Abstract
Ribosomes translating secretory or membrane proteins are targeted to the protein translocation pore (translocon) in the membrane by the signal recognition particle (SRP) pathway. SRP recognizes hydrophobic signal sequences emerging from the peptide exit region of the ribosome and, with the help of the SRP receptor, mediates the transfer of the translating ribosome to the translocon. The formation of the targeting complex is enhanced by signaling from inside the peptide exit tunnel to the SRP-binding region around the peptide exit, leading to early targeting before the appearance of the nascent peptide outside the ribosome. Furthermore, secondary structure formation of nascent transmembrane segments within the exit tunnel of translocon-bound ribosomes strongly influences the passage of membrane proteins through the translocon. This chapter describes the mechanisms that regulate the early recruitment of SRP to translating ribosomes and the interaction of the latter with the translocon, focusing on the influence of nascent peptide-induced signaling from the exit tunnel to the SRP/translocon-binding site of the ribosome.
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References
Akopian D, Shen K, Zhang X, Shan SO (2013) Signal recognition particle: an essential protein-targeting machine. Annu Rev Biochem 82:693–721
Becker T, Bhushan S, Jarasch A, Armache JP, Funes S, Jossinet F, Gumbart J, Mielke T, Berninghausen O, Schulten K, Westhof E, Gilmore R, Mandon EC, Beckmann R (2009) Structure of monomeric yeast and mammalian Sec61 complexes interacting with the translating ribosome. Science 326:1369–1373
Berndt U, Oellerer S, Zhang Y, Johnson AE, Rospert S (2009) A signal-anchor sequence stimulates signal recognition particle binding to ribosomes from inside the exit tunnel. Proc Natl Acad Sci USA 106:1398–1403
Bibi E (2011) Early targeting events during membrane protein biogenesis in Escherichia coli. Biochim Biophys Acta 1808:841–850
Bingel-Erlenmeyer R, Kohler R, Kramer G, Sandikci A, Antolic S, Maier T, Schaffitzel C, Wiedmann B, Bukau B, Ban N (2008) A peptide deformylase-ribosome complex reveals mechanism of nascent chain processing. Nature (Lond) 452:108–111
Bornemann T, Jöckel J, Rodnina MV, Wintermeyer W (2008) Signal sequence-independent membrane targeting of ribosomes containing short nascent peptides within the exit tunnel. Nat Struct Mol Biol 15:494–499
Buskiewicz I, Deuerling E, Gu SQ, Jockel J, Rodnina MV, Bukau B, Wintermeyer W (2004) Trigger factor binds to ribosome-signal-recognition particle (SRP) complexes and is excluded by binding of the SRP receptor. Proc Natl Acad Sci USA 101:7902–7906
Daniel CJ, Conti B, Johnson AE, Skach WR (2008) Control of translocation through the Sec61 translocon by nascent polypeptide structure within the ribosome. J Biol Chem 283:20864–20873
Deuerling E, Patzelt H, Vorderwulbecke S, Rauch T, Kramer G, Schaffitzel E, Mogk A, Schulze-Specking A, Langen H, Bukau B (2003) Trigger factor and DnaK possess overlapping substrate pools and binding specificities. Mol Microbiol 47:1317–1328
Estrozi LF, Boehringer D, Shan SO, Ban N, Schaffitzel C (2011) Cryo-EM structure of the E. coli translating ribosome in complex with SRP and its receptor. Nat Struct Mol Biol 18:88–90
Ferbitz L, Maier T, Patzelt H, Bukau B, Deuerling E, Ban N (2004) Trigger factor in complex with the ribosome forms a molecular cradle for nascent proteins. Nature (Lond) 431:590–596
Flanagan JJ, Chen JC, Miao Y, Shao Y, Lin J, Bock PE, Johnson AE (2003) Signal recognition particle binds to ribosome-bound signal sequences with fluorescence-detected subnanomolar affinity that does not diminish as the nascent chain lengthens. J Biol Chem 278:18628–18637
Frauenfeld J, Gumbart J, Sluis EO, Funes S, Gartmann M, Beatrix B, Mielke T, Berninghausen O, Becker T, Schulten K, Beckmann R (2011) Cryo-EM structure of the ribosome-SecYE complex in the membrane environment. Nat Struct Mol Biol 18:614–621
Grudnik P, Bange G, Sinning I (2009) Protein targeting by the signal recognition particle. Biol Chem 390:775–782
Gu SQ, Peske F, Wieden HJ, Rodnina MV, Wintermeyer W (2003) The signal recognition particle binds to protein L23 at the peptide exit of the Escherichia coli ribosome. RNA 9:566–573
Holtkamp W, Lee S, Bornemann T, Senyushkina T, Rodnina MV, Wintermeyer W (2012) Dynamic switch of SRP from scanning to targeting. Nat Struct Mol Biol 19:1332–1337
