Stimulation of -1 programmed ribosomal frameshifting by a metabolite-responsive RNA pseudoknot

RNA

Volumn 16, Issue 6, 2010, Pages 1236-1244

  Chou, Ming Yuan ^a   Lin, Szu Chieh ^a   Chang, Kung Yao ^a  

^a NATIONAL CHUNG HSING UNIVERSITY   (Taiwan)

Author keywords

1 ribosomal frameshifting; Pseudoknot; Riboswitch

Indexed keywords

RNA; S ADENOSYLHOMOCYSTEINE;

1 PROGRAMMED RIBOSOMAL FRAMESHIFTING; ARTICLE; CELL STRAIN HEK293; CONFORMATION; CONTROLLED STUDY; GENE EXPRESSION; GENETIC ENGINEERING; HUMAN; HUMAN CELL; HUMAN CELL CULTURE; IN VITRO STUDY; MUTAGENESIS; PRIORITY JOURNAL; RIBOSWITCH; RNA SEQUENCE; TRANSLATION REGULATION;

ADENOSYLHOMOCYSTEINASE; BASE SEQUENCE; CELL CULTURE TECHNIQUES; CELL LINE; FRAMESHIFTING, RIBOSOMAL; GENE EXPRESSION; HIV-1; HUMANS; KIDNEY; LUCIFERASES; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; PROTEIN BIOSYNTHESIS; RNA; RNA, CATALYTIC; RNA, MESSENGER; TRANSCRIPTION, GENETIC;

EUKARYOTA; PROKARYOTA;

EID: 77952677666     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.1922410     Document Type: Article

References (44)

