title: Recognition and discrimination of target mRNAs by Sib RNAs, a cis-encoded sRNA family.
abstract: 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.
authors.affiliation: Department of Chemistry, KAIST, Daejeon 305-701 and Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 305-806, Korea.
authors.forename: Kook
authors.initials: K
authors.lastname: Han
authors.forename: Kwang-Sun
authors.initials: KS
authors.lastname: Kim
authors.forename: Geunu
authors.initials: G
authors.lastname: Bak
authors.forename: Hongmarn
authors.initials: H
authors.lastname: Park
authors.forename: Younghoon
authors.initials: Y
authors.lastname: Lee
mesh_terms: 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
chemical_list: D001427:Bacterial Toxins; D012329:RNA, Bacterial; D012333:RNA, Messenger; D022661:RNA, Untranslated
references.citation: Bioinformatics. 2004 Mar 22;20(5):599-603
references.pmid: 15033865
references.citation: Mol Microbiol. 2002 Jul;45(2):333-49
references.pmid: 12123448
references.citation: Curr Opin Microbiol. 2007 Apr;10(2):117-24
references.pmid: 17376733
references.citation: Curr Opin Microbiol. 2007 Apr;10(2):102-9
references.pmid: 17387036
references.citation: Cell. 2009 Feb 20;136(4):615-28
references.pmid: 19239884
references.citation: J Biol Chem. 2005 Mar 4;280(9):7901-8
references.pmid: 15618228
references.citation: Nucleic Acids Res. 1990 Aug 25;18(16):4809-15
references.pmid: 1697676
references.citation: Mol Microbiol. 2003 May;48(3):657-70
references.pmid: 12694612
references.citation: Curr Biol. 2004 Dec 29;14(24):2271-6
references.pmid: 15620655
references.citation: Annu Rev Microbiol. 1994;48:713-42
references.pmid: 7826024
references.citation: J Biol Chem. 1997 Jul 11;272(28):17502-10
references.pmid: 9211896
references.citation: Nucleic Acids Res. 2005 Mar 21;33(5):1678-89
references.pmid: 15781494
references.citation: Biochemistry. 2008 Jan 15;47(2):762-70
references.pmid: 18092807
references.citation: Curr Biol. 2001 Sep 4;11(17):1369-73
references.pmid: 11553332
references.citation: Cell. 2000 Jun 9;101(6):613-23
references.pmid: 10892648
references.citation: Trends Biochem Sci. 1998 Dec;23(12):451-4
references.pmid: 9868360
references.citation: Proc Natl Acad Sci U S A. 2006 May 2;103(18):7054-8
references.pmid: 16636284
references.citation: Microbiol Mol Biol Rev. 2008 Dec;72(4):579-89, Table of Contents
references.pmid: 19052321
references.citation: Curr Biol. 2001 Jun 26;11(12):941-50
references.pmid: 11448770
references.citation: J Mol Biol. 1999 Dec 17;294(5):1115-25
references.pmid: 10600370
references.citation: J Bacteriol. 2007 May;189(9):3479-88
references.pmid: 17337574
references.citation: Nucleic Acids Res. 2003 Nov 15;31(22):6435-43
references.pmid: 14602901
references.citation: Curr Opin Microbiol. 2007 Apr;10(2):134-9
references.pmid: 17383928
references.citation: Nat Struct Mol Biol. 2009 Aug;16(8):804-6
references.pmid: 19654618
references.citation: Annu Rev Microbiol. 2004;58:303-28
references.pmid: 15487940
references.citation: Mol Microbiol. 2001 Oct;42(2):527-37
references.pmid: 11703673
references.citation: Proc Natl Acad Sci U S A. 2000 May 23;97(11):5978-83
references.pmid: 10811905
references.citation: Gene. 1989 Apr 15;77(1):51-9
references.pmid: 2744487
references.citation: J Bacteriol. 2004 Oct;186(20):6698-705
references.pmid: 15466020
references.citation: J Bacteriol. 2005 Oct;187(19):6641-50
references.pmid: 16166525
references.citation: Mol Microbiol. 1999 Jun;32(5):1090-102
references.pmid: 10361310
references.citation: Nucleic Acids Res. 2003 Apr 1;31(7):1813-20
references.pmid: 12654996
references.citation: Mol Microbiol. 2008 Dec;70(5):1076-93
references.pmid: 18710431
references.citation: Nucleic Acids Res. 2004 Nov 18;32(20):6057-68
references.pmid: 15550566
references.citation: Nat Struct Mol Biol. 2009 Aug;16(8):840-6
references.pmid: 19620966
references.citation: Crit Rev Biochem Mol Biol. 2005 Mar-Apr;40(2):93-113
references.pmid: 15814430
references.citation: Mol Microbiol. 2007 May;64(3):738-54
references.pmid: 17462020
references.citation: Annu Rev Biochem. 2005;74:199-217
references.pmid: 15952886
references.citation: Int J Biochem Cell Biol. 2002 Feb;34(2):116-29
references.pmid: 11809414
references.citation: Mol Microbiol. 2005 Dec;58(5):1421-9
references.pmid: 16313626
references.citation: Curr Opin Microbiol. 2004 Apr;7(2):140-4
references.pmid: 15063850
references.citation: EMBO J. 2000 Nov 1;19(21):5905-15
references.pmid: 11060041
references.citation: Genes Dev. 2001 Jul 1;15(13):1637-51
references.pmid: 11445539
references.citation: Biosystems. 2002 Mar-May;65(2-3):157-77
references.pmid: 12069726