Alternative genetic code for amino acids and transfer RNA revisited

Hamashima, Kiyofumi; Kanai, Akio

doi:10.1515/bmc-2013-0002

Cited by 9 publications

(12 citation statements)

References 72 publications

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“…Recent studies have identified a number of non-canonical tRNA species that were previously mis-annotated or undetected due to their unusual recognition elements, anticodon sequences and irregular secondary structures (6–15). Interestingly, although the function of many of them remains unknown (5,6,8), some of these non-canonical tRNAs are known to be responsible for changes to the universal meaning of the genetic code (7,10–15). Therefore, proper identification of tRNA genes is important to identify genetic code variations in nature (10,13).…”

Section: Introductionmentioning

confidence: 99%

Transfer RNAs with novel cloverleaf structures

Mukai¹,

Vargas-Rodriguez²,

Englert³

et al. 2016

Nucleic Acids Res

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We report the identification of novel tRNA species with 12-base pair amino-acid acceptor branches composed of longer acceptor stem and shorter T-stem. While canonical tRNAs have a 7/5 configuration of the branch, the novel tRNAs have either 8/4 or 9/3 structure. They were found during the search for selenocysteine tRNAs in terabytes of genome, metagenome and metatranscriptome sequences. Certain bacteria and their phages employ the 8/4 structure for serine and histidine tRNAs, while minor cysteine and selenocysteine tRNA species may have a modified 8/4 structure with one bulge nucleotide. In Acidobacteria, tRNAs with 8/4 and 9/3 structures may function as missense and nonsense suppressor tRNAs and/or regulatory noncoding RNAs. In δ-proteobacteria, an additional cysteine tRNA with an 8/4 structure mimics selenocysteine tRNA and may function as opal suppressor. We examined the potential translation function of suppressor tRNA species in Escherichia coli; tRNAs with 8/4 or 9/3 structures efficiently inserted serine, alanine and cysteine in response to stop and sense codons, depending on the identity element and anticodon sequence of the tRNA. These findings expand our view of how tRNA, and possibly the genetic code, is diversified in nature.

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Section: Introductionmentioning

confidence: 99%

Transfer RNAs with novel cloverleaf structures

Mukai¹,

Vargas-Rodriguez²,

Englert³

et al. 2016

Nucleic Acids Res

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“…We have previously identified nematode-specific novel tRNA genes, designated nev-tRNAs, e.g., nev-tRNA Gly (CCC) and nev-tRNA Ile (UAU), which contain 15–20-nt V-arm structures and are solely charged with Leu instead of Gly or Ile in vitro [ 8 , 16 ]. To obtain further evidence of the functionality of nev-tRNAs in cells, the following two characteristics were analyzed: (1) their maturation, with the addition of 3′ CCA; and (2) their subcellular localization.…”

Section: Resultsmentioning

confidence: 99%

“…This faithful translation of the genetic code is a central pillar of molecular biology, and is maintained by the accuracy of tRNA aminoacylation and codon–anticodon matching. Therefore, any deviation from these sequential molecular recognition rules reflects the imperfection of the translation process, resulting in ‘genetic code ambiguity’ [ 6 – 8 ]. A number of instances of natural codon reassignment suggest that genetic code ambiguity has evolutionary implications.…”

Section: Introductionmentioning

confidence: 99%

“…Recent genome sequencing projects have identified a large number of eukaryotic tRNA isodecoders, tRNA molecules that share the same anticodons but differ in their molecular sequences, which sometimes contribute to the genome architecture and evolution [ 8 , 13 ]. Several genomes of nematodes in the genus Caenorhabditis encode tRNA Gly (CCC) and tRNA Ile (UAU) molecules with an additional stem–loop structure in the variable region [ 14 ], called the “variable arm” (V-arm), although tRNAs containing the V-arm are generally restricted to tRNA Leu and tRNA Ser in eukaryotes [ 15 ].…”

