4.7 Review

The Evolution of Life Is a Road Paved with the DNA Quadruplet Symmetry and the Supersymmetry Genetic Code

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Editorial Material Biochemistry & Molecular Biology

Genetic Code Expansion: Another Solution to Codon Assignments

Kensaku Sakamoto

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2023)

Review Genetics & Heredity

Why Were [GADV]-amino Acids and GNC Codons Selected and How Was GNC Primeval Genetic Code Established?

Kenji Ikehara

Summary: The correspondence relations between codons and amino acids are determined by the genetic code, which is crucial for the life system composed of genes and proteins. This article discusses the origin and evolution of the genetic code, proposing the GNC-SNS primitive genetic code hypothesis. It explores the selection of four [GADV]-amino acids and four GNCs in the first genetic code, as well as the establishment of correspondence relations between them. The comprehensive analysis integrates theories on frozen-accident, coevolution, and adaptation to explain the origin of the genetic code.
Article Multidisciplinary Sciences

Samples returned from the asteroid Ryugu are similar to Ivuna-type carbonaceous meteorites

Tetsuya Yokoyama et al.

Summary: Carbonaceous meteorites from C-type asteroids were examined using samples from asteroid (162173) Ryugu. The samples resemble carbonaceous chondrite meteorites, particularly the CI group, and are made up of minerals formed in aqueous fluids. These minerals were altered at a temperature of 37 degrees Celsius about 5.2 million years after the formation of the first solids in the Solar System. The Ryugu samples have a composition similar to the Sun's photosphere.

SCIENCE (2023)

Article Biochemical Research Methods

The identification of a robust leucine dehydrogenase from a directed soil metagenome for efficient synthesis of L-2-aminobutyric acid

Yan Liu et al.

Summary: Through directed screening, a robust leucine dehydrogenase, TvLeuDH, was identified from a metagenomic library. TvLeuDH exhibited high substrate tolerance and excellent enzymatic activity towards 2-oxobutyric acid. A three-enzyme co-expression system was established, resulting in the conversion of 1.5 M L-threonine to L-2-ABA with a 99% molar conversion rate and a space-time yield of 51.5 g/L/h. This study reveals the great potential of directed metagenomics for industrial biotechnology.

BIOTECHNOLOGY JOURNAL (2023)

Article Biochemistry & Molecular Biology

On the origin of the genetic code

Masayuki Seki

Summary: The mechanisms underlying the generation of the genetic code have been a mystery since it was decoded in 1965. This study proposes a hypothesis on the emergence of the code, suggesting that it was driven by sequential selective pressures. According to the hypothesis, specific aminoacyl-RNAs were selected as subunits of ribozymes, with aminoacyl-RNA acting as cofactors. The duplication of specific sites allowed for the emergence of different active pockets in ribozymes, leading to the development of metabolic pathways in organisms.

GENES & GENETIC SYSTEMS (2023)

Article Biology

The error minimization of the genetic code would have been determined by natural selection and not by a neutral evolution

Massimo Di Giulio

Summary: The mechanisms by which the error minimization observed in the genetic code has been produced are discussed in this paper. The author analyzes whether the error minimization is a result of natural selection or an emergent property. Criticism is given towards Massey's simulations and Koonin's interpretations, as well as Janzen et al.'s opinion on the neutral origin of error minimization. The level of optimization achieved by the genetic code suggests an intervention of natural selection rather than a neutral process.

BIOSYSTEMS (2023)

Article Computer Science, Artificial Intelligence

Cracking the genetic code with neural networks

Marc Joiret et al.

Summary: The goal of this study was to determine if a neural network could independently rediscover the mapping between codons and amino acids to decode the genetic code. Different deep learning neural network architectures were compared to evaluate the accuracy of the codon-to-amino-acid mapping. The study also examined the impact of codon embedding and the use of unbalanced representations of amino acids for deciphering rare codons.

FRONTIERS IN ARTIFICIAL INTELLIGENCE (2023)

Article Biology

The Canonical Table of the Genetic Code as a periodic system of triplets

Vladimir A. Karasev

Summary: The Canonical Table of the Genetic Code (CTGC) is constructed theoretically based on the similarity between the conformation of proteins and 4-arc chain graphs. Compared with previously described tables, this CTGC more accurately reflects the properties of the genetic code.

BIOSYSTEMS (2022)

Review Biochemistry & Molecular Biology

Recent Advances in Genetic Code Expansion Techniques for Protein Phosphorylation Studies

Xuewen Qin et al.

Summary: Protein phosphorylation is a crucial posttranslational modification involved in cell signaling. The use of genetic code expansion has advanced the study of protein phosphorylation.

