ArticleArchaea (Vancouver, B.C.)2014
Unique characteristics of the pyrrolysine system in the 7th order of methanogens: implications for the evolution of a genetic code expansion cassette.
Article in Archaea (Vancouver, B.C.), 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 50 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
50 citing papers in PubMed, 76 citations in OpenAlex.
- Directed evolution of aminoacyl-tRNA synthetases through in vivo hypermutation.Nature communications · 2025Article
- Pyrrolysine Aminoacyl-tRNA Synthetase as a Tool for Expanding the Genetic Code.International journal of molecular sciences · 2025Review
- Efficient suppression of premature termination codons with alanine by engineered chimeric pyrrolysine tRNAs.Nucleic acids research · 2024Article
- Engineering Pyrrolysine Systems for Genetic Code Expansion and Reprogramming.Chemical reviews · 2024Review
- Evolution of Pyrrolysyl-tRNA Synthetase: From Methanogenesis to Genetic Code Expansion.Chemical reviews · 2024Review
- Navigating the archaeal frontier: insights and projections from bioinformatic pipelines.Frontiers in microbiology · 2024Article
- Article
- Evolution of termination codons of proteins and the TAG-TGA paradox.Scientific reports · 2023Article
- Quintuply orthogonal pyrrolysyl-tRNA synthetase/tRNANature chemistry · 2023Article
- Site-specific dual encoding and labeling of proteins via genetic code expansion.Cell chemical biology · 2023Review
- Update of the Pyrrolysyl-tRNA Synthetase/tRNAJournal of bacteriology · 2023Review
- The evolving role of methanogenic archaea in mammalian microbiomes.Frontiers in microbiology · 2023Review
- Ancestral archaea expanded the genetic code with pyrrolysine.The Journal of biological chemistry · 2022Article
- Reconsidering the in vivo functions of Clostridial Stickland amino acid fermentations.Anaerobe · 2022Review
- Unconventional genetic code systems in archaea.Frontiers in microbiology · 2022Review
- Review
- Reprogramming the genetic code.Nature reviews. Genetics · 2021Review
- Directed Evolution of theInternational journal of molecular sciences · 2021Article
- New Insights into the Ecology and Physiology ofMicroorganisms · 2020Article
- Article
Corrections and comments
- Erratum issued
Authors and funding
6 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Pyrrolysine (Pyl), the 22nd proteogenic amino acid, was restricted until recently to few organisms. Its translational use necessitates the presence of enzymes for synthesizing it from lysine, a dedicated amber stop codon suppressor tRNA, and a specific amino-acyl tRNA synthetase. The three genomes of the recently proposed Thermoplasmata-related 7th order of methanogens contain the complete genetic set for Pyl synthesis and its translational use. Here, we have analyzed the genomic features of the Pyl-coding system in these three genomes with those previously known from Bacteria and Archaea and analyzed the phylogeny of each component. This shows unique peculiarities, notably an amber tRNA(Pyl) with an imperfect anticodon stem and a shortened tRNA(Pyl) synthetase. Phylogenetic analysis indicates that a Pyl-coding system was present in the ancestor of the seventh order of methanogens and appears more closely related to Bacteria than to Methanosarcinaceae, suggesting the involvement of lateral gene transfer in the spreading of pyrrolysine between the two prokaryotic domains. We propose that the Pyl-coding system likely emerged once in Archaea, in a hydrogenotrophic and methanol-H2-dependent methylotrophic methanogen. The close relationship between methanogenesis and the Pyl system provides a possible example of expansion of a still evolving genetic code, shaped by metabolic requirements.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.