Nonsense-Mediated mRNA Decay Effectors Are Essential for Zebrafish Embryonic Development and Survival

ABSTRACT The nonsense-mediated mRNA decay (NMD) pathway promotes rapid degradation of mRNAs containing premature translation termination codons (PTCs or nonsense codons), preventing accumulation of potentially detrimental truncated proteins. In metazoa, seven genes (upf1, upf2, upf3, smg1, smg5, smg6, and smg7) have been identified as essential for NMD; here we show that the zebrafish genome encodes orthologs of upf1, upf2, smg1, and smg5 to smg7 and two upf3 paralogs. We also show that Upf1 is required for degradation of PTC-containing mRNAs in zebrafish embryos. Moreover, its depletion has a severe impact on embryonic development, early patterning, and viability. Similar phenotypes are observed in Upf2-, Smg5-, or Smg6-depleted embryos, suggesting that zebrafish embryogenesis requires an active NMD pathway. Using cultured cells, we demonstrate that the ability of a PTC to trigger NMD is strongly stimulated by downstream exon-exon boundaries. Thus, as in mammals and plants but in contrast to invertebrates and fungi, NMD is coupled to splicing in zebrafish. Our results together with previous studies show that NMD effectors are essential for vertebrate embryogenesis and suggest that the coupling of splicing and NMD has been maintained in vertebrates but lost in fungi and invertebrates.

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Nonsense-mediated mRNA decay

Biochemical Society Transactions ◽

10.1042/bst0360514 ◽

2008 ◽

Vol 36 (3) ◽

pp. 514-516 ◽

Cited By ~ 25

Author(s):

Jikai Wen ◽

Saverio Brogna

Keyword(s):

Mammalian Cells ◽

Mrna Decay ◽

Translation Termination ◽

Mrna Splicing ◽

Current Understanding ◽

Coupled Processes ◽

Recent Developments ◽

Nonsense Mediated Mrna Decay ◽

Premature Translation Termination

Translation and mRNA decay are coupled processes; the link is most obvious in the case of NMD (nonsense-mediated mRNA decay). NMD is a mechanism that drastically reduces the level of mRNA harbouring PTCs (premature translation termination codons). The defining event in NMD is premature translation termination and the key question is: what distinguishes premature from normal translation termination? Surprisingly, in mammalian cells, PTC recognition is linked to pre-mRNA splicing. Here, we review the current understanding in view of recent developments.

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Recognition of nonsense mRNA: towards a unified model

Biochemical Society Transactions ◽

10.1042/bst0360497 ◽

2008 ◽

Vol 36 (3) ◽

pp. 497-501 ◽

Cited By ~ 32

Author(s):

Oliver Mühlemann

Keyword(s):

Gene Expression ◽

Present Article ◽

Protein Complex ◽

Mrna Decay ◽

Translation Termination ◽

Physical Distance ◽

Unified Model ◽

Nonsense Mediated Mrna Decay ◽

Correct Translation ◽

Premature Translation Termination

Among the different cellular surveillance mechanisms that ensure accurate gene expression, nonsense-mediated mRNA decay rapidly degrades mRNAs harbouring PTCs (premature translation-termination codons) and thereby prevents the accumulation of potentially deleterious proteins with C-terminal truncations. In the present article, I review recent data from yeast, fluitflies, nematode worms and human cells and endeavour to merge these results into a unified model for recognition of nonsense mRNA. According to this model, the distinction between translation termination at PTCs and at ‘normal’ termination codons relies on the physical distance between the terminating ribosome and PABP [poly(A)-binding protein]. Correct translation termination is promoted by a PABP-mediated signal to the terminating ribosome, whereas the absence of this signal leads to the assembly of an mRNA decay-promoting protein complex including the conserved NMD factors UPF (up-frameshift) 1–3.

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UPF1 P-body localization

Biochemical Society Transactions ◽

10.1042/bst0360698 ◽

2008 ◽

Vol 36 (4) ◽

pp. 698-700 ◽

Cited By ~ 9

Author(s):

Saverio Brogna ◽

Preethi Ramanathan ◽

Jikai Wen

Keyword(s):

Mrna Decay ◽

Translation Termination ◽

Processing Bodies ◽

Cytoplasmic Granules ◽

P Bodies ◽

The Core ◽

Nonsense Mediated Mrna Decay ◽

Premature Translation Termination

NMD (nonsense-mediated mRNA decay) is a mechanism that degrades transcripts containing PTCs (premature translation termination codons). NMD is a translation-associated process that is expected to take place throughout the cytoplasm. However, recent studies have indicated that the core NMD factors UPF1 (up-frameshift-1), UPF2 and UPF3 can associate with P-bodies (processing bodies), which are large cytoplasmic granules replete with proteins involved in general mRNA decay and related processes. It has been proposed that UPF1 directs PTC-containing mRNAs to P-bodies and triggers decay. Here, we discuss the link between P-bodies and NMD in view of recent studies that suggest that P-bodies are not required for NMD in Drosophila.

