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Structural studies on decoding, termination and translocation in the bacterial ribosome

  • Chapter
Ribosomes

Abstract

With the determination of the atomic structures of the ribosomal subunits in 2000, focus has shifted in the last decade to the study of functional states of the ribosome with a view to helping elucidate the mechanisms underlying the various steps of translation. Some of these studies could be carried out using crystals of the ribosomal subunits, recognition of codon-anticodon pairing by the ribosome during decoding in the 30S subunit, or studies on peptidyl transferase intermediates in the 50S subunit. Others, such as the interaction of elongation or release factors with the ribosome require high-resolution crystal forms of the intact 70S ribosome. In this chapter, we review our studies on decoding using the 30S subunit, which could use crystals of the subunit that diffracted to high resolution. However, other functional studies such as those on elongation and termination required new crystal forms of the 70S ribosome that also diffracted to high-resolution.

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References

  • Agrawal RK, Sharma MR, Kiel MC, Hirokawa G, Booth TM, Spahn CM, Grassucci RA, Kaji A, Frank J (2004) Visualization of ribosome-recycling factor on the Escherichia coli 70S ribosome: functional implications. Proc Natl Acad Sci USA 101: 8900–8905

    Article  PubMed  CAS  Google Scholar 

  • Battle DJ, Doudna JA (2002) Specificity of RNA-RNA helix recognition. Proc Natl Acad Sci 99: 11676–11681

    Article  PubMed  CAS  Google Scholar 

  • 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: 966–970

    Article  PubMed  CAS  Google Scholar 

  • Borovinskaya MA, Pai RD, Zhang W, Schuwirth BS, Holton JM, Hirokawa G, Kaji H, Kaji A, Cate JH (2007) Structural basis for aminoglycoside inhibition of bacterial ribosome recycling. Nat Struct Mol Biol 14: 727–732

    Article  PubMed  CAS  Google Scholar 

  • Bretscher MS (1968) Translocation in protein synthesis: a hybrid structure model. Nature 218: 675–677

    Article  PubMed  CAS  Google Scholar 

  • Brodersen DE, Carter AP, Clemons WM, Jr., Morgan-Warren RJ, Murphy FVIV, Ogle JM, Tarry MJ, Wimberly B, Ramakrishnan V (2002) Atomic structures of the 30S subunit and its complexes with ligands and antibiotics. Cold Spring Harb Symp Quant Biol 66: 17–32

    Article  Google Scholar 

  • Carter AP, Clemons WM, Jr., Brodersen DE, Morgan-Warren RJ, Wimberly BT, Ramakrishnan V (2000) Functional insights from the structure of the 30S ribosomal subunit and its interactions with antibiotics. Nature 407: 340–348

    Article  PubMed  CAS  Google Scholar 

  • Diaconu M, Kothe U, Schlunzen F, Fischer N, Harms JM, Tonevitsky AG, Stark H, Rodnina MV, Wahl MC (2005) Structural basis for the function of the ribosomal L7/12 stalk in factor binding and GTPase activation. Cell 121: 991–1004

    Article  PubMed  CAS  Google Scholar 

  • Fourmy D, Recht MI, Blanchard SC, Puglisi JD (1996) Structure of the A site of Escherichia coli 16S ribosomal RNA complexed with an aminoglycoside antibiotic. Science 274: 1367–1371

    Article  PubMed  CAS  Google Scholar 

  • Frank J, Agrawal RK (2000) A ratchet-like inter-subunit reorganization of the ribosome during translocation. Nature 406: 319–332

    Article  CAS  Google Scholar 

  • Frolova LY, Tsivkovskii RY, Sivolobova GF, Oparina NY, Serpinsky OI, Blinov VM, Tatkov SI, Kisselev LL (1999) Mutations in the highly conserved GGQ motif of class 1 polypeptide release factors abolish ability of human eRF1 to trigger peptidyl-tRNA hydrolysis. RNA 5: 1014–1020

    Article  PubMed  CAS  Google Scholar 

  • Gao N, Zavialov AV, Li W, Sengupta J, Valle M, Gursky RP, Ehrenberg M, Frank J (2005) Mechanism for the disassembly of the posttermination complex inferred from cryo-EM studies. Mol Cell 18: 663–674

    Article  PubMed  CAS  Google Scholar 

  • Gao YG, Selmer M, Dunham CM, Weixlbaumer A, Kelley AC, Ramakrishnan V (2009) The structure of the ribosome with elongation factor G trapped in the posttranslocational state. Science 326: 694–699

    Article  PubMed  CAS  Google Scholar 

  • Gavrilova LP, Kostiashkina OE, Koteliansky VE, Rutkevitch NM, Spirin AS (1976) Factor-free (“non-enzymic”) and factor-dependent systems of translation of polyuridylic acid by Escherichia coli ribosomes. J Mol Biol 101: 537–552

