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Domain 4:

Synthesis and Processing of Macromolecules

How We Got to Where We Are: the Ribosome in the 21st Century

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  • Author: Peter B. Moore1
  • Editor: Susan T. Lovett2
  • VIEW AFFILIATIONS HIDE AFFILIATIONS
    Affiliations: 1: Departments of Chemistry and of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520; 2: Brandeis University, Waltham, MA
  • Received 04 April 2007 Accepted 21 June 2007 Published 12 September 2007
  • Address correspondence to Peter B. Moore peter.moore@yale.edu
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  • Abstract:

    This article is a short, informal history of the ribosome field that begins with the emergence of the field in the 1930s and ends with a description of its state in 2007, the year this essay was written. The growth in our understanding of both the role of the ribosome in protein synthesis and its structure is emphasized. Starting in 2000, the field experienced a massive upheaval as a result of the publication of the first atomic-resolution crystal structures for ribosomes. However, by 2007, the field had recovered sufficiently so that one could begin to understand how it was likely to evolve in its "poststructural" era. For that reason, this essay is about as useful as a short history of the ribosome field today as it was several years ago, when it was written.

  • Citation: Moore P. 2007. How We Got to Where We Are: the Ribosome in the 21st Century, EcoSal Plus 2007; doi:10.1128/ecosalplus.2.5.1

Key Concept Ranking

Three-Dimensional Electron Microscopy
0.44328484
16s rRNA Sequencing
0.43254915
Endoplasmic Reticulum
0.36233547
Ribosomes
0.34858993
0.44328484