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Nonsense-mediated mRNA decay factors cure most [PSI+] prion variants

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1717495115 ◽

2018 ◽

Vol 115 (6) ◽

pp. E1184-E1193 ◽

Cited By ~ 12

Author(s):

Moonil Son ◽

Reed B. Wickner

Keyword(s):

Protein Interactions ◽

Mrna Decay ◽

Rna Binding ◽

Translation Termination ◽

Amyloid Formation ◽

Multifunctional Protein ◽

Nonsense Mediated Mrna Decay ◽

Nonsense Codons ◽

Almost All

The yeast prion [PSI+] is a self-propagating amyloid of Sup35p with a folded in-register parallel β-sheet architecture. In a genetic screen for antiprion genes, using the yeast knockout collection,UPF1/NAM7andUPF3, encoding nonsense-mediated mRNA decay (NMD) factors, were frequently detected. Almost all [PSI+] variants arising in the absence of Upf proteins were eliminated by restored normal levels of these proteins, and [PSI+] arises more frequently inupfmutants. Upf1p, complexed with Upf2p and Upf3p, is a multifunctional protein with helicase, ATP-binding, and RNA-binding activities promoting efficient translation termination and degradation of mRNAs with premature nonsense codons. We find that the curing ability of Upf proteins is uncorrelated with these previously reported functions but does depend on their interaction with Sup35p and formation of the Upf1p–Upf2p–Upf3p complex (i.e., the Upf complex). Indeed, Sup35p amyloid formation in vitro is inhibited by substoichiometric Upf1p. Inhibition of [PSI+] prion generation and propagation by Upf proteins may be due to the monomeric Upf proteins and the Upf complex competing with Sup35p amyloid fibers for available Sup35p monomers. Alternatively, the association of the Upf complex with amyloid filaments may block the addition of new monomers. Our results suggest that maintenance of normal protein–protein interactions prevents prion formation and can even reverse the process.

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Caenorhabditis elegans SMG-2 Selectively Marks mRNAs Containing Premature Translation Termination Codons

Molecular and Cellular Biology ◽

10.1128/mcb.00410-07 ◽

2007 ◽

Vol 27 (16) ◽

pp. 5630-5638 ◽

Cited By ~ 39

Author(s):

Lisa Johns ◽

Andrew Grimson ◽

Sherry L. Kuchma ◽

Carrie Loushin Newman ◽

Philip Anderson

Keyword(s):

Caenorhabditis Elegans ◽

Mammalian Cells ◽

Translation Termination ◽

Yeast Two Hybrid ◽

Eukaryotic Mrnas ◽

Nonsense Mediated Mrna Decay ◽

Endogenous Genes ◽

Alternatively Spliced ◽

Two Hybrid ◽

Premature Translation Termination

ABSTRACT Eukaryotic mRNAs containing premature translation termination codons (PTCs) are rapidly degraded by a process termed “nonsense-mediated mRNA decay” (NMD). We examined protein-protein and protein-RNA interactions among Caenorhabditis elegans proteins required for NMD. SMG-2, SMG-3, and SMG-4 are orthologs of yeast (Saccharomyces cerevisiae) and mammalian Upf1, Upf2, and Upf3, respectively. A combination of immunoprecipitation and yeast two-hybrid experiments indicated that SMG-2 interacts with SMG-3, SMG-3 interacts with SMG-4, and SMG-2 interacts indirectly with SMG-4 via shared interactions with SMG-3. Such interactions are similar to those observed in yeast and mammalian cells. SMG-2-SMG-3-SMG-4 interactions require neither SMG-2 phosphorylation, which is abolished in smg-1 mutants, nor SMG-2 dephosphorylation, which is reduced or eliminated in smg-5 mutants. SMG-2 preferentially associates with PTC-containing mRNAs. We monitored the association of SMG-2, SMG-3, and SMG-4 with mRNAs of five endogenous genes whose mRNAs are alternatively spliced to either contain or not contain PTCs. SMG-2 associates with both PTC-free and PTC-containing mRNPs, but it strongly and preferentially associates with (“marks”) those containing PTCs. SMG-2 marking of PTC-mRNPs is enhanced by SMG-3 and SMG-4, but SMG-3 and SMG-4 are not detectably associated with the same mRNPs. Neither SMG-2 phosphorylation nor dephosphorylation is required for selective association of SMG-2 with PTC-containing mRNPs, indicating that SMG-2 is phosphorylated only after premature terminations have been discriminated from normal terminations. We discuss these observations with regard to the functions of SMG-2 and its phosphorylation during NMD.

