scholarly journals Rab1b and ARF5 are novel RNA-binding proteins involved in IRES-driven RNA localization

2018 ◽  
Author(s):  
Javier Fernandez-Chamorro ◽  
Rosario Francisco-Velilla ◽  
Jorge Ramajo ◽  
Encarnación Martinez-Salas
Keyword(s):  
Binding Proteins ◽  
Protein Transport ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Rna Localization ◽  
Dominant Negative ◽  
Dominant Negative Mutant ◽  
Entry Site ◽  
Initiation Of Translation ◽  
Domain 3

ABSTRACTInternal ribosome entry site (IRES) elements are organized in domains that guide internal initiation of translation. Here we have combined proteomic and imaging analysis to study novel IRES interactors recognizing specific RNA structural subdomains. Besides known IRES-binding proteins, we identified novel factors belonging to networks involved in RNA and protein transport. Among those, Rab1b and ARF5, two components of the ER-Golgi, revealed direct binding to IRES transcripts. However, these proteins exert different effects on translation. While a dominant-negative mutant of Rab1b decreased IRES function, ARF5 silencing stimulated IRES activity. RNA FISH studies revealed novel features of the IRES element. First, IRES-RNA formed clusters within the cell cytoplasm, whereas cap-RNA displayed disperse punctuated distribution. Second, the IRES-driven RNA colocalized with ARF5 and Rab1b, but not with the dominant-negative of Rab1b. Thus, our data suggest a role for domain 3 of the IRES in RNA localization around ER-Golgi, a ribosome-rich cellular compartment.

scholarly journals Rab1b and ARF5 are novel RNA-binding proteins involved in FMDV IRES–driven RNA localization

2019 ◽  
Vol 2 (1) ◽  
pp. e201800131 ◽  
Author(s):  
Javier Fernandez-Chamorro ◽  
Rosario Francisco-Velilla ◽  
Jorge Ramajo ◽  
Encarnación Martinez-Salas
Keyword(s):  
Binding Proteins ◽  
Protein Transport ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Rna Localization ◽  
Dominant Negative ◽  
Entry Site ◽  
Initiation Of Translation ◽  
Mouth Disease Virus ◽  
Domain 3

Internal ribosome entry site (IRES) elements are organized in domains that guide internal initiation of translation. Here, we have combined proteomic and imaging analysis to study novel foot-and-mouth disease virus IRES interactors recognizing specific RNA structural subdomains. Besides known picornavirus IRES–binding proteins, we identified novel factors belonging to networks involved in RNA and protein transport. Among those, Rab1b and ARF5, two components of the ER-Golgi, revealed direct binding to IRES transcripts. However, whereas Rab1b stimulated IRES function, ARF5 diminished IRES activity. RNA-FISH studies revealed novel features of the IRES element. First, IRES-RNA formed clusters within the cell cytoplasm, whereas cap-RNA displayed disperse punctate distribution. Second, the IRES-driven RNA localized in close proximity with ARF5 and Rab1b, but not with the dominant-negative of Rab1b that disorganizes the Golgi. Thus, our data suggest a role for domain 3 of the IRES in RNA localization around ER-Golgi, a ribosome-rich cellular compartment.

scholarly journals The 36-kilodalton embryonic-type cytoplasmic polyadenylation element-binding protein in Xenopus laevis is ElrA, a member of the ELAV family of RNA-binding proteins.

