The mechanism of eukaryotic translation initiation: New insights and challenges

Cold Spring Harbor Perspectives in Biology

Volumn 4, Issue 10, 2012, Pages

  Hinnebusch, Alan G ^a   Lorsch, Jon R ^b  

^a EUNICE KENNEDY SHRIVER NATIONAL INSTITUTE OF CHILD HEALTH AND HUMAN DEVELOPMENT   (United States)

^b JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

INITIATION FACTOR;

ARTICLE; BIOLOGICAL MODEL; EUKARYOTIC CELL; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; PHYSIOLOGY; RIBOSOME; RIBOSOME SUBUNIT; RNA TRANSLATION;

EUKARYOTIC CELLS; EUKARYOTIC INITIATION FACTORS; GENE EXPRESSION REGULATION; MODELS, GENETIC; PEPTIDE CHAIN INITIATION, TRANSLATIONAL; RIBOSOME SUBUNITS; RIBOSOMES;

EID: 84863889691     PISSN: None     EISSN: 19430264     Source Type: Journal    
DOI: 10.1101/cshperspect.a011544     Document Type: Article

References (137)

1. Abaeva IS, Marintchev A, Pisareva VP, Hellen CU, Pestova TV. 2011. Bypassing of stems versus linear base-by-base inspection of mammalian mRNAs during ribosomal scanning. EMBO J 30: 115-129.
2. Acker MG, Shin BS, Dever TE, Lorsch JR. 2006. Interaction between eukaryotic initiation factors 1A and 5B is required for efficient ribosomal subunit joining. J Bio Chem 281: 8469-8475.
3. Acker MG, Shin BS, Nanda JS, Saini AK, Dever TE, Lorsc JR. 2009. Kinetic analysis of late steps of eukaryotic translation initiation. J Mol Biol 385: 491-506.
4. Agris PF. 2008. Bringing order to translation: The contributions of transfer RNA anticodon-domain modifications. EMBO Rep 9: 629-635.
5. Algire MA, Maag D, Savio P, Acker MG, Tarun SZ Jr, Sach AB, Asano K, Nielsen KH, Olsen DS, Phan L, et al. 2002. Development and characterization of a reconstituted yeast translation initiation system. RNA 8: 382-397.
6. Algire MA, Maag D, Lorsch JR. 2005. Pi release from eIF2, not GTP hydrolysis, is the step controlled by start-site selection during eukaryotic translation initiation. Mol Cell 20: 251-262.
7. Alone PV, Dever TE. 2006. Direct binding of translation initiation factor eIF2g-G domain to its GTPase-activating and GDP-GTP exchange factors eIF5 and eIF2B 1. J Biol Chem 281: 12636-12644.
8. Alone PV, Cao C, Dever TE. 2008. Translation initiation factor 2g mutant alters start codon selection independent of Met-tRNA binding. Mol Cell Biol 28: 6877-6888.
9. Metis an important translation initiation intermediate in vivo. Genes Dev 14: 2534-2546.
10. Asano K, Shalev A, Phan L, Nielsen K, Clayton J, Valášek L, Donahue TF, Hinnebusch AG. 2001. Multiple roles for the carboxyl terminal domain of eIF5 in translation initiation complex assembly and GTPase activation. EMBO J 20: 2326-2337.
11. Ben-Shem A, Garreau de Loubresse N, Melnikov S, Jenner L, Yusupova G, Yusupov M. 2011. The structure of the eukaryotic ribosome at 3.0A ° resolution. Science 334: 1524-1529.
12. Berset C, Zurbriggen A, Djafarzadeh S, Altmann M, Trachsel H. 2003. RNA-binding activity of translation initiation factor eIF4G1 from Saccharomyces cerevisiae. RNA 9: 871-880.
13. Berthelot K, Muldoon M, Rajkowitsch L, Hughes J, McCarth JE. 2004. Dynamics and processivity of 40S ribosome scanning on mRNA in yeast. Mol Microbiol 51: 987-1001.
14. Bi X, Ren J, Goss DJ. 2000. Wheat germ translation initiation factor eIF4B affects eIF4A and eIFiso4F helicase activity by increasing the ATP
15. Bulygin KN, Khairulina YS, Kolosov PM, Ven'yaminova AG, Graifer DM, Vorobjev YN, Frolova LY, Kisselev LL, Karpov GG. 2010. Three distinct peptides from the N domain of translation termination factor eRF1 surround stop codon in the ribosome. RNA 16: 1902-1914.
