Structural architecture of an RNA that competitively inhibits RNase L

RNA

Volumn 18, Issue 1, 2012, Pages 88-99

  Keel, Amanda Y ^a   Jha, Babal Kant ^b   Kieft, Jeffrey S ^a,c  

^a UNIVERSITY OF COLORADO SCHOOL OF MEDICINE   (United States)

^b LERNER RESEARCH INSTITUTE   (United States)

^c HOWARD HUGHES MEDICAL INSTITUTE   (United States)

Author keywords

Antiviral countermeasure; Kissing hairpins; Poliovirus; RNA structure; RNase L

Indexed keywords

COMPETITIVE INHIBITOR RNA; RIBONUCLEASE L; RIBOSOME RNA; UNCLASSIFIED DRUG; VIRUS RNA;

ARTICLE; ENZYME INHIBITION; NONHUMAN; POLIOMYELITIS VIRUS; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DENATURATION; PROTEIN FOLDING; PROTEIN FUNCTION; PROTEIN MOTIF; PROTEIN RNA BINDING; PROTEIN STABILITY; PROTEIN TERTIARY STRUCTURE; RNA STRUCTURE; RNA TRANSPORT; X RAY CRYSTALLOGRAPHY;

ANIMALS; BASE SEQUENCE; BINDING, COMPETITIVE; ENDORIBONUCLEASES; HOT TEMPERATURE; MOLECULAR SEQUENCE DATA; MUTATION; NUCLEIC ACID CONFORMATION; NUCLEIC ACID DENATURATION; RNA; SCATTERING, SMALL ANGLE; X-RAY DIFFRACTION;

EID: 84055212199     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.030007.111     Document Type: Article

References (51)

