Anticodons

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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.

  • 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'.

  • 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.

  • chapter 9 modified uridines in the first positions of anti codons of trnas and mechanisms of codon recognition
    Journal of chromatography library, 1990
    Co-Authors: Shigeyuki Yokoyama, Tatsuo Miyazawa
    Abstract:

    Publisher Summary Proton nuclear magnetic resonance (NMR) analyses have been made of the conformational characteristics of modified nucleotides as found in the first position of the Anticodons of transfer RNAs (tRNAs), namely the derivatives of 5-methyl-2-thiouridine 5'-monophosphate (pxm 5 s 2 U) and derivatives of 5-hydroxyuridine 5'-monophosphate (pxo 5 U). In pxm 5 s 2 U, the C 3'-endo form is remarkably more stable than the C 2'-endo form for the ribose ring, because of the effects of the bulky 2-thiocarbonyl group and long-chain 5-substituent. By contrast, in pxo 5 U, the C 2'-endo form is much more stable than the C 3'-endo form, because of the interaction between the 5-substituent and 5'-phosphate group. The enthalpy differences between the C 2'-endo form and the C 3'-endo form have been obtained as 1.1, -0.7, and 0.1 kca1 /mol for pxm 5 s 2 U, pxo 5 U, and unmodified uridine 5'-monophosphate, respectively. The xm 5 s 2 U in the first position of the anticodon takes only the C 3'-endo form to recognize A as the third letter of the codon, whereas xo 5 U takes the C 2'-endo form as well as the C 3'-endo form to recognize U, A, and G as the third letter of the codon on the ribosome.

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.

  • 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.

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.

  • 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 .

  • 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.

Dieter Söll - One of the best experts on this subject based on the ideXlab platform.

  • recoding of the selenocysteine uga codon by cysteine in the presence of a non canonical trnacys and elongation factor selb
    RNA Biology, 2018
    Co-Authors: Oscar Vargasrodriguez, Markus Englert, Anna Merkuryev, Takahito Mukai, Dieter Söll
    Abstract:

    ABSTRACTIn many organisms, the UGA stop codon is recoded to insert selenocysteine (Sec) into proteins. Sec incorporation in bacteria is directed by an mRNA element, known as the Sec-insertion sequence (SECIS), located downstream of the Sec codon. Unlike other aminoacyl-tRNAs, Sec-tRNASec is delivered to the ribosome by a dedicated elongation factor, SelB. We recently identified a series of tRNASec-like tRNA genes distributed across Bacteria that also encode a canonical tRNASec. These tRNAs contain sequence elements generally recognized by cysteinyl-tRNA synthetase (CysRS). While some of these tRNAs contain a UCA Sec anticodon, most have a GCA Cys anticodon. tRNASec with GCA Anticodons are known to recode UGA codons. Here we investigate the clostridial Desulfotomaculum nigrificans tRNASec-like tRNACys, and show that this tRNA is acylated by CysRS, recognized by SelB, and capable of UGA recoding with Cys in Escherichia coli. We named this non-canonical group of tRNACys as ‘tRNAReC’ (Recoding with Cys). We p...

  • Transfer RNA identity change in anticodon variants of E. coli tRNA(Phe) in vivo.
    Molecules and Cells, 2000
    Co-Authors: Hyun S. Kim, Ick Young Kim, Dieter Söll, Yong Lee
    Abstract:

