Noncoding RNA genes identified in AT-rich hyperthermophiles

Noncoding RNA (ncRNA) genes that produce functional RNAs instead of encoding proteins seem to be somewhat more prevalent than previously thought. However, estimating their number and importance is difficult because systematic identification of ncRNA genes remains challenging. Here, we exploit a strong, surprising DNA composition bias in genomes of some hyperthermophilic organisms: simply screening for GC-rich regions in the AT-rich Methanococcus jannaschii and Pyrococcus furiosus genomes efficiently detects both known and new RNA genes with a high degree of secondary structure. A separate screen based on comparative analysis also successfully identifies noncoding RNA genes in P. furiosus. Nine of the 30 new candidate genes predicted by these screens have been verified to produce discrete, apparently noncoding transcripts with sizes ranging from 97 to 277 nucleotides.

[1]  J. Lobry,et al.  Relationships Between Genomic G+C Content, RNA Secondary Structures, and Optimal Growth Temperature in Prokaryotes , 1997, Journal of Molecular Evolution.

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

[3]  Mark Borodovsky,et al.  GENMARK: Parallel Gene Recognition for Both DNA Strands , 1993, Comput. Chem..

[4]  I-Min A. Dubchak,et al.  A computational approach to identify genes for functional RNAs in genomic sequences. , 2001, Nucleic acids research.

[5]  S. Eddy,et al.  Computational identification of noncoding RNAs in E. coli by comparative genomics , 2001, Current Biology.

[6]  S. Karlin,et al.  Prediction of complete gene structures in human genomic DNA. , 1997, Journal of molecular biology.

[7]  S. Eddy,et al.  Homologs of small nucleolar RNAs in Archaea. , 2000, Science.

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

[9]  J. Sabina,et al.  Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. , 1999, Journal of molecular biology.

[10]  H. Margalit,et al.  Novel small RNA-encoding genes in the intergenic regions of Escherichia coli , 2001, Current Biology.

[11]  M. Adams,et al.  Key Role for Sulfur in Peptide Metabolism and in Regulation of Three Hydrogenases in the Hyperthermophilic ArchaeonPyrococcus furiosus , 2001, Journal of bacteriology.

[12]  Elena Rivas,et al.  Noncoding RNA gene detection using comparative sequence analysis , 2001, BMC Bioinformatics.

[13]  S. Eddy.  Non–coding RNA genes and the modern RNA world , 2001, Nature Reviews Genetics.

[14]  K. Sowers,et al.  Gene transfer systems for the Archaea. , 1999, Trends in microbiology.

[15]  J. Cooper.  [40] Thiamine pyrophosphatase from rabbit brain , 1970 .

[16]  D. Grogan.  Hyperthermophiles and the problem of DNA instability , 1998, Molecular microbiology.

[17]  D. Cowan,et al.  Biomolecular stability and life at high temperatures , 2000, Cellular and Molecular Life Sciences CMLS.

[18]  J. Harris,et al.  New insight into RNase P RNA structure from comparative analysis of the archaeal RNA. , 2001, RNA.

[19]  J. Bachellerie,et al.  Archaeal homologs of eukaryotic methylation guide small nucleolar RNAs: lessons from the Pyrococcus genomes. , 2000, Journal of molecular biology.

[20]  P. Schattner.  Searching for RNA genes using base-composition statistics. , 2002, Nucleic acids research.

[21]  T. Speed,et al.  Biological Sequence Analysis , 1998 .

[22]  Nilay Shah,et al.  Production planning for the rational use of energy in multiproduct continuous plants , 1993 .

[23]  S. Eddy,et al.  tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. , 1997, Nucleic acids research.

[24]  W. D. de Vos,et al.  Characterization of the celB gene coding for beta-glucosidase from the hyperthermophilic archaeon Pyrococcus furiosus and its expression and site-directed mutation in Escherichia coli , 1995, Journal of bacteriology.

[25]  Jan Barciszewski,et al.  RNA Biochemistry and Biotechnology , 1999 .

[26]  R. Durbin,et al.  RNA sequence analysis using covariance models. , 1994, Nucleic acids research.

[27]  F. Robb,et al.  Complete sequence and gene organization of the genome of a hyper-thermophilic archaebacterium, Pyrococcus horikoshii OT3. , 1998, DNA research : an international journal for rapid publication of reports on genes and genomes.

[28]  G. Storz,et al.  Identification of novel small RNAs using comparative genomics and microarrays. , 2001, Genes & development.