Measuring the tolerance of the genetic code to altered codon size

SummaryProtein translation using four-base codons occurs in both natural and synthetic systems. What constraints contributed to the universal adoption of a triplet-codon, rather than quadruplet-codon, genetic code? Here, we investigate the tolerance of the E. coli genetic code to tRNA mutations that increase codon size. We found that tRNAs from all twenty canonical isoacceptor classes can be converted to functional quadruplet tRNAs (qtRNAs), many of which selectively incorporate a single amino acid in response to a specified four-base codon. However, efficient quadruplet codon translation often requires multiple tRNA mutations, potentially constraining evolution. Moreover, while tRNAs were largely amenable to quadruplet conversion, only nine of the twenty aminoacyl tRNA synthetases tolerate quadruplet anticodons. These constitute a functional and mutually orthogonal set, but one that sharply limits the chemical alphabet available to a nascent all-quadruplet code. Our results illuminate factors that led to selection and maintenance of triplet codons in primordial Earth and provide a blueprint for synthetic biologists to deliberately engineer an all-quadruplet expanded genetic code.

Analysis of Genetic Variability in the Caprine Class II MHC CLA DRB3.2(Cahi DRB3.2) gene locus of the Sangamneri goat breed of India

The objective of this study was to assess the genetic variability present across the Class II MHC DRB 3.2 gene locus in the Sangamneri goat breed of India. Sixty three single nucleotide variations were observed in CLA-DRB3.2 gene of eleven Sangamneri animals. Sixteen haplotypes with Haplotype diversity of 0.974 were found. Besides the snp(s) having two alleles, both triple and tetra allelic single nucleotide variations were present. Thus, the Class II DRB 3.2 gene of the Sangamneri goat breed animals (CLA-DRB3.2/ Cahi DRB3.2) was exhibiting a very high degree of genetic polymorphism. Of the sixty three single nucleotide variations, fifty variations were non-synonymous i.e. they resulted in a change in the corresponding amino acid encoded by the triplet codon in which they were existing. Both conservative and non-conservative amino acid changes were observed to occur. Rich diversity of the DRB3.2 gene reflected well on the ability of the Sangamneri animals to survive in the harsh climatic condition(s), exposed to all kinds of pathogen(s) existing in the environment.

Synchronized Oscillations in Double-Helix B-DNA Molecules with Mirror-Symmetric Codons

A fully analytical treatment of the base-pair and codon dynamics in double-stranded DNA molecules is introduced, by means of a realistic treatment that considers different mass values for G, A, T, and C nucleotides and takes into account the intrinsic three-dimensional, helicoidal geometry of DNA in terms of a Hamitonian in cylindrical coordinates. Within the framework of the Peyrard–Dauxois–Bishop model, we consider the coupling between stretching and stacking radial oscillations as well as the twisting motion of each base pair around the helix axis. By comparing the linearized dynamical equations for the angular and radial variables corresponding to the bp local scale with those of the longer triplet codon scale, we report an underlying hierarchical symmetry. The existence of synchronized collective oscillations of the base-pairs and their related codon triplet units are disclosed from the study of their coupled dynamical equations. The possible biological role of these correlated, long-range oscillation effects in double standed DNA molecules containing mirror-symmetric codons of the form XXX, XX’X, X’XX’, YXY, and XYX is discussed in terms of the dynamical equations solutions and their related dispersion relations.

The ATP Hypothesis: A New Conceptual Framework for the Origin of the Genetic Code

More than half a century has passed since the discovery of the genetic code, but its origin is still one of the greatest mysteries in life science, although a plenty of theories have been proposed so far, as none can explain satisfactorily why the genetic code evolved in such a way, especially in the context of the biochemical system, a relation of part to whole. Here, a new hypothesis is proposed, according to which ATP is at the origin of the genetic code by its coevolution with the pristine biochemical system of the protocell. This hypothesis shows how primitive life with its genetic code emerged through a series of processes from energy flow to information communication mediated by ATP. First, ATP is the only energetic product of photosynthesis, and is at the energetic heart of the extant biochemical systems. Second, ATP serves as not only an energy carrier but also an informatization molecule, as ATP could energetically elongate chains of both polynucleotides and polypeptides, thus providing a bridge between these molecules and eventually mediating biochemical innovation in the protocell from energy transformation to informatization, a process for creating and managing information. Informatization was inevitably coupled with structuralization (processes for organizing or incorporating cellular structures), cyclizing polynucleotides and polypeptides into a feedback loop of reciprocal causation. The triplet codon might be only for stereochemical handling of amino acids through, e.g., Watson–Crick pairing interactions. It is only the evolutionary completion of the genetic code from RNA to DNA that, contrary to the central dogma, marked the dawn of cellular life, when Darwinian evolution began to operate. The ATP hypothesis sheds light on the origin of life, together with the formation of both photosynthetic and biochemical systems, which remains largely unknown thus far.

Fourier spectral density of the coronavirus genome

We present an analysis of the coronavirus RNA genome via a study of its Fourier spectral density based on a binary representation of the nucleotide sequence. We find that at low frequencies, the power spectrum presents a small and distinct departure from the behavior expected from an uncorrelated sequence. We provide a couple of simple models to characterize such deviations. Away from a small low-frequency domain, the spectrum presents largely stochastic fluctuations about fixed values which vary inversely with the genome size generally. It exhibits no other peaks apart from those associated with triplet codon usage. We uncover an interesting, new scaling law for the coronavirus genome: the complexity of the genome scales linearly with the power-law exponent that characterizes the enveloping curve of the low-frequency domain of the spectral density.

