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 An Exclusively Nuclear RNA-Binding Protein Affects Asymmetric Localization of ASH1 mRNA and Ash1p in Yeast

2001 ◽  
Vol 153 (2) ◽  
pp. 307-318 ◽  
Author(s):  
Roy M. Long ◽  
Wei Gu ◽  
Xiuhua Meng ◽  
Graydon Gonsalvez ◽  
Robert H. Singer ◽  
...  
Keyword(s):  
Rna Binding ◽  
Rna Binding Proteins ◽  
Mrna Localization ◽  
Yeast Cells ◽  
Rna Structures ◽  
Nuclear Factors ◽  
Mother Cells ◽  
Ash1 Mrna

The localization of ASH1 mRNA to the distal tip of budding yeast cells is essential for the proper regulation of mating type switching in Saccharomyces cerevisiae. A localization element that is predominantly in the 3′-untranslated region (UTR) can direct this mRNA to the bud. Using this element in the three-hybrid in vivo RNA-binding assay, we identified a protein, Loc1p, that binds in vitro directly to the wild-type ASH1 3′-UTR RNA, but not to a mutant RNA incapable of localizing to the bud nor to several other mRNAs. LOC1 codes for a novel protein that recognizes double-stranded RNA structures and is required for efficient localization of ASH1 mRNA. Accordingly, Ash1p gets symmetrically distributed between daughter and mother cells in a loc1 strain. Surprisingly, Loc1p was found to be strictly nuclear, unlike other known RNA-binding proteins involved in mRNA localization which shuttle between the nucleus and the cytoplasm. We propose that efficient cytoplasmic ASH1 mRNA localization requires a previous interaction with specific nuclear factors.

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 Complex Minisatellite Rearrangements Generated in the Total or Partial Absence of Rad27/hFEN1 Activity Occur in a Single Generation and Are Rad51 and Rad52 Dependent

2006 ◽  
Vol 26 (17) ◽  
pp. 6675-6689 ◽  
Author(s):  
Judith Lopes ◽  
Cyril Ribeyre ◽  
Alain Nicolas
Keyword(s):  
Pedigree Analysis ◽  
Model System ◽  
Yeast Cells ◽  
Single Generation ◽  
Daughter Cells ◽  
Double Deletion ◽  
Mother And Daughter ◽  
Complex Events ◽  
High Degree ◽  
Insight Into

ABSTRACT Genomes contain tandem repeat blocks that are at risk of expansion or contraction. The mechanisms of destabilization of the human minisatellite CEB1 (arrays of 36- to 43-bp repeats) were investigated in a previously developed model system, in which CEB1-0.6 (14 repeats) and CEB1-1.8 (42 repeats) alleles were inserted into the genome of Saccharomyces cerevisiae. As in human cells, CEB1 is stable in mitotically growing yeast cells but is frequently rearranged in the absence of the Rad27/hFEN1 protein involved in Okazaki fragments maturation. To gain insight into this mode of destabilization, the CEB1-1.8 and CEB1-0.6 human alleles and 47 rearrangements derived from a CEB1-1.8 progenitor in rad27Δ cells were sequenced. A high degree of polymorphism of CEB1 internal repeats was observed, attesting to a large variety of homology-driven rearrangements. Simple deletion, double deletion, and highly complex events were observed. Pedigree analysis showed that all rearrangements, even the most complex, occurred in a single generation and were inherited equally by mother and daughter cells. Finally, the rearrangement frequency was found to increase with array size, and partial complementation of the rad27Δ mutation by hFEN1 demonstrated that the production of novel CEB1 alleles is Rad52 and Rad51 dependent. Instability can be explained by an accumulation of unresolved flap structures during replication, leading to the formation of recombinogenic lesions and faulty repair, best understood by homology-dependent synthesis-strand displacement and annealing.

Development of an RNA-protein crosslinker to capture protein interactions with diverse RNA structures in cells

RNA ◽  
2021 ◽  
pp. rna.078896.121
Author(s):  
Yan Han ◽  
Xuzhen Guo ◽  
Tiancai Zhang ◽  
Jiangyun Wang ◽  
Keqiong Ye
Keyword(s):  
Protein Interactions ◽  
Rna Structure ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
High Specificity ◽  
Ester Group ◽  
Yeast Cells ◽  
Primary Amines ◽  
Low Efficiency ◽  
In Cells

Characterization of RNA-protein interaction is fundamental for understanding metabolism and function of RNA. UV crosslinking has been widely used to map the targets of RNA-binding proteins, but is limited by low efficiency, requirement for zero-distance contact and biases for single-stranded RNA structure and certain residues of RNA and protein. Here, we report the development of an RNA-protein crosslinker (AMT-NHS) composed of a psoralen derivative and an N-hydroxysuccinimide ester group, which react with RNA bases and primary amines of protein, respectively. We show that AMT-NHS can penetrate into living yeast cells and crosslink Cbf5 to H/ACA snoRNAs with high specificity. The crosslinker induced different crosslinking patterns than UV and targeted both single- and double-stranded regions of RNA. The crosslinker provides a new tool to capture diverse RNA-protein interactions in cells.

