301
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Assenholt J, Mouaikel J, Andersen KR, Brodersen DE, Libri D, Jensen TH. Exonucleolysis is required for nuclear mRNA quality control in yeast THO mutants. RNA (NEW YORK, N.Y.) 2008; 14:2305-13. [PMID: 18824516 PMCID: PMC2578857 DOI: 10.1261/rna.1108008] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Production of aberrant messenger ribonucleoprotein particles (mRNPs) is subject to quality control (QC). In yeast strains carrying mutations of the THO complex, transcription induction triggers a number of interconnected QC phenotypes: (1) rapid degradation of several mRNAs; (2) retention of a fraction of THO-dependent mRNAs in transcription site-associated foci; and (3) formation of a high molecular weight DNA/protein complex in the 3'-ends of THO target genes. Here, we demonstrate that the 3'-5' exonucleolytic domain of the nuclear exosome factor Rrp6p is necessary for establishing all QC phenotypes associated with THO mutations. The N terminus of Rrp6p is also important presumably through its binding to the Rrp6p co-factor Rrp47p. Interestingly, the 3'-5' exonucleolytic activity of Dis3p, the only other active exonuclease of the nuclear exosome, can also contribute to RNA QC in THO mutants, while other nuclear 3'-5' exonucleases cannot. Our data show that exonucleolytic attack by the nuclear exosome is needed both for provoking mRNP QC and for its ensuing elimination of faulty RNA.
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Affiliation(s)
- Jannie Assenholt
- Centre for mRNP Biogenesis and Metabolism, Department of Molecular Biology, The Faculty of Science, Aarhus University, DK-8000 Aarhus C, Denmark
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302
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Callahan KP, Butler JS. Evidence for core exosome independent function of the nuclear exoribonuclease Rrp6p. Nucleic Acids Res 2008; 36:6645-55. [PMID: 18940861 PMCID: PMC2588529 DOI: 10.1093/nar/gkn743] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The RNA exosome processes and degrades RNAs in archaeal and eukaryotic cells. Exosomes from yeast and humans contain two active exoribonuclease components, Rrp6p and Dis3p/Rrp44p. Rrp6p is concentrated in the nucleus and the dependence of its function on the nine-subunit core exosome and Dis3p remains unclear. We found that cells lacking Rrp6p accumulate poly(A)+ rRNA degradation intermediates distinct from those found in cells depleted of Dis3p, or the core exosome component Rrp43p. Depletion of Dis3p in the absence of Rrp6p causes a synergistic increase in the levels of degradation substrates common to the core exosome and Rrp6p, but has no effect on Rrp6p-specific substrates. Rrp6p lacking a portion of its C-terminal domain no longer co-purifies with the core exosome, but continues to carry out RNA 3'-end processing of 5.8S rRNA and snoRNAs, as well as the degradation of certain truncated Rrp6-specific rRNA intermediates. However, disruption of Rrp6p-core exosome interaction results in the inability of the cell to efficiently degrade certain poly(A)+ rRNA processing products that require the combined activities of Dis3p and Rrp6p. These findings indicate that Rrp6p may carry out some of its critical functions without physical association with the core exosome.
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Affiliation(s)
- Kevin P Callahan
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY 14642, USA
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303
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Schmid M, Jensen TH. The exosome: a multipurpose RNA-decay machine. Trends Biochem Sci 2008; 33:501-10. [PMID: 18786828 DOI: 10.1016/j.tibs.2008.07.003] [Citation(s) in RCA: 193] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2008] [Revised: 07/03/2008] [Accepted: 07/07/2008] [Indexed: 10/21/2022]
Abstract
The diversity of RNAs in the cell continues to amaze. In addition to the 'classic' species of mRNA, tRNA, rRNA, snRNA and snoRNA, it is now clear that the majority of genomic information is transcribed into RNA molecules. The resulting complexity of the transcriptome poses a serious challenge to cells because they must manage numerous RNA-processing reactions, yet, at the same time, eradicate surplus and aberrant material without destroying functional RNA. The 3'-->5' exonucleolytic RNA exosome is emerging as a major facilitator of such events. Recent structural and functional data regarding this fascinating complex and its many co-factors illuminate its diverse biochemical properties and indicate mechanisms by which RNAs are targeted for either processing or degradation.
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Affiliation(s)
- Manfred Schmid
- Centre for mRNP Biogenesis and Metabolism, Department of Molecular Biology, University of Aarhus, C.F. Møllers Alle, Bldg. 130, 8000 Aarhus C., Denmark
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304
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Andersen KR, Jensen TH, Brodersen DE. Take the "A" tail--quality control of ribosomal and transfer RNA. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2008; 1779:532-7. [PMID: 18657638 DOI: 10.1016/j.bbagrm.2008.06.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2008] [Revised: 05/30/2008] [Accepted: 06/30/2008] [Indexed: 11/16/2022]
Abstract
The overall fidelity of RNA biosynthesis and processing is very high. This goes for both mRNAs, which are turned over relatively quickly, and for stable RNAs, such as the components of the translational apparatus, the transfer and ribosomal RNAs. However, no enzymatic process is completely error-free, so to minimize the number of non-functional transcripts, the cell has degradation pathways in place to efficiently deal with those mistakes that inevitably occur. Though several "RNA surveillance" or "RNA quality control" systems have been described that are able to specifically eliminate misfolded and non-functional RNAs, we still do not understand neither what precise features define a faulty RNA, nor the molecular basis for recognition of such molecules. Nonetheless, our knowledge about the controlled degradation of both stable and labile RNAs is now converging into a unified picture that points to the poly(A) tail as a key discriminator of RNA quality in both bacteria and eukaryotes.
