Please use this identifier to cite or link to this item:
標題: DU177 RNA假結刺激程式化-1轉譯框架移轉的重要結構特徵探討
The important structural features of the DU177 RNA pseudoknot in stimulating programmed -1 ribosomal frameshifting
作者: 周銘源
Chou, Ming-Yuan
關鍵字: frameshifting;轉譯框架移轉;-1PRF;RNA pseudoknot;ribosome translocation;程式化-1轉譯框架移轉;核醣核酸假結;核醣體轉譯位移
出版社: 生物化學研究所
引用: 1. Beremand, M. N., and Blumenthal, T. (1979) Overlapping genes in RNA phage: a new protein implicated in lysis, Cell 18, 257-266. 2. Kurland, C. G. (1992) Translational accuracy and the fitness of bacteria, Annu Rev Genet 26, 29-50. 3. Jacks, T., and Varmus, H. E. (1985) Expression of the Rous sarcoma virus pol gene by ribosomal frameshifting, Science 230, 1237-1242. 4. Pande, S., Vimaladithan, A., Zhao, H., and Farabaugh, P. J. (1995) Pulling the ribosome out of frame by +1 at a programmed frameshift site by cognate binding of aminoacyl-tRNA, Mol Cell Biol 15, 298-304. 5. Jacks, T., Madhani, H. D., Masiarz, F. R., and Varmus, H. E. (1988) Signals for ribosomal frameshifting in the Rous sarcoma virus gag-pol region, Cell 55, 447-458. 6. Jacks, T., Townsley, K., Varmus, H. E., and Majors, J. (1987) Two efficient ribosomal frameshifting events are required for synthesis of mouse mammary tumor virus gag-related polyproteins, Proc Natl Acad Sci U S A 84, 4298-4302. 7. Hizi, A., Henderson, L. E., Copeland, T. D., Sowder, R. C., Hixson, C. V., and Oroszlan, S. (1987) Characterization of mouse mammary tumor virus gag-pro gene products and the ribosomal frameshift site by protein sequencing, Proc Natl Acad Sci U S A 84, 7041-7045. 8. Stahl, G., McCarty, G. P., and Farabaugh, P. J. (2002) Ribosome structure: revisiting the connection between translational accuracy and unconventional decoding, Trends Biochem Sci 27, 178-183. 9. Somogyi, P., Jenner, A. J., Brierley, I., and Inglis, S. C. (1993) Ribosomal pausing during translation of an RNA pseudoknot, Mol Cell Biol 13, 6931-6940. 10. Tsuchihashi, Z. (1991) Translational frameshifting in the Escherichia coli dnaX gene in vitro, Nucleic Acids Res 19, 2457-2462. 11. Tu, C., Tzeng, T. H., and Bruenn, J. A. (1992) Ribosomal movement impeded at a pseudoknot required for frameshifting, Proc Natl Acad Sci U S A 89, 8636-8640. 12. Plant, E. P., Jacobs, K. L., Harger, J. W., Meskauskas, A., Jacobs, J. L., Baxter, J. L., Petrov, A. N., and Dinman, J. D. (2003) The 9-A solution: how mRNA pseudoknots promote efficient programmed -1 ribosomal frameshifting, RNA 9, 168-174. 13. Kontos, H., Napthine, S., and Brierley, I. (2001) Ribosomal pausing at a frameshifter RNA pseudoknot is sensitive to reading phase but shows little correlation with frameshift efficiency, Mol Cell Biol 21, 8657-8670. 14. Namy, O., Moran, S. J., Stuart, D. I., Gilbert, R. J., and Brierley, I. (2006) A mechanical explanation of RNA pseudoknot function in programmed ribosomal frameshifting, Nature 441, 244-247. 15. Wen, J. D., Lancaster, L., Hodges, C., Zeri, A. C., Yoshimura, S. H., Noller, H. F., Bustamante, C., and Tinoco, I. (2008) Following translation by single ribosomes one codon at a time, Nature 452, 598-603. 16. Moran, S. J., Flanagan, J. F. t., Namy, O., Stuart, D. I., Brierley, I., and Gilbert, R. J. (2008) The mechanics of translocation: a molecular "spring-and-ratchet" system, Structure 16, 664-672. 17. Giedroc, D. P., and Cornish, P. V. (2009) Frameshifting RNA pseudoknots: structure and mechanism, Virus Res 139, 193-208. 18. Plant, E. P., and Dinman, J. D. (2005) Torsional restraint: a new twist on frameshifting pseudoknots, Nucleic Acids Res 33, 1825-1833. 