Detection of 5'- and 3'-UTR-derived small RNAs and cis-encoded antisense RNAs in Escherichia coli.
Evidence is accumulating that small, noncoding RNAs are important regulatory molecules. Computational and experimental searches have led to the identification of approximately 60 small RNA genes in Escherichia coli. However, most of these studies focused on the intergenic regions and assumed that small RNAs were >50 nt. Thus, the previous screens missed small RNAs encoded on the antisense strand of protein-coding genes and small RNAs of <50 nt. To identify additional small RNAs, we carried out a cloning-based screen focused on RNAs of 30-65 nt. In this screen, we identified RNA species corresponding to fragments of rRNAs, tRNAs and known small RNAs. Several of the small RNAs also corresponded to 5'- and 3'-untranslated regions (UTRs) and internal fragments of mRNAs. Four of the 3'-UTR-derived RNAs were highly abundant and two showed expression patterns that differed from the corresponding mRNAs, suggesting independent functions for the 3'-UTR-derived small RNAs. We also detected three previously unidentified RNAs encoded in intergenic regions and RNAs from the long direct repeat and hok/sok elements. In addition, we identified a few small RNAs that are expressed opposite protein-coding genes and could base pair with 5' or 3' ends of the mRNAs with perfect complementarity.
Kawano
Mitsuoki
M
Cell Biology and Metabolism Branch, National Institute of Child Health and Human Development Building 18T, Room 101, Bethesda, MD 20892-5430, USA.
Reynolds
April A
AA
Miranda-Rios
Juan
J
Storz
Gisela
G
D020413:3' Untranslated Regions / Q000737:chemistry*; D020121:5' Untranslated Regions / Q000737:chemistry*; D003001:Cloning, Molecular; D021901:DNA, Intergenic; D004926:Escherichia coli / Q000235:genetics*; D016372:RNA, Antisense / Q000032:analysis / Q000235:genetics*; D012329:RNA, Bacterial / Q000032:analysis / Q000235:genetics; D012333:RNA, Messenger / Q000737:chemistry; D012335:RNA, Ribosomal / Q000737:chemistry; D012343:RNA, Transfer / Q000737:chemistry; D022661:RNA, Untranslated / Q000032:analysis / Q000235:genetics*; D012091:Repetitive Sequences, Nucleic Acid
D020413:3' Untranslated Regions; D020121:5' Untranslated Regions; D021901:DNA, Intergenic; D016372:RNA, Antisense; D012329:RNA, Bacterial; D012333:RNA, Messenger; D012335:RNA, Ribosomal; D022661:RNA, Untranslated; D012343:RNA, Transfer
Mol Microbiol. 1999 Jun;32(5):1090-102
10361310
Annu Rev Genet. 1997;31:1-31
9442888
Annu Rev Biochem. 2005;74:199-217
15952886
Annu Rev Genet. 1999;33:193-227
10690408
Mol Microbiol. 2000 Mar;35(6):1560-72
10760155
Mol Microbiol. 2000 Aug;37(4):856-68
10972807
Nat Biotechnol. 2000 Dec;18(12):1262-8
11101804
Genes Dev. 2001 Jan 15;15(2):188-200
11157775
Genes Dev. 2001 Jul 1;15(13):1637-51
11445539
Curr Biol. 2001 Jun 26;11(12):941-50
11448770
Curr Biol. 2001 Sep 4;11(17):1369-73
11553332
Science. 2001 Oct 26;294(5543):853-8
11679670
Adv Genet. 2002;46:361-98
11931231
Biosystems. 2002 Mar-May;65(2-3):157-77
12069726
Mol Microbiol. 2002 Jul;45(2):333-49
12123448
Mol Microbiol. 2002 Jul;45(2):423-38
12123454
Nucleic Acids Res. 2002 Sep 1;30(17):3732-8
12202758
Nucleic Acids Res. 2003 Apr 1;31(7):1813-20
12654996
Cold Spring Harb Symp Quant Biol. 2001;66:353-62
12762038
J Mol Biol. 2003 Oct 17;333(2):261-78
14529615
Proc Natl Acad Sci U S A. 2003 Oct 14;100(21):12057-62
14523230
Genes Dev. 2003 Nov 1;17(21):2688-97
14597663
Nucleic Acids Res. 2003 Nov 15;31(22):6435-43
14602901
J Biol Chem. 2003 Nov 14;278(46):45041-4
12941949
Cell Mol Life Sci. 2003 Oct;60(10):2100-14
14618258
Mol Microbiol. 2003 Nov;50(4):1111-24
14622403
Nucleic Acids Res. 2003 Dec 1;31(23):6748-57
14627808
Curr Opin Microbiol. 2004 Apr;7(2):140-4
15063850
Nature. 2004 Jun 3;429(6991):571-4
15175754
J Bacteriol. 2004 Oct;186(20):6698-705
15466020
Annu Rev Microbiol. 2004;58:303-28
15487940
Cell. 1984 Jul;37(3):1015-26
6378385
J Mol Biol. 1989 Aug 20;208(4):575-86
2478711
Biochimie. 1989 Sep-Oct;71(9-10):1005-12
2574599
J Bacteriol. 1991 Jul;173(14):4247-53
1906060
J Bacteriol. 1991 Jul;173(14):4254-62
2066329
Microbiology. 1996 Jul;142 ( Pt 7):1635-9
8757727
FEMS Microbiol Rev. 1999 Jun;23(3):371-90
10371039