Table of Contents Author Guidelines Submit a Manuscript
Archaea
Volume 2012, Article ID 260909, 11 pages
http://dx.doi.org/10.1155/2012/260909
Research Article

tRNA-Derived Fragments Target the Ribosome and Function as Regulatory Non-Coding RNA in Haloferax volcanii

1Department of Chemistry and Biochemistry, University of Bern, Freiestraße 3, 3012 Bern, Switzerland
2Graduate School for Cellular and Biomedical Sciences, University of Bern, 3012 Bern, Switzerland
3Division of Genomics and RNomics, Innsbruck Biocenter, Innsbruck Medical University , Innrain 80/82, 6020 Innsbruck, Austria
4Laboratory of Computational Genomics, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, 61-712 Poznan, Poland

Received 14 September 2012; Revised 16 November 2012; Accepted 28 November 2012

Academic Editor: Anita Marchfelder

Copyright © 2012 Jennifer Gebetsberger et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. A. Hüttenhofer, P. Schattner, and N. Polacek, “Non-coding RNAs: hope or hype?” Trends in Genetics, vol. 21, no. 5, pp. 289–297, 2005. View at Publisher · View at Google Scholar · View at Scopus
  2. P. P. Amaral, M. E. Dinger, T. R. Mercer, and J. S. Mattick, “The eukaryotic genome as an RNA machine,” Science, vol. 319, no. 5871, pp. 1787–1789, 2008. View at Publisher · View at Google Scholar · View at Scopus
  3. C. Ender, A. Krek, M. R. Friedländer et al., “A human snoRNA with microRNA-like functions,” Molecular Cell, vol. 32, no. 4, pp. 519–528, 2008. View at Publisher · View at Google Scholar · View at Scopus
  4. M. Brameier, A. Herwig, R. Reinhardt, L. Walter, and J. Gruber, “Human box C/D snoRNAs with miRNA like functions: expanding the range of regulatory RNAs,” Nucleic Acids Research, vol. 39, no. 2, pp. 675–686, 2011. View at Publisher · View at Google Scholar · View at Scopus
  5. H. Kawaji, M. Nakamura, Y. Takahashi et al., “Hidden layers of human small RNAs,” BMC Genomics, vol. 9, article 157, 2008. View at Publisher · View at Google Scholar · View at Scopus
  6. Z. Li, C. Ender, G. Meister, P. S. Moore, Y. Chang, and B. John, “Extensive terminal and asymmetric processing of small RNAs from rRNAs, snoRNAs, snRNAs, and tRNAs,” Nucleic Acids Research, vol. 40, no. 14, pp. 6787–6799, 2012. View at Publisher · View at Google Scholar
  7. M. Zywicki, K. Bakowska-Zywicka, and N. Polacek, “Revealing stable processing products from ribosome-associated small RNAs by deep-sequencing data analysis,” Nucleic Acids Research, vol. 40, no. 9, pp. 4013–4024, 2012. View at Publisher · View at Google Scholar
  8. D. M. Thompson and R. Parker, “Stressing out over tRNA cleavage,” Cell, vol. 138, no. 2, pp. 215–219, 2009. View at Publisher · View at Google Scholar · View at Scopus
  9. Y. S. Lee, Y. Shibata, A. Malhotra, and A. Dutta, “A novel class of small RNAs: tRNA-derived RNA fragments (tRFs),” Genes and Development, vol. 23, no. 22, pp. 2639–2649, 2009. View at Publisher · View at Google Scholar · View at Scopus
  10. M. Bühler, N. Spies, D. P. Bartel, and D. Moazed, “TRAMP-mediated RNA surveillance prevents spurious entry of RNAs into the Schizosaccharomyces pombe siRNA pathway,” Nature Structural and Molecular Biology, vol. 15, no. 10, pp. 1015–1023, 2008. View at Publisher · View at Google Scholar · View at Scopus
  11. C. Cole, A. Sobala, C. Lu et al., “Filtering of deep sequencing data reveals the existence of abundant Dicer-dependent small RNAs derived from tRNAs,” RNA, vol. 15, no. 12, pp. 2147–2160, 2009. View at Publisher · View at Google Scholar · View at Scopus
  12. D. Haussecker, Y. Huang, A. Lau, P. Parameswaran, A. Z. Fire, and M. A. Kay, “Human tRNA-derived small RNAs in the global regulation of RNA silencing,” RNA, vol. 16, no. 4, pp. 673–695, 2010. View at Publisher · View at Google Scholar · View at Scopus
  13. P. Ivanov, M. M. Emara, J. Villen, S. P. Gygi, and P. Anderson, “Angiogenin-induced tRNA fragments inhibit translation initiation,” Molecular Cell, vol. 43, no. 4, pp. 613–623, 2011. View at Publisher · View at Google Scholar
  14. C. Jöchl, M. Rederstorff, J. Hertel et al., “Small ncRNA transcriptome analysis from Aspergillus fumigatus suggests a novel mechanism for regulation of protein synthesis,” Nucleic Acids Research, vol. 36, no. 8, pp. 2677–2689, 2008. View at Publisher · View at Google Scholar · View at Scopus
  15. S. Yamasaki, P. Ivanov, G. F. Hu, and P. Anderson, “Angiogenin cleaves tRNA and promotes stress-induced translational repression,” Journal of Cell Biology, vol. 185, no. 1, pp. 35–42, 2009. View at Publisher · View at Google Scholar · View at Scopus
  16. S. Zhang, L. Sun, and F. Kragler, “The phloem-delivered RNA pool contains small noncoding RNAs and interferes with translation,” Plant Physiology, vol. 150, no. 1, pp. 378–387, 2009. View at Publisher · View at Google Scholar · View at Scopus
