Relationships between proteasomes and RNA

Schmid, Hans‐Peter; Pouch, Marie-Noëlle; Petit, Franck; Dadet, Marie-Helène; Badaoui, Saloua; Boissonnet, Gérard; Buri, Jacques; Norris, Victor; Briand, Yves

doi:10.1007/bf00990969

Cited by 15 publications

(11 citation statements)

References 40 publications

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“…Although these two processes are not connected in this region of the yeast network, several protein interactions link them in the networks of worm and fly (e.g., Pros25-Rack1-Msi or Pros25-Rack1-Tbph). These findings are consistent with previously documented association of proteasomes with mRNA-binding proteins, although the exact nature of this association has been controversial (30,31). A related functional link between the proteasome and nucleic acid synthesis was detected in our earlier network comparison of yeast and the bacteria H. pylori (13).…”

Section: Discussionsupporting

confidence: 92%

Conserved patterns of protein interaction in multiple species

Sharan

Suthram²,

Ryan³

et al. 2005

Proc. Natl. Acad. Sci. U.S.A.

712

624

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To elucidate cellular machinery on a global scale, we performed a multiple comparison of the recently available protein-protein interaction networks of Caenorhabditis elegans, Drosophila melanogaster, and Saccharomyces cerevisiae. This comparison integrated protein interaction and sequence information to reveal 71 network regions that were conserved across all three species and many exclusive to the metazoans. We used this conservation, and found statistically significant support for 4,645 previously undescribed protein functions and 2,609 previously undescribed protein interactions. We tested 60 interaction predictions for yeast by two-hybrid analysis, confirming approximately half of these. Significantly, many of the predicted functions and interactions would not have been identified from sequence similarity alone, demonstrating that network comparisons provide essential biological information beyond what is gleaned from the genome.comparative analysis ͉ multiple alignment ͉ protein network ͉ yeast two-hybrid A major challenge of postgenomic biology is to understand the complex networks of interacting genes, proteins, and small molecules that give rise to biological form and function. Advances in whole-genome approaches are now enabling us to characterize these networks systematically, by using procedures such as the two-hybrid assay (1) and protein coimmunoprecipitation (2) to screen for protein-protein interactions. To date, these technologies have generated large interaction networks for bacteria (3), yeast (4-7), and, recently, fruit fly (8) and nematode worm (9).The large amount of protein interaction data now available presents opportunities and challenges in understanding evolution and function. Such challenges involve assigning functional roles to interactions (10), separating true protein-protein interactions from false positives (11), and, ultimately, organizing large-scale interaction data into models of cellular signaling and regulatory machinery. As is often the case in biology, an approach based on evolutionary cross-species comparisons provides a valuable framework for addressing these challenges. However, although methods for comparing DNA and protein sequences have been a mainstay of bioinformatics over the past 30 years, development of similar tools at other levels of biological information, including protein interactions (12-14), metabolic networks (15-17), or gene expression data (18)(19)(20), is just beginning.Recently, we devised a method called PATHBLAST (13) for comparing the protein interaction networks of two species. Just as BLAST performs rapid pairwise alignment of protein sequences (21), PATHBLAST is based on efficient alignment of two protein networks to identify conserved network regions. Here, we extend this approach to present a computational framework for alignment and comparison of more than two protein networks. We apply this multiple network alignment strategy to compare the recently available protein networks for worm, fly, and yeast, and show that although any single net...

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Section: Discussionsupporting

confidence: 92%

Conserved patterns of protein interaction in multiple species

Sharan

Suthram²,

Ryan³

et al. 2005

Proc. Natl. Acad. Sci. U.S.A.

712

624

View full text Add to dashboard Cite

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“…We and others have shown previously that proteasomes co-purify with a fraction of RNA species ranging from 1000 to 18-20 nucleotides [28, 29]. In fact, the abundance of the RNA fraction associated with proteasomes was calculated and varied from 0.0016% up tо 0.2% of total RNA depending on the organism and specific tissue used for experiments [30].…”

Section: Resultsmentioning

confidence: 99%

“…That proteasomal 20S particles were associated with low molecular weight (lmw) RNA species has been known for decades [19, 20, 28, 30]. However, neither the exact composition nor the function(s) of these lmw RNAs were characterised in details.…”

Section: Discussionmentioning

confidence: 99%

“…That proteasome preparations often contain small RNA species ranging from 20 to 120 nucleotides [28] prompted us to test whether proteasome-associated RNAs (pa-RNAs) belonged to the family microRNAs (miRNAs). Given the fact that DNA damage controls both proteolytic and endonuclease activities of proteasomes, we also examined how genotoxic stress induced by DR affected the repertoire of these small RNAs associated with the proteasome.…”

