Comparative analysis of the protein components from 5S rRNA . protein complexes of halophilic archaebacteria

ABSTRACT Nucleophosmin (NPM/B23) is a key regulator in the regulation of a number of processes including centrosome duplication, maintenance of genomic integrity, and ribosome biogenesis. While the mechanisms underlying NPM function are largely uncharacterized, NPM loss results in severe dysregulation of developmental and growth-related events. We show that NPM utilizes a conserved CRM1-dependent nuclear export sequence in its amino terminus to enable its shuttling between the nucleolus/nucleus and cytoplasm. In search of NPM trafficking targets, we biochemically purified NPM-bound protein complexes from HeLa cell lysates. Consistent with NPM's proposed role in ribosome biogenesis, we isolated ribosomal protein L5 (rpL5), a known chaperone for the 5S rRNA. Direct interaction of NPM with rpL5 mediated the colocalization of NPM with maturing nuclear 60S ribosomal subunits, as well as newly exported and assembled 80S ribosomes and polysomes. Inhibition of NPM shuttling or loss of NPM blocked the nuclear export of rpL5 and 5S rRNA, resulting in cell cycle arrest and demonstrating that NPM and its nuclear export provide a unique and necessary chaperoning activity to rpL5/5S.

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Analysis of the intracellular localization and assembly of Ro ribonucleoprotein particles by microinjection into Xenopus laevis oocytes.

The Journal of Cell Biology ◽

10.1083/jcb.125.5.981 ◽

1994 ◽

Vol 125 (5) ◽

pp. 981-988 ◽

Cited By ~ 55

Author(s):

F H Simons ◽

G J Pruijn ◽

W J van Venrooij

Keyword(s):

Xenopus Laevis ◽

Nuclear Export ◽

Protein Complexes ◽

Intracellular Localization ◽

Xenopus Laevis Oocytes ◽

Transport Mechanisms ◽

Ribonucleoprotein Particles ◽

Protein Components ◽

Rna Protein Complexes ◽

Ro Ribonucleoprotein

Xenopus laevis oocytes have been used to determine the intracellular localization of components of Ro ribonucleoprotein particles (Ro RNPs) and to study the assembly of these RNA-protein complexes. Microinjection of the protein components of human Ro RNPs, i.e., La, Ro60, and Ro52, in X. laevis oocytes showed that all three proteins are able to enter the nucleus, albeit with different efficiencies. In contrast, the RNA components of human Ro RNPs (the Y RNAs) accumulate in the X. laevis cytoplasm upon injection. Localization studies performed at low temperatures indicated that both nuclear import of Ro RNP proteins and nuclear export of Y RNAs are mediated by active transport mechanisms. Immunoprecipitation experiments using monospecific anti-La and anti-Ro60 antibodies showed that the X. laevis La and Ro60 homologues were cross-reactive with the respective antibodies and that both X. laevis proteins were able to interact with human Y1 RNA. Further analyses indicated that: (a) association of X. laevis La and Ro60 with Y RNAs most likely takes place in the nucleus; (b) once formed, Ro RNPs are rapidly exported out of the nucleus; and (c) the association with La is lost during or shortly after nuclear export.

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Interaction of HIV Tat model peptides with tRNA and 5S rRNA.

Acta Biochimica Polonica ◽

10.18388/abp.1997_4407 ◽

1997 ◽

Vol 44 (3) ◽

pp. 591-600 ◽

Cited By ~ 2

Author(s):

M Giel-Pietraszuk ◽

M Z Barciszewska ◽

P Mucha ◽

P Rekowski ◽

G Kupryszewski ◽

...

Keyword(s):

Synthetic Peptides ◽

Protein Complexes ◽

5S Rrna ◽

Lupinus Luteus ◽

Rich Region ◽

Rna Molecules ◽

Hiv Tat ◽

Immunodeficiency Virus ◽

Arginine Residues ◽

Tar Rna

New data are presented on the interaction of model synthetic peptides containing an arginine-rich region of human immunodeficiency virus (HIV-Tat), with native RNA molecules: tRNA(Phe) of Saccharomyces cerevisiae and 5S rRNA from Lupinus luteus. Both RNA species form complexes with the Tat1 (GRKKRRQRRRA) and Tat2 (GRKKRRQRRRAPQDSQTHQASLSKQPA) peptides, as shown by electrophoretic gel shift and RNase footprint assays, and CD measurements. The nucleotide sequence UGGG located in the dihydrouridine loop of tRNAPhe as well as in the loop D of 5S rRNA is specifically protected against RNases. Our data indicate direct interactions of guanine of RNA moieties with arginine residues. These interactions seem similar to those observed in DNA-protein complexes, but different from those previously observed in the TAR RNA-Tat complexes.

