scholarly journals Is there quality control of localized mRNAs?

2014 ◽  
Vol 204 (6) ◽  
pp. 863-868 ◽  
Author(s):  
Robert Walters ◽  
Roy Parker
Keyword(s):  
Quality Control ◽  
Mrna Localization ◽  
Mrna Degradation ◽  
Eukaryotic Cells ◽  
Mrna Turnover ◽  
Local Production ◽  
Translation Repression ◽  
Additional Layer ◽  
In Cells

In eukaryotic cells many mRNAs are localized to specific regions of the cytosol, thereby allowing the local production of proteins. The process of mRNA localization can be coordinated with mRNA turnover, which can also be spatially controlled to increase the degree of mRNA localization. The coordination of mRNA localization, translation repression during transport, and mRNA degradation suggests the hypothesis that an additional layer of mRNA quality control exists in cells to degrade mRNAs that fail to be appropriately localized.

Regulated and quality-control mRNA turnover pathways in eukaryotes

2010 ◽  
Vol 38 (6) ◽  
pp. 1506-1510 ◽  
Author(s):  
Boris Reznik ◽  
Jens Lykke-Andersen
Keyword(s):  
Quality Control ◽  
Rna Processing ◽  
Rna Localization ◽  
Rna Degradation ◽  
Eukaryotic Cells ◽  
Mrna Turnover ◽  
Surveillance Systems ◽  
Rna Turnover ◽  
Rna Surveillance ◽  
Multiple Levels

Gene expression can be regulated at multiple levels, including transcription, RNA processing, RNA localization, translation and, finally, RNA turnover. RNA degradation may occur at points along the processing pathway or during translation as it undergoes quality control by RNA surveillance systems. Alternatively, mRNAs may be subject to regulated degradation, often mediated by cis-encoded determinants in the mRNA sequence that, through the recruitment of trans factors, determine the fate of the mRNA. The aim of the present review is to highlight mechanisms of regulated and quality-control RNA degradation in eukaryotic cells, with an emphasis on mammals.

scholarly journals Interrogating the degradation pathways of unstable mRNAs with XRN1-resistant sequences

2016 ◽  
Vol 7 (1) ◽  
Author(s):  
Volker Boehm ◽  
Jennifer V. Gerbracht ◽  
Marie-Charlotte Marx ◽  
Niels H. Gehring
Keyword(s):  
Gene Expression ◽  
Mrna Decay ◽  
Mrna Degradation ◽  
Eukaryotic Cells ◽  
Mrna Turnover ◽  
Degradation Pathways ◽  
Messenger Rnas ◽  
Endonucleolytic Cleavage ◽  
Nonsense Mediated Mrna Decay ◽  
Cytokine Mrnas

Abstract The turnover of messenger RNAs (mRNAs) is a key regulatory step of gene expression in eukaryotic cells. Due to the complexity of the mammalian degradation machinery, the contribution of decay factors to the directionality of mRNA decay is poorly understood. Here we characterize a molecular tool to interrogate mRNA turnover via the detection of XRN1-resistant decay fragments (xrFrag). Using nonsense-mediated mRNA decay (NMD) as a model pathway, we establish xrFrag analysis as a robust indicator of accelerated 5′–3′ mRNA decay. In tethering assays, monitoring xrFrag accumulation allows to distinguish decapping and endocleavage activities from deadenylation. Moreover, xrFrag analysis of mRNA degradation induced by miRNAs, AU-rich elements (AREs) as well as the 3′ UTRs of cytokine mRNAs reveals the contribution of 5′–3′ decay and endonucleolytic cleavage. Our work uncovers formerly unrecognized modes of mRNA turnover and establishes xrFrag as a powerful tool for RNA decay analyses.

scholarly journals RNase L reprograms translation by widespread mRNA turnover escaped by antiviral mRNAs

