Figure 1 - uploaded by Tracy Nissan
Content may be subject to copyright.
Mechanism of messenger RNA (mRNA) degradation. The degradation of mRNA begins on the newly cytoplasmic mRNA. The decay process is regulated by elements on each end of the mRNA. The mRNA has a 7-methyl-guanosine cap at the 5′ end and a poly(A) tail at the 3′ end. The poly(A) length is approximately 60 nucleotides upon export. In the cytoplasm, the mRNA is initially deadenylated by Pan2/3 and then primarily by the Ccr4/Pop2/Not deadenylase complex, resulting in a median poly(A) length of approximately 30 nucleotides. Once the poly(A) tail is shortened to a length that is no longer able to bind Pab1p, the mRNA can be degraded from the 3′5′ direction by the exosome. The 5′3′ degradation pathway requires the mRNA to be first decapped by the decapping complex Dcp1/2 and then degraded by the Xrn1p exonuclease enzyme.
Source publication
Messenger RNA (mRNA) degradation is an important element of gene expression that can be modulated by alterations in translation, such as reductions in initiation or elongation rates. Reducing translation initiation strongly affects mRNA degradation by driving mRNA toward the assembly of a decapping complex, leading to decapping. While mRNA stabilit...
Contexts in source publication
Context 1
... the 3 ′ end of an mRNA is the poly-adenosine or poly(A) tail. Sim- ilarly, linked to the 5 ′ end is a methyl-7-guanosine cap ( Figure 1). Integrating these ends is the transla- tion initiation factor eIF4F, which is the cap-binding complex (see below). ...
Context 2
... the 5 ′ cap must be exposed; therefore suggesting that the translation initiation factors eIF4G and eIF4E must be released from the mRNA. 25 Finally, following the recruitment of the decapping complex, the phosphate bond that links the cap to the body of the mRNA is hydrolyzed, leaving a monophosphorylated 5 ′ end (Figure 1). 21,26 Removal of the mRNA cap allows 5 ′ →3 ′ degradation to proceed by the exonuclease Xrn1p. ...
Context 3
... Removal of the mRNA cap allows 5 ′ →3 ′ degradation to proceed by the exonuclease Xrn1p. 23 Alternatively, oligoadenylated mRNA can be degraded from the 3 ′ →5 ′ direction by the exosome (Figure 1). The core exosome complex consists of a ring of six RNase PH-like proteins and three smaller RNA-binding proteins, which are required for its for- mation and stabilization. ...
Similar publications
The oocyte-to-embryo transition (OET) is thought to be mainly driven by post-transcriptional gene regulation. However, expression of both RNAs and proteins during the OET has not been comprehensively assayed. Furthermore, specific molecular mechanisms that regulate gene expression during OET are largely unknown. Here, we quantify and analyze transc...
Citations
... Since UTRs are important mediators of regulation of translation and degradation (15,16), we wondered whether some of the genes with extreme UCSF values encode UTRs that modulate mRNA stability. In the distribution of the residuals, the bottom and top 2.5 percent of the genes have a UCSF less than −0.72 and more than 0.87, respectively (Fig. 1B). ...
The half-life of mRNAs, as well as their translation, increases in proportion to the optimal codons, indicating a tight coupling of codon-dependent differential translation and degradation. Little is known about the regulation of this coupling. We found that the mRNA stability gain in yeast depends on the mRNA coding sequence length. Below a critical length, codon optimality fails to affect the stability of mRNAs although they can be efficiently translated into short peptides and proteins. Above this threshold length, codon optimality–dependent differential mRNA stability emerges in a switch-like fashion, which coincides with a similar increase in the polysome propensity of the mRNAs. This threshold length can be tuned by the untranslated regions (UTR). Some of these UTRs can destabilize mRNAs without reducing translation, which plays a role in controlling the amplitude of the oscillatory expression of cell cycle genes. Our findings help understand the translation of short peptides from noncoding RNAs and the translation by localized monosomes in neurons.