JOURNAL OF MOLECULAR BIOLOGY (2022)

Review Biochemistry & Molecular Biology

Genetic Code Expansion Through Quadruplet Codon Decoding

Jiantao Guo et al.

Summary: Noncanonical amino acid mutagenesis is a powerful tool for studying protein structure and function. Quadruplet codons have attracted attention for creating additional blank codons in noncanonical amino acid mutagenesis. This review discusses the methodologies and applications of quadruplet codon decoding in genetic code expansion both in vitro and in vivo.

JOURNAL OF MOLECULAR BIOLOGY (2022)

Review Biochemistry & Molecular Biology

Codon usage bias

Sujatha Thankeswaran Parvathy et al.

Summary: Codon usage bias is a common phenomenon observed in bacteria, plants, and animals, with consistent and characteristic patterns across different species and genes. The formation of codon bias is influenced by factors such as genome composition, gene expression levels, and gene length. Understanding codon usage bias can provide insights into phylogenetic relationships and gene evolution among organisms.

MOLECULAR BIOLOGY REPORTS (2022)

Editorial Material Biochemistry & Molecular Biology

Film-like organelles equip cells with multiple genetic codes

Neil C. Taylor et al.

Summary: This study demonstrates the use of 2D phase separation to engineer spatially separated organelles within eukaryotic cells, allowing independent translation of proteins incorporating noncanonical amino acids.

TRENDS IN BIOCHEMICAL SCIENCES (2022)

Review Biochemistry & Molecular Biology

Genetic Code Engineering by Natural and Unnatural Base Pair Systems for the Site-Specific Incorporation of Non-Standard Amino Acids Into Proteins

Michiko Kimoto et al.

Summary: This review discusses the current methods for incorporating new amino acids into proteins by designing new codon-anticodon interactions, including unnatural base pairs systems for expanding the genetic alphabet.

FRONTIERS IN MOLECULAR BIOSCIENCES (2022)

Editorial Material Genetics & Heredity

Locking in a synthetic genetic code

Kirsty Minton

NATURE REVIEWS GENETICS (2022)

Article Biology

Trinucleotide k-circular codes II: Biology

J. Christian Michel et al.

Summary: In this article, the concept of (≥ k)-circular codes is introduced, and the difference between circular codes and k-circular codes is explained. Through describing the characteristics of trinucleotide circular codes, the importance of circularity and the relationship between balance and self-complementarity are studied, as well as the combinatorial hierarchy of trinucleotide k-circular codes.

BIOSYSTEMS (2022)

Article Biology

The structure of the genetic code as an optimal graph clustering problem

Pawel Blazej et al.

Summary: This article introduces a new method using graph theory to evaluate the quality of the genetic code structure. By measuring the conductance, which represents the robustness of codon groups against potential changes in translation, the study shows that the standard genetic code is far from optimal according to conductance. However, many codon groups in its structure reach the minimum conductance for their size.

JOURNAL OF MATHEMATICAL BIOLOGY (2022)

Article Multidisciplinary Sciences

On the origin and evolution of the asteroid Ryugu: A comprehensive geochemical perspective

Eizo Nakamura et al.

Summary: This comprehensive analysis of 16 particles returned from the C-type asteroid Ryugu by the Hayabusa2 mission reveals important findings about its composition and origin. The particles consist of phyllosilicate matrix, porosity, minor phases, and organic matter. The abundances of elements in the particles are similar to those found in CI chondrites, suggesting that Ryugu sampled the most primitive protosolar nebula reservoirs. The analysis also suggests that complex soluble organic matter formed during aqueous alteration on the Ryugu progenitor planetesimal.

PROCEEDINGS OF THE JAPAN ACADEMY SERIES B-PHYSICAL AND BIOLOGICAL SCIENCES (2022)

Article Biochemistry & Molecular Biology

A crescendo of competent coding (c3) contains the Standard Genetic Code

Michael Yarus

Summary: The Standard Genetic Code (SGC) can be formed by merging partial codes evolved in different individuals. This process can be achieved through the evolution of accurate third-position Crick wobble. The fusion of these code fragments leads to the creation of an SGC, which can be reached sooner and more frequently compared to other coding tables or nonfusing codes.
Article Multidisciplinary Sciences

A Novel Real Coded Genetic Algorithm for Software Mutation Testing

Deepti Bala Mishra et al.

Summary: Information Technology has rapidly developed in recent years, playing a critical role in the symmetry of software systems. In the field of software testing, white-box unit-level testing is the foundation for all other techniques, as it considers the source code to conduct comprehensive testing. This research paper proposes a new approach that integrates path coverage-based testing with a Fault Detection Matrix to achieve maximum mutation coverage.

