Cap-dependent and cap-independent translation in eukaryotic systems

Gene

Volumn 332, Issue 1-2, 2004, Pages 1-11

  Merrick, William C ^a  

^a CASE WESTERN RESERVE UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Cryptic promoters; eIF; eukaryotic initiation factor; GAPDH; Internal initiation; Internal ribosome entry site; internal ribosome entry site; IRE; IRES; iron responsive element; Protein synthesis; Re initiation; Translation artifacts; untranslated region; UTR

Indexed keywords

INITIATION FACTOR; INITIATION FACTOR 1; INITIATION FACTOR 2; INITIATION FACTOR 3; INITIATION FACTOR 5; RNA;

ARTIFACT; BIOCHEMISTRY; EUKARYOTE; HUMAN; IRON RESPONSIVE ELEMENT; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN ANALYSIS; PROTEIN FUNCTION; PROTEIN SYNTHESIS; REVIEW; RNA TRANSLATION; TRANSLATION INITIATION;

ANIMALS; EUKARYOTIC CELLS; EUKARYOTIC INITIATION FACTORS; HUMANS; MODELS, GENETIC; PROTEIN BIOSYNTHESIS; RIBOSOMES; RNA CAPS;

BACTERIA (MICROORGANISMS); EUKARYOTA;

EID: 2442466927     PISSN: 03781119     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.gene.2004.02.051     Document Type: Review

References (87)

