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Lv M, Yao Y, Li F, Xu L, Yang L, Gong Q, Xu YZ, Shi Y, Fan YJ, Tang Y. Structural insights reveal the specific recognition of roX RNA by the dsRNA-binding domains of the RNA helicase MLE and its indispensable role in dosage compensation in Drosophila. Nucleic Acids Res 2019; 47:3142-3157. [PMID: 30649456 PMCID: PMC6451107 DOI: 10.1093/nar/gky1308] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 12/19/2018] [Accepted: 12/24/2018] [Indexed: 02/04/2023] Open
Abstract
In Drosophila, dosage compensation globally upregulates the expression of genes located on male single X-chromosome. Maleless (MLE) helicase plays an essential role to incorporate the roX lncRNA into the dosage compensation complex (MSL-DCC), and such function is essentially dependent on its dsRNA-binding domains (dsRBDs). Here, we report a 2.90Å crystal structure of tandem dsRBDs of MLE in complex with a 55mer stem-loop of roX2 (R2H1). MLE dsRBDs bind to R2H1 cooperatively and interact with two successive minor grooves and a major groove of R2H1, respectively. The recognition of R2H1 by MLE dsRBDs involves both shape- and sequence-specificity. Moreover, dsRBD2 displays a stronger RNA affinity than dsRBD1, and mutations of key residues in either MLE dsRBD remarkably reduce their affinities for roX2 both in vitro and in vivo. In Drosophila, the structure-based mle mutations generated using the CRISPR/Cas9 system, are partially male-lethal and indicate the inter-regulation among the components of the MSL-DCC at multiple levels. Hence, our research provides structural insights into the interactions between MLE dsRBDs and R2H1 and facilitates a deeper understanding of the mechanism by which MLE tandem dsRBDs play an indispensable role in specific recognition of roX and the assembly of the MSL-DCC in Drosophila dosage compensation.
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Affiliation(s)
- Mengqi Lv
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Yixiang Yao
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Fudong Li
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Ling Xu
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Lingna Yang
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Qingguo Gong
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Yong-Zhen Xu
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Yunyu Shi
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China.,CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yu-Jie Fan
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China.,Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yajun Tang
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China
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Das S, Biswas S, Chaudhuri S, Bhattacharyya A, Das B. A Nuclear Zip Code in SKS1 mRNA Promotes Its Slow Export, Nuclear Retention, and Degradation by the Nuclear Exosome/DRN in Saccharomyces cerevisiae. J Mol Biol 2019; 431:3626-3646. [DOI: 10.1016/j.jmb.2019.07.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Revised: 06/26/2019] [Accepted: 07/01/2019] [Indexed: 01/12/2023]
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Zhou D, Lai M, Luo A, Yu CY. An RNA Metabolism and Surveillance Quartet in the Major Histocompatibility Complex. Cells 2019; 8:E1008. [PMID: 31480283 PMCID: PMC6769589 DOI: 10.3390/cells8091008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 08/27/2019] [Accepted: 08/29/2019] [Indexed: 02/07/2023] Open
Abstract
At the central region of the mammalian major histocompatibility complex (MHC) is a complement gene cluster that codes for constituents of complement C3 convertases (C2, factor B and C4). Complement activation drives the humoral effector functions for immune response. Sandwiched between the genes for serine proteinase factor B and anchor protein C4 are four less known but critically important genes coding for essential functions related to metabolism and surveillance of RNA during the transcriptional and translational processes of gene expression. These four genes are NELF-E (RD), SKIV2L (SKI2W), DXO (DOM3Z) and STK19 (RP1 or G11) and dubbed as NSDK. NELF-E is the subunit E of negative elongation factor responsible for promoter proximal pause of transcription. SKIV2L is the RNA helicase for cytoplasmic exosomes responsible for degradation of de-polyadenylated mRNA and viral RNA. DXO is a powerful enzyme with pyro-phosphohydrolase activity towards 5' triphosphorylated RNA, decapping and exoribonuclease activities of faulty nuclear RNA molecules. STK19 is a nuclear kinase that phosphorylates RNA-binding proteins during transcription. STK19 is also involved in DNA repair during active transcription and in nuclear signal transduction. The genetic, biochemical and functional properties for NSDK in the MHC largely stay as a secret for many immunologists. Here we briefly review the roles of (a) NELF-E on transcriptional pausing; (b) SKIV2L on turnover of deadenylated or expired RNA 3'→5' through the Ski-exosome complex, and modulation of inflammatory response initiated by retinoic acid-inducible gene 1-like receptor (RLR) sensing of viral infections; (c) DXO on quality control of RNA integrity through recognition of 5' caps and destruction of faulty adducts in 5'→3' fashion; and (d) STK19 on nuclear protein phosphorylations. There is compelling evidence that a dysregulation or a deficiency of a NSDK gene would cause a malignant, immunologic or digestive disease.
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Affiliation(s)
- Danlei Zhou
- The Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH 43205, USA.
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China.
- Department of Pediatrics, The Ohio State University, Columbus, OH 43205, USA.
| | - Michalea Lai
- The Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH 43205, USA
- Department of Pediatrics, The Ohio State University, Columbus, OH 43205, USA
| | - Aiqin Luo
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China.
| | - Chack-Yung Yu
- The Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH 43205, USA.
- Department of Pediatrics, The Ohio State University, Columbus, OH 43205, USA.
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54
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Lange H, Ndecky SYA, Gomez-Diaz C, Pflieger D, Butel N, Zumsteg J, Kuhn L, Piermaria C, Chicher J, Christie M, Karaaslan ES, Lang PLM, Weigel D, Vaucheret H, Hammann P, Gagliardi D. RST1 and RIPR connect the cytosolic RNA exosome to the Ski complex in Arabidopsis. Nat Commun 2019; 10:3871. [PMID: 31455787 PMCID: PMC6711988 DOI: 10.1038/s41467-019-11807-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 08/05/2019] [Indexed: 02/01/2023] Open
Abstract
The RNA exosome is a key 3’−5’ exoribonuclease with an evolutionarily conserved structure and function. Its cytosolic functions require the co-factors SKI7 and the Ski complex. Here we demonstrate by co-purification experiments that the ARM-repeat protein RESURRECTION1 (RST1) and RST1 INTERACTING PROTEIN (RIPR) connect the cytosolic Arabidopsis RNA exosome to the Ski complex. rst1 and ripr mutants accumulate RNA quality control siRNAs (rqc-siRNAs) produced by the post-transcriptional gene silencing (PTGS) machinery when mRNA degradation is compromised. The small RNA populations observed in rst1 and ripr mutants are also detected in mutants lacking the RRP45B/CER7 core exosome subunit. Thus, molecular and genetic evidence supports a physical and functional link between RST1, RIPR and the RNA exosome. Our data reveal the existence of additional cytosolic exosome co-factors besides the known Ski subunits. RST1 is not restricted to plants, as homologues with a similar domain architecture but unknown function exist in animals, including humans. Cytosolic RNA degradation by the RNA exosome requires the Ski complex. Here the authors show that the proteins RST1 and RIPR assist the RNA exosome and the Ski complex in RNA degradation, thereby preventing the production of secondary siRNAs from endogenous mRNAs.
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Affiliation(s)
- Heike Lange
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France.
| | - Simon Y A Ndecky
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Carlos Gomez-Diaz
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - David Pflieger
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Nicolas Butel
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
| | - Julie Zumsteg
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Lauriane Kuhn
- Plateforme protéomique Strasbourg Esplanade FR1589 du CNRS, Université de Strasbourg, Strasbourg, France
| | - Christina Piermaria
- Plateforme protéomique Strasbourg Esplanade FR1589 du CNRS, Université de Strasbourg, Strasbourg, France
| | - Johana Chicher
- Plateforme protéomique Strasbourg Esplanade FR1589 du CNRS, Université de Strasbourg, Strasbourg, France
| | - Michael Christie
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Ezgi S Karaaslan
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | | | - Detlef Weigel
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Hervé Vaucheret
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
| | - Philippe Hammann
- Plateforme protéomique Strasbourg Esplanade FR1589 du CNRS, Université de Strasbourg, Strasbourg, France
| | - Dominique Gagliardi
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France.
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Zhang E, Khanna V, Dacheux E, Namane A, Doyen A, Gomard M, Turcotte B, Jacquier A, Fromont‐Racine M. A specialised SKI complex assists the cytoplasmic RNA exosome in the absence of direct association with ribosomes. EMBO J 2019; 38:e100640. [PMID: 31304628 PMCID: PMC6627227 DOI: 10.15252/embj.2018100640] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 04/25/2019] [Accepted: 05/13/2019] [Indexed: 11/09/2022] Open
Abstract
The Ski2-Ski3-Ski8 (SKI) complex assists the RNA exosome during the 3' to 5' degradation of cytoplasmic transcripts. Previous reports showed that the SKI complex is involved in the 3' to 5' degradation of mRNAs, including 3' untranslated regions (UTRs) and devoid of ribosomes. Paradoxically, we recently showed that the SKI complex directly interacts with ribosomes during the co-translational mRNA decay and that this interaction is necessary for its RNA degradation promoting activity. Here, we characterised a new SKI-associated factor, Ska1, that associates with a subpopulation of the SKI complex. We showed that Ska1 is specifically involved in the degradation of long 3'UTR-containing mRNAs, poorly translated mRNAs as well as other RNA regions not associated with ribosomes, such as cytoplasmic lncRNAs. We further show that the overexpression of SKA1 antagonises the SKI-ribosome association. We propose that the Ska1-SKI complex assists the cytoplasmic exosome in the absence of direct association of the SKI complex with ribosomes.
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Affiliation(s)
- Elodie Zhang
- Génétique des Interactions MacromoléculairesInstitut PasteurUMR3525 CNRSParisFrance
- Sorbonne UniversitéCollège DoctoralParisFrance
| | - Varun Khanna
- Génétique des Interactions MacromoléculairesInstitut PasteurUMR3525 CNRSParisFrance
- Hub Bioinformatique et BiostatistiqueInstitut Pasteur ‐ C3BIUSR 3756 IP CNRSParisFrance
| | - Estelle Dacheux
- Génétique des Interactions MacromoléculairesInstitut PasteurUMR3525 CNRSParisFrance
| | - Abdelkader Namane
- Génétique des Interactions MacromoléculairesInstitut PasteurUMR3525 CNRSParisFrance
| | - Antonia Doyen
- Génétique des Interactions MacromoléculairesInstitut PasteurUMR3525 CNRSParisFrance
| | - Maïté Gomard
- Génétique des Interactions MacromoléculairesInstitut PasteurUMR3525 CNRSParisFrance
| | - Bernard Turcotte
- Department of MedicineMcGill University Health CentreMontréalQCCanada
| | - Alain Jacquier
- Génétique des Interactions MacromoléculairesInstitut PasteurUMR3525 CNRSParisFrance
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56
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Sarkar D, Paira S, Das B. Nuclear mRNA degradation tunes the gain of the unfolded protein response in Saccharomyces cerevisiae. Nucleic Acids Res 2019; 46:1139-1156. [PMID: 29165698 PMCID: PMC5814838 DOI: 10.1093/nar/gkx1160] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 11/10/2017] [Indexed: 12/14/2022] Open
Abstract
Unfolded protein response (UPR) is triggered by the accumulation of unfolded proteins in the endoplasmic reticulum (ER), which is accomplished by a dramatic induction of genes encoding ER chaperones. Activation of these genes involves their rapid transcription by Hac1p, encoded by the HAC1 precursor transcript harboring an intron and a bipartite element (3′-BE) in the 3′-UTR. ER stress facilitates intracellular targeting and recruitment of HAC1 pre-mRNA to Ire1p foci (requiring 3′-BE), leading to its non-spliceosomal splicing mediated by Ire1p/Rlg1p. A critical concentration of the pre-HAC1 harboring a functional 3′-BE element is governed by its 3′→5′ decay by the nuclear exosome/DRN. In the absence of stress, pre-HAC1 mRNA undergoes a rapid and kinetic 3′→5′ decay leading to a precursor pool, the majority of which lack the BE element. Stress, in contrast, causes a diminished decay, thus resulting in the production of a population with an increased abundance of pre-HAC1 mRNA carrying an intact BE, which facilitates its more efficient recruitment to Ire1p foci. This mechanism plays a crucial role in the timely activation of UPR and its prompt attenuation following the accomplishment of homeostasis. Thus, a kinetic mRNA decay provides a novel paradigm for mRNA targeting and regulation of gene expression.
