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note
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A clone (Sso cosmid number 33) containing the aFIB and aNOP56 genes from S. solfataricus was provided by M. A. Ragan and C. W. Sensen. We used Southern hybridization to identify a 5-kb Xba I restriction fragment containing the corresponding genes from S. acidocaldarius; the fragment was cloned (pPD 1238), and its sequence was determined. The 165 rRNA sequences from S. acidocaldarius and S. solfataricus are 90% identical; the aFIB and aNOP56 predicted amino acid sequences are 76% and 65% identical, respectively. The S. acidocaldarius aFIB protein is 45% and 46% identical to the yeast and human proteins, and aNOP56 protein is 32% identical to the yeast and human proteins. Our choice of the name aNOP56 is arbitrary, because the aNOPSS sequence is also similar to eukaryotic NOP5/ NOP58; the eukaryotic SIK1/NOP56 and NOP5/NOP58 proteins appear to be paralogs that arose by a gene duplication in Eukarya. The GenBank accession numbers for the aNOP56 and aFIB protein sequences from S. acidocaldarius are AF201092 and AF201093, respectively.
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22
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0343882715
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note
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Southern hybridizations confirmed the existence of single-copy genes for sR1, sR2, sR5, and sR13 in S. acidocaldarius genomic DNA. Genomic clones of the S. acidocaldarius sR1 and S. solfataricus sR1 were isolated and sequenced. In both cases, the sRNA genes overlap the 3′ end of the corresponding aspartate aminotransferase genes. The translation termination codons UAA for S. acidocaldarius and UAG for S. solfataricus fall within the D' box guide regions in the two sRNAs (Fig. 4A).
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23
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on 15 June
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S. F. Altschul et al., Nucleic Acids Res. 25, 3389 (1997). The BLAST searches against the nonredundant nucleotide database were performed at www. ncbi.nlm.nih.gov/BLAST/ on 15 June 1999.
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G. J. Olsen et al., J. Mol. Evol. 22, 301 (1985); D. A. Stahl, K. R. Luehrsen, C. R. Woese, N. R. Pace, Nucleic Acids Res. 9, 6129 (1981); E. Dams, P. Londei, P. Cammarano, A. Vandenberghe, R. De Wachter, Nucleic Acids Res. 11, 4667 (1983); P. Durovic and P. P. Dennis, Mol. Microbiol. 13, 229 (1994). As a result of strain misidentification, the 165 RNA sequence published in the first paper is now recognized to be from S. acidocaldarius and not S. solfataricus as originally indicated. The two originally published 5S sequences are identical and both are derived from S. solfataricus. The S. acidocaldarius 5S sequence has been published more recently along with a brief documentation of the strain misidentification problem [P. Durovic, U. Kutay, C. Schleper, P. P. Dennis, J. Bacteriol. 176, 514 (1994)].
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G. J. Olsen et al., J. Mol. Evol. 22, 301 (1985); D. A. Stahl, K. R. Luehrsen, C. R. Woese, N. R. Pace, Nucleic Acids Res. 9, 6129 (1981); E. Dams, P. Londei, P. Cammarano, A. Vandenberghe, R. De Wachter, Nucleic Acids Res. 11, 4667 (1983); P. Durovic and P. P. Dennis, Mol. Microbiol. 13, 229 (1994). As a result of strain misidentification, the 165 RNA sequence published in the first paper is now recognized to be from S. acidocaldarius and not S. solfataricus as originally indicated. The two originally published 5S sequences are identical and both are derived from S. solfataricus. The S. acidocaldarius 5S sequence has been published more recently along with a brief documentation of the strain misidentification problem [P. Durovic, U. Kutay, C. Schleper, P. P. Dennis, J. Bacteriol. 176, 514 (1994)].
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G. J. Olsen et al., J. Mol. Evol. 22, 301 (1985); D. A. Stahl, K. R. Luehrsen, C. R. Woese, N. R. Pace, Nucleic Acids Res. 9, 6129 (1981); E. Dams, P. Londei, P. Cammarano, A. Vandenberghe, R. De Wachter, Nucleic Acids Res. 11, 4667 (1983); P. Durovic and P. P. Dennis, Mol. Microbiol. 13, 229 (1994). As a result of strain misidentification, the 165 RNA sequence published in the first paper is now recognized to be from S. acidocaldarius and not S. solfataricus as originally indicated. The two originally published 5S sequences are identical and both are derived from S. solfataricus. The S. acidocaldarius 5S sequence has been published more recently along with a brief documentation of the strain misidentification problem [P. Durovic, U. Kutay, C. Schleper, P. P. Dennis, J. Bacteriol. 176, 514 (1994)].
