Abaeva,, I. S., Marintchev,, A., Pisareva,, V. P., Hellen,, C. U., & Pestova,, T. V. (2010). Bypassing of stems versus linear base‐by‐base inspection of mammalian mRNAs during ribosomal scanning. The EMBO Journal, 30(1), 115–129. https://doi.org/10.1038/emboj.2010.302
Abaeva,, I. S., Pestova,, T. V., & Hellen,, C. U. (2016). Attachment of ribosomal complexes and retrograde scanning during initiation on the Halastavi arva virus IRES. Nucleic Acids Research, 44(5), 2362–2377. https://doi.org/10.1093/nar/gkw016
Abdelhaleem,, M. (2005). RNA helicases: Regulators of differentiation. Clinical Biochemistry, 38(6), 499–503. https://doi.org/10.1016/j.clinbiochem.2005.01.010
Acker,, M. G., Shin,, B. S., Nanda,, J. S., Saini,, A. K., Dever,, T. E., & Lorsch,, J. R. (2009). Kinetic analysis of late steps of eukaryotic translation initiation. Journal of Molecular Biology, 385(2), 491–506. https://doi.org/10.1016/j.jmb.2008.10.029
Afonina,, Z. A., Myasnikov,, A. G., Shirokov,, V. A., Klaholz,, B. P., & Spirin,, A. S. (2014). Formation of circular polyribosomes on eukaryotic mRNA without cap‐structure and poly(A)‐tail: A cryo electron tomography study. Nucleic Acids Research, 42(14), 9461–9469. https://doi.org/10.1093/nar/gku599
Aitken,, C. E., & Lorsch,, J. R. (2012). A mechanistic overview of translation initiation in eukaryotes. Nature Structural %26 Molecular Biology, 19(6), 568–576. https://doi.org/10.1038/nsmb.2303
Akulich,, K. A., Andreev,, D. E., Terenin,, I. M., Smirnova,, V. V., Anisimova,, A. S., Makeeva,, D. S., … Dmitriev,, S. E. (2016). Four translation initiation pathways employed by the leaderless mRNA in eukaryotes. Scientific Reports, 6, 37905. https://doi.org/10.1038/srep37905
Algire,, M. A., Maag,, D., & Lorsch,, J. R. (2005). Pi release from eIF2, not GTP hydrolysis, is the step controlled by start‐site selection during eukaryotic translation initiation. Molecular Cell, 20(2), 251–262.
Alone,, P. V., & Dever,, T. E. (2006). Direct binding of translation initiation factor eIF2gamma‐G domain to its GTPase‐activating and GDP‐GTP exchange factors eIF5 and eIF2B epsilon. The Journal of Biological Chemistry, 281(18), 12636–12644. https://doi.org/10.1074/jbc.M511700200
Altmann,, M., Sonenberg,, N., & Trachsel,, H. (1989). Translation in Saccharomyces cerevisiae: Initiation factor 4E‐dependent cell‐free system. Molecular and Cellular Biology, 9(10), 4467–4472.
Andaya,, A., Villa,, N., Jia,, W., Fraser,, C. S., & Leary,, J. A. (2014). Phosphorylation stoichiometries of human eukaryotic initiation factors. International Journal of Molecular Sciences, 15(7), 11523–11538. https://doi.org/10.3390/ijms150711523
Anderson,, W. F., Bosch,, L., Gros,, F., Grunberg‐Manago,, M., Ochoa,, S., Rich,, A., & Staehelin,, T. (1974). Initiation of protein synthesis in prokaryotic and eukaryotic systems. Summary of EMBO workshop. FEBS Letters, 48(1), 1–6.
Andreev,, D. E., O`Connor,, P. B., Loughran,, G., Dmitriev,, S. E., Baranov,, P. V., & Shatsky,, I. N. (2017). Insights into the mechanisms of eukaryotic translation gained with ribosome profiling. Nucleic Acids Research, 45(2), 513–526. https://doi.org/10.1093/nar/gkw1190
Andreou,, A. Z., Harms,, U., & Klostermeier,, D. (2017). eIF4B stimulates eIF4A ATPase and unwinding activities by direct interaction through its 7‐repeats region. RNA Biology, 14(1), 113–123. https://doi.org/10.1080/15476286.2016.1259782
Archer,, S. K., Shirokikh,, N. E., Beilharz,, T. H., & Preiss,, T. (2016). Dynamics of ribosome scanning and recycling revealed by translation complex profiling. Nature, 535(7613), 570–574. https://doi.org/10.1038/nature18647
Archer,, S. K., Shirokikh,, N. E., Hallwirth,, C. V., Beilharz,, T. H., & Preiss,, T. (2015). Probing the closed‐loop model of mRNA translation in living cells. RNA Biology, 12(3), 248–254. https://doi.org/10.1080/15476286.2015.1017242
Arribas‐Layton,, M., Wu,, D., Lykke‐Andersen,, J., & Song,, H. (2013). Structural and functional control of the eukaryotic mRNA decapping machinery. Biochimica et Biophysica Acta, 1829(6–7), 580–589. https://doi.org/10.1016/j.bbagrm.2012.12.006
Asano,, K. (2014). Why is start codon selection so precise in eukaryotes? Translation, 2(1), e28387. https://doi.org/10.4161/trla.28387
Asano,, K., Clayton,, J., Shalev,, A., & Hinnebusch,, A. G. (2000). A multifactor complex of eukaryotic initiation factors, eIF1, eIF2, eIF3, eIF5, and initiator tRNA(Met) is an important translation initiation intermediate in vivo. Genes %26 Development, 14(19), 2534–2546.
Asano,, K., Phan,, L., Anderson,, J., & Hinnebusch,, A. G. (1998). Complex formation by all five homologues of mammalian translation initiation factor 3 subunits from yeast Saccharomyces cerevisiae. The Journal of Biological Chemistry, 273(29), 18573–18585.
Asano,, K., Shalev,, A., Phan,, L., Nielsen,, K., Clayton,, J., Valasek,, L., … Hinnebusch,, A. G. (2001). Multiple roles for the C‐terminal domain of eIF5 in translation initiation complex assembly and GTPase activation. The EMBO Journal, 20(9), 2326–2337.
Avdulov,, S., Herrera,, J., Smith,, K., Peterson,, M., Gomez‐Garcia,, J. R., Beadnell,, T. C., … Polunovsky,, V. A. (2015). eIF4E threshold levels differ in governing normal and neoplastic expansion of mammary stem and luminal progenitor cells. Cancer Research, 75(4), 687–697. https://doi.org/10.1158/0008-5472.CAN-14-2571
Aylett,, C. H., & Ban,, N. (2017). Eukaryotic aspects of translation initiation brought into focus. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, 372(1716), 20160186. https://doi.org/10.1098/rstb.2016.0186
Aylett,, C. H., Boehringer,, D., Erzberger,, J. P., Schaefer,, T., & Ban,, N. (2015). Structure of a yeast 40S‐eIF1‐eIF1A‐eIF3‐eIF3j initiation complex. Nature Structural %26 Molecular Biology, 22(3), 269–271. https://doi.org/10.1038/nsmb.2963
Ban,, N., Nissen,, P., Hansen,, J., Moore,, P. B., & Steitz,, T. A. (2000). The complete atomic structure of the large ribosomal subunit at 2.4 A resolution. Science, 289(5481), 905–920.
Baralle,, F. E., & Brownlee,, G. G. (1978). AUG is the only recognisable signal sequence in the 5′ non‐coding regions of eukaryotic mRNA. Nature, 274(5666), 84–87.
Baranov,, P. V., & Michel,, A. M. (2016). Illuminating translation with ribosome profiling spectra. Nature Methods, 13(2), 123–124. https://doi.org/10.1038/nmeth.3738
Baron‐Benhamou,, J., Fortes,, P., Inada,, T., Preiss,, T., & Hentze,, M. W. (2003). The interaction of the cap‐binding complex (CBC) with eIF4G is dispensable for translation in yeast. RNA, 9(6), 654–662.
Barondes,, S. H., & Nirenberg,, M. W. (1962). Fate of a synthetic polynucleotide directing cell‐free protein synthesis II. Association with ribosomes. Science, 138(3542), 813–817. https://doi.org/10.1126/science.138.3542.813
Beilharz,, T. H., & Preiss,, T. (2007). Widespread use of poly(A) tail length control to accentuate expression of the yeast transcriptome. RNA, 13(7), 982–997. https://doi.org/10.1261/rna.569407
Berset,, C., Zurbriggen,, A., Djafarzadeh,, S., Altmann,, M., & Trachsel,, H. (2003). RNA‐binding activity of translation initiation factor eIF4G1 from Saccharomyces cerevisiae. RNA, 9(7), 871–880.
Berthelot,, K., Muldoon,, M., Rajkowitsch,, L., Hughes,, J., & McCarthy,, J. E. (2004). Dynamics and processivity of 40S ribosome scanning on mRNA in yeast. Molecular Microbiology, 51(4), 987–1001.
Besse,, F., & Ephrussi,, A. (2008). Translational control of localized mRNAs: Restricting protein synthesis in space and time. Nature Reviews. Molecular Cell Biology, 9(12), 971–980. https://doi.org/10.1038/nrm2548
Bhat,, M., Robichaud,, N., Hulea,, L., Sonenberg,, N., Pelletier,, J., & Topisirovic,, I. (2015). Targeting the translation machinery in cancer. Nature Reviews. Drug Discovery, 14(4), 261–278. https://doi.org/10.1038/nrd4505
Bhattacharyya,, D., Diamond,, P., & Basu,, S. (2015). An independently folding RNA G‐quadruplex domain directly recruits the 40S ribosomal subunit. Biochemistry, 54(10), 1879–1885. https://doi.org/10.1021/acs.biochem.5b00091
Bieniossek,, C., Schutz,, P., Bumann,, M., Limacher,, A., Uson,, I., & Baumann,, U. (2006). The crystal structure of the carboxy‐terminal domain of human translation initiation factor eIF5. Journal of Molecular Biology, 360(2), 457–465. https://doi.org/10.1016/j.jmb.2006.05.021
Bitterman,, P. B., & Polunovsky,, V. A. (2012). Translational control of cell fate: From integration of environmental signals to breaching anticancer defense. Cell Cycle, 11(6), 1097–1107. https://doi.org/10.4161/cc.11.6.19610
Bogorad,, A. M., Lin,, K. Y., & Marintchev,, A. (2017). Novel mechanisms of eIF2B action and regulation by eIF2alpha phosphorylation. Nucleic Acids Research, 45(20), 11962–11979. https://doi.org/10.1093/nar/gkx845
Borman,, A. M., Michel,, Y. M., & Kean,, K. M. (2000). 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 Research, 28(21), 4068–4075.
Both,, G. W., Furuichi,, Y., Muthukrishnan,, S., & Shatkin,, A. J. (1975). Ribosome binding to reovirus mRNA in protein synthesis requires 5′ terminal 7‐methylguanosine. Cell, 6(2), 185–195.
Bramham,, C. R., Jensen,, K. B., & Proud,, C. G. (2016). Tuning Specific Translation in Cancer Metastasis and Synaptic Memory: Control at the MNK‐eIF4E Axis. Trends in Biochemical Sciences, 41(10), 847–858. https://doi.org/10.1016/j.tibs.2016.07.008
Brina,, D., Miluzio,, A., Ricciardi,, S., & Biffo,, S. (2015). eIF6 anti‐association activity is required for ribosome biogenesis, translational control and tumor progression. Biochimica et Biophysica Acta, 1849(7), 830–835. https://doi.org/10.1016/j.bbagrm.2014.09.010
Browning,, K. S., & Bailey‐Serres,, J. (2015). Mechanism of cytoplasmic mRNA translation. Arabidopsis Book, 13, e0176. https://doi.org/10.1199/tab.0176
Buchwald,, G., Ebert,, J., Basquin,, C., Sauliere,, J., Jayachandran,, U., Bono,, F., … Conti,, E. (2010). Insights into the recruitment of the NMD machinery from the crystal structure of a core EJC‐UPF3b complex. Proceedings of the National Academy of Sciences of the United States of America, 107(22), 10050–10055. https://doi.org/10.1073/pnas.1000993107
Caruthers,, J. M., Johnson,, E. R., & McKay,, D. B. (2000). Crystal structure of yeast initiation factor 4A, a DEAD‐box RNA helicase. Proceedings of the National Academy of Sciences of the United States of America, 97(24), 13080–13085. https://doi.org/10.1073/pnas.97.24.13080
Castagnetti,, S., Hentze,, M. W., Ephrussi,, A., & Gebauer,, F. (2000). Control of oskar mRNA translation by Bruno in a novel cell‐free system from Drosophila ovaries. Development, 127(5), 1063–1068.
Castello,, A., Fischer,, B., Eichelbaum,, K., Horos,, R., Beckmann,, B. M., Strein,, C., … Hentze,, M. W. (2012). Insights into RNA biology from an atlas of mammalian mRNA‐binding proteins. Cell, 149(6), 1393–1406. https://doi.org/10.1016/j.cell.2012.04.031
Cate,, J. H. (2017). Human eIF3: From `blobology` to biological insight. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, 372(1716), 20160176. https://doi.org/10.1098/rstb.2016.0176
Cate,, J. H., Yusupov,, M. M., Yusupova,, G. Z., Earnest,, T. N., & Noller,, H. F. (1999). X‐ray crystal structures of 70S ribosome functional complexes. Science, 285(5436), 2095–2104.
Chapat,, C., Jafarnejad,, S. M., Matta‐Camacho,, E., Hesketh,, G. G., Gelbart,, I. A., Attig,, J., … Sonenberg,, N. (2017). Cap‐binding protein 4EHP effects translation silencing by microRNAs. Proceedings of the National Academy of Sciences of the United States of America, 114(21), 5425–5430. https://doi.org/10.1073/pnas.1701488114
Chappell,, S. A., Edelman,, G. M., & Mauro,, V. P. (2006). Ribosomal tethering and clustering as mechanisms for translation initiation. Proceedings of the National Academy of Sciences of the United States of America, 103(48), 18077–18082. https://doi.org/10.1073/pnas.0608212103
Charlesworth,, A., Meijer,, H. A., & de Moor,, C. H. (2013). Specificity factors in cytoplasmic polyadenylation. WIREs RNA, 4(4), 437–461. https://doi.org/10.1002/wrna.1171
Chen,, C. Y., & Sarnow,, P. (1995). Initiation of protein synthesis by the eukaryotic translational apparatus on circular RNAs. Science, 268(5209), 415–417.
Chen,, H., Meisburger,, S. P., Pabit,, S. A., Sutton,, J. L., Webb,, W. W., & Pollack,, L. (2012). Ionic strength‐dependent persistence lengths of single‐stranded RNA and DNA. Proceedings of the National Academy of Sciences of the United States of America, 109(3), 799–804. https://doi.org/10.1073/pnas.1119057109
Cheng,, S., Sultana,, S., Goss,, D. J., & Gallie,, D. R. (2008). Translation initiation factor 4B homodimerization, RNA binding, and interaction with Poly(A)‐binding protein are enhanced by zinc. The Journal of Biological Chemistry, 283(52), 36140–36153. https://doi.org/10.1074/jbc.M807716200
Cheung,, Y. N., Maag,, D., Mitchell,, S. F., Fekete,, C. A., Algire,, M. A., Takacs,, J. E., … Hinnebusch,, A. G. (2007). Dissociation of eIF1 from the 40S ribosomal subunit is a key step in start codon selection in vivo. Genes %26 Development, 21(10), 1217–1230.
