ArticleBMC genomics2008
RNomics and Modomics in the halophilic archaea Haloferax volcanii: identification of RNA modification genes.
Article in BMC genomics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 57 papers.
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Who cites it
57 citing papers in PubMed, 82 citations in OpenAlex.
- Structural basis of nucleotide-dependent conformational switching of a CBS-family protein on the archaeal 50S ribosome.Science China. Life sciences · 2026Article
- OTTR-seq profiling reveals dynamic tRNA modification landscapes across diverse archaeal species.Genome biology · 2026Article
- Update of the Methyltransferase Gene Family: Classification, Evolution and Biological Functions.Human genomics · 2026Review
- The Landscape of tRNA Modifications in Archaea.bioRxiv : the preprint server for biology · 2025Article
- Review
- Structural insight into the novel Thermus thermophilus SPOUT methyltransferase RlmR catalysing Um2552 formation in the 23S rRNA A-loop: a case of convergent evolution.Nucleic acids research · 2025Article
- Comprehensive nucleoside analysis of archaeal RNA modification profiles reveals an mCell reports · 2025Article
- The Ptch/SPOUT1 methyltransferase deposits an mScience advances · 2024Article
- Landscape of RNA pseudouridylation in archaeon Sulfolobus islandicus.Nucleic acids research · 2024Article
- Detection of ac4C in human mRNA is preserved upon data reassessment.Molecular cell · 2024Article
- Plant ribosomes as a score to fathom the melody of 2'-RNA biology · 2024Review
- Human TRMT1 catalyzes mScience China. Life sciences · 2023Article
- Nanopore-based RNA sequencing deciphers the formation, processing, and modification steps of rRNA intermediates in archaea.RNA (New York, N.Y.) · 2023Article
- Identification of URNA (New York, N.Y.) · 2023Article
- "Superwobbling" and tRNA-34 Wobble and tRNA-37 Anticodon Loop Modifications in Evolution and Devolution of the Genetic Code.Life (Basel, Switzerland) · 2022Review
- A Comparative Perspective on Ribosome Biogenesis: Unity and Diversity Across the Tree of Life.Methods in molecular biology (Clifton, N.J.) · 2022Review
- Adaptor Molecules Epitranscriptome Reprograms Bacterial Pathogenicity.International journal of molecular sciences · 2021Review
- A comprehensive review of m6A/m6Am RNA methyltransferase structures.Nucleic acids research · 2021Review
- Insights into synthesis and function of KsgA/Dim1-dependent rRNA modifications in archaea.Nucleic acids research · 2021Article
- Review
Corrections and comments
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Authors and funding
5 authors at 4 institutions in 2 countries.
Funding
Abstract
backgroundNaturally occurring RNAs contain numerous enzymatically altered nucleosides. Differences in RNA populations (RNomics) and pattern of RNA modifications (Modomics) depends on the organism analyzed and are two of the criteria that distinguish the three kingdoms of life. If the genomic sequences of the RNA molecules can be derived from whole genome sequence information, the modification profile cannot and requires or direct sequencing of the RNAs or predictive methods base on the presence or absence of the modifications genes.
resultsBy employing a comparative genomics approach, we predicted almost all of the genes coding for the t+rRNA modification enzymes in the mesophilic moderate halophile Haloferax volcanii. These encode both guide RNAs and enzymes. Some are orthologous to previously identified genes in Archaea, Bacteria or in Saccharomyces cerevisiae, but several are original predictions.
conclusionThe number of modifications in t+rRNAs in the halophilic archaeon is surprisingly low when compared with other Archaea or Bacteria, particularly the hyperthermophilic organisms. This may result from the specific lifestyle of halophiles that require high intracellular salt concentration for survival. This salt content could allow RNA to maintain its functional structural integrity with fewer modifications. We predict that the few modifications present must be particularly important for decoding, accuracy of translation or are modifications that cannot be functionally replaced by the electrostatic interactions provided by the surrounding salt-ions. This analysis also guides future experimental validation work aiming to complete the understanding of the function of RNA modifications in Archaeal translation.
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