Abstract
Although we tend to think that the ribosome can link together amino acids in any order, we have found that certain sequences interfere with protein synthesis. Characterization of stalling peptides found in bacteria has revealed multiple mechanisms of translational inhibition. Given that natural motifs differ in sequence and contain only three or four essential residues, peptide-mediated stalling may be quite widespread. To examine the scope of this phenomenon, we performed genetic selections in Escherichia coli to identify additional stalling motifs from random libraries. We characterized the mechanism of stalling with purified components using pre-steady-state kinetic methods. Some motifs block termination by inhibiting catalysis by release factors. In others, peptidyl transfer to certain aminoacyl-tRNAs is inhibited. Residues upstream of a stalling motif can either enhance or suppress these effects. One theme that emerges from these studies is the poor reactivity of proline, both as a peptidyl donor, at the C-terminus of the nascent peptide, and as a peptidyl acceptor, as prolyl-tRNA. This effect is compounded at three or more consecutive Pro codons. The translation factor EF-P alleviates stalling at polyproline sequences but has little or no effect on the motifs identified in our selections. Although our stalling motifs are in some sense artificial, several are underrepresented in bacterial proteomes, suggesting that they have been selected against, and analysis of ribosome profiling datasets reveals evidence of stalling where they occur in endogenous E. coli proteins.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Bjornsson A, Mottagui-Tabar S, Isaksson LA (1996) Structure of the C-terminal end of the nascent peptide influences translation termination. EMBO J 15(7):1696–1704
Blaha G, Stanley RE, Steitz TA (2009) Formation of the first peptide bond: the structure of EF-P bound to the 70S ribosome. Science 325(5943):966–970. doi:10.1126/science.1175800
Chiba S, Lamsa A, Pogliano K (2009) A ribosome-nascent chain sensor of membrane protein biogenesis in Bacillus subtilis. EMBO J 28(22):3461–3475. doi:10.1038/emboj.2009.280
Chiba S, Kanamori T, Ueda T, Akiyama Y, Pogliano K, Ito K (2011) Recruitment of a species-specific translational arrest module to monitor different cellular processes. Proc Natl Acad Sci USA 108(15):6073–6078. doi:10.1073/pnas.1018343108
Collier J, Bohn C, Bouloc P (2004) SsrA tagging of Escherichia coli SecM at its translation arrest sequence. J Biol Chem 279(52):54193–54201
Cruz-Vera LR, Rajagopal S, Squires C, Yanofsky C (2005) Features of ribosome-peptidyl-tRNA interactions essential for tryptophan induction of tna operon expression. Mol Cell 19(3):333–343
Doerfel LK, Wohlgemuth I, Kothe C, Peske F, Urlaub H, Rodnina MV (2013) EF-P is essential for rapid synthesis of proteins containing consecutive proline residues. Science 339(6115):85–88. doi:10.1126/science.1229017
Doronina VA, Wu C, de Felipe P, Sachs MS, Ryan MD, Brown JD (2008) Site-specific release of nascent chains from ribosomes at a sense codon. Mol Cell Biol 28(13):4227–4239
Dove SL, Joung JK, Hochschild A (1997) Activation of prokaryotic transcription through arbitrary protein–protein contacts. Nature (Lond) 386(6625):627–630. doi:10.1038/386627a0
Garza-Sanchez F, Janssen BD, Hayes CS (2006) Prolyl-tRNA(Pro) in the A-site of SecM-arrested ribosomes inhibits the recruitment of transfer-messenger RNA. J Biol Chem 281(45):34258–34268
