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Recognition of γ-Subunit by β-Subunit in Translation Initiation Factor 2. Stabilization of the GTP-Bound State of I/F 2 in Archaea and Eukaryotes

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Abstract

Eukaryotic and archaeal translation initiation factor 2 (e/aIF2) functions as a heterotrimeric complex. It consists of three subunits (α, β, γ). α- and β-subunits are bound to γ-subunit by hydrogen bonds and van der Waals interactions, but do not contact each other. Although main functions of the factor are performed by the γ-subunit, reliable formation of αγ and βγ complexes is necessary for its proper functioning. In this work, we introduced mutations in the recognition part of the βγ interface and showed that hydrophobic effect plays a crucial role in the recognition of subunits both in eukaryotes and archaea. Shape and properties of the groove on the surface of γ-subunit facilitates transition of the disordered recognition part of the β-subunit into an α-helix containing approximately the same number of residues in archaea and eukaryotes. In addition, based on the newly obtained data, it was concluded that in archaea and eukaryotes, transition of the γ-subunit to the active state leads to additional contact between the region of switch 1 and C-terminal part of the β-subunit, which stabilizes helical conformation of the switch.

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Abbreviations

ZFD:

zinc finger domain

References

  1. Algire, M. A., Maag, D., and Lorsch, J. R. (2005) Pi release from eIF2, not GTP hydrolysis, is the step controlled by start-site selection during eukaryotic translation initiation, Mol. Cell, 20, 251-262, https://doi.org/10.1016/j.molcel.2005.09.08.

    Article  CAS  PubMed  Google Scholar 

  2. Kapp, L. D., and Lorsch, J. R. (2004) The molecular mechanisms of eukaryotic translation, Annu. Rev. Biochem., 73, 657-704, https://doi.org/10.1146/annurev.biochem.73.030403.080419.

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Sokabe, M., Yao, M., Sakai, N., Toya, S., and Tanaka, I. (2006) Structure of archaeal translational initiation factor 2bg-GDP reveals significant conformational change of the b-subunit and switch 1 region, Proc. Natl. Acad. Sci. USA, 103, 13016-13021, https://doi.org/10.1073/pnas.0604165103.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Yatime, L., Mechulam, Y., Blanquet, S., and Schmitt, E. (2007) Structure of an archaeal heterotrimeric initiation factor 2 reveals a nucleotide state between the GTP and the GDP states, Proc. Natl. Acad. Sci. USA, 104, 18445-18450, https://doi.org/10.1073/pnas.0706784104.

    Article  PubMed  PubMed Central  Google Scholar 

  6. Stolboushkina, E., Nikonov, S., Nikulin, A., Bläsi, U., Manstein, D. J., Fedorov, R., Garber, M., and Nikonov, O. (2008) Crystal structure of the intact archaeal translation initiation factor 2 demonstrates very high conformational flexibility in the α- and β-subunits, J. Mol. Biol., 382, 680-691, https://doi.org/10.1016/j.jmb.2008.07.039.

    Article  CAS  PubMed  Google Scholar 

  7. Adomavicius, T., Guaita, M., Zhou, Y., Jennings, M. D., Latif, Z., Roseman, A. M., and Pavitt, G. D. (2019) The structural basis of translational control by eIF2 phosphorylation, Nat. Commun., 10, 2136-2146, https://doi.org/10.1038/s41467-019-10167-3.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Querido, J., Sokabe, M., Kraatz, S., Gordiyenko, Y., Skehel, J. M., et al. (2020) Structure of a human 48S translational initiation complex, Science, 369, 1220-1227, https://doi.org/10.1126/science.aba4904.

    Article  CAS  PubMed Central  Google Scholar 

  9. Thoms, M., Buschauer, R., Ameismeier, M., Koepke, L., Denk, T., et al. (2020) Structural basis for translational shutdown and immune evasion by the Nsp1 protein of SARS-CoV-2, Science, 369, 1249-1255, https://doi.org/10.1126/science.abc8665.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Thompson, G. M., Pacheco, E., Melo, E. O., and Castilho, B. A. (2000) Conserved sequences in the β subunit of archaeal and eukaryal translation initiation factor 2 (eIF2), absent from eIF5, mediate interaction with eIF2γ, Biochem. J., 347, 703-709, https://doi.org/10.1042/bj3470703.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Kashiwagi, K., Yokoyama, T., Nishimoto, M., Takahashi, M., Sakamoto, A., et al. (2019) Structural basis for eIF2B inhibition in integrated stress response, Science, 364, 495-499, https://doi.org/10.1126/science.AAW4104.

