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The mechanism of eukaryotic translation initiation and principles of its regulation

Key Points

  • Translation is a cyclical process in which ribosomal subunits that participate in initiation are derived by recycling of post-termination ribosomal complexes (post-TCs) that have completed the previous round of translation. Post-TCs first dissociate into free 60S subunits and 40S subunits bound to mRNA and with a P-site deacylated tRNA. Release of tRNA and mRNA from recycled 40S subunits requires eukaryotic initiation factor 3 (eIF3), eIF1 and eIF1A. Deacylated tRNA, which is removed from the P-site of the ribosomal 40S subunit, is replaced by Met-tRNAMeti, which binds as a ternary complex with eIF2-GTP.

  • Initiation on most eukaryotic mRNAs involves scanning by ribosomal 43S preinitiation complexes on the 5′ untranslated region (UTR) from the 5′ cap-proximal point of initial attachment to the initiation codon. The mechanism of scanning is incompletely understood, but requires an 'open' conformation of the 40S subunit, which is induced by eIF1 and eIF1A, is coupled to the activities of the DEAD-box RNA helicase eIF4A, its cofactor eIF4B and eIF4G, and may involve additional DEAD box- or DExH box-containing proteins such as DExH box protein 29 (DHX29; higher eukaryotes) and DEAD box helicase 1 (Ded1; yeast).

  • In a current model for initiation codon recognition, establishment of codon–anticodon base pairing is accompanied by displacement of eIF1 from the P-site, which switches the 40S subunit to a closed conformation that is locked onto mRNA and relieves repression of eIF5-induced hydrolysis of eIF2-bound GTP and Pi release. eIF5B then mediates the dissociation of eIF2–GDP, eIF1 and eIF1A from the interface surface of the 40S subunit and the joining to it of a 60S ribosomal subunit, to form an 80S ribosome with initiator tRNA in the P-site.

  • Regulation of eIF activity by reversible phosphorylation affects most mRNAs that are translated by the canonical scanning-dependent mode of initiation. The best-characterized examples are phosphorylation of mammalian eIF2 by any of four stress-activated kinases (which leads to a reduction in the level of eIF2–GTP–Met-tRNAMeti ternary complexes) and of mammalian 4E-binding proteins, mainly by mTOR (in response to mitogens and growth factors), which releases eIF4E for assimilation into eIF4F and promotes translation.

  • Sequence-specific RNA-binding proteins have the potential to selectively regulate specific mRNAs or classes of mRNA. 3′ UTR-binding proteins commonly repress translation by forming an inhibitory closed loop with a 5′ cap-binding protein (which may be eIF4E) and an intermediate bridging protein, whereas poly(A)-binding protein (PABP) bound to the 3′ poly(A) tail enhances initiation, possibly by tethering eIF4F so that it is available, despite dissociation from the 5′ cap, to promote further rounds of initiation on the same mRNA without having to be recruited de novo from solution.

  • MicroRNAs have recently emerged as important regulators of translation that also act by binding to the 3′ UTR. The mechanism of repression has not yet been fully elucidated, but appears to have two components, both mediated by the carboxy-terminal domain of the protein GW182: true repression of translation and an accelerated rate of deadenylation-dependent mRNA degradation.

Abstract

Protein synthesis is principally regulated at the initiation stage (rather than during elongation or termination), allowing rapid, reversible and spatial control of gene expression. Progress over recent years in determining the structures and activities of initiation factors, and in mapping their interactions in ribosomal initiation complexes, have advanced our understanding of the complex translation initiation process. These developments have provided a solid foundation for studying the regulation of translation initiation by mechanisms that include the modulation of initiation factor activity (which affects almost all scanning-dependent initiation) and through sequence-specific RNA-binding proteins and microRNAs (which affect individual mRNAs).

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Figure 1: Model of the canonical pathway of eukaryotic translation initiation.
Figure 2: Architecture of ribosomal initiation complexes.
Figure 3: eIF4GI domain structure, interactions and position in a scanning 43S complex.
Figure 4: The mechanism of regulation of ATF4 and ATF5 mRNA translation.
Figure 5: Models of miRNA-mediated repression of translation of target mRNAs.

Accession codes

Accessions

GenBank/EMBL/DDBJ

References

  1. 1

    Pestova, T. V., Lorsch, J. R. & Hellen, C. U. T. in Translational Control in Biology and Medicine (eds. Mathews, M. B., Sonenberg, N. & Hershey, J. W. B.) 87–128 (Cold Spring Harbor Laboratory Press, New York, 2007).

