The current status of vertebrate cellular mRNA IRESs

Cold Spring Harbor Perspectives in Biology

Volumn 5, Issue 2, 2013, Pages

  Jackson, Richard J ^a  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

INITIATION FACTOR; MESSENGER RNA; VIRUS RNA;

ANIMAL; ARTICLE; BINDING SITE; CHEMISTRY; CLASSIFICATION; CONFORMATION; GENETICS; METABOLISM; PHYSIOLOGY; RIBOSOME; RNA TRANSLATION; VERTEBRATE;

ANIMALS; BINDING SITES; NUCLEIC ACID CONFORMATION; PEPTIDE CHAIN INITIATION, TRANSLATIONAL; PEPTIDE INITIATION FACTORS; RIBOSOMES; RNA, MESSENGER; RNA, VIRAL; VERTEBRATES;

EID: 84875129451     PISSN: None     EISSN: 19430264     Source Type: Journal    
DOI: 10.1101/cshperspect.a011569     Document Type: Article

References (87)

1. Alexander L, Lu HH, Wimmer E. 1994. Polioviruses containing picornavirus type 1 and/or type 2 internal ribosomal entry site elements: Genetic hybrids and the expression of a foreign gene. Proc Natl Acad Sci 91: 1406-1410.
2. Ali IK, Jackson RJ. 2001. The translation of capped mRNAs has an absolute requirement for the central domain of eIF4G but not for the cap-binding initiation factor eIF4E. Cold Spring Harb Symp Quant Biol 66: 377-387.
3. Ali IK, McKendrick L, Morley SJ, Jackson RJ. 2001. Activity of the hepatitis Avirus IRES requires association between the cap-binding translation initiation factor (eIF4E) and eIF4G. J Virol 75: 7854-7863.
4. 0 end dependent translation initiation of mammalian mRNAs. Nucleic Acids Res 37: 6135-6147.
5. 0-UTR: Implications for ELK-1 expression. Nucleic Acids Res 35: 4649-4663.
6. Baird SD, Turcotte M, Korneluk RG, Holcik M. 2006. Searching for IRES. RNA 12: 1755-1785.
7. Baranick BT, Lemp NA, Nagashima J, Hiraoka K, Kasahara N, Logg CR. 2008. Splicing mediates the activity of four putative cellular internal ribosome entry sites. Proc Natl Acad Sci 105: 4733-4738.
8. Barreau C, Dutertre S, Paillard L, Osborne HB. 2006. Liposome-mediated RNA transfection should be used with caution. RNA 12: 1790-1793.
9. Bedard KM, Daijogo S, Semler BL. 2007. A nucleo-cytoplasmic SR protein functions in viral IRES-mediated translation initiation. EMBO J 26: 459-467.
10. 0 -UTRs. RNA 12: 1074-1083.
11. Borman AM, Michel YM, Kean KM. 2001. Detailed analysis of the requirements of hepatitis Avirus internal ribosome entry segment for the eukaryotic initiation factor complex eIF4F. J Virol 75: 7864-7871.
12. Boussadia O, Niepmann M, Créancier L, Prats AC, Dautry F, Jacquemin-Sablon H. 2003. Unr is required in vivo for efficient initiation of translation from the internal ribosome entrysites of both rhinovirus and poliovirus. JVirol 77: 3353-3359.
13. Braunstein S, Karpisheva K,Pola C, Goldberg J, Hochman T, Yee H, Cangiarella J, Arju R, Formenti SC, Schneider RJ. 2007. A hypoxia-controlled cap-dependent to cap-independent translation switch in breast cancer. Mol Cell 28: 501-512.
14. Bushe ll M, Stoneley M, Kong YW, Hamilton TL, Spriggs KA, Dobbyn HC, Qin X, Sarnow P, Willis AE. 2006. Polypyrimidine tract binding proteins regulates IRES-mediated gene expression during apoptosis. Mol Cell 23: 401-412.
15. Byrd MP, Zamora M, Lloyd RE. 2005. Translation of eukaryotic translation initiation factor 4GI (eIF4GI) proceeds from multiple mRNAs containing a novel cap-dependent internal ribosome entry site (IRES) that is active during poliovirus infection. J Biol Chem 280: 18610- 18622.