The ATP Hypothesis: A New Conceptual Framework for the Origin of the Genetic Code

The origin of the genetic code is the key to revealing the origin of life on Earth, as it is a prerequisite for the existence of life. More than half a century has passed since the discovery of the genetic code, but its origin is still one of the greatest mysteries. Is the origin of the genetic code truly unknowable? Does the code truly require external design? Here, a hypothesis is proposed, according to which ATP is at the origin of the genetic code by its coevolution with the pristine biochemical system. ATP has several properties that make it suitable as a plausible initiator of the genetic code. First, ATP is the only energetic product of photosynthesis. Second, ATP is at the heart of the extant biochemical systems. Third, ATP serves as a carrier of both energy and information. Fourth, ATP could energetically elongate chains of both polynucleotides and polypeptides, thus providing a bridge between these molecules and eventually mediating prebiotic biochemical innovation from energy transformation to informatization. This hypothesis shows how primitive life emerged through a series of processes from energy to information flow mediated by ATP. Informatization (processes for creating and managing information) was inevitably coupled with structuralization (processes for organizing or incorporating cellular structures), cyclizing polynucleotides and polypeptides into a feedback loop of reciprocal causation. The triplet codon might be only for stereochemical handling of amino acids through, e.g., Watson–Crick pairing interactions. It is only the evolutionary completion of the genetic code from RNA to DNA that, contrary to the central dogma, marked the dawn of cellular life, when Darwinian evolution began to operate. The ATP hypothesis sheds light on the origin of life, together with the formation of both photosynthetic and biochemical systems, which remains largely unknown thus far.

ATP-Hypothesis: A New Conceptual Framework for the Origins of Genetic Codes

The origin of genetic codes is the key to reveal life’s origin on the earth as it is a prerequisite for the existence of life. More than half a century has passed since the discovery of genetic codes, while their origin is still one of the greatest mysteries. Are the origins of genetic codes really unknowable? Do they really require external design? Here, I present an ATP-hypothesis that explains how the genetic codes came into being with the coevolution of biochemical system. ATP has several properties that make it suitable as the initiator of the origin of genetic codes. First, ATP is the only energetic product of photosynthesis. Second, ATP is at the heart of the extant biochemical systems. Third, ATP serves as carriers of both energy and information. Fourth, ATP could energetically elongate chains of both polynucleotides and polypeptides, thus providing a bridge between them, and eventually mediating prebiotic biochemical transaction from energy to information. This hypothesis shows how primitive life emerged through a series of processes from energy to information mediated by ATP. Informatization (processes of creating and managing information) was inevitably coupled with structuralization (processes of organizing or incorporating into a cellular structure), making polynucleotides and polypeptides be cyclized into a system of reciprocal causation. The triplet codon might just be for stereo-chemical handing of amino acid through e.g. Watson–Crick pairing interactions. It is an evolutionary completion for genetic codes from RNA to DNA, only which, a reverse to the Central Dogma, marked the dawn of cellular life when Darwinian evolution began to operate. ATP-hypothesis shades lights on the origin of life, together with the formations of both photosynthesis and biochemical systems, which have been largely unknown so far.

ATP-Hypothesis: A New Conceptual Framework for the Origins of Genetic Codes

The origin of genetic codes is the key to reveal life’s origin on the earth as it is a prerequisite for the existence of life. More than half a century has passed since the discovery of genetic codes, while their origin is still one of the greatest mysteries. Are the origins of genetic codes really unknowable? Do they really require external design? Here, we present an ATP-hypothesis that explains how the genetic codes came into being with the coevolution of biochemical system. ATP has several properties that make it suitable as the initiator of the origin of genetic codes. First, ATP is the only energetic product of photosynthesis. Second, ATP is at the heart of the extant biochemical systems. Third, ATP serves as carriers of both energy and information. Fourth, ATP could energetically elongate chains of both polynucleotides and polypeptides, thus providing a bridge between them, and eventually mediating prebiotic transaction from energy to information. This hypothesis shows how primitive life emerged through a series of processes from energy to information. Informatization (processes of creating and managing information) was inevitably coupled with structuralization (processes of organizing or incorporating into a cellular structure), making polynucleotides and polypeptides be cyclized into a system of reciprocal causation. The triplet codon might just be for stereo-chemical handing of amino acid through e.g. Watson–Crick pairing interactions. This hypothesis shades lights on the origin of life, together with the formations of both photosynthesis and biochemical systems, which have been largely unknown so far.

Neural Network Evolving Algorithm Based on the Triplet Codon Encoding Method

Artificial intelligence research received more and more attention nowadays. Neural Evolution (NE) is one very important branch of AI, which waves the power of evolutionary algorithms to generate Artificial Neural Networks (ANNs). How to use the evolutionary advantages of network topology and weights to solve the application of Artificial Neural Networks is the main problem in the field of NE. In this paper, a novel DNA encoding method based on the triple codon is proposed. Additionally, a NE algorithm Triplet Codon Encoding Neural Network Evolving Algorithm (TCENNE) based on this encoding method is presented to verify the rationality and validity of the coding design. The results show that TCENNE is very effective and more robust than NE algorithms, due to the coding design. Also, it is shown that it can realize the co-evolution of network topology and weights and outperform other neural evolution systems in challenging reinforcement learning tasks.