The subgenomic promoter of brome mosaic virus folds into a stem-loop structure capped by a pseudo-triloop that is structurally similar to the triloop of the genomic promoter

RNA

Volumn 18, Issue 5, 2012, Pages 992-1000

  Skov, Joan ^a   Gaudin, Mathieu ^a   Podbevšek, Peter ^a   Olsthoorn, René C L ^b   Petersen, Michael ^a  

^a UNIVERSITY OF SOUTHERN DENMARK   (Denmark)

^b LEIDEN UNIVERSITY   (Netherlands)

Author keywords

BMV; Brome mosaic virus; NMR spectroscopy; Pseudo triloop; RNA replication; RNA dependent RNA polymerase

Indexed keywords

ADENINE; GENOMIC RNA; RNA DIRECTED RNA POLYMERASE; SHORT HAIRPIN RNA; URACIL;

ARTICLE; BASE PAIRING; CONTROLLED STUDY; GENE STRUCTURE; MOSAIC VIRUS; NONHUMAN; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PRIORITY JOURNAL; PROMOTER REGION; RNA CAPPING; RNA FOLDING; RNA SYNTHESIS; RNA TRANSCRIPTION; VIRUS GENOME;

BASE PAIRING; BASE SEQUENCE; BROMOVIRUS; GENOME, VIRAL; INVERTED REPEAT SEQUENCES; MODELS, MOLECULAR; MUTATION; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; NUCLEIC ACID CONFORMATION; PROMOTER REGIONS, GENETIC; RNA, VIRAL; THERMODYNAMICS;

EID: 84859953908     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.029918.111     Document Type: Article

References (36)