Chi,, Q., Wang,, G., & Jiang,, J. (2013). The persistence length and length per base of single‐stranded DNA obtained from fluorescence correlation spectroscopy measurements using mean field theory. Physica A: Statistical Mechanics and its Applications, 392(5), 1072–1079. https://doi.org/10.1016/j.physa.2012.09.022
Choi,, S. K., Lee,, J. H., Zoll,, W. L., Merrick,, W. C., & Dever,, T. E. (1998). Promotion of met‐tRNAiMet binding to ribosomes by yIF2, a bacterial IF2 homolog in yeast. Science, 280(5370), 1757–1760.
Choudhuri,, A., Maitra,, U., & Evans,, T. (2013). Translation initiation factor eIF3h targets specific transcripts to polysomes during embryogenesis. Proceedings of the National Academy of Sciences of the United States of America, 110(24), 9818–9823. https://doi.org/10.1073/pnas.1302934110
Christensen,, A. K., & Bourne,, C. M. (1999). Shape of large bound polysomes in cultured fibroblasts and thyroid epithelial cells. The Anatomical Record, 255(2), 116–129.
Chu,, J., Cargnello,, M., Topisirovic,, I., & Pelletier,, J. (2016). Translation initiation factors: Reprogramming protein synthesis in cancer. Trends in Cell Biology, 26(12), 918–933. https://doi.org/10.1016/j.tcb.2016.06.005
Clancy,, J. L., Wei,, G. H., Echner,, N., Humphreys,, D. T., Beilharz,, T. H., & Preiss,, T. (2011). mRNA isoform diversity can obscure detection of miRNA‐mediated control of translation. RNA, 17(6), 1025–1031. https://doi.org/10.1261/rna.2567611
Clayton,, C. E. (2016). Gene expression in Kinetoplastids. Current Opinion in Microbiology, 32, 46–51. https://doi.org/10.1016/j.mib.2016.04.018
Clemons, Jr., W. M., May,, J. L., Wimberly,, B. T., McCutcheon,, J. P., Capel,, M. S., & Ramakrishnan,, V. (1999). Structure of a bacterial 30S ribosomal subunit at 5.5 A resolution. Nature, 400(6747), 833–840. https://doi.org/10.1038/23631
Coldwell,, M. J., Sack,, U., Cowan,, J. L., Barrett,, R. M., Vlasak,, M., Sivakumaran,, K., & Morley,, S. J. (2012). Multiple isoforms of the translation initiation factor eIF4GII are generated via use of alternative promoters, splice sites and a non‐canonical initiation codon. The Biochemical Journal, 448(1), 1–11. https://doi.org/10.1042/BJ20111765
Conte,, M. R., Kelly,, G., Babon,, J., Sanfelice,, D., Youell,, J., Smerdon,, S. J., & Proud,, C. G. (2006). Structure of the eukaryotic initiation factor (eIF) 5 reveals a fold common to several translation factors. Biochemistry, 45(14), 4550–4558. https://doi.org/10.1021/bi052387u
Cuchalova,, L., Kouba,, T., Herrmannova,, A., Danyi,, I., Chiu,, W. L., & Valasek,, L. (2010). The RNA recognition motif of eukaryotic translation initiation factor 3g (eIF3g) is required for resumption of scanning of posttermination ribosomes for reinitiation on GCN4 and together with eIF3i stimulates linear scanning. Molecular and Cellular Biology, 30(19), 4671–4686. https://doi.org/10.1128/MCB.00430-10
D`Ambrogio,, A., Nagaoka,, K., & Richter,, J. D. (2013). Translational control of cell growth and malignancy by the CPEBs. Nature Reviews. Cancer, 13(4), 283–290. https://doi.org/10.1038/nrc3485
de Breyne,, S., Simonet,, V., Pelet,, T., & Curran,, J. (2003). Identification of a cis‐acting element required for shunt‐mediated translational initiation of the Sendai virus Y proteins. Nucleic Acids Research, 31(2), 608–618.
Decroly,, E., & Canard,, B. (2017). Biochemical principles and inhibitors to interfere with viral capping pathways. Current Opinion in Virology, 24, 87–96. https://doi.org/10.1016/j.coviro.2017.04.003
Delagoutte,, E., & von Hippel,, P. H. (2001). Molecular mechanisms of the functional coupling of the helicase (gp41) and polymerase (gp43) of bacteriophage T4 within the DNA replication fork. Biochemistry, 40(14), 4459–4477.
des Georges,, A., Dhote,, V., Kuhn,, L., Hellen,, C. U., Pestova,, T. V., Frank,, J., & Hashem,, Y. (2015). Structure of mammalian eIF3 in the context of the 43S preinitiation complex. Nature, 525(7570), 491–495. https://doi.org/10.1038/nature14891
Dhote,, V., Sweeney,, T. R., Kim,, N., Hellen,, C. U., & Pestova,, T. V. (2012). Roles of individual domains in the function of DHX29, an essential factor required for translation of structured mammalian mRNAs. Proceedings of the National Academy of Sciences of the United States of America, 109(46), E3150–E3159. https://doi.org/10.1073/pnas.1208014109
Dmitriev,, S. E., Terenin,, I. M., Andreev,, D. E., Ivanov,, P. A., Dunaevsky,, J. E., Merrick,, W. C., & Shatsky,, I. N. (2010). GTP‐independent tRNA delivery to the ribosomal P‐site by a novel eukaryotic translation factor. The Journal of Biological Chemistry, 285(35), 26779–26787. https://doi.org/10.1074/jbc.M110.119693
Dominguez,, D. I., Ryabova,, L. A., Pooggin,, M. M., Schmidt‐Puchta,, W., Futterer,, J., & Hohn,, T. (1998). Ribosome shunting in cauliflower mosaic virus. Identification of an essential and sufficient structural element. The Journal of Biological Chemistry, 273(6), 3669–3678.
Dong,, J., Munoz,, A., Kolitz,, S. E., Saini,, A. K., Chiu,, W. L., Rahman,, H., … Hinnebusch,, A. G. (2014). Conserved residues in yeast initiator tRNA calibrate initiation accuracy by regulating preinitiation complex stability at the start codon. Genes %26 Development, 28(5), 502–520. https://doi.org/10.1101/gad.236547.113
Dresios,, J., Chappell,, S. A., Zhou,, W., & Mauro,, V. P. (2006). An mRNA‐rRNA base‐pairing mechanism for translation initiation in eukaryotes. Nature Structural %26 Molecular Biology, 13(1), 30–34. https://doi.org/10.1038/nsmb1031
Duncan,, R., Milburn,, S. C., & Hershey,, J. W. (1987). Regulated phosphorylation and low abundance of HeLa cell initiation factor eIF‐4F suggest a role in translational control. Heat shock effects on eIF‐4F. The Journal of Biological Chemistry, 262(1), 380–388.
Elfakess,, R., & Dikstein,, R. (2008). A translation initiation element specific to mRNAs with very short 5`UTR that also regulates transcription. PLoS One, 3(8), e3094. https://doi.org/10.1371/journal.pone.0003094
Elfakess,, R., Sinvani,, H., Haimov,, O., Svitkin,, Y., Sonenberg,, N., & Dikstein,, R. (2011). Unique translation initiation of mRNAs‐containing TISU element. Nucleic Acids Research, 39(17), 7598–7609. https://doi.org/10.1093/nar/gkr484
Elkon,, R., Ugalde,, A. P., & Agami,, R. (2013). Alternative cleavage and polyadenylation: Extent, regulation and function. Nature Reviews. Genetics, 14(7), 496–506. https://doi.org/10.1038/nrg3482
Emanuilov,, I., Sabatini,, D. D., Lake,, J. A., & Freienstein,, C. (1978). Localization of eukaryotic initiation factor 3 on native small ribosomal subunits. Proceedings of the National Academy of Sciences of the United States of America, 75(3), 1389–1393.
Erzberger,, J. P., Stengel,, F., Pellarin,, R., Zhang,, S., Schaefer,, T., Aylett,, C. H., … Ban,, N. (2014). Molecular architecture of the 40SeIF1eIF3 translation initiation complex. Cell, 158(5), 1123–1135. https://doi.org/10.1016/j.cell.2014.07.044
Fabian,, M. R., Sonenberg,, N., & Filipowicz,, W. (2010). Regulation of mRNA translation and stability by microRNAs. Annual Review of Biochemistry, 79, 351–379. https://doi.org/10.1146/annurev-biochem-060308-103103
Fan,, S., Jia,, M. Z., & Gong,, W. (2010). Crystal structure of the C‐terminal region of human p97/DAP5. Proteins, 78(10), 2385–2390. https://doi.org/10.1002/prot.22735
Faye,, M. D., & Holcik,, M. (2015). The role of IRES trans‐acting factors in carcinogenesis. Biochimica et Biophysica Acta, 1849(7), 887–897. https://doi.org/10.1016/j.bbagrm.2014.09.012
Fekete,, C. A., Mitchell,, S. F., Cherkasova,, V. A., Applefield,, D., Algire,, M. A., Maag,, D., … Hinnebusch,, A. G. (2007). N‐ and C‐terminal residues of eIF1A have opposing effects on the fidelity of start codon selection. The EMBO Journal, 26(6), 1602–1614.
Fernandez,, I. S., Bai,, X. C., Hussain,, T., Kelley,, A. C., Lorsch,, J. R., Ramakrishnan,, V., & Scheres,, S. H. (2013). Molecular architecture of a eukaryotic translational initiation complex. Science, 342(6160), 1240585. https://doi.org/10.1126/science.1240585
Fijalkowska,, D., Verbruggen,, S., Ndah,, E., Jonckheere,, V., Menschaert,, G., & Van Damme,, P. (2017). eIF1 modulates the recognition of suboptimal translation initiation sites and steers gene expression via uORFs. Nucleic Acids Research, 45(13), 7997–8013. https://doi.org/10.1093/nar/gkx469
Fleming,, K., Ghuman,, J., Yuan,, X., Simpson,, P., Szendroi,, A., Matthews,, S., & Curry,, S. (2003). Solution structure and RNA interactions of the RNA recognition motif from eukaryotic translation initiation factor 4B. Biochemistry, 42(30), 8966–8975. https://doi.org/10.1021/bi034506g
Fletcher,, C. M., Pestova,, T. V., Hellen,, C. U., & Wagner,, G. (1999). Structure and interactions of the translation initiation factor eIF1. The EMBO Journal, 18(9), 2631–2637.
Frank,, J. (2017). The mechanism of translation. F1000Research, 6, 198. https://doi.org/10.12688/f1000research.9760.1
Frank,, J., & Gonzalez, Jr., R. L. (2010). Structure and dynamics of a processive Brownian motor: The translating ribosome. Annual Review of Biochemistry, 79, 381–412. https://doi.org/10.1146/annurev-biochem-060408-173330
Fraser,, C. S. (2015). Quantitative studies of mRNA recruitment to the eukaryotic ribosome. Biochimie, 114, 58–71. https://doi.org/10.1016/j.biochi.2015.02.017
Fraser,, C. S., Lee,, J. Y., Mayeur,, G. L., Bushell,, M., Doudna,, J. A., & Hershey,, J. W. (2004). The j‐subunit of human translation initiation factor eIF3 is required for the stable binding of eIF3 and its subcomplexes to 40 S ribosomal subunits in vitro. The Journal of Biological Chemistry, 279(10), 8946–8956.
Freire,, E. R., Sturm,, N. R., Campbell,, D. A., & de Melo Neto,, O. P. (2017). The role of cytoplasmic mRNA cap‐binding protein complexes in Trypanosoma brucei and other Trypanosomatids. Pathogens, 6(4), 55. https://doi.org/10.3390/pathogens6040055
Frydryskova,, K., Masek,, T., Borcin,, K., Mrvova,, S., Venturi,, V., & Pospisek,, M. (2016). Distinct recruitment of human eIF4E isoforms to processing bodies and stress granules. BMC Molecular Biology, 17(1), 21. https://doi.org/10.1186/s12867-016-0072-x
Fuchs,, G., Petrov,, A. N., Marceau,, C. D., Popov,, L. M., Chen,, J., O`Leary,, S. E., … Puglisi,, J. D. (2015). Kinetic pathway of 40S ribosomal subunit recruitment to hepatitis C virus internal ribosome entry site. Proceedings of the National Academy of Sciences of the United States of America, 112(2), 319–325. https://doi.org/10.1073/pnas.1421328111
Furuichi,, Y. (2014). Caps on eukaryotic mRNAs. In eLS. Chichester: John Wiley %26 Sons Ltd.
Futterer,, J., Kiss‐Laszlo,, Z., & Hohn,, T. (1993). Nonlinear ribosome migration on cauliflower mosaic virus 35S RNA. Cell, 73(4), 789–802.
Gandin,, V., Masvidal,, L., Hulea,, L., Gravel,, S. P., Cargnello,, M., McLaughlan,, S., … Topisirovic,, I. (2016). nanoCAGE reveals 5` UTR features that define specific modes of translation of functionally related MTOR‐sensitive mRNAs. Genome Research, 26(5), 636–648. https://doi.org/10.1101/gr.197566.115
Garcia‐Garcia,, C., Frieda,, K. L., Feoktistova,, K., Fraser,, C. S., & Block,, S. M. (2015). RNA BIOCHEMISTRY. Factor‐dependent processivity in human eIF4A DEAD‐box helicase. Science, 348(6242), 1486–1488. https://doi.org/10.1126/science.aaa5089
Gebauer,, F., & Hentze,, M. W. (2004). Molecular mechanisms of translational control. Nature Reviews. Molecular Cell Biology, 5(10), 827–835.
Gebauer,, F., Preiss,, T., & Hentze,, M. W. (2012). From cis‐regulatory elements to complex RNPs and back. Cold Spring Harbor Perspectives in Biology, 4(7), a012245. https://doi.org/10.1101/cshperspect.a012245
Ghosh,, S., & Lasko,, P. (2015). Loss‐of‐function analysis reveals distinct requirements of the translation initiation factors eIF4E, eIF4E‐3, eIF4G and eIF4G2 in Drosophila spermatogenesis. PLoS One, 10(4), e0122519. https://doi.org/10.1371/journal.pone.0122519
Gilbert,, R. J., Gordiyenko,, Y., von der Haar,, T., Sonnen,, A. F., Hofmann,, G., Nardelli,, M., … McCarthy,, J. E. (2007). Reconfiguration of yeast 40S ribosomal subunit domains by the translation initiation multifactor complex. Proceedings of the National Academy of Sciences of the United States of America, 104(14), 5788–5793. https://doi.org/10.1073/pnas.0606880104
Gingras,, A. C., Raught,, B., & Sonenberg,, N. (1999). eIF4 initiation factors: Effectors of mRNA recruitment to ribosomes and regulators of translation. Annual Review of Biochemistry, 68, 913–963. https://doi.org/10.1146/annurev.biochem.68.1.913
Green,, K. M., Glineburg,, M. R., Kearse,, M. G., Flores,, B. N., Linsalata,, A. E., Fedak,, S. J., … Todd,, P. K. (2017). RAN translation at C9orf72‐associated repeat expansions is selectively enhanced by the integrated stress response. Nature Communications, 8(1), 2005. https://doi.org/10.1038/s41467-017-02200-0
Green,, K. M., Linsalata,, A. E., & Todd,, P. K. (2016). RAN translation‐What makes it run? Brain Research, 1647, 30–42. https://doi.org/10.1016/j.brainres.2016.04.003
Gross,, J. D., Moerke,, N. J., von der Haar,, T., Lugovskoy,, A. A., Sachs,, A. B., McCarthy,, J. E., & Wagner,, G. (2003). Ribosome loading onto the mRNA cap is driven by conformational coupling between eIF4G and eIF4E. Cell, 115(6), 739–750.
