scholarly journals Processing bodies control the selective translation for optimal development of Arabidopsis young seedlings

2019 ◽  
Vol 116 (13) ◽  
pp. 6451-6456 ◽  
Author(s):  
Geng-Jen Jang ◽  
Jun-Yi Yang ◽  
Hsu-Liang Hsieh ◽  
Shu-Hsing Wu
Keyword(s):  
Translational Repression ◽  
Light Conditions ◽  
Wild Type ◽  
Translation Control ◽  
Processing Bodies ◽  
P Bodies ◽  
Plant Seeds ◽  
Before And After ◽  
Selective Translation ◽  
Specific Mrnas

Germinated plant seeds buried in soil undergo skotomorphogenic development before emergence to reach the light environment. Young seedlings transitioning from dark to light undergo photomorphogenic development. During photomorphogenesis, light alters the transcriptome and enhances the translation of thousands of mRNAs during the dark-to-light transition inArabidopsisyoung seedlings. About 1,500 of these mRNAs have comparable abundance before and after light treatment, which implies widespread translational repression in dark-grown seedlings. Processing bodies (p-bodies), the cytoplasmic granules found in diverse organisms, can balance the storage, degradation, and translation of mRNAs. However, the function of p-bodies in translation control remains largely unknown in plants. Here we found that anArabidopsismutant defective in p-body formation (Decapping 5;dcp5-1) showed reduced fitness under both dark and light conditions. Comparative transcriptome and translatome analyses of wild-type anddcp5-1seedlings revealed that p-bodies can attenuate the premature translation of specific mRNAs in the dark, including those encoding enzymes for protochlorophyllide synthesis and PIN-LIKES3 for auxin-dependent apical hook opening. When the seedlings protrude from soil, light perception by photoreceptors triggers a reduced accumulation of p-bodies to release the translationally stalled mRNAs for active translation of mRNAs encoding proteins needed for photomorphogenesis. Our data support a key role for p-bodies in translation repression, an essential mechanism for proper skotomorphogenesis and timely photomorphogenesis in seedlings.

On track with P-bodies

2010 ◽  
Vol 38 (1) ◽  
pp. 242-251 ◽  
Author(s):  
Meeta Kulkarni ◽  
Sevim Ozgur ◽  
Georg Stoecklin
Keyword(s):  
Light Microscopy ◽  
Mrna Decay ◽  
Molecular Level ◽  
Somatic Cells ◽  
Present Review ◽  
Dual Function ◽  
Processing Bodies ◽  
P Bodies ◽  
Specific Mrnas ◽  
Transient Interactions

P-bodies (processing bodies) are cytoplasmic foci visible by light microscopy in somatic cells of vertebrate and invertebrate origin as well as in yeast, plants and trypanosomes. At the molecular level, P-bodies are dynamic aggregates of specific mRNAs and proteins that serve a dual function: first, they harbour mRNAs that are translationally silenced, and such mRNA can exit again from P-bodies to re-engage in translation. Secondly, P-bodies recruit mRNAs that are targeted for deadenylation and degradation by the decapping/Xrn1 pathway. Whereas certain proteins are core constituents of P-bodies, others involved in recognizing short-lived mRNAs can only be trapped in P-bodies when mRNA decay is attenuated. This reflects the very transient interactions by which many proteins associate with P-bodies. In the present review, we summarize recent findings on the function, assembly and motility of P-bodies. An updated list of proteins and RNAs that localize to P-bodies will help in keeping track of this fast-growing field.

RNA granules and cytoskeletal links

2014 ◽  
Vol 42 (4) ◽  
pp. 1206-1210 ◽  
Author(s):  
Dipen Rajgor ◽  
Catherine M. Shanahan
Keyword(s):  
Mammalian Cells ◽  
Dynamic Properties ◽  
Translational Repression ◽  
Processing Bodies ◽  
P Bodies ◽  
Rna Granules ◽  
Messenger Ribonucleoprotein ◽  
Cytoskeletal Networks ◽  
And Control ◽  
Lower Eukaryote

In eukaryotic cells, non-translating mRNAs can accumulate into cytoplasmic mRNP (messenger ribonucleoprotein) granules such as P-bodies (processing bodies) and SGs (stress granules). P-bodies contain the mRNA decay and translational repression machineries and are ubiquitously expressed in mammalian cells and lower eukaryote species including Saccharomyces cerevisiae, Drosophila melanogaster and Caenorhabditis elegans. In contrast, SGs are only detected during cellular stress when translation is inhibited and form from aggregates of stalled pre-initiation complexes. SGs and P-bodies are related to NGs (neuronal granules), which are essential in the localization and control of mRNAs in neurons. Importantly, RNA granules are linked to the cytoskeleton, which plays an important role in mediating many of their dynamic properties. In the present review, we discuss how P-bodies, SGs and NGs are linked to cytoskeletal networks and the importance of these linkages in maintaining localization of their RNA cargoes.

