1
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Khalique A, Mattijssen S, Haddad AF, Chaudhry S, Maraia RJ. Targeting mitochondrial and cytosolic substrates of TRIT1 isopentenyltransferase: Specificity determinants and tRNA-i6A37 profiles. PLoS Genet 2020; 16:e1008330. [PMID: 32324744 PMCID: PMC7200024 DOI: 10.1371/journal.pgen.1008330] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Revised: 05/05/2020] [Accepted: 03/18/2020] [Indexed: 11/29/2022] Open
Abstract
The tRNA isopentenyltransferases (IPTases), which add an isopentenyl group to N6 of A37 (i6A37) of certain tRNAs, are among a minority of enzymes that modify cytosolic and mitochondrial tRNAs. Pathogenic mutations to the human IPTase, TRIT1, that decrease i6A37 levels, cause mitochondrial insufficiency that leads to neurodevelopmental disease. We show that TRIT1 encodes an amino-terminal mitochondrial targeting sequence (MTS) that directs mitochondrial import and modification of mitochondrial-tRNAs. Full understanding of IPTase function must consider the tRNAs selected for modification, which vary among species, and in their cytosol and mitochondria. Selection is principally via recognition of the tRNA A36-A37-A38 sequence. An exception is unmodified tRNATrpCCA-A37-A38 in Saccharomyces cerevisiae, whereas tRNATrpCCA is readily modified in Schizosaccharomyces pombe, indicating variable IPTase recognition systems and suggesting that additional exceptions may account for some of the tRNA-i6A37 paucity in higher eukaryotes. Yet TRIT1 had not been characterized for restrictive type substrate-specific recognition. We used i6A37-dependent tRNA-mediated suppression and i6A37-sensitive northern blotting to examine IPTase activities in S. pombe and S. cerevisiae lacking endogenous IPTases on a diversity of tRNA-A36-A37-A38 substrates. Point mutations to the TRIT1 MTS that decrease human mitochondrial import, decrease modification of mitochondrial but not cytosolic tRNAs in both yeasts. TRIT1 exhibits clear substrate-specific restriction against a cytosolic-tRNATrpCCA-A37-A38. Additional data suggest that position 32 of tRNATrpCCA is a conditional determinant for substrate-specific i6A37 modification by the restrictive IPTases, Mod5 and TRIT1. The cumulative biochemical and phylogenetic sequence analyses provide new insights into IPTase activities and determinants of tRNA-i6A37 profiles in cytosol and mitochondria.
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Affiliation(s)
- Abdul Khalique
- Intramural Research Program of the Eunice Kennedy Shriver National Institute of Child Health and Human Development, of the National Institutes of Health, Bethesda, Maryland, United States of America
| | - Sandy Mattijssen
- Intramural Research Program of the Eunice Kennedy Shriver National Institute of Child Health and Human Development, of the National Institutes of Health, Bethesda, Maryland, United States of America
| | - Alexander F. Haddad
- Intramural Research Program of the Eunice Kennedy Shriver National Institute of Child Health and Human Development, of the National Institutes of Health, Bethesda, Maryland, United States of America
| | - Shereen Chaudhry
- Intramural Research Program of the Eunice Kennedy Shriver National Institute of Child Health and Human Development, of the National Institutes of Health, Bethesda, Maryland, United States of America
| | - Richard J. Maraia
- Intramural Research Program of the Eunice Kennedy Shriver National Institute of Child Health and Human Development, of the National Institutes of Health, Bethesda, Maryland, United States of America
- Commissioned Corps, United States Public Health Service, Rockville, Maryland, United States of America
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2
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Schweizer U, Bohleber S, Fradejas-Villar N. The modified base isopentenyladenosine and its derivatives in tRNA. RNA Biol 2017; 14:1197-1208. [PMID: 28277934 PMCID: PMC5699536 DOI: 10.1080/15476286.2017.1294309] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Base 37 in tRNA, 3′-adjacent to the anticodon, is occupied by a purine base that is thought to stabilize codon recognition by stacking interactions on the first Watson-Crick base pair. If the first codon position forms an A.U or U.A base pair, the purine is likely further modified in all domains of life. One of the first base modifications found in tRNA is N6-isopentenyl adenosine (i6A) present in a fraction of tRNAs in bacteria and eukaryotes, which can be further modified to 2-methyl-thio-N6-isopentenyladenosine (ms2i6A) in a subset of tRNAs. Homologous tRNA isopentenyl transferase enzymes have been identified in bacteria (MiaA), yeast (Mod5, Tit1), roundworm (GRO-1), and mammals (TRIT1). In eukaryotes, isopentenylation of cytoplasmic and mitochondrial tRNAs is mediated by products of the same gene. Accordingly, a patient with homozygous mutations in TRIT1 has mitochondrial disease. The role of i6A in a subset of tRNAs in gene expression has been linked with translational fidelity, speed of translation, skewed gene expression, and non-sense suppression. This review will not cover the action of i6A as a cytokinin in plants or the potential function of Mod5 as a prion in yeast.