References

1. Rheinberger H-J. 2004. A history of protein biosynthesis and ribosome research, p 1–51. In Nierhaus KH and Wilson DN (ed), Protein Synthesis and Ribosome Structure. Wiley-VCH Verlag, Weinheim, Germany. [CrossRef]
2. Brachet J. 1941. La detection histochimique et le microdosage des acides pentosenucleique. Enzymologia 10:87–96.
3. Caspersson T. 1941. The protein metabolism of the cell. Naturwissenschaften 29:33–43. [CrossRef]
4. Claude A. 1941. Particulate components of cytoplasm. Cold Spring Harbor Symp Quant Biol 9:263–271.
5. Brachet J. 1952. The role of the nucleus and cytoplasm in synthesis and morphogenesis. Symp Soc Exp Biol 6:173–200.
6. Claude A. 1943. The constitution of protoplasm. Science 97:451–455. [PubMed][CrossRef]
7. Palade GE. 1955. A small particulate component of the cytoplasm. J Biophys Biochem Cytol 1:59–68.[PubMed]
8. Palade GE, Porter KR. 1954. Studies on the endoplasmic reticulum. I. Its identification in cells in situ. J Exp Med 100:641–656. [PubMed][CrossRef]
9. Palade GE, Siekevitz P. 1956. Liver microsomes, an integrated morphological and biochemical study. J Biophys Biochem Cytol 2:171–200.[PubMed]
10. Keller EB, Zamecnik PC, Loftfield RB. 1954. The role of microsomes in the incorporation of amino acids into proteins. J Histochem Cytochem 2:378–386.[PubMed]
11. Palade GE. 1992. Intracellular aspects of the process of protein secretion, p 177–206. In Lindsten J (ed), Nobel Lectures in Physiology or Medicine, 1971–1980. World Scientific Publishing Co., Singapore.
12. Chao FC. 1957. Dissociation of macromolecular ribonucleoprotein of yeast. Arch Biochem Biophys 70:426–431. [PubMed][CrossRef]
13. Chao FC, Schachman HK. 1956. The isolation and characterization of a macromolecular ribonucleoprotein from yeast. Arch Biochem Biophys 61:220–230. [PubMed][CrossRef]
14. Tissières A, Watson JD. 1958. Ribonucleoprotein particles from Escherichia coli. Nature 182:778–780. [PubMed][CrossRef]
15. Crick FHC. 1958. On protein synthesis. Symp Soc Exp Biol 12:138–163.[PubMed]
16. Hoagland MB, Zamecnik PC, Stephenson ML. 1957. Intermediate reactions in protein biosynthesis. Biochim Biophys Acta 24:215–216. [PubMed][CrossRef]
17. Brenner S, Jacob F, Meselson M. 1961. An unstable intermediate carrying information from genes to ribosomes for protein synthesis. Nature 190:567–581. [CrossRef]
18. Gros F, Hiatt H, Gilbert G, Kurland CG, Risebrough RW, Watson JD. 1961. Unstable ribonucleic acid revealed by pulse labelling of E. coli. Nature 190:581–585. [PubMed][CrossRef]
19. Watson JD. 1964. The synthesis of proteins upon ribosomes. Bull Soc Chim Biol 46:1399–1425.[PubMed]
20. Roberts RB. 1958. Microsomal Particles and Protein Synthesis. Pergamon Press, New York, NY.
21. Traut RR, Moore PB, Delius H, Noller HF, Tissières A. 1967. Ribosomal proteins of E. coli I. Demonstration of primary structure differences. Proc Natl Acad Sci USA 57:1294–1301. [PubMed][CrossRef]
22. Hardy SJS. 1975. The stoichiometry of the ribosomal proteins of Escherichia coli. Mol Gen Genet 140:253–274. [PubMed][CrossRef]
23. Waller JP. 1964. Fractionation of the ribosomal protein from Escherichia coli. J Mol Biol 10:319–336. [PubMed][CrossRef]
24. Traub P, Nomura M. 1968. Structure and function of E. coli ribosomes. V. Reconstitution of functionally active 30S ribosomal particles from RNA and proteins. Proc Natl Acad Sci USA 59:777–784. [PubMed][CrossRef]
25. Brosius J, Palmer ML, Kennedy PJ, Noller HF. 1978. Complete nucleotide sequence of a 16S ribosomal RNA gene from Escherichia coli. Proc Natl Acad Sci USA 75:4801–4805. [PubMed][CrossRef]
26. Noller HF, Woese CR. 1981. Secondary structure of 16S ribosomal RNA. Science 212:403–411. [PubMed][CrossRef]
27. Huxley HE, Zubay G. 1960. Electron microscopic observations on the structure of microsomal particles from Escherichia coli. J Mol Biol 2:10–18. [CrossRef]
28. Lake JA. 1976. Ribosome structure determined by electron microscopy of Escherichia coli small subunits, large subunits and monomeric ribosomes. J Mol Biol 105:131–159. [PubMed][CrossRef]
29. Frank J, Zhu J, Penczek P, Li Y, Srivastava S, Verschoor A, Rademacher M, Grassucci R, Lata RK, Agrawal RK. 1995. A model for protein synthesis based on cryo-electron microscopy of the E. coli ribosome. Nature 376:441–444. [PubMed][CrossRef]
30. Yonath A, Mussig J, Tesche B, Lorenz S, Erdmann VA, Wittmann HG. 1980. Crystallization of the large ribosomal subunits from Bacillus stearothermophilus. Biochem Int 1:428–435.
31. Hope H, Frolow F, von Bohlen K, Makowski I, Kratky C, Halfori Y, Danz H, Webster P, Bartles KS, Wittmann HG, Yonath A. 1989. Cryocrystallography of ribosomal particles. Acta Crystallogr B45:190–199.
32. von Bohlen K, Makowski I, Hansen HAS, Bartels H, Berkovitch-Yellin Z, Zaytzev-Bushan A, Meyer S, Paulke C, Franscheschi F, Yonath A. 1991. Characterization and preliminary attempts for derivitization of crystals of large ribosomal subunits from Haloarcula marismortui diffracting to 3 Á resolution. J Mol Biol 222:11–15. [PubMed][CrossRef]
33. Ban N, Freeborn B, Nissen P, Penczek P, Grassucci RA, Sweet R, Frank J, Moore PB, Steitz TA. 1998. A 9 Á resolution X-ray crystallographic map of the large ribosomal subunit. Cell 93:1105–1115. [PubMed][CrossRef]
34. Selmer M, Dunham CM, Murphy FVI, Weixibaumer A, Petry S, Kelley AC, Weir JR, Ramakrishnan V. 2006. Structure of the 70S ribosome complexed with mRNA and tRNA. Science 313:1935–1942. [PubMed][CrossRef]
35. DeLano WL. 2002. The PyMol Molecular Graphics System. DeLano Scientific, San Carlos, CA.
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/content/journal/ecosalplus/10.1128/ecosalplus.2.5.1
2007-09-12
2017-12-15

Abstract:

This article is a short, informal history of the ribosome field that begins with the emergence of the field in the 1930s and ends with a description of its state in 2007, the year this essay was written. The growth in our understanding of both the role of the ribosome in protein synthesis and its structure is emphasized. Starting in 2000, the field experienced a massive upheaval as a result of the publication of the first atomic-resolution crystal structures for ribosomes. However, by 2007, the field had recovered sufficiently so that one could begin to understand how it was likely to evolve in its "poststructural" era. For that reason, this essay is about as useful as a short history of the ribosome field today as it was several years ago, when it was written.

