Thematische Bibliographien / Near-cognate tRNA / Zeitschriftenartikel
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Zeitschriftenartikel zum Thema „Near-cognate tRNA“

Autor: Grafiati
Veröffentlicht am 28. Juni 2021
Zuletzt aktualisiert am 29. Juli 2025

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1

Nguyen, Ha An, S. Sunita, and Christine M. Dunham. "Disruption of evolutionarily correlated tRNA elements impairs accurate decoding." Proceedings of the National Academy of Sciences 117, no. 28 (2020): 16333–38. http://dx.doi.org/10.1073/pnas.2004170117.

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Bacterial transfer RNAs (tRNAs) contain evolutionarily conserved sequences and modifications that ensure uniform binding to the ribosome and optimal translational accuracy despite differences in their aminoacyl attachments and anticodon nucleotide sequences. In the tRNA anticodon stem−loop, the anticodon sequence is correlated with a base pair in the anticodon loop (nucleotides 32 and 38) to tune the binding of each tRNA to the decoding center in the ribosome. Disruption of this correlation renders the ribosome unable to distinguish correct from incorrect tRNAs. The molecular basis for how the
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2

Blanchet, Sandra, David Cornu, Isabelle Hatin, Henri Grosjean, Pierre Bertin, and Olivier Namy. "Deciphering the reading of the genetic code by near-cognate tRNA." Proceedings of the National Academy of Sciences 115, no. 12 (2018): 3018–23. http://dx.doi.org/10.1073/pnas.1715578115.

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Some codons of the genetic code can be read not only by cognate, but also by near-cognate tRNAs. This flexibility is thought to be conferred mainly by a mismatch between the third base of the codon and the first of the anticodon (the so-called “wobble” position). However, this simplistic explanation underestimates the importance of nucleotide modifications in the decoding process. Using a system in which only near-cognate tRNAs can decode a specific codon, we investigated the role of six modifications of the anticodon, or adjacent nucleotides, of the tRNAs specific for Tyr, Gln, Lys, Trp, Cys,
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3

Vimaladithan, A., and P. J. Farabaugh. "Special peptidyl-tRNA molecules can promote translational frameshifting without slippage." Molecular and Cellular Biology 14, no. 12 (1994): 8107–16. http://dx.doi.org/10.1128/mcb.14.12.8107-8116.1994.

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Recently we described an unusual programmed +1 frameshift event in yeast retrotransposon Ty3. Frameshifting depends on the presence of peptidyl-tRNA(AlaCGC) on the GCG codon in the ribosomal P site and on a translational pause stimulated by the slowly decoded AGU codon. Frameshifting occurs on the sequence GCG-AGU-U by out-of-frame binding of a valyl-tRNA to GUU without slippage of peptidyl-tRNA(AlaCGC). This mechanism challenges the conventional understanding that frameshift efficiency must correlate with the ability of mRNA-bound tRNA to slip between cognate or near-cognate codons. Though fr
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Vimaladithan, A., and P. J. Farabaugh. "Special peptidyl-tRNA molecules can promote translational frameshifting without slippage." Molecular and Cellular Biology 14, no. 12 (1994): 8107–16. http://dx.doi.org/10.1128/mcb.14.12.8107.

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Recently we described an unusual programmed +1 frameshift event in yeast retrotransposon Ty3. Frameshifting depends on the presence of peptidyl-tRNA(AlaCGC) on the GCG codon in the ribosomal P site and on a translational pause stimulated by the slowly decoded AGU codon. Frameshifting occurs on the sequence GCG-AGU-U by out-of-frame binding of a valyl-tRNA to GUU without slippage of peptidyl-tRNA(AlaCGC). This mechanism challenges the conventional understanding that frameshift efficiency must correlate with the ability of mRNA-bound tRNA to slip between cognate or near-cognate codons. Though fr
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5

Ieong, Ka-Weng, Gabriele Indrisiunaite, Arjun Prabhakar, Joseph D. Puglisi, and Måns Ehrenberg. "N 6-Methyladenosines in mRNAs reduce the accuracy of codon reading by transfer RNAs and peptide release factors." Nucleic Acids Research 49, no. 5 (2021): 2684–99. http://dx.doi.org/10.1093/nar/gkab033.

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Abstract We used quench flow to study how N6-methylated adenosines (m6A) affect the accuracy ratio between kcat/Km (i.e. association rate constant (ka) times probability (Pp) of product formation after enzyme-substrate complex formation) for cognate and near-cognate substrate for mRNA reading by tRNAs and peptide release factors 1 and 2 (RFs) during translation with purified Escherichia coli components. We estimated kcat/Km for Glu-tRNAGlu, EF-Tu and GTP forming ternary complex (T3) reading cognate (GAA and Gm6AA) or near-cognate (GAU and Gm6AU) codons. ka decreased 10-fold by m6A introduction
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O’Connor, Michael. "tRNA imbalance promotes −1 frameshifting via near-cognate decoding." Journal of Molecular Biology 279, no. 4 (1998): 727–36. http://dx.doi.org/10.1006/jmbi.1998.1832.

