNA. Although no tRNA acetyltransferase activity by a GST-Tan1 fusion protein was detected, a gel-shift assay revealed that Tan1p binds tRNA, suggesting a direct role in synthesis of ac(4)C(12). The absence of the TAN1 gene in the sup61-T47:2C mutant caused a decreased level of mature, indicating that ac(4)C(12) and/or Tan1p is important for tRNA stability.
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8
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Kalhor HR, Clarke S. Novel methyltransferase for modified uridine residues at the wobble position of tRNA. Mol Cell Biol 2004; 23:9283-92. [PMID: 14645538 PMCID: PMC309612 DOI: 10.1128/mcb.23.24.9283-9292.2003] [Citation(s) in RCA: 128] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We have identified a novel tRNA methyltransferase in Saccharomyces cerevisiae that we designate Trm9. This enzyme, the product of the YML014w gene, catalyzes the esterification of modified uridine nucleotides, resulting in the formation of 5-methylcarbonylmethyluridine in tRNA(Arg3) and 5-methylcarbonylmethyl-2-thiouridine in tRNA(Glu). In intact yeast cells, disruption of the TRM9 gene results in the complete loss of these modified wobble bases and increased sensitivity at 37 degrees C to paromomycin, a translational inhibitor. These results suggest a role for this potentially reversible methyl esterification reaction when cells are under stress.
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MESH Headings
- Amino Acid Sequence
- Base Sequence
- DNA, Fungal/genetics
- Gene Deletion
- Genes, Fungal
- Methylation
- Molecular Sequence Data
- Mutation
- Protein Biosynthesis
- RNA, Fungal/chemistry
- RNA, Fungal/metabolism
- RNA, Transfer/chemistry
- RNA, Transfer/metabolism
- RNA, Transfer, Arg/chemistry
- RNA, Transfer, Arg/metabolism
- RNA, Transfer, Glu/chemistry
- RNA, Transfer, Glu/metabolism
- Saccharomyces cerevisiae/enzymology
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae Proteins/genetics
- Saccharomyces cerevisiae Proteins/metabolism
- Sequence Homology, Amino Acid
- Substrate Specificity
- Temperature
- Uridine/chemistry
- tRNA Methyltransferases/genetics
- tRNA Methyltransferases/metabolism
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Affiliation(s)
- Hamid R Kalhor
- Department of Chemistry and Biochemistry, UCLA Molecular Biology Institute, University of California-Los Angeles, 611 Charles E. Young Drive East, Los Angeles, CA 90095, USA
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9
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Ryckelynck M, Giegé R, Frugier M. Yeast tRNA(Asp) charging accuracy is threatened by the N-terminal extension of aspartyl-tRNA synthetase. J Biol Chem 2003; 278:9683-90. [PMID: 12486031 DOI: 10.1074/jbc.m211035200] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
This study evaluates the role of the N-terminal extension from yeast aspartyl-tRNA synthetase in tRNA aspartylation. The presence of an RNA-binding motif in this extension, conserved in eukaryotic class IIb aminoacyl-tRNA synthetases, provides nonspecific tRNA binding properties to this enzyme. Here, it is assumed that the additional contacts the 70 amino acid-long appendix of aspartyl-tRNA synthetase makes with tRNA could be important in expression of aspartate identity in yeast. Using in vitro transcripts mutated at identity positions, it is demonstrated that the extension grants better aminoacylation efficiency but reduced specificity to the synthetase, increasing considerably the risk of noncognate tRNA mischarging. Yeast tRNA(Glu(UUC)) and tRNA(Asn(GUU)) were identified as the most easily mischarged tRNA species. Both have a G at the discriminator position, and their anticodon differs only by one change from the GUC aspartate anticodon.