Gruner,, S., Peter,, D., Weber,, R., Wohlbold,, L., Chung,, M. Y., Weichenrieder,, O., … Izaurralde,, E. (2016). The structures of eIF4E‐eIF4G complexes reveal an extended Interface to regulate translation initiation. Molecular Cell, 64(3), 467–479. https://doi.org/10.1016/j.molcel.2016.09.020
Gualerzi,, C., Risuleo,, G., & Pon,, C. L. (1977). Initial rate kinetic analysis of the mechanism of initiation complex formation and the role of initiation factor IF‐3. Biochemistry, 16(8), 1684–1689.
Gunisova,, S., Beznoskova,, P., Mohammad,, M. P., Vlckova,, V., & Valasek,, L. S. (2016). In‐depth analysis of cis‐determinants that either promote or inhibit reinitiation on GCN4 mRNA after translation of its four short uORFs. RNA, 22(4), 542–558. https://doi.org/10.1261/rna.055046.115
Gunisova,, S., & Valasek,, L. S. (2014). Fail‐safe mechanism of GCN4 translational control—uORF2 promotes reinitiation by analogous mechanism to uORF1 and thus secures its key role in GCN4 expression. Nucleic Acids Research, 42(9), 5880–5893. https://doi.org/10.1093/nar/gku204
Haimov,, O., Sinvani,, H., & Dikstein,, R. (2015). Cap‐dependent, scanning‐free translation initiation mechanisms. Biochimica et Biophysica Acta, 1849(11), 1313–1318. https://doi.org/10.1016/j.bbagrm.2015.09.006
Halstead,, J. M., Lionnet,, T., Wilbertz,, J. H., Wippich,, F., Ephrussi,, A., Singer,, R. H., & Chao,, J. A. (2015). Translation. An RNA biosensor for imaging the first round of translation from single cells to living animals. Science, 347(6228), 1367–1671. https://doi.org/10.1126/science.aaa3380
Han,, S. J., Vaccari,, S., Nedachi,, T., Andersen,, C. B., Kovacina,, K. S., Roth,, R. A., & Conti,, M. (2006). Protein kinase B/Akt phosphorylation of PDE3A and its role in mammalian oocyte maturation. The EMBO Journal, 25(24), 5716–5725. https://doi.org/10.1038/sj.emboj.7601431
Harding,, H. P., Novoa,, I., Zhang,, Y., Zeng,, H., Wek,, R., Schapira,, M., & Ron,, D. (2000). Regulated translation initiation controls stress‐induced gene expression in mammalian cells. Molecular Cell, 6(5), 1099–1108.
Harrison,, P. F., Powell,, D. R., Clancy,, J. L., Preiss,, T., Boag,, P. R., Traven,, A., … Beilharz,, T. H. (2015). PAT‐seq: A method to study the integration of 3`‐UTR dynamics with gene expression in the eukaryotic transcriptome. RNA, 21(8), 1502–1510. https://doi.org/10.1261/rna.048355.114
Hashem,, Y., des Georges,, A., Dhote,, V., Langlois,, R., Liao,, H. Y., Grassucci,, R. A., … Frank,, J. (2013a). Structure of the mammalian ribosomal 43S preinitiation complex bound to the scanning factor DHX29. Cell, 153(5), 1108–1119. https://doi.org/10.1016/j.cell.2013.04.036
Hashem,, Y., des Georges,, A., Dhote,, V., Langlois,, R., Liao,, H. Y., Grassucci,, R. A., … Frank,, J. (2013b). Hepatitis‐C‐virus‐like internal ribosome entry sites displace eIF3 to gain access to the 40S subunit. Nature, 503(7477), 539–543. https://doi.org/10.1038/nature12658
He,, H., von der Haar,, T., Singh,, C. R., Ii,, M., Li,, B., Hinnebusch,, A. G., … Asano,, K. (2003). The yeast eukaryotic initiation factor 4G (eIF4G) HEAT domain interacts with eIF1 and eIF5 and is involved in stringent AUG selection. Molecular and Cellular Biology, 23(15), 5431–5445.
Hecht,, A., Glasgow,, J., Jaschke,, P. R., Bawazer,, L. A., Munson,, M. S., Cochran,, J. R., … Salit,, M. (2017). Measurements of translation initiation from all 64 codons in E. coli. Nucleic Acids Research, 45(7), 3615–3626. https://doi.org/10.1093/nar/gkx070
Hellens,, R. P., Brown,, C. M., Chisnall,, M. A., Waterhouse,, P. M., & Macknight,, R. C. (2016). The emerging world of small ORFs. Trends in Plant Science, 21(4), 317–328. https://doi.org/10.1016/j.tplants.2015.11.005
Hemmings‐Mieszczak,, M., & Hohn,, T. (1999). A stable hairpin preceded by a short open reading frame promotes nonlinear ribosome migration on a synthetic mRNA leader. RNA, 5(9), 1149–1157.
Hemmings‐Mieszczak,, M., Hohn,, T., & Preiss,, T. (2000). Termination and peptide release at the upstream open reading frame are required for downstream translation on synthetic shunt‐competent mRNA leaders. Molecular and Cellular Biology, 20(17), 6212–6223.
Hentze,, M. W., Castello,, A., Schwarzl,, T., & Preiss,, T. (2018). A brave new world of RNA‐binding proteins. Nature Reviews Molecular Cell Biology. https://doi.org/10.1038/nrm.2017.130
Hershey,, J. W. (2010). Regulation of protein synthesis and the role of eIF3 in cancer. Brazilian Journal of Medical and Biological Research, 43(10), 920–930.
Hershey,, J. W., Sonenberg,, N., & Mathews,, M. B. (2012). Principles of translational control: An overview. Cold Spring Harbor Perspectives in Biology, 4(12), a011528. https://doi.org/10.1101/cshperspect.a011528
Hershey,, J. W., Yanov,, J., & Fakunding,, J. L. (1979). Purification of protein synthesis initiation factors IF‐1, IF‐2, and IF‐3 from Escherichia coli. Methods in Enzymology, 60, 3–11.
Heywood,, S. M. (1973). Letter: Is there specificity in the initiation of protein synthesis in eukaryotic cells? Developmental Biology, 31(1), F1–F2.
Hinnebusch,, A. G. (2005). Translational regulation of GCN4 and the general amino acid control of yeast. Annual Review of Microbiology, 59(1), 407–450. https://doi.org/10.1146/annurev.micro.59.031805.133833
Hinnebusch,, A. G. (2014). The scanning mechanism of eukaryotic translation initiation. Annual Review of Biochemistry, 83, 779–812. https://doi.org/10.1146/annurev-biochem-060713-035802
Hinnebusch,, A. G. (2017). Structural insights into the mechanism of scanning and start codon recognition in eukaryotic translation initiation. Trends in Biochemical Sciences, 42(8), 589–611. https://doi.org/10.1016/j.tibs.2017.03.004
Hinnebusch,, A. G., Asano,, K., Olsen,, D. S., Phan,, L., Nielsen,, K. H., & Valasek,, L. (2004). Study of translational control of eukaryotic gene expression using yeast. Annals of the New York Academy of Sciences, 1038, 60–74. https://doi.org/10.1196/annals.1315.012
Hinnebusch,, A. G., Ivanov,, I. P., & Sonenberg,, N. (2016). Translational control by 5′‐untranslated regions of eukaryotic mRNAs. Science, 352(6292), 1413–1416. https://doi.org/10.1126/science.aad9868
Hsu,, H. L., Shi,, B., & Gartenhaus,, R. B. (2005). The MCT‐1 oncogene product impairs cell cycle checkpoint control and transforms human mammary epithelial cells. Oncogene, 24(31), 4956–4964. https://doi.org/10.1038/sj.onc.1208680
Hu,, M. C., Tranque,, P., Edelman,, G. M., & Mauro,, V. P. (1999). rRNA‐complementarity in the 5′ untranslated region of mRNA specifying the Gtx homeodomain protein: Evidence that base‐ pairing to 18S rRNA affects translational efficiency. Proceedings of the National Academy of Sciences of the United States of America, 96(4), 1339–1344.
Humphreys,, D. T., Westman,, B. J., Martin,, D. I., & Preiss,, T. (2005). MicroRNAs control translation initiation by inhibiting eukaryotic initiation factor 4E/cap and poly(A) tail function. Proceedings of the National Academy of Sciences of the United States of America, 102(47), 16961–16966. https://doi.org/10.1073/pnas.0506482102
Hussain,, T., Llacer,, J. L., Fernandez,, I. S., Munoz,, A., Martin‐Marcos,, P., Savva,, C. G., … Ramakrishnan,, V. (2014). Structural changes enable start codon recognition by the eukaryotic translation initiation complex. Cell, 159(3), 597–607. https://doi.org/10.1016/j.cell.2014.10.001
Hussain,, T., Llacer,, J. L., Wimberly,, B. T., Kieft,, J. S., & Ramakrishnan,, V. (2016). Large‐scale movements of IF3 and tRNA during bacterial translation initiation. Cell, 167(1), 133–144. https://doi.org/10.1016/j.cell.2016.08.074
Ingolia,, N. T., Ghaemmaghami,, S., Newman,, J. R., & Weissman,, J. S. (2009). Genome‐wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science, 324(5924), 218–223. https://doi.org/10.1126/science.1168978
Ingolia,, N. T., Lareau,, L. F., & Weissman,, J. S. (2011). Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes. Cell, 147(4), 789–802. https://doi.org/10.1016/j.cell.2011.10.002
Ivanov,, I. P., Loughran,, G., Sachs,, M. S., & Atkins,, J. F. (2010). Initiation context modulates autoregulation of eukaryotic translation initiation factor 1 (eIF1). Proceedings of the National Academy of Sciences of the United States of America, 107(42), 18056–18060. https://doi.org/10.1073/pnas.1009269107
Jackson,, R., & Standart,, N. (2015). The awesome power of ribosome profiling. RNA, 21(4), 652–654. https://doi.org/10.1261/rna.049908.115
Jackson,, R. J. (2013). The current status of vertebrate cellular mRNA IRESs. Cold Spring Harbor Perspectives in Biology, 5(2), a011569. https://doi.org/10.1101/cshperspect.a011569
Jackson,, R. J., Hellen,, C. U., & Pestova,, T. V. (2010). The mechanism of eukaryotic translation initiation and principles of its regulation. Nature Reviews. Molecular Cell Biology, 11(2), 113–127. https://doi.org/10.1038/nrm2838
Jackson,, R. J., Hellen,, C. U., & Pestova,, T. V. (2012). Termination and post‐termination events in eukaryotic translation. Advances in Protein Chemistry and Structural Biology, 86, 45–93. https://doi.org/10.1016/B978-0-12-386497-0.00002-5
Jalkanen,, A. L., Coleman,, S. J., & Wilusz,, J. (2014). Determinants and implications of mRNA poly(A) tail size—does this protein make my tail look big? Seminars in Cell %26 Developmental Biology, 34, 24–32. https://doi.org/10.1016/j.semcdb.2014.05.018
Jang,, S. K., & Paek,, K. Y. (2016). Cap‐dependent translation is mediated by `RNA looping` rather than `ribosome scanning`. RNA Biology, 13(1), 1–5. https://doi.org/10.1080/15476286.2015.1107700
Jansen,, R. P., Niessing,, D., Baumann,, S., & Feldbrugge,, M. (2014). mRNA transport meets membrane traffic. Trends in Genetics, 30(9), 408–417. https://doi.org/10.1016/j.tig.2014.07.002
Jennings,, M. D., Kershaw,, C. J., Adomavicius,, T., & Pavitt,, G. D. (2017). Fail‐safe control of translation initiation by dissociation of eIF2alpha phosphorylated ternary complexes. eLife, 6, e24542. https://doi.org/10.7554/eLife.24542
Jennings,, M. D., Kershaw,, C. J., White,, C., Hoyle,, D., Richardson,, J. P., Costello,, J. L., … Pavitt,, G. D. (2016). eIF2beta is critical for eIF5‐mediated GDP‐dissociation inhibitor activity and translational control. Nucleic Acids Research, 44(20), 9698–9709. https://doi.org/10.1093/nar/gkw657
Jennings,, M. D., & Pavitt,, G. D. (2014). A new function and complexity for protein translation initiation factor eIF2B. Cell Cycle, 13(17), 2660–2665. https://doi.org/10.4161/15384101.2014.948797
Jivotovskaya,, A. V., Valasek,, L., Hinnebusch,, A. G., & Nielsen,, K. H. (2006). Eukaryotic translation initiation factor 3 (eIF3) and eIF2 can promote mRNA binding to 40S subunits independently of eIF4G in yeast. Molecular and Cellular Biology, 26(4), 1355–1372. https://doi.org/10.1128/MCB.26.4.1355-1372.2006
Johnson,, A. G., Grosely,, R., Petrov,, A. N., & Puglisi,, J. D. (2017). Dynamics of IRES‐mediated translation. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, 372(1716), 20160177. https://doi.org/10.1098/rstb.2016.0177
Joshi,, C. P., Zhou,, H., Huang,, X., & Chiang,, V. L. (1997). Context sequences of translation initiation codon in plants. Plant Molecular Biology, 35(6), 993–1001.