... Surprisingly, the data support that G-content in A-tail is negatively correlated with the binding efficiency of PABP on A-tail and further the gene with higher G-content has lower translation efficiency [31]. PABP is believed to identify the pure poly(A) primarily, and the binding of human PABP or yeast Pab1p to mRNA poly(A) tail requires 11-12 contiguous A-nucleotides [48][49][50]. Guanosine in poly(A) tail separates the tail into interspersed A-segments, supposed to reduce binding efficiency between PABP and A-tail and also translation efficiency of Arabidopsis genes ( Figure 1C) [31]. The mixed tailing in mammals is generated by TENT4A/4B, whereas the producing mechanism in Arabidopsis is unclear. ...
Terminal nucleotidyltransferases (TENTs) could generate a ‘mixed tail’ or ‘U-rich tail’ consisting of different nucleotides at the 30 end of RNA by non-templated nucleotide addition to protect or degrade cellular messenger RNA. Recently, there has been increasing evidence that the decoration of virus RNA terminus with a mixed tail or U-rich tail is a critical way to affect viral RNA stability in virus-infected cells. This paper first briefly introduces the cellular function of the
TENT family and non-canonical tails, then comprehensively reviews their roles in virus invasion and antiviral immunity, as well as the significance of the TENT family in antiviral therapy. This review will contribute to understanding the role and mechanism of non-canonical RNA tailing in survival competition between the virus and host.
... It is tempting to speculate that the higher contribution of 3' to 5' mRNA decay puts additional pressure on co-translational surveillance due to interference between translation and decay. It was previously suggested that the dominance of 5' to 3' mRNA decay in eukaryotic cytoplasm helps to avoid clashes between translation and decay since both processes follow the same direction on mRNA [32,33]. ...
Cytoplasmic mRNA decay is effected by exonucleolytic degradation in in either the 5' to 3' or 3' to 5' direction. Pervasive terminal uridylation is implicated in mRNA degradation, however, despite its conservation throughout eucaryotes, its functional relevance for bulk mRNA turnover remains poorly understood.
In this study, we employed genome-wide 3'-RACE technique to elucidate the role of uridylation in governing mRNA decay directionality. The observed widespread uridylation of shortened poly(A) tails promotes efficient 5' to 3' mRNA decay, ensuring timely and controlled mRNA degradation. Conversely, the inhibition of this uridylation process disrupts the delicate balance, leading to excessive deadenylation and enhanced 3' to 5' mRNA decay accompanied by oligouridylation of de-adenylated mRNAs. Strikingly we found that in fission yeast uridylation of poly(A) tails and oligouridylation of non-polyadenylated substrates are catalysed by different terminal uridyltransferases. Our study sheds new light on the intricate regulatory mechanisms underlying bulk mRNA turnover, emphasizing the role of uridylation in modulating mRNA decay pathways.
... Down-regulation of these proteins suggests the overall synthesis of proteins to minimize cell growth [31]. This may be partly attributed to external stress that causes mRNA degradation and inhibits translation [85]. ...
Acetic acid and furfural (AF) are two major inhibitors of microorganisms during lignocellulosic ethanol production. In our previous study, we successfully engineered Zymomonas mobilis 532 (ZM532) strain by genome shuffling, but the molecular mechanisms of tolerance to inhibitors were still unknown. Therefore, this study investigated the responses of ZM532 and its wild‑type Z. mobilis (ZM4) to AF using multi‑omics approaches (transcriptomics, genomics, and label free quantitative proteomics). Based on RNA‑Seq data, two differentially expressed genes, ZMO_RS02740 (upregulated) and ZMO_RS06525 (down‑regulated) were knocked out and over‑expressed through CRISPR‑Cas technology to investigate their roles in AF tolerance. Overall, we identified 1865 and 14 novel DEGs in ZM532 and wild‑type ZM4. In contrast, 1532 proteins were identified in ZM532 and wild‑type ZM4. Among these, we found 96 important genes in ZM532 involving acid resistance mechanisms and survival rates against stressors. Furthermore, our knockout results demonstrated that growth activity and glucose consumption of mutant strains ZM532∆ZMO_RS02740 and ZM4∆ZMO_RS02740 decreased with increased fermentation time from 42 to 55 h and ethanol production up to 58% in ZM532 than that in ZM532∆ZMO_RS02740. Hence, these findings suggest ZMO_RS02740 as a protective strategy for ZM ethanol production under stressful conditions.
