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Origins of Protein Translation
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Origins of Protein Translation

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Biology".

Deadline for manuscript submissions: closed (31 May 2020) | Viewed by 17434

Special Issue Editors

Dr. Hervé Seligmann

E-Mail Website
Guest Editor
The Hebrew University of Jerusalem, Israel
Interests: tRNA; mitochondrial genome; developmental instability; self-correcting codes; genetic code
Prof. Dr. Jacques Demongeot

E-Mail Website
Guest Editor
Faculty of Medicine, University Grenoble Alpes, Saint Martin d'Heres, France
Interests: theoretical biology; biostatistics; medical informatics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Protein translation as it occurs in modern cells is a complex process requiring coadapted interactions between multiple types of RNAs and proteins (RNAs: mRNA, tRNAs, rRNAs; proteins: elongation and termination factors, ribosomal proteins, tRNA synthetases), functioning under a set of rules resumed in the genetic code. How did such a complex system evolve, and what were the less complex, but functional systems preceding it? Did nonribosomal peptide synthesis, and pre-tRNA mRNA translations by direct codon-amino acid interactions precede modern translation? What defined the specific genetic code codon-amino acid assignments? Was there a different genetic code before the one we know?
This Special Issue on the origins of protein translation welcomes experiment- and theory-oriented research articles and reviews about the above, and related topics, focusing on prebiotic and early life self-organization of any components of protein translation.

Dr. Hervé Seligmann
Prof. Jacques Demongeot
Guest Editors

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Keywords

  • tRNA
  • codon
  • anticodon
  • ribosome
  • tRNA synthetase

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Published Papers (4 papers)

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Research

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22 pages, 2118 KiB  
Article
Impedance Matching and the Choice Between Alternative Pathways for the Origin of Genetic Coding
by Peter R. Wills and Charles W. Carter, Jr.
Int. J. Mol. Sci. 2020, 21(19), 7392; https://doi.org/10.3390/ijms21197392 - 7 Oct 2020
Cited by 10 | Viewed by 2402
Abstract
We recently observed that errors in gene replication and translation could be seen qualitatively to behave analogously to the impedances in acoustical and electronic energy transducing systems. We develop here quantitative relationships necessary to confirm that analogy and to place it into the [...] Read more.
We recently observed that errors in gene replication and translation could be seen qualitatively to behave analogously to the impedances in acoustical and electronic energy transducing systems. We develop here quantitative relationships necessary to confirm that analogy and to place it into the context of the minimization of dissipative losses of both chemical free energy and information. The formal developments include expressions for the information transferred from a template to a new polymer, Iσ; an impedance parameter, Z; and an effective alphabet size, neff; all of which have non-linear dependences on the fidelity parameter, q, and the alphabet size, n. Surfaces of these functions over the {n,q} plane reveal key new insights into the origin of coding. Our conclusion is that the emergence and evolutionary refinement of information transfer in biology follow principles previously identified to govern physical energy flows, strengthening analogies (i) between chemical self-organization and biological natural selection, and (ii) between the course of evolutionary trajectories and the most probable pathways for time-dependent transitions in physics. Matching the informational impedance of translation to the four-letter alphabet of genes uncovers a pivotal role for the redundancy of triplet codons in preserving as much intrinsic genetic information as possible, especially in early stages when the coding alphabet size was small. Full article
(This article belongs to the Special Issue Origins of Protein Translation)
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14 pages, 2100 KiB  
Article
Flexible NAD+ Binding in Deoxyhypusine Synthase Reflects the Dynamic Hypusine Modification of Translation Factor IF5A
by Meirong Chen, Zuoqi Gai, Chiaki Okada, Yuxin Ye, Jian Yu and Min Yao
Int. J. Mol. Sci. 2020, 21(15), 5509; https://doi.org/10.3390/ijms21155509 - 31 Jul 2020
Cited by 4 | Viewed by 3161
Abstract
The eukaryotic and archaeal translation factor IF5A requires a post-translational hypusine modification, which is catalyzed by deoxyhypusine synthase (DHS) at a single lysine residue of IF5A with NAD+ and spermidine as cofactors, followed by hydroxylation to form hypusine. While human DHS catalyzed [...] Read more.
The eukaryotic and archaeal translation factor IF5A requires a post-translational hypusine modification, which is catalyzed by deoxyhypusine synthase (DHS) at a single lysine residue of IF5A with NAD+ and spermidine as cofactors, followed by hydroxylation to form hypusine. While human DHS catalyzed reactions have been well characterized, the mechanism of the hypusination of archaeal IF5A by DHS is not clear. Here we report a DHS structure from Pyrococcus horikoshii OT3 (PhoDHS) at 2.2 Å resolution. The structure reveals two states in a single functional unit (tetramer): two NAD+-bound monomers with the NAD+ and spermidine binding sites observed in multi-conformations (closed and open), and two NAD+-free monomers. The dynamic loop region V288–P299, in the vicinity of the active site, adopts different positions in the closed and open conformations and is disordered when NAD+ is absent. Combined with NAD+ binding analysis, it is clear that PhoDHS can exist in three states: apo, PhoDHS-2 equiv NAD+, and PhoDHS-4 equiv NAD+, which are affected by the NAD+ concentration. Our results demonstrate the dynamic structure of PhoDHS at the NAD+ and spermidine binding site, with conformational changes that may be the response to the local NAD+ concentration, and thus fine-tune the regulation of the translation process via the hypusine modification of IF5A. Full article
(This article belongs to the Special Issue Origins of Protein Translation)
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10 pages, 523 KiB  
Article
Codon Directional Asymmetry Suggests Swapped Prebiotic 1st and 2nd Codon Positions
by Hervé Seligmann and Jacques Demongeot
Int. J. Mol. Sci. 2020, 21(1), 347; https://doi.org/10.3390/ijms21010347 - 5 Jan 2020
Cited by 8 | Viewed by 2886
Abstract
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Origins of Protein Translation)
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Review

