title: C/D box sRNA-guided 2'-O-methylation patterns of archaeal rRNA molecules.
abstract: BACKGROUND
  In archaea and eukaryotes, ribonucleoprotein complexes containing small C/D box s(no)RNAs use base pair complementarity to target specific sites within ribosomal RNA for 2'-O-ribose methylation. These modifications aid in the folding and stabilization of nascent rRNA molecules and their assembly into ribosomal particles. The genomes of hyperthermophilic archaea encode large numbers of C/D box sRNA genes, suggesting an increased necessity for rRNA stabilization at extreme growth temperatures.
  
  
  RESULTS
  We have identified the complete sets of C/D box sRNAs from seven archaea using RNA-Seq methodology. In total, 489 C/D box sRNAs were identified, each containing two guide regions. A combination of computational and manual analyses predicts 719 guide interactions with 16S and 23S rRNA molecules. This first pan-archaeal description of guide sequences identifies (i) modified rRNA nucleotides that are frequently conserved between species and (ii) regions within rRNA that are hotspots for 2'-O-methylation. Gene duplication, rearrangement, mutational drift and convergent evolution of sRNA genes and guide sequences were observed. In addition, several C/D box sRNAs were identified that use their two guides to target locations distant in the rRNA sequence but close in the secondary and tertiary structure. We propose that they act as RNA chaperones and facilitate complex folding events between distant sequences.
  
  
  CONCLUSIONS
  This pan-archaeal analysis of C/D box sRNA guide regions identified conserved patterns of rRNA 2'-O-methylation in archaea. The interaction between the sRNP complexes and the nascent rRNA facilitates proper folding and the methyl modifications stabilize higher order rRNA structure within the assembled ribosome.
authors: Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch Strasse 10, 35043, Marburg, Germany. dennisp@janelia.hhmi.org.|Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Dr, Ashburn, VA, 20147, USA. dennisp@janelia.hhmi.org.
authors: Patrick P
authors: PP
authors: Dennis
authors: Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch Strasse 10, 35043, Marburg, Germany. trippv@students.uni-marburg.de.
authors: Vanessa
authors: V
authors: Tripp
authors: Department of Biomolecular Engineering, University of California, 1156 High Street, Santa Cruz, CA, 95064, USA. llui@soe.ucsc.edu.
authors: Lauren
authors: L
authors: Lui
authors: Department of Biomolecular Engineering, University of California, 1156 High Street, Santa Cruz, CA, 95064, USA. lowe@soe.ucsc.edu.
authors: Todd
authors: T
authors: Lowe
authors: Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch Strasse 10, 35043, Marburg, Germany. lennart.randau@mpi-marburg.mpg.de.
authors: Lennart
authors: L
authors: Randau
mesh_terms: D001105:Archaea / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D019295:Computational Biology / Q000379:methods; D019143:Evolution, Molecular; D014644:Genetic Variation; D008745:Methylation; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D020871:RNA Stability; D019642:RNA, Archaeal / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D012335:RNA, Ribosomal / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D020537:RNA, Small Nucleolar / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D017423:Sequence Analysis, RNA / Q000379:methods
chemical_list: D019642:RNA, Archaeal; D012335:RNA, Ribosomal; D020537:RNA, Small Nucleolar