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RNA Networks in Prokaryotes I: CRISPRs and Riboswitches

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Book cover RNA Infrastructure and Networks

Part of the book series: Advances in Experimental Medicine and Biology ((AEMB,volume 722))

  • 2012 Accesses

Abstract

As with eukaryotes, prokaryotes employ a variety of mechanisms to allow the various types of RNA to interact and perform complex functions as a network. This chapter will detail prokaryotic molecular systems, such as riboswitches and CRISPRs, to show how they perform unique functions within the cell. These systems can interact with each other to gain a higher level of control and here we highlight some examples of such interactions including the cleavage of certain riboswitches by RNaseP, and endoribonuclease cleavage of pre-crRNAs in the CRISPR system. Thanks to such insights, we are beginning to get a glimpse of the prokaryotic RNA infrastructure, just as we have done with eukaryotes.

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References

  1. Serganov A. The long and the short of riboswitches. Curr Opin Struct Biol 2009; 19(3):251–259.

    Article  PubMed  CAS  Google Scholar 

  2. Garst AD, Batey RT. A switch in time: detailing the life of a riboswitch. Biochim Biophys Acta 2009; 1789(9–10):584–591.

    PubMed  CAS  Google Scholar 

  3. Mandal M, Boese B, Barrick JE et al. Riboswitches control fundamental biochemical pathways in Bacillus subtilis and other bacteria. Cell 2003; 113(5):577–586.

    Article  PubMed  CAS  Google Scholar 

  4. Weinberg Z, Wang JX, Bogue J et al. Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea, and their metagenomes. Genome Biol 2010; 11(3):R31.

    Article  PubMed  Google Scholar 

  5. Wachter A, Tunc-Ozdemir M, Grove BC et al. Riboswitch control of gene expression in plants by splicing and alternative 3′ end processing of mRNAs. Plant Cell 2007; 19(11):3437–3450.

    Article  PubMed  CAS  Google Scholar 

  6. Cheah MT, Wachter A, Sudarsan N et al. Control of alternative RNA splicing and gene expression by eukaryotic riboswitches. Nature 2007; 447(7143):497–500.

    Article  PubMed  CAS  Google Scholar 

  7. Edwards TE, Klein DJ, Ferre-D’Amare AR. Riboswitches: small-molecule recognition by gene regulatory RNAs. Curr Opin Struct Biol 2007; 17(3):273–279.

    Article  PubMed  CAS  Google Scholar 

  8. Ravnum S, Andersson DI. An adenosyl-cobalamin (coenzyme-B12)-repressed translational enhancer in the cob mRNA of Salmonella typhimurium. Mol Microbiol 2001; 39(6): 1585–1594.

    Article  PubMed  CAS  Google Scholar 

  9. Nahvi A, Barrick JE, Breaker RR. Coenzyme B12 riboswitches are widespread genetic control elements in prokaryotes. Nucleic Acids Res 2004; 32(1):143–150.

    Article  PubMed  CAS  Google Scholar 

  10. Winkler WC, Nahvi A, Sudarsan N et al. An mRNA structure that controls gene expression by binding S-adenosylmethionine. Nat Struct Biol 2003; 10(9):701–707.

    Article  PubMed  CAS  Google Scholar 

  11. Corbino KA, Barrick JE, Lim J et al. Evidence for a second class of S-adenosylmethionine riboswitches and other regulatory RNA motifs in alpha-proteobacteria. Genome Biol 2005; 6(8):R70.

    Article  PubMed  Google Scholar 

  12. Montange RK, Batey RT. Structure of the S-adenosylmethionine riboswitch regulatory mRNA element. Nature 2006; 441(7097):1172–1175.

    Article  PubMed  CAS  Google Scholar 

  13. Gutierrez-Preciado A, Henkin TM, Grundy FJ et al. Biochemical features and functional implications of the RNA-based T-box regulatory mechanism. Microbiol Mol Biol Rev 2009; 73(1):36–61.

