FOR 1805: Ribosome Dynamics in Regulation of Speed and Accuracy of Translation
Final Report Abstract
Translation of the genetic information from a nucleotide sequence into a functional protein is a central biological process. The aim of this collaborative FOR1805 project was to uncover dynamic aspects of ribosome function in translation at different levels, from an atomic analysis to global-scale behavior. Using both prokaryotes and eukaryotes as model systems our results provide insights into common principles and divergent features in translation dynamics as well as regulation across the domains of life. We used a combination of interdisciplinary approaches, including high-resolution structural studies (single-particle/multi-particle cryo-EM), biophysical (rapid kinetics, molecular dynamics simulation, stochastic modeling), and biochemical (quantitative mass spectrometry, biochemical methods with singlemolecule and single-nucleotide resolution combined with the power of highly parallel deep sequencing) approaches. The team of scientists we have assembled consolidated the scientific expertise across Germany on ribosome function and protein translation. The individual projects used cutting-edge approaches and technologies, thus providing a multifaceted methodological spectrum to approach our complex scientific goal from multiple angles. Merging the research activities on translation across Germany and through this unique consolidated expertise collectively our results provided insights on (i) the role of various translation factors on the metastable energy landscape of the translating ribosome, (ii) the speed and accuracy in translation of single codon and whole open-reading frame, (iii) the impact of external factors (antibiotics, environmental stress) on translation fidelity and processivity, and (iv) the link between translation and protein folding, assembly and function. The strong collaborative nature of our research resulted in large number of publications. In total 70 original publications and 15 reviews were published from the individual projects with 15 original peerreviewed publications jointly co-authored by PIs from our Research Unit. Collectively, we generated unprecedented insights molecular aspects of the ribosome function and dynamics and advanced our understanding on how the ribosome, as a macromolecular machine, integrates different processes during translation and how how translation, as a crucial physiological process, controls cell vitality.
Publications
- EF-P is essential for rapid synthesis of proteins containing consecutive proline residues. Science 339, 85-88 (2013)
Doerfel, L.K., Wohlgemuth, I., Kothe, C., Peske, F., Urlaub, H., and Rodnina, M.V.
(See online at https://doi.org/10.1126/science.1229017) - Energy barriers and driving forces in tRNA translocation through the ribosome. Nature Struct. Mol. Biol. 20, 1390-1396 (2013)
Bock LV, Blau C, Schröder GF, Davydov II, Fischer N, Stark H, Rodnina MV, Vaiana AC, Grubmüller H
(See online at https://doi.org/10.1038/nsmb.2690) - Deducing the kinetics of protein synthesis in vivo from the transition rates measured in vitro. PLoS Comput Biol 10, e1003909 (2014)
Rudorf, S., Thommen, M., Rodnina, M.V., and Lipowsky, R
(See online at https://doi.org/10.1371/journal.pcbi.1003909) - Cryo-EM structure of the tetracycline resistance protein TetM in complex with a translating ribosome at 3.9-Å resolution. (2015) Proc Natl Acad Sci USA. 112, 5401-6 (2015)
Arenz S, Nguyen F, Beckmann R, Wilson DN
(See online at https://doi.org/10.1073/pnas.1501775112) - Entropic Contribution of Elongation Factor P to Proline Positioning at the Catalytic Center of the Ribosome. J Am Chem Soc. 137, 12997-3006 (2015)
Doerfel LK, Wohlgemuth I, Kubyshkin V, Starosta AL, Wilson DN, Budisa N, Rodnina MV
(See online at https://doi.org/10.1021/jacs.5b07427) - Operon structure and cotranslational subunit association direct protein assembly in bacteria, Science. 350, 678-80 (2015)
Shieh, Y. W., Minguez, P., Bork, P., Auburger, J. J., Guilbride, D. L., Kramer, G. & Bukau, B
(See online at https://doi.org/10.1126/science.aac8171) - A combined cryo-EM and molecular dynamics approach reveals the mechanism of ErmBL-mediated translation arrest. Nature Comm. 7, 12026 (2016)
Arenz S, Bock LV, Graf M, Innis CA, Beckmann R, Grubmüller H, Vaiana AC, Wilson DN
(See online at https://doi.org/10.1038/ncomms12026) - Discharging tRNAs: a tug of war between translation and detoxification in Escherichia coli. Nucl. Acids. Res. 44, 8324-8334 (2016)
Avcilar-Kucukgoze I, Bartholomäus A, Cordero Varela JA, Kaml RF, Neubauer P, Budisa N, Ignatova Z
(See online at https://doi.org/10.1093/nar/gkw697) - Essential structural elements in tRNA(Pro) for EF-P-mediated alleviation of translation stalling. Nat Commun 7, 11657 (2016)
Katoh, T., Wohlgemuth, I., Nagano, M., Rodnina, M.V., and Suga, H
(See online at https://doi.org/10.1038/ncomms11657) - Global profiling of SRP interaction with nascent polypeptides, Nature. 536, 219-23 (2016)
Schibich, D., Gloge, F., Pohner, I., Bjorkholm, P., Wade, R. C., von Heijne, G., Bukau, B. and Kramer, G
(See online at https://doi.org/10.1038/nature19070) - Structural insights into ribosomal rescue by Dom34 and Hbs1 at near-atomic resolution. Nature Commun. 20, 13521 (2016)
Hilal, T., Yamamoto, H., Loerke, J., Bürger, J., Mielke, T., & Spahn, C.M.T.
