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Dieter Soll - One of the best experts on this subject based on the ideXlab platform.
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15. Aminoacyl-tRNA Synthetases
The Enzymes, 2008Co-Authors: Dieter Soll, Paul SchimmelAbstract:Publisher Summary The Aminoacyl-tRNA synthetases are a family of enzymes that play a key role in protein biosynthesis. This chapter discusses the molecular and catalytic properties of Aminoacyl-tRNA synthetases. It also discusses the genetics and regulation of Aminoacyl-tRNA synthetases. In procaryotes they are contained in the nonsedimentable supernatant of cell extracts. In eucaryotic organisms, Aminoacyl-tRNA synthetases are found in the organelles, and in many cases these differ from the corresponding cytoplasmic enzymes. The latter may not exist in a “free state” in the cytoplasm. In mammalian cells, for instance, large, fast sedimenting complexes have been found, which contain some or all Aminoacyl-tRNA synthetases together with tRNA or other parts of the protein synthesizing machinery. The occurrence of some Aminoacyl-tRNA synthetases in mammalian viruses has also recently been reported. In eucaryotic organisms, Aminoacyl-tRNA synthetases different from those found in the cytoplasm are contained in organelles as part of their separate protein synthesizing machinery. In mitochondria, some of these enzymes are specific for mitochondrial tRNA's and will not aminoacylate tRNA from the cytoplasm of the same organism. To date these enzymes are little characterized, and it is not known whether specific Aminoacyl-tRNA synthetases for all 20 amino acids are present in the mitochondrion.
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Cys-tRNA^Cys formation and cysteine biosynthesis in methanogenic archaea: two faces of the same problem?
Cellular and Molecular Life Sciences CMLS, 2004Co-Authors: Satwik Kamtekar, D. Tumbula-hansen, B Ruan, Anselm Sauerwald, D. Kennedy, Ivan Ahel, Dieter SollAbstract:Aminoacyl-tRNA (transfer RNA) synthetases are essential components of the cellular translation machinery as they provide the ribosome with Aminoacyl-tRNAs. Aminoacyl-tRNA synthesis is generally well understood. However, the mechanism of Cys-tRNA^Cys formation in three methanogenic archaea ( Methanocaldococcus jannaschii , Methanothermobacter thermautotrophicus and Methanopyrus kandleri ) is still unknown, since no recognizable gene for a canonical cysteinyl-tRNA synthetase could be identified in the genome sequences of these organisms. Here we review the different routes recently proposed for Cys-tRNA^Cys formation and discuss its possible link with cysteine biosynthesis in these methanogenic archaea.
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Aminoacyl-tRNA synthesis.
Annual review of biochemistry, 2000Co-Authors: M Ibba, Dieter SollAbstract:Aminoacyl-tRNAs are substrates for translation and are pivotal in determining how the genetic code is interpreted as amino acids. The function of Aminoacyl-tRNA synthesis is to precisely match amino acids with tRNAs containing the corresponding anticodon. This is primarily achieved by the direct attachment of an amino acid to the corresponding tRNA by an Aminoacyl-tRNA synthetase, although intrinsic proofreading and extrinsic editing are also essential in several cases. Recent studies of Aminoacyl-tRNA synthesis, mainly prompted by the advent of whole genome sequencing and the availability of a vast body of structural data, have led to an expanded and more detailed picture of how Aminoacyl-tRNAs are synthesized. This article reviews current knowledge of the biochemical, structural, and evolutionary facets of Aminoacyl-tRNA synthesis.
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Archaeal Aminoacyl-tRNA Synthesis: Unique Determinants of a Universal Genetic Code?