    Google Scholar 

  2. 2

    Pisarev, A. V., Hellen, C. U. T. & Pestova, T. V. Recycling of eukaryotic posttermination ribosomal complexes. Cell 131, 286–299 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. 3

    Unbehaun, A., Borukhov, S. I., Hellen, C. U. T. & Pestova, T. V. 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 (2004). This biochemical study shows that eIF1 is a negative regulator of hydrolysis of eIF2-bound GTP, which inhibits the commitment step in initiation until codon–anticodon base pairing is established. eIF1 thus ensures the fidelity of initiation both after and during scanning.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. 4

    Fraser, C. S., Berry, K. E., Hershey, J. W. & Doudna, J. A. eIF3j is located in the decoding center of the human 40S ribosomal subunit. Mol. Cell 26, 811–819 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. 5

    Rees, D. C., Johnson, E. & Lewinson, O. ABC transporters: the power to change. Nature Rev. Mol. Cell Biol. 10, 218–227 (2009).

    Article  CAS  Google Scholar 

  6. 6

    Spahn, C. M. et al. Structure of the 80S ribosome from Saccharomyces cerevisiae-tRNA-ribosome and subunit-subunit interactions. Cell 107, 373–386 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. 7

    Schüler, M. et al. 2006. Structure of the ribosome-bound cricket paralysis virus IRES RNA. Nature Struct. Mol. Biol. 13, 1092–1096 (2006). This cryoelectron microscopy reconstruction of a dicistrovirus IRES bound to the 80S ribosome shows details at subnanometre resolution of the IRES—ribosome interaction, and reveals the potential for conformational changes in the IRES that enable it to promote successive steps in an exceptional mechanism of internal initiation.

    Article  CAS  Google Scholar 

  8. 8

    Siridechadilok, B., Fraser, C. S., Hall, R. J., Doudna, J. A. & Nogales, E. Structural roles for human translation factor eIF3 in initiation of protein synthesis. Science 310, 1513–1515 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. 9

    Yatime, L., Mechulam, Y., Blanquet, S. & Schmitt, E. Structure of an archaeal heterotrimeric initiation factor 2 reveals a nucleotide state between the GTP and the GDP states. Proc. Natl Acad. Sci. USA 104, 18445–18450 (2007).

    Article  PubMed  PubMed Central  Google Scholar 

  10. 10

    Lomakin, I. B., Kolupaeva, V. G., Marintchev, A., Wagner, G. & Pestova, T. V. Position of eukaryotic initiation factor eIF1 on the 40S ribosomal subunit determined by directed hydroxyl radical probing. Genes Dev. 17, 2786–2797 (2003). The first mapping of an eIF-binding site on a ribosome by directed hydroxyl radical probing, which shows that eIF1 binds the 40S subunit platform near the P-site, in a position that would enable it to maintain the fidelity of initiation codon selection indirectly by influencing the conformation of the platform and the positions of mRNA and initiator tRNA in initiation complexes.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. 11

    Simonetti, A. et al. Structure of the 30S translation initiation complex. Nature 455, 416–420 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. 12

    Allen, G. S., Zavialov, A., Gursky, R., Ehrenberg, M. & Frank, J. The cryo-EM structure of a translation initiation complex from Escherichia coli . Cell 121, 703–712 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. 13

    Yu, Y. et al. Position of eukaryotic translation initiation factor eIF1A on the 40S ribosomal subunit mapped by directed hydroxyl radical probing. Nucleic Acids Res. 37, 5167–5182 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. 14

    Passmore, L. A. et al. The eukaryotic translation initiation factors eIF1 and eIF1A induce an open conformation of the 40S ribosome. Mol. Cell 26, 41–50 (2007). Cryoelectron microscopy reconstructions of yeast 40S subunits bound to eIF1 and eIF1A, showing induced conformational changes that open the mRNA-binding channel in a scanning-competent conformation, which reverses on initiation codon recognition and consequent eIF1 release to clamp down on the mRNA.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. 15

    Pestova, T. V. & Kolupaeva, V. G. The roles of individual eukaryotic translation initiation factors in ribosomal scanning and initiation codon selection. Genes Dev. 16, 2906–2922 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. 16

    von der Haar, T., Gross, J. D., Wagner, G. & McCarthy, J. E. The mRNA cap-binding protein eIF4E in post-transcriptional gene expression. Nature Struct. Mol. Biol. 11, 503–511 (2004).

    Article  CAS  Google Scholar 

  17. 17

    Gross, J. D. et al. Ribosome loading onto the mRNA cap is driven by conformational coupling between eIF4G and eIF4E. Cell 115, 739–750 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. 18

    Volpon, L., Osborne, M. J., Topisirovic, I., Siddiqui, N. & Borden, K. L. Cap-free structure of eIF4E suggests a basis for conformational regulation by its ligands. EMBO J. 25, 5138–5149 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. 19

    Andersen, C. B. et al. Structure of the exon junction core complex with a trapped DEAD-box ATPase bound to RNA. Science 313, 1968–1972 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. 20

    Rogers, G. W. Jr., Richter, N. J., Lima, W. F. & Merrick, W. C. Modulation of the helicase activity of eIF4A by eIF4B, eIF4H, and eIF4F. J. Biol. Chem. 276, 30914–30922 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. 21

    Schütz, P. et al. Crystal structure of the yeast eIF4A–eIF4G complex: an RNA-helicase controlled by protein–protein interactions. Proc. Natl Acad. Sci. USA 105, 9564–9569 (2008).