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Affiliation(s)
- Kasper R Andersen
- Centre for mRNP Biogenesis and Metabolism, Department of Molecular Biology, University of Aarhus, Gustav Wieds Vej 10c, DK-8000 Aarhus C, Denmark
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305
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Kammler S, Lykke-Andersen S, Jensen TH. The RNA Exosome Component hRrp6 Is a Target for 5-Fluorouracil in Human Cells. Mol Cancer Res 2008; 6:990-5. [DOI: 10.1158/1541-7786.mcr-07-2217] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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306
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Portnoy V, Schuster G. Mycoplasma gallisepticum as the first analyzed bacterium in which RNA is not polyadenylated. FEMS Microbiol Lett 2008; 283:97-103. [PMID: 18399989 DOI: 10.1111/j.1574-6968.2008.01157.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The addition of poly(A)-tails to RNA is a phenomenon common to almost all organisms. In addition to most eukaryotic mRNAs possessing a stable poly(A)-tail, RNA is polyadenylated as part of a degradation mechanism in prokaryotes, organelles, and the eukaryotic nucleus. To date, only very few systems have been described wherein RNA is metabolized without polyadenylation, including several archaea and yeast mitochondria. The minimal genome of the parasitic bacteria, Mycoplasma, does not encode homologs of any known polyadenylating enzyme. Here, we analyze polyadenylation in Mycoplasma gallisepticum. Our results suggest this organism as being the first described bacterium in which RNA is not polyadenylated.
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Affiliation(s)
- Victoria Portnoy
- Department of Biology, Technion - Israel Institute of Technology, Haifa, Israel
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307
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Vasiljeva L, Kim M, Terzi N, Soares LM, Buratowski S. Transcription termination and RNA degradation contribute to silencing of RNA polymerase II transcription within heterochromatin. Mol Cell 2008; 29:313-23. [PMID: 18280237 DOI: 10.1016/j.molcel.2008.01.011] [Citation(s) in RCA: 111] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2007] [Revised: 12/12/2007] [Accepted: 01/30/2008] [Indexed: 01/19/2023]
Abstract
Within the heterochromatin of budding yeast, RNA polymerase II (RNAPII) transcription is repressed by the Sir2 deacetylase. Although heterochromatic silencing is generally thought to be due to limited accessibility of the underlying DNA, there are several reports of RNAPII and basal transcription factors within silenced regions. Analysis of the rDNA array revealed cryptic RNAPII transcription within the "nontranscribed" spacer region. These transcripts are terminated by the Nrd1/Sen1 complex and degraded by the exosome. Mutations in this pathway lead to decreased silencing and dramatic chromatin changes in the rDNA locus. Interestingly, Nrd1 mutants also show higher levels of rDNA recombination, suggesting that the cryptic RNAPII transcription might have a physiological role in regulating rDNA copy number. The Nrd1/Sen1/exosome pathway also contributes to silencing at telomeric loci. These results suggest that silencing of heterochromatic genes in Saccharomyces cerevisiae occurs at both transcriptional and posttranscriptional levels.
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Affiliation(s)
- Lidia Vasiljeva
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
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308
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Navarro MVAS, Oliveira CC, Zanchin NIT, Guimarães BG. Insights into the mechanism of progressive RNA degradation by the archaeal exosome. J Biol Chem 2008; 283:14120-31. [PMID: 18353775 DOI: 10.1074/jbc.m801005200] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Initially identified in yeast, the exosome has emerged as a central component of the RNA maturation and degradation machinery both in Archaea and eukaryotes. Here we describe a series of high-resolution structures of the RNase PH ring from the Pyrococcus abyssi exosome, one of them containing three 10-mer RNA strands within the exosome catalytic chamber, and report additional nucleotide interactions involving positions N5 and N7. Residues from all three Rrp41-Rrp42 heterodimers interact with a single RNA molecule, providing evidence for the functional relevance of exosome ring-like assembly in RNA processivity. Furthermore, an ADP-bound structure showed a rearrangement of nucleotide interactions at site N1, suggesting a rationale for the elimination of nucleoside diphosphate after catalysis. In combination with RNA degradation assays performed with mutants of key amino acid residues, the structural data presented here provide support for a model of exosome-mediated RNA degradation that integrates the events involving catalytic cleavage, product elimination, and RNA translocation. Finally, comparisons between the archaeal and human exosome structures provide a possible explanation for the eukaryotic exosome inability to catalyze phosphate-dependent RNA degradation.
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309
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Wilusz CJ, Wilusz J. New ways to meet your (3') end oligouridylation as a step on the path to destruction. Genes Dev 2008; 22:1-7. [PMID: 18172159 DOI: 10.1101/gad.1634508] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Carol J Wilusz
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado 80523, USA.
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310
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Barbas A, Matos RG, Amblar M, López-Viñas E, Gomez-Puertas P, Arraiano CM. New insights into the mechanism of RNA degradation by ribonuclease II: identification of the residue responsible for setting the RNase II end product. J Biol Chem 2008; 283:13070-6. [PMID: 18337246 DOI: 10.1074/jbc.m709989200] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
RNase II is a key exoribonuclease involved in the maturation, turnover, and quality control of RNA. RNase II homologues are components of the exosome, a complex of exoribonucleases. The structure of RNase II unraveled crucial aspects of the mechanism of RNA degradation. Here we show that mutations in highly conserved residues at the active site affect the activity of the enzyme. Moreover, we have identified the residue that is responsible for setting the end product of RNase II. In addition, we present for the first time the models of two members of the RNase II family, RNase R from Escherichia coli and human Rrp44, also called Dis3. Our findings improve the present model for RNA degradation by the RNase II family of enzymes.
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Affiliation(s)
- Ana Barbas
- Instituto de Tecnologia Química e Biológica/Universidade Nova de Lisboa, Apartado 127, 2781-901 Oeiras, Portugal
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311
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Lorentzen E, Basquin J, Tomecki R, Dziembowski A, Conti E. Structure of the Active Subunit of the Yeast Exosome Core, Rrp44: Diverse Modes of Substrate Recruitment in the RNase II Nuclease Family. Mol Cell 2008; 29:717-28. [DOI: 10.1016/j.molcel.2008.02.018] [Citation(s) in RCA: 129] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2007] [Revised: 01/07/2008] [Accepted: 02/28/2008] [Indexed: 10/22/2022]
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312
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Degradation of a polyadenylated rRNA maturation by-product involves one of the three RRP6-like proteins in Arabidopsis thaliana. Mol Cell Biol 2008; 28:3038-44. [PMID: 18285452 DOI: 10.1128/mcb.02064-07] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Yeast Rrp6p and its human counterpart, PM/Scl100, are exosome-associated proteins involved in the degradation of aberrant transcripts and processing of precursors to stable RNAs, such as the 5.8S rRNA, snRNAs, and snoRNAs. The activity of yeast Rrp6p is stimulated by the polyadenylation of its RNA substrates. We identified three RRP6-like proteins in Arabidopsis thaliana: AtRRP6L3 is restricted to the cytoplasm, whereas AtRRP6L1 and -2 have different intranuclear localizations. Both nuclear RRP6L proteins are functional, since AtRRP6L1 complements the temperature-sensitive phenotype of a yeast rrp6Delta strain and mutation of AtRRP6L2 leads to accumulation of an rRNA maturation by-product. This by-product corresponds to the excised 5' part of the 18S-5.8S-25S rRNA precursor and accumulates as a polyadenylated transcript, suggesting that RRP6L2 is involved in poly(A)-mediated RNA degradation in plant nuclei. Interestingly, the rRNA maturation by-product is a substrate of AtRRP6L2 but not of AtRRP6L1. This result and the distinctive subcellular distribution of AtRRP6L1 to -3 indicate a specialization of RRP6-like proteins in Arabidopsis.