Gong F, Yanofsky C (2002) Instruction of translating ribosome by nascent peptide. Science 297(5588):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(16):8997–9001
Hanawa-Suetsugu K, Sekine S, Sakai H, Hori-Takemoto C, Terada T, Unzai S, Tame JR, Kuramitsu S, Shirouzu M, Yokoyama S (2004) Crystal structure of elongation factor P from Thermus thermophilus HB8. Proc Natl Acad Sci USA 101(26):9595–9600. doi:10.1073/pnas.0308667101
Hayes CS, Bose B, Sauer RT (2002) Proline residues at the C terminus of nascent chains induce SsrA tagging during translation termination. J Biol Chem 277(37):33825–33832
Hentzen D, Mandel P, Garel JP (1972) Relation between aminoacyl-tRNA stability and the fixed amino acid. Biochim Biophys Acta 281(2):228–232
Ingolia NT, Ghaemmaghami S, Newman JR, Weissman JS (2009) Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science 324(5924):218–223. doi:10.1126/science.1168978
Ito K, Chiba S (2013) Arrest peptides: cis-acting modulators of translation. Annu Rev Biochem 82:171–202
Ivanova N, Pavlov MY, Felden B, Ehrenberg M (2004) Ribosome rescue by tmRNA requires truncated mRNAs. J Mol Biol 338(1):33–41
Janzen DM, Frolova L, Geballe AP (2002) Inhibition of translation termination mediated by an interaction of eukaryotic release factor 1 with a nascent peptidyl-tRNA. Mol Cell Biol 22(24):8562–8570
Johansson M, Ieong KW, Trobro S, Strazewski P, Aqvist J, Pavlov MY, Ehrenberg M (2011) pH-sensitivity of the ribosomal peptidyl transfer reaction dependent on the identity of the A-site aminoacyl-tRNA. Proc Natl Acad Sci USA 108(1):79–84. doi:10.1073/pnas.1012612107
Joung JK, Ramm EI, Pabo CO (2000) A bacterial two-hybrid selection system for studying protein-DNA and protein–protein interactions. Proc Natl Acad Sci USA 97(13):7382–7387. doi:10.1073/pnas.110149297
Keiler KC, Waller PR, Sauer RT (1996) Role of a peptide tagging system in degradation of proteins synthesized from damaged messenger RNA. Science 271(5251):990–993
Levchenko I, Seidel M, Sauer RT, Baker TA (2000) A specificity-enhancing factor for the ClpXP degradation machine. Science 289(5488):2354–2356
Li X, Hirano R, Tagami H, Aiba H (2006) Protein tagging at rare codons is caused by tmRNA action at the 3′-end of nonstop mRNA generated in response to ribosome stalling. RNA 12(2):248–255
Li GW, Oh E, Weissman JS (2012) The anti-Shine–Dalgarno sequence drives translational pausing and codon choice in bacteria. Nature (Lond) 484(7395):538–541. doi:10.1038/nature10965
Lovett PS, Rogers EJ (1996) Ribosome regulation by the nascent peptide. Microbiol Rev 60(2):366–385
Moore SD, Sauer RT (2007) The tmRNA system for translational surveillance and ribosome rescue. Annu Rev Biochem 76:101–124
Mottagui-Tabar S, Isaksson LA (1997) Only the last amino acids in the nascent peptide influence translation termination in Escherichia coli genes. FEBS Lett 414(1):165–170
Muto H, Ito K (2008) Peptidyl-prolyl-tRNA at the ribosomal P-site reacts poorly with puromycin. Biochem Biophys Res Commun 366(4):1043–1047
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(4):545–552
Nakatogawa H, Ito K (2002) The ribosomal exit tunnel functions as a discriminating gate. Cell 108(5):629–636
Nissen P, Hansen J, Ban N, Moore PB, Steitz TA (2000) The structural basis of ribosome activity in peptide bond synthesis. Science 289(5481):920–930
Nurizzo D, Shewry SC, Perlin MH, Brown SA, Dholakia JN, Fuchs RL, Deva T, Baker EN, Smith CA (2003) The crystal structure of aminoglycoside-3′-phosphotransferase-IIa, an enzyme responsible for antibiotic resistance. J Mol Biol 327(2):491–506
