scholarly journals Little evidence the standard genetic code is optimized for resource conservation

2021 ◽  
Author(s):  
Hana Rozhoňová ◽  
Joshua L. Payne
Keyword(s):  
Genetic Code ◽  
Null Model ◽  
Resource Conservation ◽  
Molecular Volume ◽  
Standard Genetic Code ◽  
Highly Sensitive ◽  
Nitrogen Conservation ◽  
Polar Requirement

AbstractShenhav & Zeevi (Science, 2020, 370:683-687) propose nitrogen and carbon conservation as optimization principles in the standard genetic code that are not confounded by the established optimizations for polar requirement and hydropathy. We show their results for nitrogen conservation are highly sensitive to their choice of null model and their results for carbon conservation are confounded by molecular volume.

scholarly journals Golden and Harmonic Mean in the Genetic Code

2017 ◽  
Author(s):  
Miloje M. Rakocevic
Keyword(s):  
Amino Acids ◽  
Genetic Code ◽  
Harmonic Mean ◽  
Standard Genetic Code ◽  
International Conference ◽  
Theoretical Approaches ◽  
Code Table ◽  
Nucleotide Triplet ◽  
Polar Requirement

In previous two works (Rakočević, 1998; 2013), we have shown the determination of genetic code by golden and harmonic mean within standard Genetic Code Table, i.e. nucleotide triplet table, whereas in this paper we show the same determination through a specific connection between two tables – of nucleotide doublets Table and triplets Table, over polarity of amino acids, measured by Cloister energy in general, and by hydropathy and polar requirement, partialy. [This is the expanded version of the article published in Proceedings of the 2nd International Conference “Theoretical Approaches to BioInformation Systems” (TABIS.2013), September 17–22, 2013, Belgrade, Serbia. That first version is also stored, as Version 1, in OSF Preprints.]

scholarly journals A unified model of the standard genetic code

2017 ◽  
Vol 4 (3) ◽  
pp. 160908 ◽  
Author(s):  
Marco V. José ◽  
Gabriel S. Zamudio ◽  
Eberto R. Morgado
Keyword(s):  
Genetic Code ◽  
Algebraic Model ◽  
The Other ◽  
Three Dimensions ◽  
Major Groove ◽  
Standard Genetic Code ◽  
Trna Synthetases ◽  
Aminoacyl Trna Synthetases ◽  
Primeval Rny Code ◽  
Polar Requirement

The Rodin–Ohno (RO) and the Delarue models divide the table of the genetic code into two classes of aminoacyl-tRNA synthetases (aaRSs I and II) with recognition from the minor or major groove sides of the tRNA acceptor stem, respectively. These models are asymmetric but they are biologically meaningful. On the other hand, the standard genetic code (SGC) can be derived from the primeval RNY code (R stands for purines, Y for pyrimidines and N any of them). In this work, the RO-model is derived by means of group actions, namely, symmetries represented by automorphisms, assuming that the SGC originated from a primeval RNY code. It turns out that the RO-model is symmetric in a six-dimensional (6D) hypercube. Conversely, using the same automorphisms, we show that the RO-model can lead to the SGC. In addition, the asymmetric Delarue model becomes symmetric by means of quotient group operations. We formulate isometric functions that convert the class aaRS I into the class aaRS II and vice versa. We show that the four polar requirement categories display a symmetrical arrangement in our 6D hypercube. Altogether these results cannot be attained, neither in two nor in three dimensions. We discuss the present unified 6D algebraic model, which is compatible with both the SGC (based upon the primeval RNY code) and the RO-model.

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 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

scholarly journals Resource conservation manifests in the genetic code

Science ◽  
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.

scholarly journals Extreme genetic code optimality from a molecular dynamics calculation of amino acid polar requirement

2009 ◽  
Vol 79 (6) ◽  
Author(s):  
Thomas Butler ◽  
Nigel Goldenfeld ◽  
Damien Mathew ◽  
Zaida Luthey-Schulten
Keyword(s):  
Molecular Dynamics ◽  
Amino Acid ◽  
Genetic Code ◽  
Dynamics Calculation ◽  
Polar Requirement

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

PLoS ONE ◽  
2018 ◽  
Vol 13 (8) ◽  
pp. e0201715 ◽  
Author(s):  
Paweł Błażej ◽  
Małgorzata Wnętrzak ◽  
Dorota Mackiewicz ◽  
Paweł Mackiewicz
Keyword(s):  
Evolutionary Algorithm ◽  
Genetic Code ◽  
Standard Genetic Code ◽  
Codon Positions

scholarly journals Computational Analysis of Genetic Code Variations Optimized for the Robustness against Point Mutations with Wobble-like Effects

Life ◽  
2021 ◽  
Vol 11 (12) ◽  
pp. 1338
Author(s):  
Elena Fimmel ◽  
Markus Gumbel ◽  
Martin Starman ◽  
Lutz Strüngmann
Keyword(s):  
Genetic Code ◽  
Computational Analysis ◽  
Point Mutations ◽  
Weighted Graph ◽  
Single Nucleotide Variants ◽  
Negative Effects ◽  
Standard Genetic Code ◽  
Single Nucleotide ◽  
Random Code ◽  
Optimal Weights

It is believed that the codon–amino acid assignments of the standard genetic code (SGC) help to minimize the negative effects caused by point mutations. All possible point mutations of the genetic code can be represented as a weighted graph with weights that correspond to the probabilities of these mutations. The robustness of a code against point mutations can be described then by means of the so-called conductance measure. This paper quantifies the wobble effect, which was investigated previously by applying the weighted graph approach, and seeks optimal weights using an evolutionary optimization algorithm to maximize the code’s robustness. One result of our study is that the robustness of the genetic code is least influenced by mutations in the third position—like with the wobble effect. Moreover, the results clearly demonstrate that point mutations in the first, and even more importantly, in the second base of a codon have a very large influence on the robustness of the genetic code. These results were compared to single nucleotide variants (SNV) in coding sequences which support our findings. Additionally, it was analyzed which structure of a genetic code evolves from random code tables when the robustness is maximized. Our calculations show that the resulting code tables are very close to the standard genetic code. In conclusion, the results illustrate that the robustness against point mutations seems to be an important factor in the evolution of the standard genetic code.

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