Insights into the biology of IRES elements through riboproteomic approaches

Journal of Biomedicine and Biotechnology

Volumn 2010, Issue , 2010, Pages

  Pacheco, Almudena ^a,b   Martinez Salas, Encarnacion ^a  

^a CENTRO DE BIOLOGÍA MOLECULAR SEVERO OCHOA   (Spain)

^b FOX CHASE CANCER CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RNA BINDING PROTEIN; VIRUS RNA; MESSENGER RNA;

GENE EXPRESSION REGULATION; HEPATITIS C VIRUS; INTERNAL RIBOSOME ENTRY SITE; NONHUMAN; PICORNAVIRUS; PROTEIN PROCESSING; PROTEIN RNA BINDING; PROTEOMICS; REVIEW; RIBOPROTEOMICS; RNA METABOLISM; RNA TRANSLATION; TRANSLATION INITIATION; GENETICS; METABOLISM; REGULATORY RNA SEQUENCE; RIBOSOME; VIRUS GENOME;

EUKARYOTA; HEPATITIS C VIRUS; PICORNAVIRIDAE;

GENOME, VIRAL; HEPACIVIRUS; PEPTIDE CHAIN INITIATION, TRANSLATIONAL; PICORNAVIRIDAE; REGULATORY SEQUENCES, RIBONUCLEIC ACID; RIBOSOMES; RNA, MESSENGER; RNA-BINDING PROTEINS;

EID: 77951901108     PISSN: 11107243     EISSN: 11107251     Source Type: Journal    
DOI: 10.1155/2010/458927     Document Type: Review

References (138)

1. T. V. Pestova, J. R. Lorsch, and C. U. T. Hellen, "The mechanism of translation initiation in eukaryotes," in Translation Control in Biology and Medicine, M. B. Mathews, N. Sonen-berg, and J. W. B. Hershey, Eds., pp. 87-128, Cold Spring Harbor laboratory, Cold Spring Harbor, NY, USA, 2007.
2. S. K. Jang, H.-G. Krausslich, M. J. H. Nicklin, G. M. Duke, A. C. Palmenberg, and E. Wimmer, "A segment of the 5' nontranslated region of encephalomyocarditis virus RNA directs internal entry of ribosomes during in vitro translation," Journal of Virology, vol. 62, no. 8, pp. 2636-2643, 1988.
3. J. Pelletier and N. Sonenberg, "Internal initiation of translation of eukaryotic mRNA directed by a sequence derived from poliovirus RNA," Nature, vol. 334, no. 6180, pp. 320-325, 1988.
4. E. Martínez-Salas, A. Pacheco, P. Serrano, and N. Fernandez, "New insights into internal ribosome entry site elements relevant for viral gene expression," Journal of General Virology, vol. 89, no. 3, pp. 611-626, 2008.
5. T. V. Pestova, I. N. Shatsky, S. P. Fletcher, R. J. Jackson, and C. U. T. Hellen, "A prokaryotic-like mode of cytoplasmic eukaryotic ribosome binding to the initiation codon during internal translation initation of hepatitis C and classical swine fever virus RNAs," Genes and Development, vol. 12, no. 1, pp. 67-83, 1998. (Pubitemid 28083659)
6. C. M. T. Spahn, J. S. Kieft, R. A. Grassucci, et al., "Hepatitis C virus IRES RNA-induced changes in the conformation of the 40S ribosomal subunit," Science, vol. 291, no. 5510, pp. 1959-1962, 2001. (Pubitemid 32216995)
7. S. D. Baird, M. Turcotte, R. G. Korneluk, and M. Holcik, "Searching for IRES," RNA, vol. 12, no. 10, pp. 1755-1785, 2006. (Pubitemid 44484249)
8. O. Fernández-Miragall, S. Lopez de Quinto, and E. Martínez-Salas, "Relevance of RNA structure for the activity of picornavirus IRES elements," Virus Research, vol. 139, no. 2, pp. 172-182, 2009.
9. M. Sáiz, S. Gomez, E. Martínez-Salas, and F. Sobrino, "Deletion or substitution of the aphthovirus 3' NCR abrogates infectivity and virus replication," Journal of General Virology, vol. 82, no. 1, pp. 93-101, 2001. (Pubitemid 32045799)
10. S. Lopez de Quinto, M. Saíz, D. de La Morena, F. Sobrino, and E. Martínez-Salas, "IRES-driven translation is stimulated separately by the FMDV 3'-NCR and poly(A) sequences," Nucleic Acids Research, vol. 30, no. 20, pp. 4398-4405, 2002. (Pubitemid 35277250)
11. E. Dobrikova, P. Florez, S. Bradrick, andM. Gromeier, "Activity of a type 1 picornavirus internal ribosomal entry site is determined by sequences within the 3' nontranslated region," Proceedings of the National Academy of Sciences of the United States of America, vol. 100, no. 25, pp. 15125-15130, 2003. (Pubitemid 37518027)
12. S. Lopez de Quinto and E. Martínez-Salas, "Involvement of the aphthovirus RNA region located between the two functional AUGs in start codon selection," Virology, vol. 255, no. 2, pp. 324-336, 1999. (Pubitemid 29393344)
13. D. E. Andreev, O. Fernández-Miragall, J. Ramajo, et al., "Differential factor requirement to assemble translation initiation complexes at the alternative start codons of foot-and-mouth disease virus RNA," RNA, vol. 13, no. 8, pp. 1366-1374,2007. (Pubitemid 47080480)
14. E. Martínez-Salas, "The impact of RNA structure on picornavirus IRES activity," Trends in Microbiology, vol. 16, no. 5, pp. 230-237, 2008.