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313
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Genome-wide high-resolution mapping of exosome substrates reveals hidden features in the Arabidopsis transcriptome. Cell 2008; 131:1340-53. [PMID: 18160042 DOI: 10.1016/j.cell.2007.10.056] [Citation(s) in RCA: 240] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2007] [Revised: 10/01/2007] [Accepted: 10/25/2007] [Indexed: 11/21/2022]
Abstract
The exosome complex plays a central and essential role in RNA metabolism. However, comprehensive studies of exosome substrates and functional analyses of its subunits are lacking. Here, we demonstrate that as opposed to yeast and metazoans the plant exosome core possesses an unanticipated functional plasticity and present a genome-wide atlas of Arabidopsis exosome targets. Additionally, our study provides evidence for widespread polyadenylation- and exosome-mediated RNA quality control in plants, reveals unexpected aspects of stable structural RNA metabolism, and uncovers numerous novel exosome substrates. These include a select subset of mRNAs, miRNA processing intermediates, and hundreds of noncoding RNAs, the vast majority of which have not been previously described and belong to a layer of the transcriptome that can only be visualized upon inhibition of exosome activity. These first genome-wide maps of exosome substrates will aid in illuminating new fundamental components and regulatory mechanisms of eukaryotic transcriptomes.
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314
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Portnoy V, Palnizky G, Yehudai-Resheff S, Glaser F, Schuster G. Analysis of the human polynucleotide phosphorylase (PNPase) reveals differences in RNA binding and response to phosphate compared to its bacterial and chloroplast counterparts. RNA (NEW YORK, N.Y.) 2008; 14:297-309. [PMID: 18083836 PMCID: PMC2212259 DOI: 10.1261/rna.698108] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2007] [Accepted: 10/24/2007] [Indexed: 05/25/2023]
Abstract
PNPase is a major exoribonuclease that plays an important role in the degradation, processing, and polyadenylation of RNA in prokaryotes and organelles. This phosphorolytic processive enzyme uses inorganic phosphate and nucleotide diphosphate for degradation and polymerization activities, respectively. Its structure and activities are similar to the archaeal exosome complex. The human PNPase was recently localized to the intermembrane space (IMS) of the mitochondria, and is, therefore, most likely not directly involved in RNA metabolism, unlike in bacteria and other organelles. In this work, the degradation, polymerization, and RNA-binding properties of the human PNPase were analyzed and compared to its bacterial and organellar counterparts. Phosphorolytic activity was displayed at lower optimum concentrations of inorganic phosphate. Also, the RNA-binding properties to ribohomopolymers varied significantly from those of its bacterial and organellar enzymes. The purified enzyme did not preferentially bind RNA harboring a poly(A) tail at the 3' end, compared to a molecule lacking this tail. Several site-directed mutations at conserved amino acid positions either eliminated or modified degradation/polymerization activity in different manners than observed for the Escherichia coli PNPase and the archaeal and human exosomes. In light of these results, a possible function of the human PNPase in the mitochondrial IMS is discussed.
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Affiliation(s)
- Victoria Portnoy
- Department of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel
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315
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Cristodero M, Böttcher B, Diepholz M, Scheffzek K, Clayton C. The Leishmania tarentolae exosome: purification and structural analysis by electron microscopy. Mol Biochem Parasitol 2008; 159:24-9. [PMID: 18279979 DOI: 10.1016/j.molbiopara.2007.12.012] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2007] [Revised: 12/20/2007] [Accepted: 12/28/2007] [Indexed: 11/16/2022]
Abstract
The eukaryotic exosome is a complex of at least 11 proteins that is required for various 3'-5' exoribonucleolytic RNA processing and degradation reactions. The minimal core consists of 6 RNase PH and 3 S1 domain subunits; various additional proteins may be associated. We describe here the purification of native exosome from Leishmania tarentolae. The yield is sufficient for structural studies of the native exosome. Electron microscopy and image reconstruction of negatively stained preparations revealed the expected six-membered ring structure at 35 A resolution. An additional density suggested that RRP6 and its partner EAP3 (equivalent to Rrp47) might be located at the top of the exosome and at the side of the hexameric ring. No exonuclease or polyadenylation activity was detected in the exosome preparations.
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Affiliation(s)
- Marina Cristodero
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Im Neuenheimer Feld 282, D-69120 Heidelberg, Germany
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316
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Belostotsky D. Chapter 21 Transcriptome Targets of the Exosome Complex in Plants. Methods Enzymol 2008; 448:429-43. [DOI: 10.1016/s0076-6879(08)02621-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
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317
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Abstract
Proper degradation of plant messenger RNA is crucial for the maintenance of cellular and organismal homeostasis, and it must be properly regulated to enable rapid adjustments in response to endogenous and external cues. Only a few dedicated studies have been done so far to address the fundamental mechanisms of mRNA decay in plants, especially as compared with fungal and mammalian model systems. Consequently, our systems-level understanding of plant mRNA decay remains fairly rudimentary. Nevertheless, a number of serendipitous findings in recent years have reasserted the central position of the regulated mRNA decay in plant physiology. In addition, the meteoric rise to prominence of the plant small RNA field has spawned a renewed interest in the general plant mRNA turnover pathways. Combined with the advent of widely accessible microarray platforms, these advances allow for a renewed hope of rapid progress in our understanding of the fundamental rules governing regulated mRNA degradation in plants. This chapter summarizes recent findings in this field.
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Affiliation(s)
- D A Belostotsky
- School of Biological Sciences, University of Missouri-Kansas City, Kansas City, MO 64110, USA.
