The genetic code is not optimized for resource conservation

Evolution of genetic codes is studied as change in the choice of enzymes that are used to synthesize amino acids from the genetic information of nucleic acids. We propose the following theory: the differentiation of physiological states of a cell allows for a choice of enzymes, and this choice is later fixed genetically through evolution. To demonstrate this theory, a dynamical systems model consisting of the concentrations of metabolites, enzymes, amino acyl tRNA synthetase, and tRNA–amino acid complexes in a cell is introduced and studied numerically. It is shown that the biochemical states of cells are differentiated by cell-cell interactions, and each differentiated type starts to use a different synthetase. Through the mutation of genes, this difference in the genetic code is amplified and stabilized. The relevance of this theory to the evolution of non-universal genetic code in mitochondria is suggested. The present theory is based on our recent theory of isologous symbiotic speciation, which is briefly reviewed. According to the theory, phenotypes of organisms are first differentiated into distinct types through the interaction and developmental dynamics, even though they have identical genotypes; later, with mutation in the genotype, the genotype also differentiates into discrete types, while maintaining the “symbiotic” relationship between the types. Relevance of the theory to natural as well as artificial evolution is discussed.

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tRNA Modification and Genetic Code Variations in Animal Mitochondria

Journal of Nucleic Acids ◽

10.4061/2011/623095 ◽

2011 ◽

Vol 2011 ◽

pp. 1-12 ◽

Cited By ~ 34

Author(s):

Kimitsuna Watanabe ◽

Shin-ichi Yokobori

Keyword(s):

Genetic Code ◽

Conclusive Evidence ◽

Modified Nucleosides ◽

Termination Codon ◽

Trna Modification ◽

Animal Evolution ◽

Universal Genetic Code ◽

Genetic Codes ◽

Wobble Position ◽

Code Changes

In animal mitochondria, six codons have been known as nonuniversal genetic codes, which vary in the course of animal evolution. They are UGA (termination codon in the universal genetic code changes to Trp codon in all animal mitochondria), AUA (Ile to Met in most metazoan mitochondria), AAA (Lys to Asn in echinoderm and some platyhelminth mitochondria), AGA/AGG (Arg to Ser in most invertebrate, Arg to Gly in tunicate, and Arg to termination in vertebrate mitochondria), and UAA (termination to Tyr in a planaria and a nematode mitochondria, but conclusive evidence is lacking in this case). We have elucidated that the anticodons of tRNAs deciphering these nonuniversal codons ( for UGA, for AUA, for AAA, and and for AGA/AGG) are all modified; has 5-carboxymethylaminomethyluridine or 5-taurinomethyluridine, has 5-formylcytidine or 5-taurinomethyluridine, has 7-methylguanosine and has 5-taurinomethyluridine in their anticodon wobble position, and has pseudouridine in the anticodon second position. This review aims to clarify the structural relationship between these nonuniversal codons and the corresponding tRNA anticodons including modified nucleosides and to speculate on the possible mechanisms for explaining the evolutional changes of these nonuniversal codons in the course of animal evolution.

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Refactoring the Genetic Code for Increased Evolvability

10.1101/128058 ◽

2017 ◽

Author(s):

Gur Pines ◽

James D. Winkler ◽

Assaf Pines ◽

Ryan T. Gill

Keyword(s):

Genetic Code ◽

Directed Evolution ◽

Single Gene ◽

Point Mutations ◽

Saturation Mutagenesis ◽

Mutagenic Potential ◽

Single Nucleotide ◽

Common Error ◽

Mutational Landscape ◽

Genetic Codes

AbstractThe standard genetic code is robust to mutations and base-pairing errors during transcription and translation. Point mutations are most likely to be synonymous or preserve the chemical properties of the original amino acid. Saturation mutagenesis experiments suggest that in some cases the best performing mutant requires a replacement of more than a single nucleotide within a codon. These replacements are essentially inaccessible to common error-based laboratory engineering techniques that alter single nucleotide per mutation event, due to the extreme rarity of adjacent mutations. In this theoretical study, we suggest a radical reordering of the genetic code that maximizes the mutagenic potential of single nucleotide replacements. We explore several possible genetic codes that allow a greater degree of accessibility to the mutational landscape and may result in a hyper-evolvable organism serving as an ideal platform for directed evolution experiments. We then conclude by evaluating potential applications for recoded organisms within the synthetic biology field.Significance StatementThe conservative nature of the genetic code prevents bioengineers from efficiently accessing the full mutational landscape of a gene using common error-prone methods. Here we present two computational approaches to generate alternative genetic codes with increased accessibility. These new codes allow mutational transition to a larger pool of amino acids and with a greater degree of chemical differences, using a single nucleotide replacement within the codon, thus increasing evolvability both at the single gene and at the genome levels. Given the widespread use of these techniques for strain and protein improvement along with more fundamental evolutionary biology questions, the use of recoded organisms that maximize evolvability should significantly improve the efficiency of directed evolution, library generation and fitness maximization.

