76
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Kim SI, Nalaskowska M, Germond JE, Pridmore D, Söll D. Asn-tRNA in Lactobacillus bulgaricus is formed by asparaginylation of tRNA and not by transamidation of Asp-tRNA. Nucleic Acids Res 1996; 24:2648-51. [PMID: 8758990 PMCID: PMC146019 DOI: 10.1093/nar/24.14.2648] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
In many organisms (e.g., gram-positive eubacteria) Gin-tRNA is not formed by direct glutaminylation of tRNAGln but by a specific transamidation of Glu-tRNAGln. We wondered whether a similar transamidation pathway also operates in the formation of Asn-tRNA in these organisms. Therefore we tested in S-100 preparations of Lactobacillus bulgaricus, a gram-positive eubacterium, for the conversion by an amidotransferase of [14C]Asp-tRNA to [14C]Asn-tRNA. As no transamidation was observed, we searched for genes for asparaginyl-tRNA synthetase (AsnRS). Two DNA fragments (from different locations of the L.bulgaricus chromosome) were found each containing an ORF whose sequence resembled that of the Escherichia coli asnS gene. The derived amino acid sequences of the two ORFs (432 amino acids) were the same and 41% identical with E.coli AsnRS. When one of the ORFs was expressed in E.coli, it complemented the temperature sensitivity of an E.coli asnS mutant. S-100 preparations of this transformant showed increased charging of unfractionated L.bulgaricus tRNA with asparagine. Deletion of the 3'-terminal region of the L.bulgaricus AsnRS gene led to loss of its complementation and aminoacylation properties. This indicates that L.bulgaricus contains a functional AsnRS. Thus, the transamidation pathway operates only for Gin-tRNAGln formation in this organism, and possibly in all gram-positive eubacteria.
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77
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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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78
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Rudinger J, Hillenbrandt R, Sprinzl M, Giegé R. Antideterminants present in minihelix(Sec) hinder its recognition by prokaryotic elongation factor Tu. EMBO J 1996; 15:650-7. [PMID: 8599948 PMCID: PMC449983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
During protein biosynthesis, all aminoacylated elongator tRNAs except selenocysteine-inserting tRNA Sec form ternary complexes with activated elongation factor. tRNA Sec is bound by its own translation factor, an elongation factor analogue, e.g. the SELB factor in prokaryotes. An apparent reason for this discrimination could be related to the unusual length of tRNA Sec amino acid-acceptor branch formed by 13 bp. However, it has been recently shown that an aspartylated minihelix of 13 bp derived from yeast tRNA Asp is an efficient substrate for Thermus thermophilus EF-Tu-GTP, suggesting that features other than the length of tRNA Sec prevent its recognition by EF-Tu-GTP. A stepwise mutational analysis of a minihelix derived from tRNA Sec in which sequence elements of tRNA Asp were introduced showed that the sequence of the amino acid- acceptor branch of Escherichia coli tRNA Sec contains a specific structural element that hinders its binding to T.thermophilus EF-Tu-GTP. This antideterminant is located in the 8th, 9th and 10th bp in the acceptor branch of tRNA Sec, corresponding to the last base pair in the amino acid acceptor stem and the two first pairs in the T-stem. The function of this C7.G66/G49.U65/C50.G64 box was tested by its transplantation into a minihelix derived from tRNA Asp, abolishing its recognition by EF-Tu-GTP. The specific role of this nucleotide combination is further supported by its absence in all known prokaryotic elongator tRNAs.
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MESH Headings
- Base Sequence
- Biological Evolution
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Guanosine Triphosphate/metabolism
- Molecular Sequence Data
- Nucleic Acid Conformation
- Peptide Elongation Factor Tu/metabolism
- RNA, Antisense/chemistry
- RNA, Antisense/genetics
- RNA, Antisense/metabolism
- RNA, Transfer, Amino Acid-Specific/chemistry
- RNA, Transfer, Amino Acid-Specific/genetics
- RNA, Transfer, Amino Acid-Specific/metabolism
- RNA, Transfer, Asp/chemistry
- RNA, Transfer, Asp/genetics
- RNA, Transfer, Asp/metabolism
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae/metabolism
- Thermus thermophilus/metabolism
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79
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Lee YC, Lee BJ, Hwang DS, Kang HS. Purification and characterization of mitochondrial ribonuclease P from Aspergillus nidulans. EUROPEAN JOURNAL OF BIOCHEMISTRY 1996; 235:289-96. [PMID: 8631344 DOI: 10.1111/j.1432-1033.1996.00289.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Mitochondrial ribonuclease (RNase) P from Aspergillus nidulans was purified to near homogeneity using whole-cell extract as the starting material. A 4400-fold purification with a yield of 5.2% was achieved by ammonium sulfate fractionation, heat treatment, and five types of column chromatography, including tRNA-affinity column chromatography. This enzyme, which has a molecular mass of 232 kDa determined by glycerol gradient sedimentation analysis, appears to be composed of seven polypeptides and an RNA moiety. These seven polypeptides consistently copurified with the RNase P activity through two ion-exchange chromatography columns and in a glycerol gradient. As judged by nuclease sensitivity, the enzyme requires an RNA component for its activity. The 3'-end-labeled RNAs that copurified with the enzyme displayed identical sequences but had variable lengths for the 5' end, indicating that they originated from a common RNA molecule, the putative RNA component of RNase P. The purified enzyme cleaved mitochondrial precursor tRNAHis, resulting in an 8-bp acceptor stem. This implies that the purified RNase P is a mitochondrial enzyme and that an additional guanylate residue (at position -1) of tRNAHis in A. nidulans mitochondria is generated by a mode that is analogous to the generation of their counterparts in prokaryotes and chloroplasts.
