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The Non-monophyletic Origin of the tRNA Molecule
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{"work":{"id":123290399,"created_at":"2024-08-27T07:36:06.511-07:00","from_world_paper_id":258654849,"updated_at":"2025-01-27T19:35:20.333-08:00","_data":{"publisher":"Elsevier BV","ai_abstract":"The paper discusses the non-monophyletic origin of the tRNA molecule, proposing that tRNA genes evolved from separate minigenes encoding distinct RNA hairpin structures after the time of the last universal common ancestor (LUCA). It supports this theory by outlining observations of separate tRNA genes in organisms like Nanoarchaeum equitans and suggests that this evolutionary pathway refutes the idea of a monophyletic origin for tRNA.","publication_date":"1999,,","publication_name":"Journal of Theoretical Biology"},"document_type":"paper","pre_hit_view_count_baseline":null,"quality":"low","language":"en","title":"The Non-monophyletic Origin of the tRNA Molecule","broadcastable":false,"draft":null,"has_indexable_attachment":true,"indexable":true,"seo_quality":null}}["work"]; window.loswp.workCoauthors = [78314817]; window.loswp.locale = "en"; window.loswp.countryCode = "SG"; window.loswp.cwvAbTestBucket = ""; window.loswp.designVariant = "ds_vanilla"; window.loswp.fullPageMobileSutdModalVariant = "full_page_mobile_sutd_modal"; window.loswp.useOptimizedScribd4genScript = false; window.loginModal = {}; window.loginModal.appleClientId = 'edu.academia.applesignon'; window.userInChina = "false";</script><script defer="" src="https://accounts.google.com/gsi/client"></script><div class="ds-loswp-container"><div class="ds-work-card--grid-container"><div class="ds-work-card--container js-loswp-work-card"><div class="ds-work-card--cover"><div class="ds-work-cover--wrapper"><div class="ds-work-cover--container"><button class="ds-work-cover--clickable js-swp-download-button" data-signup-modal="{"location":"swp-splash-paper-cover","attachmentId":117756794,"attachmentType":"pdf"}"><img alt="First page of “The Non-monophyletic Origin of the tRNA Molecule”" class="ds-work-cover--cover-thumbnail" src="https://0.academia-photos.com/attachment_thumbnails/117756794/mini_magick20240827-1-riuzzv.png?1724769430" /><img alt="PDF Icon" class="ds-work-cover--file-icon" src="//a.academia-assets.com/images/single_work_splash/adobe_icon.svg" /><div class="ds-work-cover--hover-container"><span class="material-symbols-outlined" style="font-size: 20px" translate="no">download</span><p>Download Free PDF</p></div><div class="ds-work-cover--ribbon-container">Download Free PDF</div><div class="ds-work-cover--ribbon-triangle"></div></button></div></div></div><div class="ds-work-card--work-information"><h1 class="ds-work-card--work-title">The Non-monophyletic Origin of the tRNA Molecule</h1><div class="ds-work-card--work-authors ds-work-card--detail"><a class="ds-work-card--author js-wsj-grid-card-author ds2-5-body-md ds2-5-body-link" data-author-id="78314817" href="https://independent.academia.edu/MassimoDiGiulio"><img alt="Profile image of Massimo Di Giulio" class="ds-work-card--author-avatar" src="https://0.academia-photos.com/78314817/26680239/25180795/s65_massimo.di_giulio.jpg" />Massimo Di Giulio</a></div><div class="ds-work-card--detail"><p class="ds-work-card--detail ds2-5-body-sm">1999, Journal of Theoretical Biology</p><div class="ds-work-card--work-metadata"><div class="ds-work-card--work-metadata__stat"><span class="material-symbols-outlined" style="font-size: 20px" translate="no">visibility</span><p class="ds2-5-body-sm" id="work-metadata-view-count">…</p></div><div class="ds-work-card--work-metadata__stat"><span class="material-symbols-outlined" style="font-size: 20px" translate="no">description</span><p class="ds2-5-body-sm">2 pages</p></div><div class="ds-work-card--work-metadata__stat"><span class="material-symbols-outlined" style="font-size: 20px" translate="no">link</span><p class="ds2-5-body-sm">1 file</p></div></div><script>(async () => { const workId = 123290399; 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It supports this theory by outlining observations of separate tRNA genes in organisms like Nanoarchaeum equitans and suggests that this evolutionary pathway refutes the idea of a monophyletic origin for tRNA.