16. 0 untranslated region. Oncogene 23: 267-277.
17. Cobbold LC, Spriggs KA, Haines SJ, Dobbyn HC, Hayes C, de Moor CH, Lilley KS, Bushell M, Willis AE. 2008. Identification of internal ribosome entry segment (IRES)trans-acting factors for the Myc family of IRESs. Mol Cell Biol 28: 40-49.
18. Costa-Mattioli M, Svitkin Y, Sonenberg N. 2004. La autoantigen is necessary for optimal function of the poliovirus and hepatitis C virus internal ribosome entry site in vivo and in vitro. Mol Cell Biol 24: 6861-6870.
19. de Breyne S, Yu Y, Pestova TV, Hellen CU. 2008. Factor requirements for translation initiation on the Simian picornavirus internal ribosomal entry site. RNA 14: 367-380.
20. de Breyne S, Yu Y, Unbehaun A, Pestova TV, Hellen CUT. 2009. Direct functional interaction of initiation factor eIF4G with type 1 internal ribosomal entry sites. Proc Natl Acad Sci 106: 9197-91202.
21. 0-untranslated region of the human retrotransposon LINE-1 mRNA is strictly cap-dependent rather than internal ribosome entry site mediated. Mol Cell Biol 27: 4685-4697.
22. 0-untranslated region of the mRNA for eIF4G, a factor involved in the picornavirus-induced switch from cap-dependent to internal initiation. J Biol Chem 271: 623-626.
23. Hellen CUT, de Breyne S. 2007. A distinct group of hepacivirus/pestivirus-like internal ribosomal entry sites in members of diverse picornavirus genera: Evidence for modular exchange of functional noncoding RNA elements by recombination. J Virol 81: 5850-5863.
24. Holcík M, Gordon BW, Korneluk RG. 2003. The internal ribosome entry site-mediated translation of antiapoptotic protein XIAP is modulated by the heterogeneous nuclear ribonucleoproteins C1 and C2. Mol Cell Biol 23: 280-288.
25. Hundsdoerfer P, Thoma C, Hentze MW. 2005. Eukaryotic translation initiation factor 4GI and p97 promote cellular internal ribosome entry sequence-driven translation. Proc Natl Acad Sci 102: 13421-13426.
26. Hunt SL, Jackson RJ. 1999. Polypyrimidine-tract binding protein (PTB) is necessary, but not sufficient, for efficient internal initiation of translation of human rhinovirus-2 RNA. RNA 5: 344-359.
27. Hunt SL, Hsuan JJ, Totty N, Jackson RJ. 1999. Unr, a cellular cytoplasmic RNA-binding protein with five cold shock domains, is required for internal initiation of translation of human rhinovirus RNA. Genes Dev 13: 437-448.
28. 0 noncoding sequence of the genome. J Virol 63: 5354-5363.
29. Jackson RJ. 1991. Potassium salts influence the fidelity of mRNA translation initiation inrabbit reticulocytelysates: Unique features of encephalomyocarditis virus RNA translation. Biochim Biophys Acta 1088: 345-358.
30. Jackson RJ, Kaminski A. 1995. Internal initiation of translation in eukaryotes: The picornavirus paradigm and beyond. RNA 1: 985-1000.
31. Jang SK, Wimmer E. 1990. 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 Dev 4: 1560-1572.
32. Johannes G, Sarnow P. 1998. Cap-independent polysomal association of natural mRNAs encoding c-myc, BiP, and eIF4G conferred by internal ribosome entry site. RNA 4: 1500-1513.
