The Evolution of the Genetic Code Revisited

Travers, Andrew

doi:10.1007/s11084-006-9041-6

Cited by 23 publications

(30 citation statements)

References 22 publications

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“…The natural genetic code is a result of selection in the early evolution, and it has a number of superiorities when compared with the other possible genetic codes [47][48][49][50][51][52][53][54][55][56][57][58].…”

Section: Resultsmentioning

confidence: 99%

The shiftability of protein coding genes: the genetic code was optimized for frameshift tolerating

Wang

Chen

et al. 2015

Preprint

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The genetic code defines the relationship between a protein and its coding DNA sequence. It was presumed that most frameshifts would yield non-functional, truncated or cytotoxic products. In this study, we report that in E. coli a frameshift β-lactamase (bla) gene is still functional if all of the inner stop codons were readthrough or replaced by a sense codon. By analyzing a large dataset including all available protein coding genes in major model organisms, it is demonstrated that in any species, and in any protein-coding genes, the three translational products from the three different reading frames, are always similar to each other and with constant ~50% similarities and ~100% coverages, and the similarities is predefined by the genetic code rather than the sequences themselves, suggesting that the genetic code was optimized for frameshift tolerating in the early evolution, which endows every protein coding gene a shiftability, an inherent and everlasting ability to tolerate frameshift mutations, and serves as an innate mechanism for cells to deal with the frameshift problem. In addition, it is likely that every protein-coding gene can be translated into three isoforms from the three different reading frames, we proposed a new gene expression paradigm, "one gene, three translations", which is an amendment to the "one gene, one/multiple peptides" hypotheses.

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Section: Resultsmentioning

confidence: 99%

The shiftability of protein coding genes: the genetic code was optimized for frameshift tolerating

Wang

Chen

et al. 2015

Preprint

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“…On the other hand, Travers has argued, based on codonanticodon thermostability, that the non-universal codes principally appeared by divergent evolution at a stage when only a few amino acids were assigned [19]. Based on the melting and stacking stabilities of the first two codon-anticodon base steps, he hypothesized that amino acids encoded by the most stable base steps (GC for Ala, GT for Val, AC for Thr, GG for Gly, CC for Pro, GA for Glu/Asp, TC for Ser, and CG for Arg) were assigned before the divergence of non-plant mitochondrial codes, and that less stable base steps (CT, AG, AT, AA, TT, TG, TA) correlated with the divergent usage of the non-universal codes.…”

Section: Fig (5)mentioning

confidence: 99%

“…It can be easily understood by comparing the number of atoms in the mononucleotides, UMP, CMP, AMP, and GMP (34)(35)(36)(37)(38), with that in the [GADV]-amino acids (10)(11)(12)(13)(14)(15)(16)(17)(18)(19). Thus, it would be much more difficult to synthesize the four nucleotides under prebiotic conditions than to synthesize the four amino acids.…”

Section: Weak Points Of the Rna World Theorymentioning

confidence: 99%

Origin and Evolutionary Process of the Genetic Code

Ikehara

Niihara²

2007

CMC

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The genetic code plots the relationship between a triplet base sequence on RNA and an amino acid that corresponds to a protein associated with a required function in organisms. Accurate knowledge about the genetic code, including its origin and evolutionary process, would be helpful for determining the causes of genetic disorders and discovering new medical treatments, as well as for understanding the origin of life. This review begins with discussion of several well-known theories on the origin of the genetic code. Then, a GNC-SNS primitive genetic code hypothesis, which we originally proposed, is explained in relation to the weak points of other theories. S and N denote G or C and any of the four bases, respectively. We also introduce our hypothesis of the GADV-protein world hypothesis on the origin of life, where GADV stands for the four amino acids, Gly[G], Ala[A], Asp[D] and Val[V]. Next, we discuss the reason why genetic disorders, which should be triggered by base replacements, are repressed at a low level under the universal genetic code. Finally, we explain the current difficulties we faced in treating genetic disorders, suggesting a prospect for a new type of treatments of these disorders.

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“…At the very beginning, this recording system would not have recorded any meaningful messages, but through mutation and natural selection, messages associated with useful peptides were continuously enhanced and conserved, giving rise to this type of biological information. This hypothesis is supported by the notion that the tRNA aminoacylated with earliest amino acids, such as glycine, alanine, valine and glutamic acid, which could be synthesized abioticly under primitive earth conditions [27], generally have the highest GC content in their anticodon and have the most stable interaction with the mRNA through Watson-Crick base pairing [28], and this could be essential for the proposed helicase activity. In fact, the coding regions in general have higher G + C content compared to the non-coding regions even in modern genes [29,30], which might be the traceable mark of this process.…”

Section: Open Accessmentioning

confidence: 95%

The origin of biological information and programmed protein synthesis

Liú¹

2013

AJMB

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Biological information is one of the most important characteristics of life, and it enables life to evolve to higher complexity and adapt to the environment by mutation and natural selection. However, the origin of this information recording and retrieval system remains a mystery. To understand the origin of biological information will lead us to one step closer to understand the origin of life on earth. Biological information is encoded in DNA and translated into protein by the ribosome in all free living organisms. The information has to be translated into proteins to carry out its biological functions, so the evolution of the ribosome must be integrated with the development of biological information. In this article, I propose that the small ribosomal subunit evolved from a ribozyme that acted as an RNA helicase in the ancient RNA world, and the involvement of tRNAs and the large ribosomal subunit evolved to enhance the helicase activity and to overcome the higher energy requirement for high GC content RNA helices. This process could have developed as a primitive recording mechanism: since Watson-Crick base paring is a natural property of RNA, each time the proto-small ribosomal subunit came to a particular GC-rich helix, tRNA-like molecules and the proto-large ribosomal subunit would have to be engaged to generate the helicase activity, and consequently the same polypeptide would be synthesized as a by-product. Simple recorded messages then evolved into useful biological information through continuous mutation and natural selection. This hypothesis provides logical and incremental steps for the development of programmed protein synthesis. I also argue that the helicase activity is preserved in the modern ribosome and that from our knowledge of the ribosome, and we can deduce the possible mechanisms of the helicase activity.

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The Evolution of the Genetic Code Revisited

Cited by 23 publications

References 22 publications

The shiftability of protein coding genes: the genetic code was optimized for frameshift tolerating

The shiftability of protein coding genes: the genetic code was optimized for frameshift tolerating

Origin and Evolutionary Process of the Genetic Code

The origin of biological information and programmed protein synthesis

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