1. Algire M.A., Maag D., Savio P., Acker M.G., Tarun S.Z. Jr., Sachs A.B., Asano K., Nielsen K.H., Olsen D.S., Phan L., Hinnebusch A.G., Lorsch J.R. Development and characterization of a reconstituted yeast translation initiation system. RNA. 8:2002;382-397
2. Anthony D.D., Merrick W.C. Eukaryotic initiation factor 4F: implications for a role in internal initiation of translation. J. Biol. Chem. 266:1991;10218-10226
3. Arraiano C.M., Maquat L.E. Post-transcriptional control of gene expression: effectors of mRNA decay. Mol. Microbiol. 49:2003;267-276
4. Benne R., Hershey J.W.B. The mechanism of action of protein synthesis initiation factors from rabbit reticulocytes. J. Biol. Chem. 253:1978;3078-3087
5. Bergamini G., Preiss T., Hentze M.W. Picornavirus IRESes and the poly(A) tail jointly promote cap-independent translation in a mammalian cell-free system. RNA. 6:2000;1781-1790
6. Chevrier D., Vezina C., Bastille J., Linard C., Sonenberg N., Boileau G. Higher order structures of the 5′-proximal region decrease the efficiency of translation of the porcine pro-opiomelanocortin mRNA. J. Biol. Chem. 263:1988;902-910
7. Cornelis S., Bruynooghe Y., Denecker G., Van Huffel S., Tinton S., Beyaert R. Identification and characterization of a novel cell cycle-regulated internal ribosome entry site. Mol. Cell. Biol. 5:2000;597-605
8. Decker C.J., Parker R. mRNA decay enzymes: decappers conserved between yeast and mammals. Proc. Natl. Acad. Sci. U. S. A. 99:2002;12512-12514
9. Dever T.E. Translation initiation: adept at adapting. TIBS. 24:1999;398-403
10. Dmitriev S.E., Terenin I.M., Dunaevsky Y.E., Merrick W.C., Shatsky I.N. Assembly of 48S translation initiation complexes from purified components with mRNAs that have some base pairing within their 5′ untranslated regions. Mol. Cell. Biol. 23:2003;8925-8933
11. Dreyfuss G., Kim V.N., Kataoka N. Messenger RNA-binding proteins and the messages they carry. Nat. Rev. 3:2002;195-205
12. Dumas E., Staedel C., Colombat M., Reigadas S., Chabas S., Astier-Gin T., Cahour A., Litvak S., Ventura M. A promoter activity is present in the DNA sequence corresponding to the hepatitis C virus 5′ UTR. Nucleic Acids Res. 31:2003;1275-1281
13. Edskes H.K., Gray V.T., Wickner R.B. The [URE3] prion is an aggregated form of Ure2p that can be cured by overexpression of Ure2p fragments. Proc. Natl. Acad. Sci. U. S. A. 96:1999;1498-1503
14. Fillebeen C., Chahine D., Caltagirone A., Segal P., Pantopoulos K. A phosphomimetic mutation at Ser-138 renders iron regulatory protein 1 sensitive to iron-dependent degradation. Mol. Cell. Biol. 23:2003;6973-6981
15. Gao X., Ruan K.C., Liu W.Y. Exploration of RNA 3′ terminal locations in rat ribosome. Mol. Cell. Biochem. 225:2001;161-165
16. Godefroy-Colburn T., Thach R.E. The role of mRNA competition in regulating translation: IV. Kinetic model. J. Biol. Chem. 256:1981;11762-11773
17. Godefroy-Colburn T., Ravelonandro M., Pinck L. Cap accessibility correlates with the initiation efficiency of alfalfa mosaic virus RNAs. Eur. J. Biochem. 147:1985;549-552
18. Gossen B., Caughman S.W., Harford J.B., Klausner R.D., Hentze M.W. Translational repression by a complex between the iron-responsive element of ferritin mRNA and its specific cytoplasmic binding protein is position dependent in vivo. EMBO J. 9:1990;4127-4133
19. Grundmann O., Mosch H-U., Braus G.H. Repression of GCN4 mRNA translation by nitrogen starvation in Saccharomyces cerevisiae. J. Biol. Chem. 276:2001;25661-25671
20. Han B., Zhang J.-T. Regulation of gene expression by internal ribosome entry sites or cryptic promoters: the eIF4G story. Mol. Cell. Biol. 22:2002;7372-7384
21. Hecht K., Bailey J.E., Minas W. Polycistronic gene expression in yeast versus cryptic promoter elements. FEMS Yeast Res. 2:2002;215-224
22. Hellen C.U.T., Sarnow P. Internal ribosome entry sites in eukaryotic mRNA molecules. Genes Dev. 15:2001;1593-1612
23. Hensold J.O., Barth-Baus D., Stratton C.A. Inducers of erythroleukemic differentiation cause messenger RNAs that lack poly(A)-binding protein to accumulate in translationally inactive, salt-labile 80S ribosomal complexes. J. Biol. Chem. 271:1996;23246-23254
24. Hershey J.W.B., Merrick W.C. Pathway and mechanism of initiation of protein synthesis. Sonenberg N., Hershey J.W.B., Mathews M. Translation Control of Gene Expression. 2000;33-88 Cold Spring Harbor Press, Cold Spring Harbor, NY
25. Hinnebusch A.G. Translational control of GCN4: gene-specific regulation by phosphorylation of eIF2. Hershey J.W.B., Mathews M., Sonenberg N. Translation Control. 1996;199-244 Cold Spring Harbor Press, Cold Spring Harbor, NY
26. Hinnebusch A.G. Translational regulation of GCN4: a window on factors that control initiator-tRNA binding to the ribosome. J. Biol. Chem. 272:1997;21661-21664
27. Hinnebusch A.G., Natarajan K. Gcn4p, a master regulator of gene expression, is controlled at multiple levels by diverse signals of starvation and stress. Eukaryot. Cell. 1:2002;22-32