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MESH Headings
- Aspergillus nidulans/enzymology
- Aspergillus nidulans/genetics
- Aspergillus nidulans/metabolism
- Base Sequence
- Binding Sites
- DNA Primers/genetics
- Endoribonucleases/genetics
- Endoribonucleases/isolation & purification
- Endoribonucleases/metabolism
- Kinetics
- Mitochondria/enzymology
- Molecular Sequence Data
- Nucleic Acid Conformation
- Protein Conformation
- RNA Precursors/chemistry
- RNA Precursors/genetics
- RNA Precursors/metabolism
- RNA Processing, Post-Transcriptional
- RNA, Catalytic/genetics
- RNA, Catalytic/isolation & purification
- RNA, Catalytic/metabolism
- RNA, Fungal/chemistry
- RNA, Fungal/genetics
- RNA, Fungal/metabolism
- RNA, Transfer, Asp/chemistry
- RNA, Transfer, Asp/genetics
- RNA, Transfer, Asp/metabolism
- Ribonuclease P
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80
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Grosjean H, Edqvist J, Stråby KB, Giegé R. Enzymatic formation of modified nucleosides in tRNA: dependence on tRNA architecture. J Mol Biol 1996; 255:67-85. [PMID: 8568876 DOI: 10.1006/jmbi.1996.0007] [Citation(s) in RCA: 93] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Information is still quite limited concerning the structural requirements in tRNA molecules for their post-transcriptional maturation by base and ribose modification enzymes. To address this question, we have chosen as the model system yeast tRNAAsp that has a known three-dimensional structure and the in vivo modifying machinery of the Xenopus laevis oocyte able to act on microinjected tRNA precursors. We have systematically compared the modification pattern of wild-type tRNAAsp with that of a series of structural mutants (21 altogether) altered at single or multiple positions in the D-, T-and the anticodon branch, as well as in the variable region. The experimental system allowed us to analyze the effects of structural perturbations in tRNA on the enzymatic formation of modified nucleosides at 12 locations scattered over the tRNA cloverleaf. We found that the formation of m1G37 and psi 40 in the anticodon loop and stem and psi 13 in the D-stem, were extremely sensitive to 3D perturbations. In contrast, the formation of T54, psi 55 and m1A58 in the T-loop, m5C49 in the T-stem and m2G6 in the amino acid accepting stem were essentially insensitive to change in the overall tRNA architecture; these modified nucleosides were also formed in appropriate minimalist (stems and loops) tRNA domains. The formation of m2G26 at the junction between the anticodon and the D-stem, of Q34 and manQ34 in the anticodon loop were sensitive only to drastic structural perturbation of the tRNA. Altogether, these results reflect the existence of different modes of tRNA recognition by the many different modifying enzymes. A classification of this family of maturation enzymes into two major groups, according to their sensitivities to structural perturbations in tRNA, is proposed.
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81
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Tomita K, Ueda T, Watanabe K. Two nucleotides 5'-adjacent to the anticodon of rat cytoplasmic tRNA(Asp) are not edited. Biochimie 1996; 78:1001-6. [PMID: 9150878 DOI: 10.1016/s0300-9084(97)86723-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Cytoplasmic tRNA(Asp) of rat liver was purified by the solid-phase hybridization method and its nucleotide sequence was analyzed by Donis-Keller's method. The results suggested that the two nucleotides next to the anticodon were identical to its gene sequence, a finding that is inconsistent with a previous report demonstrating by several methods that C32 and T33 on the tRNA(Asp) gene are post-transcriptionally converted to U32 and C33, respectively (Beier et al (1992) Nucleic Acids Res 20, 2679-2683). Our results indicate that the tRNA hybridized to an oligonucleotide, designed on the basis of the tRNA(Asp) gene sequence, undergoes no editing and possesses C32 and U33 as predicted from the DNA sequence. Analysis of cDNA synthesized from the purified tRNA(Asp) by the RT-PCR method supported the finding that RNA editing is not involved in the maturation process of rat cytoplasmic tRNA(Asp).