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Affiliation(s)
- Ulrich Schweizer
- a Institut für Biochemie und Molekularbiologie, Rheinische Friedrich-Wilhelms-Universität Bonn , Bonn , Germany
| | - Simon Bohleber
- a Institut für Biochemie und Molekularbiologie, Rheinische Friedrich-Wilhelms-Universität Bonn , Bonn , Germany
| | - Noelia Fradejas-Villar
- a Institut für Biochemie und Molekularbiologie, Rheinische Friedrich-Wilhelms-Universität Bonn , Bonn , Germany
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3
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Lamichhane TN, Arimbasseri AG, Rijal K, Iben JR, Wei FY, Tomizawa K, Maraia RJ. Lack of tRNA-i6A modification causes mitochondrial-like metabolic deficiency in S. pombe by limiting activity of cytosolic tRNATyr, not mito-tRNA. RNA (NEW YORK, N.Y.) 2016; 22:583-96. [PMID: 26857223 PMCID: PMC4793213 DOI: 10.1261/rna.054064.115] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 12/28/2015] [Indexed: 05/17/2023]
Abstract
tRNA-isopentenyl transferases (IPTases) are highly conserved enzymes that form isopentenyl-N(6)-A37 (i6A37) on subsets of tRNAs, enhancing their translation activity. Nuclear-encoded IPTases modify select cytosolic (cy-) and mitochondrial (mt-) tRNAs. Mutation in human IPTase, TRIT1, causes disease phenotypes characteristic of mitochondrial translation deficiency due to mt-tRNA dysfunction. Deletion of the Schizosaccharomyces pombe IPTase (tit1-Δ) causes slow growth in glycerol, as well as in rapamycin, an inhibitor of TOR kinase that maintains metabolic homeostasis. Schizosaccharomyces pombe IPTase modifies three different cy-tRNAs(Ser) as well as cy-tRNA(Tyr), cy-tRNA(Trp), and mt-tRNA(Trp). We show that lower ATP levels in tit1-Δ relative to tit1(+) cells are also more decreased by an inhibitor of oxidative phosphorylation, indicative of mitochondrial dysfunction. Here we asked if the tit1-Δ phenotypes are due to hypomodification of cy-tRNA or mt-tRNA. A cytosol-specific IPTase that modifies cy-tRNA, but not mt-tRNA, fully rescues the tit1-Δ phenotypes. Moreover, overexpression of cy-tRNAs also rescues the phenotypes, and cy-tRNA(Tyr) alone substantially does so. Bioinformatics indicate that cy-tRNA(Tyr) is most limiting for codon demand in tit1-Δ cells and that the cytosolic mRNAs most loaded with Tyr codons encode carbon metabolilizing enzymes, many of which are known to localize to mitochondria. Thus, S. pombe i6A37 hypomodification-associated metabolic deficiency results from hypoactivity of cy-tRNA, mostly tRNA(Tyr), and unlike human TRIT1-deficiency does not impair mitochondrial translation due to mt-tRNA hypomodification. We discuss species-specific aspects of i6A37. Specifically relevant to mitochondria, we show that its hypermodified version, ms2i6A37 (2-methylthiolated), which occurs on certain mammalian mt-tRNAs (but not cy-tRNAs), is not found in yeast.
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Affiliation(s)
- Tek N Lamichhane
- Section on Molecular and Cell Biology, Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Aneeshkumar G Arimbasseri
- Section on Molecular and Cell Biology, Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Keshab Rijal
- Section on Molecular and Cell Biology, Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - James R Iben
- Molecular Genetics Laboratory, Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Fan Yan Wei
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, 860-0862 Kumamoto, Japan
| | - Kazuhito Tomizawa
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, 860-0862 Kumamoto, Japan
| | - Richard J Maraia
- Section on Molecular and Cell Biology, Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA Commissioned Corps, US Public Health Service, Rockville, Maryland 20016, USA
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4
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Lack of tRNA modification isopentenyl-A37 alters mRNA decoding and causes metabolic deficiencies in fission yeast. Mol Cell Biol 2013; 33:2918-29. [PMID: 23716598 DOI: 10.1128/mcb.00278-13] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
tRNA isopentenyltransferases (Tit1) modify tRNA position 37, adjacent to the anticodon, to N6-isopentenyladenosine (i6A37) in all cells, yet the tRNA subsets selected for modification vary among species, and their relevance to phenotypes is unknown. We examined the function of i6A37 in Schizosaccharomyces pombe tit1+ and tit1-Δ cells by using a β-galactosidase codon-swap reporter whose catalytic activity is sensitive to accurate decoding of codon 503. i6A37 increased the activity of tRNACys at a cognate codon and that of tRNATyr at a near-cognate codon, suggesting that i6A37 promotes decoding activity generally and increases fidelity at cognate codons while decreasing fidelity at noncognate codons. S. pombe cells lacking tit1+ exhibit slow growth in glycerol or rapamycin. While existing data link wobble base U34 modifications to translation of functionally related mRNAs, whether this might extend to the anticodon-adjacent position 37 was unknown. Indeed, we found a biased presence of i6A37-cognate codons in high-abundance mRNAs for ribosome subunits and energy metabolism, congruent with the observed phenotypes and the idea that i6A37 promotes translational efficiency. Polysome profiles confirmed the decreased translational efficiency of mRNAs in tit1-Δ cells. Because subsets of i6A37-tRNAs differ among species, as do their cognate codon-sensitive mRNAs, these genomic variables may underlie associated phenotypic differences.
