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Chapter 26 : Ribosomal Elongation Cycle
Authors:
Knud H. Nierhaus1,
Marylena Dabrowski1,
Edda Einfeldt1,
Detlev Kamp1,
Viter Marquez1,
Sebastian Patzke1,
Markus A. Schäfer1,
Ulrich Stelzl1,
Christian Spahn2,
Nils Burkhardt3,
Gundo Diedrich3,
Gregor Blaha4,
Regine Willumeit5,
Heinrich B. Stuhrmann6
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Affiliations:
1: Max-Planck-Institut für Molekulare Genetik, AG Ribosomen, Ihnestraβe 73, D-14195 Berlin, Germany;
2: Max-Planck-Institut für Molekulare Genetik, AG Ribosomen, Ihnestraβe 73, D-14195 Berlin, Germany, and Wadsworth Center, New York State Department of Health, Empire State Plaza, P.O. Box 509, Albany, NY 12201-0509;
3: Max-Planck-Institut für Molekulare Genetik, AG Ribosomen, Ihnestraβe 73, D-14195 Berlin, and BAYER AGWuppertal, Gebäude 405, Abteilung MST, D-42096 Wuppertal, Germany;
4: Max-Planck-Institut für Molekulare Genetik, AG Ribosomen, Ihnestraβe 73, D-14195 Berlin, and GKSS Research Center, Max-Planck-Straβe, 21502 Geesthacht, Germany;
5: GKSS Research Center, Max-Planck-Straβe, 21502 Geesthacht, Germany;
6: GKSS Research Center, Max-Planck-Straβe, 21502 Geesthacht, Germany, and Institut de Biologie Structurale, 41 Avenue des Martyrs, F-38027 Grenoble, CEDEX 1, France
Content Type: Monograph
Publication Year:
2000
Category: Microbial Genetics and Molecular Biology
Book DOI:
10.1128/9781555818142
Chapter DOI:
10.1128/9781555818142.ch26
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Abstract:
This chapter provides a brief review of the reactions of the elongation cycle, and discusses recent data that clarify and explain some points of the divergent aspects of the current models of the elongation cycle. It shows that the location and the features of the deacylated tRNA in either the P or E site are extremely sensitive to the buffer conditions applied. These data explain the discrepancies of the current models of the elongation cycle and the controversy about the features and importance of the E site. It shows that the striking differences can be traced back to differences in the buffer systems used by the two groups. It presents contact patterns of deacylated tRNA with the ribosomal subunits and the P/E hybrid site, and contact patterns of tRNAs in the ribosomal pre and post states. Escherichia coli cells grow happily in D2O instead of H2O, thus replacing all the protons with deuterons. The crystal structure of the ternary complex has demonstrated that EF-Tu is more than 50 Å from the anticodon. The central enzymatic activity of the ribosome is the formation of the peptide bond that is formed at an active center on the large ribosomal subunit, the PTF center. Different affinity-labeling approaches were applied to identify components at or near the peptidyltransferase (PTF) center. As a topographical method, affinity labeling cannot directly identify the component actually involved in the enzymatic activity.
Citation:
Nierhaus K, Dabrowski M, Einfeldt E, Kamp D, Marquez V, Patzke S, Schäfer M, Stelzl U, Spahn C, Burkhardt N, Diedrich G, Blaha G, Willumeit R, Stuhrmann H.
2000.
Ribosomal Elongation Cycle,
p 319-336.
In
Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed),
The Ribosome.
ASM Press, Washington, DC.
doi: 10.1128/9781555818142.ch26
Figures
Ribosomal Elongation Cycle
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Citation:
Nierhaus K, Dabrowski M, Einfeldt E, Kamp D, Marquez V, Patzke S, Schäfer M, Stelzl U, Spahn C, Burkhardt N, Diedrich G, Blaha G, Willumeit R, Stuhrmann H.
2000.
Ribosomal Elongation Cycle,
p 319-336.
In
Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed),
The Ribosome.
