Gingras, A. C., Raught, B. & Sonenberg, N. eIF4 initiation factors: effectors of mRNA recruitment to ribosomes and regulators of translation. Annu. Rev. Biochem. 68, 913–963 (1999).
Hinnebusch, A. G. & Lorsch, J. R. The mechanism of eukaryotic translation initiation: new insights and challenges. Cold Spring Harb. Perspect. Biol. 4, a011544 (2012).
Merrick, W. C. eIF4F: a retrospective. J. Biol. Chem. 290, 24091–24099 (2015).
Abramson, R. D. et al. The ATP-dependent interaction of eukaryotic initiation factors with mRNA. J. Biol. Chem. 262, 3826–3832 (1987).
Kaye, N. M., Emmett, K. J., Merrick, W. C. & Jankowsky, E. Intrinsic RNA binding by the eukaryotic initiation factor 4F depends on a minimal RNA length but not on the m7G cap. J. Biol. Chem. 284, 17742–17750 (2009).
von der Haar, T. & McCarthy, J. E. Intracellular translation initiation factor levels in Saccharomyces cerevisiae and their role in cap-complex function. Mol. Microbiol. 46, 531–544 (2002).
Martinez-Salas, E., Francisco-Velilla, R., Fernandez-Chamorro, J. & Embarek, A. M. Insights into structural and mechanistic features of viral IRES elements. Front. Microbiol. 8, 2629 (2017).
Jia, Y., Polunovsky, V., Bitterman, P. B. & Wagner, C. R. Cap-dependent translation initiation factor eIF4E: an emerging anticancer drug target. Med. Res. Rev. 32, 786–814 (2012).
Otero, L. J., Ashe, M. P. & Sachs, A. B. The yeast poly(A)-binding protein Pab1p stimulates in vitro poly(A)-dependent and cap-dependent translation by distinct mechanisms. EMBO J. 18, 3153–3163 (1999).
He, H. et al. The yeast eukaryotic initiation factor 4G (eIF4G) HEAT domain interacts with eIF1 and eIF5 and is involved in stringent AUG selection. Mol. Cell. Biol. 23, 5431–5445 (2003).
Yourik, P. et al. Yeast eIF4A enhances recruitment of mRNAs regardless of their structural complexity. eLife 6, e31476 (2017).
Kumar, P., Hellen, C. U. & Pestova, T. V. Toward the mechanism of eIF4F-mediated ribosomal attachment to mammalian capped mRNAs. Genes Dev. 30, 1573–1588 (2016).
Gruner, S. et al. The structures of eIF4E-eIF4G complexes reveal an extended interface to regulate translation initiation. Mol. Cell 64, 467–479 (2016).
Oberer, M., Marintchev, A. & Wagner, G. Structural basis for the enhancement of eIF4A helicase activity by eIF4G. Genes Dev. 19, 2212–2223 (2005).
Rajagopal, V., Park, E. H., Hinnebusch, A. G. & Lorsch, J. R. Specific domains in yeast translation initiation factor eIF4G strongly bias RNA unwinding activity of the eIF4F complex toward duplexes with 5′-overhangs. J. Biol. Chem. 287, 20301–20312 (2012).
Cetin, B. & O’Leary, S. E. mRNA- and factor-driven dynamic variability controls eIF4F-cap recognition for translation initiation. Nucleic Acids Res. 50, 8240–8261 (2022).
O’Sullivan, M. H. & Fraser, C. S. Monitoring RNA restructuring in a human cell-free extract reveals eIF4A-dependent and eIF4A-independent unwinding activity. J. Biol. Chem. 299, 104936 (2023).
Lanker, S. et al. Interactions of the eIF-4F subunits in the yeast Saccharomyces cerevisiae. J. Biol. Chem. 267, 21167–21171 (1992).
Feoktistova, K., Tuvshintogs, E., Do, A. & Fraser, C. S. Human eIF4E promotes mRNA restructuring by stimulating eIF4A helicase activity. Proc. Natl Acad. Sci. USA 110, 13339–13344 (2013).
Cetin, B., Song, G. J. & O’Leary, S. E. Heterogeneous dynamics of protein-RNA interactions across transcriptome-derived messenger RNA populations. J. Am. Chem. Soc. 142, 21249–21253 (2020).
Sokabe, M. & Fraser, C. S. A helicase-independent activity of eIF4A in promoting mRNA recruitment to the human ribosome. Proc. Natl Acad. Sci. USA 114, 6304–6309 (2017).
Sen, N. D., Zhou, F., Ingolia, N. T. & Hinnebusch, A. G. Genome-wide analysis of translational efficiency reveals distinct but overlapping functions of yeast DEAD-box RNA helicases Ded1 and eIF4A. Genome Res. 25, 1196–1205 (2015).
