scholarly journals Evolution and Unprecedented Variants of the Mitochondrial Genetic Code in a Lineage of Green Algae

2019 ◽  
Vol 11 (10) ◽  
pp. 2992-3007 ◽  
Author(s):  
David Žihala ◽  
Marek Eliáš
Keyword(s):  
Genetic Code ◽  
Protein Sequences ◽  
Dynamic Evolution ◽  
Translation System ◽  
Release Factor ◽  
Standard Genetic Code ◽  
Green Algal ◽  
Mitochondrial Genetic Code ◽  
Species Analysis ◽  
Direct Support

Abstract Mitochondria of diverse eukaryotes have evolved various departures from the standard genetic code, but the breadth of possible modifications and their phylogenetic distribution are known only incompletely. Furthermore, it is possible that some codon reassignments in previously sequenced mitogenomes have been missed, resulting in inaccurate protein sequences in databases. Here we show, considering the distribution of codons at conserved amino acid positions in mitogenome-encoded proteins, that mitochondria of the green algal order Sphaeropleales exhibit a diversity of codon reassignments, including previously missed ones and some that are unprecedented in any translation system examined so far, necessitating redefinition of existing translation tables and creating at least seven new ones. We resolve a previous controversy concerning the meaning the UAG codon in Hydrodictyaceae, which beyond any doubt encodes alanine. We further demonstrate that AGG, sometimes together with AGA, encodes alanine instead of arginine in diverse sphaeroplealeans. Further newly detected changes include Arg-to-Met reassignment of the AGG codon and Arg-to-Leu reassignment of the CGG codon in particular species. Analysis of tRNAs specified by sphaeroplealean mitogenomes provides direct support for and molecular underpinning of the proposed reassignments. Furthermore, we point to unique mutations in the mitochondrial release factor mtRF1a that correlate with changes in the use of termination codons in Sphaeropleales, including the two independent stop-to-sense UAG reassignments, the reintroduction of UGA in some Scenedesmaceae, and the sense-to-stop reassignment of UCA widespread in the group. Codon disappearance seems to be the main drive of the dynamic evolution of the mitochondrial genetic code in Sphaeropleales.

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 Frameshifts and wild-type protein sequences are always highly similar because the genetic code is optimal for frameshift tolerance

2016 ◽  
Author(s):  
Xiaolong Wang ◽  
Quanjiang Dong ◽  
Gang Chen ◽  
Jianye Zhang ◽  
Yongqiang Liu ◽  
...  
Keyword(s):  
Amino Acid ◽  
Genetic Code ◽  
Protein Sequences ◽  
Loss Of Function ◽  
Wild Type ◽  
Standard Genetic Code ◽  
Type Protein ◽  
Wild Type Protein ◽  
Codon Pairs ◽  
Reading Frames

AbstractFrameshift mutation yields truncated, dysfunctional product proteins, leading to loss-of-function, genetic disorders or even death. Frameshift mutations have been considered as mostly harmful and of little importance for the molecular evolution of proteins. Frameshift protein sequences, encoded by the alternative reading frames of a coding gene, have been therefore considered as meaningless. However, existing studies had shown that frameshift genes/proteins are widely existing and sometimes functional. It is puzzling how a frameshift kept its structure and functionality while its amino-acid sequence is changed substantially. Here we demonstrate that the protein sequences of the frameshifts are highly conservative when compared with the wild-type protein sequence, and the similarities among the three protein sequences encoded in the three reading frames of a coding gene are defined mainly by the genetic code. In the standard genetic code, amino acid substitutions assigned to frameshift codon substitutions are far more conservative than those assigned to random substitutions. The frameshift tolerability of the standard genetic code ranks in the top 1.0-5.0% of all possible genetic codes, showing that the genetic code is optimal in terms of frameshift tolerance. In some higher species, the shiftability is further optimized at gene- or genome-level by a biased usage of codons and codon pairs, in which frameshift-tolerable codons/codon pairs are overrepresented in their genomes.

scholarly journals Rapid Genetic Code Evolution in Green Algal Mitochondrial Genomes

2019 ◽  
Vol 36 (4) ◽  
pp. 766-783 ◽  
Author(s):  
Emmanuel Noutahi ◽  
Virginie Calderon ◽  
Mathieu Blanchette ◽  
Nadia El-Mabrouk ◽  
Bernd Franz Lang
Keyword(s):  
Genetic Code ◽  
Synonymous Codon ◽  
Trna Synthetase ◽  
Mitochondrial Genomes ◽  
Green Plants ◽  
Codon Recognition ◽  
Green Algal ◽  
Mitochondrial Genetic Code ◽  
Depth Study ◽  
Gene Duplication And Loss

