scholarly journals The standard genetic code facilitates exploration of the space of functional nucleotide sequences

2017 ◽  
Author(s):  
Shubham Tripathi ◽  
Michael W. Deem
Keyword(s):  
Genetic Diversity ◽  
Genetic Code ◽  
Time Scales ◽  
Large Fraction ◽  
Standard Genetic Code ◽  
Universal Genetic Code ◽  
Functional Sequence ◽  
Fitness Advantage ◽  
Standard Code ◽  
Intermediate Time

AbstractThe standard genetic code is well known to be optimized for minimizing the phenotypic effects of single nucleotide substitutions, a property that was likely selected for during the emergence of a universal code. Given the fitness advantage afforded by high standing genetic diversity in a population in a dynamic environment, it is possible that selection to explore a large fraction of the space of functional proteins also occurred. To determine whether selection for such a property played a role during the emergence of the nearly universal genetic code, we investigated the number of functional variants of the Escherichia coli PhoQ protein explored at different time scales under translation using different genetic codes. We found that the standard genetic code is highly optimal for exploring a large fraction of the space of functional PhoQ variants at intermediate time scales as compared to random codes. Environmental changes, in response to which genetic diversity in a population provides a fitness advantage, are likely to have occurred at these intermediate time scales. Our results indicate that the ability of the standard code to explore a large fraction of the space of functional sequence variants arises from a balance between robustness and flexibility and is largely independent of the property of the standard code to minimize the phenotypic effects of mutations. We propose that selection to explore a large fraction of the functional sequence space while minimizing the phenotypic effects of mutations contributed towards the emergence of the standard code as the universal genetic code.

Alternative genetic code for amino acids and transfer RNA revisited

2013 ◽  
Vol 4 (3) ◽  
pp. 309-318 ◽  
Author(s):  
Kiyofumi Hamashima ◽  
Akio Kanai
Keyword(s):  
Genetic Code ◽  
Translational Control ◽  
Trna Synthetase ◽  
Evolutionary Divergence ◽  
Aminoacyl Trna Synthetase ◽  
Standard Genetic Code ◽  
Standard Code ◽  
Rna Biosynthesis ◽  
Nematode Worm ◽  
Eukaryotic Genomes

AbstractThe genetic code is highly conserved among all organisms and its evolution is thought to be strictly limited. However, an increasing number of studies have reported non-standard codes in prokaryotic and eukaryotic genomes. Most of these deviations from the standard code are attributable to tRNA changes relating to, for example, codon/anticodon base pairing and tRNA/aminoacyl-tRNA synthetase recognition. In this review, we focus on tRNA, a key molecule in the translation of the genetic code, and summarize the most recently published information on the evolutionary divergence of the tRNAs. Surprisingly, although higher eukaryotes, such as the nematode (worm), utilize the standard genetic code, newly identified nematode-specific tRNAs (nev-tRNAs) translate nucleotides in a manner that transgresses the code. Furthermore, a variety of additional functions of tRNAs, beyond their translation of the genetic code, have emerged rapidly. We also review these intriguing new aspects of tRNA, which have potential impacts on translational control, RNA silencing, antibiotic resistance, RNA biosynthesis, and transcriptional regulation.

scholarly journals Motility at the Origin of Life: Its Characterization and a Model

2014 ◽  
Vol 20 (1) ◽  
pp. 55-76 ◽  
Author(s):  
Tom Froese ◽  
Nathaniel Virgo ◽  
Takashi Ikegami
Keyword(s):  
Origin Of Life ◽  
Time Scales ◽  
Morphological Changes ◽  
Reaction Diffusion ◽  
Dissipative Structures ◽  
Reaction Diffusion Systems ◽  
Diffusion Systems ◽  
Inclusive Approach ◽  
Intermediate Time ◽  
The Origin Of Life