... Acute glucose withdrawal further post-transcriptionally inhibits translation initiation [117], partly causing mRNAs to aggregate in so-called processing bodies or stress granules. Growth-associated transcripts are withdrawn from translation or actively degraded once located in said agglomerates [118,119]. Bresson et al. provide additional evidence that RiBi and RP genes are specifically flagged for TRAMP-mediated mRNA degradation following glucose withdrawal, with both gene sets exhibiting different degradation dynamics [120]. High PKA activity reportedly inhibits p-body and stress granule formation [121] and more remarkably, the assembly of these structures is independent of TORC1 or Snf1 signaling [122]. ...
Commercial-scale bioreactors create an unnatural environment for microbes from an evolutionary point of view. Mixing insufficiencies expose individual cells to fluctuating nutrient concentrations on a second-to-minute scale while transcriptional and translational capacities limit the microbial adaptation time from minutes to hours. This mismatch carries the risk of inadequate adaptation effects, especially considering that nutrients are available at optimal concentrations on average. Consequently, industrial bioprocesses that strive to maintain microbes in a phenotypic sweet spot, during lab-scale development, might suffer performance losses when said adaptive misconfigurations arise during scale-up. Here, we investigated the influence of fluctuating glucose availability on the gene-expression profile in the industrial yeast Ethanol Red™. The stimulus-response experiment introduced 2 min glucose depletion phases to cells growing under glucose limitation in a chemostat. Even though Ethanol Red™ displayed robust growth and productivity, a single 2 min depletion of glucose transiently triggered the environmental stress response. Furthermore, a new growth phenotype with an increased ribosome portfolio emerged after complete adaptation to recurring glucose shortages. The results of this study serve a twofold purpose. First, it highlights the necessity to consider the large-scale environment already at the experimental development stage, even when process-related stressors are moderate. Second, it allowed the deduction of strain engineering guidelines to optimize the genetic background of large-scale production hosts.
... Our data demonstrated that the translation of mRNAs with more m 6 A sites decreased after YTHDF1 KD (Supplementary Fig. S5B). We also observed a decrease at mRNA level ( Supplementary Fig. S5B), which could be explained by the fact that mRNA stability is tightly regulated by translation and they are always positively associated (32). ...
... Our data showed that YTHDF1 promotes the translation of a group of genes, whereas YTHDF2 was reported to facilitate the degradation of tumor suppressor mRNAs in AML (19). We also observed a decrease in mRNA level, which could be explained by the fact that mRNA stability is tightly regulated by translation and they are always positively associated (32). The possibility that YTHDF1 might promote mRNA stability is not excluded. ...
N6-methyladenosine (m6A), the most abundant modification in mRNAs, has been defined as a crucial modulator in the progression of acute myelogenous leukemia (AML). Identification of the key regulators of m6A modifications in AML could provide further insights into AML biology and uncover more effective therapeutic strategies for patients with AML. Here, we report overexpression of YTHDF1, an m6A reader protein, in human AML samples at the protein level with enrichment in leukemia stem cells (LSC). Whereas YTHDF1 was dispensable for normal hematopoiesis in mice, depletion of YTHDF1 attenuated self-renewal, proliferation, and leukemic capacity of primary human and mouse AML cells in vitro and in vivo. Mechanistically, YTHDF1 promoted the translation of cyclin E2 in an m6A-dependent manner. Structure-based virtual screening of FDA-approved drugs identified tegaserod as a potential YTHDF1 inhibitor. Tegaserod blocked the direct binding of YTHDF1 with m6A-modified mRNAs and inhibited YTHDF1-regulated cyclin E2 translation. Moreover, tegaserod reduced the viability of patient-derived AML cells in vitro and prolonged survival in patient-derived xenograft models. Together, our study defines YTHDF1 as an integral regulator of AML progression by regulating the expression of m6A-modified mRNAs, which might serve as a potential therapeutic target for AML.