    Article  PubMed  CAS  Google Scholar 

  14. Cromie MJ, Shi Y, Latifi T et al. An RNA sensor for intracellular Mg(2+). Cell 2006; 125(1):71–84.

    Article  PubMed  CAS  Google Scholar 

  15. O’Connor K, Fletcher SA, Csonka LN. Increased expression of Mg(2+) transport proteins enhances the survival of Salmonella enterica at high temperature. Proc Natl Acad Sci USA 2009; 106(41): 17522–17527.

    Article  PubMed  Google Scholar 

  16. Waldminghaus T, Heidrich N, Brantl S et al. Four U: a novel type of RNA thermometer in Salmonella. Mol Microbiol 2007; 65(2):413–424.

    Article  PubMed  CAS  Google Scholar 

  17. Mandal M, Lee M, Barrick JE et al. A glycine-dependent riboswitch that uses cooperative binding to control gene expression. Science 2004; 306(5694):275–279.

    Article  PubMed  CAS  Google Scholar 

  18. Sudarsan N, Hammond MC, Block KF et al. Tandem riboswitch architectures exhibit complex gene control functions. Science 2006; 314(5797):300–304.

    Article  PubMed  CAS  Google Scholar 

  19. Jansen R, Embden JD, Gaastra W et al. Identification of genes that are associated with DNA repeats in prokaryotes. Mol Microbiol 2002; 43(6):1565–1575.

    Article  PubMed  CAS  Google Scholar 

  20. Ishino Y, Shinagawa H, Makino K et al. Nucleotide sequence of the iap gene, responsible for alkaline phosphatase isozyme conversion in Escherichia coli, and identification of the gene product. J Bacteriol 1987; 169(12):5429–5433.

    PubMed  CAS  Google Scholar 

  21. Mojica FJ, Diez-Villasenor C, Soria E et al. Biological significance of a family of regularly spaced repeats in the genomes of Archaea, Bacteria and mitochondria. Mol Microbiol 2000; 36(1):244–246.

    Article  PubMed  CAS  Google Scholar 

  22. Marraffini LA, Sontheimer EJ. CRISPR interference: RNA-directed adaptive immunity in bacteria and archaea. Nat Rev Genet 2010; 11(3):181–190.

    Article  PubMed  CAS  Google Scholar 

  23. Mojica FJ, Ferrer C, Juez G et al. Long stretches of short tandem repeats are present in the largest replicons of the Archaea Haloferax mediterranei and Haloferax volcanii and could be involved in replicon partitioning. Mol Microbiol 1995; 17(1):85–93.

    Article  PubMed  CAS  Google Scholar 

  24. Makarova KS, Aravind L, Grishin NV et al. A DNA repair system specific for thermophilic Archaea and bacteria predicted by genomic context analysis. Nucleic Acids Res 2002; 30(2):482–496.

    Article  PubMed  CAS  Google Scholar 

  25. Bolotin A, Quinquis B, Sorokin A et al. Clustered regularly interspaced short palindrome repeats (CRISPRs) have spacers of extrachromosomal origin. Microbiology 2005; 151(Pt 8):2551–2561.

    Article  PubMed  CAS  Google Scholar 

  26. Mojica FJ, Diez-Villasenor C, Garcia-Martinez J et al. Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements. J Mol Evol 2005; 60(2): 174–182.

    Article  PubMed  CAS  Google Scholar 

  27. Pourcel C, Salvignol G, Vergnaud G. CRISPR elements in Yersiniapestis acquire new repeats by preferential uptake of bacteriophage DNA, and provide additional tools for evolutionary studies. Microbiology 2005; 151(Pt 3):653–663.

    Article  PubMed  CAS  Google Scholar 

  28. Barrangou R, Fremaux C, Deveau H et al. CRISPR provides acquired resistance against viruses in prokaryotes. Science 2007; 315(5819):1709–1712.

    Article  PubMed  CAS  Google Scholar 

  29. Deveau H, Barrangou R, Garneau JE et al. Phage response to CRISPR-encoded resistance in Streptococcus thermophilus. J Bacteriol 2008; 190(4):1390–1400.