15. G. J. Belsham, "Divergent picornavirus IRES elements," Virus Research, vol. 139, no. 2, pp. 183-192, 2009.
16. P. J. Lukavsky, "Structure and function of HCV IRES domains," Virus Research, vol. 139, no. 2, pp. 166-171, 2009.
17. J. S. Kieft, "Comparing the three-dimensional structures of Dicistroviridae IGR IRES RNAs with other viral RNA structures," Virus Research, vol. 139, no. 2, pp. 148-156,2009.
18. S. Lopez de Quinto and E. Martínez-Salas, "Conserved structural motifs located in distal loops of aphthovirus internal ribosome entry site domain 3 are required for internal initiation of translation," Journal of Virology, vol. 71, no. 5, pp. 4171-4175, 1997. (Pubitemid 27172441)
19. M. E. M. Robertson, R. A. Seamons, and G. J. Belsham, "A selection system for functional internal ribosome entry site (IRES) elements: analysis of the requirement for a conserved GNRA tetraloop in the encephalomyocarditis virus IRES," RNA, vol. 5, no. 9, pp. 1167-1179, 1999. (Pubitemid 29422759)
20. O. Fernández-Miragall and E. Martínez-Salas, "Structural organization of a viral IRES depends on the integrity of the GNRA motif," RNA, vol. 9, no. 11, pp. 1333-1344, 2003. (Pubitemid 37310864)
21. O. Fernández-Miragall, R. Ramos, J. Ramajo, and E. Martínez-Salas, "Evidence of reciprocal tertiary interactions between conserved motifs involved in organizing RNA structure essential for internal initiation of translation," RNA, vol. 12, no. 2, pp. 223-234, 2006. (Pubitemid 43121927)
22. P. Serrano, J. Gomez, and E. Martínez-Salas, " Characterization of a cyanobacterial RNase P ribozyme recognition motif in the IRES of foot-and-mouth disease virus reveals a unique structural element," RNA, vol. 13, no. 6, pp. 849-859, 2007. (Pubitemid 46799819)
23. P. Serrano, J. Ramajo, and E. Martínez-Salas, "Rescue of internal initiation of translation by RNA complementation provides evidence for a distribution of functions between individual IRES domains," Virology, vol. 388, no. 1, pp. 221-229, 2009.
24. V. G. Kolupaeva, T. V. Pestova, C. U. T. Hellen, and I. N. Shatsky, "Translation eukaryotic initiation factor 4G recognizes a specific structural element within the internal ribosome entry site of encephalomyocarditis virus RNA," Journal of Biological Chemistry, vol. 273, no. 29, pp. 18599-18604, 1998. (Pubitemid 28334791)
25. S. de Breyne, Y. Yu, A. Unbehaun, T. V. Pestova, and C. U. T. Hellen, "Direct functional interaction of initiation factor eIF4G with type 1 internal ribosomal entry sites," Proceedings of the National Academy of Sciences of the United States of America, vol. 106, no. 23, pp. 9197-9202, 2009.
26. S. Lopez de Quinto, E. Lafuente, and E. Martínez-Salas, "IRES interaction with translation initiation factors: functional characterization of novel RNA contacts with eIF3, eIF4B, andeIF4GII," RNA, vol. 7, no. 9, pp. 1213-1226,2001. (Pubitemid 32831351)
27. S. Lopez de Quinto and E. Martínez-Salas, "Interaction of the elF4G initiation factor with the aphthovirus IRES is essential for internal translation initiation in vivo," RNA, vol. 6, no. 10, pp. 1380-1392, 2000.
28. A. T. Clark, M. E. M. Robertson, G. L. Conn, and G. J. Belsham, "Conserved nucleotides within the J domain of the encephalomyocarditis virus internal ribosome entry site are required for activity and for interaction with eIF4G," Journal of Virology, vol. 77, no. 23, pp. 12441-12449, 2003. (Pubitemid 37430641)
29. A. J. Dorner, B. L. Semler, R. J. Jackson, R. Hanecak, E. Duprey, and E. Wimmer, "In vitro translation of poliovirus RNA: utilization of internal initiation sites in reticulocyte lysate," Journal of Virology, vol. 50, no. 2, pp. 507-514, 1984. (Pubitemid 14135780)
30. J. R. Gebhard and E. Ehrenfeld, "Specific interactions of HeLa cell proteins with proposed translation domains of the poliovirus 5' noncoding region," Journal of Virology, vol. 66, no. 5, pp. 3101-3109, 1992.
31. B. M. Lunde, C. Moore, and G. Varani, "RNA-binding proteins: modular design for efficient function," Nature Reviews Molecular Cell Biology, vol. 8, no. 6, pp. 479-490, 2007. (Pubitemid 46809150)
32. K. E. Lukong, K. Chang, E. W. Khandjian, and S. Richard, "RNA-binding proteins in human genetic disease," Trends in Genetics, vol. 24, no. 8, pp. 416-425, 2008.