Kahvejian,, A., Svitkin,, Y. V., Sukarieh,, R., M`Boutchou,, M. N., & Sonenberg,, N. (2005). Mammalian poly(A)‐binding protein is a eukaryotic translation initiation factor, which acts via multiple mechanisms. Genes %26 Development, 19(1), 104–113. https://doi.org/10.1101/gad.1262905
Kamenska,, A., Simpson,, C., & Standart,, N. (2014). eIF4E‐binding proteins: New factors, new locations, new roles. Biochemical Society Transactions, 42(4), 1238–1245. https://doi.org/10.1042/BST20140063
Kaminishi,, T., Wilson,, D. N., Takemoto,, C., Harms,, J. M., Kawazoe,, M., Schluenzen,, F., … Yokoyama,, S. (2007). A snapshot of the 30S ribosomal subunit capturing mRNA via the Shine–Dalgarno interaction. Structure, 15(3), 289–297. https://doi.org/10.1016/j.str.2006.12.008
Kang,, M. K., & Han,, S. J. (2011). Post‐transcriptional and post‐translational regulation during mouse oocyte maturation. BMB Reports, 44(3), 147–157. https://doi.org/10.5483/BMBRep.2011.44.3.147
Kanitz,, A., Gypas,, F., Gruber,, A. J., Gruber,, A. R., Martin,, G., & Zavolan,, M. (2015). Comparative assessment of methods for the computational inference of transcript isoform abundance from RNA‐seq data. Genome Biology, 16, 150. https://doi.org/10.1186/s13059-015-0702-5
Karaskova,, M., Gunisova,, S., Herrmannova,, A., Wagner,, S., Munzarova,, V., & Valasek,, L. (2012). Functional characterization of the role of the N‐terminal domain of the c/Nip1 subunit of eukaryotic initiation factor 3 (eIF3) in AUG recognition. The Journal of Biological Chemistry, 287(34), 28420–28434. https://doi.org/10.1074/jbc.M112.386656
Kasiappan,, R., Shih,, H. J., Chu,, K. L., Chen,, W. T., Liu,, H. P., Huang,, S. F., … Hsu,, H. L. (2009). Loss of p53 and MCT‐1 overexpression synergistically promote chromosome instability and tumorigenicity. Molecular Cancer Research, 7(4), 536–548. https://doi.org/10.1158/1541-7786.MCR-08-0422
Kearse,, M. G., & Wilusz,, J. E. (2017). Non‐AUG translation: A new start for protein synthesis in eukaryotes. Genes %26 Development, 31(17), 1717–1731. https://doi.org/10.1101/gad.305250.117
Kim,, S., Streets,, A. M., Lin,, R. R., Quake,, S. R., Weiss,, S., & Majumdar,, D. S. (2011). High‐throughput single‐molecule optofluidic analysis. Nature Methods, 8(3), 242–245. https://doi.org/10.1038/nmeth.1569
Klein,, C., Terrao,, M., Inchaustegui Gil,, D., & Clayton,, C. (2015). Polysomes of Trypanosoma brucei: Association with initiation factors and RNA‐binding proteins. PLoS One, 10(8), e0135973. https://doi.org/10.1371/journal.pone.0135973
Koh,, D. C., Edelman,, G. M., & Mauro,, V. P. (2013). Physical evidence supporting a ribosomal shunting mechanism of translation initiation for BACE1 mRNA. Translation (Austin), 1(1), e24400. https://doi.org/10.4161/trla.24400
Kolitz,, S. E., & Lorsch,, J. R. (2010). Eukaryotic initiator tRNA: Finely tuned and ready for action. FEBS Letters, 584(2), 396–404. https://doi.org/10.1016/j.febslet.2009.11.047
Kolupaeva,, V. G., Pestova,, T. V., & Hellen,, C. U. (2000). An enzymatic footprinting analysis of the interaction of 40S ribosomal subunits with the internal ribosomal entry site of hepatitis C virus. Journal of Virology, 74(14), 6242–6250.
Konagurthu,, A. S., Whisstock,, J. C., Stuckey,, P. J., & Lesk,, A. M. (2006). MUSTANG: a multiple structural alignment algorithm. Proteins, 64(3), 559–574. https://doi.org/10.1002/prot.20921
Korostelev,, A., & Noller,, H. F. (2007). The ribosome in focus: New structures bring new insights. Trends in Biochemical Sciences, 32(9), 434–441. https://doi.org/10.1016/j.tibs.2007.08.002
Kozak,, M. (1978). How do eucaryotic ribosomes select initiation regions in messenger RNA? Cell, 15(4), 1109–1123.
Kozak,, M. (1979). Inability of circular mRNA to attach to eukaryotic ribosomes. Nature, 280(5717), 82–85.
Kozak,, M. (1980). Influence of mRNA secondary structure on binding and migration of 40S ribosomal subunits. Cell, 19(1), 79–90.
Kozak,, M. (1987). An analysis of 5′‐noncoding sequences from 699 vertebrate messenger RNAs. Nucleic Acids Research, 15(20), 8125–8148.
Kozak,, M. (1988). Leader length and secondary structure modulate mRNA function under conditions of stress. Molecular and Cellular Biology, 8(7), 2737–2744.
Kozak,, M. (1990). Downstream secondary structure facilitates recognition of initiator codons by eukaryotic ribosomes. Proceedings of the National Academy of Sciences of the United States of America, 87(21), 8301–8305.
Kozak,, M. (1991). A short leader sequence impairs the fidelity of initiation by eukaryotic ribosomes. Gene Expression, 1(2), 111–115.
Kozak,, M. (1992). Regulation of translation in eukaryotic systems. Annual Review of Cell Biology, 8, 197–225.
Kozak,, M. (2001). New ways of initiating translation in eukaryotes? Molecular and Cellular Biology, 21(6), 1899–1907. https://doi.org/10.1128/MCB.21.6.1899-1907.2001
Kozak,, M. (2003). Alternative ways to think about mRNA sequences and proteins that appear to promote internal initiation of translation. Gene, 318, 1–23.
Kozak,, M., & Shatkin,, A. J. (1976). Characterization of ribosome‐protected fragments from reovirus messenger RNA. The Journal of Biological Chemistry, 251(14), 4259–4266.
Kozak,, M., & Shatkin,, A. J. (1977). Sequences and properties of two ribosome binding sites from the small size class of reovirus messenger RNA. The Journal of Biological Chemistry, 252(19), 6895–6908.
Kozak,, M., & Shatkin,, A. J. (1978). Migration of 40 S ribosomal subunits on messenger RNA in the presence of edeine. The Journal of Biological Chemistry, 253(18), 6568–6577.
Kozlov,, G., Menade,, M., Rosenauer,, A., Nguyen,, L., & Gehring,, K. (2010). Molecular determinants of PAM2 recognition by the MLLE domain of poly(A)‐binding protein. Journal of Molecular Biology, 397(2), 397–407. https://doi.org/10.1016/j.jmb.2010.01.032
Krieger,, E., & Vriend,, G. (2014). YASARA view—molecular graphics for all devices—from smartphones to workstations. Bioinformatics, 30(20), 2981–2982. https://doi.org/10.1093/bioinformatics/btu426
Kropiwnicka,, A., Kuchta,, K., Lukaszewicz,, M., Kowalska,, J., Jemielity,, J., Ginalski,, K., … Zuberek,, J. (2015). Five eIF4E isoforms from Arabidopsis thaliana are characterized by distinct features of cap analogs binding. Biochemical and Biophysical Research Communications, 456(1), 47–52. https://doi.org/10.1016/j.bbrc.2014.11.032
Kubacka,, D., Kamenska,, A., Broomhead,, H., Minshall,, N., Darzynkiewicz,, E., & Standart,, N. (2013). Investigating the consequences of eIF4E2 (4EHP) interaction with 4E‐transporter on its cellular distribution in HeLa cells. PLoS One, 8(8), e72761. https://doi.org/10.1371/journal.pone.0072761
Kull,, F. J., & Endow,, S. A. (2013). Force generation by kinesin and myosin cytoskeletal motor proteins. Journal of Cell Science, 126(Pt. 1), 9–19. https://doi.org/10.1242/jcs.103911
Kumar,, P., Hellen,, C. U., & Pestova,, T. V. (2016). Toward the mechanism of eIF4F‐mediated ribosomal attachment to mammalian capped mRNAs. Genes %26 Development, 30(13), 1573–1588. https://doi.org/10.1101/gad.282418.116
Kuriyan,, J., & O`Donnell,, M. (1993). Sliding clamps of DNA polymerases. Journal of Molecular Biology, 234(4), 915–925. https://doi.org/10.1006/jmbi.1993.1644
Labno,, A., Tomecki,, R., & Dziembowski,, A. (2016). Cytoplasmic RNA decay pathways—enzymes and mechanisms. Biochimica et Biophysica Acta, 1863(12), 3125–3147. https://doi.org/10.1016/j.bbamcr.2016.09.023
Lacerda,, R., Menezes,, J., & Romao,, L. (2017). More than just scanning: The importance of cap‐independent mRNA translation initiation for cellular stress response and cancer. Cellular and Molecular Life Sciences, 74(9), 1659–1680. https://doi.org/10.1007/s00018-016-2428-2
Lammich,, S., Schobel,, S., Zimmer,, A. K., Lichtenthaler,, S. F., & Haass,, C. (2004). Expression of the Alzheimer protease BACE1 is suppressed via its 5′‐untranslated region. EMBO Reports, 5(6), 620–625. https://doi.org/10.1038/sj.embor.7400166
Lee,, A. S., Kranzusch,, P. J., Doudna,, J. A., & Cate,, J. H. (2016). eIF3d is an mRNA cap‐binding protein that is required for specialized translation initiation. Nature, 536(7614), 96–99. https://doi.org/10.1038/nature18954
LeFebvre,, A. K., Korneeva,, N. L., Trutschl,, M., Cvek,, U., Duzan,, R. D., Bradley,, C. A., … Rhoads,, R. E. (2006). Translation initiation factor eIF4G‐1 binds to eIF3 through the eIF3e subunit. The Journal of Biological Chemistry, 281(32), 22917–22932. https://doi.org/10.1074/jbc.M605418200
Legnini,, I., Di Timoteo,, G., Rossi,, F., Morlando,, M., Briganti,, F., Sthandier,, O., … Bozzoni,, I. (2017). Circ‐ZNF609 is a circular RNA that can be translated and functions in Myogenesis. Molecular Cell, 66(1), 22–37. https://doi.org/10.1016/j.molcel.2017.02.017
Lejeune,, F., Ranganathan,, A. C., & Maquat,, L. E. (2004). eIF4G is required for the pioneer round of translation in mammalian cells. Nature Structural %26 Molecular Biology, 11(10), 992–1000.
Lewis,, S. M., Cerquozzi,, S., Graber,, T. E., Ungureanu,, N. H., Andrews,, M., & Holcik,, M. (2008). The eIF4G homolog DAP5/p97 supports the translation of select mRNAs during endoplasmic reticulum stress. Nucleic Acids Research, 36(1), 168–178. https://doi.org/10.1093/nar/gkm1007
Liang,, H., He,, S., Yang,, J., Jia,, X., Wang,, P., Chen,, X., … Yin,, Y. (2014). PTENalpha, a PTEN isoform translated through alternative initiation, regulates mitochondrial function and energy metabolism. Cell Metabolism, 19(5), 836–848. https://doi.org/10.1016/j.cmet.2014.03.023
Liberman,, N., Gandin,, V., Svitkin,, Y. V., David,, M., Virgili,, G., Jaramillo,, M., … Sonenberg,, N. (2015). DAP5 associates with eIF2beta and eIF4AI to promote internal ribosome entry site driven translation. Nucleic Acids Research, 43(7), 3764–3775. https://doi.org/10.1093/nar/gkv205
Lin,, S., Choe,, J., Du,, P., Triboulet,, R., & Gregory,, R. I. (2016). The m(6)A Methyltransferase METTL3 promotes translation in human cancer cells. Molecular Cell, 62(3), 335–345. https://doi.org/10.1016/j.molcel.2016.03.021
Lind,, C., & Aqvist,, J. (2016). Principles of start codon recognition in eukaryotic translation initiation. Nucleic Acids Research, 44(17), 8425–8432. https://doi.org/10.1093/nar/gkw534
Lind,, C., Esguerra,, M., & Aqvist,, J. (2017). A close‐up view of codon selection in eukaryotic initiation. RNA Biology, 14(7), 815–819. https://doi.org/10.1080/15476286.2017.1308998
Liu,, F., Putnam,, A., & Jankowsky,, E. (2008). ATP hydrolysis is required for DEAD‐box protein recycling but not for duplex unwinding. Proceedings of the National Academy of Sciences of the United States of America, 105(51), 20209–20214. https://doi.org/10.1073/pnas.0811115106
Llacer,, J. L., Hussain,, T., Marler,, L., Aitken,, C. E., Thakur,, A., Lorsch,, J. R., … Ramakrishnan,, V. (2015). Conformational differences between open and closed states of the eukaryotic translation initiation complex. Molecular Cell, 59(3), 399–412. https://doi.org/10.1016/j.molcel.2015.06.033
Lomakin,, I. B., Kolupaeva,, V. G., Marintchev,, A., Wagner,, G., & Pestova,, T. V. (2003). Position of eukaryotic initiation factor eIF1 on the 40S ribosomal subunit determined by directed hydroxyl radical probing. Genes %26 Development, 17(22), 2786–2797.
Lomakin,, I. B., Shirokikh,, N. E., Yusupov,, M. M., Hellen,, C. U., & Pestova,, T. V. (2006). The fidelity of translation initiation: Reciprocal activities of eIF1, IF3 and YciH. The EMBO Journal, 25(1), 196–210.
Lomakin,, I. B., & Steitz,, T. A. (2013). The initiation of mammalian protein synthesis and mRNA scanning mechanism. Nature, 500(7462), 307–311. https://doi.org/10.1038/nature12355
Lomakin,, I. B., Stolboushkina,, E. A., Vaidya,, A. T., Zhao,, C., Garber,, M. B., Dmitriev,, S. E., & Steitz,, T. A. (2017). Crystal structure of the human ribosome in complex with DENR‐MCT‐1. Cell Reports, 20(3), 521–528. https://doi.org/10.1016/j.celrep.2017.06.025
Lorsch,, J. R., & Dever,, T. E. (2010). Molecular view of 43 S complex formation and start site selection in eukaryotic translation initiation. The Journal of Biological Chemistry, 285(28), 21203–21207. https://doi.org/10.1074/jbc.R110.119743
Lu,, W. T., Wilczynska,, A., Smith,, E., & Bushell,, M. (2014). The diverse roles of the eIF4A family: You are the company you keep. Biochemical Society Transactions, 42(1), 166–172. https://doi.org/10.1042/BST20130161
Luna,, R. E., Arthanari,, H., Hiraishi,, H., Nanda,, J., Martin‐Marcos,, P., Markus,, M. A., … Wagner,, G. (2012). The C‐terminal domain of eukaryotic initiation factor 5 promotes start codon recognition by its dynamic interplay with eIF1 and eIF2beta. Cell Reports, 1(6), 689–702. https://doi.org/10.1016/j.celrep.2012.04.007
Luttermann,, C., & Meyers,, G. (2007). A bipartite sequence motif induces translation reinitiation in feline calicivirus RNA. The Journal of Biological Chemistry, 282(10), 7056–7065. https://doi.org/10.1074/jbc.M608948200
Luttermann,, C., & Meyers,, G. (2009). The importance of inter‐ and intramolecular base pairing for translation reinitiation on a eukaryotic bicistronic mRNA. Genes %26 Development, 23(3), 331–344. https://doi.org/10.1101/gad.507609
Luttermann,, C., & Meyers,, G. (2014). Two alternative ways of start site selection in human norovirus reinitiation of translation. The Journal of Biological Chemistry, 289(17), 11739–11754. https://doi.org/10.1074/jbc.M114.554030
Maag,, D., Fekete,, C. A., Gryczynski,, Z., & Lorsch,, J. R. (2005). A conformational change in the eukaryotic translation preinitiation complex and release of eIF1 signal recognition of the start codon. Molecular Cell, 17(2), 265–275. https://doi.org/10.1016/j.molcel.2004.11.051
Maag,, D., & Lorsch,, J. R. (2003). Communication between eukaryotic translation initiation factors 1 and 1A on the yeast small ribosomal subunit. Journal of Molecular Biology, 330(5), 917–924.
Maicas,, E., Shago,, M., & Friesen,, J. D. (1990). Translation of the Saccharomyces cerevisiae tcm1 gene in the absence of a 5′‐untranslated leader. Nucleic Acids Research, 18(19), 5823–5828.