16. Carter AP, ClemonsWMJr, Brodersen DE, Morgan-Warre RJ, Hartsch T, Wimberly BT, Ramakrishnan V. 2001. Crystal structure of an initiation factor bound to the 30S ribosomal subunit. Science 291: 498-501.
17. Caruthers JM, Johnson ER, McKay DB. 2000. Crystal structure of yeast initiation factor 4A, a DEAD-box RNA helicase. Proc Natl Acad Sci 97: 13080-13085.
18. Cheung YN, Maag D, Mitchell SF, Fekete CA, Algire MA, Takacs JE, Shirokikh N, Pestova T, Lorsch JR, Hinnebusc AG. 2007. Dissociation of eIF1 from the 40S ribosomal subunit is a key step in start codon selection in vivo. Gene Dev 21: 1217-1230.
19. Chiu WL, Wagner S, Herrmannova A, Burela L, Zhang F, Saini AK, Valasek L, Hinnebusch AG. 2010. The C-terminal region of eukaryotic translation initiation factor 3a (eIF3a) promotesmRNA recruitment, scanning, and, together with eIF3j and the eIF3b RNA recognition motif, selection of AUG start codons. Mol Cell Biol 30: 4415-4434.
20. Conte MR, Kelly G, Babon J, Sanfelice D, Youell J, Smerdo SJ, Proud CG. 2006. Structure of the eukaryotic initiation factor (eIF) 5 reveals a fold common to several translation factors. Biochemistry 45: 4550-4558.
21. Das S, Ghosh R, Maitra U. 2001. Eukaryotic translation initiation factor 5 functions as a GTPase-activating protein. J Biol Chem 276: 6720-6726.
22. Daugeron MC, Lenstra TL, Frizzarin M, El Yacoubi B, Liu X, Baudin-Baillieu A, Lijnzaad P, Decourty L, Saveanu C, Jacquier A, et al. 2011. Gcn4 misregulation reveals a direct role for the evolutionary conserved EKC/KEOPS in the t6A modification of tRNAs. Nucleic Acids Res 39: 6148-6160.
23. Dennis MD, Person MD, Browning KS. 2009. Phosphorylation of plant translation initiation factors by CK2 enhances the in vitro interaction of multifactor complex components. J Biol Chem 284: 20615-20628.
24. Dev K, Qiu H, Dong J, Zhang F, Barthlme D, Hinnebusc AG. 2010. The b/Gcd7 subunit of eukaryotic translation initiation factor 2B (eIF2B), a guanine nucleotide exchange factor, is crucial for binding eIF2 in vivo. Mo Cell Biol 30: 5218-5233.
25. Dever TE, Dar AC, Sicheri F. 2007. The elF2a kinases. InTranslational control in biology and medicine (ed. Mathews M, Sonenberg N, Hershey JWB), pp. 319-344.
26. Cold SpringHarbor Laboratory Press, Cold SpringHarbor, NY. Dmitriev SE, Terenin IM, Dunaevsky YE, MerrickWC, Shatsk IN. 2003. Assembly of 48S translation initiation complexes from purified components with mRNAs that have some base pairing within their 50 untranslated regions. Mol Cell Biol 23: 8925-8933.
27. Dmitriev SE, Terenin IM, Andreev DE, Ivanov PA, Dunaevsk JE, MerrickWC, Shatsky IN. 2010. GTP-independent tRNA delivery to the ribosomal P-site by a novel eukaryotic translation factor. J Biol Chem 285: 26779-26787.
28. Donahue T. 2000. Genetic approaches to translation initiation in Saccharomyces cerevisiae. In Translational control of gene expression (ed. Sonenberg N, Hershey JWB, Mathews MB), pp. 487-502.
29. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY. Dong J, Nanda JS, Rahman H, Pruitt MR, Shin BS, Won CM, Lorsch JR, Hinnebusch AG. 2008. Genetic identification of yeast 18S rRNA residues required for efficient recruitment of initiator tRNA(Met) and AUG selection. Genes Dev 22: 2242-2255.
30. El Yacoubi B, Lyons B, Cruz Y, Reddy R, Nordin B, Agnelli F, Williamson JR, Schimmel P, Swairjo MA, de Crecy-Lagar V. 2009. The universal YrdC/Sua5 family is required for the formation of threonylcarbamoyladenosine in tRNA. Nucleic Acids Res 37: 2894-2909.
