Conservation analysis of small RNA genes in Escherichia coli

Bioinformatics

Volumn 20, Issue 5, 2004, Pages 599-603

  Zhang, Yong ^a   Zhang, Zhihua ^a   Ling, Lunjiang ^a   Shi, Baochen ^a   Chen, Runsheng ^a  

^a INSTITUTE OF BIOPHYSICS   (China)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL RNA; RIBOSOME RNA; TRANSFER RNA;

ARTICLE; BACTERIAL GENE; BACTERIAL GENETICS; CONTROLLED STUDY; ESCHERICHIA COLI; GENE FUNCTION; GENE NUMBER; GENETIC ANALYSIS; GENETIC CODE; GENETIC CONSERVATION; GENETIC DISTANCE; GENETIC SIMILARITY; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; QUANTITATIVE ANALYSIS; RNA GENE;

ESCHERICHIA COLI;

EID: 1842612028     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btg457     Document Type: Article

References (24)

1. Altschul,S.F., Madden,T.L., Schaffer,A.A., Zhang,J., Zhang,Z., Miller,W. and Lipman,D.J. (1997) Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
2. Argaman,L., Hershberg,R., Vogel,J., Bejerano,G., Wagner,E.G., Margalit,H. and Altuvia,S. (2001) Novel small RNA-encoding genes in the intergenic regions of Escherichia coli. Curr. Biol., 11, 941-950.
3. Blattner,F.R., Plunkett,G., III, Bloch,C.A., Perna,N.T., Burland,V., Riley,M., Collado-Vides,J., Glasner,J.D., Rode,C.K., Mayhew,G.F. et al. (1997) The complete genome sequence of Escherichia coli K-12. Science, 277, 1453-1474.
4. Carter,R.J., Dubchak,I. and Holbrook,S.R. (2001) A computational approach to identify genes for functional RNAs in genomic sequences. Nucleic Acids Res., 29, 3928-3938.
5. Chen,S., Lesnik,E.A., Hall,T.A., Sampath,R., Griffey,R.H., Ecker,D.J. and Blyn,L.B. (2002) A bioinformatics based approach to discover small RNA genes in the Escherichia coli genome. Biosystems, 65, 157-177.
6. Eddy,S. (2001) Non-coding RNA genes and the modern RNA world. Nat. Rev. Genet., 2, 919-929.
7. Filipowicz,W. (2000) Imprinted expression of small nucleolar RNAs in brain: Time for RNomics. Proc. Natl Acad. Sci. USA, 97, 14035-14037.
8. Hershberg,R., Altuvia,S. and Margalit,H. (2003) A survey of small RNA-encoding genes in Escherichia coli. Nucleic Acids Res., 31, 1813-1820.
9. Hershberg,R., Bejerano,G., Santos-Zavaleta,A. and Margalit,H. (2001) PromEC: An updated database of Escherichia coli mRNA promoters with experimentally identified transcriptional start sites. Nucleic Acids Res., 29, 277.
10. Huttenhofer,A., Brosius,J. and Bachellerie,J.P. (2002) RNomics: Identification and function of small, non-messenger RNAs. Curr. Opin. Chem. Biol., 6, 835-843.
11. Kroger,M. and Wahl,R. (1996) Compilation of DNA sequences of Escherichia coli K12 (ECD and ECDC; update 1995). Nucleic Acids Res., 24, 29-31.
12. Majdalani,N., Chen,S., Murrow,J., St John,K. and Gottesman,S. (2001) Regulation of RpoS by a novel small RNA: The characterization of RprA. Mol. Microbiol., 39, 1382-1394.
13. Masse,E. and Gottesman,S. (2002) A small RNA regulates the expression of genes involved in iron metabolism in Escherichia coli. Proc. Natl Acad. Sci. USA, 99, 4620-4625.
14. Rivas,E., Klein,R.J., Jones,T.A. and Eddy,S.R. (2001) Computational identitication of noncoding RNAs in E. coli by comparative genomics. Curr. Biol., 11, 1369-1373.
15. Rudd,K.E. (1999) Novel intergenic repeats of Escherichia coli K-12. Res. Microbiol., 150, 653-664.
16. Rudd,K.E. (2000) EcoGene: A genome sequence database for Escherichia coli K-12. Nucleic Acids Res., 28, 60-64.
17. Storz,G. (2002) An expanding universe of noncoding RNAs. Science, 296, 1260-1263.
18. Thompson,J.D., Higgins,D.G. and Gibson,T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22, 4673-4680.
19. Tjaden,B., Saxena,R.M., Stolyar,S., Haynor, D.R., Kolker,E. and Rosenow,C. (2002) Transcriptome analysis of Escherichia coli using high-density oligonucleotide probe arrays. Nucleic Acids Res., 30, 3732-3738.
20. Urbanowski,M.L., Stauffer,L.T. and Stauffer,G.V. (2000) The gcvB gene encodes a small untranslated RNA involved in expression of the dipeptide and oligopeptide transport systems in Escherichia coli. Mol. Microbiol., 37, 856-868.
21. Wahl,R. and Kroger,M. (1995) ECDC - a totally integrated and interactively usable genetic map of Escherichia coli K12, Microbiol. Res., 150, 7-61.
22. Wassarman,K.M. (2002) Small RNAs in bacteria: Diverse regulators of gene expression in response to environmental changes. Cell, 109, 141-144.
23. Wassarman,K.M., Repoila,F., Rosenow,C., Storz,G. and Gottesman,S. (2001) Identification of novel small RNAs using comparative genomics and microarrays. Genes Dev., 15, 1637-1651.
24. Wassarman,K.M., Zhang,A. and Storz,G. (1999) Small RNAs in Escherichia coli. Trends Microbiol., 7, 37-45.