A functional involvement of ABCE1, eukaryotic ribosome recycling factor, in nonstop mRNA decay in Drosophila melanogaster cells

Kashima, Isao; Takahashi, Masaki; Hashimoto, Yoshifumi; Sakota, Eri; Nakamura, Yoshikazu; Inada, Toshifumu

doi:10.1016/j.biochi.2014.08.001

Cited by 15 publications

(17 citation statements)

References 39 publications

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“…To construct the small 30S subunit of the S. solfataricus ribosome, the homology models of the archaeal ribosomal proteins were aligned to the known small ribosomal subunit from S. cerevisiae (pdb: 3U5G, 3U5F)36. Yeast ribosomal proteins are thereby named according to the new nomenclature of ribosomal proteins, while the archaeal r-proteins hold their UniProt entry name going along with the MS analysis19. A model of ABCE1 in the closed state is positioned according to the cryo-EM map of the pre-recycling complex (pdb: 3J16)8.…”

Section: Methodsmentioning

confidence: 99%

“…Nevertheless, in accordance to its strong sequence conservation, ABCE1 proved to be indispensable for the fundamental process of ribosome recycling25. ABCE1 is able to recycle post-termination complexes after canonical translation as well as vacant ribosomes and stalled ribosomal complexes, which are further processed by messenger RNA (mRNA) surveillance mechanisms218192021. During canonical translation, ABCE1 is recruited to the post-termination complex after dissociation of the GTPase eRF3/aEF1α (ref.…”

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confidence: 99%

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Structure of the ribosome post-recycling complex probed by chemical cross-linking and mass spectrometry

et al. 2016

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Ribosome recycling orchestrated by the ATP binding cassette (ABC) protein ABCE1 can be considered as the final—or the first—step within the cyclic process of protein synthesis, connecting translation termination and mRNA surveillance with re-initiation. An ATP-dependent tweezer-like motion of the nucleotide-binding domains in ABCE1 transfers mechanical energy to the ribosome and tears the ribosome subunits apart. The post-recycling complex (PRC) then re-initiates mRNA translation. Here, we probed the so far unknown architecture of the 1-MDa PRC (40S/30S·ABCE1) by chemical cross-linking and mass spectrometry (XL-MS). Our study reveals ABCE1 bound to the translational factor-binding (GTPase) site with multiple cross-link contacts of the helix–loop–helix motif to the S24e ribosomal protein. Cross-linking of the FeS cluster domain to the ribosomal protein S12 substantiates an extreme lever-arm movement of the FeS cluster domain during ribosome recycling. We were thus able to reconstitute and structurally analyse a key complex in the translational cycle, resembling the link between translation initiation and ribosome recycling.

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Section: Methodsmentioning

confidence: 99%

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confidence: 99%

Structure of the ribosome post-recycling complex probed by chemical cross-linking and mass spectrometry

et al. 2016

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“…In addition to the nucleotide and amino acid building blocks, all three steps require energy and are interdependent, as nucleic acids and proteins are both essential for each process. Likewise, Fe-S clusters are also required at each step as cofactors of the DNA polymerase (see references in Table 1 and Kaguni et al, 1983 ; Peck et al, 1992 ; Sahashi et al, 2014 ; Stiban et al, 2014 ), of the essential subunit of the basal transcription factor TFIIH Xpd (Reynaud et al, 1999 ; Chen et al, 2003 ; Aguilar-Fuentes et al, 2006 ; Li et al, 2010 ) and of Pixie, which is required for ribosome biosynthesis and the initiation of translation (Andersen and Leevers, 2007 ; Kashima et al, 2014 ). Thus, DNA replication, transcription, and translation rest on the CIA providing Fe-S cluster to DNA polymerase, Xpd, and Pixie, respectively.…”

Section: Fe-s and Moco Enzymesmentioning

confidence: 99%

Iron Sulfur and Molybdenum Cofactor Enzymes Regulate the Drosophila Life Cycle by Controlling Cell Metabolism

