Diverse relationships between metal ions and the ribosome

2021 ◽  
Author(s):  
Genki Akanuma
Keyword(s):  
Gene Expression ◽  
Secondary Structure ◽  
Metal Ions ◽  
Structural Stability ◽  
Ribosomal Rna ◽  
Ribosomal Proteins ◽  
Rna Binding ◽  
Cellular Homeostasis ◽  
Ribosomal Subunits ◽  
Translational Activity

Abstract The ribosome requires metal ions for structural stability and translational activity. These metal ions are important for stabilizing the secondary structure of ribosomal RNA, binding of ribosomal proteins to the ribosome, and for interaction of ribosomal subunits. In this review, various relationships between ribosomes and metal ions, especially Mg2+ and Zn2+, are presented. Mg2+ regulates gene expression by modulating the translational stability and synthesis of ribosomes, which in turn contribute to the cellular homeostasis of Mg2+. In addition, Mg2+ can partly complement the function of ribosomal proteins. Conversely, a reduction in the cellular concentration of Zn2+ induces replacement of ribosomal proteins, which mobilizes free-Zn2+ in the cell and represses translation activity. Evolutional relationships between these metal ions and the ribosome are also discussed.

scholarly journals Association of Nonribosomal Nucleolar Proteins in Ribonucleoprotein Complexes during Interphase and Mitosis

1999 ◽  
Vol 10 (1) ◽  
pp. 77-90 ◽  
Author(s):  
Serafı́n Piñol-Roma
Keyword(s):  
Ribosomal Proteins ◽  
Rna Binding ◽  
Rrna Synthesis ◽  
28S Rrna ◽  
Ribosomal Subunits ◽  
Interphase Cell ◽  
Ribonucleoprotein Complexes ◽  
Nucleolar Proteins ◽  
M Phase ◽  
Nucleolar Rna

rRNA precursors are bound throughout their length by specific proteins, as the pre-rRNAs emerge from the transcription machinery. The association of pre-rRNA with proteins as ribonucleoprotein (RNP) complexes persists during maturation of 18S, 5.8S, and 28S rRNA, and through assembly of ribosomal subunits in the nucleolus. Preribosomal RNP complexes contain, in addition to ribosomal proteins, an unknown number of nonribosomal nucleolar proteins, as well as small nucleolar RNA-ribonucleoproteins (sno-RNPs). This report describes the use of a specific, rapid, and mild immunopurification approach to isolate and analyze human RNP complexes that contain nonribosomal nucleolar proteins, as well as ribosomal proteins and rRNA. Complexes immunopurified with antibodies to nucleolin—a major nucleolar RNA-binding protein—contain several distinct specific polypeptides that include, in addition to nucleolin, the previously identified nucleolar proteins B23 and fibrillarin, proteins with electrophoretic mobilities characteristic of ribosomal proteins including ribosomal protein S6, and a number of additional unidentified proteins. The physical association of these proteins with one another is mediated largely by RNA, in that the complexes dissociate upon digestion with RNase. Complexes isolated from M-phase cells are similar in protein composition to those isolated from interphase cell nuclear extracts. Therefore, the predominant proteins that associate with nucleolin in interphase remain in RNP complexes during mitosis, despite the cessation of rRNA synthesis and processing in M-phase. In addition, precursor rRNA, as well as processed 18S and 28S rRNA and candidate rRNA processing intermediates, is found associated with the immunopurified complexes. The characteristics of the rRNP complexes described here, therefore, indicate that they represent bona fide precursors of mature cytoplasmic ribosomal subunits.

Protein binding and subunit association activity in particles reconstituted from Escherichia coli MRE600 50S ribosomal components

1976 ◽  
Vol 54 (5) ◽  
pp. 470-476
Author(s):  
F. K. Chu ◽  
P. Y. Maeba
Keyword(s):  
Escherichia Coli ◽  
Protein Binding ◽  
Ribosomal Rna ◽  
Ribosomal Proteins ◽  
Rna Binding ◽  
5S Rna ◽  
Ribonucleoprotein Particles ◽  
Incubation Method ◽  
Do So

Reconstituted 37S and 48S ribonucleoprotein particles were constructed by incubating Escherichia coli ribosomal RNA with total 50S ribosomal proteins by a sequential incubation method. By comparing the protein compositions of the two types of particles, the proteins that bind to 37S complexes to form 48S particles have been determined. Although only 48S particles could associate with 30S subunits, isolated 37S reconstituted particles could do so if incubated with exogenous 50S proteins. The proteins that bind under these conditions and confer upon particles the ability to associate are L2, L11, L15, L18 and L25. The involvement of these proteins in 5S RNA binding is discussed.

