scholarly journals Global Analysis of mRNA, Translation, and Protein Localization: Local Translation Is a Key Regulator of Cell Protrusions

2015 ◽  
Vol 35 (3) ◽  
pp. 344-357 ◽  
Author(s):  
Faraz K. Mardakheh ◽  
Angela Paul ◽  
Sandra Kümper ◽  
Amine Sadok ◽  
Hugh Paterson ◽  
...  
Keyword(s):  
Protein Localization ◽  
Global Analysis ◽  
Mrna Translation ◽  
Local Translation

scholarly journals Specific Anchoring and Local Translation of Poxviral ATI mRNA at Cytoplasmic Inclusion Bodies

2019 ◽  
Vol 94 (4) ◽  
Author(s):  
George C. Katsafanas ◽  
Bernard Moss
Keyword(s):  
Inclusion Bodies ◽  
Actin Polymerization ◽  
Rna Binding ◽  
Protein Localization ◽  
Cytoplasmic Inclusion ◽  
Mrna Translation ◽  
Translation Initiation Factor ◽  
Initiation Factor ◽  
Local Translation ◽  
Virion Assembly

ABSTRACT On-site translation of mRNAs provides an efficient means of subcellular protein localization. In eukaryotic cells, the transport of cellular mRNAs to membraneless sites usually occurs prior to translation and involves specific sequences known as zipcodes that interact with RNA binding and motor proteins. Poxviruses replicate in specialized cytoplasmic factory regions where DNA synthesis, transcription, translation, and virion assembly occur. Some poxviruses embed infectious virus particles outside of factories in membraneless protein bodies with liquid gel-like properties known as A-type inclusions (ATIs) that are comprised of numerous copies of the viral 150-kDa ATI protein. Here, we demonstrate by fluorescent in situ hybridization that these inclusions are decorated with ATI mRNA. On-site translation is supported by the localization of a translation initiation factor eIF4E and by ribosome-bound nascent chain ribopuromycylation. Nascent peptide-mediated anchoring of ribosome-mRNA translation complexes to the inclusions is suggested by release of the mRNA by puromycin, a peptide chain terminator. Following puromycin washout, relocalization of ATI mRNA at inclusions depends on RNA and protein synthesis but requires neither microtubules nor actin polymerization. Further studies show that the ATI mRNAs remain near the sites of transcription in the factory regions when stop codons are introduced near the N terminus of the ATI or large truncations are made at the N or C termini. Instead of using a zipcode, we propose that ATI mRNA localization is mediated by ribosome-bound nascent ATI polypeptides that interact with ATI protein in inclusions and thereby anchor the complex for multiple rounds of mRNA translation. IMPORTANCE Poxvirus genome replication, transcription, translation, and virion assembly occur at sites within the cytoplasm known as factories. Some poxviruses sequester infectious virions outside of the factories in inclusion bodies comprised of numerous copies of the 150-kDa ATI protein, which can provide stability and protection in the environment. We provide evidence that ATI mRNA is anchored by nascent peptides and translated at the inclusion sites rather than in virus factories. Association of ATI mRNA with inclusion bodies allows multiple rounds of local translation and prevents premature ATI protein aggregation and trapping of virions within the factory.

scholarly journals Nanoparticle-based local translation reveals mRNA as a translation-coupled scaffold with anchoring function

2019 ◽  
Vol 116 (27) ◽  
pp. 13346-13351 ◽  
Author(s):  
Shunnichi Kashida ◽  
Dan Ohtan Wang ◽  
Hirohide Saito ◽  
Zoher Gueroui
Keyword(s):  
Messenger Rna ◽  
Protein Localization ◽  
Continuous Production ◽  
Protein Domains ◽  
Mrna Translation ◽  
Actin Binding ◽  
Local Translation ◽  
Local Formation ◽  
Complex Processes ◽  
Cell Extracts

The spatial regulation of messenger RNA (mRNA) translation is central to cellular functions and relies on numerous complex processes. Biomimetic approaches could bypass these endogenous complex processes, improve our comprehension of the regulation, and allow for controlling local translation regulations and functions. However, the causality between local translation and nascent protein function remains elusive. Here, we developed a nanoparticle (NP)-based strategy to magnetically control mRNA spatial patterns in mammalian cell extracts and investigate how local translation impacts nascent protein localization and function. By monitoring the translation of the magnetically localized mRNAs, we show that mRNA–NP complexes operate as a source for the continuous production of proteins from defined positions. By applying this approach to actin-binding proteins, we triggered the local formation of actin cytoskeletons and identified the minimal requirements for spatial control of the actin filament network. In addition, our bottom-up approach identified a role for mRNA as a translation-coupled scaffold for the function of nascent N-terminal protein domains. Our approach will serve as a platform for regulating mRNA localization and investigating the function of nascent protein domains during translation.

scholarly journals Nanoparticle-based local translation reveals mRNA as translation-coupled scaffold with anchoring function

