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

Guimarães, Romeu Cardoso

doi:10.3390/life7020016

Cited by 19 publications

(5 citation statements)

References 131 publications

(183 reference statements)

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“…In addition, mean CDA decreases with the order of inclusion of amino acids in the genetic code, according to the majorities of genetic code inclusion hypotheses as reviewed in [14], in agreement with genetic code evolutionary hypotheses that assume that class II tRNA synthetases and their cognate amino acids were first included in the genetic code [15,16]. This negative correlation is strongest (r = −0.775) with the genetic code inclusion order derived from the genetic code origin self-referential model [17] (presumed earliest to presumed latest amino acids: G, S, L, D, N, E, P, K, F, R, A, C, T, V, H, Q, I, M, Y and W).…”

Section: Cda and Properties Of The Translational Apparatus The Genetsupporting

confidence: 73%

Codon Directional Asymmetry Suggests Swapped Prebiotic 1st and 2nd Codon Positions

Seligmann

Demongeot

2020

IJMS

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Background: Codon directional asymmetry (CDA) classifies the 64 codons into palindromes (XYX, CDA = 0), and 5′- and 3′-dominant (YXX and XXY, CDA < 0 and CDA > 0, respectively). Previously, CDA was defined by the purine/pyrimidine divide (A,G/C,T), where X is either a purine or a pyrimidine. For the remaining codons with undefined CDA, CDA was defined by the 5′ or 3′ nucleotide complementary to Y. This CDA correlates with cognate amino acid tRNA synthetase classes, antiparallel beta sheet conformation index and the evolutionary order defined by the self-referential genetic code evolution model (CDA < 0: class I, high beta sheet index, late genetic code inclusion). Methods: We explore associations of CDAs defined by nucleotide classifications according to complementarity strengths (A:T, weak; C:G, strong) and keto-enol/amino-imino groupings (G,T/A,C), also after swapping 1st and 2nd codon positions with amino acid physicochemical and structural properties. Results: Here, analyses show that for the eight codons whose purine/pyrimidine-based CDA requires using the rule of complementarity with the midposition, using weak interactions to define CDA instead of complementarity increases associations with tRNA synthetase classes, antiparallel beta sheet index and genetic code evolutionary order. CDA defined by keto-enol/amino-imino groups, 1st and 2nd codon positions swapped, correlates with amino acid parallel beta sheet formation indices and Doolittle’s hydropathicities. Conclusions: Results suggest (a) prebiotic swaps from N2N1N3 to N1N2N3 codon structures, (b) that tRNA-mediated translation replaced direct codon-amino acid interactions, and (c) links between codon structures and cognate amino acid properties.

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Section: Cda and Properties Of The Translational Apparatus The Genetsupporting

confidence: 73%

Codon Directional Asymmetry Suggests Swapped Prebiotic 1st and 2nd Codon Positions

Seligmann

Demongeot

2020

IJMS

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“…Arg is also coded by GC-rich codons, but the authors omitted it from the earliest encoded amino acids since most (but not all) simulation experiments suggested that Arg was not present under prebiotic conditions [8]. The coevolution hypothesis of the genetic code proposed that the encoding of new amino acids was determined by the evolution of their synthetic pathways within the primordial biochemical system [1,9,10]. While this hypothesis may be valid for certain late amino acids, it is unlikely to be correct for the earliest of them, as this would demand complex protein-based enzymatic activities.…”

Section: Introductionmentioning

confidence: 99%

Universal Codons with Enrichment from GC to AU Nucleotide Composition Reveal a Chronological Assignment from Early to Late Along with LUCA Formation

Gospodinov

Kunnev

2020

Life

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The emergence of a primitive genetic code should be considered the most essential event during the origin of life. Almost a complete set of codons (as we know them) should have been established relatively early during the evolution of the last universal common ancestor (LUCA) from which all known organisms descended. Many hypotheses have been proposed to explain the driving forces and chronology of the evolution of the genetic code; however, none is commonly accepted. In the current paper, we explore the features of the genetic code that, in our view, reflect the mechanism and the chronological order of the origin of the genetic code. Our hypothesis postulates that the primordial RNA was mostly GC-rich, and this bias was reflected in the order of amino acid codon assignment. If we arrange the codons and their corresponding amino acids from GC-rich to AU-rich, we find that: 1. The amino acids encoded by GC-rich codons (Ala, Gly, Arg, and Pro) are those that contribute the most to the interactions with RNA (if incorporated into short peptides). 2. This order correlates with the addition of novel functions necessary for the evolution from simple to longer folded peptides. 3. The overlay of aminoacyl-tRNA synthetases (aaRS) to the amino acid order produces a distinctive zonal distribution for class I and class II suggesting an interdependent origin. These correlations could be explained by the active role of the bridge peptide (BP), which we proposed earlier in the evolution of the genetic code.

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“…Thus, primordial tRNA-like molecules (not real tRNAs) of the same origin may have evolved (Figure 6). Based on the knowledge of the tRNA-rRNA homologies [48], tRNA dimers may also have been mimics of the ribosome [49]. On the other hand, faced with the metabolic paradoxes of purine and pyrimidine biosynthesis, i.e., purine and pyrimidine rings are synthesized from glycine and aspartic acid, respectively [50], one possibility may be peptide nucleic acids (PNA) as a precursor to RNA [51].…”

Section: Discussionmentioning

confidence: 99%

Peptide Bond Formation between Aminoacyl-Minihelices by a Scaffold Derived from the Peptidyl Transferase Center

Kawabata

Kawashima

Mutsuro‐Aoki

et al. 2022

Life

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The peptidyl transferase center (PTC) in the ribosome is composed of two symmetrically arranged tRNA-like units that contribute to peptide bond formation. We prepared units of the PTC components with putative tRNA-like structure and attempted to obtain peptide bond formation between aminoacyl-minihelices (primordial tRNAs, the structures composed of a coaxial stack of the acceptor stem on the T-stem of tRNA). One of the components of the PTC, P1c2UGGU (74-mer), formed a dimer and a peptide bond was formed between two aminoacyl-minihelices tethered by the dimeric P1c2UGGU. Peptide synthesis depended on both the existence of the dimeric P1c2UGGU and the sequence complementarity between the ACCA-3′ sequence of the minihelix. Thus, the tRNA-like structures derived from the PTC could have originated as a scaffold of aminoacyl-minihelices for peptide bond formation through an interaction of the CCA sequence of minihelices. Moreover, with the same origin, some would have evolved to constitute the present PTC of the ribosome, and others to function as present tRNAs.

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

Cited by 19 publications

References 131 publications

Codon Directional Asymmetry Suggests Swapped Prebiotic 1st and 2nd Codon Positions

Codon Directional Asymmetry Suggests Swapped Prebiotic 1st and 2nd Codon Positions

Universal Codons with Enrichment from GC to AU Nucleotide Composition Reveal a Chronological Assignment from Early to Late Along with LUCA Formation

Peptide Bond Formation between Aminoacyl-Minihelices by a Scaffold Derived from the Peptidyl Transferase Center

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