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5
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Lamichhane TN, Blewett NH, Maraia RJ. Plasticity and diversity of tRNA anticodon determinants of substrate recognition by eukaryotic A37 isopentenyltransferases. RNA (NEW YORK, N.Y.) 2011; 17:1846-57. [PMID: 21873461 PMCID: PMC3185917 DOI: 10.1261/rna.2628611] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
The N(6)-(isopentenyl)adenosine (i(6)A) modification of some tRNAs at position A37 is found in all kingdoms and facilitates codon-specific mRNA decoding, but occurs in different subsets of tRNAs in different species. Here we examine yeasts' tRNA isopentenyltransferases (i.e., dimethylallyltransferase, DMATase, members of the Δ(2)-isopentenylpyrophosphate transferase, IPPT superfamily) encoded by tit1(+) in Schizosaccharomyces pombe and MOD5 in Saccharomyces cerevisiae, whose homologs are Escherichia coli miaA, the human tumor suppressor TRIT1, and the Caenorhabditis elegans life-span gene product GRO-1. A major determinant of miaA activity is known to be the single-stranded tRNA sequence, A36A37A38, in a stem-loop. tRNA(Trp)(CCA) from either yeast is a Tit1p substrate, but neither is a Mod5p substrate despite the presence of A36A37A38. We show that Tit1p accommodates a broader range of substrates than Mod5p. tRNA(Trp)(CCA) is distinct from Mod5p substrates, which we sort into two classes based on the presence of G at position 34 and other elements. A single substitution of C34 to G converts tRNA(Trp)(CCA) to a Mod5p substrate in vitro and in vivo, consistent with amino acid contacts to G34 in existing Mod5p-tRNA(Cys)(GCA) crystal structures. Mutation of Mod5p in its G34 recognition loop region debilitates it differentially for its G34 (class I) substrates. Multiple alignments reveal that the G34 recognition loop sequence of Mod5p differs significantly from Tit1p, which more resembles human TRIT1 and other DMATases. We show that TRIT1 can also modify tRNA(Trp)(CCA) consistent with broad recognition similar to Tit1p. This study illustrates previously unappreciated molecular plasticity and biological diversity of the tRNA-isopentenyltransferase system of eukaryotes.
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Affiliation(s)
- Tek N. Lamichhane
- Intramural Research Program on Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Nathan H. Blewett
- Intramural Research Program on Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Richard J. Maraia
- Intramural Research Program on Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
- Commissioned Corps, US Public Health Service, Washington, DC 20201, USA
- Corresponding author.E-mail .
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6
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Alexandrov A, Grayhack EJ, Phizicky EM. tRNA m7G methyltransferase Trm8p/Trm82p: evidence linking activity to a growth phenotype and implicating Trm82p in maintaining levels of active Trm8p. RNA (NEW YORK, N.Y.) 2005; 11:821-30. [PMID: 15811913 PMCID: PMC1370766 DOI: 10.1261/rna.2030705] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
We show that Saccharomyces cerevisiae strains lacking Trm8p/Trm82p tRNA m7G methyltransferase are temperature-sensitive in synthetic media containing glycerol. Bacterial TRM8 orthologs complement the growth defect of trm8-Delta, trm82-Delta, and trm8-Delta trm82-Delta double mutants, suggesting that bacteria employ a single subunit for Trm8p/Trm82p function. The growth phenotype of trm8 mutants correlates with lack of tRNA m7G methyltransferase activity in vitro and in vivo, based on analysis of 10 mutant alleles of trm8 and bacterial orthologs, and suggests that m7G modification is the cellular function important for growth. Initial examination of the roles of the yeast subunits shows that Trm8p has most of the functions required to effect m7G modification, and that a major role of Trm82p is to maintain cellular levels of Trm8p. Trm8p efficiently cross-links to pre-tRNAPhe in vitro in the presence or absence of Trm82p, in addition to its known residual tRNA m7G modification activity and its SAM-binding domain. Surprisingly, the levels of Trm8p, but not its mRNA, are severely reduced in a trm82-Delta strain. Although Trm8p can be produced in the absence of Trm82p by deliberate overproduction, the resulting protein is inactive, suggesting that a second role of Trm82p is to stabilize Trm8p in an active conformation.
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Affiliation(s)
- Andrei Alexandrov
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine, 601 Elmwood Ave., Box 712, Rochester, NY 14642, USA
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7
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Warner GJ, Berry MJ, Moustafa ME, Carlson BA, Hatfield DL, Faust JR. Inhibition of selenoprotein synthesis by selenocysteine tRNA[Ser]Sec lacking isopentenyladenosine. J Biol Chem 2000; 275:28110-9. [PMID: 10821829 DOI: 10.1074/jbc.m001280200] [Citation(s) in RCA: 133] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A common posttranscriptional modification of tRNA is the isopentenylation of adenosine at position 37, creating isopentenyladenosine (i(6)A). The role of this modified nucleoside in protein synthesis of higher eukaryotes is not well understood. Selenocysteyl (Sec) tRNA (tRNA([Ser]Sec)) decodes specific UGA codons and contains i(6)A. To address the role of the modified nucleoside in this tRNA, we constructed a site-specific mutation, which eliminates the site of isopentenylation, in the Xenopus tRNA([Ser]Sec) gene. Transfection of the mutant tRNA([Ser]Sec) gene resulted in 80% and 95% reduction in the expression of co-transfected selenoprotein genes encoding type I and II iodothyronine deiodinases, respectively. A similar decrease in type I deiodinase synthesis was observed when transfected cells were treated with lovastatin, an inhibitor of the biosynthesis of the isopentenyl moiety. Neither co-transfection with the mutant tRNA gene nor lovastatin treatment reduced type I deiodinase mRNA levels. Also, mutant tRNA expression did not alter initiation of translation or degradation of the type I deiodinase protein. Furthermore, isopentenylation of tRNA([Ser]Sec) was not required for synthesis of Sec on the tRNA. We conclude that isopentenylation of tRNA([Ser]Sec) is required for efficient translational decoding of UGA and synthesis of selenoproteins.
