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RNA Networks in Prokaryotes II: tRNA Processing and Small RNAs

  • Lesley J. Collins
  • Patrick J. Biggs
Part of the Advances in Experimental Medicine and Biology book series (AEMB, volume 722)

Abstract

It is becoming clear that in prokaryotes RNAs interact and perform complex functions as a network similar to what we have uncovered in eukaryotes. This chapter will continue the discussion of prokaryotic molecular systems, showing how these systems can interact with each other to gain a higher level of control within the cell. Our examples include RNase P, the tRNA cleaving molecule that, as well as performing other functions, also cleaves certain ribo switches; and the glmS gene under the control of both a ribozyme in its 5′ untranslated region and two small RNAs. With further investigation of nonprotein coding RNA interactions (i.e., the RNA infrastructure), in bacteria and archaea, we gain greater understanding of the influence that small strands of RNA sequence can have over the entire cell.

Keywords

Methanothermobacter Thermoautotrophicus 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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References

  1. 1.
    Esakova O, Krasilnikov AS. Of proteins and RNA: the RNase P/MRP family. RNA2010; 16(9):1725–1747.PubMedCrossRefGoogle Scholar
  2. 2.
    Lai LB, Vioque A, Kirsebom LA et al. Unexpected diversity of RNase P, an ancient tRNA processing enzyme: challenges and prospects. FEBS Lett 2010; 584(2):287–296.PubMedCrossRefGoogle Scholar
  3. 3.
    Marvin MC, Engelke DR. Broadening the mission of an RNA enzyme. J Cell Biochem2009; 108(6): 1244–1251.PubMedCrossRefGoogle Scholar
  4. 4.
    Marvin MC, Engelke DR. RNase P: increased versatility through protein complexity? RNA Biol 2009; 6(1):40–42.PubMedCrossRefGoogle Scholar
  5. 5.
    Cho IM, Lai LB, Susanti D et al. Ribosomal protein L7Ae is a subunit of archaeal RNase P. Proc Natl Acad Sci USA 2010; 107(33): 14573–14578.CrossRefGoogle Scholar
  6. 6.
    Jarrous N, Gopalan V. Archaeal/Eukaryal RNase P: subunits, functions and RNA diversification. Nucleic Acids Res 2010.Google Scholar
  7. 7.
    Pulukkunat DK, Gopalan V. Studies on Methanocaldococcus jannaschii RNase P reveal insights into the roles of RNA and protein cofactors in RNase P catalysis. Nucleic Acids Res 2008; 36(12):4172–4180.PubMedCrossRefGoogle Scholar
  8. 8.
    Koutmou KS, Zahler NH, Kurz JC et al. Protein-precursortRNA contact leads to sequence-specific recognition of 5’ leaders by bacterial ribonuclease P. J Mol Biol 2010; 396(1):195–208.CrossRefGoogle Scholar
  9. 9.
    Mohanty BK, Kushner SR. Ribonuclease P processes polycistronic tRNA transcripts in Escherichia coli independent of ribonuclease E. Nucleic Acids Res 2007; 35(22):7614–7625.CrossRefGoogle Scholar
  10. 10.
    Mans RM, Guerrier-Takada C, Altman S et al. Interaction of RNase P from Escherichia coli with pseudoknotted structures in viral RNAs. Nucleic Acids Res 1990; 18(12):3479–3487.PubMedCrossRefGoogle Scholar
  11. 11.
    Bai Y, Rider PJ, Liu F. Catalytic M1GS RNA as an antiviral agent in animals. Methods Mol Biol 2010; 629:339–353.PubMedGoogle Scholar
  12. 12.