1. Barton DJ, O'Donnell BJ, Flanegan JB. 2001. 5′ cloverleaf in poliovirus RNA is a cis-acting replication element required for negative-strand synthesis. EMBO J 20: 1439-1448. (Pubitemid 32233983)
2. Blouin S, Lafontaine DA. 2007. A loop-loop interaction and a K-turn motif located in the lysine aptamer domain are important for the riboswitch gene regulation control. RNA 13: 1256-1267. (Pubitemid 47080471)
3. Blouin S, Chinnappan R, Lafontaine DA. 2011. Folding of the lysine riboswitch: importance of peripheral elements for transcriptional regulation. Nucleic Acids Res 39: 3373-3387.
4. Casey G, Neville PJ, Plummer SJ, Xiang Y, Krumroy LM, Klein EA, Catalona WJ, Nupponen N, Carpten JD, Trent JM, et al. 2002. RNASEL Arg462Gln variant is implicated in up to 13% of prostate cancer cases. Nat Genet 32: 581-583. (Pubitemid 35435169)
5. Chakrabarti A, Jha BK, Silverman RH. 2011. New insights into the role of RNase L in innate immunity. J Interferon Cytokine Res 31: 49-57.
6. Chang KY, Tinoco I Jr. 1997. The structure of an RNA "kissing" hairpin complex of the HIV TAR hairpin loop and its complement. J Mol Biol 269: 52-66.
7. Costantino D, Kieft JS. 2005. A preformed compact ribosome-binding domain in the cricket paralysis-like virus IRES RNAs. RNA 11: 332-343. (Pubitemid 40270825)
8. Cullen BR. 2009. Viral RNAs: lessons from the enemy. Cell 136: 592-597.
9. DeAbreu DM, Olive JE, Collins RA. 2011. Additional roles of a peripheral loop-loop interaction in the Neurospora VS ribozyme. Nucleic Acids Res 39: 6223-6228.
10. Dong B, Silverman RH. 1997. A bipartite model of 2-5A-dependent RNase L. J Biol Chem 272: 22236-22242. (Pubitemid 27382855)
11. Dreher TW. 2009. Role of tRNA-like structures in controlling plant virus replication. Virus Res 139: 217-229.
12. Filbin ME, Kieft JS. 2009. Toward a structural understanding of IRES RNA function. Curr Opin Struct Biol 19: 267-276.
13. Flanegan JB, Petterson RF, Ambros V, Hewlett NJ, Baltimore D. 1977. Covalent linkage of a protein to a defined nucleotide sequence at the 5′-terminus of virion and replicative intermediate RNAs of poliovirus. Proc Natl Acad Sci 74: 961-965. (Pubitemid 8068723)
14. Gardner CL, Ryman KD. 2010. Yellow fever: a reemerging threat. Clin Lab Med 30: 237-260.
15. Garst AD, Heroux A, Rambo RP, Batey RT. 2008. Crystal structure of the lysine riboswitch regulatory mRNA element. J Biol Chem 283: 22347-22351.
16. Giedroc DP, Cornish PV. 2009. Frameshifting RNA pseudoknots: structure and mechanism. Virus Res 139: 193-208.
17. Goodfellow IG, Kerrigan D, Evans DJ. 2003. Structure and function analysis of the poliovirus cis-acting replication element (CRE). RNA 9: 124-137. (Pubitemid 36206308)
18. Gorbalenya AE, Enjuanes L, Ziebuhr J, Snijder EJ. 2006. Nidovirales: evolving the largest RNA virus genome. Virus Res 117: 17-37.
19. Hammond JA, Rambo RP, Filbin ME, Kieft JS. 2009. Comparison and functional implications of the 3D architectures of viral tRNA-like structures. RNA 15: 294-307.
20. Hammond JA, Rambo RP, Kieft JS. 2010. Multi-domain packing in the aminoacylatable 3′ end of a plant viral RNA. J Mol Biol 399: 450-463.
21. Han JQ, Townsend HL, Jha BK, Paranjape JM, Silverman RH, Barton DJ. 2007. A phylogenetically conserved RNA structure in the poliovirus open reading frame inhibits the antiviral endoribonuclease RNase L. J Virol 81: 5561-5572. (Pubitemid 46846996)
22. 2661 region of 23S rRNA is located at the ribosomal binding sites of both elongation factors. Biochimie 69: 911-923.
23. Hogle JM, Chow M, Filman DJ. 1985. Three-dimensional structure of poliovirus at 2.9 Å resolution. Science 229: 1358-1365. (Pubitemid 16222374)
24. Katz SL. 2006. Polio: new challenges in 2006. J Clin Virol 36: 163-165.
25. Kieft JS, Costantino DA, Filbin ME, Hammond J, Pfingsten JS. 2007. Structural methods for studying IRES function. Methods Enzymol 430: 333-371.
26. Kitamura N, Adler C, Wimmer E. 1980. Structure and expression of the picornavirus genome. Ann N Y Acad Sci 354: 183-201. (Pubitemid 11134767)