    Article  PubMed  PubMed Central  Google Scholar 

  22. 22

    Marintchev, A. et al. 2009. Topology and regulation of the human eIF4A/4G/4H helicase complex in translation initiation. Cell 136, 447–460 (2009). In this study, modelling based on known structures of factor domains, NMR, quantitative binding assays and site-directed mutagenesis were used to derive a model of the eIF4A–eIF4G–eIF4H (or eIF4A–eIF4G–eIF4B) helicase complex and to propose hypotheses for its dynamic organization, location and modus operandi on the scanning ribosomal complex.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. 23

    LeFebvre, A. K. et al. Translation initiation factor eIF4G-1 binds to eIF3 through the eIF3e subunit. J. Biol. Chem. 281, 22917–22932 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. 24

    Kozak, M. Structural features in eukaryotic mRNAs that modulate the initiation of translation. J. Biol. Chem. 266, 19867–19870 (1991).

    CAS  PubMed  PubMed Central  Google Scholar 

  25. 25

    Pisarev, A. V., Kolupaeva, V. G., Yusupov, M. M., Hellen, C. U. T & Pestova, T. V. Ribosomal position and contacts of mRNA in eukaryotic translation initiation complexes. EMBO J. 27, 1609–1621 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. 26

    Jackson, R. J. The ATP requirement for initiation of eukaryotic translation varies according to the mRNA species. Eur. J. Biochem. 200, 285–294 (1991).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. 27

    Svitkin, Y. V. et al. The requirement for eukaryotic initiation factor 4A (elF4A) in translation is in direct proportion to the degree of mRNA 5′ secondary structure. RNA 7, 382–394 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. 28

    Matsuda, D. & Dreher, T. W. Close spacing of AUG initiation codons confers dicistronic character on a eukaryotic mRNA. RNA 12, 1338–1349 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. 29

    Pisareva, V. P. et al. Translation initiation on mammalian mRNAs with structured 5′UTRs requires DExH-box protein DHX29. Cell 135, 1237–1250 (2008). Identifies DHX29 as a novel initiation factor that promotes ribosomal scanning, particularly on highly structured 5′ UTRs, in a translation system reconstituted from highly purified factors.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. 30

    Parsyan, A. et al. The helicase protein, DHX29 promotes translation initiation, cell proliferation and tumorigenesis. Proc. Natl Acad. Sci. USA Dec 11 2009 (doi: 10.1073/pnas.0909773106). Reports the importance of DHX29 for initiation in vivo.

  31. 31

    Chuang, R. Y., Weaver, P. L., Liu, Z. & Chang, T. H. Requirement of the DEAD-Box protein ded1p for messenger RNA translation. Science 275, 1468–1471 (1997).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. 32

    de la Cruz, J., Iost, I., Kressler, D. & Linder, P. The p20 and Ded1 proteins have antagonistic roles in eIF4E-dependent translation in Saccharomyces cerevisiae . Proc. Natl Acad. Sci. USA 94, 5201–5206 (1997).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. 33

    Marsden, S., Nardelli, M., Linder, P. & McCarthy, J. E. Unwinding single RNA molecules using helicases involved in eukaryotic translation initiation. J. Mol. Biol. 361, 327–335 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. 34

    Tarn, W. Y. & Chang, T. H. The current understanding of Ded1p/DDX3 homologs from yeast to human. RNA Biol. 6, 17–20 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. 35

    Imataka, H., Olsen, H. S. & Sonenberg, N. A new translational regulator with homology to eukaryotic translation initiation factor 4G. EMBO J. 16, 817–825 (1997).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. 36

    Hundsdoerfer, P., Thoma, C. & Hentze, M. W. Eukaryotic translation initiation factor 4GI and p97 promote cellular internal ribosome entry sequence-driven translation. Proc. Natl Acad. Sci. USA 102, 13421–13426 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. 37

    Ramírez-Valle, F., Braunstein, S., Zavadil, J., Formenti, S. C. & Schneider, R. J. eIF4GI links nutrient sensing by mTOR to cell proliferation and inhibition of autophagy. J. Cell Biol. 181, 293-307 (2008).

  38. 38

    Pestova, T. V., Borukhov, S. I. & Hellen, C. U. T. Eukaryotic ribosomes require initiation factors 1 and 1A to locate initiation codons. Nature 394, 854–859 (1998).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. 39

    Pisarev, A. V. et al. Specific functional interactions of nucleotides at key -3 and +4 positions flanking the initiation codon with components of the mammalian 48S translation initiation complex. Genes Dev. 20, 624–636 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. 40

    Donahue, T. F. in Translational Control of Gene Expression (eds. Sonenberg, N., Hershey, J. W. B., & Mathews, M. B.) 487–502 (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, 2000).