2018 ◽  
Author(s):  
James M Burke ◽  
Stephanie L Moon ◽  
Evan T Lester ◽  
Tyler Matheny ◽  
Roy Parker
Keyword(s):  
Translation Initiation ◽  
Mammalian Cells ◽  
Mrna Degradation ◽  
Stress Granule ◽  
Mrna Turnover ◽  
Rnase L ◽  
Protein Kinase R ◽  
Double Stranded Rna ◽  
Translation Repression ◽  
Eif2α Phosphorylation

SUMMARYIn response to foreign and endogenous double-stranded RNA (dsRNA), protein kinase R (PKR) and ribonuclease L (RNase L) reprogram translation in mammalian cells. PKR inhibits translation initiation through eIF2α phosphorylation, which triggers stress granule (SG) formation and promotes translation of stress responsive mRNAs. The mechanisms of RNase L-driven translation repression, its contribution to SG assembly, and its regulation of dsRNA stress-induced mRNAs are unknown. We demonstrate that RNase L drives translational shut-off in response to dsRNA by promoting widespread turnover of mRNAs. This alters stress granule assembly and reprograms translation by only allowing for the translation of mRNAs resistant to RNase L degradation, including numerous antiviral mRNAs such asIFN-β. Individual cells differentially activate dsRNA responses revealing variation that can affect cellular outcomes. This identifies bulk mRNA degradation and the resistance of antiviral mRNAs as the mechanism by which RNaseL reprograms translation in response to dsRNA.

scholarly journals Chemical Biology Framework to Illuminate Proteostasis

2020 ◽  
Vol 89 (1) ◽  
pp. 529-555 ◽  
Author(s):  
Rebecca M. Sebastian ◽  
Matthew D. Shoulders
Keyword(s):  
Quality Control ◽  
Protein Folding ◽  
Chemical Biology ◽  
Control Factors ◽  
Network Composition ◽  
Network Component ◽  
Selection Of ◽  
In Cells

Protein folding in the cell is mediated by an extensive network of >1,000 chaperones, quality control factors, and trafficking mechanisms collectively termed the proteostasis network. While the components and organization of this network are generally well established, our understanding of how protein-folding problems are identified, how the network components integrate to successfully address challenges, and what types of biophysical issues each proteostasis network component is capable of addressing remains immature. We describe a chemical biology–informed framework for studying cellular proteostasis that relies on selection of interesting protein-folding problems and precise researcher control of proteostasis network composition and activities. By combining these methods with multifaceted strategies to monitor protein folding, degradation, trafficking, and aggregation in cells, researchers continue to rapidly generate new insights into cellular proteostasis.

scholarly journals Cytoplasmic foci are sites of mRNA decay in human cells

2004 ◽  
Vol 165 (1) ◽  
pp. 31-40 ◽  
Author(s):  
Nicolas Cougot ◽  
Sylvie Babajko ◽  
Bertrand Séraphin
Keyword(s):  
Mrna Decay ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Human Cells ◽  
Eukaryotic Cells ◽  
Mrna Turnover ◽  
Expression Control ◽  
Gene Expression Control ◽  
Cytoplasmic Structures

Understanding gene expression control requires defining the molecular and cellular basis of mRNA turnover. We have previously shown that the human decapping factors hDcp2 and hDcp1a are concentrated in specific cytoplasmic structures. Here, we show that hCcr4, hDcp1b, hLsm, and rck/p54 proteins related to 5′–3′ mRNA decay also localize to these structures, whereas DcpS, which is involved in cap nucleotide catabolism, is nuclear. Functional analysis using fluorescence resonance energy transfer revealed that hDcp1a and hDcp2 interact in vivo in these structures that were shown to differ from the previously described stress granules. Our data indicate that these new structures are dynamic, as they disappear when mRNA breakdown is abolished by treatment with inhibitors. Accumulation of poly(A)+ RNA in these structures, after RNAi-mediated inactivation of the Xrn1 exonuclease, demonstrates that they represent active mRNA decay sites. The occurrence of 5′–3′ mRNA decay in specific subcellular locations in human cells suggests that the cytoplasm of eukaryotic cells may be more organized than previously anticipated.

