Inhibition of translation initiation following glucose depletion in yeast facilitates a rationalization of mRNA content

2010 ◽  
Vol 38 (4) ◽  
pp. 1131-1136 ◽  
Author(s):  
Jennifer Lui ◽  
Susan G. Campbell ◽  
Mark P. Ashe
Keyword(s):  
Translation Initiation ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Regulation Of Gene Expression ◽  
Yeast Cells ◽  
Transcriptional Level ◽  
Diauxic Shift ◽  
P Bodies ◽  
Glucose Levels ◽  
Glucose Depletion

Glucose is the preferred carbon source for most eukaryotes and so it is important that cells can sense and react rapidly to fluctuations in glucose levels. It is becoming increasingly clear that the regulation of gene expression at the post-transcriptional level is important in the adaptation to changes in glucose levels, possibly as this could engender more rapid alterations in the concentrations of key proteins, such as metabolic enzymes. Following the removal of glucose from yeast cells a rapid inhibition of translation is observed. As a consequence, mRNPs (messenger ribonucleoproteins) relocalize into cytoplasmic granules known as P-bodies (processing bodies) and EGP-bodies. mRNA decay components localize into P-bodies, and thus these assemblies are likely to represent sites where mRNAs are targeted for degradation. In contrast, EGP-bodies lack any decay components and contain the eukaryotic translation initiation factors eIF4E, eIF4G and Pab1p, as well as other RNA-binding proteins. Therefore EGP-bodies probably constitute sites where mRNAs are earmarked for storage. So, it is possible that cells distinguish between transcripts and target them to either P-bodies or EGP-bodies depending on their functional value. The localization of mRNAs into these granules following glucose starvation may serve to preserve mRNAs that are involved in the diauxic shift to ethanol growth and entry into stationary phase, as well as to degrade mRNAs that are solely involved in glucose fermentation.

scholarly journals Integrated multi-omics reveals common properties underlying stress granule and P-body formation

2020 ◽  
Author(s):  
Christopher J. Kershaw ◽  
Michael G. Nelson ◽  
Jennifer Lui ◽  
Christian P. Bates ◽  
Martin D. Jennings ◽  
...  
Keyword(s):  
Phase Separation ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Regulation Of Gene Expression ◽  
Low Complexity ◽  
P Bodies ◽  
Binding Domains ◽  
Glucose Depletion ◽  
Before And After ◽  
Mrna Content

ABSTRACTNon-membrane-bound compartments such as P-bodies (PBs) and stress granules (SGs) play important roles in the regulation of gene expression following environmental stresses. We have systematically determined the protein and mRNA composition of PBs and SGs formed in response to a common stress condition imposed by glucose depletion. We find that high molecular weight (HMW) complexes exist prior to glucose depletion that may act as seeds for the further condensation of proteins forming mature PBs and SGs. Both before and after glucose depletion, these HMW complexes are enriched for proteins containing low complexity and RNA binding domains. The mRNA content of these HMW complexes is enriched for long, structured mRNAs that become more poorly translated following glucose depletion. Many proteins and mRNAs are shared between PBs and SGs including several multivalent RNA binding proteins that may promote condensate interactions during liquid-liquid phase separation. Even where the precise identity of mRNAs and proteins localizing to PBs and SGs is distinct, the mRNAs and proteins share common biophysical and chemical features that likely trigger their phase separation.

scholarly journals Proteomic analysis of Dhh1 complexes reveals a role for Hsp40 chaperone Ydj1 in yeast P-body assembly

2015 ◽  
Author(s):  
Gregory A. Cary ◽  
Dani B.N. Vinh ◽  
Patrick May ◽  
Rolf Kuestner ◽  
Aimee M. Dudley
Keyword(s):  
Rna Binding ◽  
Rna Binding Proteins ◽  
Active Role ◽  
Low Complexity ◽  
Mitochondrial Rna ◽  
P Bodies ◽  
Glucose Depletion ◽  
Catalytic Rnas ◽  
Rnp Granules

