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1.
Biosystems ; 222: 104796, 2022 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-36306879

RESUMO

tRNAs presumably accreted into modern ribosomal RNAs. Previous analyses showed similar secondary structures for ancient rRNA subelements and theoretical minimal RNA rings, candidate tRNA ancestors rationally designed from tRNA-unrelated principles. Here, analyses test which tRNA secondary structure subelements resemble ancient/recent rRNA subelements. Results show that ribosomal RNA subelements evolved from structures resembling 1. Upper half part of the tRNA secondary structure; and 2. Towards structures resembling (a) tRNA 5' stem-loop hairpins in large rRNA subunit and (b) tRNA lower half part in small rRNA subunit (stop and start codons conservation model). tRNAs and rRNAs presumably originated from the tRNA upper half part including the acceptor stem. Modern split 5' and 3' tRNA genes (spliced at anticodons) apparently reproduce ancestral-like states, because the acceptor stem protocode suggests acceptor stems evolved from spliced anticodon-like stem-loop hairpins, strengthening central roles for acceptor stem CCA-addition at translation origins. The Root-Bernstein hypothesis on the existence of tRNA structural symmetries presumably reflects late 5' tRNA stem-loop hairpin duplications, some integrating rRNAs. Analyses of tRNA subelements similarities with rRNA subelements suggest tRNAs evolved and re-evolved by different duplication-fusions, along different structural subdivision models. Hence, sequential/parallel processes, perhaps in the same ancestral organism(s) produced polyphyletic tRNAs. Results confirm RNA ring usefulness for understanding prebiotic and early life evolution, and their similarities with primordial protein coding and tRNA genes.


Assuntos
Evolução Molecular , RNA Ribossômico , RNA Ribossômico/genética , RNA de Transferência/metabolismo , Anticódon/genética , RNA/genética , Conformação de Ácido Nucleico
2.
Biology (Basel) ; 10(7)2021 Jul 05.
Artigo em Inglês | MEDLINE | ID: mdl-34356478

RESUMO

We present spread parameters for first and second waves of the COVID-19 pandemic for USA states, and for consecutive nonoverlapping periods of 20 days for the USA and 51 countries across the globe. We studied spread rates in the USA states and 51 countries, and analyzed associations between spread rates at different periods, and with temperature, elevation, population density and age. USA first/second wave spread rates increase/decrease with population density, and are uncorrelated with temperature and median population age. Spread rates are systematically inversely proportional to those estimated 80-100 days later. Ascending/descending phases of the same wave only partially explain this. Directions of correlations with factors such as temperature and median age flip. Changes in environmental trends of the COVID-19 pandemic remain unpredictable; predictions based on classical epidemiological knowledge are highly uncertain. Negative associations between population density and spread rates, observed in independent samples and at different periods, are most surprising. We suggest that systematic negative associations between spread rates 80-100 days apart could result from confinements selecting for greater contagiousness, a potential double-edged sword effect of confinements.

4.
Gene ; 769: 145208, 2021 Feb 15.
Artigo em Inglês | MEDLINE | ID: mdl-33031892

RESUMO

Genetic code codon-amino acid assignments evolve for 15 (AAA, AGA, AGG, ATA, CGG, CTA, CTG. CTC, CTT, TAA, TAG, TCA, TCG, TGA and TTA (GNN codons notably absent)) among 64 codons (23.4%) across the 31 genetic codes (NCBI list completed with recently suggested green algal mitochondrial genetic codes). Their usage in 25 theoretical minimal RNA rings is examined. RNA rings are designed in silico to code once over the shortest length for all 22 coding signals (start and stop codons and each amino acid according to the standard genetic code). Though designed along coding constraints, RNA rings resemble ancestral tRNA loops, assigning to each RNA ring a putative anticodon, a cognate amino acid and an evolutionary genetic code integration rank for that cognate amino acid. Analyses here show 1. biases against/for evolvable codons in the two first vs last thirds of RNA ring coding sequences, 2. RNA rings with evolvable codons have recent cognates, and 3. evolvable codon and cytosine numbers in RNA ring compositions are positively correlated. Applying alternative genetic codes to RNA rings designed for nonredundant coding according to the standard genetic code reveals unsuspected properties of the standard genetic code and of RNA rings, notably on codon assignment evolvability and the special role of cytosine in relation to codon assignment evolvability and of the genetic code's coding structure.