33. Kafasla P, Morgner N, Pöyry TA, Curry S, Robinson CV, Jackson RJ. 2009. Polypyrimidine tract binding protein stabilizes the encephalomyocarditis virus IRES structure via binding multiple sites in a unique orientation. Mol Cell 34: 556-568.
34. Kafasla P, Morgner N, Robinson CV, Jackson RJ. 2010. Polypyrimidine tract binding protein stimulates the poliovirus IRES by modulating eIF4G binding. EMBO J 29: 3710-3722.
35. Kaminski A, Jackson RJ. 1998. The polypyrimidine tract binding protein (PTB) requirement for internal initiation of translation of cardiovirus RNAs is conditional rather than absolute. RNA 4: 626-638.
36. Kaminski A, Howell MT, Jackson RJ. 1990. Initiation of encephalomyocarditis virus RNA translation: The authentic initiation site is not selected by a scanning mechanism. EMBO J 9: 3753-3759.
37. Kaminski A, Belsham GJ, Jackson RJ. 1994. Translation of encephalomyocarditis virus RNA: Parameters influencing the selectionof the internal initiation site. EMBOJ 13: 1673-1681.
38. Kaminski A, Pöyry TAA, Skene PJ, Jackson RJ. 2010. Mechanism of initiation site selection promoted by the human rhinovirus 2 internal ribosome entry site. J Virol 84: 6578-6589.
39. King HA, Cobbold LC, Willis AE. 2010. The role of IRES trans-acting factors in regulating translation initiation. Biochem Soc Trans 38: 1581-1586.
40. Koeller DM, Casey JL, Hentze MW, Gerhardt EM, Chan LN, Klausner RD, Harford JB. 1989. Acytosolic protein binds to structural elements within the iron regulatory region of the transferrin receptor mRNA. Proc Natl Acad Sci 86: 3574-3578.
41. Kolupaeva VG, Pestova TV, Hellen CU, Shatsky IN. 1998. Translation eukaryotic initiation factor 4G recognizes a specific structural element within the internal ribosome entry site of encephalomyocarditis virus RNA. J Biol Chem 273: 18599-18604.
42. Kolupaeva VG, Lomakin IB, Pestova TV, Hellen CUT. 2003. Eukaryotic initiation factors 4G and 4A mediate conformational changes downstream of the initiation codon of the encephalomyocarditis virus internal ribosomal entry site. Mol Cell Biol 23: 687-698.
43. Kozak M. 2003. Alternative ways to think about mRNA sequences and proteins that appear to promote internal initiation of translation. Gene 318: 1-23.
44. Kozak M. 2005. A second look at cellular mRNA sequences said to function as internal ribosome entry sites. Nucleic Acids Res 33: 6593-6602.
45. Le Hir H, Nott A, Moore MJ. 2003. How introns influence and enhance eukaryotic gene expression. Trends Biochem Sci 28: 215-220.
46. Lemp NA, Hiraoka K, Kasahara N, Logg CR. 2012. Cryptic transcripts from the ubiquitous pMB1 origin of replication confound functional tests for cis-regulatory elements. Nucleic Acids Res doi: 10.1093/nar/gks451.
47. Kip1. Nucleic Acids Res 33: 3763-3771.
48. Lomakin IV, Hellen CUT, Pestova TV. 2000. Physical association of eukaryotic initiation factor 4G (eIF4G) with eIF4A stronglyenhances binding of eIF4G to the internal ribosomal entry site of encephalomyocarditis virus is required for internal initiation of translation. Mol Cell Biol 20: 6019-6029.
49. 0 untranslated region. J Virol 65: 5895-5901.
50. 0 -untranslated regions of plant viral RNAs. Biochem Soc Trans 35: 1629-1633.
51. Mokrejs M, Masek T, Vopalensky A, Hlubucek P, Delbos P, Pospisek M. 2010. IRESite-a tool for the examination of viral and cellular internal ribosome entry sites. Nucleic Acids Res 38: D131-D136.
