A survey of small RNA-encoding genes in Escherichia coli

Nucleic Acids Research

Volumn 31, Issue 7, 2003, Pages 1813-1820

  Hershberg, Ruth ^a   Altuvia, Shoshy ^a   Margalit, Hanah ^a  

^a HEBREW UNIVERSITY OF JERUSALEM   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL RNA;

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; BACTERIAL GENETICS; CONTROLLED STUDY; ESCHERICHIA COLI; GENE FUNCTION; GENE IDENTIFICATION; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC CODE; GENETIC CONSERVATION; GENETIC VARIABILITY; INFORMATION PROCESSING; MULTIGENE FAMILY; NONHUMAN; PREDICTION; PRIORITY JOURNAL; REVIEW; SEQUENCE HOMOLOGY;

BASE COMPOSITION; ESCHERICHIA COLI; GENES, BACTERIAL; GENOME, BACTERIAL; RNA, BACTERIAL;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; NEGIBACTERIA; PROKARYOTA;

EID: 0037387973     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkg297     Document Type: Review

References (44)

1. Hildebrandt,M. and Nellen,W. (1992) Differential antisense transcription from the Dictyostelium EB4 gene locus: implications on antisense-mediated regulation of mRNA stability. Cell, 69, 197-204.
2. Lankenau,S., Corces,V.G. and Lankenau,D.H. (1994) The Drosophila micropia retrotransposon encodes a testis-specific antisense RNA complementary to reverse transcriptase. Mol. Cell. Biol., 14, 1764-1775.
3. Morfeldt,E., Taylor,D., von Gabain,A. and Arvidson,S. (1995) Activation of alpha-toxin translation in Staphylococcus aureus by the trans-encoded antisense RNA, RNAIII. EMBO J., 14, 4569-4577.
4. Sharp,T.V., Schwemmle,M., Jeffrey,I., Laing,K., Mellor,H., Proud,C.G., Hilse,K. and Clemens,M.J. (1993) Comparative analysis of the regulation of the interferon-inducible protein kinase PKR by Epstein-Barr virus RNAs EBER-1 and EBER-2 and adenovirus VAI RNA. Nucleic Acids Res., 21, 4483-4490.
5. Wagner,E.G. and Simons,R.W. (1994) Antisense RNA control in bacteria, phages, and plasmids. Annu. Rev. Microbiol., 48, 713-742.
6. Wassarman,K.M., Zhang,A. and Storz,G. (1999) Small RNAs in Escherichia coli. Trends Microbiol., 7, 37-45.
7. Wightman,B., Ha,I. and Ruvkun,G. (1993) Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C.elegans. Cell, 75, 855-862.
8. Eddy,S.R. (2001) Non-coding RNA genes and the modern RNA world. Nature Rev. Genet., 2, 919-929.
9. Wassarman,K.M. (2002) Small RNAs in bacteria: diverse regulators of gene expression in response to environmental changes. Cell, 109, 141-144.
10. Storz,G. (2002) An expanding universe of noncoding RNAs. Science, 296, 1260-1263.
11. Eddy,S.R. (2002) Computational genomics of noncoding RNA genes. Cell, 109, 137-140.
12. 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.
13. 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.
14. Rivas,E., Klein,R.J., Jones,T.A. and Eddy,S.R. (2001) Computational identification of noncoding RNAs in E.coli by comparative genomics. Curr. Biol., 11, 1369-1373.
15. 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.
16. 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.
17. 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.
18. 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.
19. 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.
20. Rudd,K.E. (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res., 28, 60-64.
21. 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., Gregor,J., Davis,N.W., Kirkpatrick,H.A., Goeden,M.A., Rose,D.J., Mau,B. and Shao,Y. (1997) The complete genome sequence of Escherichia coli K-12. Science, 277, 1453-1474.