scholarly journals RGG-motif protein Sbp1 is required for Processing body (P-body) disassembly

2021 ◽  
Author(s):  
Raju Roy ◽  
Ishwarya Achappa Kuttanda ◽  
Nupur Bhatter ◽  
Purusharth I Rajyaguru
Keyword(s):  
Mrna Decay ◽  
Glucose Deprivation ◽  
Low Complexity ◽  
Wild Type ◽  
Processing Bodies ◽  
P Bodies ◽  
Rna Granules ◽  
Processing Body ◽  
Mrna Fate

AbstractRNA granules are conserved mRNP complexes that play an important role in determining mRNA fate by affecting translation repression and mRNA decay. Processing bodies (P-bodies) harbor enzymes responsible for mRNA decay and proteins involved in modulating translation. Although many proteins have been identified to play a role in P-body assembly, a bonafide disassembly factor remains unknown. In this report, we identify RGG-motif translation repressor protein Sbp1 as a disassembly factor of P-bodies. Disassembly of Edc3 granules but not the Pab1 granules (a conserved stress granule marker) that arise upon sodium azide and glucose deprivation stress are defective in Δsbp1. Disassembly of other P-body proteins such as Dhh1 and Scd6 is also defective in Δsbp1. Complementation experiments suggest that the wild type Sbp1 but not an RGG-motif deletion mutant rescues the Edc3 granule disassembly defect in Δsbp1. We observe that purified Edc3 forms assemblies, which is promoted by the presence of RNA and NADH. Strikingly, addition of purified Sbp1 leads to significantly decreased Edc3 assemblies. Although low complexity sequences have been in general implicated in assembly, our results reveal the role of RGG-motif (a low-complexity sequence) in the disassembly of P-bodies.

Yeast mRNA localization: protein asymmetry, organelle localization and response to stress

2014 ◽  
Vol 42 (4) ◽  
pp. 1256-1260 ◽  
Author(s):  
Mariavittoria Pizzinga ◽  
Mark P. Ashe
Keyword(s):  
Gene Expression ◽  
Transcriptional Control ◽  
Mrna Localization ◽  
Translational Repression ◽  
Yeast Saccharomyces Cerevisiae ◽  
Processing Bodies ◽  
Control Of Gene Expression ◽  
P Bodies ◽  
Response To Stress ◽  
Kinetics Of

The localization of mRNA forms a key facet of the post-transcriptional control of gene expression and recent evidence suggests that it may be considerably more widespread than previously anticipated. For example, defined mRNA-containing granules can be associated with translational repression or activation. Furthermore, mRNA P-bodies (processing bodies) harbour much of the mRNA decay machinery and stress granules are thought to play a role in mRNA storage. In the present review, we explore the process of mRNA localization in the yeast Saccharomyces cerevisiae, examining connections between organellar mRNA localization and the response to stress. We also review recent data suggesting that even where there is a global relocalization of mRNA, the specificity and kinetics of this process can be regulated.

Pat1 proteins: a life in translation, translation repression and mRNA decay

2010 ◽  
Vol 38 (6) ◽  
pp. 1602-1607 ◽  
Author(s):  
Aline Marnef ◽  
Nancy Standart
Keyword(s):  
Gene Expression ◽  
Transcriptional Control ◽  
Mrna Decay ◽  
Current Knowledge ◽  
Translational Repression ◽  
Processing Bodies ◽  
P Bodies ◽  
Expression Control ◽  
Gene Expression Control ◽  
Sequential Binding

Pat1 proteins are conserved across eukaryotes. Vertebrates have evolved two Pat1 proteins paralogues, whereas invertebrates and yeast only possess one such protein. Despite their lack of known domains or motifs, Pat1 proteins are involved in several key post-transcriptional mechanisms of gene expression control. In yeast, Pat1p interacts with translating mRNPs (messenger ribonucleoproteins), and is responsible for translational repression and decapping activation, ultimately leading to mRNP degradation. Drosophila HPat and human Pat1b (PatL1) proteins also have conserved roles in the 5′→3′ mRNA decay pathway. Consistent with their functions in silencing gene expression, Pat1 proteins localize to P-bodies (processing bodies) in yeast, Drosophila, Caenorhabditis elegans and human cells. Altogether, Pat1 proteins may act as scaffold proteins allowing the sequential binding of repression and decay factors on mRNPs, eventually leading to their degradation. In the present mini-review, we present the current knowledge on Pat1 proteins in the context of their multiple functions in post-transcriptional control.

