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1.
Nucleic Acids Res ; 46(17): 9081-9093, 2018 09 28.
Article in English | MEDLINE | ID: mdl-29893896

ABSTRACT

We have previously shown that 5' halves from tRNAGlyGCC and tRNAGluCUC are the most enriched small RNAs in the extracellular space of human cell lines, and especially in the non-vesicular fraction. Extracellular RNAs are believed to require protection by either encapsulation in vesicles or ribonucleoprotein complex formation. However, deproteinization of non-vesicular tRNA halves does not affect their retention in size-exclusion chromatography. Thus, we considered alternative explanations for their extracellular stability. In-silico analysis of the sequence of these tRNA-derived fragments showed that tRNAGly 5' halves can form homodimers or heterodimers with tRNAGlu 5' halves. This capacity is virtually unique to glycine tRNAs. By analyzing synthetic oligonucleotides by size exclusion chromatography, we provide evidence that dimerization is possible in vitro. tRNA halves with single point substitutions preventing dimerization are degraded faster both in controlled nuclease digestion assays and after transfection in cells, showing that dimerization can stabilize tRNA halves against the action of cellular nucleases. Finally, we give evidence supporting dimerization of endogenous tRNAGlyGCC 5' halves inside cells. Considering recent reports have shown that 5' tRNA halves from Ala and Cys can form tetramers, our results highlight RNA intermolecular structures as a new layer of complexity in the biology of tRNA-derived fragments.


Subject(s)
Dimerization , RNA Stability , RNA, Transfer, Glu/metabolism , RNA, Transfer, Gly/metabolism , Ribonucleases/metabolism , 5' Flanking Region , Base Sequence , Glutamic Acid/metabolism , Glycine/metabolism , Humans , MCF-7 Cells , Nucleic Acid Conformation , RNA, Transfer, Glu/chemistry , RNA, Transfer, Gly/chemistry
2.
Nucleic Acids Res ; 45(22): 12601-12610, 2017 Dec 15.
Article in English | MEDLINE | ID: mdl-29155943

ABSTRACT

A bacterial translation factor EF-P alleviates ribosomal stalling caused by polyproline sequence by accelerating Pro-Pro formation. EF-P recognizes a specific D-arm motif found in tRNAPro isoacceptors, 9-nt D-loop closed by a stable D-stem sequence, for Pro-selective peptidyl-transfer acceleration. It is also known that the T-stem sequence on aminoacyl-tRNAs modulates strength of the interaction with EF-Tu, giving enhanced incorporation of non-proteinogenic amino acids such as some N-methyl amino acids. Based on the above knowledge, we logically engineered tRNA's D-arm and T-stem sequences to investigate a series of tRNAs for the improvement of consecutive incorporation of d-amino acids and an α, α-disubstituted amino acid. We have devised a chimera of tRNAPro1 and tRNAGluE2, referred to as tRNAPro1E2, in which T-stem of tRNAGluE2 was engineered into tRNAPro1. The combination of EF-P with tRNAPro1E2NNN pre-charged with d-Phe, d-Ser, d-Ala, and/or d-Cys has drastically enhanced expression level of not only linear peptides but also a thioether-macrocyclic peptide consisting of the four consecutive d-amino acids over the previous method using orthogonal tRNAs.


Subject(s)
Amino Acids/genetics , DNA, Recombinant/genetics , RNA, Transfer, Amino Acyl/genetics , RNA, Transfer/genetics , Amino Acid Sequence , Amino Acids/metabolism , Base Sequence , Nucleic Acid Conformation , Peptide Elongation Factor Tu/metabolism , Peptide Elongation Factors/metabolism , Protein Binding , RNA, Transfer/chemistry , RNA, Transfer/metabolism , RNA, Transfer, Amino Acyl/metabolism , RNA, Transfer, Glu/chemistry , RNA, Transfer, Glu/genetics , RNA, Transfer, Glu/metabolism , RNA, Transfer, Pro/chemistry , RNA, Transfer, Pro/genetics , RNA, Transfer, Pro/metabolism
3.
RNA ; 22(3): 467-76, 2016 Mar.
Article in English | MEDLINE | ID: mdl-26729921

ABSTRACT

In mammalian cells under oxidative stress, the methionyl-tRNA synthetase (MetRS) misacylates noncognate tRNAs at frequencies as high as 10% distributed among up to 28 tRNA species. Instead of being detrimental for the cell, misincorporation of methionine residues in the proteome reduces the risk of oxidative damage to proteins, which aids the oxidative stress response. tRNA microarrays have been essential for the detection of the full pattern of misacylated tRNAs, but have limited capacity to investigate the misacylation and mistranslation mechanisms in live cells. Here we develop a dual-fluorescence reporter to specifically measure methionine misincorporation at glutamic acid codons GAA and GAG via tRNA(Glu) mismethionylation in human cells. Our method relies on mutating a specific Met codon in the active site of the fluorescent protein mCherry to a Glu codon that renders mCherry nonfluorescent when translation follows the genetic code. Mistranslation utilizing mismethionylated tRNA(Glu) restores fluorescence in proportion to the amount of misacylated tRNA(Glu). This cellular approach works well for both transient transfection and established stable HEK293 lines. It is rapid, straightforward, and well suited for high-throughput activity analysis under a wide range of physiological conditions. As a proof of concept, we apply this method to characterize the effect of human tRNA(Glu) isodecoders on mistranslation and discuss the implications of our findings.


