scholarly journals RNF219 attenuates global mRNA decay through inhibition of CCR4-NOT complex-mediated deadenylation

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Fabian Poetz ◽  
Joshua Corbo ◽  
Yevgen Levdansky ◽  
Alexander Spiegelhalter ◽  
Doris Lindner ◽  
...  
Keyword(s):  
Half Life ◽  
Direct Interaction ◽  
Low Complexity ◽  
Mrna Degradation ◽  
Mrna Turnover ◽  
Hdac Inhibition ◽  
Linear Motif ◽  
Active Ring ◽  
Induced Changes ◽  
Mrna Half Life

AbstractThe CCR4-NOT complex acts as a central player in the control of mRNA turnover and mediates accelerated mRNA degradation upon HDAC inhibition. Here, we explored acetylation-induced changes in the composition of the CCR4-NOT complex by purification of the endogenously tagged scaffold subunit NOT1 and identified RNF219 as an acetylation-regulated cofactor. We demonstrate that RNF219 is an active RING-type E3 ligase which stably associates with CCR4-NOT via NOT9 through a short linear motif (SLiM) embedded within the C-terminal low-complexity region of RNF219. By using a reconstituted six-subunit human CCR4-NOT complex, we demonstrate that RNF219 inhibits deadenylation through the direct interaction of the α-helical SLiM with the NOT9 module. Transcriptome-wide mRNA half-life measurements reveal that RNF219 attenuates global mRNA turnover in cells, with differential requirement of its RING domain. Our results establish RNF219 as an inhibitor of CCR4-NOT-mediated deadenylation, whose loss upon HDAC inhibition contributes to accelerated mRNA turnover.

scholarly journals Inhibition of protein synthesis stabilizes histone mRNA.

1984 ◽  
Vol 4 (10) ◽  
pp. 2082-2090 ◽  
Author(s):  
E Stimac ◽  
V E Groppi ◽  
P Coffino
Keyword(s):  
Protein Synthesis ◽  
Half Life ◽  
Mrna Turnover ◽  
Approach To Equilibrium ◽  
Histone Mrna ◽  
Rapid Degradation ◽  
Permeabilized Cells ◽  
Fivefold Increase ◽  
Inhibition Of Protein Synthesis ◽  
Mrna Half Life

The inhibition of protein synthesis in exponentially growing S49 cells leads to a specific fivefold increase in histone mRNA in 30 min. The rate of transcription of histone mRNA, measured in intact or digitonin-permeabilized cells, is increased slightly, if at all, by cycloheximide inhibition of protein synthesis. Both approach-to-equilibrium labeling and pulse-chase experiments show that cycloheximide prolongs histone mRNA half-life from approximately 30 min to greater than 2 h. Histone mRNA made before the addition of cycloheximide becomes stable after the inhibition of protein synthesis, whereas removal of the inhibitor is followed by rapid degradation of histone mRNA. This suggests that the increased stability of histone mRNA during inhibition of protein synthesis results not from alteration of the structure of the mRNA, but from the loss of an activity in the cell which regulates histone mRNA turnover.

Inhibition of protein synthesis stabilizes histone mRNA

1984 ◽  
Vol 4 (10) ◽  
pp. 2082-2090
Author(s):  
E Stimac ◽  
V E Groppi ◽  
P Coffino
Keyword(s):  
Protein Synthesis ◽  
Half Life ◽  
Mrna Turnover ◽  
Approach To Equilibrium ◽  
Histone Mrna ◽  
Rapid Degradation ◽  
Permeabilized Cells ◽  
Fivefold Increase ◽  
Inhibition Of Protein Synthesis ◽  
Mrna Half Life

The inhibition of protein synthesis in exponentially growing S49 cells leads to a specific fivefold increase in histone mRNA in 30 min. The rate of transcription of histone mRNA, measured in intact or digitonin-permeabilized cells, is increased slightly, if at all, by cycloheximide inhibition of protein synthesis. Both approach-to-equilibrium labeling and pulse-chase experiments show that cycloheximide prolongs histone mRNA half-life from approximately 30 min to greater than 2 h. Histone mRNA made before the addition of cycloheximide becomes stable after the inhibition of protein synthesis, whereas removal of the inhibitor is followed by rapid degradation of histone mRNA. This suggests that the increased stability of histone mRNA during inhibition of protein synthesis results not from alteration of the structure of the mRNA, but from the loss of an activity in the cell which regulates histone mRNA turnover.