Structures of prokaryotic ribosomal proteins: implications for RNA binding and evolution

1995 ◽  
Vol 73 (11-12) ◽  
pp. 979-986 ◽  
Author(s):  
V. Ramakrishnan ◽  
Sue Ellen Gerchman ◽  
Jadwiga H. Kycia ◽  
Christopher Davies ◽  
Barbara L. Golden ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
High Resolution ◽  
Ribosomal Rna ◽  
Ribosomal Proteins ◽  
Bacillus Stearothermophilus ◽  
Rna Binding ◽  
X Ray ◽  
X Ray Crystallography ◽  
Binding Regions

After along hiatus, the pace of determination of the structures of ribosomal proteins has accelerated dramatically. We discuss here the structures of five ribosomal proteins from Bacillus stearothermophilus: S5, S17, L6, L9, and L14. These structures represent several new motifs. Each of these structures has revealed new insights, and we have developed criteria for recognizing RNA-binding regions of each protein and correlating the structures with such properties as antibiotic resistance. The information here should also prove invaluable in an eventual high-resolution picture of the intact ribosome.Key words: ribosome, ribosomal proteins, ribosomal RNA, X-ray crystallography, NMR.

scholarly journals An RNA-binding switch drives ribosome biogenesis and tumorigenesis downstream of RAS oncogene

2021 ◽  
Author(s):  
Muhammad S Azman ◽  
Martin Dodel ◽  
Federica Capraro ◽  
Rupert Faraway ◽  
Maria Dermit ◽  
...  
Keyword(s):  
Gene Expression ◽  
Ribosomal Rna ◽  
Ribosome Biogenesis ◽  
Rna Binding ◽  
Binding Activity ◽  
Ras Signaling ◽  
Cancer Cell Proliferation ◽  
Inhibit Tumor Growth ◽  
Oncogenic Ras

Oncogenic RAS signaling reprograms gene expression through both transcriptional and post-transcriptional mechanisms. While transcriptional regulation downstream of RAS is relatively well-characterized, how RAS post-transcriptionally modulates gene expression to promote malignancy is unclear. Using quantitative RNA Interactome Capture analysis, we reveal that oncogenic RAS signaling reshapes the RNA-bound proteomic landscape of cancer cells, with a network of nuclear proteins centered around Nucleolin displaying enhanced RNA-binding activity. We show that Nucleolin is phosphorylated downstream of RAS, which increases its binding to pre-ribosomal-RNA (rRNA), boosts rRNA production, and promotes ribosome biogenesis. This Nucleolin-dependent enhancement of ribosome biogenesis is crucial for RAS-induced cancer cell proliferation, and can be targeted therapeutically to inhibit tumor growth. Our results reveal that oncogenic RAS signaling drives ribosome biogenesis by regulating the RNA-binding activity of Nucleolin, and highlights the crucial role of this process in RAS-mediated tumorigenesis.

scholarly journals The size and conformation of Artemia (brine-shrimp) ribosomal RNA free in solution

1982 ◽  
Vol 205 (3) ◽  
pp. 495-501 ◽  
Author(s):  
K Donceel ◽  
P Nieuwenhuysen ◽  
J Clauwaert
Keyword(s):  
Ribosomal Rna ◽  
Diffusion Coefficients ◽  
Brine Shrimp ◽  
Ribosomal Proteins ◽  
Hydrodynamic Radius ◽  
Ribosomal Subunit ◽  
Ribosomal Subunits ◽  
Rrna Species ◽  
Reported Data ◽  
And Diffusion

The RNA was isolated from the large ribosomal subunits of the brine shrimp Artemia, and its conformation free in solution was studied by determining its sedimentation and diffusion coefficients. A comparison was made of the hydrodynamic radius of the ribosomal subunit and its isolated RNA in various buffers. The conformation of the rRNA free in solution is more extended than when it is incorporated in the ribosome. This is not only the case when the rRNA solution lacks bivalent and polyvalent cations, but even in the presence of Mg2+ and spermidine, which cause a tightening of RNA. Thus the ribosomal proteins should induce a further tightening of the rRNA during the assembly of the ribosome. In the discussion, the reported data on Escherichia coli rRNA species are presented in such a way that large discrepancies between various studied are revealed, and that they can be compared with the data reported here on the larger rRNA of an eukaryote.

scholarly journals Yeast Asc1p and Mammalian RACK1 Are Functionally Orthologous Core 40S Ribosomal Proteins That Repress Gene Expression

2004 ◽  
Vol 24 (18) ◽  
pp. 8276-8287 ◽  
Author(s):  
Vincent R. Gerbasi ◽  
Connie M. Weaver ◽  
Salisha Hill ◽  
David B. Friedman ◽  
Andrew J. Link
Keyword(s):  
Gene Expression ◽  
Translational Control ◽  
Ribosomal Proteins ◽  
Translational Activity ◽  
Eukaryotic Gene ◽  
Associated Proteins ◽  
Yeast Ribosomes ◽  
Specific Proteins ◽  
Conserved Core