    The anticodon sequence is a major recognition element for most aminoacyl-tRNA synthetases. We investigated the in vivo effects of changing the anticodon on the aminoacylation specificity in the example of E. coli tRNAPhe. Constructing different anticodon mutants of E. coli tRNAPhe by site-directed mutagenesis, we isolated 22 anticodon mutant tRNAPhe; the Anticodons corresponded to 16 amino acids and an opal stop codon. To examine whether the mutant tRNAs had changed their amino acid acceptor specificity in vivo, we tested the viability of E. coli strains containing these tRNAPhe genes in a medium which permitted tRNA induction. Fourteen mutant tRNA genes did not affect host viability. However, eight mutant tRNA genes were toxic to the host and prevented growth, presumably because the anticodon mutants led to translational errors. Many mutant tRNAs which did not affect host viability were not aminoacylated in vivo. Three mutant tRNAs containing anticodon sequences corresponding to lysine (UUU), methionine (CAU) and threonine (UGU) were charged with the amino acid corresponding to their anticodon, but not with phenylalanine. These three tRNAs and tRNAPhe are located in the same cluster in a sequence similarity dendrogram of total E. coli tRNAs. The results support the idea that such tRNAs arising from in vivo evolution are derived by anticodon change from the same ancestor tRNA.

  • anticodon and acceptor stem nucleotides in trna gln are major recognition elements for e coli glutaminyl trna synthetase
    Nature, 1991
    Co-Authors: Martina Jahn, John M Rogers, Dieter Söll
    Abstract:

    THE correct attachment of amino acids to their corresponding (cognate) transfer RNA catalysed by aminoacyl-tRNA synthetases is a key factor in ensuring the fidelity of protein biosynthesis. Previous studies have demonstrated that the interaction of Escherichia coli tRNAGln with glutaminyl-tRNA synthetase (GlnRS) provides an excellent system1 to study this highly specific recognition process, also referred to as 'tRNA identity'2. Accurate acylation of tRNA depends mainly on two principles: a set of nucleotides in the tRNA molecule (identity elements) responsible for proper discrimination by aminoacyl-tRNA synthetases1–3 and competition between different synthetases for tRNAs4–6. Elements of glutamine identity are located in the anticodon2, 7–9 and in the acceptor stem region, including the discriminator base5, 10–13. We report here the production of more than 20 tRNAGln2 mutants at positions likely to be involved in tRNA discrimination by the enzyme. Unmodified tRNA, containing the wild-type anticodon and U or G at its 5′-terminus, can be aminocylated by GlnRS with similar kinetic parameters to native tRNAGln2. By in vitro aminoacylation the mutant tRNAs showed decreases of up to 3 x 105-fold in the specificity constant (kcat/KM)14 with the major contribution of kcat. Despite these large changes, some of these mutant tRNAs are efficient amber suppressors in vivo. Our results show that strong elements for glutamine identity reside in the anticodon region and in positions 2 and 3 of the acceptor stem, and that the contribution of different identity elements to the overall discrimination varies significantly. We discuss our data in the light of the crystal structure of the GlnRS :tRNAGln complex15, 16.

Hervé Seligmann - One of the best experts on this subject based on the ideXlab platform.

  • First arrived, first served: competition between codons for codon-amino acid stereochemical interactions determined early genetic code assignments
    The Science of Nature, 2020
    Co-Authors: Hervé Seligmann
    Abstract:

    Stereochemical nucleotide-amino acid interactions, in the form of noncovalent nucleotide-amino acid interactions, potentially produced the genetic code’s codon-amino acid assignments. Empirical estimates of single nucleotide-amino acid affinities on surfaces and in solution are used to test whether trinucleotide-amino acid affinities determined genetic code assignments pending the principle “first arrived, first served”: presumed early amino acids have greater codon-amino acid affinities than ulterior ones. Here, these single nucleotide affinities are used to approximate all 64 × 20 trinucleotide-amino acid affinities. Analyses show that (1) on surfaces, genetic code codon-amino acid assignments tend to match high affinities for the amino acids that integrated earliest the genetic code (according to Wong’s metabolic coevolution hypothesis between nucleotides and amino acids) and (2) in solution, the same principle holds for the anticodon-amino acid assignments. Affinity analyses match best genetic code assignments when assuming that trinucleotides competed for amino acids, rather than amino acids for trinucleotides. Codon-amino acid affinities stick better to genetic code assignments than anticodon-amino acid affinities. Presumably, two independent coding systems, on surfaces and in solution, converged, and formed the current translation system. Proto-translation on surfaces by direct codon-amino acid interactions without tRNA-like adaptors coadapted with a system emerging in solution by proto-tRNA anticodon-amino acid interactions. These systems assigned identical or similar cognates to codons on surfaces and to Anticodons in solution. Results indicate that a prebiotic metabolism predated genetic code self-organization.