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A UPF1 variant drives conditional remodeling of nonsense-mediated mRNA decay

10.1101/2021.01.27.428318 ◽

2021 ◽

Author(s):

Sarah E. Fritz ◽

Soumya Ranganathan ◽

J. Robert Hogg

Keyword(s):

Gene Expression ◽

Mrna Decay ◽

Gene Expression Regulation ◽

Translation Termination ◽

Translational Repression ◽

The Core ◽

Human Genes ◽

Rna Quality Control ◽

Nonsense Mediated Mrna Decay

AbstractThe nonsense-mediated mRNA decay (NMD) pathway monitors translation termination to degrade transcripts with premature stop codons and regulate thousands of human genes. Due to the major role of NMD in RNA quality control and gene expression regulation, it is important to understand how the pathway responds to changing cellular conditions. Here we show that an alternative mammalian-specific isoform of the core NMD factor UPF1, termed UPF1LL, enables condition-dependent remodeling of NMD specificity. UPF1LL associates more stably with potential NMD target mRNAs than the major UPF1SL isoform, expanding the scope of NMD to include many transcripts normally immune to the pathway. Unexpectedly, the enhanced persistence of UPF1LL on mRNAs supports induction of NMD in response to rare translation termination events. Thus, while canonical NMD is abolished by translational repression, UPF1LL activity is enhanced, providing a mechanism to rapidly rewire NMD specificity in response to cellular stress.

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Screening Readthrough Compounds to Suppress Nonsense Mutations: Possible Application to β-Thalassemia

Journal of Clinical Medicine ◽

10.3390/jcm9020289 ◽

2020 ◽

Vol 9 (2) ◽

pp. 289 ◽

Cited By ~ 3

Author(s):

Monica Borgatti ◽

Emiliano Altamura ◽

Francesca Salvatori ◽

Elisabetta D’Aversa ◽

Nicola Altamura

Keyword(s):

Genetic Disease ◽

Chelation Therapy ◽

Translation Termination ◽

Premature Termination Codon ◽

Nonsense Suppression ◽

Current Status ◽

Nonsense Mutations ◽

Nonsense Mediated Mrna Decay ◽

Mrna Destabilization ◽

Premature Translation Termination

Several types of thalassemia (including β039-thalassemia) are caused by nonsense mutations in genes controlling globin production, leading to premature translation termination and mRNA destabilization mediated by the nonsense mediated mRNA decay. Drugs (for instance, aminoglycosides) can be designed to suppress premature translation termination by inducing readthrough (or nonsense suppression) at the premature termination codon. These findings have introduced new hopes for the development of a pharmacologic approach to cure this genetic disease. In the present review, we first summarize the principle and current status of the chemical relief for the expression of functional proteins from genes otherwise unfruitful for the presence of nonsense mutations. Second, we compare data available on readthrough molecules for β0-thalassemia. The examples reported in the review strongly suggest that ribosomal readthrough should be considered as a therapeutic approach for the treatment of β0-thalassemia caused by nonsense mutations. Concluding, the discovery of molecules, exhibiting the property of inducing β-globin, such as readthrough compounds, is of great interest and represents a hope for several patients, whose survival will depend on the possible use of drugs rendering blood transfusion and chelation therapy unnecessary.

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Nonsense-Mediated mRNA Decay Mutation in Aspergillus nidulans

Eukaryotic Cell ◽

10.1128/ec.00220-06 ◽

2006 ◽

Vol 5 (11) ◽

pp. 1838-1846 ◽

Cited By ~ 13

Author(s):

Igor Y. Morozov ◽

Susana Negrete-Urtasun ◽

Joan Tilburn ◽

Christine A. Jansen ◽

Mark X. Caddick ◽

...

Keyword(s):

Aspergillus Nidulans ◽

Mrna Decay ◽

Premature Termination ◽

Regulation Of Gene Expression ◽

Premature Termination Codon ◽

Termination Codon ◽

Urate Oxidase ◽

Genes Encoding ◽

Nonsense Mediated Mrna Decay ◽

Nonsense Codons

ABSTRACT An Aspergillus nidulans mutation, designated nmdA1, has been selected as a partial suppressor of a frameshift mutation and shown to truncate the homologue of the Saccharomyces cerevisiae nonsense-mediated mRNA decay (NMD) surveillance component Nmd2p/Upf2p. nmdA1 elevates steady-state levels of premature termination codon-containing transcripts, as demonstrated using mutations in genes encoding xanthine dehydrogenase (hxA), urate oxidase (uaZ), the transcription factor mediating regulation of gene expression by ambient pH (pacC), and a protease involved in pH signal transduction (palB). nmdA1 can also stabilize pre-mRNA (unspliced) and wild-type transcripts of certain genes. Certain premature termination codon-containing transcripts which escape NMD are relatively stable, a feature more in common with certain nonsense codon-containing mammalian transcripts than with those in S. cerevisiae. As in S. cerevisiae, 5′ nonsense codons are more effective at triggering NMD than 3′ nonsense codons. Unlike the mammalian situation but in common with S. cerevisiae and other lower eukaryotes, A. nidulans is apparently impervious to the position of premature termination codons with respect to the 3′ exon-exon junction.