33. E. Martínez-Salas, O. Fernández-Miragall, S. Reigadas, A. Pacheco, and P. Serrano, "Internal ribosome entry site elements in eukaryotic genomes," Current Genomics, vol. 5, no. 3, pp. 259-277, 2004. (Pubitemid 38477352)
34. K. Sawicka, M. Bushell, K. A. Spriggs, and A. E. Willis, "Polypyrimidine-tract-binding protein: a multifunctional RNA-binding protein," Biochemical Society Transactions, vol. 36, no. 4, pp. 641-647, 2008.
35. S. Reigadas, A. Pacheco, J. Ramajo, S. Lopez de Quinto, andE. Martínez-Salas, "Specific interference between two unrelated internal ribosome entry site elements impairs translation efficiency," FEBS Letters, vol. 579, no. 30, pp. 6803-6808, 2005. (Pubitemid 41773690)
36. A. Pacheco, S. Reigadas, and E. Martínez-Salas, "Ribopro-teomic analysis of polypeptides interacting with the internal ribosome-entry site element of foot-and-mouth disease viral RNA," Proteomics, vol. 8, no. 22, pp. 4782-4790, 2008.
37. Y. Yu, H. Ji, J. A. Doudna, and J. A. Leary, "Mass spectrometric analysis of the human 40S ribosomal subunit: native and HCV IRES-bound complexes," Protein Science, vol. 14, no. 6, pp. 1438-1446, 2005. (Pubitemid 41007909)
38. S. Weinlich, S. Hüttelmaier, A. Schierhorn, S.-E. Behrens, A. Ostareck-Lederer, and D. H. Ostareck, "IGF2BP1 enhances HCV IRES-mediated translation initiation via the 3'UTR," RNA, vol. 15, no. 8, pp. 1528-1542, 2009.
39. N. Luz and E. Beck, "A cellular 57 kDa protein binds to two regions of the internal translation initiation site of foot-and-mouth disease virus," FEBS Letters, vol. 269, no. 2, pp. 311-314, 1990. (Pubitemid 20273815)
40. S. K. Jang and E. Wimmer, "Cap-independent translation of encephalomyocarditis virus RNA: structural elements of the internal ribosomal entry site and involvement of a cellular 57-kD RNA-binding protein," Genes and Development, vol. 4, no. 9, pp. 1560-1572, 1990.
41. A. Borman, M. T. Howell, J. G. Patton, and R. J. Jackson, "The involvement of a spliceosome component in internal initiation of human rhinovirus RNA translation," Journal of General Virology, vol. 74, no. 9, pp. 1775-1788, 1993. (Pubitemid 23272342)
42. V. G. Kolupaeva, C. U. T. Hellen, and I. N. Shatsky, "Structural analysis of the interaction of the pyrimidine tract-binding protein with the internal ribosomal entry site of encephalomyocarditis virus and foot-and-mouth disease virus RNAs," RNA, vol. 2, no. 12, pp. 1199-1212, 1996. (Pubitemid 26419216)
43. P. Kafasla, N. Morgner, T. A. A. Pöyry, S. Curry, C. V. Robinson, and R. J. Jackson, "Polypyrimidine tract binding protein stabilizes the encephalomyocarditis virus IRES structure via binding multiple sites in a unique orientation," Molecular Cell, vol. 34, no. 5, pp. 556-568, 2009.
44. M. R. Conte, T. Grüne, J. Ghuman, et al., "Structure of tandem RNA recognition motifs from polypyrimidine tract binding protein reveals novel features of the RRM fold," EMBO Journal, vol. 19, no. 12, pp. 3132-3141, 2000. (Pubitemid 30386783)
45. P. M. Florez, O. M. Sessions, E. J. Wagner, M. Gromeier, and M. A. Garcia-Blanco, "The polypyrimidine tract binding protein is required for efficient picornavirus gene expression and propagation," Journal of Virology, vol. 79, no. 10, pp. 6172-6179, 2005. (Pubitemid 40617222)
46. Y. K. Kim, B. Hahm, and S. K. Jang, "Polypyrimidine tract-binding protein inhibits translation of bip mRNA," Journal of Molecular Biology, vol. 304, no. 2, pp. 119-133, 2000.
47. E. V. Pilipenko, E. G. Viktorova, S. T. Guest, V. I. Agol, and R. P. Roos, "Cell-specific proteins regulate viral RNA translation and virus-induced disease," EMBO Journal, vol. 20, no. 23, pp. 6899-6908, 2001. (Pubitemid 33134219)
48. M. K. Merrill, E. Y Dobrikova, and M. Gromeier, "Cell-type-specific repression of internal ribosome entry site activity by double-stranded RNA-binding protein 76," Journal of Virology, vol. 80, no. 7, pp. 3147-3156, 2006.
