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1.
Genes (Basel) ; 15(9)2024 Sep 11.
Article in English | MEDLINE | ID: mdl-39336786

ABSTRACT

From the most ancient RNAs, which followed an RNY pattern and folded into small hairpins, modern RNA molecules evolved by two different pathways, dubbed Extended Genetic Code 1 and 2, finally conforming to the current standard genetic code. Herein, we describe the evolutionary path of the RNAome based on these evolutionary routes. In general, all the RNA molecules analysed contain portions encoded by both genetic codes, but crucial features seem to be better recovered by Extended 2 triplets. In particular, the whole Peptidyl Transferase Centre, anti-Shine-Dalgarno motif, and a characteristic quadruplet of the RNA moiety of RNAse-P are clearly unveiled. Differences between bacteria and archaea are also detected; in most cases, the biological sequences are more stable than their controls. We then describe an evolutionary trajectory of the RNAome formation, based on two complementary evolutionary routes: one leading to the formation of essentials, while the other complemented the molecules, with the cooperative assembly of their constituents giving rise to modern RNAs.


Subject(s)
Archaea , Evolution, Molecular , RNA , Archaea/genetics , Bacteria/genetics , Genetic Code , Nucleic Acid Conformation , RNA/genetics , RNA, Bacterial/genetics
2.
Genes (Basel) ; 14(12)2023 11 29.
Article in English | MEDLINE | ID: mdl-38136981

ABSTRACT

It is widely accepted that the earliest RNA molecules were folded into hairpins or mini-helixes. Herein, we depict the 2D and 3D conformations of those earliest RNA molecules with only RNY triplets, which Eigen proposed as the primeval genetic code. We selected 26 species (13 bacteria and 13 archaea). We found that the free energy of RNY hairpins was consistently lower than that of their corresponding shuffled controls. We found traces of the three ribosomal RNAs (16S, 23S, and 5S), tRNAs, 6S RNA, and the RNA moieties of RNase P and the signal recognition particle. Nevertheless, at this stage of evolution there was no genetic code (as seen in the absence of the peptidyl transferase centre and any vestiges of the anti-Shine-Dalgarno sequence). Interestingly, we detected the anticodons of both glycine (GCC) and threonine (GGU) in the hairpins of proto-tRNA.


Subject(s)
Evolution, Molecular , Genetic Code , RNA, Transfer/genetics , RNA/genetics , Bacteria/genetics
3.
Life (Basel) ; 13(10)2023 Sep 30.
Article in English | MEDLINE | ID: mdl-37895385

ABSTRACT

Aminoacyl-tRNA synthetases (aaRSs) originated from an ancestral bidirectional gene (mirror symmetry), and through the evolution of the genetic code, the twenty aaRSs exhibit a symmetrical distribution in a 6-dimensional hypercube of the Standard Genetic Code. In this work, we assume a primeval RNY code and the Extended Genetic RNA code type II, which includes codons of the types YNY, YNR, and RNR. Each of the four subsets of codons can be represented in a 4-dimensional hypercube. Altogether, these 4 subcodes constitute the 6-dimensional representation of the SGC. We identify the aaRSs symmetry groups in each of these hypercubes. We show that each of the four hypercubes contains the following sets of symmetries for the two known Classes of synthetases: RNY: dihedral group of order 4; YNY: binary group; YNR: amplified octahedral group; and RNR: binary group. We demonstrate that for each hypercube, the group of symmetries in Class 1 is the same as the group of symmetries in Class 2. The biological implications of these findings are discussed.

4.
Theory Biosci ; 142(3): 211-219, 2023 Sep.
Article in English | MEDLINE | ID: mdl-37402895

ABSTRACT

In this work, we formulate the following question: How the distribution of aminoacyl-tRNA synthetases (aaRSs) went from an ancestral bidirectional gene (mirror symmetry) to the symmetrical distribution of aaRSs in a six-dimensional hypercube of the Standard Genetic Code (SGC)? We assume a primeval RNY code, two Extended Genetic RNA codes type 1 and 2, and the SGC. We outline the types of symmetries of the distribution of aaRSs in each code. The symmetry groups of aaRSs in each code are described, until the symmetries of the SGC display a mirror symmetry. Considering both Extended RNA codes the 20 aaRSs were already present before the Last Universal Ancestor. These findings reveal intricacies in the diversification of aaRSs accompanied by the evolution of the genetic code.


