ArticleGenome biology2011
Discovery of permuted and recently split transfer RNAs in Archaea.
Article in Genome biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed, 62 citations in OpenAlex.
- From water to land: evolution of tRNA gene repertoires in photosynthetic organisms.The EMBO journal · 2026Review
- Archaeal RNA processing and regulation: expanding the functional landscape.Microbiology and molecular biology reviews : MMBR · 2025Review
- Structural basis of substrate diversity and functional evolution of archaeal RNA-splicing endonucleases.Nucleic acids research · 2025Article
- tRNAscan-SE 2.0: improved detection and functional classification of transfer RNA genes.Nucleic acids research · 2021Article
- Phylogeny and evolution of chloroplast tRNAs in Adoxaceae.Ecology and evolution · 2021Article
- Recent Insights Into the Structure, Function, and Evolution of the RNA-Splicing Endonucleases.Frontiers in genetics · 2019Review
- Structural Basis for tRNA Mimicry by a Bacterial Y RNA.Structure (London, England : 1993) · 2018Article
- Dimerization confers increased stability to nucleases in 5' halves from glycine and glutamic acid tRNAs.Nucleic acids research · 2018Article
- The RNA-splicing endonuclease from the euryarchaeaon Methanopyrus kandleri is a heterotetramer with constrained substrate specificity.Nucleic acids research · 2018Article
- Intercompartmental Piecewise Gene Transfer.Genes · 2017Review
- Binding Properties of Split tRNA to the C-terminal Domain of Methionyl-tRNA Synthetase of Nanoarchaeum equitans.Journal of molecular evolution · 2017Article
- Novel Genomic and Evolutionary Perspective of Cyanobacterial tRNAs.Frontiers in genetics · 2017Article
- AccessFold: predicting RNA-RNA interactions with consideration for competing self-structure.Bioinformatics (Oxford, England) · 2016Article
- Evolutionary Insights into RNA trans-Splicing in Vertebrates.Genome biology and evolution · 2016Review
- A Comprehensive tRNA Genomic Survey Unravels the Evolutionary History of tRNA Arrays in Prokaryotes.Genome biology and evolution · 2015Article
- Pyrobaculum yellowstonensis Strain WP30 Respires on Elemental Sulfur and/or Arsenate in Circumneutral Sulfidic Geothermal Sediments of Yellowstone National Park.Applied and environmental microbiology · 2015Article
- Precise mapping and dynamics of tRNA-derived fragments (tRFs) in the development of Triops cancriformis (tadpole shrimp).BMC genetics · 2015Article
- Disrupted tRNA Genes and tRNA Fragments: A Perspective on tRNA Gene Evolution.Life (Basel, Switzerland) · 2015Review
- Experimental confirmation of a whole set of tRNA molecules in two archaeal species.International journal of molecular sciences · 2015Article
- Capture, Unfolding, and Detection of Individual tRNA Molecules Using a Nanopore Device.Frontiers in bioengineering and biotechnology · 2015Article
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
backgroundAs in eukaryotes, precursor transfer RNAs in Archaea often contain introns that are removed in tRNA maturation. Two unrelated archaeal species display unique pre-tRNA processing complexity in the form of split tRNA genes, in which two to three segments of tRNAs are transcribed from different loci, then trans-spliced to form a mature tRNA. Another rare type of pre-tRNA, found only in eukaryotic algae, is permuted, where the 3' half is encoded upstream of the 5' half, and must be processed to be functional.
resultsUsing an improved version of the gene-finding program tRNAscan-SE, comparative analyses and experimental verifications, we have now identified four novel trans-spliced tRNA genes, each in a different species of the Desulfurococcales branch of the Archaea: tRNA(Asp(GUC)) in Aeropyrum pernix and Thermosphaera aggregans, and tRNA(Lys(CUU)) in Staphylothermus hellenicus and Staphylothermus marinus. Each of these includes features surprisingly similar to previously studied split tRNAs, yet comparative genomic context analysis and phylogenetic distribution suggest several independent, relatively recent splitting events. Additionally, we identified the first examples of permuted tRNA genes in Archaea: tRNA(iMet(CAU)) and tRNA(Tyr(GUA)) in Thermofilum pendens, which appear to be permuted in the same arrangement seen previously in red alga.
conclusionsOur findings illustrate that split tRNAs are sporadically spread across a major branch of the Archaea, and that permuted tRNAs are a new shared characteristic between archaeal and eukaryotic species. The split tRNA discoveries also provide new clues to their evolutionary history, supporting hypotheses for recent acquisition via viral or other mobile elements.
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