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17 pages, 1899 KiB  
Review
The Alanine World Model for the Development of the Amino Acid Repertoire in Protein Biosynthesis
by Vladimir Kubyshkin and Nediljko Budisa
Int. J. Mol. Sci. 2019, 20(21), 5507; https://doi.org/10.3390/ijms20215507 - 5 Nov 2019
Cited by 32 | Viewed by 7699
Abstract
A central question in the evolution of the modern translation machinery is the origin and chemical ethology of the amino acids prescribed by the genetic code. The RNA World hypothesis postulates that templated protein synthesis has emerged in the transition from RNA to [...] Read more.
A central question in the evolution of the modern translation machinery is the origin and chemical ethology of the amino acids prescribed by the genetic code. The RNA World hypothesis postulates that templated protein synthesis has emerged in the transition from RNA to the Protein World. The sequence of these events and principles behind the acquisition of amino acids to this process remain elusive. Here we describe a model for this process by following the scheme previously proposed by Hartman and Smith, which suggests gradual expansion of the coding space as GC–GCA–GCAU genetic code. We point out a correlation of this scheme with the hierarchy of the protein folding. The model follows the sequence of steps in the process of the amino acid recruitment and fits well with the co-evolution and coenzyme handle theories. While the starting set (GC-phase) was responsible for the nucleotide biosynthesis processes, in the second phase alanine-based amino acids (GCA-phase) were recruited from the core metabolism, thereby providing a standard secondary structure, the α-helix. In the final phase (GCAU-phase), the amino acids were appended to the already existing architecture, enabling tertiary fold and membrane interactions. The whole scheme indicates strongly that the choice for the alanine core was done at the GCA-phase, while glycine and proline remained rudiments from the GC-phase. We suggest that the Protein World should rather be considered the Alanine World, as it predominantly relies on the alanine as the core chemical scaffold. Full article
(This article belongs to the Special Issue Origins of Protein Translation)
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