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Affiliation(s)
- Michaël Ryckelynck
- Département Mécanismes et Macromolécules de la Synthèse Protéique et Cristallogenèse, UPR 9002, Institut de Biologie Moléculaire et Cellulaire du CNRS, 15 rue René Descartes, F-67084 Strasbourg Cedex, France
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10
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Becker HD, Giegé R, Kern D. Identity of prokaryotic and eukaryotic tRNA(Asp) for aminoacylation by aspartyl-tRNA synthetase from Thermus thermophilus. Biochemistry 1996; 35:7447-58. [PMID: 8652522 DOI: 10.1021/bi9601058] [Citation(s) in RCA: 54] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The aspartate identity of tRNA for AspRS from Thermus thermophilus has been investigated by kinetic analysis of the aspartylation reaction of different tRNA molecules and their variants as well as of tRNAPhe variants with transplanted aspartate identity elements. It is shown that G10, G34, U35, C36, C38, and G73 determine recognition and aspartylation of yeast and T.thermophilus tRNA(Asp) by the thermophilic AspRS. This set of nucleotides specifies also tRNA aspartylation in the homologous yeast and Escherichia coli systems. Structural considerations indicate that the major aspartate identity elements interact with amino acids conserved in all AspRSs. It follows that the structural features of tRNA and synthetase specifying aspartylation are mainly conserved in various structural contexts and in organisms adapted to different life conditions. Mutations of tRNA identity elements provoke drastic losses of charging in the heterologous system involving yeast tRNA(Asp) and T. thermophilus AspRS. In the homologous systems, the mutational effects are less pronounced. However, effects in E. coli and T. thermophilus exceed those in yeast which are particularly moderate, indicating variations in the individual contributions of identity elements for aspartylation in prokaryotes and eukaryotes. Analysis of multiple tRNA mutants reveals cooperativity between the cluster of determinants of the anticodon loop and the additional determinants G10 and G73 for efficient aspartylation in the thermophilic system, suggesting that conformational changes trigger formation of the functional tRNA/synthetase complex.
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MESH Headings
- Amino Acid Sequence
- Anticodon
- Aspartate-tRNA Ligase/chemistry
- Aspartate-tRNA Ligase/metabolism
- Base Sequence
- Escherichia coli
- Kinetics
- Molecular Sequence Data
- Nucleic Acid Conformation
- RNA, Transfer, Asp/biosynthesis
- RNA, Transfer, Asp/metabolism
- RNA, Transfer, Phe/biosynthesis
- RNA, Transfer, Phe/metabolism
- Recombinant Proteins/chemistry
- Recombinant Proteins/metabolism
- Saccharomyces cerevisiae
- Sequence Homology, Amino Acid
- Substrate Specificity
- Thermus thermophilus/enzymology
- Transcription, Genetic
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Affiliation(s)
- H D Becker
- Unité Propre de Recherches 9002 Structure des Macromolécules Biologiques et Mécanismes de Reconnaissance, Institut de Biologie Moléculaire et Cellulaire, Centre national de la Recherche Scientifique, Strasbourg, France
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11
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Krieg R, Stucka R, Clark S, Feldmann H. The use of a synthetic tRNA gene as a novel approach to study in vivo transcription and chromatin structure in yeast. Nucleic Acids Res 1991; 19:3849-55. [PMID: 1861977 PMCID: PMC328473 DOI: 10.1093/nar/19.14.3849] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
To monitor in vivo transcription and chromatin structure of yeast tRNA genes, we constructed a synthetic tRNA gene that can be used as a reporter. Constructs in which this synthetic tRNA gene is combined with different flanking regions can be integrated into the genome as single copies. The artificial tRNA gene is tagged by the insertion of an intron-like sequence that cannot be spliced out from the precursor and transcripts can thus be identified and quantitated. By several criteria, the artificial tRNA gene behaves like a resident tRNA gene. By measuring the accessibility towards DNaseI in chromatin, we found that the artificial tRNA gene exhibits the same characteristic pattern as resident tRNA genes. Three DNaseI-sensitive sites across the transcribed part of the gene and the immediate flanking regions reflect the formation of the stable transcription complex; positioned nucleosomes are observed in the upstream flanking region. We are confident that the system we have established will prove useful for studying regulatory aspects of tRNA gene expression as well as aspects of pre-tRNA processing and splicing.