P-bodies (PB) are ribonucleoprotein (RNP) complexes that aggregate into cytoplasmic foci when cells are exposed to stress. While the conserved mRNA decay and translational repression machineries are known components of PB, how and why cells assemble RNP complexes into large foci remain unclear. Using mass spectrometry to analyze proteins immunoisolated with the core PB protein Dhh1, we show that a considerable number of proteins contain low-complexity (LC) sequences, similar to proteins highly represented in mammalian RNP granules. We also show that the Hsp40 chaperone Ydj1, which contains an LC domain and controls prion protein aggregation, is required for the formation of Dhh1-GFP foci upon glucose depletion. New classes of proteins that reproducibly co-enrich with Dhh1-GFP during PB induction include proteins involved in nucleotide or amino acid metabolism, glycolysis, tRNA aminoacylation, and protein folding. Many of these proteins have been shown to form foci in response to other stresses. Finally, analysis of RNA associated with Dhh1-GFP shows enrichment of mRNA encoding the PB protein Pat1 and catalytic RNAs along with their associated mitochondrial RNA-binding proteins, suggesting an active role for RNA in PB function. Thus, global characterization of PB composition has uncovered proteins and RNA that are important for PB assembly.

scholarly journals Age-induced P-bodies become detrimental and shorten the lifespan of yeast

2021 ◽  
Author(s):  
Joonhyuk Choi ◽  
Shuhao Wang ◽  
Yang Li ◽  
Nan Hao ◽  
Brian M Zid
Keyword(s):  
Irreversible Process ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Model System ◽  
Yeast Cells ◽  
P Bodies ◽  
Daughter Cells ◽  
Progressive Loss ◽  
External Stresses ◽  
Mother Cells

Aging is an irreversible process characterized by a progressive loss of homeostasis in cells, which often manifests as protein aggregates. Recently, it has been speculated that aggregates of RNA-binding proteins (RBPs) may go through pathological transitions during aging and drive the progression of age-associated neurodegenerative diseases. Using Saccharomyces cerevisiae as a model system of aging, we find that P-bodies - an RBP granule that is formed and can be beneficial for cell growth during stress conditions - naturally form during aging without any external stresses and an increase in P-body intensity is negatively correlated with the future lifespan of yeast cells. When mother cells transfer age-induced P-bodies to daughter cells, the mother cells extend lifespan, while the daughter cells grow poorly, suggesting that these age-induced P-bodies may be directly pathological. Furthermore, we find that suppressing acidification of the cytosol during aging slows down the increase in the intensity of P-body foci and extends lifespan. Our data suggest that acidification of the cytosol may facilitate the pathological transition of RBP granules during aging.

scholarly journals Regulation of Klf16 by Double Strand RNA-binding Protein STAU1 in Adipocyte Differentiation in vitro

2020 ◽  
Author(s):  
Ya Qun Guan ◽  
Xuan Yu Meng ◽  
Xiao Di Liang ◽  
Ting Ting Hu ◽  
Nurbierye Nuermamati ◽  
...  
Keyword(s):  
Rna Binding ◽  
Adipocyte Differentiation ◽  
Rna Binding Proteins ◽  
Binding Protein ◽  
Adipogenic Differentiation ◽  
Regulation Of Gene Expression ◽  
Rna Binding Protein ◽  
Negative Regulator ◽  
Transcriptional Level

Abstract Background: Adipogenesis is an essential process in organismal development and plays a significant role in adipose tissue homeostasis. Post-transcriptional regulation of gene expression plays a key role in adipogenesis and involves many RNA-binding proteins (RBPs). In mammals, Staufen1 (STAU1) is a conserved RBP(RNA Binding Protein )consisting of several dsRBP (double strand RNA). STAU1 plays an important role in the Stau1-mediated mRNA decay (SMD) pathway, which is related to adipocyte formation, myocyte development, and neural differentiation. Klf16 (Kruppel like transcription factor 16) is a negative regulator that inhibits adipocyte differentiation. AIM:This study was conducted to determine the role of Klf16 in adipocyte differentiation in the context of the SMD pathway.Methods: 3T3-L1 cells were induced and cultured in vitro by cocktail method, Knockdown and Overexpression of STAU1 and KLF16. Then, adipocyte differentiation andexpression of adipogenic-related genes (STAU1, KLF16, PPARγ, and Lipin1) were measured by RT-qPCR and Western blot.RNA immunoprecipitation (RIP) method verified that STAU1 protein can bind to KLF16.Results: The results revealed that STAU1 regulates Klf16 expression at the post-transcriptional level during the adipogenic differentiation of 3T3-L1 cells.STAU1 candirectly bind the 3′UTR of Klf16 mRNA. Klf16 mRNA was found to be degraded through the SMD pathway, thus promoting adipocyte differentiation.Conclusions: In this study, the mechanism of adipocyte differentiation regulation at the post-transcriptional level is demonstrated, and Klf16 is shown as a substrate of the SMD pathway, thus providing new insights into adipogenesis.