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82
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Rees B, Cavarelli J, Moras D. Conformational flexibility of tRNA: structural changes in yeast tRNA(Asp) upon binding to aspartyl-tRNA synthetase. Biochimie 1996; 78:624-31. [PMID: 8955905 DOI: 10.1016/s0300-9084(96)80008-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The availability of several X-ray structures at atomic resolution of tRNA(Asp) from yeast, both in its free state and complexed with its cognate tRNA-synthetase, enables a detailed examination of the conformational changes due to interaction with the enzyme. Although the molecule conserves its general L shape, its conformation undergoes important modifications. They may be described as a bending of the two arms which brings the 3' acceptor end and the anticodon part closer together, completed by a drastic change of the anticodon loop, which puts the anticodon bases in a more exposed position, facilitating their interaction with the synthetase. The packing interactions in the crystals are also discussed. Finally, the results of protection studies by chemical probes in solution are discussed in view of the RNA-protein contacts observed in the crystals.
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83
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Mörl M, Dörner M, Pääbo S. C to U editing and modifications during the maturation of the mitochondrial tRNA(Asp) in marsupials. Nucleic Acids Res 1995; 23:3380-4. [PMID: 7567446 PMCID: PMC307214 DOI: 10.1093/nar/23.17.3380] [Citation(s) in RCA: 55] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
In marsupial mitochondria, the nucleotide residue at the second position of the anticodon of the tRNA for aspartic acid is changed post-transcriptionally such that the translational machinery recognizes it as a uracil rather than the cytosine residue encoded in the gene. By postlabeling nucleotide analysis, we show here that the cytosine residue is converted to a conventional uracil residue in an RNA editing event that affects approximately half of the tRNA molecules under steady state conditions. Furthermore, we have identified three different tRNA(Asp) species which all carry three pseudouridines and two methylations but have the anticodons GCC, GUC and QUC respectively, the latter representing a rare example of queuine incorporation into a mitochondrial tRNA. This allows us to describe a likely sequential order of modification of the tRNA(Asp), where methylations and conversions of uridines to pseudouridines precede the editing event, while the exchange of guanine by queuine takes place after the C to U editing event.
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84
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Vlassov VV, Zuber G, Felden B, Behr JP, Giegé R. Cleavage of tRNA with imidazole and spermine imidazole constructs: a new approach for probing RNA structure. Nucleic Acids Res 1995; 23:3161-7. [PMID: 7667092 PMCID: PMC307173 DOI: 10.1093/nar/23.16.3161] [Citation(s) in RCA: 72] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Hydrolysis of RNA in imidazole buffer and by spermine-imidazole conjugates has been investigated. The RNA models were yeast tRNA(Asp) and a transcript derived from the 3'-terminal sequence of tobacco mosaic virus RNA representing a minihelix capable of being enzymatically aminoacylated with histidine. Imidazole buffer and spermine-imidazole conjugates in the presence of free imidazole cleave phosphodiester bonds in the folded RNAs in a specific fashion. Imidazole buffer induces cleavages preferentially in single-stranded regions because nucleotides in these regions have more conformational freedom and can assume more easily the geometry needed for formation of the hydrolysis intermediate state. Spermine-imidazole constructs supplemented with free imidazole cleave tRNA(Asp) within single-stranded regions after pyrimidine residues with a marked preference for pyrimidine-A sequences. Hydrolysis patterns suggest a cleavage mechanism involving an attack by the imidazole residue of the electrostatically bound spermine-imidazole and by free imidazole at the most accessible single-stranded regions of the RNA. Cleavages in a viral RNA fragment recapitulating a tRNA-like domain were found in agreement with the model of this molecule that accounts for its functional properties, thus illustrating the potential of the imidazole-derived reagents as structural probes for solution mapping of RNAs. The cleavage reactions are simple to perform, provide information reflecting the state of the ribose-phosphate backbone of RNA and can be used for mapping single- and double-stranded regions in RNAs.
