RNA Binding by the Brome Mosaic Virus Capsid Protein and the Regulation of Viral RNA Accumulation

Journal of Molecular Biology

Volumn 391, Issue 2, 2009, Pages 314-326

  Yi, Guanghui ^a   Vaughan, Robert C ^a   Yarbrough, Ian ^a   Dharmaiah, S ^a   Kao, C Cheng ^a  

^a INDIANA UNIVERSITY   (United States)

Author keywords

brome mosaic virus; capsid protein; positive strand RNA virus; RNA replication; translation

Indexed keywords

CAPSID PROTEIN; MUTANT PROTEIN; RNA DIRECTED RNA POLYMERASE; VIRUS RNA;

ARTICLE; ASSAY; BINDING AFFINITY; CONTROLLED STUDY; DOWN REGULATION; GENE EXPRESSION REGULATION; HERB; INOCULATION; MOSAIC VIRUS; NONHUMAN; PEPTIDE ANALYSIS; PLANT LEAF; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN RNA BINDING; REPORTER GENE; RNA BINDING; RNA ELEMENT; RNA REPLICATION; RNA STRUCTURE; RNA SYNTHESIS; RNA TRANSLATION; TRANSLATION REGULATION; VIRUS CAPSID; VIRUS PARTICLE;

BROME MOSAIC VIRUS; MIRIDAE; NICOTIANA BENTHAMIANA; RNA VIRUSES;

EID: 67650700208     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2009.05.065     Document Type: Article

References (43)