scholarly journals Highly accessible AU-rich regions in 3’ untranslated regions are hotspots for binding of proteins and miRNAs

2016 ◽  
Author(s):  
Mireya Plass ◽  
Simon H. Rasmussen ◽  
Anders Krogh
Keyword(s):  
Transcriptional Regulation ◽  
Mirna Target ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Regulation Of Gene Expression ◽  
Regulatory Control ◽  
Hek293 Cells ◽  
Transcriptional Level ◽  
Target Sites ◽  
Post Transcriptional Regulation

AbstractBackgroundMicroRNAs (miRNAs) are endogenous short non-coding RNAs involved in the regulation of gene expression at the post-transcriptional level typically by promoting destabilization or translational repression of target RNAs. Sometimes this regulation is absent or different, which likely is the result of interactions with other post-transcriptional factors, particularly RNA-binding proteins (RBPs). Despite the importance of the interactions between RBPs and miRNAs, little is known about how they affect post-transcriptional regulation in a global scale.ResultsIn this study, we have analyzed CLIP datasets of 49 RBPs in HEK293 cells with the aim of understanding the interplay between RBPs and miRNAs in post-transcriptional regulation. Our results show that RBPs bind preferentially in conserved regulatory hotspots that frequently contain miRNA target sites. This organization facilitates the competition and cooperation among RBPs and the regulation of miRNA target site accessibility. In some cases RBP enrichment on target sites correlates with miRNA expression, suggesting coordination between the regulatory factors. However, in most cases, competition among factors is the most plausible interpretation of our data. Upon AGO2 knockdown, transcripts that contain such hotspots that overlap target sites of expressed miRNAs in 3’UTRs are significantly less up-regulated than transcripts without them, suggesting that RBP binding limits miRNA accessibility.ConclusionsWe show that RBP binding is concentrated in regulatory hotspots in 3’UTRs. The presence of these hotspots facilitates the interaction among post-transcriptional regulators, that interact or compete with each other under different conditions. These hotspots are enriched in genes with regulatory functions such as DNA binding and RNA binding. Taken together, our results suggest that hotspots are important regulatory regions that define an extra layer of auto-regulatory control of post-transcriptional regulation.

scholarly journals Characterization of the RNA-Binding Protein TcSgn1 in Trypanosoma cruzi

2021 ◽  
Vol 9 (5) ◽  
pp. 986
Author(s):  
Camila Oliveira ◽  
André P. Gerber ◽  
Samuel Goldenberg ◽  
Lysangela R. Alves
Keyword(s):  
Gene Expression ◽  
Trypanosoma Cruzi ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Binding Protein ◽  
Regulation Of Gene Expression ◽  
Rna Binding Protein ◽  
Transcriptional Level ◽  
Rna Recognition Motif ◽  
Ribonucleoprotein Complexes

RNA-binding proteins (RBPs) participate in several steps of post-transcriptional regulation of gene expression, such as splicing, messenger RNA transport, mRNA localization, and translation. Gene-expression regulation in trypanosomatids occurs primarily at the post-transcriptional level, and RBPs play important roles in the process. Here, we characterized the RBP TcSgn1, which contains one RNA recognition motif (RRM). TcSgn1 is a close ortholog of yeast Saccharomyces cerevisiae protein ScSgn1, which plays a role in translational regulation in the cytoplasm. We found that TcSgn1 in Trypanosoma cruzi is localized in the nucleus in exponentially growing epimastigotes. By performing immunoprecipitation assays of TcSgn1, we identified hundreds of mRNAs associated with the protein, a significant fraction of them coding for nucleic acids binding, transcription, and endocytosis proteins. In addition, we show that TcSgn1 is capable of interacting directly with the poly(A) tail of the mRNAs. The study of parasites under nutritional stress showed that TcSgn1 was localized in cytoplasmic granules in addition to localizing in the nucleus. Similar to ScSgn1, we observed that TcSgn1 also interacts with the PABP1 protein, suggesting that this protein may play a role in regulating gene expression in T. cruzi. Taken together, our results show that RNA-binding protein TcSgn1 is part of ribonucleoprotein complexes associated with nuclear functions, stress response, and RNA metabolism.

scholarly journals RNA-binding proteins La and HuR cooperatively modulate translation repression of PDCD4 mRNA

