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Andre R. O. Cavalcanti - One of the best experts on this subject based on the ideXlab platform.
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Tandem stop Codons in ciliates that reassign stop Codons.
Journal of Molecular Evolution, 2009Co-Authors: Marie Adachi, Andre R. O. CavalcantiAbstract:Tandem stop Codons are extra stop Codons hypothesized to be present downstream of genes to act as a backup in case of read-through of the real stop codon. Although seemingly absent from Escherichia coli, recent studies have confirmed the presence of such Codons in yeast. In this paper we will analyze the genomes of two ciliate species—Paramecium tetraurelia and Tetrahymena thermophila—that reassign the stop Codons TAA and TAG to glutamine, for the presence of tandem stop Codons. We show that there are more tandem stop Codons downstream of both Paramecium and Tetrahymena genes than expected by chance given the base composition of the downstream regions. This excess of tandem stop Codons is larger in Tetrahymena and Paramecium than in yeast. We propose that this might be caused by a higher frequency of stop codon read-through in these species than in yeast, possibly because of a leaky termination machinery resulting from stop codon reassignment.
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patterns of codon usage in two ciliates that reassign the genetic code tetrahymena thermophila and paramecium tetraurelia
Protist, 2008Co-Authors: Hannah M W Salim, Karen Ring, Andre R. O. CavalcantiAbstract:We used the recently sequenced genomes of the ciliates Tetrahymena thermophila and Paramecium tetraurelia to analyze the codon usage patterns in both organisms; we have analyzed codon usage bias, Gln codon usage, GC content and the nucleotide contexts of initiation and termination Codons in Tetrahymena and Paramecium. We also studied how these trends change along the length of the genes and in a subset of highly expressed genes. Our results corroborate some of the trends previously described in Tetrahymena, but also negate some specific observations. In both genomes we found a strong bias toward Codons with low GC content; however, in highly expressed genes this bias is smaller and Codons ending in GC tend to be more frequent. We also found that codon bias increases along gene segments and in highly expressed genes and that the context surrounding initiation and termination Codons are always AT rich. Our results also suggest differences in the efficiency of translation of the reassigned stop Codons between the two species and between the reassigned Codons. Finally, we discuss some of the possible causes for such translational efficiency differences.
Daniel L Dunkelmann - One of the best experts on this subject based on the ideXlab platform.
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Total synthesis of Escherichia coli with a recoded genome
Nature, 2019Co-Authors: Julius Fredens, Kaihang Wang, Daniel De La Torre, Louise F H Funke, Wesley E Robertson, Yonka Christova, Tiongsun Chia, Wolfgang H Schmied, Daniel L Dunkelmann, Václav BeránekAbstract:Nature uses 64 Codons to encode the synthesis of proteins from the genome, and chooses 1 sense codon—out of up to 6 synonyms—to encode each amino acid. Synonymous codon choice has diverse and important roles, and many synonymous substitutions are detrimental. Here we demonstrate that the number of Codons used to encode the canonical amino acids can be reduced, through the genome-wide substitution of target Codons by defined synonyms. We create a variant of Escherichia coli with a four-megabase synthetic genome through a high-fidelity convergent total synthesis. Our synthetic genome implements a defined recoding and refactoring scheme—with simple corrections at just seven positions—to replace every known occurrence of two sense Codons and a stop codon in the genome. Thus, we recode 18,214 Codons to create an organism with a 61-codon genome; this organism uses 59 Codons to encode the 20 amino acids, and enables the deletion of a previously essential transfer RNA. High-fidelity convergent total synthesis is used to produce Escherichia coli with a 61-codon synthetic genome that uses 59 Codons to encode all of the canonical amino acids.
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total synthesis of escherichia coli with a recoded genome
Nature, 2019Co-Authors: Julius Fredens, Kaihang Wang, Daniel De La Torre, Louise F H Funke, Wesley E Robertson, Yonka Christova, Tiongsun Chia, Wolfgang H Schmied, Daniel L DunkelmannAbstract:Nature uses 64 Codons to encode the synthesis of proteins from the genome, and chooses 1 sense codon—out of up to 6 synonyms—to encode each amino acid. Synonymous codon choice has diverse and important roles, and many synonymous substitutions are detrimental. Here we demonstrate that the number of Codons used to encode the canonical amino acids can be reduced, through the genome-wide substitution of target Codons by defined synonyms. We create a variant of Escherichia coli with a four-megabase synthetic genome through a high-fidelity convergent total synthesis. Our synthetic genome implements a defined recoding and refactoring scheme—with simple corrections at just seven positions—to replace every known occurrence of two sense Codons and a stop codon in the genome. Thus, we recode 18,214 Codons to create an organism with a 61-codon genome; this organism uses 59 Codons to encode the 20 amino acids, and enables the deletion of a previously essential transfer RNA.
Kaihang Wang - One of the best experts on this subject based on the ideXlab platform.
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Total synthesis of Escherichia coli with a recoded genome
Nature, 2019Co-Authors: Julius Fredens, Kaihang Wang, Daniel De La Torre, Louise F H Funke, Wesley E Robertson, Yonka Christova, Tiongsun Chia, Wolfgang H Schmied, Daniel L Dunkelmann, Václav BeránekAbstract:Nature uses 64 Codons to encode the synthesis of proteins from the genome, and chooses 1 sense codon—out of up to 6 synonyms—to encode each amino acid. Synonymous codon choice has diverse and important roles, and many synonymous substitutions are detrimental. Here we demonstrate that the number of Codons used to encode the canonical amino acids can be reduced, through the genome-wide substitution of target Codons by defined synonyms. We create a variant of Escherichia coli with a four-megabase synthetic genome through a high-fidelity convergent total synthesis. Our synthetic genome implements a defined recoding and refactoring scheme—with simple corrections at just seven positions—to replace every known occurrence of two sense Codons and a stop codon in the genome. Thus, we recode 18,214 Codons to create an organism with a 61-codon genome; this organism uses 59 Codons to encode the 20 amino acids, and enables the deletion of a previously essential transfer RNA. High-fidelity convergent total synthesis is used to produce Escherichia coli with a 61-codon synthetic genome that uses 59 Codons to encode all of the canonical amino acids.
