Mutuality in Discrete and Compositional Information: Perspectives for Synthetic Genetic Codes

Guimarães, Romeu Cardoso

doi:10.1007/s12559-011-9116-1

Cited by 4 publications

(4 citation statements)

References 90 publications

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“…The stabilized couple would evolve into a aRS-tRNA cognate set given that (1) this initial binding would at least not harm the protein synthesis activity and in case (2) the specificity would show benefits to the chemical system in which they are immersed, starting with e.g., facilitation of the flows through reduction of turbulence and of mass and energy gradients, among other effects. The two components of this cycle produce the compositional (various recognition sites in the enzyme and in the tRNA) to discrete (one triplet—the anticodon—and one amino acid) correspondences and also the self-stimulatory properties that are at the core of the living systems [ 5 , 6 ].…”

Section: Contextmentioning

confidence: 99%

“…The suggested process of encoding ( Figure 5 ) does not involve a typical decision process due to being almost ‘automatic’: the formation of the highest ΔG pair in the module (in the central rows of the matrix, G NG :C NC [ 5 ]) is followed by lowered concentrations of five other pairs that members of the first pair would be involved with. Two dimers are left at high concentrations, for the second encoding round, the low ΔG pairs (G NA :Y NU, in the top and bottom rows of the matrix).…”

Section: Functionality In the Modular Organizationmentioning

confidence: 99%

“…It is possible that they would be involved in integration of the networks of dimers (the NSC, diagonal, with the SC, horizontal) or in regulatory processes but this has not been specifically tested, except graphically. An integrative role is plainly acceptable for the protein associations in the Multi-aRS Complexes [ 31 ], and the aRSs in the complex would be further associated through the dimers they bring in together with them ([ 5 , 17 ]; an update is available as Supplementary Information 1 ), including the SC subnetworks.…”

Section: Functionality In the Modular Organizationmentioning

confidence: 99%

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

Guimarães

2017

Life

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The proposal that the genetic code was formed on the basis of (proto)tRNA Dimer-Directed Protein Synthesis 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 stable and apt 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 sink-effective 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.

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Section: Contextmentioning

confidence: 99%

Section: Functionality In the Modular Organizationmentioning

confidence: 99%

Section: Functionality In the Modular Organizationmentioning

confidence: 99%

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

Guimarães

2017

Life

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“…The two components of this cycle produce the compositional to discrete correspondences and also the selfstimulatory properties that are at the core of the living systems [5,6].…”

mentioning

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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Roots of Complexity in the Self-referential Genetic Code

Guimarães

2019

Emergence and Modularity in Life Sciences

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Mutuality in Discrete and Compositional Information: Perspectives for Synthetic Genetic Codes

Cited by 4 publications

References 90 publications

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

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

Roots of Complexity in the Self-referential Genetic Code

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Mutuality in Discrete and Compositional Information: Perspectives for Synthetic Genetic Codes

Cited by 4 publications

References 90 publications

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

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

Roots of Complexity in the Self-referential Genetic Code

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