Nonstop-mRNA decay machinery is involved in the clearance of mRNA 5′-fragments produced by RNAi and NMD in Drosophila melanogaster cells

Hashimoto, Yoshifumi; Takahashi, Masaki; Sakota, Eri; Nakamura, Yoshikazu

doi:10.1016/j.bbrc.2017.01.092

Cited by 30 publications

(46 citation statements)

References 28 publications

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“…We and others have recently shown that translation surveillance factors including skih-2 and pelo-1 act in NMD after a committed step of mRNA decay (Arribere and Fire 2018;Hashimoto et al 2017). The effect of skih-2 and pelo-1 on NMD targets is not detectable at the level of RNAseq, but is detectable as an accumulation of 15-18nt Ribo-seq footprints that represent a population of stalled ribosomes.…”

Section: Nonu-1 Acts In No-go Mrna Decaymentioning

confidence: 99%

“…Another possibility is that SKI's role in surveillance is misunderstood. While it is widely known that one function of the SKI complex is to destabilize the upstream (5') mRNA fragment during translation surveillance (e.g., (Doma and Parker 2006;Hashimoto et al 2017)), it is unclear if this effect is responsible for the phenotypic suppression of Nonstop reporters by SKI. Alternative models include functional suppression by SKI's effects on ribosome recycling or initiation (Searfoss and Wickner 2000;Searfoss et al 2001), which is also consistent with recent structural data showing a direct role for SKI on the ribosome and near the 5'ends of ORFs (Schmidt et al 2016).…”

Section: The Role Of Nonu-1 In Translation Surveillancementioning

confidence: 99%

“…Central to both Nonstop and No-Go Decay is the process of ribosome stalling. Recent work has also shown that ribosomes stall during Nonsense-Mediated mRNA Decay, effectively funneling NMD targets into Nonstop Decay (Hashimoto et al 2017;Arribere and Fire 2018). Despite substantial mechanistic insight into translation surveillance pathways (reviewed in (Joazeiro 2017)), how ribosomal stalling communicates with mRNA decay machinery remains a central unsolved question.…”

Section: Introductionmentioning

confidence: 99%

“…Mounting evidence points to endonucleolytic cleavage of the mRNA in the vicinity of stalled ribosomes as an important early event in translation surveillance (e.g., (Doma and Parker 2006;Guydosh and Green 2014;Ikeuchi et al 2019;Navickas et al)). While the identity of the critical nuclease(s) remain unknown, target mRNAs are eventually cleared in part by 3'>5' degradation facilitated by the SKI RNA helicase in conjunction with the exosome (Doma and Parker 2006;van Hoof et al 2002;Hashimoto et al 2017;Arribere and Fire 2018). Knowledge of the identity and functions of factors that interface between translation and mRNA decay will illuminate a critical junction in gene expression and regulation.…”

Section: Introductionmentioning

confidence: 99%

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NONU-1 encodes a conserved endonuclease required for mRNA translation surveillance

Glover

Burroughs

Egelhofer

et al. 2019

Preprint

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Cellular translation surveillance rescues ribosomes that stall on problematic mRNAs. During translation surveillance, endonucleolytic cleavage of the problematic mRNA is a critical step in rescuing stalled ribosomes. However, the nuclease(s) responsible remain unknown. Here we identify NONU-1 as a novel endoribonuclease required for translation surveillance pathways including No-Go and Nonstop mRNA Decay. We show that: (1) NONU-1 reduces Nonstop and No-Go mRNA levels; (2) NONU-1 contains an Smr RNase domain required for mRNA decay and with properties similar to the unknown endonuclease; and (3) the domain architecture and catalytic residues of NONU-1 are conserved throughout metazoans and eukaryotes, respectively. We extend our results in C. elegans to homologous factors in S. cerevisiae, showing conservation of function of the NONU-1 protein across billions of years of evolution.Our work establishes the identity of a previously unknown factor critical to translation surveillance and will inform mechanistic studies at the intersection of translation and mRNA decay. 1 5 10 15 20 25 2 30 35 40 45 50 that organism. NONU-1 contains a conserved IF3-C fold domain previously implicated in processing RNA. Our results identify a critical new component of the translation surveillance machinery in two model organisms and suggest why this factor has been recalcitrant to discovery in S. cerevisiae. RESULTS nonu-1 encodes a novel factor required for Nonstop mRNA DecayWe previously developed a phenotypic reporter in C. elegans that allowed us to identify Nonstop mRNA Decay factors via reverse and forward genetics ( Figure 1A, (Arribere and Fire 2018)).Briefly, the reporter was constructed using the unc-54 locus as expression and function of this gene has been extensively studied (Brenner 1974;Epstein et al. 1974;Dibb et al. 1985Dibb et al. , 1989Moerman et al. 1982;Bejsovec and Anderson 1988;Anderson and Brenner 1984) and unc-54 has been used in previous suppressor screens (Hodgkin et al. 1989). To construct a Nonstop reporter at the unc-54 locus we first integrated a GFP at the C-terminus of UNC-54 by CRISPR/Cas9. We also removed all stop codons from the 3'UTR and integrated a ribosomal skipping T2A sequence between the C-terminal GFP and the remainder of the 3'UTR. The T2A sequence is a viral-derived peptide that cotranslationally releases the upstream protein and allows UNC-54::GFP to escape Nonstop protein decay (so-called "Ribosome Quality Control", (Bengtson and Joazeiro 2010;Shao et al. 2013;Shen et al. 2015)). We hereafter refer to the unc-54::gfp::t2a::nonstop reporter as unc-54 (Nonstop). Animals with the unc-54 (Nonstop) reporter deficient in Nonstop mRNA Decay exhibit derepression of the locus, as evidenced by increased GFP fluorescence, mRNA expression, and egg laying (unc-54 encodes a muscle myosin required in the vulva for egg laying) ( Figure 1B, (Arribere and Fire 2018)).Although our initial screen successfully identified C. elegans' skih-2 and ttc-37 (homologs of S. cerevisiae SKI2 and SKI3, respectively), ...

