scholarly journals Crick Wobble and Superwobble in Standard Genetic Code Evolution

Author(s):  
Michael Yarus

AbstractWobble coding is inevitable during evolution of the Standard Genetic Code (SGC). It ultimately splits half of NN U/C/A/G coding boxes with different assignments. Further, it contributes to pervasive SGC order by reinforcing close spacing for identical SGC assignments. But wobble cannot appear too soon, or it will inhibit encoding and more decisively, obstruct evolution of full coding tables. However, these prior results assumed Crick wobble, NN U/C and NN A/G, read by a single adaptor RNA. Superwobble translates NN U/C/A/G codons, using one adaptor RNA with an unmodified 5′ anticodon U (appropriate to earliest coding) in modern mitochondria, plastids, and mycoplasma. Assuming the SGC was selected when evolving codes most resembled it, characteristics of the critical selection events can be calculated. For example, continuous superwobble infrequently evolves SGC-like coding tables. So, continuous superwobble is a very improbable origin hypothesis. In contrast, late-arising superwobble shares late Crick wobble’s frequent resemblance to SGC order. Thus late superwobble is possible, but yields SGC-like assignments less frequently than late Crick wobble. Ancient coding ambiguity, most simply, arose from Crick wobble alone. This is consistent with SGC assignments to NAN codons.

2020 ◽  
Author(s):  
Kuba Nowak ◽  
Paweł Błażej ◽  
Małgorzata Wnetrzak ◽  
Dorota Mackiewicz ◽  
Paweł Mackiewicz

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.


PLoS ONE ◽  
2018 ◽  
Vol 13 (10) ◽  
pp. e0205450 ◽  
Author(s):  
Paweł Błażej ◽  
Małgorzata Wnętrzak ◽  
Dorota Mackiewicz ◽  
Paweł Mackiewicz

PLoS ONE ◽  
2018 ◽  
Vol 13 (8) ◽  
pp. e0201715 ◽  
Author(s):  
Paweł Błażej ◽  
Małgorzata Wnętrzak ◽  
Dorota Mackiewicz ◽  
Paweł Mackiewicz

Life ◽  
2021 ◽  
Vol 11 (12) ◽  
pp. 1338
Author(s):  
Elena Fimmel ◽  
Markus Gumbel ◽  
Martin Starman ◽  
Lutz Strüngmann

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.


2017 ◽  
Author(s):  
Miloje M. Rakocevic

In previous two works [1], [2] 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.


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