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Chapter 12 : Structure of the Yeast Ribosomal Stalk

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Abstract:

The stalk of the large ribosomal subunit is involved in the interaction of the elongation factors with the ribosome, as biochemical data have clearly indicated and as has been directly confirmed by electron microscopy. The eukaryotic ribosomal-stalk elements are functionally equivalent to the bacterial components, but while some of them are highly conserved, others have evolved notably. The highly probable presence of the acidic proteins in the ribosome as monomers, together with the existence of one specific binding site for each 12-kDa protein in the particles, favors the homogeneous rather than the heterogeneous ribosomal-stalk model in yeast. The data available on the assembly of the yeast stalk are not abundant. An analysis of two strains carrying a disruption of the genes encoding the two proteins of the same type, either P1 or P2, has shown that their ribosomes do not carry any 12-kDa acidic protein. The experimental evidence indicates that the in vitro assembly of the yeast ribosomal stalk involves a number of consecutive binding steps which are apparently initiated by the interaction of the P1 proteins and is followed by the binding of the P2 polypeptides.

Citation: Ballesta J, Guarinos E, Zurdo J, Parada P, Nusspaumer G, Lalioti V, Perez-Fernandez J, Remacha M. 2000. Structure of the Yeast Ribosomal Stalk, p 115-126. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch12

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Figures

Image of Figure 1
Figure 1

Models of acidic protein distribution in the yeast ribosomal stalk. (A) Heterogeneous model. Ribosomes carry one dimer of a P1 and another of a P2 protein type. Four associations of the four acidic proteins are possible: P1-P2, P1-P2, P1-P2, P1-P2. (B) Homogeneous model. All ribosomes carry one monomer of the four acidic proteins simultaneously.

Citation: Ballesta J, Guarinos E, Zurdo J, Parada P, Nusspaumer G, Lalioti V, Perez-Fernandez J, Remacha M. 2000. Structure of the Yeast Ribosomal Stalk, p 115-126. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch12
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Figure 2

Cross-linking of P1-cys62. D7, with a disrupted P1 gene, was transformed with plasmid pFL37-P1-cys62 carrying a P1 protein in which a unique cysteine was introduced in position 62. Ribosomes (20 μg) from the transformed strain were treated in 10 μl of buffer with -phenanthroline-Cu ( ) to oxidize the cysteine SH groups, and the ribosomes were resolved by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (lane 2). Similarly, a preparation of purified recombinant P1-cys62 protein (5 μg) was treated in the same way and resolved in the same gel (lane 3). As a control, ribosomes from untransformed D7 were treated in the same way (lane 1). Proteins were blotted to nitrocellulose membranes and detected with P1-specific antibodies.

Citation: Ballesta J, Guarinos E, Zurdo J, Parada P, Nusspaumer G, Lalioti V, Perez-Fernandez J, Remacha M. 2000. Structure of the Yeast Ribosomal Stalk, p 115-126. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch12
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Image of Figure 3
Figure 3

Affinity chromatography of ribosomes in Ni (Ni-nitrilotriacetic acid) columns. (A) A P2-HisT protein was constructed by fusing a six-His tail to the C-terminal end of protein P2 in plasmid pFL392-His6. The tagged protein was expressed in D4 lacking P2, and a ribosome preparation from the transformed strain was loaded into a 1-ml Ni affinity column. The column was washed with 10 ml of 10 mM Tris-HCl (pH 7.4), 10 mM MgCl, and 100 mM KCl buffer containing increasing concentrations of imidazol. Aliquots of the eluted fractions were resolved in sodium dodecyl sulfatepolyacrylamide gels, and the presence of ribosomes in the fractions was checked by estimating the stalk protein P0 by Western blotting with a specific monoclonal antibody. (B) Ribosomes from a control strain carrying a wild-type P2 protein were obtained and processed as for panel A. Lanes: 1, excluded volume; 2 to 6, fractions eluted with buffer containing 0, 10, 40, 70, and 100 mM imidazol.

Citation: Ballesta J, Guarinos E, Zurdo J, Parada P, Nusspaumer G, Lalioti V, Perez-Fernandez J, Remacha M. 2000. Structure of the Yeast Ribosomal Stalk, p 115-126. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch12
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Figure 4

Isoelectrofocusing of ribosomes from the affinity chromatography columns. An aliquot of the loaded sample (L) and of the 100 mM imidazol-eluted fraction (R) were resolved in polyacrylamide gels in a 2.5 to 5.0 pH gradient as previously described ( ). The gels were silver stained. The positions of the different acidic proteins are marked. The upper band corresponds in each case to the phosphorylated form of the protein.

Citation: Ballesta J, Guarinos E, Zurdo J, Parada P, Nusspaumer G, Lalioti V, Perez-Fernandez J, Remacha M. 2000. Structure of the Yeast Ribosomal Stalk, p 115-126. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch12
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Figure 5

Isoelectrofocusing of ribosomes from disrupted strains lacking acidic proteins. Ribosomes (0.5 mg) from D4, D5, D6, and D7 lacking proteins P2ö, P2, P1, and P1, respectively, were resolved as for Fig. 4. wt, wild type.