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MESH Headings
- Animals
- Base Sequence
- Blotting, Northern
- Chromatin/ultrastructure
- Cloning, Molecular
- DNA, Fungal
- Electrophoresis, Polyacrylamide Gel
- Genes, Synthetic
- Molecular Sequence Data
- Nucleic Acid Conformation
- RNA Precursors/metabolism
- RNA Splicing
- RNA, Fungal
- RNA, Transfer/genetics
- Saccharomyces cerevisiae/genetics
- Templates, Genetic
- Transcription, Genetic
- Transformation, Genetic
- Xenopus/genetics
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Affiliation(s)
- R Krieg
- Institut für Physiologische Chemie, Physikalische Biochemie und Zellbiologie, Universität München, FRG
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12
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Sprinzl M, Dank N, Nock S, Schön A. Compilation of tRNA sequences and sequences of tRNA genes. Nucleic Acids Res 1991; 19 Suppl:2127-71. [PMID: 2041802 PMCID: PMC331350 DOI: 10.1093/nar/19.suppl.2127] [Citation(s) in RCA: 100] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Affiliation(s)
- M Sprinzl
- Laboratorium für Biochemie, Universität Bayreuth, FRG
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13
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Peterson D, Schön A, Söll D. The nucleotide sequences of barley cytoplasmic glutamate transfer RNAs and structural features essential for formation of δ-aminolevulinic acid. PLANT MOLECULAR BIOLOGY 1988; 11:293-299. [PMID: 24272342 DOI: 10.1007/bf00027386] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/1988] [Accepted: 05/23/1988] [Indexed: 06/02/2023]
Abstract
In chloroplasts and a number of prokaryotes, δ-aminolevulinic acid (ALA), the universal precursor of porphyrins, is synthesized by a multistep enzymatic pathway with glutamyl-tRNA(Glu) as an intermediate. The ALA synthesizing system from barley chloroplasts is highly specific in its tRNA requirement for chloroplast tRNA(Glu); a number of other Glu-tRNAs are inactive in ALA formation although they can be glutamylated by chloroplast aminoacyl-tRNA synthetases. In order to obtain more information about the structural features defining the ability of a tRNA to be recognized by the ALA synthesizing enzymes, we purified and sequenced two cytoplasmic tRNA(Glu) species from barley embryos which are inactive in ALA synthesis. By using glutamylated tRNAs as a substrate for the overall reaction, we showed that Glu-tRNA reductase is the enzyme responsible for tRNA discrimination.
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Affiliation(s)
- D Peterson
- Department of Molecular Biophysics & Biochemistry, Yale University, P.O. Box 6666, 06511, New Haven, CT, USA
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14
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Sandmeyer SB, Bilanchone VW, Clark DJ, Morcos P, Carle GF, Brodeur GM. Sigma elements are position-specific for many different yeast tRNA genes. Nucleic Acids Res 1988; 16:1499-515. [PMID: 3279393 PMCID: PMC336330 DOI: 10.1093/nar/16.4.1499] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
We determined the DNA sequence of seventeen sigma elements and flanking regions in order to investigate the extent of the association between the yeast repetitive element, sigma, and tRNA genes. Fifteen of seventeen sigma elements analyzed begin at position -19 to -16 with respect to the 5' end of a tRNA-coding sequence. This region is close to the initiation point of tRNA gene transcription and contains a sequence which is modestly conserved for a number of tRNA genes. Two pairs of identical sigma elements occur as the long terminal repeats of a sequence which, together with flanking sigma elements, has the structural properties of a retrotransposon; this element has been named Ty3 (manuscript submitted). Hybridization analysis of yeast chromosomal DNA separated by orthogonal field alternation gel electrophoresis (OFAGE) showed that Ty3 and isolated sigma elements are distributed over many chromosomes in the yeast genome.
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Affiliation(s)
- S B Sandmeyer
- Department of Microbiology and Molecular Genetics, California College of Medicine, University of California, Irvine 92717
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15
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Stucka R, Hauber J, Feldmann H. One member of the tRNA(Glu) gene family in yeast codes for a minor GAGtRNA(Glu) species and is associated with several short transposable elements. Curr Genet 1987; 12:323-8. [PMID: 2833361 DOI: 10.1007/bf00405754] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
During characterization of the whole tRNA-(Glu) family from the yeast, Saccharomyces cerevisiae, we isolated one cosmid clone bearing a tRNA(Glu) gene copy that is deviant from the major tRNA(Glu3) gene members in only five positions. This divergent tRNA-(Glu) is a minor species and is represented by a single gene copy. One of the nucleotide exchanges concerns the anticodon which is modified from T-T-C in the tRNA(Glu3) gene to C-T-C which implies that this tRNA serves the codon triplet G-A-G. Two other minor yeast tRNA species have been reported which appear to be particularly designed for the translation of those codons that have a G in its third (Wobble) position. The low abundance of such minor tRNA species correlates positively to the low occurrence of most of the N-N-G codons in yeast. Furthermore, the GAGtRNA-(Glu) locus represents another case of the general phenomenon in which the majority of the tRNA genes in yeast are associated with one or several transposable elements forming complex patterns. In this particular case, divergent segments of delta and tau are present in the 5' flanking region of the tRNA gene and arranged in a novel configuration. The sequence data lend support to the view that tau is not an evolutionary young element as was earlier anticipated.