</p></div></div><div class="ds-top-related-works--grid-container"><div class="ds-related-content--container ds-top-related-works--container"><h2 class="ds-related-content--heading">Related papers</h2><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="0" data-entity-id="123290395" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/123290395/The_non_monophyletic_origin_of_the_tRNA_molecule_and_the_origin_of_genes_only_after_the_evolutionary_stage_of_the_last_universal_common_ancestor_LUCA_">The non-monophyletic origin of the tRNA molecule and the origin of genes only after the evolutionary stage of the last universal common ancestor (LUCA)</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="78314817" href="https://independent.academia.edu/MassimoDiGiulio">Massimo Di Giulio</a></div><p class="ds-related-work--metadata ds2-5-body-xs">Journal of Theoretical Biology, 2006</p><p class="ds-related-work--abstract ds2-5-body-sm">A model has been proposed suggesting that the tRNA molecule must have originated by direct duplication of an RNA hairpin structure On the origin of the transfer RNA molecule. J. Theor. Biol. 159,[199][200][201][202][203][204][205][206][207][208][209][210][211][212][213][214]. A non-monophyletic origin of this molecule has also been theorized . The non-monophyletic origin of tRNA molecule. J. Theor. Biol. 197,[403][404][405][406][407][408][409][410][411][412][413][414]. In other words, the tRNA genes evolved only after the evolutionary stage of the last universal common ancestor (LUCA) through the assembly of two minigenes codifying for different RNA hairpin structures, which is what the exon theory of genes suggests when it is applied to the model of tRNA origin. Recent observations strongly corroborate this theorization because it has been found that some tRNA genes are completely separate in two minigenes codifying for the 5 0 and 3 0 halves of this molecule [Randau, L., et al., 2005a. Nanoarchaeum equitans creates functional tRNAs from separate genes for their 5 0 -and 3 0 -halves. Nature 433, 537-541]. In this paper it is shown that these tRNA genes codifying for the 5 0 and 3 0 halves of this molecule are the ancestral form from which the tRNA genes continuously codifying for the complete tRNA molecule are thought to have evolved. This, together with the very existence of completely separate tRNA genes codifying for their 5 0 and 3 0 halves, proves a non-monophyletic origin for tRNA genes, as a monophyletic origin would exclude the existence of these genes which have, on the contrary, been observed. Here the polyphyletic origin of genes codifying for proteins is also suggested and discussed. Moreover, a hypothesis is advanced to suggest that the LUCA might have had a fragmented genome made up of RNA and the possibility that 'Paleokaryotes' may exist is outlined. Finally, the characteristic of the indivisibility of homology that these polyphyletic origins seem to remove at the sequence level is discussed.</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"The non-monophyletic origin of the tRNA molecule and the origin of genes only after the evolutionary stage of the last universal common ancestor (LUCA)","attachmentId":117756793,"attachmentType":"pdf","work_url":"https://www.academia.edu/123290395/The_non_monophyletic_origin_of_the_tRNA_molecule_and_the_origin_of_genes_only_after_the_evolutionary_stage_of_the_last_universal_common_ancestor_LUCA_","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/123290395/The_non_monophyletic_origin_of_the_tRNA_molecule_and_the_origin_of_genes_only_after_the_evolutionary_stage_of_the_last_universal_common_ancestor_LUCA_"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="1" data-entity-id="100841874" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/100841874/A_Comparison_Among_the_Models_Proposed_to_Explain_the_Origin_of_the_tRNA_Molecule_A_Synthesis">A Comparison Among the Models Proposed to Explain the Origin of the tRNA Molecule: A Synthesis</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="78314817" href="https://independent.academia.edu/MassimoDiGiulio">Massimo Di Giulio</a></div><p class="ds-related-work--metadata ds2-5-body-xs">Journal of Molecular Evolution, 2009</p><p class="ds-related-work--abstract ds2-5-body-sm">A comparison is made among all the models proposed to explain the origin of the tRNA molecule. The conclusion reached is that, for the model predicting that the tRNA molecule originated after