    Article  PubMed  CAS  Google Scholar 

  • Hansson S, Singh R, Gudkov AT, Liljas A, Logan DT (2005) Structural insights into fusidic acid resistance and sensitivity in EF-G. J Mol Biol 348: 939–949

    Article  PubMed  CAS  Google Scholar 

  • Harms JM, Wilson DN, Schluenzen F, Connell SR, Stachelhaus T, Zaborowska Z, Spahn CM, Fucini P (2008) Translational regulation via L11: molecular switches on the ribosome turned on and off by thiostrepton and micrococcin. Mol Cell 30: 26–38

    Article  PubMed  CAS  Google Scholar 

  • Hirashima A, Kaji A (1973) Role of elongation factor G and a protein factor on the release of ribosomes from messenger ribonucleic acid. J Biol Chem 248: 7580–7587

    PubMed  CAS  Google Scholar 

  • Ito K, Uno M, Nakamura Y (1998) Single amino acid substitution in prokaryote polypeptide release factor 2 permits it to terminate translation at all three stop codons. Proc Natl Acad Sci USA 95: 8165–8169

    Article  PubMed  CAS  Google Scholar 

  • Ito K, Uno M, Nakamura Y (2000) A tripeptide ‘anticodon’ deciphers stop codons in messenger RNA. Nature 403: 680–684

    Article  PubMed  CAS  Google Scholar 

  • Jin H, Kelley AC, Loakes D, Ramakrishnan V (2010) Structure of the 70S ribosome bound to release factor 2 and a substrate analog provides insights into catalysis of peptide release. Proc Natl Acad Sci USA 107: 8593–8598

    Article  PubMed  Google Scholar 

  • Kazemie M (1976) Binding of aminoacyl-tRNA to reconstituted subparticles of Escherichia coli large ribosomal subunits. Eur JBiochem 67: 373–378

    Article  CAS  Google Scholar 

  • Klaholz BP, Pape T, Zavialov AV, Myasnikov AG, Orlova EV, Vestergaard B, Ehrenberg M, van Heel M (2003) Structure of the Escherichia coli ribosomal termination complex with release factor 2. Nature 421: 90–94

    Article  PubMed  CAS  Google Scholar 

  • Korostelev A, Zhu J, Asahara H, Noller HF (2010) Recognition of the amber UAG stop codon by release factor RF1. EMBO J 29: 2577–2585

    Article  PubMed  CAS  Google Scholar 

  • Korostelev A, Asahara H, Lancaster L, Laurberg M, Hirschi A, Zhu J, Trakhanov S, Scott WG, Noller HF (2008) Crystal structure of a translation termination complex formed with release factor RF2. Proc Natl Acad Sci USA 105: 19684–19689

    Article  PubMed  Google Scholar 

  • Korostelev A, Trakhanov S, Laurberg M, Noller HF (2006) Crystal structure of a 70S ribosome-tRNA complex reveals functional interactions and rearrangements. Cell 126: 1065–1077

    Article  PubMed  CAS  Google Scholar 

  • Laurberg M, Kristensen O, Martemyanov K, Gudkov AT, Nagaev I, Hughes D, Liljas A (2000) Structure of a mutant EF-G reveals domain III and possibly the fusidic acid binding site. J Mol Biol 303: 593–603

    Article  PubMed  CAS  Google Scholar 

  • Laurberg M, Asahara H, Korostelev A, Zhu J, Trakhanov S, Noller HF (2008) Structural basis for translation termination on the 70S ribosome. Nature 454: 852–857

    Article  PubMed  CAS  Google Scholar 

  • Maguire BA, Beniaminov AD, Ramu H, Mankin AS, Zimmermann RA (2005) A protein component at the heart of an RNA machine: the importance of protein l27for the function of the bacterial ribosome. Mol Cell 20: 427–435

    Article  PubMed  CAS  Google Scholar 

  • Moazed D, Noller HF (1989) Intermediate states in the movement of transfer RNA in the ribosome. Nature 342: 142–148

    Article  PubMed  CAS  Google Scholar 

  • Moore VG, Atchison RE, Thomas G, Moran M, Noller HF (1975) Identification of a ribosomal protein essential for peptidyl transferase activity. Proc Natl Acad Sci USA 72: 844–848

    Article  PubMed  CAS  Google Scholar 

  • Mora L, Heurgue-Hamard V, Champ S, Ehrenberg M, Kisselev LL, Buckingham RH (2003) The essential role of the invariant GGQ motif in the function and stability in vivo of bacterial release factors RF1 and RF2. Mol Microbiol 47: 267–275

    Article  PubMed  CAS  Google Scholar 

  • Nissen P, Hansen J, Ban N, Moore PB, Steitz TA (2000) The structural basis of ribosome activity in peptide bond synthesis. Science 289: 920–930