31. El Yacoubi B, Hatin I, Deutsch C, Kahveci T, Rousset JP, Iwata-Reuyl D, Murzin AG, de Crecy-Lagard V. 2011. A role for the universal Kae1/Qri7/YgjD (COG0533) family in tRNA modification. EMBO J 30: 882-893.
32. Fekete CA, Mitchell SF, Cherkasova VA, Applefield D, Algir MA, Maag D, Saini A, Lorsch JR, Hinnebusch AG. 2007. N-and C-terminal residues of eIF1A have opposing effects on the fidelity of start codon selection. EMBO J 26: 1602-1614.
33. Fringer JM, Acker MG, Fekete CA, Lorsch JR, Dever TE. 2007. Coupled release of eukaryotic translation initiation factors 5B and 1A from 80S ribosomes following subunit joining. Mol Cell Biol 27: 2384-2397.
34. Gomez E, Pavitt GD. 2000. Identification of domains and residues within the 1 subunit of eukaryotic translation initiation factor 2B (eIF2b) required for guanine nucleotide exchange reveals a novel activation function promoted by eIF2B complex formation. Mol Cell Biol 20: 3965-3976.
35. Gomez E, Mohammad SS, Pavitt GD. 2002. Characterization of the minimal catalytic domain within eIF2B: The guanine-nucleotide exchange factor for translation initiation. EMBO J 21: 5292-5301.
36. He H, von der Haar T, Singh CR, Ii M, Li B, Hinnebusch AG, McCarthy JE, Asano K. 2003. The yeast eukaryotic initiation factor 4G (eIF4G) HEAT domain interacts with eIF1 and eIF5 and is involved in stringent AUG selection. Mol Cell Biol 23: 5431-5445.
37. Hershey JWB, MerrickWC. 2000. Pathway and mechanism of initiation of protein synthesis. In Translational control of gene expression (ed. Sonenberg N, Hershey JWB, Mathews MB), pp. 33-88. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
38. Hilbert M, Kebbel F, Gubaev A, KlostermeierD. 2011. eIF4G stimulates the activity of the DEAD box protein eIF4A by a conformational guidance mechanism. Nucleic Acids Res 39: 2260-2270.
39. Hilliker A, Gao Z, Jankowsky E, Parker R. 2011. The DEADbox protein Ded1 modulates translation by the formation and resolution of an eIF4F-mRNA complex. Mol Cell 43: 962-972.
40. Hinnebusch AG. 2011. Molecular mechanism of scanning and start codon selection in eukaryotes. Microbiol Mol Biol Rev 75: 434-467.
41. Hinnebusch AG, Dever TE, Asano K. 2007. Mechanism of translation initiation in the yeast Saccharomyces cerevisiae. In Translational control in biology and medicine (ed. Mathews M, Sonenberg N, Hershey JWB), pp. 225-268.
42. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY. Hinton TM, Coldwell MJ, Carpenter GA, Morley SJ, Pai VM. 2007. Functional analysis of individual binding activities of the scaffold protein eIF4G. J Biol Chem 282: 1695-1708.
43. Ingolia NT, Ghaemmaghami S, Newman JR, Weissman JS. 2009. Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science 324: 218-223.
44. Ivanov IP, Loughran G, Sachs MS, Atkins JF. 2010. Initiation context modulates autoregulation of eukaryotic translation initiation factor 1 (eIF1). Proc Natl Acad Sci 107: 18056-18060.
45. Jennings MD, Pavitt GD. 2010. eIF5 has GDI activity necessary for translational control by eIF2 phosphorylation. Nature 465: 378-381.
46. Jivotovskaya AV, Valasek L, Hinnebusch AG, Nielsen KH. 2006. Eukaryotic translation initiation factor 3 (eIF3) and eIF2 can promote mRNA binding to 40S subunits independently of eIF4G in yeast. Mol Cell Biol 26: 1355-1372.
47. Kahvejian A, Svitkin YV, Sukarieh R, M'Boutchou MN, Sonenber N. 2005. Mammalian poly(A)-binding protein is a eukaryotic translation initiation factor, which acts via multiple mechanisms. Genes Dev 19: 104-113.
48. Kapp LD, Lorsch JR. 2004. GTP-dependent recognition of the methionine moiety on initiator tRNA by translation factor eIF2. J Mol Biol 335: 923-936.
49. Kapp LD, Kolitz SE, Lorsch JR. 2006. Yeast initiator tRNA identity elements cooperate to influence multiple steps of translation initiation. RNA 12: 751-764.