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7

Wohlgemuth, Ingo, Corinna Pohl, Joerg Mittelstaet, Andrey L. Konevega, and Marina V. Rodnina. "Evolutionary optimization of speed and accuracy of decoding on the ribosome." Philosophical Transactions of the Royal Society B: Biological Sciences 366, no. 1580 (2011): 2979–86. http://dx.doi.org/10.1098/rstb.2011.0138.

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Speed and accuracy of protein synthesis are fundamental parameters for the fitness of living cells, the quality control of translation, and the evolution of ribosomes. The ribosome developed complex mechanisms that allow for a uniform recognition and selection of any cognate aminoacyl-tRNA (aa-tRNA) and discrimination against any near-cognate aa-tRNA, regardless of the nature or position of the mismatch. This review describes the principles of the selection—kinetic partitioning and induced fit—and discusses the relationship between speed and accuracy of decoding, with a focus on bacterial tran
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Pernod, Ketty, Laure Schaeffer, Johana Chicher, et al. "The nature of the purine at position 34 in tRNAs of 4-codon boxes is correlated with nucleotides at positions 32 and 38 to maintain decoding fidelity." Nucleic Acids Research 48, no. 11 (2020): 6170–83. http://dx.doi.org/10.1093/nar/gkaa221.

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Abstract Translation fidelity relies essentially on the ability of ribosomes to accurately recognize triplet interactions between codons on mRNAs and anticodons of tRNAs. To determine the codon-anticodon pairs that are efficiently accepted by the eukaryotic ribosome, we took advantage of the IRES from the intergenic region (IGR) of the Cricket Paralysis Virus. It contains an essential pseudoknot PKI that structurally and functionally mimics a codon-anticodon helix. We screened the entire set of 4096 possible combinations using ultrahigh-throughput screenings combining coupled transcription/tra
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9

Zhang, Jingji, Ka-Weng Ieong, Magnus Johansson, and Måns Ehrenberg. "Accuracy of initial codon selection by aminoacyl-tRNAs on the mRNA-programmed bacterial ribosome." Proceedings of the National Academy of Sciences 112, no. 31 (2015): 9602–7. http://dx.doi.org/10.1073/pnas.1506823112.

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We used a cell-free system with pureEscherichia colicomponents to study initial codon selection of aminoacyl-tRNAs in ternary complex with elongation factor Tu and GTP on messenger RNA-programmed ribosomes. We took advantage of the universal rate-accuracy trade-off for all enzymatic selections to determine how the efficiency of initial codon readings decreased linearly toward zero as the accuracy of discrimination against near-cognate and wobble codon readings increased toward the maximal asymptote, thedvalue. We report data on the rate-accuracy variation for 7 cognate, 7 wobble, and 56 near-c
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Roy, Bijoyita, Westley J. Friesen, Yuki Tomizawa, et al. "Ataluren stimulates ribosomal selection of near-cognate tRNAs to promote nonsense suppression." Proceedings of the National Academy of Sciences 113, no. 44 (2016): 12508–13. http://dx.doi.org/10.1073/pnas.1605336113.

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A premature termination codon (PTC) in the ORF of an mRNA generally leads to production of a truncated polypeptide, accelerated degradation of the mRNA, and depression of overall mRNA expression. Accordingly, nonsense mutations cause some of the most severe forms of inherited disorders. The small-molecule drug ataluren promotes therapeutic nonsense suppression and has been thought to mediate the insertion of near-cognate tRNAs at PTCs. However, direct evidence for this activity has been lacking. Here, we expressed multiple nonsense mutation reporters in human cells and yeast and identified the
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Schrock, Madison N., Krishna Parsawar, Kelly T. Hughes, and Fabienne F. V. Chevance. "D-stem mutation in an essential tRNA increases translation speed at the cost of fidelity." PLOS Genetics 21, no. 2 (2025): e1011569. https://doi.org/10.1371/journal.pgen.1011569.

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The efficiency with which aminoacyl-tRNA and GTP-bound translation elongation factor EF-Tu recognizes the A-site codon of the ribosome is dependent on codons and tRNA species present in the polypeptide (P) and exit (E) codon sites. To understand how codon context affects the efficiency of codon recognition by tRNA-bound EF-Tu, a genetic system was developed to select for fast translation through slow-translating codon combinations. Selection for fast translation through the slow-translated UCA-UAC pair, flanked by histidine codons, resulted in the isolation of an A25G base substitution mutant
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Beznosková, Petra, Laure Bidou, Olivier Namy, and Leoš Shivaya Valášek. "Increased expression of tryptophan and tyrosine tRNAs elevates stop codon readthrough of reporter systems in human cell lines." Nucleic Acids Research 49, no. 9 (2021): 5202–15. http://dx.doi.org/10.1093/nar/gkab315.