    Scif E, Altman S. RNase P cleaves the adenine riboswitch and stabilizes pbuE mRNA in Bacillus subtilis. RNA 2008; 14(6): 1237–1243.CrossRefGoogle Scholar
  13. 13.
    Altman S,W esolowski D, Guerrier-Takada C et al. RNase P cleavestransient structures in some riboswitches. Proc Natl Acad Sci U S A 2005; 102(32):11284–11289.PubMedCrossRefGoogle Scholar
  14. 14.
    De Lay N, Gottesman S. The Crp-activated small noncoding regulatory RNA CyaR (RyeE) links nutritional status to group behavior. J Bacteriol 2009; 191(2):461–476.PubMedCrossRefGoogle Scholar
  15. 15.
    Gottesman S, Storz G. Bacterial small RNA regulators: versatile roles and rapidly evolving variations. Cold Spring Harb Perspect Biol 2010; [Epub ahead of print].Google Scholar
  16. 16.
    Waters LS, Storz G. Regulatory RNAs in bacteria. Cell 2009; 136(4):615–628.PubMedCrossRefGoogle Scholar
  17. 17.
    Mandin P, Gottesman S. Integrating anaerobic/aerobic sensing and the general stress response through the ArcZ small RNA. EMBO J 2010; 29(18):3094–3107.PubMedCrossRefGoogle Scholar
  18. 18.
    Martinez-Antonio A, Janga SC, Thieffry D. Functional organisation of Escherichia coli transcriptional regulatory network. J Mol Biol 2008; 381(1):238–247.PubMedCrossRefGoogle Scholar
  19. 19.
    Gorke B, Vogel J. Noncoding RNA control of the making and breaking of sugars. Genes & development 2008;22(21):2914–2925.CrossRefGoogle Scholar
  20. 20.
    Masse E, Salvail H, Desnoyers G et al. Small RNAs controlling iron metabolism. Curr Opin Microbiol 2007; 10(2):140–145.PubMedCrossRefGoogle Scholar
  21. 21.
    Svenningsen SL, Tu KC, Bassler BL. Gene dosage compensation calibrates four regulatory RNAs to control Vibrio cholerae quorum sensing. EMBO J 2009; 28(4):429–439.PubMedCrossRefGoogle Scholar
  22. 22.
    Shimoni Y, Friedlander G, Hetzroni G et al. Regulation of gene expression by small non-coding RNAs: a quantitative view. Mol Syst Biol 2007; 3:138.PubMedCrossRefGoogle Scholar
  23. 23.
    Papenfort K, Said N, Welsink T et al. Specific and pleiotropic patterns of mRNA regulation by ArcZ, a conserved, Hfq-dependent small RNA. Mol Microbiol 2009; 74(1):139–158.PubMedCrossRefGoogle Scholar
  24. 24.
    Soper T, Mandin P, Majdalani N et al. Positive regulation by small RNAs and the role of Hfq. Proc Natl Acad Sci U S A 2010; 107(21):9602–9607.PubMedCrossRefGoogle Scholar
  25. 25.
    Hardwick SW, Chan VS, Broadhurst RW et al. An RNA degradosome assembly in Caulobacter crescentus. Nucleic Acids Res 2010; 39(4): 1449–1459.PubMedCrossRefGoogle Scholar
  26. 26.
    Janga SC, Babu MM. Transcript stability in the protein interaction network of Escherichia coli. Mol Biosyst 2009; 5(2):154–162.PubMedCrossRefGoogle Scholar
  27. 27.
    Worrall JA, Gorna M, Crump NT et al. Reconstitution and analysis of the multienzyme Escherichia coli RNA degradosome. J Mol Biol 2008; 382(4):870–883.PubMedCrossRefGoogle Scholar
  28. 28.
    Evguenieva-Hackenberg E, Klug G. RNA degradation in Archaea and Gram-negative bacteria different from Escherichia coli. Prog Mol Biol Transi Sci 2009; 85:275–317.CrossRefGoogle Scholar
  29. 29.
    Kaberdin VR, Lin-Chao S. Unraveling new roles for minor components of the E. coli RNA degradosome. RNA Biol 2009; 6(4):402–405.PubMedCrossRefGoogle Scholar
  30. 30.
    Monod J. Recherches sur la croissance des cultures bactériennes. Paris: Hermann & cie; 1942.Google Scholar
