Codon reassignment (codon capture) in evolution

1989 ◽  
Vol 28 (4) ◽  
pp. 271-278 ◽  
Author(s):  
Syozo Osawa ◽  
Thomas H. Jukes
Keyword(s):  
Codon Reassignment ◽  
Codon Capture

scholarly journals A novel nuclear genetic code alteration in yeasts and the evolution of codon reassignment in eukaryotes

2016 ◽  
Author(s):  
Stefanie Mühlhausen ◽  
Peggy Findeisen ◽  
Uwe Plessmann ◽  
Henning Urlaub ◽  
Martin Kollmar
Keyword(s):  
Genetic Code ◽  
Trna Synthetase ◽  
Amino Acid Sequences ◽  
Codon Reassignment ◽  
Proteomics Data ◽  
Pachysolen Tannophilus ◽  
Sequence Comparisons ◽  
Codon Capture ◽  
Cellular Translation ◽  
Sense Codon

AbstractThe genetic code is the universal cellular translation table to convert nucleotide into amino acid sequences. Changes to sense codons are expected to be highly detrimental. However, reassignments of single or multiple codons in mitochondria and nuclear genomes demonstrated that the code can evolve. Still, alterations of nuclear genetic codes are extremely rare leaving hypotheses to explain these variations, such as the ‘codon capture’, the ‘genome streamlining’ and the ‘ambiguous intermediate’ theory, in strong debate. Here, we report on a novel sense codon reassignment inPachysolen tannophilus, a yeast related to the Pichiaceae. By generating proteomics data and using tRNA sequence comparisons we show that inPachysolenCUG codons are translated as alanine and not as the universal leucine. The polyphyly of the CUG-decoding tRNAs in yeasts is best explained by atRNA loss driven codon reassignmentmechanism. Loss of the CUG-tRNA in the ancient yeast is followed by gradual decrease of respective codons and subsequent codon capture by tRNAs whose anticodon is outside the aminoacyl-tRNA synthetase recognition region. Our hypothesis applies to all nuclear genetic code alterations and provides several testable predictions. We anticipate more codon reassignments to be uncovered in existing and upcoming genome projects.

scholarly journals Sense codon reassignment enables viral resistance and encoded polymer synthesis

Science ◽  
2021 ◽  
Vol 372 (6546) ◽  
pp. 1057-1062
Author(s):  
Wesley E. Robertson ◽  
Louise F. H. Funke ◽  
Daniel de la Torre ◽  
Julius Fredens ◽  
Thomas S. Elliott ◽  
...  
Keyword(s):  
Stop Codon ◽  
Synonymous Codon ◽  
Viral Resistance ◽  
Release Factor ◽  
Codon Reassignment ◽  
Efficient Synthesis ◽  
Noncanonical Amino Acids ◽  
Laboratory Evolution ◽  
Transfer Rnas ◽  
Sense Codon

It is widely hypothesized that removing cellular transfer RNAs (tRNAs)—making their cognate codons unreadable—might create a genetic firewall to viral infection and enable sense codon reassignment. However, it has been impossible to test these hypotheses. In this work, following synonymous codon compression and laboratory evolution in Escherichia coli, we deleted the tRNAs and release factor 1, which normally decode two sense codons and a stop codon; the resulting cells could not read the canonical genetic code and were completely resistant to a cocktail of viruses. We reassigned these codons to enable the efficient synthesis of proteins containing three distinct noncanonical amino acids. Notably, we demonstrate the facile reprogramming of our cells for the encoded translation of diverse noncanonical heteropolymers and macrocycles.

The evolution of CUG codon reassignment in Candida albicans

2000 ◽  
Vol 28 (5) ◽  
pp. A186-A186
Author(s):  
J. M. O'sullivan ◽  
E. Chukeatirote ◽  
S. Massey ◽  
B. Davenport ◽  
P. J. Brown ◽  
...  
Keyword(s):  
Candida Albicans ◽  
Codon Reassignment

Codon reassignment in Candida species: An evolutionary conundrum

Biochimie ◽  
1996 ◽  
Vol 78 (11-12) ◽  
pp. 993-999 ◽  
Author(s):  
M.F. Tuite ◽  
M.A.S. Santos
Keyword(s):  
Candida Species ◽  
Codon Reassignment

scholarly journals Dissecting the Contribution of Release Factor Interactions to Amber Stop Codon Reassignment Efficiencies of the Methanocaldococcus jannaschii Orthogonal Pair