scholarly journals Scavenger Decapping Activity Facilitates 5′ to 3′ mRNA Decay

2005 ◽  
Vol 25 (22) ◽  
pp. 9764-9772 ◽  
Author(s):  
Hudan Liu ◽  
Megerditch Kiledjian
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Mrna Stability ◽  
Mrna Decay ◽  
Hydrolytic Activity ◽  
Mrna Degradation ◽  
Mrna Turnover ◽  
Threefold Increase ◽  
Mechanistic Analysis ◽  
Decapping Enzyme ◽  
Mrna Half Life

ABSTRACT mRNA degradation occurs through distinct pathways, one primarily from the 5′ end of the mRNA and the second from the 3′ end. Decay from the 3′ end generates the m7GpppN cap dinucleotide, which is subsequently hydrolyzed to m7Gp and ppN in Saccharomyces cerevisiae by a scavenger decapping activity termed Dcs1p. Although Dcs1p functions in the last step of mRNA turnover, we demonstrate that its activity modulates earlier steps of mRNA decay. Disruption of the DCS1 gene manifests a threefold increase of the TIF51A mRNA half-life. Interestingly, the hydrolytic activity of Dcs1p was essential for the altered mRNA turnover, as Dcs1p, but not a catalytically inactive Dcs1p mutant, complemented the increased mRNA stability. Mechanistic analysis revealed that 5′ to 3′ exoribonucleolytic activity was impeded in the dcs1Δ strain, resulting in the accumulation of uncapped mRNA. These data define a new role for the Dcs1p scavenger decapping enzyme and demonstrate a novel mechanism whereby the final step in the 3′ mRNA decay pathway can influence 5′ to 3′ exoribonucleolytic activity.

scholarly journals Genome-scale conserved molecular principles of mRNA half-life regulation

2020 ◽  
Author(s):  
Sudipto Basu ◽  
Saurav Mallik ◽  
Suman Hait ◽  
Sudip Kundu
Keyword(s):  
Molecular Species ◽  
Half Life ◽  
Structural Features ◽  
Mrna Degradation ◽  
Molecular Structures ◽  
Precise Control ◽  
Ribonucleoprotein Complexes ◽  
Specific Degradation ◽  
Genome Scale ◽  
Mrna Half Life

AbstractPrecise control of protein and mRNA degradation is essential for cellular metabolism and homeostasis. Controlled and specific degradation of both molecular species necessitates their engagements with the respective degradation machineries; this engagement involves a disordered/unstructured segment of the substrate traversing the degradation tunnel of the machinery and accessing the catalytic sites. Here, we report that mRNAs comprising longer terminal and/or internal unstructured segments have significantly shorter half-lives; the lengths of the 5′ terminal, 3′ terminal and internal unstructured segments that affect mRNA half-life are compatible with molecular structures of the 5′ exo- 3′ exo- and endo-ribonuclease machineries. Sequestration into ribonucleoprotein complexes elongates mRNA half-life, presumably by burying ribonuclease engagement sites under oligomeric interfaces. After gene duplication, differences in terminal unstructured lengths, proportions of internal unstructured segments and oligomerization modes result in significantly altered half-lives of paralogous mRNAs. Side-by-side comparison of molecular principles underlying controlled protein and mRNA degradation unravels their remarkable mechanistic similarities, and suggests how the intrinsic structural features of the two molecular species regulate their half-lives on genome-scale and during evolution.

The KH-type splicing regulatory protein (KSRP) regulates type III interferon expression post-transcriptionally

2019 ◽  
Vol 476 (2) ◽  
pp. 333-352 ◽  
Author(s):  
Lisa Schmidtke ◽  
Katharina Schrick ◽  
Sabrina Saurin ◽  
Rudolf Käfer ◽  
Fabian Gather ◽  
...  
Keyword(s):  
Half Life ◽  
Rna Binding ◽  
Binding Protein ◽  
Regulatory Protein ◽  
Rna Binding Protein ◽  
Luciferase Reporter ◽  
Regulatory Function ◽  
Type Iii ◽  
Type Iii Ifn ◽  
Mrna Half Life

