1
|
Halpern A, Bartsch LR, Ibrahim K, Harrison SA, Ahn M, Christodoulou J, Lane N. Biophysical Interactions Underpin the Emergence of Information in the Genetic Code. Life (Basel) 2023; 13:life13051129. [PMID: 37240774 DOI: 10.3390/life13051129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 04/25/2023] [Accepted: 04/30/2023] [Indexed: 05/28/2023] Open
Abstract
The genetic code conceals a 'code within the codons', which hints at biophysical interactions between amino acids and their cognate nucleotides. Yet, research over decades has failed to corroborate systematic biophysical interactions across the code. Using molecular dynamics simulations and NMR, we have analysed interactions between the 20 standard proteinogenic amino acids and 4 RNA mononucleotides in 3 charge states. Our simulations show that 50% of amino acids bind best with their anticodonic middle base in the -1 charge state common to the backbone of RNA, while 95% of amino acids interact most strongly with at least 1 of their codonic or anticodonic bases. Preference for the cognate anticodonic middle base was greater than 99% of randomised assignments. We verify a selection of our results using NMR, and highlight challenges with both techniques for interrogating large numbers of weak interactions. Finally, we extend our simulations to a range of amino acids and dinucleotides, and corroborate similar preferences for cognate nucleotides. Despite some discrepancies between the predicted patterns and those observed in biology, the existence of weak stereochemical interactions means that random RNA sequences could template non-random peptides. This offers a compelling explanation for the emergence of genetic information in biology.
Collapse
Affiliation(s)
- Aaron Halpern
- UCL Centre for Life's Origins and Evolution (CLOE), Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Lilly R Bartsch
- UCL Centre for Life's Origins and Evolution (CLOE), Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Kaan Ibrahim
- UCL Centre for Life's Origins and Evolution (CLOE), Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Stuart A Harrison
- UCL Centre for Life's Origins and Evolution (CLOE), Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Minkoo Ahn
- Department of Structural and Molecular Biology, Institute of Structural and Molecular Biology (ISMB), University College London, London WC1E 6BT, UK
| | - John Christodoulou
- Department of Structural and Molecular Biology, Institute of Structural and Molecular Biology (ISMB), University College London, London WC1E 6BT, UK
| | - Nick Lane
- UCL Centre for Life's Origins and Evolution (CLOE), Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| |
Collapse
|
2
|
Harrison SA, Palmeira RN, Halpern A, Lane N. A biophysical basis for the emergence of the genetic code in protocells. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2022; 1863:148597. [PMID: 35868450 DOI: 10.1016/j.bbabio.2022.148597] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 06/27/2022] [Accepted: 07/13/2022] [Indexed: 11/17/2022]
Abstract
The origin of the genetic code is an abiding mystery in biology. Hints of a 'code within the codons' suggest biophysical interactions, but these patterns have resisted interpretation. Here, we present a new framework, grounded in the autotrophic growth of protocells from CO2 and H2. Recent work suggests that the universal core of metabolism recapitulates a thermodynamically favoured protometabolism right up to nucleotide synthesis. Considering the genetic code in relation to an extended protometabolism allows us to predict most codon assignments. We show that the first letter of the codon corresponds to the distance from CO2 fixation, with amino acids encoded by the purines (G followed by A) being closest to CO2 fixation. These associations suggest a purine-rich early metabolism with a restricted pool of amino acids. The second position of the anticodon corresponds to the hydrophobicity of the amino acid encoded. We combine multiple measures of hydrophobicity to show that this correlation holds strongly for early amino acids but is weaker for later species. Finally, we demonstrate that redundancy at the third position is not randomly distributed around the code: non-redundant amino acids can be assigned based on size, specifically length. We attribute this to additional stereochemical interactions at the anticodon. These rules imply an iterative expansion of the genetic code over time with codon assignments depending on both distance from CO2 and biophysical interactions between nucleotide sequences and amino acids. In this way the earliest RNA polymers could produce non-random peptide sequences with selectable functions in autotrophic protocells.