49. M. K. Merrill and M. Gromeier, "The double-stranded RNA binding protein 76:NF45 heterodimer inhibits translation initiation at the rhinovirus type 2 internal ribosome entry site," Journal of Virology, vol. 80, no. 14, pp. 6936-6942,2006. (Pubitemid 44025192)
50. Y Song, E. Tzima, K. Ochs, et al., "Evidence for an RNA chaperone function of polypyrimidine tract-binding protein in picornavirus translation," RNA, vol. 11, no. 12, pp. 1809-1824, 2005. (Pubitemid 41720031)
51. E. V. Pilipenko, T. V. Pestova, V. G. Kolupaeva, et al., "A cell cycle-dependent protein serves as a template-specific translation initiation factor," Genes and Development, vol. 14, no. 16, pp. 2028-2045, 2000. (Pubitemid 30637353)
52. T. P. Monie, A. J. Perrin, J. R. Birtley, et al., "Structural insights into the transcriptional and translational roles of Ebp1," EMBO Journal, vol. 26, no. 17, pp. 3936-3944, 2007. (Pubitemid 47367486)
53. O. Boussadia, M. Niepmann, L. Créancier, A.-C. Prats, F. Dautry, and H. Jacquemin-Sablon, "Unr is required in vivo for efficient initiation of translation from the internal ribosome entry sites of both rhinovirus and poliovirus," Journal of Virology, vol. 77, no. 6, pp. 3353-3359, 2003. (Pubitemid 36297254)
54. E. C. Anderson, S. L. Hunt, and R. J. Jackson, "Internal initiation of translation from the human rhinovirus-2 internal ribosome entry site requires the binding of Unr to two distinct sites on the 5' untranslated region," Journal of General Virology, vol. 88, no. 11, pp. 3043-3052, 2007. (Pubitemid 350131244)
55. H. Lu, W. Li, W. S. Noble, D. Payan, and D. C. Anderson, "Riboproteomics of the hepatitis C virus internal ribosomal entry site," Journal of Proteome Research, vol. 3, no. 5, pp. 949-957, 2004. (Pubitemid 39425650)
56. J. R. Evans, S. A. Mitchell, K. A. Spriggs, et al., "Members of the poly (rC) binding protein family stimulate the activity of the c-myc internal ribosome entry segment in vitro and in vivo," Oncogene, vol. 22, no. 39, pp. 8012-8020, 2003. (Pubitemid 37175865)
57. S. A. Mitchell, K. A. Spriggs, M. J. Coldwell, R. J. Jackson, and A. E. Willis, "The Apaf-1 internal ribosome entry segment attains the correct structural conformation for function via interactions with PTB and Unr," Molecular Cell, vol. 11, no. 3, pp. 757-771, 2003. (Pubitemid 36385128)
58. B. Schepens, S. A. Tinton, Y Bruynooghe, et al., "A role for hnRNP C1/C2 and Unr in internal initiation of translation during mitosis," EMBO Journal, vol. 26, no. 1, pp. 158-169, 2007. (Pubitemid 46094708)
59. H. Matsui, H. Asou, and T. Inaba, "Cytokines direct the regulation of Bim mRNA stability by heat-shock cognate protein 70," Molecular Cell, vol. 25, no. 1, pp. 99-112, 2007. (Pubitemid 46049065)
60. K. M. Bedard, S. Daijogo, and B. L. Semler, "A nucleo-cytoplasmic SR protein functions in viral IRES-mediated translation initiation," EMBO Journal, vol. 26, no. 2, pp. 459-467, 2007. (Pubitemid 46160946)
61. A. Pacheco, S. Lopez de Quinto, J. Ramajo, N. Fernandez, and E. Martínez-Salas, "A novel role for Gemin5 in mRNA translation," Nucleic Acids Research, vol. 37, no. 2, pp. 582-590, 2009.
62. D. J. Battle, C.-K. Lau, L. Wan, H. Deng, F. Lotti, andG. Drey-fuss, "The Gemin5 protein of the SMN complex identifies snRNAs," Molecular Cell, vol. 23, no. 2, pp. 273-279, 2006. (Pubitemid 44062371)
63. C. L. Will and R. Lührmann, "Spliceosomal UsnRNP biogenesis, structure and function," Current Opinion in Cell Biology, vol. 13, no. 3, pp. 290-301, 2001. (Pubitemid 32429493)
64. I. Fierro-Monti, S. Mohammed, R. Matthiesen, et al., "Quantitative proteomics identifies Gemin5, a scaffolding protein involved in ribonucleoprotein assembly, as a novel partner for eukaryotic initiation factor 4E," Journal of Proteome Research, vol. 5, no. 6, pp. 1367-1378, 2006. (Pubitemid 43865807)
65. G. Michlewski, J. R. Sanford, and J. F. Cáceres, "The splicing factor SF2/ASF regulates translation initiation by enhancing phosphorylation of 4E-BP1," Molecular Cell, vol. 30, no. 2, pp. 179-189, 2008. (Pubitemid 351626689)
66. M. Kiledjian and G. Dreyfuss, "Primary structure and binding activity of the hnRNP U protein: binding RNA through RGG box," EMBO Journal, vol. 11, no. 7, pp. 2655-2664, 1992.
67. J. H. Kim, B. Hahm, Y. K. Kim, M. Choi, and S. K. Jang, "Protein-protein interaction among hnRNPs shuttling between nucleus and cytoplasm," Journal of Molecular Biology, vol. 298, no. 3, pp. 395-405, 2000.
