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 The evolutionary history of Saccharomyces species inferred from completed mitochondrial genomes and revision in the ‘yeast mitochondrial genetic code’

DNA Research ◽  
2017 ◽  
Vol 24 (6) ◽  
pp. 571-583 ◽  
Author(s):  
Pavol Sulo ◽  
Dana Szabóová ◽  
Peter Bielik ◽  
Silvia Poláková ◽  
Katarína Šoltys ◽  
...  
Keyword(s):  
Genetic Code ◽  
Evolutionary History ◽  
Mitochondrial Genomes ◽  
Mitochondrial Genetic Code ◽  
History Of

scholarly journals Case for the genetic code as a triplet of triplets

2017 ◽  
Vol 114 (18) ◽  
pp. 4745-4750 ◽  
Author(s):  
Fabienne F. V. Chevance ◽  
Kelly T. Hughes
Keyword(s):  
Genetic Code ◽  
Context Effects ◽  
Synonymous Codon ◽  
Elongation Factor ◽  
Mrna Translation ◽  
Codon Recognition ◽  
Hydrogen Bond Interactions ◽  
Codon Context ◽  
A Site

The efficiency of codon translation in vivo is controlled by many factors, including codon context. At a site early in theSalmonella flgMgene, the effects on translation of replacing codons Thr6 and Pro8 offlgMwith synonymous alternates produced a 600-fold range in FlgM activity. Synonymous changes at Thr6 and Leu9 resulted in a twofold range in FlgM activity. The level of FlgM activity produced by any codon arrangement was directly proportional to the degree of in vivo ribosome stalling at synonymous codons. Synonymous codon suppressors that corrected the effect of a translation-defective synonymousflgMallele were restricted to two codons flanking the translation-defective codon. The various codon arrangements had no apparent effects onflgMmRNA stability or predicted mRNA secondary structures. Our data suggest that efficient mRNA translation is determined by a triplet-of-triplet genetic code. That is, the efficiency of translating a particular codon is influenced by the nature of the immediately adjacent flanking codons. A model explains these codon-context effects by suggesting that codon recognition by elongation factor-bound aminoacyl-tRNA is initiated by hydrogen bond interactions between the first two nucleotides of the codon and anticodon and then is stabilized by base-stacking energy over three successive codons.

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.

Structural Basis for Genetic-Code Expansion with Various Bulky Lysine Derivatives by an Engineered Pyrrolysyl-tRNA Synthetase

2018 ◽  
Author(s):  
Tatsuo Yanagisawa ◽  
Mitsuo Kuratani ◽  
Eiko Seki ◽  
Nobumasa Hino ◽  
Kensaku Sakamoto ◽  
...  
Keyword(s):  
Genetic Code ◽  
Trna Synthetase ◽  
Structural Basis ◽  
Genetic Code Expansion

scholarly journals Transferability of N-terminal mutations of pyrrolysyl-tRNA synthetase in one species to that in another species on unnatural amino acid incorporation efficiency

Amino Acids ◽  
2020 ◽  
Author(s):  
Thomas L. Williams ◽  
Debra J. Iskandar ◽  
Alexander R. Nödling ◽  
Yurong Tan ◽  
Louis Y. P. Luk ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Genetic Code ◽  
Unnatural Amino Acids ◽  
Trna Synthetase ◽  
Unnatural Amino Acid ◽  
Amino Acid Incorporation ◽  
Acid Incorporation ◽  
Genetic Code Expansion ◽  
Incorporation Efficiency

AbstractGenetic code expansion is a powerful technique for site-specific incorporation of an unnatural amino acid into a protein of interest. This technique relies on an orthogonal aminoacyl-tRNA synthetase/tRNA pair and has enabled incorporation of over 100 different unnatural amino acids into ribosomally synthesized proteins in cells. Pyrrolysyl-tRNA synthetase (PylRS) and its cognate tRNA from Methanosarcina species are arguably the most widely used orthogonal pair. Here, we investigated whether beneficial effect in unnatural amino acid incorporation caused by N-terminal mutations in PylRS of one species is transferable to PylRS of another species. It was shown that conserved mutations on the N-terminal domain of MmPylRS improved the unnatural amino acid incorporation efficiency up to five folds. As MbPylRS shares high sequence identity to MmPylRS, and the two homologs are often used interchangeably, we examined incorporation of five unnatural amino acids by four MbPylRS variants at two temperatures. Our results indicate that the beneficial N-terminal mutations in MmPylRS did not improve unnatural amino acid incorporation efficiency by MbPylRS. Knowledge from this work contributes to our understanding of PylRS homologs which are needed to improve the technique of genetic code expansion in the future.

scholarly journals Aminoacylation and translational quality control strategy employed by leucyl-tRNA synthetase from a human pathogen with genetic code ambiguity

2013 ◽  
Vol 41 (21) ◽  
pp. 9825-9838 ◽  
Author(s):  
Xiao-Long Zhou ◽  
Zhi-Peng Fang ◽  
Zhi-Rong Ruan ◽  
Meng Wang ◽  
Ru-Juan Liu ◽  
...  
Keyword(s):  
Quality Control ◽  
Genetic Code ◽  
Control Strategy ◽  
Trna Synthetase ◽  
Human Pathogen ◽  
Code Ambiguity ◽  
Quality Control Strategy

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.

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