scholarly journals Human UPF1 Participates in Small RNA-Induced mRNA Downregulation

2009 ◽  
Vol 29 (21) ◽  
pp. 5789-5799 ◽  
Author(s):  
Hua Jin ◽  
Mi Ra Suh ◽  
Jinju Han ◽  
Kyu-Hyeon Yeom ◽  
Yoontae Lee ◽  
...  
Keyword(s):  
Small Rna ◽  
Rna Silencing ◽  
Translational Repression ◽  
Helicase Domain ◽  
Small Interfering Rnas ◽  
Wild Type ◽  
Processing Bodies ◽  
Mirna Targets ◽  
Underlying Mechanisms ◽  
Argonaute 1

ABSTRACT MicroRNAs (miRNAs) are endogenous antisense regulators that trigger endonucleolytic mRNA cleavage, translational repression, and/or mRNA decay. miRNA-mediated gene regulation is important for numerous biological pathways, yet the underlying mechanisms are still under rigorous investigation. Here we identify human UPF1 (hUPF1) as a protein that contributes to RNA silencing. When hUPF1 is knocked down, miRNA targets are upregulated. The depletion of hUPF1 also increases the off-target messages of small interfering RNAs (siRNAs), which are imperfectly complementary to transfected siRNAs. Conversely, when overexpressed, wild-type hUPF1 downregulates miRNA targets. The helicase domain mutant of hUPF1 fails to suppress miRNA targets. hUPF1 interacts with human Argonaute 1 (hAGO1) and hAGO2 and colocalizes with hAGO1 and hAGO2 in processing bodies, which are known to be the sites for translational repression and mRNA destruction. We further find that the amounts of target messages bound to hAGO2 are reduced when hUPF1 is depleted. Our data thus suggest that hUPF1 may participate in RNA silencing by facilitating the binding of the RNA-induced silencing complex to the target and by accelerating the decay of the mRNA.

scholarly journals IP6K1 upregulates the formation of processing bodies by influencing protein-protein interactions on the mRNA cap

2021 ◽  
Author(s):  
Akruti Shah ◽  
Rashna Bhandari
Keyword(s):  
Protein Interactions ◽  
Inositol Phosphate ◽  
Translational Repression ◽  
Protein Protein Interactions ◽  
Processing Bodies ◽  
Activator Proteins ◽  
Mrna Decapping ◽  
P Bodies ◽  
Decapping Enzyme ◽  
Translational Suppression

Inositol hexakisphosphate kinase 1 (IP6K1) is a small molecule kinase that catalyzes the conversion of the inositol phosphate IP6 to 5-IP7. We show that IP6K1 acts independent of its catalytic activity to upregulate the formation of processing bodies (P-bodies), which are cytoplasmic ribonucleoprotein granules that store translationally repressed mRNA. IP6K1 does not localize to P-bodies, but instead binds to ribosomes, where it interacts with the mRNA decapping complex - the scaffold protein EDC4, activator proteins DCP1A/B, decapping enzyme DCP2, and RNA helicase DDX6. Along with its partner 4E-T, DDX6 is known to nucleate protein-protein interactions on the 5’ mRNA cap to facilitate P-body formation. IP6K1 binds the translation initiation complex eIF4F on the mRNA cap, augmenting the interaction of DDX6 with 4E-T and the cap binding protein eIF4E. Cells with reduced IP6K1 show downregulated microRNA-mediated translational suppression and increased stability of DCP2-regulated transcripts. Our findings unveil IP6K1 as a novel facilitator of proteome remodelling on the mRNA cap, tipping the balance in favour of translational repression over initiation, thus leading to P-body assembly.

Ultrastructure of Melanin Formation in Curvularia sp., Alternaria sp., and Drechslera Sorokiniana

1977 ◽  
Vol 35 ◽  
pp. 398-399
Author(s):  
M. H. Wheeler ◽  
W. J. Tolmsoff ◽  
A. A. Bell
Keyword(s):  
Potassium Phosphate ◽  
Thielaviopsis Basicola ◽  
Wild Type ◽  
Potassium Phosphate Buffer ◽  
Transmission Microscopy ◽  
Electron Transmission ◽  
Melanin Formation ◽  
Before And After ◽  
Alternaria Sp ◽  
Electron Transmission Microscopy