Subject(s)
Fluorescent Dyes , Methionine/genetics , Protein Biosynthesis , Base Sequence , Humans , Molecular Sequence Data , Nucleic Acid Conformation , RNA, Transfer, Glu/chemistry , RNA, Transfer, Glu/genetics
4.
Nature ; 467(7315): 612-6, 2010 Sep 30.
Article in English | MEDLINE | ID: mdl-20882017

ABSTRACT

In most bacteria and all archaea, glutamyl-tRNA synthetase (GluRS) glutamylates both tRNA(Glu) and tRNA(Gln), and then Glu-tRNA(Gln) is selectively converted to Gln-tRNA(Gln) by a tRNA-dependent amidotransferase. The mechanisms by which the two enzymes recognize their substrate tRNA(s), and how they cooperate with each other in Gln-tRNA(Gln) synthesis, remain to be determined. Here we report the formation of the 'glutamine transamidosome' from the bacterium Thermotoga maritima, consisting of tRNA(Gln), GluRS and the heterotrimeric amidotransferase GatCAB, and its crystal structure at 3.35 A resolution. The anticodon-binding body of GluRS recognizes the common features of tRNA(Gln) and tRNA(Glu), whereas the tail body of GatCAB recognizes the outer corner of the L-shaped tRNA(Gln) in a tRNA(Gln)-specific manner. GluRS is in the productive form, as its catalytic body binds to the amino-acid-acceptor arm of tRNA(Gln). In contrast, GatCAB is in the non-productive form: the catalytic body of GatCAB contacts that of GluRS and is located near the acceptor stem of tRNA(Gln), in an appropriate site to wait for the completion of Glu-tRNA(Gln) formation by GluRS. We identified the hinges between the catalytic and anticodon-binding bodies of GluRS and between the catalytic and tail bodies of GatCAB, which allow both GluRS and GatCAB to adopt the productive and non-productive forms. The catalytic bodies of the two enzymes compete for the acceptor arm of tRNA(Gln) and therefore cannot assume their productive forms simultaneously. The transition from the present glutamylation state, with the productive GluRS and the non-productive GatCAB, to the putative amidation state, with the non-productive GluRS and the productive GatCAB, requires an intermediate state with the two enzymes in their non-productive forms, for steric reasons. The proposed mechanism explains how the transamidosome efficiently performs the two consecutive steps of Gln-tRNA(Gln) formation, with a low risk of releasing the unstable intermediate Glu-tRNA(Gln).


Subject(s)
Glutamate-tRNA Ligase/chemistry , Glutamate-tRNA Ligase/metabolism , Nitrogenous Group Transferases/chemistry , Nitrogenous Group Transferases/metabolism , RNA, Transfer, Gln/chemistry , RNA, Transfer, Gln/metabolism , Thermotoga maritima/enzymology , Anticodon/genetics , Biocatalysis , Crystallography, X-Ray , Electrophoretic Mobility Shift Assay , Models, Molecular , Molecular Conformation , Protein Binding , RNA, Transfer, Gln/biosynthesis , RNA, Transfer, Glu/chemistry , RNA, Transfer, Glu/metabolism , Staphylococcus aureus/enzymology , Substrate Specificity
5.
Nucleic Acids Res ; 42(10): 6487-96, 2014 Jun.
Article in English | MEDLINE | ID: mdl-24711368

ABSTRACT

Dnmt2 enzymes are conserved in eukaryotes, where they methylate C38 of tRNA-Asp with high activity. Here, the activity of one of the very few prokaryotic Dnmt2 homologs from Geobacter species (GsDnmt2) was investigated. GsDnmt2 was observed to methylate tRNA-Asp from flies and mice. Unexpectedly, it had only a weak activity toward its matching Geobacter tRNA-Asp, but methylated Geobacter tRNA-Glu with good activity. In agreement with this result, we show that tRNA-Glu is methylated in Geobacter while the methylation is absent in tRNA-Asp. The activities of Dnmt2 enzymes from Homo sapiens, Drosophila melanogaster, Schizosaccharomyces pombe and Dictyostelium discoideum for methylation of the Geobacter tRNA-Asp and tRNA-Glu were determined showing that all these Dnmt2s preferentially methylate tRNA-Asp. Hence, the GsDnmt2 enzyme has a swapped transfer ribonucleic acid (tRNA) specificity. By comparing the different tRNAs, a characteristic sequence pattern was identified in the variable loop of all preferred tRNA substrates. An exchange of two nucleotides in the variable loop of murine tRNA-Asp converted it to the corresponding variable loop of tRNA-Glu and led to a strong reduction of GsDnmt2 activity. Interestingly, the same loss of activity was observed with human DNMT2, indicating that the variable loop functions as a specificity determinant in tRNA recognition of Dnmt2 enzymes.