1997 ◽  
Vol 17 (11) ◽  
pp. 6402-6409 ◽  
Author(s):  
L Wu ◽  
P J Good ◽  
J D Richter
Keyword(s):  
Xenopus Laevis ◽  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Binding Protein ◽  
Dominant Negative ◽  
Cytoplasmic Polyadenylation ◽  
Element Binding Protein

The translational activation of several maternal mRNAs in Xenopus laevis is dependent on cytoplasmic poly(A) elongation. Messages harboring the UUUUUAU-type cytoplasmic polyadenylation element (CPE) in their 3' untranslated regions (UTRs) undergo polyadenylation and translation during oocyte maturation. This CPE is bound by the protein CPEB, which is essential for polyadenylation. mRNAs that have the poly(U)12-27 embryonic-type CPE (eCPE) in their 3' UTRs undergo polyadenylation and translation during the early cleavage and blastula stages. A 36-kDa eCPE-binding protein in oocytes and embryos has been identified by UV cross-linking. We now report that this 36-kDa protein is ElrA, a member of the ELAV family of RNA-binding proteins. The proteins are identical in size, antibody directed against ElrA immunoprecipitates the 36-kDa protein, and the two proteins have the same RNA binding specificity in vitro. C12 and activin receptor mRNAs, both of which contain eCPEs, are detected in immunoprecipitated ElrA-mRNP complexes from eggs and embryos. In addition, this in vivo interaction requires the eCPE. Although a number of experiments failed to define a role for ElrA in cytoplasmic polyadenylation, the expression of a dominant negative ElrA protein in embryos results in an exogastrulation phenotype. The possible functions of ElrA in gastrulation are discussed.

scholarly journals FMRP promotes RNA localization to neuronal projections through interactions between its RGG domain and G-quadruplex RNA sequences

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Raeann Goering ◽  
Laura I Hudish ◽  
Bryan B Guzman ◽  
Nisha Raj ◽  
Gary J Bassell ◽  
...  
Keyword(s):  
Fragile X Syndrome ◽  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Fragile X ◽  
Rna Localization ◽  
Null Mouse ◽  
Rna Sequences ◽  
Rna Molecules ◽  
G Quadruplex

The sorting of RNA molecules to subcellular locations facilitates the activity of spatially restricted processes. We have analyzed subcellular transcriptomes of FMRP-null mouse neuronal cells to identify transcripts that depend on FMRP for efficient transport to neurites. We found that these transcripts contain an enrichment of G-quadruplex sequences in their 3′ UTRs, suggesting that FMRP recognizes them to promote RNA localization. We observed similar results in neurons derived from Fragile X Syndrome patients. We identified the RGG domain of FMRP as important for binding G-quadruplexes and the transport of G-quadruplex-containing transcripts. Finally, we found that the translation and localization targets of FMRP were distinct and that an FMRP mutant that is unable to bind ribosomes still promoted localization of G-quadruplex-containing messages. This suggests that these two regulatory modes of FMRP may be functionally separated. These results provide a framework for the elucidation of similar mechanisms governed by other RNA-binding proteins.

scholarly journals Nuclear RNP complex assembly initiates cytoplasmic RNA localization

2004 ◽  
Vol 165 (2) ◽  
pp. 203-211 ◽  
Author(s):  
Tracy L. Kress ◽  
Young J. Yoon ◽  
Kimberly L. Mowry
Keyword(s):  
Protein Interactions ◽  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Rna Localization ◽  
Rna Sequences ◽  
Cytoplasmic Rna ◽  
Rnp Complex ◽  
Maternal Mrnas ◽  
Protein Components

Cytoplasmic localization of mRNAs is a widespread mechanism for generating cell polarity and can provide the basis for patterning during embryonic development. A prominent example of this is localization of maternal mRNAs in Xenopus oocytes, a process requiring recognition of essential RNA sequences by protein components of the localization machinery. However, it is not yet clear how and when such protein factors associate with localized RNAs to carry out RNA transport. To trace the RNA–protein interactions that mediate RNA localization, we analyzed RNP complexes from the nucleus and cytoplasm. We find that an early step in the localization pathway is recognition of localized RNAs by specific RNA-binding proteins in the nucleus. After transport into the cytoplasm, the RNP complex is remodeled and additional transport factors are recruited. These results suggest that cytoplasmic RNA localization initiates in the nucleus and that binding of specific RNA-binding proteins in the nucleus may act to target RNAs to their appropriate destinations in the cytoplasm.