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Affiliation(s)
- Debasish Sarkar
- Department of Life Science and Biotechnology, Jadavpur University, Kolkata 700 032, West Bengal, India
| | - Sunirmal Paira
- Department of Life Science and Biotechnology, Jadavpur University, Kolkata 700 032, West Bengal, India
| | - Biswadip Das
- Department of Life Science and Biotechnology, Jadavpur University, Kolkata 700 032, West Bengal, India
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57
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D'Orazio KN, Wu CCC, Sinha N, Loll-Krippleber R, Brown GW, Green R. The endonuclease Cue2 cleaves mRNAs at stalled ribosomes during No Go Decay. eLife 2019; 8:e49117. [PMID: 31219035 PMCID: PMC6598757 DOI: 10.7554/elife.49117] [Citation(s) in RCA: 105] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 06/19/2019] [Indexed: 01/04/2023] Open
Abstract
Translation of problematic sequences in mRNAs leads to ribosome collisions that trigger a series of quality control events including ribosome rescue, degradation of the stalled nascent polypeptide, and targeting of the mRNA for decay (No Go Decay or NGD). Using a reverse genetic screen in yeast, we identify Cue2 as the conserved endonuclease that is recruited to stalled ribosomes to promote NGD. Ribosome profiling and biochemistry provide strong evidence that Cue2 cleaves mRNA within the A site of the colliding ribosome. We demonstrate that NGD primarily proceeds via Xrn1-mediated exonucleolytic decay and Cue2-mediated endonucleolytic decay normally constitutes a secondary decay pathway. Finally, we show that the Cue2-dependent pathway becomes a major contributor to NGD in cells depleted of factors required for the resolution of stalled ribosome complexes. Together these results provide insights into how multiple decay processes converge to process problematic mRNAs in eukaryotic cells..
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Affiliation(s)
- Karole N D'Orazio
- Department of Molecular Biology and GeneticsHoward Hughes Medical Institute, Johns Hopkins University School of MedicineBaltimoreUnited States
| | - Colin Chih-Chien Wu
- Department of Molecular Biology and GeneticsHoward Hughes Medical Institute, Johns Hopkins University School of MedicineBaltimoreUnited States
| | - Niladri Sinha
- Department of Molecular Biology and GeneticsHoward Hughes Medical Institute, Johns Hopkins University School of MedicineBaltimoreUnited States
| | - Raphael Loll-Krippleber
- Donnelly Centre for Cellular and Biomolecular Research, Department of BiochemistryUniversity of TorontoTorontoCanada
| | - Grant W Brown
- Donnelly Centre for Cellular and Biomolecular Research, Department of BiochemistryUniversity of TorontoTorontoCanada
| | - Rachel Green
- Department of Molecular Biology and GeneticsHoward Hughes Medical Institute, Johns Hopkins University School of MedicineBaltimoreUnited States
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58
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Phospho-peptide binding domains in S. cerevisiae model organism. Biochimie 2019; 163:117-127. [PMID: 31194995 DOI: 10.1016/j.biochi.2019.06.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Accepted: 06/06/2019] [Indexed: 02/07/2023]
Abstract
Protein phosphorylation is one of the main mechanisms by which signals are transmitted in eukaryotic cells, and it plays a crucial regulatory role in almost all cellular processes. In yeast, more than half of the proteins are phosphorylated in at least one site, and over 20,000 phosphopeptides have been experimentally verified. However, the functional consequences of these phosphorylation events for most of the identified phosphosites are unknown. A family of protein interaction domains selectively recognises phosphorylated motifs to recruit regulatory proteins and activate signalling pathways. Nine classes of dedicated modules are coded by the yeast genome: 14-3-3, FHA, WD40, BRCT, WW, PBD, and SH2. The recognition specificity relies on a few residues on the target protein and has coevolved with kinase specificity. In the present study, we review the current knowledge concerning yeast phospho-binding domains and their networks. We emphasise the relevance of both positive and negative amino acid selection to orchestrate the highly regulated outcomes of inter- and intra-molecular interactions. Finally, we hypothesise that only a small fraction of yeast phosphorylation events leads to the creation of a docking site on the target molecule, while many have a direct effect on the protein or, as has been proposed, have no function at all.
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59
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Poulton C, Pathak G, Mina K, Lassman T, Azmanov DN, McCormack E, Broley S, Dreyer L, Gration D, Taylor E, OSullivan M, Siafarikis A, Ravikumara M, Dawkins H, Pachter N, Baynam G. Tricho-hepatic-enteric syndrome (THES) without intractable diarrhoea. Gene 2019; 699:110-114. [PMID: 30844479 DOI: 10.1016/j.gene.2019.02.059] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 02/08/2019] [Accepted: 02/09/2019] [Indexed: 01/15/2023]
Abstract
Tricho-hepatic-enteric syndrome (THES) is a genetically heterogeneous rare syndrome (OMIM: 222470 (THES1) and 614602 (THES2)) that typically presents in the neonatal period with intractable diarrhoea, intra-uterine growth retardation (IUGR), facial dysmorphism, and hair and skin changes. THES is associated with pathogenic variants in either TTC37 or SKIV2L; both are components of the human SKI complex, an RNA exosome cofactor. We report an 8 year old girl who was diagnosed with THES by the Undiagnosed Disease Program-WA with compound heterozygous pathogenic variants in SKIV2L. While THES was considered in the differential diagnosis, the absence of protracted diarrhoea delayed definitive diagnosis. We therefore suggest that SKIV2L testing should be considered in cases otherwise suggestive of THES, but without the characteristic diarrhoea. We expand the phenotypic spectrum while reviewing the current knowledge on SKIV2L.
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Affiliation(s)
- C Poulton
- Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, Australia; Undiagnosed Disease Program, Perth Children's Hospital Foundation, Nedlands, Australia.
| | - G Pathak
- Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, Australia
| | - K Mina
- Douglass Hanly Moir Pathology, Macquarie Park, New South Wales, Australia
| | - T Lassman
- Telethon Kids Institute, Nedlands, Western Australia, Australia
| | - D N Azmanov
- Department of Diagnostic Genomics, PathWest Laboratory Medicine Western Australia, Nedlands, Western Australia, Australia
| | - E McCormack
- Faculty of Science, Doctor of Medicine Program, University of Western Australia, Perth, Western Australia, Australia
| | - S Broley
- Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, Australia; Undiagnosed Disease Program, Perth Children's Hospital Foundation, Nedlands, Australia
| | - L Dreyer
- Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, Australia; Undiagnosed Disease Program, Perth Children's Hospital Foundation, Nedlands, Australia
| | - D Gration
- Western Australia Register for Developmental Abnormalities, King Edward Memorial Hospital for Women Perth, Australia
| | - E Taylor
- Department of Paediatrics, Perth Children's Hospital Foundation, Nedlands, Australia
| | - M OSullivan
- Department of Immunology, Perth Children's Hospital Foundation, Nedlands, Australia
| | - A Siafarikis
- Department of Endocrinology, Perth Children's Hospital Foundation, Nedlands, Australia
| | - M Ravikumara
- Department of Gastroenterology, Perth Children's Hospital Foundation, Nedlands, Australia
| | - H Dawkins
- Centre for Population Health Research, Curtin University of Technology, Bentley, Australia
| | - N Pachter
- Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, Australia
| | - G Baynam
- Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, Australia; Undiagnosed Disease Program, Perth Children's Hospital Foundation, Nedlands, Australia; School of Paediatrics and Child Health, The University of Western Australia, Perth, Australia
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60
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Urdaneta EC, Vieira-Vieira CH, Hick T, Wessels HH, Figini D, Moschall R, Medenbach J, Ohler U, Granneman S, Selbach M, Beckmann BM. Purification of cross-linked RNA-protein complexes by phenol-toluol extraction. Nat Commun 2019; 10:990. [PMID: 30824702 PMCID: PMC6397201 DOI: 10.1038/s41467-019-08942-3] [Citation(s) in RCA: 134] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 02/11/2019] [Indexed: 12/30/2022] Open
Abstract
Recent methodological advances allowed the identification of an increasing number of RNA-binding proteins (RBPs) and their RNA-binding sites. Most of those methods rely, however, on capturing proteins associated to polyadenylated RNAs which neglects RBPs bound to non-adenylate RNA classes (tRNA, rRNA, pre-mRNA) as well as the vast majority of species that lack poly-A tails in their mRNAs (including all archea and bacteria). We have developed the Phenol Toluol extraction (PTex) protocol that does not rely on a specific RNA sequence or motif for isolation of cross-linked ribonucleoproteins (RNPs), but rather purifies them based entirely on their physicochemical properties. PTex captures RBPs that bind to RNA as short as 30 nt, RNPs directly from animal tissue and can be used to simplify complex workflows such as PAR-CLIP. Finally, we provide a global RNA-bound proteome of human HEK293 cells and the bacterium Salmonella Typhimurium.
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Affiliation(s)
- Erika C Urdaneta
- IRI Life Sciences, Humboldt University, Philippstr. 13, 10115, Berlin, Germany
| | - Carlos H Vieira-Vieira
- Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125, Berlin, Germany
| | - Timon Hick
- IRI Life Sciences, Humboldt University, Philippstr. 13, 10115, Berlin, Germany
| | - Hans-Herrmann Wessels
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125, Berlin, Germany
- Department of Biology, Humboldt University, Philippstr. 13, 10115, Berlin, Germany
| | - Davide Figini
- IRI Life Sciences, Humboldt University, Philippstr. 13, 10115, Berlin, Germany
| | - Rebecca Moschall
- Biochemistry I, University of Regensburg, Universitätsstrasse 31, 93053, Regensburg, Germany
| | - Jan Medenbach
- Biochemistry I, University of Regensburg, Universitätsstrasse 31, 93053, Regensburg, Germany
| | - Uwe Ohler
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125, Berlin, Germany
- Department of Biology, Humboldt University, Philippstr. 13, 10115, Berlin, Germany
| | - Sander Granneman
- Centre for Systems and Synthetic Biology (SynthSys), University of Edinburgh, Max Born Crescent, Edinburgh, EH9 3BF, UK
| | - Matthias Selbach
- Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125, Berlin, Germany
| | - Benedikt M Beckmann
- IRI Life Sciences, Humboldt University, Philippstr. 13, 10115, Berlin, Germany.
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61
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Szaker HM, Darkó É, Medzihradszky A, Janda T, Liu HC, Charng YY, Csorba T. miR824/AGAMOUS-LIKE16 Module Integrates Recurring Environmental Heat Stress Changes to Fine-Tune Poststress Development. FRONTIERS IN PLANT SCIENCE 2019; 10:1454. [PMID: 31824525 PMCID: PMC6886564 DOI: 10.3389/fpls.2019.01454] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 10/18/2019] [Indexed: 05/19/2023]
Abstract
Plant development is continually fine-tuned based on environmental factors. How environmental perturbations are integrated into the developmental programs and how poststress adaptation is regulated remains an important topic to dissect. Vegetative to reproductive phase change is a very important developmental transition that is complexly regulated based on endogenous and exogenous cues. Proper timing of flowering is vital for reproductive success. It has been shown previously that AGAMOUS LIKE 16 (AGL16), a MADS-box transcription factor negatively regulates flowering time transition through FLOWERING LOCUS T (FT), a central downstream floral integrator. AGL16 itself is negatively regulated by the microRNA miR824. Here we present a comprehensive molecular analysis of miR824/AGL16 module changes in response to mild and recurring heat stress. We show that miR824 accumulates gradually in response to heat due to the combination of transient transcriptional induction and posttranscriptional stability. miR824 induction requires heat shock cis-elements and activity of the HSFA1 family and HSFA2 transcription factors. Parallel to miR824 induction, its target AGL16 is decreased, implying direct causality. AGL16 posttranscriptional repression during heat stress, however, is more complex, comprising of a miRNA-independent, and a miR824-dependent pathway. We also show that AGL16 expression is leaf vein-specific and overlaps with miR824 (and FT) expression. AGL16 downregulation in response to heat leads to a mild derepression of FT. Finally, we present evidence showing that heat stress regulation of miR824/AGL16 is conserved within Brassicaceae. In conclusion, due to the enhanced post-transcriptional stability of miR824, stable repression of AGL16 is achieved following heat stress. This may serve to fine-tune FT levels and alter flowering time transition. Stress-induced miR824, therefore, can act as a "posttranscriptional memory factor" to extend the acute impact of environmental fluctuations in the poststress period.
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Affiliation(s)
- Henrik Mihály Szaker
- Agricultural Biotechnology Institute, NARIC, Godollo, Hungary
- Faculty of Natural Sciences, Eötvös Lóránd University, Budapest, Hungary
| | - Éva Darkó
- Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Martonvásár, Hungary
| | | | - Tibor Janda
- Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Martonvásár, Hungary
| | - Hsiang-chin Liu
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Yee-yung Charng
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Tibor Csorba
- Agricultural Biotechnology Institute, NARIC, Godollo, Hungary
- *Correspondence: Tibor Csorba,
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Saramago M, da Costa PJ, Viegas SC, Arraiano CM. The Implication of mRNA Degradation Disorders on Human DISease: Focus on DIS3 and DIS3-Like Enzymes. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1157:85-98. [PMID: 31342438 DOI: 10.1007/978-3-030-19966-1_4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
RNA degradation is considered a critical posttranscriptional regulatory checkpoint, maintaining the correct functioning of organisms. When a specific RNA transcript is no longer required in the cell, it is signaled for degradation through a number of highly regulated steps. Ribonucleases (or simply RNases) are key enzymes involved in the control of RNA stability. These enzymes can perform the RNA degradation alone or cooperate with other proteins in RNA degradation complexes. Important findings over the last years have shed light into eukaryotic RNA degradation by members of the RNase II/RNB family of enzymes. DIS3 enzyme belongs to this family and represents one of the catalytic subunits of the multiprotein complex exosome. This RNase has a diverse range of functions, mainly within nuclear RNA metabolism. Humans encode two other DIS3-like enzymes: DIS3L (DIS3L1) and DIS3L2. DIS3L1 also acts in association with the exosome but is strictly cytoplasmic. In contrast, DIS3L2 acts independently of the exosome and shows a distinctive preference for uridylated RNAs. These enzymes have been shown to be involved in important cellular processes, such as mitotic control, and associated with human disorders like cancer. This review shows how the impairment of function of each of these enzymes is implicated in human disease.
