Home LiteratureArticle Details
PMID: 17576690 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

In vitro analysis of the interaction between the small RNA SR1 and its primary target ahrC mRNA.

Nucleic acids research ·Vol. 35 ·No. 13 ·2007-00-00 ·Pages 4331-46

Heidrich N, Moll I, Brantl S

Abstract

Small regulatory RNAs (sRNAs) from bacterial chromosomes became the focus of research over the past five years. However, relatively little is known in terms of structural requirements, kinetics of interaction with their targets and degradation in contrast to well-studied plasmid-encoded antisense RNAs. Here, we present a detailed in vitro analysis of SR1, a sRNA of Bacillus subtilis that is involved in regulation of arginine catabolism by basepairing with its target, ahrC mRNA. The secondary structures of SR1 species of different lengths and of the SR1/ahrC RNA complex were determined and functional segments required for complex formation narrowed down. The initial contact between SR1 and its target was shown to involve the 5' part of the SR1 terminator stem and a region 100 bp downstream from the ahrC transcriptional start site. Toeprinting studies and secondary structure probing of the ahrC/SR1 complex indicated that SR1 inhibits translation initiation by inducing structural changes downstream from the ahrC RBS. Furthermore, it was demonstrated that Hfq, which binds both SR1 and ahrC RNA was not required to promote ahrC/SR1 complex formation but to enable the translation of ahrC mRNA. The intracellular concentrations of SR1 were calculated under different growth conditions.