50. Kaye NM, Emmett KJ, Merrick WC, Jankowsky E. 2009. Intrinsic RNA binding by the eukaryotic initiation factor 4F depends on a minimal RNA length but not on the m7G cap. J Biol Chem 284: 17742-17750.
51. Kim JH, Park SM, Park JH, Keum SJ, Jang SK. 2011. eIF2A mediates translation of hepatitis C viral mRNA under stress conditions. EMBO J 30: 2454-2464.
52. Kolitz SE, Takacs JE, Lorsch JR. 2009. Kinetic and thermodynamic analysis of the role of start codon/anticodon base pairing during eukaryotic translation initiation. RNA 15: 138-152.
53. Kolupaeva VG, Unbehaun A, Lomakin IB, Hellen CU, Pestov TV. 2005. Binding of eukaryotic initiation factor 3 to ribosomal 40S subunits and its role in ribosomal dissociation and anti-association. RNA 11: 470-486.
54. Korneeva NL, Lamphear BJ, Hennigan FL, Rhoads RE. 2000. Mutually cooperative binding of eukaryotic translation initiation factor (eIF) 3 and eIF4A to human eIF4G-1. J Biol Chem 275: 41369-41376.
55. Krishnamoorthy T, Pavitt GD, Zhang F, Dever TE, Hinnebusc AG. 2001. Tight binding of the phosphorylated a subunit of initiation factor 2 (eIF2a) to the regulatory subunits of guanine nucleotide exchange factor eIF2B is required for inhibition of translation initiation. Mol Cel Biol 21: 5018-5030.
56. Lawless C, Pearson RD, Selley JN, Smirnova JB, Grant CM, Ashe MP, Pavitt GD, Hubbard SJ. 2009. Upstream sequence elements direct post-transcriptional regulation of gene expression under stress conditions in yeast. BMC Genomics 10: 7-26.
57. Lee JH, Pestova TV, Shin BS, Cao C, Choi SK, Dever TE. 2002. Initiation factor eIF5B catalyzes second GTP-dependent step in eukaryotic translation initiation. Pro Natl Acad Sci 99: 16689-16694.
58. LeFebvre AK, Korneeva NL, Trutschl M, CvekU, Duzan RD, Bradley CA, Hershey JW, Rhoads RE. 2006. Translation initiation factor eIF4G-1 binds to eIF3 through the eIF3e subunit. J Biol Chem 281: 22917-22932.
59. LinCA, Ellis SR, True HL. 2009. The Sua5 protein is essential for normal translational regulation in yeast. Mol Cell Biol 30: 354-363.
60. Lindqvist L, Imataka H, Pelletier J. 2008. Cap-dependent eukaryotic initiation factor-mRNA interactions probed by cross-linking. RNA 14: 960-969.
61. Liu F, Putnam A, Jankowsky E. 2008. ATP hydrolysis is required for DEAD-box protein recycling but not for duplex unwinding. Proc Natl Acad Sci 105: 20209-20214.
62. Lomakin IB, Kolupaeva VG, Marintchev A, Wagner G, Pestov TV. 2003. Position of eukaryotic initiation factor eIF1 on the 40S ribosomal subunit determined by directed hydroxyl radical probing. Genes Dev 17: 2786-2797.
63. Lomakin IB, Shirokikh NE, Yusupov MM, Hellen CU, Pestov TV. 2006. The fidelity of translation initiation: Reciprocal activities of eIF1, IF3 and YciH. EMBO J 25: 196-210.
64. Lorsch JR, Dever TE. 2010. Molecular view of 43 S complex formation and start site selection in eukaryotic translation initiation. J Biol Chem 285: 21203-21207.
65. Loughran G, Sachs MS, Atkins JF, Ivanov IP. 2012. Stringency of start codon selection modulates autoregulation of translation initiation factor eIF5. Nucleic Acids Res 40: 2898-2906.
66. Maag D, Lorsch JR. 2003. Communication between eukaryotic translation initiation factors 1 and 1A on the yeast small ribosomal subunit. J Mol Biol 330: 917-924.
67. Maag D, Fekete CA, Gryczynski Z, Lorsch JR. 2005. A conformational change in the eukaryotic translation preinitiation complex and release of eIF1 signal recognition of the start codon. Mol Cell 17: 265-275.
68. Maag D, Algire MA, Lorsch JR. 2006. Communication between eukaryotic translation initiation factors 5 and 1A within the ribosomal pre-initiation complex plays a role in start site selection. J Mol Biol 356: 724-737.