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Biochimie
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Maden, B.E.H.1
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Ajuh, P.M.5
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31
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0032518163
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The search algorithm and general snoRNA gene model remained as originally described (3), although yeast/ human snoRNA training data were replaced by 5. acidocaldarius training data. Alignments of box features (C, D', and D) from S. acidocaldarius sRNAs sR1 to sR17 (Table 1) were used to create log odds weight matrices reflecting the frequency of each nucleotide at each position in each box feature. The lengths of the rRNA complementary region and the gaps between box features were scored with binned length distributions. Overall, training data for the nucleotide content of the box features did not change substantially between the yeast/human and archaeal models, but the distribution of lengths between features did vary; archaeal sRNAs appear to be much more compact than those in eukaryotes, and the rRNA complementary regions are shorter, commonly 8 to 11 nt long compared with 10 to 14 nt complementarities most often found in S. cerevisiae snoRNAs. We used final snoRNA scores to rank candidates within each genome and inspected hits manually by descending score. Hits that completely overlapped >600 nt open reading frames called by Glimmer 1.04 [S. Salzberg, A. Delcher, S. Kasif, O. White, Nucleic Acids Res. 26, 544 (1998)] were discarded. No absolute score cutoff was used because each species' candidates matched the S. acidocaldarius-trained model to a different degree, and we had no estimate of the total number of genes to be found or the variability of sequence features for each different species.
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Nucleic Acids Res.
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Salzberg, S.1
Delcher, A.2
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White, O.4
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32
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0343011199
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note
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Two-thirds of the S. solfataricus genome was completed at the time of our searches. The Web sites for accessing the archaeal genomes are as follows: S. solfataricus, niji.imb.nrc.ca/sulfolobus/; M. jannaschii and A. fulgidus, www.tigr.org/tdb/; A. pernix, www. mild.nite.go.jp/APEK1/; M. thermoautotrophicum, www.biosci.ohio-state.edu/~genomes/mthermo/; P. abyssi, www.genoscope.cns.fr/Pab/; P. horikoshii, www. bio.nite.go.jp/ot3db_index.html; and P. furiosus, www. genome.utah.edu/sequence.html. We gratefully acknowledge the Sulfolobus solfataricus P2 Genome Project (niji.imb.nrc.ca/sulfhome), Genoscope (www. genoscope.cns.fr), and the Utah Genome Center, Department of Human Genetics, University of Utah (www.genome.utah.edu) for access to unpublished genome sequence data.
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All newly identified archaeal snoRNAs and annotation are also available at rna.wustl.edu/snoRNAdb
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Supplemental information is available at www. sciencemag.org/feature/data/1047007.shl. All newly identified archaeal snoRNAs and annotation are also available at rna.wustl.edu/snoRNAdb/.
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35
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note
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Numerous candidate sRNAs that had one or more imperfect features were found in the genomes of the S. solfataricus, M. jannaschii, A. fulgidus, A. pernix, and M. thermoautotrophicum, but in the absence of identified ribose methylation sites or other confirmatory information, their authenticity remains uncertain. In particular, no strong candidates were identified within M. thermoautotrophicum, although we believe at least some of the search hits are legitimate (broader sRNA training data and/or the opportunity to test several dozen candidates experimentally are needed).
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note
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For each Pyrococcus sRNA homology group, the sequence identity for end-to-end alignments of interspecies members was 80 to 98%.
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J. D. Thompson, D. C. Higgins, T. J. Gibson, Nucleic Acids Res. 22, 4673 (1994). For our alignments, we anchored the 5′ ends of the 16S rRNA with the conserved sequence GGUUGAUCCU; this block occupies positions 16 to 25 in all the 16S sequences in our alignment. The 23S sequences were anchored with the conserved sequence GGAUGGCUCG. In the respective 23S sequences in our alignment, this block occupies positions 21 to 30 in Afu, 22 to 31 in Mja, 33 to 42 in Pho, 20 to 29 in Ape, 28 to 37 in Sso, and 33 to 42 in Sac.
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note
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We thank J. W. Brown for generously providing M. jannaschii total RNA used in verifying sRNA predictions. Work in P.P.D.'s laboratory was supported by the Medical Research Council of Canada, grant MT6340; work in S.R.E.'s laboratory was supported by NIH National Human Genome Research Institute grant HG01363.
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