Identification of dengue RNA binding proteins using RNA chromatography and quantitative mass spectrometry

Methods in Molecular Biology

Volumn 1138, Issue , 2014, Pages 253-270

  Ward, Alex M ^a   Gunaratne, J ^a   Garcia Blanco, Mariano A ^a  

^a NONE

Author keywords

Dengue virus; Quantitative mass spectrometry; RNA affinity chromatography; RNA aptamer; RNA binding proteins; SILAC; Tobramycin

Indexed keywords

APTAMER; RNA BINDING PROTEIN; TOBRAMYCIN; VIRUS RNA; CELL EXTRACT; VIRUS PROTEIN;

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; ADHERENT CELL; AMINO ACID SEQUENCE; ARTICLE; CELL LYSATE; CELL POPULATION; CHROMATOGRAPHY; CONTROLLED STUDY; DENGUE VIRUS 2; FLOW RATE; HUMAN; IN VITRO STUDY; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; NONHUMAN; POLYACRYLAMIDE GEL ELECTROPHORESIS; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN ANALYSIS; PROTEIN RNA BINDING; QUANTITATIVE ANALYSIS; RNA CHROMATOGRAPHY; WESTERN BLOTTING; AFFINITY CHROMATOGRAPHY; ANIMAL; CELL LINE; CONFORMATION; DENGUE VIRUS; ISOLATION AND PURIFICATION; ISOTOPE LABELING; METHODOLOGY;

DENGUE VIRUS;

ANIMALS; CELL EXTRACTS; CELL LINE; CHROMATOGRAPHY, AFFINITY; CHROMATOGRAPHY, LIQUID; DENGUE VIRUS; ISOTOPE LABELING; MASS SPECTROMETRY; NUCLEIC ACID CONFORMATION; RNA, VIRAL; RNA-BINDING PROTEINS; VIRAL PROTEINS;

EID: 84905924113     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-4939-0348-1_16     Document Type: Article

References (43)