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318
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Greimann JC, Lima CD. Reconstitution of RNA exosomes from human and Saccharomyces cerevisiae cloning, expression, purification, and activity assays. Methods Enzymol 2008; 448:185-210. [PMID: 19111177 PMCID: PMC2773543 DOI: 10.1016/s0076-6879(08)02610-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Eukaryotic RNA exosomes participate in 3' to 5'-processing and degradation of RNA in the nucleus and cytoplasm. RNA exosomes are multisubunit complexes composed of at least nine distinct proteins that form the exosome core. Although the eukaryotic exosome core shares structural and sequence similarity to phosphorolytic archaeal exosomes and bacterial PNPase, the eukaryotic exosome core has diverged from its archaeal and bacterial cousins and appears devoid of phosphorolytic activity. In yeast, the processive hydrolytic 3' to 5'-exoribonuclease Rrp44 associates with exosomes in the nucleus and cytoplasm. Although human Rrp44 appears homologous to yeast Rrp44, it has not yet been shown to associate with human exosomes. In the nucleus, eukaryotic exosomes interact with Rrp6, a distributive hydrolytic 3' to 5'-exoribonuclease. To facilitate analysis of eukaryotic RNA exosomes, we will describe procedures used to clone, express, purify, and reconstitute the nine-subunit human exosome and nine-, ten-, and eleven-subunit yeast exosomes. We will also discuss procedures to assess exoribonuclease activity for reconstituted exosomes.
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Affiliation(s)
- Jaclyn C. Greimann
- Structural Biology Program, Sloan-Kettering Institute, New York, NY 10065
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319
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Lorentzen E, Conti E. Expression, reconstitution, and structure of an archaeal RNA degrading exosome. Methods Enzymol 2008; 447:417-35. [PMID: 19161854 DOI: 10.1016/s0076-6879(08)02220-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The exosome is a protein complex that participates in a wide variety of RNA processing, degradation, and quality-control pathways. The exosome is conserved in all eukaryotes studied to date and is also present in many archaeal organisms, albeit in a simpler form. To gain insights into the architecture of the exosome complex, we have chosen the hyperthermophilic archaeum Sulfolobus solfataricus as a model system. Here we describe the coexpression, purification, and crystal structure determination of archaeal exosome complexes. To understand how the archaeal exosome binds and degrades RNA, we designed RNA substrates for degradation experiments exploiting the knowledge of the geometric constraints of the exosome structure. Furthermore, we describe several crystal structures in which RNA substrates were diffused into crystals and how anomalous scattering from 5-iodo-uridine-modified RNA was used to locate low-occupancy RNA binding sites.
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Affiliation(s)
- Esben Lorentzen
- Birkbeck College London, Institute of Structural Molecular Biology, London, United Kingdom
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320
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Bernstein J, Patterson DN, Wilson GM, Toth EA. Characterization of the essential activities of Saccharomyces cerevisiae Mtr4p, a 3'->5' helicase partner of the nuclear exosome. J Biol Chem 2007; 283:4930-42. [PMID: 18096702 DOI: 10.1074/jbc.m706677200] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Mtr4p belongs to the Ski2p family of DEVH-box containing proteins and is required for processing and degradation of a variety of RNA substrates in the nucleus. In particular, Mtr4p is required for creating the 5.8 S ribosomal RNA from its 7 S precursor, proper 3'-end processing of the U4 small nuclear RNA and some small nucleolar RNAs, and degradation of aberrant mRNAs and tRNAs. In these studies we have shown that Mtr4p has RNA-dependent ATPase (or dATPase) activity that is stimulated effectively by likely substrates (e.g. tRNA) but surprisingly weakly by poly(A). Using an RNA strand-displacement assay, we have demonstrated that Mtr4p can, in the presence of ATP or dATP, unwind the duplex region of a partial duplex RNA substrate in the 3'-->5' direction. We have examined the ability of Mtr4p to bind model RNA substrates in the presence of nucleotides that mimic the stages (i.e. ATP-bound, ADP-bound, and nucleotide-free) of the unwinding reaction. Our results demonstrate that the presence of a non-hydrolyzable ATP analog allows Mtr4p to discriminate between partial duplex RNA substrates, binding a 3'-tailed substrate with 5-fold higher affinity than a 5'-tailed substrate. In addition, Mtr4p displays a marked preference for binding to poly(A) RNA relative to an oligoribonucleotide of the same length and a random sequence. This binding exhibits apparent cooperativity and different dynamic behavior from binding to the random single-stranded RNA. This unique binding mode might be employed primarily for degradation.
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Affiliation(s)
- Jade Bernstein
- Department of Biochemistry and Molecular Biology, and Marlene and Stewart Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
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321
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Slomovic S, Portnoy V, Yehudai-Resheff S, Bronshtein E, Schuster G. Polynucleotide phosphorylase and the archaeal exosome as poly(A)-polymerases. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2007; 1779:247-55. [PMID: 18177749 DOI: 10.1016/j.bbagrm.2007.12.004] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2007] [Revised: 11/29/2007] [Accepted: 12/06/2007] [Indexed: 02/02/2023]
Abstract
The addition of poly(A)-tails to RNA is a phenomenon common to almost all organisms. Not only homopolymeric poly(A)-tails, comprised exclusively of adenosines, but also heteropolymeric poly(A)-rich extensions, which include the other three nucleotides as well, have been observed in bacteria, archaea, chloroplasts, and human cells. Polynucleotide phosphorylase (PNPase) and the archaeal exosome, which bear strong similarities to one another, both functionally and structurally, were found to polymerize the heteropolymeric tails in bacteria, spinach chloroplasts, and archaea. As phosphorylases, these enzymes use diphosphate nucleotides as substrates and can reversibly polymerize or degrade RNA, depending on the relative concentrations of nucleotides and inorganic phosphate. A possible scenario, illustrating the evolution of RNA polyadenylation and its related functions, is presented, in which PNPase (or the archaeal exosome) was the first polyadenylating enzyme to evolve and the heteropolymeric tails that it produced, functioned in a polyadenylation-stimulated RNA degradation pathway. Only at a later stage in evolution, did the poly(A)-polymerases that use only ATP as a substrate, hence producing homopolymeric adenosine extensions, arise. Following the appearance of homopolymeric tails, a new role for polyadenylation evolved; RNA stability. This was accomplished by utilizing stable poly(A)-tails associated with the mature 3' ends of transcripts. Today, stable polyadenylation coexists with unstable heteropolymeric and homopolymeric tails. Therefore, the heteropolymeric poly(A)-rich tails, observed in bacteria, organelles, archaea, and human cells, represent an ancestral stage in the evolution of polyadenylation.