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MESH Headings
- Base Sequence
- Binding Sites
- Buffers
- Hydrolysis
- Imidazoles
- Molecular Probes
- Molecular Sequence Data
- Molecular Structure
- Nucleic Acid Conformation
- RNA, Fungal/chemistry
- RNA, Fungal/genetics
- RNA, Fungal/metabolism
- RNA, Transfer, Asp/chemistry
- RNA, Transfer, Asp/genetics
- RNA, Transfer, Asp/metabolism
- RNA, Viral/chemistry
- RNA, Viral/genetics
- RNA, Viral/metabolism
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae/metabolism
- Spermine
- Tobacco Mosaic Virus/genetics
- Tobacco Mosaic Virus/metabolism
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85
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Eriani G, Cavarelli J, Martin F, Ador L, Rees B, Thierry JC, Gangloff J, Moras D. The class II aminoacyl-tRNA synthetases and their active site: evolutionary conservation of an ATP binding site. J Mol Evol 1995; 40:499-508. [PMID: 7783225 DOI: 10.1007/bf00166618] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Previous sequence analyses have suggested the existence of two distinct classes of aminoacyl-tRNA synthetase. The partition was established on the basis of exclusive sets of sequence motifs (Eriani et al. [1990] Nature 347:203-306). X-ray studies have now well defined the structural basis of the two classes: the class I enzymes share with dehydrogenases and kinases the classic nucleotide binding fold called the Rossmann fold, whereas the class II enzymes possess a different fold, not found elsewhere, built around a six-stranded antiparallel beta-sheet. The two classes of synthetases catalyze the same global reaction that is the attachment of an amino acid to the tRNA, but differ as to where on the terminal adenosine of the tRNA the amino acid is placed: class I enzymes act on the 2' hydroxyl whereas the class II enzymes prefer the 3' hydroxyl group. The three-dimensional structure of aspartyl-tRNA synthetase from yeast, a typical class II enzyme, is described here, in relation to its function. The crucial role of the sequence motifs in substrate binding and enzyme structure is high-lighted. Overall these results underline the existence of an intimate evolutionary link between the aminoacyl-tRNA synthetases, despite their actual structural diversity.
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86
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Mueller SO, Slany RK. Structural analysis of the interaction of the tRNA modifying enzymes Tgt and QueA with a substrate tRNA. FEBS Lett 1995; 361:259-64. [PMID: 7698334 DOI: 10.1016/0014-5793(95)00169-a] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The enzymes tRNA guanine-transglycosylase (Tgt) and S-adenosylmethionine :tRNA ribosyltransferase-isomerase (QueA) participate in the biosynthesis of the hypermodified tRNA nucleoside queuosine (Q) in Escherichia coli. Here we show by HPLC analysis and gel retardation that both enzymes interact with an in vitro transcribed tRNA(ASP) from yeast, specifically modified with a Q precursor molecule. RNase I footprinting experiments showed strong protein tRNA contacts in the anticodon stem-loop and a minor interaction with the dihydrouridine loop. This suggests that all identity elements for the recognition of Q-specific tRNAs are clustered in the anticodon region and explains earlier results that both enzymes accept a RNA microhelix with the sequence of an anticodon stem-loop as substrate.
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87
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Tsunoda M, Takenaka A, Cavarelli J, Rees B, Thierry JC, Moras D. Electrostatic potential in aminoacylation by aspartyl-tRNAs synthetase. NUCLEIC ACIDS SYMPOSIUM SERIES 1995:65-66. [PMID: 8841554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Based upon the X-ray structures of complexes between tRNAAsp and aspRS including ATP or Asp-AMP, several electrostatic potentials were calculated by solving the Poisson-Boltzmann equation. The potentials indicate clearly that a Mg2+ ion is essential for binding of ATP and that aspartate is identified electrostatically. The alpha-carboxyl group is forced to contact with the alpha-phosphorus atom of ATP, suggesting its inversion to form an Asp-AMP. When the cognate tRNA is bound to the aspRS:Asp-AMP complex, the 3'-hydroxyl group is located in an electrostatically favorable position to transfer the amino acid as a class II aminoacylation.
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88
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Puttaraju M, Beebe JA, Niranjanakumari S, Been MD, Fierke CA. Generation and characterization of circular Bacillus subtilis RNase P RNA; activation by RNase P protein. NUCLEIC ACIDS SYMPOSIUM SERIES 1995:92-94. [PMID: 8643411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
A circular form of Bacillus subtilis ribonuclease P RNA (C-P RNA) was generated in vitro by splicing permuted intron-exon (PIE) sequences containing the P RNA sequence. Steady-state cleavage of pre-tRNA(Asp) catalyzed by circular P RNA is slightly faster than the linear form. Furthermore, steady-state turnover catalyzed by circular RNase P RNA is activated by the addition of the Bacillus subtilis protein component of RNase P, to a rate constant equal to the linear holoenzyme under identical conditions. Also, the circles are resistant to nuclease degradation, have less sequence heterogeneity, and may enhance the formation of a unique structure. Therefore, circular forms of RNase P RNA should prove useful for mutagenesis and structural studies.
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89
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Abstract
Two new enzymatic probes have been used for structural investigations of native and unmodified transcript tRNA molecules. Both probes were single-strand-specific nucleases isolated from higher plants. The results obtained after enzymatic hydrolysis of tRNAs support the earlier hypothesis that posttranscriptional modifications in tRNA help to stabilize its structure and make it more rigid.