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Abstract Regulation of translation via stop codon readthrough (SC-RT) expands not only tissue-specific but also viral proteomes in humans and, therefore, represents an important subject of study. Understanding this mechanism and all involved players is critical also from a point of view of prospective medical therapies of hereditary diseases caused by a premature termination codon. tRNAs were considered for a long time to be just passive players delivering amino acid residues according to the genetic code to ribosomes without any active regulatory roles. In contrast, our recent yeast work iden
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13

Thomas, Erica N., Carrie L. Simms, Hannah E. Keedy, and Hani S. Zaher. "Insights into the base-pairing preferences of 8-oxoguanosine on the ribosome." Nucleic Acids Research 47, no. 18 (2019): 9857–70. http://dx.doi.org/10.1093/nar/gkz701.

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Abstract Of the four bases, guanine is the most susceptible to oxidation, which results in the formation of 8-oxoguanine (8-oxoG). In protein-free DNA, 8-oxodG adopts the syn conformation more frequently than the anti one. In the syn conformation, 8-oxodG base pairs with dA. The equilibrium between the anti and syn conformations of the adduct are known to be altered by the enzyme recognizing 8-oxodG. We previously showed that 8-oxoG in mRNA severely disrupts tRNA selection, but the underlying mechanism for these effects was not addressed. Here, we use miscoding antibiotics and ribosome mutants
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Mittelstaet, Joerg, Andrey L. Konevega, and Marina V. Rodnina. "Distortion of tRNA upon Near-cognate Codon Recognition on the Ribosome." Journal of Biological Chemistry 286, no. 10 (2011): 8158–64. http://dx.doi.org/10.1074/jbc.m110.210021.

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15

Khonsari, Bahar, and Roland Klassen. "Impact of Pus1 Pseudouridine Synthase on Specific Decoding Events in Saccharomyces cerevisiae." Biomolecules 10, no. 5 (2020): 729. http://dx.doi.org/10.3390/biom10050729.

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Pus1-dependent pseudouridylation occurs in many tRNAs and at multiple positions, yet the functional impact of this modification is incompletely understood. We analyzed the consequences of PUS1 deletion on the essential decoding of CAG (Gln) codons by tRNAGlnCUG in yeast. Synthetic lethality was observed upon combining the modification defect with destabilized variants of tRNAGlnCUG, pointing to a severe CAG-decoding defect of the hypomodified tRNA. In addition, we demonstrated that misreading of UAG stop codons by a tRNAGlnCUG variant is positively affected by Pus1. Genetic approaches further
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16

Ng, Martin Y., Hong Li, Mikel D. Ghelfi, Yale E. Goldman, and Barry S. Cooperman. "Ataluren and aminoglycosides stimulate read-through of nonsense codons by orthogonal mechanisms." Proceedings of the National Academy of Sciences 118, no. 2 (2021): e2020599118. http://dx.doi.org/10.1073/pnas.2020599118.

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During protein synthesis, nonsense mutations, resulting in premature stop codons (PSCs), produce truncated, inactive protein products. Such defective gene products give rise to many diseases, including cystic fibrosis, Duchenne muscular dystrophy (DMD), and some cancers. Small molecule nonsense suppressors, known as TRIDs (translational read-through–inducing drugs), stimulate stop codon read-through. The best characterized TRIDs are ataluren, which has been approved by the European Medicines Agency for the treatment of DMD, and G418, a structurally dissimilar aminoglycoside. Previously [1], we
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Keedy, Hannah E., Erica N. Thomas, and Hani S. Zaher. "Decoding on the ribosome depends on the structure of the mRNA phosphodiester backbone." Proceedings of the National Academy of Sciences 115, no. 29 (2018): E6731—E6740. http://dx.doi.org/10.1073/pnas.1721431115.

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During translation, the ribosome plays an active role in ensuring that mRNA is decoded accurately and rapidly. Recently, biochemical studies have also implicated certain accessory factors in maintaining decoding accuracy. However, it is currently unclear whether the mRNA itself plays an active role in the process beyond its ability to base pair with the tRNA. Structural studies revealed that the mRNA kinks at the interface of the P and A sites. A magnesium ion appears to stabilize this structure through electrostatic interactions with the phosphodiester backbone of the mRNA. Here we examined t
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Beznosková, Petra, Zuzana Pavlíková, Jakub Zeman, Colin Echeverría Aitken, and Leoš S. Valášek. "Yeast applied readthrough inducing system (YARIS): an invivo assay for the comprehensive study of translational readthrough." Nucleic Acids Research 47, no. 12 (2019): 6339–50. http://dx.doi.org/10.1093/nar/gkz346.

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Abstract Stop codon readthrough—the decoding of a stop codon by a near-cognate tRNA—is employed by viruses to balance levels of enzymatic and structural proteins and by eukaryotic cells to enable isoform-specific protein synthesis in response to external stimuli. Owing to the prevalence of premature termination codons in human disease, readthrough has emerged as an attractive therapeutic target. A growing list of various features, for example the +4 nucleotide immediately following the stop codon, modulate readthrough levels, underscoring the need for systematic investigation of readthrough. H
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19

Akins, R. A., R. L. Kelley, and A. M. Lambowitz. "Characterization of mutant mitochondrial plasmids of Neurospora spp. that have incorporated tRNAs by reverse transcription." Molecular and Cellular Biology 9, no. 2 (1989): 678–91. http://dx.doi.org/10.1128/mcb.9.2.678-691.1989.