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(1):50–54
Poole ES, Brown CM, Tate WP (1995) The identity of the base following the stop codon determines the efficiency of in vivo translational termination in Escherichia coli. EMBO J 14(1):151–158
Ramu H, Mankin A, Vazquez-Laslop N (2009) Programmed drug-dependent ribosome stalling. Mol Microbiol 71(4):811–824. doi:10.1111/j.1365-2958.2008.06576.x
Ramu H, Vazquez-Laslop N, Klepacki D, Dai Q, Piccirilli J, Micura R, Mankin AS (2011) Nascent peptide in the ribosome exit tunnel affects functional properties of the A-site of the peptidyl transferase center. Mol Cell 41(3):321–330. doi:10.1016/j.molcel.2010.12.031
Roche ED, Sauer RT (1999) SsrA-mediated peptide tagging caused by rare codons and tRNA scarcity. EMBO J 18(16):4579–4589
Roche ED, Sauer RT (2001) Identification of endogenous SsrA-tagged proteins reveals tagging at positions corresponding to stop codons. J Biol Chem 276(30):28509–28515
Shaw JJ, Green R (2007) Two distinct components of release factor function uncovered by nucleophile partitioning analysis. Mol Cell 28(3):458–467. doi:10.1016/j.molcel.2007.09.007
Sunohara T, Jojima K, Tagami H, Inada T, Aiba H (2004) Ribosome stalling during translation elongation induces cleavage of mRNA being translated in Escherichia coli. J Biol Chem 279(15):15368–15375. doi:10.1074/jbc.M312805200
Tanner DR, Cariello DA, Woolstenhulme CJ, Broadbent MA, Buskirk AR (2009) Genetic identification of nascent peptides that induce ribosome stalling. J Biol Chem 284(50):34809–34818
Ude S, Lassak J, Starosta AL, Kraxenberger T, Wilson DN, Jung K (2013) Translation elongation factor EF-P alleviates ribosome stalling at polyproline stretches. Science 339(6115):82–85. doi:10.1126/science.1228985
Vazquez-Laslop N, Thum C, Mankin AS (2008) Molecular mechanism of drug-dependent ribosome stalling. Mol Cell 30(2):190–202
Wah DA, Levchenko I, Rieckhof GE, Bolon DN, Baker TA, Sauer RT (2003) Flexible linkers leash the substrate binding domain of SspB to a peptide module that stabilizes delivery complexes with the AAA+ ClpXP protease. Mol Cell 12(2):355–363
Wohlgemuth I, Brenner S, Beringer M, Rodnina MV (2008) Modulation of the rate of peptidyl transfer on the ribosome by the nature of substrates. J Biol Chem 283(47):32229–32235
Woolstenhulme CJ, Parajuli S, Healey DW, Valverde DP, Petersen EN, Starosta AL, Guydosh NR, Johnson WE, Wilson DN, Buskirk AR (2013) Nascent peptides that block protein synthesis in bacteria. Proc Natl Acad Sci USA 110(10):E878–E887. doi:10.1073/pnas.1219536110
Yanagitani K, Kimata Y, Kadokura H, Kohno K (2011) Translational pausing ensures membrane targeting and cytoplasmic splicing of XBP1u mRNA. Science 331(6017):586–589. doi:10.1126/science.1197142
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(2):201–211
Youngman EM, Brunelle JL, Kochaniak AB, Green R (2004) The active site of the ribosome is composed of two layers of conserved nucleotides with distinct roles in peptide bond formation and peptide release. Cell 117(5):589–599
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2014 Springer Japan
About this chapter
Cite this chapter
Woolstenhulme, C.J., Buskirk, A.R. (2014). Isolation of Ribosome Stalling Motifs from Random Libraries. In: Ito, K. (eds) Regulatory Nascent Polypeptides. Springer, Tokyo. https://doi.org/10.1007/978-4-431-55052-5_13
Download citation
DOI: https://doi.org/10.1007/978-4-431-55052-5_13
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)