22. Schattner,P. (2002) Searching for RNA genes using base-composition statistics. Nucleic Acids Res., 30, 2076-2082.
23. Klein,R.J., Misulovin,Z. and Eddy,S.R. (2002) Noncoding RNA genes identified in AT-rich hyperthermophiles. Proc. Natl Acad. Sci. USA, 99, 7542-7547.
24. Altschul,S.F., Gish,W., Miller,W., Myers,E.W. and Lipman,D.J. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
25. 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.
26. Zwieb,C., Gorodkin,J., Knudsen,B., Burks,J. and Wower,J. (2003) tmRDB (tmRNA database). Nucleic Acids Res., 31, 446-447.
27. Eddy,S.R. (2002) A memory-efficient dynamic programming algorithm for optimal alignment of a sequence to an RNA secondary structure. BMC Bioinformatics, 3, 18.
28. Huynen,M., Snel,B., Lathe,W.,III and Bork,P. (2000) Predicting protein function by genomic context: quantitative evaluation and qualitative inferences. Genome Res., 10, 1204-1210.
29. Dandekar,T., Snel,B., Huynen,M. and Bork,P. (1998) Conservation of gene order: a fingerprint of proteins that physically interact. Trends Biochem. Sci., 23, 324-328.
30. Yanai,I., Mellor,J.C. and DeLisi,C. (2002) Identifying functional links between genes using conserved chromosomal proximity. Trends Genet., 18, 176-179.
31. Karzai,A.W., Susskind,M.M. and Sauer,R.T. (1999) SmpB, a unique RNA-binding protein essential for the peptide-tagging activity of SsrA (tmRNA). EMBO J., 18, 3793-3799.
32. Smith,T.F. and Waterman,M.S. (1981) Identification of common molecular subsequences. J. Mol. Biol., 147, 195-197.
33. Rudd,K.E. (1999) Novel intergenic repeats of Escherichia coli K-12. Res. Microbiol., 150, 653-664.
34. Brown,S. and Fournier,M.J. (1984) The 4.5 S RNA gene of Escherichia coli is essential for cell growth. J. Mol. Biol., 178, 533-550.
35. Tetart,F. and Bouche,J.P. (1992) Regulation of the expression of the cell-cycle gene ftsZ by DicF antisense RNA. Division does not require a fixed number of FtsZ molecules. Mol. Microbiol., 6, 615-620.
36. Sledjeski,D. and Gottesman,S. (1995) A small RNA acts as an antisilencer of the H-NS-silenced rcsA gene of Escherichia coli. Proc. Natl Acad. Sci. USA, 92, 2003-2007.
37. Mizuno,T., Chou,M.Y. and Inouye,M. (1984) A unique mechanism regulating gene expression: translational inhibition by a complementary RNA transcript (micRNA). Proc. Natl Acad. Sci. USA, 81, 1966-1970.
38. Keiler,K.C., Waller,P.R. and Sauer,R.T. (1996) Role of a peptide tagging system in degradation of proteins synthesized from damaged messenger RNA. Science, 271, 990-993.
39. Liu,M.Y., Gui,G., Wei,B., Preston,J.F.,III, Oakford,L., Yuksel,U., Giedroc,D.P. and Romeo,T. (1997) The RNA molecule CsrB binds to the global regulatory protein CsrA and antagonizes its activity in Escherichia coli. J. Biol. Chem., 272, 17502-17510.
40. Brownlee,G.G. (1971) Sequence of 6S RNA of E. coli. Nature New Biol., 229, 147-149.
41. Jain,S.K., Gurevitz,M. and Apirion,D. (1982) A small RNA that complements mutants in the RNA processing enzyme ribonuclease P. J. Mol. Biol., 162, 515-533.
42. 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.
43. Polayes,D.A., Rice,P.W. and Dahlberg,J.E. (1988) DNA polymerase I activity in Escherichia coli is influenced by spot 42 RNA. J. Bacteriol., 170, 2083-2088.
44. Argaman,L. and Altuvia,S. (2000) fhlA repression by OxyS RNA: kissing complex formation at two sites results in a stable antisense-target RNA complex. J. Mol. Biol., 300, 1101-1112.