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Figures

Image of Figure 1
Figure 1

This micrograph shows what the endoplasmic reticulum looks like under an electron microscope when fixed, stained, and thin-sectioned specimens of pancreatic tissue are examined. The specks abundant in this view are ribosomes.

Reprinted from ( 11 ), with permission of the publisher.

Citation: Moore P. 2007. How We Got to Where We Are: the Ribosome in the 21st Century, EcoSal Plus 2007; doi:10.1128/ecosalplus.2.5.1
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Image of Figure 2
Figure 2

This cartoon appears in the article Watson published in 1964, which did much to fix the idea in everyone’s mind that the ribosome has two principal sites for tRNA binding, one that interacts preferentially with peptidyl-tRNAs, the P site, and a second at which aminoacyl-tRNAs bind as they enter the peptide bond formation process, the A site ( 19 ). The left panel shows a piece of mRNA attached to the 30S subunit, forming base pairs with two tRNAs that both also interact with the large subunit, one carrying a nascent peptide and the other an aminoacyl-tRNA. In the middle panel, we see the state of affairs that exists after the nascent peptide has been transferred to the amino group of the amino acid of what used to be the aminoacyl-tRNA. The right panel shows the situation that prevails after the peptidyl-tRNA moves from the site where it forms initially to the site it must occupy if another amino acid is to be added to the growing chain. AA, amino acid; n, amino acid in nascent peptide.

Reprinted from ( 19 ) with permission of the publisher.

Citation: Moore P. 2007. How We Got to Where We Are: the Ribosome in the 21st Century, EcoSal Plus 2007; doi:10.1128/ecosalplus.2.5.1
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Image of Figure 3
Figure 3

This micrograph is a portion of Plate IIIb from an article on ribosome structure published by Huxley and Zubay in 1960 ( 27 ). The particles are embedded in phosphotungstic acid, which is a negative stain, and the division of the particles into two, unequal, subunits is plainly visible.

Reprinted from the ( 27 ) with permission of the publisher.

Citation: Moore P. 2007. How We Got to Where We Are: the Ribosome in the 21st Century, EcoSal Plus 2007; doi:10.1128/ecosalplus.2.5.1
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Image of Figure 4
Figure 4

The image shown is a photograph of the plaster models of the large subunit (left) and the small subunit (right) given by James Lake circa 1977. They correspond to the shapes he reported for these objects in 1976 ( 28 ). The maximum linear dimension of the ribosome is about 250 Å, and at this resolution, only a specialist can distinguish the ribosomes of one prokaryotic species from those of another. The ribosomal subunits of eukaryotes are similar in shape but somewhat larger, i.e., about 300 Å in maximum linear dimension.

Citation: Moore P. 2007. How We Got to Where We Are: the Ribosome in the 21st Century, EcoSal Plus 2007; doi:10.1128/ecosalplus.2.5.1
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Image of Figure 5
Figure 5

Selmer and coworkers recently published a 2.8-Å-resolution structure of the 70S ribosome from ( 34 ), the highest-resolution structure of a complete ribosome that is presently available. The particle is oriented so that the viewer looks into the interface between the two subunits from the direction that aminoacyl-tRNAs are delivered to the particle by elongation factor EF-Tu. The RNA components of the large subunit are dark blue, and its protein components are light blue. The RNA components of the small subunit are dark green, while its proteins are light brown. A tRNA (dark red) can be seen to be bound at the P site, while beyond it, in magenta, a tRNA bound at the E site can just be seen. The pink fragment seen at the small-subunit end of the P site-bound tRNA is a fragment of mRNA. All components are shown in a stick representation in which only non-hydrogen atoms are taken into account. This image was prepared using PyMol ( 35 ).

Reprinted from ( 34 ) with permission of the publisher.

Citation: Moore P. 2007. How We Got to Where We Are: the Ribosome in the 21st Century, EcoSal Plus 2007; doi:10.1128/ecosalplus.2.5.1
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