Recognition and discrimination of target mRNAs by Sib RNAs, a cis-encoded sRNA family.
Five Sib antitoxin RNAs, members of a family of cis-encoded small regulatory RNAs (sRNAs) in Escherichia coli, repress their target mRNAs, which encode Ibs toxins. This target repression occurs only between cognate sRNA-mRNA pairs with an exception of ibsA. We performed co-transformation assays to assess the ability of SibC derivatives to repress ibsC expression, thereby revealing the regions of SibC that are essential for ibsC mRNA recognition. SibC has two target recognition domains, TRD1 and TRD2, which function independently. The target site for TRD1 is located within the ORF of ibsC, whereas the target site for TRD2 is located in the translational initiation region. The TRD1 sequence is sufficient to repress ibsC expression. In contrast, TRD2 requires a specific structure in addition to the recognition sequence. An in vitro structural probing analysis showed that the initial interactions at these two recognition sites allowed base-pairing to progress into the flanking sequences. Displacement of the TRD1 and TRD2 domains of SibC by the corresponding domains of SibD changed the target specificity of SibC from ibsC to ibsD, suggesting that these two elements modulate the cognate target recognition of each Sib RNA by discriminating among non-cognate ibs mRNAs.
Han
Kook
K
Department of Chemistry, KAIST, Daejeon 305-701 and Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 305-806, Korea.
Kim
Kwang-Sun
KS
Bak
Geunu
G
Park
Hongmarn
H
Lee
Younghoon
Y
D001427:Bacterial Toxins / Q000235:genetics*; D001483:Base Sequence; D004926:Escherichia coli / Q000235:genetics*; D015964:Gene Expression Regulation, Bacterial; D008969:Molecular Sequence Data; D012329:RNA, Bacterial / Q000737:chemistry* / Q000378:metabolism; D012333:RNA, Messenger / Q000737:chemistry / Q000378:metabolism; D022661:RNA, Untranslated / Q000737:chemistry* / Q000378:metabolism; D017384:Sequence Deletion; D014170:Transformation, Genetic
D001427:Bacterial Toxins; D012329:RNA, Bacterial; D012333:RNA, Messenger; D022661:RNA, Untranslated
Bioinformatics. 2004 Mar 22;20(5):599-603
15033865
Mol Microbiol. 2002 Jul;45(2):333-49
12123448
Curr Opin Microbiol. 2007 Apr;10(2):117-24
17376733
Curr Opin Microbiol. 2007 Apr;10(2):102-9
17387036
Cell. 2009 Feb 20;136(4):615-28
19239884
J Biol Chem. 2005 Mar 4;280(9):7901-8
15618228
Nucleic Acids Res. 1990 Aug 25;18(16):4809-15
1697676
Mol Microbiol. 2003 May;48(3):657-70
12694612
Curr Biol. 2004 Dec 29;14(24):2271-6
15620655
Annu Rev Microbiol. 1994;48:713-42
7826024
J Biol Chem. 1997 Jul 11;272(28):17502-10
9211896
Nucleic Acids Res. 2005 Mar 21;33(5):1678-89
15781494
Biochemistry. 2008 Jan 15;47(2):762-70
18092807
Curr Biol. 2001 Sep 4;11(17):1369-73
11553332
Cell. 2000 Jun 9;101(6):613-23
10892648
Trends Biochem Sci. 1998 Dec;23(12):451-4
9868360
Proc Natl Acad Sci U S A. 2006 May 2;103(18):7054-8
16636284
Microbiol Mol Biol Rev. 2008 Dec;72(4):579-89, Table of Contents
19052321
Curr Biol. 2001 Jun 26;11(12):941-50
11448770
J Mol Biol. 1999 Dec 17;294(5):1115-25
10600370
J Bacteriol. 2007 May;189(9):3479-88
17337574
Nucleic Acids Res. 2003 Nov 15;31(22):6435-43
14602901
Curr Opin Microbiol. 2007 Apr;10(2):134-9
17383928
Nat Struct Mol Biol. 2009 Aug;16(8):804-6
19654618
Annu Rev Microbiol. 2004;58:303-28
15487940
Mol Microbiol. 2001 Oct;42(2):527-37
11703673
Proc Natl Acad Sci U S A. 2000 May 23;97(11):5978-83
10811905
Gene. 1989 Apr 15;77(1):51-9
2744487
J Bacteriol. 2004 Oct;186(20):6698-705
15466020
J Bacteriol. 2005 Oct;187(19):6641-50
16166525
Mol Microbiol. 1999 Jun;32(5):1090-102
10361310
Nucleic Acids Res. 2003 Apr 1;31(7):1813-20
12654996
Mol Microbiol. 2008 Dec;70(5):1076-93
18710431
Nucleic Acids Res. 2004 Nov 18;32(20):6057-68
15550566
Nat Struct Mol Biol. 2009 Aug;16(8):840-6
19620966
Crit Rev Biochem Mol Biol. 2005 Mar-Apr;40(2):93-113
15814430
Mol Microbiol. 2007 May;64(3):738-54
17462020
Annu Rev Biochem. 2005;74:199-217
15952886
Int J Biochem Cell Biol. 2002 Feb;34(2):116-29
11809414
Mol Microbiol. 2005 Dec;58(5):1421-9
16313626
Curr Opin Microbiol. 2004 Apr;7(2):140-4
15063850
EMBO J. 2000 Nov 1;19(21):5905-15
11060041
Genes Dev. 2001 Jul 1;15(13):1637-51
11445539
Biosystems. 2002 Mar-May;65(2-3):157-77
12069726