Significance
The m6A reader YTHDF1 is required for progression of acute myelogenous leukemia and can be targeted with the FDA-approved drug tegaserod to suppress leukemia growth.
... Combined with the feedforward role of PKA, multiple feedback mechanisms exist with the potential to act as signal amplifiers. For instance, Ashe et al. (2000) reported severe inhibition of translation initiation within 30-60 s after glucose depletion, which can induce rapid RiBi and RP mRNA degradation (Huch & Nissan, 2014). In our experiment, ample nutrient conditions 2 min after the start of the s-LSL cycle superimposed the initiated decay of translationassociated genes. ...
In fed-batch operated industrial bioreactors, glucose-limited feeding is commonly applied for optimal control of cell growth and product formation. Still, microbial cells such as yeasts and bacteria are frequently exposed to glucose starvation conditions in poorly mixed zones or far away from the feedstock inlet point. Despite its commonness, studies mimicking related stimuli are still underrepresented in scale-up/scale-down considerations. This may surprise as the transition from glucose limitation to starvation has the potential to provoke regulatory responses with negative consequences for production performance. In order to shed more light, we performed gene-expression analysis of Saccharomyces cerevisiae grown in intermittently fed chemostat cultures to study the effect of limitation-starvation transitions. The resulting glucose concentration gradient was representative for the commercial scale and compelled cells to tolerate about 76 s with sub-optimal substrate supply. Special attention was paid to the adaptation status of the population by discriminating between first time and repeated entry into the starvation regime. Unprepared cells reacted with a transiently reduced growth rate governed by the general stress response. Yeasts adapted to the dynamic environment by increasing internal growth capacities at the cost of rising maintenance demands by 2.7%. Evidence was found that multiple protein kinase A (PKA) and Snf1-mediated regulatory circuits were initiated and ramped down still keeping the cells in an adapted trade-off between growth optimization and down-regulation of stress response. From this finding, primary engineering guidelines are deduced to optimize both the production host's genetic background and the design of scale-down experiments.
... ActD blocks the transcription of RNA from DNA and is frequently used to analyze mRNA stability via this property (Yang et al., 2003). Following transcription blockade, mRNA half-life becomes a function of how effectively this mRNA is translated (Huch and Nissan, 2014), which is dependent on an array of epi and co-transcriptional factors. Therefore, it can be assumed that genes that are up or down regulated after ActD treatment are doing so not because of transcriptional changes, but due to changes in their stability. ...
Ferroptosis is a non-apoptotic cell death mechanism characterized by the generation of lipid peroxides. While many effectors in the ferroptosis pathway have been mapped, its epitranscriptional regulation is not yet fully understood. Ferroptosis can be induced via system xCT inhibition (Class I) or GPX4 inhibition (Class II). Previous works have revealed important differences in cellular response to different ferroptosis inducers. Importantly, blocking mRNA transcription or translation appears to protect cells against Class I ferroptosis inducing agents but not Class II. In this work, we examined the impact of blocking transcription (via Actinomycin D) or translation (via Cycloheximide) on Erastin (Class I) or RSL3 (Class II) induced ferroptosis. Blocking transcription or translation protected cells against Erastin but was detrimental against RSL3. Cycloheximide led to increased levels of GSH alone or when co-treated with Erastin via the activation of the reverse transsulfuration pathway. RNA sequencing analysis revealed early activation of a strong alternative splice program before observed changes in transcription. mRNA stability analysis revealed divergent mRNA stability changes in cellular response to Erastin or RSL3. Importantly, codon optimality biases were drastically different in either condition. Our data also implicated translation repression and rate as an important determinant of the cellular response to ferroptosis inducers. Given that mRNA stability and codon usage can be influenced via the tRNA epitranscriptome, we evaluated the role of a tRNA modifying enzyme in ferroptosis stress response. Alkbh1, a tRNA demethylase, led to translation repression and increased the resistance to Erastin but made cells more sensitive to RSL3.