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total synthesis of escherichia coli with a recoded genome
Nature, 2019Co-Authors: Julius Fredens, Kaihang Wang, Daniel De La Torre, Louise F H Funke, Wesley E Robertson, Yonka Christova, Tiongsun Chia, Wolfgang H Schmied, Daniel L DunkelmannAbstract:Nature uses 64 Codons to encode the synthesis of proteins from the genome, and chooses 1 sense codon—out of up to 6 synonyms—to encode each amino acid. Synonymous codon choice has diverse and important roles, and many synonymous substitutions are detrimental. Here we demonstrate that the number of Codons used to encode the canonical amino acids can be reduced, through the genome-wide substitution of target Codons by defined synonyms. We create a variant of Escherichia coli with a four-megabase synthetic genome through a high-fidelity convergent total synthesis. Our synthetic genome implements a defined recoding and refactoring scheme—with simple corrections at just seven positions—to replace every known occurrence of two sense Codons and a stop codon in the genome. Thus, we recode 18,214 Codons to create an organism with a 61-codon genome; this organism uses 59 Codons to encode the 20 amino acids, and enables the deletion of a previously essential transfer RNA.
Julius Fredens - One of the best experts on this subject based on the ideXlab platform.
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Total synthesis of Escherichia coli with a recoded genome
Nature, 2019Co-Authors: Julius Fredens, Kaihang Wang, Daniel De La Torre, Louise F H Funke, Wesley E Robertson, Yonka Christova, Tiongsun Chia, Wolfgang H Schmied, Daniel L Dunkelmann, Václav BeránekAbstract:Nature uses 64 Codons to encode the synthesis of proteins from the genome, and chooses 1 sense codon—out of up to 6 synonyms—to encode each amino acid. Synonymous codon choice has diverse and important roles, and many synonymous substitutions are detrimental. Here we demonstrate that the number of Codons used to encode the canonical amino acids can be reduced, through the genome-wide substitution of target Codons by defined synonyms. We create a variant of Escherichia coli with a four-megabase synthetic genome through a high-fidelity convergent total synthesis. Our synthetic genome implements a defined recoding and refactoring scheme—with simple corrections at just seven positions—to replace every known occurrence of two sense Codons and a stop codon in the genome. Thus, we recode 18,214 Codons to create an organism with a 61-codon genome; this organism uses 59 Codons to encode the 20 amino acids, and enables the deletion of a previously essential transfer RNA. High-fidelity convergent total synthesis is used to produce Escherichia coli with a 61-codon synthetic genome that uses 59 Codons to encode all of the canonical amino acids.
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total synthesis of escherichia coli with a recoded genome
Nature, 2019Co-Authors: Julius Fredens, Kaihang Wang, Daniel De La Torre, Louise F H Funke, Wesley E Robertson, Yonka Christova, Tiongsun Chia, Wolfgang H Schmied, Daniel L DunkelmannAbstract:Nature uses 64 Codons to encode the synthesis of proteins from the genome, and chooses 1 sense codon—out of up to 6 synonyms—to encode each amino acid. Synonymous codon choice has diverse and important roles, and many synonymous substitutions are detrimental. Here we demonstrate that the number of Codons used to encode the canonical amino acids can be reduced, through the genome-wide substitution of target Codons by defined synonyms. We create a variant of Escherichia coli with a four-megabase synthetic genome through a high-fidelity convergent total synthesis. Our synthetic genome implements a defined recoding and refactoring scheme—with simple corrections at just seven positions—to replace every known occurrence of two sense Codons and a stop codon in the genome. Thus, we recode 18,214 Codons to create an organism with a 61-codon genome; this organism uses 59 Codons to encode the 20 amino acids, and enables the deletion of a previously essential transfer RNA.
Václav Beránek - One of the best experts on this subject based on the ideXlab platform.
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Total synthesis of Escherichia coli with a recoded genome
Nature, 2019Co-Authors: Julius Fredens, Kaihang Wang, Daniel De La Torre, Louise F H Funke, Wesley E Robertson, Yonka Christova, Tiongsun Chia, Wolfgang H Schmied, Daniel L Dunkelmann, Václav BeránekAbstract:Nature uses 64 Codons to encode the synthesis of proteins from the genome, and chooses 1 sense codon—out of up to 6 synonyms—to encode each amino acid. Synonymous codon choice has diverse and important roles, and many synonymous substitutions are detrimental. Here we demonstrate that the number of Codons used to encode the canonical amino acids can be reduced, through the genome-wide substitution of target Codons by defined synonyms. We create a variant of Escherichia coli with a four-megabase synthetic genome through a high-fidelity convergent total synthesis. Our synthetic genome implements a defined recoding and refactoring scheme—with simple corrections at just seven positions—to replace every known occurrence of two sense Codons and a stop codon in the genome. Thus, we recode 18,214 Codons to create an organism with a 61-codon genome; this organism uses 59 Codons to encode the 20 amino acids, and enables the deletion of a previously essential transfer RNA. High-fidelity convergent total synthesis is used to produce Escherichia coli with a 61-codon synthetic genome that uses 59 Codons to encode all of the canonical amino acids.