Problem and paradigms: Unconventional methods in codon reading

Lagerkvist, Ulf

doi:10.1002/bies.950040509

Cited by 12 publications

(11 citation statements)

References 27 publications

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“…Two out of three decoding postulates that a tRNA pairing with only the first two codon bases (usually a G and a C) can be sufficient for translation and that any base can occur at the third (wobble) codon position (opposite position 34 of the tRNA; Figure 1). This mechanism is supported by several examples (Lagerkvist, 1986). It has also been suggested to occur in chloroplasts (Shinozaki et al, 1986) and supported by in vitro experiments using wheat (Triticum aestivum) germ extracts and bean (Phaseolus vulgaris) chloroplast tRNAs (Pfitzinger et al, 1990).…”

Section: Introductionmentioning

confidence: 70%

Arabidopsis tRNA Adenosine Deaminase Arginine Edits the Wobble Nucleotide of Chloroplast tRNAArg(ACG) and Is Essential for Efficient Chloroplast Translation

et al. 2009

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RNA editing changes the coding/decoding information relayed by transcripts via nucleotide insertion, deletion, or conversion. Editing of tRNA anticodons by deamination of adenine to inosine is used both by eukaryotes and prokaryotes to expand the decoding capacity of individual tRNAs. This limits the number of tRNA species required for codon-anticodon recognition. We have identified the Arabidopsis thaliana gene that codes for tRNA adenosine deaminase arginine (TADA), a chloroplast tRNA editing protein specifically required for deamination of chloroplast (cp)-tRNA Arg (ACG) to cp-tRNA Arg (ICG). Land plant TADAs have a C-terminal domain similar in sequence and predicted structure to prokaryotic tRNA deaminases and also have very long N-terminal extensions of unknown origin and function. Biochemical and mutant complementation studies showed that the C-terminal domain is sufficient for cognate tRNA deamination both in vitro and in planta. Disruption of TADA has profound effects on chloroplast translation efficiency, leading to reduced yields of chloroplast-encoded proteins and impaired photosynthetic function. By contrast, chloroplast transcripts accumulate to levels significantly above those of wild-type plants. Nevertheless, absence of cp-tRNA Arg (ICG) is compatible with plant survival, implying that two out of three CGN codon recognition occurs in chloroplasts, though this mechanism is less efficient than wobble pairing.

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Section: Introductionmentioning

confidence: 70%

Arabidopsis tRNA Adenosine Deaminase Arginine Edits the Wobble Nucleotide of Chloroplast tRNAArg(ACG) and Is Essential for Efficient Chloroplast Translation

et al. 2009

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“…SS5). This enzyme acts on all tRNAs harboring a U 35 in the middle position of anticodon, thus G 34 -containing tRNAs specific for His, Asn, Asp of the 2-synonymous codon family boxes. The Tgt enzyme (COG0345) is almost universally found in both Bacteria and Eukarya ( [87]).…”

Section: Tyr/stop-or-gln (Uan 3 ) Decoding Boxmentioning

confidence: 99%

Deciphering synonymous codons in the three domains of life: Co‐evolution with specific tRNA modification enzymes

2009

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a b s t r a c tThe strategies organisms use to decode synonymous codons in cytosolic protein synthesis are not uniform. The complete isoacceptor tRNA repertoire and the type of modified nucleoside found at the wobble position 34 of their anticodons were analyzed in all kingdoms of life. This led to the identification of four main decoding strategies that are diversely used in Bacteria, Archaea and Eukarya. Many of the modern tRNA modification enzymes acting at position 34 of tRNAs are present only in specific domains and obviously have arisen late during evolution. In an evolutionary fine-tuning process, these enzymes must have played an essential role in the progressive introduction of new amino acids, and in the refinement and standardization of the canonical nuclear genetic code observed in all extant organisms (functional convergent evolutionary hypothesis).

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“…Lagerkvist suggested the following interpretation: ''codons may be read according to the two-out-of three principle that relies mainly on the Watson-Crick base pairs formed with the first two codon positions, while the mispaired nucleotides in the third codon and anticodon wobble positions make a comparatively small contribution to the total stability of the reading interaction'' (Lagerkvist 1986).…”

Section: Introductionmentioning

confidence: 99%

Degeneracy of the genetic code and stability of the base pair at the second position of the anticodon

Lehmann¹,

Libchaber²

2008

RNA

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Problem and paradigms: Unconventional methods in codon reading

Cited by 12 publications

References 27 publications

Arabidopsis tRNA Adenosine Deaminase Arginine Edits the Wobble Nucleotide of Chloroplast tRNAArg(ACG) and Is Essential for Efficient Chloroplast Translation

Arabidopsis tRNA Adenosine Deaminase Arginine Edits the Wobble Nucleotide of Chloroplast tRNAArg(ACG) and Is Essential for Efficient Chloroplast Translation

Deciphering synonymous codons in the three domains of life: Co‐evolution with specific tRNA modification enzymes

Degeneracy of the genetic code and stability of the base pair at the second position of the anticodon

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