Harms, U., Andreou, A. Z., Gubaev, A. & Klostermeier, D. eIF4B, eIF4G and RNA regulate eIF4A activity in translation initiation by modulating the eIF4A conformational cycle. Nucleic Acids Res. 42, 7911–7922 (2014).
Andreou, A. Z. & Klostermeier, D. eIF4B and eIF4G jointly stimulate eIF4A ATPase and unwinding activities by modulation of the eIF4A conformational cycle. J. Mol. Biol. 426, 51–61 (2014).
O’Leary, S. E., Petrov, A., Chen, J. & Puglisi, J. D. Dynamic recognition of the mRNA cap by Saccharomyces cerevisiae eIF4E. Structure 21, 2197–2207 (2013).
Krause, L., Willing, F., Andreou, A. Z. & Klostermeier, D. The domains of yeast eIF4G, eIF4E and the cap fine-tune eIF4A activities through an intricate network of stimulatory and inhibitory effects. Nucleic Acids Res. 50, 6497–6510 (2022).
Schutz, P. et al. Crystal structure of the yeast eIF4A-eIF4G complex: an RNA-helicase controlled by protein-protein interactions. Proc. Natl Acad. Sci. USA 105, 9564–9569 (2008).
Rozen, F. et al. Bidirectional RNA helicase activity of eucaryotic translation initiation factors 4A and 4F. Mol. Cell. Biol. 10, 1134–1144 (1990).
Ray, B. K. et al. ATP-dependent unwinding of messenger RNA structure by eukaryotic initiation factors. J. Biol. Chem. 260, 7651–7658 (1985).
Mitchell, S. F. et al. The 5′-7-methylguanosine cap on eukaryotic mRNAs serves both to stimulate canonical translation initiation and to block an alternative pathway. Mol. Cell 39, 950–962 (2010).
Marcotrigiano, J. et al. A conserved HEAT domain within eIF4G directs assembly of the translation initiation machinery. Mol. Cell 7, 193–203 (2001).
Hershey, P. E. et al. The Cap-binding protein eIF4E promotes folding of a functional domain of yeast translation initiation factor eIF4G1. J. Biol. Chem. 274, 21297–21304 (1999).
Rogers, G. W. Jr, Komar, A. A. & Merrick, W. C. eIF4A: the godfather of the DEAD box helicases. Prog. Nucleic Acid Res. Mol. Biol. 72, 307–331 (2002).
Lindqvist, L., Imataka, H. & Pelletier, J. Cap-dependent eukaryotic initiation factor-mRNA interactions probed by cross-linking. RNA 14, 960–969 (2008).
Liu, X., Schuessler, P. J., Sahoo, A. & Walker, S. E. Reconstitution and analyses of RNA interactions with eukaryotic translation initiation factors and ribosomal preinitiation complexes. Methods 162-163, 42–53 (2019).
Hilbert, M., Kebbel, F., Gubaev, A. & Klostermeier, D. eIF4G stimulates the activity of the DEAD box protein eIF4A by a conformational guidance mechanism. Nucleic Acids Res. 39, 2260–2270 (2011).
Andreou, A. Z., Harms, U. & Klostermeier, D. eIF4B stimulates eIF4A ATPase and unwinding activities by direct interaction through its 7-repeats region. RNA Biol. 14, 113–123 (2017).
Querido, J. B. et al. The structure of a human translation initiation complex reveals two independent roles for the helicase eIF4A. Nat. Struct. Mol. Biol. 31, 455–464 (2024).
Haizel, S. A., Bhardwaj, U., Gonzalez, R. L. Jr, Mitra, S. & Goss, D. J. 5′-UTR recruitment of the translation initiation factor eIF4GI or DAP5 drives cap-independent translation of a subset of human mRNAs. J. Biol. Chem. 295, 11693–11706 (2020).
Acker, M. G., Kolitz, S. E., Mitchell, S. F., Nanda, J. S. & Lorsch, J. R. Reconstitution of yeast translation initiation. Methods Enzymol. 430, 111–145 (2007).
Wang, J. et al. eIF5B gates the transition from translation initiation to elongation. Nature 573, 605–608 (2019).
Jarmoskaite, I., AlSadhan, I., Vaidyanathan, P. P. & Herschlag, D. How to measure and evaluate binding affinities. eLife 9, e57264 (2020).
Buttner, L., Javadi-Zarnaghi, F. & Hobartner, C. Site-specific labeling of RNA at internal ribose hydroxyl groups: terbium-assisted deoxyribozymes at work. J. Am. Chem. Soc. 136, 8131–8137 (2014).
Graham, J. S., Johnson, R. C. & Marko, J. F. Concentration-dependent exchange accelerates turnover of proteins bound to double-stranded DNA. Nucleic Acids Res. 39, 2249–2259 (2011).