(+)-Scytalone [3,4-dihydro-3,6,8-trihydroxy-l-(2Hj-naphthalenone] and 1,8-di- hydroxynaphthalene (DHN) have been proposed as intermediates of melanin synthesis in the fungi Verticillium dahliae (1, 2, 3, 4) and Thielaviopsis basicola (4, 5). Scytalone is enzymatically dehydrated by V. dahliae to 1,3,8-trihydroxynaphthalene which is then reduced to (-)-vermelone [(-)-3,4- dihydro-3,8-dihydroxy-1(2H)-naphthalenone]. Vermelone is subsequently dehydrated to DHN which is enzymatically polymerized to melanin.Melanin formation in Curvularia sp., Alternaria sp., and Drechslera soro- kiniana was examined by light and electron-transmission microscopy. Wild-type isolates of each fungus were compared with albino mutants before and after treatment with 1 mM scytalone or 0.1 mM DHN in 50 mM potassium phosphate buffer, pH 7.0. Both chemicals were converted to dark pigments in the walls of hyphae and conidia of the albino mutants. The darkened cells were similar in appearance to corresponding cells of the wild types under the light microscope.

scholarly journals RNA decay in processing bodies is indispensable for adipogenesis

2021 ◽  
Vol 12 (4) ◽  
Author(s):  
Ryotaro Maeda ◽  
Daisuke Kami ◽  
Akira Shikuma ◽  
Yosuke Suzuki ◽  
Toshihiko Taya ◽  
...  
Keyword(s):  
Lipid Droplets ◽  
Adipogenic Differentiation ◽  
Negative Regulator ◽  
Translational Repression ◽  
Rna Decay ◽  
Significant Suppression ◽  
Intracellular Lipid ◽  
Processing Bodies ◽  
Binding Partner ◽  
The Stability

AbstractThe RNA decay pathway plays key regulatory roles in cell identities and differentiation processes. Although adipogenesis is transcriptionally and epigenetically regulated and has been thoroughly investigated, how RNA metabolism that contributes to the stability of phenotype-shaping transcriptomes participates in differentiation remains elusive. In this study, we investigated Ddx6, an essential component of processing bodies (PBs) that executes RNA decay and translational repression in the cytoplasm and participates in the cellular transition of reprogramming. Upon adipogenic induction, Ddx6 dynamically accumulated to form PBs with a binding partner, 4E-T, at the early phase prior to emergence of intracellular lipid droplets. In contrast, preadipocytes with Ddx6 knockout (KO) or 4E-T knockdown (KD) failed to generate PBs, resulting in significant suppression of adipogenesis. Transcription factors related to preadipocytes and negative regulators of adipogenesis that were not expressed under adipogenic stimulation were maintained in Ddx6-KO and 4E-T-KD preadipocytes under adipogenic induction. Elimination of Dlk1, a major negative regulator of adipogenesis, in 3T3L1 Ddx6-KO cells did not restore adipogenic differentiation capacity to any extent. Similar to murine cells, human primary mesenchymal stem cells, which can differentiate into adipocytes upon stimulation with adipogenic cocktails, required DDX6 to maturate into adipocytes. Therefore, RNA decay of the entire parental transcriptome, rather than removal of a strong negative regulator, could be indispensable for adipogenesis.

scholarly journals A microfluidic device enabling drug resistance analysis of leukemia cells via coupled dielectrophoretic detection and impedimetric counting

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Yağmur Demircan Yalçın ◽  
Taylan Berkin Töral ◽  
Sertan Sukas ◽  
Ender Yıldırım ◽  
Özge Zorlu ◽  
...  
Keyword(s):  
Drug Resistance ◽  
K562 Cells ◽  
Leukemia Cells ◽  
Drug Resistant ◽  
Wild Type ◽  
Gene Expressions ◽  
Before And After ◽  
The Difference ◽  
Selection Of ◽  
Resistant Cells

AbstractWe report the development of a lab-on-a-chip system, that facilitates coupled dielectrophoretic detection (DEP-D) and impedimetric counting (IM-C), for investigating drug resistance in K562 and CCRF-CEM leukemia cells without (immuno) labeling. Two IM-C units were placed upstream and downstream of the DEP-D unit for enumeration, respectively, before and after the cells were treated in DEP-D unit, where the difference in cell count gave the total number of trapped cells based on their DEP characteristics. Conductivity of the running buffer was matched the conductivity of cytoplasm of wild type K562 and CCRF-CEM cells. Results showed that DEP responses of drug resistant and wild type K562 cells were statistically discriminative (at p = 0.05 level) at 200 mS/m buffer conductivity and at 8.6 MHz working frequency of DEP-D unit. For CCRF-CEM cells, conductivity and frequency values were 160 mS/m and 6.2 MHz, respectively. Our approach enabled discrimination of resistant cells in a group by setting up a threshold provided by the conductivity of running buffer. Subsequent selection of drug resistant cells can be applied to investigate variations in gene expressions and occurrence of mutations related to drug resistance.

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