Subject(s)
Bacterial Proteins/metabolism , Geobacter/enzymology , RNA, Transfer, Glu/metabolism , tRNA Methyltransferases/metabolism , Animals , Humans , Methylation , Mice , Nucleic Acid Conformation , RNA, Transfer, Asp/chemistry , RNA, Transfer, Asp/metabolism , RNA, Transfer, Glu/chemistry , Substrate Specificity
6.
Proc Natl Acad Sci U S A ; 110(31): 12756-61, 2013 Jul 30.
Article in English | MEDLINE | ID: mdl-23858450

ABSTRACT

T-box riboswitches control transcription of downstream genes through the tRNA-binding formation of terminator or antiterminator structures. Previously reported T-boxes were described as single-specificity riboswitches that can bind specific tRNA anticodons through codon-anticodon interactions with the nucleotide triplet of their specifier loop (SL). However, the possibility that T-boxes might exhibit specificity beyond a single tRNA had been overlooked. In Clostridium acetobutylicum, the T-box that regulates the operon for the essential tRNA-dependent transamidation pathway harbors a SL with two potential overlapping codon positions for tRNA(Asn) and tRNA(Glu). To test its specificity, we performed extensive mutagenic, biochemical, and chemical probing analyses. Surprisingly, both tRNAs can efficiently bind the SL in vitro and in vivo. The dual specificity of the T-box is allowed by a single base shift on the SL from one overlapping codon to the next. This feature allows the riboswitch to sense two tRNAs and balance the biosynthesis of two amino acids. Detailed genomic comparisons support our observations and suggest that "flexible" T-box riboswitches are widespread among bacteria, and, moreover, their specificity is dictated by the metabolic interconnection of the pathways under control. Taken together, our results support the notion of a genome-dependent codon ambiguity of the SLs. Furthermore, the existence of two overlapping codons imposes a unique example of tRNA-dependent regulation at the transcriptional level.


Subject(s)
Anticodon/metabolism , Clostridium acetobutylicum/metabolism , RNA, Bacterial/metabolism , RNA, Transfer, Asn/metabolism , RNA, Transfer, Glu/metabolism , Riboswitch/physiology , Anticodon/chemistry , Anticodon/genetics , Asparagine/biosynthesis , Asparagine/genetics , Clostridium acetobutylicum/chemistry , Clostridium acetobutylicum/genetics , Glutamic Acid/biosynthesis , Glutamic Acid/genetics , RNA, Bacterial/chemistry , RNA, Bacterial/genetics , RNA, Transfer, Asn/chemistry , RNA, Transfer, Asn/genetics , RNA, Transfer, Glu/chemistry , RNA, Transfer, Glu/genetics
7.
Nucleic Acids Res ; 41(1): 667-76, 2013 Jan 07.
Article in English | MEDLINE | ID: mdl-23161686

ABSTRACT

In the yeast Saccharomyces cerevisiae, the aminoacyl-tRNA synthetases (aaRS) GluRS and MetRS form a complex with the auxiliary protein cofactor Arc1p. The latter binds the N-terminal domains of both synthetases increasing their affinity for the transfer-RNA (tRNA) substrates tRNA(Met) and tRNA(Glu). Until now, structural information was available only on the enzymatic domains of the individual aaRSs but not on their complexes with associated cofactors. We have analysed the yeast Arc1p-complexes in solution by small-angle X-ray scattering (SAXS). The ternary complex of MetRS and GluRS with Arc1p, displays a peculiar extended star-like shape, implying possible flexibility of the complex. We reconstituted in vitro a pentameric complex and demonstrated by electrophoretic mobility shift assay that the complex is active and contains tRNA(Met) and tRNA(Glu), in addition to the three protein partners. SAXS reveals that binding of the tRNAs leads to a dramatic compaction of the pentameric complex compared to the ternary one. A hybrid low-resolution model of the pentameric complex is constructed rationalizing the compaction effect by the interactions of negatively charged tRNA backbones with the positively charged tRNA-binding domains of the synthetases.


Subject(s)
Glutamate-tRNA Ligase/chemistry , Methionine-tRNA Ligase/chemistry , RNA, Transfer, Glu/chemistry , RNA, Transfer, Met/chemistry , RNA-Binding Proteins/chemistry , Saccharomyces cerevisiae Proteins/chemistry , Electrophoretic Mobility Shift Assay , Glutamate-tRNA Ligase/metabolism , Methionine-tRNA Ligase/metabolism , Models, Molecular , Protein Structure, Tertiary , RNA, Transfer, Glu/metabolism , RNA, Transfer, Met/metabolism , RNA-Binding Proteins/metabolism , Saccharomyces cerevisiae/enzymology , Saccharomyces cerevisiae Proteins/metabolism , Scattering, Small Angle , X-Ray Diffraction
8.
Nucleic Acids Res ; 39(11): 4818-26, 2011 Jun.
Article in English | MEDLINE | ID: mdl-21306992