1. Weaver SC, Reisen WK (2010) Present and future arboviral threats. Antiviral Res 85(2):328-345
2. Mackey TK, Liang BA (2012) Threats from emerging and re-emerging neglected tropical diseases (NTDs). Infect Ecol Epidemiol 2
3. Lindenbach B, Thiel HJ, Rice CM (2007) Flaviviridae: the viruses and their replication. Vol. I. Field’s virology, 5th edn. Lippincott, Williams and Wilkins, Philadelphia, PA
4. Ward AM, Bidet K, Yinglin A, Ler SG, Hogue K, Blackstock W, Gunaratne J, Garcia-Blanco MA (2011) Quantitative mass spectrometry of DENV-2 RNA-interacting proteins reveals that the DEAD-box RNA helicase DDX6 binds the DB1 and DB2 3′ UTR structures. RNA Biol 8(6):1173-1186
5. Alvarez DE, De Lella Ezcurra AL, Fucito S, Gamarnik AV (2005) Role of RNA structures present at the 3′UTR of dengue virus on translation, RNA synthesis, and viral replication. Virology 339(2):200-212
6. Alvarez DE, Filomatori CV, Gamarnik AV (2008) Functional analysis of dengue virus cyclization sequences located at the 5′ and 3′UTRs. Virology 375(1):223-235
7. Alvarez DE, Lodeiro MF, Luduena SJ, Pietrasanta LI, Gamarnik AV (2005) Long-range RNA-RNA interactions circularize the dengue virus genome. J Virol 79(11):6631-6643
8. Anwar A, Leong KM, Ng ML, Chu JJ, Garcia-Blanco MA (2009) The polypyrimidine tractbinding protein is required for efficient dengue virus propagation and associates with the viral replication machinery. J Biol Chem 284(25):17021-17029
9. Brinton MA, Dispoto JH (1988) Sequence and secondary structure analysis of the 5′-terminal region of flavivirus genome RNA. Virology 162(2):290-299
10. Brinton MA, Fernandez AV, Dispoto JH (1986) The 3′-nucleotides of flavivirus genomic RNA form a conserved secondary structure. Virology 153(1):113-121
11. Chiu WW, Kinney RM, Dreher TW (2005) Control of translation by the 5′-and 3′-terminal regions of the dengue virus genome. J Virol 79(13):8303-8315
12. Clyde K, Harris E (2006) RNA secondary structure in the coding region of dengue virus type 2 directs translation start codon selection and is required for viral replication. J Virol 80(5):2170-2182
13. Emara MM, Liu H, Davis WG, Brinton MA (2008) Mutation of mapped TIA-1/TIAR binding sites in the 3′ terminal stem-loop of West Nile virus minus-strand RNA in an infectious clone negatively affects genomic RNA amplification. J Virol 82(21):10657-10670
14. Filomatori CV, Lodeiro MF, Alvarez DE, Samsa MM, Pietrasanta L, Gamarnik AV (2006) A 5′ RNA element promotes dengue virus RNA synthesis on a circular genome. Genes Dev 20(16):2238-2249
15. Garcia-Montalvo BM, Medina F, del Angel RM (2004) La protein binds to NS5 and NS3 and to the 5′ and 3′ ends of Dengue 4 virus RNA. Virus Res 102(2):141-150
16. Grange T, Bouloy M, Girard M (1985) Stable secondary structures at the 3′-end of the genome of yellow fever virus (17 D vaccine strain). FEBS Lett 188(1):159-163
17. Hahn CS, Hahn YS, Rice CM, Lee E, Dalgarno L, Strauss EG, Strauss JH (1987) Conserved elements in the 3′ untranslated region of flavivirus RNAs and potential cyclization sequences. J Mol Biol 198(1):33-41
18. Holden KL, Harris E (2004) Enhancement of dengue virus translation: role of the 3′ untranslated region and the terminal 3′ stem-loop domain. Virology 329(1):119-133
19. Holden KL, Stein DA, Pierson TC, Ahmed AA, Clyde K, Iversen PL, Harris E (2006) Inhibition of dengue virus translation and RNA synthesis by a morpholino oligomer targeted to the top of the terminal 3′ stem-loop structure. Virology 344(2):439-452
20. Olsthoorn RC, Bol JF (2001) Sequence comparison and secondary structure analysis of the 3′ noncoding region of flavivirus genomes reveals multiple pseudoknots. RNA 7(10):1370-1377
21. Paranjape SM, Harris E (2007) Y box-binding protein-1 binds to the dengue virus 3′-untranslated region and mediates antiviral effects. J Biol Chem 282(42):30497-30508
22. Polacek C, Foley JE, Harris E (2009) Conformational changes in the solution structure of the dengue virus 5′ end in the presence and absence of the 3′ untranslated region. J Virol 83(2):1161-1166
23. Takegami T, Washizu M, Yasui K (1986) Nucleotide sequence at the 3′ end of Japanese encephalitis virus genomic RNA. Virology 152(2):483-486
24. Yocupicio-Monroy M, Padmanabhan R, Medina F, del Angel RM (2007) Mosquito La protein binds to the 3′ untranslated region of the positive and negative polarity dengue virus RNAs and relocates to the cytoplasm of infected cells. Virology 357(1):29-40
25. Lei Y, Huang Y, Zhang H, Yu L, Zhang M, Dayton A (2011) Functional interaction between cellular p100 and the dengue virus 3′ UTR. J Gen Virol 92(Pt 4):796-806
26. Li W, Li Y, Kedersha N, Anderson P, Emara M, Swiderek KM, Moreno GT, Brinton MA (2002) Cell proteins TIA-1 and TIAR interact with the 3′ stem-loop of the West Nile virus complementary minus-strand RNA and facilitate virus replication. J Virol 76(23):11989-12000
27. Hartmuth K, Vornlocher HP, Luhrmann R (2004) Tobramycin affinity tag purification of spliceosomes. Methods Mol Biol 257:47-64
28. Srisawat C, Engelke DR (2001) Streptavidin aptamers: affinity tags for the study of RNAs and ribonucleoproteins. RNA 7(4):632-641
29. Klug SJ, Famulok M (1994) All you wanted to know about SELEX. Mol Biol Rep 20(2):97-107
30. Caputi M, Mayeda A, Krainer AR, Zahler AM (1999) hnRNP A/B proteins are required for inhibition of HIV-1 pre-mRNA splicing. EMBO J 18(14):4060-4067
31. Stellato C, Gubin MM, Magee JD, Fang X, Fan J, Tartar DM, Chen J, Dahm GM, Calaluce R, Mori F, Jackson GA, Casolaro V, Franklin CL, Atasoy U (2011) Coordinate regulation of GATA-3 and Th2 cytokine gene expression by the RNA-binding protein HuR. J Immunol 187(1):441-449
32. Mann M (2006) Functional and quantitative proteomics using SILAC. Nat Rev Mol Cell Biol 7(12):952-958
33. Ong SE, Blagoev B, Kratchmarova I, Kristensen DB, Steen H, Pandey A, Mann M (2002) Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol Cell Proteomics 1(5):376-386
34. Butter F, Scheibe M, Morl M, Mann M (2009) Unbiased RNA-protein interaction screen by quantitative proteomics. Proc Natl Acad Sci U S A 106(26):10626-10631
35. Mittler G, Butter F, Mann M (2009) A SILACbased DNA protein interaction screen that identifies candidate binding proteins to functional DNA elements. Genome Res 19(2):284-293
36. Ong SE, Mann M (2006) A practical recipe for stable isotope labeling by amino acids in cell culture (SILAC). Nat Protoc 1(6):2650-2660
37. Schulze WX, Mann M (2004) A novel proteomic screen for peptide-protein interactions. J Biol Chem 279(11):10756-10764
38. Selbach M, Mann M (2006) Protein interaction screening by quantitative immunoprecipitation combined with knockdown (QUICK). Nat Methods 3(12):981-983
39. Shevchenko A, Tomas H, Havlis J, Olsen JV, Mann M (2006) In-gel digestion for mass spectrometric characterization of proteins and proteomes. Nat Protoc 1(6):2856-2860
40. Cox J, Mann M (2008) MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteomewide protein quantification. Nat Biotechnol 26(12):1367-1372
41. Lossner C, Warnken U, Pscherer A, Schnolzer M (2011) Preventing arginine-toproline conversion in a cell-line-independent manner during cell cultivation under stable isotope labeling by amino acids in cell culture (SILAC) conditions. Anal Biochem 412(1): 123-125
42. Rigbolt KT, Blagoev B (2010) Proteome-wide quantitation by SILAC. Methods Mol Biol 658:187-204
43. Trinkle-Mulcahy L, Boulon S, Lam YW, Urcia R, Boisvert FM, Vandermoere F, Morrice NA, Swift S, Rothbauer U, Leonhardt H, Lamond A (2008) Identifying specific protein interaction partners using quantitative mass spectrometry and bead proteomes. J Cell Biol 183(2):223-239