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Affiliation(s)
- Margarida Saramago
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Paulo J da Costa
- Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge, Lisboa, Portugal.,Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, University of Lisbon, Lisboa, Portugal
| | - Sandra C Viegas
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal.
| | - Cecília M Arraiano
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal.
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63
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Schmid M, Jensen TH. The Nuclear RNA Exosome and Its Cofactors. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1203:113-132. [PMID: 31811632 DOI: 10.1007/978-3-030-31434-7_4] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
The RNA exosome is a highly conserved ribonuclease endowed with 3'-5' exonuclease and endonuclease activities. The multisubunit complex resides in both the nucleus and the cytoplasm, with varying compositions and activities between the two compartments. While the cytoplasmic exosome functions mostly in mRNA quality control pathways, the nuclear RNA exosome partakes in the 3'-end processing and complete decay of a wide variety of substrates, including virtually all types of noncoding (nc) RNAs. To handle these diverse tasks, the nuclear exosome engages with dedicated cofactors, some of which serve as activators by stimulating decay through oligoA addition and/or RNA helicase activities or, as adaptors, by recruiting RNA substrates through their RNA-binding capacities. Most nuclear exosome cofactors contain the essential RNA helicase Mtr4 (MTR4 in humans). However, apart from Mtr4, nuclear exosome cofactors have undergone significant evolutionary divergence. Here, we summarize biochemical and functional knowledge about the nuclear exosome and exemplify its cofactor variety by discussing the best understood model organisms-the budding yeast Saccharomyces cerevisiae, the fission yeast Schizosaccharomyces pombe, and human cells.
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Affiliation(s)
- Manfred Schmid
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark
| | - Torben Heick Jensen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark.
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64
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Abstract
The bacterial endoribonuclease RNase E occupies a pivotal position in the control of gene expression, as its actions either commit transcripts to an irreversible fate of rapid destruction or unveil their hidden functions through specific processing. Moreover, the enzyme contributes to quality control of rRNAs. The activity of RNase E can be directed and modulated by signals provided through regulatory RNAs that guide the enzyme to specific transcripts that are to be silenced. Early in its evolutionary history, RNase E acquired a natively unfolded appendage that recruits accessory proteins and RNA. These accessory factors facilitate the activity of RNase E and include helicases that remodel RNA and RNA-protein complexes, and polynucleotide phosphorylase, a relative of the archaeal and eukaryotic exosomes. RNase E also associates with enzymes from central metabolism, such as enolase and aconitase. RNase E-based complexes are diverse in composition, but generally bear mechanistic parallels with eukaryotic machinery involved in RNA-induced gene regulation and transcript quality control. That these similar processes arose independently underscores the universality of RNA-based regulation in life. Here we provide a synopsis and perspective of the contributions made by RNase E to sustain robust gene regulation with speed and accuracy.
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65
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Szádeczky-Kardoss I, Gál L, Auber A, Taller J, Silhavy D. The No-go decay system degrades plant mRNAs that contain a long A-stretch in the coding region. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 275:19-27. [PMID: 30107878 DOI: 10.1016/j.plantsci.2018.07.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 07/18/2018] [Accepted: 07/19/2018] [Indexed: 05/04/2023]
Abstract
RNA quality control systems identify and degrade aberrant mRNAs, thereby preventing the accumulation of faulty proteins. Non-stop decay (NSD) and No-go decay (NGD) are closely related RNA quality control systems that act during translation. NSD degrades mRNAs lacking a stop codon, while NGD recognizes and decays mRNAs that contain translation elongation inhibitory structures. NGD has been intensively studied in yeast and animals but it has not been described in plants yet. In yeast, NGD is induced if the elongating ribosome is stalled by a strong inhibitory structure. Then, the mRNA is cleaved by an unknown nuclease and the cleavage fragments are degraded. Here we show that NGD also operates in plant. We tested several potential NGD cis-elements and found that in plants, unlike in yeast, only long A-stretches induce NGD. These long A-stretches trigger endonucleolytic cleavage, and then the 5' fragments are degraded in a Pelota-, HBS1- and SKI2- dependent manner, while XRN4 eliminates the 3' fragment. We also show that plant NGD operates gradually, the longer the A-stretch, the more efficient the cleavage. Our data suggest that mechanistically NGD is conserved in eukaryotes, although the NGD inducing cis-elements could be different. Moreover, we found that Arabidopsis AtPelota1 functions in both NGD and NSD, while AtPelota2 represses these quality control systems. The function of plant NGD will be discussed.
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Affiliation(s)
| | - Luca Gál
- Agricultural Biotechnology Institute, Szent-Györgyi 4, H-2100, Gödöllő, Hungary
| | - Andor Auber
- Agricultural Biotechnology Institute, Szent-Györgyi 4, H-2100, Gödöllő, Hungary
| | - János Taller
- University Pannonia Georgikon, Festetics 7, 8360, Keszthely, Hungary
| | - Dániel Silhavy
- Agricultural Biotechnology Institute, Szent-Györgyi 4, H-2100, Gödöllő, Hungary.
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66
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Droll D, Wei G, Guo G, Fan Y, Baumgarten S, Zhou Y, Xiao Y, Scherf A, Zhang Q. Disruption of the RNA exosome reveals the hidden face of the malaria parasite transcriptome. RNA Biol 2018; 15:1206-1214. [PMID: 30235972 PMCID: PMC7000224 DOI: 10.1080/15476286.2018.1517014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Abstract
Antisense transcription emerges as a key regulator of important biological processes in the human malaria parasite Plasmodium falciparum. RNA-processing factors, however, remain poorly characterized in this pathogen. Here, we purified the multiprotein RNA exosome complex of malaria parasites by affinity chromatography, using HA-tagged PfRrp4 and PfDis3 as the ligands. Seven distinct core exosome subunits (PfRrp41, PfMtr3, PfRrp42, PfRrp45, PfRrp4, PfRrp40, PfCsl4) and two exoribonuclease proteins PfRrp6 and PfDis3 are identified by mass spectrometry. Western blot analysis detects Dis3 and Rrp4 predominantly in the cytoplasmic fraction during asexual blood stage development. An inducible gene knock out of the PfDis3 subunit reveals the upregulation of structural and coding RNA, but the vast majority belongs to antisense RNA. Furthermore, we detect numerous types of cryptic unstable transcripts (CUTs) linked to virulence gene families including antisense RNA in the rif gene family. Our work highlights the limitations of steady-state RNA analysis to predict transcriptional activity and link the RNA surveillance machinery directly with post-transcriptional control and gene expression in malaria parasites.
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Affiliation(s)
- Dorothea Droll
- a Unité Biologie des Interactions Hôte-Parasite, Département de Parasites et Insectes Vecteurs , Institut Pasteur , Paris , France.,b CNRS, ERL 9195 , Paris , France.,c INSERM, Unit U1201 , Paris , France
| | - Guiying Wei
- d Research Center for Translational Medicine, Key Laboratory of Arrhythmias of the Ministry of Education of China, East Hospital , Tongji University School of Medicine , Shanghai , China
| | - Gangqiang Guo
- d Research Center for Translational Medicine, Key Laboratory of Arrhythmias of the Ministry of Education of China, East Hospital , Tongji University School of Medicine , Shanghai , China
| | - Yanting Fan
- d Research Center for Translational Medicine, Key Laboratory of Arrhythmias of the Ministry of Education of China, East Hospital , Tongji University School of Medicine , Shanghai , China
| | - Sebastian Baumgarten
- a Unité Biologie des Interactions Hôte-Parasite, Département de Parasites et Insectes Vecteurs , Institut Pasteur , Paris , France.,b CNRS, ERL 9195 , Paris , France.,c INSERM, Unit U1201 , Paris , France
| | - Yiqing Zhou
- e CAS Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology , Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences , Shanghai , China
| | - Youli Xiao
- e CAS Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology , Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences , Shanghai , China
| | - Artur Scherf
- a Unité Biologie des Interactions Hôte-Parasite, Département de Parasites et Insectes Vecteurs , Institut Pasteur , Paris , France.,b CNRS, ERL 9195 , Paris , France.,c INSERM, Unit U1201 , Paris , France
| | - Qingfeng Zhang
- d Research Center for Translational Medicine, Key Laboratory of Arrhythmias of the Ministry of Education of China, East Hospital , Tongji University School of Medicine , Shanghai , China
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67
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Kalisiak K, Kuliński TM, Tomecki R, Cysewski D, Pietras Z, Chlebowski A, Kowalska K, Dziembowski A. A short splicing isoform of HBS1L links the cytoplasmic exosome and SKI complexes in humans. Nucleic Acids Res 2018; 45:2068-2080. [PMID: 28204585 PMCID: PMC5389692 DOI: 10.1093/nar/gkw862] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 08/25/2016] [Accepted: 09/20/2016] [Indexed: 12/18/2022] Open
Abstract
The exosome complex is a major eukaryotic exoribonuclease that requires the SKI complex for its activity in the cytoplasm. In yeast, the Ski7 protein links both complexes, whereas a functional equivalent of the Ski7 has remained unknown in the human genome. Proteomic analysis revealed that a previously uncharacterized short splicing isoform of HBS1L (HBS1LV3) is the long-sought factor linking the exosome and SKI complexes in humans. In contrast, the canonical HBS1L variant, HBS1LV1, which acts as a ribosome dissociation factor, does not associate with the exosome and instead interacts with the mRNA surveillance factor PELOTA. Interestingly, both HBS1LV1 and HBS1LV3 interact with the SKI complex and HBS1LV1 seems to antagonize SKI/exosome supercomplex formation. HBS1LV3 contains a unique C-terminal region of unknown structure, with a conserved RxxxFxxxL motif responsible for exosome binding and may interact with the exosome core subunit RRP43 in a way that resembles the association between Rrp6 RNase and Rrp43 in yeast. HBS1LV3 or the SKI complex helicase (SKI2W) depletion similarly affected the transcriptome, deregulating multiple genes. Furthermore, half-lives of representative upregulated mRNAs were increased, supporting the involvement of HBS1LV3 and SKI2W in the same mRNA degradation pathway, essential for transcriptome homeostasis in the cytoplasm.
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Affiliation(s)
- Katarzyna Kalisiak
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Tomasz M. Kuliński
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Rafał Tomecki
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Dominik Cysewski
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Zbigniew Pietras
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland
- International Institute of Molecular and Cell Biology in Warsaw, Ks. Trojdena 4, 02-109 Warsaw, Poland
| | - Aleksander Chlebowski
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Katarzyna Kowalska
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Andrzej Dziembowski
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland
- To whom correspondence should be addressed. Tel: +48 22 5922033; Fax: +48 22 6584176;
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68
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Structure of activated transcription complex Pol II-DSIF-PAF-SPT6. Nature 2018; 560:607-612. [PMID: 30135578 DOI: 10.1038/s41586-018-0440-4] [Citation(s) in RCA: 255] [Impact Index Per Article: 42.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 07/17/2018] [Indexed: 11/09/2022]
Abstract
Gene regulation involves activation of RNA polymerase II (Pol II) that is paused and bound by the protein complexes DRB sensitivity-inducing factor (DSIF) and negative elongation factor (NELF). Here we show that formation of an activated Pol II elongation complex in vitro requires the kinase function of the positive transcription elongation factor b (P-TEFb) and the elongation factors PAF1 complex (PAF) and SPT6. The cryo-EM structure of an activated elongation complex of Sus scrofa Pol II and Homo sapiens DSIF, PAF and SPT6 was determined at 3.1 Å resolution and compared to the structure of the paused elongation complex formed by Pol II, DSIF and NELF. PAF displaces NELF from the Pol II funnel for pause release. P-TEFb phosphorylates the Pol II linker to the C-terminal domain. SPT6 binds to the phosphorylated C-terminal-domain linker and opens the RNA clamp formed by DSIF. These results provide the molecular basis for Pol II pause release and elongation activation.
