scholarly journals No accident: genetic codes freeze in error–correcting patterns of the standard genetic code

2002 ◽  
Vol 357 (1427) ◽  
pp. 1625-1642 ◽  
Author(s):  
David H. Ardell ◽  
Guy Sella
Keyword(s):  
Information Processing ◽  
Genetic Code ◽  
Genetic Model ◽  
Random Pattern ◽  
Biological Organization ◽  
Standard Genetic Code ◽  
Protein Coding ◽  
Evolutionary Forces ◽  
Protein Coding Genes ◽  
Genetic Codes

The standard genetic code poses a challenge in understanding the evolution of information processing at a fundamental level of biological organization. Genetic codes are generally coadapted with, or ‘frozen‘ by, the protein–coding genes that they translate, and so cannot easily change by natural selection. Yet the standard code has a significantly non–random pattern that corrects common errors in the transmission of information in protein–coding genes. Because of the freezing effect and for other reasons, this pattern has been proposed not to be due to selection but rather to be incidental to other evolutionary forces or even entirely accidental. We present results from a deterministic population genetic model of code–message coevolution. We explicitly represent the freezing effect of genes on genetic codes and the perturbative effect of changes in genetic codes on genes. We incorporate characteristic patterns of mutation and translational error, namely, transition bias and positional asymmetry, respectively. Repeated selection over small successive changes produces genetic codes that are substantially, but not optimally, error correcting. In particular, our model reproduces the error–correcting patterns of the standard genetic code. Aspects of our model and results may be applicable to the general problem of adaptation to error in other natural information–processing systems.

scholarly journals Improved annotation of protein-coding genes boundaries in metazoan mitochondrial genomes

2019 ◽  
Vol 47 (20) ◽  
pp. 10543-10552 ◽  
Author(s):  
Alexander Donath ◽  
Frank Jühling ◽  
Marwa Al-Arab ◽  
Stephan H Bernhart ◽  
Franziska Reinhardt ◽  
...  
Keyword(s):  
De Novo ◽  
Stop Codon ◽  
Difficult Problem ◽  
Mitochondrial Genomes ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Genetic Codes ◽  
Annotation Server ◽  
Codon Positions ◽  
Mitochondrial Transcripts

Abstract With the rapid increase of sequenced metazoan mitochondrial genomes, a detailed manual annotation is becoming more and more infeasible. While it is easy to identify the approximate location of protein-coding genes within mitogenomes, the peculiar processing of mitochondrial transcripts, however, makes the determination of precise gene boundaries a surprisingly difficult problem. We have analyzed the properties of annotated start and stop codon positions in detail, and use the inferred patterns to devise a new method for predicting gene boundaries in de novo annotations. Our method benefits from empirically observed prevalances of start/stop codons and gene lengths, and considers the dependence of these features on variations of genetic codes. Albeit not being perfect, our new approach yields a drastic improvement in the accuracy of gene boundaries and upgrades the mitochondrial genome annotation server MITOS to an even more sophisticated tool for fully automatic annotation of metazoan mitochondrial genomes.

Many alternative and theoretical genetic codes are more robust to amino acid replacements than the standard genetic code

2019 ◽  
Vol 464 ◽  
pp. 21-32 ◽  
Author(s):  
Paweł Błażej ◽  
Małgorzata Wnętrzak ◽  
Dorota Mackiewicz ◽  
Przemysław Gagat ◽  
Paweł Mackiewicz
Keyword(s):  
Amino Acid ◽  
Genetic Code ◽  
Standard Genetic Code ◽  
Genetic Codes

scholarly journals The shiftability of protein coding genes: the genetic code was optimized for frameshift tolerating

2015 ◽  
Author(s):  
Xiaolong Wang ◽  
Xuxiang Wang ◽  
Gang Chen ◽  
Jianye Zhang ◽  
Yongqiang Liu ◽  
...  
Keyword(s):  
Genetic Code ◽  
Model Organisms ◽  
Large Dataset ◽  
Protein Coding ◽  
E Coli ◽  
Protein Coding Genes ◽  
New Gene ◽  
Sense Codon ◽  
The Relationship ◽  
Reading Frames

