The Triplet Code From First Principles

Trifonov, Edward N.

doi:10.1080/07391102.2004.10506975

Cited by 232 publications

(282 citation statements)

References 55 publications

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“…These results suggest that Leu, Ile, His, and Lys may have once occupied the entire codon block, and specific codons were later conceded to the other amino acids. Specifically, the data provide evidence for the capture of AUG from Ile to Met, consistent with what is considered a key codon capture event (24,25), as well as unique evidence that Phe may have captured the UUY codons from Leu. Our data also suggest that a subset of codons of Lys and His were reassigned to Asn and Gln, respectively.…”

Section: Codons or Anticodons For Select Amino Acids Are Enriched Neamentioning

confidence: 68%

“…Our finding on ribosomal anticodon-amino acid enrichment, when compared with the consensus chronology of amino acids built on 60 criteria (24), revealed a distinct stage for the evolution of the canonical code. Except for Asp, all other amino acids that are significantly enriched with their anticodons in the ribosome are at the later stage of amino acid expansion (Table 1), starting from Leu (ranked No.…”

Section: Codons or Anticodons For Select Amino Acids Are Enriched Neamentioning

confidence: 96%

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Imprints of the genetic code in the ribosome

Johnson

Wang

2010

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

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The establishment of the genetic code remains elusive nearly five decades after the code was elucidated. The stereochemical hypothesis postulates that the code developed from interactions between nucleotides and amino acids, yet supporting evidence in a biological context is lacking. We show here that anticodons are selectively enriched near their respective amino acids in the ribosome, and that such enrichment is significantly correlated with the canonical code over random codes. Ribosomal anticodon-amino acid enrichment further reveals that specific codons were reassigned during code evolution, and that the code evolved through a two-stage transition from ancient amino acids without anticodon interaction to newer additions with anticodon interaction. The ribosome thus serves as a molecular fossil, preserving biological evidence that anticodonamino acid interactions shaped the evolution of the genetic code.evolution of the genetic code | stereochemical hypothesis | anticodonamino acid association | codon reassignment | RNA-protein interaction T he origin and evolution of the genetic code is a critical transition in the evolution of all modern organisms (1). Understanding why the genetic code evolved to its modern form is as important, if not more so, as knowing the code itself (2), as it is central to understanding major evolutionary breakthroughs. However, the universality of the code is also its downfall with regard to studying its formation, as no organisms exist containing a primitive or intermediate genetic code for comparison. Although multiple hypotheses have been proposed to explain why codons are selectively assigned to specific amino acids (3, 4), empirical data are extremely rare and difficult to obtain (5-8), leaving many theories in the realm of conjecture. One theory addressing this challenging question is the stereochemical hypothesis, which postulates that the genetic code developed from interactions between anticodon-or codon-containing polynucleotides and their respective amino acids (5, 9). This theory is supported by RNA aptamer experiments, in which RNA molecules evolved to bind specific amino acids in vitro are enriched with anticodon and codon elements for the amino acid (6-8, 10). Codons for arginine have also been found to confer binding specificity for arginine in the self-splicing group I introns (11). Nonetheless, the biological relevance of these aptamers and introns to genetic code evolution is unknown, and no further in vivo data exist to support this hypothesis.If chemical or physical interactions between nucleotides and amino acids did influence the evolution of the genetic code, relics of this evolution may be present in modern cells. In particular, we may uncover such imprints within RNA-binding proteins and RNAprotein interactions. The ribosome presents an excellent model for the study of these potential interactions, as it is a large ribonucleoprotein complex with some 50 proteins interacting extensively with the ribosomal RNAs (rRNAs) for stability and structure (Fig. 1A) (...

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Section: Codons or Anticodons For Select Amino Acids Are Enriched Neamentioning

confidence: 68%

Section: Codons or Anticodons For Select Amino Acids Are Enriched Neamentioning

confidence: 96%

Imprints of the genetic code in the ribosome

Johnson

Wang

2010

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

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“…Roughly speaking, the frequencies of G, A, D, V, P, L, T, R, H, W tend to decrease, the frequencies of S, E, I, N, K, F, Y tend to increase, and the frequencies of Q, C, M tend to keep constant. The magnitudes of variations are different: frequencies of G, A, V, P, R decrease more rapidly than that of D, L, T, H, W, while frequencies of I, N, K, F, Y increase more rapidly than that of S, E. We found that the evolutionary trends of amino acids are related to the amino acid chronology [13]: most of the amino acids whose frequencies tend to decrease (or increase) are among the earlier (or later) recruited amino acids according to the amino acid chronology. The variation trends of amino acid frequencies are intrinsic properties of molecular evolution, which are irrelative to the choice of orders in sorting species.…”

Section: General Variation Trends Of Amino Acid Frequenciesmentioning

confidence: 78%

Genetic code evolution as an initial driving force for molecular evolution

Zhang

2009

Physica A: Statistical Mechanics and its Applications

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There is an intrinsic relationship between the molecular evolution in primordial period and the properties of genomes and proteomes of contemporary species. The genomic data may help us understand the driving force of evolution of life at molecular level. In absence of evidence, numerous problems in molecular evolution had to fall into a twilight zone of speculation and controversy in the past. Here we show that delicate structures of variations of genomic base compositions and amino acid frequencies resulted from the genetic code evolution. And the driving force of evolution of life also originated in the genetic code evolution. The theoretical results on the variations of amino acid frequencies and genomic base compositions agree with the experimental observations very well, not only in the variation trends but also in some fine structures. Inversely, the genomic data of contemporary species can help reconstruct the genetic code chronology and amino acid chronology in primordial period. Our results may shed light on the intrinsic mechanism of molecular evolution and the genetic code evolution.

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“…The genetic code likely evolved from a primitive, smaller group of amino acids to the modern complement of 20 amino acids via a series of ambiguous intermediate codes (7,17). According to this hypothesis, each codon block would originally have included a greater number of codons that recursively cycled between ambiguity and specific coding, until eventually the modern codon assignments evolved.…”

mentioning

confidence: 99%

“…With the exception of phenylalanine, the NUN-encoded amino acids are structurally similar. (Phenylalanine may have "captured codons" from the NUN block, as a later addition to the genetic code [17].) Therefore, the cognate aminoacyl-tRNA synthetases would naturally be more permissive towards these related amino acids.…”

mentioning

confidence: 99%