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Shigeyuki Yokoyama – One of the best experts on this subject based on the ideXlab platform.

  • Structural insights into the first step of RNA-dependent cysteine biosynthesis in archaea
    Nature Structural & Molecular Biology, 2007
    Co-Authors: Ryuya Fukunaga, Shigeyuki Yokoyama

    Abstract:

    Cysteine is ligated to tRNA^Cys by cysteinyl-tRNA synthetase in most organisms. However, in methanogenic archaea lacking cysteinyl-tRNA synthetase, O -phosphoserine is ligated to tRNA^Cys by O -phosphoseryl–tRNA synthetase (SepRS), and the phosphoseryl-tRNA^Cys is converted to cysteinyl-tRNA^Cys. In this study, we determined the crystal structure of the SepRS tetramer in complex with tRNA^Cys and O -phosphoserine at 2.6-Å resolution. The catalytic domain of SepRS recognizes the negatively charged side chain of O -phosphoserine at a noncanonical site, using the dipole moment of a conserved α-helix. The unique C-terminal domain specifically recognizes the anticodon GCA of tRNA^Cys. On the basis of the structure, we engineered SepRS to recognize tRNA^Cys mutants with the Anticodons UCA and CUA and clarified the anticodon recognition mechanism by crystallography. The mutant SepRS-tRNA pairs may be useful for translational incorporation of O -phosphoserine into proteins in response to the stop codons UGA and UAG.

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  • Structural basis for anticodon recognition by discriminating glutamyl-tRNA synthetase.
    Nature Structural & Molecular Biology, 2001
    Co-Authors: Shun-ichi Sekine, Osamu Nureki, Atsushi Shimada, D.g. Vassylyev, Shigeyuki Yokoyama

    Abstract:

    Glutamyl-tRNA synthetases (GluRSs) are divided into two distinct types, with regard to the presence or absence of glutaminyl-tRNA synthetase (GlnRS) in the genetic translation systems. In the original 19-synthetase systems lacking GlnRS, the ‘non-discriminating’ GluRS glutamylates both tRNAGlu and tRNAGln. In contrast, in the evolved 20-synthetase systems with GlnRS, the ‘discriminating’ GluRS aminoacylates only tRNAGlu. Here we report the 2.4 A resolution crystal structure of a ‘discriminating’ GluRS·tRNAGlu complex from Thermus thermophilus. The GluRS recognizes the tRNAGlu anticodon bases via two α-helical domains, maintaining the base stacking. We show that the discrimination between the Glu and Gln Anticodons (34YUC36 and 34YUG36, respectively) is achieved by a single arginine residue (Arg 358). The mutation of Arg 358 to Gln resulted in a GluRS that does not discriminate between the Glu and Gln Anticodons. This change mimics the reverse course of GluRS evolution from anticodon ‘non-dicsriminating’ to ‘discriminating’.

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  • in vitrocodon reading specificities of unmodified trna molecules with different Anticodons on the sequence background ofescherichia colitrnaser1
    Biochemical and Biophysical Research Communications, 1999
    Co-Authors: Kazuyuki Takai, Hiroshi Takaku, Shigeyuki Yokoyama

    Abstract:

    The codon-reading properties of wobble-position variants of the unmodified form of Escherichia coli tRNASer1 (the UGA anticodon) were measured in a cell-free translation system. Two variants, with the AGA and CGA Anticodons, each exclusively read a single codon, UCU and UCG, respectively. The only case of efficient wobbling occurred with the variant with the GGA anticodon, which reads the UCU codon in addition to the UCC codon. Surprisingly, this wobble reading is more efficient than the Watson-Crick reading by the variant with the AGA anticodon. Furthermore, we prepared tRNA variants with AA, UC, and CU, instead of GA, in the second and third positions and measured their relative efficiencies in the reading of codons starting with UU, GA, and AG, respectively. The specificity concerning the wobble position is essentially the same as that in the case of the codons starting with UC.

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Richard Cordaux – One of the best experts on this subject based on the ideXlab platform.