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69
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Structural basis for MTR4-ZCCHC8 interactions that stimulate the MTR4 helicase in the nuclear exosome-targeting complex. Proc Natl Acad Sci U S A 2018; 115:E5506-E5515. [PMID: 29844170 PMCID: PMC6004480 DOI: 10.1073/pnas.1803530115] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Aberrant or unwanted transcripts can be degraded by the RNA exosome with the help of the nuclear exosome-targeting (NEXT) complex. NEXT, composed of RNA-binding protein RBM7, scaffold ZCCHC8, and helicase MTR4, is implicated in stress response, neurodegeneration, and viral ribogenesis. Here, we characterize the activities of NEXT that support its role in exosome-mediated decay. NEXT catalyzes 3′→5′ helicase activity and disrupts RNA:RNA and DNA:RNA duplexes more efficiently than MTR4. Optimal activity is observed when substrates include a uridine-rich motif, for interactions with RBM7, and a 3′ poly(A) tail. The ZCCHC8 C-terminal domain binds the helicase core and can stimulate MTR4 helicase/ATPase activities. Our results highlight the interplay among NEXT subunits to ensure effective targeting of substrates. The nuclear exosome-targeting (NEXT) complex functions as an RNA exosome cofactor and is involved in surveillance and turnover of aberrant transcripts and noncoding RNAs. NEXT is a ternary complex composed of the RNA-binding protein RBM7, the scaffold zinc-knuckle protein ZCCHC8, and the helicase MTR4. While RNA interactions with RBM7 are known, it remains unclear how NEXT subunits collaborate to recognize and prepare substrates for degradation. Here, we show that MTR4 helicase activity is enhanced when associated with RBM7 and ZCCHC8. While uridine-rich substrates interact with RBM7 and are preferred, optimal activity is observed when substrates include a polyadenylated 3′ end. We identify a bipartite interaction of ZCCHC8 with MTR4 and uncover a role for the conserved C-terminal domain of ZCCHC8 in stimulating MTR4 helicase and ATPase activities. A crystal structure reveals that the ZCCHC8 C-terminal domain binds the helicase core in a manner that is distinct from that observed for Saccharomyces cerevisiae exosome cofactors Trf4p and Air2p. Our results are consistent with a model whereby effective targeting of substrates by NEXT entails recognition of elements within the substrate and activation of MTR4 helicase activity.
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70
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Szádeczky-Kardoss I, Csorba T, Auber A, Schamberger A, Nyikó T, Taller J, Orbán TI, Burgyán J, Silhavy D. The nonstop decay and the RNA silencing systems operate cooperatively in plants. Nucleic Acids Res 2018; 46:4632-4648. [PMID: 29672715 PMCID: PMC5961432 DOI: 10.1093/nar/gky279] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 03/28/2018] [Accepted: 04/11/2018] [Indexed: 12/27/2022] Open
Abstract
Translation-dependent mRNA quality control systems protect the protein homeostasis of eukaryotic cells by eliminating aberrant transcripts and stimulating the decay of their protein products. Although these systems are intensively studied in animals, little is known about the translation-dependent quality control systems in plants. Here, we characterize the mechanism of nonstop decay (NSD) system in Nicotiana benthamiana model plant. We show that plant NSD efficiently degrades nonstop mRNAs, which can be generated by premature polyadenylation, and stop codon-less transcripts, which are produced by endonucleolytic cleavage. We demonstrate that in plants, like in animals, Pelota, Hbs1 and SKI2 proteins are required for NSD, supporting that NSD is an ancient and conserved eukaryotic quality control system. Relevantly, we found that NSD and RNA silencing systems cooperate in plants. Plant silencing predominantly represses target mRNAs through endonucleolytic cleavage in the coding region. Here we show that NSD is required for the elimination of 5' cleavage product of mi- or siRNA-guided silencing complex when the cleavage occurs in the coding region. We also show that NSD and nonsense-mediated decay (NMD) quality control systems operate independently in plants.
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Affiliation(s)
| | - Tibor Csorba
- Agricultural Biotechnology Institute, Szent-Györgyi 4, H-2100 Gödöllő, Hungary
| | - Andor Auber
- Agricultural Biotechnology Institute, Szent-Györgyi 4, H-2100 Gödöllő, Hungary
| | - Anita Schamberger
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok körútja 2, 1117 Budapest, Hungary
| | - Tünde Nyikó
- Agricultural Biotechnology Institute, Szent-Györgyi 4, H-2100 Gödöllő, Hungary
| | - János Taller
- University Pannonia Georgikon, Festetics 7, 8360 Keszthely, Hungary
| | - Tamás I Orbán
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok körútja 2, 1117 Budapest, Hungary
| | - József Burgyán
- Agricultural Biotechnology Institute, Szent-Györgyi 4, H-2100 Gödöllő, Hungary
| | - Dániel Silhavy
- Agricultural Biotechnology Institute, Szent-Györgyi 4, H-2100 Gödöllő, Hungary
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71
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Wang Y, Wang Q, Wei X, Shao J, Zhao J, Zhang Z, Chen Z, Bai Y, Wang N, Wang Y, Li M, Zhai X. Global scientific trends on exosome research during 2007-2016: a bibliometric analysis. Oncotarget 2018; 8:48460-48470. [PMID: 28477015 PMCID: PMC5564662 DOI: 10.18632/oncotarget.17223] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Accepted: 03/22/2017] [Indexed: 12/12/2022] Open
Abstract
Background Exosomes are small vesicles of endosomal origin, and they can be used for the diagnosis and the treatment. However, limited data were for the evaluation of the trend of exosome researches. This study aims to investigate the trend of exosome researches and compare the contribution of research from different regions, organizations and authors. Methods Exosome related publications from 2007 to 2016 were retrieved from the Web of Science database. Excel, GraphPad Prism 5 and VOSviewer software were used to analyze the research trend. Results A total of 1852 papers were identified and were cited 62967 times. The United States accounted for 38.8% of the articles, 42.0% of the citations, and the highest H-index (76). China ranked the second in the number of articles, but the sixth in citation frequency (4337) and the fourth in H-index (36). The journals, PLoS ONE and J Biol Chem had the highest number of publications. The author, Gabrielsson S., has published the most papers in this field (22). The keyword “ribonucleic acid” was mentioned the most at 746 times, and the words, “stem cell”, “drug resistance” and “monocyte cell factor” were the latest hotspots appeared around 2015. Conclusion Literature growth related to exosome is expanding rapidly. The quality of the articles from China still requires improvement. Recent studies focus on the relationship with tumor, and “stem cell”, “drug resistance” and “michigan cancer foundation-7” may be the newest topics that should be closely followed in exosome research.
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Affiliation(s)
- Yiran Wang
- Department of Oncology, Changhai Hospital, Second Military Medical University, Shanghai, China.,Graduate Management Unit, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Qijin Wang
- Department of Endocrinology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Xianzhao Wei
- Department of Orthopedics, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Jie Shao
- Department of Orthopedics, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Jian Zhao
- Department of Orthopedics, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Zicheng Zhang
- Graduate Management Unit, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Ziqiang Chen
- Department of Orthopedics, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Yushu Bai
- Department of Orthopedics, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Ning Wang
- Department of Oncology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Yajie Wang
- Department of Oncology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Ming Li
- Department of Orthopedics, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Xiao Zhai
- Department of Orthopedics, Changhai Hospital, Second Military Medical University, Shanghai, China
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72
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Bourgeois P, Esteve C, Chaix C, Béroud C, Lévy N, Fabre A, Badens C. Tricho-Hepato-Enteric Syndrome mutation update: Mutations spectrum of TTC37 and SKIV2L, clinical analysis and future prospects. Hum Mutat 2018. [PMID: 29527791 DOI: 10.1002/humu.23418] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Tricho-Hepato-Enteric syndrome (THES) is a very rare autosomal recessive syndromic enteropathy caused by mutations of either TTC37 or SKIV2L genes. Very little is known of these two gene products in mammals nor of the pathophysiology of the disease. Since the identification of the genes, we have set up the molecular diagnostic of THES in routine, gathering a large cohort with clinical and molecular data. Here, we report the phenotype and genotype analysis of this cohort together with an extensive literature review of THES cases worldwide, that is, 96 individuals harboring mutations in one gene or the other. We set up locus-specific databases for both genes and reviewed the type of mutation as well as their localization in the proteins. No hot spot is evidenced for any type of mutation. The phenotypic analysis was first made on the whole cohort but is limited due to heterogeneity in clinical descriptions. We then examined the lab diagnostic cohort in detail for clinical manifestations. For the first time, we are able to suggest that patients lacking SKIV2L seem more severely affected than those lacking TTC37, in terms of liver damage and prenatal growth impairment.
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Affiliation(s)
- Patrice Bourgeois
- Molecular genetics Laboratory, Medical genetics and Cell biology Department, La Timone children's hospital, Assistance-Publique des Hôpitaux de Marseille (APHM), Marseille, France.,GMGF, Aix Marseille Univ, Marseille, France
| | | | - Charlène Chaix
- Molecular genetics Laboratory, Medical genetics and Cell biology Department, La Timone children's hospital, Assistance-Publique des Hôpitaux de Marseille (APHM), Marseille, France
| | - Christophe Béroud
- Molecular genetics Laboratory, Medical genetics and Cell biology Department, La Timone children's hospital, Assistance-Publique des Hôpitaux de Marseille (APHM), Marseille, France.,GMGF, Aix Marseille Univ, Marseille, France
| | - Nicolas Lévy
- Molecular genetics Laboratory, Medical genetics and Cell biology Department, La Timone children's hospital, Assistance-Publique des Hôpitaux de Marseille (APHM), Marseille, France.,GMGF, Aix Marseille Univ, Marseille, France
| | | | - Alexandre Fabre
- GMGF, Aix Marseille Univ, Marseille, France.,Multidisciplinary Pediatric Service - La Timone Children's Hospital, Assistance-Publique des Hôpitaux de Marseille (APHM), Marseille, France
| | - Catherine Badens
- Molecular genetics Laboratory, Medical genetics and Cell biology Department, La Timone children's hospital, Assistance-Publique des Hôpitaux de Marseille (APHM), Marseille, France.,GMGF, Aix Marseille Univ, Marseille, France
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73
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Morton DJ, Kuiper EG, Jones SK, Leung SW, Corbett AH, Fasken MB. The RNA exosome and RNA exosome-linked disease. RNA (NEW YORK, N.Y.) 2018; 24:127-142. [PMID: 29093021 PMCID: PMC5769741 DOI: 10.1261/rna.064626.117] [Citation(s) in RCA: 98] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The RNA exosome is an evolutionarily conserved, ribonuclease complex that is critical for both processing and degradation of a variety of RNAs. Cofactors that associate with the RNA exosome likely dictate substrate specificity for this complex. Recently, mutations in genes encoding both structural subunits of the RNA exosome and its cofactors have been linked to human disease. Mutations in the RNA exosome genes EXOSC3 and EXOSC8 cause pontocerebellar hypoplasia type 1b (PCH1b) and type 1c (PCH1c), respectively, which are similar autosomal-recessive, neurodegenerative diseases. Mutations in the RNA exosome gene EXOSC2 cause a distinct syndrome with various tissue-specific phenotypes including retinitis pigmentosa and mild intellectual disability. Mutations in genes that encode RNA exosome cofactors also cause tissue-specific diseases with complex phenotypes. How mutations in these genes give rise to distinct, tissue-specific diseases is not clear. In this review, we discuss the role of the RNA exosome complex and its cofactors in human disease, consider the amino acid changes that have been implicated in disease, and speculate on the mechanisms by which exosome gene mutations could underlie dysfunction and disease.