69. Majumdar R, Bandyopadhyay A, Maitra U. 2003. Mammalian translation initiation factor eIF1 functions with eIF1A and eIF3 in the formation of a stable 40 S preinitiation complex. J Biol Chem 278: 6580-6587.
70. Marck C, Grosjean H. 2002. tRNomics: Analysis of tRNA genes from 50 genomes of Eukarya, Archaea, and bacteria reveals anticodon-sparing strategies and domain-specific features. RNA 8: 1189-1232.
71. Marintchev A, Kolupaeva VG, Pestova TV, Wagner G. 2003. Mapping the binding interface between human eukaryotic initiation factors 1A and 5B: A new interaction between old partners. Proc Natl Acad Sci 100: 1535-1540.
72. Marintchev A, Edmonds K, Marintcheva B, Hendrickson E, Oberer M, Suzuki C, Herdy B, Sonenberg N, Wagner G. 2009. Topology and regulation of the human eIF4A/4G/ 4H helicase complex in translation initiation. Cell 136: 447-460.
73. Marshall RA, Aitken CE, Puglisi JD. 2009. GTP hydrolysis by IF2 guides progression of the ribosome into elongation. Mol Cell 35: 37-47.
74. Martin-Marcos P, Hinnebusch AG, Tamame M. 2007. Ribosomal protein L33 is required for ribosome biogenesis, subunit joining and repression of GCN4 translation. Mo Cell Biol 27: 5968-5985.
75. Martin-Marcos P, Cheung YN, Hinnebusch AG. 2011. Functional elements in initiation factors 1, 1A and 2b discriminate against poor AUG context and non-AUG start codons. Mol Cell Biol 31: 4814-4831.
76. Mitchell SF, Walker SE, Algire MA, Park EH, Hinnebusc AG, Lorsch JR. 2010. The 50-7-methylguanosine cap on eukaryotic mRNAs serves both to stimulate canonical translation initiation and block an alternative pathway. Mol Cell 39: 950-962.
77. Nanda JS, Cheung YN, Takacs JE, Martin-Marcos P, Sain AK, Hinnebusch AG, Lorsch JR. 2009. eIF1 controls multiple steps in start codon recognition during eukaryotic translation initiation. J Mol Biol 394: 268-285.
78. Naveau M, Lazennec-Schurdevin C, Panvert M, Mechula Y, Schmitt E. 2010. tRNA binding properties of eukaryotic translation initiation factor 2 from Encephalitozoon cuniculi. Biochemistry 49: 8680-8688.
79. Nemoto N, Singh CR, Udagawa T, Wang S, Thorson E, Winter Z, Ohira T, Ii M, Valasek L, Brown SJ, et al. 2010. Yeast 18 S rRNA is directly involved in the ribosomal response to stringent AUG selection during translation initiation. J Biol Chem 285: 32200-32212.
80. Nielsen KH, Szamecz B, Valasek L, Jivotovskaya A, Shin BS, Hinnebusch AG. 2004. Functions of eIF3 downstream of 48S assembly impact AUG recognition and GCN4 translational control. EMBO J 23: 1166-1177.
81. Nielsen KH, Behrens MA, He Y, Oliveira CL, Sottrup Jense L, Hoffmann SV, Pedersen JS, Andersen GR. 2011. Synergistic activation of eIF4A by eIF4B and eIF4G. Nuclei Acids Res 39: 2678-2689.
82. Oberer M, Marintchev A, Wagner G. 2005. Structural basis for the enhancement of eIF4A helicase activity by eIF4G. Genes Dev 19: 2212-2223.
83. Olsen DS, EM S, Mathew A, Zhang F, Krishnamoorthy T, Phan L, Hinnebusch AG. 2003. Domains of eIF1A that mediate binding to eIF2, eIF3 and eIF5B and promote ternary complex recruitment in vivo. EMBO J 22: 193-204.
84. Ozes AR, Feoktistova K, Avanzino BC, Fraser CS. 2011. Duplex unwinding and ATPase activities of the DEAD-box helicase eIF4A are coupled by eIF4G and eIF4B. JMol Biol 412: 674-687.
85. Park E, Walker S, Lee J, Rothenburg S, Lorsch J, Hinnebusc A. 2011a. Multiple elements in the eIF4G1 N-terminus promote assembly of eIF4G1 PABP mRNPs in vivo. EMBO J 30: 302-316.
86. Park EH, Zhang F, Warringer J, Sunnerhagen P, Hinnebusc AG. 2011b. Depletion of eIF4G from yeast cells narrows the range of translational efficiencies genome-wide. BMC Genomics 12: 1-18.