ABSTRACT Translation of mRNA into protein is a fundamental step in eukaryotic gene expression requiring the large (60S) and small (40S) ribosome subunits and associated proteins. By modern proteomic approaches, we previously identified a novel 40S-associated protein named Asc1p in budding yeast and RACK1 in mammals. The goals of this study were to establish Asc1p or RACK1 as a core conserved eukaryotic ribosomal protein and to determine the role of Asc1p or RACK1 in translational control. We provide biochemical, evolutionary, genetic, and functional evidence showing that Asc1p or RACK1 is indeed a conserved core component of the eukaryotic ribosome. We also show that purified Asc1p-deficient ribosomes have increased translational activity compared to that of wild-type yeast ribosomes. Further, we demonstrate that asc1Δ null strains have increased levels of specific proteins in vivo and that this molecular phenotype is complemented by either Asc1p or RACK1. Our data suggest that one of Asc1p's or RACK1's functions is to repress gene expression.

scholarly journals The nucleolar DExD/H protein Hel66 is involved in ribosome biogenesis in Trypanosoma brucei

2021 ◽  
Author(s):  
Majeed Bakari-Soale ◽  
Nonso Josephat Ikenge ◽  
Marion Scheibe ◽  
Falk Butter ◽  
Nicola Gail Jones ◽  
...  
Keyword(s):  
Ribosomal Rna ◽  
Ribosomal Proteins ◽  
Ribosome Biogenesis ◽  
Growth Defect ◽  
Rrna Processing ◽  
Ribosomal Subunits ◽  
Comprehensive Picture ◽  
Severe Growth Defect ◽  
H Protein ◽  
Severe Growth

The biosynthesis of ribosomes is a complex cellular process involving ribosomal RNA, ribosomal proteins and several further trans-acting factors. DExD/H box proteins constitute the largest family of trans-acting protein factors involved in this process. Several members of this protein family have been directly implicated in ribosome biogenesis in yeast. In trypanosomes, ribosome biogenesis differs in several features from the process described in yeast. Here, we have identified the DExD/H box helicase Hel66 as being involved in ribosome biogenesis. The protein is unique to Kinetoplastida, localises to the nucleolus and its depletion via RNAi caused a severe growth defect. Loss of the protein resulted in a decrease of global translation and accumulation of rRNA processing intermediates for both the small and large ribosomal subunits. Only a few factors involved in trypanosome rRNA biogenesis have been described so far and our findings contribute to gaining a more comprehensive picture of this essential process.

scholarly journals Co-Assembly of 40S and 60S Ribosomal Proteins in Early Steps of Eukaryotic Ribosome Assembly

2019 ◽  
Vol 20 (11) ◽  
pp. 2806 ◽  
Author(s):  
Jesse M. Fox ◽  
Rebekah L. Rashford ◽  
Lasse Lindahl
Keyword(s):  
Ribosomal Rna ◽  
Ribosomal Proteins ◽  
Ribosome Assembly ◽  
Relative Timing ◽  
Ribosomal Subunits ◽  
Eukaryotic Ribosome ◽  
Rrna Molecule ◽  
Ribosomal Precursor ◽  
Its1 And Its2

In eukaryotes three of the four ribosomal RNA (rRNA) molecules are transcribed as a long precursor that is processed into mature rRNAs concurrently with the assembly of ribosomal subunits. However, the relative timing of association of ribosomal proteins with the ribosomal precursor particles and the cleavage of the precursor rRNA into the subunit-specific moieties is not known. To address this question, we searched for ribosomal precursors containing components from both subunits. Particles containing specific ribosomal proteins were targeted by inducing synthesis of epitope-tagged ribosomal proteins followed by pull-down with antibodies targeting the tagged protein. By identifying other ribosomal proteins and internal rRNA transcribed spacers (ITS1 and ITS2) in the immuno-purified ribosomal particles, we showed that eS7/S7 and uL4/L4 bind to nascent ribosomes prior to the separation of 40S and 60S specific segments, while uS4/S9, uL22, and eL13/L13 are bound after, or simultaneously with, the separation. Thus, the incorporation of ribosomal proteins from the two subunits begins as a co-assembly with a single rRNA molecule, but is finished as an assembly onto separate precursors for the two subunits.

Metal ions induced secondary structure rearrangements: mechanically interlocked lassovs.unthreaded branched-cyclic topoisomers

The Analyst ◽  
2018 ◽  
Vol 143 (10) ◽  
pp. 2323-2333 ◽  
Author(s):  
Kevin Jeanne Dit Fouque ◽  
Javier Moreno ◽  
Julian D. Hegemann ◽  
Séverine Zirah ◽  
Sylvie Rebuffat ◽  
...  
Keyword(s):  
Protein Folding ◽  
Secondary Structure ◽  
Metal Ions ◽  
Conformational Change ◽  
Structural Stability ◽  
Significant Role

Metal ions can play a significant role in a variety of important functions in protein systems including cofactor for catalysis, protein folding, assembly, structural stability and conformational change.

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