scholarly journals RNA-Binding Proteins Impacting on Internal Initiation of Translation

2013 ◽  
Vol 14 (11) ◽  
pp. 21705-21726 ◽  
Author(s):  
Encarnación Martínez-Salas ◽  
Gloria Lozano ◽  
Javier Fernandez-Chamorro ◽  
Rosario Francisco-Velilla ◽  
Alfonso Galan ◽  
...  
Keyword(s):  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Initiation Of Translation ◽  
Internal Initiation

scholarly journals La protein is required for efficient translation driven by encephalomyocarditis virus internal ribosomal entry site

1999 ◽  
Vol 80 (12) ◽  
pp. 3159-3166 ◽  
Author(s):  
Yoon Ki Kim ◽  
Sung Key Jang
Keyword(s):  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Protein A ◽  
Internal Ribosomal Entry Site ◽  
Encephalomyocarditis Virus ◽  
Entry Site ◽  
Polypyrimidine Tract Binding Protein ◽  
La Protein ◽  
Ribosomal Entry

Translation of internal ribosomal entry site (IRES)-dependent mRNAs is mediated by RNA-binding proteins as well as canonical translation factors. In order to elucidate the roles of RNA-binding proteins in IRES-dependent translation, the role of polypyrimidine tract-binding protein (PTB) and La protein in encephalomyocarditis virus (EMCV) IRES-dependent translation was investigated. PTB was required for efficient EMCV IRES-driven translation but, intriguingly, an excess of PTB suppressed it. Such a translational suppression by surplus PTB was relieved by addition of La protein. A possible role for La protein in IRES-dependent translation is discussed.

scholarly journals A massively parallel reporter assay reveals focused and broadly encoded RNA localization signals in neurons

2021 ◽  
Author(s):  
Martin Mikl ◽  
Davide Eletto ◽  
Minkyoung Lee ◽  
Atefeh Lafzi ◽  
Farah Mhamedi ◽  
...  
Keyword(s):  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Neuronal Cell ◽  
Mrna Localization ◽  
Rna Localization ◽  
Massively Parallel ◽  
Reporter Assay ◽  
Massively Parallel Reporter Assay ◽  
Localization Behavior

AbstractAsymmetric subcellular localization of mRNA is a common cellular phenomenon that is thought to contribute to spatial gene regulation. In highly polar neurons, subcellular transcript localization and translation are thought to enhance cellular efficiency and timely responses to external cues. Although mRNA localization has been observed in many tissues and numerous examples of the functional importance of this process exist, we still lack a systematic understanding of how the transcript sorting machinery works in a sequence-specific manner.Here, we addressed these gaps by combining subcellular transcriptomics and rationally designed sequence libraries. We developed a massively parallel reporter assay (MPRA) for mRNA localization and tested ~50,000 sequences for their ability to drive RNA localization to neurites of neuronal cell lines. By scanning the 3’UTR of >300 genes we identified many previously unknown localization regions and mapped the localization potential of endogenous sequences. Our data suggest two ways the localization potential can be encoded in the 3’UTR: focused localization motifs and broadly encoded localization potential based on small contributions.We identified sequence motifs enriched in dendritically localized transcripts and tested the potential of these motifs to affect the localization behavior of an mRNA. This assay revealed sequence elements with the ability to bias localization towards neurite as well as soma. Depletion of RNA binding proteins predicted or experimentally shown to bind these motifs abolished the effect on localization, suggesting that these motifs act by recruiting specific RNA-binding proteins.Based on our dataset we developed machine learning models that accurately predict the localization behavior of novel sequences. Testing this predictor on native mRNA sequencing data showed good agreement between predicted and observed localization potential, suggesting that the rules uncovered by our MPRA also apply to the localization of native transcripts.Applying similar systematic high-throughput approaches to other cell types will open the door for a comparative perspective on RNA localization across tissues and reveal the commonalities and differences of this crucial regulatory mechanism.