19. Kang, H., Hines, J. V., and Tinoco, I., Jr. (1996) Conformation of a non-frameshifting RNA pseudoknot from mouse mammary tumor virus, J Mol Biol 259, 135-147. 20. Dulude, D., Baril, M., and Brakier-Gingras, L. (2002) Characterization of the frameshift stimulatory signal controlling a programmed -1 ribosomal frameshift in the human immunodeficiency virus type 1, Nucleic Acids Res 30, 5094-5102. 21. Larsen, B., Wills, N. M., Gesteland, R. F., and Atkins, J. F. (1994) rRNA-mRNA base pairing stimulates a programmed -1 ribosomal frameshift, J Bacteriol 176, 6842-6851. 22. Rettberg, C. C., Prere, M. F., Gesteland, R. F., Atkins, J. F., and Fayet, O. (1999) A three-way junction and constituent stem-loops as the stimulator for programmed -1 frameshifting in bacterial insertion sequence IS911, J Mol Biol 286, 1365-1378. 23. Bekaert, M., and Rousset, J. P. (2005) An extended signal involved in eukaryotic -1 frameshifting operates through modification of the E site tRNA, Mol Cell 17, 61-68. 24. Napthine, S., Liphardt, J., Bloys, A., Routledge, S., and Brierley, I. (1999) The role of RNA pseudoknot stem 1 length in the promotion of efficient -1 ribosomal frameshifting, J Mol Biol 288, 305-320. 25. Liphardt, J., Napthine, S., Kontos, H., and Brierley, I. (1999) Evidence for an RNA pseudoknot loop-helix interaction essential for efficient -1 ribosomal frameshifting, J Mol Biol 288, 321-335. 26. Su, L., Chen, L., Egli, M., Berger, J. M., and Rich, A. (1999) Minor groove RNA triplex in the crystal structure of a ribosomal frameshifting viral pseudoknot, Nat Struct Biol 6, 285-292. 27. Chen, X., Kang, H., Shen, L. X., Chamorro, M., Varmus, H. E., and Tinoco, I., Jr. (1996) A characteristic bent conformation of RNA pseudoknots promotes -1 frameshifting during translation of retroviral RNA, J Mol Biol 260, 479-483. 28. Kim, Y. G., Maas, S., Wang, S. C., and Rich, A. (2000) Mutational study reveals that tertiary interactions are conserved in ribosomal frameshifting pseudoknots of two luteoviruses, RNA 6, 1157-1165. 29. Pallan, P. S., Marshall, W. S., Harp, J., Jewett, F. C., 3rd, Wawrzak, Z., Brown, B. A., 2nd, Rich, A., and Egli, M. (2005) Crystal structure of a luteoviral RNA pseudoknot and model for a minimal ribosomal frameshifting motif, Biochemistry 44, 11315-11322. 30. Plant, E. P., Rakauskaite, R., Taylor, D. R., and Dinman, J. D. (2010) Achieving a golden mean: mechanisms by which coronaviruses ensure synthesis of the correct stoichiometric ratios of viral proteins, J Virol 84, 4330-4340. 31. Dinman, J. D., and Wickner, R. B. (1992) Ribosomal frameshifting efficiency and gag/gag-pol ratio are critical for yeast M1 double-stranded RNA virus propagation, J Virol 66, 3669-3676. 32. Felsenstein, K. M., and Goff, S. P. (1988) Expression of the gag-pol fusion protein of Moloney murine leukemia virus without gag protein does not induce virion formation or proteolytic processing, J Virol 62, 2179-2182. 33. Hung, M., Patel, P., Davis, S., and Green, S. R. (1998) Importance of ribosomal frameshifting for human immunodeficiency virus type 1 particle assembly and replication, J Virol 72, 4819-4824. 34. Theimer, C. A., Blois, C. A., and Feigon, J. (2005) Structure of the human telomerase RNA pseudoknot reveals conserved tertiary interactions essential for function, Mol Cell 17, 671-682. 35. Kim, N. K., Zhang, Q., Zhou, J., Theimer, C. A., Peterson, R. D., and Feigon, J. (2008) Solution structure and dynamics of the wild-type pseudoknot of human telomerase RNA, J Mol Biol 384, 1249-1261. 36. Chen, J. L., Blasco, M. A., and Greider, C. W. (2000) Secondary structure of vertebrate telomerase RNA, Cell 100, 503-514. 