2018 ◽  
Author(s):  
Shunnichi Kashida ◽  
Dan Ohtan Wang ◽  
Hirohide Saito ◽  
Zoher Gueroui
Keyword(s):  
Protein Localization ◽  
Continuous Production ◽  
Mrna Translation ◽  
Protein Domain ◽  
Actin Binding ◽  
Local Translation ◽  
Local Formation ◽  
Complex Processes ◽  
Cell Extracts

AbstractSpatial regulations of mRNA translation are central to cellular functions and relies on numerous complex processes. Biomimetic approaches could bypass the endogenous complex processes, improve our comprehension, and allow for controlling local translation regulations and functions. However, the causality between localizing translation and nascent protein function remains elusive. Here, we develop a novel nanoparticle-based strategy to magnetically control mRNA spatial patterns in mammalian cell extracts and investigate how local translation impacts nascent protein localization and function. By monitoring translation on magnetically localized mRNAs, we show that mRNA-nanoparticle operates as a source for the continuous production of proteins from defined positions. By applying magnetic localization of mRNAs coding for Actin Binding Proteins, we trigger the local formation of actin cytoskeleton and identify minimal requirements for spatial control of actin filament network. In addition, our bottom-up approach identifies a novel role of mRNA as translation-coupled scaffold for nascent N-terminal protein domain functions. Our approach will serve as a novel platform for regulating mRNA localization and investigating a functional role of nascent protein domains during translation.

Targeting of transcripts encoding membrane proteins in polarized epithelia: RNA–protein binding studies of the SGLT1 3′-UTR

2008 ◽  
Vol 36 (3) ◽  
pp. 525-527 ◽  
Author(s):  
Christopher M. Pedder ◽  
Dianne Ford ◽  
John E. Hesketh
Keyword(s):  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Protein Localization ◽  
Complex Structure ◽  
Mrna Translation ◽  
Drosophila Embryo ◽  
Binding Studies ◽  
Polarized Epithelia ◽  
Apical Localization

mRNA stability, mRNA translation and spatial localization of mRNA species within a cell can be governed by signals in the 3′-UTR (3′-untranslated region). Local translation of proteins is essential for the development of many eukaryotic cell types, such as the Drosophila embryo, where the spatial and temporal localization of bicoid and gurken mRNAs, among others, is required to establish morphogen gradients. More recent studies have suggested that mRNA localization also occurs with transcripts coding for membrane-based or secreted proteins, and that localization at organelles such as the endoplasmic reticulum directs translation more efficiently to specific subdomains, so as to aid correct protein localization. In human epithelial cells, the mRNA coding for SGLT1 (sodium–glucose co-transporter 1), an apical membrane protein, has been shown to be localized apically in polarized cells. However, the nature of the signals and RNA-binding proteins involved are unknown. Ongoing work is aimed at identifying the localization signals in the SGLT1 3′-UTR and the corresponding binding proteins. Using a protein extract from polarized Caco-2 cells, both EMSAs (electrophoretic mobility-shift assays) and UV cross-linking assays have shown that a specific protein complex is formed with the first 300 bases of the 3′-UTR sequence. MFold predictions suggest that this region folds into a complex structure and ongoing studies using a series of strategic deletions are being carried out to identify the precise nature of the motif involved, particularly the role of the sequence or RNA secondary structure, as well as to identify the main proteins present within the complex. Such information will provide details of the post-transcriptional events that lead to apical localization of the SGLT1 transcript and may reveal mechanisms of more fundamental importance in the apical localization of proteins in polarized epithelia.

Global Analysis of Maternal mRNA Translation during Mouse Oocyte Meiotic Maturation.

2010 ◽  
Vol 83 (Suppl_1) ◽  
pp. 327-327
Author(s):  
Jing Chen ◽  
Collin Melton ◽  
NaYoung Suh ◽  
Robert Blelloch ◽  
Marco Conti
Keyword(s):  
Global Analysis ◽  
Mrna Translation ◽  
Mouse Oocyte ◽  
Meiotic Maturation ◽  
Maternal Mrna ◽  
Oocyte Meiotic Maturation

scholarly journals RNAs as Regulators of Cellular Matchmaking

2021 ◽  
Vol 8 ◽  
Author(s):  
Nikita Fernandes ◽  
J. Ross Buchan
Keyword(s):  
Protein Localization ◽  
Mrna Translation ◽  
Rna Molecules ◽  
P Bodies ◽  
Coding Regions ◽  
Cytoplasmic Rna ◽  
Chromosome Topology ◽  
Future Challenges ◽  
Non Coding Rnas ◽  
Nuclear Processes

RNA molecules are increasingly being identified as facilitating or impeding the interaction of proteins and nucleic acids, serving as so-called scaffolds or decoys. Long non-coding RNAs have been commonly implicated in such roles, particularly in the regulation of nuclear processes including chromosome topology, regulation of chromatin state and gene transcription, and assembly of nuclear biomolecular condensates such as paraspeckles. Recently, an increased awareness of cytoplasmic RNA scaffolds and decoys has begun to emerge, including the identification of non-coding regions of mRNAs that can also function in a scaffold-like manner to regulate interactions of nascently translated proteins. Collectively, cytoplasmic RNA scaffolds and decoys are now implicated in processes such as mRNA translation, decay, protein localization, protein degradation and assembly of cytoplasmic biomolecular condensates such as P-bodies. Here, we review examples of RNA scaffolds and decoys in both the nucleus and cytoplasm, illustrating common themes, the suitability of RNA to such roles, and future challenges in identifying and better understanding RNA scaffolding and decoy functions.

