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Di Giulio M. Theories of the origin of the genetic code: Strong corroboration for the coevolution theory. Biosystems 2024; 239:105217. [PMID: 38663520 DOI: 10.1016/j.biosystems.2024.105217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 04/16/2024] [Accepted: 04/18/2024] [Indexed: 04/29/2024]
Abstract
I analyzed all the theories and models of the origin of the genetic code, and over the years, I have considered the main suggestions that could explain this origin. The conclusion of this analysis is that the coevolution theory of the origin of the genetic code is the theory that best captures the majority of observations concerning the organization of the genetic code. In other words, the biosynthetic relationships between amino acids would have heavily influenced the origin of the organization of the genetic code, as supported by the coevolution theory. Instead, the presence in the genetic code of physicochemical properties of amino acids, which have also been linked to the physicochemical properties of anticodons or codons or bases by stereochemical and physicochemical theories, would simply be the result of natural selection. More explicitly, I maintain that these correlations between codons, anticodons or bases and amino acids are in fact the result not of a real correlation between amino acids and codons, for example, but are only the effect of the intervention of natural selection. Specifically, in the genetic code table we expect, for example, that the most similar codons - that is, those that differ by only one base - will have more similar physicochemical properties. Therefore, the 64 codons of the genetic code table ordered in a certain way would also represent an ordering of some of their physicochemical properties. Now, a study aimed at clarifying which physicochemical property of amino acids has influenced the allocation of amino acids in the genetic code has established that the partition energy of amino acids has played a role decisive in this. Indeed, under some conditions, the genetic code was found to be approximately 98% optimized on its columns. In this same work, it was shown that this was most likely the result of the action of natural selection. If natural selection had truly allocated the amino acids in the genetic code in such a way that similar amino acids also have similar codons - this, not through a mechanism of physicochemical interaction between, for example, codons and amino acids - then it might turn out that even different physicochemical properties of codons (or anticodons or bases) show some correlation with the physicochemical properties of amino acids, simply because the partition energy of amino acids is correlated with other physicochemical properties of amino acids. It is very likely that this would inevitably lead to a correlation between codons (or anticodons or bases) and amino acids. In other words, since the codons (anticodons or bases) are ordered in the genetic code, that is to say, some of their physicochemical properties should also be ordered by a similar order, and given that the amino acids would also appear to have been ordered in the genetic code by selection natural, then it should inevitably turn out that there is a correlation between, for example, the hydrophobicity of anticodons and that of amino acids. Instead, the intervention of natural selection in organizing the genetic code would appear to be highly compatible with the main mechanism of structuring the genetic code as supported by the coevolution theory. This would make the coevolution theory the only plausible explanation for the origin of the genetic code.
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Affiliation(s)
- Massimo Di Giulio
- The Ionian School, Early Evolution of Life Department, Genetic Code and tRNA Origin Laboratory, Via Roma 19, 67030, Alfedena, L'Aquila, Italy.
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2
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Kapral TH, Farnhammer F, Zhao W, Lu ZJ, Zagrovic B. Widespread autogenous mRNA-protein interactions detected by CLIP-seq. Nucleic Acids Res 2022; 50:9984-9999. [PMID: 36107779 PMCID: PMC9508846 DOI: 10.1093/nar/gkac756] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 07/12/2022] [Accepted: 08/24/2022] [Indexed: 02/02/2023] Open
Abstract
Autogenous interactions between mRNAs and the proteins they encode are implicated in cellular feedback-loop regulation, but their extent and mechanistic foundation are unclear. It was recently hypothesized that such interactions may be common, reflecting the role of intrinsic nucleobase-amino acid affinities in shaping the genetic code's structure. Here we analyze a comprehensive set of CLIP-seq experiments involving multiple protocols and report on widespread autogenous interactions across different organisms. Specifically, 230 of 341 (67%) studied RNA-binding proteins (RBPs) interact with their own mRNAs, with a heavy enrichment among high-confidence hits and a preference for coding sequence binding. We account for different confounding variables, including physical (overexpression and proximity during translation), methodological (difference in CLIP protocols, peak callers and cell types) and statistical (treatment of null backgrounds). In particular, we demonstrate a high statistical significance of autogenous interactions by sampling null distributions of fixed-margin interaction matrices. Furthermore, we study the dependence of autogenous binding on the presence of RNA-binding motifs and structured domains in RBPs. Finally, we show that intrinsic nucleobase-amino acid affinities favor co-aligned binding between mRNA coding regions and the proteins they encode. Our results suggest a central role for autogenous interactions in RBP regulation and support the possibility of a fundamental connection between coding and binding.