87. Parsyan A, Shahbazian D, Martineau Y, Petroulakis E, Alain T, Larsson O, Mathonnet G, Tettweiler G, Hellen CU, Pestova TV, et al. 2009. The helicase protein DHX29 promotes translation initiation, cell proliferation, and tumorigenesis. Proc Natl Acad Sci 106: 22217-22222.
88. Parsyan A, Svitkin Y, Shahbazian D, Gkogkas C, Lasko P, Merrick WC, Sonenberg N. 2011. mRNA helicases: The tacticians of translational control. Nat Rev Mol Cell Biol 12: 235-245.
89. Passmore LA, Schmeing TM, Maag D, Applefield DJ, Acke MG, Algire MA, Lorsch JR, Ramakrishnan V. 2007. The eukaryotic translation initiation factors eIF1 and eIF1A induce an open conformation of the 40S ribosome. Mol Cell 26: 41-50.
90. Paulin FE, Campbell LE, O'Brien K, Loughlin J, Proud CG. 2001. Eukaryotic translation initiation factor 5 (eIF5) acts as a classical GTPase-activator protein. Curr Biol 11: 55-59.
91. Pestova TV, Kolupaeva VG. 2002. The roles of individual eukaryotic translation initiation factors in ribosomal scanning and initiation codon selection. Genes Dev 16: 2906-2922.
92. Pestova TV, Lomakin IB, Lee JH, Choi SK, Dever TE, Helle CUT. 2000. The joining of ribosomal subunits in eukaryotes requires eIF5B. Nature 403: 332-335.
93. Pestova TV, Lorsch JR, Hellen CUT. 2007. The mechanism of translation initiation in eukaryotes. In Translational control in biology and medicine (ed. Mathews M, Sonenberg N, Hershey JWB), pp. 87-128.
94. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY. Pisarev AV, Kolupaeva VG, Pisareva VP, MerrickWC, Helle CU, Pestova TV. 2006. Specific functional interactions of nucleotides at key 23 and +4 positions flanking the initiation codon with components of the mammalian 48S translation initiation complex. Genes Dev 20: 624-636.
95. Pisarev AV, Kolupaeva VG, Yusupov MM, Hellen CU, Pestov TV. 2008. Ribosomal position and contacts of mRNA in eukaryotic translation initiation complexes. EMBO J 27: 1609-1621.
96. Pisareva VP, Pisarev AV, Komar AA, Hellen CU, Pestova TV. 2008. Translation initiation on mammalian mRNAs with structured 50UTRs requires DExH-box protein DHX29. Cell 135: 1237-1250.
97. Rabl J, Leibundgut M, Ataide SF, Haag A, Ban N. 2011. Crystal structure of the eukaryotic 40S ribosomal subunit in complex with initiation factor 1. Science 331: 730-736.
98. Rajagopal V, Park EH, Hinnebusch AG, Lorsch JR. 2012. Specific domains in yeast eIF4G strongly bias the RNA unwinding activity of the eIF4F complex towards duplexes with 50-overhangs. J Biol Chem doi: 10.1074/jbc.M112.347278.
99. Ramirez-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.
100. Reibarkh M, Yamamoto Y, Singh CR, del Rio F, Fahmy A, Le B, Luna RE, Ii M, Wagner G, Asano K. 2008. Eukaryotic initiation factor (eIF) 1 carries two distinct eIF5-binding faces important for multifactor assembly and AUG selection. J Biol Chem 283: 1094-1103.
101. Rozovsky N, Butterworth AC, Moore MJ. 2008. Interactions between eIF4AI and its accessory factors eIF4B and eIF4H. RNA 14: 2136-2148.
102. Saini AK, Nanda JS, Lorsch JR, Hinnebusch AG. 2010. Regulatory elements in eIF1A control the fidelity of start codon selection by modulating tRNA(i)(Met) binding to the ribosome. Genes Dev 24: 97-110.
103. Schmitt E, Naveau M, Mechulam Y. 2010. Eukaryotic and archaeal translation initiation factor 2: A heterotrimeric tRNA carrier. FEBS Lett 584: 405-412.
104. Schmitt E, Panvert M, Lazennec-Schurdevin C, Coureu PD, Perez J, Thompson A, Mechulam Y. 2012. Structure of the ternary initiation complex aIF2-GDPNP-methionylated initiator tRNA. Nat Struct Mol Biol 19: 450-454.