2018

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Iron sulfur (Fe-S) clusters and the molybdenum cofactor (Moco) are present at enzyme sites, where the active metal facilitates electron transfer. Such enzyme systems are soluble in the mitochondrial matrix, cytosol and nucleus, or embedded in the inner mitochondrial membrane, but virtually absent from the cell secretory pathway. They are of ancient evolutionary origin supporting respiration, DNA replication, transcription, translation, the biosynthesis of steroids, heme, catabolism of purines, hydroxylation of xenobiotics, and cellular sulfur metabolism. Here, Fe-S cluster and Moco biosynthesis in Drosophila melanogaster is reviewed and the multiple biochemical and physiological functions of known Fe-S and Moco enzymes are described. We show that RNA interference of Mocs3 disrupts Moco biosynthesis and the circadian clock. Fe-S-dependent mitochondrial respiration is discussed in the context of germ line and somatic development, stem cell differentiation and aging. The subcellular compartmentalization of the Fe-S and Moco assembly machinery components and their connections to iron sensing mechanisms and intermediary metabolism are emphasized. A biochemically active Fe-S core complex of heterologously expressed fly Nfs1, Isd11, IscU, and human frataxin is presented. Based on the recent demonstration that copper displaces the Fe-S cluster of yeast and human ferredoxin, an explanation for why high dietary copper leads to cytoplasmic iron deficiency in flies is proposed. Another proposal that exosomes contribute to the transport of xanthine dehydrogenase from peripheral tissues to the eye pigment cells is put forward, where the Vps16a subunit of the HOPS complex may have a specialized role in concentrating this enzyme within pigment granules. Finally, we formulate a hypothesis that (i) mitochondrial superoxide mobilizes iron from the Fe-S clusters in aconitase and succinate dehydrogenase; (ii) increased iron transiently displaces manganese on superoxide dismutase, which may function as a mitochondrial iron sensor since it is inactivated by iron; (iii) with the Krebs cycle thus disrupted, citrate is exported to the cytosol for fatty acid synthesis, while succinyl-CoA and the iron are used for heme biosynthesis; (iv) as iron is used for heme biosynthesis its concentration in the matrix drops allowing for manganese to reactivate superoxide dismutase and Fe-S cluster biosynthesis to reestablish the Krebs cycle.

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“…Aberrant translation arrest induced by poly-lysine sequence results in RQC in yeast 1, 2, 4, 13–20 , in Droshophila 21, 22 , and in mammalian cells 8, 9, 23–26 . The yeast Ltn1 was identified by genetic screen as a factor that is involved in the repression of aberrant nonstop products with poly-lysine sequence produced by translation of a poly(A) tail of nonstop mRNA 27 .…”

Section: Introductionmentioning

confidence: 99%

Ubiquitination of stalled ribosome triggers ribosome-associated quality control

et al. 2017

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Translation arrest by polybasic sequences induces ribosome stalling, and the arrest product is degraded by the ribosome-mediated quality control (RQC) system. Here we report that ubiquitination of the 40S ribosomal protein uS10 by the E3 ubiquitin ligase Hel2 (or RQT1) is required for RQC. We identify a RQC-trigger (RQT) subcomplex composed of the RNA helicase-family protein Slh1/Rqt2, the ubiquitin-binding protein Cue3/Rqt3, and yKR023W/Rqt4 that is required for RQC. The defects in RQC of the RQT mutants correlate with sensitivity to anisomycin, which stalls ribosome at the rotated form. Cryo-electron microscopy analysis reveals that Hel2-bound ribosome are dominantly the rotated form with hybrid tRNAs. Ribosome profiling reveals that ribosomes stalled at the rotated state with specific pairs of codons at P-A sites serve as RQC substrates. Rqt1 specifically ubiquitinates these arrested ribosomes to target them to the RQT complex, allowing subsequent RQC reactions including dissociation of the stalled ribosome into subunits.

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A functional involvement of ABCE1, eukaryotic ribosome recycling factor, in nonstop mRNA decay in Drosophila melanogaster cells

Cited by 15 publications

References 39 publications

Structure of the ribosome post-recycling complex probed by chemical cross-linking and mass spectrometry

Structure of the ribosome post-recycling complex probed by chemical cross-linking and mass spectrometry

Iron Sulfur and Molybdenum Cofactor Enzymes Regulate the Drosophila Life Cycle by Controlling Cell Metabolism

Ubiquitination of stalled ribosome triggers ribosome-associated quality control

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