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The Mauriceville and Varkud mitochondrial plasmids of Neurospora spp. are closely related, closed-circular DNAs (3.6 and 3.7 kilobases, respectively) whose nucleotide sequences and genetic organization suggest relationships to mitochondrial introns and retroelements. We have characterized nine suppressive mutants of these plasmids that outcompete mitochondrial DNA and lead to impaired growth. All nine suppressive plasmids contain small insertions, corresponding to or including a mitochondrial tRNA (tRNATrp, tRNAGly, or tRNAVal) or a tRNA-like sequence. The insertions are located at the positio
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Akins, R. A., R. L. Kelley, and A. M. Lambowitz. "Characterization of mutant mitochondrial plasmids of Neurospora spp. that have incorporated tRNAs by reverse transcription." Molecular and Cellular Biology 9, no. 2 (1989): 678–91. http://dx.doi.org/10.1128/mcb.9.2.678.

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The Mauriceville and Varkud mitochondrial plasmids of Neurospora spp. are closely related, closed-circular DNAs (3.6 and 3.7 kilobases, respectively) whose nucleotide sequences and genetic organization suggest relationships to mitochondrial introns and retroelements. We have characterized nine suppressive mutants of these plasmids that outcompete mitochondrial DNA and lead to impaired growth. All nine suppressive plasmids contain small insertions, corresponding to or including a mitochondrial tRNA (tRNATrp, tRNAGly, or tRNAVal) or a tRNA-like sequence. The insertions are located at the positio
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Sharma, Virag, Marie-Françoise Prère, Isabelle Canal, et al. "Analysis of tetra- and hepta-nucleotides motifs promoting -1 ribosomal frameshifting in Escherichia coli." Nucleic Acids Research 42, no. 11 (2014): 7210–25. http://dx.doi.org/10.1093/nar/gku386.

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Abstract Programmed ribosomal -1 frameshifting is a non-standard decoding process occurring when ribosomes encounter a signal embedded in the mRNA of certain eukaryotic and prokaryotic genes. This signal has a mandatory component, the frameshift motif: it is either a Z_ZZN tetramer or a X_XXZ_ZZN heptamer (where ZZZ and XXX are three identical nucleotides) allowing cognate or near-cognate repairing to the -1 frame of the A site or A and P sites tRNAs. Depending on the signal, the frameshifting frequency can vary over a wide range, from less than 1% to more than 50%. The present study combines
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Roy, Bijoyita, John D. Leszyk, David A. Mangus, and Allan Jacobson. "Nonsense suppression by near-cognate tRNAs employs alternative base pairing at codon positions 1 and 3." Proceedings of the National Academy of Sciences 112, no. 10 (2015): 3038–43. http://dx.doi.org/10.1073/pnas.1424127112.

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Premature termination codons (PTCs) in an mRNA ORF inactivate gene function by causing production of a truncated protein and destabilization of the mRNA. Readthrough of a PTC allows ribosomal A-site insertion of a near-cognate tRNA, leading to synthesis of a full-length protein from otherwise defective mRNA. To understand the mechanism of such nonsense suppression, we developed a yeast system that allows purification and sequence analysis of full-length readthrough products arising as a consequence of endogenous readthrough or the compromised termination fidelity attributable to the loss of Up
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Bonilla, Steve. "Single-particle cryo-EM reveals a novel form of viral 3D tRNA mimicry." Structural Dynamics 12, no. 2_Supplement (2025): A296. https://doi.org/10.1063/4.0000602.

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Certain single-stranded positive sense RNA viral genomes contain conformationally dynamic RNA structures at their 3' end that mimic tRNA. These structures are recognized by the host-cells’ aminoacyl tRNA synthetases, leading to the addition of an amino acid to the 3' end of the viral genome. The aminoacylated tRNA-like structures (TLSs) hijack the host’s biochemical machinery during infection and have been implicated in diverse and essential viral functions including viral protein production, genome replication, and packaging. Despite decades of study, the structural basis of viral tRNA mimicr
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24

Benslimane, Nesrine, Camille Loret, Pauline Chazelas, et al. "Readthrough Activators and Nonsense-Mediated mRNA Decay Inhibitor Molecules: Real Potential in Many Genetic Diseases Harboring Premature Termination Codons." Pharmaceuticals 17, no. 3 (2024): 314. http://dx.doi.org/10.3390/ph17030314.

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Nonsense mutations that generate a premature termination codon (PTC) can induce both the accelerated degradation of mutated mRNA compared with the wild type version of the mRNA or the production of a truncated protein. One of the considered therapeutic strategies to bypass PTCs is their “readthrough” based on small-molecule drugs. These molecules promote the incorporation of a near-cognate tRNA at the PTC position through the native polypeptide chain. In this review, we detailed the various existing strategies organized according to pharmacological molecule types through their different mechan
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McMurry, Jonathan L., and Michelle C. Y. Chang. "Fluorothreonyl-tRNA deacylase prevents mistranslation in the organofluorine producerStreptomyces cattleya." Proceedings of the National Academy of Sciences 114, no. 45 (2017): 11920–25. http://dx.doi.org/10.1073/pnas.1711482114.