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Affiliation(s)
- G J Warner
- Tufts University School of Medicine, Department of Physiology, Boston, Massachusetts 02111, USA
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8
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Buvoli M, Buvoli A, Leinwand LA. Suppression of nonsense mutations in cell culture and mice by multimerized suppressor tRNA genes. Mol Cell Biol 2000; 20:3116-24. [PMID: 10757796 PMCID: PMC85606 DOI: 10.1128/mcb.20.9.3116-3124.2000] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We demonstrate here the first experimental suppression of a premature termination codon in vivo by using an ochre suppressor tRNA acting in an intact mouse. Multicopy tRNA expression plasmids were directly injected into skeletal muscle and into the hearts of transgenic mice carrying a reporter gene with an ochre mutation. A strategy for modulation of suppressor efficiency, applicable to diverse systems and based on tandem multimerization of the tRNA gene, is developed. The product of suppression (chloramphenicol acetyltransferase) accumulates linearly with increases in suppressor tRNA concentration to the point where the ochre-suppressing tRNA(Ser) is in four- to fivefold excess over the endogenous tRNA(Ser). The subsequent suppressor activity plateau seems to be attributable to accumulation of unmodified tRNAs. These results define many salient variables for suppression in vivo, for example, for tRNA suppression employed as gene therapy for nonsense defects.
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Affiliation(s)
- M Buvoli
- Department of Molecular Biology, University of Colorado at Boulder, Boulder, Colorado 80309, USA
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9
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Niederberger C, Gräub R, Costa A, Desgrès J, Schweingruber ME. The tRNA N2,N2-dimethylguanosine-26 methyltransferase encoded by gene trm1 increases efficiency of suppression of an ochre codon in Schizosaccharomyces pombe. FEBS Lett 1999; 464:67-70. [PMID: 10611485 DOI: 10.1016/s0014-5793(99)01679-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
In the majority of eukaryotic tRNAs, the guanosine at position 26 is modified by a dimethyl group, but so far a function of this modification has not been detected. We isolated the Schizosaccharomyces pombe gene, trm1, encoding the tRNA N2, N2-dimethylguanosine-26 methyltransferase. Strains having the gene deleted completely lack N2,N2-dimethylguanosine. In strains carrying the weak ochre tRNA suppressor sup3-i, deletion of trm1 abolishes suppression indicating that the trm1 deletion acts as an antisuppressor mutation. The result suggests that in vivo N2, N2-dimethylguanosine-26 increases the capacity of the sup3-i serine tRNA to translate the UAA (ochre) codon.
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Affiliation(s)
- C Niederberger
- Institute of General Microbiology, Baltzerstrasse 4, CH-3012, Bern, Switzerland
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10
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Agris PF. The importance of being modified: roles of modified nucleosides and Mg2+ in RNA structure and function. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1996; 53:79-129. [PMID: 8650309 DOI: 10.1016/s0079-6603(08)60143-9] [Citation(s) in RCA: 210] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- P F Agris
- Department of Biochemistry, North Carolina State University, Raleigh 27695, USA
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11
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Persson BC, Esberg B, Olafsson O, Björk GR. Synthesis and function of isopentenyl adenosine derivatives in tRNA. Biochimie 1994; 76:1152-60. [PMID: 7748950 DOI: 10.1016/0300-9084(94)90044-2] [Citation(s) in RCA: 68] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Isopentenyl adenosine derivatives can be found next to the anticodon (position 37) in tRNA from both the Bacteria and Eucarya domains. These modified nucleosides improve the efficiency of tRNA in translation, can increase and decrease translational fidelity, and make the tRNA less codon context sensitive. In bacteria the synthesis of isopentenyl adenosine derivatives seems to be linked to iron metabolism and central metabolic pathways.
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Affiliation(s)
- B C Persson
- Department of Microbiology, Umeå University, Sweden
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12
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Katunin V, Soboleva N, Mahkno V, Sedelnikova E, Zhenodarova S, Kirillov S. Effect of the nucleotide-37 on the interaction of tRNA(Phe) with the P site of Escherichia coli ribosomes. Biochimie 1994; 76:51-7. [PMID: 7518255 DOI: 10.1016/0300-9084(94)90062-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The method of anticodon loop replacement has been used to make derivatives of yeast tRNA(Phe) with the substitution at position 37 (tRNA(Phe)GAAA) and at the anticodon(tRNA(Phe)GCAG). A quantitative study of the interaction of various types of deacylated yeast tRNA(Phe) (tRNA(Phe)+Y, tRNA(Phe)GAAA, tRNA(Phe)-Y) with the P site of the [70S ribosome*poly(U)]-complex was carried out at different Mg2+ concentrations and temperatures. The presence and nature of the nucleotide situated at the 3'-end of the anticodon are essential for such interaction in E coli ribosomes. Replacement of the Y base with the unmodified adenosine decreases the interaction enthalpy from 39 kcal/mol to 24 kcal/mol, whereas its removal reduces the interaction enthalpy to 16 kcal/mol. Replacement of the second anticodon nucleotide, adenosine, with cytosine further reduces the enthalpy to 6 kcal/mol, which is typical of tRNA-P site interaction in the absence of poly(U). In the absence of poly(U) the affinity of tRNA(PheY) for the P site of the 70S ribosome is five times lower than the affinity of tRNA(Phe+Y) or tRNA(Phe)GCAG. Thus, in the ribosome the modified nucleotide stabilizes the codon-anticodon interaction through its stacking interaction with the codon-anticodon base stack. In addition, this decreases the free energy of binding as a result of the interaction of the modified nucleotide itself with the hydrophobic center of the P site.
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Affiliation(s)
- V Katunin
- Petersburg Nuclear Physics Institute, Russian Academy of Science, Leningrad Region
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13
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Abstract
As an aid to the fission yeast genome project, we describe a database for Schizosaccharomyces pombe consisting of both genetic and physical information. As presented, it is therefore both an updated gene list of all the nuclear genes of the fission yeast, and provides an estimate of the physical distance between two mapped genes. Additionally, a field indicates whether the sequence of the gene is available. Currently, sequence information is available for 135 of the 501 known genes.