Collapse
Affiliation(s)
- Stuart A Harrison
- Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London WC1E 6BT, United Kingdom of Great Britain and Northern Ireland
| | - Raquel Nunes Palmeira
- Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London WC1E 6BT, United Kingdom of Great Britain and Northern Ireland
| | - Aaron Halpern
- Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London WC1E 6BT, United Kingdom of Great Britain and Northern Ireland
| | - Nick Lane
- Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London WC1E 6BT, United Kingdom of Great Britain and Northern Ireland.
| |
Collapse
|
3
|
The Uroboros Theory of Life's Origin: 22-Nucleotide Theoretical Minimal RNA Rings Reflect Evolution of Genetic Code and tRNA-rRNA Translation Machineries. Acta Biotheor 2019; 67:273-297. [PMID: 31388859 DOI: 10.1007/s10441-019-09356-w] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 07/31/2019] [Indexed: 02/06/2023]
Abstract
Theoretical minimal RNA rings attempt to mimick life's primitive RNAs. At most 25 22-nucleotide-long RNA rings code once for each biotic amino acid, a start and a stop codon and form a stem-loop hairpin, resembling consensus tRNAs. We calculated, for each RNA ring's 22 potential splicing positions, similarities of predicted secondary structures with tRNA vs. rRNA secondary structures. Assuming rRNAs partly derived from tRNA accretions, we predict positive associations between relative secondary structure similarities with rRNAs over tRNAs and genetic code integration orders of RNA ring anticodon cognate amino acids. Analyses consider for each secondary structure all nucleotide triplets as potential anticodon. Anticodons for ancient, chemically inert cognate amino acids are most frequent in the 25 RNA rings. For RNA rings with primordial cognate amino acids according to tRNA-homology-derived anticodons, tRNA-homology and coding sequences coincide, these are separate for predicted cognate amino acids that presumably integrated late the genetic code. RNA ring secondary structure similarity with rRNA over tRNA secondary structures associates best with genetic code integration orders of anticodon cognate amino acids when assuming split anticodons (one and two nucleotides at the spliced RNA ring 5' and 3' extremities, respectively), and at predicted anticodon location in the spliced RNA ring's midst. Results confirm RNA ring homologies with tRNAs and CDs, ancestral status of tRNA half genes split at anticodons, the tRNA-rRNA axis of RNA evolution, and that single theoretical minimal RNA rings potentially produce near-complete proto-tRNA sets. Hence genetic code pre-existence determines 25 short circular gene- and tRNA-like RNAs. Accounting for each potential splicing position, each RNA ring potentially translates most amino acids, realistically mimicks evolution of the tRNA-rRNA translation machinery. These RNA rings 'of creation' remind the uroboros' (snake biting its tail) symbolism for creative regeneration.
Collapse
|
4
|
Demongeot J, Norris V. Emergence of a "Cyclosome" in a Primitive Network Capable of Building "Infinite" Proteins. Life (Basel) 2019; 9:E51. [PMID: 31216720 PMCID: PMC6617141 DOI: 10.3390/life9020051] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 06/08/2019] [Accepted: 06/13/2019] [Indexed: 01/02/2023] Open
Abstract
We argue for the existence of an RNA sequence, called the AL (for ALpha) sequence, which may have played a role at the origin of life; this role entailed the AL sequence helping generate the first peptide assemblies via a primitive network. These peptide assemblies included "infinite" proteins. The AL sequence was constructed on an economy principle as the smallest RNA ring having one representative of each codon's synonymy class and capable of adopting a non-functional but nevertheless evolutionarily stable hairpin form that resisted denaturation due to environmental changes in pH, hydration, temperature, etc. Long subsequences from the AL ring resemble sequences from tRNAs and 5S rRNAs of numerous species like the proteobacterium, Rhodobacter sphaeroides. Pentameric subsequences from the AL are present more frequently than expected in current genomes, in particular, in genes encoding some of the proteins associated with ribosomes like tRNA synthetases. Such relics may help explain the existence of universal sequences like exon/intron frontier regions, Shine-Dalgarno sequence (present in bacterial and archaeal mRNAs), CRISPR and mitochondrial loop sequences.