The Biological bulletin, 1999Co-Authors: M Ibba, Alan W. Curnow, James L. Bono, Patricia A. Rosa, Carl R. Woese, Dieter SollAbstract:The accurate synthesis of Aminoacyl-tRNAs is essential for faithful translation of the genetic code and is assumed to be one of the most highly conserved processes in biology. Recently, this dogmatic view has been called into question by the sequences of a number of archaeal genomes; for example, the genomic sequence of Methanococcus jannaschii does not contain open reading frames (ORFs) encoding homologs of the asparaginyl-, cysteinyl-, glutaminyl-, and lysyl-tRNA synthetases (l-3). Furthermore, the full complement of Aminoacyl-tRNAs necessary for translation is not entirely formed by the Aminoacyl-tRNA synthetases (AARS). In a significant number of cases, the AARSs activate a non-cognate amino acid, and the generation of the correct Aminoacyl-tRNA pair is brought about subsequently by a second protein. The use of such pathways for the formation of Gln-tRNAG’” (via Glu-tRNAG’“) and SectRNAS”” (vin Ser-tRNAS”” ) is well documented in all the living kingdoms (4, 5). Moreover, in several Archaea, an additional Aminoacyl-tRNA, Asn-tRNA*““, is also formed by transformation of a mischarged tRNA rather than by direct aminoacylation with asparaginyl-tRNA synthetase. Biochemical evidence indicates that aspartyl-tRNA synthetase initially synthesizes Asp-tRNA*““, which is subsequently converted to Asn-tRNA*“” in a distinct tRNAdependent transamidation reaction (6). The use of two-step (indirect) aminoacylation pathways for the formation of Asn-tRNA*“” and Gln-tRNAG’” in
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Aminoacyl-tRNA synthesis: divergent routes to a common goal
Trends in biochemical sciences, 1997Co-Authors: M Ibba, Alan W. Curnow, Dieter SollAbstract:Aminoacyl-tRNAs are key components in protein synthesis. They are formed directly by correct acylation of tRNA (by Aminoacyl-tRNA synthetases) or indirectly by tRNA-dependent transformation of misacylated tRNAs. The accuracy of Aminoacyl-tRNA synthesis is enhanced by a number of further protein-RNA or protein-protein interactions, some of which are restricted to Archaea, and might reflect adaptation mechanisms to diverse conditions.
Anna V. El'skaya - One of the best experts on this subject based on the ideXlab platform.
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Rabbit translation elongation factor 1α stimulates the activity of homologous Aminoacyl-tRNA synthetase
FEBS Letters, 1996Co-Authors: Boris Negrutskii, T V Budkevich, V F Shalak, G V Turkovskaya, Anna V. El'skayaAbstract:Functional and structural sequestration of Aminoacyl-tRNA has been recently found in eukaryotic cells and the Aminoacyl-tRNA channeling has been suggested [B.S. Negrutskii et al., Proc. Natl. Acad. Sci. 91 (1994) 964–968], but molecular details and mechanism of the process remained unclear. In this paper we have verified a possible interaction between rabbit Aminoacyl-tRNA synthetase and homologous translation elongation factor 1α (EF-1α), the proteins which may play a role of sequential components involved into the transfer of the Aminoacyl-tRNA along the protein synthetic metabolic chain. The stimulation of the phenylalanyl-tRNA synthetase activity by EF-1α is found. The effect is shown to be specific towards the origin of tRNA and elongation factor molecules. The data obtained favor the direct transfer mechanism of the Aminoacyl-tRNA channeling process during eukaryotic protein synthesis.
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Rabbit translation elongation factor 1 alpha stimulates the activity of homologous Aminoacyl-tRNA synthetase.
FEBS letters, 1996Co-Authors: Boris Negrutskii, T V Budkevich, V F Shalak, G V Turkovskaya, Anna V. El'skayaAbstract:Functional and structural sequestration of Aminoacyl-tRNA has been recently found in eukaryotic cells and the Aminoacyl-tRNA channeling has been suggested [B.S. Negrutskii et al., Proc. Natl. Acad. Sci. 91 (1994) 964-968], but molecular details and mechanism of the process remained unclear. In this paper we have verified a possible interaction between rabbit Aminoacyl-tRNA synthetase and homologous translation elongation factor 1 alpha (EF-1 alpha), the proteins which may play a role of sequential components involved in the transfer of the Aminoacyl-tRNA along the protein synthetic metabolic chain. The stimulation of the phenylalanyl-tRNA synthetase activity by EF-1 alpha is found. The effect is shown to be specific towards the origin of tRNA and elongation factor molecules. The data obtained favor the direct transfer mechanism of the Aminoacyl-tRNA channeling process during eukaryotic protein synthesis.