37. Gilbert, S. D., Rambo, R. P., Van Tyne, D., and Batey, R. T. (2008) Structure of the SAM-II riboswitch bound to S-adenosylmethionine, Nat Struct Mol Biol 15, 177-182. 38. Toor, N., Keating, K. S., Taylor, S. D., and Pyle, A. M. (2008) Crystal structure of a self-spliced group II intron, Science 320, 77-82. 39. Grentzmann, G., Ingram, J. A., Kelly, P. J., Gesteland, R. F., and Atkins, J. F. (1998) A dual-luciferase reporter system for studying recoding signals, RNA 4, 479-486. 40. Ellinger, T., and Ehricht, R. (1998) Single-step purification of T7 RNA polymerase with a 6-histidine tag, Biotechniques 24, 718-720. 41. Milligan, J. F., and Uhlenbeck, O. C. (1989) Synthesis of small RNAs using T7 RNA polymerase, Methods Enzymol 180, 51-62. 42. Puglisi, J. D., Wyatt, J. R., and Tinoco, I., Jr. (1988) A pseudoknotted RNA oligonucleotide, Nature 331, 283-286. 43. Wang, J. X., Lee, E. R., Morales, D. R., Lim, J., and Breaker, R. R. (2008) Riboswitches that sense S-adenosylhomocysteine and activate genes involved in coenzyme recycling, Mol Cell 29, 691-702. 44. Su, M. C., Chang, C. T., Chu, C. H., Tsai, C. H., and Chang, K. Y. (2005) An atypical RNA pseudoknot stimulator and an upstream attenuation signal for -1 ribosomal frameshifting of SARS coronavirus, Nucleic Acids Res 33, 4265-4275. 45. Kim, Y. G., Su, L., Maas, S., O''Neill, A., and Rich, A. (1999) Specific mutations in a viral RNA pseudoknot drastically change ribosomal frameshifting efficiency, Proc Natl Acad Sci U S A 96, 14234-14239. 46. Chen, G., Chang, K. Y., Chou, M. Y., Bustamante, C., and Tinoco, I., Jr. (2009) Triplex structures in an RNA pseudoknot enhance mechanical stability and increase efficiency of -1 ribosomal frameshifting, Proc Natl Acad Sci U S A 106, 12706-12711. 47. Lowman, H. B., and Draper, D. E. (1986) On the recognition of helical RNA by cobra venom V1 nuclease, J Biol Chem 261, 5396-5403. 48. Vary, C. P., and Vournakis, J. N. (1984) RNA structure analysis using T2 ribonuclease: detection of pH and metal ion induced conformational changes in yeast tRNAPhe, Nucleic Acids Res 12, 6763-6778. 49. Soukup, G. A., and Breaker, R. R. (1999) Relationship between internucleotide linkage geometry and the stability of RNA, RNA 5, 1308-1325. 50. Chen, J. L., and Greider, C. W. (2005) Functional analysis of the pseudoknot structure in human telomerase RNA, Proc Natl Acad Sci U S A 102, 8080-8085. 51. Fresco, J. R., and Su, D. F. (1962) Polynucleotides. IV. Synthesis of polyriboguanylic acid catalyzed by polynucleotide phosphorylase, J Biol Chem 237, PC3305-PC3306. 52. ten Dam, E. B., Verlaan, P. W., and Pleij, C. W. (1995) Analysis of the role of the pseudoknot component in the SRV-1 gag-pro ribosomal frameshift signal: loop lengths and stability of the stem regions, RNA 1, 146-154. 53. Thompson, D. V. M., WI), Van Oosbree, Thomas R. (Madison, WI). (1994) Coupled transcription and translation in eukaryotic cell-free extract, Promega Corporation (Madison, WI), United States. 54. Chou, M. Y., and Chang, K. Y. (2010) An intermolecular RNA triplex provides insight into structural determinants for the pseudoknot stimulator of -1 ribosomal frameshifting, Nucleic Acids Res 38, 1676-1685. 55. Qiao, F., and Cech, T. R. (2008) Triple-helix structure in telomerase RNA contributes to catalysis, Nat Struct Mol Biol 15, 634-640. 56. Jenner, L. B., Demeshkina, N., Yusupova, G., and Yusupov, M. (2010) Structural aspects of messenger RNA reading frame maintenance by the ribosome, Nat Struct Mol Biol 17, 555-560. 57. Chou, M. Y., Lin, S. C., and Chang, K. Y. (2010) Stimulation of -1 programmed ribosomal frameshifting by a metabolite-responsive RNA pseudoknot, RNA 16, 1236-1244. 