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Affiliation(s)
- Derrick J Morton
- Department of Biology, Emory University, NE, Atlanta, Georgia 30322, USA
| | - Emily G Kuiper
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Stephanie K Jones
- Department of Biology, Emory University, NE, Atlanta, Georgia 30322, USA
- Genetics and Molecular Biology Graduate Program, Emory University, NE, Atlanta, Georgia 30322, USA
| | - Sara W Leung
- Department of Biology, Emory University, NE, Atlanta, Georgia 30322, USA
| | - Anita H Corbett
- Department of Biology, Emory University, NE, Atlanta, Georgia 30322, USA
| | - Milo B Fasken
- Department of Biology, Emory University, NE, Atlanta, Georgia 30322, USA
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74
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Fabre A, Petit LM, Hansen LF, Wewer AV, Esteve C, Chaix C, Bourgeois P, Badens C, Paerregaard A. A new mutation in the C-terminal end of TTC37
leading to a mild form of syndromic diarrhea/tricho-hepato-enteric syndrome in seven patients from two families. Am J Med Genet A 2018; 176:727-732. [DOI: 10.1002/ajmg.a.38618] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 12/13/2017] [Accepted: 01/01/2018] [Indexed: 11/11/2022]
Affiliation(s)
- Alexandre Fabre
- Service de Pédiatrie Multidisciplinaire; Hopital de la Timone; APHM; Marseille France
- Aix Marseille Univ; INSERM, MMG; Marseille France
| | - Laetitia-Marie Petit
- Aix Marseille Univ; INSERM, MMG; Marseille France
- Unité de gastro-entérologie, Hépatologie et Nutrition Pédiatriques; Departement de l'enfant et de l'Adolescent; Hopitaux Universitaires de Geneve; Geneve Switzerland
| | - Lars F. Hansen
- Department of Paediatrics; Hvidovre University Hospital; Copenhagen Denmark
| | - Anne V. Wewer
- Department of Paediatrics; Hvidovre University Hospital; Copenhagen Denmark
| | | | - Charlène Chaix
- Service de biologie moléculaire; Hopital de la Timone Enfant, APHM; Marseille France
| | - Patrice Bourgeois
- Aix Marseille Univ; INSERM, MMG; Marseille France
- Service de biologie moléculaire; Hopital de la Timone Enfant, APHM; Marseille France
| | - Catherine Badens
- Aix Marseille Univ; INSERM, MMG; Marseille France
- Service de biologie moléculaire; Hopital de la Timone Enfant, APHM; Marseille France
| | - Anders Paerregaard
- Department of Paediatrics; Hvidovre University Hospital; Copenhagen Denmark
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75
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Razew M, Warkocki Z, Taube M, Kolondra A, Czarnocki-Cieciura M, Nowak E, Labedzka-Dmoch K, Kawinska A, Piatkowski J, Golik P, Kozak M, Dziembowski A, Nowotny M. Structural analysis of mtEXO mitochondrial RNA degradosome reveals tight coupling of nuclease and helicase components. Nat Commun 2018; 9:97. [PMID: 29311576 PMCID: PMC5758563 DOI: 10.1038/s41467-017-02570-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2017] [Accepted: 12/11/2017] [Indexed: 01/08/2023] Open
Abstract
Nuclease and helicase activities play pivotal roles in various aspects of RNA processing and degradation. These two activities are often present in multi-subunit complexes from nucleic acid metabolism. In the mitochondrial exoribonuclease complex (mtEXO) both enzymatic activities are tightly coupled making it an excellent minimal system to study helicase-exoribonuclease coordination. mtEXO is composed of Dss1 3'-to-5' exoribonuclease and Suv3 helicase. It is the master regulator of mitochondrial gene expression in yeast. Here, we present the structure of mtEXO and a description of its mechanism of action. The crystal structure of Dss1 reveals domains that are responsible for interactions with Suv3. Importantly, these interactions are compatible with the conformational changes of Suv3 domains during the helicase cycle. We demonstrate that mtEXO is an intimate complex which forms an RNA-binding channel spanning its entire structure, with Suv3 helicase feeding the 3' end of the RNA toward the active site of Dss1.
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Affiliation(s)
- Michal Razew
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, Trojdena 4, 02-109, Warsaw, Poland
| | - Zbigniew Warkocki
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106, Warsaw, Poland
| | - Michal Taube
- Faculty of Physics, Adam Mickiewicz University, ul. Umultowska 89, 61-614, Poznan, Poland
| | - Adam Kolondra
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106, Warsaw, Poland
| | - Mariusz Czarnocki-Cieciura
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, Trojdena 4, 02-109, Warsaw, Poland
| | - Elzbieta Nowak
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, Trojdena 4, 02-109, Warsaw, Poland
| | - Karolina Labedzka-Dmoch
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106, Warsaw, Poland
| | - Aleksandra Kawinska
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106, Warsaw, Poland
| | - Jakub Piatkowski
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106, Warsaw, Poland
| | - Pawel Golik
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106, Warsaw, Poland
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106, Warsaw, Poland
| | - Maciej Kozak
- Faculty of Physics, Adam Mickiewicz University, ul. Umultowska 89, 61-614, Poznan, Poland
| | - Andrzej Dziembowski
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106, Warsaw, Poland
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106, Warsaw, Poland
| | - Marcin Nowotny
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, Trojdena 4, 02-109, Warsaw, Poland.
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76
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Falk S, Tants JN, Basquin J, Thoms M, Hurt E, Sattler M, Conti E. Structural insights into the interaction of the nuclear exosome helicase Mtr4 with the preribosomal protein Nop53. RNA (NEW YORK, N.Y.) 2017; 23:1780-1787. [PMID: 28883156 PMCID: PMC5688999 DOI: 10.1261/rna.062901.117] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Accepted: 09/05/2017] [Indexed: 05/24/2023]
Abstract
The nuclear exosome and the associated RNA helicase Mtr4 participate in the processing of several ribonucleoprotein particles (RNP), including the maturation of the large ribosomal subunit (60S). S. cerevisiae Mtr4 interacts directly with Nop53, a ribosomal biogenesis factor present in late pre-60S particles containing precursors of the 5.8S rRNA. The Mtr4-Nop53 interaction plays a pivotal role in the maturation of the 5.8S rRNA, providing a physical link between the nuclear exosome and the pre-60S RNP. An analogous interaction between Mtr4 and another ribosome biogenesis factor, Utp18, directs the exosome to an earlier preribosomal particle. Nop53 and Utp18 contain a similar Mtr4-binding motif known as the arch-interacting motif (AIM). Here, we report the 3.2 Å resolution crystal structure of S. cerevisiae Mtr4 bound to the interacting region of Nop53, revealing how the KOW domain of the helicase recognizes the AIM sequence of Nop53 with a network of hydrophobic and electrostatic interactions. The AIM-interacting residues are conserved in Mtr4 and are not present in the related cytoplasmic helicase Ski2, rationalizing the specificity and versatility of Mtr4 in the recognition of different AIM-containing proteins. Using nuclear magnetic resonance (NMR), we show that the KOW domain of Mtr4 can simultaneously bind an AIM-containing protein and a structured RNA at adjacent surfaces, suggesting how it can dock onto RNPs. The KOW domains of exosome-associated helicases thus appear to have evolved from the KOW domains of ribosomal proteins and to function as RNP-binding modules in the context of the nuclear exosome.
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Affiliation(s)
- Sebastian Falk
- Max-Planck-Institute of Biochemistry, Department of Structural Cell Biology, D-82152 Martinsried, Germany
| | - Jan-Niklas Tants
- Center for Integrated Protein Science Munich at Chair of Biomolecular NMR Spectroscopy, Department Chemie, Technische Universität München, 85748 Garching, Germany
- Institute of Structural Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Jerôme Basquin
- Max-Planck-Institute of Biochemistry, Department of Structural Cell Biology, D-82152 Martinsried, Germany
| | - Matthias Thoms
- Heidelberg University Biochemistry Center (BZH), INF 328, D-69120 Heidelberg, Germany
| | - Ed Hurt
- Heidelberg University Biochemistry Center (BZH), INF 328, D-69120 Heidelberg, Germany
| | - Michael Sattler
- Center for Integrated Protein Science Munich at Chair of Biomolecular NMR Spectroscopy, Department Chemie, Technische Universität München, 85748 Garching, Germany
- Institute of Structural Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Elena Conti
- Max-Planck-Institute of Biochemistry, Department of Structural Cell Biology, D-82152 Martinsried, Germany
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77
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Jamar NH, Kritsiligkou P, Grant CM. The non-stop decay mRNA surveillance pathway is required for oxidative stress tolerance. Nucleic Acids Res 2017; 45:6881-6893. [PMID: 28472342 PMCID: PMC5499853 DOI: 10.1093/nar/gkx306] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 04/12/2017] [Indexed: 01/09/2023] Open
Abstract
Reactive oxygen species (ROS) are toxic by-products of normal aerobic metabolism. ROS can damage mRNAs and the translational apparatus resulting in translational defects and aberrant protein production. Three mRNA quality control systems monitor mRNAs for translational errors: nonsense-mediated decay, non-stop decay (NSD) and no-go decay (NGD) pathways. Here, we show that factors required for the recognition of NSD substrates and components of the SKI complex are required for oxidant tolerance. We found an overlapping requirement for Ski7, which bridges the interaction between the SKI complex and the exosome, and NGD components (Dom34/Hbs1) which have been shown to function in both NSD and NGD. We show that ski7 dom34 and ski7 hbs1 mutants are sensitive to hydrogen peroxide stress and accumulate an NSD substrate. We further show that NSD substrates are generated during ROS exposure as a result of aggregation of the Sup35 translation termination factor, which increases stop codon read-through allowing ribosomes to translate into the 3΄-end of mRNAs. Overexpression of Sup35 decreases stop codon read-through and rescues oxidant tolerance consistent with this model. Our data reveal an unanticipated requirement for the NSD pathway during oxidative stress conditions which prevents the production of aberrant proteins from NSD mRNAs.
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Affiliation(s)
- Nur H Jamar
- The University of Manchester, Faculty of Biology, Medicine and Health, Manchester M13 9PT, UK.,School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Malaysia
| | - Paraskevi Kritsiligkou
- The University of Manchester, Faculty of Biology, Medicine and Health, Manchester M13 9PT, UK
| | - Chris M Grant
- The University of Manchester, Faculty of Biology, Medicine and Health, Manchester M13 9PT, UK
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78
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Abstract
Numerous surveillance pathways sculpt eukaryotic transcriptomes by degrading unneeded, defective, and potentially harmful noncoding RNAs (ncRNAs). Because aberrant and excess ncRNAs are largely degraded by exoribonucleases, a key characteristic of these RNAs is an accessible, protein-free 5' or 3' end. Most exoribonucleases function with cofactors that recognize ncRNAs with accessible 5' or 3' ends and/or increase the availability of these ends. Noncoding RNA surveillance pathways were first described in budding yeast, and there are now high-resolution structures of many components of the yeast pathways and significant mechanistic understanding as to how they function. Studies in human cells are revealing the ways in which these pathways both resemble and differ from their yeast counterparts, and are also uncovering numerous pathways that lack equivalents in budding yeast. In this review, we describe both the well-studied pathways uncovered in yeast and the new concepts that are emerging from studies in mammalian cells. We also discuss the ways in which surveillance pathways compete with chaperone proteins that transiently protect nascent ncRNA ends from exoribonucleases, with partner proteins that sequester these ends within RNPs, and with end modification pathways that protect the ends of some ncRNAs from nucleases.
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Affiliation(s)
- Cedric Belair
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute , National Institutes of Health , Frederick , Maryland 21702 , United States
| | - Soyeong Sim
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute , National Institutes of Health , Frederick , Maryland 21702 , United States
| | - Sandra L Wolin
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute , National Institutes of Health , Frederick , Maryland 21702 , United States
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79
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Schmidt C, Kowalinski E, Shanmuganathan V, Defenouillère Q, Braunger K, Heuer A, Pech M, Namane A, Berninghausen O, Fromont-Racine M, Jacquier A, Conti E, Becker T, Beckmann R. The cryo-EM structure of a ribosome-Ski2-Ski3-Ski8 helicase complex. Science 2017; 354:1431-1433. [PMID: 27980209 DOI: 10.1126/science.aaf7520] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Revised: 09/26/2016] [Accepted: 11/21/2016] [Indexed: 01/06/2023]
Abstract
Ski2-Ski3-Ski8 (Ski) is a helicase complex functioning with the RNA-degrading exosome to mediate the 3'-5' messenger RNA (mRNA) decay in turnover and quality-control pathways. We report that the Ski complex directly associates with 80S ribosomes presenting a short mRNA 3' overhang. We determined the structure of an endogenous ribosome-Ski complex using cryo-electron microscopy (EM) with a local resolution of the Ski complex ranging from 4 angstroms (Å) in the core to about 10 Å for intrinsically flexible regions. Ribosome binding displaces the autoinhibitory domain of the Ski2 helicase, positioning it in an open conformation near the ribosomal mRNA entry tunnel. We observe that the mRNA 3' overhang is threaded directly from the small ribosomal subunit to the helicase channel of Ski2, primed for ongoing exosome-mediated 3'-5' degradation.
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Affiliation(s)
- Christian Schmidt
- Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, Feodor-Lynen-Strasse 25, University of Munich, 81377 Munich, Germany
| | - Eva Kowalinski
- Max Planck Institute of Biochemistry, Department of Structural Cell Biology, Am Klopferspitz 18, 82152 Martinsried, Munich, Germany
| | - Vivekanandan Shanmuganathan
- Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, Feodor-Lynen-Strasse 25, University of Munich, 81377 Munich, Germany
| | - Quentin Defenouillère
- Institut Pasteur, Génétique des Interactions Macromoléculaires, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 3525, Rue du Docteur Roux 25-28, 75724 Paris, France.,Sorbonne Universités, UPMC Paris 6, Complexité du Vivant, 75252 Paris Cedex 05, France
| | - Katharina Braunger
- Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, Feodor-Lynen-Strasse 25, University of Munich, 81377 Munich, Germany
| | - André Heuer
- Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, Feodor-Lynen-Strasse 25, University of Munich, 81377 Munich, Germany
| | - Markus Pech
- Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, Feodor-Lynen-Strasse 25, University of Munich, 81377 Munich, Germany
| | - Abdelkader Namane
- Institut Pasteur, Génétique des Interactions Macromoléculaires, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 3525, Rue du Docteur Roux 25-28, 75724 Paris, France
| | - Otto Berninghausen
- Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, Feodor-Lynen-Strasse 25, University of Munich, 81377 Munich, Germany
| | - Micheline Fromont-Racine
- Institut Pasteur, Génétique des Interactions Macromoléculaires, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 3525, Rue du Docteur Roux 25-28, 75724 Paris, France
| | - Alain Jacquier
- Institut Pasteur, Génétique des Interactions Macromoléculaires, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 3525, Rue du Docteur Roux 25-28, 75724 Paris, France
| | - Elena Conti
- Max Planck Institute of Biochemistry, Department of Structural Cell Biology, Am Klopferspitz 18, 82152 Martinsried, Munich, Germany.
| | - Thomas Becker
- Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, Feodor-Lynen-Strasse 25, University of Munich, 81377 Munich, Germany.
| | - Roland Beckmann
- Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, Feodor-Lynen-Strasse 25, University of Munich, 81377 Munich, Germany.
