A new understanding of the decoding principle on the ribosome

Nature - Tập 484 Số 7393 - Trang 256-259 - 2012
N. Demeshkina1,2,3,4, L. Jenner1,2,3,4, Éric Westhof5, Marat Yusupov6
1CNRS, UMR7104, Illkirch 67400, France
2Département de Biologie et de Génomique Structurales, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch 67400, France
3INSERM, U964, Illkirch 67400, France
4Université de Strasbourg > > > > > >
5Architecture et Réactivité de l’ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire, CNRS, Strasbourg 67084, France,
6CNRS, UMR7104, Illkirch 67400, France, Strasbourg, 67000, France

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Tài liệu tham khảo

Rodnina, M. V. & Wintermeyer, W. Fidelity of aminoacyl-tRNA selection on the ribosome: kinetic and structural mechanisms. Annu. Rev. Biochem. 70, 415–435 (2001)

Rodnina, M. V., Gromadski, K. B., Kothe, U. & Wieden, H. J. Recognition and selection of tRNA in translation. FEBS Lett. 579, 938–942 (2005)

Zaher, H. S. & Green, R. Fidelity at the molecular level: lessons from protein synthesis. Cell 136, 746–762 (2009)

Gromadski, K. B., Daviter, T. & Rodnina, M. V. A uniform response to mismatches in codon-anticodon complexes ensures ribosomal fidelity. Mol. Cell 21, 369–377 (2006)

Lee, T. H., Blanchard, S. C., Kim, H. D., Puglisi, J. D. & Chu, S. The role of fluctuations in tRNA selection by the ribosome. Proc. Natl Acad. Sci. USA 104, 13661–13665 (2007)

Li, W. et al. Recognition of aminoacyl-tRNA: a common molecular mechanism revealed by cryo-EM. EMBO J. 27, 3322–3331 (2008)

Schmeing, T. M. et al. The crystal structure of the ribosome bound to EF-Tu and aminoacyl-tRNA. Science 326, 688–694 (2009)

Schuette, J. C. et al. GTPase activation of elongation factor EF-Tu by the ribosome during decoding. EMBO J. 28, 755–765 (2009)

Voorhees, R. M., Schmeing, T. M., Kelley, A. C. & Ramakrishnan, V. The mechanism for activation of GTP hydrolysis on the ribosome. Science 330, 835–838 (2010)

Ehrenberg, M., Kurland, C. G. & Ruusala, T. Counting cycles of EF-Tu to measure proofreading in translation. Biochimie 68, 261–273 (1986)

Voorhees, R. M., Weixlbaumer, A., Loakes, D., Kelley, A. C. & Ramakrishnan, V. Insights into substrate stabilization from snapshots of the peptidyl transferase center of the intact 70S ribosome. Nature Struct. Mol. Biol. 16, 528–533 (2009)

Jenner, L., Demeshkina, N., Yusupova, G. & Yusupov, M. Structural rearrangements of the ribosome at the tRNA proofreading step. Nature Struct. Mol. Biol. 17, 1072–1078 (2010)

Geggier, P. et al. Conformational sampling of aminoacyl-tRNA during selection on the bacterial ribosome. J. Mol. Biol. 399, 576–595 (2010)

Whitford, P. C. et al. Accommodation of aminoacyl-tRNA into the ribosome involves reversible excursions along multiple pathways. RNA 16, 1196–1204 (2010)

Moazed, D. & Noller, H. F. Binding of tRNA to the ribosomal A and P sites protects two distinct sets of nucleotides in 16 S rRNA. J. Mol. Biol. 211, 135–145 (1990)

Powers, T. & Noller, H. F. Selective perturbation of G530 of 16 S rRNA by translational miscoding agents and a streptomycin-dependence mutation in protein S12. J. Mol. Biol. 235, 156–172 (1994)

Yoshizawa, S., Fourmy, D. & Puglisi, J. D. Recognition of the codon–anticodon helix by ribosomal RNA. Science 285, 1722–1725 (1999)

Ogle, J. M. et al. Recognition of cognate transfer RNA by the 30S ribosomal subunit. Science 292, 897–902 (2001)

Ogle, J. M., Murphy, F. V., Tarry, M. J. & Ramakrishnan, V. Selection of tRNA by the ribosome requires a transition from an open to a closed form. Cell 111, 721–732 (2002)

Selmer, M. et al. Structure of the 70S ribosome complexed with mRNA and tRNA. Science 313, 1935–1942 (2006)

Jenner, L. B., Demeshkina, N., Yusupova, G. & Yusupov, M. Structural aspects of messenger RNA reading frame maintenance by the ribosome. Nature Struct. Mol. Biol. 17, 555–560 (2010)

BPS Database of RNA Base-pair Structures . http://bps.rutgers.edu/bps (2008)

Bebenek, K., Pedersen, L. C. & Kunkel, T. A. Replication infidelity via a mismatch with Watson–Crick geometry. Proc. Natl Acad. Sci. USA 108, 1862–1867 (2011)

Auffinger, P. & Westhof, E. An extended structural signature for the tRNA anticodon loop. RNA 7, 334–341 (2001)

Pape, T., Wintermeyer, W. & Rodnina, M. V. Conformational switch in the decoding region of 16S rRNA during aminoacyl-tRNA selection on the ribosome. Nature Struct. Biol. 7, 104–107 (2000)

Cochella, L. & Green, R. An active role for tRNA in decoding beyond codon:anticodon pairing. Science 308, 1178–1180 (2005)

Dale, T. & Uhlenbeck, O. C. Amino acid specificity in translation. Trends Biochem. Sci. 30, 659–665 (2005)

Schmeing, T. M., Voorhees, R. M., Kelley, A. C. & Ramakrishnan, V. How mutations in tRNA distant from the anticodon affect the fidelity of decoding. Nature Struct. Mol. Biol. 18, 432–436 (2011)

Mueller, M., Wang, M. & Schulze-Briese, C. Optimal fine φ-slicing for single-photon-counting pixel detectors. Acta Crystallogr. D 68, 42–56 (2012)

Adams, P. D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D 66, 213–221 (2010)

Praaenikar, J., Afonine, P. V., Guncar, G., Adams, P. D. & Turk, D. Averaged kick maps: less noise, more signal and probably less bias. Acta Crystallogr. D 65, 921–931 (2009)