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MESH Headings
- Base Sequence
- Fungi/chemistry
- Molecular Sequence Data
- Nucleic Acid Conformation
- Plants/enzymology
- RNA Processing, Post-Transcriptional
- RNA, Transfer/chemistry
- RNA, Transfer/metabolism
- RNA, Transfer, Asp/chemistry
- RNA, Transfer, Asp/metabolism
- RNA, Transfer, Phe/chemistry
- RNA, Transfer, Phe/metabolism
- Ribonucleosides/chemistry
- Single-Strand Specific DNA and RNA Endonucleases/metabolism
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90
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Poterszman A, Delarue M, Thierry JC, Moras D. Synthesis and recognition of aspartyl-adenylate by Thermus thermophilus aspartyl-tRNA synthetase. J Mol Biol 1994; 244:158-67. [PMID: 7966328 DOI: 10.1006/jmbi.1994.1716] [Citation(s) in RCA: 54] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The crystal structures of Thermus thermophilus aspartyl-tRNA synthetase and of its complex with ATP, Mg2+ and aspartic acid, show in situ formation of the amino acid adenylate and furnish experimental evidence for the modes of recognition of aspartic acid and ATP. The amino acid fits in a predefined specific site in which it replaces water molecules without significant conformational changes of the binding residues. This mode of selection is reminiscent of the lock and key concept. The pocket is closed by the movement of a histidine side chain from a neighbouring loop acting as a valve. ATP binding is driven by the stacking of the adenine upon the otherwise fixed aromatic ring of the class-II-invariant phenylalanine Phe235. Specific recognition is achieved by interactions with the flexible side chains of other class-II-conserved residues. Conformational changes have been identified which allow the description of a reaction pathway including both lock-and-key and induced-fit interactions. This pathway can presumably be extended to all class II aaRS.
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91
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LaGrandeur TE, Hüttenhofer A, Noller HF, Pace NR. Phylogenetic comparative chemical footprint analysis of the interaction between ribonuclease P RNA and tRNA. EMBO J 1994; 13:3945-52. [PMID: 7521296 PMCID: PMC395314 DOI: 10.1002/j.1460-2075.1994.tb06710.x] [Citation(s) in RCA: 72] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Ribonuclease P RNA is the catalytic moiety of the ribonucleoprotein enzyme that endonucleolytically cleaves precursor sequences from the 5' ends of pre-tRNAs. The bacterial RNase P RNA-tRNA complex was examined with a footprinting approach, utilizing chemical modification to determine RNase P RNA nucleotides that potentially contact tRNA. RNase P RNA was modified with dimethylsulfate or kethoxal in the presence or absence of tRNA, and sites of modification were detected by primer extension. Comparison of the results reveals RNase P bases that are protected from modification upon binding tRNA. Analyses were carried out with RNase P RNAs from three different bacteria: Escherichia coli, Chromatium vinosum and Bacillus subtilis. Discrete bases of these RNAs that lie within conserved, homologous portions of the secondary structures are similarly protected. One protection among all three RNAs was attributed to the precursor segment of pre-tRNA. Experiments using pre-tRNAs containing precursor segments of variable length demonstrate that a precursor segment of only 2-4 nucleotides is sufficient to confer this protection. Deletion of the 3'-terminal CCA sequence of tRNA correlates with loss of protection of a particular loop in the RNase P RNA secondary structure. Analysis of mutant tRNAs containing sequential 3'-terminal deletions suggests a relative orientation of the bound tRNA CCA to that loop.
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MESH Headings
- Bacillus subtilis/chemistry
- Bacillus subtilis/metabolism
- Base Sequence
- Binding Sites
- Chromatium/chemistry
- Chromatium/metabolism
- DNA Mutational Analysis
- DNA Primers/metabolism
- Endoribonucleases/chemistry
- Endoribonucleases/metabolism
- Escherichia coli/chemistry
- Escherichia coli/metabolism
- Escherichia coli Proteins
- Macromolecular Substances
- Models, Molecular
- Molecular Sequence Data
- Phylogeny
- RNA Processing, Post-Transcriptional
- RNA, Bacterial/chemistry
- RNA, Bacterial/metabolism
- RNA, Catalytic/chemistry
- RNA, Catalytic/metabolism
- RNA, Transfer, Asp/chemistry
- RNA, Transfer, Asp/genetics
- RNA, Transfer, Asp/metabolism
- Ribonuclease P
- Species Specificity
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92
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Pütz J, Florentz C, Benseler F, Giegé R. A single methyl group prevents the mischarging of a tRNA. NATURE STRUCTURAL BIOLOGY 1994; 1:580-2. [PMID: 7634096 DOI: 10.1038/nsb0994-580] [Citation(s) in RCA: 98] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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93
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Beebe JA, Fierke CA. A kinetic mechanism for cleavage of precursor tRNA(Asp) catalyzed by the RNA component of Bacillus subtilis ribonuclease P. Biochemistry 1994; 33:10294-304. [PMID: 7520753 DOI: 10.1021/bi00200a009] [Citation(s) in RCA: 108] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
A kinetic mechanism is presented for the cleavage of Bacillus subtilis precursor tRNA(Asp) catalyzed by the RNA component of B. subtilis ribonuclease P (RNase P) under optimal conditions (50 mM Tris Cl (pH 8.0), 100 mM MgCl2, and 800 mM NH4Cl, 37 degrees C). This kinetic mechanism was derived from measuring pre-steady-state, steady-state, single-turnover, and binding kinetics using a combination of quench-flow, gel filtration, and gel shift techniques. A minimal kinetic description involves the following: (1) binding of pre-tRNA(Asp) to RNase P RNA rapidly (6.3 x 10(6) M-1 s-1), but slower than the diffusion-controlled limit; (2) cleavage of the phosphodiester bond with a rate constant of 6 s-1; (3) dissociation of products in a kinetically preferred pathway, with the 5' RNA fragment dissociating first (> or = 0.2 s-1) followed by rate-limiting tRNA dissociation (0.02 s-1); and (4) formation of a second conformer of RNase P RNA during the catalytic cycle that is less stable and binds pre-tRNA(Asp) significantly more slowly (7 x 10(4) M-1 s-1). This scheme involves the isolation of individual steps in the reaction sequence, is consistent with steady-state data, and pinpoints the rate-determining step under a variety of conditions. This kinetic mechanism will facilitate a more accurate definition of the role of metals, pH, and the protein component in each step of the reaction and provide an essential background for understanding the influence of structural changes on the catalytic activity.