scholarly journals Receptor-specific interactome as a hub for rapid cue-induced selective translation in axons

2019 ◽  
Author(s):  
Max Koppers ◽  
Roberta Cagnetta ◽  
Toshiaki Shigeoka ◽  
Lucia C.S. Wunderlich ◽  
Sixian Zhao ◽  
...  
Keyword(s):  
Rna Binding ◽  
Rna Binding Proteins ◽  
Axon Growth ◽  
Mrna Translation ◽  
Local Translation ◽  
Simultaneous Exposure ◽  
Surface Receptors ◽  
Guidance Cue ◽  
Selective Translation ◽  
Specific Mrnas

AbstractDuring neuronal wiring, extrinsic cues trigger the local translation of specific mRNAs in axons via cell surface receptors. The coupling of ribosomes to receptors has been proposed as a mechanism linking signals to local translation but it is not known how broadly this mechanism operates, nor whether it can selectively regulate mRNA translation. We report that receptor-ribosome coupling is employed by multiple guidance cue receptors and this interaction is mRNA-dependent. We find that different receptors bind to distinct sets of mRNAs and RNA-binding proteins. Cue stimulation induces rapid dissociation of ribosomes from receptors and the selective translation of receptor-specific mRNAs in retinal axon growth cones. Further, we show that receptor-ribosome dissociation and cue-induced selective translation are inhibited by simultaneous exposure to translation-repressive cues, suggesting a novel mode of signal integration. Our findings reveal receptor-specific interactomes and provide a general model for the rapid, localized and selective control of cue-induced translation.

scholarly journals Receptor-specific interactome as a hub for rapid cue-induced selective translation in axons

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Max Koppers ◽  
Roberta Cagnetta ◽  
Toshiaki Shigeoka ◽  
Lucia CS Wunderlich ◽  
Pedro Vallejo-Ramirez ◽  
...  
Keyword(s):  
Rna Binding ◽  
Rna Binding Proteins ◽  
Mrna Translation ◽  
Retinal Ganglion ◽  
Local Translation ◽  
Surface Receptors ◽  
Guidance Cue ◽  
Extrinsic Cues ◽  
Selective Translation ◽  
Specific Mrnas

Extrinsic cues trigger the local translation of specific mRNAs in growing axons via cell surface receptors. The coupling of ribosomes to receptors has been proposed as a mechanism linking signals to local translation but it is not known how broadly this mechanism operates, nor whether it can selectively regulate mRNA translation. We report that receptor-ribosome coupling is employed by multiple guidance cue receptors and this interaction is mRNA-dependent. We find that different receptors associate with distinct sets of mRNAs and RNA-binding proteins. Cue stimulation of growing Xenopus retinal ganglion cell axons induces rapid dissociation of ribosomes from receptors and the selective translation of receptor-specific mRNAs. Further, we show that receptor-ribosome dissociation and cue-induced selective translation are inhibited by co-exposure to translation-repressive cues, suggesting a novel mode of signal integration. Our findings reveal receptor-specific interactomes and suggest a generalizable model for cue-selective control of the local proteome.

scholarly journals Super-resolution ribosome profiling reveals unannotated translation events in Arabidopsis

2016 ◽  
Vol 113 (45) ◽  
pp. E7126-E7135 ◽  
Author(s):  
Polly Yingshan Hsu ◽  
Lorenzo Calviello ◽  
Hsin-Yen Larry Wu ◽  
Fay-Wei Li ◽  
Carl J. Rothfels ◽  
...  
Keyword(s):  
Global Analysis ◽  
Super Resolution ◽  
Mrna Translation ◽  
Ribosome Profiling ◽  
Optimization Strategy ◽  
Plant Genomics ◽  
Reading Frame ◽  
Periodic Property ◽  
Evolutionarily Conserved ◽  
Small Orfs

Deep sequencing of ribosome footprints (ribosome profiling) maps and quantifies mRNA translation. Because ribosomes decode mRNA every 3 nt, the periodic property of ribosome footprints could be used to identify novel translated ORFs. However, due to the limited resolution of existing methods, the 3-nt periodicity is observed mostly in a global analysis, but not in individual transcripts. Here, we report a protocol applied to Arabidopsis that maps over 90% of the footprints to the main reading frame and thus offers super-resolution profiles for individual transcripts to precisely define translated regions. The resulting data not only support many annotated and predicted noncanonical translation events but also uncover small ORFs in annotated noncoding RNAs and pseudogenes. A substantial number of these unannotated ORFs are evolutionarily conserved, and some produce stable proteins. Thus, our study provides a valuable resource for plant genomics and an efficient optimization strategy for ribosome profiling in other organisms.

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