1. Callaway A., Giesman-Cookmeyer D., Gillock E.T., Sit T.L., and Lommel S.A. The multifunctional capsid proteins of plant RNA viruses. Annu. Rev. Phytopathol. 39 (2001) 419-460
2. Guogas L.M., Laforest S.M., and Gehrke L. Coat protein activation of alfalfa mosaic virus replication is concentration dependent. J. Virol. 79 (2005) 5752-5761
3. Neeleman L., Olsthoorn R.C., Linthorst H.J., and Bol J.F. Translation of a nonpolyadenylated viral RNA is enhanced by binding of viral coat protein or polyadenylation of the RNA. Proc. Natl Acad. Sci. USA 98 (2001) 14286-14291
4. Bol J.F. Replication of alfamo- and ilarviruses: role of the coat protein. Annu. Rev. Phytopathol. 43 (2005) 39-62
5. Witherell G.W., Gott J.M., and Uhlenbeck O.C. Specific interaction between RNA phage coat proteins and RNA. Prog. Nucleic Acid Res. Mol. Biol. 40 (1991) 185-220
6. Lucas R.W., Larson S.B., and McPherson A. The crystallographic structure of brome mosaic virus. J. Mol. Biol. 317 (2002) 95-108
7. Rao A.L. Genome packaging by spherical plant RNA viruses. Annu. Rev. Phytopathol. 44 (2006) 61-87
8. Noueiry A.O., and Ahlquist P. Brome mosaic virus RNA replication: revealing the role of the host in RNA virus replication. Annu. Rev. Phytopathol. 41 (2003) 77-98
9. Gopinath K., Dragnea B., and Kao C.C. Interaction between brome mosaic virus proteins and RNAs: effects on RNA replication, protein expression and RNA stability. J. Virol. 79 (2005) 14222-14234
10. Yi G., Letteney E., Kim C.H., and Kao C.C. Brome mosaic virus capsid protein regulates accumulation of viral replication proteins by binding to the replicase assembly RNA element. RNA 15 (2009) 615-626
11. Zhu J., Gopinath K., Murali A., Yi G., Hayward S.D., Zhu H., and Kao C. RNA-binding proteins that inhibit RNA virus infection. Proc. Natl Acad. Sci. USA 104 (2007) 3129-3134
12. Kim C.H., and Kao C. A mutant viral RNA promoter with an altered conformation retains efficient recognition by a viral RNA replicase through a solution-exposed adenine. RNA 7 (2001) 1476-1485
13. Kim C.H., Kao C., and Tinoco I. RNA motifs that determine specificity between a viral replicase and its promoter. Nat. Struct. Biol. 7 (2000) 415-423
14. Kim Y.C., Russell W.K., Ranjith-Kuman C.T., Thomson M., Russell D.H., and Kao C.C. Functional analysis of RNA binding by the hepatitis C virus RNA-dependent RNA polymerase. J. Biol. Chem. 280 (2005) 38011-38019
15. Gelvin S.B. Agrobacterium-mediated plant transformation: the biology behind the "gene-jockeying" tool. Microbiol. Mol. Biol. Rev. 67 (2003) 16-37
16. Chapman M.R., and Kao C.C. A minimal RNA promoter for minus-strand RNA synthesis by the brome mosaic virus polymerase complex. J. Mol. Biol. 286 (1999) 709-720
17. Ranjith-Kumar C.T., Zhang X., and Kao C.C. Enhancer-like activity of a brome mosaic virus RNA promoter. J. Virol. 77 (2003) 1830-1839
18. She Y.M., Haber S., Seifers D.L., Loboda A., Chernushevich I., Perreault H., et al. Determination of the complete amino acid sequence for the coat protein of brome mosaic virus by time-of-flight mass spectrometry: evidence for mutations associated with change of propagation host. J. Biol. Chem. 276 (2001) 20039-20047
19. Bhardwaj K., Palaninathan S., Alcantara J.M., Yi L.L., Guarino L., Sacchettini J.C., and Kao C.C. Structural and functional analysis of the severe acute respiratory syndrome coronavirus endoribonuclease Nsp15. J. Biol. Chem. 283 (2008) 3655-3664
20. Ranjith-Kumar C.T., Duffy K.E., Jordan J.L., Eaton-Bassiri A., Vaughan R., Hoose S., et al. Single-stranded oligonucleotides can inhibit cytokine production induced by human toll-like receptor 3. Mol. Cell. Biol. 28 (2008) 4507-4519
21. Rao A.L., and Grantham G.L. Biological significance of the seven amino-terminal basic residues of brome mosaic virus coat protein. Virology 211 (1995) 42-52
22. Rao A.L., and Grantham G.L. Molecular studies on bromovirus capsid protein: II. Functional analysis of the amino-terminal arginine-rich motif and its role in encapsidation, movement, and pathology. Virology 226 (1996) 294-305
23. Speir J.A., Munshi S., Wang G., Baker T.S., and Johnson S.E. Structures of the native and swollen forms of cowpea chlorotic mottle virus determined by X-ray crystallography and cryo-electron microscopy. Structure 15 (1995) 63-78
24. Shepherd C.M., Borelli I.A., Lander G., Natarajan P., Siddavanahalli V., Bajaj C., et al. VIPERdb: a relational database for structural virology. Nucleic Acids Res. 34 (2006) D386-D389
25. Pettersen E.F., Goddard T.D., Huang C.C., Couch G.S., Greenblatt D.M., Meng E.C., and Ferrin T.E. UCSF Chimera-a visualization system for exploratory research and analysis. J. Comput. Chem. 25 (2004) 1605-1612
26. Ludtke S.J., Baldwin P.R., and Chiu W. EMAN: semiautomated software for high-resolution single-particle reconstructions. J. Struct. Biol. 128 (1999) 82-97
27. Niesen F.H., Berglund H., and Vedadi M. The use of differential scanning fluorimetry to detect ligand interactions that promote protein stability. Nat. Protoc. 2 (2007) 2212-2221
28. Dragnea B., Chen C., Kwak E.S., Stein B., and Kao C.C. Gold nanoparticles as spectroscopic enhancers for in vitro studies on single viruses. J. Am. Chem. Soc. 125 (2003) 6374-6375
29. Takeda A., Kaido M., Okuno T., and Mise K. The C terminus of the movement protein of brome mosaic virus controls the requirement for coat protein in cell-to-cell movement and plays a role in long-distance movement. J. Gen. Virol. 85 (2004) 1751-1761
30. Calhoun S.L., Speir J.A., and Rao A.L. In vivo particle polymorphism results from deletion of a N-terminal peptide molecular switch in brome mosaic virus capsid protein. Virology 364 (2007) 407-421
31. Okinaka Y., Mise K., Suzuki E., Okuno T., and Furusawa I. The C terminus of brome mosaic virus coat protein controls viral cell-to-cell and long-distance movement. J. Virol. 75 (2001) 5385-5390
32. Okinaka Y., Mise K., Okuno T., and Furusawa I. Characterization of a novel barley protein, HCP1, that interacts with the brome mosaic virus coat protein. Mol. Plant-Microbe Interact. 16 (2003) 352-359
33. Kim S.H., Ryabov E.V., Kalinina N.O., Rakitina D.V., Gillespie T., MacFarlane S., et al. Cajal bodies and the nucleolus are required for a plant virus systemic infection. EMBO J. 26 (2007) 2169-2179
34. Kim S.H., Macfarlane S., Kalinina N.O., Rakitina D.V., Ryabov E.V., Gillespie T., et al. Interaction of a plant virus-encoded protein with the major nucleolar protein fibrillarin is required for systemic virus infection. Proc. Natl Acad. Sci. USA 104 (2007) 11115-11120
35. French R., and Ahlquist P. Intercistronic as well as terminal sequence are required for efficient amplification of brome mosaic virus RNA3. J. Virol. 61 (1987) 1457-1465
36. Pogue G.P., and Hall T.C. The requirement for a 5′ stem-loop structure in brome mosaic virus replication supports a new model for viral positive-strand RNA initiation. J. Virol. 66 (1992) 674-684
37. Reichert V.L., Choi M., Petrillo J.E., and Gehrke L. Alfalfa mosaic virus coat protein bridges RNA and RNA-dependent RNA polymerase in vitro. Virology 364 (2007) 214-226
38. Ahlquist P. Parallels among positive-strand RNA viruses, reverse-transcribing viruses and double-stranded RNA viruses. Nat. Rev. Microbiol. 4 (2006) 371-382
39. Chen J., and Ahlquist P. Brome mosaic virus polymerase-like protein 2a is directed to the endoplasmic reticulum by helicase-like viral protein 1a. J. Virol. 74 (2000) 4310-4318
40. Chen J., Noueiry A.O., and Ahlquist P. Brome mosaic virus protein 1a recruits viral RNA2 to RNA replication through a 5′ proximal RNA2 signal. J. Virol. 75 (2001) 3207-3219
41. Kao C.C., and Ahlquist P. Identification of domains required for direct interaction of the helicase-like and polymerase-like RNA replication proteins of brome mosaic virus. J. Virol. 66 (1992) 7293-7302
42. Johnson K.N., Tang L., Johnson J.E., and Ball L.A. Heterologous RNA encapsidated in Pariacoto virus-like particles forms a dodecahedral cage similar to genomic RNA in wild-type virions. J. Virol. 78 (2004) 11371-11378
43. Yi G., and Kao C. cis- and trans-acting functions of brome mosaic virus protein 1a in genomic RNA1 replication. J. Virol. 82 (2008) 3045-3053