  • The Uroboros Theory of Life’s Origin: 22-Nucleotide Theoretical Minimal RNA Rings Reflect Evolution of Genetic Code and tRNA-rRNA Translation Machineries
    Acta Biotheoretica, 2019
    Co-Authors: Jacques Demongeot, Hervé Seligmann
    Abstract:

    Theoretical minimal RNA rings attempt to mimick life’s primitive RNAs. At most 25 22-nucleotide-long RNA rings code once for each biotic amino acid, a start and a stop codon and form a stem-loop hairpin, resembling consensus tRNAs. We calculated, for each RNA ring’s 22 potential splicing positions, similarities of predicted secondary structures with tRNA vs. rRNA secondary structures. Assuming rRNAs partly derived from tRNA accretions, we predict positive associations between relative secondary structure similarities with rRNAs over tRNAs and genetic code integration orders of RNA ring anticodon cognate amino acids. Analyses consider for each secondary structure all nucleotide triplets as potential anticodon. Anticodons for ancient, chemically inert cognate amino acids are most frequent in the 25 RNA rings. For RNA rings with primordial cognate amino acids according to tRNA-homology-derived Anticodons, tRNA-homology and coding sequences coincide, these are separate for predicted cognate amino acids that presumably integrated late the genetic code. RNA ring secondary structure similarity with rRNA over tRNA secondary structures associates best with genetic code integration orders of anticodon cognate amino acids when assuming split Anticodons (one and two nucleotides at the spliced RNA ring 5′ and 3′ extremities, respectively), and at predicted anticodon location in the spliced RNA ring’s midst. Results confirm RNA ring homologies with tRNAs and CDs, ancestral status of tRNA half genes split at Anticodons, the tRNA-rRNA axis of RNA evolution, and that single theoretical minimal RNA rings potentially produce near-complete proto-tRNA sets. Hence genetic code pre-existence determines 25 short circular gene- and tRNA-like RNAs. Accounting for each potential splicing position, each RNA ring potentially translates most amino acids, realistically mimicks evolution of the tRNA-rRNA translation machinery. These RNA rings ‘of creation’ remind the uroboros’ (snake biting its tail) symbolism for creative regeneration.

  • Putative Anticodons in mitochondrial tRNA sidearm loops: Pocketknife tRNAs?
    Journal of Theoretical Biology, 2013
    Co-Authors: Hervé Seligmann
    Abstract:

    The hypothesis that tRNA sidearm loops bear Anticodons assumes crossovers between anticodon and sidearms, or translation by expressed aminoacylated tRNA halves forming single stem-loops. Only the latter might require ribosomal adaptations. Drosophila mitochondrial codon usages coevolve with sidearm numbers bearing matching putative Anticodons (comparing different codon families in one genome, macroevolution) and when comparing different genomes for single codon families (microevolution). Coevolution between Drosophila and yeast mitochondrial antisense tRNAs and codon usages partly confounds microevolutionary patterns for putative sidearm Anticodons. Some tRNA sidearm loops have more than seven nucleotides, putative expanded Anticodons potentially matching quadruplet codons (tetracodons, codons expanded by a fourth silent position, forming tetragenes (predicted by alignment analyses of Drosophila mitochondrial genomes)). Tetracodon numbers coevolve with expanded tRNA sidearm loops. Sidearm coevolution with amino acid usages and tetragenes occurs for putative Anticodons in 5' and 3' sidearms loops (D and TΨC loops, respectively), are stronger for the D-loop. Results slightly favour isolated stem-loops upon crossover hypotheses. An alternative hypothesis, that patterns observed for sidearm 'Anticodons' do not imply translational activity, but recognition signals for tRNA synthetases that aminoacylate tRNAs, is incompatible with tetracodon/tetra-anticodon coevolution. Hence analyses strengthen translational hypotheses for tRNA sidearm Anticodons, tetragenes, and antisense tRNAs.