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Affiliation(s)
- R Stucka
- Institut für Physiologische Chemie, Physikalische Biochemie und Zellbiologie, Universität München, Federal Republic of Germany
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16
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Mendenhall MD, Leeds P, Fen H, Mathison L, Zwick M, Sleiziz C, Culbertson MR. Frameshift suppressor mutations affecting the major glycine transfer RNAs of Saccharomyces cerevisiae. J Mol Biol 1987; 194:41-58. [PMID: 3039147 DOI: 10.1016/0022-2836(87)90714-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Mutations have been identified in Saccharomyces cerevisiae glycine tRNA genes that result in suppression of +1 frameshift mutations in glycine codons. Wild-type and suppressor alleles of genes encoding the two major glycine tRNAs, tRNA(GCC) and tRNA(UCC), were examined in this study. The genes were identified by genetic complementation and by hybridization to a yeast genomic library using purified tRNA probes. tRNA(UCC) is encoded by three genes, whereas approximately 15 genes encode tRNA(GCC). The frameshift suppressor genes suf1+, suf4+ and suf6+ were shown to encode the wild-type tRNA(UCC) tRNA. The suf1+ and suf4+ genes were identical in DNA sequence, whereas the suf6+ gene, whose DNA sequence was not determined, was shown by a hybridization experiment to encode tRNA(UCC). The ultraviolet light-induced SU F1-1 and spontaneous SU F4-1 suppressor mutations were each shown to differ from wild-type at two positions in the anticodon, including a +1 base-pair insertion and a base-pair substitution. These changes resulted in a CCCC four-base anticodon rather than the CCU three-base anticodon found in wild-type. The RNA sequence of tRNA(UCC) was shown to contain a modified uridine in the wobble position. Mutant tRNA(CCCC) isolated from a SU F1-1 strain lacked this modification. Three unlinked genes that encode wild-type tRNA(GCC), suf20+, trn2, and suf17+, were identical in DNA sequence to the previously described suf16+ frameshift suppressor gene. Spontaneous suppressor mutations at the SU F20 and SU F17 loci were analyzed. The SU F20-2 suppressor allele contained a CCCC anticodon. This allele was derived in two serial selections through two independent mutational events, a +1 base insertion and a base substitution in the anticodon. Presumably, the original suppressor allele, SU F20-1, contained the single base insertion. The SU F17-1 suppressor allele also contained a CCCC anticodon resulting from two mutations, a +1 insertion and a base substitution. However, this allele contained an additional base substitution at position 33 adjacent to the 5' side of the four-base anticodon. The possible origin and significance of multiple mutations leading to frameshift suppression is discussed.
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17
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Abstract
Human tRNA(CUCGlu) has been isolated by direct hybridization of the tRNA to 28S ribosomal RNA. We now report the isolation of mouse tRNA(CUCGlu) using the same procedure. Partial sequence analysis of the mouse tRNA shows that it is identical to the human tRNA and to a cloned rat tDNA(CUCGlu) sequence. This mouse tRNA(CUCGlu), however, differs by one nucleotide from a previously cloned mouse tDNA(CUCGlu) sequence, suggesting that the tDNA may be a pseudogene. Further evolutionary comparison of these and other glutamate tRNAs and tDNAs has provided evidence to suggest that two other tDNA(Glu) sequences arose by mutation of functional tRNAGlu genes such that their anticodon sequences were converted from one glutamate isoacceptor to the other. These tDNA sequences may also represent pseudogenes.
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Affiliation(s)
- F L Smardo
- Department of Biochemistry, University of Kansas Medical Center, Kansas City 66103
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18
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Patwardhan S, Cherayil JD. 5-Methyl-2-thiouridine in the tRNA of Candida tropicalis and its localization in lysine tRNA. J Bacteriol 1985; 162:55-60. [PMID: 3845081 PMCID: PMC218952 DOI: 10.1128/jb.162.1.55-60.1985] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
35S incorporation studies showed that Candida tropicalis tRNA contained two thionucleosides, one of which was identified as 5-methyl-2-thiouridine. The other thionucleoside was alkali labile, and it appeared to be an ester. Pulse-chase experiments suggested that the two thionucleosides were structurally related. 5-Methyl-2-thiouridine was present in one of the lysine tRNAs. This is the first report of the presence of this nucleoside in a yeast tRNA.