Abstract Type III interferons (IFNs) are the latest members of the IFN family. They play an important role in immune defense mechanisms, especially in antiviral responses at mucosal sites. Moreover, they control inflammatory reactions by modulating neutrophil and dendritic cell functions. Therefore, it is important to identify cellular mechanisms involved in the control of type III IFN expression. All IFN family members contain AU-rich elements (AREs) in the 3′-untranslated regions (3′-UTR) of their mRNAs that determine mRNA half-life and consequently the expressional level of these cytokines. mRNA stability is controlled by different proteins binding to these AREs leading to either stabilization or destabilization of the respective target mRNA. The KH-type splicing regulatory protein KSRP (also named KHSRP) is an important negative regulator of ARE-containing mRNAs. Here, we identify the interferon lambda 3 (IFNL3) mRNA as a new KSRP target by pull-down and immunoprecipitation experiments, as well as luciferase reporter gene assays. We characterize the KSRP-binding site in the IFNL3 3′-UTR and demonstrate that KSRP regulates the mRNA half-life of the IFNL3 transcript. In addition, we detect enhanced expression of IFNL3 mRNA in KSRP−/− mice, establishing a negative regulatory function of KSRP in type III IFN expression also in vivo. Besides KSRP the RNA-binding protein AUF1 (AU-rich element RNA-binding protein 1) also seems to be involved in the regulation of type III IFN mRNA expression.

Depression of nuclear transcription and extension of mRNA half-life under anoxia in Artemia franciscana embryos

2000 ◽  
Vol 203 (7) ◽  
pp. 1123-1130 ◽  
Author(s):  
F. van Breukelen ◽  
R. Maier ◽  
S.C. Hand
Keyword(s):  
Half Life ◽  
Mammalian Cells ◽  
Transcriptional Activity ◽  
Artemia Franciscana ◽  
Mrna Levels ◽  
Compensatory Mechanisms ◽  
Depressed State ◽  
Initiation Of Transcription ◽  
Mrna Half Life

Transcriptional activity, as assessed by nuclear run-on assays, was constant during 10 h of normoxic development for embryos of the brine shrimp Artemia franciscana. Exposure of embryos to only 4 h of anoxia resulted in a 79.3+/−1 % decrease in levels of in-vivo-initiated transcripts, and transcription was depressed by 88. 2+/−0.7 % compared with normoxic controls after 24 h of anoxia (means +/− s.e.m., N=3). Initiation of transcription was fully restored after 1 h of normoxic recovery. Artificially lowering the intracellular pH of aerobic embryos to the value reflective of anoxia (pH 6.7) showed that acidification alone explained over half the transcriptional arrest. Initiation of transcription was not rescued by application of 80 % carbon monoxide under anoxia, which suggests that heme-based oxygen sensing is not involved in this global arrest. When these transcriptional data are combined with the finding that mRNA levels are unchanged for at least 6 h of anoxia, it is clear that the half-life of mRNA is extended at least 8.5-fold compared with that in aerobic embryos. In contrast to the activation of compensatory mechanisms to cope with anoxia that occurs in mammalian cells, A. franciscana embryos enter a metabolically depressed state in which gene expression and mRNA turnover are cellular costs apparently not compatible with survival and in which extended tolerance supercedes the requirement for continued metabolic function.

Mixed tailing by TENT4A and TENT4B shields mRNA from rapid deadenylation

Science ◽  
2018 ◽  
Vol 361 (6403) ◽  
pp. 701-704 ◽  
Author(s):  
Jaechul Lim ◽  
Dongwan Kim ◽  
Young-suk Lee ◽  
Minju Ha ◽  
Mihye Lee ◽  
...  
Keyword(s):  
Gene Regulation ◽  
Half Life ◽  
Messenger Rna ◽  
Mrna Translation ◽  
Posttranscriptional Gene Regulation ◽  
And Function ◽  
Mrna Half Life ◽  
In Cells

RNA tails play integral roles in the regulation of messenger RNA (mRNA) translation and decay. Guanylation of the poly(A) tail was discovered recently, yet the enzymology and function remain obscure. Here we identify TENT4A (PAPD7) and TENT4B (PAPD5) as the enzymes responsible for mRNA guanylation. Purified TENT4 proteins generate a mixed poly(A) tail with intermittent non-adenosine residues, the most common of which is guanosine. A single guanosine residue is sufficient to impede the deadenylase CCR4-NOT complex, which trims the tail and exposes guanosine at the 3′ end. Consistently, depletion of TENT4A and TENT4B leads to a decrease in mRNA half-life and abundance in cells. Thus, TENT4A and TENT4B produce a mixed tail that shields mRNA from rapid deadenylation. Our study unveils the role of mixed tailing and expands the complexity of posttranscriptional gene regulation.

