Abstract
As the nascent polypeptide chain is being synthesized, it passes through a tunnel within the large ribosomal subunit. Rather than a passive conduit for the nascent chain, accumulating evidence indicates that specific nascent polypeptide chains can establish distinct interactions with the ribosomal tunnel to induce translation arrest. Cryo-EM structures of nascent peptide-dependent stalled ribosome complexes (SRC) have provided the first structural insights into how the nascent polypeptide chain interacts with the ribosomal tunnel to inhibit ribosome function.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Alderete JP, Jarrahian S, Geballe AP (1999) Translational effects of mutations and polymorphisms in a repressive upstream open reading frame of the human cytomegalovirus UL4 gene. J Virol 73:8330–8337
Bhushan S, Gartmann M, Halic M, Armache JP, Jarasch A, Mielke T, Berninghausen O, Wilson DN, Beckmann R (2010a) Alpha-helical nascent polypeptide chains visualized within distinct regions of the ribosomal exit tunnel. Nat Struct Mol Biol 17:313–317
Bhushan S, Meyer H, Starosta AL, Becker T, Mielke T, Berninghausen O, Sattler M, Wilson DN, Beckmann R (2010b) Structural basis for translational stalling by human cytomegalovirus (hCMV) and fungal arginine attenuator peptide (AAP). Mol Cell 40:138–146
Bhushan S, Hoffmann T, Seidelt B, Frauenfeld J, Mielke T, Berninghausen O, Wilson DN, Beckmann R (2011) SecM-stalled ribosomes adopt an altered geometry at the peptidyltransferase center. PLoS Biol 19:e1000581
Butkus ME, Prundeanu LB, Oliver DB (2003) Translocon “pulling” of nascent SecM controls the duration of its translational pause and secretion-responsive secA regulation. J Bacteriol 185:6719–6722
Cao JH, Geballe AP (1996) Inhibition of nascent-peptide release at translation termination. Mol Cell Biol 16:7109–7114
Cruz-Vera LR, Yanofsky C (2008) Conserved residues Asp16 and Pro24 of TnaC-tRNAPro participate in tryptophan induction of Tna operon expression. J Bacteriol 190:4791–4797
Cruz-Vera L, Rajagopal S, Squires C, Yanofsky C (2005) Features of ribosome-peptidyl-tRNA interactions essential for tryptophan induction of tna operon expression. Mol Cell 19:333–343
Cruz-Vera LR, New A, Squires C, Yanofsky C (2007) Ribosomal features essential for tna operon induction: tryptophan binding at the peptidyl transferase center. J Bacteriol 189:3140–3146
Degnin CR, Schleiss MR, Cao J, Geballe AP (1993) Translational inhibition mediated by a short upstream open reading frame in the human cytomegalovirus gpUL4 (gp48) transcript. J Virol 67:5514–5521
Delbecq P, Calvo O, Filipkowski RK, Pierard A, Messenguy F (2000) Functional analysis of the leader peptide of the yeast gene CPA1 and heterologous regulation by other fungal peptides. Curr Genet 38:105–112
Fang P, Spevak C, Wu C, Sachs M (2004) A nascent polypeptide domain that can regulate translation elongation. Proc Natl Acad Sci USA 101:4059–4064
Freitag M, Dighde N, Sachs MS (1996) A UV-induced mutation in Neurospora that affects translational regulation in response to arginine. Genetics 142:117–127
Fulle S, Gohlke H (2009) Statics of the ribosomal exit tunnel: implications for cotranslational peptide folding, elongation regulation, and antibiotics binding. J Mol Biol 387:502–517
Geballe AP, Spaete RR, Mocarski ES (1986) A cis-acting element within the 5′ leader of a cytomegalovirus beta transcript determines kinetic class. Cell 46:865–872
Gong F, Yanofsky C (2002) Instruction of translating ribosome by nascent peptide. Science 297:1864–1867
Gong F, Ito K, Nakamura Y, Yanofsky C (2001) The mechanism of tryptophan induction of tryptophanase operon expression: tryptophan inhibits release factor-mediated cleavage of TnaC-peptidyl-tRNA(Pro). Proc Natl Acad Sci USA 98:8997–9001
Hansen JL, Schmeing TM, Moore PB, Steitz TA (2002) Structural insights into peptide bond formation. Proc Natl Acad Sci USA 99:11670–11675
Hofer A, Bussiere C, Johnson AW (2007) Mutational analysis of the ribosomal protein Rpl10 from yeast. J Biol Chem 282:32630–32639