52. Nagy E, Maquat LE. 1998. A rule for termination-codon positionwithin intron-containing genes: When nonsense affects RNA abundance. Trends Biochem Sci 23: 198-199.
53. Nicholson R, Pelletier J, Le S-Y, Sonenberg N. 1991. Structural and functional analysis of the ribosome landing pad of poliovirus type 2: In vivo translation studies. J Virol 65: 5886-5894.
54. Oberstrass FC, Auweter SD, Erat M, Hargous Y, Henning A, Wenter P, Reymond L, Amir-Ahmady B, Pitsch S, Black DL, et al. 2005. Structure of PTB bound to RNA: Specific binding and implications for splicing regulation. Science 309: 2054-2057.
55. Özeş AR, Feoktistova K, Avanzino BC, Fraser CS. 2011. Duplex unwinding and ATPase activities of the DEAD-box helicase eIF4A are coupledbyeIF4G and eIF4B. J Mol Biol 412: 674-687.
56. Pelletier J, Sonenberg N. 1988. Internal initiation of translation of eukaryotic mRNA directed by a sequence derived from poliovirus RNA. Nature 334: 320-325.
57. Pelletier J, Flynn ME, Kaplan G, Racaniello V, Sonenberg N. 1988. Mutational analysis of upstream AUG codons of poliovirus RNA. J Virol 62: 4486-4492.
58. 0 nontranslated region of poliovirus can function as an initiation codon in vitro and in vivo. Virology 204: 729-737.
59. Pestova TV, Hellen CUT, Shatsky IN. 1996. Canonical eukaryotic initiation factors determine initiation of translation by internal ribosomal entry. Mol Cell Biol 16: 6859-6869.
60. Pestova TV, Shatsky IN, Fletcher SP, Jackson RJ, Hellen CUT. 1998. A prokaryotic-like mode of cytoplasmic eukaryotic ribosome binding to the initiation codon during internal translation initiation of hepatitis C and classical swine fever virus RNAs. Genes Dev 12: 67-83.
61. Pestova TV, de Breyne S, Pisarev AV, Abaeva IS, Hellen CU. 2008. EIF2-dependent and eIF2-independent modes of initiation on the CSFV IRES: A common role of domain II. EMBO J 27: 1060-1072.
62. Pilipenko EV, Pestova TV, Kolupaeva VG, Khitrina EV, Poperechnaya AN, Agol VI, Hellen CUT. 2000. A cell cycle-dependent protein serves as a template-specific translation initiation factor. Genes Dev 14: 2028- 2045.
63. 0 noncoding region of poliovirus RNA. J Virol 66: 5313-5319.
64. Prévôt D, Décimo D, Herbreteau CH, Roux F, Garin J, Darlix JL, Ohlmann T. 2003. Characterization of a novel RNAbinding region of eIF4GI critical for ribosomal scanning. EMBO J 22: 1909-1921.
65. Qin X, Sarnow P. 2004. Preferential translation of internal ribosome entry site-containing mRNAs during the mitotic cycle in mammalian cells. J Biol Chem 279: 13721- 13728.
66. Ramírez-Valle F, Braunstein S, Zavadil J, Formenti SC, Schneider RJ. 2008. eIF4GI links nutrient sensing by mTOR to cell proliferation and inhibition of autophagy. J Cell Biol 181: 293-307.
67. 0 cistron expression by inducing production of monocistronic mRNA in the bgal/CAT bicistronic reporter system. RNA 15: 1980-1985.
68. Sasaki J, Nakashima N. 2000. Methionine-independent initiation of translation in the capsid protein of an insect RNAvirus. Proc Natl Acad Sci 97: 1512-1515.
69. Schepens B, Tinton SA, Bruynooghe Y, Parthoens E, Haegman M, Beyaert R, Cornelis S. 2007. A role for hnRNP C1/C2 and Unr in internal initiation of translation during mitosis. EMBO J 26: 158-169.