  • Untangling Heteroplasmy, Structure, and Evolution of an Atypical Mitochondrial Genome by PacBio Sequencing.
    Genetics, 2017
    Co-Authors: Jean Peccoud, Mohamed Amine Chebbi, Alexandre Cormier, Bouziane Moumen, Clément Gilbert, Isabelle Marcadé, Christopher Chandler, Richard Cordaux

    Abstract:

    The highly compact mitochondrial (mt) genome of terrestrial isopods (Oniscidae) presents two unusual features. First, several loci can individually encode two tRNAs, thanks to single nucleotide polymorphisms at anticodon sites. Within-individual variation (heteroplasmy) at these loci is thought to have been maintained for millions of years because individuals that do not carry all tRNA genes die, resulting in strong balancing selection. Second, the oniscid mtDNA genome comes in two conformations: a ∼14 kb linear monomer and a ∼28 kb circular dimer comprising two monomer units fused in palindrome. We hypothesized that heteroplasmy actually results from two genome units of the same dimeric molecule carrying different tRNA genes at mirrored loci. This hypothesis, however, contradicts the earlier proposition that dimeric molecules result from the replication of linear monomers-a process that should yield totally identical genome units within a dimer. To solve this contradiction, we used the SMRT (PacBio) technology to sequence mirrored tRNA loci in single dimeric molecules. We show that dimers do present different tRNA genes at mirrored loci; thus covalent linkage, rather than balancing selection, maintains vital variation at Anticodons. We also leveraged unique features of the SMRT technology to detect linear monomers closed by hairpins and carrying noncomplementary bases at Anticodons. These molecules contain the necessary information to encode two tRNAs at the same locus, and suggest new mechanisms of transition between linear and circular mtDNA. Overall, our analyses clarify the evolution of an atypical mt genome where dimerization counterintuitively enabled further mtDNA compaction.

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  • Multiple Conserved Heteroplasmic Sites in tRNA Genes in the Mitochondrial Genomes of Terrestrial Isopods (Oniscidea).
    G3, 2015
    Co-Authors: Christopher H Chandler, Bouziane Moumen, Myriam Badawi, Pierre Grève, Richard Cordaux

    Abstract:

    Mitochondrial genome structure and organization are relatively conserved among metazoans. However, in many isopods, especially the terrestrial isopods (Oniscidea), the mitochondrial genome consists of both ∼14-kb linear monomers and ∼28-kb circular dimers. This unusual organization is associated with an ancient and conserved constitutive heteroplasmic site. This heteroplasmy affects the anticodon of a tRNA gene, allowing this single locus to function as a “dual” tRNA gene for two different amino acids. Here, we further explore the evolution of these unusual mitochondrial genomes by assembling complete mitochondrial sequences for two additional Oniscidean species, Trachelipus rathkei and Cylisticus convexus. Strikingly, we find evidence of two additional heteroplasmic sites that also alter tRNA Anticodons, creating additional dual tRNA genes, and that are conserved across both species. These results suggest that the unique linear/circular organization of isopods’ mitochondrial genomes may facilitate the evolution of stable mitochondrial heteroplasmies, and, conversely, once such heteroplasmies have evolved, they constrain the multimeric structure of the mitochondrial genome in these species. Finally, we outline some possible future research directions to identify the factors influencing mitochondrial genome evolution in this group.

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Sylvain Blanquet – One of the best experts on this subject based on the ideXlab platform.

  • Discrimination by Escherichia coli initiation factor IF3 against initiation on non-canonical codons relies on complementarity rules.
    Journal of Molecular Biology, 1999
    Co-Authors: Thierry Meinnel, C. Sacerdot, Sylvain Blanquet, Mathias Springer

    Abstract:

