We are analyzing https://link.springer.com/article/10.1186/1471-2164-9-470.

Title:
RNomics and Modomics in the halophilic archaea Haloferax volcanii: identification of RNA modification genes | BMC Genomics
Description:
Background Naturally 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. Results By 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. Conclusion The 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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Keywords {🔍}

google, scholar, pubmed, rna, cas, trna, volcanii, modification, rrna, modified, trnas, position, genes, coli, found, archaea, modifications, archaeal, structure, formation, acids, ribosomal, figure, analysis, positions, nucleic, res, enzymes, family, additional, table, nucleotides, biol, present, sequence, identified, cog, box, genome, ribosome, mol, anticodon, file, conserved, grosjean, srna, sequences, guide, decoding, yeast,

Topics {✒️}

valérie de crécy-lagard copurified s-adenosyl-l-homocysteine uk/cgi-bin/plant_snorna/home s-adenosyl-l-methionine ssu cell-free protein-synthesizing system discussion post-transcriptional modification cis-acting archaeal pre-trnatrp post-transcriptional modification mapping single post-transcriptional modification université de paris-sud chemin de borde-rouge l-shaped spatial conformation de crécy-lagard de crécy lagard post-transcriptional nucleotide modification open access article ferre-d'amare ar canonical l-shaped conformation article download pdf clouet-d'orval single-gene knockout mutants signature search tool peptidyl transferase center universal pyrimidine t8/c8 christine gaspin s-adenosylmethionine-dependent methyltransferase fact post-transcriptionally deaminated complementary watson-crick counterpart author information authors full size image trna-sel/sec coding closely phylogenetically related o'farrell hc e-site trnas sit post-transcriptional modification comprehensive multi-species collection atp-dependent tils family ancient c5-methylated enzyme forming rna-rna interactions archaeal pre-trnatrp nucleotides cbf5p/nop10p dependent complex peptidyl transferase centre multi-site specific enzyme p-site-bound trna schematic 3d-architecture model minor base n4-acetylcytidine /snornadb/archaea/pyro-annote p-site trnas sit post-transcriptional modifications rna-guided rna modification

Questions {❓}

However for tRNA-Leu (?
Lafontaine DLJ, Preiss T, Tollervey D: Yeast 18S rRNA dimethylase Dim1p: a quality control mechanism in ribosome synthesis?
Edu/cgi-bin/hgTracks?
Uk/interpro/IEntry?
Volcanii genome suggests that ?
Volcanii tRNA-Leu (UAA) was reported not to be modified, while the U-34 residue in tRNA-Leu (?

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WebPage:
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         headline:RNomics and Modomics in the halophilic archaea Haloferax volcanii: identification of RNA modification genes
         description:Naturally 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. By 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. The 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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      headline:RNomics and Modomics in the halophilic archaea Haloferax volcanii: identification of RNA modification genes
      description:Naturally 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. By 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. The 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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         Modify Nucleotide
         Peptidyl Transferase Center
         Modify Nucleoside
         Wobble Position
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         Life Sciences
         general
         Microarrays
         Proteomics
         Animal Genetics and Genomics
         Microbial Genetics and Genomics
         Plant Genetics and Genomics
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            address:
               name:IGM, Université de Paris-sud, Orsay, France
               type:PostalAddress
            type:Organization
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            address:
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      affiliation:
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      name:Institut de Biologie et de Technologies de Saclay (iBiTecS), Commissariat à l'Energie Atomique (CEA), Gif sur Yvette, France
      name:Department of Biochemistry and Molecular Biology, University of Massachussets, Amerherst, USA
      name:Department of Microbiology and Department of Microbiology and Cell Science, University of Florida, Gainsville, USA

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