Genes ◽  
2018 ◽  
Vol 9 (11) ◽  
pp. 546 ◽  
Author(s):  
David Schwark ◽  
Margaret Schmitt ◽  
John Fisk
Keyword(s):  
Stop Codon ◽  
Release Factor ◽  
Codon Reassignment ◽  
Methanocaldococcus Jannaschii ◽  
E Coli ◽  
Amber Stop Codon ◽  
Orthogonal Pair ◽  
Amber Codon ◽  
Quantitative Contribution ◽  
Stop Codon Reassignment

Non-canonical amino acids (ncAAs) are finding increasing use in basic biochemical studies and biomedical applications. The efficiency of ncAA incorporation is highly variable, as a result of competing system composition and codon context effects. The relative quantitative contribution of the multiple factors affecting incorporation efficiency are largely unknown. This manuscript describes the use of green fluorescent protein (GFP) reporters to quantify the efficiency of amber codon reassignment using the Methanocaldococcus jannaschii orthogonal pair system, commonly employed for ncAA incorporation, and quantify the contribution of release factor 1 (RF1) to the overall efficiency of amino acid incorporation. The efficiencies of amber codon reassignments were quantified at eight positions in GFP and evaluated in multiple combinations. The quantitative contribution of RF1 competition to reassignment efficiency was evaluated through comparisons of amber codon suppression efficiencies in normal and genomically recoded Escherichia coli strains. Measured amber stop codon reassignment efficiencies for eight single stop codon GFP variants ranged from 51 to 117% in E. coli DH10B and 76 to 104% in the RF1 deleted E. coli C321.ΔA.exp. Evaluation of efficiency changes in specific sequence contexts in the presence and absence of RF1 suggested that RF1 specifically interacts with +4 Cs and that the RF1 interactions contributed approximately half of the observed sequence context-dependent variation in measured reassignment efficiency. Evaluation of multisite suppression efficiencies suggests that increasing demand for translation system components limits multisite incorporation in cells with competing RF1.

scholarly journals Trans-Species Polymorphism in Mitochondrial Genome of Camarodont Sea Urchins

Genes ◽  
2019 ◽  
Vol 10 (8) ◽  
pp. 592
Author(s):  
Evgeniy S. Balakirev
Keyword(s):  
Sea Urchins ◽  
Stop Codon ◽  
Global Ocean ◽  
Abrupt Climate Change ◽  
Local Alignment ◽  
Codon Reassignment ◽  
Length Difference ◽  
Search Tool ◽  
Alternative Hypotheses ◽  
Mesocentrotus Nudus

Mitochondrial (mt) genomes of the sea urchins Strongylocentrotus intermedius and Mesocentrotus nudus demonstrate the identical patterns of intraspecific length variability of the ND6 gene, consisting of 489 bp (S variant) and 498 bp (L variant), respectively. For both species, the ND6 length difference is due to the 488A>G substitution, which changes the stop codon TAG in S variant for a tryptophan codon TGG in L variant and elongates the corresponding ND6 protein by three additional amino acids, Trp-Leu-Trp. The phylogenetic analysis based on mt genomes of sea urchins and related echinoderm groups from GenBank has shown the S and L ND6 variants as shared among the camarodont sea urchins; the rest of the echinoderms demonstrate the S variant only. The data suggest that the ND6 488A>G substitution can be the first example of the trans-species polymorphism in sea urchins, persisting at least since the time of the Odontophora diversification at the Eocene/Oligocene boundary (approximately 34 million years ago), which was characterized by an abrupt climate change and significant global ocean cooling. Alternative hypotheses, including the convergent RNA editing and/or codon reassignment, are not supported by direct comparisons of the ND6 gene sequences with the corresponding transcripts using the basic local alignment search tool (BLAST) of full sea urchin transcriptomes.

Toward the experimental codon reassignment in vivo : protein building with an expanded amino acid repertoire

1999 ◽  
Vol 13 (1) ◽  
pp. 41-51 ◽  
Author(s):  
NEDILJKO BUDISA ◽  
CAROLINE MINKS ◽  
STEFAN ALEFELDER ◽  
WALTRAUD WENGER ◽  
FUMIN DONG ◽  
...  
Keyword(s):  
Amino Acid ◽  
Codon Reassignment

scholarly journals The Distinction Between Recoding and Codon Reassignment: Figure 1.—

Genetics ◽  
2010 ◽  
Vol 185 (4) ◽  
pp. 1535-1536 ◽  
Author(s):  
John F. Atkins ◽  
Pavel V. Baranov
Keyword(s):  
Codon Reassignment
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