Assuntos
Códon , Evolução Molecular , RNA Circular/genética , Simulação por Computador , Código Genético , RNA de Transferência/genética
5.
Bioessays ; 43(3): e2000071, 2021 03.
Artigo em Inglês | MEDLINE | ID: mdl-33319381

RESUMO

Theoretical minimal RNA rings are candidate primordial genes evolved for non-redundant coding of the genetic code's 22 coding signals (one codon per biogenic amino acid, a start and a stop codon) over the shortest possible length: 29520 22-nucleotide-long RNA rings solve this min-max constraint. Numerous RNA ring properties are reminiscent of natural genes. Here we present analyses showing that all RNA rings lack dinucleotide CG (a mutable, chemically instable dinucleotide coding for Arginine), bearing a resemblance to known CG-depleted genomes. CG in "incomplete" RNA rings (not coding for all coding signals, with only 3-12 nucleotides) gradually decreases towards CG absence in complete, 22-nucleotide-long RNA rings. Presumably, feedback loops during RNA ring growth during evolution (when amino acid assignment fixed the genetic code) assigned Arg to codons lacking CG (AGR) to avoid CG. Hence, as a chemical property of base pairs, CG mutability restructured the genetic code, thereby establishing itself as genetically encoded biological information.


Assuntos
RNA de Transferência , RNA , Arginina/genética , Códon/genética , Evolução Molecular , Retroalimentação , Código Genético , RNA/genética
6.
Life (Basel) ; 11(1)2020 Dec 23.
Artigo em Inglês | MEDLINE | ID: mdl-33374866

RESUMO

We propose combinatorial fusion rules that describe the codon assignment in the standard genetic code simply and uniformly for all canonical amino acids. These rules become obvious if the origin of the standard genetic code is considered as a result of a fusion of four protocodes: two dominant AU and GC protocodes and two recessive AU and GC protocodes. The biochemical meaning of the fusion rules consists of retaining the complementarity between cognate codons of the small hydrophobic amino acids and large charged or polar amino acids within the protocodes. The proto tRNAs were assembled in form of two kissing hairpins with 9-base and 10-base loops in the case of dominant protocodes and two 9-base loops in the case of recessive protocodes. The fusion rules reveal the connection between the stop codons, the non-canonical amino acids, pyrrolysine and selenocysteine, and deviations in the translation of mitochondria. Using fusion rules, we predicted the existence of additional amino acids that are essential for the development of the standard genetic code. The validity of the proposed partition of the genetic code into dominant and recessive protocodes is considered referring to state-of-the-art hypotheses. The formation of two aminoacyl-tRNA synthetase classes is compatible with four-protocode partition.

7.
Med Hypotheses ; 144: 110245, 2020 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-33254550

RESUMO

(1) Background: RNA viruses and especially coronaviruses could act inside host cells not only by building their own proteins, but also by perturbing the cell metabolism. We show the possibility of miRNA-like inhibitions by the SARS-CoV-2 concerning for example the hemoglobin and type I interferons syntheses, hence highly perturbing oxygen distribution in vital organs and immune response as described by clinicians; (2) Hypothesis: We hypothesize that short RNA sequences (about 20 nucleotides in length) from the SARS-CoV-2 virus genome can inhibit the translation of human proteins involved in oxygen metabolism, olfactory perception and immune system. (3) Methods: We compare RNA subsequences of SARS-CoV-2 protein S and RNA-dependent RNA polymerase genes to mRNA sequences of beta-globin and type I interferons; (4) Results: RNA subsequences longer than eight nucleotides from SARS-CoV-2 genome could hybridize subsequences of the mRNA of beta-globin and of type I interferons; (5) Conclusions: Beyond viral protein production, COVID-19 might affect vital processes like host oxygen transport and immune response.