SYMMETRY-BASEL (2022)

Article Genetics & Heredity

An Explanation of Exceptions from Chargaff's Second Parity Rule/Strand Symmetry of DNA Molecules

Marija Rosandic et al.

Summary: The article reveals the symmetrical nature of quadruplets in DNA structure and the violation of CSPR rule, offering new hypotheses for the creation and evolution of DNA.
Article Biology

Tandemly repeated NBPF HOR copies (Olduvai triplets): Possible impact on human brain evolution

Matko Gluncic et al.

Summary: The study identified tandemly organized NBPF higher order repeats in human and nonhuman primate genomes, with a discontinuous jump in copy number as species evolved. Point mutations were found in some NBPF monomers not organized in canonical repeats.

LIFE SCIENCE ALLIANCE (2022)

Article Biology

Relational model of the standard genetic code

Pasko Konjevoda et al.

Summary: This paper presents an alternative approach to interpret and manage the genetic code by using the relational data model. The Standard Genetic Code table is divided into four tables based on different bases. By adopting coding function with the third base, a specific protein synthesis without ambiguity is enabled, in accordance with the concept of ambiguity reduction in the origin of biological codes.

BIOSYSTEMS (2021)

Article Biochemistry & Molecular Biology

Evolution of the Standard Genetic Code

Michael Yarus

Summary: The researcher computed paths to the Standard Genetic Code (SGC) and found that SGC-like coding emerged from traditional evolutionary mechanisms. They defined progress values to objectively measure evolution and discovered that SGC evolution is critically sensitive to disorder from random assignments, slowing down near coding completion.

JOURNAL OF MOLECULAR EVOLUTION (2021)

Article Biology

A computational screen for alternative genetic codes in over 250,000 genomes

Yekaterina Shulgina et al.

Summary: The genetic code, once thought to be a 'frozen accident,' has been found to evolve to some extent through the discovery of alternative genetic codes. The development of a computational method called Codetta allowed the prediction of amino acid decoding from nucleotide sequence data. By analyzing over 250,000 bacterial and archaeal genome sequences, five new codon reassignments for arginine were discovered, with evolutionary forces like low GC content driving these changes. The study demonstrates the utility of Codetta in understanding how genetic codes evolve and ensuring accuracy in protein databases.
Article Biology

The origin of the genetic code and origin of ideas

Massimo Di Giulio

Summary: The observation of Ser coding and the differences in codons alone cannot explain the origin of the genetic code without additional assumptions. The hypotheses of ancestral amino acids, poly-G mRNA as the first to be translated, and tRNA duplication as mechanisms lack solid evidence. Furthermore, the discussion lacked consideration of a coevolution theory in explaining the origin of the genetic code.

JOURNAL OF THEORETICAL BIOLOGY (2021)

Article Biology

The novel Ideal Symmetry Genetic Code table - Common purine-pyrimidine symmetry net for all RNA and DNA species

Marija Rosandic et al.

Summary: This study explores the symmetries within the genetic code, revealing the physicochemical properties of purine-pyrimidine symmetry and demonstrating how tRNA cognate anticodons can recognize synonymous codons during mRNA decoding. The research highlights the significance of symmetries in the genetic code throughout evolution.

JOURNAL OF THEORETICAL BIOLOGY (2021)

Article Biochemistry & Molecular Biology

Is the Genetic Code Optimized for Resource Conservation?

Haiqing Xu et al.

Summary: A recent study suggesting that the standard genetic code is optimized for resource conservation is found to be theoretically untenable. After correcting methodological problems, it is concluded that there is no evidence supporting the optimization of the SGC for nitrogen or carbon conservation.

MOLECULAR BIOLOGY AND EVOLUTION (2021)

Article Mathematics, Interdisciplinary Applications

SYMMETRY AND ASYMMETRY IN BIOINFORMATICS: FROM GENETIC CODE TO LIFE

Matthew He

SYMMETRY-CULTURE AND SCIENCE (2021)

Article Biochemistry & Molecular Biology

Evolution of the genetic code

Lei Lei et al.

Summary: This study presents a detailed model that explains the positions of all amino acids in the genetic code and describes the evolution of the code. Furthermore, it discusses the evolution pattern of aaRS enzymes and the biological selection for the earliest evolution of the code and protocell evolution.

TRANSCRIPTION-AUSTIN (2021)

Article Biology

Rumer's transformation: A symmetry puzzle standing for half a century

Diego L. Gonzalez et al.