Subject(s)
Amino Acyl-tRNA Synthetases , Evolution, Molecular , Genetic Code , Amino Acyl-tRNA Synthetases/genetics , RNA, Transfer/genetics , RNA
5.
Acta Biotheor ; 70(1): 7, 2021 Dec 17.
Article in English | MEDLINE | ID: mdl-34919168

ABSTRACT

The origin of the genetic code has been attributed in part to an accidental assignment of codons to amino acids. Although several lines of evidence indicate the subsequent expansion and improvement of the genetic code, the hypothesis of Francis Crick concerning a frozen accident occurring at the early stage of genetic code evolution is still widely accepted. Considering Crick's hypothesis, mathematical descriptions of hypothetical scenarios involving a huge number of possible coexisting random genetic codes could be very important to explain the origin and evolution of a selected genetic code. This work aims to contribute in this regard, that is, it provides a theoretical framework in which statistical parameters of error functions are calculated. Given a genetic code and an amino acid property, the functional code robustness is estimated by means of a known error function. In this work, using analytical calculations, general expressions for the average and standard deviation of the error function distributions of completely random codes with standard stop codons were obtained. As a possible biological application of these results, any set of amino acids and any pure or mixed amino acid properties can be used in the calculations, such that, in case of having to select a set of amino acids to create a genetic code, possible advantages of natural selection of the genetic codes could be discussed.


Subject(s)
Evolution, Molecular , Genetic Code , Animals , Codon, Terminator , Genetic Code/genetics
6.
J Mol Evol ; 89(9-10): 611-617, 2021 12.
Article in English | MEDLINE | ID: mdl-34505179

ABSTRACT

The evolutionary history of Class I aminoacyl-tRNA synthetases (aaRS) through the reconstruction of ancestral sequences is presented. From structural molecular modeling, we sought to understand its relationship with the acceptor arms and the tRNA anticodon loop, how this relationship was established, and the possible implications in determining the genetic code and the translation system. The results of the molecular docking showed that in 7 out 9 aaRS, the acceptor arm and the anticodon loop bond practically in the same region. Domain accretion process in aaRS and repositioning of interactions between tRNAs and aaRS are illustrated. Based on these results, we propose that the operational code and the anticodon code coexisted, competing for the aaRS catalytic region, while consequently contributed to the stabilization of these proteins.


Subject(s)
Amino Acyl-tRNA Synthetases , Genetic Code , Amino Acyl-tRNA Synthetases/genetics , Anticodon/genetics , Molecular Docking Simulation , RNA, Transfer/genetics
7.
Mol Phylogenet Evol ; 162: 107208, 2021 09.
Article in English | MEDLINE | ID: mdl-34029719

ABSTRACT

The transition to a heterotrophic lifestyle in angiosperms is characterized by convergent evolutionary changes. Plastid genome remodeling includes dramatic functional and physical reductions with the highest degrees observed in fully heterotrophic plants. Genes related to photosynthesis are generally absent or pseudogenized, while a few genes related to other metabolic processes that take place within the plastid are almost invariably maintained. The family Balanophoraceae consists of root holoparasites that present reduced plastid genomes with an extraordinarily elevated AT content and the single genetic code change ever documented in land plant plastomes (the stop codon TAG now codes for tryptophan). Here, we studied the plastomes of Lophophytum leandri and Ombrophytum subterraneum (Balanophoraceae) that showed the remarkable absence of the gene trnE, a highly biased nucleotide composition, and an independent genetic code change (the standard stop codon TGA codes for tryptophan). This is the second genetic code change identified in land plant plastomes. Analysis of the transcriptome of Lophophytum indicated that the entire C5 pathway typical of plants is conserved despite the lack of trnE in its plastome. A hypothetical model of plastome evolution in the Balanophoraceae is presented.


Subject(s)
AT Rich Sequence/genetics , Balanophoraceae/genetics , Evolution, Molecular , Genetic Code , Genome, Plastid , Genes, Plant/genetics , Phylogeny
8.
J Mol Evol ; 89(6): 357-369, 2021 07.
Article in English | MEDLINE | ID: mdl-33934169

