Evolutionary Steps in the Emergence of Life Deduced from the Bottom-Up Approach and GADV Hypothesis (Top-Down Approach)

Ikehara, Kenji

doi:10.3390/life6010006

Cited by 27 publications

(40 citation statements)

References 57 publications

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“…The first functional amino acid containing entities might not have been individual amino acids, but dipeptides or even sort oligopeptides. Ikehara (Ikehara, 2016), for example, proposed that oligomers of the VADG amino acids were the first to appear. The longer peptides first scenarios are problematic as while one can select on random sequences, without heredity there could be no evolution (Zachar and Szathmáry, 2010), i.e.…”

Section: Introductionmentioning

confidence: 99%

The evolution of the genetic code: Impasses and challenges

Kun

Radványi

2018

Biosystems

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The origin of the genetic code and translation is a "notoriously difficult problem". In this survey we present a list of questions that a full theory of the genetic code needs to answer. We assess the leading hypotheses according to these criteria. The stereochemical, the coding coenzyme handle, the coevolution, the four-column theory, the error minimization and the frozen accident hypotheses are discussed. The integration of these hypotheses can account for the origin of the genetic code. But experiments are badly needed. Thus we suggest a host of experiments that could (in)validate some of the models. We focus especially on the coding coenzyme handle hypothesis (CCH). The CCH suggests that amino acids attached to RNA handles enhanced catalytic activities of ribozymes. Alternatively, amino acids without handles or with a handle consisting of a single adenine, like in contemporary coenzymes could have been employed. All three scenarios can be tested in in vitro compartmentalized systems.

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Section: Introductionmentioning

confidence: 99%

The evolution of the genetic code: Impasses and challenges

Kun

Radványi

2018

Biosystems

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“…The chronology offered by the self-referential model clashes with the traditional studies on the origins of the code [69][70][71][72][73][74][75][76][77][78]. These are centered on the set of amino acids that are produced in relative abundance under prebiotic conditions, possibly representing what would be expected from early Earth geochemical systems.…”

Section: Metabolic Pathwaysmentioning

confidence: 99%

Self-Referential Encoding on Modules of Anticodon Pairs—Roots of the Biological Flow System

Guimarães

2017

Preprint

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Abstract:The proposal that the genetic code was formed on the basis of protein synthesis directed by tRNA dimers is reviewed and updated. The tRNAs paired through the anticodon loops are an indication on the process. Dimers are considered mimics of the ribosomes -structures that hold tRNAs together and facilitate the transferase reaction, and of the translation process -anticodons are at the same time codons for each other. The primitive protein synthesis system gets stabilized when the product peptides are able to bind the producers therewith establishing a self-stimulating production cycle. The chronology of amino acid encoding starts with Glycine and Serine, indicating the metabolic support of the Glycine-Serine C1-assimilation pathway, which is also consistent with evidence on origins of bioenergetics mechanisms. Since it is not possible to reach for substrates simpler than C1 and compounds in the identified pathway are apt for generating the other central metabolic routes, it is considered that protein synthesis is the beginning and center of a succession of sinkeffective mechanisms that drive the formation and evolution of the metabolic flow system. Plasticity and diversification of proteins construct the cellular system following the orientation given by the flow and implementing it. Nucleic acid monomers participate in bioenergetics and the polymers are conservative memory systems for the synthesis of proteins. Protoplasmic fission is the final sink-effective mechanism, part of cell reproduction, guaranteeing that proteins don't accumulate to saturation, which would trigger inhibition.Keywords: genetic code; tRNA dimers; self-reference; modularity; error-compensation; metabolism chronology; protein stability; punctuation system Living beings are metabolic flow systems that self-construct on the basis of memories and adapt / evolve on the basis of constitutive plasticity. Life is the ontogenetic and evolutionary process instantiated by living beings. ContextCellular structures and functions are composed by a network that may be divided into a mostly internal segment of macromolecules, the proteins and the nucleic acids, and another of micromolecules, that communicate and exchange intimately with the environment. The genetic encoding/decoding system is a key mechanism in both of these processes. It participates in the informational, the polymer sequence order-based self-referential cycle that is the cellular nucleoprotein core, the specifically endogenous and molecular identifier of living beings (Figure 1). The decoding system mediates the translation of genetic sequences -string memories -into proteins, which are the main functional working components of the cell system. The protein synthesis machinery is centered on ribosomes, while the mRNAs, tRNAs and synthetases carry the translation signals, Preprints (www.preprints.org) | NOT PEER-REVIEWED |