ABSTRACT

Transfer RNA (tRNA) contains a number of complex 'hypermodified' nucleosides that are essential for a number of genetic processes. Intermediate forms of these nucleosides are rarely found in tRNA despite the fact that modification is not generally a complete process. We propose that the modification machinery is tuned into an efficient 'assembly line' that performs the modification steps at similar, or sequentially increasing, rates to avoid build-up of possibly deleterious intermediates. To investigate this concept, we measured steady-state kinetics for the final two steps of the biosynthesis of the mnm(5)s(2)U nucleoside in Escherichia coli tRNA(Glu), which are both catalysed by the bifunctional MnmC enzyme. High-performance liquid chromatography-based assays using selectively under-modified tRNA substrates gave a K(m) value of 600 nM and k(cat) 0.34 s(-1) for the first step, and K(m) 70 nM and k(cat) 0.31 s(-1) for the second step. These values show that the second reaction occurs faster than the first reaction, or at a similar rate at very high substrate concentrations. This result indicates that the enzyme is kinetically tuned to produce fully modified mnm(5)(s(2))U while avoiding build-up of the nm(5)(s(2))U intermediate. The assay method developed here represents a general approach for the comparative analysis of tRNA-modifying enzymes.


Subject(s)
Escherichia coli Proteins/metabolism , Multienzyme Complexes/metabolism , RNA, Transfer, Glu/metabolism , Thiouridine/analogs & derivatives , Chromatography, High Pressure Liquid/methods , Kinetics , RNA, Transfer, Glu/chemistry , Thiouridine/metabolism
9.
Nature ; 442(7101): 419-24, 2006 Jul 27.
Article in English | MEDLINE | ID: mdl-16871210

ABSTRACT

Uridine at the first anticodon position (U34) of glutamate, lysine and glutamine transfer RNAs is universally modified by thiouridylase into 2-thiouridine (s2U34), which is crucial for precise translation by restricting codon-anticodon wobble during protein synthesis on the ribosome. However, it remains unclear how the enzyme incorporates reactive sulphur into the correct position of the uridine base. Here we present the crystal structures of the MnmA thiouridylase-tRNA complex in three discrete forms, which provide snapshots of the sequential chemical reactions during RNA sulphuration. On enzyme activation, an alpha-helix overhanging the active site is restructured into an idiosyncratic beta-hairpin-containing loop, which packs the flipped-out U34 deeply into the catalytic pocket and triggers the activation of the catalytic cysteine residues. The adenylated RNA intermediate is trapped. Thus, the active closed-conformation of the complex ensures accurate sulphur incorporation into the activated uridine carbon by forming a catalytic chamber to prevent solvent from accessing the catalytic site. The structures of the complex with glutamate tRNA further reveal how MnmA specifically recognizes its three different tRNA substrates. These findings provide the structural basis for a general mechanism whereby an enzyme incorporates a reactive atom at a precise position in a biological molecule.


Subject(s)
Nucleic Acid Conformation , RNA, Transfer, Glu/chemistry , RNA, Transfer, Glu/metabolism , Sulfur/metabolism , Anticodon , Catalysis , Crystallography, X-Ray , Enzyme Activation , Escherichia coli/enzymology , Escherichia coli Proteins/chemistry , Escherichia coli Proteins/metabolism , Models, Molecular , Protein Conformation , RNA, Transfer, Glu/genetics
10.
Proc Natl Acad Sci U S A ; 106(38): 16209-14, 2009 Sep 22.
Article in English | MEDLINE | ID: mdl-19805282

ABSTRACT

Mammalian mitochondrial (mt) tRNAs, which are required for mitochondrial protein synthesis, are all encoded in the mitochondrial genome, while mt aminoacyl-tRNA synthetases (aaRSs) are encoded in the nuclear genome. However, no mitochondrial homolog of glutaminyl-tRNA synthetase (GlnRS) has been identified in mammalian genomes, implying that Gln-tRNA(Gln) is synthesized via an indirect pathway in the mammalian mitochondria. We demonstrate here that human mt glutamyl-tRNA synthetase (mtGluRS) efficiently misaminoacylates mt tRNA(Gln) to form Glu-tRNA(Gln). In addition, we have identified a human homolog of the Glu-tRNA(Gln) amidotransferase, the hGatCAB heterotrimer. When any of the hGatCAB subunits were inactivated by siRNA-mediated knock down in human cells, the Glu-charged form of tRNA(Gln) accumulated and defects in respiration could be observed. We successfully reconstituted in vitro Gln-tRNA(Gln) formation catalyzed by the recombinant mtGluRS and hGatCAB. The misaminoacylated form of tRNA(Gln) has a weak binding affinity to the mt elongation factor Tu (mtEF-Tu), indicating that the misaminoacylated form of tRNA(Gln) is rejected from the translational apparatus to maintain the accuracy of mitochondrial protein synthesis.