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80
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Zinder JC, Lima CD. Targeting RNA for processing or destruction by the eukaryotic RNA exosome and its cofactors. Genes Dev 2017; 31:88-100. [PMID: 28202538 PMCID: PMC5322736 DOI: 10.1101/gad.294769.116] [Citation(s) in RCA: 151] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
In this review, Zinder and Lima highlight recent advances that have illuminated roles for the RNA exosome and its cofactors in specific biological pathways, alongside studies that attempted to dissect these activities through structural and biochemical characterization of nuclear and cytoplasmic RNA exosome complexes. The eukaryotic RNA exosome is an essential and conserved protein complex that can degrade or process RNA substrates in the 3′-to-5′ direction. Since its discovery nearly two decades ago, studies have focused on determining how the exosome, along with associated cofactors, achieves the demanding task of targeting particular RNAs for degradation and/or processing in both the nucleus and cytoplasm. In this review, we highlight recent advances that have illuminated roles for the RNA exosome and its cofactors in specific biological pathways, alongside studies that attempted to dissect these activities through structural and biochemical characterization of nuclear and cytoplasmic RNA exosome complexes.
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Affiliation(s)
- John C Zinder
- Tri-Institutional Training Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA.,Structural Biology Program, Sloan Kettering Institute, New York, New York, 10065, USA
| | - Christopher D Lima
- Structural Biology Program, Sloan Kettering Institute, New York, New York, 10065, USA.,Howard Hughes Medical Institute, New York, New York, 10065 USA
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81
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Li L, Lingaraju M, Basquin C, Basquin J, Conti E. Structure of a SMG8-SMG9 complex identifies a G-domain heterodimer in the NMD effector proteins. RNA (NEW YORK, N.Y.) 2017; 23:1028-1034. [PMID: 28389433 PMCID: PMC5473137 DOI: 10.1261/rna.061200.117] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 04/04/2017] [Indexed: 06/07/2023]
Abstract
Nonsense-mediated mRNA decay (NMD) is a eukaryotic mRNA degradation pathway involved in surveillance and post-transcriptional regulation, and executed by the concerted action of several trans-acting factors. The SMG1 kinase is an essential NMD factor in metazoans and is associated with two recently identified and yet poorly characterized proteins, SMG8 and SMG9. We determined the 2.5 Å resolution crystal structure of a SMG8-SMG9 core complex from C. elegans We found that SMG8-SMG9 is a G-domain heterodimer with architectural similarities to the dynamin-like family of GTPases such as Atlastin and GBP1. The SMG8-SMG9 heterodimer forms in the absence of nucleotides, with interactions conserved from worms to humans. Nucleotide binding occurs at the G domain of SMG9 but not of SMG8. Fitting the GDP-bound SMG8-SMG9 structure in EM densities of the human SMG1-SMG8-SMG9 complex raises the possibility that the nucleotide site of SMG9 faces SMG1 and could impact the kinase conformation and/or regulation.
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Affiliation(s)
- Liang Li
- Department of Structural Cell Biology, Max-Planck-Institute of Biochemistry, D-82152 Martinsried, Germany
| | - Mahesh Lingaraju
- Department of Structural Cell Biology, Max-Planck-Institute of Biochemistry, D-82152 Martinsried, Germany
| | - Claire Basquin
- Department of Structural Cell Biology, Max-Planck-Institute of Biochemistry, D-82152 Martinsried, Germany
| | - Jérome Basquin
- Department of Structural Cell Biology, Max-Planck-Institute of Biochemistry, D-82152 Martinsried, Germany
| | - Elena Conti
- Department of Structural Cell Biology, Max-Planck-Institute of Biochemistry, D-82152 Martinsried, Germany
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82
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Bobik K, McCray TN, Ernest B, Fernandez JC, Howell KA, Lane T, Staton M, Burch-Smith TM. The chloroplast RNA helicase ISE2 is required for multiple chloroplast RNA processing steps in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 91:114-131. [PMID: 28346704 DOI: 10.1111/tpj.13550] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2016] [Revised: 03/14/2017] [Accepted: 03/21/2017] [Indexed: 05/06/2023]
Abstract
INCREASED SIZE EXCLUSION LIMIT2 (ISE2) is a chloroplast-localized RNA helicase that is indispensable for proper plant development. Chloroplasts in leaves with reduced ISE2 expression have previously been shown to exhibit reduced thylakoid contents and increased stromal volume, indicative of defective development. It has recently been reported that ISE2 is required for the splicing of group II introns from chloroplast transcripts. The current study extends these findings, and presents evidence for ISE2's role in multiple aspects of chloroplast RNA processing beyond group II intron splicing. Loss of ISE2 from Arabidopsis thaliana leaves resulted in defects in C-to-U RNA editing, altered accumulation of chloroplast transcripts and chloroplast-encoded proteins, and defective processing of chloroplast ribosomal RNAs. Potential ISE2 substrates were identified by RNA immunoprecipitation followed by next-generation sequencing (RIP-seq), and the diversity of RNA species identified supports ISE2's involvement in multiple aspects of chloroplast RNA metabolism. Comprehensive phylogenetic analyses revealed that ISE2 is a non-canonical Ski2-like RNA helicase that represents a separate sub-clade unique to green photosynthetic organisms, consistent with its function as an essential protein. Thus ISE2's evolutionary conservation may be explained by its numerous roles in regulating chloroplast gene expression.
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Affiliation(s)
- Krzysztof Bobik
- Department of Biochemistry and Cellular & Molecular Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Tyra N McCray
- School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Ben Ernest
- School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Jessica C Fernandez
- Department of Biochemistry and Cellular & Molecular Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Katharine A Howell
- Plant Energy Biology, ARC Center of Excellence, University of Western Australia, Perth, Australia
| | - Thomas Lane
- Department of Entomology and Plant Pathology, University of Tennessee Institute of Agriculture, Knoxville, TN, 37996, USA
| | - Margaret Staton
- School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA
- Department of Entomology and Plant Pathology, University of Tennessee Institute of Agriculture, Knoxville, TN, 37996, USA
| | - Tessa M Burch-Smith
- Department of Biochemistry and Cellular & Molecular Biology, University of Tennessee, Knoxville, TN, 37996, USA
- School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA
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83
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Guydosh NR, Green R. Translation of poly(A) tails leads to precise mRNA cleavage. RNA (NEW YORK, N.Y.) 2017; 23:749-761. [PMID: 28193672 PMCID: PMC5393183 DOI: 10.1261/rna.060418.116] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 02/09/2017] [Indexed: 05/07/2023]
Abstract
Translation of poly(A) tails leads to mRNA cleavage but the mechanism and global pervasiveness of this "nonstop/no-go" decay process is not understood. Here we performed ribosome profiling (in a yeast strain lacking exosome function) of short 15-18 nucleotides mRNA footprints to identify ribosomes stalled at 3' ends of mRNA decay intermediates. In this background, we found mRNA cleavage extending hundreds of nucleotides upstream of ribosome stalling in poly(A) and predominantly in one reading frame. These observations suggest that decay-triggering endonucleolytic cleavage is closely associated with the ribosome. Surprisingly, ribosomes appeared to accumulate (i.e., stall) in the transcriptome when as few as three consecutive ORF-internal lysine codons were positioned in the A, P, and E sites though significant mRNA degradation was not observed. Endonucleolytic cleavage was found, however, at sites of premature polyadenylation (encoding polylysine) and rescue of the ribosomes stalled at these sites was dependent on Dom34. These results suggest this process may be critical when changes in the polyadenylation site occur during development, tumorigenesis, or when translation termination/recycling is impaired.
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Affiliation(s)
- Nicholas R Guydosh
- Howard Hughes Medical Institute, Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Rachel Green
- Howard Hughes Medical Institute, Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
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84
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Tsuzuki M, Motomura K, Kumakura N, Takeda A. Interconnections between mRNA degradation and RDR-dependent siRNA production in mRNA turnover in plants. JOURNAL OF PLANT RESEARCH 2017; 130:211-226. [PMID: 28197782 DOI: 10.1007/s10265-017-0906-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2016] [Accepted: 12/08/2016] [Indexed: 06/06/2023]
Abstract
Accumulation of an mRNA species is determined by the balance between the synthesis and the degradation of the mRNA. Individual mRNA molecules are selectively and actively degraded through RNA degradation pathways, which include 5'-3' mRNA degradation pathway, 3'-5' mRNA degradation pathway, and RNA-dependent RNA polymerase-mediated mRNA degradation pathway. Recent studies have revealed that these RNA degradation pathways compete with each other in mRNA turnover in plants and that plants have a hidden layer of non-coding small-interfering RNA production from a set of mRNAs. In this review, we summarize the current information about plant mRNA degradation pathways in mRNA turnover and discuss the potential roles of a novel class of the endogenous siRNAs derived from plant mRNAs.
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Affiliation(s)
- Masayuki Tsuzuki
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, 153-8902, Japan
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Kazuki Motomura
- Institute of Transformative Bio-Molecules, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8601, Japan
| | - Naoyoshi Kumakura
- Center for Sustainable Resource Science, RIKEN, Suehiro-cho 1-7-22, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Atsushi Takeda
- Department of Biotechnology, Graduate School of Life Sciences, Ritsumeikan University, Shiga, 525-8577, Japan.
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85
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Kurihara Y. Activity and roles of Arabidopsis thaliana XRN family exoribonucleases in noncoding RNA pathways. JOURNAL OF PLANT RESEARCH 2017; 130:25-31. [PMID: 27988817 DOI: 10.1007/s10265-016-0887-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 10/28/2016] [Indexed: 05/20/2023]
Abstract
RNA metabolism is mediated by several sophisticated exo- or endo- ribonucleases. XRN family proteins are the conserved 5'-3' exoribonucleases in eukaryotes. A. thaliana genome encodes three XRN homologs (AtXRN2, AtXRN3 and AtXRN4) and their independent or redundant roles, which are possibly plant-specific in some cases, have been reported. AtXRN2 acts in maturation of ribosomal RNAs partially with AtXRN3. AtXRN3 is also involved in elimination of 3' remnants of microRNA precursors and in termination of mRNA transcription events. AtXRN4 degrades not only a small fraction of mRNAs in stress response but also 3' cleavage products of miRNA-mediated cleavage of target mRNAs. Moreover, all AtXRNs are important factors to suppress unexpected RNA silencing occurrence. Thus, this review summarizes and discusses multiple roles of AtXRN exoribonucleases and their relationship with noncoding RNA pathways including RNA silencing pathways.
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Affiliation(s)
- Yukio Kurihara
- Synthetic Genomics Research Group, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.
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86
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Falk S, Finogenova K, Melko M, Benda C, Lykke-Andersen S, Jensen TH, Conti E. Structure of the RBM7-ZCCHC8 core of the NEXT complex reveals connections to splicing factors. Nat Commun 2016; 7:13573. [PMID: 27905398 PMCID: PMC5146272 DOI: 10.1038/ncomms13573] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 10/13/2016] [Indexed: 01/24/2023] Open
Abstract
The eukaryotic RNA exosome participates extensively in RNA processing and degradation. In human cells, three accessory factors (RBM7, ZCCHC8 and hMTR4) interact to form the nuclear exosome targeting (NEXT) complex, which directs a subset of non-coding RNAs for exosomal degradation. Here we elucidate how RBM7 is incorporated in the NEXT complex. We identify a proline-rich segment of ZCCHC8 as the interaction site for the RNA-recognition motif (RRM) of RBM7 and present the crystal structure of the corresponding complex at 2.0 Å resolution. On the basis of the structure, we identify a proline-rich segment within the splicing factor SAP145 with strong similarity to ZCCHC8. We show that this segment of SAP145 not only binds the RRM region of another splicing factor SAP49 but also the RRM of RBM7. These dual interactions of RBM7 with the exosome and the spliceosome suggest a model whereby NEXT might recruit the exosome to degrade intronic RNAs. RBM7 and ZCCHC8 are two core subunits of the Nuclear Exosome Targeting complex, which regulates the degradation of selected non-coding RNAs in human cells. Here, the authors use structural and biochemical methods to show how ZCCHC8 recruits RBM7 in the complex, leaving the RNA binding site accessible and revealing possible implications for splicing.