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Subcellular distribution and properties of rabbit liver Aminoacyl-tRNA synthetases under myocardial ischemia
Molecular and Cellular Biochemistry, 1993Co-Authors: Leonid L. Ivanov, Zenius Martinkus, Ol'ga V. Kharchenko, Sana Sara, Leonardas Lukoshevichius, Antanas Prashkevichius, Anna V. El'skayaAbstract:Subcellular distribution of Aminoacyl-tRNA synthetase activities has been studied in normal rabbit liver and under experimental myocardial ischemia (EMI). An increase in the activity of a number of Aminoacyl-tRNA synthetases in postmitochondrial and postribosomal supernatants from rabbit liver has been determined 12 hr after EMI. Gel chromatography of the postribosomal supernatant on Sepharose 6B shows that Aminoacyl-tRNA synthetase activities are distributed among the fractions with M_r 1.82×10^6, 0.84×10^6 (high-M_r Aminoacyl-tRNA synthetase complexes) and 0.12–0.35×10^6. In the case of EMI Aminoacyl-tRNA synthetase activities are partly redistributed from the 1.82×10^6 complex into the 0.84×10^6 complex. The catalytic properties of both free and complex leucyl-tRNA synthetases have been compared. K_M for all the substrates are the values of the same order in norm and under EMI. A decrease in some Aminoacyl-tRNA synthetase activities associated with polyribosomes has been observed 12 hr after EMI. The interaction of Aminoacyl-tRNA synthetases with polyribosomes stimulates the catalytic activity of some enzymes and protects them from heat inactivation in vitro . It is assumed that the changes in association of Aminoacyl-tRNA synthetases with high-M_r complexes and compartmentalization of these enzymes on polyribosomes may be related to the alteration of protein biosynthesis under myocardial ischemia.
Wang-yi Liu - One of the best experts on this subject based on the ideXlab platform.
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Effects of the active aldehyde group generated by RNA N-glycosidase in the sarcin/ricin domain of rat 28S ribosomal RNA on peptide elongation.
Biological Chemistry, 2000Co-Authors: Wang-yi LiuAbstract:Effects of the active aldehyde group of ribose C1' at position 4324 of rat 28S rRNA, in the inactivated ribosome generated by RNA N-glycosidases (trichosanthin, A-chain of cinnamomin and ricin), on peptide elongation have been studied. The aldehyde group inhibits the activities of eEF1A-dependent Aminoacyl-tRNA binding to the inactivated ribosome and eEF1A-dependent GTPase, but increases eEF2-dependent activity. At a high concentration of RNA N-glycosidase, the generated aldehyde group also inhibits Aminoacyl-tRNA binding to the inactivated ribosome in the absence of elongation factor and translocation activity. When the aldehyde group is reduced into a hydroxyl group by sodium borohydride or blocked with an amino acid through nucleophilic addition, the activities of eEF1A-dependent Aminoacyl-tRNA binding and eEF1A-dependent GTPase of the inactivated ribosome are partially restored, but the altered activities of eEF2-dependent GTPase, translocation and Aminoacyl-tRNA binding in the absence of elongation factor are not normalized. Thus, reduction or blockage of the aldehyde group with sodium borohydride or amino acids might change the conformation of the S/R domain in rat 28S ribosomal RNA to meet the requirement for eEF1A-dependent reactions, but not eEF2-involved reactions.
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effects of the active aldehyde group generated by rna n glycosidase in the sarcin ricin domain of rat 28s ribosomal rna on peptide elongation
Biological Chemistry, 2000Co-Authors: Wang-yi LiuAbstract:Effects of the active aldehyde group of ribose C1' at position 4324 of rat 28S rRNA, in the inactivated ribosome generated by RNA N-glycosidases (trichosanthin, A-chain of cinnamomin and ricin), on peptide elongation have been studied. The aldehyde group inhibits the activities of eEF1A-dependent Aminoacyl-tRNA binding to the inactivated ribosome and eEF1A-dependent GTPase, but increases eEF2-dependent activity. At a high concentration of RNA N-glycosidase, the generated aldehyde group also inhibits Aminoacyl-tRNA binding to the inactivated ribosome in the absence of elongation factor and translocation activity. When the aldehyde group is reduced into a hydroxyl group by sodium borohydride or blocked with an amino acid through nucleophilic addition, the activities of eEF1A-dependent Aminoacyl-tRNA binding and eEF1A-dependent GTPase of the inactivated ribosome are partially restored, but the altered activities of eEF2-dependent GTPase, translocation and Aminoacyl-tRNA binding in the absence of elongation factor are not normalized. Thus, reduction or blockage of the aldehyde group with sodium borohydride or amino acids might change the conformation of the S/R domain in rat 28S ribosomal RNA to meet the requirement for eEF1A-dependent reactions, but not eEF2-involved reactions.