1. Adkins S, Kao CC. 1998. Subgenomic RNA promoters dictate the mode of recognition by bromoviral RNA-dependent RNA polymerases. Virology 252: 1-8. (Pubitemid 28564126)
2. Brunger AT. 1996. X-PLOR version 3.851. Yale University Press, New Haven, CT.
3. Cornell WD, Cieplak P, Bayly I, Gould IR, Merz KM, Ferguson DM, Spellmeyer DC, Fox T, Caldwell JW, Kollman PA. 1995. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J Am Chem Soc 117: 5179-5197.
4. Cromsigt JAMTC, Hilbers CW, Wijmenga SS. 2001. Prediction of proton chemical shifts in RNA. J Biol NMR 21: 11-29. (Pubitemid 32962608)
5. Delaglio F, Grzesiek S, Vuister GW, Zhu G, Pfeifer J, Bax A. 1995. NMRpipe: A multidimensional spectral processing system based on UNIX pipes. J Biol NMR 6: 277-293.
6. Flodell S, Schleucher J, Cromsigt J, Ippel H, Kidd-Ljunggren K, Wijmenga S. 2002. The apical stem-loop of the hepatitis B virus encapsidation signal folds into a stable tri-loop with two underlying pyrimidine bulges. Nucleic Acids Res 30: 4803-4811. (Pubitemid 35331761)
7. Flodell S, Petersen M, Girard F, Zdunek J, Schleucher J, Kidd- Ljunggren K, Wijmenga SS. 2006. Structure of the apical loop of the Hepatitis B virus encapsidation signal. Nucleic Acids Res 34: 4449-4457. (Pubitemid 44567044)
8. Foloppe N, Hartmann B, Nilsson L, MacKerell AD. 2002. Intrinsic conformational energetics associated with the glycosyl torsion in DNA: A quantum mechanical study. Biophys J 82: 1554-1569. (Pubitemid 34204773)
9. Gopinath K, Dragnea B, Kao C. 2005. Interaction between Brome mosaic virus proteins and RNAs: effects on RNA replication, protein expression, and RNA stability. J Virol 79: 14222-14234. (Pubitemid 41552720)
10. Haasnoot PCJ, Brederode FT, Olsthoorn RCL, Bol JF. 2000. A conserved hairpin structure in Alfamovirus and Bromovirus sub-genomic promoters is required for efficient RNA synthesis in vitro. RNA 6: 708-716. (Pubitemid 30318466)
11. Haasnoot PCJ, Olsthoorn RCL, Bol JF. 2002. The Brome mosaic virus subgenomic promoter hairpin is structurally similar to the iron-responsive element and functionally equivalent to the minus-strand core promoter stem-loop C. RNA 8: 110-122. (Pubitemid 34260170)
12. Haasnoot PC, Bol JF, Olsthoorn RC. 2003. A plant virus replication system to assay the formation of RNA pseudotriloop motifs in RNA-protein interactions. Proc Natl Acad Sci 100: 12596-12600. (Pubitemid 37339944)
13. Kao CC, Sivakumaran K. 2000. Brome mosaic virus, good for an RNA virologist's basic needs. Mol Plant Pathol 1: 91-97.
14. Kao CC, Ni P, Hema M, Huang XL, Dragnea B. 2011. The coat protein leads the way: An update on basic and applied studies with the Brome mosaic virus coat protein. Mol Plant Pathol 12: 403-412.
15. Kim CH, Tinoco I. 2001. Structural and thermodynamic studies on mutant RNA motifs that impair the specificity between a viral replicase and its promoter. J Mol Biol 307: 827-839. (Pubitemid 33027662)
16. Kim CH, Kao CC, Tinoco I. 2000. RNA motifs that determine specificity between a viral replicase and its promoter. Nat Struct Biol 7: 415-423. (Pubitemid 30250007)
17. Koradi R, Billeter M, Wüthrich K. 1996. MOLMOL: A program for display and analysis of macromolecular structures. J Mol Graph 14: 51-55. (Pubitemid 26152976)
18. Lavery R, Sklenar H. 1988. The definition of generalized helicoidal parameters and for axis curvature of irregular nucleic acids. J Biomol Struct Dyn 6: 63-91.
19. Luy B, Marino JP. 2000. Direct evidence for Watson-Crick base pairs in a dynamic region of RNA structure. J Am Chem Soc 122: 8095-8096. (Pubitemid 30659441)
20. Marsh LE, Dreher TW, Hall TC. 1988. Mutational analysis of the core and modulator sequences of the BMV RNA3 subgenomic promoter. Nucleic Acids Res 16: 981-995.
21. Mergny JL, Lacroix L. 2003. Analysis of thermal melting curves. Oligonucleotides 13: 515-537. (Pubitemid 38296149)
22. Miller WA, Koev G. 2000. Synthesis of subgenomic RNAs by positive-strand RNA viruses. Virology 273: 1-8. (Pubitemid 30602002)
23. Miller WA, Dreher TW, Hall TC. 1985. Synthesis of Brome mosaic virus subgenomic RNA in vitro by internal initiation on (-)-sense genomic RNA. Nature 313: 68-70. (Pubitemid 15192309)
24. Olsthoorn RC, Haasnoot PC, Bol JF. 2004. Similarities and differences between the subgenomic and minus-strand promoters of an RNA plant virus. J Virol 78: 4048-4053. (Pubitemid 38437211)
25. Rao ALN. 2001 Bromoviruses. In Encyclopedia of plant pathology (ed. OC Maloy, TD Murray), pp. 155-158. John Wiley & Sons, Toronto.
26. Sarma RH, Mynott RJ, Wood DJ, Hruska FE. 1973. Determination of the preferred conformations constrained along the C4′-C5′ and C5′-O5′ bonds of β-5′-nucleotides in solution. Four-bond 31P-1H coupling. J Am Chem Soc 95: 6457-6459.
27. Shu Z, Bevilacqua PC. 1999. Isolation and characterization of thermodynamically stable and unstable RNA hairpins from a triloop combinatorial library. Biochemistry 38: 15369-15379. (Pubitemid 129520371)
28. Siegel RW, Bellon L, Beigelman L, Kao CC. 1998. Moieties in an RNA promoter specifically recognized by a viral RNA-dependent RNA polymerase. Proc Natl Acad Sci 95: 11613-11618.
29. Sivakumaran K, Choi S-K, Hema M, Kao CC. 2004. Requirements for Brome mosaic virus subgenomic RNA synthesis in vivo and replicase-core promoter interactions in vitro. J Virol 78: 6091-6101. (Pubitemid 38715907)
30. Smirnyagina E, Hsu YH, Chua N, Ahlquist P. 1994. Second-site mutations in the Brome mosaic-virus RNA3 intercistronic region partially suppress a defect in coat protein messenger-RNA transcription. Virology 198: 427-436.
31. Sztuba-Solinska J, Stollar V, Bujarski JJ. 2011. Subgenomic messenger RNAs: mastering regulation of (+)-strand RNA virus life cycle. Virology 412: 245-255.
32. Varani G, Aboul-ela F, Allain FHT. 1996. NMR investigation of RNA structures. Prog Nucl Magn Reson Spectrosc 29: 51-127.
33. Wijmenga SS, van Buuren BNM. 1998. The use of NMR methods for conformational studies of nucleic acids. Prog Nucl Magn Reson Spectrosc 32: 287-387. (Pubitemid 128638273)
34. Yi G, Letteney E, Kim CH, Kao CC. 2009a. Brome mosaic virus capsid protein regulates accumulation of viral replication proteins by binding to the replicase assembly RNA element. RNA 15: 615-626.
35. Yi GH, Vaughan RC, Yarbrough I, Dharmaiah S, Kao CC. 2009b. RNA binding by the Brome mosaic virus capsid protein and the regulation of viral RNA accumulation. J Mol Biol 391: 314-326.
36. Zhu J, Gopinath K, Murali A, Yi GH, Hayward SD, Zhu H, Kao C. 2007. RNA-binding proteins that inhibit RNA virus infection. Proc Natl Acad Sci 104: 3129-3134. (Pubitemid 46364125)