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94
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Frugier M, Söll D, Giegé R, Florentz C. Identity switches between tRNAs aminoacylated by class I glutaminyl- and class II aspartyl-tRNA synthetases. Biochemistry 1994; 33:9912-21. [PMID: 8060999 DOI: 10.1021/bi00199a013] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
High-resolution X-ray structures for the tRNA/aminoacyl-tRNA synthetase complexes between Escherichia coli tRNAGln/GlnRS and yeast tRNAAsp/AspRS have been determined. Positive identity nucleotides that direct aminoacylation specificity have been defined in both cases; E. coli tRNAGln identity is governed by 10 elements scattered in the tRNA structure, while specific aminoacylation of yeast tRNAAsp is dependent on 5 positions. Both identity sets are partially overlapping and share 3 nucleotides. Interestingly, the two enzymes belong to two different classes described for aminoacyl-tRNA synthetases. The class I glutaminyl-tRNA synthetase and the class II aspartyl-tRNA synthetase recognize their cognate tRNA from opposite sides. Mutants derived from glutamine and aspartate tRNAs have been created by progressively introducing identity elements from one tRNA into the other one. Glutaminylation and aspartylation assays of the transplanted tRNAs show that identity nucleotides from a tRNA originally aminoacylated by a synthetase from one class are still recognized if they are presented to the enzyme in a structural framework corresponding to a tRNA aminoacylated by a synthetase belonging to the other class. The simple transplantation of the glutamine identity set into tRNAAsp is sufficient to obtain glutaminylatable tRNA, but additional subtle features seem to be important for the complete conversion of tRNAGln in an aspartylatable substrate. This study defines C38 in yeast tRNAAsp as a new identity nucleotide for aspartylation. We show also in this paper that, during the complex formation, aminoacyl-tRNA synthetases are at least partially responsible for conformational changes which involve structural constraints in tRNA molecules.
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95
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Edqvist J, Blomqvist K, Stråby KB. Structural elements in yeast tRNAs required for homologous modification of guanosine-26 into dimethylguanosine-26 by the yeast Trm1 tRNA-modifying enzyme. Biochemistry 1994; 33:9546-51. [PMID: 8068629 DOI: 10.1021/bi00198a021] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
In eukaryotic tRNAs, guanosines in position 26 (G26), located at the junction between the D-stem and the anticodon stem of tRNA, are usually modified to N2,N2-dimethylguanosine (m2(2)G). Although G26 is a prerequisite for biosynthesis of m2(2)G26, it is not self-sufficient for the formation of the dimethylated G26, since in exceptional cases eukaryotic tRNAs have an unmodified G26. In the yeast Saccharomyces cerevisiae the only tRNA species with an unmodified G26 is tRNAAsp. Using in vitro transcripts of this tRNA, as well as of yeast tRNAPhe, a tRNA containing m2(2)G26 in vivo, we have investigated the requirements on tRNA sequences and structures for the formation of m2(2)G26 by the yeast enzyme, i.e. in a homologous in vitro system. We have now demonstrated that G26 was efficiently dimethylated in vitro also after deletion of the entire anticodon stem and loop. We conclude that the elements necessary for a productive interaction between G26 in nuclear coded yeast tRNAs and the yeast G26 modifying enzyme are located within the core of the tRNA. For modification of G26 to m2(2)G26 via monomethylated G26, important primary and secondary structural elements in the tRNAs are a size of at least five nucleotides in the variable loop together with two G-C base pairs in the D-stem. This is the first case reported where the minimal requirements on nuclear coded tRNAs for a yeast modifying enzyme has been elucidated.
