The Standard Genetic Code can Evolve from a Two-Letter GC Code Without Information Loss or Costly Reassignments

Frank, A.; Froese, Tom

doi:10.1007/s11084-018-9559-4

Cited by 16 publications

(11 citation statements)

References 35 publications

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“…It was recently shown that the standard genetic code can evolve from a two-letter GC code without information loss or costly reassignments (Frank and Froese, 2018). An expanded (e. g. quadruplet) codons can be thought of in the context of expanding the existing genetic code (Chen & Schindlinger, 2010).…”

Section: Discussionmentioning

confidence: 99%

The Smooth Evolution of the Universal Genetic Code. Main Episodes

Pawłowski¹

2019

ijSciences

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The possible scenario of the origin and evolution of genetic code is proposed, being primarily implicated by the working hypothesis which states that the chronological order of amino acids evolutionary implementation monotonically correlates with their increasing mass. It fulfills the minimalistic claim of the smallest changes of the evolving system at increasing complexity, hereinafter called "the smooth evolution". The working hypothesis was postulated concerning the results of statistical analysis indicating a strong correlation between amino acid mass and the chosen parameters of contemporary genetic code, which are expected to change in a certain individual direction during the evolution of the initial genetic system. It was additionally supplemented by the most common hypotheses adopted from the literature, as stereochemical, 'frozen accident' and coevolutional. The developed scenario allows a detailed description of the twenty-two consecutive episodes of the history of code definition and the estimation of its dynamics. It reveals the main eras of evolution conditioned by the environmental and structural constraints. It also lets the estimation of the evolutionary frequencies of codon sense expansion, and redefinition. Dominating trends and amino acids were indicated. The underlying assumptions, limits, exceptions, and the future of the code evolution have been discussed.

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Section: Discussionmentioning

confidence: 99%

The Smooth Evolution of the Universal Genetic Code. Main Episodes

Pawłowski¹

2019

ijSciences

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“…Such approaches have been much criticized and abandoned. The central argument is that the reading frame with dinucleotides is incompatible with the reading frame with trinucleotides, leading to gene sequences unreadable, problem synthesized shortly with the following sentence "letters belonging to the first position of the next codon would be consistently misread as being the last letter of the preceding codon" (Frank and Froese, 2018). We prove in this paper the existence of mixed circular codes, in particular of dinucleotides and trinucleotides.…”

Section: Discussionmentioning

confidence: 82%

Mixed circular codes

Fimmel

Michel

Pirot

et al. 2019

Mathematical Biosciences

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By an extensive statistical analysis in genes of bacteria, archaea, eukaryotes, plasmids and viruses, a maximal C 3-self-complementary trinucleotide circular code has been found to have the highest average occurrence in the reading frame of the ribosome during translation. Circular codes may play an important role in maintaining the correct reading frame. On the other hand, as several evolutionary theories propose primeval codes based on dinucleotides, trinucleotides and tetranucleotides, mixed circular codes are investigated. By using a graph-theoretical approach of circular codes recently developed, we study mixed circular codes, which are the union of a dinucleotide circular code, a trinucleotide circular code and a tetranucleotide circular code. Maximal mixed circular codes of (di,tri)-nucleotides, (tri,tetra)-nucleotides and (di,tri,tetra)-nucleotides are constructed, respectively. In particular, we show that any maximal dinucleotide circular code of size 6 can be embedded into a maximal mixed (di,tri)-nucleotide circular code such that its trinucleotide component is a maximal C 3-comma-free code. The growth function of self-complementary mixed circular codes of dinucleotides and trinucleotides is given. Self-complementary mixed circular codes could have been involved in primitive genetic processes.

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“…Genetic information is molecular memory recorded by triplet codon, but its origin has been investigated and debated for a long time (e.g., [1,2,3,4,5]. It is a miracle of nature that a set of genetic codes was able to produce tens of millions of different species on the earth.…”

Section: Introductionmentioning

confidence: 99%

ATP-Hypothesis: A New Conceptual Framework for the Origins of Genetic Codes

Xie¹

2020

Preprint

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The origin of genetic codes is the key to reveal life’s origin on the earth as it is a prerequisite for the existence of life. More than half a century has passed since the discovery of genetic codes, while their origin is still one of the greatest mysteries. Are the origins of genetic codes really unknowable? Do they really require external design? Here, I present an ATP-hypothesis that explains how the genetic codes came into being with the coevolution of biochemical system. ATP has several properties that make it suitable as the initiator of the origin of genetic codes. First, ATP is the only energetic product of photosynthesis. Second, ATP is at the heart of the extant biochemical systems. Third, ATP serves as carriers of both energy and information. Fourth, ATP could energetically elongate chains of both polynucleotides and polypeptides, thus providing a bridge between them, and eventually mediating prebiotic biochemical transaction from energy to information. This hypothesis shows how primitive life emerged through a series of processes from energy to information mediated by ATP. Informatization (processes of creating and managing information) was inevitably coupled with structuralization (processes of organizing or incorporating into a cellular structure), making polynucleotides and polypeptides be cyclized into a system of reciprocal causation. The triplet codon might just be for stereo-chemical handing of amino acid through e.g. Watson–Crick pairing interactions. It is an evolutionary completion for genetic codes from RNA to DNA, only which, a reverse to the Central Dogma, marked the dawn of cellular life when Darwinian evolution began to operate. ATP-hypothesis shades lights on the origin of life, together with the formations of both photosynthesis and biochemical systems, which have been largely unknown so far.

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The Standard Genetic Code can Evolve from a Two-Letter GC Code Without Information Loss or Costly Reassignments

Cited by 16 publications

References 35 publications

The Smooth Evolution of the Universal Genetic Code. Main Episodes

The Smooth Evolution of the Universal Genetic Code. Main Episodes

Mixed circular codes

ATP-Hypothesis: A New Conceptual Framework for the Origins of Genetic Codes

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