ABSTRACT

We use large-scale mutagenesis data and computer simulations to quantify the mutational robustness of protein-coding genes by taking into account constraints arising from protein function and the genetic code. Analyses of the distribution of amino acid substitutions from 18 mutagenesis studies revealed an average of 45% of neutral variants; while mutagenesis data of 12 proteins artificially designed under no other constraints but stability, reach an average of 60%. Simulations using a lattice protein model allow us to contrast these estimates to the expected mutational robustness of protein families by generating unbiased samples of foldable sequences, which we find to have 30% of neutral variants. In agreement with mutagenesis data of designed proteins, the model shows that maximally robust protein families might access up to twice the amount of neutral variants observed in the unbiased samples (i.e. 60%). A biophysical model of protein-ligand binding suggests that constraints associated to molecular function have only a moderate impact on robustness of approximately 5 to 10% of neutral variants; and that the direction of this effect depends on the relation between functional performance and thermodynamic stability. Although the genetic code constraints the access of a gene's nucleotide sequence to only 30% of the full distribution of amino acid mutations, it provides an extra 15 to 20% of neutral variants to the estimations above, such that the expected, observed, and maximal robustness of protein-coding genes are approximately 50, 65, and 75%, respectively. We discuss our results in the light of three main hypothesis put forward to explain the existence of mutationally robust genes.


Subject(s)
Genetic Code , Proteins , Humans , Models, Genetic , Mutagenesis , Mutation , Proteins/genetics , Thermodynamics
9.
Acta Biotheor ; 69(1): 67-78, 2021 Mar.
Article in English | MEDLINE | ID: mdl-32783083

ABSTRACT

The theory of chemical symbiosis (TCS) suggests that biological systems started with the collaboration of two polymeric molecules existing in early Earth: nucleic acids and peptides. Chemical symbiosis emerged when RNA-like nucleic acid polymers happened to fold into 3D structures capable to bind amino acids together, forming a proto peptidyl-transferase center. This folding catalyzed the formation of quasi-random small peptides, some of them capable to bind this ribozyme structure back and starting to form an initial layer that would produce the larger subunit of the ribosome by accretion. TCS suggests that there is no chicken-and-egg problem into the emergence of biological systems as RNAs and peptides were of equal importance to the origin of life. Life has initially emerged when these two macromolecules started to interact in molecular symbiosis. Further, we suggest that life evolved into progenotes and cells due to the emergence of new layers of symbiosis. Mutualism is the strongest force in biology, capable to create novelties by emergent principles; on which the whole is bigger than the sum of the parts. TCS aims to apply the Margulian view of biology into the origins of life field.


Subject(s)
Evolution, Molecular , Models, Theoretical , Origin of Life , Peptide Fragments/metabolism , Proteins/metabolism , RNA/metabolism , Symbiosis , Humans , Models, Biological , Peptide Fragments/chemistry , Proteins/chemistry , RNA/chemistry
10.
Viruses ; 12(1)2020 01 15.
Article in English | MEDLINE | ID: mdl-31952167

ABSTRACT

We report high rates of detection (35.36%, 29/82) of genogroup-I (GI) picobirnaviruses (PBVs) in non-diarrheic fecal samples from the small Indian mongoose (Urva auropunctata). In addition, we identified a novel PBV-like RNA-dependent RNA polymerase (RdRp) gene sequence that uses an alternative mitochondrial genetic code (that of mold or invertebrate) for translation. The complete/nearly complete gene segment-2/RdRp gene sequences of seven mongoose PBV GI strains and the novel PBV-like strain were obtained by combining a modified non-specific primer-based amplification method with conventional RT-PCRs, facilitated by the inclusion of a new primer targeting the 3'-untranslated region (UTR) of PBV gene segment-2. The mongoose PBV and PBV-like strains retained the various features that are conserved in gene segment-2/RdRps of other PBVs. However, high genetic diversity was observed among the mongoose PBVs within and between host species. This is the first report on detection of PBVs in the mongoose. Molecular characterization of the PBV and PBV-like strains from a new animal species provided important insights into the various features and complex diversity of PBV gene segment-2/putative RdRps. The presence of the prokaryotic ribosomal binding site in the mongoose PBV genomes, and analysis of the novel PBV-like RdRp gene sequence that uses an alternative mitochondrial genetic code (especially that of mold) for translation corroborated recent speculations that PBVs may actually infect prokaryotic or fungal host cells.


Subject(s)
Genetic Code , Genome, Viral , Herpestidae/virology , Picobirnavirus/genetics , RNA Virus Infections/veterinary , Animals , Feces/virology , Genetic Variation , Genotype , Host Specificity , Mitochondria/genetics , Phylogeny , Picobirnavirus/classification , Picobirnavirus/isolation & purification , RNA, Viral/genetics , RNA-Dependent RNA Polymerase/genetics , Saint Kitts and Nevis
11.
Orig Life Evol Biosph ; 48(2): 259-272, 2018 Jun.
Article in English | MEDLINE | ID: mdl-29959584

