Bacterial Ribosomes

Abstract

Ribosomes are complex ribonucleoproteins that provide the platform for protein biosynthesis in all organisms.

Keywords: protein biosynthesis; translation; messenger RNA; transfer RNA

Figure 1.

Cryoelectron microscopy of the Escherichia coli ribosome, with the small subunit (50S) in yellow, the large subunit in blue. The space between the subunits (intersubunit space) is where most of the ligands interact with the ribosome.

Figure 2.

Morphology of Escherichia coli ribosomal subunits, and locations of ribosomal proteins, as determined by immunoelectron microscopy. Top row: Three‐dimensional cryoelectron microscopy maps of (a) the 30S subunit, (b) the 50S subunit and (c) the 70S ribosome (Frank et al., ). Bottom row: Models of the two subunits and the 70S ribosome, as derived from visual interpretation of 2D projections from conventional electron microscopy of negatively stained specimen with approximate locations of some of the ribosomal proteins, marked by numbers. Locations of r‐protein are determined by immunoelectron microscopy. Reproduced from Stöffler‐Meilicke and Stöffler with permission by the American Society for Microbiology Press, Washington DC.

Figure 3.

The elongation cycle, showing three‐dimensional positions of tRNAs and elongation factors, as obtained by cryoelectron microscopy technique, overlaid on the 1.5‐nm resolution map of the Escherichia coli 70S ribosome. Top: tRNA positions in the pretranslocational state. The aminoacyl‐tRNA (pink) is present in the A site and peptidyl‐tRNA (green), carrying a growing polypeptide chain, in the P site. Right: Posttranslocational state. After peptide bond formation, A‐ (pink) and P‐ (green) site tRNAs have moved to P (green) and E (yellow) sites, respectively, in an EF‐G‐dependent translocation reaction. EF‐G (purple) momentarily interacts with ribosome to facilitate the translocation reaction. Bottom: Posttranslocational state with tRNAs occupying P and E sites. EF‐G has been released, after GTP hydrolysis in GDP form, to vacate the overlapping binding site for the next ternary complex. Left: At this stage, a new aminoacyl‐tRNA (grey, then pink) enters into the cycle in the form of a ternary complex with EF‐Tu (red) and GTP, and binds to the ribosome in the A/T state. Recently, another E site, the E2 site (brown), has been suggested, in which the deacylated tRNA temporarily resides without maintaining codon–anticodon interaction. While the EF‐Tu part of the ternary complex leaves the ribosome, following GTP hydrolysis, aminoacyl‐tRNA moves to its proper A‐site position to engage in peptide‐bond formation, and deacylated tRNA is released from the E2 site.

close

References

Ævarsson A, Brazhnikov E, Garber M et al. (1994) Three‐dimensional structure of the ribosomal translocase: elongation factor G from Thermus thermophilus. EMBO Journal 13: 3669–3677.

Agrawal RK, Penczek P, Grassucci RA, Li Y, Leith A, Nierhaus KH and Frank J (1996) Direct visualization of A‐, P‐, and E‐site transfer RNAs in the Escherichia coli ribosome. Science 271: 1000–1002.

Agrawal RK, Penczek P, Grassucci RA and Frank J (1998) Visualization of elongation factor G on the Escherichia coli 70S ribosome: the mechanism of translocation. Proceedings of the National Academy of Sciences of the USA 95: 6134–6138.

Bernabeu C and Lake JA (1982) Nascent polypeptide chains emerge from the exit domain of the large ribosomal subunit: Immune mapping of the nascent chain. Proceedings of the National Academy of Sciences of the USA 79: 3111–3115.

Capel MS, Engleman DM, Freeborn BR et al. (1987) A complete mapping of the proteins in the small ribosomal subunit of Escherichia coli. Science 238: 1403–1406.

Czworkowski J, Wang J, Steitz TA and Moore PB (1994) The crystal structure of elongation factor G complexed with GDP, at 2.7Å. EMBO Journal 13: 3661–3668.

Dahlberg AE (1989) The functional role of ribosomal RNA in protein synthesis. Cell 57: 525–529.

Frank J and Agrawal RK (1998) The movement of tRNA through the ribosome. Biophysical Journal 74: 589–594.