Collapse
Affiliation(s)
- Jacques Demongeot
- Faculty of Medicine, Université Grenoble Alpes, AGEIS EA 7407 Tools for e-Gnosis Medical, 38700 La Tronche, France.
| | - Vic Norris
- Laboratory of Microbiology Signals and Microenvironment, Université de Rouen, 76821 Mont-Saint-Aignan CEDEX, France.
| |
Collapse
|
5
|
Fontecilla-Camps JC. Geochemical Continuity and Catalyst/Cofactor Replacement in the Emergence and Evolution of Life. Angew Chem Int Ed Engl 2018; 58:42-48. [DOI: 10.1002/anie.201808438] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 08/27/2018] [Indexed: 12/29/2022]
|
6
|
Fontecilla-Camps JC. Geochemische Kontinuität und Katalysator/Cofaktor-Austausch für Ursprung und Evolution des Lebens. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201808438] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
|
7
|
Tamura K. Origins and Early Evolution of the tRNA Molecule. Life (Basel) 2015; 5:1687-99. [PMID: 26633518 PMCID: PMC4695843 DOI: 10.3390/life5041687] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 11/25/2015] [Accepted: 11/26/2015] [Indexed: 11/16/2022] Open
Abstract
Modern transfer RNAs (tRNAs) are composed of ~76 nucleotides and play an important role as "adaptor" molecules that mediate the translation of information from messenger RNAs (mRNAs). Many studies suggest that the contemporary full-length tRNA was formed by the ligation of half-sized hairpin-like RNAs. A minihelix (a coaxial stack of the acceptor stem on the T-stem of tRNA) can function both in aminoacylation by aminoacyl tRNA synthetases and in peptide bond formation on the ribosome, indicating that it may be a vestige of the ancestral tRNA. The universal CCA-3' terminus of tRNA is also a typical characteristic of the molecule. "Why CCA?" is the fundamental unanswered question, but several findings give a comprehensive picture of its origin. Here, the origins and early evolution of tRNA are discussed in terms of various perspectives, including nucleotide ligation, chiral selectivity of amino acids, genetic code evolution, and the organization of the ribosomal peptidyl transferase center (PTC). The proto-tRNA molecules may have evolved not only as adaptors but also as contributors to the composition of the ribosome.
Collapse
Affiliation(s)
- Koji Tamura
- Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo 125-8585, Japan.
- Research Institute for Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan.
| |
Collapse
|
8
|
The RNA World: 4,000,000,050 years old. Life (Basel) 2015; 5:1583-6. [PMID: 26791312 PMCID: PMC4695837 DOI: 10.3390/life5041583] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 10/13/2015] [Indexed: 12/26/2022] Open
|
9
|
Tamura K. Beyond the Frozen Accident: Glycine Assignment in the Genetic Code. J Mol Evol 2015; 81:69-71. [PMID: 26289730 DOI: 10.1007/s00239-015-9694-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 08/11/2015] [Indexed: 10/23/2022]
Abstract
tRNA with a terminal UCCA-3' forms a structure in which the 3'-sequence folds back. The adenine of glycyl-AMP can base-pair with the uridine of the UCCA-3' region, which places the glycine residue in close proximity to the 3'-terminal adenosine of tRNA, possibly enabling the transfer of glycine from glycyl-AMP to tRNA. Thus, the UCCA-3'-containing tRNA (as seen in eubacterial tRNA(Gly)s) would possess an intrinsic property of glycylation by glycyl-AMP. This model provides a new perspective on the origins of the glycine assignment in the genetic code, beyond the "frozen accident" hypothesis.
Collapse
Affiliation(s)
- Koji Tamura
- Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo, 125-8585, Japan. .,Research Institute for Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan.
| |
Collapse
|