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Affiliation(s)
- G G Lennon
- Biomed. Div. L-452, Lawrence Livermore National Laboratory, Livermore, CA 94550
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14
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Hopper AK. Genetic methods for study of trans-acting genes involved in processing of precursors to yeast cytoplasmic transfer RNAs. Methods Enzymol 1990; 181:400-21. [PMID: 2199759 DOI: 10.1016/0076-6879(90)81139-l] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
All of the strategies to identify mutants defective in pre-tRNA processing have proved to be useful. However, in some of these strategies (such as inability to derepress a nonsense suppressor, correction of processing-defective substrates, and reverse genetics) only a single mutant has been isolated. This is not because the methods have proved to be inefficient, but rather because the field is still in infancy. Further work is needed to saturate the types of mutants found by each procedure. Undoubtedly, new strategies will be designed.
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15
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Chapter 1 Synthesis and Function of Modified Nucleosides in tRNA. ACTA ACUST UNITED AC 1990. [DOI: 10.1016/s0301-4770(08)61487-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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16
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Wilson RK, Roe BA. Presence of the hypermodified nucleotide N6-(delta 2-isopentenyl)-2-methylthioadenosine prevents codon misreading by Escherichia coli phenylalanyl-transfer RNA. Proc Natl Acad Sci U S A 1989; 86:409-13. [PMID: 2643111 PMCID: PMC286479 DOI: 10.1073/pnas.86.2.409] [Citation(s) in RCA: 52] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The overall structure of transfer RNA is optimized for its various functions by a series of unique post-transcriptional nucleotide modifications. Since many of these modifications are conserved from prokaryotes through higher eukaryotes, it has been proposed that most modified nucleotides serve to optimize the ability of the tRNA to accurately interact with other components of the protein synthesizing machinery. When a cloned synthetic Escherichia coli tRNAPhe gene was transfected into a bacterial host that carried a defective phenylalanine tRNA-synthetase gene, tRNAPhe was overexpressed by 11-fold. As a result of this overexpression, an undermodified tRNAPhe species was produced that lacked only N6-(delta 2-isopentenyl)-2-methylthioadenosine (ms2i6A), a hypermodified nucleotide found immediately 3' to the anticodon of all major E. coli tRNAs that read UNN codons. To investigate the role of ms2i6A in E. coli tRNA, we compared the aminoacylation kinetics and in vitro codon-reading properties of the ms2i6A-lacking and normal fully modified tRNAPhe species. The results of these experiments indicate that while ms2i6A is not required for normal aminoacylation of tRNAPhe, its presence stabilizes codon-anticodon interaction and thereby prevents misreading of the genetic code.
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MESH Headings
- Adenosine/analogs & derivatives
- Amino Acid Sequence
- Base Sequence
- Chemical Fractionation
- Chromatography, Thin Layer
- Cloning, Molecular
- Codon/genetics
- Escherichia coli/genetics
- Gene Expression Regulation
- Isopentenyladenosine/analogs & derivatives
- Isopentenyladenosine/genetics
- Isopentenyladenosine/metabolism
- Kinetics
- Molecular Sequence Data
- Phenylalanine-tRNA Ligase/genetics
- Protein Biosynthesis
- RNA Processing, Post-Transcriptional
- RNA, Messenger/genetics
- RNA, Transfer, Amino Acid-Specific/metabolism
- RNA, Transfer, Phe/biosynthesis
- RNA, Transfer, Phe/genetics
- RNA, Transfer, Phe/isolation & purification
- RNA, Transfer, Phe/metabolism
- Transcription, Genetic
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Affiliation(s)
- R K Wilson
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman 73019
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17
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Modifiers of ochre suppressors in Saccharomyces cerevisiae that exhibit ochre suppressor-dependent amber suppression. Curr Genet 1988. [DOI: 10.1007/bf00419992] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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18
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Effect of intron mutations on processing and function of Saccharomyces cerevisiae SUP53 tRNA in vitro and in vivo. Mol Cell Biol 1987. [PMID: 3537724 DOI: 10.1128/mcb.6.7.2663] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Saccharomyces cerevisiae leucine-inserting amber suppressor tRNA gene SUP53 (a tRNALeu3 allele) was used to investigate the relationship between precursor tRNA structure and mature tRNA function. This gene encodes a pre-tRNA which contains a 32-base intron. The mature tRNASUP53 contains a 5-methylcytosine modification of the anticodon wobble base. Mutations were made in the SUP53 intron. These mutant genes were transcribed in an S. cerevisiae nuclear extract preparation. In this extract, primary tRNA gene transcripts are end-processed and base modified after addition of cofactors. The base modifications made in vitro were examined, and the mutant pre-tRNAs were analyzed for their ability to serve as substrates for partially purified S. cerevisiae tRNA endonuclease and ligase. Finally, the suppressor function of these mutant tRNA genes was assayed after their integration into the S. cerevisiae genome. Mutant analysis showed that the totally intact precursor tRNA, rather than any specific sequence or structure of the intron, was necessary for efficient nonsense suppression by tRNASUP53. Less efficient suppressor activity correlated with the absence of the 5-methylcytosine modification. Most of the intron-altered precursor tRNAs were successfully spliced in vitro, indicating that modifications are not critical for recognition by the tRNA endonuclease and ligase.