ASM Press, Washington, DC.
doi: 10.1128/9781555818142.ch26
/content/10.1128/9781555818142.chap26.fig26-1
Figure 1
Models of the elongation cycle. (A) Hybrid-site model. (B) Allosteric three-site model. For explanations, see the text.
10.1128/9781555818142/fig26-1_thmb.gif
10.1128/9781555818142/fig26-1.gif
Figure 1
Models of the elongation cycle. (A) Hybrid-site model. (B) Allosteric three-site model. For explanations, see the text.
Citation:
Nierhaus K, Dabrowski M, Einfeldt E, Kamp D, Marquez V, Patzke S, Schäfer M, Stelzl U, Spahn C, Burkhardt N, Diedrich G, Blaha G, Willumeit R, Stuhrmann H.
2000.
Ribosomal Elongation Cycle,
p 319-336.
In
Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed),
The Ribosome.
ASM Press, Washington, DC.
doi: 10.1128/9781555818142.ch26
/content/10.1128/9781555818142.chap26.fig26-2
Figure 2
Relative accessibilities of the phosphate groups of a phosphorothioated tRNA on either subunit and a 70S ribosome. The relative accessibility of a phosphate position means the accessibility relative to that of the corresponding position of a deacylated tRNA in solution. (Left) Accessibility graphs of tRNAs bound to ribosomal subunits or 70S ribosomes, always in the presence of poly(U). The y axes indicate the relative accessibilities (1, full accessibility; 0, full protection); the x axis gives the nucleotide position. (A) Comparison of the accessibility pattern of a tRNA bound to the P site of a 70S ribosome (red) with that of a tRNA bound to 30S subunits (green). (B) Same as graph A except that the pattern obtained with 50S subunits is shown (blue). (Right) The same patterns projected onto the three-dimensional model of tRNA with a color code for the accessibility of a phosphate group. (Taken from Schäfer et al., unpublished .)
10.1128/9781555818142/fig26-2_thmb.gif
10.1128/9781555818142/fig26-2.gif
Figure 2
Relative accessibilities of the phosphate groups of a phosphorothioated tRNA on either subunit and a 70S ribosome. The relative accessibility of a phosphate position means the accessibility relative to that of the corresponding position of a deacylated tRNA in solution. (Left) Accessibility graphs of tRNAs bound to ribosomal subunits or 70S ribosomes, always in the presence of poly(U). The y axes indicate the relative accessibilities (1, full accessibility; 0, full protection); the x axis gives the nucleotide position. (A) Comparison of the accessibility pattern of a tRNA bound to the P site of a 70S ribosome (red) with that of a tRNA bound to 30S subunits (green). (B) Same as graph A except that the pattern obtained with 50S subunits is shown (blue). (Right) The same patterns projected onto the three-dimensional model of tRNA with a color code for the accessibility of a phosphate group. (Taken from Schäfer et al., unpublished .)
Citation:
Nierhaus K, Dabrowski M, Einfeldt E, Kamp D, Marquez V, Patzke S, Schäfer M, Stelzl U, Spahn C, Burkhardt N, Diedrich G, Blaha G, Willumeit R, Stuhrmann H.
2000.
Ribosomal Elongation Cycle,
p 319-336.
In
Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed),
The Ribosome.
ASM Press, Washington, DC.
doi: 10.1128/9781555818142.ch26
/content/10.1128/9781555818142.chap26.fig26-3
Figure 3
Contact border of a deacylated tRNA at the 70S P site separating the tRNA regions contacting the small and the large ribosomal subunit. (Taken from Schäfer et al., unpublished .)
10.1128/9781555818142/fig26-3_thmb.gif
10.1128/9781555818142/fig26-3.gif
Figure 3
Contact border of a deacylated tRNA at the 70S P site separating the tRNA regions contacting the small and the large ribosomal subunit. (Taken from Schäfer et al., unpublished .)
Citation:
Nierhaus K, Dabrowski M, Einfeldt E, Kamp D, Marquez V, Patzke S, Schäfer M, Stelzl U, Spahn C, Burkhardt N, Diedrich G, Blaha G, Willumeit R, Stuhrmann H.