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19
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Gałat A, Serafinowski P, Koput J. A circular dichroism study of modified nucleosides. Biochim Biophys Acta Gen Subj 1984. [DOI: 10.1016/0304-4165(84)90210-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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20
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Laten HM, Cramer JH, Rownd RH. Thiolated nucleotides in yeast transfer RNA. BIOCHIMICA ET BIOPHYSICA ACTA 1983; 741:1-6. [PMID: 6351920 DOI: 10.1016/0167-4781(83)90002-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
By culturing Saccharomyces cerevisiae in growth medium containing Mg35SO4, we have determined the extent and variation of tRNA thiolation in this yeast. We find that 5-methoxycarbonylmethyl-2-thiouridine (mcm5s2U)1 is the major, if not only, thiolated derivative in S. cerevisiae tRNA. In addition, a comparison of the chromatographic mobility of mcm5s2Up on cellulose thin layers with those reported for unknown uridine derivatives found in purified yeast tRNA digests, leads to the conclusion that at least two of these tRNAs contain this modification.
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21
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Chan JC, Yang JA, Dunn MJ, Agris PF, Wong TW. The nucleotide sequence of a glutamate tRNA from rat liver. Nucleic Acids Res 1982; 10:4605-8. [PMID: 6813824 PMCID: PMC321115 DOI: 10.1093/nar/10.15.4605] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
A glutamate tRNA from rat liver was purified. By means of post-labeling techniques, its nucleotide sequence was shown to be: pU-C-C-C-A-C-A-U-m1G-G-U-C-psi-A-G-C- G-G-D-D-A-G-G-A-U-U-C-C-U-G-G-psi-U-mcm5s2U-U-C-A-C-C-C-A-G-G-C-G- G-C-m5C-m5C-G-G-G-Tm-psi-C-G-A-C-U-C-C-C-G-G-U-G-U-G-G-G-A-A-C-C-AOH. The sequence is remarkably similar to that of tRNA4Glu from Drosophila melanogaster. Only 10 out of 75 nucleotides in the two tRNAs are different.
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22
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Ikemura T. Correlation between the abundance of yeast transfer RNAs and the occurrence of the respective codons in protein genes. Differences in synonymous codon choice patterns of yeast and Escherichia coli with reference to the abundance of isoaccepting transfer RNAs. J Mol Biol 1982; 158:573-97. [PMID: 6750137 DOI: 10.1016/0022-2836(82)90250-9] [Citation(s) in RCA: 509] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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23
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Chan JC, Yang JA, Dunn MJ, Agris PF, Wong TW. The nucleotide sequence of a glutamine tRNA from rat liver. Nucleic Acids Res 1982; 10:3755-8. [PMID: 6921629 PMCID: PMC320749 DOI: 10.1093/nar/10.12.3755] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
A glutamate tRNA from rat liver was purified. By means of post-labeling techniques, its nucleotide sequence was shown to be: pU-C-C-C-A-C-A-U-m1G-G-U-C-psi-A-G-C- G-G-D-D-A-G-G-A-U-U-C-C-U-G-G-psi-U-mcm5S2U-U-C-A-C-C-C-A-G-G-C-G- G-C-m5C-m5C-G-G-G-Tm-psi-C-G-A-C-U-C-C-C-G-G-U-G-U-G-G-G-A-A-C-C-AOH. The sequence is remarkably similar to that of tRNAGlu from Drosophila melanogaster. Only 10 out of 75 nucleotides in the two tRNAs are different.
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Feldmann H, Olah J, Friedenreich H. Sequence of a yeast DNA fragment containing a chromosomal replicator and a tRNA Glu 3 gene. Nucleic Acids Res 1981; 9:2949-59. [PMID: 6269065 PMCID: PMC326904 DOI: 10.1093/nar/9.12.2949] [Citation(s) in RCA: 37] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The sequence of a 1.9 kb Bam x Hind III fragment from yeast has been determined. This fragment is part of a yeast 6.7 kb Hind III segment cloned into pBR322 (pY20). The fragment carries a single gene for a glutamate tRNA which has no intron. According to genetic analyses [1] this fragment also contains a yeast chromosomal replicator. We have analyzed the sequence for potential open reading frames and for several structural features which are thought to be involved in the initiation of DNA replication. Hybridization studies have revealed that portions of this sequence are repeated within the yeast genome.