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Resolving Missing Protein Problems Using Functional Class Scoring

10.21203/rs.3.rs-1201188/v1 ◽

2022 ◽

Author(s):

Bertrand Jernhan Wong ◽

Weijia Kong ◽

Limsoon Wong ◽

Wilson Wen Bin Goh

Keyword(s):

Protein Complexes ◽

Functional Class ◽

P Value ◽

Proteomics Data ◽

Individual Protein ◽

Data Independent Acquisition ◽

Technological Advances ◽

Incomplete Coverage ◽

Protein Components ◽

Using Data

Abstract Despite technological advances in proteomics, incomplete coverage and inconsistency issues persist, resulting in “data holes”. These data holes cause the missing protein problem (MPP), where relevant proteins are persistently unobserved, or sporadically observed across samples. This hinders biomarker and drug discovery from proteomics data. Network-based approaches are powerful: The Functional Class Scoring (FCS) method using protein complexes was able to easily recover missed proteins with weak or partial support. However, there are limitations: The verification approach (in determining missing protein recovery) is potentially biased as the test data was based on relatively outdated Data-Dependent Acquisition (DDA) proteomics and FCS does not provide a scoring scheme for individual protein components (in significant complexes). To address these issues: First, we devised a more rigorous evaluation of FCS based on same-sample technical replicates. And second, we evaluate using data from more recent Data-Independent Acquisition (DIA) technologies (viz. SWATH).Although cross-replicate examination reveals some inconsistencies amongst same-class samples, tissue-differentiating signal is nonetheless strongly conserved. This confirms FCS as a viable method that selects biologically meaningful networks. We also report that predicted missing proteins are statistically significant based on FCS p-values. Although cross-replicate verification rates are not spectacular, the predicted missing proteins as a whole, have higher peptide support than non-predicted proteins. FCS also has the capacity to predict missing proteins that are often lost due to weak specific peptide support. As a yet unresolved limitation, we find that FCS cannot assign meaningful probabilities to individual protein components (no relationship between actual probability of verification and FCS-assigned probability) as it only provides a p-value at the level of complexes.

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Structural analysis of 5S rRNA, 5S rRNA-protein complexes and ribosomes employing RNase H and d(GTTCGG)

European Journal of Biochemistry ◽

10.1111/j.1432-1033.1987.tb10793.x ◽

1987 ◽

Vol 163 (2) ◽

pp. 239-246 ◽

Cited By ~ 10

Author(s):

Siegfried LORENZ ◽

Roland K. HARTMANN ◽

Norbert PIEL ◽

Norbert ULBRICH ◽

Volker A. ERDMANN

Keyword(s):

Structural Analysis ◽

Protein Complexes ◽

Rnase H ◽

5S Rrna

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Structural analysis of three prokaryotic 5S rRNA species and selected 5S rRNA-ribosomal-protein complexes by means of Pb(II)-induced hydrolysis

European Journal of Biochemistry ◽

10.1111/j.1432-1033.1992.tb16670.x ◽

1992 ◽

Vol 204 (2) ◽

pp. 575-581 ◽

Cited By ~ 24

Author(s):

Jerzy CIESIOLKA ◽

Siegfried LORENZ ◽

Volker A. ERDMANN

Keyword(s):

Structural Analysis ◽

Ribosomal Protein ◽

Protein Complexes ◽

5S Rrna ◽

Rrna Species

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Structure and Assembly of the Nuclear Pore Complex

Annual Review of Biophysics ◽

10.1146/annurev-biophys-052118-115308 ◽

2019 ◽

Vol 48 (1) ◽

pp. 515-536 ◽

Cited By ~ 40

Author(s):

Bernhard Hampoelz ◽

Amparo Andres-Pons ◽

Panagiotis Kastritis ◽

Martin Beck

Keyword(s):

Posttranslational Modifications ◽

Current Knowledge ◽

Protein Complexes ◽

Hierarchical Organization ◽

Nuclear Pore ◽

Nuclear Pore Complexes ◽

Multiple Copies ◽

Architectural Principles ◽

Protein Components ◽

Pore Complexes

Nuclear pore complexes (NPCs) mediate nucleocytoplasmic exchange. They are exceptionally large protein complexes that fuse the inner and outer nuclear membranes to form channels across the nuclear envelope. About 30 different protein components, termed nucleoporins, assemble in multiple copies into an intricate cylindrical architecture. Here, we review our current knowledge of the structure of nucleoporins and how those come together in situ. We delineate architectural principles on several hierarchical organization levels, including isoforms, posttranslational modifications, nucleoporins, and higher-order oligomerization of nucleoporin subcomplexes. We discuss how cells exploit this modularity to faithfully assemble NPCs.

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