Subject(s)
Amino Acyl-tRNA Synthetases/metabolism , Mitochondria/metabolism , RNA, Transfer, Amino Acyl/biosynthesis , RNA, Transfer, Gln/biosynthesis , Amino Acid Sequence , Amino Acyl-tRNA Synthetases/genetics , Animals , Blotting, Northern , Cattle , Glutamate-tRNA Ligase/genetics , Glutamate-tRNA Ligase/metabolism , Green Fluorescent Proteins/genetics , Green Fluorescent Proteins/metabolism , HeLa Cells , Humans , Kinetics , Microscopy, Fluorescence , Molecular Sequence Data , Nitrogenous Group Transferases/genetics , Nitrogenous Group Transferases/metabolism , Nucleic Acid Conformation , Protein Subunits/genetics , Protein Subunits/metabolism , RNA Interference , RNA, Transfer, Amino Acyl/chemistry , RNA, Transfer, Gln/chemistry , RNA, Transfer, Glu/biosynthesis , RNA, Transfer, Glu/chemistry , Recombinant Fusion Proteins/genetics , Recombinant Fusion Proteins/metabolism , Sequence Homology, Amino Acid , Transfection , Transfer RNA Aminoacylation
11.
Nucleic Acids Res ; 36(4): 1072-80, 2008 Mar.
Article in English | MEDLINE | ID: mdl-18096622

ABSTRACT

Kluyveromyces lactis gamma-toxin is a tRNA endonuclease that cleaves Saccharomyces cerevisiae [see text] between position 34 and position 35. All three substrate tRNAs carry a 5-methoxycarbonylmethyl-2-thiouridine (mcm(5)s(2)U) residue at position 34 (wobble position) of which the mcm(5) group is required for efficient cleavage. However, the different cleavage efficiencies of mcm(5)s(2)U(34)-containing tRNAs suggest that additional features of these tRNAs affect cleavage. In the present study, we show that a stable anticodon stem and the anticodon loop are the minimal requirements for cleavage by gamma-toxin. A synthetic minihelix RNA corresponding to the anticodon stem loop (ASL) of the natural substrate [see text] is cleaved at the same position as the natural substrate. In [see text], the nucleotides U(34)U(35)C(36)A(37)C(38) are required for optimal gamma-toxin cleavage, whereas a purine at position 32 or a G in position 33 dramatically reduces the cleavage of the ASL. Comparing modified and partially modified forms of E. coli and yeast [see text] reinforced the strong stimulatory effects of the mcm(5) group, revealed a weak positive effect of the s(2) group and a negative effect of the bacterial 5-methylaminomethyl (mnm(5)) group. The data underscore the high specificity of this yeast tRNA toxin.


Subject(s)
Anticodon/chemistry , Endoribonucleases/metabolism , Kluyveromyces/enzymology , Mycotoxins/metabolism , Anticodon/metabolism , Base Sequence , Molecular Sequence Data , Mutation , RNA, Transfer, Gln/chemistry , RNA, Transfer, Gln/metabolism , RNA, Transfer, Glu/chemistry , RNA, Transfer, Glu/metabolism , RNA, Transfer, Lys/chemistry , RNA, Transfer, Lys/metabolism , Substrate Specificity , Thiouridine/analogs & derivatives , Thiouridine/chemistry
12.
J Bacteriol ; 191(5): 1604-9, 2009 Mar.
Article in English | MEDLINE | ID: mdl-19103926

ABSTRACT

In Escherichia coli, release factor 1 (RF1) is one of two RFs that mediate termination; it specifically recognizes UAA and UAG stop codons. A mutant allele, prfA1, coding for an RF1 that causes temperature-sensitive (Ts) growth at 42 degrees C, was used to select for temperature-resistant (Ts(+)) suppressors. This study describes one such suppressor that is the result of an IS10 insertion into the cysB gene, giving a Cys(-) phenotype. CysB is a transcription factor regulating the cys regulon, mainly as an activator, which explains the Cys(-) phenotype. We have found that suppression is a consequence of the lost ability to donate sulfur to enzymes involved in the synthesis of thiolated nucleosides. From genetic analyses we conclude that it is the lack of the 5-methylaminomethyl-2-thiouridine (mnm(5)s(2)U) modification of the wobble base of tRNA(Glu), tRNA(Lys), and/or tRNA(Gln) that causes the suppressor phenotype.