Assuntos
COVID-19/virologia , Interferon Tipo I/metabolismo , MicroRNAs/metabolismo , Oxigênio/metabolismo , SARS-CoV-2/genética , Glicoproteína da Espícula de Coronavírus/genética , Globinas beta/metabolismo , COVID-19/metabolismo , Genoma Viral , Hemoglobinas/metabolismo , Humanos , Sistema Imunitário , Fases de Leitura Aberta , Pandemias , Mapeamento de Interação de Proteínas , RNA Mensageiro/metabolismo , Ribossomos/metabolismo , Olfato , Replicação Viral , Tratamento Farmacológico da COVID-19
8.
Biology (Basel) ; 9(8)2020 Aug 14.
Artigo em Inglês | MEDLINE | ID: mdl-32823981

RESUMO

(1) Background: Here, we characterize COVID-19's waves, following a study presenting negative associations between first wave COVID-19 spread parameters and temperature. (2) Methods: Visual examinations of daily increases in confirmed COVID-19 cases in 124 countries, determined first and second waves in 28 countries. (3) Results: The first wave spread rate increases with country mean elevation, median population age, time since wave onset, and decreases with temperature. Spread rates decrease above 1000 m, indicating high ultraviolet lights (UVs) decrease the spread rate. The second wave associations are the opposite, i.e., spread increases with temperature and young age, and decreases with time since wave onset. The earliest second waves started 5-7 April at mutagenic high elevations (Armenia, Algeria). The second waves also occurred at the warm-to-cold season transition (Argentina, Chile). Second vs. first wave spread decreases in most (77%) countries. In countries with late first wave onset, spread rates better fit second than first wave-temperature patterns. In countries with ageing populations (for example, Japan, Sweden, and Ukraine), second waves only adapted to spread at higher temperatures, not to infect the young. (4) Conclusions: First wave viruses evolved towards lower spread. Second wave mutant COVID-19 strain(s) adapted to higher temperature, infecting younger ages and replacing (also in cold conditions) first wave COVID-19 strains. Counterintuitively, low spread strains replace high spread strains, rendering prognostics and extrapolations uncertain.

9.
C R Biol ; 343(1): 111-122, 2020 Jun 05.
Artigo em Inglês | MEDLINE | ID: mdl-32720493

RESUMO

Nucleotide affinities for noncovalent interactions with amino acids produce associations between mRNAs and cognate peptides, potentially regulating ribosomal translation. Correlations between nucleotide affinities and residue hydrophobicity are explored for 25 theoretical minimal RNA rings, 22 nucleotide-long RNAs designed in silico to code for each amino acid once after three translation rounds, and forming stem-loop hairpins. This design presumably mimicks life's first RNAs. RNA rings resemble consensual tRNAs, suggesting proto-tRNA function, predicted anticodon and cognate amino acid. The 25 RNA rings and their presumed evolutionary order, deduced from the genetic code integration order of the amino acid cognate to their predicted anticodon, produces noteworthy associations with several ancient properties of the cell's translational machinery. Here we use this system to explore the evolution of codon affinity-residue hydrophobicity correlations, assuming these reflect pre-tRNA and pre-ribosomal translations. This hypothesis expects that correlations decrease with genetic code inclusion orders of RNA ring cognates. RNA ring associations between nucleotide affinities and residue hydrophobicities resemble those from modern natural genes/proteins. Association strengths decrease with genetic code inclusion ranks of proto-tRNA cognate amino acids. In silico design of minimal RNA rings didn't account for affinities between RNA and peptides coded by these RNAs. Yet, interactions between RNA rings and translated cognate peptides resemble modern natural genes. This property is strongest for ancient RNA rings, weakest for recent RNA rings, spanning a period during which modern tRNA- and ribosome-based translation presumably evolved. Results indicate that translation lacking tRNA-like adaptors based on codon-amino acid affinities and the genetic code pre-existed tRNA-mediated translation. Theoretical minimal RNA rings appear valid prebiotic peptide-RNA world models for the transition between pre-tRNA- and tRNA-mediated translations.