Kamar, R. I. et al. Facilitated dissociation of transcription factors from single DNA binding sites. Proc. Natl Acad. Sci. USA 114, E3251–E3257 (2017).
Kosar, Z., Attar, A. G. & Erbas, A. Facilitated dissociation of nucleoid-associated proteins from DNA in the bacterial confinement. Biophys. J. 121, 1119–1133 (2022).
Luo, Y., North, J. A., Rose, S. D. & Poirier, M. G. Nucleosomes accelerate transcription factor dissociation. Nucleic Acids Res. 42, 3017–3027 (2014).
MacDougall, D. D. & Gonzalez, R. L. Jr Translation initiation factor 3 regulates switching between different modes of ribosomal subunit joining. J. Mol. Biol. 427, 1801–1818 (2015).
Wang, J. et al. Rapid 40S scanning and its regulation by mRNA structure during eukaryotic translation initiation. Cell 185, 4474–4487 (2022).
Rajyaguru, P., She, M. & Parker, R. Scd6 targets eIF4G to repress translation: RGG motif proteins as a class of eIF4G-binding proteins. Mol. Cell 45, 244–254 (2012).
Gupta, N., Lorsch, J. R. & Hinnebusch, A. G. Yeast Ded1 promotes 48S translation pre-initiation complex assembly in an mRNA-specific and eIF4F-dependent manner. eLife 7, e38892 (2018).
Linder, P. & Jankowsky, E. From unwinding to clamping—the DEAD box RNA helicase family. Nat. Rev. Mol. Cell Biol. 12, 505–516 (2011).
Sen, N. D. et al. Functional interplay between DEAD-box RNA helicases Ded1 and Dbp1 in preinitiation complex attachment and scanning on structured mRNAs in vivo. Nucleic Acids Res. 47, 8785–8806 (2019).
Sharma, D. & Jankowsky, E. The Ded1/DDX3 subfamily of DEAD-box RNA helicases. Crit. Rev. Biochem. Mol. Biol. 49, 343–360 (2014).
Brito Querido, J. et al. The structure of a human translation initiation complex reveals two independent roles for the helicase eIF4A. Nat. Struct. Mol. Biol. 31, 455–464 (2024).
Bohlen, J., Fenzl, K., Kramer, G., Bukau, B. & Teleman, A. A. Selective 40S footprinting reveals cap-tethered ribosome scanning in human cells. Mol. Cell 79, 561–574 (2020).
Pause, A., Methot, N., Svitkin, Y., Merrick, W. C. & Sonenberg, N. 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. EMBO J. 13, 1205–1215 (1994).
Livingston, N. M. et al. Bursting translation on single mRNAs in live cells. Mol. Cell 83, 2276–2289 (2023).
Zinshteyn, B., Rojas-Duran, M. F. & Gilbert, W. V. Translation initiation factor eIF4G1 preferentially binds yeast transcript leaders containing conserved oligo-uridine motifs. RNA 23, 1365–1375 (2017).
Tamarkin-Ben-Harush, A., Vasseur, J. J., Debart, F., Ulitsky, I. & Dikstein, R. Cap-proximal nucleotides via differential eIF4E binding and alternative promoter usage mediate translational response to energy stress. eLife 6, e21907 (2017).
Lakowicz, J. R. Principles of Fluorescence Spectroscopy 3rd edn (Springer, 2006).
Blanchard, S. C., Kim, H. D., Gonzalez, R. L. Jr, Puglisi, J. D. & Chu, S. tRNA dynamics on the ribosome during translation. Proc. Natl Acad. Sci. USA 101, 12893–12898 (2004).
Blanchard, S. C., Gonzalez, R. L., Kim, H. D., Chu, S. & Puglisi, J. D. tRNA selection and kinetic proofreading in translation. Nat. Struct. Mol. Biol. 11, 1008–1014 (2004).
Edelstein, A., Amodaj, N., Hoover, K., Vale, R. & Stuurman, N. Computer control of microscopes using microManager. Curr. Protoc. Mol. Biol. https://doi.org/10.1002/0471142727.mb1420s92 (2010).
Ray, K. K. et al. Entropic control of the free-energy landscape of an archetypal biomolecular machine. Proc. Natl Acad. Sci. USA 120, e2220591120 (2023).
Verma, A. R. et al. Increasing the accuracy of single-molecule data analysis using tMAVEN. Biophys J. 123, 2765–2780 (2024).
Bronson, J. E., Fei, J., Hofman, J. M., Gonzalez, R. L. Jr & Wiggins, C. H. Learning rates and states from biophysical time series: a Bayesian approach to model selection and single-molecule FRET data. Biophys. J. 97, 3196–3205 (2009).
Schindelin, J. et al. Fiji: an open-source platform for biological-image analysis. Nat. Methods 9, 676–682 (2012).