Due to recent advances in synthetic biology and artificial life, the origin of life is currently a hot topic of research. We review the literature and argue that the two traditionally competing replicator-first and metabolism-first approaches are merging into one integrated theory of individuation and evolution. We contribute to the maturation of this more inclusive approach by highlighting some problematic assumptions that still lead to an ximpoverished conception of the phenomenon of life. In particular, we argue that the new consensus has so far failed to consider the relevance of intermediate time scales. We propose that an adequate theory of life must account for the fact that all living beings are situated in at least four distinct time scales, which are typically associated with metabolism, motility, development, and evolution. In this view, self-movement, adaptive behavior, and morphological changes could have already been present at the origin of life. In order to illustrate this possibility, we analyze a minimal model of lifelike phenomena, namely, of precarious, individuated, dissipative structures that can be found in simple reaction-diffusion systems. Based on our analysis, we suggest that processes on intermediate time scales could have already been operative in prebiotic systems. They may have facilitated and constrained changes occurring in the faster- and slower-paced time scales of chemical self-individuation and evolution by natural selection, respectively.

scholarly journals Some theoretical aspects of reprogramming the standard genetic code

2020 ◽  
Author(s):  
Kuba Nowak ◽  
Paweł Błażej ◽  
Małgorzata Wnetrzak ◽  
Dorota Mackiewicz ◽  
Paweł Mackiewicz
Keyword(s):  
Amino Acids ◽  
Genetic Code ◽  
Dna Sequences ◽  
Theoretical Perspective ◽  
Optimal Number ◽  
Optimal Size ◽  
Coding System ◽  
Standard Genetic Code ◽  
Nucleotide Mutation ◽  
Code Extension

1AbstractReprogramming of the standard genetic code in order to include non-canonical amino acids (ncAAs) opens a new perspective in medicine, industry and biotechnology. There are several methods of engineering the code, which allow us for storing new genetic information in DNA sequences and transmitting it into the protein world. Here, we investigate the problem of optimal genetic code extension from theoretical perspective. We assume that the new coding system should encode both canonical and new ncAAs using 64 classical codons. What is more, the extended genetic code should be robust to point nucleotide mutation and minimize the possibility of reversion from new to old information. In order to do so, we follow graph theory to study the properties of optimal codon sets, which can encode 20 canonical amino acids and stop coding signal. Finally, we describe the set of vacant codons that could be assigned to new amino acids. Moreover, we discuss the optimal number of the newly incorporated ncAAs and also the optimal size of codon blocks that are assigned to ncAAs.

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

2008 ◽  
pp. 100-109 ◽  
Author(s):  
Paweł Mackiewicz ◽  
Przemysław Biecek ◽  
Dorota Mackiewicz ◽  
Joanna Kiraga ◽  
Krystian Baczkowski ◽  
...  
Keyword(s):  
Genetic Code ◽  
Selection Pressure ◽  
Mutational Pressure ◽  
Universal Genetic Code

scholarly journals Correction: Optimization of the standard genetic code according to three codon positions using an evolutionary algorithm

PLoS ONE ◽  
2018 ◽  
Vol 13 (10) ◽  
pp. e0205450 ◽  
Author(s):  
Paweł Błażej ◽  
Małgorzata Wnętrzak ◽  
Dorota Mackiewicz ◽  
Paweł Mackiewicz
Keyword(s):  
Evolutionary Algorithm ◽  
Genetic Code ◽  
Standard Genetic Code ◽  
Codon Positions

Evolution of Genetic Codes through Isologous Diversification of Cellular States

2000 ◽  
Vol 6 (4) ◽  
pp. 283-305 ◽  
Author(s):  
Hiroaki Takagi ◽  
Kunihiko Kaneko ◽  
Tetsuya Yomo
Keyword(s):  
Genetic Code ◽  
Present Theory ◽  
Trna Synthetase ◽  
Recent Theory ◽  
Symbiotic Relationship ◽  
Universal Genetic Code ◽  
Systems Model ◽  
Genetic Codes ◽  
A Cell ◽  
Developmental Dynamics

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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