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19
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Antisuppressor mutations and sulfur-carrying nucleosides in transfer RNAs of Schizosaccharomyces pombe. J Biol Chem 1986. [DOI: 10.1016/s0021-9258(18)66573-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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20
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Yarus M, Cline S, Raftery L, Wier P, Bradley D. The translational efficiency of tRNA is a property of the anticodon arm. J Biol Chem 1986. [DOI: 10.1016/s0021-9258(18)67412-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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21
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Strobel MC, Abelson J. Effect of intron mutations on processing and function of Saccharomyces cerevisiae SUP53 tRNA in vitro and in vivo. Mol Cell Biol 1986; 6:2663-73. [PMID: 3537724 PMCID: PMC367823 DOI: 10.1128/mcb.6.7.2663-2673.1986] [Citation(s) in RCA: 55] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The Saccharomyces cerevisiae leucine-inserting amber suppressor tRNA gene SUP53 (a tRNALeu3 allele) was used to investigate the relationship between precursor tRNA structure and mature tRNA function. This gene encodes a pre-tRNA which contains a 32-base intron. The mature tRNASUP53 contains a 5-methylcytosine modification of the anticodon wobble base. Mutations were made in the SUP53 intron. These mutant genes were transcribed in an S. cerevisiae nuclear extract preparation. In this extract, primary tRNA gene transcripts are end-processed and base modified after addition of cofactors. The base modifications made in vitro were examined, and the mutant pre-tRNAs were analyzed for their ability to serve as substrates for partially purified S. cerevisiae tRNA endonuclease and ligase. Finally, the suppressor function of these mutant tRNA genes was assayed after their integration into the S. cerevisiae genome. Mutant analysis showed that the totally intact precursor tRNA, rather than any specific sequence or structure of the intron, was necessary for efficient nonsense suppression by tRNASUP53. Less efficient suppressor activity correlated with the absence of the 5-methylcytosine modification. Most of the intron-altered precursor tRNAs were successfully spliced in vitro, indicating that modifications are not critical for recognition by the tRNA endonuclease and ligase.
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22
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Pleiotropic effects induced by modification deficiency next to the anticodon of tRNA from Salmonella typhimurium LT2. J Bacteriol 1986; 166:1013-21. [PMID: 2423501 PMCID: PMC215226 DOI: 10.1128/jb.166.3.1013-1021.1986] [Citation(s) in RCA: 70] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
A strain of Salmonella typhimurium LT2 was isolated, which harbors a mutation acting as an antisuppressor toward an amber suppressor derivative, supF30, of tRNATyr1. The mutant is deficient in cis-2-methylthioribosylzeatin[N6-(4-hydroxyisopentenyl)-2-me thylthioadenosine, ms2io6A], which is a modification normally present next to the anticodon (position 37) in tRNA reading codons starting with uridine. The gene miaA, defective in the mutant, is located close to and counterclockwise of the purA gene at 96 min on the chromosomal map of S. typhimurium with the gene order mutL miaA purA. Growth rate of the mutant was reduced 20 to 50%, and the effect was more pronounced in media supporting fast growth. Translational chain elongation rate at 37 degrees C was reduced from 16 amino acids per s in the wild-type cell to 11 amino acids per s in the miaA1 mutant in the four different growth media tested. The cellular yield in limiting glucose, glycerol, or succinate medium was reduced for the miaAI mutant compared with wild-type cells, with 49, 41, and 57% reductions, respectively. The miaAI mutation renders the cell more sensitive or resistant toward several amino acid analogs, suggesting that the deficiency in ms2io6A influences the regulation of several amino acid biosynthetic operons. We suggest that tRNAPhe, lacking ms2io6A, translates a UUU codon in the early histidine leader sequence with lowered efficiency, leading to repression of the his operon.
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23
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Abstract
The translational activity of a transfer RNA at a codon varies at different message sites, although the codon does not vary. The source of this effect, which may help to determine the level of gene expression, is generally agreed to be in nearby message sequences. By making every possible nucleotide combination between position 33 of the transfer RNA and the major context nucleotide of the message, it was shown that base-pairing between the two nucleotides is not the source of this context effect on translation in vivo.
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24
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Laten HM, Zahareas-Doktor S. Presence and source of free isopentenyladenosine in yeasts. Proc Natl Acad Sci U S A 1985; 82:1113-5. [PMID: 3883351 PMCID: PMC397204 DOI: 10.1073/pnas.82.4.1113] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Cytokinins are a class of naturally occurring compounds that regulate growth and differentiation in tissues of higher plants. Many cytokinins are isopentenylated derivatives of adenine and its riboside, adenosine. By virtue of the post-transcriptional isopentenylation of specific anticodon loop adenosine residues in certain tRNA sequences, cytokinins are nearly universal, but tRNA-independent (de novo) cytokinin synthesis has been demonstrated in a few species. Using a radioimmunoassay, we have demonstrated that haploid strains of Saccharomyces cerevisiae and Schizosaccharomyces pombe contain, respectively, 0.8 and 0.9 microgram of the free cytokinin, N6-(delta 2-isopentenyl)adenosine, per g of cells (wet weight). Strains of both species characterized by mutations that result in deficiencies of isopentenylated tRNAs have somewhat elevated levels of free N6-(delta 2-isopentenyl)adenosine. These findings lead to the conclusion that the major, if not exclusive, source of free cytokinins in these two yeasts is a synthetic pathway independent of isopentenylated RNA turnover.
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25
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Laten HM, Timmons RM, Suid S. An antisuppressor mutant of Saccharomyces cerevisiae deficient in isopentenylated tRNA has reduced delta 2-isopentenylpyrophosphate: tRNA-delta 2-isopentenyl transferase activity. FEBS Lett 1985; 179:307-10. [PMID: 3881278 DOI: 10.1016/0014-5793(85)80540-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
We have previously reported the isolation and initial characterization of a mutation in Saccharomyces cerevisiae, designated mod5-1, that reduces the capacity of altered tyrosine tRNAs to suppress ochre nonsense mutations. The mutation results in the virtual elimination of the modified tRNA nucleoside, N6-delta 2-(isopentenyl) adenosine, normally found adjacent to the anticodons of certain tRNA species. We demonstrate here that MOD5 codes for delta 2-isopentenylpyrophosphate: tRNA-delta 2-isopentenyl transferase, or a protein that regulates its synthesis.