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Fluorine is an element with unusual properties that has found significant utility in the design of synthetic small molecules, ranging from therapeutics to materials. In contrast, only a few fluorinated compounds made by living organisms have been found to date, most of which derive from the fluoroacetate/fluorothreonine biosynthetic pathway first discovered inStreptomyces cattleya. While fluoroacetate has long been known to act as an inhibitor of the tricarboxylic acid cycle, the fate of the amino acid fluorothreonine is still not well understood. Here, we show that fluorothreonine can be misi
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Guinto, Ferdiemar C., Rebecca W. Alexander, and Freddie R. Salsbury. "Substrate recognition and near-cognate discrimination by the wobble-base modifying enzyme tRNA-isoleucine lysidine synthase (TilS)." Biophysical Journal 122, no. 3 (2023): 216a. http://dx.doi.org/10.1016/j.bpj.2022.11.1288.

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Beyer, Jenna N., Parisa Hosseinzadeh, Ilana Gottfried-Lee, et al. "Overcoming Near-Cognate Suppression in a Release Factor 1-Deficient Host with an Improved Nitro-Tyrosine tRNA Synthetase." Journal of Molecular Biology 432, no. 16 (2020): 4690–704. http://dx.doi.org/10.1016/j.jmb.2020.06.014.

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28

Kondo, Jiro, and Mai Koganei. "Structural Bases for the Fitness Cost of the Antibiotic-Resistance and Lethal Mutations at Position 1408 of 16S rRNA." Molecules 25, no. 1 (2019): 159. http://dx.doi.org/10.3390/molecules25010159.

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To understand a structural basis for the fitness cost of the A1408G antibiotic-resistance mutation in the ribosomal A-site RNA, we have determined crystal structures of its A1408C and A1408U lethal mutants, and made comparison with previously solved structures of the wild type and the antibiotic-resistant mutant. The A-site RNA containing an asymmetric internal loop functions as a molecular switch to discriminate a single cognate tRNA from several near-cognate tRNAs by its conformational ON/OFF switching. Overall structures of the “off” states of the A1408C/U lethal mutants are very similar to
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Suzuki, Takeo, Kenjyo Miyauchi, Tsutomu Suzuki, et al. "Taurine-containing Uridine Modifications in tRNA Anticodons Are Required to Decipher Non-universal Genetic Codes in Ascidian Mitochondria." Journal of Biological Chemistry 286, no. 41 (2011): 35494–98. http://dx.doi.org/10.1074/jbc.m111.279810.

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Variations in the genetic code are found frequently in mitochondrial decoding systems. Four non-universal genetic codes are employed in ascidian mitochondria: AUA for Met, UGA for Trp, and AGA/AGG(AGR) for Gly. To clarify the decoding mechanism for the non-universal genetic codes, we isolated and analyzed mitochondrial tRNAs for Trp, Met, and Gly from an ascidian, Halocynthia roretzi. Mass spectrometric analysis identified 5-taurinomethyluridine (τm5U) at the anticodon wobble positions of tRNAMet(AUR), tRNATrp(UGR), and tRNAGly(AGR), suggesting that τm5U plays a critical role in the accurate d
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Zhang, Hong, Zhihui Lyu, Yongqiang Fan, et al. "Metabolic stress promotes stop-codon readthrough and phenotypic heterogeneity." Proceedings of the National Academy of Sciences 117, no. 36 (2020): 22167–72. http://dx.doi.org/10.1073/pnas.2013543117.

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Accurate protein synthesis is a tightly controlled biological process with multiple quality control steps safeguarded by aminoacyl-transfer RNA (tRNA) synthetases and the ribosome. Reduced translational accuracy leads to various physiological changes in both prokaryotes and eukaryotes. Termination of translation is signaled by stop codons and catalyzed by release factors. Occasionally, stop codons can be suppressed by near-cognate aminoacyl-tRNAs, resulting in protein variants with extended C termini. We have recently shown that stop-codon readthrough is heterogeneous among single bacterial ce
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Jobin, Parker G., Nestor Solis, Yoan Machado, et al. "Moonlighting matrix metalloproteinase substrates: Enhancement of proinflammatory functions of extracellular tyrosyl-tRNA synthetase upon cleavage." Journal of Biological Chemistry 295, no. 8 (2019): 2186–202. http://dx.doi.org/10.1074/jbc.ra119.010486.

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Tyrosyl-tRNA synthetase ligates tyrosine to its cognate tRNA in the cytoplasm, but it can also be secreted through a noncanonical pathway. We found that extracellular tyrosyl-tRNA synthetase (YRS) exhibited proinflammatory activities. In addition to acting as a monocyte/macrophage chemoattractant, YRS initiated signaling through Toll-like receptor 2 (TLR2) resulting in NF-κB activation and release of tumor necrosis factor α (TNFα) and multiple chemokines, including MIP-1α/β, CXCL8 (IL8), and CXCL1 (KC) from THP1 monocyte and peripheral blood mononuclear cell–derived macrophages. Furthermore, Y
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Pisareva, Vera P., and Andrey V. Pisarev. "DHX29 reduces leaky scanning through an upstream AUG codon regardless of its nucleotide context." Nucleic Acids Research 44, no. 9 (2016): 4252–65. http://dx.doi.org/10.1093/nar/gkw240.