68. A. V. Makeyev and S. A. Liebhaber, "The poly(C)-binding proteins: a multiplicity of functions and a search for mechanisms," RNA, vol. 8, no. 3, pp. 265-278, 2002. (Pubitemid 34311177)
69. M. Lynch, L. Chen, M. J. Ravitz, et al., "hnRNP K binds a core polypyrimidine element in the eukaryotic translation initiation factor 4E (eIF4E) promoter, and its regulation of eIF4E contributes to neoplastic transformation," Molecular and Cellular Biology, vol. 25, no. 15, pp. 6436-6453, 2005. (Pubitemid 41023220)
70. P.-T. Lee, P.-C. Liao, W.-C. Chang, and J. T. Tseng, "Epidermal growth factor increases the interaction between nucleolin and heterogeneous nuclear ribonucleoprotein K/poly(C) binding protein 1 complex to regulate the gastrin mRNA turnover," Molecular Biology of the Cell, vol. 18, no. 12, pp. 5004-5013, 2007. (Pubitemid 350246700)
71. B. Collier, B. Gorgoni, C. Loveridge, H. J. Cooke, and N. K. Gray, "The DAZL family proteins are PABP-binding proteins that regulate translation in germ cells," EMBO Journal, vol. 24, no. 14, pp. 2656-2666, 2005. (Pubitemid 41076321)
72. L. B. Blyn, J. S. Towner, B. L. Semler, and E. Ehrenfeld, "Requirement of poly(rC) binding protein 2 for translation of poliovirus RNA," Journal of Virology, vol. 71, no. 8, pp. 6243-6246, 1997. (Pubitemid 27304973)
73. A. V. Gamarnik, N. Böddeker, and R. Andino, "Translation and replication of human rhinovirus type 14 and mengovirus in Xenopus oocytes," Journal of Virology, vol. 74, no. 24, pp. 11983-11987, 2000. (Pubitemid 32222351)
74. K. Choi, J. H. Kim, X. Li, et al., "Identification of cellular proteins enhancing activities of internal ribosomal entry sites by competition with oligodeoxynucleotides," Nucleic Acids Research, vol. 32, no. 4, pp. 1308-1317, 2004. (Pubitemid 38854732)
75. P. Sean, J. H. C. Nguyen, and B. L. Semler, "Altered interactions between stem-loop IV within the 5' noncoding region of coxsackievirus RNA and poly(rC) binding protein 2: effects on IRES-mediated translation and viral infectivity," Virology, vol. 389, no. 1-2, pp. 45-58, 2009.
76. B. L. Walter, J. H. C. Nguyen, E. Ehrenfeld, and B. L. Semler, "Differential utilization of poly(rC) binding protein 2 in translation directed by picornavirus IRES elements," RNA, vol. 5, no. 12, pp. 1570-1585, 1999.
77. E. Martínez-Salas, S. Lopez de Quinto, R. Ramos, and O. Fernández-Miragall, "IRES elements: features of the RNA structure contributing to their activity," Biochimie, vol. 84, no. 8, pp. 755-763, 2002. (Pubitemid 35363460)
78. R. Perera, S. Daijogo, B. L. Walter, J. H. C. Nguyen, and B. L. Semler, "Cellular protein modification by poliovirus: the two faces of poly(rC)-binding protein," Journal of Virology, vol. 81, no. 17, pp. 8919-8932, 2007. (Pubitemid 47311436)
79. J. Graff, J. Cha, L. B. Blyn, and E. Ehrenfeld, "Interaction of poly(rC) binding protein 2 with the 5' noncoding region of hepatitis A virus RNA and its effects on translation," Journal of Virology, vol. 72, no. 12, pp. 9668-9675, 1998. (Pubitemid 28520830)
80. C. Candé, N. Vahsen, D. Métivier, et al., "Regulation of cytoplasmic stress granules by apoptosis-inducing factor," Journal of Cell Science, vol. 117, no. 19, pp. 4461-4468, 2004. (Pubitemid 39360072)
81. K. Fujimura, J. Katahira, F. Kano, Y. Yoneda, and M. Murata, "Selective localization of PCBP2 to cytoplasmic processing bodies," Biochimica et Biophysica Acta, vol. 1793, no. 5, pp. 878-887, 2009.
82. F. Parker, F. Maurier, I. Delumeau, et al., "A Ras-GTPase-activating protein SH3-domain-binding protein," Molecular and Cellular Biology, vol. 16, no. 6, pp. 2561-2569, 1996. (Pubitemid 26161259)
83. S. Solomon, Y. Xu, B. Wang, et al., "Distinct structural features of caprin-1 mediate its interaction with G3BP-1 and its induction of phosphorylation of eukaryotic translation initiation factor 2a, entry to cytoplasmic stress granules, and selective interaction with a subset of mRNAs," Molecular and Cellular Biology, vol. 27, no. 6, pp. 2324-2342, 2007. (Pubitemid 46418485)
84. H. Tourrière, K. Chebli, L. Zekri, et al., "The RasGAP-associated endoribonuclease G3BP assembles stress granules," Journal of Cell Biology, vol. 160, no. 6, pp. 823-831, 2003. (Pubitemid 36350838)
85. P. Tingting, F. Caiyun, Y. Zhigang, Y. Pengyuan, and Y Zhenghong, "Subproteomic analysis of the cellular proteins associated with the 3' untranslated region of the hepatitis C virus genome in human liver cells," Biochemical and Biophysical Research Communications, vol. 347, no. 3, pp. 683-691, 2006. (Pubitemid 44092638)
86. K. E. Gustin and P. Sarnow, "Effects of poliovirus infection on nucleo-cytoplasmic trafficking and nuclear pore complex composition," EMBO Journal, vol. 20, no. 1-2, pp. 240-249, 2001. (Pubitemid 32099120)
87. H. Ginisty, H. Sicard, B. Roger, and P. Bouvet, "Structure and functions of nucleolin," Journal of Cell Science, vol. 112, no. 6, pp. 761-772, 1999. (Pubitemid 29179310)
88. S. Waggoner and P. Sarnow, "Viral ribonucleoprotein complex formation and nucleolar-cytoplasmic relocalization of nucleolin in poliovirus-infected cells," Journal of Virology, vol. 72, no. 8, pp. 6699-6709, 1998. (Pubitemid 28323988)
89. R. E. Izumi, B. Valdez, R. Banerjee, M. Srivastava, and A. Dasgupta, "Nucleolin stimulates viral internal ribosome entry site-mediated translation," Virus Research, vol. 76, no. 1, pp. 17-29, 2001. (Pubitemid 32480132)
90. J.-Y Lin, M.-L. Li, and S.-R. Shih, "Far upstream element binding protein 2 interacts with enterovirus 71 internal ribosomal entry site and negatively regulates viral translation," Nucleic Acids Research, vol. 37, no. 1, pp. 47-59, 2009.