2020 ◽  
pp. jbc.RA120.014894
Author(s):  
Ravi Kumar ◽  
Dipak Kumar Poria ◽  
Partho Sarothi Ray
Keyword(s):  
Inflammatory Response ◽  
Chronic Inflammation ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Critical Role ◽  
Regulation Of Gene Expression ◽  
Mrna Translation ◽  
Suppressor Gene ◽  
Cooperative Action ◽  
Translation Repression

Post-transcriptional regulation of gene expression plays a critical role in controlling the inflammatory response. An uncontrolled inflammatory response results in chronic inflammation, often leading to tumorigenesis. Programmed cell death 4 (PDCD4) is a pro-inflammatory tumor-suppressor gene which helps to prevent the transition from chronic inflammation to cancer. PDCD4 mRNA translation is regulated by an interplay between the oncogenic microRNA miR-21 and the RNA-binding protein (RBP) HuR in response to LPS stimulation, but the role of other regulatory factors remain unknown. Here we report that the RBP Lupus antigen (La) interacts with the 3’UTR of PDCD4 mRNA and prevents miR-21-mediated translation repression. While LPS causes nuclear-cytoplasmic translocation of HuR, it enhances cellular La expression. Remarkably, La and HuR were found to bind cooperatively to the PDCD4 mRNA and mitigate miR-21-mediated translation repression. The cooperative action of La and HuR reduced cell proliferation and enhanced apoptosis, reversing the pro-oncogenic function of miR-21. Together, these observations demonstrate a cooperative interplay between two RBPs, triggered differentially by the same stimulus, which exerts a synergistic effect on PDCD4 expression and thereby helps maintain a balance between inflammation and tumorigenesis.

scholarly journals RNA-binding proteins and circadian rhythms in Arabidopsis thaliana

2001 ◽  
Vol 356 (1415) ◽  
pp. 1755-1759 ◽  
Author(s):  
Dorothee Staiger
Keyword(s):  
Arabidopsis Thaliana ◽  
Feedback Loop ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Transcriptional Level ◽  
Reverse Genetic ◽  
Genetic Approach ◽  
Circadian Oscillators ◽  
Clock Proteins ◽  
Reverse Genetic Approach

An Arabidopsis transcript preferentially expressed at the end of the daily light period codes for the RNA–binding protein At GRP7. A reverse genetic approach in Arabidopsis thaliana has revealed its role in the generation of circadian rhythmicity: At GRP7 is part of a negative feedback loop through which it influences the oscillations of its own transcript. Biochemical and genetic experiments indicate a mechanism for this autoregulatory circuit: At grp7 gene transcription is rhythmically activated by the circadian clock during the day. The At GPR7 protein accumulates with a certain delay and represses further accumulation of its transcript, presumably at the post–transcriptional level. In this respect, the At GRP7 feedback loop differs from known circadian oscillators in the fruitfly Drosophila and mammals based on oscillating clock proteins that repress transcription of their own genes with a 24 h rhythm. It is proposed that the At GRP7 feedback loop may act within an output pathway from the Arabidopsis clock.

scholarly journals The Role of Translation Initiation Regulation in Haematopoiesis

2012 ◽  
Vol 2012 ◽  
pp. 1-10 ◽  
Author(s):  
Godfrey Grech ◽  
Marieke von Lindern
Keyword(s):  
Gene Expression ◽  
Translation Initiation ◽  
Translational Control ◽  
Molecular Mechanisms ◽  
Rna Binding ◽  
Regulation Of Gene Expression ◽  
Mrna Translation ◽  
Translation Control ◽  
Haematological Disorders

Organisation of RNAs into functional subgroups that are translated in response to extrinsic and intrinsic factors underlines a relatively unexplored gene expression modulation that drives cell fate in the same manner as regulation of the transcriptome by transcription factors. Recent studies on the molecular mechanisms of inflammatory responses and haematological disorders indicate clearly that the regulation of mRNA translation at the level of translation initiation, mRNA stability, and protein isoform synthesis is implicated in the tight regulation of gene expression. This paper outlines how these posttranscriptional control mechanisms, including control at the level of translation initiation factors and the role of RNA binding proteins, affect hematopoiesis. The clinical relevance of these mechanisms in haematological disorders indicates clearly the potential therapeutic implications and the need of molecular tools that allow measurement at the level of translational control. Although the importance of miRNAs in translation control is well recognised and studied extensively, this paper will exclude detailed account of this level of control.

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