An Amino Acid-Swapped Genetic Code

Fujino, Tomoshige; Tozaki, Masahiro; Murakami, Hiroshi

doi:10.1021/acssynbio.0c00196

Cited by 15 publications

(16 citation statements)

References 58 publications

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“…In previous studies, ,, tRNAs were enzymatically transcribed using T7 RNA polymerase as those with extra 5′ sequences, followed by the removal of the extra sequences using RNaseP. This processing step is essential because T7 RNA polymerase requires guanine as the first transcription site, , and some tRNAs do not start with guanine.…”

Section: Resultsmentioning

confidence: 99%

“…In Escherichia coli, a set of tRNAs with 41 different anticodons serves this function, although, theoretically, 21 tRNAs are sufficient for encoding the 20 amino acids and formylmethionine. In previous studies, in vitro translation using 21 chemically synthesized or in-vitro-transcribed − tRNA sets has been demonstrated. However, in these studies, tRNAs were synthesized and purified before being used for translation.…”

Section: Introductionmentioning

confidence: 99%

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Transfer RNA Synthesis-Coupled Translation and DNA Replication in a Reconstituted Transcription/Translation System

2022

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Transfer RNAs (tRNAs) are key molecules involved in translation. In vitro synthesis of tRNAs and their coupled translation are important challenges in the construction of a self-regenerative molecular system. Here, we first purified EF-Tu and ribosome components in a reconstituted translation system of Escherichia coli to remove residual tRNAs. Next, we expressed 15 types of tRNAs in the repurified translation system and performed translation of the reporter luciferase gene depending on the expression. Furthermore, we demonstrated DNA replication through expression of a tRNA encoded by DNA, mimicking information processing within the cell. Our findings highlight the feasibility of an in vitro selfreproductive system, in which tRNAs can be synthesized from replicating DNA.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Transfer RNA Synthesis-Coupled Translation and DNA Replication in a Reconstituted Transcription/Translation System

2022

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“…It has been shown that the dynamics of protein phosphorylation at these two amino acid residues can regulate cellular activities in bacteria and eukaryotes [ 53 ]. In addition, the most common mutation pattern was Ser→Leu (42.95%, 95% CI: 22.65~63.25), which was also found in Mycobacterium tuberculosis, influenza virus, or Escherichia coli [ 54 , 55 , 56 ]. Indeed, the mutation feature of Ser→Leu has been demonstrated to significantly reduce the replication and hemagglutinin (HA) cleavage of the H1N2 swine influenza virus and is an influential factor in attenuating viral pathogenicity [ 57 ].…”

Section: Discussionmentioning

confidence: 99%

Drug Resistance (Dapsone, Rifampicin, Ofloxacin) and Resistance-Related Gene Mutation Features in Leprosy Patients: A Systematic Review and Meta-Analysis

Li,

Yang

et al. 2022

IJMS

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Dapsone (DDS), Rifampicin (RIF) and Ofloxacin (OFL) are drugs recommended by the World Health Organization (WHO) for the treatment of leprosy. In the context of leprosy, resistance to these drugs occurs mainly due to mutations in the target genes (Folp1, RpoB and GyrA). It is important to monitor antimicrobial resistance in patients with leprosy. Therefore, we performed a meta-analysis of drug resistance in Mycobacterium leprae and the mutational profile of the target genes. In this paper, we limited the study period to May 2022 and searched PubMed, Web of Science (WOS), Scopus, and Embase databases for identified studies. Two independent reviewers extracted the study data. Mutation and drug-resistance rates were estimated in Stata 16.0. The results demonstrated that the drug-resistance rate was 10.18% (95% CI: 7.85–12.51). Subgroup analysis showed the highest resistance rate was in the Western Pacific region (17.05%, 95% CI:1.80 to 13.78), and it was higher after 2009 than before [(11.39%, 7.46–15.33) vs. 6.59% (3.66–9.53)]. We can conclude that the rate among new cases (7.25%, 95% CI: 4.65–9.84) was lower than the relapsed (14.26%, 95 CI%: 9.82–18.71). Mutation rates of Folp1, RpoB and GyrA were 4.40% (95% CI: 3.02–5.77), 3.66% (95% CI: 2.41–4.90) and 1.28% (95% CI: 0.87–1.71) respectively, while the rate for polygenes mutation was 1.73% (0.83–2.63). For further analysis, we used 368 drug-resistant strains as research subjects and found that codons (Ser, Pro, Ala) on RpoB, Folp1 and GyrA are the most common mutation sites in the determining region (DRDR). In addition, the most common substitution patterns of Folp1, RpoB, and GyrA are Pro→Leu, Ser→Leu, and Ala→Val. This study found that a higher proportion of patients has developed resistance to these drugs, and the rate has increased since 2009, which continue to pose a challenge to clinicians. In addition, the amino acid alterations in the sequence of the DRDR regions and the substitution patterns mentioned in the study also provide new ideas for clinical treatment options.

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“…Although swapping the amino acid identity of sense codons presents a possible way to prevent horizontal gene transfer [23][24][25] , it was impossible to test this hypothesis in vivo until now. To establish a serine TCR -to-leucine swapped genetic code (Figure 3A), we utilized Syn61∆3, which genome-wide lacks annotated instances of TCR codons and their corresponding tRNA genes, and sought to identify tRNAs capable of efficiently translating TCR codons as leucine.…”

Section: Creation Of An Amino-acid-swapped Genetic Codementioning

confidence: 99%

Swapped genetic code blocks viral infections and gene transfer

Nyerges

Vinke

Flynn

et al. 2022

Preprint

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Removing cellular transfer RNAs (tRNAs), making their cognate codons unreadable, creates a genetic firewall that prevents viral replication and horizontal gene transfer. However, numerous viruses and mobile genetic elements encode parts of the translational apparatus, including tRNAs, potentially rendering a genetic-code-based firewall ineffective. In this paper, we show that such horizontally transferred tRNA genes can enable viral replication in Escherichia coli cells despite the genome-wide lack of three codons and the previously essential cognate tRNAs and release factor 1. By repurposing viral tRNAs, we then develop recoded cells bearing an amino-acid-swapped genetic code that reassigns two of the six serine codons to leucine during translation. This amino-acid-swapped genetic code renders cells completely resistant to viral infections by mistranslating viral proteomes and prevents the escape of synthetic genetic information by engineered reliance on serine codons to produce leucine-requiring proteins. Finally, we also repurpose the third free codon to biocontain this virus-resistant host via dependence on an amino acid not found in nature.

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An Amino Acid-Swapped Genetic Code

Cited by 15 publications

References 58 publications

Transfer RNA Synthesis-Coupled Translation and DNA Replication in a Reconstituted Transcription/Translation System

Transfer RNA Synthesis-Coupled Translation and DNA Replication in a Reconstituted Transcription/Translation System

Drug Resistance (Dapsone, Rifampicin, Ofloxacin) and Resistance-Related Gene Mutation Features in Leprosy Patients: A Systematic Review and Meta-Analysis

Swapped genetic code blocks viral infections and gene transfer

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