Les affinités nucléotidiques des interactions non covalentes avec les acides aminés produisent des associations entre les ARNm et les peptides apparentés, régulant potentiellement la traduction ribosomale. Les corrélations entre les affinités nucléotidiques et l'hydrophobicité des résidus sont explorées pour 25 ARNs circulaires théoriques d'une longueur minimale de 22 nucléotides, conçus in silico pour coder chaque acide aminé une fois et une seule après trois tours de traduction et former des structures « hairpin ¼ (épingle à cheveux) maximales. Cette conception imite vraisemblablement les premiers ARNs de la vie. Les ARNs circulaires ressemblent à des ARNts consensuels, suggérant une fonction de proto-ARNt, mettant en jeu un anticodon prédit et un acide aminé apparenté. Les 25 ARNs circulaires et leur ordre d'évolution présumé, déduits de l'ordre d'intégration dans le code génétique de l'acide aminé apparenté à leur anticodon prédit, montrent des associations remarquables avec plusieurs propriétés anciennes du mécanisme de traduction de la cellule. Ici, nous les utilisons pour explorer l'évolution des corrélations entre hydrophobicité d'un résidu et affinité à son codon, en supposant qu'elles reflètent des propriétés de la traduction pré-ARNt et pré-ribosomique. Cette hypothèse suppose que les corrélations diminuent avec les ordres d'inclusion dans le code génétique du codon apparenté à un ARN circulaire. Les associations entre les affinités des nucléotides et les hydrophobicités des résidus ressemblent à celles existant actuellement entre gènes et protéines. Les forces d'association diminuent avec les rangs d'inclusion dans le code génétique des acides aminés apparentés au proto-ARNt. La conception des ARNs circulaires minimaux ne tient pas compte des affinités entre ceux-ci et les peptides qu'ils codent. Cependant, les interactions entre les ARNs circulaires et leurs peptides apparentés ressemblent à celles observées pour les gènes naturels actuels. Cette propriété est plus forte pour les ARNs circulaires anciens et plus faible pour les récents, couvrant une période au cours de laquelle la traduction moderne à base d'ARNts et de ribosomes a probablement évolué. Les résultats indiquent que la traduction usant d'adaptateurs fondés sur les affinités codon-acide aminé et sur le code génétique primitif a préexisté à une traduction médiée par l'ARNt. Les ARNs circulaires minimaux théoriques apparaissent ainsi comme des modèles prébiotiques pour la transition entre les traductions à médiation pré-ARNt et ARNt.


Assuntos
Aminoácidos/genética , Nucleotídeos/genética , RNA de Transferência/genética , RNA/genética , Códon , Simulação por Computador , Evolução Molecular , Código Genético
10.
Biosystems ; 196: 104180, 2020 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-32534170

RESUMO

During the noncanonical deletion transcription, k nucleotides are systematically skipped/deleted after each transcribed trinucleotide producing deletion-RNAs (delRNAs). Peptides matching delRNAs either result from (a) canonical translation of delRNAs; or (b) noncanonical translation of regular transcripts along expanded codons. Only along frame "0" (start site) (a) and (b) produce identical peptides. Here, mitochondrial mass spectrometry data analyses assume expanded codon/del-transcription with 3 + k (k from 0 to 12) nucleotides. Detected peptides map preferentially on previously identified delRNAs. More peptides were detected for k (1-12) when del-transcriptional and expanded codon translations start sites coincide (i.e. the 0th frame) than for frames +1 or +2. Hence, both (a) and (b) produced peptides identified here. Biases for frame 0 decrease for k > 2, reflecting codon/anticodon expansion limits. Further analyses find preferential pyrrolysine insertion at stop codons, suggesting Pyl-specific mitochondrial suppressor tRNAs loaded by Pyl-specific tRNA synthetases with unknown origins. Pyl biases at stops are stronger for regular than expanded codons suggesting that Pyl-tRNAs are less competitive with near-cognate tRNAs in expanded codon contexts. Statistical biases for these findings exclude that detected peptides are experimental and/or bioinformatic artefacts implying both del-transcription and expanded codons translation occur in human mitochondria.


Assuntos
Códon de Terminação/genética , Lisina/análogos & derivados , Mitocôndrias/genética , Fragmentos de Peptídeos/genética , Biossíntese de Proteínas/fisiologia , Códon de Terminação/metabolismo , Humanos , Lisina/genética , Lisina/metabolismo , Mitocôndrias/metabolismo , Fragmentos de Peptídeos/metabolismo , RNA de Transferência/genética , RNA de Transferência/metabolismo
11.
Biology (Basel) ; 9(5)2020 May 03.
Artigo em Inglês | MEDLINE | ID: mdl-32375234

RESUMO

(1) Background: The virulence of coronavirus diseases due to viruses like SARS-CoV or MERS-CoV decreases in humid and hot weather. The putative temperature dependence of infectivity by the new coronavirus SARS-CoV-2 or covid-19 has a high predictive medical interest. (2) Methods: External temperature and new covid-19 cases in 21 countries and in the French administrative regions were collected from public data. Associations between epidemiological parameters of the new case dynamics and temperature were examined using an ARIMA model. (3) Results: We show that, in the first stages of the epidemic, the velocity of contagion decreases with country- or region-wise temperature. (4) Conclusions: Results indicate that high temperatures diminish initial contagion rates, but seasonal temperature effects at later stages of the epidemy remain questionable. Confinement policies and other eviction rules should account for climatological heterogeneities, in order to adapt the public health decisions to possible geographic or seasonal gradients.