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Section: Nonu-1 Acts In No-go Mrna Decaymentioning

confidence: 99%

Section: The Role Of Nonu-1 In Translation Surveillancementioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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NONU-1 encodes a conserved endonuclease required for mRNA translation surveillance

Glover

Burroughs

Egelhofer

et al. 2019

Preprint

View full text Add to dashboard Cite

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“…nor show any evidence for aberrant splicing that would give rise to premature termination codons ( Figure S3B), ruling out NMD [42][43][44] . NSD is triggered by ribosome read through into the 3' UTR, but all Tst-regulated RNAs are annotated transcripts that encode stop codons suggesting that NSD is also not involved [45][46][47] .…”

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confidence: 99%

RNA degradation sculpts the maternal transcriptome duringDrosophilaoogenesis

Blatt

Wong-Deyrup

McCarthy

et al. 2020

Preprint

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AbstractIn sexually reproducing animals, the oocyte contributes a large supply of RNAs that are essential to launch development upon fertilization. The mechanisms that regulate the composition of the maternal RNA contribution during oogenesis are unclear. Here, we show that a subset of RNAs expressed during the early stages of oogenesis is subjected to regulated degradation during oocyte specification. Failure to remove these RNAs results in oocyte dysfunction and death. We identify the RNA-degrading Super Killer complex and No-Go Decay factor Pelota as key regulators of oogenesis via targeted clearance of RNAs expressed in germline stem cells. These regulators target RNAs enriched for cytidine sequences bound by the protein Half pint. Thus, RNA degradation helps orchestrate a germ cell-to-maternal transition by sculpting the maternal RNA contribution to the zygote.

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PolyA tracks, polybasic peptides, poly‐translational hurdles

Arthur

Djuranović

2018

WIREs RNA

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The abundance of messenger RNA (mRNA) is one of the major determinants of protein synthesis. As such, factors that influence mRNA stability often contribute to gene regulation. Polyadenylation of the 3' end of mRNA transcripts, the poly(A) tail, has long been recognized as one of these regulatory elements given its influence on translation efficiency and mRNA stability. Unwanted translation of the poly(A) tail signals to the cell an aberrant polyadenylation event or the lack of stop codons, which makes this sequence an important element in translation fidelity and mRNA surveillance response. Consequently, investigations into the effects of the poly(A) tail lead to the discoveries that poly-lysine as well as other polybasic peptide sequences and, to a much greater extent, polyA mRNA sequences within the open reading frame influence mRNA stability and translational efficiency. Conservation and evolutionary selection of codon usage in polyA track sequences across multiple organisms suggests a biological significance for coding polyA tracks in the regulation of gene expression. Here, we discuss the cellular responses and consequences of coding polyA track translation and synthesis of polybasic peptides. This article is categorized under Translation > Translation Mechanisms Translation > Translation Regulation RNA Turnover and Surveillance > Turnover/Surveillance Mechanisms.

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Nonstop-mRNA decay machinery is involved in the clearance of mRNA 5′-fragments produced by RNAi and NMD in Drosophila melanogaster cells

Cited by 30 publications

References 28 publications

NONU-1 encodes a conserved endonuclease required for mRNA translation surveillance

NONU-1 encodes a conserved endonuclease required for mRNA translation surveillance

RNA degradation sculpts the maternal transcriptome duringDrosophilaoogenesis

PolyA tracks, polybasic peptides, poly‐translational hurdles

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