... mRNA degradation can be triggered by various quality control mechanisms (e.g. nonsensemediated decay), but degradation is also thought to be cou-pled to the translation of the mRNA by ribosomes (3,4). Seminal work established the main degradation pathway in eukaryotes: mRNA is deadenylated by the Ccr4-Not complex, decapped by the Dcp1-Dcp2 complex, and degraded by the highly processive 5 -3 exoribonuclease Xrn1 (5)(6)(7)(8)(9)(10). ...
In the last decade, multiple studies demonstrated that cells maintain a balance of mRNA production and degradation, but the mechanisms by which cells implement this balance remain unknown. Here, we monitored cells' total and recently-transcribed mRNA profiles immediately following an acute depletion of Xrn1-the main 5'-3' mRNA exonuclease-which was previously implicated in balancing mRNA levels. We captured the detailed dynamics of the adaptation to rapid degradation of Xrn1 and observed a significant accumulation of mRNA, followed by a delayed global reduction in transcription and a gradual return to baseline mRNA levels. We found that this transcriptional response is not unique to Xrn1 depletion; rather, it is induced earlier when upstream factors in the 5'-3' degradation pathway are perturbed. Our data suggest that the mRNA feedback mechanism monitors the accumulation of inputs to the 5'-3' exonucleolytic pathway rather than its outputs.
... DDX6 (RCK) enhances the translation of a subset of proliferation mRNAs in epidermal progenitor cells (Y. Wang et al., 2015) and facilitates the interplay between miRNA mediated post-transcriptional gene silencing (Roy and Jacobson 2013;Huch and Nissan 2014). DDX6 additionally stabilises autophagy mRNAs through association with DCP2 (Hu et al., 2015) and enhances 5′-3′ mRNA decay by facilitating XRN1 access for decapping (Coller et al., 2001;Fischer and Weis 2002). ...
Short repeated sequences of 3−6 nucleotides are causing a growing number of over 50 microsatellite expansion disorders, which mainly present with neurodegenerative features. Although considered rare diseases in relation to the relatively low number of cases, these primarily adult-onset conditions, often debilitating and fatal in absence of a cure, collectively pose a large burden on healthcare systems in an ageing world population. The pathological mechanisms driving disease onset are complex implicating several non-exclusive mechanisms of neuronal injury linked to RNA and protein toxic gain- and loss- of functions. Adding to the complexity of pathogenesis, microsatellite repeat expansions are polymorphic and found in coding as well as in non-coding regions of genes. They form secondary and tertiary structures involving G-quadruplexes and atypical helices in repeated GC-rich sequences. Unwinding of these structures by RNA helicases plays multiple roles in the expression of genes including repeat-associated non-AUG (RAN) translation of polymeric-repeat proteins with aggregating and cytotoxic properties. Here, we will briefly review the pathogenic mechanisms mediated by microsatellite repeat expansions prior to focus on the RNA helicases eIF4A, DDX3X and DHX36 which act as modifiers of RAN translation in C9ORF72-linked amyotrophic lateral sclerosis/frontotemporal dementia (C9ORF72-ALS/FTD) and Fragile X-associated tremor/ataxia syndrome (FXTAS). We will further review the RNA helicases DDX5/17, DHX9, Dicer and UPF1 which play additional roles in the dysregulation of RNA metabolism in repeat expansion disorders. In addition, we will contrast these with the roles of other RNA helicases such as DDX19/20, senataxin and others which have been associated with neurodegeneration independently of microsatellite repeat expansions. Finally, we will discuss the challenges and potential opportunities that are associated with the targeting of RNA helicases for the development of future therapeutic approaches.