Section: Introductionmentioning

confidence: 99%

“…Several genomes of nematodes in the genus Caenorhabditis encode tRNA Gly (CCC) and tRNA Ile (UAU) molecules with an additional stem–loop structure in the variable region [ 14 ], called the “variable arm” (V-arm), although tRNAs containing the V-arm are generally restricted to tRNA Leu and tRNA Ser in eukaryotes [ 15 ]. In a previous study, we designated these “nematode-specific V-arm-containing tRNAs” (nev-tRNAs) and demonstrated their weak expression in C. elegans [ 8 , 16 ]. In vitro aminoacylation assays have clearly shown that these tRNAs are solely charged with Leu, instead of glycine (Gly) or isoleucine (Ile).…”

Section: Introductionmentioning

confidence: 99%

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Analysis of Genetic Code Ambiguity Arising from Nematode-Specific Misacylated tRNAs

et al. 2015

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The faithful translation of the genetic code requires the highly accurate aminoacylation of transfer RNAs (tRNAs). However, it has been shown that nematode-specific V-arm-containing tRNAs (nev-tRNAs) are misacylated with leucine in vitro in a manner that transgresses the genetic code. nev-tRNAGly (CCC) and nev-tRNAIle (UAU), which are the major nev-tRNA isotypes, could theoretically decode the glycine (GGG) codon and isoleucine (AUA) codon as leucine, causing GGG and AUA codon ambiguity in nematode cells. To test this hypothesis, we investigated the functionality of nev-tRNAs and their impact on the proteome of Caenorhabditis elegans. Analysis of the nucleotide sequences in the 3’ end regions of the nev-tRNAs showed that they had matured correctly, with the addition of CCA, which is a crucial posttranscriptional modification required for tRNA aminoacylation. The nuclear export of nev-tRNAs was confirmed with an analysis of their subcellular localization. These results show that nev-tRNAs are processed to their mature forms like common tRNAs and are available for translation. However, a whole-cell proteome analysis found no detectable level of nev-tRNA-induced mistranslation in C. elegans cells, suggesting that the genetic code is not ambiguous, at least under normal growth conditions. Our findings indicate that the translational fidelity of the nematode genetic code is strictly maintained, contrary to our expectations, although deviant tRNAs with misacylation properties are highly conserved in the nematode genome.

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Codon usage bias

2021

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Codon usage bias is the preferential or non-random use of synonymous codons, a ubiquitous phenomenon observed in bacteria, plants and animals. Different species have consistent and characteristic codon biases. Codon bias varies not only with species, family or group within kingdom, but also between the genes within an organism. Codon usage bias has evolved through mutation, natural selection, and genetic drift in various organisms. Genome composition, GC content, expression level and length of genes, position and context of codons in the genes, recombination rates, mRNA folding, and tRNA abundance and interactions are some factors influencing codon bias. The factors shaping codon bias may also be involved in evolution of the universal genetic code. Codon-usage bias is critical factor determining gene expression and cellular function by influencing diverse processes such as RNA processing, protein translation and protein folding. Codon usage bias reflects the origin, mutation patterns and evolution of the species or genes. Investigations of codon bias patterns in genomes can reveal phylogenetic relationships between organisms, horizontal gene transfers, molecular evolution of genes and identify selective forces that drive their evolution. Most important application of codon bias analysis is in the design of transgenes, to increase gene expression levels through codon optimization, for development of transgenic crops. The review gives an overview of deviations of genetic code, factors influencing codon usage or bias, codon usage bias of nuclear and organellar genes, computational methods to determine codon usage and the significance as well as applications of codon usage analysis in biological research, with emphasis on plants.

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Alternative genetic code for amino acids and transfer RNA revisited

Cited by 9 publications

References 72 publications

Transfer RNAs with novel cloverleaf structures

Transfer RNAs with novel cloverleaf structures

Analysis of Genetic Code Ambiguity Arising from Nematode-Specific Misacylated tRNAs

Codon usage bias

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