    Google Scholar 

  41. 41

    Maag, D., Algire, M. A. & Lorsch, J. R. 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 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. 42

    Maag, D., Fekete, C. A., Gryczynski, Z. & Lorsch, J. R. A conformational change in the eukaryotic translation preinitiation complex and release of eIF1 signal recognition of the start codon. Mol. Cell 17, 265–275 (2005). Together with references 3 and 14, this study shows that start codon recognition induces a conformational change in ribosomal initiation complexes and the displacement of eIF1, probably resulting in closure of the mRNA-binding channel and in triggering hydrolysis of eIF2-bound GTP, respectively, thereby committing the arrested 48S complex to the initiation codon.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. 43

    Cheung, Y.N. et al. Dissociation of eIF1 from the 40S ribosomal subunit is a key step in start codon selection in vivo . Genes Dev. 21, 1217–1230 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. 44

    Fekete, C. A. et al. N- and C-terminal residues of eIF1A have opposing effects on the fidelity of start codon selection. EMBO J. 26, 1602–1614 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. 45

    Paulin, F. E., Campbell, L. E., O'Brien, K., Loughlin, J. & Proud, C. G. Eukaryotic translation initiation factor 5 (eIF5) acts as a classical GTPase-activator protein. Curr. Biol. 11, 55–59 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. 46

    Marintchev, A. & Wagner, G. Translation initiation: structures, mechanisms and evolution. Q. Rev. Biophys. 37, 197–284 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. 47

    Algire, M. A., Maag, D. & Lorsch, J. R. Pi release from eIF2, not GTP hydrolysis, is the step controlled by start-site selection during eukaryotic translation initiation. Mol. Cell 20, 251–262 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. 48

    Kapp, L. D. & Lorsch, J. R. GTP-dependent recognition of the methionine moiety on initiator tRNA by translation factor eIF2. J. Mol. Biol. 335, 923–936 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. 49

    Pestova, T. V. et al. The joining of ribosomal subunits in eukaryotes requires eIF5B. Nature 403, 332–335 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. 50

    Unbehaun, A. et al. Position of eukaryotic initiation factor eIF5B on the 80S ribosome mapped by directed hydroxyl radical probing. EMBO J. 26, 3109–3123 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. 51

    Olsen, D. S. et al. Domains of eIF1A that mediate binding to eIF2, eIF3 and eIF5B and promote ternary complex recruitment in vivo . EMBO J. 22, 193–204 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. 52

    Marintchev, A., Kolupaeva, V. G., Pestova, T. V. & Wagner, G. Mapping the binding interface between human eukaryotic initiation factors 1A and 5B: a new interaction between old partners. Proc. Natl Acad. Sci. USA 100, 1535–1540 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. 53

    Acker, M. G., Shin, B. S., Dever, T. E. & Lorsch, J. R. Interaction between eukaryotic initiation factors 1A and 5B is required for efficient ribosomal subunit joining. J. Biol. Chem. 281, 8469–8475 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  54. 54

    Acker, M. G. et al. Kinetic analysis of late steps of eukaryotic translation initiation. J. Mol. Biol. 385, 491–506 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  55. 55

    Calvo, S. E, Pagliarini, D. J. & Mootha, V. K. Upstream open reading frames cause widespread reduction of protein expression and are polymorphic among humans. Proc. Natl Acad. Sci. USA 106, 7507–7512 (2009).

    Article  PubMed  PubMed Central  Google Scholar 

  56. 56

    Resch, A. M., Ogurtsov, A. Y., Rogozin, I. B., Shabalina, S. A. & Koonin, E. V. Evolution of alternative and constitutive regions of mammalian 5′UTRs. BMC Genomics 10, 162 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  57. 57

    Lawless, C. et al. Upstream sequence elements direct post-transcriptional regulation of gene expression under stress conditions in yeast. BMC Genomics 10, 7 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  58. 58

    Luukkonen, B. G. M., Tan, W. & Schwartz, S. Efficiency of reinitiation of translation on human immunodeficiency virus type 1 mRNAs is determined by the length of the upstream open reading frame and by intercistronic distance. J. Virol. 69, 4086–4094 (1995).

    CAS  PubMed  PubMed Central  Google Scholar 

  59. 59

    Kozak, M. Constraints on reinitiation of translation in mammals. Nucleic Acids Res. 29, 5226–5232 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  60. 60

    Pöyry, T. A. A, Kaminski, A. & Jackson, R. J. What determines whether mammalian ribosomes resume scanning after translation of a short upstream open reading frame? Genes Dev. 18, 62–75 (2004). Data, obtained using a panel of mRNAs that have different eIF requirements, suggesting that eIF3 and eIF4G remain weakly associated with ribosomes during translation of short uORFs and that these factors then promote the resumption of scanning, leading to reinitiation.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  61. 61

    Dever, T. E., Dar, A. C. & Sicheri, F. in Translational control in biology and medicine (eds Mathews, M. B., Sonenberg, N. & Hershey, J. W. B.) 319–344 (Cold Spring Harbor Laboratory Press, New York, 2007).