Subject(s)
Bacterial Proteins/genetics , Escherichia coli Proteins/genetics , Escherichia coli/growth & development , Peptide Termination Factors/genetics , RNA, Transfer, Gln , RNA, Transfer, Glu , RNA, Transfer, Lys , Suppression, Genetic , Temperature , Alleles , Bacterial Proteins/metabolism , Codon, Terminator , Culture Media , DNA Transposable Elements , Escherichia coli/genetics , Escherichia coli/physiology , Escherichia coli Proteins/metabolism , Gene Expression Regulation, Bacterial , Hot Temperature , Peptide Termination Factors/metabolism , Phenotype , RNA, Transfer, Gln/chemistry , RNA, Transfer, Gln/genetics , RNA, Transfer, Gln/metabolism , RNA, Transfer, Glu/chemistry , RNA, Transfer, Glu/genetics , RNA, Transfer, Glu/metabolism , RNA, Transfer, Lys/chemistry , RNA, Transfer, Lys/genetics , RNA, Transfer, Lys/metabolism , Thiouridine/analogs & derivatives , Thiouridine/metabolism
13.
Science ; 267(5206): 1958-65, 1995 Mar 31.
Article in English | MEDLINE | ID: mdl-7701318

ABSTRACT

The crystal structure of a class I aminoacyl-transfer RNA synthetase, glutamyl-tRNA synthetase (GluRS) from Thermus thermophilus, was solved and refined at 2.5 A resolution. The amino-terminal half of GluRS shows a geometrical similarity with that of Escherichia coli glutaminyl-tRNA synthetase (GlnRS) of the same subclass in class I, comprising the class I-specific Rossmann fold domain and the intervening subclass-specific alpha/beta domain. These domains were found to have two GluRS-specific, secondary-structure insertions, which then participated in the specific recognition of the D and acceptor stems of tRNA(Glu) as indicated by mutagenesis analyses based on the docking properties of GluRS and tRNA. In striking contrast to the beta-barrel structure of the GlnRS carboxyl-terminal half, the GluRS carboxyl-terminal half displayed an all-alpha-helix architecture, an alpha-helix cage, and mutagenesis analyses indicated that it had a role in the anticodon recognition.


Subject(s)
Glutamate-tRNA Ligase/chemistry , Thermus thermophilus/enzymology , Amino Acid Sequence , Amino Acyl-tRNA Synthetases/chemistry , Anticodon , Biological Evolution , Computer Graphics , Crystallography, X-Ray , Escherichia coli/enzymology , Glutamate-tRNA Ligase/metabolism , Models, Molecular , Molecular Sequence Data , Mutagenesis, Site-Directed , Protein Conformation , Protein Folding , Protein Structure, Secondary , Protein Structure, Tertiary , RNA, Transfer, Glu/chemistry , RNA, Transfer, Glu/metabolism , Sequence Alignment
14.
Nucleic Acids Res ; 34(21): 6083-94, 2006.
Article in English | MEDLINE | ID: mdl-17074748

ABSTRACT

In many prokaryotes and in organelles asparagine and glutamine are formed by a tRNA-dependent amidotransferase (AdT) that catalyzes amidation of aspartate and glutamate, respectively, mischarged on tRNAAsn and tRNAGln. These pathways supply the deficiency of the organism in asparaginyl- and glutaminyl-tRNA synthtetases and provide the translational machinery with Asn-tRNAAsn and Gln-tRNAGln. So far, nothing is known about the structural elements that confer to tRNA the role of a specific cofactor in the formation of the cognate amino acid. We show herein, using aspartylated tRNAAsn and tRNAAsp variants, that amidation of Asp acylating tRNAAsn is promoted by the base pair U1-A72 whereas the G1-C72 pair and presence of the supernumerary nucleotide U20A in the D-loop of tRNAAsp prevent amidation. We predict, based on comparison of tRNAGln and tRNAGlu sequence alignments from bacteria using the AdT-dependent pathway to form Gln-tRNAGln, that the same combination of nucleotides also rules specific tRNA-dependent formation of Gln. In contrast, we show that the tRNA-dependent conversion of Asp into Asn by archaeal AdT is mainly mediated by nucleotides G46 and U47 of the variable region. In the light of these results we propose that bacterial and archaeal AdTs use kingdom-specific signals to catalyze the tRNA-dependent formations of Asn and Gln.


Subject(s)
Asparagine/biosynthesis , Neisseria meningitidis/enzymology , Nitrogenous Group Transferases/metabolism , RNA, Bacterial/chemistry , RNA, Transfer/chemistry , Adenine/chemistry , Base Sequence , Kinetics , Nitrogenous Group Transferases/chemistry , RNA, Archaeal/chemistry , RNA, Archaeal/metabolism , RNA, Bacterial/metabolism , RNA, Transfer/metabolism , RNA, Transfer, Asn/chemistry , RNA, Transfer, Asn/metabolism , RNA, Transfer, Asp/chemistry , RNA, Transfer, Asp/metabolism , RNA, Transfer, Gln/chemistry , RNA, Transfer, Gln/metabolism , RNA, Transfer, Glu/chemistry , RNA, Transfer, Glu/metabolism , Sequence Alignment , Species Specificity , Substrate Specificity , Uridine/chemistry
15.
Mol Cell Biol ; 23(24): 9283-92, 2003 Dec.
Article in English | MEDLINE | ID: mdl-14645538

ABSTRACT

We have identified a novel tRNA methyltransferase in Saccharomyces cerevisiae that we designate Trm9. This enzyme, the product of the YML014w gene, catalyzes the esterification of modified uridine nucleotides, resulting in the formation of 5-methylcarbonylmethyluridine in tRNA(Arg3) and 5-methylcarbonylmethyl-2-thiouridine in tRNA(Glu). In intact yeast cells, disruption of the TRM9 gene results in the complete loss of these modified wobble bases and increased sensitivity at 37 degrees C to paromomycin, a translational inhibitor. These results suggest a role for this potentially reversible methyl esterification reaction when cells are under stress.