91. J. Höck, L. Weinmann, C. Ender, et al., "Proteomic and functional analysis of Argonaute-containing mRNA-protein complexes in human cells," EMBO Reports, vol. 8, no. 11, pp. 1052-1060, 2007. (Pubitemid 350042341)
92. M. Landthaler, D. Gaidatzis, A. Rothballer, et al., "Molecular characterization of human Argonaute-containing ribonucleoprotein complexes and their bound target mRNAs," RNA, vol. 14, no. 12, pp. 2580-2596, 2008.
93. K. Tsukiyama-Kohara, N. Iizuka, M. Kohara, and A. Nomoto, "Internal ribosome entry site within hepatitis C virus RNA," Journal of Virology, vol. 66, no. 3, pp. 1476-1483, 1992.
94. C. S. Fraser and J. A. Doudna, "Structural and mechanistic insights into hepatitis C viral translation initiation," Nature Reviews Microbiology, vol. 5, no. 1, pp. 29-38, 2007. (Pubitemid 44942301)
95. C. Wang, S.-Y. Le, N. Ali, and A. Siddiqui, "An RNA pseudoknot is an essential structural element of the internal ribosome entry site located within the hepatitis C virus 5' noncoding region," RNA, vol. 1, no. 5, pp. 526-537, 1995.
96. G. A. Otto and J. D. Puglisi, "The pathway of HCV IRES-mediated translation initiation," Cell, vol. 119, no. 3, pp. 369-380, 2004. (Pubitemid 39423839)
97. N. Locker, L. E. Easton, and P. J. Lukavsky, "HCV and CSFV IRES domain II mediate eIF2 release during 80S ribosome assembly," EMBO Journal, vol. 26, no. 3, pp. 795-805, 2007.
98. J. S. Kieft, K. Zhou, R. Jubin, and J. A. Doudna, "Mechanism of ribosome recruitment by hepatitis C IRES RNA," RNA, vol. 7, no. 2, pp. 194-206, 2001. (Pubitemid 33590503)
99. E. Buratti, S. Tisminetzky, M. Zotti, and F. E. Baralle, "Functional analysis of the interaction between HCV 5'UTR and putative subunits of eukaryotic translation initiation factor elF3," Nucleic Acids Research, vol. 26, no. 13, pp. 3179-3187, 1998. (Pubitemid 28288916)
100. B. Siridechadilok, C. S. Fraser, R. J. Hall, J. A. Doudna, and E. Nogales, "Molecular biology: structural roles for human translation factor elF3 in initiation of protein synthesis," Science, vol. 310, no. 5753, pp. 1513-1515, 2005. (Pubitemid 41746350)
101. I. M. Terenin, S. E. Dmitriev, D. E. Andreev, and I. N. Shatsky, "Eukaryotic translation initiation machinery can operate in a bacterial-like mode without eIF2," Nature Structural and Molecular Biology, vol. 15, no. 8, pp. 836-841, 2008.
102. S. Fukushi, M. Okada, J. Stahl, T. Kageyama, F. B. Hoshino, and K. Katayama, "Ribosomal protein S5 interacts with the internal ribosomal entry site of hepatitis C virus," Journal of Biological Chemistry, vol. 276, no. 24, pp. 20824-20826,2001.
