RNomics and Modomics in the halophilic archaea Haloferax volcanii: identification of RNA modification genes
1 Department of Microbiology and Department of Microbiology and Cell Science, University of Florida, Gainsville, FL-32611, Florida, USA
2 IGM, Université de Paris-sud, UMR 8621, Orsay, F 91405, France
3 CNRS, IGM, Orsay, F-91405, France
4 National Institute of Agronomical Research, Biometrics and Artificial Intelligence Department, Chemin de Borde-Rouge, Auzeville BP 27, 31326 Castanet-Tolosan, France
5 Institut de Biologie et de Technologies de Saclay (iBiTecS), Commissariat à l'Energie Atomique (CEA), Gif sur Yvette, F-91191, France
6 Department of Biochemistry and Molecular Biology, University of Massachussets, Amerherst, MA 01003, Massachusetts, USA
BMC Genomics 2008, 9:470 doi:10.1186/1471-2164-9-470Published: 9 October 2008
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.