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Affiliation(s)
- Sebastian Falk
- Department of Structural Cell Biology, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
| | - Ksenia Finogenova
- Department of Structural Cell Biology, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
| | - Mireille Melko
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Alle 3, 8000C Aarhus, Denmark
| | - Christian Benda
- Department of Structural Cell Biology, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
| | - Søren Lykke-Andersen
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Alle 3, 8000C Aarhus, Denmark
| | - Torben Heick Jensen
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Alle 3, 8000C Aarhus, Denmark
| | - Elena Conti
- Department of Structural Cell Biology, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
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87
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North M, Gaytán BD, Romero C, De La Rosa VY, Loguinov A, Smith MT, Zhang L, Vulpe CD. Functional Toxicogenomic Profiling Expands Insight into Modulators of Formaldehyde Toxicity in Yeast. Front Genet 2016; 7:200. [PMID: 27909446 PMCID: PMC5112362 DOI: 10.3389/fgene.2016.00200] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2016] [Accepted: 10/31/2016] [Indexed: 12/21/2022] Open
Abstract
Formaldehyde (FA) is a commercially important chemical with numerous and diverse uses. Accordingly, occupational and environmental exposure to FA is prevalent worldwide. Various adverse effects, including nasopharyngeal, sinonasal, and lymphohematopoietic cancers, have been linked to FA exposure, prompting designation of FA as a human carcinogen by U.S. and international scientific entities. Although the mechanism(s) of FA toxicity have been well studied, additional insight is needed in regard to the genetic requirements for FA tolerance. In this study, a functional toxicogenomics approach was utilized in the model eukaryotic yeast Saccharomyces cerevisiae to identify genes and cellular processes modulating the cellular toxicity of FA. Our results demonstrate mutant strains deficient in multiple DNA repair pathways-including homologous recombination, single strand annealing, and postreplication repair-were sensitive to FA, indicating FA may cause various forms of DNA damage in yeast. The SKI complex and its associated factors, which regulate mRNA degradation by the exosome, were also required for FA tolerance, suggesting FA may have unappreciated effects on RNA stability. Furthermore, various strains involved in osmoregulation and stress response were sensitive to FA. Together, our results are generally consistent with FA-mediated damage to both DNA and RNA. Considering DNA repair and RNA degradation pathways are evolutionarily conserved from yeast to humans, mechanisms of FA toxicity identified in yeast may be relevant to human disease and genetic susceptibility.
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Affiliation(s)
- Matthew North
- Department of Nutritional Science and Toxicology, University of California Berkeley, CA, USA
| | - Brandon D Gaytán
- Department of Nutritional Science and Toxicology, University of California Berkeley, CA, USA
| | - Carlos Romero
- Division of Environmental Health Sciences, School of Public Health, University of California Berkeley, CA, USA
| | - Vanessa Y De La Rosa
- Department of Nutritional Science and Toxicology, University of California Berkeley, CA, USA
| | - Alex Loguinov
- Department of Nutritional Science and Toxicology, University of California Berkeley, CA, USA
| | - Martyn T Smith
- Division of Environmental Health Sciences, School of Public Health, University of California Berkeley, CA, USA
| | - Luoping Zhang
- Division of Environmental Health Sciences, School of Public Health, University of California Berkeley, CA, USA
| | - Chris D Vulpe
- Department of Nutritional Science and Toxicology, University of California Berkeley, CA, USA
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88
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Łabno A, Tomecki R, Dziembowski A. Cytoplasmic RNA decay pathways - Enzymes and mechanisms. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2016; 1863:3125-3147. [PMID: 27713097 DOI: 10.1016/j.bbamcr.2016.09.023] [Citation(s) in RCA: 124] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 09/29/2016] [Accepted: 09/30/2016] [Indexed: 12/14/2022]
Abstract
RNA decay plays a crucial role in post-transcriptional regulation of gene expression. Work conducted over the last decades has defined the major mRNA decay pathways, as well as enzymes and their cofactors responsible for these processes. In contrast, our knowledge of the mechanisms of degradation of non-protein coding RNA species is more fragmentary. This review is focused on the cytoplasmic pathways of mRNA and ncRNA degradation in eukaryotes. The major 3' to 5' and 5' to 3' mRNA decay pathways are described with emphasis on the mechanisms of their activation by the deprotection of RNA ends. More recently discovered 3'-end modifications such as uridylation, and their relevance to cytoplasmic mRNA decay in various model organisms, are also discussed. Finally, we provide up-to-date findings concerning various pathways of non-coding RNA decay in the cytoplasm.
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Affiliation(s)
- Anna Łabno
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, Poland; Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5A, 02-106 Warsaw, Poland
| | - Rafał Tomecki
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, Poland; Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5A, 02-106 Warsaw, Poland.
| | - Andrzej Dziembowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, Poland; Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5A, 02-106 Warsaw, Poland.
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89
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Rowley PA, Ho B, Bushong S, Johnson A, Sawyer SL. XRN1 Is a Species-Specific Virus Restriction Factor in Yeasts. PLoS Pathog 2016; 12:e1005890. [PMID: 27711183 PMCID: PMC5053509 DOI: 10.1371/journal.ppat.1005890] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 08/23/2016] [Indexed: 02/07/2023] Open
Abstract
In eukaryotes, the degradation of cellular mRNAs is accomplished by Xrn1 and the cytoplasmic exosome. Because viral RNAs often lack canonical caps or poly-A tails, they can also be vulnerable to degradation by these host exonucleases. Yeast lack sophisticated mechanisms of innate and adaptive immunity, but do use RNA degradation as an antiviral defense mechanism. One model is that the RNA of yeast viruses is subject to degradation simply as a side effect of the intrinsic exonuclease activity of proteins involved in RNA metabolism. Contrary to this model, we find a highly refined, species-specific relationship between Xrn1p and the "L-A" totiviruses of different Saccharomyces yeast species. We show that the gene XRN1 has evolved rapidly under positive natural selection in Saccharomyces yeast, resulting in high levels of Xrn1p protein sequence divergence from one yeast species to the next. We also show that these sequence differences translate to differential interactions with the L-A virus, where Xrn1p from S. cerevisiae is most efficient at controlling the L-A virus that chronically infects S. cerevisiae, and Xrn1p from S. kudriavzevii is most efficient at controlling the L-A-like virus that we have discovered within S. kudriavzevii. All Xrn1p orthologs are equivalent in their interaction with another virus-like parasite, the Ty1 retrotransposon. Thus, the activity of Xrn1p against totiviruses is not simply an incidental consequence of the enzymatic activity of Xrn1p, but rather Xrn1p co-evolves with totiviruses to maintain its potent antiviral activity and limit viral propagation in Saccharomyces yeasts. Consistent with this, we demonstrated that Xrn1p physically interacts with the Gag protein encoded by the L-A virus, suggesting a host-virus interaction that is more complicated than just Xrn1p-mediated nucleolytic digestion of viral RNAs.
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Affiliation(s)
- Paul A. Rowley
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, United States of America
- Section of Molecular Biosciences, University of Texas at Austin, Austin, Texas, United States of America
| | - Brandon Ho
- Section of Molecular Biosciences, University of Texas at Austin, Austin, Texas, United States of America
| | - Sarah Bushong
- Section of Molecular Biosciences, University of Texas at Austin, Austin, Texas, United States of America
| | - Arlen Johnson
- Section of Molecular Biosciences, University of Texas at Austin, Austin, Texas, United States of America
| | - Sara L. Sawyer
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, United States of America
- Section of Molecular Biosciences, University of Texas at Austin, Austin, Texas, United States of America
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90
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Maity A, Chaudhuri A, Das B. DRN and TRAMP degrade specific and overlapping aberrant mRNAs formed at various stages of mRNP biogenesis inSaccharomyces cerevisiae. FEMS Yeast Res 2016; 16:fow088. [DOI: 10.1093/femsyr/fow088] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/29/2016] [Indexed: 01/08/2023] Open
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91
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Kowalinski E, Kögel A, Ebert J, Reichelt P, Stegmann E, Habermann B, Conti E. Structure of a Cytoplasmic 11-Subunit RNA Exosome Complex. Mol Cell 2016; 63:125-34. [PMID: 27345150 PMCID: PMC4942675 DOI: 10.1016/j.molcel.2016.05.028] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Revised: 04/26/2016] [Accepted: 05/18/2016] [Indexed: 10/28/2022]
Abstract
The RNA exosome complex associates with nuclear and cytoplasmic cofactors to mediate the decay, surveillance, or processing of a wide variety of transcripts. In the cytoplasm, the conserved core of the exosome (Exo10) functions together with the conserved Ski complex. The interaction of S. cerevisiae Exo10 and Ski is not direct but requires a bridging cofactor, Ski7. Here, we report the 2.65 Å resolution structure of S. cerevisiae Exo10 bound to the interacting domain of Ski7. Extensive hydrophobic interactions rationalize the high affinity and stability of this complex, pointing to Ski7 as a constitutive component of the cytosolic exosome. Despite the absence of sequence homology, cytoplasmic Ski7 and nuclear Rrp6 bind Exo10 using similar surfaces and recognition motifs. Knowledge of the interacting residues in the yeast complexes allowed us to identify a splice variant of human HBS1-Like as a Ski7-like exosome-binding protein, revealing the evolutionary conservation of this cytoplasmic cofactor.
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Affiliation(s)
- Eva Kowalinski
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Alexander Kögel
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Judith Ebert
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Peter Reichelt
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Elisabeth Stegmann
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Bianca Habermann
- Computational Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Elena Conti
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.
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92
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Ribosome-associated Asc1/RACK1 is required for endonucleolytic cleavage induced by stalled ribosome at the 3' end of nonstop mRNA. Sci Rep 2016; 6:28234. [PMID: 27312062 PMCID: PMC4911565 DOI: 10.1038/srep28234] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 05/31/2016] [Indexed: 12/21/2022] Open
Abstract
Dom34-Hbs1 stimulates degradation of aberrant mRNAs lacking termination codons by dissociating ribosomes stalled at the 3′ ends, and plays crucial roles in Nonstop Decay (NSD) and No-Go Decay (NGD). In the dom34Δ mutant, nonstop mRNA is degraded by sequential endonucleolytic cleavages induced by a stalled ribosome at the 3′ end. Here, we report that ribosome-associated Asc1/RACK1 is required for the endonucleolytic cleavage of nonstop mRNA by stalled ribosome at the 3′ end of mRNA in dom34Δ mutant cells. Asc1/RACK1 facilitates degradation of truncated GFP-Rz mRNA in the absence of Dom34 and exosome-dependent decay. Asc1/RACK1 is required for the sequential endonucleolytic cleavages by the stalled ribosome in the dom34Δ mutant, depending on its ribosome-binding activity. The levels of peptidyl-tRNA derived from nonstop mRNA were elevated in dom34Δasc1Δ mutant cells, and overproduction of nonstop mRNA inhibited growth of mutant cells. E3 ubiquitin ligase Ltn1 degrades the arrest products from truncated GFP-Rz mRNA in dom34Δ and dom34Δasc1Δ mutant cells, and Asc1/RACK1 represses the levels of substrates for Ltn1-dependent degradation. These indicate that ribosome-associated Asc1/RACK1 facilitates endonucleolytic cleavage of nonstop mRNA by stalled ribosomes and represses the levels of aberrant products even in the absence of Dom34. We propose that Asc1/RACK1 acts as a fail-safe in quality control for nonstop mRNA.
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93
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CryoEM structure of yeast cytoplasmic exosome complex. Cell Res 2016; 26:822-37. [PMID: 27174052 DOI: 10.1038/cr.2016.56] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Revised: 01/26/2016] [Accepted: 03/07/2016] [Indexed: 01/25/2023] Open
Abstract
The eukaryotic multi-subunit RNA exosome complex plays crucial roles in 3'-to-5' RNA processing and decay. Rrp6 and Ski7 are the major cofactors for the nuclear and cytoplasmic exosomes, respectively. In the cytoplasm, Ski7 helps the exosome to target mRNAs for degradation and turnover via a through-core pathway. However, the interaction between Ski7 and the exosome complex has remained unclear. The transaction of RNA substrates within the exosome is also elusive. In this work, we used single-particle cryo-electron microscopy to solve the structures of the Ski7-exosome complex in RNA-free and RNA-bound forms at resolutions of 4.2 Å and 5.8 Å, respectively. These structures reveal that the N-terminal domain of Ski7 adopts a structural arrangement and interacts with the exosome in a similar fashion to the C-terminal domain of nuclear Rrp6. Further structural analysis of exosomes with RNA substrates harboring 3' overhangs of different length suggests a switch mechanism of RNA-induced exosome activation in the through-core pathway of RNA processing.