103. E. Laletina, D. Graifer, A. Malygin, A. Ivanov, I. Shatsky, and G. Karpova, "Proteins surrounding hairpin IIIe of the hepatitis C virus internal ribosome entry site on the human 40S ribosomal subunit," Nucleic Acids Research, vol. 34, no. 7, pp. 2027-2036, 2006. (Pubitemid 44314201)
104. G. A. Otto, P. J. Lukavsky, A. M. Lancaster, P. Sarnow, and J. D. Puglisi, "Ribosomal proteins mediate the hepatitis C virus IRES-HeLa 40S interaction," RNA, vol. 8, no. 7, pp. 913-923, 2002. (Pubitemid 34787688)
105. H. Ji, C. S. Fraser, Y. Yu, J. Leary, and J. A. Doudna, "Coordinated assembly of human translation initiation complexes by the hepatitis C virus internal ribosome entry site RNA," Proceedings of the National Academy of Sciences of the United States of America, vol. 101, no. 49, pp. 16990-16995, 2004. (Pubitemid 39627761)
106. J. Sengupta, J. Nilsson, R. Gursky, C. M. T. Spahn, P. Nissen, and J. Frank, "Identification of the versatile scaffold protein RACK1 on the eukaryotic ribosome by cryo-EM," Nature Structural and Molecular Biology, vol. 11, no. 10, pp. 957-962, 2004. (Pubitemid 39315299)
107. O. Isken, M. Baroth, C. W. Grassmann, et al., "Nuclear factors are involved in hepatitis C virus RNA replication," RNA, vol. 13, no. 10, pp. 1675-1692, 2007. (Pubitemid 47481676)
108. C. Romero-López and A. Berzal-Herranz, "A long-range RNA-RNA interaction between the 5' and 3' ends of the HCV genome," RNA, vol. 15, no. 9, pp. 1740-1752, 2009.
109. P. Serrano, M. R. Pulido, M. Saiz, and E. Martínez-Salas, "The 3' end of the foot-and-mouth disease virus genome establishes two distinct long-range RNA-RNA interactions with the 5' and region," Journal of General Virology, vol. 87, no. 10, pp. 3013-3022, 2006. (Pubitemid 44463910)
110. R. Gosert, K. H. Chang, R. Rijnbrand, M. Yi, D. V. Sangar, and S. M. Lemon, "Transient expression of cellular polypyrimidine-tract binding protein stimulates cap-independent translation directed by both picornaviral and flaviviral internal ribosome entry sites in vivo," Molecular and Cellular Biology, vol. 20, no. 5, pp. 1583-1595, 2000. (Pubitemid 30100178)
111. Y Song, P. Friebe, E. Tzima, C. Jünemann, R. Bartenschlager, and M. Niepmann, "The hepatitis C virus RNA 3'-untranslated region strongly enhances translation directed by the internal ribosome entry site," Journal of Virology, vol. 80, no. 23, pp. 11579-11588, 2006. (Pubitemid 44788872)
112. J. H. Kim, K. Y Paek, S. H. Ha, et al., "A cellular RNA-binding protein enhances internal ribosomal entry site-dependent translation through an interaction downstream of the hepatitis C virus polyprotein initiation codon," Molecular and Cellular Biology, vol. 24, no. 18, pp. 7878-7890, 2004. (Pubitemid 39167439)
113. T. Mondal, U. Ray, A. K. Manna, R. Gupta, S. Roy, and S. Das, "Structural determinant of human La protein critical for internal initiation of translation of hepatitis C virus RNA," Journal of Virology, vol. 82, no. 23, pp. 11927-11938, 2008.
114. K. Meerovitch, Y. V. Svitkin, H. S. Lee, et al., "La autoantigen enhances and corrects aberrant translation of poliovirus RNA in reticulocyte lysate," Journal of Virology, vol. 67, no. 7, pp. 3798-3807, 1993. (Pubitemid 23180701)
115. Y. K. Kim and S. K. Jang, "La protein is required for efficient translation driven by encephalomyocarditis virus internal ribosomal entry site," Journal of General Virology, vol. 80, no. 12, pp. 3159-3166, 1999.
116. S. Cordes, Y. Kusov, T. Heise, and V. Gauss-Müller, "La autoantigen suppresses IRES-dependent translation of the hepatitis A virus," Biochemical and Biophysical Research Communications, vol. 368, no. 4, pp. 1014-1019, 2008.
117. H. M. Liu, H. Aizaki, K. S. Choi, K. Machida, J. J.-H. Ou, and M. M. C. Lai, "SYNCRIP (synaptotagmin-binding, cytoplasmic RNA-interacting protein) is a host factor involved in hepatitis C virus RNA replication," Virology, vol. 386, no. 2, pp. 249-256, 2009.
118. B. Hahm, Y K. Kim, J. H. Kim, T. Y Kim, and S. K. Jang, "Heterogeneous nuclear ribonucleoprotein L interacts with the 3' border of the internal ribosomal entry site of hepatitis C virus," Journal of Virology, vol. 72, no. 11, pp. 8782-8788, 1998. (Pubitemid 28471821)
119. B. Hwang, J. H. Lim, B. Hahm, S. K. Jang, and S.-W. Lee, "hnRNP L is required for the translation mediated by HCV IRES," Biochemical and Biophysical Research Communications, vol. 378, no. 3, pp. 584-588, 2009.
120. M. Majumder, I. Yaman, F. Gaccioli, et al., "The hnRNA-binding proteins hnRNP L and PTB are required for efficient translation of the Cat-1 arginine/lysine transporter mRNA during amino acid starvation," Molecular and Cellular Biology, vol. 29, no. 10, pp. 2899-2912, 2009.
121. K. Y Paek, C. S. Kim, S. M. Park, J. H. Kim, and S. K. Jang, "RNA-binding protein hnRNP D modulates internal ribosome entry site-dependent translation of hepatitis C Virus RNA," Journal of Virology, vol. 82, no. 24, pp. 12082-12093, 2008.