Roles for myosin Va in RNA transport and turnover

2012 ◽  
Vol 40 (6) ◽  
pp. 1416-1420 ◽  
Author(s):  
Mary W. McCaffrey ◽  
Andrew J. Lindsay
Keyword(s):  
Rna Binding ◽  
Rna Binding Proteins ◽  
Class V ◽  
Processing Bodies ◽  
Surface Receptors ◽  
P Bodies ◽  
Myosin Va ◽  
Myosin Vb ◽  
Actin Cables ◽  
The Brain

Mammals express three class V myosins. Myosin Va is widely expressed, but enriched in the brain, testes and melanocytes, myosin Vb is expressed ubiquitously, and myosin Vc is believed to be epithelium-specific. Myosin Va is the best characterized of the three and plays a key role in the transport of cargo to the plasma membrane. Its cargo includes cell-surface receptors, pigment and organelles such as the endoplasmic reticulum. It is also emerging that RNA and RNA-BPs (RNA-binding proteins) make up another class of myosin Va cargo. It has long been established that the yeast class V myosin, Myo4p, transports mRNAs along actin cables into the growing bud, and now several groups have reported a similar role for class V myosins in higher eukaryotes. Myosin Va has also been implicated in the assembly and maintenance of P-bodies (processing bodies), cytoplasmic foci that are involved in mRNA storage and degradation. The present review examines the evidence that myosin Va plays a role in the transport and turnover of mRNA.

scholarly journals Competitive binding of CUGBP1 and HuR to occludin mRNA controls its translation and modulates epithelial barrier function

2013 ◽  
Vol 24 (2) ◽  
pp. 85-99 ◽  
Author(s):  
Ting-Xi Yu ◽  
Jaladanki N. Rao ◽  
Tongtong Zou ◽  
Lan Liu ◽  
Lan Xiao ◽  
...  
Keyword(s):  
Barrier Function ◽  
Untranslated Region ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Cell Monolayer ◽  
Intestinal Epithelial ◽  
Processing Bodies ◽  
Epithelial Barrier Function ◽  
P Bodies ◽  
The Stability

RNA-binding proteins CUG-binding protein 1 (CUGBP1) and HuR are highly expressed in epithelial tissues and modulate the stability and translation of target mRNAs. Here we present evidence that CUGBP1 and HuR jointly regulate the translation of occludin and play a crucial role in the maintenance of tight junction (TJ) integrity in the intestinal epithelial cell monolayer. CUGBP1 and HuR competed for association with the same occludin 3′-untranslated region element and regulated occludin translation competitively and in opposite directions. CUGBP1 overexpression decreased HuR binding to occludin mRNA, repressed occludin translation, and compromised the TJ barrier function, whereas HuR overexpression inhibited CUGBP1 association with occludin mRNA and promoted occludin translation, thereby enhancing the barrier integrity. Repression of occludin translation by CUGBP1 was due to the colocalization of CUGBP1 and tagged occludin RNA in processing bodies (P-bodies), and this colocalization was prevented by HuR overexpression. These findings indicate that CUGBP1 represses occludin translation by increasing occludin mRNA recruitment to P-bodies, whereas HuR promotes occludin translation by blocking occludin mRNA translocation to P-bodies via the displacement of CUGBP1.

scholarly journals Stress Granule-Mediated Oxidized RNA Decay in P-Body: Hypothetical Role of ADAR1, Tudor-SN, and STAU1

2021 ◽  
Vol 8 ◽  
Author(s):  
Ravi Kumar Alluri ◽  
Zhongwei Li ◽  
Keith R. McCrae
Keyword(s):  
Oxidative Stress ◽  
Inverted Repeat ◽  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Relevant Literature ◽  
Stress Granule ◽  
P Bodies ◽  
Docking Mechanism