MeSH Terms
Bacillus subtilis/genetics Bacterial Proteins/genetics,metabolism Base Sequence Binding Sites Gene Expression Regulation, Bacterial Genes, Reporter Host Factor 1 Protein/physiology Molecular Sequence Data Nucleic Acid Conformation Peptide Chain Initiation, Translational RNA, Bacterial/chemistry,metabolism RNA, Messenger/chemistry,metabolism RNA, Untranslated/chemistry,metabolism Repressor Proteins/genetics,metabolism Ribosomes/metabolism Trans-Activators/genetics,metabolism
Chemicals
AhrC protein, Bacillus subtilis Bacterial Proteins Host Factor 1 Protein RNA, Bacterial RNA, Messenger RNA, Untranslated Repressor Proteins Trans-Activators
Authors & Affiliations
3 authors, click to expand affiliations / ORCID
Heidrich Nadja
AG Bakteriengenetik, Friedrich-Schiller-Universität Jena, Philosophenweg 12, Jena D-07743, Germany.
Moll Isabella
Brantl Sabine
References (44)
44 references, click to expand
  1. Extension inhibition analysis of translation initiation complexes.
    Methods Enzymol. 1988;164:419-25 PMID: 2468068
  2. Regulatory mechanisms employed by cis-encoded antisense RNAs.
    Curr Opin Microbiol. 2007 Apr;10(2):102-9 PMID: 17387036
  3. Antisense RNA-mediated transcriptional attenuation occurs faster than stable antisense/target RNA pairing: an in vitro study of plasmid pIP501.
    EMBO J. 1994 Aug 1;13(15):3599-607 PMID: 7520390
  4. Footprinting mRNA-ribosome complexes with chemical probes.
    EMBO J. 1994 Aug 15;13(16):3892-901 PMID: 8070416
  5. Secondary structures of Escherichia coli antisense micF RNA, the 5'-end of the target ompF mRNA, and the RNA/RNA duplex.
    Biochemistry. 1995 Mar 21;34(11):3621-31 PMID: 7534474
  6. Activation of alpha-toxin translation in Staphylococcus aureus by the trans-encoded antisense RNA, RNAIII.
    EMBO J. 1995 Sep 15;14(18):4569-77 PMID: 7556100
  7. An unusually long-lived antisense RNA in plasmid copy number control: in vivo RNAs encoded by the streptococcal plasmid pIP501.
    J Mol Biol. 1996 Jan 19;255(2):275-88 PMID: 8551520
  8. The RNA-binding protein HF-I, known as a host factor for phage Qbeta RNA replication, is essential for rpoS translation in Escherichia coli.
    Genes Dev. 1996 May 1;10(9):1143-51 PMID: 8654929
  9. Antisense RNA-mediated transcriptional attenuation: an in vitro study of plasmid pT181.
    Mol Microbiol. 2000 Mar;35(6):1469-82 PMID: 10760147
  10. Probing the structure of RNAIII, the Staphylococcus aureus agr regulatory RNA, and identification of the RNA domain involved in repression of protein A expression.
    RNA. 2000 May;6(5):668-79 PMID: 10836788
  11. A trans-acting RNA as a control switch in Escherichia coli: DsrA modulates function by forming alternative structures.
    Proc Natl Acad Sci U S A. 2000 Aug 29;97(18):9919-24 PMID: 10954740
  12. RNA expression analysis using an antisense Bacillus subtilis genome array.
    J Bacteriol. 2001 Dec;183(24):7371-80 PMID: 11717296
  13. The Sm-like Hfq protein increases OxyS RNA interaction with target mRNAs.
    Mol Cell. 2002 Jan;9(1):11-22 PMID: 11804582
  14. Antisense RNAs in bacteria and their genetic elements.
    Adv Genet. 2002;46:361-98 PMID: 11931231
  15. Spot 42 RNA mediates discoordinate expression of the E. coli galactose operon.
    Genes Dev. 2002 Jul 1;16(13):1696-706 PMID: 12101127
  16. Coupled degradation of a small regulatory RNA and its mRNA targets in Escherichia coli.
    Genes Dev. 2003 Oct 1;17(19):2374-83 PMID: 12975324
  17. Antisense-RNA mediated transcriptional attenuation: importance of a U-turn loop structure in the target RNA of plasmid pIP501 for efficient inhibition by the antisense RNA.
    J Mol Biol. 2003 Nov 7;333(5):917-29 PMID: 14583190
  18. Hfq, a new chaperoning role: binding to messenger RNA determines access for small RNA regulator.
    EMBO J. 2004 Jan 28;23(2):396-405 PMID: 14739933
  19. The bacterial Sm-like protein Hfq: a key player in RNA transactions.
    Mol Microbiol. 2004 Mar;51(6):1525-33 PMID: 15009882
  20. Construction of a Bacillus subtilis double mutant deficient in extracellular alkaline and neutral proteases.
    J Bacteriol. 1984 Oct;160(1):442-4 PMID: 6434524
  21. Integrative vector for constructing single-copy translational fusions between regulatory regions of Bacillus subtilis and the bgaB reporter gene encoding a heat-stable beta-galactosidase.
    FEMS Microbiol Lett. 1997 May 1;150(1):49-54 PMID: 9163905
  22. A small, stable RNA induced by oxidative stress: role as a pleiotropic regulator and antimutator.
    Cell. 1997 Jul 11;90(1):43-53 PMID: 9230301
  23. Bacillus subtilis histone-like protein, HBsu, is an integral component of a SRP-like particle that can bind the Alu domain of small cytoplasmic RNA.
    J Biol Chem. 1999 May 7;274(19):13569-76 PMID: 10224127
  24. Involvement of a novel transcriptional activator and small RNA in post-transcriptional regulation of the glucose phosphoenolpyruvate phosphotransferase system.
    Mol Microbiol. 2004 Nov;54(4):1076-89 PMID: 15522088
  25. Staphylococcus aureus RNAIII and the endoribonuclease III coordinately regulate spa gene expression.
    EMBO J. 2005 Feb 23;24(4):824-35 PMID: 15678100
  26. Both RNase E and RNase III control the stability of sodB mRNA upon translational inhibition by the small regulatory RNA RyhB.
    Nucleic Acids Res. 2005;33(5):1678-89 PMID: 15781494
  27. A highly conserved 6S RNA structure is required for regulation of transcription.
    Nat Struct Mol Biol. 2005 Apr;12(4):313-9 PMID: 15793584
  28. Ribonucleases J1 and J2: two novel endoribonucleases in B.subtilis with functional homology to E.coli RNase E.
    Nucleic Acids Res. 2005;33(7):2141-52 PMID: 15831787
  29. 6S RNA is a widespread regulator of eubacterial RNA polymerase that resembles an open promoter.
    RNA. 2005 May;11(5):774-84 PMID: 15811922
  30. An abundance of RNA regulators.
    Annu Rev Biochem. 2005;74:199-217 PMID: 15952886
  31. Small untranslated RNA antitoxin in Bacillus subtilis.
    J Bacteriol. 2005 Oct;187(19):6641-50 PMID: 16166525
  32. Implication of CcpN in the regulation of a novel untranslated RNA (SR1) in Bacillus subtilis.
    Mol Microbiol. 2005 Oct;58(1):189-206 PMID: 16164558
  33. Hfq-dependent regulation of OmpA synthesis is mediated by an antisense RNA.
    Genes Dev. 2005 Oct 1;19(19):2355-66 PMID: 16204185
  34. Small RNA genes expressed from Staphylococcus aureus genomic and pathogenicity islands with specific expression among pathogenic strains.
    Proc Natl Acad Sci U S A. 2005 Oct 4;102(40):14249-54 PMID: 16183745
  35. Regulation of ompA mRNA stability: the role of a small regulatory RNA in growth phase-dependent control.
    Mol Microbiol. 2005 Dec;58(5):1421-9 PMID: 16313626
  36. Genes for small, noncoding RNAs under sporulation control in Bacillus subtilis.
    J Bacteriol. 2006 Jan;188(2):532-41 PMID: 16385044
  37. Identification of small Hfq-binding RNAs in Listeria monocytogenes.
    RNA. 2006 Jul;12(7):1383-96 PMID: 16682563
  38. The small untranslated RNA SR1 from the Bacillus subtilis genome is involved in the regulation of arginine catabolism.
    Mol Microbiol. 2006 Oct;62(2):520-36 PMID: 17020585
  39. Small non-coding RNAs and the bacterial outer membrane.
    Curr Opin Microbiol. 2006 Dec;9(6):605-11 PMID: 17055775
  40. Antisense RNA-mediated transcriptional attenuation in plasmid pIP501: the simultaneous interaction between two complementary loop pairs is required for efficient inhibition by the antisense RNA.
    Microbiology. 2007 Feb;153(Pt 2):420-7 PMID: 17259613
  41. No detectable effect of RNA-binding protein Hfq absence in Staphylococcus aureus.
    BMC Microbiol. 2007;7:10 PMID: 17291347
  42. Spectroscopic observation of RNA chaperone activities of Hfq in post-transcriptional regulation by a small non-coding RNA.
    Nucleic Acids Res. 2007;35(3):999-1006 PMID: 17259214
  43. Identification of new noncoding RNAs in Listeria monocytogenes and prediction of mRNA targets.
    Nucleic Acids Res. 2007;35(3):962-74 PMID: 17259222
  44. Quantitation of ColE1-encoded replication elements.
    Proc Natl Acad Sci U S A. 1991 Jan 15;88(2):405-9 PMID: 1703297
Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
1362-4962
DOI
10.1093/nar/gkm439
Published
2007-00-00
Epub
2007-00-18
Pages
4331-46
Language
English
Region
England
NLM ID
0411011
PMCID
PMC1935000
Subset
IM
External Links
PubMed source DOI: 10.1093/nar/gkm439 PMC Full Text View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: product@genelibs.com

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2