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Affiliation(s)
- Shimyn Slomovic
- Department of Biology, Technion - Israel Institute of Technology, Haifa, Israel
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322
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Couté Y, Kindbeiter K, Belin S, Dieckmann R, Duret L, Bezin L, Sanchez JC, Diaz JJ. ISG20L2, a novel vertebrate nucleolar exoribonuclease involved in ribosome biogenesis. Mol Cell Proteomics 2007; 7:546-59. [PMID: 18065403 DOI: 10.1074/mcp.m700510-mcp200] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Proteomics analyses of human nucleoli provided molecular bases for an understanding of the multiple functions fulfilled by these nuclear domains. However, the biological roles of about 100 of the identified proteins are unpredictable. The present study describes the functional characterization of one of these proteins, ISG20L2. We demonstrate that ISG20L2 is a 3' to 5' exoribonuclease involved in ribosome biogenesis at the level of 5.8 S rRNA maturation, more specifically in the processing of the 12 S precursor rRNA. The use of truncated forms of ISG20L2 demonstrated that its N-terminal half promotes the nucleolar localization and suggested that its C-terminal half bears the exoribonuclease activity. Identification of the binding partners of ISG20L2 confirmed its involvement in the biogenesis of the large ribosomal subunit. These results strongly support the notion that, in human, as it was demonstrated in yeast, 5.8 S rRNA maturation requires several proteins in addition to the exosome complex. Furthermore this observation greatly sustains the idea that the extremely conserved need for correctly processed rRNAs in vertebrates and yeast is achieved by close but different mechanisms.
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Affiliation(s)
- Yohann Couté
- Biomedical Proteomics Research Group, Département de Biologie Structurale et Bioinformatique, Centre Médical Universitaire, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland.
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323
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Ibrahim H, Wilusz J, Wilusz CJ. RNA recognition by 3'-to-5' exonucleases: the substrate perspective. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2007; 1779:256-65. [PMID: 18078842 DOI: 10.1016/j.bbagrm.2007.11.004] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2007] [Revised: 11/08/2007] [Accepted: 11/09/2007] [Indexed: 12/30/2022]
Abstract
The 3'-to-5' exonucleolytic decay and processing of a variety of RNAs is an essential feature of RNA metabolism in all cells. The 3'-5' exonucleases, and in particular the exosome, are involved in a large number of pathways from 3' processing of rRNA, snRNA and snoRNA, to decay of mRNAs and mRNA surveillance. The potent enzymes performing these reactions are regulated to prevent processing of inappropriate substrates whilst mature RNA molecules exhibit several attributes that enable them to evade 3'-5' attack. How does an enzyme perform such selective activities on different substrates? The goal of this review is to provide an overview and perspective of available data on the underlying principles for the recognition of RNA substrates by 3'-to-5' exonucleases.
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Affiliation(s)
- Hend Ibrahim
- Colorado State University, Department of Microbiology, Immunology and Pathology, Fort Collins, CO 80525, USA
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324
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Vanacova S, Stef R. The exosome and RNA quality control in the nucleus. EMBO Rep 2007; 8:651-7. [PMID: 17603538 PMCID: PMC1905902 DOI: 10.1038/sj.embor.7401005] [Citation(s) in RCA: 105] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2007] [Accepted: 05/04/2007] [Indexed: 11/09/2022] Open
Abstract
To control the quality of RNA biogenesis in the nucleus, cells use sophisticated molecular machines. These machines recognize and degrade not only RNA trimmings--the leftovers of RNA processing--but also incorrectly processed RNAs that contain defects. By using this mechanism, cells ensure that only high-quality RNAs are engaged in protein synthesis and other cellular processes. The exosome--a complex of several exoribonucleolytic and RNA-binding proteins--is the central 3'-end RNA degradation and processing factor in this surveillance apparatus. The exosome operates with auxiliary factors that stimulate its activity and recruit its RNA substrates in the crowded cellular environment. In this review, we discuss recent structural and functional data related to the nuclear quality-control apparatus, including the long-awaited structure of the human exosome and its activity.
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Affiliation(s)
- Stepanka Vanacova
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH-4057 Basel, Switzerland
| | - Richard Stef
- National Centre for Biomolecular Research, Masaryk University, Kamenice 5/A4, CZ-62500 Brno, Czech Republic
- Tel: +420 5 49 49 24 36; Fax: +420 5 49 49 25 56;
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325
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Architecture of the yeast Rrp44 exosome complex suggests routes of RNA recruitment for 3' end processing. Proc Natl Acad Sci U S A 2007; 104:16844-9. [PMID: 17942686 DOI: 10.1073/pnas.0705526104] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The eukaryotic core exosome (CE) is a conserved nine-subunit protein complex important for 3' end trimming and degradation of RNA. In yeast, the Rrp44 protein constitutively associates with the CE and provides the sole source of processive 3'-to-5' exoribonuclease activity. Here we present EM reconstructions of the core and Rrp44-bound exosome complexes. The two-lobed Rrp44 protein binds to the RNase PH domain side of the exosome and buttresses the bottom of the exosome-processing chamber. The Rrp44 C-terminal body part containing an RNase II-type active site is anchored to the exosome through a conserved set of interactions mainly to the Rrp45 and Rrp43 subunit, whereas the Rrp44 N-terminal head part is anchored to the Rrp41 subunit and may function as a roadblock to restrict access of RNA to the active site in the body region. The Rrp44-exosome (RE) architecture suggests an active site sequestration mechanism for strict control of 3' exoribonuclease activity in the RE complex.