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Abstract During eukaryotic translation initiation, the 43S preinitiation complex (43S PIC), consisting of the 40S ribosomal subunit, eukaryotic initiation factors (eIFs) and initiator tRNA scans mRNA to find an appropriate start codon. Key roles in the accuracy of initiation codon selection belong to eIF1 and eIF1A, whereas the mammalian-specific DHX29 helicase substantially contributes to ribosomal scanning of structured mRNAs. Here, we show that DHX29 stimulates the recognition of the AUG codon but not the near-cognate CUG codon regardless of its nucleotide context during ribosomal scanning.
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Melnikov, Sergey V., Keith D. Rivera, Denis Ostapenko, et al. "Error-prone protein synthesis in parasites with the smallest eukaryotic genome." Proceedings of the National Academy of Sciences 115, no. 27 (2018): E6245—E6253. http://dx.doi.org/10.1073/pnas.1803208115.

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Microsporidia are parasitic fungi-like organisms that invade the interior of living cells and cause chronic disorders in a broad range of animals, including humans. These pathogens have the tiniest known genomes among eukaryotic species, for which they serve as a model for exploring the phenomenon of genome reduction in obligate intracellular parasites. Here we report a case study to show an apparent effect of overall genome reduction on the primary structure and activity of aminoacyl-tRNA synthetases, indispensable cellular proteins required for protein synthesis. We find that most microspori
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34

Smoljanow, Daniela, Dennis Lebeda, Julia Hofhuis, and Sven Thoms. "Defining the high-translational readthrough stop codon context." PLOS Genetics 21, no. 6 (2025): e1011753. https://doi.org/10.1371/journal.pgen.1011753.

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Translational termination is not entirely efficient and competes with elongation, which might result in translational readthrough (TR). TR occurs when a near-cognate tRNA binds to a stop codon, (mis)interpreting it as a sense codon and producing a C-terminal extension of the protein. This process is influenced by the stop codon itself and the surrounding nucleotide sequence, known as the stop codon context (SCC). To investigate the role of these cis-acting elements beyond the high-TR motif UGA CUA G, this study examines specific positions within the SCC, both upstream and downstream of the mot
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35

Kämper, U., U. Kück, A. D. Cherniack, and A. M. Lambowitz. "The mitochondrial tyrosyl-tRNA synthetase of Podospora anserina is a bifunctional enzyme active in protein synthesis and RNA splicing." Molecular and Cellular Biology 12, no. 2 (1992): 499–511. http://dx.doi.org/10.1128/mcb.12.2.499-511.1992.

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The Neurospora crassa mitochondrial tyrosyl-tRNA synthetase (mt tyrRS), which is encoded by the nuclear gene cyt-18, functions not only in aminoacylation but also in the splicing of group I introns. Here, we isolated the cognate Podospora anserina mt tyrRS gene, designated yts1, by using the N. crassa cyt-18 gene as a hybridization probe. DNA sequencing of the P. anserina gene revealed an open reading frame (ORF) of 641 amino acids which has significant similarity to other tyrRSs. The yts1 ORF is interrupted by two introns, one near its N terminus at the same position as the single intron in t
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36

Kämper, U., U. Kück, A. D. Cherniack, and A. M. Lambowitz. "The mitochondrial tyrosyl-tRNA synthetase of Podospora anserina is a bifunctional enzyme active in protein synthesis and RNA splicing." Molecular and Cellular Biology 12, no. 2 (1992): 499–511. http://dx.doi.org/10.1128/mcb.12.2.499.

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The Neurospora crassa mitochondrial tyrosyl-tRNA synthetase (mt tyrRS), which is encoded by the nuclear gene cyt-18, functions not only in aminoacylation but also in the splicing of group I introns. Here, we isolated the cognate Podospora anserina mt tyrRS gene, designated yts1, by using the N. crassa cyt-18 gene as a hybridization probe. DNA sequencing of the P. anserina gene revealed an open reading frame (ORF) of 641 amino acids which has significant similarity to other tyrRSs. The yts1 ORF is interrupted by two introns, one near its N terminus at the same position as the single intron in t
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37

Biswas, Priyanka, Dillip K. Sahu, Kalyanasis Sahu, and Rajat Banerjee. "Spectroscopic Studies of Asparaginyl-tRNA Synthetase from Entamoeba histolytica." Protein & Peptide Letters 26, no. 6 (2019): 435–48. http://dx.doi.org/10.2174/0929866526666190327122419.