105. Schutz P, Bumann M, Oberholzer AE, Bieniossek C, Trachse H, Altmann M, Baumann U. 2008. Crystal structure of the yeast eIF4A-eIF4G complex: An RNA-helicase controlled by protein-protein interactions. ProcNatl Acad Sci 105: 9564-9569.
106. Selmer M, Dunham CM, Murphy FVt, Weixlbaumer A, Petry S, Kelley AC, Weir JR, Ramakrishnan V. 2006. Structure of the 70S ribosome complexed with mRNA and tRNA. Science 313: 1935-1942.
107. Sengoku T, Nureki O, Nakamura A, Kobayashi S, Yokoyam S. 2006. Structural basis for RNA unwinding by the DEAD-box protein Drosophila Vasa. Cell 125: 287-300.
108. Shabalina SA, Ogurtsov AY, Rogozin IB, Koonin EV, Lipma DJ. 2004. Comparative analysis of orthologous eukaryotic mRNAs: Potential hidden functional signals. Nuclei Acids Res 32: 1774-1782.
109. Shin BS, Maag D, Roll-Mecak A, Arefin MS, Burley SK, Lorsch JR, Dever TE. 2002. Uncoupling of initiation factor eIF5B/IF2 GTPase and translational activities by mutations that lower ribosome affinity. Cell 111: 1015-1025.
110. Shin BS, Acker MG, Maag D, Kim JR, Lorsch JR, Dever TE. 2007. Intragenic suppressor mutations restore GTPase and translation functions of a eukaryotic initiation factor 5B switch II mutant. Mol Cell Biol 27: 1677-1685.
111. Shin BS, Kim JR, Walker SE, Dong J, Lorsch JR, Dever TE. 2011. Initiation factor eIF2g promotes eIF2-GTP-MettRNA(i)(Met) ternary complex binding to the 40S ribosome. Nat Struct Mol Biol 18: 1227-1234.
112. Singh CR, He H, Ii M, Yamamoto Y, Asano K. 2004. Efficient incorporation of eukaryotic initiation factor 1 into the multifactor complex is critical for formation of functional ribosomal preinitiation complexes in vivo. J Biol Chem 279: 31910-31920.
113. Singh CR, Curtis C, Yamamoto Y, Hall NS, Kruse DS, He H, Hannig EM, Asano K. 2005. Eukaryotic translation initiation factor 5 is critical for integrity of the scanning preinitiation complex and accurate control of GCN4 translation. Mol Cell Biol 25: 5480-5491.
114. Singh CR, Lee B, Udagawa T, Mohammad-Qureshi SS, Yamamot Y, PavittGD, Asano K. 2006. An eIF5/eIF2 complex antagonizes guanine nucleotide exchange by eIF2B during translation initiation. EMBO J 25: 4537-4546.
115. Singh CR, Udagawa T, Lee B, Wassink S, He H, Yamamoto Y, Anderson JT, Pavitt GD, Asano K. 2007. Change in nutritional status modulates the abundance of critical preinitiation intermediate complexes during translation initiation in vivo. J Mol Biol 370: 315-330.
116. Siridechadilok B, Fraser CS, Hall RJ, Doudna JA, Nogales E. 2005. Structural roles for human translation factor eIF3 in initiation of protein synthesis. Science 310: 1513-1515.
117. Skabkin MA, Skabkina OV, Dhote V, Komar AA, Hellen CU, Pestova TV. 2010. Activities of Ligatin and MCT-1/ DENR in eukaryotic translation initiation and ribosomal recycling. Genes Dev 24: 1787-1801.
118. Sokabe M, Fraser CS, Hershey JW. 2011. The human translation initiation multi-factor complex promotes methionyl-tRNAi binding to the 40S ribosomal subunit. Nucleic Acids Res 40: 905-913.
119. Spirin AS. 2009. How does a scanning ribosomal particle move along the 50-untranslated region of eukaryotic mRNA? Brownian ratchetmodel. Biochemistry 48: 10688-10692.
120. Srinivasan M, Mehta P, Yu Y, Prugar E, Koonin EV, Karza AW, Sternglanz R. 2011. The highly conserved KEOPS/ EKC complex is essential for a universal tRNA modification, t6A. EMBO J 30: 873-881.
121. Stolboushkina E, Nikonov S, Nikulin A, Blasi U, Manstei DJ, Fedorov R, Garber M, Nikonov O. 2008. Crystal structure of the intact archaeal translation initiation factor 2 demonstrates very high conformational flexibility in the a-and b-subunits. J Mol Biol 382: 680-691.