Majumdar,, R., & Maitra,, U. (2005). Regulation of GTP hydrolysis prior to ribosomal AUG selection during eukaryotic translation initiation. The EMBO Journal, 24(21), 3737–3746. https://doi.org/10.1038/sj.emboj.7600844
Manosas,, M., Camunas‐Soler,, J., Croquette,, V., & Ritort,, F. (2017). Single molecule high‐throughput footprinting of small and large DNA ligands. Nature Communications, 8(1), 304. https://doi.org/10.1038/s41467-017-00379-w
Maquat,, L. E., Tarn,, W. Y., & Isken,, O. (2010). The pioneer round of translation: Features and functions. Cell, 142(3), 368–374. https://doi.org/10.1016/j.cell.2010.07.022
Marchetti,, M., Malinowska,, A., Heller,, I., & Wuite,, G. J. L. (2017). How to switch the motor on: RNA polymerase initiation steps at the single‐molecule level. Protein Science, 26(7), 1303–1313. https://doi.org/10.1002/pro.3183
Marintchev,, A. (2013). Roles of helicases in translation initiation: A mechanistic view. Biochimica et Biophysica Acta, 1829(8), 799–809. https://doi.org/10.1016/j.bbagrm.2013.01.005
Marintchev,, A., Edmonds,, K. A., Marintcheva,, B., Hendrickson,, E., Oberer,, M., Suzuki,, C., … Wagner,, G. (2009). Topology and regulation of the human eIF4A/4G/4H helicase complex in translation initiation. Cell, 136(3), 447–460. https://doi.org/10.1016/j.cell.2009.01.014
Marintchev,, A., & Wagner,, G. (2004). Translation initiation: Structures, mechanisms and evolution. Quarterly Reviews of Biophysics, 37(3–4), 197–284.
Martin,, F., Barends,, S., Jaeger,, S., Schaeffer,, L., Prongidi‐Fix,, L., & Eriani,, G. (2011). Cap‐assisted internal initiation of translation of histone H4. Molecular Cell, 41(2), 197–209. https://doi.org/10.1016/j.molcel.2010.12.019
Martin,, F., Menetret,, J. F., Simonetti,, A., Myasnikov,, A. G., Vicens,, Q., Prongidi‐Fix,, L., … Eriani,, G. (2016). Ribosomal 18S rRNA base pairs with mRNA during eukaryotic translation initiation. Nature Communications, 7, 12622. https://doi.org/10.1038/ncomms12622
Martineau,, Y., Derry,, M. C., Wang,, X., Yanagiya,, A., Berlanga,, J. J., Shyu,, A. B., … Sonenberg,, N. (2008). Poly(A)‐binding protein‐interacting protein 1 binds to eukaryotic translation initiation factor 3 to stimulate translation. Molecular and Cellular Biology, 28(21), 6658–6667. https://doi.org/10.1128/MCB.00738-08
Martinez‐Nunez,, R. T., & Sanford,, J. R. (2016). Studying isoform‐specific mRNA recruitment to polyribosomes with Frac‐seq. Methods in Molecular Biology, 1358, 99–108. https://doi.org/10.1007/978-1-4939-3067-8_6
Martinez‐Silva,, A. V., Aguirre‐Martinez,, C., Flores‐Tinoco,, C. E., Alejandri‐Ramirez,, N. D., & Dinkova,, T. D. (2012). Translation initiation factor AteIF(iso)4E is involved in selective mRNA translation in Arabidopsis thaliana seedlings. PLoS One, 7(2), e31606. https://doi.org/10.1371/journal.pone.0031606
Martin‐Marcos,, P., Cheung,, Y. N., & Hinnebusch,, A. G. (2011). Functional elements in initiation factors 1, 1A, and 2beta discriminate against poor AUG context and non‐AUG start codons. Molecular and Cellular Biology, 31(23), 4814–4831. https://doi.org/10.1128/MCB.05819-11
Martin‐Marcos,, P., Nanda,, J. S., Luna,, R. E., Zhang,, F., Saini,, A. K., Cherkasova,, V. A., … Hinnebusch,, A. G. (2014). Enhanced eIF1 binding to the 40S ribosome impedes conformational rearrangements of the preinitiation complex and elevates initiation accuracy. RNA, 20(2), 150–167. https://doi.org/10.1261/rna.042069.113
Matsuda,, D., & Mauro,, V. P. (2014). Base pairing between hepatitis C virus RNA and 18S rRNA is required for IRES‐dependent translation initiation in vivo. Proceedings of the National Academy of Sciences of the United States of America, 111(43), 15385–15389. https://doi.org/10.1073/pnas.1413472111
Matyskiela,, M. E., Lander,, G. C., & Martin,, A. (2013). Conformational switching of the 26S proteasome enables substrate degradation. Nature Structural %26 Molecular Biology, 20(7), 781–788. https://doi.org/10.1038/nsmb.2616
Mauro,, V. P., & Matsuda,, D. (2016). Translation regulation by ribosomes: Increased complexity and expanded scope. RNA Biology, 13(9), 748–755. https://doi.org/10.1080/15476286.2015.1107701
McCormick,, C. J., Salim,, O., Lambden,, P. R., & Clarke,, I. N. (2008). Translation termination reinitiation between open reading frame 1 (ORF1) and ORF2 enables capsid expression in a bovine norovirus without the need for production of viral subgenomic RNA. Journal of Virology, 82(17), 8917–8921. https://doi.org/10.1128/JVI.02362-07
McGlincy,, N. J., & Ingolia,, N. T. (2017). Transcriptome‐wide measurement of translation by ribosome profiling. Methods, 126, 112–129. https://doi.org/10.1016/j.ymeth.2017.05.028
Merrick,, W. C. (2015). eIF4F: A retrospective. The Journal of Biological Chemistry, 290(40), 24091–24099. https://doi.org/10.1074/jbc.R115.675280
Meyer,, K. D., Patil,, D. P., Zhou,, J., Zinoviev,, A., Skabkin,, M. A., Elemento,, O., … Jaffrey,, S. R. (2015). 5` UTR m(6)A promotes cap‐independent translation. Cell, 163(4), 999–1010. https://doi.org/10.1016/j.cell.2015.10.012
Meyers,, G. (2003). Translation of the minor capsid protein of a calicivirus is initiated by a novel termination‐dependent reinitiation mechanism. The Journal of Biological Chemistry, 278(36), 34051–34060. https://doi.org/10.1074/jbc.M304874200
Meyers,, G. (2007). Characterization of the sequence element directing translation reinitiation in RNA of the calicivirus rabbit hemorrhagic disease virus. Journal of Virology, 81(18), 9623–9632. https://doi.org/10.1128/JVI.00771-07
Meyuhas,, O. (2015). Ribosomal protein S6 phosphorylation: Four decades of research. International Review of Cell and Molecular Biology, 320, 41–73. https://doi.org/10.1016/bs.ircmb.2015.07.006
Michel,, A. M., Andreev,, D. E., & Baranov,, P. V. (2014). Computational approach for calculating the probability of eukaryotic translation initiation from ribo‐seq data that takes into account leaky scanning. BMC Bioinformatics, 15, 380. https://doi.org/10.1186/s12859-014-0380-4
Mihailovich,, M., Thermann,, R., Grohovaz,, F., Hentze,, M. W., & Zacchetti,, D. (2007). Complex translational regulation of BACE1 involves upstream AUGs and stimulatory elements within the 5′ untranslated region. Nucleic Acids Research, 35(9), 2975–2985. https://doi.org/10.1093/nar/gkm191
Minshall,, N., Reiter,, M. H., Weil,, D., & Standart,, N. (2007). CPEB interacts with an ovary‐specific eIF4E and 4E‐T in early Xenopus oocytes. The Journal of Biological Chemistry, 282(52), 37389–37401. https://doi.org/10.1074/jbc.M704629200
Mitchell,, S. F., & Lorsch,, J. R. (2008). Should I stay or should I go? Eukaryotic translation initiation factors 1 and 1A control start codon recognition. The Journal of Biological Chemistry, 283(41), 27345–27349. https://doi.org/10.1074/jbc.R800031200
Mitchell,, S. F., & Parker,, R. (2014). Principles and properties of eukaryotic mRNPs. Molecular Cell, 54(4), 547–558. https://doi.org/10.1016/j.molcel.2014.04.033
Miyasaka,, H. (1999). The positive relationship between codon usage bias and translation initiation AUG context in Saccharomyces cerevisiae. Yeast, 15(8), 633–637. https://doi.org/10.1002/(SICI)1097-0061(19990615)15:8%3C633::AID-YEA407%3E3.0.CO;2-O
Mohammad,, M. P., Munzarova Pondelickova,, V., Zeman,, J., Gunisova,, S., & Valasek,, L. S. (2017). In vivo evidence that eIF3 stays bound to ribosomes elongating and terminating on short upstream ORFs to promote reinitiation. Nucleic Acids Research, 45(5), 2658–2674. https://doi.org/10.1093/nar/gkx049
Monzingo,, A. F., Dhaliwal,, S., Dutt‐Chaudhuri,, A., Lyon,, A., Sadow,, J. H., Hoffman,, D. W., … Browning,, K. S. (2007). The structure of eukaryotic translation initiation factor‐4E from wheat reveals a novel disulfide bond. Plant Physiology, 143(4), 1504–1518. https://doi.org/10.1104/pp.106.093146
Morisaki,, T., Lyon,, K., DeLuca,, K. F., DeLuca,, J. G., English,, B. P., Zhang,, Z., … Stasevich,, T. J. (2016). Real‐time quantification of single RNA translation dynamics in living cells. Science, 352(6292), 1425–1429. https://doi.org/10.1126/science.aaf0899
Morita,, M., Ler,, L. W., Fabian,, M. R., Siddiqui,, N., Mullin,, M., Henderson,, V. C., … Sonenberg,, N. (2012). A novel 4EHP‐GIGYF2 translational repressor complex is essential for mammalian development. Molecular and Cellular Biology, 32(17), 3585–3593. https://doi.org/10.1128/MCB.00455-12
Muthukrishnan,, S., Both,, G. W., Furuichi,, Y., & Shatkin,, A. J. (1975). 5`‐Terminal 7‐methylguanosine in eukaryotic mRNA is required for translation. Nature, 255(5503), 33–37.
Myasnikov,, A. G., Afonina,, Z. A., Menetret,, J. F., Shirokov,, V. A., Spirin,, A. S., & Klaholz,, B. P. (2014). The molecular structure of the left‐handed supra‐molecular helix of eukaryotic polyribosomes. Nature Communications, 5, 5294. https://doi.org/10.1038/ncomms6294
Nag,, N., Lin,, K. Y., Edmonds,, K. A., Yu,, J., Nadkarni,, D., Marintcheva,, B., & Marintchev,, A. (2016). eIF1A/eIF5B interaction network and its functions in translation initiation complex assembly and remodeling. Nucleic Acids Research, 44(15), 7441–7456. https://doi.org/10.1093/nar/gkw552
Nanda,, J. S., Saini,, A. K., Munoz,, A. M., Hinnebusch,, A. G., & Lorsch,, J. R. (2013). Coordinated movements of eukaryotic translation initiation factors eIF1, eIF1A, and eIF5 trigger phosphate release from eIF2 in response to start codon recognition by the ribosomal preinitiation complex. The Journal of Biological Chemistry, 288(8), 5316–5329. https://doi.org/10.1074/jbc.M112.440693
Napthine,, S., Lever,, R. A., Powell,, M. L., Jackson,, R. J., Brown,, T. D., & Brierley,, I. (2009). Expression of the VP2 protein of murine norovirus by a translation termination‐reinitiation strategy. PLoS One, 4(12), e8390. https://doi.org/10.1371/journal.pone.0008390
Nielsen,, K. H., Behrens,, M. A., He,, Y., Oliveira,, C. L., Jensen,, L. S., Hoffmann,, S. V., … Andersen,, G. R. (2011). Synergistic activation of eIF4A by eIF4B and eIF4G. Nucleic Acids Research, 39(7), 2678–2689. https://doi.org/10.1093/nar/gkq1206
Nousch,, M., Reed,, V., Bryson‐Richardson,, R. J., Currie,, P. D., & Preiss,, T. (2007). The eIF4G‐homolog p97 can activate translation independent of caspase cleavage. RNA, 13(3), 374–384. https://doi.org/10.1261/rna.372307
Obayashi,, E., Luna,, R. E., Nagata,, T., Martin‐Marcos,, P., Hiraishi,, H., Singh,, C. R., … Asano,, K. (2017). Molecular landscape of the ribosome pre‐initiation complex during mRNA scanning: Structural role for eIF3c and its control by eIF5. Cell Reports, 18(11), 2651–2663. https://doi.org/10.1016/j.celrep.2017.02.052
O`Leary,, S. E., Petrov,, A., Chen,, J., & Puglisi,, J. D. (2013). Dynamic recognition of the mRNA cap by Saccharomyces cerevisiae eIF4E. Structure, 21(12), 2197–2207. https://doi.org/10.1016/j.str.2013.09.016
Osborne,, M. J., Volpon,, L., Kornblatt,, J. A., Culjkovic‐Kraljacic,, B., Baguet,, A., & Borden,, K. L. (2013). eIF4E3 acts as a tumor suppressor by utilizing an atypical mode of methyl‐7‐guanosine cap recognition. Proceedings of the National Academy of Sciences of the United States of America, 110(10), 3877–3882. https://doi.org/10.1073/pnas.1216862110
Ozes,, A. R., Feoktistova,, K., Avanzino,, B. C., & Fraser,, C. S. (2011). Duplex unwinding and ATPase activities of the DEAD‐box helicase eIF4A are coupled by eIF4G and eIF4B. Journal of Molecular Biology, 412(4), 674–687. https://doi.org/10.1016/j.jmb.2011.08.004
Paek,, K. Y., Hong,, K. Y., Ryu,, I., Park,, S. M., Keum,, S. J., Kwon,, O. S., & Jang,, S. K. (2015). Translation initiation mediated by RNA looping. Proceedings of the National Academy of Sciences of the United States of America, 112(4), 1041–1046. https://doi.org/10.1073/pnas.1416883112
Palade,, G. (1975). Intracellular aspects of the process of protein synthesis. Science, 189(4206), 867. https://doi.org/10.1126/science.189.4206.867-b
Pamudurti,, N. R., Bartok,, O., Jens,, M., Ashwal‐Fluss,, R., Stottmeister,, C., Ruhe,, L., … Kadener,, S. (2017). Translation of CircRNAs. Molecular Cell, 66(1), 9–21. https://doi.org/10.1016/j.molcel.2017.02.021
Papadopoulos,, E., Jenni,, S., Kabha,, E., Takrouri,, K. J., Yi,, T., Salvi,, N., … Wagner,, G. (2014). Structure of the eukaryotic translation initiation factor eIF4E in complex with 4EGI‐1 reveals an allosteric mechanism for dissociating eIF4G. Proceedings of the National Academy of Sciences of the United States of America, 111(31), E3187–E3195. https://doi.org/10.1073/pnas.1410250111
Parsyan,, A., Svitkin,, Y., Shahbazian,, D., Gkogkas,, C., Lasko,, P., Merrick,, W. C., & Sonenberg,, N. (2011). mRNA helicases: The tacticians of translational control. Nature Reviews. Molecular Cell Biology, 12(4), 235–245. https://doi.org/10.1038/nrm3083
Passmore,, L. A., Schmeing,, T. M., Maag,, D., Applefield,, D. J., Acker,, M. G., Algire,, M. A., … Ramakrishnan,, V. (2007). The eukaryotic translation initiation factors eIF1 and eIF1A induce an open conformation of the 40S ribosome. Molecular Cell, 26(1), 41–50.
Pause,, A., Methot,, N., Svitkin,, Y., Merrick,, W. C., & Sonenberg,, N. (1994). Dominant negative mutants of mammalian translation initiation factor eIF‐4A define a critical role for eIF‐4F in cap‐dependent and cap‐independent initiation of translation. The EMBO Journal, 13(5), 1205–1215.