12.
Sci Rep ; 10(1): 7693, 2020 05 06.
Artigo em Inglês | MEDLINE | ID: mdl-32376895

RESUMO

Ribosomal RNAs are complex structures that presumably evolved by tRNA accretions. Statistical properties of tRNA secondary structures correlate with genetic code integration orders of their cognate amino acids. Ribosomal RNA secondary structures resemble those of tRNAs with recent cognates. Hence, rRNAs presumably evolved from ancestral tRNAs. Here, analyses compare secondary structure subcomponents of small ribosomal RNA subunits with secondary structures of theoretical minimal RNA rings, presumed proto-tRNAs. Two independent methods determined different accretion orders of rRNA structural subelements: (a) classical comparative homology and phylogenetic reconstruction, and (b) a structural hypothesis assuming an inverted onion ring growth where the three-dimensional ribosome's core is most ancient and peripheral elements most recent. Comparisons between (a) and (b) accretions orders with RNA ring secondary structure scales show that recent rRNA subelements are: 1. more like RNA rings with recent cognates, indicating ongoing coevolution between tRNA and rRNA secondary structures; 2. less similar to theoretical minimal RNA rings with ancient cognates. Our method fits (a) and (b) in all examined organisms, more with (a) than (b). Results stress the need to integrate independent methods. Theoretical minimal RNA rings are potential evolutionary references for any sequence-based evolutionary analyses, independent of the focal data from that study.


Assuntos
Evolução Molecular , Filogenia , Estrutura Secundária de Proteína , RNA Ribossômico/metabolismo , RNA de Transferência/metabolismo , Código Genético , RNA Ribossômico/genética , RNA de Transferência/genética , Ribossomos/metabolismo
13.
Naturwissenschaften ; 107(3): 20, 2020 May 04.
Artigo em Inglês | MEDLINE | ID: mdl-32367155

RESUMO

Stereochemical nucleotide-amino acid interactions, in the form of noncovalent nucleotide-amino acid interactions, potentially produced the genetic code's codon-amino acid assignments. Empirical estimates of single nucleotide-amino acid affinities on surfaces and in solution are used to test whether trinucleotide-amino acid affinities determined genetic code assignments pending the principle "first arrived, first served": presumed early amino acids have greater codon-amino acid affinities than ulterior ones. Here, these single nucleotide affinities are used to approximate all 64 × 20 trinucleotide-amino acid affinities. Analyses show that (1) on surfaces, genetic code codon-amino acid assignments tend to match high affinities for the amino acids that integrated earliest the genetic code (according to Wong's metabolic coevolution hypothesis between nucleotides and amino acids) and (2) in solution, the same principle holds for the anticodon-amino acid assignments. Affinity analyses match best genetic code assignments when assuming that trinucleotides competed for amino acids, rather than amino acids for trinucleotides. Codon-amino acid affinities stick better to genetic code assignments than anticodon-amino acid affinities. Presumably, two independent coding systems, on surfaces and in solution, converged, and formed the current translation system. Proto-translation on surfaces by direct codon-amino acid interactions without tRNA-like adaptors coadapted with a system emerging in solution by proto-tRNA anticodon-amino acid interactions. These systems assigned identical or similar cognates to codons on surfaces and to anticodons in solution. Results indicate that a prebiotic metabolism predated genetic code self-organization.


Assuntos
Aminoácidos/química , Aminoácidos/metabolismo , Códon/química , Códon/metabolismo , Evolução Biológica , Códon/genética , Estereoisomerismo
14.
Bioessays ; 42(6): e1900201, 2020 06.
Artigo em Inglês | MEDLINE | ID: mdl-32227358

RESUMO

The rational design of theoretical minimal RNA rings predetermines AUG as the universal start codon. This design maximizes coded amino acid diversity over minimal sequence length, defining in silico theoretical minimal RNA rings, candidate ancestral genes. RNA rings code for 21 amino acids and a stop codon after three consecutive translation rounds, and form a degradation-delaying stem-loop hairpin. Twenty-five RNA rings match these constraints, ten start with the universal initiation codon AUG. No first codon bias exists among remaining RNA rings. RNA ring design predetermines AUG as initiation codon. This is the only explanation yet for AUG as start codon. RNA ring design determines additional RNA ring gene- and tRNA-like properties described previously, because it presumably mimics constraints on life's primordial RNAs.