Citation: Ballesta J, Guarinos E, Zurdo J, Parada P, Nusspaumer G, Lalioti V, Perez-Fernandez J, Remacha M. 2000. Structure of the Yeast Ribosomal Stalk, p 115-126. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch12
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Image of Figure 6
Figure 6

Isoelectrofocusing of ribosomes reconstituted with recombinant acidic proteins. Ribosomes from D4567 lacking the four acidic proteins were incubated at 30°C in 10 mM Tris-HCl (pH 7.4), 10 mM MgCl, and 100 mM KCl with a fourfold molar excess of recombinant protein P1 (lane 3), recombinant protein P2 (lane 4), and recombinant protein P1 plus P2 (lane 5). The reconstituted ribosomes were centrifuged through two layers of 20 and 40% sucrose in 10 mM Tris-HCl (pH 7.4), 100 mM MgCl, and 500 mM KCl buffer. Ribosomes incubated in the absence of proteins (lane 2) and a mixture of both free recombinant proteins (lane 1) were included as controls. Isoelectrofocusing was carried out as for Fig. 4.

Citation: Ballesta J, Guarinos E, Zurdo J, Parada P, Nusspaumer G, Lalioti V, Perez-Fernandez J, Remacha M. 2000. Structure of the Yeast Ribosomal Stalk, p 115-126. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch12
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Figure 7

Activity of D4567 ribosomes reconstituted with recombinant proteins. Ribosomes reconstituted as indicated in the legend to Fig. 6 were tested in a poly(U)-dependent polymerization assay ( ). Bars: 1, D4567 ribosomes; 2, D4567 ribosomes plus SP fraction; 3, D4567 ribosomes plus P1; 4, D4567 ribosomes plus P2; 5, D4567 ribosomes plus P1 plus P2. The SP fraction corresponds to an NHCl-ethanol wash of wild-type ribosomes containing the four acidic proteins ( ). Control ribosomes (sample 2) polymerized 10.1 pmol of Phe per pmol of ribosomes.

Citation: Ballesta J, Guarinos E, Zurdo J, Parada P, Nusspaumer G, Lalioti V, Perez-Fernandez J, Remacha M. 2000. Structure of the Yeast Ribosomal Stalk, p 115-126. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch12
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Figure 8

Analysis of ribosomes from D45 overexpressing protein P1. (A) Ribosomes from the P2-P2-deficient D45 strain transformed with the multicopy plasmid pP1b were analyzed before (lane 2) and after (lane 3) centrifugation through a sucrose gradient as for Fig. 6. Ribosomes from W303 (lane 1) were included as a control. (B) Ribosomes from D67 (lane 2), lacking proteins P1 and P1 and containing an accumulation protein P2, in the cytoplasm ( ) were analyzed as for panel A. Lane 1, control ribosomes as in panel A.

Citation: Ballesta J, Guarinos E, Zurdo J, Parada P, Nusspaumer G, Lalioti V, Perez-Fernandez J, Remacha M. 2000. Structure of the Yeast Ribosomal Stalk, p 115-126. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch12
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Figure 9

Probable distribution of the four acidic proteins in the yeast ribosomal stalk.

Citation: Ballesta J, Guarinos E, Zurdo J, Parada P, Nusspaumer G, Lalioti V, Perez-Fernandez J, Remacha M. 2000. Structure of the Yeast Ribosomal Stalk, p 115-126. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch12
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Tables

Generic image for table
Table 1

Amino acid sequence similarity of yeast ribosomal acidic proteins

Citation: Ballesta J, Guarinos E, Zurdo J, Parada P, Nusspaumer G, Lalioti V, Perez-Fernandez J, Remacha M. 2000. Structure of the Yeast Ribosomal Stalk, p 115-126. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch12
Generic image for table
Table 2

Effect of P0 protein chimera expression on strains

Citation: Ballesta J, Guarinos E, Zurdo J, Parada P, Nusspaumer G, Lalioti V, Perez-Fernandez J, Remacha M. 2000. Structure of the Yeast Ribosomal Stalk, p 115-126. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch12
Generic image for table
Table 3

Interaction between the different yeast ribosomal-stalk components estimated by the two-hybrid system

Citation: Ballesta J, Guarinos E, Zurdo J, Parada P, Nusspaumer G, Lalioti V, Perez-Fernandez J, Remacha M. 2000. Structure of the Yeast Ribosomal Stalk, p 115-126. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch12
Generic image for table
Table 4

Estimation of protein P1 in S30 extracts from strains

Citation: Ballesta J, Guarinos E, Zurdo J, Parada P, Nusspaumer G, Lalioti V, Perez-Fernandez J, Remacha M. 2000. Structure of the Yeast Ribosomal Stalk, p 115-126. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch12

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