28. Huang H.K., Yoon H., Hannig E.M., Donahue T.F. GTP hydrolysis controls stringent selection of the AUG start codon during translation initiation in Saccharomyces cerevisiae. Genes Dev. 11:1997;2396-2413
29. Jang S.K., Krausslich H.G., Nicklin M.J., Duke G.M., Palmenberg A.C., Wimmer E. A segment of the 5′ nontranslated region of encephalomycarditis virus mRNA directs internal entry of ribosomes during in vitro translation. J. Virol. 62:1988;2636-2643
30. Jang S.K., Davies M.V., Kaufman R.J., Wimmer E. Initiation of protein synthesis by internal entry of ribosomes into the 5′ nontranslated region of encephalomycarditis virus mRNA in vivo. J. Virol. 63:1989;1651-1660
31. Johannes G., Carter M.S., Eisen M.B., Brown P.O., Sarnow P. Identification of eukaryotic mRNAs that are translated at reduced cap binding complex eIF4F concentrations using a cDNA microarray. Proc. Natl. Acad. Sci. U. S. A. 96:1999;13118-13123
32. Kean K.M. The role of mRNA 5′-noncoding and 3′-end sequences on 40S ribosomal subunit recruitment, and how RNA viruses successfully compete with cellular mRNAs to ensure their own protein synthesis. Biol. Cell. 95:2003;129-139
33. Keiper B.D., Gan W., Rhoads R.E. Protein synthesis initiation factor 4G. Int. J. Biochem. Cell Biol. 31:1999;37-41
34. Komar A.A., Lesnik T., Cullin C., Merrick W.C., Trachsel H., Altman M. Internal initiation drives the synthesis of Ure2 protein lacking the prion domain and affects [URE3] propagation in yeast cells. EMBO J. 22:2003;1199-1209
35. Kozak M. Influence of mRNA secondary structure on binding and migration of 40S ribosomal subunits. Cell. 19:1980;79-90
36. Kozak M. Role of ATP in binding and migration of 40S ribosomal subunits. Cell. 22:1980;459-467
37. Kozak M. Influences of mRNA secondary structure on initiation by eukaryotic ribosomes. Proc. Natl. Acad. Sci. U. S. A. 83:1986;2850-2854
38. Kozak M. An analysis of 5′-noncoding sequences from 699 vertebrate messenger RNAs. Nucleic Acids Res. 15:1987;8125-8148
39. Kozak M. Downstream secondary structure facilitates recognition of initiator codons by eukaryotic ribosomes. Proc. Natl. Acad. Sci. U. S. A. 87:1990;8301-8305
40. Kozak M. Initiation of translation in prokaryotes and eukaryotes. Gene. 234:1999;187-208
41. Kozak M. New ways of initiating translation in eukaryotes? Mol. Cell. Biol. 21:2001;1899-1907
42. Kozak M. New ways of initiating translation in eukaryotes: letter to the editor. Mol. Cell. Biol. 21:2001;8241-8246
43. Kozak M. Alternative ways to think about mRNA sequences and proteins that appear to promote internal initiation of translation. Gene. 318:2003;1-23
44. Kozak M., Shatkin A.J. Migration of 40S ribosomal subunits on messenger RNA in the presence of edeine. J. Biol. Chem. 253:1978;6568-6577
45. Lee J.H., Pestova T.V., Shin B-S., Cao C., Choi S.K., Dever T.E. Initiation factor eIF5B catalyzes second GTP-dependent step in eukaryotic translation initiation. Proc. Natl. Acad. Sci. U. S. A. 99:2002;16689-16694
46. Lockard R.E., Currey K., Browner M., Lawrence C., Maizel J. Secondary structure model for mouse beta Maj globin mRNA derived from enzymatic digestion data, comparative sequence and computer analysis. Nucleic Acids Res. 14:1986;5827-5841
47. Lorsch J., Herschlag D. Kinetic dissection of fundamental processes of eukaryotic translation initiation in vitro. EMBO J. 18:1999;6705-6717
48. Lu B., Li Q., Liu W.Y., Ruan K.C. Effects of hydrostatic pressure on the activity of rat ribosome and cell-free translation system. Biochem. Mol. Biol. Int. 43:1997;499-506
49. Maiti T., Das S., Maitra U. Isolation and functional characterization of a temperature sensitive mutant of the yeast Saccharomyces cerevisiae in translation initiation factor eIF5: an eIF5-dependent cell-free translation system. Gene. 244:2000;109-118
50. Martinez-Salas E., Ramos R., Lafuente E., de Quinto S.L. Functional interactions in internal translation initiation directed by viral and cellular IRES elements. J. Gen. Virol. 82:2001;973-984
51. Masison D.C., Wickner R.B. Prion-inducing domain of yeast Ure2p and protease resistance of Ure2p in prion-containing cells. Science. 270:1995;93-95
52. Masison D.C., Maddelein M.L., Wickner R.B. The prion model for [URE3] of yeast: spontaneous generation and requirements for propagation. Proc. Natl. Acad. Sci. U. S. A. 94:1997;12503-12508
53. Mazumder B., Sampath P., Seshadri V., Maitra R.K., DiCorleto P.E., Fox P.L. Regulated release of l13a from the 60S ribosomal subunit as a mechanism of transcript specific translational control. Cell. 115:2003;187-198
54. McCarthy J.E.G. Posttranslational control of gene expression in yeast. Microbiol. Mol. Biol. Rev. 62:1998;1492-1553
55. Meijer H.A., Thomas A.A.M. Control of eukaryotic protein synthesis by upstream open reading frames in the 5′-untranslated region of an mRNA. Biochem. J. 367:2002;1-11
56. Merrick W.C. Evidence that a single GTP is used in the formation of 80S initiation complexes. J. Biol. Chem. 254:1979;3708-3711
57. Merrick W.C. Assays for eukaryotic protein synthesis. Methods Enzymol. 60:1979;108-123