    Google Scholar 

  62. 62

    Vattem, K. M. & Wek, R. C. Reinitiation involving upstream ORFs regulates ATF4 mRNA translation in mammalian cells. Proc. Natl Acad. Sci. USA 101, 11269–11274 (2004). Shows how the configuration of the two uORFs in ATF4 mRNA results in stimulated ATF synthesis following PERK activation.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  63. 63

    Zhou, D. et al. Phosphorylation of eIF2 directs ATF5 translational control in response to diverse stress conditions. J. Biol. Chem. 283, 7064–7073 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  64. 64

    Raught, B. & Gringras, A.-C. in Translational control in biology and medicine (eds Mathews, M. B., Sonenberg, N. & Hershey, J. W. B.) 369–400 (Cold Spring Harbor Laboratory Press, New York, 2007).

    Google Scholar 

  65. 65

    Ueda, T., Watanabe-Fukunaga, R., Fukuyama, H., Nagata, S. & Fukunaga, R. Mnk2 and Mnk1 are essential for constitutive and inducible phosphorylation of eIF4E but not for cell growth or development. Mol. Cell Biol. 24, 6539–6549 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  66. 66

    Wendel, H. G. et al. Dissecting eIF4E action in tumorigenesis. Genes Dev. 21, 3232–3237 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  67. 67

    Pende, M. et al. S6K1−/−/S6K2−/− mice exhibit perinatal lethality and rapamycin-sensitive 5′ terminal oligopyrmidine tract mRNA translation and reveal a mitogen-activated protein kinase-dependent S6 kinase pathway. Mol. Cell Biol. 24, 3112–3124 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  68. 68

    Ruvinsky, I. et al. Ribosomal protein S6 phosphorylation is a determinant of cell size and glucose homeostasis. Genes Dev. 19, 2199–2211 (2005). Shows that transgenic knock-in mice homozygous for non-phosphorylatable rpS6 are viable and normal and show proper regulation of ribosomal protein mRNA translation.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  69. 69

    Gebauer F & Hentze, M. W. Molecular mechanisms of translational control. Nature Rev. Mol. Cell Biol. 5, 827–835 (2004).

    Google Scholar 

  70. 70

    Muckenthaler, M., Gray, N. K. & Hentze, M. W. IRP-1 binding to ferritin mRNA prevents the recruitment of the small ribosomal subunit by the cap-binding complex eIF4F. Mol. Cell 2, 383–388 (1998).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  71. 71

    Paraskeva, E., Gray, N. K., Schläger, B., Wehr, K. & Hentze, M. W. Ribosomal pausing and scanning arrest as mechanisms of translational regulation from cap-distal iron-responsive elements. Mol. Cell Biol. 19, 807–816 (1999).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  72. 72

    De Melo Neto, O. P., Standart, N. & Martins de Sa, C. Autoregulation of poly(A)-binding protein synthesis in vitro . Nucleic Acids Res. 23, 2198–2205 (1995).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  73. 73

    Hamilton, T. L., Stoneley, M., Spriggs, K. A. & Bushell, M. TOPS and their regulation. Biochem. Soc. Trans. 34, 12–16 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  74. 74

    Patursky-Polischuk, I. et al. The TSC-mTOR pathway mediates translational activation of TOP mRNAs by insulin largely in a raptor- or rictor-independent manner. Mol. Cell Biol. 29, 640–649 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  75. 75

    Kahvejian, A., Svitkin, Y. V. Sukareieh, R., M'Boutchou, M. N. & Sonenberg, N. Mammalian poly(A)-binding protein is a eukaryotic translation initiation factor, which acts via multiple mechanisms. Genes Dev. 19, 104–113 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  76. 76

    Sachs, A. B. & Davis, R. W. The poly(A) binding protein is required for poly(A) shortening and 60S ribosomal subunit-dependent translation initiation. Cell 58, 857–867 (1989).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  77. 77

    Proweller, A. & Butler, J. S. Ribosome concentration contributes to discrimination against poly(A)-mRNA during translation initiation in Saccharomyces cerevisiae . J. Biol. Chem. 272, 6004–6010 (1997).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  78. 78

    Borman, A. M., Michel, Y. M. & Kean, K. M. Biochemical characterisation of cap-poly(A) synergy in rabbit reticulocyte lysates: the eIF4G-PABP interaction increases the functional affinity of eIF4E for the capped mRNA 5′-end. Nucleic Acids Res. 28, 4068–4075 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  79. 79

    Kessler, S. H. & Sachs, A. B. RNA recognition motif 2 of yeast Pab1p is required for its functional interaction with eukaryotic translation initiation factor 4G. Mol. Cell Biol. 18, 51–57 (1998).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  80. 80

    Imataka, H., Gradi, A. & Sonenberg, N. A newly identified N terminal amino acid sequence of human eIF4G binds poly(A)-binding protein and functions in poly(A)-dependent translation. EMBO J. 17, 7480–7489 (1998).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  81. 81