122. Sun C, Todorovic A, Querol-Audi{dotless}́ J, Bai Y, Villa N, Snyder M, Ashchyan J, Lewis CS, Hartland A, Gradia S, et al. 2011. Functional reconstitution of human eukaryotic translation initiation factor 3 (eIF3). Proc Natl Acad Sci 108: 20473-20478.
123. Svitkin Y, Pause A, Haghighat A, Pyronnet S, Witherell GW, Belsham G, Sonenberg N. 2001. The requirement for eukaryotic initiation factor 4A (eIF4A) in translation is in direct proportion to the degree of mRNA 50 secondary structure. RNA 7: 382-394.
124. Svitkin YV, Evdokimova VM, Brasey A, Pestova TV, Fantus D, Yanagiya A, Imataka H, Skabkin MA, Ovchinnikov LP, Merrick WC, et al. 2009. General RNA-binding proteins have a function in poly(A)-binding protein-dependent translation. EMBO J 28: 58-68.
125. Szamecz B, Rutkai E, Cuchalova L, Munzarova V, Herrmannov A, Nielsen KH, Burela L, Hinnebusch AG, Valasek L. 2008. eIF3a cooperates with sequences 50 of uORF1 to promote resumption of scanning by post-termination ribosomes for reinitiation on GCN4 mRNA. Genes Dev 22: 2414-2425.
126. Tarun SZ, Wells SE, Deardorff JA, Sachs AB. 1997. Translation initiation factor eIF4G mediates in vitro poly (A) tail-dependent translation. Proc Natl Acad Sci 94: 9046-9051.
127. Unbehaun A, Borukhov SI, Hellen CU, Pestova TV. 2004. Release of initiation factors from 48S complexes during ribosomal subunit joining and the link between establishment of codon-anticodon base-pairing and hydrolysis of eIF2-bound GTP. Genes Dev 18: 3078-3093.
128. Valášek L, Nielsen KH, Hinnebusch AG. 2002. Direct eIF2-eIF3 contact in the multifactor complex is important for translation initiation in vivo. EMBO J 21: 5886-5898.
129. Valášek L, Mathew A, Shin BS, Nielsen KH, Szamecz B, Hinnebusch AG. 2003. The Yeast eIF3 subunits TIF32/a and NIP1/c and eIF5 make critical connections with the 40S ribosome in vivo. Genes Dev 17: 786-799.
130. Valášek L, Nielsen KH, Zhang F, Fekete CA, Hinnebusch AG. 2004. Interactions of eukaryotic translation initiation factor 3 (eIF3) subunit NIP1/c with eIF1 and eIF5 promote preinitiation complex assembly and regulate start codon selection. Mol Cell Biol 24: 9437-9455.
131. Vassilenko KS, Alekhina OM, Dmitriev SE, Shatsky IN, Spirin AS. 2011. Unidirectional constant rate motion of the ribosomal scanning particle during eukaryotic translation initiation. Nucleic Acids Res 39: 5555-5567.
132. von der Haar T, McCarthy JE. 2002. Intracellular translation initiation factor levels in Saccharomyces cerevisiae and their role in cap-complex function. Mol Microbiol 46: 531-544.
133. Yanagiya A, Svitkin YV, Shibata S, Mikami S, Imataka H, Sonenberg N. 2009. Requirement of RNA binding of mammalian eukaryotic translation initiation factor 4GI (eIF4GI) for efficient interaction of eIF4E with the mRNA cap. Mol Cell Biol 29: 1661-1669.
134. Yatime L, Mechulam Y, Blanquet S, Schmitt E. 2006. Structural switch of the g subunit in an archaeal aIF2ag heterodimer. Structure 14: 119-128.
135. Yatime L, Mechulam Y, Blanquet S, Schmitt E. 2007. Structure of an archaeal heterotrimeric initiation factor 2 reveals a nucleotide state between the GTP and the GDP states. Proc Natl Acad Sci 104: 18445-18450.
136. Yu Y, Marintchev A, Kolupaeva VG, Unbehaun A, Veryasova T, Lai SC, Hong P, Wagner G, Hellen CU, Pestova TV. 2009. Position of eukaryotic translation initiation factor eIF1A on the 40S ribosomal subunit mapped by directed hydroxyl radical probing. Nucleic Acids Res 37: 5167-5182.
137. Yu Y, Abaeva IS, Marintchev A, Pestova TV, HellenCU. 2011. Common conformational changes induced in type 2 picornavirus IRESs by cognate trans-acting factors. Nuclei Acids Res 39: 4851-4865.