The genetic code defines the relationship between a protein and its coding DNA sequence. It was presumed that most frameshifts would yield non-functional, truncated or cytotoxic products. In this study, we report that in E. coli, a frameshift β-lactamase (bla) gene is still functional if all of the inner stop codons were readthrough or replaced by a sense codon. By analyzing a large dataset including all available protein coding genes in major model organisms, it is demonstrated that in any species, and in any protein-coding genes, the three translational products from the three different reading frames, are always similar to each other and with constant ~50% similarities and ~100% coverages, and the similarities is predefined by the genetic code rather than the sequences themselves. It is likely that a coding gene can be translated into three isoforms from each of the three reading frames, we propose a new gene expression paradigm, “one transcript, three translations”, which is an amendment to the traditional “one gene, one/multiple peptides” hypotheses. Finally, we concluded that the genetic code was optimized for frameshift tolerating in the early evolution, which endows every protein coding gene a character of shiftability, an inherent and everlasting ability to tolerate frameshift mutations, and serves as an innate mechanism for cells to deal with the frameshift problem.

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

Symmetry ◽  
2018 ◽  
Vol 10 (9) ◽  
pp. 388 ◽  
Author(s):  
Marco José ◽  
Gabriel Zamudio
Keyword(s):  
Amino Acids ◽  
Genetic Code ◽  
Graph Representation ◽  
Symmetry Groups ◽  
Standard Genetic Code ◽  
Graph Representations ◽  
Symmetrical Structure ◽  
Genetic Codes ◽  
Mitochondrial Genetic Code

It has long been claimed that the mitochondrial genetic code possesses more symmetries than the Standard Genetic Code (SGC). To test this claim, the symmetrical structure of the SGC is compared with noncanonical genetic codes. We analyzed the symmetries of the graphs of codons and their respective phenotypic graph representation spanned by the RNY (R purines, Y pyrimidines, and N any of them) code, two RNA Extended codes, the SGC, as well as three different mitochondrial genetic codes from yeast, invertebrates, and vertebrates. The symmetry groups of the SGC and their corresponding phenotypic graphs of amino acids expose the evolvability of the SGC. Indeed, the analyzed mitochondrial genetic codes are more symmetrical than the SGC.

scholarly journals Packing the Standard Genetic Code in its box: 3-dimensional late Crick wobble

2021 ◽  
Author(s):  
Michael Yarus
Keyword(s):  
Amino Acid ◽  
Genetic Code ◽  
Dimensional Space ◽  
Parallel Evolution ◽  
Three Dimensional ◽  
Standard Genetic Code ◽  
3 Dimensional ◽  
Combinatorial Properties ◽  
Genetic Codes ◽  
Level Order

AbstractMinimally-evolved codes are constructed with randomly chosen Standard Genetic Code (SGC) triplets, and completed with completely random triplet assignments. Such “genetic codes” have not evolved, but retain SGC qualities. Retained qualities are inescapable, part of the logic of code evolution. For example, sensitivity of coding to arbitrary assignments, which must be <≈ 10%, is intrinsic. Such sensitivity comes from elementary combinatorial properties of coding, and constrains any SGC evolution hypothesis. Similarly, evolution of last-evolved functions is difficult, due to late kinetic phenomena, likely common across codes. Census of minimally-evolved code assignments shows that shape and size of wobble domains controls packing into a coding table, shifting the accuracy of codon assignments. Access to the SGC therefore requires a plausible pathway to limited randomness, avoiding difficult completion while packing a highly ordered, degenerate code into a fixed three-dimensional space. Late Crick wobble in a 3-dimensional genetic code previously assembled by lateral transfer satisfies these varied, simultaneous requirements. By allowing parallel evolution of SGC domains, it can yield shortened evolution to SGC-level order, and allow the code to arise in smaller populations. It effectively yields full codes. Less obviously, it unifies well-studied sources for order in amino acid coding, including a minority of stereochemical triplet-amino acid associations. Finally, fusion of its intermediates into the definitive SGC is credible, mirroring broadly-accepted later events in cellular evolution.

scholarly journals Genomics of Natural Populations: Evolutionary Forces that Establish and Maintain Gene Arrangements in Drosophila pseudoosbscura