scholarly journals OmpC regulation differs between ST131 and non-ST131 Escherichia coli clinical isolates and involves differential expression of the small RNA MicC

2020 ◽  
Vol 75 (5) ◽  
pp. 1151-1158
Author(s):  
Corey S Suelter ◽  
Nancy D Hanson
Keyword(s):  
Escherichia Coli ◽  
Half Life ◽  
Selective Advantage ◽  
Resistance Mechanisms ◽  
Northern Blotting ◽  
Rt Pcr ◽  
E Coli ◽  
Protein Levels ◽  
Porin Proteins ◽  
Mrna Half Life

Abstract Background Virulence genes and the expression of resistance mechanisms undoubtedly play a role in the successful spread of the pandemic clone Escherichia coli ST131. Porin down-regulation is a chromosomal mechanism associated with antibiotic resistance. Translation of porin proteins can be impacted by modifications in mRNA half-life and the interaction among small RNAs (sRNAs), the porin transcript and the sRNA chaperone Hfq. Modifications in the translatability of porin proteins could impact the fitness and therefore the success of E. coli ST131 isolates in the presence of antibiotic. Objectives To identify differences in the translatability of OmpC and OmpF porins for different STs of E. coli by comparing steady-state RNA levels, mRNA half-life, regulatory sRNA expression and protein production. Methods RNA expression was evaluated using real-time RT–PCR and OmpC mRNA half-life by northern blotting. OmpC, OmpF and Hfq protein levels were evaluated by immunoblotting. Results Differences between ST131 and non-ST131 isolates included: (i) the level of OmpC RNA and protein produced with mRNA expression higher for ST131 but OmpC protein levels lower compared with non-ST131 isolates; (ii) OmpC mRNA half-life (21–30 min for ST131 isolates compared with <2–23 min for non-ST131 isolates); and (iii) levels of the sRNA MicC (2- to 120-fold for ST131 isolates compared with −4- to 70-fold for non-ST131 isolates). Conclusions Mechanisms involved in the translatability of porin proteins differed among different STs of E. coli. These differences could provide a selective advantage to ST131 E. coli when confronted with an antibiotic-rich environment.

Glucocorticoids regulate NHE-3 transcription in OKP cells

1996 ◽  
Vol 270 (1) ◽  
pp. F164-F169 ◽  
Author(s):  
M. Baum ◽  
M. Amemiya ◽  
V. Dwarakanath ◽  
R. J. Alpern ◽  
O. W. Moe
Keyword(s):  
Gene Transcription ◽  
Half Life ◽  
Time Course ◽  
In Vitro Transcription ◽  
Mrna Abundance ◽  
Proton Secretion ◽  
Threefold Increase ◽  
Mrna Half Life ◽  
Synthetic Glucocorticoid

OKP cells express NHE-3, an amiloride-resistant Na+/H+ antiporter, which is likely an isoform responsible for apical proton secretion by the proximal tubule. We have previously shown that an amiloride-resistant Na+/H+ antiporter in OKP cells is regulated by dexamethasone, a synthetic glucocorticoid. The purpose of the present study was to examine the mechanism for the glucocorticoid-mediated increase in Na+/H+ antiporter activity. Incubation of OKP cells with 10(-6) M dexamethasone resulted in a two- to threefold increase in NHE-3 mRNA abundance. This increase was seen after 4 h of incubation with dexamethasone, a time course similar to that found for Na+/H+ antiporter activity. To examine the mechanism for the increase in NHE-3 mRNA abundance, mRNA half-life and in vitro transcription experiments were performed. NHE-3 mRNA had a half-life of 8 h in control and dexamethasone-treated cells. The rate of in vitro transcription was 1.8-fold greater when OKP cells were treated with dexamethasone. These data suggest that the glucocorticoid-mediated increase in Na+/H+ antiporter activity is due to an increase in NHE-3 gene transcription.

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