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Background: Aminoacyl-tRNA synthetases play an important role in catalyzing the first step in protein synthesis by attaching the appropriate amino acid to its cognate tRNA which then transported to the growing polypeptide chain. Asparaginyl-tRNA Synthetase (AsnRS) from Brugia malayi, Leishmania major, Thermus thermophilus, Trypanosoma brucei have been shown to play an important role in survival and pathogenesis. Entamoeba histolytica (Ehis) is an anaerobic eukaryotic pathogen that infects the large intestines of humans. It is a major cause of dysentery and has the potential to cause life-threa
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38

Nilsson, Kristina, Hans K. Lundgren, Tord G. Hagervall, and Glenn R. Björk. "The Cysteine Desulfurase IscS Is Required for Synthesis of All Five Thiolated Nucleosides Present in tRNA from Salmonella enterica Serovar Typhimurium." Journal of Bacteriology 184, no. 24 (2002): 6830–35. http://dx.doi.org/10.1128/jb.184.24.6830-6835.2002.

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ABSTRACT Deficiency of a modified nucleoside in tRNA often mediates suppression of +1 frameshift mutations. In Salmonella enterica serovar Typhimurium strain TR970 (hisC3737), which requires histidine for growth, a potential +1 frameshifting site, CCC-CAA-UAA, exists within the frameshifting window created by insertion of a C in the hisC gene. This site may be suppressed by peptidyl-tRNAProcmo5UGG (cmo5U is uridine-5-oxyacetic acid), making a frameshift when decoding the near-cognate codon CCC, provided that a pause occurs by, e.g., a slow entry of the tRNAGlnmnm5s2UUG (mnm5s2U is 5-methylamin
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39

Mangkalaphiban, Kotchaphorn, Feng He, Robin Ganesan, Chan Wu, Richard Baker, and Allan Jacobson. "Transcriptome-wide investigation of stop codon readthrough in Saccharomyces cerevisiae." PLOS Genetics 17, no. 4 (2021): e1009538. http://dx.doi.org/10.1371/journal.pgen.1009538.

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Translation of mRNA into a polypeptide is terminated when the release factor eRF1 recognizes a UAA, UAG, or UGA stop codon in the ribosomal A site and stimulates nascent peptide release. However, stop codon readthrough can occur when a near-cognate tRNA outcompetes eRF1 in decoding the stop codon, resulting in the continuation of the elongation phase of protein synthesis. At the end of a conventional mRNA coding region, readthrough allows translation into the mRNA 3’-UTR. Previous studies with reporter systems have shown that the efficiency of termination or readthrough is modulated by cis-act
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40

Sundararajan, Anuradha, William A. Michaud, Qiang Qian, Guillaume Stahl, and Philip J. Farabaugh. "Near-Cognate Peptidyl-tRNAs Promote +1 Programmed Translational Frameshifting in Yeast." Molecular Cell 4, no. 6 (1999): 1005–15. http://dx.doi.org/10.1016/s1097-2765(00)80229-4.

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41

Sanbonmatsu, Karissa Y. "Flipping through the Genetic Code: New Developments in Discrimination between Cognate and Near-Cognate tRNAs and the Effect of Antibiotics." Journal of Molecular Biology 426, no. 19 (2014): 3197–200. http://dx.doi.org/10.1016/j.jmb.2014.07.005.

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42

Beznosková, Petra, Stanislava Gunišová, and Leoš Shivaya Valášek. "Rules of UGA-N decoding by near-cognate tRNAs and analysis of readthrough on short uORFs in yeast." RNA 22, no. 3 (2016): 456–66. http://dx.doi.org/10.1261/rna.054452.115.

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43

Thakur, Anil, and Alan G. Hinnebusch. "eIF1 Loop 2 interactions with Met-tRNAi control the accuracy of start codon selection by the scanning preinitiation complex." Proceedings of the National Academy of Sciences 115, no. 18 (2018): E4159—E4168. http://dx.doi.org/10.1073/pnas.1800938115.

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The eukaryotic 43S preinitiation complex (PIC), bearing initiator methionyl transfer RNA (Met-tRNAi) in a ternary complex (TC) with eukaryotic initiation factor 2 (eIF2)-GTP, scans the mRNA leader for an AUG codon in favorable context. AUG recognition evokes rearrangement from an open PIC conformation with TC in a “POUT” state to a closed conformation with TC more tightly bound in a “PIN” state. eIF1 binds to the 40S subunit and exerts a dual role of enhancing TC binding to the open PIC conformation while antagonizing the PIN state, necessitating eIF1 dissociation for start codon selection. St
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44

Girodat, Dylan, Hans-Joachim Wieden, Scott C. Blanchard, and Karissa Y. Sanbonmatsu. "Geometric alignment of aminoacyl-tRNA relative to catalytic centers of the ribosome underpins accurate mRNA decoding." Nature Communications 14, no. 1 (2023). http://dx.doi.org/10.1038/s41467-023-40404-9.

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AbstractAccurate protein synthesis is determined by the two-subunit ribosome’s capacity to selectively incorporate cognate aminoacyl-tRNA for each mRNA codon. The molecular basis of tRNA selection accuracy, and how fidelity can be affected by antibiotics, remains incompletely understood. Using molecular simulations, we find that cognate and near-cognate tRNAs delivered to the ribosome by Elongation Factor Tu (EF-Tu) can follow divergent pathways of motion into the ribosome during both initial selection and proofreading. Consequently, cognate aa-tRNAs follow pathways aligned with the catalytic
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45

Saleh, Sima, and Philip J. Farabaugh. "Post-transcriptional modification to the core of tRNAs modulates translational misreading errors." RNA, October 31, 2023, rna.079797.123. http://dx.doi.org/10.1261/rna.079797.123.