scholarly journals Targeting of c-myc and β-globin coding sequences to cytoskeletal-bound polysomes by c-myc 3′ untranslated region

1994 ◽  
Vol 298 (1) ◽  
pp. 143-148 ◽  
Author(s):  
J Hesketh ◽  
G Campbell ◽  
M Piechaczyk ◽  
J M Blanchard
Keyword(s):  
In Situ Hybridization ◽  
Untranslated Region ◽  
Mrna Localization ◽  
Eukaryotic Cells ◽  
Beta Globin ◽  
Globin Mrna ◽  
Directional Information ◽  
Coding Sequences ◽  
Membrane Bound

The influence of the 3′ untranslated region on mRNA localization was investigated by measuring the distribution of myc, beta-globin and hybrid myc-globin mRNAs between free, cytoskeletal-bound and membrane-bound polysomes in cells transfected with either control or chimeric gene constructs. c-myc sequences and beta-globin-coding sequences linked to the myc 3′ untranslated region were present at greatest enrichment in cytoskeletal-bound polysomes. beta-Globin mRNA and myc-coding sequences linked to the beta-globin 3′ untranslated region were recovered largely in the free polysomes. In situ hybridization confirmed that replacement of the c-myc 3′ untranslated region by that of globin caused a relocalization of the mRNA. The results suggest that mRNA localization in differentiated eukaryotic cells depends on a mechanism that involves directional information in the 3′ untranslated region of mRNAs.

scholarly journals Single-molecule imaging of mRNA localization and regulation during the integrated stress response

2018 ◽  
Author(s):  
Johannes H. Wilbertz ◽  
Franka Voigt ◽  
Ivana Horvathova ◽  
Gregory Roth ◽  
Yinxiu Zhan ◽  
...  
Keyword(s):  
Stress Response ◽  
Single Molecule ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Mrna Localization ◽  
Mrna Degradation ◽  
Integrated Stress Response ◽  
Cellular Space ◽  
Processing Bodies ◽  
Functional Consequence

AbstractBiological phase transitions form membrane-less organelles that generate distinct cellular environments. How molecules are partitioned between these compartments and the surrounding cellular space and the functional consequence of this localization is not well understood. Here, we report the localization of mRNA to stress granules(SGs) and processing bodies(PBs), which are distinct biomolecular condensates, and its effect on translation and mRNA degradation during the integrated stress response. Using single mRNA imaging in living human cells, we find that the interactions of mRNAs with SGs and PBs have different dynamics and that specific RNA binding proteins can anchor mRNAs within these compartments. During recovery from stress, mRNAs that were within SGs and PBs are translated and degraded at similar rates as their cytosolic counterparts.

scholarly journals Ribosome quality control activity potentiates vaccinia virus protein synthesis during infection

2020 ◽  
Author(s):  
Elayanambi Sundaramoorthy ◽  
Andrew P. Ryan ◽  
Amit Fulzele ◽  
Marilyn Leonard ◽  
Matthew D. Daugherty ◽  
...  
Keyword(s):  
Quality Control ◽  
Viral Infection ◽  
Vaccinia Virus ◽  
Critical Role ◽  
Mrna Translation ◽  
Virus Protein ◽  
Viral Mrnas ◽  
Control Activity ◽  
Viral Propagation ◽  
In Cells