1. Baranov PV, Henderson CM, Anderson CB, Gesteland RF, Atkins JF, Howard MT. 2005. Programmed ribosomal frameshifting in decoding the SARS-Cov genome. Virology 332: 498-510.
2. Barrick JE, Breaker RR. 2007. The distributions, mechanisms, and structures of metabolite-binding riboswitches. Genome Biol 8: R239. doi: 10.1186/gb-2007-8-11-r239.
3. Chamorro M, Parkin N, Varmus HE. 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 89: 713-717.
4. Cheah MT, Wachter A, Sudarsan N, Breaker RR. 2007. Control of alternative RNA splicing and gene expression by eukaryotic riboswitches. Nature 447: 497-500. (Pubitemid 46816734)
5. Chen G, Chang KY, Chou MY, Bustamante C, Tinoco I Jr. 2009. Triplex structures in an RNA pseudoknot enhance mechanical stability and increase efficiency of -1 ribosomal frameshifting. Proc Natl Acad Sci 106: 12706-12711.
6. Chou M-Y, 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. doi: 10.1093/nar/gkp1107.
7. Corbino KA, Barrick JE, Lim J, Welz R, Tucker BJ, Puskarz I, Mandal M, Rudnick ND, Breaker RR. 2005. Evidence for a second class of S-adenosylmethionine riboswitches and other regulatory RNA motifs in -proteobacteria. Genome Biol 6: R70. doi: 10.1186/gb-2005-6-8-r70.
8. Dulude D, Baril M, Brakier-Gingras L. 2002. Characteriation of the frameshift stimulatory signal controlling a programmed -1 ribosomal frameshift in the human immunodeficiency virus type 1. Nucleic Acids Res 30: 5094-5102. (Pubitemid 36033026)
9. Farabaugh PJ. 1996. Programmed translational frameshifting. Microbiol Rev 60: 103-134.
10. Gesteland RF, Atkins JF. 1996. Recoding: Dynamic reprogramming of translation. Annu Rev Biochem 65: 741-768.
11. Giedroc DP, Theimer CA, Nixon PL. 2000. Structure, stability and function of RNA pseudoknots involved in stimulating ribosomal frameshifting. J Mol Biol 298: 167-185.
12. Gilbert SD, Rambo RP, Van Tyne D, Batey RT. 2008. Structure of the SAM-II riboswitch bound to S-adenosylmethionine. Nat Struct Mol Biol 15: 761-772. (Pubitemid 351207508)
13. Grentzmann G, Ingram JA, Kelly PJ, Gesteland RF, Atkins JF. 1998. A dual-luciferase reporter system for studying recoding signals. RNA 4: 479-486. (Pubitemid 28160788)
14. Grundy FJ, Henkin TM. 2006. From ribosome to riboswitch: Control of gene expression in bacteria by RNA structural rearrangements. Crit Rev Biochem Mol Biol 41: 329-338.
15. Henkin TM. 2008. Riboswitch RNAs: Using RNA to sense cellular metabolism. Genes Dev 22: 3383-3390.
16. Hermes M, Osswald H, Mattar J, Kloor D. 2004. Influence of an altered methylation potential on mRNA methylation and gene expression in HepG2 cells. Exp Cell Res 294: 325-334. (Pubitemid 38326734)
17. Hung M, Patel P, Davis S, Green SR. 1998. Importance of ribosomal frameshifting for human immunodeficiency virus type 1 particle assembly and replication. J Virol 72: 4819-4824. (Pubitemid 28215658)
18. Howard MT, Gesteland RF, Atkins JF. 2004. Efficient stimulation of site-specific ribosome frameshifting by antisense oligonucleotides. RNA 10: 1653-1661.
19. Ivanov IP, Atkins JF. 2007. Ribosomal frameshifting in decoding antizyme mRNAs from yeast and protests to humans: Close to 300 cases reveal remarkable diversity despite underlying conservation. Nucleic Acids Res 35: 1842-1858.
20. Jacobs JL, Belew AT, Rakauskaite R, Dinman JD. 2007. Identification of functional, endogenous programmed -1 ribosomal frameshift signals in the genome of Saccharomyces cerevisiae. Nucleic Acids Res 35: 165-174. (Pubitemid 46189841)
21. Kang M, Peterson R, Feigon J. 2009. Structural insights into riboswitch control of the biosynthesis of queuosine, a modified nucleotide found in the anticodon of tRNA. Mol Cell 33: 784-790.
22. Klein DJ, Edwards TE, Ferré-D'Amaré AR. 2009. Cocrystal structure of a class I preQ1 riboswitch reveals a pseudoknot recognizing an essential hypermodified nucleobase. Nat Struct Mol Biol 16: 343-344.
23. Kollmus HK, Honigman A, Panet A, Hauser H. 1994. The sequences of and distance between two cis-acting signals determine the efficiency of ribosomal frameshifting in human immunodeficiency virus type 1 and human T cell leukemia virus type II in vivo. J Virol 68: 6087-6091. (Pubitemid 24258631)
24. Kollmus HK, Hentze MW, Hauser H. 1996. Regulated ribosomal frameshifting by an RNA-protein interaction. RNA 2: 316-323. (Pubitemid 26371283)
25. Mandal M, Breaker RR. 2004. Gene regulation by riboswitches. Nat Rev Mol Cell Biol 5: 451-463.
26. Manktelow E, Shigemoto K, Brierley I. 2005. Characterization of the frameshift signal of Edr, a mammalian example of programmed -1 ribosomal frameshifting. Nucleic Acids Res 33: 1553-1563. (Pubitemid 41430102)
27. Matsufuji S, Matsufuji T, Miyazaki Y, Murakami Y, Atkins JF, Gesteland RF, Hayashi S. 1995. Autoregulatory frameshifting in decoding mammalian ornithine decarboxylase antizyme. Cell 80: 51-60.
28. 1 aptamer class in Streptococcaceae bacteria. RNA 14: 685-695.
29. Nudler E, Mironov AS. 2004. The riboswitch control of bacterial metabolism. Trends Biochem Sci 29: 11-17.
30. Olsthoorn RCL, Laurs M, Sohet F, Hilbers CW, Heus HA, Pleij CWA. 2004. Efficient stimulation of site-specific ribosome frameshifting by antisense oligonucleotides. RNA 10: 1702-1703.
31. Petros LM, Howard MT, Gesteland RF, Atkins JF. 2005. Polyamine sensing during antizyme mRNA programmed frameshifting. Biochem Biophys Res Commun 338: 1478-1489.
32. Plant EP, Dinman JD. 2005. Torsional restraint: A new twist on frameshifting pseudoknots. Nucleic Acids Res 33: 1825-1833.
33. Plant EP, Perez-Alvarado GC, Jacobs JL, Mukhopadhyay B, Henning M, Dinman JD. 2005. A three-stemmed mRNA pseudoknot in the SARS coronavirus frameshift signal. PLoS Biol 3: e172. doi: 10.1371/journal.pbio.0030172. (Pubitemid 41032211)
34. Rom E, Kahana C. 1994. Polyamines regulate the expression of ornithine decarboxylase antizyme in vitro by inducing ribosomal frame-shifting. Proc. Natl. Acad. Sci. 91: 3959-3963.
35. Serganov A, Patel D. 2007. Ribozymes, riboswitches and beyond: Regulation of gene expression without proteins. Nat Rev Genet 8: 776-790. (Pubitemid 47429208)
36. Soukup GA, Breaker RR. 1999. Relationship between internucleotide linkage geometry and the stability of RNA. RNA 5: 1308-1325.
37. 0 metabolite by an unusually small riboswitch aptamer domain. J Biol Chem 284: 11012-11016.
38. Su MC, Chang CT, Chu CH, Tsai CH, Chang KY. 2005. An atypical RNA pseudoknot stimulator and an upstream attenuation signal for -1 ribosomal frameshifting of SARS coronavirus. Nucleic Acids Res 33: 4265-4275.
39. Sudarsan N, Barrick JE, Breaker RR. 2003. Metabolite-binding RNA domains present in the genes of eukaryotes. RNA 9: 644-647. (Pubitemid 36618192)
40. Theimer CA, Blois CA, Feigon J. 2005. Structure of the human telomerase RNA pseudoknot reveals conserved tertiary interactions essential for function. Mol Cell 17: 671-682. (Pubitemid 40320917)
41. Ueland PM. 1982. Pharmacological and biochemical aspects of S-adenosylhomocysteine and S-adenosylhomocysteine hydrolase. Pharmacol Rev 34: 223-285.
42. Wang JX, Lee ER, Morales DR, Lim J, Breaker RR. 2008. Riboswitches that sense S-adenosylhomocysteine and activate genes involved in coenzyme recycling. Mol Cell 29: 691-702. (Pubitemid 351400921)
43. Weinberg Z, Barrick JE, Yao Z, Roth A, Kim JN, Gore J, Wang JX, Lee ER, Block KF, Sudarsan N, et al. 2007. Identification of 22 candidate structured RNAs in bacteria using the Cmfinder comparative genomics pipeline. Nucleic Acids Res 35: 4809-4819. (Pubitemid 47250352)
44. Wills NM, Moore B, Hammer A, Gesteland RF, Atkins JF. 2006. A functional -1 ribosomal frameshift signal in the human paraneoplastic Ma3 gene. J Biol Chem 281: 7082-7088. (Pubitemid 43847472)