Paz,, I., & Choder,, M. (2001). Eukaryotic translation initiation factor 4E‐dependent translation is not essential for survival of starved yeast cells. Journal of Bacteriology, 183(15), 4477–4483.
Pelletier,, J., Graff,, J., Ruggero,, D., & Sonenberg,, N. (2015). Targeting the eIF4F translation initiation complex: A critical nexus for cancer development. Cancer Research, 75(2), 250–263. https://doi.org/10.1158/0008-5472.CAN-14-2789
Pestova,, T. V., Borukhov,, S. I., & Hellen,, C. U. (1998). Eukaryotic ribosomes require initiation factors 1 and 1A to locate initiation codons. Nature, 394(6696), 854–859.
Pestova,, T. V., de Breyne,, S., Pisarev,, A. V., Abaeva,, I. S., & Hellen,, C. U. (2008). eIF2‐dependent and eIF2‐independent modes of initiation on the CSFV IRES: A common role of domain II. The EMBO Journal, 27(7), 1060–1072.
Pestova,, T. V., & Kolupaeva,, V. G. (2002). The roles of individual eukaryotic translation initiation factors in ribosomal scanning and initiation codon selection. Genes %26 Development, 16(22), 2906–2922.
Pestova,, T. V., Lomakin,, I. B., Lee,, J. H., Choi,, S. K., Dever,, T. E., & Hellen,, C. U. (2000). The joining of ribosomal subunits in eukaryotes requires eIF5B. Nature, 403(6767), 332–335.
Peter,, D., Weber,, R., Sandmeir,, F., Wohlbold,, L., Helms,, S., Bawankar,, P., … Izaurralde,, E. (2017). GIGYF1/2 proteins use auxiliary sequences to selectively bind to 4EHP and repress target mRNA expression. Genes %26 Development, 31(11), 1147–1161. https://doi.org/10.1101/gad.299420.117
Petrov,, A., Grosely,, R., Chen,, J., O`Leary,, S. E., & Puglisi,, J. D. (2016). Multiple parallel pathways of translation initiation on the CrPV IRES. Molecular Cell, 62(1), 92–103. https://doi.org/10.1016/j.molcel.2016.03.020
Phan,, L., Schoenfeld,, L. W., Valasek,, L., Nielsen,, K. H., & Hinnebusch,, A. G. (2001). A subcomplex of three eIF3 subunits binds eIF1 and eIF5 and stimulates ribosome binding of mRNA and tRNA(i)Met. The EMBO Journal, 20(11), 2954–2965. https://doi.org/10.1093/emboj/20.11.2954
Phan,, L., Zhang,, X., Asano,, K., Anderson,, J., Vornlocher,, H. P., Greenberg,, J. R., … Hinnebusch,, A. G. (1998). Identification of a translation initiation factor 3 (eIF3) core complex, conserved in yeast and mammals, that interacts with eIF5. Molecular and Cellular Biology, 18(8), 4935–4946.
Phelps,, C., Lee,, W., Jose,, D., von Hippel,, P. H., & Marcus,, A. H. (2013). Single‐molecule FRET and linear dichroism studies of DNA breathing and helicase binding at replication fork junctions. Proceedings of the National Academy of Sciences of the United States of America, 110(43), 17320–17325. https://doi.org/10.1073/pnas.1314862110
Pick,, E., Hofmann,, K., & Glickman,, M. H. (2009). PCI complexes: Beyond the proteasome, CSN, and eIF3 Troika. Molecular Cell, 35(3), 260–264. https://doi.org/10.1016/j.molcel.2009.07.009
Pisarev,, A. V., Kolupaeva,, V. G., Pisareva,, V. P., Merrick,, W. C., Hellen,, C. U., & Pestova,, T. V. (2006). 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 %26 Development, 20(5), 624–636. https://doi.org/10.1101/gad.1397906
Pisarev,, A. V., Kolupaeva,, V. G., Yusupov,, M. M., Hellen,, C. U., & Pestova,, T. V. (2008). Ribosomal position and contacts of mRNA in eukaryotic translation initiation complexes. The EMBO Journal, 27(11), 1609–1621.
Pisarev,, A. V., Shirokikh,, N. E., & Hellen,, C. U. (2005). Translation initiation by factor‐independent binding of eukaryotic ribosomes to internal ribosomal entry sites. Comptes Rendus Biologies, 328(7), 589–605. https://doi.org/10.1016/j.crvi.2005.02.004
Pisareva,, V. P., & Pisarev,, A. V. (2014). eIF5 and eIF5B together stimulate 48S initiation complex formation during ribosomal scanning. Nucleic Acids Research, 42(19), 12052–12069. https://doi.org/10.1093/nar/gku877
Pisareva,, V. P., & Pisarev,, A. V. (2016). DHX29 reduces leaky scanning through an upstream AUG codon regardless of its nucleotide context. Nucleic Acids Research, 44(9), 4252–4265. https://doi.org/10.1093/nar/gkw240
Pisareva,, V. P., Pisarev,, A. V., Komar,, A. A., Hellen,, C. U., & Pestova,, T. V. (2008). Translation initiation on mammalian mRNAs with structured 5`UTRs requires DExH‐box protein DHX29. Cell, 135(7), 1237–1250. https://doi.org/10.1016/j.cell.2008.10.037
Pooggin,, M. M., Futterer,, J., & Hohn,, T. (2008). Cross‐species functionality of pararetroviral elements driving ribosome shunting. PLoS One, 3(2), e1650. https://doi.org/10.1371/journal.pone.0001650
Pooggin,, M. M., Hohn,, T., & Futterer,, J. (2000). Role of a short open reading frame in ribosome shunt on the cauliflower mosaic virus RNA leader. The Journal of Biological Chemistry, 275(23), 17288–17296. https://doi.org/10.1074/jbc.M001143200
Pooggin,, M. M., Ryabova,, L. A., He,, X., Futterer,, J., & Hohn,, T. (2006). Mechanism of ribosome shunting in Rice tungro bacilliform pararetrovirus. RNA, 12(5), 841–850. https://doi.org/10.1261/rna.2285806
Powell,, M. L., Leigh,, K. E., Poyry,, T. A., Jackson,, R. J., Brown,, T. D., & Brierley,, I. (2011). Further characterisation of the translational termination‐reinitiation signal of the influenza B virus segment 7 RNA. PLoS One, 6(2), e16822. https://doi.org/10.1371/journal.pone.0016822
Poyry,, T. A., & Jackson,, R. J. (2011). Mechanisms governing the selection of translation initiation sites on foot‐and‐mouth disease virus RNA. Journal of Virology, 85(19), 10178–10188. https://doi.org/10.1128/JVI.05085-11
Poyry,, T. A., Kaminski,, A., Connell,, E. J., Fraser,, C. S., & Jackson,, R. J. (2007). The mechanism of an exceptional case of reinitiation after translation of a long ORF reveals why such events do not generally occur in mammalian mRNA translation. Genes %26 Development, 21(23), 3149–3162. https://doi.org/10.1101/gad.439507
Poyry,, T. A., Kaminski,, A., & Jackson,, R. J. (2004). What determines whether mammalian ribosomes resume scanning after translation of a short upstream open reading frame? Genes %26 Development, 18(1), 62–75. https://doi.org/10.1101/gad.276504
Preiss,, T. (2016). All ribosomes are created equal. Really? Trends in Biochemical Sciences, 41(2), 121–123. https://doi.org/10.1016/j.tibs.2015.11.009
Preiss,, T., & Hentze,, M. W. (1999). From factors to mechanisms: Translation and translational control in eukaryotes. Current Opinion in Genetics %26 Development, 9(5), 515–521.
Prosniak,, M., Dierov,, J., Okami,, K., Tilton,, B., Jameson,, B., Sawaya,, B. E., & Gartenhaus,, R. B. (1998). A novel candidate oncogene, MCT‐1, is involved in cell cycle progression. Cancer Research, 58(19), 4233–4237.
Proud,, C. G. (2011). mTOR Signalling in health and disease. Biochemical Society Transactions, 39(2), 431–436. https://doi.org/10.1042/BST0390431
Proud,, C. G. (2015). Mnks, eIF4E phosphorylation and cancer. Biochimica et Biophysica Acta, 1849(7), 766–773. https://doi.org/10.1016/j.bbagrm.2014.10.003
Ptushkina,, M., von der Haar,, T., Karim,, M. M., Hughes,, J. M., & McCarthy,, J. E. (1999). Repressor binding to a dorsal regulatory site traps human eIF4E in a high cap‐affinity state. The EMBO Journal, 18(14), 4068–4075.
Ptushkina,, M., von der Haar,, T., Vasilescu,, S., Frank,, R., Birkenhager,, R., & McCarthy,, J. E. (1998). Cooperative modulation by eIF4G of eIF4E‐binding to the mRNA 5′ cap in yeast involves a site partially shared by p20. The EMBO Journal, 17(16), 4798–4808. https://doi.org/10.1093/emboj/17.16.4798
Qu,, X., Wen,, J. D., Lancaster,, L., Noller,, H. F., Bustamante,, C., & Tinoco, Jr., I. (2011). The ribosome uses two active mechanisms to unwind messenger RNA during translation. Nature, 475(7354), 118–121. https://doi.org/10.1038/nature10126
Rabl,, J., Leibundgut,, M., Ataide,, S. F., Haag,, A., & Ban,, N. (2011). Crystal structure of the eukaryotic 40S ribosomal subunit in complex with initiation factor 1. Science, 331(6018), 730–736. https://doi.org/10.1126/science.1198308
Ranji,, A., Shkriabai,, N., Kvaratskhelia,, M., Musier‐Forsyth,, K., & Boris‐Lawrie,, K. (2011). Features of double‐stranded RNA‐binding domains of RNA helicase A are necessary for selective recognition and translation of complex mRNAs. The Journal of Biological Chemistry, 286(7), 5328–5337. https://doi.org/10.1074/jbc.M110.176339
Rice,, S., Lin,, A. W., Safer,, D., Hart,, C. L., Naber,, N., Carragher,, B. O., … Vale,, R. D. (1999). A structural change in the kinesin motor protein that drives motility. Nature, 402(6763), 778–784. https://doi.org/10.1038/45483
Richter,, J. D. (2007). CPEB: A life in translation. Trends in Biochemical Sciences, 32(6), 279–285. https://doi.org/10.1016/j.tibs.2007.04.004
Richter,, J. D., & Lasko,, P. (2011). Translational control in oocyte development. Cold Spring Harbor Perspectives in Biology, 3(9), a002758. https://doi.org/10.1101/cshperspect.a002758
Rogers, Jr., G. W., Edelman,, G. M., & Mauro,, V. P. (2004). Differential utilization of upstream AUGs in the beta‐secretase mRNA suggests that a shunting mechanism regulates translation. Proceedings of the National Academy of Sciences of the United States of America, 101(9), 2794–2799. https://doi.org/10.1073/pnas.0308576101
Rossi,, D., Kuroshu,, R., Zanelli,, C. F., & Valentini,, S. R. (2014). eIF5A and EF‐P: Two unique translation factors are now traveling the same road. WIREs RNA, 5(2), 209–222. https://doi.org/10.1002/wrna.1211
Safaee,, N., Kozlov,, G., Noronha,, A. M., Xie,, J., Wilds,, C. J., & Gehring,, K. (2012). Interdomain allostery promotes assembly of the poly(A) mRNA complex with PABP and eIF4G. Molecular Cell, 48(3), 375–386. https://doi.org/10.1016/j.molcel.2012.09.001
Saini,, A. K., Nanda,, J. S., Lorsch,, J. R., & Hinnebusch,, A. G. (2010). Regulatory elements in eIF1A control the fidelity of start codon selection by modulating tRNA(i)(Met) binding to the ribosome. Genes %26 Development, 24(1), 97–110. https://doi.org/10.1101/gad.1871910
Saini,, A. K., Nanda,, J. S., Martin‐Marcos,, P., Dong,, J., Zhang,, F., Bhardwaj,, M., … Hinnebusch,, A. G. (2015). Eukaryotic translation initiation factor eIF5 promotes the accuracy of start codon recognition by regulating Pi release and conformational transitions of the preinitiation complex. Nucleic Acids Research, 43(11), 5673–5674. https://doi.org/10.1093/nar/gkv510
Saletta,, F., Suryo Rahmanto,, Y., & Richardson,, D. R. (2010). The translational regulator eIF3a: The tricky eIF3 subunit! Biochimica et Biophysica Acta, 1806(2), 275–286. https://doi.org/10.1016/j.bbcan.2010.07.005
Sanchez,, A. M., Csibi,, A., Raibon,, A., Docquier,, A., Lagirand‐Cantaloube,, J., Leibovitch,, M. P., … Bernardi,, H. (2013). eIF3f: A central regulator of the antagonism atrophy/hypertrophy in skeletal muscle. The International Journal of Biochemistry %26 Cell Biology, 45(10), 2158–2162. https://doi.org/10.1016/j.biocel.2013.06.001
Scheper,, G. C., van der Knaap,, M. S., & Proud,, C. G. (2007). Translation matters: Protein synthesis defects in inherited disease. Nature Reviews. Genetics, 8(9), 711–723. https://doi.org/10.1038/nrg2142
Schleich,, S., Strassburger,, K., Janiesch,, P. C., Koledachkina,, T., Miller,, K. K., Haneke,, K., … Teleman,, A. A. (2014). DENR‐MCT‐1 promotes translation re‐initiation downstream of uORFs to control tissue growth. Nature, 512(7513), 208–212. https://doi.org/10.1038/nature13401
Schmitt,, E., Panvert,, M., Lazennec‐Schurdevin,, C., Coureux,, P. D., Perez,, J., Thompson,, A., & Mechulam,, Y. (2012). Structure of the ternary initiation complex aIF2‐GDPNP‐methionylated initiator tRNA. Nature Structural %26 Molecular Biology, 19(4), 450–454. https://doi.org/10.1038/nsmb.2259
Schneider,, R., Agol,, V. I., Andino,, R., Bayard,, F., Cavener,, D. R., Chappell,, S. A., … Wormington,, M. (2001). New ways of initiating translation in eukaryotes. Molecular and Cellular Biology, 21(23), 8238–8246.
Schuller,, A. P., Wu,, C. C., Dever,, T. E., Buskirk,, A. R., & Green,, R. (2017). eIF5A functions globally in translation elongation and termination. Molecular Cell, 66(2), 194–205. https://doi.org/10.1016/j.molcel.2017.03.003
Schutz,, P., Bumann,, M., Oberholzer,, A. E., Bieniossek,, C., Trachsel,, H., Altmann,, M., & Baumann,, U. (2008). Crystal structure of the yeast eIF4A‐eIF4G complex: An RNA‐helicase controlled by protein‐protein interactions. Proceedings of the National Academy of Sciences of the United States of America, 105(28), 9564–9569. https://doi.org/10.1073/pnas.0800418105
Schwanhausser,, B., Busse,, D., Li,, N., Dittmar,, G., Schuchhardt,, J., Wolf,, J., … Selbach,, M. (2011). Global quantification of mammalian gene expression control. Nature, 473(7347), 337–342. https://doi.org/10.1038/nature10098
Sen,, N. D., Zhou,, F., Harris,, M. S., Ingolia,, N. T., & Hinnebusch,, A. G. (2016). eIF4B stimulates translation of long mRNAs with structured 5` UTRs and low closed‐loop potential but weak dependence on eIF4G. Proceedings of the National Academy of Sciences of the United States of America, 113(38), 10464–10472. https://doi.org/10.1073/pnas.1612398113
Sen,, N. D., Zhou,, F., Ingolia,, N. T., & Hinnebusch,, A. G. (2015). Genome‐wide analysis of translational efficiency reveals distinct but overlapping functions of yeast DEAD‐box RNA helicases Ded1 and eIF4A. Genome Research, 25(8), 1196–1205. https://doi.org/10.1101/gr.191601.115
Sendoel,, A., Dunn,, J. G., Rodriguez,, E. H., Naik,, S., Gomez,, N. C., Hurwitz,, B., … Fuchs,, E. (2017). Translation from unconventional 5′ start sites drives tumour initiation. Nature, 541(7638), 494–499. https://doi.org/10.1038/nature21036
Shafritz,, D. A., Weinstein,, J. A., Safer,, B., Merrick,, W. C., Weber,, L. A., Hickey,, E. D., & Baglioni,, C. (1976). Evidence for role of m7G5′‐phosphate group in recognition of eukaryotic mRNA by initiation factor IF‐M3. Nature, 261(5558), 291–294.
