Reply to ‘Is LUCA a thermophilic progenote?’

Weiss, Madeline C.; Neukirchen, Sinje; Roettger, Mayo; Mrnjavac, Natalia; Nelson-Sathi, Shijulal; Martin, William; Sousa, Filipa L.

doi:10.1038/nmicrobiol.2016.230

Cited by 40 publications

(54 citation statements)

References 15 publications

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“…The bioenergetics group of William Martin pointed to the Ljungdahl-Wood autotrophic pathway, which also has some steps involving H 4 Folate/H 4 MPT carriers but is very complex with respect to the variety of cofactors required for the biosynthesis of AcetylCoA [87,88]. A portion of this route is shared with the methanogenic pathways.…”

Section: Metabolic Pathwaysmentioning

confidence: 99%

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: Metabolic Pathwaysmentioning

confidence: 99%

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

Guimarães

2017

Life

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“…These became an important kind of monomeric substrate for the dimer-directed synthesis of chains, generating peptides. Our focus on the biomass aspect, via Gly and Ser, coincides with the bioenergetic aspect that focuses on AcetylCoA [79,83,87,88,89]. Our identification of continuity with respect to Glycine seems justified but we cannot indicate the same for Serine since prebiotic concentrations of this are generally low.…”

Section: The Flow Is the Logicmentioning

confidence: 91%

“…The bioenergetics group of William Martin pointed to the Ljungdahl-Wood autotrophic pathway, which also has some steps involving H4Folate/H4MPT carriers but is very complex with respect to the variety of cofactors required for the biosynthesis of AcetylCoA [87,88]. A portion of this route is shared with the methanogenic pathways.…”

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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“…These became an important kind of monomeric substrate for the dimer-directed synthesis of chains, generating peptides. Our focus on the biomass aspect, via Gly and Ser, coincides with the bioenergetic aspect that focuses on AcetylCoA [70,73,77,78,79]. Our identification of continuity with respect to Glycine seems justified but we cannot indicate the same for Serine since prebiotic concentrations of this are generally low.…”

Section: The Flow the Logicmentioning

confidence: 91%

“…The bioenergetics group of William Martin pointed to the Ljungdahl-Wood autotrophic pathway, which also has some steps involving H4Folate/H4MPT carriers but is very complex with respect to the variety of cofactors required for the biosynthesis of AcetylCoA [77,78]. A portion of this route is shared with the methanogenic pathways.…”

Section: Metabolic Pathwaysmentioning

confidence: 99%

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

Guimarães¹

2017

Preprint

View full text Add to dashboard Cite

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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Reply to ‘Is LUCA a thermophilic progenote?’

Cited by 40 publications

References 15 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

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

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Reply to ‘Is LUCA a thermophilic progenote?’

Cited by 40 publications

References 15 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

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