Assuntos
Evolução Molecular , RNA , Viés , Códon/genética , Códon de Iniciação/genética , Biossíntese de Proteínas/genética , RNA/genética
15.
Front Genet ; 11: 42, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32117454

RESUMO

Expressed sequence tags (ESTs) provide an imprint of cellular RNA diversity irrespectively of sequence homology with template genomes. NCBI databases include many unknown RNAs from various normal and cancer cells. These are usually ignored assuming sequencing artefacts or contamination due to their lack of sequence homology with template DNA. Here, we report genomic origins of 347 ESTs previously assumed artefacts/unknown, from the FAPESP/LICR Human Cancer Genome Project. EST template detection uses systematic nucleotide exchange analyses called swinger transformations. Systematic nucleotide exchanges replace systematically particular nucleotides with different nucleotides. Among 347 unknown ESTs, 51 ESTs match mitogenome transcription, 17 and 2 ESTs are from nuclear chromosome non-coding regions, and uncharacterized nuclear genes. Identified ESTs mapped on 205 protein-coding genes, 10 genes had swinger RNAs in several biosamples. Whole cell transcriptome searches for 17 ESTs mapping on non-coding regions confirmed their transcription. The 10 swinger-transcribed genes identified more than once associate with cancer induction and progression, suggesting swinger transformation occurs mainly in highly transcribed genes. Swinger transformation is a unique method to identify noncanonical RNAs obtained from NGS, which identifies putative ncRNA transcribed regions. Results suggest that swinger transcription occurs in highly active genes in normal and genetically unstable cancer cells.

16.
J Mol Evol ; 88(3): 243-252, 2020 04.
Artigo em Inglês | MEDLINE | ID: mdl-32025759

RESUMO

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.


Assuntos
Evolução Molecular , Sequências Repetidas Invertidas , Conformação de Ácido Nucleico , RNA de Transferência/genética , Código Genético , RNA
17.
Gene ; 738: 144436, 2020 May 15.
Artigo em Inglês | MEDLINE | ID: mdl-32027954

RESUMO

Accretions of tRNAs presumably formed the large complex ribosomal RNA structures. Similarities of tRNA secondary structures with rRNA secondary structures increase with the integration order of their cognate amino acid in the genetic code, indicating tRNA evolution towards rRNA-like structures. Here analyses rank secondary structure subelements of three large ribosomal RNAs (Prokaryota: Archaea: Thermus thermophilus; Bacteria: Escherichia coli; Eukaryota: Saccharomyces cerevisiae) in relation to their similarities with secondary structures formed by presumed proto-tRNAs, represented by 25 theoretical minimal RNA rings. These ranks are compared to those derived from two independent methods (ranks provide a relative evolutionary age to the rRNA substructure), (a) cladistic phylogenetic analyses and (b) 3D-crystallography where core subelements are presumed ancient and peripheral ones recent. Comparisons of rRNA secondary structure subelements with RNA ring secondary structures show congruence between ranks deduced by this method and both (a) and (b) (more with (a) than (b)), especially for RNA rings with predicted ancient cognate amino acid. Reconstruction of accretion histories of large rRNAs will gain from adequately integrating information from independent methods. Theoretical minimal RNA rings, sequences deterministically designed in silico according to specific coding constraints, might produce adequate scales for prebiotic and early life molecular evolution.