    Article  PubMed  CAS  Google Scholar 

  • Ogle JM, Brodersen DE, Clemons WM, Jr., Tarry MJ, Carter AP, Ramakrishnan V (2001) Recognition of cognate transfer RNA by the 30S ribosomal subunit. Science 292: 897–902

    Article  PubMed  CAS  Google Scholar 

  • Ogle JM, Carter AP, Ramakrishnan V (2003) Insights into the decoding mechanism from recent ribosome structures. Trends Biochem Sci 28: 259–266

    Article  PubMed  CAS  Google Scholar 

  • Ogle JM, Murphy FV, Tarry MJ, Ramakrishnan V (2002) Selection of tRNA by the ribosome requires a transition from an open to a closed form. Cell 111: 721–732

    Article  PubMed  CAS  Google Scholar 

  • Ogle JM, Ramakrishnan V (2005) Structural Insights into Translational Fidelity. Ann Rev Biochem 74.: 129–177

    Article  PubMed  CAS  Google Scholar 

  • Pape T, Wintermeyer W, Rodnina M (1999) Induced fit in initial selection and proofreading of aminoacyl-tRNA on the ribosome. Embo J 18: 3800–3807

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Peske F, Savelsbergh A, Katunin VI, Rodnina MV, Wintermeyer W (2004) Conformational changes of the small ribosomal subunit during elongation factor G-dependent tRNA-mRNA translocation. J Mol Biol 343: 1183–1194

    Article  PubMed  CAS  Google Scholar 

  • Petry S, Brodersen DE, Murphy FVt, Dunham CM, Selmer M, Tarry MJ, Kelley AC, Ramakrishnan V (2005) Crystal structures of the ribosome in complex with release factors RF1 and RF2 bound to a cognate stop codon. Cell 123: 1255–1266

    Article  PubMed  CAS  Google Scholar 

  • Rawat UB, Zavialov AV, Sengupta J, Valle M, Grassucci RA, Linde J, Vestergaard B, Ehrenberg M, Frank J (2003) A cryo-electron microscopic study of ribosome-bound termination factor RF2. Nature 421: 87–90

    Article  PubMed  CAS  Google Scholar 

  • Rodnina MV, Savelsbergh A, Katunin VI, Wintermeyer W (1997) Hydrolysis of GTP by elongation factor G drives tRNA movement on the ribosome. Nature 385: 37–41

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • 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 438: 520–524

    Article  PubMed  CAS  Google Scholar 

  • Schmeing TM, Voorhees RM, Kelley AC, Gao YG, Murphy FVt, Weir JR, Ramakrishnan V (2009) The crystal structure of the ribosome bound to EF-Tu and aminoacyl-tRNA. Science 326: 688–694

    Article  PubMed  CAS  Google Scholar 

  • Schuette JC, Murphy FVt, Kelley AC, Weir JR, Giesebrecht J, Connell SR, Loerke J, Mielke T, Zhang W, Penczek PA, Ramakrishnan V, Spahn CM (2009) GTPase activation of elongation factor EF-Tu by the ribosome during decoding. Embo J 28: 755–765

    Article  PubMed  CAS  Google Scholar 

  • Schuwirth BS, Borovinskaya MA, Hau CW, Zhang W, Vila-Sanjurjo A, Holton JM, Cate JH (2005) Structures of the bacterial ribosome at 3.5 A resolution. Science 310: 827–834

    Article  PubMed  CAS  Google Scholar 

  • Seeman NC, Rosenberg JM, Rich A (1976) Sequence-specific recognition of double helical nucleic acids by proteins. Proc Natl Acad Sci 73: 804–808

    Article  PubMed  CAS  Google Scholar 

  • Selmer M, Dunham CM, Murphy FVt, Weixlbaumer A, Petry S, Kelley AC, Weir JR, Ramakrishnan V (2006) Structure of the 70S ribosome complexed with mRNA and tRNA. Science 313: 1935–1942

    Article  PubMed  CAS  Google Scholar 

  • Sengupta J, Nilsson J, Gursky R, Kjeldgaard M, Nissen P, Frank J (2008) Visualization of the eEF2-0S ribosome transition-state complex by cryo-electron microscopy. J Mol Biol 382: 179–187

    Article  PubMed  CAS  Google Scholar 

  • Shaw JJ, Green R (2007) Two distinct components of release factor function uncovered by nucleophile partitioning analysis. Mol Cell 28: 458–467

    Article  PubMed  CAS  Google Scholar 

  • Song H, Mugnier P, Das AK, Webb HM, Evans DR, Tuite MF, Hemmings BA, Barford D (2000) The crystal structure of human eukaryotic release factor eRF1— mechanism of stop codon recognition and peptidyl-tRNA hydrolysis. Cell 100: 311–321