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25
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Abstract
DNA sequences in a 1.7 kb Pst fragment from yeast have been determined. This fragment is part of a yeast 7.4 kb Hind III segment cloned ino pBR322 (pY 5). The fragment carries a single gene for a glutamate tRNA. The coding portion of this gene is identical in sequence to that of the tRNA Glu 3 gene from pY 20 [1]. The flanking regions differ in their sequences, but possible secondary structures within the 5'-flanking regions bear similar features. Sequence homologies between pY 5 and pY 20 were detected far outside the tRNA genes. More surprisingly, extended sequence homologies were seen between the flanking regions of the pY 20 tRNA Glu 3 gene and a tRNA Ser gene [2,3]. We have also checked the known tRNA genes for structural similarities. Hybridization studies indicate that portions of the Pst fragment are repeated within the yeast genome.
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Olson MV, Page GS, Sentenac A, Piper PW, Worthington M, Weiss RB, Hall BD. Only one of two closely related yeast suppressor tRNA genes contains an intervening sequence. Nature 1981; 291:464-9. [PMID: 6262655 DOI: 10.1038/291464a0] [Citation(s) in RCA: 72] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The yeast genes that code for the serine-inserting SUP-RL1 amber and SUQ5 ochre suppressors have been cloned and sequenced. These two unlinked genes differ by only three base pairs in their coding regions yet they encode tRNAs of different translational specificities, and while the SUP-RL1 gene has a 19-base pair intervening sequence, the SUQ5 gene has none.
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27
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Altwegg M, Kubli E. The nucleotide sequence of glutamate tRNA4 of Drosophila melanogaster. Nucleic Acids Res 1980; 8:215-23. [PMID: 6775307 PMCID: PMC327262 DOI: 10.1093/nar/8.2.215] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The nucleotide sequence of Drosophila melanogaster glutamate tRNA4 was determined to be: pU-C-C-C-A-U-A-U-G-G-U-C-psi-A-G-D-G-G-C-D-A-G-G-A-U-A-U-C-U-G-G-C (m) -U-U-U-C-A-C-C-A-G-A-A-G-G-C-C-C-G-G-G-T-psi-U-C-G-A-U-U-C-C-C-G-G-U-A-U-G-G-G-A-A-C-C-AOH. A partial modified C is found at position 32 in the anticodon loop.
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28
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Lipnick RL, Fissekis JD. Carbon-13 nmr spectra of the tRNA “wobble” nucleosides 5-carboxymethyl-, 5-carbomethoxymethyl-, and 5-carbamoylmethyluridine. J Heterocycl Chem 1980. [DOI: 10.1002/jhet.5570170139] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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29
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Mizuno H, Sundaralingam M. Stacking of Crick Wobble pair and Watson-Crick pair: stability rules of G-U pairs at ends of helical stems in tRNAs and the relation to codon-anticodon Wobble interaction. Nucleic Acids Res 1978; 5:4451-61. [PMID: 724522 PMCID: PMC342761 DOI: 10.1093/nar/5.11.4451] [Citation(s) in RCA: 83] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The occurrence of the noncomplementary G-U base pair at the end of a helix is found to be governed by stacking interactions. As a rule, a G-U pair with G on the 5'-side of a Watson-Crick base pair exhibits strikingly greater stacking overlap with the Watson-Crick base pair than a G-U pair on the 3'-side of a Watson-Crick base pair. The former arrangement is expected to be more stable and indeed is observed 29 times out of 32 in the known transfer RNA molecules. In accordance with this rule, the major wobble base pairs G-U or I-U in codon-anticodon interactions have G or I on the 5'-side of the anticodon. Similarly, in initiator tRNAs, this rule is obeyed where now the G is the first letter of the codon (5'-side). In the situation where U is in the wobble position of the anticodon, it is usually substituted at C(5) andmay also have a 2-thio group and it can read one to four codons depending on its modifications. A G at the wobble position of the anticodon can recognize the two codons ending with U or C and modification of G (unless it is I) does not change its reading properties.