Frank J, Zhu J, Penczek P, Li Y, Srivastava S et al. (1995) A model of protein synthesis based on cryo‐electron microscopy of the E. coli ribosome. Nature 376: 441–444.

Green R and Noller HF (1997) Ribosomes and translation. Annual Review of Biochemistry 66: 679–716.

Lata KR, Agrawal RK, Penczek P, Grassucci RA, Zhu J and Frank J (1996) Three‐dimensional reconstruction of the Escherichia coli 30S ribosomal subunit in ice. Journal of Molecular Biology 262: 43–52.

Malhotra A, Penczek P, Agrawal RK et al. (1998) E. coli 70S ribosome at 15Åresolution by cryo‐electron microscopy: Localization of fMET‐tRNAfMet and fitting of L1 protein. Journal of Molecular Biology 280: 103–116.

May RP, Nowotny V, Nowotny P, Voss H and Nierhaus KH (1992) Inter‐protein distances within the large subunit from Escherichia coli ribosomes. EMBO Journal 11: 373–378.

Moazed D and Noller HF (1989a) Interaction of tRNA with 23S RNA in ribosomal A, P and E sites. Cell 57: 585–597.

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

Mueller F, Stark H, Van Heel M, Rinke‐Appel J and Brimacombe R (1997) A new model for the three‐dimensional folding of Escherichia coli 16S ribosomal RNA. III. The topography of the functional center. Journal of Molecular Biology 271: 566–587.

Nierhaus KH (1990) The allosteric three‐site model for the ribosomal elongation cycle: Feature and future. Biochemistry 29: 4997–5012.

Nissen P, Kjeldgaard M, Thirup S, Polekhina G, Reshetnikova L, Clark BFC and Nyborg J (1995) Crystal structure of the ternary complex of Phe‐tRNAPhe, EF‐Tu, and a GTP analog. Science 270: 1464–1472.

Stark H, Müller F, Orlova EV et al. (1995) The 70S ribosome at 23 Å resolution: fitting the ribosomal RNA. Structure 3: 815–821.

Stark H, Orlova EV, Rinke‐Appel J et al. (1997a) Arrangement of tRNAs in pre‐ and posttranslocational ribosomes revealed by electron cryomicroscopy. Cell 88: 19–28.

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

Stöffler‐Meilicke M and Stöffler G (1990) Topography of the ribosomal proteins from Escherichia coli within the intact subunits as determined by immunoelectron microscopy and protein–protein cross‐linking. In: Hill WE, Dahlberg A, Garrett RA, Moore PB, Schlessinger D and Warner JR (eds) The Ribosome, Structure, Function, Evolution, pp. 123–133. Washington DC: ASM Press.

Yonath A, Leonard KR and Wittmann HG (1987) A tunnel in the large ribosomal subunit revealed by three‐dimensional image reconstruction. Science 236: 813–816.

Further Reading

Hill WE, Moore P, Dahlberg A, Schlessinger R, Garrett R and Warner J (1990) The Ribosome: Structure, Function, and Evolution. Washington, DC: American Society for Microbiology.

Liljas A and Al‐Karadaghi S (1997) Structural aspects of protein synthesis. Nature Structural Biology 4: 767–771.

Matheson A, Dennis P, Davies J and Hill W (1995) Frontiers in Translation. Ottawa: National Research Council Canada.

Moore PB (1998) The three‐dimensional structure of the ribosome and its components. Annual Review of Biophysical Chemistry 27: 35–58.

Nierhaus KH (1993) Solution of the ribosome riddle: how the ribosome selects the correct aminoacyl‐tRNA out of 41 similar contestants. Molecular Microbiology 9: 661–669.

Ramakrishnan V and White SW (1998) Ribosomal protein structures: insights into the architecture, machinery and evolution of the ribosome. Trends in Biochemical Sciences 23: 208–212.

Wilson KS and Noller HF (1998) Molecular movement inside the translation engine. Cell 92: 337–349.

Contact Editor close
Submit a note to the editor about this article by filling in the form below.

* Required Field

How to Cite close
Frank, Joachim, and Agrawal, Rajendra K(Apr 2001) Bacterial Ribosomes. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1038/npg.els.0000305]