    Article  PubMed  CAS  Google Scholar 

  • Stanley RE, Blaha G, Grodzicki RL, Strickler MD, Steitz TA (2010) The structures of the anti-tuberculosis antibiotics viomycin and capreomycin bound to the 70S ribosome. Nat Struct Mol Biol

    Google Scholar 

  • Stark H, Rodnina MV, Rinke-Appel J, Brimacombe R, Wintermeyer W, van Heel M (1997) Visualization of elongation factor Tu on the Escherichia coli ribosome. Nature 389: 403–406

    Article  PubMed  CAS  Google Scholar 

  • Trakhanov SD, Yusupov MM, Agalarov SC, Garber MB, Ryazantsev SN, Tischenko SV, Shirokov VA (1987) Crystallization of 70 S ribosomes and 30S ribosomal subunits from Thermus thermophilus. FEBS Lett 220: 319–322

    Article  Google Scholar 

  • Trobro S, Aqvist J (2007) A model for how ribosomal release factors induce peptidyl-tRNA cleavage in termination of protein synthesis. Mol Cell 27: 758–766

    Article  PubMed  CAS  Google Scholar 

  • Valle M, Sengupta J, Swami NK, Grassucci RA, Burkhardt N, Nierhaus KH, Agrawal RK, Frank J (2002) Cryo-EM reveals an active role for aminoacyl-tRNA in the accommodation process. Embo J 21: 3557–3567

    Article  PubMed  CAS  Google Scholar 

  • Villa E, Sengupta J, Trabuco LG, LeBarron J, Baxter WT, Shaikh TR, Grassucci RA, Nissen P, Ehrenberg M, Schulten K, Frank J (2009) Ribosome-induced changes in elongation factor Tu conformation control GTP hydrolysis. Proc Natl Acad Sci USA 106: 1063–1068

    Article  PubMed  Google Scholar 

  • Vogeley L, Palm GJ, Mesters JR, Hilgenfeld R (2001) Conformational change of elongation factor Tu (EF-Tu) induced by antibiotic binding. Crystal structure of the complex between EF-Tu. GDP and aurodox. J Biol Chem 276: 17149–17155

    Article  PubMed  CAS  Google Scholar 

  • Voorhees RM, Weixlbaumer A, Loakes D, Kelley AC, Ramakrishnan V (2009) Insights into substrate stabilization from snapshots of the peptidyl transferase center of the intact 70S ribosome. Nat Struct Mol Biol 16: 528–533

    Article  PubMed  CAS  Google Scholar 

  • Voorhees RM, Schmeing TM, Kelley AC, Ramakrishnan V. (2010) The mechanism for activation of GTP hydrolysis on the ribosome. Science 330: 835–838

    Article  PubMed  CAS  Google Scholar 

  • Weixlbaumer A, Jin H, Neubauer C, Voorhees RM, Petry S, Kelley AC, Ramakrishnan V (2008) Insights into translational termination from the structure of RF2 bound to the ribosome. Science 322: 953–956

    Article  PubMed  CAS  Google Scholar 

  • Weixlbaumer A, Petry S, Dunham CM, Selmer M, Kelley AC, Ramakrishnan V (2007) Crystal structure of the ribosome recycling factor bound to the ribosome. Nat Struct Mol Biol 14: 733–737

    Article  PubMed  CAS  Google Scholar 

  • Wilson DN, Schluenzen F, Harms JM, Yoshida T, Ohkubo T, Albrecht R, Buerger J, Kobayashi Y, Fucini P (2005) X-ray crystallography study on ribosome recycling: the mechanism of binding and action of RRF on the 50S ribosomal subunit. Embo J 24: 251–260

    Article  PubMed  CAS  Google Scholar 

  • Wower J, Kirillov SV, Wower IK, Guven S, Hixson SS, Zimmermann RA (2000) Transit of tRNA through the Escherichia coli ribosome. Cross-linking of the 3’ end of tRNA to specific nucleotides of the 23S ribosomal RNA at the A, P, and E sites. J Biol Chem 275: 37887–37894

    Article  PubMed  CAS  Google Scholar 

  • Yusupov MM, Yusupova GZ, Baucom A, Lieberman K, Earnest TN, Cate JH, Noller HF (2001) Crystal structure of the ribosome at 5.5 A resolution. Science 292: 883–896

    Article  PubMed  CAS  Google Scholar 

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  1. Venki Ramakrishnan
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Editors and Affiliations

  1. Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany

    Marina V. Rodnina  & Wolfgang Wintermeyer  & 

  2. Howard Hughes Medical Institute Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA

    Rachel Green

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Ramakrishnan, V. (2011). Structural studies on decoding, termination and translocation in the bacterial ribosome. In: Rodnina, M.V., Wintermeyer, W., Green, R. (eds) Ribosomes. Springer, Vienna. https://doi.org/10.1007/978-3-7091-0215-2_2

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