Ribosomal Proteins at the Stalk Region Modulate Functional rRNA Structures in the GTPase Center

Uchiumi, Toshio; Honma, Sachiko; Endo, Yaeta; Hachimori, Akira

doi:10.1074/jbc.m207424200

Cited by 30 publications

(49 citation statements)

References 63 publications

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“…It does not however exclude that other ribosomal motifs do not participate in elongation factor binding, provided that they are conserved in both the ribosomes. This, for example is the case for rRNA motifs such as the Sarcin-Ricin Loop and the thiostrepton loop for which accessibility is modulated by elongation factor binding (Guillot et al, 1993a(Guillot et al, , 1993bUchiumi et al, 2002a). Conversely, bacterial L7/L12 have been shown to be able to partly reconstitute the properties of yeast ribosomes depleted of P1/P2 (SanchezMadrid et al, 1981b).…”

Section: Whatever the Molecular Mechanism Supporting The Translocatiomentioning

confidence: 99%

The puzzling lateral flexible stalk of the ribosome

Gonzalo

Reboud

2003

Biology of the Cell

128

131

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The lateral flexible stalk of the large ribosomal subunit is made of several interacting proteins anchored to a conserved region of the 28S (26S) rRNA termed the GTPase-associated domain or thiostrepton loop. This structure is demonstrated to adopt puzzling changes of conformation following the different steps of the elongation cycle. Some of these proteins termed the P-proteins in eukaryotes and L10 and L7/L12 in bacteria, present little structural similarities between Eubacteria on one side and Archae and Eukaryotes on the other side. However, up to now, these proteins seem to present a similar macromolecular organisation and they have been involved in the same functions. Convincing evidence attests that these proteins participate in elongation factor binding to the ribosome, and it has been suggested that these proteins might be evolved in a GTP hydrolysis activating protein activity. Involvement of these proteins in the translational mechanism is discussed. Moreover, in eukaryotes, small P-proteins are also found as isolated proteins in a cytoplasmic pool that exchanges with the ribosome-associated P-proteins. Moreover, a part of the ribosomal proteins is phosphorylated (hence their P-protein names). The biological signification of these particularities is discussed.

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Section: Whatever the Molecular Mechanism Supporting The Translocatiomentioning

confidence: 99%

The puzzling lateral flexible stalk of the ribosome

Gonzalo

Reboud

2003

Biology of the Cell

128

131

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“…Ribosomal Subunits and the 50 S Core Particles-E. coli ribosomal subunits were prepared as described previously (20). 50 S cores deficient in L10⅐L7/L12 and L11 were prepared by extraction of the 50 S subunits from the L11-deficient E. coli mutant AM68 (32) in a solution containing 50% ethanol and 0.5 M NH 4 Cl solution at 0°C, as described previously (19).…”

Section: Methodsmentioning

confidence: 99%

“…This strong dependence on the P0⅐P1-P2 complex for the factor accessibility suggests the direct interaction between the protein complex and elongation factors. It has also been suggested that the P0⅐P1-P2 complex modulates the functional structures of the sarcin/ricin domain around 2660 as well as the 1070 regions of 23 S/28 S rRNA and makes them accessible to eukaryotic elongation factors (20). Knowledge of the molecular details on the assembly of P0, P1, and P2 proteins onto rRNA is essential to clarify protein-dependent function of the GTPase-associated center.…”

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confidence: 99%

A Mode of Assembly of P0, P1, and P2 Proteins at the GTPase-associated Center in Animal Ribosome