ABSTRACT

It is widely agreed that the standard genetic code must have been preceded by a simpler code that encoded fewer amino acids. How this simpler code could have expanded into the standard genetic code is not well understood because most changes to the code are costly. Taking inspiration from the recently synthesized six-letter code, we propose a novel hypothesis: the initial genetic code consisted of only two letters, G and C, and then expanded the number of available codons via the introduction of an additional pair of letters, A and U. Various lines of evidence, including the relative prebiotic abundance of the earliest assigned amino acids, the balance of their hydrophobicity, and the higher GC content in genome coding regions, indicate that the original two nucleotides were indeed G and C. This process of code expansion probably started with the third base, continued with the second base, and ended up as the standard genetic code when the second pair of letters was introduced into the first base. The proposed process is consistent with the available empirical evidence, and it uniquely avoids the problem of costly code changes by positing instead that the code expanded its capacity via the creation of new codons with extra letters.


Subject(s)
Evolution, Molecular , Genetic Code/genetics , Origin of Life , Codon/analysis , Models, Genetic , Nucleotides/analysis
12.
Orig Life Evol Biosph ; 48(1): 83-91, 2018 Mar.
Article in English | MEDLINE | ID: mdl-29082465

ABSTRACT

In this work, we explicitly consider the evolution of the Standard Genetic Code (SGC) by assuming two evolutionary stages, to wit, the primeval RNY code and two intermediate codes in between. We used network theory and graph theory to measure the connectivity of each phenotypic graph. The connectivity values are compared to the values of the codes under different randomization scenarios. An error-correcting optimal code is one in which the algebraic connectivity is minimized. We show that the SGC is optimal in regard to its robustness and error-tolerance when compared to all random codes under different assumptions.


Subject(s)
Evolution, Molecular , Genetic Code , Models, Genetic
13.
Life (Basel) ; 7(2)2017 Apr 06.
Article in English | MEDLINE | ID: mdl-28383509

ABSTRACT

The proposal that the genetic code was formed on the basis of (proto)tRNA Dimer-Directed Protein Synthesis is reviewed and updated. The tRNAs paired through the anticodon loops are an indication on the process. Dimers are considered mimics of the ribosomes-structures that hold tRNAs together and facilitate the transferase reaction, and of the translation process-anticodons are at the same time codons for each other. The primitive protein synthesis system gets stabilized when the product peptides are stable and apt to bind the producers therewith establishing a self-stimulating production cycle. The chronology of amino acid encoding starts with Glycine and Serine, indicating the metabolic support of the Glycine-Serine C1-assimilation pathway, which is also consistent with evidence on origins of bioenergetics mechanisms. Since it is not possible to reach for substrates simpler than C1 and compounds in the identified pathway are apt for generating the other central metabolic routes, it is considered that protein synthesis is the beginning and center of a succession of sink-effective mechanisms that drive the formation and evolution of the metabolic flow system. Plasticity and diversification of proteins construct the cellular system following the orientation given by the flow and implementing it. Nucleic acid monomers participate in bioenergetics and the polymers are conservative memory systems for the synthesis of proteins. Protoplasmic fission is the final sink-effective mechanism, part of cell reproduction, guaranteeing that proteins don't accumulate to saturation, which would trigger inhibition.

14.
R Soc Open Sci ; 4(3): 160908, 2017 Mar.
Article in English | MEDLINE | ID: mdl-28405378

ABSTRACT

The Rodin-Ohno (RO) and the Delarue models divide the table of the genetic code into two classes of aminoacyl-tRNA synthetases (aaRSs I and II) with recognition from the minor or major groove sides of the tRNA acceptor stem, respectively. These models are asymmetric but they are biologically meaningful. On the other hand, the standard genetic code (SGC) can be derived from the primeval RNY code (R stands for purines, Y for pyrimidines and N any of them). In this work, the RO-model is derived by means of group actions, namely, symmetries represented by automorphisms, assuming that the SGC originated from a primeval RNY code. It turns out that the RO-model is symmetric in a six-dimensional (6D) hypercube. Conversely, using the same automorphisms, we show that the RO-model can lead to the SGC. In addition, the asymmetric Delarue model becomes symmetric by means of quotient group operations. We formulate isometric functions that convert the class aaRS I into the class aaRS II and vice versa. We show that the four polar requirement categories display a symmetrical arrangement in our 6D hypercube. Altogether these results cannot be attained, neither in two nor in three dimensions. We discuss the present unified 6D algebraic model, which is compatible with both the SGC (based upon the primeval RNY code) and the RO-model.