Ribosomes are highly abundant cellular machines that perform the essential task of translating the genetic code into proteins. Cellular translation activity is finely tuned and proteostasis insults, such as those incurred upon viral infection, activate stress signaling pathways that result in translation reprogramming. Viral infection selectively shuts down host mRNA while redistributing ribosomes for selective translation of viral mRNAs. The intricacies of this selective ribosome shuffle from host to viral mRNAs are poorly understood. Here, we uncover a role for the ribosome associated quality control (RQC) factor ZNF598, a sensor for collided ribosomes, as a critical factor for vaccinia virus mRNA translation. Collided ribosomes are sensed by ZNF598, which ubiquitylates 40S subunit proteins uS10 and eS10 and thereby initiates RQC-dependent nascent chain degradation and ribosome recycling. We show that vaccinia infection in human cells enhances uS10 ubiquitylation indicating an increased burden on RQC pathways during viral propagation. Consistent with an increased RQC demand, we demonstrate that vaccinia virus replication is impaired in cells which either lack ZNF598 or contain a ubiquitylation deficient version of uS10. Using SILAC-based proteomics and concurrent RNAseq analysis, we determine that host translation of vaccinia virus mRNAs is compromised in cells that lack RQC activity as compared to control cells whereas there was little evidence of differences in host or viral transcription. Additionally, vaccinia virus infection resulted in a loss of cellular RQC activity, suggesting that ribosomes engaged in viral protein production recruit ZNF598 away from its function in host translation. Thus, co-option of ZNF598 by vaccinia virus plays a critical role in translational reprogramming that is needed for optimal viral propagation.

scholarly journals Differential role of cytosolic Hsp70s in longevity assurance and protein quality control

PLoS Genetics ◽  
2021 ◽  
Vol 17 (1) ◽  
pp. e1008951
Author(s):  
Rebecca Andersson ◽  
Anna Maria Eisele-Bürger ◽  
Sarah Hanzén ◽  
Katarina Vielfort ◽  
David Öling ◽  
...  
Keyword(s):  
Quality Control ◽  
Protein Quality ◽  
Protein Quality Control ◽  
Nucleotide Binding Domain ◽  
Short Lifespan ◽  
Severe Reduction ◽  
Shock Proteins ◽  
Mutant Cells ◽  
In Cells

70 kDa heat shock proteins (Hsp70) are essential chaperones of the protein quality control network; vital for cellular fitness and longevity. The four cytosolic Hsp70’s in yeast, Ssa1-4, are thought to be functionally redundant but the absence of Ssa1 and Ssa2 causes a severe reduction in cellular reproduction and accelerates replicative aging. In our efforts to identify which Hsp70 activities are most important for longevity assurance, we systematically investigated the capacity of Ssa4 to carry out the different activities performed by Ssa1/2 by overproducing Ssa4 in cells lacking these Hsp70 chaperones. We found that Ssa4, when overproduced in cells lacking Ssa1/2, rescued growth, mitigated aggregate formation, restored spatial deposition of aggregates into protein inclusions, and promoted protein degradation. In contrast, Ssa4 overproduction in the Hsp70 deficient cells failed to restore the recruitment of the disaggregase Hsp104 to misfolded/aggregated proteins, to fully restore clearance of protein aggregates, and to bring back the formation of the nucleolus-associated aggregation compartment. Exchanging the nucleotide-binding domain of Ssa4 with that of Ssa1 suppressed this ‘defect’ of Ssa4. Interestingly, Ssa4 overproduction extended the short lifespan of ssa1Δ ssa2Δ mutant cells to a lifespan comparable to, or even longer than, wild type cells, demonstrating that Hsp104-dependent aggregate clearance is not a prerequisite for longevity assurance in yeast.

scholarly journals Evidenţierea legităţilor de declanşare a epizootiilor baculovirale la H. Cunea

2020 ◽  
Author(s):  
Aurelia Stingaci ◽  
Keyword(s):  
Quality Control ◽  
Biological Material ◽  
Material Selection ◽  
Natural Populations ◽  
Local Production ◽  
Express Method ◽  
Selection For

In the paper there are presented the results of the researches of existing methods of quality control for cultures of insects for rearing is presented. A new express-method of biological material selection for H. cunea establishment has been approbated. This method may be suitable for monitoring of natural populations condition in systems of integrated plant protections of diferent agricultural, ornamental and forest crops with intensive anthropogenic loading.The results of the present study revealed the larvicidal potential of baculovirus isolates found in the larvae of H.cunea, local production of biopesticides, which will reduce the final cost of the product and will more accessible to farmer.

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