Hagiya

Naganuma

Maki

et al. 2005

Journal of Biological Chemistry

Self Cite

108

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Ribosomal P0, P1, and P2 proteins, together with the conserved domain of 28 S rRNA, constitute a major part of the GTPase-associated center in eukaryotic ribosomes. We investigated the mode of assembly in vitro by using various truncation mutants of silkworm P0. When compared with wild type (WT)-P0, the C-terminal truncation mutants C⌬65 and C⌬81 showed markedly reduced binding ability to P1 and P2, which was offset by the addition of an rRNA fragment covering the P0⅐P1-P2 binding site. The mutant C⌬107 lost the P1/P2 binding activity, whereas it retained the rRNA binding. In contrast, the N-terminal truncation mutants N⌬21-N⌬92 completely lost the rRNA binding, although they retained P1/P2 binding capability, implying an essential role of the N terminus of P0 for rRNA binding. The P0 mutants N⌬6, N⌬14, and C⌬18-C⌬81, together with P1/P2 and eL12, bound to the Escherichia coli core 50 S subunits deficient in L10⅐L7/L12 complex and L11. Analysis of incorporation of 32 P-labeled P1/P2 into the 50 S subunits with WT-P0 and C⌬81 by sedimentation analysis indicated that WT-P0 bound two copies of P1 and P2, but C⌬81 bound only one copy each. The hybrid ribosome with C⌬81 that appears to contain one P1-P2 heterodimer retained lower but considerable activities dependent on eukaryotic elongation factors. These results suggested that two P1-P2 dimers bind to close but separate regions on the C-terminal half of P0. The results were further confirmed by binding experiments using chimeric P0 mutants in which the C-terminal 81 or 107 amino acids were replaced with the homologous sequences of the archaebacterial P0.The ribosomal large subunits from all organisms contain an active site termed the "GTPase-associated center" that is responsible for the GTPase-related events in protein biosynthesis. This active site is composed of the two highly conserved domains around 1070 and 2660 (Escherichia coli numbering is used throughout) of 23 S/28 S rRNA and the ribosomal proteins bound to the 1070 region (1-3). The protein components of this site in prokaryotic ribosomes constitute a characteristic pentameric complex, L10(L7/L12) 2 (L7/L12) 2 (4, 5), in which two L7/L12 homodimers bind to the C-terminal regions of L10 (6) and constitute a highly flexible and functionally important lateral protuberance, the so-called "stalk" (7). Although the ribosomal stalk is observed by cryo-electron microscopy (8), the detailed structure of this pentameric complex has not been resolved by x-ray crystallography of ribosomes (9 -11). The chemical features of protein-protein and proteinrRNA interactions in the GTPase-associated center remain to be clarified.The animal ribosomal phosphoproteins P0 and P1/P2 (P proteins) are counterparts of prokaryotic L10 and L7/L12, respectively, although P1 and P2 are related but different proteins, unlike prokaryotic L7/L12 (12-14). In yeast cells, there are two P1-type proteins, P1␣ and P1␤, and two P2-type proteins, P2␣ and P2␤ (15). It is believed that P proteins constitute a pentameric complex, designated here as...

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“…These differences may explain why RIP display different affinities among them when assayed against different ribosomal substrates [2,17,19,21,25].…”

Section: Introductionmentioning

confidence: 99%

“…Although ribosomes are different in terms of their components among the three phylogenetic domains, Archea, Bacteria, and Eukarya, several functional regions are always conserved because they are essential to preserve the protein biosynthesis machinery [1,2]. One of them is the sarcin/ricin loop (SRL) [3,4] located in the larger rRNA molecule.…”

Section: Introductionmentioning

confidence: 99%

Modeling the highly specific ribotoxin recognition of ribosomes

García-Mayoral¹,

Garcı́a-Ortega²,

Álvarez-García³

et al. 2005

FEBS Letters

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The three-dimensional structures of the a-sarcin ribotoxin and its D(7-22) deletion mutant, both complexed with a 20-mer oligonucleotide mimicking the sarcin/ricin loop (SRL) of the ribosome, have been docked into the structure of the Halobacterium marismortui ribosome by fitting the nucleotide atomic coordinates into those of the ribosomal SRL. This study has revealed that two regions of the ribotoxin, residues 11-16 and 84-85, contact the ribosomal proteins L14 (residues 99-105) and L6 (residues 88-92), respectively. The first of these two ribotoxin regions appears to be crucial for its specific ribosome recognition.

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Ribosomal Proteins at the Stalk Region Modulate Functional rRNA Structures in the GTPase Center

Cited by 30 publications

References 63 publications

The puzzling lateral flexible stalk of the ribosome

The puzzling lateral flexible stalk of the ribosome

A Mode of Assembly of P0, P1, and P2 Proteins at the GTPase-associated Center in Animal Ribosome

Modeling the highly specific ribotoxin recognition of ribosomes

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