Jensen CG, Pedersen S (1994) Concentrations of 4.5S RNA and Ffh protein in Escherichia coli: the stability of Ffh protein is dependent on the concentration of 4.5S RNA. J Bacteriol 176:7148–7154
Kramer G, Rauch T, Rist W, Vorderwulbecke S, Patzelt H, Schulze-Specking A, Ban N, Deuerling E, Bukau B (2002) L23 protein functions as a chaperone docking site on the ribosome. Nature (Lond) 419:171–174
Lakshmipathy SK, Tomic S, Kaiser CM, Chang HC, Genevaux P, Georgopoulos C, Barral JM, Johnson AE, Hartl FU, Etchells SA (2007) Identification of nascent chain interaction sites on trigger factor. J Biol Chem 282:12186–12193
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
Liao S, Lin J, Do H, Johnson AE (1997) Both lumenal and cytosolic gating of the aqueous ER translocon pore are regulated from inside the ribosome during membrane protein integration. Cell 90:31–41
Lin PJ, Jongsma CG, Liao S, Johnson AE (2011a) Transmembrane segments of nascent polytopic membrane proteins control cytosol/ER targeting during membrane integration. J Cell Biol 195:41–54
Lin PJ, Jongsma CG, Pool MR, Johnson AE (2011b) Polytopic membrane protein folding at L17 in the ribosome tunnel initiates cyclical changes at the translocon. J Cell Biol 195:55–70
Lin KF, Sun CS, Huang YC, Chan SI, Koubek J, Wu TH, Huang JJ (2012) Cotranslational protein folding within the ribosome tunnel influences trigger-factor recruitment. Biophys J 102:2818–2827
Lu J, Deutsch C (2005) Folding zones inside the ribosomal exit tunnel. Nat Struct Mol Biol 12:1123–1129
Lu J, Hua Z, Kobertz WR, Deutsch C (2011) Nascent peptide side chains induce rearrangements in distinct locations of the ribosomal tunnel. J Mol Biol 411:499–510
Mandon EC, Trueman SF, Gilmore R (2013) Protein translocation across the rough endoplasmic reticulum. Cold Spring Harb Perspect Biol 5(2)
Menetret JF, Hegde RS, Aguiar M, Gygi SP, Park E, Rapoport TA, Akey CW (2008) Single copies of Sec61 and TRAP associate with a nontranslating mammalian ribosome. Structure 16:1126–1137
Nyathi Y, Wilkinson BM, Pool MR (2013) Co-translational targeting and translocation of proteins to the endoplasmic reticulum. Biochim Biophys Acta 1833(11):2392–2402
Oh E, Becker AH, Sandikci A, Huber D, Chaba R, Gloge F, Nichols RJ, Typas A, Gross CA, Kramer G, Weissman JS, Bukau B (2011) Selective ribosome profiling reveals the cotranslational chaperone action of trigger factor in vivo. Cell 147:1295–1308
Park E, Rapoport TA (2012) Mechanisms of Sec61/SecY-mediated protein translocation across membranes. Annu Rev Biophys 41:21–40
Pool MR (2009) A trans-membrane segment inside the ribosome exit tunnel triggers RAMP4 recruitment to the Sec61p translocase. J Cell Biol 185:889–902
Raine A, Ivanova N, Wikberg JE, Ehrenberg M (2004) Simultaneous binding of trigger factor and signal recognition particle to the E. coli ribosome. Biochimie 86:495–500
Rutkowska A, Mayer MP, Hoffmann A, Merz F, Zachmann-Brand B, Schaffitzel C, Ban N, Deuerling E, Bukau B (2008) Dynamics of trigger factor interaction with translating ribosomes. J Biol Chem 283:4124–4132
Sandikci A, Gloge F, Martinez M, Mayer MP, Wade R, Bukau B, Kramer G (2013) Dynamic enzyme docking to the ribosome coordinates N-terminal processing with polypeptide folding. Nat Struct Mol Biol 20:843–850
Shao S, Hegde RS (2011) Membrane protein insertion at the endoplasmic reticulum. Annu Rev Cell Dev Biol 27:25–56
Wilson DN, Beckmann R (2011) The ribosomal tunnel as a functional environment for nascent polypeptide folding and translational stalling. Curr Opin Struct Biol 21:274–282
Woolhead CA, McCormick PJ, Johnson AE (2004) Nascent membrane and secretory proteins differ in FRET-detected folding far inside the ribosome and in their exposure to ribosomal proteins. Cell 116:725–736
Acknowledgments
We thank Holger Stark for preparing Fig. 5.1.
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Bornemann, T., Holtkamp, W., Wintermeyer, W. (2014). Nascent Peptide-Induced Signaling from the Exit Tunnel to the Outside of the Ribosome. In: Ito, K. (eds) Regulatory Nascent Polypeptides. Springer, Tokyo. https://doi.org/10.1007/978-4-431-55052-5_5
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DOI: https://doi.org/10.1007/978-4-431-55052-5_5
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