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.

scholarly journals IP6K1 upregulates the formation of processing bodies by promoting proteome remodeling on the mRNA cap

2020 ◽  
Author(s):  
Akruti Shah ◽  
Rashna Bhandari
Keyword(s):  
Protein Interactions ◽  
Inositol Phosphate ◽  
Binding Protein ◽  
Mrna Translation ◽  
Rna Helicase ◽  
Scaffolding Protein ◽  
Processing Bodies ◽  
Activator Proteins ◽  
Mrna Decapping ◽  
P Bodies

AbstractInositol hexakisphosphate kinases (IP6Ks) are ubiquitously expressed small molecule kinases that catalyze the conversion of the inositol phosphate IP6 to 5-IP7. IP6Ks have been reported to influence cellular functions by protein-protein interactions independent of their enzymatic activity. Here, we show that IP6K1 regulates the formation of processing bodies (P-bodies), which are cytoplasmic ribonucleoprotein granules that serve as sites for storage of translationally repressed mRNA. Cells with reduced levels of IP6K1 display a dramatic reduction in the number of P-bodies, which can be restored by the expression of active or catalytically inactive IP6K1. IP6K1 does not localize to P-bodies, but instead facilitates the formation of P-bodies by promoting translation suppression. We demonstrate that IP6K1 is present on ribosomes, where it interacts with proteins that constitute the mRNA decapping complex – the scaffold protein EDC4, activator proteins DCP1A/B, and the decapping enzyme DCP2. IP6K1 also interacts with components of the eIF4F translation initiation complex – the scaffolding protein eIF4G1, the RNA helicase eIF4A2, and the cap binding protein eIF4E. The RNA helicase DDX6 and the eIF4E binding protein 4E-T are known to promote translation suppression to facilitate P-body formation. We show that IP6K1 binds to DDX6 and promotes the interaction of DDX6 and 4E-T with the cap binding protein eIF4E, and also enhances the binding between DDX6 and EDC4, thus acting to suppress mRNA translation and promote mRNA decapping. Our findings unveil IP6K1 as a novel facilitator of proteome remodelling on the mRNA cap, tipping the balance in favour of translation repression over initiation, and thus leading to the formation of P-bodies.

scholarly journals Biomolecular condensates amplify mRNA decapping by coupling protein interactions with conformational changes in Dcp1/Dcp2

2020 ◽  
Author(s):  
Ryan W. Tibble ◽  
Anaïs Depaix ◽  
Joanna Kowalska ◽  
Jacek Jemielity ◽  
John D. Gross
Keyword(s):  
Conformational Change ◽  
Conformational Changes ◽  
Protein Interactions ◽  
Mrna Degradation ◽  
Enzyme Activation ◽  
List Type ◽  
Protein Protein Interactions ◽  
Mrna Decapping ◽  
P Bodies

SUMMARYCells organize biochemical processes into biological condensates. P-bodies are cytoplasmic condensates enriched in factors important for mRNA degradation. P-bodies have been identified as sites of both mRNA storage and decay, but how these opposing outcomes may be achieved in condensates is unresolved. A critical step in mRNA degradation is removal of the 5’-7-methylguanosine cap by Dcp1/Dcp2, which is highly enriched in P-bodies. Dcp1/Dcp2 activity is repressed in condensates in vitro and requires the activator Edc3. Activation of decapping is amplified in condensates relative to the surrounding solution due to stabilization of an autoinhibited state in Dcp1/Dcp2. Edc3 couples a conformational change in the Dcp1/Dcp2 active site with alteration of the protein-protein interactions driving phase separation to activate decapping in condensates. The composition-dependent regulation of enzyme activity in condensates occurs over length scales ranging from microns to Ångstroms and may control the functional state of P-bodies and related phase-separated compartments.HIGHLIGHTSmRNA decapping in droplets is repressedCatalytically inert droplets are activated by a change in condensate compositionA switch in enzymatic activity requires a conformational change in condensatesCondensates amplify enzyme activation compared to surrounding solution

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 Edc3p and a glutamine/asparagine-rich domain of Lsm4p function in processing body assembly in Saccharomyces cerevisiae

2007 ◽  
Vol 179 (3) ◽  
pp. 437-449 ◽  
Author(s):  
Carolyn J. Decker ◽  
Daniela Teixeira ◽  
Roy Parker
Keyword(s):  
Protein Interactions ◽  
Messenger Rna ◽  
Mrna Decay ◽  
Processing Bodies ◽  
P Bodies ◽  
Rna Granules ◽  
Rich Domain ◽  
Cytoplasmic Rna ◽  
Processing Body ◽  
The Individual