    Article  PubMed  CAS  Google Scholar 

  30. Horvath P, Romero DA, Coute-Monvoisin AC et al. Diversity, activity, and evolution of CRISPR loci in Streptococcus thermophilus. J Bacteriol 2008; 190(4): 1401–1412.

    Article  PubMed  CAS  Google Scholar 

  31. Tang TH, Polacek N, Zywicki M et al. Identification of novel non-coding RNAs as potential antisense regulators in the archaeon Sulfolobus solfataricus. Mol Microbiol 2005; 55(2):469–481.

    Article  PubMed  CAS  Google Scholar 

  32. Tang TH, Bachellerie JP, Rozhdestvensky T et al. Identification of 86 candidates for small nonmessenger RNAs from the archaeon Archaeoglobus fulgidus. Proc Natl Acad Sci U S A 2002; 99(11):7536–7541.

    Article  PubMed  CAS  Google Scholar 

  33. Godde JS, Bickerton A. The repetitive DNA elements called CRISPRs and their associated genes: evidence of horizontal transfer among prokaryotes. J Mol Evol 2006; 62(6):718–729.

    Article  PubMed  CAS  Google Scholar 

  34. Haft DH, Selengut J, Mongodin EF et al. A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes. PLoS Comput Biol 2005; 1(6):e60.

    Article  PubMed  Google Scholar 

  35. Makarova KS, Grishin NV, Shabalina SA et al. A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi and hypothetical mechanisms of action. Biol Direct 2006; 1:7.

    Article  PubMed  Google Scholar 

  36. Kunin V, Sorek R, Hugenholtz P. Evolutionary conservation of sequence and secondary structures in CRISPR repeats. Genome Biol 2007; 8(4):R61.

    Article  PubMed  Google Scholar 

  37. Mojica FJ, Diez-Villasenor C, Garcia-Martinez J et al. Short motif sequences determine the targets of the prokaryotic CRISPR defence system. Microbiology 2009; 155(Pt 3):733–740.

    Article  PubMed  CAS  Google Scholar 

  38. Mojica FJ, Diez-Villasenor C. The on-off switch of CRISPR immunity against phages in Escherichia coli. Mol Microbiol 2010; 77(6):1341–1345.

    Article  PubMed  CAS  Google Scholar 

  39. Pougach K, Semenova E, Bogdanova E et al. Transcription, processing and function of CRISPR cassettes in Escherichia coli. Mol Microbiol 2010; 77(6):1367–1379.

    Article  PubMed  CAS  Google Scholar 

  40. Edwards RA, Rohwer F. Viral metagenomics. Nat Rev Microbiol 2005; 3(6):504–510.

    Article  PubMed  CAS  Google Scholar 

  41. Edgar RC. PILER-CR: fast and accurate identification of CRISPR repeats. BMC Bioinformatics 2007; 8:18.

    Article  PubMed  Google Scholar 

  42. Bland C, Ramsey TL, Sabree F et al. CRISPR recognition tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats. BMC Bioinformatics 2007; 8:209.

    Article  PubMed  Google Scholar 

  43. Grissa I, Vergnaud G, Pourcel C. The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats. BMC Bioinformatics 2007; 8:172.

    Article  PubMed  Google Scholar 

  44. Grissa I, Vergnaud G, Pourcel C. CRISPRcompar: a website to compare clustered regularly interspaced short palindromic repeats. Nucleic Acids Res 2008; 36(Web Server issue):W145–W148.

    Article  PubMed  CAS  Google Scholar 

  45. Rousseau C, Gonnet M, Le Romancer M et al. CRISPI: a CRISPR interactive database. Bioinformatics 2009; 25(24):3317–3318.

    Article  PubMed  CAS  Google Scholar 

  46. Mrazek J, Xie S, Guo X et al. AIMIE: a web-based environment for detection and interpretation of significant sequence motifs in prokaryotic genomes. Bioinformatics 2008; 24(8): 1041–1048.