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Affiliation(s)
- Thomas H Kapral
- Departmet of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Vienna, A-1030, Austria,Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, A-1030, Austria
| | - Fiona Farnhammer
- Departmet of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Vienna, A-1030, Austria,Division of Metabolism, University Children's Hospital Zurich and Children's Research Center, University of Zurich, Zurich, 8032, Switzerland,Division of Oncology, University Children's Hospital Zurich and Children's Research Center, University of Zurich, Zurich, 8032, Switzerland
| | - Weihao Zhao
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Zhi J Lu
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Bojan Zagrovic
- To whom correspondence should be addressed. Tel: +43 1 4277 52271; Fax: +43 1 4277 9522;
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Caldararo F, Di Giulio M. The genetic code is very close to a global optimum in a model of its origin taking into account both the partition energy of amino acids and their biosynthetic relationships. Biosystems 2022; 214:104613. [DOI: 10.1016/j.biosystems.2022.104613] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 01/16/2022] [Accepted: 01/17/2022] [Indexed: 01/23/2023]
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Rogers SO. Evolution of the genetic code based on conservative changes of codons, amino acids, and aminoacyl tRNA synthetases. J Theor Biol 2019; 466:1-10. [PMID: 30658052 DOI: 10.1016/j.jtbi.2019.01.022] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 01/10/2019] [Accepted: 01/14/2019] [Indexed: 11/30/2022]
Abstract
The genetic code, as arranged in the standard tabular form, displays a non-random structure relating to the characteristics of the amino acids. An alternative arrangement can be made by organizing the code according to aminoacyl-tRNA synthetases (aaRSs), codons, and reverse complement codons, which illuminates a coevolutionary process that led to the contemporary genetic code. As amino acids were added to the genetic code, they were recognized by aaRSs that interact with stereochemically similar amino acids. Single nucleotide changes in the codons and anticodons were favored over more extensive changes, such that there was a logical stepwise progression in the evolution of the genetic code. The model presented traces the evolution of the genetic code accounting for these steps. Amino acid frequencies in ancient proteins and the preponderance of GNN codons in mRNAs for ancient proteins indicate that the genetic code began with alanine, aspartate, glutamate, glycine, and valine, with alanine being in the highest proportions. In addition to being consistent in terms of conservative changes in codon nucleotides, the model also is consistent with respect to aaRS classes, aaRS attachment to the tRNA, amino acid stereochemistry, and to a large extent with amino acid physicochemistry, and biochemical pathways.
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Affiliation(s)
- Scott O Rogers
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH, United States.