Shahbazian,, D., Parsyan,, A., Petroulakis,, E., Hershey,, J., & Sonenberg,, N. (2010). eIF4B controls survival and proliferation and is regulated by proto‐oncogenic signaling pathways. Cell Cycle, 9(20), 4106–4109. https://doi.org/10.4161/cc.9.20.13630
Shatsky,, I. N., Dmitriev,, S. E., Terenin,, I. M., & Andreev,, D. E. (2010). Cap‐ and IRES‐independent scanning mechanism of translation initiation as an alternative to the concept of cellular IRESs. Molecules and Cells, 30(4), 285–293. https://doi.org/10.1007/s10059-010-0149-1
Sherrill,, K. W., & Lloyd,, R. E. (2008). Translation of cIAP2 mRNA is mediated exclusively by a stress‐modulated ribosome shunt. Molecular and Cellular Biology, 28(6), 2011–2022. https://doi.org/10.1128/MCB.01446-07
Shi,, Y., & Manley,, J. L. (2015). The end of the message: Multiple protein‐RNA interactions define the mRNA polyadenylation site. Genes %26 Development, 29(9), 889–897. https://doi.org/10.1101/gad.261974.115
Shimotohno,, K., Kodama,, Y., Hashimoto,, J., & Miura,, K. I. (1977). Importance of 5`‐terminal blocking structure to stabilize mRNA in eukaryotic protein synthesis. Proceedings of the National Academy of Sciences of the United States of America, 74(7), 2734–2738.
Shine,, J., & Dalgarno,, L. (1974). The 3′‐terminal sequence of Escherichia coli 16S ribosomal RNA: Complementarity to nonsense triplets and ribosome binding sites. Proceedings of the National Academy of Sciences of the United States of America, 71(4), 1342–1346.
Shine,, J., & Dalgarno,, L. (1975). Determinant of cistron specificity in bacterial ribosomes. Nature, 254(5495), 34–38.
Shirokikh,, N. E., Archer,, S. K., Beilharz,, T. H., Powell,, D., & Preiss,, T. (2017). Translation complex profile sequencing to study the in vivo dynamics of mRNA‐ribosome interactions during translation initiation, elongation and termination. Nature Protocols, 12(4), 697–731. https://doi.org/10.1038/nprot.2016.189
Shirokikh,, N. E., & Spirin,, A. S. (2008). Poly(A) leader of eukaryotic mRNA bypasses the dependence of translation on initiation factors. Proceedings of the National Academy of Sciences of the United States of America, 105(31), 10738–10743. https://doi.org/10.1073/pnas.0804940105
Sierra,, J. M., Meier,, D., & Ochoa,, S. (1974). Effect of development on the translation of messenger RNA in Artemia salina embryos. Proceedings of the National Academy of Sciences of the United States of America, 71(7), 2693–2697.
Simonetti,, A., Brito Querido,, J., Myasnikov,, A. G., Mancera‐Martinez,, E., Renaud,, A., Kuhn,, L., & Hashem,, Y. (2016). eIF3 peripheral subunits rearrangement after mRNA binding and start‐codon recognition. Molecular Cell, 63(2), 206–217. https://doi.org/10.1016/j.molcel.2016.05.033
Sinvani,, H., Haimov,, O., Svitkin,, Y., Sonenberg,, N., Tamarkin‐Ben‐Harush,, A., Viollet,, B., & Dikstein,, R. (2015). Translational tolerance of mitochondrial genes to metabolic energy stress involves TISU and eIF1‐eIF4GI cooperation in start codon selection. Cell Metabolism, 21(3), 479–492. https://doi.org/10.1016/j.cmet.2015.02.010
Siridechadilok,, B., Fraser,, C. S., Hall,, R. J., Doudna,, J. A., & Nogales,, E. (2005). Structural roles for human translation factor eIF3 in initiation of protein synthesis. Science, 310(5753), 1513–1515.
Skabkin,, M. A., Kiselyova,, O. I., Chernov,, K. G., Sorokin,, A. V., Dubrovin,, E. V., Yaminsky,, I. V., … Ovchinnikov,, L. P. (2004). Structural organization of mRNA complexes with major core mRNP protein YB‐1. Nucleic Acids Research, 32(18), 5621–5635. https://doi.org/10.1093/nar/gkh889
Skabkin,, M. A., Skabkina,, O. V., Dhote,, V., Komar,, A. A., Hellen,, C. U., & Pestova,, T. V. (2010). Activities of Ligatin and MCT‐1/DENR in eukaryotic translation initiation and ribosomal recycling. Genes %26 Development, 24(16), 1787–1801. https://doi.org/10.1101/gad.1957510
Skabkin,, M. A., Skabkina,, O. V., Hellen,, C. U., & Pestova,, T. V. (2013). Reinitiation and other unconventional posttermination events during eukaryotic translation. Molecular Cell, 51(2), 249–264. https://doi.org/10.1016/j.molcel.2013.05.026
Slavov,, N., Semrau,, S., Airoldi,, E., Budnik,, B., & van Oudenaarden,, A. (2015). Differential stoichiometry among core ribosomal proteins. Cell Reports, 13(5), 865–873. https://doi.org/10.1016/j.celrep.2015.09.056
Smircich,, P., Eastman,, G., Bispo,, S., Duhagon,, M. A., Guerra‐Slompo,, E. P., Garat,, B., … Sotelo‐Silveira,, J. R. (2015). Ribosome profiling reveals translation control as a key mechanism generating differential gene expression in Trypanosoma cruzi. BMC Genomics, 16, 443. https://doi.org/10.1186/s12864-015-1563-8
Smith,, E., Meyerrose,, T. E., Kohler,, T., Namdar‐Attar,, M., Bab,, N., Lahat,, O., … Frenkel,, B. (2005). Leaky ribosomal scanning in mammalian genomes: Significance of histone H4 alternative translation in vivo. Nucleic Acids Research, 33(4), 1298–1308. https://doi.org/10.1093/nar/gki248
Soetanto,, R., Hynes,, C. J., Patel,, H. R., Humphreys,, D. T., Evers,, M., Duan,, G., … Preiss,, T. (2016). Role of miRNAs and alternative mRNA 3′‐end cleavage and polyadenylation of their mRNA targets in cardiomyocyte hypertrophy. Biochimica et Biophysica Acta, 1859(5), 744–756. https://doi.org/10.1016/j.bbagrm.2016.03.010
Sokabe,, M., & Fraser,, C. S. (2014). Human eukaryotic initiation factor 2 (eIF2)‐GTP‐Met‐tRNAi ternary complex and eIF3 stabilize the 43 S preinitiation complex. The Journal of Biological Chemistry, 289(46), 31827–31836. https://doi.org/10.1074/jbc.M114.602870
Sokabe,, M., & Fraser,, C. S. (2017). A helicase‐independent activity of eIF4A in promoting mRNA recruitment to the human ribosome. Proceedings of the National Academy of Sciences of the United States of America, 114(24), 6304–6309. https://doi.org/10.1073/pnas.1620426114
Sokabe,, M., Fraser,, C. S., & Hershey,, J. W. (2012). The human translation initiation multi‐factor complex promotes methionyl‐tRNAi binding to the 40S ribosomal subunit. Nucleic Acids Research, 40(2), 905–913. https://doi.org/10.1093/nar/gkr772
Somers,, J., Poyry,, T., & Willis,, A. E. (2013). A perspective on mammalian upstream open reading frame function. The International Journal of Biochemistry %26 Cell Biology, 45(8), 1690–1700. https://doi.org/10.1016/j.biocel.2013.04.020
Sonenberg,, N., & Hinnebusch,, A. G. (2009). Regulation of translation initiation in eukaryotes: Mechanisms and biological targets. Cell, 136(4), 731–745. https://doi.org/10.1016/j.cell.2009.01.042
Soto‐Rifo,, R., Rubilar,, P. S., Limousin,, T., de Breyne,, S., Decimo,, D., & Ohlmann,, T. (2012). DEAD‐box protein DDX3 associates with eIF4F to promote translation of selected mRNAs. The EMBO Journal, 31(18), 3745–3756. https://doi.org/10.1038/emboj.2012.220
Spirin,, A. S. (2009a). How does a scanning ribosomal particle move along the 5′‐untranslated region of eukaryotic mRNA? Brownian ratchet model. Biochemistry, 48(45), 10688–10692. https://doi.org/10.1021/bi901379a
Spirin,, A. S. (2009b). The ribosome as a conveying thermal ratchet machine. The Journal of Biological Chemistry, 284(32), 21103–21119. https://doi.org/10.1074/jbc.X109.001552
Srivastava,, S., Verschoor,, A., & Frank,, J. (1992). Eukaryotic initiation factor 3 does not prevent association through physical blockage of the ribosomal subunit‐subunit interface. Journal of Molecular Biology, 226(2), 301–304.
Standart,, N., & Minshall,, N. (2008). Translational control in early development: CPEB, P‐bodies and germinal granules. Biochemical Society Transactions, 36(Pt. 4), 671–676. https://doi.org/10.1042/BST0360671
Starck,, S. R., Tsai,, J. C., Chen,, K., Shodiya,, M., Wang,, L., Yahiro,, K., … Walter,, P. (2016). Translation from the 5′ untranslated region shapes the integrated stress response. Science, 351(6272), aad3867. https://doi.org/10.1126/science.aad3867
Steitz,, J. A. (1969). Polypeptide chain initiation: Nucleotide sequences of the three ribosomal binding sites in bacteriophage R17 RNA. Nature, 224(5223), 957–964.
Steitz,, T. A. (2005). On the structural basis of peptide‐bond formation and antibiotic resistance from atomic structures of the large ribosomal subunit. FEBS Letters, 579(4), 955–958. https://doi.org/10.1016/j.febslet.2004.11.053
Steitz,, T. A., & Moore,, P. B. (2017). Perspectives on the ribosome. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, 372(1716), 20160537. https://doi.org/10.1098/rstb.2016.0537
Sugiyama,, H., Takahashi,, K., Yamamoto,, T., Iwasaki,, M., Narita,, M., Nakamura,, M., … Yamanaka,, S. (2017). Nat1 promotes translation of specific proteins that induce differentiation of mouse embryonic stem cells. Proceedings of the National Academy of Sciences of the United States of America, 114(2), 340–345. https://doi.org/10.1073/pnas.1617234114
Sun,, Y., Atas,, E., Lindqvist,, L., Sonenberg,, N., Pelletier,, J., & Meller,, A. (2012). The eukaryotic initiation factor eIF4H facilitates loop‐binding, repetitive RNA unwinding by the eIF4A DEAD‐box helicase. Nucleic Acids Research, 40(13), 6199–6207. https://doi.org/10.1093/nar/gks278
Sun,, Y., Atas,, E., Lindqvist,, L. M., Sonenberg,, N., Pelletier,, J., & Meller,, A. (2014). Single‐molecule kinetics of the eukaryotic initiation factor 4AI upon RNA unwinding. Structure, 22(7), 941–948. https://doi.org/10.1016/j.str.2014.04.014
Svitkin,, Y. V., Gradi,, A., Imataka,, H., Morino,, S., & Sonenberg,, N. (1999). Eukaryotic initiation factor 4GII (eIF4GII), but not eIF4GI, cleavage correlates with inhibition of host cell protein synthesis after human rhinovirus infection. Journal of Virology, 73(4), 3467–3472.
Sweeney,, T. R., Abaeva,, I. S., Pestova,, T. V., & Hellen,, C. U. (2014). The mechanism of translation initiation on Type 1 picornavirus IRESs. The EMBO Journal, 33(1), 76–92. https://doi.org/10.1002/embj.201386124
Takyar,, S., Hickerson,, R. P., & Noller,, H. F. (2005). mRNA helicase activity of the ribosome. Cell, 120(1), 49–58. https://doi.org/10.1016/j.cell.2004.11.042
Tang,, L., Morris,, J., Wan,, J., Moore,, C., Fujita,, Y., Gillaspie,, S., … Asano,, K. (2017). Competition between translation initiation factor eIF5 and its mimic protein 5MP determines non‐AUG initiation rate genome‐wide. Nucleic Acids Research, 45, 11941–11953. https://doi.org/10.1093/nar/gkx808
Tarun, Jr., S. Z., & Sachs,, A. B. (1996). Association of the yeast poly(A) tail binding protein with translation initiation factor eIF‐4G. The EMBO Journal, 15(24), 7168–7177.
Terenin,, I. M., Akulich,, K. A., Andreev,, D. E., Polyanskaya,, S. A., Shatsky,, I. N., & Dmitriev,, S. E. (2016). Sliding of a 43S ribosomal complex from the recognized AUG codon triggered by a delay in eIF2‐bound GTP hydrolysis. Nucleic Acids Research, 44(4), 1882–1893. https://doi.org/10.1093/nar/gkv1514
Terenin,, I. M., Smirnova,, V. V., Andreev,, D. E., Dmitriev,, S. E., & Shatsky,, I. N. (2017). A researcher`s guide to the galaxy of IRESs. Cellular and Molecular Life Sciences, 74(8), 1431–1455. https://doi.org/10.1007/s00018-016-2409-5
Thakor,, N., & Holcik,, M. (2012). IRES‐mediated translation of cellular messenger RNA operates in eIF2alpha‐ independent manner during stress. Nucleic Acids Research, 40(2), 541–552. https://doi.org/10.1093/nar/gkr701
Thakor,, N., Smith,, M. D., Roberts,, L., Faye,, M. D., Patel,, H., Wieden,, H. J., … Holcik,, M. (2017). Cellular mRNA recruits the ribosome via eIF3‐PABP bridge to initiate internal translation. RNA Biology, 14(5), 553–567. https://doi.org/10.1080/15476286.2015.1137419
Thoreen,, C. C., Chantranupong,, L., Keys,, H. R., Wang,, T., Gray,, N. S., & Sabatini,, D. M. (2012). A unifying model for mTORC1‐mediated regulation of mRNA translation. Nature, 485(7396), 109–113. https://doi.org/10.1038/nature11083
Tocilj,, A., Schlunzen,, F., Janell,, D., Gluhmann,, M., Hansen,, H. A., Harms,, J., … Yonath,, A. (1999). The small ribosomal subunit from Thermus thermophilus at 4.5 A resolution: Pattern fittings and the identification of a functional site. Proceedings of the National Academy of Sciences of the United States of America, 96(25), 14252–14257.