Subject(s)
RNA, Fungal/metabolism , RNA, Transfer/metabolism , Saccharomyces cerevisiae Proteins/metabolism , Saccharomyces cerevisiae/enzymology , tRNA Methyltransferases/metabolism , Amino Acid Sequence , Base Sequence , DNA, Fungal/genetics , Gene Deletion , Genes, Fungal , Methylation , Molecular Sequence Data , Mutation , Protein Biosynthesis , RNA, Fungal/chemistry , RNA, Transfer/chemistry , RNA, Transfer, Arg/chemistry , RNA, Transfer, Arg/metabolism , RNA, Transfer, Glu/chemistry , RNA, Transfer, Glu/metabolism , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae Proteins/genetics , Sequence Homology, Amino Acid , Substrate Specificity , Temperature , Uridine/chemistry , tRNA Methyltransferases/genetics
16.
Protein J ; 26(1): 61-73, 2007 Jan.
Article in English | MEDLINE | ID: mdl-17237992

ABSTRACT

Protein recognition of RNA has been studied using Peptide Phage Display Libraries, but in the absence of RNA modifications. Peptides from two libraries, selected for binding the modified anticodon stem and loop (ASL) of human tRNA(LyS3) having 2-thiouridine (s(2)U34) and pseudouridine (psi39), bound the modified human ASL(Lys3)(s(2)U34;psi39) preferentially and had significant homology with RNA binding proteins. Selected peptides were narrowed to a manageable number using a less sensitive, but inexpensive assay before conducting intensive characterization. The affinity and specificity of the best binding peptide (with an N-terminal fluorescein) were characterized by fluorescence spectrophotometry. The peptide exhibited the highest binding affinity for ASL(LYS3)(s(2)U34; psi39), followed by the hypermodified ASL(Lys3) (mcm(5)s(2) U34; ms(2)t(6)A37) and the unmodified ASL(Lys3), but bound poorly to singly modified ASL(Lys3) constructs (psi39, ms(2)t(6)A37, s(2)34), ASL(Lys1,2) (t(6)A37) and Escherichia coli ASL(Glu) (s(2)U34). Thus, RNA modifications are potentially important recognition elements for proteins and can be targets for selective recognition by peptides.


Subject(s)
Anticodon/metabolism , Nucleic Acid Conformation , Peptides/metabolism , RNA, Transfer, Glu/chemistry , RNA, Transfer, Lys/chemistry , Thiouridine/analogs & derivatives , Amino Acid Motifs , Anticodon/antagonists & inhibitors , Base Pairing , Codon/chemistry , Humans , Models, Chemical , Peptide Library , Protein Binding , Pseudouridine/chemistry , Spectrometry, Fluorescence , Thermodynamics , Thiouridine/chemistry
17.
Article in English | MEDLINE | ID: mdl-16582487

ABSTRACT

MnmA catalyzes a sulfuration reaction to synthesize 2-thiouridine at the wobble positions of tRNA(Glu), tRNA(Gln) and tRNA(Lys) in Escherichia coli. The binary complex of MnmA and tRNA(Glu) was crystallized in two different crystal forms: forms I and II. Cocrystallization of MnmA-tRNA(Glu) with ATP yielded form III crystals. The three crystal forms diffracted to 3.1, 3.4 and 3.4 angstroms resolution, respectively, using synchrotron radiation at SPring-8. These crystals belong to space groups C2, I2(1)2(1)2(1) and C2, with unit-cell parameters a = 225.4, b = 175.8, c = 53.0 angstroms, beta = 101.6 degrees, a = 101.5, b = 108.0, c = 211.2 A and a = 238.1, b = 102.1, c = 108.2 angstroms, beta = 117.0 degrees, respectively. The asymmetric units of these crystals are expected to contain two, one and two MnmA-tRNA(Glu) complexes, respectively.


Subject(s)
Escherichia coli Proteins/metabolism , RNA, Transfer, Glu/metabolism , Cloning, Molecular , Crystallization , Escherichia coli/metabolism , Escherichia coli Proteins/chemistry , Escherichia coli Proteins/genetics , Escherichia coli Proteins/isolation & purification , RNA, Transfer, Glu/chemistry , RNA, Transfer, Glu/isolation & purification , Recombinant Proteins/chemistry , Recombinant Proteins/isolation & purification , Recombinant Proteins/metabolism , X-Ray Diffraction
18.
Nucleic Acids Res ; 27(17): 3583-8, 1999 Sep 01.
Article in English | MEDLINE | ID: mdl-10446250

ABSTRACT

A stable conformer of Escherichia coli tRNA(Glu), obtained in the absence of Mg(2+), is inactive in the aminoacylation reaction. Probing it with diethylpyrocarbonate, dimethyl sulfate and ribonuclease V1 revealed that it has a hairpin structure with two internal loops; the helical segments at both extremities have the same structure as the acceptor stem and the anticodon arm of the native conformer of tRNA(Glu)and the middle helix is formed of nucleotides from the D-loop (G15-C20:2) and parts of the T-loop and stem (G51-C56), with G19 bulging out. This model is consistent with other known properties of this inactive conformer, including its capacity to dimerize. Therefore, this tRNA requires magnesium to acquire a conformation that can be aminoacylated, as others require a post-transcriptional modification to reach this active conformation.