2017 ◽  
Author(s):  
Zachary L. Fuller ◽  
Gwilym D. Haynes ◽  
Stephen Richards ◽  
Stephen W. Schaeffer
Keyword(s):  
Complex Traits ◽  
Gene Arrangement ◽  
Drosophila Pseudoobscura ◽  
Heterogeneous Environments ◽  
Protein Coding ◽  
Single Chromosome ◽  
Evolutionary Forces ◽  
Protein Coding Genes ◽  
Chromosomal Inversions ◽  
Outlier Loci

AbstractThe evolution of complex traits in heterogeneous environments may shape the order of genes within chromosomes. Drosophila pseudoobscura has a rich gene arrangement polymorphism that allows one to test evolutionary genetic hypotheses about how chromosomal inversions are established in populations. D. pseudoobscura has >30 gene arrangements on a single chromosome that were generated through a series of overlapping inversion mutations with > 10 inversions with appreciable frequencies and wide geographic distributions. This study analyzes the genomic sequences of 54 strains of Drosophila pseudoobscura that carry one of six different chromosomal arrangements to test whether (1) genetic drift, (2) hitchhiking with an adaptive allele, (3) direct effects of inversions to create gene disruptions caused by breakpoints, or (4) indirect effects of inversions in limiting the formation of recombinant gametes are responsible for the establishment of new gene arrangements. We found that the inversion events do not disrupt the structure of protein coding genes at the breakpoints. Population genetic analyses of 2,669 protein coding genes identified 277 outlier loci harboring elevated frequencies of arrangement-specific derived alleles. Significant linkage disequilibrium occurs among distant loci interspersed between regions with low levels of association indicating that distant allelic combinations are held together despite shared polymorphism among arrangements. Outlier genes showing evidence of genetic differentiation between arrangements are enriched for sensory perception and detoxification genes. The data presented here support the indirect effect of inversion hypothesis where chromosomal inversions are favored because they maintain linked associations among multi-locus allelic combinations among different arrangements.

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

2018 ◽  
Author(s):  
Paweł Błażej ◽  
Dariusz R. Kowalski ◽  
Dorota Mackiewicz ◽  
Małgorzata Wnetrzak ◽  
Daniyah A. Aloqalaa ◽  
...  
Keyword(s):  
Genetic Code ◽  
Graph Clustering ◽  
Standard Genetic Code ◽  
Nucleotide Substitutions ◽  
Single Nucleotide ◽  
Protein Coding ◽  
Coding Sequences ◽  
Clustering Problem ◽  
Code Structure

AbstractThe standard genetic code (SGC) is the set of rules by which genetic information is translated into proteins, from codons, i.e. triplets of nucleotides, to amino acids. The questions about the origin and the main factor responsible for the present structure of the code are still under a hot debate. Various methodologies have been used to study the features of the code and assess the level of its potential optimality. Here, we introduced a new general approach to evaluate the quality of the genetic code structure. This methodology comes from graph theory and allows us to describe new properties of the genetic code in terms of conductance. This parameter measures the robustness of codon groups against the potential changes in translation of the protein-coding sequences generated by single nucleotide substitutions. We described the genetic code as a partition of an undirected and unweighted graph, which makes the model general and universal. Using this approach, we showed that the structure of the genetic code is a solution to the graph clustering problem. We presented and discussed the structure of the codes that are optimal according to the conductance. Despite the fact that the standard genetic code is far from being optimal according to the conductance, its structure is characterised by many codon groups reaching the minimum conductance for their size. The SGC represents most likely a local minimum in terms of errors occurring in protein-coding sequences and their translation.

scholarly journals The shiftability of protein coding genes: the genetic code was optimized for frameshift tolerating

2015 ◽  
Author(s):  
Xiaolong Wang ◽  
Xuxiang Wang ◽  
Gang Chen ◽  
Jianye Zhang ◽  
Yongqiang Liu ◽  
...  
Keyword(s):  
Genetic Code ◽  
Model Organisms ◽  
Large Dataset ◽  
Protein Coding ◽  
E Coli ◽  
Protein Coding Genes ◽  
New Gene ◽  
Sense Codon ◽  
The Relationship ◽  
Reading Frames