Reactive oxygen species (ROS) generated under oxidative stress (OS) cause oxidative damage to RNA. Recent studies have suggested a role for oxidized RNA in several human disorders. Under the conditions of oxidative stress, mRNAs released from polysome dissociation accumulate and initiate stress granule (SG) assembly. SGs are highly enriched in mRNAs, containing inverted repeat (IR) Alus in 3′ UTRs, AU-rich elements, and RNA-binding proteins. SGs and processing bodies (P-bodies) transiently interact through a docking mechanism to allow the exchange of RNA species. However, the types of RNA species exchanged, and the mechanisms and outcomes of exchange are still unknown. Specialized RNA-binding proteins, including adenosine deaminase acting on RNA (ADAR1-p150), with an affinity toward inverted repeat Alus, and Tudor staphylococcal nuclease (Tudor-SN) are specifically recruited to SGs under OS along with an RNA transport protein, Staufen1 (STAU1), but their precise biochemical roles in SGs and SG/P-body docking are uncertain. Here, we critically review relevant literature and propose a hypothetical mechanism for the processing and decay of oxidized-RNA in SGs/P-bodies, as well as the role of ADAR1-p150, Tudor-SN, and STAU1.

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 An Algorithm to Quantify Inducible Protein Condensates In Eukaryotic Cells

2021 ◽  
Author(s):  
Jeremy C Hunn ◽  
Katherine M. Hutchinson ◽  
Joshua B Kelley ◽  
Daniel Reines
Keyword(s):  
Rna Binding ◽  
Rna Binding Proteins ◽  
Strain Differences ◽  
Growth Defect ◽  
Protein Distribution ◽  
Granule Formation ◽  
P Bodies ◽  
Subcellular Compartments ◽  
Manual Counting ◽  
Inducible Protein

Reorganization of cellular proteins into subcellular compartments, such as the rearrangement of RNA-binding proteins into cytoplasmic stress granules and P-bodies, is a well-recognized, widely studied physiological process currently under intense investigation. Using the assembly of a novel, inducible, nuclear granule formed from the east RNA-binding transcription termination factors Nab3 and Nrd1, we present a freely-accessible, high-throughput and unbiased algorithm written in MATLAB that detects and measures protein distribution, partitioning, and sequestration into subcellular compartments captured by fluorescence microscopy; an invaluable advancement to current image analysis methods which utilize experiment-specific custom scripts or subjective manual counting. Employing our algorithm, we quantified thousands of cells, ensuring rigorous examination of Nab3 granule formation across strains with reproducible statistical analyses. We document strain differences in Nab3 granule formation and an associated growth defect. Additionally, we applied our algorithm to immunofluorescent images of the inducible polymerization into filaments of an enzyme in human cells, demonstrating the algorithms versatility and adaptability.

scholarly journals Human CPR (Cell Cycle Progression Restoration) Genes Impart a Far– Phenotype on Yeast Cells

Genetics ◽  
1997 ◽  
Vol 147 (3) ◽  
pp. 1063-1076 ◽  
Author(s):  
Michael C Edwards ◽  
Nanette Liegeois ◽  
Joe Horecka ◽  
Ronald A DePinho ◽  
George F Sprague ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Cell Cycle Progression ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Growth Control ◽  
Yeast Cells ◽  
G1 Arrest ◽  
Mating Pheromone ◽  
Cycle Progression ◽  
Yeast Genes

Regulated cell cycle progression depends on the proper integration of growth control pathways with the basic cell cycle machinery. While many of the central molecules such as cyclins, CDKs, and CKIs are known, and many of the kinases and phosphatases that modify the CDKs have been identified, little is known about the additional layers of regulation that impinge upon these molecules. To identify new regulators of cell proliferation, we have selected for human and yeast cDNAs that when overexpressed were capable of specifically overcoming G1 arrest signals from the cell cycle branch of the mating pheromone pathway, while still maintaining the integrity of the transcriptional induction branch. We have identified 13 human CPR (cell cycle progression restoration) genes and 11 yeast OPY (overproduction-induced pheromone-resistant yeast) genes that specifically block the G1 arrest by mating pheromone. The CPR genes represent a variety of biochemical functions including a new cyclin, a tumor suppressor binding protein, chaperones, transcription factors, translation factors, RNA-binding proteins, as well as novel proteins. Several CPR genes require individual CLNs to promote pheromone resistance and those that require CLN3 increase the basal levels of Cln3 protein. Moreover, several of the yeast OPY genes have overlapping functions with the human CPR genes, indicating a possible conservation of roles.

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