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Tpa1p Is Part of an mRNP Complex That Influences Translation Termination, mRNA Deadenylation, and mRNA Turnover in Saccharomyces cerevisiae

Molecular and Cellular Biology ◽

10.1128/mcb.02448-05 ◽

2006 ◽

Vol 26 (14) ◽

pp. 5237-5248 ◽

Cited By ~ 38

Author(s):

Kim M. Keeling ◽

Joe Salas-Marco ◽

Lev Z. Osherovich ◽

David M. Bedwell

Keyword(s):

Saccharomyces Cerevisiae ◽

Mrna Decay ◽

Potential Role ◽

Translation Termination ◽

Tail Length ◽

Fold Increase ◽

Reading Frame ◽

Yeast Strains ◽

Messenger Ribonucleoprotein ◽

Nonsense Mediated Mrna Decay

ABSTRACT In this report, we show that the Saccharomyces cerevisiae protein Tpa1p (for termination and polyadenylation) influences translation termination efficiency, mRNA poly(A) tail length, and mRNA stability. Tpa1p is encoded by the previously uncharacterized open reading frame YER049W. Yeast strains carrying a deletion of the TPA1 gene (tpa1Δ) exhibited increased readthrough of stop codons, and coimmunoprecipitation assays revealed that Tpa1p interacts with the translation termination factors eRF1 and eRF3. In addition, the tpa1Δ mutation led to a 1.5- to 2-fold increase in the half-lives of mRNAs degraded by the general 5′→3′ pathway or the 3′→5′ nonstop decay pathway. In contrast, this mutation did not have any affect on the nonsense-mediated mRNA decay pathway. Examination of mRNA poly(A) tail length revealed that poly(A) tails are longer than normal in a tpa1Δ strain. Consistent with a potential role in regulating poly(A) tail length, Tpa1p was also found to coimmunoprecipitate with the yeast poly(A) binding protein Pab1p. These results suggest that Tpa1p is a component of a messenger ribonucleoprotein complex bound to the 3′ untranslated region of mRNAs that affects translation termination, deadenylation, and mRNA decay.

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Gene Set Coregulated by the Saccharomyces cerevisiae Nonsense-Mediated mRNA Decay Pathway

Eukaryotic Cell ◽

10.1128/ec.4.12.2066-2077.2005 ◽

2005 ◽

Vol 4 (12) ◽

pp. 2066-2077 ◽

Cited By ~ 15

Author(s):

Rachel Taylor ◽

Bessie Wanja Kebaara ◽

Tara Nazarenus ◽

Ashley Jones ◽

Rena Yamanaka ◽

...

Keyword(s):

Saccharomyces Cerevisiae ◽

Mrna Decay ◽

Translation Termination ◽

Yeast Cells ◽

Wild Type ◽

Transcription Activator ◽

Nonsense Mediated Mrna Decay ◽

Indirect Consequence ◽

Transcription Activators ◽

And Function

ABSTRACT The nonsense-mediated mRNA decay (NMD) pathway has historically been thought of as an RNA surveillance system that degrades mRNAs with premature translation termination codons, but the NMD pathway of Saccharomyces cerevisiae has a second role regulating the decay of some wild-type mRNAs. In S. cerevisiae, a significant number of wild-type mRNAs are affected when NMD is inactivated. These mRNAs are either wild-type NMD substrates or mRNAs whose abundance increases as an indirect consequence of NMD. A current challenge is to sort the mRNAs that accumulate when NMD is inactivated into direct and indirect targets. We have developed a bioinformatics-based approach to address this challenge. Our approach involves using existing genomic and function databases to identify transcription factors whose mRNAs are elevated in NMD-deficient cells and the genes that they regulate. Using this strategy, we have investigated a coregulated set of genes. We have shown that NMD regulates accumulation of ADR1 and GAL4 mRNAs, which encode transcription activators, and that Adr1 is probably a transcription activator of ATS1. This regulation is physiologically significant because overexpression of ADR1 causes a respiratory defect that mimics the defect seen in strains with an inactive NMD pathway. This strategy is significant because it allows us to classify the genes regulated by NMD into functionally related sets, an important step toward understanding the role NMD plays in the normal functioning of yeast cells.

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