2000.
Ribosomal Elongation Cycle,
p 319-336.
In
Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed),
The Ribosome.
ASM Press, Washington, DC.
doi: 10.1128/9781555818142.ch26
/content/10.1128/9781555818142.chap26.fig26-4
Figure 4
Deacylated tRNAs in the P and P/E sites as observed in polyamine and conventional buffer systems, respectively ( Agrawal et al., 1999 ). (Top) Mutual arrangement of tRNAs in the two sites. The anticodon regions are highlighted in red and overlap; therefore, both positions cannot be occupied simultaneously in the same ribosome. (Bottom) tRNAs in the two positions seen within the ribosome. Landmarks of the small 30S subunit: h, head; sp, spore. Landmarks of the large 50S subunit: L1, L1 protuberance; CP, central protuberance; St, L12 stalk. (Adapted from Agrawal et al., 1999 .)
10.1128/9781555818142/fig26-4_thmb.gif
10.1128/9781555818142/fig26-4.gif
Figure 4
Deacylated tRNAs in the P and P/E sites as observed in polyamine and conventional buffer systems, respectively ( Agrawal et al., 1999 ). (Top) Mutual arrangement of tRNAs in the two sites. The anticodon regions are highlighted in red and overlap; therefore, both positions cannot be occupied simultaneously in the same ribosome. (Bottom) tRNAs in the two positions seen within the ribosome. Landmarks of the small 30S subunit: h, head; sp, spore. Landmarks of the large 50S subunit: L1, L1 protuberance; CP, central protuberance; St, L12 stalk. (Adapted from Agrawal et al., 1999 .)
Citation:
Nierhaus K, Dabrowski M, Einfeldt E, Kamp D, Marquez V, Patzke S, Schäfer M, Stelzl U, Spahn C, Burkhardt N, Diedrich G, Blaha G, Willumeit R, Stuhrmann H.
2000.
Ribosomal Elongation Cycle,
p 319-336.
In
Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed),
The Ribosome.
ASM Press, Washington, DC.
doi: 10.1128/9781555818142.ch26
/content/10.1128/9781555818142.chap26.fig26-5
Figure 5
Difference patterns of thioated tRNAs. E, P, and A mark the respective tRNA binding sites. Red, positions where the relative intensities of the two states compared differed by at least a factor of 2; blue, no difference according to this criterion. (A) Differences in the protection patterns of AcPhe-tRNA before and after translocation. (B) Differences of tRNAPhe in the PPre site and AcPhe-tRNA in the PPost site. (C) Differences in the protection patterns of tRNAPhe before and after translocation. (D) Differences in the protection patterns of deacylated tRNAPhe in the PPre site and in the A site [A(deac)]. (Adapted from Dabrowski et al., 1998 .)
10.1128/9781555818142/fig26-5_thmb.gif
10.1128/9781555818142/fig26-5.gif
Figure 5
Difference patterns of thioated tRNAs. E, P, and A mark the respective tRNA binding sites. Red, positions where the relative intensities of the two states compared differed by at least a factor of 2; blue, no difference according to this criterion. (A) Differences in the protection patterns of AcPhe-tRNA before and after translocation. (B) Differences of tRNAPhe in the PPre site and AcPhe-tRNA in the PPost site. (C) Differences in the protection patterns of tRNAPhe before and after translocation. (D) Differences in the protection patterns of deacylated tRNAPhe in the PPre site and in the A site [A(deac)]. (Adapted from Dabrowski et al., 1998 .)
Citation:
Nierhaus K, Dabrowski M, Einfeldt E, Kamp D, Marquez V, Patzke S, Schäfer M, Stelzl U, Spahn C, Burkhardt N, Diedrich G, Blaha G, Willumeit R, Stuhrmann H.
2000.
Ribosomal Elongation Cycle,
p 319-336.
In
Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed),
The Ribosome.