BIOSYSTEMS (2020)

Review Nutrition & Dietetics

Potential ofChlorellaas a Dietary Supplement to Promote Human Health

Tomohiro Bito et al.

NUTRIENTS (2020)

Article Mathematics, Interdisciplinary Applications

BISYMMETRIC MATRICES AND SYMMETROLOGIC RESEARCHES IN GENETIC BIOMECHANICS

Sergey Petoukhov et al.

SYMMETRY-CULTURE AND SCIENCE (2020)

Review Microbiology

Understanding the Genetic Code

Milton H. Safer

JOURNAL OF BACTERIOLOGY (2019)

Article Multidisciplinary Sciences

Total synthesis of Escherichia coli with a recoded genome

Julius Fredens et al.

NATURE (2019)

Article Biology

Linear codes and the mitochondrial genetic code

Elena Fimmel et al.

BIOSYSTEMS (2019)

Article Biology

On the origin of degeneracy in the genetic code

D. L. Gonzalez et al.

INTERFACE FOCUS (2019)

Article Computer Science, Information Systems

Local Symmetry of Non-Coding Genetic Sequences

Marijus Radavicius et al.

INFORMATICA (2019)

Article Computer Science, Cybernetics

OPTIMAL NOISE-IMMUNE GENETIC CODES

I. V. Sergienko et al.

CYBERNETICS AND SYSTEMS ANALYSIS (2019)

Review Biology

What is code biology?

Marcello Barbieri

BIOSYSTEMS (2018)

Article Multidisciplinary Sciences

Symmetrical Properties of Graph Representations of Genetic Codes: From Genotype to Phenotype

Marco Jose et al.

SYMMETRY-BASEL (2018)

Article Multidisciplinary Sciences

A unified model of the standard genetic code

Marco V. Jose et al.

ROYAL SOCIETY OPEN SCIENCE (2017)

Article Biology

A binary representation of the genetic code

Louis R. Nemzer

BIOSYSTEMS (2017)

Article Biology

A new integrated symmetrical table for genetic codes

Jian-Jun Shu

BIOSYSTEMS (2017)

Article Biochemistry & Molecular Biology

Trinucleotide's quadruplet symmetries and natural symmetry law of DNA creation ensuing Chargaff's second parity rule

Marija Rosandic et al.

JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS (2016)

Article Biology

Evolution of the genetic code through progressive symmetry breaking

Reijer Lenstra

JOURNAL OF THEORETICAL BIOLOGY (2014)

Editorial Material Humanities, Multidisciplinary

Introduction to Code Biology

Marcello Barbieri

BIOSEMIOTICS (2014)

Article Biology

Patterns of nucleotide asymmetries in plant and animal genomes

Martin Mascher et al.

BIOSYSTEMS (2013)

Article Biochemistry & Molecular Biology

Compensatory nature of Chargaff's second parity rule

Alexandra E. Rapoport et al.

JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS (2013)

Article Computer Science, Interdisciplinary Applications

Symmetry breaking in the genetic code: Finite groups

Fernando Antoneli et al.

MATHEMATICAL AND COMPUTER MODELLING (2011)

Article Statistics & Probability

Statistical Testing of Chargaff's Second Parity Rule in Bacterial Genome Sequences

Andrew Hart et al.

STOCHASTIC MODELS (2011)

Review Biochemical Research Methods

Are There Laws of Genome Evolution?

Eugene V. Koonin

PLOS COMPUTATIONAL BIOLOGY (2011)

Article Biology

Essential molecular functions associated with the circular code evolution

Ahmed Ahmed et al.

JOURNAL OF THEORETICAL BIOLOGY (2010)

Article Mathematical & Computational Biology

Codon Populations in Single-stranded Whole Human Genome DNA Are Fractal and Fine-tuned by the Golden Ratio 1.618

Jean-Claude Perez

INTERDISCIPLINARY SCIENCES-COMPUTATIONAL LIFE SCIENCES (2010)

Article Biotechnology & Applied Microbiology

Inversions and inverted transpositions as the basis for an almost universal format of genome sequences

Guenter Albrecht-Buehler

GENOMICS (2007)

Article Biochemistry & Molecular Biology

Symmetry preservation in the evolution of the genetic code

JEM Hornos et al.

IUBMB LIFE (2004)

Article Biochemical Research Methods

Why are complementary DNA strands symmetric?

PF Baisnée et al.

BIOINFORMATICS (2002)

Article Biochemical Research Methods

Compositional symmetries in complete genomes

D Qi et al.

BIOINFORMATICS (2001)