  17. J. Straub, M. Brenneis, A. Jellen-Ritter, R. Heyer, J. Soppa, and A. Marchfelder, “Small RNAs in haloarchaea: identification, differential expression and biological function,” RNA Biology, vol. 6, no. 3, pp. 281–292, 2009. View at Google Scholar · View at Scopus
  18. P. Khaitovich, T. Tenson, P. Kloss, and A. S. Mankin, “Reconstitution of functionally active Thermus aquaticus large ribosomal subunits with in vitro-transcribed rRNA,” Biochemistry, vol. 38, no. 6, pp. 1780–1788, 1999. View at Publisher · View at Google Scholar · View at Scopus
  19. G. Ring, P. Londei, and J. Eichler, “Protein biogenesis in Archaea: addressing translation initiation using an in vitro protein synthesis system for Haloferax volcanii,” FEMS Microbiology Letters, vol. 270, no. 1, pp. 34–41, 2007. View at Publisher · View at Google Scholar · View at Scopus
  20. R. E. Monro and K. A. Marcker, “Ribosome-catalysed reaction of puromycin with a formylmethionine-containing oligonucleotide,” Journal of Molecular Biology, vol. 25, no. 2, pp. 347–350, 1967. View at Google Scholar · View at Scopus
  21. N. Polacek, S. Swaney, D. Shinabarger, and A. S. Mankin, “SPARK—a novel method to monitor ribosomal peptidyl transferase activity,” Biochemistry, vol. 41, no. 39, pp. 11602–11610, 2002. View at Publisher · View at Google Scholar · View at Scopus
  22. M. D. Erlacher, K. Lang, N. Shankaran et al., “Chemical engineering of the peptidyl transferase center reveals an important role of the 2′-hydroxyl group of A2451,” Nucleic Acids Research, vol. 33, no. 5, pp. 1618–1627, 2005. View at Publisher · View at Google Scholar · View at Scopus
  23. F. Gebauer and M. W. Hentze, “Molecular mechanisms of translational control,” Nature Reviews Molecular Cell Biology, vol. 5, no. 10, pp. 827–835, 2004. View at Publisher · View at Google Scholar · View at Scopus
  24. J. S. Mattick and I. V. Makunin, “Non-coding RNA,” Human molecular genetics, vol. 15, supplement 1, pp. R17–R29, 2006. View at Publisher · View at Google Scholar · View at Scopus
  25. C. Zwieb and S. Bhuiyan, “Archaea signal recognition particle shows the way,” Archaea, vol. 2010, Article ID 485051, 11 pages, 2010. View at Publisher · View at Google Scholar · View at Scopus
  26. B. D. Janssen and C. S. Hayes, “The tmRNA ribosome-rescue system,” Advances in Protein Chemistry and Structural Biology, vol. 86, pp. 151–191, 2012. View at Publisher · View at Google Scholar
  27. D. N. Wilson, “The A-Z of bacterial translation inhibitors,” Critical Reviews in Biochemistry and Molecular Biology, vol. 44, no. 6, pp. 393–433, 2009. View at Publisher · View at Google Scholar · View at Scopus
  28. D. M. Thompson, C. Lu, P. J. Green, and R. Parker, “tRNA cleavage is a conserved response to oxidative stress in eukaryotes,” RNA, vol. 14, no. 10, pp. 2095–2103, 2008. View at Publisher · View at Google Scholar · View at Scopus
  29. H. Fu, J. Feng, Q. Liu et al., “Stress induces tRNA cleavage by angiogenin in mammalian cells,” FEBS Letters, vol. 583, no. 2, pp. 437–442, 2009. View at Publisher · View at Google Scholar · View at Scopus
  30. R. Heyer, M. Dorr, A. Jellen-Ritter et al., “High throughput sequencing reveals a plethora of small RNAs including tRNA derived fragments in Haloferax volcanii,” RNA Biology, vol. 9, no. 7, pp. 1011–1018, 2012. View at Publisher · View at Google Scholar
  31. D. M. Thompson and R. Parker, “The RNase Rny1p cleaves tRNAs and promotes cell death during oxidative stress in Saccharomyces cerevisiae,” Journal of Cell Biology, vol. 185, no. 1, pp. 43–50, 2009. View at Publisher · View at Google Scholar · View at Scopus
  32. M. Saikia, D. Krokowski, B. J. Guan et al., “Genome-wide identification and quantitative analysis of cleaved tRNA fragments induced by cellular stress,” The Journal of Biological Chemistry, vol. 287, no. 51, pp. 42708–42725, 2012. View at Publisher · View at Google Scholar
  33. M. R. Garcia-Silva, M. Frugier, J. P. Tosar et al., “A population of tRNA-derived small RNAs is actively produced in Trypanosoma cruzi and recruited to specific cytoplasmic granules,” Molecular and Biochemical Parasitology, vol. 171, no. 2, pp. 64–73, 2010. View at Publisher · View at Google Scholar · View at Scopus
  34. H. J. Haiser, F. V. Karginov, G. J. Hannon, and M. A. Elliot, “Developmentally regulated cleavage of tRNAs in the bacterium Streptomyces coelicolor,” Nucleic Acids Research, vol. 36, no. 3, pp. 732–741, 2008. View at Publisher · View at Google Scholar · View at Scopus
  35. M. Rederstorff and A. Hüttenhofer, “CDNA library generation from ribonucleoprotein particles,” Nature Protocols, vol. 6, no. 2, pp. 166–174, 2011. View at Publisher · View at Google Scholar · View at Scopus