Processing bodies (P-bodies) are cytoplasmic RNA granules that contain translationally repressed messenger ribonucleoproteins (mRNPs) and messenger RNA (mRNA) decay factors. The physical interactions that form the individual mRNPs within P-bodies and how those mRNPs assemble into larger P-bodies are unresolved. We identify direct protein interactions that could contribute to the formation of an mRNP complex that consists of core P-body components. Additionally, we demonstrate that the formation of P-bodies that are visible by light microscopy occurs either through Edc3p, which acts as a scaffold and cross-bridging protein, or via the “prionlike” domain in Lsm4p. Analysis of cells defective in P-body formation indicates that the concentration of translationally repressed mRNPs and decay factors into microscopically visible P-bodies is not necessary for basal control of translation repression and mRNA decay. These results suggest a stepwise model for P-body assembly with the initial formation of a core mRNA–protein complex that then aggregates through multiple specific mechanisms.

scholarly journals Protection of specific maternal messenger RNAs by the P body protein CGH-1 (Dhh1/RCK) during Caenorhabditis elegans oogenesis

2008 ◽  
Vol 182 (3) ◽  
pp. 543-557 ◽  
Author(s):  
Peter R. Boag ◽  
Arzu Atalay ◽  
Stacey Robida ◽  
Valerie Reinke ◽  
T. Keith Blackwell
Keyword(s):  
Caenorhabditis Elegans ◽  
Messenger Rnas ◽  
Processing Bodies ◽  
Body Protein ◽  
Translation Inhibition ◽  
Mrna Decapping ◽  
P Bodies ◽  
Somatic Tissues ◽  
Translational Regulators ◽  
Dependent Mechanism

During oogenesis, numerous messenger RNAs (mRNAs) are maintained in a translationally silenced state. In eukaryotic cells, various translation inhibition and mRNA degradation mechanisms congregate in cytoplasmic processing bodies (P bodies). The P body protein Dhh1 inhibits translation and promotes decapping-mediated mRNA decay together with Pat1 in yeast, and has been implicated in mRNA storage in metazoan oocytes. Here, we have investigated in Caenorhabditis elegans whether Dhh1 and Pat1 generally function together, and how they influence mRNA sequestration during oogenesis. We show that in somatic tissues, the Dhh1 orthologue (CGH-1) forms Pat1 (patr-1)-dependent P bodies that are involved in mRNA decapping. In contrast, during oogenesis, CGH-1 forms patr-1–independent mRNA storage bodies. CGH-1 then associates with translational regulators and a specific set of maternal mRNAs, and prevents those mRNAs from being degraded. Our results identify somatic and germ cell CGH-1 functions that are distinguished by the involvement of PATR-1, and reveal that during oogenesis, numerous translationally regulated mRNAs are specifically protected by a CGH-1–dependent mechanism.

Identification of Edc3p as an Enhancer of mRNA Decapping in Saccharomyces cerevisiae

Genetics ◽  
2004 ◽  
Vol 166 (2) ◽  
pp. 729-739
Author(s):  
Meenakshi Kshirsagar ◽  
Roy Parker
Keyword(s):  
Mrna Decay ◽  
Temperature Sensitive ◽  
Early Step ◽  
Major Pathway ◽  
Mrna Decapping ◽  
P Bodies ◽  
Exonuclease Digestion ◽  
Decapping Enzyme ◽  
Two Hybrid ◽  
New Protein

Abstract The major pathway of mRNA decay in yeast initiates with deadenylation, followed by mRNA decapping and 5′-3′ exonuclease digestion. An in silico approach was used to identify new proteins involved in the mRNA decay pathway. One such protein, Edc3p, was identified as a conserved protein of unknown function having extensive two-hybrid interactions with several proteins involved in mRNA decapping and 5′-3′ degradation including Dcp1p, Dcp2p, Dhh1p, Lsm1p, and the 5′-3′ exonuclease, Xrn1p. We show that Edc3p can stimulate mRNA decapping of both unstable and stable mRNAs in yeast when the decapping enzyme is compromised by temperature-sensitive alleles of either the DCP1 or the DCP2 genes. In these cases, deletion of EDC3 caused a synergistic mRNA-decapping defect at the permissive temperatures. The edc3Δ had no effect when combined with the lsm1Δ, dhh1Δ, or pat1Δ mutations, which appear to affect an early step in the decapping pathway. This suggests that Edc3p specifically affects the function of the decapping enzyme per se. Consistent with a functional role in decapping, GFP-tagged Edc3p localizes to cytoplasmic foci involved in mRNA decapping referred to as P-bodies. These results identify Edc3p as a new protein involved in the decapping reaction.

scholarly journals DCP2 plays multiple roles during Drosophila development – possible case of moonlighting?