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326
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327
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Liu Q, Greimann JC, Lima CD. Reconstitution, Activities, and Structure of the Eukaryotic RNA Exosome. Cell 2007. [DOI: 10.1016/j.cell.2007.09.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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328
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Simón E, Séraphin B. A specific role for the C-terminal region of the Poly(A)-binding protein in mRNA decay. Nucleic Acids Res 2007; 35:6017-28. [PMID: 17766253 PMCID: PMC2094065 DOI: 10.1093/nar/gkm452] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
mRNA poly(A) tails affect translation, mRNA export and mRNA stability, with translation initiation involving a direct interaction between eIF4G and the poly(A)-binding protein Pab1. The latter factor contains four RNA recognition motifs followed by a C-terminal region composed of a linker and a PABC domain. We show here that yeast mutants lacking the C-terminal domains of Pab1 display specific synthetic interactions with mutants in the 5′-3′ mRNA decay pathway. Moreover, these mutations impair mRNA decay in vivo without significantly affecting mRNA export or translation. Inhibition of mRNA decay occurs through slowed deadenylation. In vitro analyses demonstrate that removal of the Pab1 linker domain directly interferes with the ability of the Pop2–Ccr4 complex to deadenylate the Pab1-bound poly(A). Binding assays demonstrate that this results from a modulation of poly(A) packaging by the Pab1 linker region. Overall, our results demonstrate a direct involvement of Pab1 in mRNA decay and reveal the modular nature of this factor, with different domains affecting various cellular processes. These data suggest new models involving the modulation of poly(A) packaging by Pab1 to control mRNA decay.
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Affiliation(s)
| | - Bertrand Séraphin
- *To whom correspondence should be addressed. +33 1 69 82 38 84+33 1 69 82 38 77
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329
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Schneider C, Anderson JT, Tollervey D. The exosome subunit Rrp44 plays a direct role in RNA substrate recognition. Mol Cell 2007; 27:324-331. [PMID: 17643380 PMCID: PMC7610968 DOI: 10.1016/j.molcel.2007.06.006] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2006] [Revised: 04/12/2007] [Accepted: 06/06/2007] [Indexed: 10/23/2022]
Abstract
The exosome plays key roles in RNA maturation and surveillance, but it is unclear how target RNAs are identified. We report the functional characterization of the yeast exosome component Rrp44, a member of the RNase II family. Recombinant Rrp44 and the purified TRAMP polyadenylation complex each specifically recognized tRNA(i)(Met) lacking a single m(1)A(58) modification, even in the presence of a large excess of total tRNA. This tRNA is otherwise mature and functional in translation in vivo but is presumably subtly misfolded. Complete degradation of the hypomodified tRNA required both Rrp44 and the poly(A) polymerase activity of TRAMP. The intact exosome lacking only the catalytic activity of Rrp44 failed to degrade tRNA(i)(Met), showing this to be a specific Rrp44 substrate. Recognition of hypomodified tRNA(i)(Met) by Rrp44 is genetically separable from its catalytic activity on other substrates, with the mutations mapping to distinct regions of the protein.
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Affiliation(s)
- Claudia Schneider
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3JR, UK
| | - James T Anderson
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53201, USA
| | - David Tollervey
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3JR, UK.
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330
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Stead JA, Costello JL, Livingstone MJ, Mitchell P. The PMC2NT domain of the catalytic exosome subunit Rrp6p provides the interface for binding with its cofactor Rrp47p, a nucleic acid-binding protein. Nucleic Acids Res 2007; 35:5556-67. [PMID: 17704127 PMCID: PMC2018643 DOI: 10.1093/nar/gkm614] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The exosome complex is a key component of the cellular RNA surveillance machinery and is required for normal 3′ end processing of many stable RNAs. Exosome activity requires additional factors such as the Ski or TRAMP complexes to activate the complex or facilitate substrate binding. Rrp47p promotes the catalytic activity of the exosome component Rrp6p, but its precise function is unknown. Here we show that recombinant Rrp47p is expressed as an apparently hexameric complex that specifically binds structured nucleic acids. Furthermore, pull-down assays demonstrated that Rrp47p interacts directly with the N-terminal region of Rrp6p that contains the functionally uncharacterized PMC2NT domain. Strains expressing a mutant form of Rrp6p lacking the N-terminal region failed to accumulate Rrp47p at normal levels, exhibited a slow growth phenotype characteristic of rrp47-Δ mutants and showed RNA processing defects consistent with loss of Rrp47p function. These findings suggest Rrp47p promotes Rrp6p activity by facilitating binding via the PMC2NT domain to structural elements within RNA. Notably, characterized Rrp6p substrates such as the 5.8S+30 species are predicted to contain helices at their 3′ termini, while others such as intergenic or antisense cryptic unstable transcripts could potentially form extensive double-stranded molecules with overlapping mRNAs.
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Affiliation(s)
| | | | | | - Phil Mitchell
- *To whom correspondence should be addressed. +44 114 222 2821+44 0114 222 2800
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331
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Malecki M, Jedrzejczak R, Stepien PP, Golik P. In vitro reconstitution and characterization of the yeast mitochondrial degradosome complex unravels tight functional interdependence. J Mol Biol 2007; 372:23-36. [PMID: 17658549 DOI: 10.1016/j.jmb.2007.06.074] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2007] [Revised: 06/13/2007] [Accepted: 06/26/2007] [Indexed: 11/23/2022]
Abstract
The mitochondrial degradosome (mtEXO), the main RNA-degrading complex of yeast mitochondria, is composed of two subunits: an exoribonuclease encoded by the DSS1 gene and an RNA helicase encoded by the SUV3 gene. We expressed both subunits of the yeast mitochondrial degradosome in Escherichia coli, reconstituted the complex in vitro and analyzed the RNase, ATPase and helicase activities of the two subunits separately and in complex. The results reveal a very strong functional interdependence. For every enzymatic activity, we observed significant changes when the relevant protein was present in the complex, compared to the activity measured for the protein alone. The ATPase activity of Suv3p is stimulated by RNA and its background activity in the absence of RNA is reduced greatly when the protein is in the complex with Dss1p. The Suv3 protein alone does not display RNA-unwinding activity and the 3' to 5' directional helicase activity requiring a free 3' single-stranded substrate becomes apparent only when Suv3p is in complex with Dss1p. The Dss1 protein alone does have some basal exoribonuclease activity, which is not ATP-dependent, but in the presence of Suv3p the activity of the entire complex is enhanced greatly and is entirely ATP-dependent, with no residual activity observed in the absence of ATP. Such absolute ATP-dependence is unique among known exoribonuclease complexes. On the basis of these results, we propose a model in which the Suv3p RNA helicase acts as a molecular motor feeding the substrate to the catalytic centre of the RNase subunit.