the assembly of two hairpin-like structures, molecular fossils have been found in the half-genes of the tRNAs of Nanoarchaeum equitans. These might be the witnesses of the transition stage predicted by the model through which the evolution of the tRNA molecule passed, thus providing considerable corroboration for this model. Keywords Corroboration/falsification of theories Á Transition stages Á Molecular fossils of genes Á Ancestral stages Á Missing link Á Hairpin structure Corroboration of the Theories in the Framework of Evolutionary Biology and Molecular Fossils</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"A Comparison Among the Models Proposed to Explain the Origin of the tRNA Molecule: A Synthesis","attachmentId":101548480,"attachmentType":"pdf","work_url":"https://www.academia.edu/100841874/A_Comparison_Among_the_Models_Proposed_to_Explain_the_Origin_of_the_tRNA_Molecule_A_Synthesis","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/100841874/A_Comparison_Among_the_Models_Proposed_to_Explain_the_Origin_of_the_tRNA_Molecule_A_Synthesis"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="2" data-entity-id="66223808" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/66223808/The_Presence_in_tRNA_Molecule_Sequences_of_the_Double_Hairpin_an_Evolutionary_Stage_Through_Which_the_Origin_of_this_Molecule_is_Thought_to_have_Passed">The Presence in tRNA Molecule Sequences of the Double Hairpin, an Evolutionary Stage Through Which the Origin of this Molecule is Thought to have Passed</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="78314817" href="https://independent.academia.edu/MassimoDiGiulio">Massimo Di Giulio</a></div><p class="ds-related-work--metadata ds2-5-body-xs">Journal of Molecular Evolution, 2011</p><p class="ds-related-work--abstract ds2-5-body-sm">We analyse 6,810 tRNAs, calculating the free energy of the corresponding double hairpin and ‘cigar’ secondary structures, for which we find a high thermodynamic and statistical significance. We also analyse these tRNAs for similarity and complementarity of their 5′ and 3′ halves or segments of them in intra-and inter-molecular comparisons. We find very clear signs that the two halves of</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"The Presence in tRNA Molecule Sequences of the Double Hairpin, an Evolutionary Stage Through Which the Origin of this Molecule is Thought to have Passed","attachmentId":77499602,"attachmentType":"pdf","work_url":"https://www.academia.edu/66223808/The_Presence_in_tRNA_Molecule_Sequences_of_the_Double_Hairpin_an_Evolutionary_Stage_Through_Which_the_Origin_of_this_Molecule_is_Thought_to_have_Passed","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/66223808/The_Presence_in_tRNA_Molecule_Sequences_of_the_Double_Hairpin_an_Evolutionary_Stage_Through_Which_the_Origin_of_this_Molecule_is_Thought_to_have_Passed"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="3" data-entity-id="13603334" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/13603334/The_Origin_and_Evolution_of_TRNA_Inferred_From_Phylogenetic_Analysis_of_Structure">The Origin and Evolution of TRNA Inferred From Phylogenetic Analysis of Structure</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="32778210" href="https://illinois.academia.edu/GustavoCaetanoAnolles">Gustavo Caetano-Anolles</a></div><p class="ds-related-work--metadata ds2-5-body-xs">Journal of Molecular Evolution, 2008</p><p class="ds-related-work--abstract ds2-5-body-sm">The evolutionary history of the two structural and functional domains of tRNA is controversial but har-bors the secrets of early translation and the genetic code. To explore the origin and evolution of tRNA, we recon-structed phylogenetic trees directly from molecular structure. Forty-two ...