    Gray, N. K., Coller, J. M., Dickson, K. S. & Wickens, M. Multiple portions of poly(A)-binding protein stimulate translation in vivo . EMBO J. 19, 4723–4733 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  82. 82

    Cakmakci, N. G., Lerner, R. S., Wagner, E. J., Zheng, L. & Marzluff, W. F. SLIP1, a factor required for activation of histone mRNA translation by the stem-loop binding protein. Mol. Cell. Biol. 28, 1182–1194 (2008). SLIP1 is shown to interact with both SLBP (bound to the 3′ stem loop of histone mRNAs) and the eIF4G subunit of eIF4F, forming a 'closed loop' that stimulates histone mRNA translation.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  83. 83

    Kleene, K. C. Poly(A) shortening accompanies the activation of translation of five mRNAs during spermiogenesis in the mouse. Development 106, 367–373 (1989).

    CAS  PubMed  PubMed Central  Google Scholar 

  84. 84

    Braun, R. E., Peschon, J. J., Behringer, R. R., Brinster, R. L. & Palmiter, R. D. Protamine 3′ untranslated sequences regulate temporal translational control and subcellular localization of growth hormone in spermatids of transgenic mice. Genes Dev. 3, 793–802 (1989).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  85. 85

    Standart, N., Dale, M., Stewart, E. & Hunt, T. Maternal mRNA from clam oocytes can be specifically unmasked in vitro by antisense RNA complementary to the 3′-untranslated region. Genes Dev. 1990 4, 2157–2168 (1990).

    CAS  Google Scholar 

  86. 86

    Sonenberg, N. & Hinnebusch, A. G. Regulation of translation initiation in eukaryotes: mechanisms and biological targets. Cell 136, 731–745 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  87. 87

    Minshall, N., Reiter, M. H., Weil, D. & Standart, N. CPEB interacts with an ovary-specific eIF4E and 4E-T in early Xenopus oocytes. J. Biol. Chem. 282, 37389–37401 (2007). Repression of maternal mRNAs in vertebrate ( X. laevis ) oocyctes is shown to involve the binding of a large CPEB-containing protein complex to the 3′ UTR, and a CPEB–4E-T–eIF4E1b tripartite interaction relay, which blocks eIF4F access to the 5′ cap.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  88. 88

    Villaescusa, J. C. et al. Cytoplasmic Prep1 interacts with 4EHP inhibiting Hoxb4 translation. PLoS One 4, e5213 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  89. 89

    Chekulaeva, M., Hentze, M. W. & Ephrussi, A. Bruno acts as a dual repressor of oskar translation, promoting mRNA oligomerization and formation of silencing particles. Cell 124, 521–533 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  90. 90

    Minshall, N. & Standart, N. The active form of Xp54 RNA helicase in translational repression is an RNA-mediated oligomer. Nucleic Acids Res. 32, 1325–1334 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  91. 91

    Tanaka, K. J. et al. RAP55, a cytoplasmic mRNP component, represses translation in Xenopus oocytes. J. Biol. Chem. 281, 40096–40106 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  92. 92

    Coller, J. & Parker, R. General translational repression by activators of mRNA decapping. Cell 122, 875–886 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  93. 93

    Klann, E. & Richter, J. D. in Translational control in biology and medicine (eds. Mathews, M. B., Sonenberg, N. & Hershey, J. W. B.) 485–506 (Cold Spring Harbor Laboratory Press, New York, 2007).

    Google Scholar 

  94. 94

    Ostarek, D. H., Ostareck-Lederer, A., Shatsky, I. N. & Hentze, M. W. Lipoxygenase mRNA silencing in erythroid differentiation: The 3′UTR regulatory complex controls 60S subunit joining. Cell 104, 281–290 (2001).

    Article  Google Scholar 

  95. 95

    Hüttelmaier, S. et al. Spatial regulation of β-actin translation by Src-dependent phosphorylation of ZBP1. Nature 438, 512–515 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  96. 96

    Johnstone, O. & Lasko, P. Interaction with eIF5B is essential for Vasa function during development. Development 131, 4167–4178 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  97. 97

    Bhattacharyya, S. N., Habermacher, R., Martine, U., Closs, E. I. & Filipowicz, W. Relief of microRNA-mediated repression in human cells subjected to stress. Cell 125, 1111–1124 (2006). One of the few studies of miRNA-mediated repression of an endogenous vertebrate mRNA, showing an inhibition of initiation that is relieved on amino acid starvation.

    Article  CAS  Google Scholar 

  98. 98

    Jackson, R. J. & Standart, N. How do microRNAs regulate gene expression? Sci. STKE 367, re1 (2007).