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Wnętrzak M, Błażej P, Mackiewicz D, Mackiewicz P. The optimality of the standard genetic code assessed by an eight-objective evolutionary algorithm. BMC Evol Biol 2018; 18:192. [PMID: 30545289 PMCID: PMC6293558 DOI: 10.1186/s12862-018-1304-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 11/22/2018] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The standard genetic code (SGC) is a unique set of rules which assign amino acids to codons. Similar amino acids tend to have similar codons indicating that the code evolved to minimize the costs of amino acid replacements in proteins, caused by mutations or translational errors. However, if such optimization in fact occurred, many different properties of amino acids must have been taken into account during the code evolution. Therefore, this problem can be reformulated as a multi-objective optimization task, in which the selection constraints are represented by measures based on various amino acid properties. RESULTS To study the optimality of the SGC we applied a multi-objective evolutionary algorithm and we used the representatives of eight clusters, which grouped over 500 indices describing various physicochemical properties of amino acids. Thanks to that we avoided an arbitrary choice of amino acid features as optimization criteria. As a consequence, we were able to conduct a more general study on the properties of the SGC than the ones presented so far in other papers on this topic. We considered two models of the genetic code, one preserving the characteristic codon blocks structure of the SGC and the other without this restriction. The results revealed that the SGC could be significantly improved in terms of error minimization, hereby it is not fully optimized. Its structure differs significantly from the structure of the codes optimized to minimize the costs of amino acid replacements. On the other hand, using newly defined quality measures that placed the SGC in the global space of theoretical genetic codes, we showed that the SGC is definitely closer to the codes that minimize the costs of amino acids replacements than those maximizing them. CONCLUSIONS The standard genetic code represents most likely only partially optimized systems, which emerged under the influence of many different factors. Our findings can be useful to researchers involved in modifying the genetic code of the living organisms and designing artificial ones.
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Affiliation(s)
- Małgorzata Wnętrzak
- Department of Genomics, Faculty of Biotechnology, University of Wrocław, ul. Joliot-Curie 14a, 50-383, Wrocław, Poland
| | - Paweł Błażej
- Department of Genomics, Faculty of Biotechnology, University of Wrocław, ul. Joliot-Curie 14a, 50-383, Wrocław, Poland
| | - Dorota Mackiewicz
- Department of Genomics, Faculty of Biotechnology, University of Wrocław, ul. Joliot-Curie 14a, 50-383, Wrocław, Poland
| | - Paweł Mackiewicz
- Department of Genomics, Faculty of Biotechnology, University of Wrocław, ul. Joliot-Curie 14a, 50-383, Wrocław, Poland.
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Facchiano A, Di Giulio M. The genetic code is not an optimal code in a model taking into account both the biosynthetic relationships between amino acids and their physicochemical properties. J Theor Biol 2018; 459:45-51. [DOI: 10.1016/j.jtbi.2018.09.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 09/04/2018] [Accepted: 09/19/2018] [Indexed: 01/22/2023]
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de Farias ST, Antonino D, Rêgo TG, José MV. Structural evolution of Glycyl-tRNA synthetases alpha subunit and its implication in the initial organization of the decoding system. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2018; 142:43-50. [PMID: 30142371 DOI: 10.1016/j.pbiomolbio.2018.08.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 07/13/2018] [Accepted: 08/14/2018] [Indexed: 11/27/2022]
Abstract
The origin and evolution of the genetic code is a fundamental challenge in modern biology. At the center of this problem is the correct interaction between amino acids and tRNAs. Aminoacyl-tRNA synthetase is the enzyme responsible for the correct binding between amino acids and tRNAs. Among the 20 canonical amino acid, glycine was the most abundant in prebiotic condition and it must have been one of the first to be incorporated into the genetic code. In this work, we derive the ancestral sequence of Glycyl-tRNA synthetase (GlyRS) and predict its 3D-structure. We show, via molecular docking experiments, the capacity of ancestral GlyRS to bind the tRNA anticodon stem loop, cofactors and substrates. These bindings exhibit high affinity and specificity. We propose that the primordial function of these interactions was to stabilize both compounds to make possible the catalysis. In this context, the anticodon stem loop did contribute to the encoding system and just with the emergence of the mRNA it was co-opted for codification. Thus, we present a model for the origin of the genetic code in which the operational and the anticodon codes did not evolve independently.
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Affiliation(s)
- Savio Torres de Farias
- Laboratório de Genética Evolutiva Paulo Leminsk, Departamento de Biologia Molecular, Universidade Federal da Paraíba, João Pessoa, Brazil.
| | - Daniel Antonino
- Laboratório de Genética Evolutiva Paulo Leminsk, Departamento de Biologia Molecular, Universidade Federal da Paraíba, João Pessoa, Brazil
| | - Thais Gaudêncio Rêgo
- Departamento de Informática, Universidade Federal da Paraíba, João Pessoa, Brazil
| | - Marco V José
- Theoretical Biology Group, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México CDMX, C.P. 04510, Mexico.