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MESH Headings
- Base Sequence
- Genes, Synthetic
- Guanosine/analogs & derivatives
- Guanosine/biosynthesis
- Guanosine/metabolism
- Molecular Sequence Data
- Mutagenesis, Site-Directed
- Nucleic Acid Conformation
- RNA Processing, Post-Transcriptional
- RNA, Transfer/genetics
- RNA, Transfer/metabolism
- RNA, Transfer, Asp/genetics
- RNA, Transfer, Asp/metabolism
- RNA, Transfer, Phe/genetics
- RNA, Transfer, Phe/metabolism
- Saccharomyces cerevisiae/enzymology
- Sequence Homology, Nucleic Acid
- Substrate Specificity
- Transcription, Genetic
- tRNA Methyltransferases/genetics
- tRNA Methyltransferases/metabolism
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96
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Rudinger J, Blechschmidt B, Ribeiro S, Sprinzl M. Minimalist aminoacylated RNAs as efficient substrates for elongation factor Tu. Biochemistry 1994; 33:5682-8. [PMID: 8180193 DOI: 10.1021/bi00185a003] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
We demonstrate here, using RNA variants derived from tRNAAsp, that the minimalist aminoacylated structure able to interact efficiently with elongation factor Tu comprises a 10 base-pair helix linked to the 3'-terminal NCCA sequence. Shorter structures can interact with the elongation factor, but with significantly decreased affinity. Conserved features in the aminoacyl acceptor branch of tRNAs, such as base pair G53-C61 and the T-loop architecture, could be replaced respectively by the inverted base pair C53-G61 and by unusual anticodon loop or tetraloop sequences. Variants of whole tRNAAsp or of the 12 base-pair aspartate minihelix, with enlarged 13 base-pair long aminoacyl acceptor branches, as in selenocysteine-inserting tRNAs that are not recognized by elongation factor Tu, keep their binding ability to this factor. These functional results are well accounted for by the crystallographic structure of the Thermus thermophilus binary EF-Tu.GTP complex, which possesses a binding cleft accommodating the minimalist 10 base-pair domain of the tRNA aminoacyl acceptor branch.
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97
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Rinaldi T, Francisci S, Zennaro E, Frontali L, Bolotin-Fukuhara M. Suppression of a mitochondrial point mutation in a tRNA gene can cast light on the mechanisms of 3' end-processing. Curr Genet 1994; 25:451-5. [PMID: 7521797 DOI: 10.1007/bf00351785] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
We used a genetic approach to study the nuclear factors involved in the biogenesis of mitochondrial tRNAs. A point mutation in the mitochondrial tRNA(Asp) gene of Saccharomyces cerevisiae had previously been shown to result in a temperature-sensitive respiratory-deficient phenotype as a result of the absence of 3' end-processing of the tRNA(Asp). Analysis of mitochondrial revertants has shown that all revertants sequenced have a G-A compensatory change at position 53, which restores the hydrogen-bond with the mutated nucleotide. We then searched for nuclear suppressors to identify the nuclear gene(s) involved in mitochondrial tRNA 3' end-processing. One such suppressor mutation was further characterized: it restores tRNA(Asp) maturation and growth at 36 degrees C on glycerol medium in heterozygous diploids, but leads to a defective growth phenotype in haploids.
