On a quest of reverse translation

Vitas, Marko; Dobovišek, Andrej

doi:10.1007/s10698-016-9260-5

Cited by 8 publications

(2 citation statements)

References 109 publications

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“…This cautious approach has not been shared in more recent studies, in which a so-called “maximum entropy production” (MEP) principle, applicable within different fields of physical, biological and environmental sciences, has been introduced as an extension of the Second Law (see for example: [ 25 – 29 ]). That principle has also been seen as relevant when considering the origin and evolution of life problem (see for example: [ 30 – 35 ]). According to that proposal, a system that is held in a far from equilibrium situation should evolve towards an increase of energy dissipation and along a pathway in which the rate of dissipation, and thus of entropy production, is maximised.…”

Section: Resultsmentioning

confidence: 99%

How and why kinetics, thermodynamics, and chemistry induce the logic of biological evolution

Pross¹,

Pascal²

2017

Beilstein J. Org. Chem.

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Thermodynamic stability, as expressed by the Second Law, generally constitutes the driving force for chemical assembly processes. Yet, somehow, within the living world most self-organisation processes appear to challenge this fundamental rule. Even though the Second Law remains an inescapable constraint, under energy-fuelled, far-from-equilibrium conditions, populations of chemical systems capable of exponential growth can manifest another kind of stability, dynamic kinetic stability (DKS). It is this stability kind based on time/persistence, rather than on free energy, that offers a basis for understanding the evolutionary process. Furthermore, a threshold distance from equilibrium, leading to irreversibility in the reproduction cycle, is needed to switch the directive for evolution from thermodynamic to DKS. The present report develops these lines of thought and argues against the validity of a thermodynamic approach in which the maximisation of the rate of energy dissipation/entropy production is considered to direct the evolutionary process. More generally, our analysis reaffirms the predominant role of kinetics in the self-organisation of life, which, in turn, allows an assessment of semi-quantitative constraints on systems and environments from which life could evolve.

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Section: Resultsmentioning

confidence: 99%

How and why kinetics, thermodynamics, and chemistry induce the logic of biological evolution

Pross¹,

Pascal²

2017

Beilstein J. Org. Chem.

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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%

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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In the Beginning was a Mutualism - On the Origin of Translation

Vitas¹,

Dobovišek

2018

Orig Life Evol Biosph

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The origin of translation is critical for understanding the evolution of life, including the origins of life. The canonical genetic code is one of the most dominant aspects of life on this planet, while the origin of heredity is one of the key evolutionary transitions in living world. Why the translation apparatus evolved is one of the enduring mysteries of molecular biology. Assuming the hypothesis, that during the emergence of life evolution had to first involve autocatalytic systems which only subsequently acquired the capacity of genetic heredity, we propose and discuss possible mechanisms, basic aspects of the emergence and subsequent molecular evolution of translation and ribosomes, as well as enzymes as we know them today. It is possible, in this sense, to view the ribosome as a digital-to-analogue information converter. The proposed mechanism is based on the abilities and tendencies of short RNA and polypeptides to fold and to catalyse biochemical reactions. The proposed mechanism is in concordance with the hypothesis of a possible chemical co-evolution of RNA and proteins in the origin of the genetic code or even more generally at the early evolution of life on Earth. The possible abundance and availability of monomers at prebiotic conditions are considered in the mechanism. The hypothesis that early polypeptides were folding on the RNA scaffold is also considered and mutualism in molecular evolutionary development of RNA and peptides is favoured.

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On a quest of reverse translation

Cited by 8 publications

References 109 publications

How and why kinetics, thermodynamics, and chemistry induce the logic of biological evolution

How and why kinetics, thermodynamics, and chemistry induce the logic of biological evolution

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

In the Beginning was a Mutualism - On the Origin of Translation

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