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Affiliation(s)
- Michal Malecki
- Department of Genetics and Biotechnology, University of Warsaw, Pawinskiego 5A, 02-106, Warsaw, Poland
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332
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Gupta R, Kus B, Fladd C, Wasmuth J, Tonikian R, Sidhu S, Krogan NJ, Parkinson J, Rotin D. Ubiquitination screen using protein microarrays for comprehensive identification of Rsp5 substrates in yeast. Mol Syst Biol 2007; 3:116. [PMID: 17551511 PMCID: PMC1911201 DOI: 10.1038/msb4100159] [Citation(s) in RCA: 127] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2007] [Accepted: 04/24/2007] [Indexed: 01/25/2023] Open
Abstract
Ubiquitin-protein ligases (E3s) are responsible for target recognition and regulate stability, localization or function of their substrates. However, the substrates of most E3 enzymes remain unknown. Here, we describe the development of a novel proteomic in vitro ubiquitination screen using a protein microarray platform that can be utilized for the discovery of substrates for E3 ligases on a global scale. Using the yeast E3 Rsp5 as a test system to identify its substrates on a yeast protein microarray that covers most of the yeast (Saccharomyces cerevisiae) proteome, we identified numerous known and novel ubiquitinated substrates of this E3 ligase. Our enzymatic approach was complemented by a parallel protein microarray protein interaction study. Examination of the substrates identified in the analysis combined with phage display screening allowed exploration of binding mechanisms and substrate specificity of Rsp5. The development of a platform for global discovery of E3 substrates is invaluable for understanding the cellular pathways in which they participate, and could be utilized for the identification of drug targets.
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Affiliation(s)
- Ronish Gupta
- Program in Cell Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Bart Kus
- Program in Cell Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Christopher Fladd
- Program in Cell Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - James Wasmuth
- Program in Molecular Structure and Function, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Raffi Tonikian
- Banting & Best Department of Medical Research, University of Toronto, Canada
- Department of Molecular and Medical Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Sachdev Sidhu
- Department of Protein Engineering, Genentech, South San Francisco, CA, USA
| | - Nevan J Krogan
- Department of Cellular and Molecular Pharmacology, University of California-San Francisco, San Francisco, CA, USA
| | - John Parkinson
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
- Program in Molecular Structure and Function, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Molecular and Medical Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Daniela Rotin
- Program in Cell Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
- Program in Cell Biology, The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario, Canada M5G 1X8. Tel.: +1 416-813-5098; Fax: +1 416-813-8456;
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333
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Lin-Chao S, Chiou NT, Schuster G. The PNPase, exosome and RNA helicases as the building components of evolutionarily-conserved RNA degradation machines. J Biomed Sci 2007; 14:523-32. [PMID: 17514363 DOI: 10.1007/s11373-007-9178-y] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2007] [Accepted: 02/27/2007] [Indexed: 01/27/2023] Open
Abstract
The structure and function of polynucleotide phosphorylase (PNPase) and the exosome, as well as their associated RNA-helicases proteins, are described in the light of recent studies. The picture raised is of an evolutionarily conserved RNA-degradation machine which exonucleolytically degrades RNA from 3' to 5'. In prokaryotes and in eukaryotic organelles, a trimeric complex of PNPase forms a circular doughnut-shaped structure, in which the phosphorolysis catalytic sites are buried inside the barrel-shaped complex, while the RNA binding domains create a pore where RNA enters, reminiscent of the protein degrading complex, the proteasome. In some archaea and in the eukaryotes, several different proteins form a similar circle-shaped complex, the exosome, that is responsible for 3' to 5' exonucleolytic degradation of RNA as part of the processing, quality control, and general RNA degradation process. Both PNPase in prokaryotes and the exosome in eukaryotes are found in association with protein complexes that notably include RNA helicase.
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Affiliation(s)
- Sue Lin-Chao
- Institute of Molecular Biology, Academia Sinica, Taipei, 11529, Taiwan.
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334
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Hartung S, Hopfner KP. The exosome, plugged. EMBO Rep 2007; 8:456-7. [PMID: 17471261 PMCID: PMC1866209 DOI: 10.1038/sj.embor.7400961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2007] [Accepted: 03/13/2007] [Indexed: 11/09/2022] Open
Affiliation(s)
- Sophia Hartung
- Center of Integrated Protein Science and Gene Center, Ludwig-Maximilians University of Munich, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
| | - Karl-Peter Hopfner
- Center of Integrated Protein Science and Gene Center, Ludwig-Maximilians University of Munich, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
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335
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Reinisch KM, Wolin SL. Emerging themes in non-coding RNA quality control. Curr Opin Struct Biol 2007; 17:209-14. [PMID: 17395456 DOI: 10.1016/j.sbi.2007.03.012] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2006] [Revised: 01/26/2007] [Accepted: 03/16/2007] [Indexed: 01/15/2023]
Abstract
Quality control pathways for non-coding RNAs such as tRNAs and rRNAs are widespread. In both prokaryotes and eukaryotes, poly(A) polymerases target aberrant non-coding RNAs for degradation. In yeast, a nuclear complex that includes the poly(A) polymerase Trf4p works together with the exosome in degrading a broad array of non-coding RNAs, several of which are aberrant. Yeast also have additional pathways for the degradation of defective RNAs and other pathways may exist in higher eukaryotes. One possibility is that cells recognize specific, still undiscovered, features common to misfolded RNAs; however, an alternative is that RNA quality control proteins interact with relatively general RNA structures, whereas correctly folded RNAs are sequestered by specific RNA-binding proteins and thus protected from degradation. Recently available structures of protein and ribonucleoprotein complexes involved in non-coding RNA quality control are providing a more detailed understanding of this process.
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Affiliation(s)
- Karin M Reinisch
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06510, USA.
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336
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Lorentzen E, Dziembowski A, Lindner D, Seraphin B, Conti E. RNA channelling by the archaeal exosome. EMBO Rep 2007; 8:470-6. [PMID: 17380186 PMCID: PMC1866195 DOI: 10.1038/sj.embor.7400945] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2006] [Revised: 01/24/2007] [Accepted: 02/05/2007] [Indexed: 11/09/2022] Open
Abstract
Exosomes are complexes containing 3' --> 5' exoribonucleases that have important roles in processing, decay and quality control of various RNA molecules. Archaeal exosomes consist of a hexameric core of three active RNase PH subunits (ribosomal RNA processing factor (Rrp)41) and three inactive RNase PH subunits (Rrp42). A trimeric ring of subunits with putative RNA-binding domains (Rrp4/cep1 synthetic lethality (Csl)4) is positioned on top of the hexamer on the opposite side to the RNA degrading sites. Here, we present the 1.6 A resolution crystal structure of the nine-subunit exosome of Sulfolobus solfataricus and the 2.3 A structure of this complex bound to an RNA substrate designed to be partly trimmed rather than completely degraded. The RNA binds both at the active site on one side of the molecule and on the opposite side in the narrowest constriction of the central channel. Multiple substrate-binding sites and the entrapment of the substrate in the central channel provide a rationale for the processive degradation of extended RNAs and the stalling of structured RNAs.
