Homologs of small nucleolar RNAs in Archaea.

In eukaryotes, dozens of posttranscriptional modifications are directed to specific nucleotides in ribosomal RNAs (rRNAs) by small nucleolar RNAs (snoRNAs). We identified homologs of snoRNA genes in both branches of the Archaea. Eighteen small sno-like RNAs (sRNAs) were cloned from the archaeon Sulfolobus acidocaldarius by coimmunoprecipitation with archaeal fibrillarin and NOP56, the homologs of eukaryotic snoRNA-associated proteins. We trained a probabilistic model on these sRNAs to search for more sRNAs in archaeal genomic sequences. Over 200 additional sRNAs were identified in seven archaeal genomes representing both the Crenarchaeota and the Euryarchaeota. snoRNA-based rRNA processing was therefore probably present in the last common ancestor of Archaea and Eukarya, predating the evolution of a morphologically distinct nucleolus.

[1]  N. Pace,et al.  An unusual 5S rRNA, from Sulfolobus acidocaldarius, and its implications for a general 5S rRNA structure. , 1981, Nucleic acids research.

[2]  R. de Wachter,et al.  Sequences of the 5S rRNAs of the thermo-acidophilic archaebacterium Sulfolobus solfataricus (Caldariella acidophila) and the thermophilic eubacteria Bacillus acidocaldarius and Thermus aquaticus. , 1983, Nucleic acids research.

[3]  R. Gupta.  Halobacterium volcanii tRNAs. Identification of 41 tRNAs covering all amino acids, and the sequences of 33 class I tRNAs. , 1984, The Journal of biological chemistry.

[4]  O. Kandler,et al.  Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. , 1990, Proceedings of the National Academy of Sciences of the United States of America.

[5]  D. Tollervey,et al.  The small nucleolar RNP protein NOP1 (fibrillarin) is required for pre‐rRNA processing in yeast. , 1991, The EMBO journal.

[6]  J. Thompson,et al.  CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. , 1994, Nucleic acids research.

[7]  K. A. Amiri.  Fibrillarin-like proteins occur in the domain Archaea , 1994, Journal of bacteriology.

[8]  Strain identification and 5S rRNA gene characterization of the hyperthermophilic archaebacterium Sulfolobus acidocaldarius , 1994, Journal of bacteriology.

[9]  P. Dennis,et al.  Separate pathways for excision and processing of 16S and 23S rRNA from the primary rRNA operon transcript from the hyperthermophilic archaebacterium Sulfolobus acldocaldarius: similarities to eukaryotic rRNA processing , 1994, Molecular microbiology.

[10]  M. Fournier,et al.  The small nucleolar RNAs. , 1995, Annual review of biochemistry.

[11]  B. Maden,et al.  Classical and novel approaches to the detection and localization of the numerous modified nucleotides in eukaryotic ribosomal RNA. , 1995, Biochimie.

[12]  Tamás Kiss,et al.  Site-Specific Ribose Methylation of Preribosomal RNA: A Novel Function for Small Nucleolar RNAs , 1996, Cell.

[13]  J. Bachellerie,et al.  Targeted ribose methylation of RNA in vivo directed by tailored antisense RNA guides , 1996, Nature.

[14]  Laurie Smith,et al.  The RNA World of the Nucleolus: Two Major Families of Small RNAs Defined by Different Box Elements with Related Functions , 1996, Cell.

[15]  J. Steitz,et al.  A small nucleolar RNA requirement for site-specific ribose methylation of rRNA in Xenopus. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[16]  Thomas L. Madden,et al.  Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.

[17]  D. Armbruster,et al.  Splicing of Intron-containing tRNATrp by the ArchaeonHaloferax volcanii Occurs Independent of Mature tRNA Structure* , 1997, The Journal of Biological Chemistry.

[18]  Tamás Kiss,et al.  Site-Specific Pseudouridine Formation in Preribosomal RNA Is Guided by Small Nucleolar RNAs , 1997, Cell.

[19]  D. Tollervey,et al.  Nucleolar KKE/D repeat proteins Nop56p and Nop58p interact with Nop1p and are required for ribosome biogenesis , 1997, Molecular and cellular biology.

[20]  J. Ni,et al.  Small Nucleolar RNAs Direct Site-Specific Synthesis of Pseudouridine in Ribosomal RNA , 1997, Cell.

[21]  M. Caizergues-Ferrer,et al.  A small nucleolar RNP protein is required for pseudouridylation of eukaryotic ribosomal RNAs , 1997, The EMBO journal.

[22]  J. Brockenbrough,et al.  Nop5p Is a Small Nucleolar Ribonucleoprotein Component Required for Pre-18 S rRNA Processing in Yeast* , 1998, The Journal of Biological Chemistry.

[23]  T. Pederson,et al.  The plurifunctional nucleolus. , 1998, Nucleic acids research.

[24]  S. Salzberg,et al.  Microbial gene identification using interpolated Markov models. , 1998, Nucleic acids research.

[25]  J. Steitz,et al.  Modification of U6 spliceosomal RNA is guided by other small RNAs. , 1998, Molecular cell.

[26]  Kathleen R. Noon,et al.  Posttranscriptional Modifications in 16 S and 23 S rRNAs of the Archaeal Hyperthermophile Sulfolobus solfataricus , 1998 .

[27]  William Arbuthnot Sir Lane,et al.  Purification and characterization of the nuclear RNase P holoenzyme complex reveals extensive subunit overlap with RNase MRP. , 1998, Genes & development.

[28]  D. Tollervey,et al.  Birth of the snoRNPs: the evolution of the modification-guide snoRNAs. , 1998, Trends in biochemical sciences.

[29]  Z. Kiss-László,et al.  Sequence and structural elements of methylation guide snoRNAs essential for site‐specific ribose methylation of pre‐rRNA , 1998, The EMBO journal.

[30]  J. Bachellerie,et al.  Evolutionarily conserved structural features in the ITS2 of mammalian pre-rRNAs and potential interactions with the snoRNA U8 detected by comparative analysis of new mouse sequences. , 1999, Nucleic acids research.

[31]  S. Eddy,et al.  A computational screen for methylation guide snoRNAs in yeast. , 1999, Science.

[32]  J. Steitz,et al.  Guided tours: from precursor snoRNA to functional snoRNP. , 1999, Current opinion in cell biology.