scholarly journals RNA-Binding Proteins HuR and PTB Promote the Translation of Hypoxia-Inducible Factor 1α

2007 ◽  
Vol 28 (1) ◽  
pp. 93-107 ◽  
Author(s):  
Stefanie Galbán ◽  
Yuki Kuwano ◽  
Rudolf Pullmann ◽  
Jennifer L. Martindale ◽  
Hyeon Ho Kim ◽  
...  
Keyword(s):  
Binding Proteins ◽  
Rna Binding ◽  
De Novo ◽  
Rna Binding Proteins ◽  
Hypoxia Inducible Factor ◽  
Mrna Levels ◽  
Entry Site ◽  
Hypoxia Inducible Factor 1Α ◽  
Ribonucleoprotein Complexes ◽  
Polypyrimidine Tract Binding Protein

ABSTRACT The levels of hypoxia-inducible factor 1α (HIF-1α) are tightly controlled. Here, we investigated the posttranscriptional regulation of HIF-1α expression in human cervical carcinoma HeLa cells responding to the hypoxia mimetic CoCl2. Undetectable in untreated cells, HIF-1α levels increased dramatically in CoCl2-treated cells, while HIF-1α mRNA levels were unchanged. HIF-1α translation was potently elevated by CoCl2 treatment, as determined by de novo translation analysis and by monitoring the polysomal association of HIF-1α mRNA. An internal ribosome entry site in the HIF-1α 5′ untranslated region (UTR) was found to enhance translation constitutively, but it did not further induce translation in response to CoCl2 treatment. Instead, we postulated that RNA-binding proteins HuR and PTB, previously shown to bind HIF-1α mRNA, participated in its translational upregulation after CoCl2 treatment. Indeed, both RNA-binding proteins were found to bind HIF-1α mRNA in a CoCl2-inducible manner as assessed by immunoprecipitation of endogenous ribonucleoprotein complexes. Using a chimeric reporter, polypyrimidine tract-binding protein (PTB) was found to bind the HIF-1α 3′UTR, while HuR associated principally with the 5′UTR. Lowering PTB expression or HuR expression using RNA interference reduced HIF-1α translation and expression levels but not HIF-1α mRNA abundance. Conversely, HIF-1α expression and translation in response to CoCl2 were markedly elevated after HuR overexpression. We propose that HuR and PTB jointly upregulate HIF-1α translation in response to CoCl2.

scholarly journals Translation of Polioviral mRNA Is Inhibited by Cleavage of Polypyrimidine Tract-Binding Proteins Executed by Polioviral 3Cpro

2002 ◽  
Vol 76 (5) ◽  
pp. 2529-2542 ◽  
Author(s):  
Sung Hoon Back ◽  
Yoon Ki Kim ◽  
Woo Jae Kim ◽  
Sungchan Cho ◽  
Hoe Rang Oh ◽  
...  
Keyword(s):  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Binding Protein ◽  
Internal Ribosomal Entry Site ◽  
Polypyrimidine Tract ◽  
Entry Site ◽  
Polypyrimidine Tract Binding ◽  
Polypyrimidine Tract Binding Protein ◽  
Target Sites

ABSTRACT The translation of polioviral mRNA occurs through an internal ribosomal entry site (IRES). Several RNA-binding proteins, such as polypyrimidine tract-binding protein (PTB) and poly(rC)-binding protein (PCBP), are required for the poliovirus IRES-dependent translation. Here we report that a poliovirus protein, 3Cpro (and/or 3CDpro), cleaves PTB isoforms (PTB1, PTB2, and PTB4). Three 3Cpro target sites (one major target site and two minor target sites) exist in PTBs. PTB fragments generated by poliovirus infection are redistributed to the cytoplasm from the nucleus, where most of the intact PTBs are localized. Moreover, these PTB fragments inhibit polioviral IRES-dependent translation in a cell-based assay system. We speculate that the proteolytic cleavage of PTBs may contribute to the molecular switching from translation to replication of polioviral RNA.

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