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Genomics Insights: The DNA Habitat and its RNA Inhabitants: At the Dawn of RNA Sociology

Genomics Insights ◽

10.4137/gei.s11490 ◽

2013 ◽

Vol 6 ◽

pp. GEI.S11490 ◽

Cited By ~ 20

Author(s):

Luis P. Villarreal ◽

Guenther Witzany

Keyword(s):

Genetic Code ◽

Evolutionary Novelty ◽

Agent Based ◽

Cellular Processes ◽

Genetic Codes ◽

Physical Chemical ◽

Persistent Viruses ◽

Virus Research ◽

Biological Concepts ◽

Regulatory Rnas

Most molecular biological concepts derive from physical chemical assumptions about the genetic code that are basically more than 40 years old. Additionally, systems biology, another quantitative approach, investigates the sum of interrelations to obtain a more holistic picture of nucleotide sequence order. Recent empirical data on genetic code compositions and rearrangements by mobile genetic elements and noncoding RNAs, together with results of virus research and their role in evolution, does not really fit into these concepts and compel a reexamination. In this review, we try to find an alternate hypothesis. It seems plausible now that if we look at the abundance of regulatory RNAs and persistent viruses in host genomes, we will find more and more evidence that the key players that edit the genetic codes of host genomes are consortia of RNA agents and viruses that drive evolutionary novelty and regulation of cellular processes in all steps of development. This agent-based approach may lead to a qualitative RNA sociology that investigates and identifies relevant behavioral motifs of cooperative RNA consortia. In addition to molecular biological perspectives, this may lead to a better understanding of genetic code evolution and dynamics.

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Optimisation of Asymmetric Mutational Pressure and Selection Pressure Around the Universal Genetic Code

Computational Science – ICCS 2008 - Lecture Notes in Computer Science ◽

10.1007/978-3-540-69389-5_13 ◽

2008 ◽

pp. 100-109 ◽

Cited By ~ 8

Author(s):

Paweł Mackiewicz ◽

Przemysław Biecek ◽

Dorota Mackiewicz ◽

Joanna Kiraga ◽

Krystian Baczkowski ◽

...

Keyword(s):

Genetic Code ◽

Selection Pressure ◽

Mutational Pressure ◽

Universal Genetic Code

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The Universal Genetic Code and Non-Canonical Variants ☆

Reference Module in Life Sciences ◽

10.1016/b978-0-12-809633-8.07327-1 ◽

2017 ◽

Author(s):

A.S. Rodin ◽

S. Branciamore

Keyword(s):

Genetic Code ◽

Universal Genetic Code

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Characterization and Incidence of the First Member of the Genus Mitovirus Identified in the Phytopathogenic Species Fusarium oxysporum

Viruses ◽

10.3390/v12030279 ◽

2020 ◽

Vol 12 (3) ◽

pp. 279 ◽

Cited By ~ 1

Author(s):

Almudena Torres-Trenas ◽

Encarnación Pérez-Artés

Keyword(s):

Phylogenetic Analysis ◽

Amino Acid ◽

Genetic Code ◽

Fusarium Oxysporum ◽

Amino Acid Residues ◽

Fusarium Spp ◽

Stem Loop ◽

Universal Genetic Code ◽

The Family ◽

Amino Acid Tryptophan

A novel mycovirus named Fusarium oxysporum f. sp. dianthi mitovirus 1 (FodMV1) has been identified infecting a strain of Fusarium oxysporum f. sp. dianthi from Colombia. The genome of FodMV1 is 2313 nt long, and comprises a 172-nt 5’-UTR, a 2025-nt single ORF encoding an RdRp of 675 amino acid residues, and a 113-nt 3´-UTR. Homology BlastX searches identifies FodMV1 as a novel member of the genus Mitovirus in the family Narnaviridae. As the rest of mitoviruses, the genome of FodMV1 presents a high percentage of A+U (58.8%) and contains a number of UGA codons that encode the amino acid tryptophan rather than acting as stop codons as in the universal genetic code. Another common feature with other mitoviruses is that the 5′- and 3′-UTR regions of FodMV1 can be folded into potentially stable stem-loop structures. Result from phylogenetic analysis place FodMV1 in a different clade than the rest of mitoviruses described in other Fusarium spp. Incidence of FodMV1-infections in the collection of F. oxysporum f. sp. dianthi isolates analyzed is relatively high. Of particular interest is the fact that FodMV1 has been detected infecting isolates from two geographical areas as distant as Spain and Colombia.

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Resource conservation manifests in the genetic code

Science ◽

10.1126/science.aaz9642 ◽

2020 ◽

Vol 370 (6517) ◽

pp. 683-687

Author(s):

Liat Shenhav ◽

David Zeevi

Keyword(s):

Genetic Code ◽

Nutrient Limitation ◽

Nitrogen Availability ◽

Resource Conservation ◽

Marine Microbes ◽

Carbon And Nitrogen ◽

Selective Pressures ◽

Domains Of Life ◽

Cell Data ◽

Competition For Resources

Nutrient limitation drives competition for resources across organisms. However, much is unknown about how selective pressures resulting from nutrient limitation shape microbial coding sequences. Here, we study this “resource-driven selection” by using metagenomic and single-cell data of marine microbes, alongside environmental measurements. We show that a significant portion of the selection exerted on microbes is explained by the environment and is associated with nitrogen availability. Notably, this resource conservation optimization is encoded in the structure of the standard genetic code, providing robustness against mutations that increase carbon and nitrogen incorporation into protein sequences. This robustness generalizes to codon choices from multiple taxa across all domains of life, including the human genome.

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