Topisirovic,, I., Svitkin,, Y. V., Sonenberg,, N., & Shatkin,, A. J. (2011). Cap and cap‐binding proteins in the control of gene expression. WIREs RNA, 2(2), 277–298. https://doi.org/10.1002/wrna.52
Tranque,, P., Hu,, M. C., Edelman,, G. M., & Mauro,, V. P. (1998). rRNA complementarity within mRNAs: A possible basis for mRNA‐ribosome interactions and translational control. Proceedings of the National Academy of Sciences of the United States of America, 95(21), 12238–12243.
Tseng,, H. Y., Chen,, Y. A., Jen,, J., Shen,, P. C., Chen,, L. M., Lin,, T. D., … Hsu,, H. L. (2017). Oncogenic MCT‐1 activation promotes YY1‐EGFR‐MnSOD signaling and tumor progression. Oncogene, 6(4), e313. https://doi.org/10.1038/oncsis.2017.13
Tuller,, T., Ruppin,, E., & Kupiec,, M. (2009). Properties of untranslated regions of the S. cerevisiae genome. BMC Genomics, 10, 391. https://doi.org/10.1186/1471-2164-10-391
Turner,, R. E., Pattison,, A. D., & Beilharz,, T. H. (2017). Alternative polyadenylation in the regulation and dysregulation of gene expression. Seminars in Cell %26 Developmental Biology, 75, 61–69. https://doi.org/10.1016/j.semcdb.2017.08.056
Uemura,, S., Dorywalska,, M., Lee,, T. H., Kim,, H. D., Puglisi,, J. D., & Chu,, S. (2007). Peptide bond formation destabilizes Shine–Dalgarno interaction on the ribosome. Nature, 446(7134), 454–457. https://doi.org/10.1038/nature05625
Unbehaun,, A., Borukhov,, S. I., Hellen,, C. U., & Pestova,, T. V. (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 %26 Development, 18(24), 3078–3093.
Vaidya,, A. T., Lomakin,, I. B., Joseph,, N. N., Dmitriev,, S. E., & Steitz,, T. A. (2017). Crystal structure of the C‐terminal domain of human eIF2D and its implications on eukaryotic translation initiation. Journal of Molecular Biology, 429(18), 2765–2771. https://doi.org/10.1016/j.jmb.2017.07.015
Valasek,, L., Nielsen,, K. H., & Hinnebusch,, A. G. (2002). Direct eIF2‐eIF3 contact in the multifactor complex is important for translation initiation in vivo. The EMBO Journal, 21(21), 5886–5898.
Valasek,, L., Nielsen,, K. H., Zhang,, F., Fekete,, C. A., & Hinnebusch,, A. G. (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. Molecular and Cellular Biology, 24(21), 9437–9455.
Valasek,, L. S. (2012). `Ribozoomin`—translation initiation from the perspective of the ribosome‐bound eukaryotic initiation factors (eIFs). Current Protein %26 Peptide Science, 13(4), 305–330.
Valasek,, L. S., Zeman,, J., Wagner,, S., Beznoskova,, P., Pavlikova,, Z., Mohammad,, M. P., … Gunisova,, S. (2017). Embraced by eIF3: Structural and functional insights into the roles of eIF3 across the translation cycle. Nucleic Acids Research, 45, 10948–10968. https://doi.org/10.1093/nar/gkx805
van der Weyden,, L., White,, J. K., Adams,, D. J., & Logan,, D. W. (2011). The mouse genetics toolkit: Revealing function and mechanism. Genome Biology, 12(6), 224. https://doi.org/10.1186/gb-2011-12-6-224
Vassilenko,, K. S., Alekhina,, O. M., Dmitriev,, S. E., Shatsky,, I. N., & Spirin,, A. S. (2011). Unidirectional constant rate motion of the ribosomal scanning particle during eukaryotic translation initiation. Nucleic Acids Research, 39(13), 5555–5567. https://doi.org/10.1093/nar/gkr147
Vattem,, K. M., & Wek,, R. C. (2004). Reinitiation involving upstream ORFs regulates ATF4 mRNA translation in mammalian cells. Proceedings of the National Academy of Sciences of the United States of America, 101(31), 11269–11274.
Villa,, N., Do,, A., Hershey,, J. W., & Fraser,, C. S. (2013). Human eukaryotic initiation factor 4G (eIF4G) protein binds to eIF3c, ‐d, and ‐e to promote mRNA recruitment to the ribosome. The Journal of Biological Chemistry, 288(46), 32932–32940. https://doi.org/10.1074/jbc.M113.517011
Villalba,, A., Coll,, O., & Gebauer,, F. (2011). Cytoplasmic polyadenylation and translational control. Current Opinion in Genetics %26 Development, 21(4), 452–457. https://doi.org/10.1016/j.gde.2011.04.006
Viphakone,, N., Voisinet‐Hakil,, F., & Minvielle‐Sebastia,, L. (2008). Molecular dissection of mRNA poly(A) tail length control in yeast. Nucleic Acids Research, 36(7), 2418–2433. https://doi.org/10.1093/nar/gkn080
Visweswaraiah,, J., & Hinnebusch,, A. G. (2017). Interface between 40S exit channel protein uS7/Rps5 and eIF2alpha modulates start codon recognition in vivo. eLife, 6, e22572. https://doi.org/10.7554/eLife.22572
Voigts‐Hoffmann,, F., Klinge,, S., & Ban,, N. (2012). Structural insights into eukaryotic ribosomes and the initiation of translation. Current Opinion in Structural Biology, 22(6), 768–777. https://doi.org/10.1016/j.sbi.2012.07.010
von der Haar,, T., Gross,, J. D., Wagner,, G., & McCarthy,, J. E. (2004). The mRNA cap‐binding protein eIF4E in post‐transcriptional gene expression. Nature Structural %26 Molecular Biology, 11(6), 503–511. https://doi.org/10.1038/nsmb779
von Hippel,, P. H., & Delagoutte,, E. (2001). A general model for nucleic acid helicases and their "coupling" within macromolecular machines. Cell, 104(2), 177–190.
Walker,, S. E., Zhou,, F., Mitchell,, S. F., Larson,, V. S., Valasek,, L., Hinnebusch,, A. G., & Lorsch,, J. R. (2013). Yeast eIF4B binds to the head of the 40S ribosomal subunit and promotes mRNA recruitment through its N‐terminal and internal repeat domains. RNA, 19(2), 191–207. https://doi.org/10.1261/rna.035881.112
Walters,, B., & Thompson,, S. R. (2016). Cap‐independent translational control of carcinogenesis. Frontiers in Oncology, 6, 128. https://doi.org/10.3389/fonc.2016.00128
Wang,, H., McManus,, J., & Kingsford,, C. (2016). Isoform‐level ribosome occupancy estimation guided by transcript abundance with Ribomap. Bioinformatics, 32(12), 1880–1882. https://doi.org/10.1093/bioinformatics/btw085
Warner,, J. R., Rich,, A., & Hall,, C. E. (1962). Electron microscope studies of ribosomal clusters synthesizing hemoglobin. Science, 138(3548), 1399–1403. https://doi.org/10.1126/science.138.3548.1399
Weber,, L. A., Hickey,, E. D., & Baglioni,, C. (1978). Influence of potassium salt concentration and temperature on inhibition of mRNA translation by 7‐methylguanosine5`‐monophosphate. The Journal of Biological Chemistry, 253(1), 178–183.
Wei,, C. C., Balasta,, M. L., Ren,, J., & Goss,, D. J. (1998). Wheat germ poly(A) binding protein enhances the binding affinity of eukaryotic initiation factor 4F and (iso)4F for cap analogues. Biochemistry, 37(7), 1910–1916. https://doi.org/10.1021/bi9724570
Weill,, L., Belloc,, E., Bava,, F. A., & Mendez,, R. (2012). Translational control by changes in poly(A) tail length: Recycling mRNAs. Nature Structural %26 Molecular Biology, 19(6), 577–585. https://doi.org/10.1038/nsmb.2311
Weisser,, M., Schafer,, T., Leibundgut,, M., Bohringer,, D., Aylett,, C. H. S., & Ban,, N. (2017). Structural and functional insights into human re‐initiation complexes. Molecular Cell, 67(3), 447–456 e447. https://doi.org/10.1016/j.molcel.2017.06.032
Weisser,, M., Voigts‐Hoffmann,, F., Rabl,, J., Leibundgut,, M., & Ban,, N. (2013). The crystal structure of the eukaryotic 40S ribosomal subunit in complex with eIF1 and eIF1A. Nature Structural %26 Molecular Biology, 20(8), 1015–1017. https://doi.org/10.1038/nsmb.2622
Wilson,, D. N., & Doudna Cate,, J. H. (2012). The structure and function of the eukaryotic ribosome. Cold Spring Harbor Perspectives in Biology, 4(5), a011536. https://doi.org/10.1101/cshperspect.a011536
Wittenberg,, A. D., Azar,, S., Klochendler,, A., Stolovich‐Rain,, M., Avraham,, S., Birnbaum,, L., … Meyuhas,, O. (2016). Phosphorylated ribosomal protein S6 is required for Akt‐driven hyperplasia and malignant transformation, but not for hypertrophy, aneuploidy and hyperfunction of pancreatic beta‐cells. PLoS One, 11(2), e0149995. https://doi.org/10.1371/journal.pone.0149995
Wolfe,, A. L., Singh,, K., Zhong,, Y., Drewe,, P., Rajasekhar,, V. K., Sanghvi,, V. R., … Wendel,, H. G. (2014). RNA G‐quadruplexes cause eIF4A‐dependent oncogene translation in cancer. Nature, 513(7516), 65–70. https://doi.org/10.1038/nature13485
Wolin,, S. L., & Walter,, P. (1988). Ribosome pausing and stacking during translation of a eukaryotic mRNA. The EMBO Journal, 7(11), 3559–3569.
Wortham,, N. C., & Proud,, C. G. (2015). eIF2B: Recent structural and functional insights into a key regulator of translation. Biochemical Society Transactions, 43(6), 1234–1240. https://doi.org/10.1042/BST20150164
Wu,, B., Eliscovich,, C., Yoon,, Y. J., & Singer,, R. H. (2016). Translation dynamics of single mRNAs in live cells and neurons. Science, 352(6292), 1430–1435. https://doi.org/10.1126/science.aaf1084
Xue,, S., Tian,, S., Fujii,, K., Kladwang,, W., Das,, R., & Barna,, M. (2015). RNA regulons in Hox 5` UTRs confer ribosome specificity to gene regulation. Nature, 517(7532), 33–38. https://doi.org/10.1038/nature14010
Yamamoto,, H., Unbehaun,, A., Loerke,, J., Behrmann,, E., Collier,, M., Burger,, J., … Spahn,, C. M. (2014). Structure of the mammalian 80S initiation complex with initiation factor 5B on HCV‐IRES RNA. Nature Structural %26 Molecular Biology, 21(8), 721–727. https://doi.org/10.1038/nsmb.2859
Yamamoto,, H., Unbehaun,, A., & Spahn,, C. M. T. (2017). Ribosomal chamber music: Toward an understanding of IRES mechanisms. Trends in Biochemical Sciences, 42(8), 655–668. https://doi.org/10.1016/j.tibs.2017.06.002
Yanagiya,, A., Svitkin,, Y. V., 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. Molecular and Cellular Biology, 29(6), 1661–1669. https://doi.org/10.1128/MCB.01187-08
Yarunin,, A., Harris,, R. E., Ashe,, M. P., & Ashe,, H. L. (2011). Patterning of the Drosophila oocyte by a sequential translation repression program involving the d4EHP and Belle translational repressors. RNA Biology, 8(5), 904–912. https://doi.org/10.4161/rna.8.5.16325
Yazaki,, K., Yoshida,, T., Wakiyama,, M., & Miura,, K. (2000). Polysomes of eukaryotic cells observed by electron microscopy. Journal of Electron Microscopy, 49(5), 663–668.
Yoder‐Hill,, J., Pause,, A., Sonenberg,, N., & Merrick,, W. C. (1993). The p46 subunit of eukaryotic initiation factor (eIF)‐4F exchanges with eIF‐4A. The Journal of Biological Chemistry, 268(8), 5566–5573.
Yu,, Y., Marintchev,, A., Kolupaeva,, V. G., Unbehaun,, A., Veryasova,, T., Lai,, S. C., … Pestova,, T. V. (2009). Position of eukaryotic translation initiation factor eIF1A on the 40S ribosomal subunit mapped by directed hydroxyl radical probing. Nucleic Acids Research, 37(15), 5167–5182. https://doi.org/10.1093/nar/gkp519
Yueh,, A., & Schneider,, R. J. (1996). Selective translation initiation by ribosome jumping in adenovirus‐infected and heat‐shocked cells. Genes %26 Development, 10(12), 1557–1567.
Yueh,, A., & Schneider,, R. J. (2000). Translation by ribosome shunting on adenovirus and hsp70 mRNAs facilitated by complementarity to 18S rRNA. Genes %26 Development, 14(4), 414–421.
Yusupova,, G. Z., Yusupov,, M. M., Cate,, J. H., & Noller,, H. F. (2001). The path of messenger RNA through the ribosome. Cell, 106(2), 233–241.
Zhang,, F., & Hinnebusch,, A. G. (2011). An upstream ORF with non‐AUG start codon is translated in vivo but dispensable for translational control of GCN4 mRNA. Nucleic Acids Research, 39(8), 3128–3140. https://doi.org/10.1093/nar/gkq1251
Zhang,, F., Saini,, A. K., Shin,, B. S., Nanda,, J., & Hinnebusch,, A. G. (2015). Conformational changes in the P site and mRNA entry channel evoked by AUG recognition in yeast translation preinitiation complexes. Nucleic Acids Research, 43(4), 2293–2312. https://doi.org/10.1093/nar/gkv028
Zhang,, Y., You,, J., Wang,, X., & Weber,, J. (2015). The DHX33 RNA helicase promotes mRNA translation initiation. Molecular and Cellular Biology, 35(17), 2918–2931. https://doi.org/10.1128/MCB.00315-15
Zhao,, P., Liu,, Q., Miller,, W. A., & Goss,, D. J. (2017). Eukaryotic translation initiation factor 4G (eIF4G) coordinates interactions with eIF4A, eIF4B, and eIF4E in binding and translation of the barley yellow dwarf virus 3′ cap‐independent translation element (BTE). The Journal of Biological Chemistry, 292(14), 5921–5931. https://doi.org/10.1074/jbc.M116.764902
Zhou,, M., Sandercock,, A. M., Fraser,, C. S., Ridlova,, G., Stephens,, E., Schenauer,, M. R., … Robinson,, C. V. (2008). Mass spectrometry reveals modularity and a complete subunit interaction map of the eukaryotic translation factor eIF3. Proceedings of the National Academy of Sciences of the United States of America, 105(47), 18139–18144. https://doi.org/10.1073/pnas.0801313105
Zinoviev,, A., Hellen,, C. U., & Pestova,, T. V. (2015). Multiple mechanisms of reinitiation on bicistronic calicivirus mRNAs. Molecular Cell, 57(6), 1059–1073. https://doi.org/10.1016/j.molcel.2015.01.039
Zuberek,, J., Kubacka,, D., Jablonowska,, A., Jemielity,, J., Stepinski,, J., Sonenberg,, N., & Darzynkiewicz,, E. (2007). Weak binding affinity of human 4EHP for mRNA cap analogs. RNA, 13(5), 691–697.