ASM Press, Washington, DC.
doi: 10.1128/9781555818142.ch26
/content/10.1128/9781555818142.chap26.fig26-6
Figure 6
The α-ε model of the elongation cycle. E, P, and A mark the respective tRNA binding sites. The essential feature is a movable ribosomal α-ε domain that connects both subunits through the intersubunit space, binds both tRNAs of an elongating ribosome, and carries them from the A and P sites to the P and E sites, respectively, during translocation. The model keeps all the features of the allosteric three-site model (Fig. 1B) but explains the reciprocal linkage between the A and E sites by the fact that the α-ε domain moves out of the A site during translocation, leaving the decoding center alone at the A site, rather than by an allosteric coupling. Yellow and green, the two binding regions of the α-ε domain; blue, the decoding center at the A site.
10.1128/9781555818142/fig26-6_thmb.gif
10.1128/9781555818142/fig26-6.gif
Figure 6
The α-ε model of the elongation cycle. E, P, and A mark the respective tRNA binding sites. The essential feature is a movable ribosomal α-ε domain that connects both subunits through the intersubunit space, binds both tRNAs of an elongating ribosome, and carries them from the A and P sites to the P and E sites, respectively, during translocation. The model keeps all the features of the allosteric three-site model (Fig. 1B) but explains the reciprocal linkage between the A and E sites by the fact that the α-ε domain moves out of the A site during translocation, leaving the decoding center alone at the A site, rather than by an allosteric coupling. Yellow and green, the two binding regions of the α-ε domain; blue, the decoding center at the A site.
Citation:
Nierhaus K, Dabrowski M, Einfeldt E, Kamp D, Marquez V, Patzke S, Schäfer M, Stelzl U, Spahn C, Burkhardt N, Diedrich G, Blaha G, Willumeit R, Stuhrmann H.
2000.
Ribosomal Elongation Cycle,
p 319-336.
In
Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed),
The Ribosome.
ASM Press, Washington, DC.
doi: 10.1128/9781555818142.ch26
/content/10.1128/9781555818142.chap26.fig26-7
Figure 7
tRNA arrangement in PRE (left-hand panels) and POST (right-hand panels) states. The green and red tRNAs are thought to be at the A and P sites, respectively, of PRE states and at the P and E sites, respectively, of POST states. (A and B) 70S ribosome; (C and D) 30S subunit; (E and F) 50S subunit. (From Nierhaus et al., 1998 .)
10.1128/9781555818142/fig26-7_thmb.gif
10.1128/9781555818142/fig26-7.gif
Figure 7
tRNA arrangement in PRE (left-hand panels) and POST (right-hand panels) states. The green and red tRNAs are thought to be at the A and P sites, respectively, of PRE states and at the P and E sites, respectively, of POST states. (A and B) 70S ribosome; (C and D) 30S subunit; (E and F) 50S subunit. (From Nierhaus et al., 1998 .)
Citation:
Nierhaus K, Dabrowski M, Einfeldt E, Kamp D, Marquez V, Patzke S, Schäfer M, Stelzl U, Spahn C, Burkhardt N, Diedrich G, Blaha G, Willumeit R, Stuhrmann H.
2000.
Ribosomal Elongation Cycle,
p 319-336.
In
Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed),
The Ribosome.
ASM Press, Washington, DC.
doi: 10.1128/9781555818142.ch26
/content/10.1128/9781555818142.chap26.fig26-8
Figure 8
The tRNAs present on the elongating ribosome in the PRE and POST states. (A) tRNA position observed in poly(U)-programmed ribosomes saturated with deacylated tRNAs in the presence of the conventional buffer system. (B) tRNAs in the POST state in the presence of the polyamine system (adapted from Agrawal et al., 1998). (C) Same as panel B, but the top of the 70S ribosome has been cut off. (D) Same as panel B, but a slice of the ribosome is shown with the tRNAs kept at the P and E sites. A, P, and E mark the respective tRNA binding sites, and E2 marks the corresponding tRNA position. Landmarks of the small subunit: ch, tentative mRNA channel through the neck of the 30S subunit; h, head; pt, platform; 1b, part of bridge 1 connecting the subunits. Landmarks of the large subunit: CP, central protuberance; St, L12 stalk.