    Translation initiation factor IF3, one of three factors specifically required for translation initiation in Escherichia coli, inhibits initiation on any codon other than the three canonical initiation codons, AUG, GUG, or UUG. This discrimination against initiation on non-canonical codons could be due to either direct recognition of the two last bases of the codon and their cognate bases on the anticodon or to some ability to “feel” codon-anticodon complementarity. To investigate the importance of codon-anticodon complementarity in the discriminatory role of IF3, we constructed a derivative of tRNALeuthat has all the known characteristics of an initiator tRNA except the CAU anticodon. This tRNA is efficiently formylated by methionyl-tRNAfMettransformylase and charged by leucyl-tRNA synthetase irrespective of the sequence of its anticodon. These initiator tRNALeuderivatives (called tRNALI) allow initiation at all the non-canonical codons tested, provided that the complementarity between the codon and the anticodon of the initiator tRNALeuis respected. More remarkably, the discrimination by IF3, normally observed with non-canonical codons, is neutralised if a tRNALIcarrying a complementary anticodon is used for initiation. This suggests that IF3 somehow recognises codon-anticodon complementarity, at least at the second and third position of the codon, rather than some specific bases in either the codon or the anticodon.

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  • two acidic residues of escherichia coli methionyl trna synthetase act as negative discriminants towards the binding of non cognate trna Anticodons
    Journal of Molecular Biology, 1993
    Co-Authors: Emmanuelle Schmitt, Thierry Meinnel, Yves Mechulam, Michel Panvert, Sylvain Blanquet

    Abstract:

    Abstract Escherichia coli methionyl-tRNA synthetase recognizes its cognate tRNAs according to the sequence of the CAU anticodon. In order to identify residues of methionyl-tRNA synthetase involved in tRNA anticodon recognition, enzyme variants created by cassette mutagenesis were genetically screened for their acquired ability to charge tRNA Met m derivatives with an ochre or an amber anticodon and, consequently, to cause the suppression of a stop codon in an indicator gene. The selected enzymes are called suppressors. Mutations were firstly directed towards the region of the synthetase encompassing residues 451 to 467. Several dozens of suppressor enzymes were compared. Statistical analysis of the mutations suggested that the substitution of an Asp side-chain at position 456 was sufficient to render possible the charging of the ochre or amber suppressor tRNAs. Point mutants at this position were therefore constructed. Their behaviour demonstrated that various tRNA Met derivatives having a non-Met anticodon could be aminoacylated in vitro provided only that the side-chain of residue 456 was no longer acidic. In turn, the Asp456 residue is not essential to the CAU anticodon recognition, since its substitution does not impair the aminoacylation of wild-type tRNA Met . The analysis was enlarged to a second region from residue 437 to residue 454. The mutagenesis highlighted two other positions, one of which, Asn452, appeared involved in wild-type tRNA Met binding. The second position, Asp449, plays a role very similar to that of Asp456. It is concluded that both Asp449 and 456 behave as “antideterminants”, contributing together to the rejection by the enzyme of tRNAs carrying non-Met Anticodons. Finally, it is shown that the activities of some particular methionyl-tRNA synthetase variants, which have been made indifferent to the sequence of the anticodon of a tRNA Met , are tightly dependent on the presence of the nucleotide determinants specific to the acceptor stem of tRNA Met .

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  • Selection of suppressor methionyl-tRNA synthetases: mapping the tRNA anticodon binding site.
    Proceedings of the National Academy of Sciences of the United States of America, 1991
    Co-Authors: Thierry Meinnel, Sylvain Blanquet, Yves Mechulam, D Le Corre, Michel Panvert, Guy Fayat

    Abstract:

    Abstract
    Accurate aminoacylation of a tRNA by Escherichia coli methionyl-tRNA synthetase (MTS) is specified by the CAU anticodon. A genetic screening procedure was designed to isolate MTS mutants able to aminoacylate a methionine amber tRNA (CUA anticodon). Selected suppressor MTS enzymes all possess one or several mutations in the vicinity of Trp-461, a residue that is the major contributor to the stability of complexes formed with tRNAs having the cognate CAU anticodon. Analysis of catalytic properties of purified suppressor enzymes shows that they have acquired an additional specificity toward the amber anticodon without complete disruption of the methionine anticodon site. It is concluded that both positive and negative discrimination toward the binding of tRNA anticodon sequences is restricted to a limited region of the synthetase, residues 451-467.

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