Boris Negrutskii - One of the best experts on this subject based on the ideXlab platform.
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mRNA-Independent way to regulate translation elongation rate in eukaryotic cells
IUBMB life, 2018Co-Authors: Boris Negrutskii, Marc Mirande, Dmytro Vlasenko, Pavlo Futernyk, Anna El'skayaAbstract:The question of what governs the translation elongation rate in eukaryotes has not yet been completely answered. Earlier, different availability of different tRNAs was considered as a main factor involved, however, recent data revealed that the elongation rate does not always depend on tRNA availability. Here, we offer another, codon-independent approach to explain specific tRNA-dependence of the elongation rate in eukaryotes. We hypothesize that the exit rate of eukaryotic translation elongation factor 1A (eEF1A)*GDP from the 80S ribosome depends on the protein affinity to specific Aminoacyl-tRNA remaining on the ribosome after GTP hydrolysis. Subsequently, a slower dissociation of eEF1A*GDP from certain Aminoacyl-tRNAs in the ribosome can negatively influence the ribosomal elongation rate in a tRNA-dependent and mRNA-independent way. The specific tRNA-dependent departure rate of eEF1A*GDP from the ribosome is suggested to be a novel factor contributing to the overall translation elongation control in eukaryotic cells. © 2018 IUBMB Life, 2018.
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Rabbit translation elongation factor 1 alpha stimulates the activity of homologous Aminoacyl-tRNA synthetase.
FEBS letters, 1996Co-Authors: Boris Negrutskii, T V Budkevich, V F Shalak, G V Turkovskaya, Anna V. El'skayaAbstract:Functional and structural sequestration of Aminoacyl-tRNA has been recently found in eukaryotic cells and the Aminoacyl-tRNA channeling has been suggested [B.S. Negrutskii et al., Proc. Natl. Acad. Sci. 91 (1994) 964-968], but molecular details and mechanism of the process remained unclear. In this paper we have verified a possible interaction between rabbit Aminoacyl-tRNA synthetase and homologous translation elongation factor 1 alpha (EF-1 alpha), the proteins which may play a role of sequential components involved in the transfer of the Aminoacyl-tRNA along the protein synthetic metabolic chain. The stimulation of the phenylalanyl-tRNA synthetase activity by EF-1 alpha is found. The effect is shown to be specific towards the origin of tRNA and elongation factor molecules. The data obtained favor the direct transfer mechanism of the Aminoacyl-tRNA channeling process during eukaryotic protein synthesis.
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Rabbit translation elongation factor 1α stimulates the activity of homologous Aminoacyl-tRNA synthetase
FEBS Letters, 1996Co-Authors: Boris Negrutskii, T V Budkevich, V F Shalak, G V Turkovskaya, Anna V. El'skayaAbstract:Functional and structural sequestration of Aminoacyl-tRNA has been recently found in eukaryotic cells and the Aminoacyl-tRNA channeling has been suggested [B.S. Negrutskii et al., Proc. Natl. Acad. Sci. 91 (1994) 964–968], but molecular details and mechanism of the process remained unclear. In this paper we have verified a possible interaction between rabbit Aminoacyl-tRNA synthetase and homologous translation elongation factor 1α (EF-1α), the proteins which may play a role of sequential components involved into the transfer of the Aminoacyl-tRNA along the protein synthetic metabolic chain. The stimulation of the phenylalanyl-tRNA synthetase activity by EF-1α is found. The effect is shown to be specific towards the origin of tRNA and elongation factor molecules. The data obtained favor the direct transfer mechanism of the Aminoacyl-tRNA channeling process during eukaryotic protein synthesis.
Marina V. Rodnina - One of the best experts on this subject based on the ideXlab platform.