58. Edwards, A., Reyes, F., Heroux, A., and Batey, R. T. (2010) Crystal structure of the SAH riboswitch aptamer, In The fifteenth annual meeting of the RNA society. 59. Kollmus, H., Hentze, M. W., and Hauser, H. (1996) Regulated ribosomal frameshifting by an RNA-protein interaction, RNA 2, 316-323. 60. Park, S. J., Jung, Y. H., Kim, Y. G., and Park, H. J. (2008) Identification of novel ligands for the RNA pseudoknot that regulate -1 ribosomal frameshifting, Bioorg Med Chem 16, 4676-4684. 61. Chamorro, M., Parkin, N., and Varmus, H. E. (1992) An RNA pseudoknot and an optimal heptameric shift site are required for highly efficient ribosomal frameshifting on a retroviral messenger RNA, Proc Natl Acad Sci U S A 89, 713-717. 62. Michiels, P. J., Versleijen, A. A., Verlaan, P. W., Pleij, C. W., Hilbers, C. W., and Heus, H. A. (2001) Solution structure of the pseudoknot of SRV-1 RNA, involved in ribosomal frameshifting, J Mol Biol 310, 1109-1123. 63. Nixon, P. L., Rangan, A., Kim, Y. G., Rich, A., Hoffman, D. W., Hennig, M., and Giedroc, D. P. (2002) Solution structure of a luteoviral P1-P2 frameshifting mRNA pseudoknot, J Mol Biol 322, 621-633. 64. Nagaswamy, U., Larios-Sanz, M., Hury, J., Collins, S., Zhang, Z., Zhao, Q., and Fox, G. E. (2002) NCIR: a database of non-canonical interactions in known RNA structures, Nucleic Acids Res 30, 395-397.

Programmed -1 ribosomal frameshifting (-1 PRF), which is known to be caused by the slippery sequence and the stimulator sequence, modulates the moving direction and distance of a translating ribosome. Upon reaching the slippery sequence, the translation complex tends to shift into the -1 reading frame. However, the tRNAs in the translation complex can still form stable codon-anticodon interactions after shifting into the -1 frame because of the composition of the slippery sequence. The stimulator sequence, properly distant from the slippery sequence, is regarded to be the main source to pause the translation complex on the slippery sequence and cause -1 PRF, and thus the lever that controls -1 PRF efficiency.
We found DU177, an RNA pseudoknot derived from the human telomerase RNA, can stimulate -1 PRF. With its detailed structural data, we tried to understand the important structural features of the DU177 pseudoknot responsible for its -1 PRF efficiency through mutagenesis. Our results indicated both the interactions between stem and loop and the stacking junction of the two stem helixes have greater effect on the -1 PRF stimulating property of the DU177 pseudoknot than the loop nucleotides near the RNA entry channel of the ribosome when -1 PRF occurred. We divided the DU177 pseudoknot into a hairpin structure on mRNA and an oligo RNA, and we found -1 PRF occurred after the stem loop interactions applying on the hairpin structure. In addition to confirming the importance of stem loop interactions and junction stacking in -1 PRF, we also found an single-strand RNA inducible -1 PRF stimulator.
The inducible -1 PRF stimulator was converted to stimulate -1 PRF after the binding of its responsive molecule and is suitable for application in the study of -1 PRF mechanism. Because of the correlation between translation elongation mechanism and -1 PRF, the study might help in understanding the details of translation translocation. Besides, the inducible -1 PRF stimulator might directly be applied on living organisms and has the potential to become an inducible translation control system in bioassay and medicine.
其他識別: U0005-2707201016092700
Appears in Collections:生物化學研究所

Show full item record

Google ScholarTM


Items in DSpace are protected by copyright, with all rights reserved, unless otherwise indicated.