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Protein synthesis on the ribosome involves the successive rapid recruitment of cognate aminoacyl-tRNAs and rejection the much more numerous incorrect near or non-cognates. The principal feature of translation elongation is that at every step many incorrect aa-tRNAs unsuccessfully enter the A site for each cognate accepted. Normal levels of translational accuracy require that cognate tRNAs have relatively similar rates of acceptance by the ribosome. To achieve that, tRNAs evolved to compensate for differences in amino acid properties and codon-anticodon strength. Part of that response involved
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46

She, Richard, Jingchuan Luo, and Jonathan S. Weissman. "Translational fidelity screens in mammalian cells reveal eIF3 and eIF4G2 as regulators of start codon selectivity." Nucleic Acids Research, May 5, 2023. http://dx.doi.org/10.1093/nar/gkad329.

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Abstract The translation initiation machinery and the ribosome orchestrate a highly dynamic scanning process to distinguish proper start codons from surrounding nucleotide sequences. Here, we performed genome-wide CRISPRi screens in human K562 cells to systematically identify modulators of the frequency of translation initiation at near-cognate start codons. We observed that depletion of any eIF3 core subunit promoted near-cognate start codon usage, though sensitivity thresholds of each subunit to sgRNA-mediated depletion varied considerably. Double sgRNA depletion experiments suggested that e
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47

Loveland, Anna B., Eugene Bah, Rohini Madireddy, et al. "Ribosome•RelA structures reveal the mechanism of stringent response activation." eLife 5 (July 19, 2016). http://dx.doi.org/10.7554/elife.17029.

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Stringent response is a conserved bacterial stress response underlying virulence and antibiotic resistance. RelA/SpoT-homolog proteins synthesize transcriptional modulators (p)ppGpp, allowing bacteria to adapt to stress. RelA is activated during amino-acid starvation, when cognate deacyl-tRNA binds to the ribosomal A (aminoacyl-tRNA) site. We report four cryo-EM structures of E. coli RelA bound to the 70S ribosome, in the absence and presence of deacyl-tRNA accommodating in the 30S A site. The boomerang-shaped RelA with a wingspan of more than 100 Å wraps around the A/R (30S A-site/RelA-bound)
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48

Valasek, Leos Shivaya, Michaela Kucerova, Jakub Zeman, and Petra Beznoskova. "Cysteine tRNA acts as a stop codon readthrough-inducing tRNA in the human HEK293T cell line." RNA, May 23, 2023, rna.079688.123. http://dx.doi.org/10.1261/rna.079688.123.

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Under certain circumstances, any of the three termination codons can be read through by a near-cognate tRNA; i.e. a tRNA whose two out of three anticodon nucleotides base-pair with those of the stop codon. Unless programmed to synthetize C-terminally extended protein variants with expanded physiological roles, readthrough represents an undesirable translational error. On the other side of a coin, a significant number of human genetic diseases is associated with the introduction of nonsense mutations (premature termination codons - PTCs) into coding sequences, where stopping is not desirable. H
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49

Holm, Mikael, Chandra Sekhar Mandava, Måns Ehrenberg, and Suparna Sanyal. "The mechanism of error induction by the antibiotic viomycin provides insight into the fidelity mechanism of translation." eLife 8 (June 7, 2019). http://dx.doi.org/10.7554/elife.46124.

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Applying pre-steady state kinetics to an Escherichia-coli-based reconstituted translation system, we have studied how the antibiotic viomycin affects the accuracy of genetic code reading. We find that viomycin binds to translating ribosomes associated with a ternary complex (TC) consisting of elongation factor Tu (EF-Tu), aminoacyl tRNA and GTP, and locks the otherwise dynamically flipping monitoring bases A1492 and A1493 into their active conformation. This effectively prevents dissociation of near- and non-cognate TCs from the ribosome, thereby enhancing errors in initial selection. Moreover
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50

Matsuura, Jin, Shinichiro Akichika, Fan-Yan Wei, et al. "Human DUS1L catalyzes dihydrouridine modification at tRNA positions 16/17, and DUS1L overexpression perturbs translation." Communications Biology 7, no. 1 (2024). http://dx.doi.org/10.1038/s42003-024-06942-8.

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AbstractHuman cytoplasmic tRNAs contain dihydrouridine modifications at positions 16 and 17 (D16/D17). The enzyme responsible for D16/D17 formation and its cellular roles remain elusive. Here, we identify DUS1L as the human tRNA D16/D17 writer. DUS1L knockout in the glioblastoma cell lines LNZ308 and U87 causes loss of D16/D17. D formation is reconstituted in vitro using recombinant DUS1L in the presence of NADPH or NADH. DUS1L knockout/overexpression in LNZ308 cells shows that DUS1L supports cell growth. Moreover, higher DUS1L expression in glioma patients is associated with poorer prognosis.
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