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26
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27
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Temperature sensitive allosuppressor mutants of the fission yeast S. pombe influence cell cycle control over mitosis. ACTA ACUST UNITED AC 1984. [DOI: 10.1007/bf00328067] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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28
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Hagervall TG, Björk GR. Undermodification in the first position of the anticodon of supG-tRNA reduces translational efficiency. MOLECULAR & GENERAL GENETICS : MGG 1984; 196:194-200. [PMID: 6387394 DOI: 10.1007/bf00328050] [Citation(s) in RCA: 37] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Two mutants of Escherichia coli, trmC1 and trmC2, which are both defective in the synthesis of 5-methylaminomethyl-2-thiouridine (mnm5s2U) were utilized to study the function of this complex modified nucleoside. Transfer RNAs specific for glutamine, glutamic acid and lysine as well as a specific ochre suppressor derived from lysine tRNA (tRNAUAAlys encoded by the supG allele), contain this modified nucleoside at position 34 (the wobble position). It was found that two different undermodified derivatives of mnm5s2U were present in the two trmC mutants, which suggests that the two mutations affect two different enzymatic activities. Using the lacI-Z fusion system (Miller and Albertini 1983), we found that the efficiency of supG-mediated suppression was reduced to 30%-90% of the wild-type value in the trmC mutants. The modification-deficient supG-tRNA in the mutants showed a higher sensitivity to codon context than the normal tRNAUAAlys.
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29
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Vacher J, Grosjean H, Houssier C, Buckingham RH. The effect of point mutations affecting Escherichia coli tryptophan tRNA on anticodon-anticodon interactions and on UGA suppression. J Mol Biol 1984; 177:329-42. [PMID: 6379198 DOI: 10.1016/0022-2836(84)90460-1] [Citation(s) in RCA: 62] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
tRNA species in Escherichia coli that translate codons starting with U contain 2-methyl-thio-N6-isopentenyl-adenosine in position 37, 3' adjacent to the anticodon. The role of this hypermodification in protein synthesis and trp operon attenuation has been investigated. Temperature-jump relaxation methods have been applied to study the interaction between E. coli tRNAPro, with anticodon VGG (V is uridine-5-oxyacetic acid) complementary to that of tRNATrp, and three species of E. coli tRNATrp: wild type tRNATrp (with ms2i6A37 and G24), UGA suppressor tRNATrp (with ms2i6A37 and A24 in the dihydrouridine stem but the same anticodon CCA), and the same suppressor molecule but ms2i6A-deficient as a result of the mutation miaA. Complex formation between tRNAPro and ms2i6A-containing tRNATrp shows thermodynamic parameters close to those found for several other pairs of tRNA with complementary anticodons. However, ms2i6A-deficient tRNATrp makes less stable complexes with tRNAPro, which dissociate eightfold faster. No effect on the complementary anticodon interaction of the mutation in the dihydrouridine stem can be detected. When the tRNA analogous to the opal codon, E. coli tRNASerIV (anticodon VGA) replaces tRNAPro in similar experiments, very weak complexes are observed with both normally hypermodified species of tRNATrp, the wild type and UGA suppressor; these show a lifetime about 50-fold shorter than with tRNAPro, but are again similar. No complex formation is detectable with the ms2i6A-deficient species. This may explain why the hypermodification is necessary for the efficient suppression of the UGA terminator of Q beta coat protein in vitro. The data on complexes with tRNAPro suggest that deficiency in ms2i6A may also reduce the efficiency of UGG reading. Thus, miaA may affect trp operon attenuation by slowing translation of the tandem UGG codons in the leader sequence. Temperature-jump differential spectra suggest that ms2i6 stabilizes the anticodon interaction by improved stacking of base 37.
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An antisuppressor mutation of Schizosaccharomyces pombe affects the post-transcriptional modification of the “wobble” base in the anticodon of tRNAs. J Biol Chem 1984. [DOI: 10.1016/s0021-9258(17)43226-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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31
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Kersten H. On the biological significance of modified nucleosides in tRNA. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1984; 31:59-114. [PMID: 6397775 DOI: 10.1016/s0079-6603(08)60375-x] [Citation(s) in RCA: 54] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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32
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Laten HM. Antisuppression of class I suppressors in an isopentenylated-transfer RNA deficient mutant of Saccharomyces cerevisiae. Curr Genet 1984; 8:29-32. [DOI: 10.1007/bf00405428] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/1983] [Indexed: 11/25/2022]
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33
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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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34
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Tuite MF, Cox BS, McLaughlin CS. In vitro nonsense suppression in [psi+] and [psi-] cell-free lysates of Saccharomyces cerevisiae. Proc Natl Acad Sci U S A 1983; 80:2824-8. [PMID: 6344070 PMCID: PMC393924 DOI: 10.1073/pnas.80.10.2824] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
An homologous in vitro assay for yeast nonsense suppressors was used to examine the effect of the cytoplasmically inherited genetic determinant [psi] on the efficiency of in vitro nonsense suppression. The efficiency of all three types of yeast tRNA-mediated nonsense suppressor (ochre, amber, and UGA) is much greater in cell-free lysates prepared from a sup+ [psi+] strain than in lysates prepared from an isogeneic sup+ [psi-] strain. Lysates prepared from a [psi-] strain, into which the [psi+] determinant was reintroduced by kar1-mediated cytoduction, support efficient suppression. Evidence is also presented that [psi-] lysates contain an inhibitor of in vitro nonsense suppression.