    Google Scholar 

  99. 99

    Pillai, R. S., Artus, C. G. & Filipowicz, W. Tethering of human Ago proteins to mRNA mimics the miRNA-mediated repression of protein synthesis. RNA 10, 1518–1525 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  100. 100

    Zipprich, J. T., Bhattacharyya, S. Mathys, H. & Filipowicz, W. Importance of the C-terminal domain of the human GW182 protein TNRC6C for translational repression. RNA 15, 781–793 (2009). Tethering the C-terminal domain of GW182 to the 3′ UTR is shown to recapitulate miRNA-mediated repression of translation.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  101. 101

    Eulalio, A., Tritschler, F. & Izaurralde, E. The GW182 protein family in animal cells: New insights into domains required for miRNA-mediated gene silencing. RNA 15, 1433–1442 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  102. 102

    Behm-Ansmant, I. et al. mRNA degradation by miRNAs and GW182 requires both CCR:NOT deadenylase and DCP1:DCP2 decapping enzymes. Genes Dev. 20, 1885–1898 (2006). Tethering GW182 to the 3′ UTR in the absence of AGO or miRNAs is shown to result in both translational repression and accelerated mRNA degradation through the normal deadenylation-dependent route.

    Article  PubMed  PubMed Central  Google Scholar 

  103. 103

    Fabian, M. R. et al. Mammalian miRNA RISC recruits CAF1 and PABP to affect PABP-dependent deadenylation. Mol. Cell 35, 868–880 (2009).

    CAS  Google Scholar 

  104. 104

    Zekri, L., Huntzinge, E., Heimstädt, S. & Izaurralde, E. The silencing domain of GW182 interacts with PABPC1 to promote translational repression and degradation of miRNA targets and is required for target release. Mol. Cell Biol. 29, 6220–6231 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  105. 105

    Kong, Y. W. et al. The mechanism of micro-RNA-mediated translation repression is determined by the promoter of the target gene. Proc. Natl Acad. Sci. USA 105, 8866–8871 (2008).

    Article  PubMed  PubMed Central  Google Scholar 

  106. 106

    Nottrott, S., Simard, M. J. & Richter, J. D. Human let-7a miRNA blocks protein production on actively translating polyribosomes. Nature Struct. Mol. Biol. 13, 1108–1114 (2006).

    Article  CAS  Google Scholar 

  107. 107

    Eulalio, A., Huntzinger E & Izaurralde, E. GW182 interaction with Argonaute is essential for miRNA-mediated translational repression and mRNA decay. Nature Struct. Mol. Biol. 15, 346–353 (2008).

    Article  CAS  Google Scholar 

  108. 108

    Mathonnet, G. et al. MicroRNA inhibition of translation initiation in vitro by targeting the cap-binding complex elF4F. Science 317, 1764–1767 (2007). Recapitulation of miRNA-mediated repression in a mouse cell-free extract suggests that miRNAs directly or indirectly inhibit eIF4F function.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  109. 109

    Thermann, R. & Hentze, M. W. Drosphila miR2 induces pseudo-polysomes and inhibits translation initiation. Nature 447, 875–878 (2007).

    Article  CAS  Google Scholar 

  110. 110

    Standart, N. & Jackson, R. J. MicroRNAs repress translation of m7Gppp-capped target mRNAs in vitro by inhibiting initiation and promoting deadenylation. Genes Dev. 21, 1975–1982 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  111. 111

    Wu, L., Fan, J. & Belasco, J. G. MicroRNAs direct rapid deadenylation of mRNA. Proc. Natl Acad. Sci. USA 103, 4034–4039 (2006).

    Article  CAS  Google Scholar 

  112. 112

    Pestova, T. V., Hellen, C. U. & Shatsky, I. N. Canonical eukaryotic initiation factors determine initiation of translation by internal ribosomal entry. Mol. Cell. Biol. 16, 6859–6869 (1996).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  113. 113

    Pestova, T. V., Shatsky, I. N. & Hellen, C. U. T. Functional dissection of eukaryotic initiation factor 4F: the 4A subunit and the central domain of the 4G subunit are sufficient to mediate internal entry of 43S preinitiation complexes. Mol. Cell Biol. 16, 6870–6878 (1996).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  114. 114

    de Breyne, S., Yu, Y., Unbehaun, A., Pestova, T. V. & Hellen, C. U. T. Direct functional interaction of initiation factor eIF4G with type 1 internal ribosomal entry sites. Proc. Natl Acad. Sci. USA 106, 9197–9202 (2009).

    Article  PubMed  PubMed Central  Google Scholar 

  115. 115

    Pestova, T. V., Shatsky, I. N., Fletcher, S. P., Jackson, R. J. & Hellen, C. U. T. 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 (1998).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  116. 116

    Wilson, J. E., Pestova, T. V., Hellen, C. U. T. & Sarnow, P. Initiation of protein synthesis from the A site of the ribosome. Cell 102, 511–520 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  117. 117

    Jackson, R. J. Alternative mechanisms of initiating translation of mammalian mRNAs. Biochem. Soc. Trans. 33, 1231–1241 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  118. 118

    Baranick, B. T. et al. Splicing mediates the activity of four putative cellular internal ribosome entry sites. Proc. Natl Acad. Sci. USA 105, 4733–4738 (2009).