</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"The Origin and Evolution of TRNA Inferred From Phylogenetic Analysis of Structure","attachmentId":45164187,"attachmentType":"pdf","work_url":"https://www.academia.edu/13603334/The_Origin_and_Evolution_of_TRNA_Inferred_From_Phylogenetic_Analysis_of_Structure","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/13603334/The_Origin_and_Evolution_of_TRNA_Inferred_From_Phylogenetic_Analysis_of_Structure"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="4" data-entity-id="115659022" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/115659022/Evolution_of_tRNA_into_rRNA_secondary_structures">Evolution of tRNA into rRNA secondary structures</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="30601357" href="https://otmed.academia.edu/HerveSeligmann">Herve Seligmann</a></div><p class="ds-related-work--metadata ds2-5-body-xs">Gene Reports, 2019</p><p class="ds-related-work--abstract ds2-5-body-sm">RNA and protein structures enable reconstructing ancient evolution because: 1. structures evolve more slowly than primary sequences; 2. Ancient self-organized patterns reappear spontaneously and/or 3. re-evolve secondarily. Previous analyses grouped RNA secondary structures in (a) presumably primitive, short RNAs rich in external loops (topping stems) and few bulges (unpaired nucleotides within stems); and (b) longer, more derived RNAs with more bulges, presumed regulatory endonuclease targets. These represent the main axis of RNA evolution from (a) tRNA-like to (b) rRNA-like. We suggest that relative similarity of tRNAs to (a) reflects antiquity, and to (b) the opposite, predicting that tRNA scores on this tRNA-rRNA axis converge with genetic code inclusion orders of tRNA cognate amino acids. This occurs in particular according to amino acids ranked inversely to tRNA isoacceptor diversity, and mainly in evolutionarily ancient organisms. Putatively, in some organisms, tRNA cloverleaves sometimes recover convergence with genetic code inclusion orders of cognate amino acids, probably because original ancient evolutionary processes integrated functional constraints, i.e., tRNA distinguishability to avoid misacylations. Results confirm the direction, evolutionary and biological relevance of the tRNA-rRNA secondary structure axis as RNA's major evolutionary axis, a potential calibrator of biomolecular evolution. adaptive components integral to the original evolving self-organizing system, notably self-correction properties (Seligmann, 2018a). 1.1. Genetic code inclusion order of amino acid-codon assignments A large number of hypotheses predict the order of amino acid integration in the genetic code, meaning their assignment to codons. These follow diverse approaches, from physicochemical properties of amino acids, i.e., their chemical inertness (Trifonov, 1999), structural complexity (Dufton, 1997; Trifonov and Bettecken, 1997) and stereochemical affinities with nucleotide triplets (Yarus and Christian, 1989; Yarus et al., 2009; Yarus, 2017), including differences between Land D-amino acid enantiomers and their preferences for interacting with D-RNA (Root-Bernstein, 2007; Han et al., 2010; Michel and Seligmann, 2014), to coevolution between metabolic pathways, for example Nfixation (Davis, 1999) and parallels between metabolism of amino acids and their codon assignment (Wong, 1975, 2005). Many hypotheses produce similar/congruent genetic code integration orders for amino acids (Trifonov, 2000, 2004), but it is plausible that different components of the complex translation machinery whose sum produces the genetic code had at least partly independent</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"Evolution of tRNA into rRNA secondary structures","attachmentId":112004984,"attachmentType":"pdf","work_url":"https://www.academia.edu/115659022/Evolution_of_tRNA_into_rRNA_secondary_structures","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/115659022/Evolution_of_tRNA_into_rRNA_secondary_structures"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="5" data-entity-id="88758002" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/88758002/tRNA_evolution_from_the_proto_tRNA_minihelix_world">tRNA evolution from the proto-tRNA minihelix world</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="44971148" href="https://independent.academia.edu/SanjayAdithya">Adithya Sanjay</a></div><p class="ds-related-work--metadata ds2-5-body-xs">Transcription, 2016</p><p class="ds-related-work--abstract ds2-5-body-sm">Multiple models have been advanced for the evolution of cloverleaf tRNA. Here, the conserved archaeal tRNA core (75-nt) is posited to have evolved from ligation of three proto-tRNA minihelices (31-nt) and two-symmetrical 9-nt deletions within joined acceptor stems (93-18 D 75-nt). The primary evidence for this conclusion is that the 5-nt stem 7-nt anticodon loop and the 5-nt stem 7-nt T loop are structurally homologous and related by coding sequence. We posit that the D loop was