    Article  PubMed  CAS  Google Scholar 

  47. Deveau H, Garneau JE, Moineau S. CRISPR/Cas system and its role in phage-bacteria interactions. Annu Rev Microbiol 2010; 64:475–493.

    Article  PubMed  CAS  Google Scholar 

  48. Sorek R, Kunin V, Hugenholtz P. CRISPR—a widespread system that provides acquired resistance against phages in bacteria and archaea. Nat Rev Microbiol 2008; 6(3):181–186.

    Article  PubMed  CAS  Google Scholar 

  49. Stern A, Keren L, Wurtzel O et al. Self-targeting by CRISPR: gene regulation or autoimmunity? Trends Genet 2010; 26(8):335–340.

    Article  PubMed  CAS  Google Scholar 

  50. Sebaihia M, Wren BW, Mullany P et al. The multidrug-resistant human pathogen Clostridium difficile has a highly mobile, mosaic genome. Nat Genet 2006; 38(7):779–786.

    Article  PubMed  Google Scholar 

  51. Marraffini LA, Sontheimer EJ. Self versus nonself discrimination during CRISPR RNA-directed immunity. Nature 2010; 463(7280):568–571.

    Article  PubMed  CAS  Google Scholar 

  52. Aklujkar M, Lovley DR. Interference with histidyl-tRNA synthetase by a CRISPR spacer sequence as a factor in the evolution of Pelobacter carbinolicus. BMC Evol Biol 2010; 10:230.

    Article  PubMed  Google Scholar 

  53. Brouns SJ, Jore MM, Lundgren M et al. Small CRISPR RNAs guide antiviral defense in prokaryotes. Science 2008; 321(5891):960–964.

    Article  PubMed  CAS  Google Scholar 

  54. Li Y, Liu X, Huang L et al. Potential coexistence of both bacterial and eukaryotic small RNA biogenesis and functional related protein homologs in Archaea. J Genet Genomics 2010; 37(8):493–503.

    Article  PubMed  CAS  Google Scholar 

  55. Haurwitz RE, Jinek M, Wiedenheft B et al. Sequence-and structure-specific RNA processing by a CRISPR endonuclease. Science 2010; 329(5997):1355–1358.

    Article  PubMed  Google Scholar 

  56. Touchon M, Rocha EP. The small, slow and specialized CRISPR and anti-CRISPR of Escherichia and Salmonella. PLoS One 2010; 5(6):e11126.

    Article  PubMed  Google Scholar 

  57. Stern A, Sorek R. Thephage-host arms race: shapingthe evolution of microbes. Bioessays 2011; 33(1):43–51.

    Article  PubMed  CAS  Google Scholar 

  58. 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.

    Article  PubMed  CAS  Google Scholar 

  59. Kunst F, Ogasawara N, Moszer I et al. The complete genome sequence of the gram-positive bacterium Bacillus subtilis. Nature 1997; 390(6657):249–256.

    Article  PubMed  CAS  Google Scholar 

  60. Gardner PP, Daub J, Tate JG et al. Rfam: updates to the RNA families database. Nucleic Acids Res 2009; 37(Database issue):D136–D140.

    Article  PubMed  CAS  Google Scholar 

  61. Darty K, Denise A, Ponty Y. VARNA: Interactive drawing and editing of the RNA secondary structure. Bioinformatics 2009; 25(15):1974–1975.

    Article  PubMed  CAS  Google Scholar 

  62. Horvath P, Barrangou R. CRISPR/Cas, the immune system of bacteria and archaea. Science 2010; 327(5962): 167–170.

    Article  PubMed  CAS  Google Scholar 

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Biggs, P.J., Collins, L.J. (2011). RNA Networks in Prokaryotes I: CRISPRs and Riboswitches. In: Collins, L.J. (eds) RNA Infrastructure and Networks. Advances in Experimental Medicine and Biology, vol 722. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-0332-6_13

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