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MESH Headings
- Base Sequence
- Diploidy
- Genes, Fungal
- Molecular Sequence Data
- Nucleic Acid Conformation
- Phenotype
- Point Mutation
- RNA/chemistry
- RNA/genetics
- RNA/metabolism
- RNA Processing, Post-Transcriptional
- RNA, Fungal/chemistry
- RNA, Fungal/genetics
- RNA, Fungal/metabolism
- RNA, Mitochondrial
- RNA, Transfer, Asp/chemistry
- RNA, Transfer, Asp/genetics
- RNA, Transfer, Asp/metabolism
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae/metabolism
- Suppression, Genetic
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98
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Chen YL, Wu RT. Altered queuine modification of transfer RNA involved in the differentiation of human K562 erythroleukemia cells in the presence of distinct differentiation inducers. Cancer Res 1994; 54:2192-8. [PMID: 7513611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Altered queuine modification of tRNA has been correlated to neoplasia and cell differentiation, but much of the existing evidence is only circumstantial. In the present study, we used several distinct differentiation inducers to measure changes in Q-family tRNA species during the erythroid differentiation of human K562 erythroleukemia cells. Treatment of K562 cells with 3.6 microM 1-beta-D-arabinofuranosylcytosine (ara-C), 1 mM sodium butyrate, 0.1 mM hemin, or 5 microM 5-azacytidine resulted in growth inhibition, erythroid differentiation, and changes in queuine content of tRNA. In the presence of the irreversible inducer ara-C, the queuine content of tRNA increased markedly when the cells differentiated into benzidine-positive erythroid cells, and cell growth was inhibited. The increase in the queuine content of tRNA in differentiated K562 cells was an irreversible event. In cells incubated with the reversible inducer sodium butyrate, an increase in the queuine content of tRNA was correlated with the increase in benzidine-positive erythroid cells throughout the culturing period. After removal of the drug at 48 h, the queuine content of tRNA decreased concomitant with a decrease in benzidine-positive cells. Treatment with another reversible inducer, hemin, caused only a transient increase in the queuine content of tRNA, which was not correlated with the steady increase in benzidine-positive erythroid cells. The agent 5-azacytidine slightly inhibited cell growth but did not significantly change the percentage of benzidine-positive cells and the queuine content of tRNA. We further clarified the changes in queuine content of tRNA by analyzing the Q-containing isoacceptors of Q-family tRNA species including tRNA(Tyr), tRNA(His), tRNA(Asp), and tRNA(Asn) by RPC-5 chromatography, and found that the change in queuine content of tRNA(Tyr) was greater than the other Q-family tRNA species during induction by ara-C, sodium butyrate, and hemin. Our results indicate that the change in queuine content of tRNA is an irreversible event of terminal differentiation in ara-C induction and is a transient event of reversible differentiation in hemin induction. Sodium butyrate induction might represent a status between irreversible and reversible differentiation. Q-containing isoacceptors of tRNA might potentially play an important biological role during K562 cell differentiation.
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MESH Headings
- Aspartate-tRNA Ligase
- Azacitidine/pharmacology
- Butyrates/pharmacology
- Butyric Acid
- Cell Differentiation/drug effects
- Cell Division/drug effects
- Cell Line
- Cytarabine/pharmacology
- Guanine/analogs & derivatives
- Guanine/analysis
- Guanine/metabolism
- Hemin/pharmacology
- Humans
- Kinetics
- Leukemia, Erythroblastic, Acute
- RNA, Transfer, Amino Acyl/chemistry
- RNA, Transfer, Amino Acyl/metabolism
- RNA, Transfer, Asp/metabolism
- RNA, Transfer, His/metabolism
- RNA, Transfer, Tyr/metabolism
- Time Factors
- Tumor Cells, Cultured
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99
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Podyminogin MA, Vlassov VV, Giegé R. Synthetic RNA-cleaving molecules mimicking ribonuclease A active center. Design and cleavage of tRNA transcripts. Nucleic Acids Res 1993; 21:5950-6. [PMID: 7507235 PMCID: PMC310480 DOI: 10.1093/nar/21.25.5950] [Citation(s) in RCA: 60] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
RNA cleaving molecules were synthesized by conjugating imidazole residues imitating the essential imidazoles in the active center of pancreatic ribonuclease to an intercalating compound, derivative of phenazine capable of binding to the double stranded regions of polynucleotides. Action of the molecules on tRNA was investigated. It was found, that some of the compounds bearing two imidazole residues cleave tRNA under physiological conditions. The cleavage reaction shows a bell-shaped pH dependence with a maximum at pH 7.0 indicating participation of protonated and non-protonated imidazole residues in the process. Under the conditions stabilizing the tRNA structure, a tRNAAsp transcript was cleaved preferentially at the junctions of the stem and loop regions of the cloverleaf tRNA fold, at the five positions C56, C43, C20.1, U13, and U8, with a marked preference for C56. This cleavage pattern is consistent with a hydrolysis mechanism involving non-covalent binding of the compounds to the double-stranded regions of tRNA followed by an attack of the imidazole residues at the juxtaposed flexible single-stranded regions of the molecule. The compounds provide new probes for the investigation of RNA structure in solution and potential reactive groups for antisense oligonucleotide derivatives.
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100
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Frugier M, Florentz C, Schimmel P, Giegé R. Triple aminoacylation specificity of a chimerized transfer RNA. Biochemistry 1993; 32:14053-61. [PMID: 8268184 DOI: 10.1021/bi00213a039] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
We report here the rational design and construction of a chimerized transfer RNA with tripartite aminoacylation specificity. A yeast aspartic acid specific tRNA was transformed into a highly efficient acceptor of alanine and phenylalanine and a moderate acceptor of valine. The transformation was guided by available knowledge of the requirements for aminoacylation by each of the three amino acids and was achieved by iterative changes in the local sequence context and the structural framework of the variable loop and the two variable regions of the dihydrouridine loop. The changes introduced to confer efficient acceptance of the three amino acids eliminate aminoacylation with aspartate. The interplay of determinants and antideterminants for different specific aminoacylations, and the constraints imposed by the structural framework, suggest that a tRNA with an appreciable capacity for more than three efficient aminoacylations may be inherently difficult to achieve.
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