The genetic code defines the relationship between a protein and its coding DNA sequence. It was presumed that most frameshifts would yield non-functional, truncated or cytotoxic products. In this study, we report that in E. coli, a frameshift β-lactamase (bla) gene is still functional if all of the inner stop codons were readthrough or replaced by a sense codon. By analyzing a large dataset including all available protein coding genes in major model organisms, it is demonstrated that in any species, and in any protein-coding genes, the three translational products from the three different reading frames, are always similar to each other and with constant ~50% similarities and ~100% coverages, and the similarities is predefined by the genetic code rather than the sequences themselves. It is likely that a coding gene can be translated into three isoforms from each of the three reading frames, we propose a new gene expression paradigm, “one transcript, three translations”, which is an amendment to the traditional “one gene, one/multiple peptides” hypotheses. Finally, we concluded that the genetic code was optimized for frameshift tolerating in the early evolution, which endows every protein coding gene a character of shiftability, an inherent and everlasting ability to tolerate frameshift mutations, and serves as an innate mechanism for cells to deal with the frameshift problem.

scholarly journals Dihedral Group in The Ancient Genetic

2020 ◽  
Vol 16 (1) ◽  
pp. 13
Author(s):  
Isah Aisah ◽  
Eddy Djauhari ◽  
Asep Singgih
Keyword(s):  
Genetic Code ◽  
Dihedral Group ◽  
Symmetry Groups ◽  
Permutation Symmetry ◽  
Standard Genetic Code ◽  
Dihedral Groups ◽  
Genetic Codes ◽  
Living Things ◽  
Code Group ◽  
Nucleotide Bases

The standard genetic code consist of four nucleotide bases which encode genes to produce amino acids needed by living things. The addition of new base  (Dummy) causes a sequence of bases to become five nucleotide bases called ancient genetic codes. The five base set is denoted by , where B forms group through matching , , , , and   from set . Ancient genetic codes can be reviewed as algebraic structures as a vector spaces and other structures as symmetry groups. In this article, discussed the properties of symmetry groups from ancient genetic codes that will produce dihedral groups. The study began by constructing an expanded nucleotide base isomorphism with . The presence of base  causes  to have a cardinality of 24, denoted as  with .  isomorphic with  which is denoted by . Group  had three clasess of partitions based on strong-weak, purin-pyrimidin types, and amino-keto nucleotide groups which are denoted as , , and . All three classes are subgroups of . By using the rules of rotation and reflection in the four-side plane, it was found that only one group fulfilled the rule was named the dihedral group. Keywords: ancient genetic code, group, subgroup, permutation, symmetry group , dihedral group.

scholarly journals Fitting the standard genetic code into its triplet table

2021 ◽  
Vol 118 (36) ◽  
pp. e2021103118
Author(s):  
Michael Yarus
Keyword(s):  
Amino Acid ◽  
Genetic Code ◽  
Dimensional Space ◽  
Parallel Evolution ◽  
Three Dimensional ◽  
Standard Genetic Code ◽  
Basic Part ◽  
Combinatorial Properties ◽  
Genetic Codes ◽  
Level Order

Minimally evolved codes are constructed here; these have randomly chosen standard genetic code (SGC) triplets, completed with completely random triplet assignments. Such “genetic codes” have not evolved, but retain SGC qualities. Retained qualities are basic, part of the underpinning of coding. For example, the sensitivity of coding to arbitrary assignments, which must be < ∼10%, is intrinsic. Such sensitivity comes from the elementary combinatorial properties of coding and constrains any SGC evolution hypothesis. Similarly, assignment of last-evolved functions is difficult because of late kinetic phenomena, likely common across codes. Census of minimally evolved code assignments shows that shape and size of wobble domains controls the code’s fit into a coding table, strongly shifting accuracy of codon assignments. Access to the SGC therefore requires a plausible pathway to limited randomness, avoiding difficult completion while fitting a highly ordered, degenerate code into a preset three-dimensional space. Three-dimensional late Crick wobble in a genetic code assembled by lateral transfer between early partial codes satisfies these varied, simultaneous requirements. By allowing parallel evolution of SGC domains, this origin can yield shortened evolution to SGC-level order and allow the code to arise in smaller populations. It effectively yields full codes. Less obviously, it unifies previously studied chemical, biochemical, and wobble order in amino acid assignment, including a stereochemical minority of triplet–amino acid associations. Finally, fusion of intermediates into the final SGC is credible, mirroring broadly accepted later cellular evolution.

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