  31. 31.
    Fujita Y. Carbon catabolite control of the metabolic network in Bacillus subtilis. Biosci Biotechnol Biochem 2009; 73(2):245–259.PubMedCrossRefGoogle Scholar
  32. 32.
    Sonnleitner E, Abdou L, Haas D. Small RNA as global regulator of carbon catabolite repression in Pseudomonas aeruginosa. Proc Natl Acad Sci U S A 2009; 106(51):21866–21871.PubMedCrossRefGoogle Scholar
  33. 33.
    Vogel J, Papenfort K. Small non-coding RNAs and the bacterial outer membrane. Curr Opin Microbiol 2006; 9(6):605–611.PubMedCrossRefGoogle Scholar
  34. 34.
    Figueroa-Bossi N, Valentini M, Malleret L et al. Caught at its own game: regulatory small RNA inactivated by an inducible transcript mimicking its target. Genes & development 2009; 23(17):2004–2015.CrossRefGoogle Scholar
  35. 35.
    Wadler CS, Vanderpool CK. Characterization of homologs of the small RNA SgrS reveals diversity in function. Nucleic Acids Res 2009; 37(16):5477–5485.PubMedCrossRefGoogle Scholar
  36. 36.
    Reichenbach B, Gopel Y, Gorke B. Dual control by perfectly overlapping sigma 54-and sigma 70-promoters adjusts small RNA GlmY expression to different environmental signals. Mol Microbiol 2009; 74(5): 1054–1070.PubMedCrossRefGoogle Scholar
  37. 37.
    Winkler WC, Nahvi A, Roth A et al. Control of gene expression by anatural metabolite-responsive ribozyme. Nature 2004; 428(6980):281–286.PubMedCrossRefGoogle Scholar
  38. 38.
    McCarthy TJ, Plog MA, Floy SA et al. Ligand requirements for glmS ribozyme self-cleavage. Chem Biol 2005; 12(11):1221–1226.PubMedCrossRefGoogle Scholar
  39. 39.
    Collins JA, Irnov I, Baker S et al. Mechanism of mRNA destabilization by the glmS ribozyme. Genes Dev 2007;21(24):3356–3368.PubMedCrossRefGoogle Scholar
  40. 40.
    Abe T, Sakaki K, Fujihara A et al. tmRNA-dependent trans-translation is required for sporulation in Bacillus subtilis. Mol Microbiol 2008; 69(6):1491–1498.PubMedCrossRefGoogle Scholar
  41. 41.
    Wower J, Wower IK, Zwieb C. Making the jump: new insights into the mechanism of trans-translation. J Biol 2008; 7(5): 17.PubMedCrossRefGoogle Scholar
  42. 42.
    Une M, Kurita D, Muto A et al. Trans-translation by tmRNA and SmpB. Nucleic Acids Symp Ser (Oxf) 2009; (53):305–306.Google Scholar
  43. 43.
    Hayes CS, Keiler KC. Beyond ribosome rescue: tmRNA and co-translational processes. FEBS Lett 2010; 584(2):413–419.PubMedCrossRefGoogle Scholar
  44. 44.
    Liu Y, Wu N, Dong J et al. SsrA (tmRNA) acts as an antisense RNA to regulate Staphylococcus aureus pigment synthesis by base pairing with crtMN mRNA. FEBS Lett 2010; 584(20):4325–4329.PubMedCrossRefGoogle Scholar
  45. 45.
    Kuo HK, Krasich R, Bhagwat AS et al. Importance of the tmRNA system for cell survival when transcription is blocked by DNA-protein cross-links. Mol Microbiol 2010; 78(3):686–700.PubMedCrossRefGoogle Scholar

Copyright information

© Landes Bioscience and Springer Science+Business Media, LLC 2011

Authors and Affiliations

  • Lesley J. Collins
    • 1
  • Patrick J. Biggs
    • 2
  1. 1.Institute of Fundamental SciencesMassey UniversityPalmerston NorthNew Zealand
  2. 2.Institute of Veterinary, Animal and Biomedical SciencesMassey UniversityPalmerston NorthNew Zealand

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