generated from a third minihelix (31-nt) in which the stem and loop became rearranged after 9-nt acceptor stem deletions and cloverleaf folding. The most 3-5-nt segment of the D loop and the 5-nt V loop are apparent remnants of the joined acceptor stems (14-9 D 5-nt). Before refolding in the tRNA cloverleaf, we posit that the 3 0-5-nt segment of the D loop and the 5-nt V loop were paired, and, in the tRNA cloverleaf, frequent pairing of positions 29 (D loop) and 47 (V loop) remains (numbered on a 75-nt tRNA cloverleaf core). Amazingly, after >3.5 billion years of evolutionary pressure on the tRNA cloverleaf structure, a model can be constructed that convincingly describes the genesis of 75/75-nt conserved archaeal tRNA core positions. Judging from the tRNA structure, cloverleaf tRNA appears to represent at least a second-generation scheme (and possibly a thirdgeneration scheme) that replaced a robust 31-nt minihelix protein-coding system, evidence for which is preserved in the cloverleaf structure. Understanding tRNA evolution provides insights into ribosome and rRNA evolution.</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"tRNA evolution from the proto-tRNA minihelix world","attachmentId":92673065,"attachmentType":"pdf","work_url":"https://www.academia.edu/88758002/tRNA_evolution_from_the_proto_tRNA_minihelix_world","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/88758002/tRNA_evolution_from_the_proto_tRNA_minihelix_world"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="6" data-entity-id="30626344" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/30626344/tRNA_rRNA_sequence_homologies_A_model_for_the_origin_of_a_common_ancestral_molecule_and_prospects_for_its_reconstruction">tRNA-rRNA sequence homologies: A model for the origin of a common ancestral molecule, and prospects for its reconstruction</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="18191518" href="https://cpmtc-igc-ufmg.academia.edu/RomeuGuimaraes">Romeu C Guimaraes</a></div><p class="ds-related-work--metadata ds2-5-body-xs">Origins of Life, 1984</p><p class="ds-related-work--abstract ds2-5-body-sm">A model is proposed for the early evolution of the coding mechanism. A primordial RNA embodies the functions of today's nucleic acids in a single molecule. The molecule is generated by successive rounds of self priming and-templating. After proximity is as functions can be partitioned among more efficient specializel molecules. The prediction of sequence homologies in later forms prompted a search for matches between t-and r-RNAs. These are described. Their distributions of their origins. The existance of overlapping homologies indicates an approach to the reconstruction of an ancestral molecule.</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"tRNA-rRNA sequence homologies: A model for the origin of a common ancestral molecule, and prospects for its reconstruction","attachmentId":51073655,"attachmentType":"pdf","work_url":"https://www.academia.edu/30626344/tRNA_rRNA_sequence_homologies_A_model_for_the_origin_of_a_common_ancestral_molecule_and_prospects_for_its_reconstruction","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/30626344/tRNA_rRNA_sequence_homologies_A_model_for_the_origin_of_a_common_ancestral_molecule_and_prospects_for_its_reconstruction"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="7" data-entity-id="81721628" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/81721628/More_Pieces_of_Ancient_than_Recent_Theoretical_Minimal_Proto_tRNA_Like_RNA_Rings_in_Genes_Coding_for_tRNA_Synthetases">More Pieces of Ancient than Recent Theoretical Minimal Proto-tRNA-Like RNA Rings in Genes Coding for tRNA Synthetases</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="214735294" href="https://independent.academia.edu/JDemongeot">Jacques Demongeot</a></div><p class="ds-related-work--metadata ds2-5-body-xs">Journal of Molecular Evolution, 2019</p><p class="ds-related-work--abstract ds2-5-body-sm">Theoretical minimal RNA rings were designed to mimick life's primordial RNAs by forming stem-loop hairpins and coding once for each of the 20 amino acids, a start and a stop codon. At most 25 22-nucleotide long RNA rings follow these criteria. These align well with a consensus tRNA sequence, predicting for each RNA ring an anticodon and an associated cognate amino acid. Hypotheses on cognate amino acid order of