70. Shatsky IN, Dmitriev SE, Terenin IM, Andreev DE. 2010. Capand IRES-independent scanning mechanism of translation initiation as an alternative to the concept of cellular IRESs. Mol Cells 30: 285-293.
71. Sherrill KW, Lloyd RE. 2008. Translation of cIAP2 mRNA is mediated exclusively by a stress-modulated ribosome shunt. Mol Cell Biol 28: 2011-2022.
72. Sherrill KW, Byrd MP, Van Eden ME, Lloyd RE. 2004. BCL-2 translation is mediated via internal ribosome entry during cell stress. J Biol Chem 279: 29066-29074.
73. Shiroki K, Ohsawa C, Sugi N, Wakiyama M, Miura K, Watanabe M, Suzuki Y, Sugano S. 2002. Internal ribosome entry site-mediated translation of Smad5 in vivo: Requirement for a nuclear event. Nucleic Acids Res 30: 2851-2861.
74. Silvera D, Arju R, Darvishian F, Levine PH, Zolfaghari L, Goldberg J, Hochman T, Formenti SC, Schneider RJ. 2009. Essential role for eIF4GI overexpression inthe pathogenesis of inflammatory breast cancer. Nat Cell Biol 11: 903-908.
75. Stoneley M, Willis AE. 2004. Cellular internal ribosome entry segments: Structures, trans-acting factors and regulation of gene expression. Oncogene 23: 3200-3207.
76. Stoneley M, Subkhankulova T, Le Quesne JP, Coldwell MJ, Jopling CL, Belsham GJ, Willis AE. 2000. Analysis of the c-myc IRES; a potential role for cell-type specific transacting factors and the nuclear compartment. Nucleic Acids Res 28: 687-694.
77. Svitkin YV, Meerovitch K, Lee HS, Dholakia JN, Kenan DJ, Agol VI, Sonenberg N. 1994. Internal translation initiation on poliovirus RNA: Further characterization of La function in poliovirus translation in vitro. J Virol 68: 1544-1550.
78. Thoma C, Bergamini G, Galy B, Hundsdoerfer P, Hentze MW. 2004. Enhancement of IRES-mediated translation of the c-myc and BiP mRNAs by the poly(A) tail is independent of intact eIF4G and PABP. Mol Cell 15: 925-935.
79. van Eden ME, Byrd MP, Sherrill KW, Lloyd RE. 2004. Demonstrating internal ribosome entry sites in eukaryotic mRNAs using stringent RNA test procedures. RNA 10: 720-730.
80. Vopálenský V, Masek T, Horváth O, Vicenová B, Mokrejs M, Posísek M. 2008. Firefly luciferase gene contains a cryptic promoter. RNA 14: 1720-1729.
81. Walter BL, Nguyen JH, Ehrenfeld E, Semler BL. 1999. Differential utilization of poly(rC) binding protein 2 in translation directed by picornavirus IRES elements. RNA 5: 1570-1585.
82. 0-UTR. Nucleic Acids Res 33: 2248-2258.
83. Wilson JE, Pestova TV, Hellen CU, Sarnow P. 2000. Initiation of protein synthesis from the A site of the ribosome. Cell 102: 511-520.
84. Young RM, Wang S-J, Gordan JD, Ji X, Liebhaber SA, Simon MC. 2008. Hypoxia-mediated selective mRNA translation by an internal ribosome entry site-independent mechanism. J Biol Chem 283: 16309-16319.
85. Yu Y, Sweeney TR, Kafasla P, Jackson RJ, Pestova TV, Hellen CUT. 2011. The mechanism of translation initiation on Aichivirus RNA mediated by a novel type of picornavirus IRES. EMBO J 30: 4423-4436.
86. Yueh A, Schneider RJ. 1996. Selective translation initiation by ribosome jumping in adenovirus-infected and heatshocked cells. Genes Dev 10: 1557-1567.
87. Yueh A, Schneider RJ. 2000. Translation by ribosome shunting on adenovirus and hsp70 mRNAs facilitated by complementarity to 18S rRNA. Genes Dev 14: 414-421.