  • Pocketknife tRNA hypothesis: Anticodons in mammal mitochondrial tRNA side-arm loops translate proteins?
    BioSystems, 2013
    Co-Authors: Hervé Seligmann
    Abstract:

    Abstract Peptide elongation proceeds by tRNA Anticodons recognizing mRNA codons coding for the tRNA's cognate amino acid. Putatively, tRNAs possess three Anticodons because tRNA side and anticodon-arms form similar stem-loop structures. Two lines of evidence indicate that mammal mitochondrial tRNA sidearms function as Anticodons: numbers of TΨC-arm ‘Anticodons’ matching specific cognates coevolve with that cognate's usage in mitochondrial genomes; and predicted ‘tetragene’ numbers, genes coded by quadruplet codons (tetracodons), coevolve with numbers of expanded Anticodons in D-arms, as previously observed between tetragenes and antisense tRNA expanded Anticodons. Sidearms with long stems and high GC contents contribute most to tRNA sidearm-tetragene coevolution. Results are compatible with two hypothetical mechanisms for translation by side-arms: crossovers exchange anticodon- and side-arms; tRNA sidearms are excised, aminoacylated and function as isolated stem-loop hairpins (more probable for long, respectively stable branches). Isolated sidearms would resemble recently described armless ‘minimal’ tRNAs. Isolated hairpins might most parsimoniously explain observed patterns. tRNA genes templating for three, rather than one functional tRNA, compress minimal genome size. Results suggest fused tRNA halves form(ed) modern tRNAs, isolated tRNA subparts occasionally translate proteins. Results confirm translational activity by antisense tRNAs, whose Anticodons also coevolve with codon usages. Accounting for antisense Anticodons improves results for sidearm Anticodons.

  • putative mitochondrial polypeptides coded by expanded quadruplet codons decoded by antisense trnas with unusual Anticodons
    BioSystems, 2012
    Co-Authors: Hervé Seligmann
    Abstract:

    Abstract Weak triplet codon–anticodon interactions render ribosome-free translation unlikely. Some modern tRNAs read quadruplet codons (tetracodons), suggesting vestigial ribosome-free translation. Here, mitochondrial genomes are explored for tetracoded overlapping protein coding (tetra)genes. Occasional single tetracodons within regular mitochondrial genes coevolve positively/negatively with antisense tRNAs with predicted reduced/expanded Anticodons (depending on taxon), suggesting complex tetra-decoding mechanisms. Transcripts of antisense tRNAs with unusual Anticodons are more abundant than of homologues with regular Anticodons. Assuming overlapping tetracoding with silent 4th tetracodon position, BLAST aligns 10 putative tetragenes spanning 17% of regular human mitochondrial protein coding tricodons with 14 GenBank proteins. Various tests including predicted peptide secondary structures, 3rd codon position (of the regular main frame of the protein coding gene) conservation against replicational deamination mutation gradients, and circular code usage (overlapping genes avoid using circular code codons) confirm tetracoding in these overlapping tetragenes with silent 4th position, but not for BLAST-predicted tetragenes assuming silent 2nd or 3rd positions. This converges with tetradecoding mechanisms that are more compatible with silent 4th, than at other, tetracodon positions. Tetracoding increases with (a) GC-contents, perhaps conserved or switched on in high temperature conditions; (b) usage of theoretically predicted ‘tessera’ tetracodons; (c) 12s rRNA stability; and d) antisense tRNA numbers with predicted expanded Anticodons. Most detected tetragenes are not evolutionarily conserved, apparently reflect specific, transient adaptations. Tetracoding increases with mammal longevity.