inclusion in the genetic code produce evolutionary ranks for theoretical RNA rings. This evolutionary hypothesis predicts that pieces of RNA rings with more ancient cognate amino acid should be more frequent in modern genes than those from RNA rings with late cognate amino acids. Analyses of genes for tRNA synthetases, among the most ancient proteins, from archaeal, bacterial, eukaryote and viral superkingdoms overall confirm these predictions, least for tRNA synthetases with early cognate amino acids and for the neogene-enriched genome of the giant virus Tupanvirus. Hence early tRNA synthetase genes and late RNA rings evolved separately. Results indicate that RNA rings and tRNA synthetases with the same cognate amino acid are less separated for relatively recent cognate amino acids, suggesting that over evolutionary time the components of the molecular apparatus became more integrated, perhaps in cell-like membrane-bound systems. Results confirm that theoretical considerations in the design of minimal RNA rings recreated RNAs close to the actual primordial RNA population that produce genes by accretion, and confirm the hypothesis of homology of minimal RNA rings with tRNAs and their proto-tRNA status.</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"More Pieces of Ancient than Recent Theoretical Minimal Proto-tRNA-Like RNA Rings in Genes Coding for tRNA Synthetases","attachmentId":87667890,"attachmentType":"pdf","work_url":"https://www.academia.edu/81721628/More_Pieces_of_Ancient_than_Recent_Theoretical_Minimal_Proto_tRNA_Like_RNA_Rings_in_Genes_Coding_for_tRNA_Synthetases","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/81721628/More_Pieces_of_Ancient_than_Recent_Theoretical_Minimal_Proto_tRNA_Like_RNA_Rings_in_Genes_Coding_for_tRNA_Synthetases"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="8" data-entity-id="125634432" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/125634432/RNA_Rings_Strengthen_Hairpin_Accretion_Hypotheses_for_tRNA_Evolution_A_Reply_to_Commentaries_by_Z_F_Burton_and_M_Di_Giulio">RNA Rings Strengthen Hairpin Accretion Hypotheses for tRNA Evolution: A Reply to Commentaries by Z.F. Burton and M. Di Giulio</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="30601357" href="https://otmed.academia.edu/HerveSeligmann">Herve Seligmann</a></div><p class="ds-related-work--metadata ds2-5-body-xs">Journal of Molecular Evolution, 2020</p><p class="ds-related-work--abstract ds2-5-body-sm">Theoretical minimal RNA ring design ensures coding over the shortest length once for each coding signal (start and stop codons, and each amino acid) and their hairpin configuration. These constraints define 25 RNA rings which surprisingly resemble ancestral tRNA loops, suggesting commonalities between RNA ring design and proto-tRNAs. RNA rings share several other properties with tRNAs, suggesting that primordial RNAs were multifunctional peptide coding sequences and structural RNAs. Two hypotheses, respectively, by M. Di Giulio and Z.F. Burton, derived from cloverleaf structural symmetries suggest that two and three, respectively, stem-loop hairpins agglutinated into tRNAs. Their authors commented that their respective structure-based hypotheses reflect better tRNA structure than RNA rings. Unlike these hypotheses, RNA ring design uses no tRNA-derived information, rendering model predictive power comparisons senseless. Some analyses of RNA ring primary and secondary structures stress RNA ring splicing in their predicted anticodon's midst, indicating ancestrality of split tRNAs, as the two-piece model predicts. Advancement of knowledge, rather than of specific hypotheses, gains foremost by examining independent hypotheses for commonalities, and only secondarily for discordances. RNA rings mimick ancestral biomolecules including tRNAs, and their evolution, and constitute an interesting synthetic system for early prebiotic evolution tests/simulations.