    Article  CAS  PubMed  Google Scholar 

  12. Laurino, J. P., Thompson, G. M., Pacheco, E., and Castilho, B. A. (1999) The β subunit of eukaryotic translation initiation factor 2 binds mRNA through the lysine repeats and a region comprising the C2-C2 motif, Mol. Cell. Biol., 19, 173-181, https://doi.org/10.1128/MCB.19.1.173.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Hashimoto, N. N., Carnevalli, L. S., and Castilho, B. A. (2002) Translation initiation at non-AUG codons mediated by a weakened association of eukaryotic initiation factor (eIF) 2 subunits, Biochem. J., 367, 359-368, https://doi.org/10.1042/bj20020556.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Huang, H. K., Yoon, H., Hanning, E. M., and Donahue, T. F. (1997) GTP hydrolysis controls stringent selection of the AUG start codon during translation initiation in Saccharomyces cerevisiae, Genes Dev., 11, 2396-2413, https://doi.org/10.1101/gad.11.18.2396.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Donahue, T. F., Cigan, A. M., Pabich, E. K., and Valavicius, B. C. (1988) Mutations at a Zn(II) finger motif in the yeast eIF-2 β gene alter ribosomal start-site selection during the scanning process, Cell, 54, 621-632, https://doi.org/10.1016/s0092-8674(88)80006-0.

    Article  CAS  PubMed  Google Scholar 

  16. Castilho-Valavicius, B., Thompson, G. M., and Donahue, T. F. (1992) Mutation analysis of the Cys-X2-Cys-X19-Cys-X2-Cys motif in the β subunit of eukaryotic translation initiation factor 2, Gene Expr., 2, 297-309.

    CAS  PubMed  Google Scholar 

  17. Borck, G., Shin, B.-S., Stiller, B., Mimouni-Bloch, A., Thiele, H., Kim, J.-R., et al. (2012) eIF2γ mutation that disrupts eIF2 complex integrity links intellectual disability to impaired translation initiation, Mol. Cell, 48, 641-646, https://doi.org/10.1016/j.molcel.2012.09.005.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Nikonov, O. S., Kravchenko, O. V., Nevskaya, N. A., Stolboushkina, E. A., Garber, M. B., and Nikonov, S. V. (2021) Effect of the Ile222Thr missense mutation in SsoIF2γ on the affinity of γ and β subunits of aIF2, Crystallogr. Rep., 66, 797-801, https://doi.org/10.1134/S106377452105015119.

    Article  CAS  Google Scholar 

  19. Mirdita, M., Schütze, K., Moriwaki, Y., Heo, L., Ovchinnikov, S., and Steinegger, M. (2022) ColabFold: making protein folding accessible to all, Nat. Methods, 19, 679-682, https://doi.org/10.1038/s41592-022-01488-1.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Žídek, A., Potapenko, A., et al. (2021) Highly accurate protein structure prediction with AlphaFold, Nature, 596, 583-589, https://doi.org/10.1038/s41586-021-03819-2.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Mirdita, M., Steinegger, M., and Söding, J. (2019) MMseqs2 desktop and local web server app for fast, interactive sequence searches, Bioinformatics, 35, 2856-2858, https://doi.org/10.1093/bioinformatics/bty1057.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Steinegger, M., Meier, M., Mirdita, M., Vöhringer, H., Haunsberger, S. J., and Söding, J. (2019) HH-suite3 for fast remote homology detection and deep protein annotation, BMC Bioinformatics, 20, 473, https://doi.org/10.1186/s12859-019-3019-7.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Eastman, P., Swails, J., Chodera, J. D., McGibbon, R. T., Zhao, Y., et al. (2017) OpenMM 7: Rapid development of high performance algorithms for molecular dynamics, PLoS Comput. Biol., 13, e1005659, https://doi.org/10.1371/journal.pcbi.1005659.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Emsley, P., Lohkamp, B., Scott, W., and Cowtan, K. (2010) Features and Development of Coot, Acta Crystallogr. Sec. D Biol. Crystallogr., 66, 486-501, https://doi.org/10.1107/S0907444910007493.