Section: Introductionmentioning

confidence: 99%

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DNA damage modulates interactions between microRNAs and the 26S proteasome

et al. 2014

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26S proteasomes are known as major non-lysosomal cellular machines for coordinated and specific destruction of ubiquitinylated proteins. The proteolytic activities of proteasomes are controlled by various post-translational modifications in response to environmental cues, including DNA damage. Besides proteolysis, proteasomes also associate with RNA hydrolysis and splicing. Here, we extend the functional diversity of proteasomes by showing that they also dynamically associate with microRNAs (miRNAs) both in the nucleus and cytoplasm of cells. Moreover, DNA damage induced by an anti-cancer drug, doxorubicin, alters the repertoire of proteasome-associated miRNAs, enriching the population of miRNAs that target cell cycle checkpoint regulators and DNA repair proteins. Collectively, these data uncover yet another potential mode of action for proteasomes in the cell via their dynamic association with microRNAs.

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“…Furthermore, proteasomes are involved in cell cycle control (25,29) and in early steps of the immune response, such as major histocompatibility complex class I-restricted antigen processing (5,26). Proteasomes are also involved in transcriptional regulation (47,56), and recent reports suggest that they may also participate in the pathways of cellular RNA breakdown (52,59). It is possible that the Mov34 interaction with the JEV 3Ј-NCR helps in binding of the proteasome with the viral RNA for its subsequent involvement in transcription or other activities listed above.…”

Section: Discussionmentioning

confidence: 99%

Mov34 Protein from Mouse Brain Interacts with the 3′ Noncoding Region of Japanese Encephalitis Virus

Vrati

2000

J Virol

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The plus-sense RNA genome of Japanese encephalitis virus (JEV) contains noncoding regions (NCRs) of 95 and 585 bases at its 5 and 3 ends, respectively. The last 83 nucleotides of the 3-NCR are predicted to form stable stem-loop (SL) structures. The shape of this 3-SL structure is highly conserved among divergent flaviviruses even though only small stretches of nucleotide sequence contained within these structures are conserved. These SL structures have been predicted to function as cis-acting signals for RNA replication and as such may bind to viral and cellular proteins that may be involved in viral replication. We have studied the interaction of the JEV 3-NCR RNA with host proteins using gel retardation assays. We show that the JEV 3-SL structure RNA forms three complexes with proteins from the S100 cytoplasmic extract prepared from the neonatal mouse brain. These complexes could be obtained Japanese encephalitis virus (JEV) is a flavivirus with a plussense, single-stranded RNA genome of ϳ11 kb. The genomic RNA contains a single open reading frame capable of encoding a polyprotein of ϳ3,400 amino acids which is subsequently cleaved into three structural (capsid, pre-M, and envelope) and seven nonstructural (NS1, NS2A, NS2B, NS3, NS4A, NS4B, and NS5) proteins. The coding region in the genome is flanked by 5Ј and 3Ј noncoding regions (NCRs) of 95 and 585 bases (63). The size and sequence of the 3Ј-NCR vary among different flaviviruses although its secondary structure comprising stable stem-loop (SL) formations is predicted to be highly conserved. The last 80 to 90 bases at the extreme 3Ј end of the genome have been predicted to form stable SL structures in different flaviviruses (10,11,63,65). There are only small stretches of nucleotide sequences, mostly located in the loop regions of these SL structures, that are conserved among flaviviruses (10). Conservation of the location and the shape of these SL structures in the 3Ј-NCR of flaviviruses indicates that they may have some functional significance.During the course of flavivirus replication, a minus-sense RNA is synthesized from the plus-sense genomic RNA. This intermediate form of RNA serves as template for the synthesis of the plus-sense genomic RNA which is synthesized to 10-to 100-fold-higher levels than the minus-sense RNA (12, 62). Both the nucleotide sequence and the structural elements of the 3Ј-NCR such as the 3Ј-SL structure are predicted to contain cis-acting signals for the initiation of the viral RNA transcription, and thus, they may specifically interact with viral or cellular proteins during viral RNA replication (12,71).A number of host proteins have been shown to be associated with the RNA-dependent RNA polymerase of phage Q␤ (9), brome mosaic virus (53), cucumber mosaic virus (34), tobacco mosaic virus (48), vesicular stomatitis virus (19), measles virus (44), influenza virus (46), and poliovirus (33, 43). Moreover, a variety of host proteins has been shown to interact with putative cis-acting elements of Sindbis virus (50), mouse hepatitis ...

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Relationships between proteasomes and RNA

Cited by 15 publications

References 40 publications

Conserved patterns of protein interaction in multiple species

Conserved patterns of protein interaction in multiple species

DNA damage modulates interactions between microRNAs and the 26S proteasome

Mov34 Protein from Mouse Brain Interacts with the 3′ Noncoding Region of Japanese Encephalitis Virus

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