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Di Giulio M. On Earth, there would be a number of fundamental kinds of primary cells – cellular domains – greater than or equal to four. J Theor Biol 2018; 443:10-17. [DOI: 10.1016/j.jtbi.2018.01.025] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 01/10/2018] [Accepted: 01/19/2018] [Indexed: 11/15/2022]
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Zamudio GS, José MV. Phenotypic Graphs and Evolution Unfold the Standard Genetic Code as the Optimal. ORIGINS LIFE EVOL B 2017; 48:83-91. [PMID: 29082465 DOI: 10.1007/s11084-017-9552-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2017] [Accepted: 10/16/2017] [Indexed: 10/18/2022]
Abstract
In this work, we explicitly consider the evolution of the Standard Genetic Code (SGC) by assuming two evolutionary stages, to wit, the primeval RNY code and two intermediate codes in between. We used network theory and graph theory to measure the connectivity of each phenotypic graph. The connectivity values are compared to the values of the codes under different randomization scenarios. An error-correcting optimal code is one in which the algebraic connectivity is minimized. We show that the SGC is optimal in regard to its robustness and error-tolerance when compared to all random codes under different assumptions.
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Affiliation(s)
- Gabriel S Zamudio
- Theoretical Biology Group, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, C.P. 04510, Ciudad de México CDMX, Mexico
| | - Marco V José
- Theoretical Biology Group, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, C.P. 04510, Ciudad de México CDMX, Mexico.
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Seligmann H, Warthi G. Genetic Code Optimization for Cotranslational Protein Folding: Codon Directional Asymmetry Correlates with Antiparallel Betasheets, tRNA Synthetase Classes. Comput Struct Biotechnol J 2017; 15:412-424. [PMID: 28924459 PMCID: PMC5591391 DOI: 10.1016/j.csbj.2017.08.001] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Revised: 07/20/2017] [Accepted: 08/05/2017] [Indexed: 12/14/2022] Open
Abstract
A new codon property, codon directional asymmetry in nucleotide content (CDA), reveals a biologically meaningful genetic code dimension: palindromic codons (first and last nucleotides identical, codon structure XZX) are symmetric (CDA = 0), codons with structures ZXX/XXZ are 5'/3' asymmetric (CDA = - 1/1; CDA = - 0.5/0.5 if Z and X are both purines or both pyrimidines, assigning negative/positive (-/+) signs is an arbitrary convention). Negative/positive CDAs associate with (a) Fujimoto's tetrahedral codon stereo-table; (b) tRNA synthetase class I/II (aminoacylate the 2'/3' hydroxyl group of the tRNA's last ribose, respectively); and (c) high/low antiparallel (not parallel) betasheet conformation parameters. Preliminary results suggest CDA-whole organism associations (body temperature, developmental stability, lifespan). Presumably, CDA impacts spatial kinetics of codon-anticodon interactions, affecting cotranslational protein folding. Some synonymous codons have opposite CDA sign (alanine, leucine, serine, and valine), putatively explaining how synonymous mutations sometimes affect protein function. Correlations between CDA and tRNA synthetase classes are weaker than between CDA and antiparallel betasheet conformation parameters. This effect is stronger for mitochondrial genetic codes, and potentially drives mitochondrial codon-amino acid reassignments. CDA reveals information ruling nucleotide-protein relations embedded in reversed (not reverse-complement) sequences (5'-ZXX-3'/5'-XXZ-3').