15.
BMC Genomics ; 18(1): 227, 2017 03 13.
Article in English | MEDLINE | ID: mdl-28288557

ABSTRACT

BACKGROUND: For a long time synonymous single nucleotide polymorphisms were considered as silent mutations. However, nowadays it is well known that they can affect protein conformation and function, leading to altered disease susceptibilities, differential prognosis and/or drug responses, among other clinically relevant genetic traits. This occurs through different mechanisms: by disrupting the splicing signals of precursor mRNAs, affecting regulatory binding-sites of transcription factors and miRNAs, or by modifying the secondary structure of mRNAs. RESULTS: In this paper we considered 22 human genetic diseases or traits, linked to 35 synonymous single nucleotide polymorphisms in 27 different genes. We performed a local sequence context analysis in terms of the ribosomal pause propensity affected by synonymous single nucleotide polymorphisms. We found that synonymous mutations related to the above mentioned mechanisms presented small pause propensity changes, whereas synonymous mutations that were not related to those mechanisms presented large pause propensity changes. On the other hand, we did not observe large variations in the codon usage of codons associated with these mutations. Furthermore, we showed that the changes in the pause propensity associated with benign sSNPs are significantly lower than the pause propensity changes related to sSNPs associated to diseases. CONCLUSIONS: These results suggest that the genetic diseases or traits related to synonymous mutations with large pause propensity changes, could be the consequence of another mechanism underlying non-silent synonymous mutations. Namely, alternative protein configuration related, in turn, to alterations in the ribosome-mediated translational attenuation program encoded by pairs of consecutive codons, not codons. These findings shed light on the latter mechanism based on the perturbation of the co-translational folding process.


Subject(s)
Codon , Disease Susceptibility , Polymorphism, Single Nucleotide , Silent Mutation , Genetic Association Studies , Genome, Human , Humans , Models, Biological , Protein Biosynthesis , RNA, Messenger/genetics , Ribosomes/metabolism
16.
Life (Basel) ; 7(1)2017 Feb 13.
Article in English | MEDLINE | ID: mdl-28208827

ABSTRACT

In this work, we determine the biological and mathematical properties that are sufficient and necessary to uniquely determine both the primeval RNY (purine-any base-pyrimidine) code and the standard genetic code (SGC). These properties are: the evolution of the SGC from the RNY code; the degeneracy of both codes, and the non-degeneracy of the assignments of aminoacyl-tRNA synthetases (aaRSs) to amino acids; the wobbling property; the consideration that glycine was the first amino acid; the topological and symmetrical properties of both codes.

17.
J Theor Biol ; 335: 245-8, 2013 Oct 21.
Article in English | MEDLINE | ID: mdl-23871958

ABSTRACT

The origin and evolution of life on the planet is one of the most intriguing challenges in life sciences and, for some researchers, it is centered in the origin of the genetic code. Many hypotheses about the origin and evolution of tRNA have been proposed and in this work a new suggestion is proposed based on the reconstruction of tRNA ancestor sequences. Ancestral sequences of 22 types of tRNA molecules were built by maximum likelihood from 9758 sequences currently reported from different organisms. Phylogenetic analysis showed that the main force for evolutionary diversification of tRNA molecules was a change in the second base of the anticodon. The data revealed that diversification is not correlated with the characteristic of the specified amino acid, indicating that the correlation between tRNA and amino acid was given indirectly, and possibly should have been mediated by proto-aminoacyl-tRNA synthetases.


Subject(s)
Anticodon/genetics , Evolution, Molecular , Models, Genetic , Phylogeny , Amino Acyl-tRNA Synthetases/genetics
18.
J Carcinog Mutagen ; 1(Suppl 5): 1-12, 2013 Jul 29.
Article in English | MEDLINE | ID: mdl-25177526

ABSTRACT

Epigenetic modifications constitute the next frontier in tumor biology research. Post-translation modification of histones dynamically influences gene expression independent of alterations to the DNA sequence. These mechanisms are often mediated by histone linkers or by proteins associated with the recruitment of DNA-binding proteins, HDAC I and II interacting proteins and transcriptional activators, coactivators or corepressors. Early evidence suggested that histones and their modifiers are involved in sophisticated processes that modulate tumor behavior and cellular phenotype. In this review, we discuss how recent discoveries about chromatin modifications, particularly histone acetylation, are shaping our knowledge of cell biology and our understanding of the molecular circuitry governing tumor progression and consider whether recent insights may extend to novel therapeutic approaches. Furthermore, we discuss the latest oncogenomic findings in Head and Neck Squamous Cell Carcinoma (HNSCC) from studies using Next Generation Sequencing (NGS) technology and highlight the impact of mutations identified in histones and their modifiers.

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