2019 ◽  
Author(s):  
Rohit Kunar ◽  
Jagat K Roy
Keyword(s):  
Protein Expression ◽  
Early Development ◽  
Multiple Roles ◽  
Dorsal Closure ◽  
Larval Brain ◽  
Living World ◽  
Mrna Decapping ◽  
P Bodies ◽  
Active Expression ◽  
Decapping Enzyme

AbstractmRNA decapping proteins (DCPs) are components of the P-bodies in the cell which are hubs of mRNAs targeted for decay and they provide the cell with a reversible pool of mRNAs in response to cellular demands. The Drosophila genome codes for two decapping proteins, DCP1 and DCP2 out of which DCP2 is the cognate decapping enzyme. The present endeavour explores the endogenous promoter firing, transcript and protein expression of DCP2 in Drosophila wherein, besides a ubiquitous expression across development, we identify active expression paradigm during dorsal closure and a plausible moonlighting expression in the Corazonin neurons of the larval brain. We also demonstrate that the ablation of DCP2 leads to embryonic lethality and defects in vital morphogenetic processes whereas a knockdown of DCP2 in the Corazonin neurons reduces the sensitivity to ethanol in adults, thereby ascribing novel regulatory roles to DCP2. Our findings unravel novel putative roles for DCP2 and identify it as a candidate for studies on the regulated interplay of essential molecules during early development in Drosophila, nay the living world.

scholarly journals Numerous interactions act redundantly to assemble a tunable size of P bodies in Saccharomyces cerevisiae

2017 ◽  
Vol 114 (45) ◽  
pp. E9569-E9578 ◽  
Author(s):  
Bhalchandra S. Rao ◽  
Roy Parker
Keyword(s):  
Protein Interactions ◽  
Growth Conditions ◽  
Protein Protein Interactions ◽  
Protein Assemblies ◽  
P Bodies ◽  
Multiple Protein ◽  
Body Components ◽  
Rnp Granules ◽  
General Translation ◽  
Liquid Liquid Phase Separation

Eukaryotic cells contain multiple RNA–protein assemblies referred to as RNP granules, which are thought to form through multiple protein–protein interactions analogous to a liquid–liquid phase separation. One class of RNP granules consists of P bodies, which consist of nontranslating mRNAs and the general translation repression and mRNA degradation machinery. P bodies have been suggested to form predominantly through interactions of Edc3 and a prion-like domain on Lsm4. In this work, we provide evidence that P-body assembly can be driven by multiple different protein–protein and/or protein–RNA interactions, including interactions involving Dhh1, Psp2, and Pby1. Moreover, the relative importance of specific interactions can vary with different growth conditions. Based on these observations, we develop a summative model wherein the P-body assembly phenotype of a given mutant can be predicted from the number of currently known protein–protein interactions between P-body components.

scholarly journals New methods for capturing the mystery lipid, PtdIns5P

2010 ◽  
Vol 428 (3) ◽  
pp. e1-e2 ◽  
Author(s):  
Jonathan M. Backer
Keyword(s):  
Protein Interactions ◽  
Inositol Phosphate ◽  
Coincidence Detection ◽  
Protein Protein Interactions ◽  
Detection Mechanism ◽  
Intact Cells ◽  
New Methods ◽  
Binding Domains ◽  
Biochemical Journal ◽  
Phox Homology

The enormous versatility of phosphatidylinositol as a mediator of intracellular signalling is due to its variable phosphorylation on every combination of the 3′, 4′ and 5′ positions, as well as an even more complex range of phosphorylated products when inositol phosphate is released by phospholipase C activity. The phosphoinositides are produced by distinct enzymes in distinct intracellular membranes, and recruit and regulate downstream signalling proteins containing binding domains [PH (pleckstrin homology), PX (Phox homology), FYVE etc.] that are relatively specific for these lipids. Specific recruitment of downstream proteins presumably involves a coincidence detection mechanism, in which a combination of lipid–protein and protein–protein interactions define specificity. Of the seven intrucellular phosphoinositide, quantification of PtdIns5P levels in intact cells has remained difficult. In this issue of the Biochemical Journal, Sarkes and Rameh describe a novel HPLC-based approach which makes possible an analysis of the subcellular distribution of PtdIns5P and other phosphoinositides.

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