10.1128/9781555818142/fig26-8_thmb.gif
10.1128/9781555818142/fig26-8.gif
Figure 8
The tRNAs present on the elongating ribosome in the PRE and POST states. (A) tRNA position observed in poly(U)-programmed ribosomes saturated with deacylated tRNAs in the presence of the conventional buffer system. (B) tRNAs in the POST state in the presence of the polyamine system (adapted from Agrawal et al., 1998). (C) Same as panel B, but the top of the 70S ribosome has been cut off. (D) Same as panel B, but a slice of the ribosome is shown with the tRNAs kept at the P and E sites. A, P, and E mark the respective tRNA binding sites, and E2 marks the corresponding tRNA position. Landmarks of the small subunit: ch, tentative mRNA channel through the neck of the 30S subunit; h, head; pt, platform; 1b, part of bridge 1 connecting the subunits. Landmarks of the large subunit: CP, central protuberance; St, L12 stalk.
Citation:
Nierhaus K, Dabrowski M, Einfeldt E, Kamp D, Marquez V, Patzke S, Schäfer M, Stelzl U, Spahn C, Burkhardt N, Diedrich G, Blaha G, Willumeit R, Stuhrmann H.
2000.
Ribosomal Elongation Cycle,
p 319-336.
In
Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed),
The Ribosome.
ASM Press, Washington, DC.
doi: 10.1128/9781555818142.ch26
References
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Agrawal, R. K.,, P. Penczek,, R. A. Grassucci,, N. Burkhardt,, K. H. Nierhaus,, and J. Frank. 1999. Effect of buffer conditions on the position of tRNA on the 70S ribosome as visualized by cryoelectron microscopy. J. Biol. Chem. 274: 8723– 8729.
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Agraval, R. K.,, N. Burkhardt,, K. H. Nierhaus,, and J. Frank. Unpublished data.
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Bilgin, N.,, L. A. Kirsebom,, M. Ehrenberg,, and C. G. Kurland. 1988. Mutations in ribosomal proteins L7/L12 perturb EF-G and EF-Tu functions. Biochimie 70: 611– 618.
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Tables
Ribosomal Elongation Cycle
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Stuhrmann, foaf_surname=Stuhrmann, pub_isAffiliatedWith=[com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/affiliation/10.1128/9781555818142.chap26-aff6]]}]]
Citation:
Nierhaus K, Dabrowski M, Einfeldt E, Kamp D, Marquez V, Patzke S, Schäfer M, Stelzl U, Spahn C, Burkhardt N, Diedrich G, Blaha G, Willumeit R, Stuhrmann H.
2000.
Ribosomal Elongation Cycle,
p 319-336.
In
Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed),
The Ribosome.
ASM Press, Washington, DC.
doi: 10.1128/9781555818142.ch26
/content/10.1128/9781555818142.chap26.tab26-1
Table 1
Two views of the E site
Table 1
Two views of the E site
Citation:
Nierhaus K, Dabrowski M, Einfeldt E, Kamp D, Marquez V, Patzke S, Schäfer M, Stelzl U, Spahn C, Burkhardt N, Diedrich G, Blaha G, Willumeit R, Stuhrmann H.
2000.
Ribosomal Elongation Cycle,
p 319-336.
In
Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed),
The Ribosome.
ASM Press, Washington, DC.
doi: 10.1128/9781555818142.ch26
/content/10.1128/9781555818142.chap26.tab26-2
Table 2
Concentrations of ions and polyamines important for ribosomal functions
Table 2
Concentrations of ions and polyamines important for ribosomal functions
Citation:
Nierhaus K, Dabrowski M, Einfeldt E, Kamp D, Marquez V, Patzke S, Schäfer M, Stelzl U, Spahn C, Burkhardt N, Diedrich G, Blaha G, Willumeit R, Stuhrmann H.
2000.
Ribosomal Elongation Cycle,
p 319-336.
In
Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed),
The Ribosome.
ASM Press, Washington, DC.
doi: 10.1128/9781555818142.ch26