    Article  Google Scholar 

  119. 119

    Silvera, D. et al. Essential role for eIF4GI overexpression in the pathogenesis of inflammatory breast cancer. Nature Cell Biol. 11, 903–908 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  120. 120

    Braunstein, S. et al. A hypoxia-controlled cap-dependent to cap-independent translation switch in breast cancer. Mol. Cell 28, 501–512 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  121. 121

    Stebbins-Boaz, B., Cao, Q., de Moor, C. H., Mendez, R. & Richter, J. D. Maskin is a CPEB-associated factor that transiently interacts with eIF4E. Mol. Cell 4, 1017–1027 (1999).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgements

We thank J. Doudna, A. Marintchev and L. Passmore for figures. Research in the authors' laboratories is supported by grants from the Biotechnology and Biological Sciences Research Council and The Wellcome Trust (RJJ), the National Institutes of Health (NIH) National Institute of Allergy and Infectious Diseases (CUTH) and the NIH National Institute of General Medical Sciences (TVP).

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Tatyana V. Pestova and Christopher U. T. Hellen have filed a patent on DHX29 and its use to identify therapeutic regulators of gene expression.

Supplementary information

Supplementary information S1 (box) | The involvement of eIF6 in translation initiation (PDF 253 kb)

41580_2010_BFnrm2838_MOESM252_ESM.pdf

Supplementary information S2 (box) | Reinitiation after translation of a short upstream ORF (uORF); instructive differences between yeast and vertebrates. (PDF 263 kb)

Supplementary information S3 (box) | Proteolytic cleavage of initiation factors (PDF 254 kb)

41580_2010_BFnrm2838_MOESM254_ESM.pdf

Supplementary information S4 (box) | Similarities and differences between the mechanisms of regulation of yeast GCN4 and mammalian ATF4/5 mRNAs (PDF 253 kb)

41580_2010_BFnrm2838_MOESM255_ESM.pdf

Supplementary information S5 (box) | Does the "closed loop" configuration resulting from PABP-eIF4G interaction promote ribosome recycling? (PDF 241 kb)

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DATABASES

Protein Data bank 

1JGO

1JGP

Glossary

Met-tRNAMeti

The unique initiator tRNA, aminoacylated with methionine, that is used to initiate protein synthesis. Its anticodon is complementary to the AUG initiation codon; it forms a specific ternary complex with eIF2 and GTP and it binds to the ribosomal P-site.

P-site

The site on a ribosome that holds the tRNA that is linked to the growing peptide chain (peptidyl-tRNA).

Internal ribosome entry site

A structure that is located in the 5′ UTR or ORF of some mRNAs of cellular or viral origin. It mediates translation initiation independently of the 5′ end of mRNA by recruiting the ribosome directly to an internal position on the mRNA.

ATP-binding cassette (ABC) family

A family of proteins that typically contain two nucleotide-binding domains (NBDs), which form two composite nucleotide-binding sites. The transition between the closed ATP-bound and open ADP-bound states induces a tweezer-like powerstroke between NBDs, which causes conformational changes in associated domains and/or macromolecules.

18S rRNA

Ribosomal RNA of the 40S ribosomal subunit. It determines the overall shape of the 40S subunit and is the main component of its decoding centre. It is also involved in formation of the main contacts between 40S and 60S ribosomal subunits.

A-site

The site on a ribosome that holds the new, incoming aminoacyl-tRNA.

E-site

The site on a ribosome that accommodates deacylated tRNA before it is released from the ribosome.

DEAD-box RNA helicase

An RNA helicase that contains the DEAD (Asp-Glu-Ala-Asp) or DExD/H (Asp-Glu-X-Asp,His; where X represents any amino acid) motifs. These proteins use the energy of ATP hydrolysis to unwind RNA.

RRM domain

(RNA-recognition motif). A protein domain that contains two short consensus sequences embedded in a structurally conserved region of 80 amino acids.

HEAT domain

A protein domain of 37–47 amino acids that consists of tandemly repeated pairs of antiparallel α-helices. HEAT domains have a superhelical structure and often function as protein–protein interaction surfaces.

GTPase-activating protein

A protein that stimulates the intrinsic ability of a GTPase to hydrolyse GTP to GDP.

Arginine finger

A catalytic residue that was first defined for RasGAPs, and that supplies a catalytic arginine residue into the active site of Ras to increase the reaction rate.

MicroRNA

A small RNA of 21 nucleotides that regulates the expression of mRNAs with which it is partially complementary in sequence.

KH domain

(K-homology domain). A protein domain, originally identified in the human hnRNP-K protein, that is important for RNA binding and probably binds RNA directly.

Argonaute

A family of proteins that are characterized by the presence of two homology domains: PAZ and PIWI. These proteins are essential for diverse RNA silencing pathways.

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Jackson, R., Hellen, C. & Pestova, T. The mechanism of eukaryotic translation initiation and principles of its regulation. Nat Rev Mol Cell Biol 11, 113–127 (2010). https://doi.org/10.1038/nrm2838

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