Subject(s)
Escherichia coli/genetics , Magnesium/metabolism , Magnesium/physiology , RNA, Transfer, Glu/chemistry , Adenosine/metabolism , Alkylating Agents/metabolism , Cytosine/metabolism , Diethyl Pyrocarbonate/metabolism , Endoribonucleases/metabolism , Nucleic Acid Conformation , Protein Denaturation , Sulfuric Acid Esters/metabolism
19.
Nucleic Acids Res ; 31(20): 6035-42, 2003 Oct 15.
Article in English | MEDLINE | ID: mdl-14530451

ABSTRACT

Discrimination between cognate and non-cognate tRNAs by aminoacyl-tRNA synthetases occurs at several steps of the aminoacylation pathway. We have measured changes of solvation and counter-ion distribution at various steps of the aminoacylation pathway of glutamyl- and glutaminyl-tRNA synthetases. The decrease in the association constant with increasing KCl concentration is relatively small for cognate tRNA binding when compared to known DNA-protein interactions. The electro-neutral nature of the tRNA binding domain may be largely responsible for this low ion release stoichiometry, suggesting that a relatively large electrostatic component of the DNA-protein interaction free energy may have evolved for other purposes, such as, target search. Little change in solvation upon tRNA binding is seen. Non-cognate tRNA binding actually increases with increasing KCl concentration indicating that charge repulsion may be a significant component of binding free energy. Thus, electrostatic interactions may have been used to discriminate between cognate and non-cognate tRNAs in the binding step. The catalytic constant of glutaminyl-tRNA synthetase increases with increasing osmotic pressure indicating a water release of 8.4 +/- 1.4 mol/mol in the transition state, whereas little change is seen in the case of glutamyl-tRNA synthetase. We propose that the significant amount of water release in the transition state, in the case of glutaminyl-tRNA synthetase, is due to additional contact of the protein with the tRNA in the transition state.


Subject(s)
Amino Acyl-tRNA Synthetases/chemistry , Glutamate-tRNA Ligase/chemistry , RNA, Transfer, Amino Acyl/chemistry , RNA, Transfer, Glu/chemistry , Amino Acyl-tRNA Synthetases/metabolism , Dose-Response Relationship, Drug , Glutamate-tRNA Ligase/metabolism , Kinetics , Potassium Chloride/pharmacology , Protein Binding/drug effects , RNA, Transfer, Amino Acyl/metabolism , RNA, Transfer, Glu/metabolism , Solvents/chemistry , Water/chemistry
20.
Nucleic Acids Res ; 32(9): 2768-75, 2004.
Article in English | MEDLINE | ID: mdl-15150343

ABSTRACT

Escherichia coli encodes YadB, a protein displaying 34% identity with the catalytic core of glutamyl-tRNA synthetase but lacking the anticodon-binding domain. We show that YadB is a tRNA modifying enzyme that evidently glutamylates the queuosine residue, a modified nucleoside at the wobble position of the tRNA(Asp) QUC anticodon. This conclusion is supported by a variety of biochemical data and by the inability of the enzyme to glutamylate tRNA(Asp) isolated from an E.coli tRNA-guanosine transglycosylase minus strain deprived of the capacity to exchange guanosine 34 with queuosine. Structural mimicry between the tRNA(Asp) anticodon stem and the tRNA(Glu) amino acid acceptor stem in prokaryotes encoding YadB proteins indicates that the function of these tRNA modifying enzymes, which we rename glutamyl-Q tRNA(Asp) synthetases, is conserved among prokaryotes.


Subject(s)
Anticodon/metabolism , Escherichia coli/enzymology , Escherichia coli/genetics , Glutamate-tRNA Ligase/chemistry , Glutamate-tRNA Ligase/metabolism , Nucleoside Q/metabolism , RNA, Transfer, Asp/metabolism , Acylation , Anticodon/chemistry , Anticodon/genetics , Base Sequence , Biological Evolution , Conserved Sequence , Glutamate-tRNA Ligase/genetics , Molecular Mimicry , Nucleoside Q/genetics , Periodic Acid/pharmacology , RNA, Bacterial/chemistry , RNA, Bacterial/genetics , RNA, Bacterial/metabolism , RNA, Transfer, Asp/chemistry , RNA, Transfer, Asp/genetics , RNA, Transfer, Glu/chemistry , RNA, Transfer, Glu/genetics , RNA, Transfer, Glu/metabolism
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