</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"RNA Rings Strengthen Hairpin Accretion Hypotheses for tRNA Evolution: A Reply to Commentaries by Z.F. Burton and M. Di Giulio","attachmentId":119641175,"attachmentType":"pdf","work_url":"https://www.academia.edu/125634432/RNA_Rings_Strengthen_Hairpin_Accretion_Hypotheses_for_tRNA_Evolution_A_Reply_to_Commentaries_by_Z_F_Burton_and_M_Di_Giulio","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/125634432/RNA_Rings_Strengthen_Hairpin_Accretion_Hypotheses_for_tRNA_Evolution_A_Reply_to_Commentaries_by_Z_F_Burton_and_M_Di_Giulio"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="9" data-entity-id="92172166" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/92172166/RNA_Ligation_and_the_Origin_of_tRNA">RNA Ligation and the Origin of tRNA</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="248515885" href="https://independent.academia.edu/UmaNagaswamy">Uma Nagaswamy</a></div><p class="ds-related-work--metadata ds2-5-body-xs">Origins of Life and Evolution of Biospheres - ORIGINS LIFE EVOL BIOSPHERE, 2003</p><p class="ds-related-work--abstract ds2-5-body-sm">A straightforward origin of transfer RNA,(tRNA), is difficult to envision because of the apparentlycomplex idiosyncratic interaction between the D-loop and T-loop. Recently, multiple examples of the T-loop structuralmotif have been identified in ribosomal RNA. These examplesshow that the long-range interactions between the T-loop andD-loops seen in tRNA are not an essential part of the motifbut rather are facilitated by it. Thus, the core T-loopstructure could already have existed in a small RNA prior tothe emergence of the tRNA. The tRNA might then have arisenby expansion of an RNA that carried the motif. With thisidea in mind, Di Giulio&#x27;s earlier hypothesis that tRNAevolved by a simple duplication or ligation of a minihelixRNA was re-examined. It is shown that an essentially moderntRNA structure can in fact be generated by the ligation oftwo 38-nucleotide RNA minihelices of appropriate sequence.Although rare, such sequences occur with sufficientfrequency, (1 in 3 × 107), that...</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"RNA Ligation and the Origin of tRNA","attachmentId":95252176,"attachmentType":"pdf","work_url":"https://www.academia.edu/92172166/RNA_Ligation_and_the_Origin_of_tRNA","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/92172166/RNA_Ligation_and_the_Origin_of_tRNA"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div></div></div><div class="ds-sticky-ctas--wrapper js-loswp-sticky-ctas hidden"><div class="ds-sticky-ctas--grid-container"><div class="ds-sticky-ctas--container"><button class="ds2-5-button js-swp-download-button" data-signup-modal="{"location":"continue-reading-button--sticky-ctas","attachmentId":117756794,"attachmentType":"pdf","workUrl":null}">See full PDF</button><button class="ds2-5-button ds2-5-button--secondary js-swp-download-button" data-signup-modal="{"location":"download-pdf-button--sticky-ctas","attachmentId":117756794,"attachmentType":"pdf","workUrl":null}"><span class="material-symbols-outlined" style="font-size: 20px" translate="no">download</span>Download PDF</button></div></div></div><div class="ds-below-fold--grid-container"><div class="ds-work--container js-loswp-embedded-document"><div class="attachment_preview" data-attachment="Attachment_117756794" style="display: none"><div class="js-scribd-document-container"><div class="scribd--document-loading js-scribd-document-loader" style="display: block;"><img alt="Loading..." src="//a.academia-assets.com/images/loaders/paper-load.gif" /><p>Loading Preview</p></div></div><div style="text-align: center;"><div class="scribd--no-preview-alert js-preview-unavailable"><p>Sorry, preview is currently unavailable. You can download the paper by clicking the button above.</p></div></div></div></div><div class="ds-sidebar--container js-work-sidebar"><div class="ds-related-content--container"><h2 class="ds-related-content--heading">Related papers</h2><div class="ds-related-work--container js-related-work-sidebar-card" data-collection-position="0" data-entity-id="48479585" data-sort-order="default"><a class="ds-related-work--title js-related-work-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/48479585/Evolution_of_transfer_RNA_and_the_origin_of_the_translation_system">Evolution of transfer RNA and the origin of the translation system</a><div class="ds-related-work--metadata"><a class="js-related-work-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="124859264" href="https://independent.academia.edu/DrMarcoJose">Dr. Marco Jose</a></div><p class="ds-related-work--metadata ds2-5-body-xs">Frontiers in Genetics, 2014</p><div 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class="ds-related-work--container