58. Merrick W.C. Initiation of protein biosynthesis in eukaryotes. BAMBED. 31:2003;378-385
59. Morris D.R., Geballe A.P. Upstream open reading frames as regulators of mRNA translation. Mol. Cell. Biol. 20:2000;8635-8642
60. Mueller P.P., Hinnebusch A.G. Multiple upstream AUG codons mediate translational control of GCN4. Cell. 45:1986;201-207
61. Nielsen P.J., Trachsel H. The mouse protein synthesis factor 4A gene family includes two related functional genes which are differentially expressed. EMBO J. 7:1988;2097-2105
62. Pain V.M. Initiation of protein synthesis in eukaryotic cells. Eur. J. Biochem. 236:1996;747-767
63. Paraskeva E., Hentze M.W. Iron-sulphur clusters as genetic regulatory switches: the bifunctional iron regulatory protein-1. FEBS Lett. 389:1996;40-43
64. Parkin N.T., Cohen E.A., Darveau A., Rosen C., Haseltine W., Sonenberg N. Mutational analysis of the 5′ non-coding region of human immunodeficiency virus type 1: effects of secondary structure on translation. EMBO J. 7:1988;2831-2837
65. Paulous S., Malnou C.E., Michel Y.M., Kean K.M., Borman A.M. Comparison of the capacity of different viral internal ribosome entry segments to direct translation initiation in poly(A)-dependent reticulocyte lysates. Nucleic Acids Res. 31:2003;722-733
66. Pelletier J., Sonenberg N. Internal initiation of translation of eukaryotic mRNA directed by a sequence derived from poliovirus RNA. Nature. 334:1988;320-325
67. Pestova T.V., Hellen C.U.T. The structure and function of initiation factors in eukaryotic protein synthesis. Cell. Mol. Life Sci. 57:2000;651-674
68. Pestova T.V., Kolupaeva V.G. The roles of individual eukaryotic translation initiation factors in ribosomal scanning and initiation codon selection. Genes Dev. 16:2002;2906-2922
69. Pestova T.V., Borukhov S.I., Hellen C.U.T. Eukaryotic ribosomes require initiation factors 1 and 1A to locate initiation codons. Nature. 394:1998;854-859
70. Pestova T.V., Lomakin I.B., Lee J.H., Choi S.K., Dever T.E., Hellen C.U.T. The joining of ribosomal subunits requires eIF5B. Nature. 403:2000;332-335
71. Pestova T.V., Kolupaeva V.G., Lomakin I.B., Pilipenko E.V., Shatsky I.N., Agol V.I., Hellen C.U.T. Molecular mechanisms of translation initiation in eukaryotes. Proc. Natl. Acad. Sci. U. S. A. 98:2001;7029-7036
72. Ray B.K., Brendler T.G., Adya S., Daniels-McQuessn S., Miller J.K., Hershey J.W.B., Grifo J.A., Merrick W.C., Thach R.E. Role of mRNA competition in regulating translation: further characterization of mRNA discriminatory initiation factors. Proc. Natl. Acad. Sci. U. S. A. 80:1983;663-667
73. Rouault T.A., Klausner R.D., Harford J.B. Translation control of ferritin. Hershey J.W.B., Mathews M., Sonenberg N. Translation Control. 1996;335-362 Cold Spring Harbor Press, Cold Spring Harbor, N.Y
74. Ryabova L.A., Pooggin M.M., Hohn T. Viral strategies of translation initiation: ribosomal shunt and reinitiation. Prog. Nucleic Acid Res. 72:2002;1-39
75. Sarnow P. Viral internal ribosome entry site elements: novel ribosome-RNA complexes and roles in viral pathogenesis. J. Virol. 77:2003;2801-2806
76. Schneider R.J., Mohr I. Translation initiation and viral tricks. TIBS. 28:2002;130-136
77. Trachsel H., Erni B., Schrier M.H., Staehelin T. Initiation of mammalian protein synthesis: II. The assembly of the initiation complex with purified initiation factors. J. Mol. Biol. 116:1977;755-767
78. Vagner S., Galy B., Pyronnet S. Irresistible IRES. Attracting the translational machinery to internal ribosome entry sites. EMBO Rep. 21:2001;893-898
79. van Eyll O., Michiels T. Non-AUG initiated internal translation of the L* protein of Theiler's virus and importance of this protein for viral persistence. J. Virol. 76:2002;10665-10673
80. Van Venrooij W.J., van Eekelen C.A.G., Jansen R.T.P., Princen J.M.G. Specific poly-A-binding protein of 76, 000 molecular weight in polyribosomes is not present on poly A of free cytoplasmic mRNP. Nature. 270:1977;189-191
81. Verge V., Vonlanthen M., Masson J-M., Trachsel H., Altman M. Localization of a promoter in the putative internal ribosome entry site of the Saccharomyces cerevisiae TIF4631 gene. RNA. 10:2004;277-286
82. von der Haar T., McCarthy J.E.G. Intracellular translation initiation factor levels in Saccharomyces cerevisiae and their role in cap-complex formation. Mol. Microbiol. 46:2002;531-544
83. Webster's New Collegiate Dictionary. 1977;793 G. & C. Merriam, Springfield, MA
84. Wilkie G.S., Dickson K.S., Gray N.K. Regulation of mRNA translation by 5′- and 3′-UTR binding factors. TIBS. 28:2003;182-188
85. Yeuh A., Schneider R.J. Selective translation by ribosome jumping in adenovirus infected and heat shocked cells. Genes Dev. 10:1996;1557-1567
86. Yeuh A., Schneider R.J. Translation by ribosome shunting on adenovirus and Hsp70 mRNAs facilitated by complementarity to 18S rRNA. Genes Dev. 14:2000;414-421
87. Zoll W.L., Horton L.E., Komar A.A., Hensold J.O., Merrick W.C. Characterization of mammalian eIF2A and identification of the yeast homolog. J. Biol. Chem. 277:2002;37079-37087