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Affiliation(s)
- Hervé Seligmann
- Aix-Marseille Univ, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS UMR7278, IRD 198, INSERM U1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, Postal code 13385, France
- Dept. Ecol Evol Behav, Alexander Silberman Inst Life Sci, The Hebrew University of Jerusalem, IL-91904 Jerusalem, Israel
| | - Ganesh Warthi
- Aix-Marseille Univ, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS UMR7278, IRD 198, INSERM U1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, Postal code 13385, France
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Zamudio GS, José MV. On the Uniqueness of the Standard Genetic Code. Life (Basel) 2017; 7:life7010007. [PMID: 28208827 PMCID: PMC5370407 DOI: 10.3390/life7010007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 02/07/2017] [Accepted: 02/08/2017] [Indexed: 11/16/2022] Open
Abstract
In this work, we determine the biological and mathematical properties that are sufficient and necessary to uniquely determine both the primeval RNY (purine-any base-pyrimidine) code and the standard genetic code (SGC). These properties are: the evolution of the SGC from the RNY code; the degeneracy of both codes, and the non-degeneracy of the assignments of aminoacyl-tRNA synthetases (aaRSs) to amino acids; the wobbling property; the consideration that glycine was the first amino acid; the topological and symmetrical properties of both codes.
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Affiliation(s)
- Gabriel S Zamudio
- Theoretical Biology Group, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México D.F. 04510, Mexico.
| | - Marco V José
- Theoretical Biology Group, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México D.F. 04510, Mexico.
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Some pungent arguments against the physico-chemical theories of the origin of the genetic code and corroborating the coevolution theory. J Theor Biol 2017; 414:1-4. [DOI: 10.1016/j.jtbi.2016.11.014] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Revised: 10/26/2016] [Accepted: 11/16/2016] [Indexed: 10/20/2022]
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Liu Z, Rigger L, Rossi JC, Sutherland JD, Pascal R. Mixed Anhydride Intermediates in the Reaction of 5(4H)-Oxazolones with Phosphate Esters and Nucleotides. Chemistry 2016; 22:14940-14949. [PMID: 27534830 PMCID: PMC5074369 DOI: 10.1002/chem.201602697] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Indexed: 12/13/2022]
Abstract
5(4H)‐Oxazolones can be formed through the activation of acylated α‐amino acids or of peptide C termini. They constitute potentially activated intermediates in the abiotic chemistry of peptides that preceded the origin of life or early stages of biology and are capable of yielding mixed carboxylic‐phosphoric anhydrides upon reaction with phosphate esters and nucleotides. Here, we present the results of a study aimed at investigating the chemistry that can be built through this interaction. As a matter of fact, the formation of mixed anhydrides with mononucleotides and nucleic acid models is shown to take place at positions involving a mono‐substituted phosphate group at the 3’‐ or 5’‐terminus but not at the internal phosphodiester linkages. In addition to the formation of mixed anhydrides, the subsequent intramolecular acyl or phosphoryl transfers taking place at the 3’‐terminus are considered to be particularly relevant to the common prebiotic chemistry of α‐amino acids and nucleotides.
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Affiliation(s)
- Ziwei Liu
- Institut des Biomolécules Max Mousseron, CNRS, Université de Montpellier, École nationale supérieure de chimie de Montpellier (ENSCM), Place E. Bataillon, 34095, Montpellier Cedex 5, France
| | - Lukas Rigger
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, CB2 0QH, UK
| | - Jean-Christophe Rossi
- Institut des Biomolécules Max Mousseron, CNRS, Université de Montpellier, École nationale supérieure de chimie de Montpellier (ENSCM), Place E. Bataillon, 34095, Montpellier Cedex 5, France
| | - John D Sutherland
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, CB2 0QH, UK
| | - Robert Pascal
- Institut des Biomolécules Max Mousseron, CNRS, Université de Montpellier, École nationale supérieure de chimie de Montpellier (ENSCM), Place E. Bataillon, 34095, Montpellier Cedex 5, France.
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Abstract
A semi-synthetic organism with an extended genetic alphabet heralds a new era in synthetic biology.
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Affiliation(s)
- Roy D Sleator
- Department of Biological Sciences; Cork Institute of Technology; Cork, Ireland
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