AbstractGenetic code deviations involving stop codons have been previously reported in mitochondrial genomes of several green plants (Viridiplantae), most notably chlorophyte algae (Chlorophyta). However, as changes in codon recognition from one amino acid to another are more difficult to infer, such changes might have gone unnoticed in particular lineages with high evolutionary rates that are otherwise prone to codon reassignments. To gain further insight into the evolution of the mitochondrial genetic code in green plants, we have conducted an in-depth study across mtDNAs from 51 green plants (32 chlorophytes and 19 streptophytes). Besides confirming known stop-to-sense reassignments, our study documents the first cases of sense-to-sense codon reassignments in Chlorophyta mtDNAs. In several Sphaeropleales, we report the decoding of AGG codons (normally arginine) as alanine, by tRNA(CCU) of various origins that carry the recognition signature for alanine tRNA synthetase. In Chromochloris, we identify tRNA variants decoding AGG as methionine and the synonymous codon CGG as leucine. Finally, we find strong evidence supporting the decoding of AUA codons (normally isoleucine) as methionine in Pycnococcus. Our results rely on a recently developed conceptual framework (CoreTracker) that predicts codon reassignments based on the disparity between DNA sequence (codons) and the derived protein sequence. These predictions are then validated by an evaluation of tRNA phylogeny, to identify the evolution of new tRNAs via gene duplication and loss, and structural modifications that lead to the assignment of new tRNA identities and a change in the genetic code.

scholarly journals Mitogenomes Reveal Alternative Initiation Codons and Lineage-Specific Gene Order Conservation in Echinoderms

2020 ◽  
Author(s):  
Zheng Bin Randolph Quek ◽  
Jia Jin Marc Chang ◽  
Yin Cheong Aden Ip ◽  
Yong Kit Samuel Chan ◽  
Danwei Huang
Keyword(s):  
Genetic Code ◽  
Gene Order ◽  
Mitochondrial Genes ◽  
Specific Gene ◽  
Standard Genetic Code ◽  
Mitochondrial Genetic Code ◽  
Gene Order Conservation ◽  
Mitochondrial Code ◽  
Lineage Specific Gene

Abstract The mitochondrial genetic code is much more varied than the standard genetic code. The invertebrate mitochondrial code, for instance, comprises six initiation codons, including five alternative start codons. However, only two initiation codons are known in the echinoderm and flatworm mitochondrial code, the canonical ATG and alternative GTG. Here, we analyzed 23 Asteroidea mitogenomes, including ten newly sequenced species and unambiguously identified at least two other start codons, ATT and ATC, both of which also initiate translation of mitochondrial genes in other invertebrates. These findings underscore the diversity of the genetic code and expand upon the suite of initiation codons among echinoderms to avoid erroneous annotations. Our analyses have also uncovered the remarkable conservation of gene order among asteroids, echinoids, and holothuroids, with only an interchange between two gene positions in asteroids over ∼500 Ma of echinoderm evolution.

scholarly journals Isolation of a rat mitochondrial release factor. Accommodation of the changed genetic code for termination.

1987 ◽  
Vol 262 (8) ◽  
pp. 3548-3552
Author(s):  
C.C. Lee ◽  
K.M. Timms ◽  
C.N. Trotman ◽  
W.P. Tate
Keyword(s):  
Genetic Code ◽  
Release Factor

scholarly journals Widespread use of the “ascidian” mitochondrial genetic code in tunicates

F1000Research ◽  
2020 ◽  
Vol 8 ◽  
pp. 2072
Author(s):  
Julien Pichon ◽  
Nicholas M. Luscombe ◽  
Charles Plessy
Keyword(s):  
Genetic Code ◽  
Stop Codon ◽  
Mitochondrial Protein ◽  
Sequence Alignments ◽  
Additional Species ◽  
Multiple Sequence ◽  
Oikopleura Dioica ◽  
Mitochondrial Genetic Code ◽  
Mitochondrial Sequences ◽  
Mitochondrial Code

Background: Ascidians, a tunicate class, use a mitochondrial genetic code that is distinct from vertebrates and other invertebrates. Though it has been used to translate the coding sequences from other tunicate species on a case-by-case basis, it is has not been investigated whether this can be done systematically. This is an important because a) some tunicate mitochondrial sequences are currently translated with the invertebrate code by repositories such as NCBI GenBank, and b) uncertainties about the genetic code to use can complicate or introduce errors in phylogenetic studies based on translated mitochondrial protein sequences. Methods: We collected publicly available nucleotide sequences for non-ascidian tunicates including appendicularians such as Oikopleura dioica, translated them using the ascidian mitochondrial code, and built multiple sequence alignments covering all tunicate classes. Results: All tunicates studied here appear to translate AGR codons to glycine instead of serine (invertebrates) or as a stop codon (vertebrates), as initially described in ascidians. Among Oikopleuridae, we suggest further possible changes in the use of the ATA (Ile → Met) and TGA (Trp → Arg) codons. Conclusions: We recommend using the ascidian mitochondrial code in automatic translation pipelines of mitochondrial sequences for all tunicates. Further investigation is required for additional species-specific differences.

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.

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