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Conditional Switch between Frameshifting Regimes upon Translation of dnaX mRNA
Molecular Cell, 2017Co-Authors: Neva Caliskan, Ingo Wohlgemuth, Natalia Korniy, Michael Pearson, Frank Peske, Marina V. RodninaAbstract:Summary Ribosome frameshifting during translation of bacterial dnaX can proceed via different routes, generating a variety of distinct polypeptides. Using kinetic experiments, we show that –1 frameshifting predominantly occurs during translocation of two tRNAs bound to the slippery sequence codons. This pathway depends on a stem-loop mRNA structure downstream of the slippery sequence and operates when Aminoacyl-tRNAs are abundant. However, when Aminoacyl-tRNAs are in short supply, the ribosome switches to an alternative frameshifting pathway that is independent of a stem-loop. Ribosome stalling at a vacant 0-frame A-site codon results in slippage of the P-site peptidyl-tRNA, allowing for –1-frame decoding. When the –1-frame Aminoacyl-tRNA is lacking, the ribosomes switch into –2 frame. Quantitative mass spectrometry shows that the –2-frame product is synthesized in vivo . We suggest that switching between frameshifting routes may enrich gene expression at conditions of Aminoacyl-tRNA limitation.
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Ribosome interactions of Aminoacyl-tRNA and elongation factor Tu in the codon-recognition complex
Nature structural biology, 2002Co-Authors: Holger Stark, Marina V. Rodnina, Hans-joachim Wieden, Friedrich Zemlin, Wolfgang Wintermeyer, M. Van HeelAbstract:The mRNA codon in the ribosomal A-site is recognized by Aminoacyl-tRNA (aa-tRNA) in a ternary complex with elongation factor Tu (EF-Tu) and GTP. Here we report the 13 A resolution three-dimensional reconstruction determined by cryo-electron microscopy of the kirromycin-stalled codon-recognition complex. The structure of the ternary complex is distorted by binding of the tRNA anticodon arm in the decoding center. The aa-tRNA interacts with 16S rRNA, helix 69 of 23S rRNA and proteins S12 and L11, while the sarcin-ricin loop of 23S rRNA contacts domain 1 of EF-Tu near the nucleotide-binding pocket. These results provide a detailed snapshot view of an important functional state of the ribosome and suggest mechanisms of decoding and GTPase activation.
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gtp consumption of elongation factor tu during translation of heteropolymeric mrnas
Proceedings of the National Academy of Sciences of the United States of America, 1995Co-Authors: Marina V. Rodnina, Wolfgang WintermeyerAbstract:Abstract The stoichiometry of elongation factor Tu (EF-Tu) and GTP in the complex with Aminoacyl-tRNA and the consumption of GTP during peptide bond formation on the ribosome were studied in the Escherichia coli system. The ribosomes were programmed either with two different heteropolymeric mRNAs coding for Met-Phe-Thr-Ile ... (mMFTI) or Met-Phe-Phe-Gly ... (mMFFG) or with poly(U). The composition of the complex of EF-Tu, GTP, and Phe-tRNA(Phe) was studied by gel chromatography. With equimolar amounts of factor and Phe-tRNA(Phe), a pentameric complex, (EF-Tu.GTP)2.Phe-tRNA(Phe), was observed, whereas the classical ternary complex, EF-Tu.GTP.Phe-tRNA(Phe), was found only when Phe-tRNA(Phe) was in excess. Upon binding of the purified pentameric complex to ribosomes carrying fMet-tRNA(fMet) in the peptidyl site and exposing a Phe codon in the aminoacyl site, only one out of two GTPs of the pentameric complex was hydrolyzed per Phe-tRNA bound and peptide bond formed, regardless of the mRNA used. In the presence of EF-G, the stoichiometry of one GTP hydrolyzed per peptide bond formed was found on mMFTI when one or two elongation cycles were completed. In contrast, on mMFFG, which contains two contiguous Phe codons, UUU-UUC, two GTP molecules of the pentameric complex were hydrolyzed per Phe incorporated into dipeptide, whereas the incorporation of the second Phe to form tripeptide consumed only one GTP. Thus, generally one GTP is hydrolyzed by EF-Tu per Aminoacyl-tRNA bound and peptide bond formed, and more than one GTP is hydrolyzed only when a particular mRNA sequence, such as a homopolymeric stretch, is translated. The role of the additional GTP hydrolysis is not known; it may be related to frameshifting of peptidyl-tRNA during translocation.