js-related-work-sidebar-card" data-collection-position="1" data-entity-id="116463882" data-sort-order="default"><a class="ds-related-work--title js-related-work-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/116463882/Evolution_from_Possible_Primitive_tRNA_Viroids_to_Early_Poly_tRNA_Derived_mRNAs_A_New_Approach_from_the_Poly_tRNA_Theory">Evolution from Possible Primitive tRNA-Viroids to Early Poly-tRNA-Derived mRNAs: A New Approach from the Poly-tRNA Theory</a><div class="ds-related-work--metadata"><a class="js-related-work-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="4832437" href="https://niigata-u.academia.edu/Nao263Furuichi">Naotaka Furuichi</a></div><p class="ds-related-work--metadata ds2-5-body-xs">2005</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" 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</span><a class="js-related-work-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="46533447" href="https://independent.academia.edu/BSteer">Brian Steer</a></div><p class="ds-related-work--metadata ds2-5-body-xs">Proceedings of the National Academy of Sciences, 1998</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"Genetic code origins: tRNAs older than their synthetases?","attachmentId":44484259,"attachmentType":"pdf","work_url":"https://www.academia.edu/24124807/Genetic_code_origins_tRNAs_older_than_their_synthetases","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-related-work-grid-card-view-pdf" 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Derivative Amino Acids in Archea GENE 396 (2007) 75-83</a><div class="ds-related-work--metadata"><a class="js-related-work-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="1025767" href="https://unal-co.academia.edu/LuisEugenioAndradePerez">Luis Eugenio Andrade Perez</a></div><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"Burbano Hernan y Andrade Eugenio Analysis of tRNA Abstract Shapes of Precursor and Derivative Amino Acids in Archea GENE 396 (2007) 75-83","attachmentId":30632797,"attachmentType":"pdf","work_url":"https://www.academia.edu/2631139/Burbano_Hernan_y_Andrade_Eugenio_Analysis_of_tRNA_Abstract_Shapes_of_Precursor_and_Derivative_Amino_Acids_in_Archea_GENE_396_2007_75_83","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span 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class="ds-related-work--metadata"><a class="js-related-work-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="67662229" href="https://independent.academia.edu/JacquesDaniel6">Jacques Daniel</a></div><p class="ds-related-work--metadata ds2-5-body-xs">arXiv: Populations and Evolution, 2020</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"On some predictions of the poly-tRNA model for the origin and evolution of genetic coding","attachmentId":84310047,"attachmentType":"pdf","work_url":"https://www.academia.edu/76685247/On_some_predictions_of_the_poly_tRNA_model_for_the_origin_and_evolution_of_genetic_coding","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link 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href="https://unal.academia.edu/EugenioAndrade">Eugenio Andrade</a></div><p class="ds-related-work--metadata ds2-5-body-xs">2007</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"Analysis of tRNA abstract shapes of precursor/derivative amino acids in Archaea","attachmentId":75113018,"attachmentType":"pdf","work_url":"https://www.academia.edu/62300447/Analysis_of_tRNA_abstract_shapes_of_precursor_derivative_amino_acids_in_Archaea","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-related-work-grid-card-view-pdf" href="https://www.academia.edu/62300447/Analysis_of_tRNA_abstract_shapes_of_precursor_derivative_amino_acids_in_Archaea"><span 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data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"Evolution of tRNA-like sequences and genome variability","attachmentId":53104351,"attachmentType":"pdf","work_url":"https://www.academia.edu/32984768/Evolution_of_tRNA_like_sequences_and_genome_variability","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-related-work-grid-card-view-pdf" href="https://www.academia.edu/32984768/Evolution_of_tRNA_like_sequences_and_genome_variability"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-related-work-sidebar-card" data-collection-position="12" data-entity-id="70553993" data-sort-order="default"><a 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