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94
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Towler BP, Jones CI, Viegas SC, Apura P, Waldron JA, Smalley SK, Arraiano CM, Newbury SF. The 3'-5' exoribonuclease Dis3 regulates the expression of specific microRNAs in Drosophila wing imaginal discs. RNA Biol 2016; 12:728-41. [PMID: 25892215 PMCID: PMC4615222 DOI: 10.1080/15476286.2015.1040978] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Dis3 is a highly conserved exoribonuclease which degrades RNAs in the 3'-5' direction. Mutations in Dis3 are associated with a number of human cancers including multiple myeloma and acute myeloid leukemia. In this work, we have assessed the effect of a Dis3 knockdown on Drosophila imaginal disc development and on expression of mature microRNAs. We find that Dis3 knockdown severely disrupts the development of wing imaginal discs in that the flies have a “no wing” phenotype. Use of RNA-seq to quantify the effect of Dis3 knockdown on microRNA expression shows that Dis3 normally regulates a small subset of microRNAs, with only 11 (10.1%) increasing in level ≥2-fold and 6 (5.5%) decreasing in level ≥2-fold. Of these microRNAs, miR-252–5p is increased 2.1-fold in Dis3-depleted cells compared to controls while the level of the miR-252 precursor is unchanged, suggesting that Dis3 can act in the cytoplasm to specifically degrade this mature miRNA. Furthermore, our experiments suggest that Dis3 normally interacts with the exosomal subunit Rrp40 in the cytoplasm to target miR-252–5p for degradation during normal wing development. Another microRNA, miR-982–5p, is expressed at lower levels in Dis3 knockdown cells, while the miR-982 precursor remains unchanged, indicating that Dis3 is involved in its processing. Our study therefore reveals an unexpected specificity for this ribonuclease toward microRNA regulation, which is likely to be conserved in other eukaryotes and may be relevant to understanding its role in human disease.
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Affiliation(s)
- Benjamin P Towler
- a Brighton and Sussex Medical School; Medical Research Building; University of Sussex; Falmer , Brighton , UK
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95
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Prabu JR, Müller M, Thomae AW, Schüssler S, Bonneau F, Becker PB, Conti E. Structure of the RNA Helicase MLE Reveals the Molecular Mechanisms for Uridine Specificity and RNA-ATP Coupling. Mol Cell 2016; 60:487-99. [PMID: 26545078 DOI: 10.1016/j.molcel.2015.10.011] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Revised: 08/10/2015] [Accepted: 10/02/2015] [Indexed: 10/22/2022]
Abstract
The MLE helicase remodels the roX lncRNAs, enabling the lncRNA-mediated assembly of the Drosophila dosage compensation complex. We identified a stable MLE core comprising the DExH helicase module and two auxiliary domains: a dsRBD and an OB-like fold. MLEcore is an unusual DExH helicase that can unwind blunt-ended RNA duplexes and has specificity for uridine nucleotides. We determined the 2.1 Å resolution structure of MLEcore bound to a U10 RNA and ADP-AlF4. The OB-like and dsRBD folds bind the DExH module and contribute to form the entrance of the helicase channel. Four uridine nucleotides engage in base-specific interactions, rationalizing the conservation of uridine-rich sequences in critical roX substrates. roX2 binding is orchestrated by MLE's auxiliary domains, which is prerequisite for MLE localization to the male X chromosome. The structure visualizes a transition-state mimic of the reaction and suggests how eukaryotic DEAH/RHA helicases couple ATP hydrolysis to RNA translocation.
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Affiliation(s)
- J Rajan Prabu
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Marisa Müller
- Biomedical Center and Center for Integrated Protein Science, Ludwig-Maximilians-University, 82152 Martinsried, Germany
| | - Andreas W Thomae
- Biomedical Center and Center for Integrated Protein Science, Ludwig-Maximilians-University, 82152 Martinsried, Germany
| | - Steffen Schüssler
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Fabien Bonneau
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Peter B Becker
- Biomedical Center and Center for Integrated Protein Science, Ludwig-Maximilians-University, 82152 Martinsried, Germany.
| | - Elena Conti
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany.
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96
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Audin MJC, Wurm JP, Cvetkovic MA, Sprangers R. The oligomeric architecture of the archaeal exosome is important for processive and efficient RNA degradation. Nucleic Acids Res 2016; 44:2962-73. [PMID: 26837575 PMCID: PMC4824110 DOI: 10.1093/nar/gkw062] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 01/25/2016] [Indexed: 11/30/2022] Open
Abstract
The exosome plays an important role in RNA degradation and processing. In archaea, three Rrp41:Rrp42 heterodimers assemble into a barrel like structure that contains a narrow RNA entrance pore and a lumen that contains three active sites. Here, we demonstrate that this quaternary structure of the exosome is important for efficient RNA degradation. We find that the entrance pore of the barrel is required for nM substrate affinity. This strong interaction is crucial for processive substrate degradation and prevents premature release of the RNA from the enzyme. Using methyl TROSY NMR techniques, we establish that the 3′ end of the substrate remains highly flexible inside the lumen. As a result, the RNA jumps between the three active sites that all equally participate in substrate degradation. The RNA jumping rate is, however, much faster than the cleavage rate, indicating that not all active site:substrate encounters result in catalysis. Enzymatic turnover therefore benefits from the confinement of the active sites and substrate in the lumen, which ensures that the RNA is at all times bound to one of the active sites. The evolution of the exosome into a hexameric complex and the optimization of its catalytic efficiency were thus likely co-occurring events.
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Affiliation(s)
- Maxime J C Audin
- Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany
| | - Jan Philip Wurm
- Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany
| | - Milos A Cvetkovic
- Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany
| | - Remco Sprangers
- Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany
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Li Y, Burclaff J, Anderson JT. Mutations in Mtr4 Structural Domains Reveal Their Important Role in Regulating tRNAiMet Turnover in Saccharomyces cerevisiae and Mtr4p Enzymatic Activities In Vitro. PLoS One 2016; 11:e0148090. [PMID: 26820724 PMCID: PMC4731217 DOI: 10.1371/journal.pone.0148090] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Accepted: 01/12/2016] [Indexed: 12/24/2022] Open
Abstract
RNA processing and turnover play important roles in the maturation, metabolism and quality control of a large variety of RNAs thereby contributing to gene expression and cellular health. The TRAMP complex, composed of Air2p, Trf4p and Mtr4p, stimulates nuclear exosome-dependent RNA processing and degradation in Saccharomyces cerevisiae. The Mtr4 protein structure is composed of a helicase core and a novel so-called arch domain, which protrudes from the core. The helicase core contains highly conserved helicase domains RecA-1 and 2, and two structural domains of unclear functions, winged helix domain (WH) and ratchet domain. How the structural domains (arch, WH and ratchet domain) coordinate with the helicase domains and what roles they are playing in regulating Mtr4p helicase activity are unknown. We created a library of Mtr4p structural domain mutants for the first time and screened for those defective in the turnover of TRAMP and exosome substrate, hypomodified tRNAiMet. We found these domains regulate Mtr4p enzymatic activities differently through characterizing the arch domain mutants K700N and P731S, WH mutant K904N, and ratchet domain mutant R1030G. Arch domain mutants greatly reduced Mtr4p RNA binding, which surprisingly did not lead to significant defects on either in vivo tRNAiMet turnover, or in vitro unwinding activities. WH mutant K904N and Ratchet domain mutant R1030G showed decreased tRNAiMet turnover in vivo, as well as reduced RNA binding, ATPase and unwinding activities of Mtr4p in vitro. Particularly, K904 was found to be very important for steady protein levels in vivo. Overall, we conclude that arch domain plays a role in RNA binding but is largely dispensable for Mtr4p enzymatic activities, however the structural domains in the helicase core significantly contribute to Mtr4p ATPase and unwinding activities.
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Affiliation(s)
- Yan Li
- College of Veterinary Medicine, Agricultural University of Hebei, Baoding, Hebei, 071001, China
| | - Joseph Burclaff
- Division of Biology and Biomedical Sciences, Washington University, St. Louis, MO, 63110, United States of America
| | - James T. Anderson
- Department of Biological Sciences, Marquette University, Milwaukee, WI, 53233, United States of America
- * E-mail:
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98
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The regulation and functions of the nuclear RNA exosome complex. Nat Rev Mol Cell Biol 2016; 17:227-39. [PMID: 26726035 DOI: 10.1038/nrm.2015.15] [Citation(s) in RCA: 269] [Impact Index Per Article: 33.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The RNA exosome complex is the most versatile RNA-degradation machine in eukaryotes. The exosome has a central role in several aspects of RNA biogenesis, including RNA maturation and surveillance. Moreover, it is emerging as an important player in regulating the expression levels of specific mRNAs in response to environmental cues and during cell differentiation and development. Although the mechanisms by which RNA is targeted to (or escapes from) the exosome are still not fully understood, general principles have begun to emerge, which we discuss in this Review. In addition, we introduce and discuss novel, previously unappreciated functions of the nuclear exosome, including in transcription regulation and in the maintenance of genome stability.
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99
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Post-transcriptional gene silencing in plants: a double-edged sword. SCIENCE CHINA-LIFE SCIENCES 2015; 59:271-6. [PMID: 26718356 DOI: 10.1007/s11427-015-4972-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 09/08/2015] [Indexed: 01/08/2023]
Abstract
In plants, post-transcriptional gene silencing (PTGS) protects the genome from foreign genes and restricts the expression of certain endogenous genes for proper development. Here, we review the recent progress about how the unwanted PTGS is avoided in plants. As a decision-making step of PTGS, aberrant transcripts from most endogenous coding genes are strictly sorted to the bidirectional RNA decay pathways in cytoplasm but not to the short interference RNA (siRNA)-mediated PTGS, with the exception of a few development-relevant endogenous siRNA-producing genes. We also discuss a finely balanced PTGS threshold model that plants fully take advantage of the power of PTGS without self-harm.
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100
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Reddy BPN, Shrestha S, Hart KJ, Liang X, Kemirembe K, Cui L, Lindner SE. A bioinformatic survey of RNA-binding proteins in Plasmodium. BMC Genomics 2015; 16:890. [PMID: 26525978 PMCID: PMC4630921 DOI: 10.1186/s12864-015-2092-1] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2015] [Accepted: 10/15/2015] [Indexed: 11/10/2022] Open
Abstract
Background The malaria parasites in the genus Plasmodium have a very complicated life cycle involving an invertebrate vector and a vertebrate host. RNA-binding proteins (RBPs) are critical factors involved in every aspect of the development of these parasites. However, very few RBPs have been functionally characterized to date in the human parasite Plasmodium falciparum. Methods Using different bioinformatic methods and tools we searched P. falciparum genome to list and annotate RBPs. A representative 3D models for each of the RBD domain identified in P. falciparum was created using I-TESSAR and SWISS-MODEL. Microarray and RNAseq data analysis pertaining PfRBPs was performed using MeV software. Finally, Cytoscape was used to create protein-protein interaction network for CITH-Dozi and Caf1-CCR4-Not complexes. Results We report the identification of 189 putative RBP genes belonging to 13 different families in Plasmodium, which comprise 3.5 % of all annotated genes. Almost 90 % (169/189) of these genes belong to six prominent RBP classes, namely RNA recognition motifs, DEAD/H-box RNA helicases, K homology, Zinc finger, Puf and Alba gene families. Interestingly, almost all of the identified RNA-binding helicases and KH genes have cognate homologs in model species, suggesting their evolutionary conservation. Exploration of the existing P. falciparum blood-stage transcriptomes revealed that most RBPs have peak mRNA expression levels early during the intraerythrocytic development cycle, which taper off in later stages. Nearly 27 % of RBPs have elevated expression in gametocytes, while 47 and 24 % have elevated mRNA expression in ookinete and asexual stages. Comparative interactome analyses using human and Plasmodium protein-protein interaction datasets suggest extensive conservation of the PfCITH/PfDOZI and PfCaf1-CCR4-NOT complexes. Conclusions The Plasmodium parasites possess a large number of putative RBPs belonging to most of RBP families identified so far, suggesting the presence of extensive post-transcriptional regulation in these parasites. Taken together, in silico identification of these putative RBPs provides a foundation for future functional studies aimed at defining a unique network of post-transcriptional regulation in P. falciparum. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2092-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- B P Niranjan Reddy
- Department of Entomology, Center for Malaria Research, Pennsylvania State University, 501 ASI Bldg, University Park, PA, 16802, USA
| | - Sony Shrestha
- Department of Entomology, Center for Malaria Research, Pennsylvania State University, 501 ASI Bldg, University Park, PA, 16802, USA
| | - Kevin J Hart
- Department of Biochemistry and Molecular Biology, Center for Malaria Research, Pennsylvania State University, W223 Millennium Science Complex, University Park, PA, 16802, USA
| | - Xiaoying Liang
- Department of Entomology, Center for Malaria Research, Pennsylvania State University, 501 ASI Bldg, University Park, PA, 16802, USA
| | - Karen Kemirembe
- Department of Entomology, Center for Malaria Research, Pennsylvania State University, 501 ASI Bldg, University Park, PA, 16802, USA
| | - Liwang Cui
- Department of Entomology, Center for Malaria Research, Pennsylvania State University, 501 ASI Bldg, University Park, PA, 16802, USA.
| | - Scott E Lindner
- Department of Biochemistry and Molecular Biology, Center for Malaria Research, Pennsylvania State University, W223 Millennium Science Complex, University Park, PA, 16802, USA.
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