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35
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Johnson PF, Abelson J. The yeast tRNATyr gene intron is essential for correct modification of its tRNA product. Nature 1983; 302:681-7. [PMID: 6339954 DOI: 10.1038/302681a0] [Citation(s) in RCA: 108] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Precise deletion of the intervening sequence of a yeast tRNATyr ochre suppressor gene (SUP6) significantly reduced its suppressor activity relative to that of the unaltered gene. This is probably the result of the absence of the pseudouridine modification, normally present at the middle anticodon position of mature suppressor tRNA, in tRNA synthesized in vivo from the deleted gene.
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36
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Munz P, Dorsch-H�sler K, Leupold U. The genetic fine structure of nonsense suppressors in Schizosaccharomyces pombe. Curr Genet 1983; 7:101-8. [DOI: 10.1007/bf00365633] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/1982] [Indexed: 10/26/2022]
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37
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Palmer DT, Blum PH, Artz SW. Effects of the hisT mutation of Salmonella typhimurium on translation elongation rate. J Bacteriol 1983; 153:357-63. [PMID: 6401282 PMCID: PMC217379 DOI: 10.1128/jb.153.1.357-363.1983] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The hisT mutation in Salmonella typhimurium which results in loss of pseudouridine base modifications in the anticodon regions of many tRNAs was shown to reduce the rate of protein synthesis in vivo by about 20 to 25% as compared with that measured in hisT strains. Reduced protein synthesis rate occurred predominantly at the level of translation rather than transcription. Increased sensitivity of hisT mutants to growth inhibition by antibiotics that inhibit translation elongation, but not by those that inhibit translation initiation, transcription initiation, or transcription elongation, indicates that the hisT mutation leads to a defect in one or more of the steps in the polypeptide chain elongation mechanism. These results can account for effects of the hisT mutation on regulation of certain amino acid biosynthetic operons, including the his, leu, and ilv operons.
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38
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Bruce AG, Atkins JF, Wills N, Uhlenbeck O, Gesteland RF. Replacement of anticodon loop nucleotides to produce functional tRNAs: amber suppressors derived from yeast tRNAPhe. Proc Natl Acad Sci U S A 1982; 79:7127-31. [PMID: 6961400 PMCID: PMC347291 DOI: 10.1073/pnas.79.23.7127] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The method of anticodon loop replacement has been used to make derivatives of yeast tRNAPhe. By constructing tRNAs with a CUA anticodon, complementary to the amber (UAG) terminator, functional amber suppressor tRNAs were produced. The activity of these tRNAs was assayed in a mammalian cell-free protein synthesizing system. The level of suppression reflects the efficiency of codon recognition. tRNAs were constructed with either A, C, U, or G on the 3' side of the CUA anticodon. The tRNAs containing the purines were efficient amber suppressors, whereas those containing pyrimidines were inefficient.
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39
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Martin NC, Hopper AK. Isopentenylation of both cytoplasmic and mitochondrial tRNA is affected by a single nuclear mutation. J Biol Chem 1982. [DOI: 10.1016/s0021-9258(18)33857-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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40
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19 Nucleotide Modification in RNA. ACTA ACUST UNITED AC 1982. [DOI: 10.1016/s1874-6047(08)60291-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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41
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Prather NE, Murgola EJ, Mims BH. Primary structure of an unusual glycine tRNA UGA suppressor. Nucleic Acids Res 1981; 9:6421-8. [PMID: 7033934 PMCID: PMC327613 DOI: 10.1093/nar/9.23.6421] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
We have determined the nucleotide sequences of two UGA-suppressing glycine transfer RNAs. The suppressor tRNAs were previously shown to translate both UGA and UGG and to have arisen as a consequence of mutation in glyT, the gene for the GGA/G-reading glycine tRNA of Escherichia coli. In each mutant tRNA, the primary sequence change was the substitution of adenine for cytosine in the 3' position of the anticodon. In addition, a portion of mutant glyT tRNA molecules contained N6-(delta 2-isopentenyl)-2-thiomethyl adenine adjacent to the 3' end of the anticodon (nucleotide 37). The presence or absence of this hypermodification may be a determinant in some of the biological properties of the mutant tRNA.
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43
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Kurjan J, Hall BD, Gillam S, Smith M. Mutations at the yeast SUP4 tRNATyr locus: DNA sequence changes in mutants lacking suppressor activity. Cell 1980; 20:701-9. [PMID: 6998562 DOI: 10.1016/0092-8674(80)90316-5] [Citation(s) in RCA: 94] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Yeast strains harboring indepjendent mutations within the SUP4 tyrosine tRNA gene have been selected by virtue of their inactivating effect upon the SUP4-o UAA suppressor. Three fourths of the mutations at SUP4 are point alterations; the rest resemble the deletions described by Rothstein (1979). A meiotic genetic fine structure map of the locus was made by crossing 69 of the mutants in all combinations and testing for the frequency of SUP4-o recombinants. The sequences of SUP4 genes cloned from 32 mutant strains were determined by the dideoxynucleotide terminator method, using as primer a synthetic oligodeoxynucleotide corresponding to a sequence adjoining the SUP4 3' terminus. The positions of the DNA sequence alterations showed good colinearity with the positions of the mutations on the genetic map. One of the 26 mutant sites found by DNA sequencing lies within the intervening sequence. At this site three repeat mutations were found, each changing AT leads to TA. Whereas mutations were generally rather uniformly distributed throughout the tRNATyr coding sequence, none occurred in the DNA sequences flanking the mature tRNATyr sequence or in a 12 nucleotide sequence including the 10 bp which constitute the 3' side of the intervening sequence.
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