    Article  CAS  Google Scholar 

  25. Nikonov, O., Stolboushkina, E., Arkhipova, V., Kravchenko, O., Nikonov, S., and Garber, M. (2014) Conformational transitions in the γ subunit of the archaeal translation initiation factor 2, Acta Cryst., D70, 658-667, https://doi.org/10.1107/S1399004713032240.

    Article  CAS  Google Scholar 

  26. Dubiez, E., Aleksandrov, A., Lazennec-Schurdevin, C., Mechulam, Y., and Schmitt, E. (2015) Identification of a second GTP-bound magnesium ion in archaeal initiation factor 2, Nucleic Acids Res., 43, 2946-2957, https://doi.org/10.1093/nar/gkv053.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Gutierrez, P., Osborne, M. J., Siddiqui, N., Trempe, J. F., Arrowsmith, C., and Gehring, K. (2004) Structure of the archaeal translation initiation factor aIF2β from Methanobacterium thermoautotrophicum: implications for translation initiation, Protein Sci., 13, 659-667, https://doi.org/10.1110/ps.03506604.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Vasile, F., Pechkova, E., and Nicolini, C. (2008) Solution structure of the β-subunit of the translation initiation factor aIF2 from archaebacteria Sulfolobus solfataricus, Proteins, 70, 1112-1115, https://doi.org/10.1002/Prot.21797.

    Article  CAS  PubMed  Google Scholar 

  29. Schmitt, E., Naveau, M., and Mechulam, Y. (2010) Eukaryotic and archaeal translation initiation factor 2: a heterotrimeric tRNA carrier, FEBS Lett., 584, 405-412, https://doi.org/10.1016/j.febslet.2009.11.002.

    Article  CAS  PubMed  Google Scholar 

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Acknowledgments

The authors are grateful to E. A. Stolboushkina for providing plasmids pET-11a with the gene encoding the γ-subunit of the translation initiation factor 2 of the archaea S. solfataricus (wild type and mutated at position 181), as well as pET-11c with the EIF2S2 gene; U. Dzhus for providing SceIF2β; A. G. Gabdulkhakov for collecting X-ray diffraction data. We express our gratitude to S. E. Permyakov for the opportunity to conduct experiments on the ProteOn XPR36 at the Institute of Biological Instrumentation of the Russian Academy of Sciences.

Funding

The work was financially supported by the State Budget Project no. AAAA-A19-119122490038-8.

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Authors and Affiliations

  1. Institute of Protein Research, Russian Academy of Sciences, 142290, Pushchino, Moscow Region, Russia

    Oleg S. Nikonov, Ekaterina Yu. Nikonova, Anastasiia G. Tarabarova, Alisa O. Mikhaylina, Olesya V. Kravchenko, Natalia A. Nevskaya & Stanislav V. Nikonov

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  1. Oleg S. Nikonov
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  2. Ekaterina Yu. Nikonova
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  3. Anastasiia G. Tarabarova
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  4. Alisa O. Mikhaylina
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  5. Olesya V. Kravchenko
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  6. Natalia A. Nevskaya
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  7. Stanislav V. Nikonov
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Contributions

S. V. Nikonov – work management; E. Yu. Nikonova, A. G. Tarabarova, O. S. Nikonov – conducting experiments; A. O. Mikhailina – conducting SPR measurements; O. V. Kravchenko – determination of the structure of the mutant form; O. S. Nikonov, N. A. Nevskaya, S. V. Nikonov – discussion of the results of the study; O. S. Nikonov – AlphaFold modeling and drawing of figures; S. V. Nikonov, N. A. Nevskaya – writing and editing the text of the manuscript.

Corresponding author

Correspondence to Oleg S. Nikonov.

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The authors declare no conflict of interests in financial or any other sphere. This article does not contain any studies with human participants or animals performed by any of the authors.

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Nikonov, O.S., Nikonova, E.Y., Tarabarova, A.G. et al. Recognition of γ-Subunit by β-Subunit in Translation Initiation Factor 2. Stabilization of the GTP-Bound State of I/F 2 in Archaea and Eukaryotes. Biochemistry Moscow 88, 221–230 (2023). https://doi.org/10.1134/S0006297923020062

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