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Affiliation(s)
- Esben Lorentzen
- European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, D-69117, Heidelberg, Germany
- Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, D-82152, Martinsried, Germany
- Tel: +49 6221 3878537; Fax: +49 6221 387 8519; E-mail:
| | - Andrzej Dziembowski
- Equipe Labellisée La Ligue, CGM, CNRS UPR2167, Associée à l'Université Pierre et Marie Curie, Avenue de la Terrasse, 91198 Gif sur Yvette Cedex, France
| | - Doris Lindner
- European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, D-69117, Heidelberg, Germany
| | - Bertrand Seraphin
- Equipe Labellisée La Ligue, CGM, CNRS UPR2167, Associée à l'Université Pierre et Marie Curie, Avenue de la Terrasse, 91198 Gif sur Yvette Cedex, France
| | - Elena Conti
- European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, D-69117, Heidelberg, Germany
- Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, D-82152, Martinsried, Germany
- Tel: +49 6221 3878537; Fax: +49 6221 387 8519; E-mail:
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337
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Murakami H, Goto DB, Toda T, Chen ES, Grewal SI, Martienssen RA, Yanagida M. Ribonuclease activity of Dis3 is required for mitotic progression and provides a possible link between heterochromatin and kinetochore function. PLoS One 2007; 2:e317. [PMID: 17380189 PMCID: PMC1820850 DOI: 10.1371/journal.pone.0000317] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2007] [Accepted: 03/05/2007] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND Cellular RNA metabolism has a broad range of functional aspects in cell growth and division, but its role in chromosome segregation during mitosis is only poorly understood. The Dis3 ribonuclease is a key component of the RNA-processing exosome complex. Previous isolation of the dis3-54 cold-sensitive mutant of fission yeast Schizosaccharomyces pombe suggested that Dis3 is also required for correct chromosome segregation. METHODOLOGY/PRINCIPAL FINDINGS We show here that the progression of mitosis is arrested in dis3-54, and that segregation of the chromosomes is blocked by activation of the mitotic checkpoint control. This block is dependent on the Mad2 checkpoint protein. Double mutant and inhibitor analyses revealed that Dis3 is required for correct kinetochore formation and function, and that this activity is monitored by the Mad2 checkpoint. Dis3 is a member of the highly conserved RNase II family and is known to be an essential subunit of the exosome complex. The dis3-54 mutation was found to alter the RNaseII domain of Dis3, which caused a reduction in ribonuclease activity in vitro. This was associated with loss of silencing of an ura4(+) reporter gene inserted into the outer repeats (otr) and central core (cnt and imr) regions of the centromere. On the other hand, centromeric siRNA maturation and formation of the RITS RNAi effector complex was normal in the dis3-54 mutant. Micrococcal nuclease assay also suggested the overall chromatin structure of the centromere was not affected in dis3-54 mutant. CONCLUSIONS/SIGNIFICANCE RNase activity of Dis3, a core subunit of exosome, was found to be required for proper kinetochore formation and establishment of kinetochore-microtubule interactions. Moreover, Dis3 was suggested to contribute to kinetochore formation through an involvement in heterochromatic silencing at both outer centromeric repeats and within the central core region. This activity is likely monitored by the mitotic checkpoint, and distinct from that of RNAi-mediated heterochromatin formation directly targeting outer centromeric repeats.
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Affiliation(s)
- Hiroaki Murakami
- CREST Research Program, Japan Science and Technology Corporation, Department of Gene Mechanisms, Graduate School of Biostudies, Kyoto University, Yoshida-Honmachi, Sakyo-ku, Kyoto, Japan
| | - Derek B. Goto
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Takashi Toda
- Laboratory of Cell Regulation, Cancer Research UK, London Research Institute, Lincoln's Inn Fields Laboratories, London, United Kingdom
| | - Ee Sin Chen
- Laboratory of Molecular Cell Biology, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Shiv I. Grewal
- Laboratory of Molecular Cell Biology, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Robert A. Martienssen
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Mitsuhiro Yanagida
- CREST Research Program, Japan Science and Technology Corporation, Department of Gene Mechanisms, Graduate School of Biostudies, Kyoto University, Yoshida-Honmachi, Sakyo-ku, Kyoto, Japan
- * To whom correspondence should be addressed. E-mail:
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338
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Hooker TS, Lam P, Zheng H, Kunst L. A core subunit of the RNA-processing/degrading exosome specifically influences cuticular wax biosynthesis in Arabidopsis. THE PLANT CELL 2007; 19:904-13. [PMID: 17351114 PMCID: PMC1867365 DOI: 10.1105/tpc.106.049304] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2006] [Revised: 02/01/2007] [Accepted: 02/23/2007] [Indexed: 05/14/2023]
Abstract
The cuticle is an extracellular matrix composed of cutin polyester and waxes that covers aerial organs of land plants and protects them from environmental stresses. The Arabidopsis thaliana cer7 mutant exhibits reduced cuticular wax accumulation and contains considerably lower transcript levels of ECERIFERUM3/WAX2/YORE-YORE (CER3/WAX2/YRE), a key wax biosynthetic gene. We show here that CER7 protein is a putative 3'-5' exoribonuclease homologous to yeast Ribonuclease PH45 (RRP45p), a core subunit of the RNA processing and degrading exosome that controls the expression of CER3/WAX2/YRE. We propose that CER7 acts by degrading a specific mRNA species encoding a negative regulator of CER3/WAX2/YRE transcription. A second RRP45p homolog found in Arabidopsis, designated At RRP45a, is partially functionally redundant with CER7, and complete loss of RRP45 function in Arabidopsis is lethal. To our knowledge, CER7 is currently the only example of a core exosomal subunit specifically influencing a cellular process.
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Affiliation(s)
- Tanya S Hooker
- Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
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