Ito K, Chiba S (2013) Arrest peptides: cis-acting modulators of translation. Annu Rev Biochem 82:171–202
Ito K, Chiba S, Pogliano K (2010) Divergent stalling sequences sense and control cellular physiology. Biochem Biophys Res Commun 393:1–5
Lawrence MG, Lindahl L, Zengel JM (2008) Effects on translation pausing of alterations in protein and RNA components of the ribosome exit tunnel. J Bacteriol 190:5862–5869
Muto H, Nakatogawa H, Ito K (2006) Genetically encoded but nonpolypeptide prolyl-tRNA functions in the A site for SecM-mediated ribosomal stall. Mol Cell 22:545–552
Nakatogawa H, Ito K (2001) Secretion monitor, SecM, undergoes self-translation arrest in the cytosol. Mol Cell 7:185–192
Nakatogawa H, Ito K (2002) The ribosomal exit tunnel functions as a discriminating gate. Cell 108:629–636
Pavlov MY, Watts RE, Tan Z, Cornish VW, Ehrenberg M, Forster AC (2009) Slow peptide bond formation by proline and other N-alkylamino acids in translation. Proc Natl Acad Sci USA 106:50–54
Schmeing TM, Huang KS, Strobel SA, Steitz TA (2005) An induced-fit mechanism to promote peptide bond formation and exclude hydrolysis of peptidyl-tRNA. Nature (Lond) 438:520–524
Seidelt B, Innis CA, Wilson DN, Gartmann M, Armache JP, Villa E, Trabuco LG, Becker T, Mielke T, Schulten K et al (2009) Structural insight into nascent polypeptide chain-mediated translational stalling. Science 326:1412–1415
Selmer M, Dunham C, Murphy FT, Weixlbaumer A, Petry S, Kelley A, Weir J, Ramakrishnan V (2006) Structure of the 70S ribosome complexed with mRNA and tRNA. Science 313:1935–1942
Simonovic M, Steitz TA (2009) A structural view on the mechanism of the ribosome-catalyzed peptide bond formation. Biochim Biophys Acta 1789:612–623
Trabuco LG, Villa E, Mitra K, Frank J, Schulten K (2008) Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics. Structure 16:673–683
Vazquez-Laslop N, Thum C, Mankin AS (2008) Molecular mechanism of drug-dependent ribosome stalling. Mol Cell 30:190–202
Vazquez-Laslop N, Ramu H, Klepacki D, Kannan K, Mankin AS (2010) The key function of a conserved and modified rRNA residue in the ribosomal response to the nascent peptide. EMBO J 29:3108–3117
Wang Z, Sachs MS (1997a) Arginine-specific regulation mediated by the Neurospora crassa arg-2 upstream open reading frame in a homologous, cell-free in vitro translation system. J Biol Chem 272:255–261
Wang Z, Sachs MS (1997b) Ribosome stalling is responsible for arginine-specific translational attenuation in Neurospora crassa. Mol Cell Biol 17:4904–4913
Weixlbaumer A, Jin H, Neubauer C, Voorhees R, Petry S, Kelley A, Ramakrishnan V (2008) Insights into translational termination from the structure of RF2 bound to the ribosome. Science 322:953–956
Wilson DN, Beckmann R (2011) The ribosomal tunnel as a functional environment for nascent polypeptide folding and translational stalling. Curr Opin Struct Biol 21:1–10
Wilson DN, Bhushan S, Becker T, Beckmann R (2011) Nascent polypeptide chains within the ribosomal tunnel analyzed by cryo-EM. In: Rodnina MV, Wintermeyer W, Green R (eds) The ribosome: structure, function, & evolution. Springer, New York, pp 387–398
Yang R, Cruz-Vera LR, Yanofsky C (2009) 23S rRNA nucleotides in the peptidyl transferase center are essential for tryptophanase operon induction. J Bacteriol 191:3445–3450
Yap MN, Bernstein HD (2009) The plasticity of a translation arrest motif yields insights into nascent polypeptide recognition inside the ribosome tunnel. Mol Cell 34:201–211
Author information
Authors and Affiliations
Corresponding authors
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2014 Springer Japan
About this chapter
Cite this chapter
Wilson, D.N., Beckmann, R. (2014). Structures of Nascent Polypeptide Chain-Dependent-Stalled Ribosome Complexes. In: Ito, K. (eds) Regulatory Nascent Polypeptides. Springer, Tokyo. https://doi.org/10.1007/978-4-431-55052-5_3
Download citation
DOI: https://doi.org/10.1007/978-4-431-55052-5_3
Published:
Publisher Name: Springer, Tokyo
Print ISBN: 978-4-431-55051-8
Online ISBN: 978-4-431-55052-5
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)