(See online at https://doi.org/10.1038/ncomms13521) - Structures of ribosome-bound initiation factor 2 reveal the mechanism of subunit association. Science Adv. 2, e1501502 (2016)
Sprink, T., Ramrath, D.J., Yamamoto, H., Yamamoto, K., Loerke, J., Ismer, J., Hildebrand, P.W., Scheerer, P., Bürger, J., Mielke, T., & Spahn, C.M.T.
(See online at https://doi.org/10.1126/sciadv.1501502) - The pathway to GTPase activation of elongation factor SelB on the ribosome. Nature 540, 80-85 (2016)
Fischer N, Neumann P, Bock LV, Maracci C, Wang Z, Paleskava A, Konevega AL, Schröder GF, Grubmüller H, Ficner R, Rodnina MV, Stark H
(See online at https://doi.org/10.1038/nature20560) - An antimicrobial peptide that inhibits translation by trapping release factors on the ribosome. Nat Struct Mol Biol. 24, 752-757 (2017)
Florin T, Maracci C, Graf M, Karki P, Klepacki D, Berninghausen O, Beckmann R, Vázquez-Laslop N, Wilson DN, Rodnina MV, Mankin AS
(See online at https://doi.org/10.1038/nsmb.3439) - Structural Basis for Polyproline-Mediated Ribosome Stalling and Rescue by the Translation Elongation Factor EF-P. Mol. Cell 68 (3), 515–527 (2017)
Huter P, Arenz S, Bock LV, Graf M, Frister JO, Heuer A, Peil L, Starosta AL, Wohlgemuth I, Peske F, Novacek J, Berninghausen O, Grubmüller H, Tenson T, Beckmann R, Rodnina MV, Vaiana AC, Wilson DN
(See online at https://doi.org/10.1016/j.molcel.2017.10.014) - The force-sensing peptide VemP employs extreme compaction and secondary structure formation to induce ribosomal stalling. Elife. pii: e25642 (2017)
Su,T., Cheng, J., Sohmen, D., Hedman, R., Berninghausen, O., von Heijne, G., Wilson, D.N., Beckmann, R.
(See online at https://doi.org/10.7554/eLife.25642) - Decomposition of timedependent fluorescence signals reveals codon-specific kinetics of protein synthesis. Nucleic Acids Research 46, e130 (2018)
Haase, N., Holtkamp, W. ,Lipowsky, R., Rodnina, M., and Rudorf, S.
(See online at https://doi.org/10.1093/nar/gky740) - Structure of hybernating 100S ribosome reveals an inactive conformation of the ribosomal S1. Nature Microbiol. 3, 1115-1121 (2018)
Beckert, B., Turk, M., Czech, A., Berninghausen, O., Beckmann, R., Ignatova, Z., Plitzko, J.M. & Wilson. D.N.
(See online at https://doi.org/10.1038/s41564-018-0237-0) - The RNA-binding protein Hfq is important for ribosome biogenesis and affects translation fidelity. EMBO J. 37, e97631 (2018)
Andrade, J.M., dos Santos, R.F., Chelysheva, I. Ignatova Z. and Arraiano, C.M.
(See online at https://doi.org/10.15252/embj.201797631) - Visualization of translation termination intermediates trapped by the Apidaecin 137 peptide during RF3-mediated recycling of RF1. Nat Commun. 9, 3053 (2018)
Graf M, Huter P, Maracci C, Peterek M, Rodnina MV, Wilson DN
(See online at https://doi.org/10.1038/s41467-018-05465-1)