122. J.-Y. Lin, S.-R. Shih, M. Pan, et al., "hnRNP A1 interacts with the 3' untranslated regions of enterovirus 71 and Sindbis virus RNA and is required for viral replication," Journal of Virology, vol. 83, no. 12, pp. 6106-6114, 2009.
123. S. Bonnal, F. Pileur, C. Orsini, et al., "Heterogeneous nuclear ribonucleoprotein A1 is a novel internal ribosome entry site trans-acting factor that modulates alternative initiation of translation of the fibroblast growth factor 2 mRNA," Journal of Biological Chemistry, vol. 280, no. 6, pp. 4144-4153, 2005. (Pubitemid 40288579)
124. A. Cammas, F. Pileur, S. Bonnal, et al., "Cytoplasmic relo-calization of heterogeneous nuclear ribonucleoprotein A1 controls translation initiation of specific mRNAs," Molecular Biology of the Cell, vol. 18, no. 12, pp. 5048-5059, 2007. (Pubitemid 350246704)
125. A. Kukalev, Y. Nord, C. Palmberg, T. Bergman, and P. Percipalle, "Actin and hnRNP U cooperate for productive transcription by RNA polymerase II," Nature Structural and Molecular Biology, vol. 12, no. 3, pp. 238-244, 2005. (Pubitemid 43079365)
126. P. Percipalle, A. Jonsson, D. Nashchekin, et al., "Nuclear actin is associated with a specific subset of hnRNP A/B-type proteins," Nucleic Acids Research, vol. 30, no. 8, pp. 1725-1734, 2002. (Pubitemid 34679749)
127. D. E. Schultz, C. C. Hardin, and S. M. Lemon, "Specific interaction of glyceraldehyde 3-phosphate dehydrogenase with the 5'-nontranslated RNA of hepatitis a virus," Journal of Biological Chemistry, vol. 271, no. 24, pp. 14134-14142, 1996.
128. M. Yi, D. E. Schultz, and S. M. Lemon, "Functional significance of the interaction of hepatitis A virus RNA with glyceraldehyde 3-phosphate dehydrogenase (GAPDH): opposing effects of GAPDH and polypyrimidine tract binding protein on internal ribosome entry site function," Journal of Virology, vol. 74, no. 14, pp. 6459-6468, 2000. (Pubitemid 30429813)
129. R. Mukhopadhyay, J. Jia, A. Arif, P. S. Ray, and P. L. Fox, "The GAIT system: a gatekeeper of inflammatory gene expression," Trends in Biochemical Sciences, vol. 34, no. 7, pp. 324-331, 2009.
130. F. V. Fuller-Pace, "DExD/H box RNA helicases: multifunctional proteins with important roles in transcriptional regulation," Nucleic Acids Research, vol. 34, no. 15, pp. 4206-4215, 2006. (Pubitemid 44542200)
131. T. R. Hartman, S. Qian, C. Bolinger, S. Fernandez, D. R. Schoenberg, and K. Boris-Lawrie, "RNA helicase A is necessary for translation of selected messenger RNAs," Nature Structural and Molecular Biology, vol. 13, no. 6, pp. 509-516, 2006. (Pubitemid 43848905)
132. H.-C. Chen, W.-C. Lin, Y.-G. Tsay, S.-C. Lee, andC.-J. Chang, "An RNA helicase, DDX1, interacting with poly(A) RNA and heterogeneous nuclear ribonucleoprotein K," Journal of Biological Chemistry, vol. 277, no. 43, pp. 40403-40409,2002. (Pubitemid 35215615)
133. M. Rodróguez Pulido, P. Serrano, M. Sáiz, and E. Martínez-Salas, "Foot-and-mouth disease virus infection induces proteolytic cleavage of PTB, eIF3a,b, and PABP RNA-binding proteins," Virology, vol. 364, no. 2, pp. 466-474, 2007.
134. J. P. White, A. M. Cardenas, W. E. Marissen, and R. E. Lloyd, "Inhibition of cytoplasmic mRNA stress granule formation by a viral proteinase," Cell Host and Microbe, vol. 2, no. 5, pp. 295-305, 2007. (Pubitemid 350056396)
135. V. Guerniou, R. Gillet, F. Berrée, B. Carboni, and B. Felden, "Targeted inhibition of the hepatitis C internal ribosomal entry site genomic RNA with oligonucleotide conjugates," Nucleic Acids Research, vol. 35, no. 20, pp. 6778-6787, 2007. (Pubitemid 350201798)
136. C. Romero-López, R. Díaz-González, A. Barroso-del Jesus, and A. Berzal-Herranz, "Inhibition of hepatitis C virus replication and internal ribosome entry site-dependent translation by an RNA molecule," Journal of General Virology, vol. 90, no. 7, pp. 1659-1669, 2009.
137. M. F. Rosas, E. Martínez-Salas, and F. Sobrino, "Stable expression of antisense RNAs targeted to the 5' non-coding region confers heterotypic inhibition to foot-and-mouth disease virus infection," Journal of General Virology, vol. 84, no. 2, pp. 393-402, 2003. (Pubitemid 36175714)
138. A. Vagnozzi, D. A. Stein, P. L. Iversen, and E. Rieder, "Inhibition of foot-and-mouth disease virus infections in cell cultures with antisense morpholino oligomers," Journal of Virology, vol. 81, no. 21, pp. 11669-11680, 2007. (Pubitemid 47623799)