Assuntos
RNA Ribossômico/genética , RNA de Transferência/genética , Subunidades Ribossômicas Maiores/genética , Simulação por Computador , Escherichia coli/genética , Evolução Molecular , Código Genético , Conformação de Ácido Nucleico , Filogenia , RNA/genética , RNA Ribossômico/fisiologia , RNA de Transferência/fisiologia , Subunidades Ribossômicas Maiores/metabolismo , Saccharomyces cerevisiae/genética , Thermus thermophilus/genética
18.
Biosystems ; 191-192: 104116, 2020 May.
Artigo em Inglês | MEDLINE | ID: mdl-32081715

RESUMO

Deaminations C->T and A->G are frequent mutations producing nucleotide content gradients across genomes proportional to singlestrandedness during replication/transcription. Hence, within single codons, deamination risks increase from first to third codon positions, while second codon positions are functionally most crucial. Here genetic codes are analyzed assuming that after anticodons protected codons from deaminations, first and second codon positions swapped (N2N1N3->N1N2N3), with lowest deamination risks for N2 in presumed primitive N2N1N3 codons. N2N1N3, not standard N1N2N3, codon structure minimizes deaminations inversely proportionally to cognate amino acid hydrophobicity and parallel betasheet conformational preference. For N1N2N3, deamination minimization increases with genetic code integration order of cognate amino acids: during the presumed N2N1N3->N1N2N3 codon structure transition, protein synthesis combined direct codon-amino acid interactions for late amino acids and tRNA-based translation for early amino acids. Hence N2N1N3 codons would correspond to tRNA-free translation by spontaneous codon-amino acid affinities, and tRNA-mediated translation presumably caused N2N1N3->N1N2N3 swaps. Results show that rational, not arbitrary rules link codon and amino acid structures. Some analyses detect mitochondrial RNAs and peptides in public data corresponding to systematic position swaps, suggesting occasional swapping polymerase activity.


Assuntos
Aminoácidos/genética , Anticódon/genética , Códon/genética , Código Genético/genética , Biossíntese de Proteínas/genética , Sequência de Aminoácidos , Aminoácidos/química , Anticódon/química , Sequência de Bases , Códon/química , Desaminação , Humanos , Interações Hidrofóbicas e Hidrofílicas , Modelos Genéticos , Nucleotídeos/genética , Conformação Proteica em Folha beta , RNA de Transferência/química , RNA de Transferência/genética , Homologia de Sequência do Ácido Nucleico
19.
Int J Mol Sci ; 21(1)2020 Jan 05.
Artigo em Inglês | MEDLINE | ID: mdl-31948054

RESUMO

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.


Assuntos
Aminoácidos/genética , Aminoacil-tRNA Sintetases/metabolismo , Códon , Purinas/química , Pirimidinas/química , Aminoácidos/química , Evolução Molecular , Código Genético , Ligação de Hidrogênio , Interações Hidrofóbicas e Hidrofílicas , Modelos Genéticos , Nucleotídeos/química , Biossíntese de Proteínas
20.
BMC Genet ; 21(1): 7, 2020 01 23.
Artigo em Inglês | MEDLINE | ID: mdl-31973715

RESUMO

BACKGROUND: Theoretical minimal RNA rings code by design over the shortest length once for each of the 20 amino acids, a start and a stop codon, and form stem-loop hairpins. This defines at most 25 RNA rings of 22 nucleotides. As a group, RNA rings mimick numerous prebiotic and early life biomolecular properties: tRNAs, deamination gradients and replication origins, emergence of codon preferences for the natural circular code, and contents of early protein coding genes. These properties result from the RNA ring's in silico design, based mainly on coding nonredundancy among overlapping translation frames, as the genetic code's codon-amino acid assignments determine. RNA rings resemble ancestral tRNAs, defining RNA ring anticodons and corresponding cognate amino acids. Surprisingly, all examined RNA ring properties coevolve with genetic code integration ranks of RNA ring cognates, as if RNA rings mimick prebiotic and early life evolution. METHODS: Distances between RNA rings were calculated using different evolutionary models. Associations between these distances and genetic code evolutionary hypotheses detect evolutionary models best describing RNA ring diversification. RESULTS: Here pseudo-phylogenetic analyses of RNA rings produce clusters corresponding to the primordial code in tRNA acceptor stems, more so when substitution matrices from neutrally evolving pseudogenes are used rather than from functional protein coding genes reflecting selection for conserving amino acid properties. CONCLUSIONS: Results indicate RNA rings with recent cognates evolved from those with early cognates. Hence RNA rings, as designed by the genetic code's structure, simulate tRNA stem evolution and prebiotic history along neutral chemistry-driven mutation regimes.


Assuntos
Anticódon , Evolução Molecular , Modelos Genéticos , RNA de Transferência/química , RNA de Transferência/genética , RNA/química , RNA/genética , Aminoácidos , Sequência de Bases , Códon , Mutação
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