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“…The chronology offered by the self-referential model clashes with the traditional studies on the origins of the code [60][61][62][63][64][65][66][67][68][69]. These are centered on the set of amino acids that are produced in relative abundance under prebiotic conditions, possibly representing what would be expected from early Earth geochemical systems.…”

Section: Metabolic Pathwaysmentioning

confidence: 99%

Self-Referential Encoding on Modules of Anticodon Pairs—Roots of the Biological Flow System

Guimarães¹

2017

Preprint

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Abstract:The proposal that the genetic code was formed on the basis of protein synthesis directed by tRNA dimers is reviewed and updated. The tRNAs paired through the anticodon loops are an indication on the process. Dimers are considered mimics of the ribosomes -structures that hold tRNAs together and facilitate the transferase reaction, and of the translation process -anticodons are at the same time codons for each other. The primitive protein synthesis system gets stabilized when the product peptides are able to bind the producers therewith establishing a self-stimulating production cycle. The chronology of amino acid encoding starts with Glycine and Serine, indicating the metabolic support of the Glycine-Serine C1-assimilation pathway, which is also consistent with evidence on origins of bioenergetics mechanisms. Since it is not possible to reach for substrates simpler than C1 and compounds in the identified pathway are apt for generating the other central metabolic routes, it is considered that protein synthesis is the beginning and center of a succession of sinkeffective mechanisms that drive the formation and evolution of the metabolic flow system. Plasticity and diversification of proteins construct the cellular system following the orientation given by the flow and implementing it. Nucleic acid monomers participate in bioenergetics and the polymers are conservative memory systems for the synthesis of proteins. Protoplasmic fission is the final sink-effective mechanism, part of cell reproduction, guaranteeing that proteins don't accumulate to saturation, which would trigger inhibition.Keywords: genetic code; tRNA dimers; self-reference; modularity; error-compensation; metabolism chronology; protein stability; punctuation system Living beings are metabolic flow systems that self-construct on the basis of memories.Life is the ontogenetic and evolutionary process instantiated by living beings. ContextThe genetic encoding/decoding system is a key mechanism in the cellular processes. It participates in the informational, the polymer sequence order-based self-referential cycle that is the cellular nucleoprotein core, the specifically endogenous and molecular identifier of living beings (Figure 1). The decoding system mediates the translation of genetic sequences -string memories -into proteins, which are the main functional working components of the cell system. The protein synthesis machinery is centered on ribosomes, while the mRNAs, tRNAs and synthetases carry the translation signals, which establish the correspondences -codes -between mRNA and tRNA base triplets, and the amino acids. It may be said, with some simplification, that the main function of the other -inter-genic -sequences and of the multitude of RNAs that do not code for proteins would be regulatory, in the sense of retrieving information, processing and preparing it for coordinated expression in Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted:

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Evolutionary Steps in the Emergence of Life Deduced from the Bottom-Up Approach and GADV Hypothesis (Top-Down Approach)

Cited by 27 publications

References 57 publications

The evolution of the genetic code: Impasses and challenges

The evolution of the genetic code: Impasses and challenges

Self-Referential Encoding on Modules of Anticodon Pairs—Roots of the Biological Flow System

Self-Referential Encoding on Modules of Anticodon Pairs—Roots of the Biological Flow System

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Evolutionary Steps in the Emergence of Life Deduced from the Bottom-Up Approach and GADV Hypothesis (Top-Down Approach)

Cited by 27 publications

References 57 publications

The evolution of the genetic code: Impasses and challenges

The evolution of the genetic code: Impasses and challenges

Self-Referential Encoding on Modules of Anticodon Pairs&mdash;Roots of the Biological Flow System

Self-Referential Encoding on Modules of Anticodon Pairs&mdash;Roots of the Biological Flow System

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Self-Referential Encoding on Modules of Anticodon Pairs—Roots of the Biological Flow System

Self-Referential Encoding on Modules of Anticodon Pairs—Roots of the Biological Flow System