27. Lancaster L, Lambert NJ, Maklan EJ, Horan LH, Noller HF. 2008. The sarcin-ricin loop of 23S rRNA is essential for assembly of the functional core of the 50S ribosomal subunit. RNA 14: 1999-2012.
28. Lee YF, Nomoto A, Detjen BM, Wimmer E. 1977. A protein covalently linked to poliovirus genome RNA. Proc Natl Acad Sci 74: 59-63. (Pubitemid 8025870)
29. Leontis NB, Westhof E. 1998. A common motif organizes the structure of multi-helix loops in 16 S and 23 S ribosomal RNAs. J Mol Biol 283: 571-583. (Pubitemid 28486721)
30. Lescoute A, Westhof E. 2006. Topology of three-way junctions in folded RNAs. RNA 12: 83-93. (Pubitemid 43037456)
31. Liang SL, Quirk D, Zhou A. 2006. RNase L: its biological roles and regulation. IUBMB Life 58: 508-514. (Pubitemid 44470236)
32. Lipfert J, Ouellet J, Norman DG, Doniach S, Lilley DM. 2008. The complete VS ribozyme in solution studied by small-angle X-ray scattering. Structure 16: 1357-1367.
33. Martin A, Lemon SM. 2006. Hepatitis A virus: from discovery to vaccines. Hepatology 43: S164-S172.
34. Moazed D, Robertson JM, Noller HF. 1988. Interaction of elongation factors EF-G and EF-Tu with a conserved loop in 23S RNA. Nature 334: 362-364.
35. Nijs J, De Meirleir K. 2005. Impairments of the 2-5A synthetase/RNase L pathway in chronic fatigue syndrome. In Vivo 19: 1013-1021.
36. Nomoto A, Kitamura N, Golini F, Wimmer E. 1977. The 5′-terminal structures of poliovirion RNA and poliovirus mRNA differ only in the genome-linked protein VPg. Proc Natl Acad Sci 74: 5345-5349.
37. Paul AV, Rieder E, Kim DW, van Boom JH, Wimmer E. 2000. Identification of an RNA hairpin in poliovirus RNA that serves as the primary template in the in vitro uridylylation of VPg. J Virol 74: 10359-10370.
38. Pelletier J, Sonenberg N. 1988. Internal initiation of translation of eukaryotic mRNA directed by a sequence derived from poliovirus RNA. Nature 334: 320-325.
39. Racaniello VR, Baltimore D. 1981. Molecular cloning of poliovirus cDNA and determination of the complete nucleotide sequence of the viral genome. Proc Natl Acad Sci 78: 4887-4891. (Pubitemid 12225586)
40. Rastogi T, Beattie TL, Olive JE, Collins RA. 1996. A long-range pseudoknot is required for activity of the Neurospora VS ribozyme. EMBO J 15: 2820-2825. (Pubitemid 26176259)
41. Rezza G. 2007. Prevention and control of emerging infections: a challenge for the 3rd millennium. New Microbiol 30: 358-361. (Pubitemid 47264906)
42. Steil BP, Barton DJ. 2009. Cis-active RNA elements (CREs) and picornavirus RNA replication. Virus Res 139: 240-252.
43. Stoddard CD, Montange RK, Hennelly SP, Rambo RP, Sanbonmatsu KY, Batey RT. 2010. Free state conformational sampling of the SAM-I riboswitch aptamer domain. Structure 18: 787-797.
44. Svergun DI, Petoukhov MV, Koch MH. 2001. Determination of domain structure of proteins from X-ray solution scattering. Biophys J 80: 2946-2953. (Pubitemid 32521666)
45. Teixeira MG, Barreto ML. 2009. Diagnosis and management of dengue. BMJ 339: b4338. doi: 10.1136/bmj.b4338.
46. Thakur CS, Xu Z, Wang Z, Novince Z, Silverman RH. 2005. A convenient and sensitive fluorescence resonance energy transfer assay for RNase L and 2′,5′ oligoadenylates. Methods Mol Med 116: 103-113.
47. Townsend HL, Jha BK, Han JQ, Maluf NK, Silverman RH, Barton DJ. 2008a. A viral RNA competitively inhibits the antiviral endoribonuclease domain of RNase L. RNA 14: 1026-1036. (Pubitemid 351717484)
48. Townsend HL, Jha BK, Silverman RH, Barton DJ. 2008b. A putative loop E motif and an H-H kissing loop interaction are conserved and functional features in a group C enterovirus RNA that inhibits ribonuclease L. RNA Biol 5: 263-272.
49. Xiang Y, Wang Z, Murakami J, Plummer S, Klein EA, Carpten JD, Trent JM, Isaacs WB, Casey G, Silverman RH. 2003. Effects of RNase L mutations associated with prostate cancer on apoptosis induced by 2′,5′-oligoadenylates. Cancer Res 63: 6795-6801. (Pubitemid 37322961)
50. Zhang W, Dunkle JA, Cate JH. 2009. Structures of the ribosome in intermediate states of ratcheting. Science 325: 1014-1017.
51. Zoll J, Heus HA, van Kuppeveld FJ, Melchers WJ. 2009. The structure-function relationship of the enterovirus 3′-UTR. Virus Res 139: 209-216.