Surprising contribution to aminoacylation and translation of non-Watson–Crick pairs in tRNA

McClain, William H.

doi:10.1073/pnas.0600592103

Cited by 15 publications

(14 citation statements)

References 28 publications

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“…Some chimeras (data not shown) allowed efficient suppression in the absence of Cyc, suggesting that the resulting tRNAs were charged by endogenous E. coli tRNA synthetases. Edman degradation (data not shown) of a reporter protein based on the E. coli dihydrofolate reductase (DHFR) system containing a UAG codon in position 3 (18) revealed the presence of glutamine (80%), threonine (12%), and In vivo binding of tRNA Pyl to PylRS was determined by the yeast three-hybrid method as described in Materials and Methods. L represents loss of aminoacylation efficiency and is calculated as (k cat/KM mutant)/(kcat/KM wild type).…”

Section: Effect Of Mutations In Trna Pyl On In Vitro Charging By and mentioning

confidence: 99%

Pyrrolysine is not hardwired for cotranslational insertion at UAG codons

Ambrogelly¹,

Gundllapalli²,

Herring³

et al. 2007

Proc. Natl. Acad. Sci. U.S.A.

119

126

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Pyrrolysine (Pyl), the 22nd naturally encoded amino acid, gets acylated to its distinctive UAG suppressor tRNA Pyl by the cognate pyrrolysyl-tRNA synthetase (PylRS). Here we determine the RNA elements required for recognition and aminoacylation of tRNA Pyl in vivo by using the Pyl analog N--cyclopentyloxycarbonyl-L-lysine. Forty-two Methanosarcina barkeri tRNA Pyl variants were tested in Escherichia coli for suppression of the lac amber A24 mutation; then relevant tRNA Pyl mutants were selected to determine in vivo binding to M. barkeri PylRS in a yeast three-hybrid system and to measure in vitro tRNA Pyl aminoacylation. tRNA Pyl identity elements include the discriminator base, the first base pair of the acceptor stem, the T-stem base pair G51:C63, and the anticodon flanking nucleotides U33 and A37. Transplantation of the tRNA Pyl identity elements into the mitochondrial bovine tRNA Ser scaffold yielded chimeric tRNAs active both in vitro and in vivo. Because the anticodon is not important for PylRS recognition, a tRNA Pyl variant could be constructed that efficiently suppressed the lac opal U4 mutation in E. coli. These data suggest that tRNA Pyl variants may decode numerous codons and that tRNA Pyl :PylRS is a fine orthogonal tRNA:synthetase pair that facilitated the late addition of Pyl to the genetic code.orthogonal tRNA ͉ suppression ͉ tRNA identity ͉ pyrrolysyl-tRNA synthetase ͉ aminoacyl-tRNA synthetase

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Section: Effect Of Mutations In Trna Pyl On In Vitro Charging By and mentioning

confidence: 99%

Pyrrolysine is not hardwired for cotranslational insertion at UAG codons

Ambrogelly¹,

Gundllapalli²,

Herring³

et al. 2007

Proc. Natl. Acad. Sci. U.S.A.

119

126

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“…Stop codons also have a similar phenomena, with TAA, TAG and single nucleotide T common while AGG and AGA are rarely used (Cao, Wu and Yan, 2006). As previously reported (McClain, 2006), the start codons for the NAD4L gene and ATP6 gene in Os. tetraspis are TTG and ACA, both of them being unconventional.…”

Section: Genomes and Gene Featuresmentioning

confidence: 79%

“…Similarly, the putative tRNA Arg in Pa. trigonatus contains two non-Watson-Crick base pairs (both A/C) and one mismatch (A/A), appearing to be a new interesting example of mis-and unpaired bp (Roos, Aggarwal and Janke, 2007). It has been shown that non-Watson-Crick G/U and A/C pairings may play an important role in aminoacetylation and translation, primarily because of the conformational flexibility they provided, and unpaired nucleotides in stem regions may yield additional flexibility of the tRNA structure (McClain, 2006).…”

Section: Genomes and Gene Featuresmentioning

confidence: 98%

Two complete mitochondrial genomes of Crocodylus and implications for crocodilians phylogeny

Yan

Feng

et al. 2010

Amphib Reptilia

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The complete mitochondrial (mt) genomes of two crocodilians: Crocodylus palustris and Crocodylus mindorensis, were sequenced in order to examine their gene and genome features. Additionally, we intended to increase the amount of molecular data suitable for phylogenetic analysis. Their gene orders conform to other crocodilians that have been sequenced, except the arrangement of two tRNA genes differ from other vertebrates, showing that the gene order of crocodilians is remarkably conserved. Phylogenetic analyses (maximum likelihood, Bayesian inference) based on the mt protein-coding genes at the nucleotide level were performed among crocodilians for which complete mt genomes were available. The results suggest that the gharial (Gavialis gangeticus) joins the false gharial (Tomistoma schlegelii) on a common branch, that constitutes a sister group to traditional Crocodylidae. In this report, Mecistops cataphractus is evidently most closely related to Osteolaemus tetraspis. They are isolated as sister taxon from the main clades in Crocodylus. Regarding Paleosuchus, it appears as sister group to Caiman within the Alligatoridae. In particular, relationships among species of Crocodylus (true crocodiles) are discussed.

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“…Base pair 49-65 that has been shown to directly influence the translation (McClain 2006) is the only locus outside the anticodon domain (ACD) where the presence of covariations was found in all three domains of life (Fig. 6A,B).…”

Section: T Stemmentioning

confidence: 99%

Analysis of genomic tRNA sets from Bacteria, Archaea, and Eukarya points to anticodon–codon hydrogen bonds as a major determinant of tRNA compositional variations

Targanski¹,

Cherkasova²

2008

RNA

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Analysis of 100 complete sets of the cytoplasmic elongator tRNA genes from Bacteria, Archaea, and Eukarya pointed to correspondences between types of anticodon and composition of the rest of the tRNA body. The number of the hydrogen bonds formed between the complementary nucleotides in the anticodon-codon duplex appeared as a major quantitative parameter determining covariations in all three domains of life. Our analysis has supported and advanced the ''extended anticodon'' concept that is based on the argument that the decoding performance of the anticodon is enhanced by selection of a matching anticodon stem-loop sequence, as reported by Yarus in 1982. In addition to the anticodon stem-loop, we have found covariations between the anticodon nucleotides and the composition of the distant regions of their respective tRNAs that include dihydrouridine (D) and thymidyl (T) stem-loops. The majority of the covariable tRNA positions were found at the regions with the increased dynamic potential-such as stem-loop and stem-stem junctions. The consistent occurrences of the covariations on the multigenomic level suggest that the number and pattern of the hydrogen bonds in the anticodon-codon duplex constitute a major factor in the course of translation that is reflected in the fine-tuning of the tRNA composition and structure.

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Surprising contribution to aminoacylation and translation of non-Watson–Crick pairs in tRNA

Cited by 15 publications

References 28 publications

Pyrrolysine is not hardwired for cotranslational insertion at UAG codons

Pyrrolysine is not hardwired for cotranslational insertion at UAG codons

Two complete mitochondrial genomes of Crocodylus and implications for crocodilians phylogeny

Analysis of genomic tRNA sets from Bacteria, Archaea, and Eukarya points to anticodon–codon hydrogen bonds as a major determinant of tRNA compositional variations

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