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30
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Weissenbach J, Dirheimer G. Pairing properties of the methylester of 5-carboxymethyl uridine in the wobble position of yeast tRNA3Arg. BIOCHIMICA ET BIOPHYSICA ACTA 1978; 518:530-4. [PMID: 350282 DOI: 10.1016/0005-2787(78)90171-5] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
At optimum magnesium concentration (10 mM) both yeast tRNA1Arg and tRNA3Arg are able to bind to poly (A,G) and A-G-A in presence of Escherichia coli robisomes. With A-G-G only tRNA1Arg ginds, wherea tRNA3Arg (anticodon mcm5 U-C-U) is not bound. This result means that the methylcarboxymethyl substituant in position 5 of U prevents its wobble with G.
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31
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Berman HM, Marcu D, Narayanan P. Modified bases in tRNA: the structures of 5-carbamoylmethyl- and 5-carboxymethyl uridine. Nucleic Acids Res 1978; 5:893-903. [PMID: 643621 PMCID: PMC342031 DOI: 10.1093/nar/5.3.893] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The crystal structures of two nucleosides, 5-carbamoylmethyluridine (1) and 5-carboxymethyluridine (2), were determined from three-dimensional x-ray diffraction data, and refined to R = 0.036 and R = 0.047, respectively. Compound 1 is in the C3'-endo conformation with chi +5.2 degrees (anti), psiinfinity = +63.4 degrees and psialpha = +180.0 degrees (tt); 2 is in the C2'endo conformation with chi +49.4 degrees (anti), psiinfinity -60.5 degrees and psialpha +60.0 degrees (gg). For each derivative, the plane of the side chain substituent is skewed with respect to the plane of the nucleobase; for 1, the carboxamide group is on the same side of the uracil plane vis a vis the ribose ring; for 2, the carboxyl group is on the opposite side of this plane. No base pairing is observed for either structure. Incorporation of structure 1 into a 3'-stacked tRNA anticodon appears to place 08 within hydrogen bonding distance of the 02' hydroxyl of ribose 33, which may limit the ability of such a molecule of tRNA to "wobble".
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32
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Feldman M. Minor components in transfer RNA: The location-function relationships. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 1978. [DOI: 10.1016/0079-6107(78)90018-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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33
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Goddard JP. The structures and functions of transfer RNA. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 1978. [DOI: 10.1016/0079-6107(78)90021-4] [Citation(s) in RCA: 57] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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Ortwerth BJ, Carlson JV. Lysine transfer RNA from liver: a sulfur-containing species that codes for AAG. Arch Biochem Biophys 1977; 178:278-84. [PMID: 836035 DOI: 10.1016/0003-9861(77)90192-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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35
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Lapointe J, Delcuve G, Duplain L. Derepressed levels of glutamate synthase and glutamine synthetase in Escherichia coli mutants altered in glutamyl-transfer ribonucleic acid synthetase. J Bacteriol 1975; 123:843-50. [PMID: 239924 PMCID: PMC235805 DOI: 10.1128/jb.123.3.843-850.1975] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The levels of glutamate synthase and of glutamine synthetase are both derepressed 10-fold in strain JP1449 of Escherichia coli carrying a thermosensitive mutation in the glutamyl-transfer ribonucleic acid (tRNA) synthetase and growing exponentially but at a reduced rate at a partially restrictive temperature, compared with the levels in strain AB347 isogenic with strain JP1449 except for this thermosensitive mutation and the marker aro. These two enzymes catalyze one of the two pathways for glutamate biosynthesis in E. coli, the other being defined by the glutamate dehydrogenase. We observed a correlation between the percentage of charged tRNAGlu and the level of glutamate synthase in various mutants reported to have an altered glutamyl-tRNA synthetase activity. These results suggest that a glutamyl-tRNA might be involved in the repression of the biosynthesis of the glutamate synthase and of the glutamine synthetase and would couple the regulation of the biosynthesis of these two enzymes, which can work in tandem to synthesize glutamate when the ammonia concentration is low in E. coli but whose structural genes are quite distant from each other. No derepression of the level of the glutamate dehydrogenase was observed in mutant strain JP1449 under the conditions where the levels of the glutamine synthetase and of the glutamate synthase were derepressed. This result indicates that the two pathways for glutamate biosynthesis in E. coli are under different regulatory controls. The glutamate has been reported to be probably the key regulatory element of the biosynthesis of the glutamate dehydrogenase. Our results indicate that the cell has chosen the level of glutamyl-tRNA as a more sensitive probe to regulate the biosynthesis of the enzymes of the other pathway, which must be energized at a low ammonia concentration.
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