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Puno MR, Lima CD. Structural basis for RNA surveillance by the human nuclear exosome targeting (NEXT) complex. Cell 2022; 185:2132-2147.e26. [PMID: 35688134 PMCID: PMC9210550 DOI: 10.1016/j.cell.2022.04.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 03/04/2022] [Accepted: 04/08/2022] [Indexed: 02/07/2023]
Abstract
RNA quality control relies on co-factors and adaptors to identify and prepare substrates for degradation by ribonucleases such as the 3' to 5' ribonucleolytic RNA exosome. Here, we determined cryogenic electron microscopy structures of human nuclear exosome targeting (NEXT) complexes bound to RNA that reveal mechanistic insights to substrate recognition and early steps that precede RNA handover to the exosome. The structures illuminate ZCCHC8 as a scaffold, mediating homodimerization while embracing the MTR4 helicase and flexibly anchoring RBM7 to the helicase core. All three subunits collaborate to bind the RNA, with RBM7 and ZCCHC8 surveying sequences upstream of the 3' end to facilitate RNA capture by MTR4. ZCCHC8 obscures MTR4 surfaces important for RNA binding and extrusion as well as MPP6-dependent recruitment and docking onto the RNA exosome core, interactions that contribute to RNA surveillance by coordinating RNA capture, translocation, and extrusion from the helicase to the exosome for decay.
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Affiliation(s)
- M Rhyan Puno
- Structural Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Christopher D Lima
- Structural Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA; Howard Hughes Medical Institute, 1275 York Avenue, New York, NY 10065, USA.
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2
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Saito Y, Hawley BR, Puno MR, Sarathy SN, Lima CD, Jaffrey SR, Darnell RB, Keeney S, Jain D. YTHDC2 control of gametogenesis requires helicase activity but not m 6A binding. Genes Dev 2022; 36:180-194. [PMID: 35058317 PMCID: PMC8887132 DOI: 10.1101/gad.349190.121] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 01/05/2022] [Indexed: 11/30/2022]
Abstract
Mechanisms regulating meiotic progression in mammals are poorly understood. The N6-methyladenosine (m6A) reader and 3' → 5' RNA helicase YTHDC2 switches cells from mitotic to meiotic gene expression programs and is essential for meiotic entry, but how this critical cell fate change is accomplished is unknown. Here, we provide insight into its mechanism and implicate YTHDC2 in having a broad role in gene regulation during multiple meiotic stages. Unexpectedly, mutation of the m6A-binding pocket of YTHDC2 had no detectable effect on gametogenesis and mouse fertility, suggesting that YTHDC2 function is m6A-independent. Supporting this conclusion, CLIP data defined YTHDC2-binding sites on mRNA as U-rich and UG-rich motif-containing regions within 3' UTRs and coding sequences, distinct from the sites that contain m6A during spermatogenesis. Complete loss of YTHDC2 during meiotic entry did not substantially alter translation of its mRNA binding targets in whole-testis ribosome profiling assays but did modestly affect their steady-state levels. Mutation of the ATPase motif in the helicase domain of YTHDC2 did not affect meiotic entry, but it blocked meiotic prophase I progression, causing sterility. Our findings inform a model in which YTHDC2 binds transcripts independent of m6A status and regulates gene expression during multiple stages of meiosis by distinct mechanisms.
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Affiliation(s)
- Yuhki Saito
- Laboratory of Molecular Neuro-oncology, Howard Hughes Medical Institute, Rockefeller University, New York, New York 10065, USA
| | - Ben R Hawley
- Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, New York 10065, USA
| | - M Rhyan Puno
- Structural Biology Program, Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Shreya N Sarathy
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, New Jersey 08854, USA
| | - Christopher D Lima
- Structural Biology Program, Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Samie R Jaffrey
- Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, New York 10065, USA
| | - Robert B Darnell
- Laboratory of Molecular Neuro-oncology, Howard Hughes Medical Institute, Rockefeller University, New York, New York 10065, USA
| | - Scott Keeney
- Molecular Biology Program, Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Devanshi Jain
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, New Jersey 08854, USA
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Puno MR, Lima CD. Methods to assess helicase and translocation activities of human nuclear RNA exosome and RNA adaptor complexes. Methods Enzymol 2022; 673:453-473. [PMID: 35965016 PMCID: PMC9382703 DOI: 10.1016/bs.mie.2022.03.060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The nuclear RNA exosome collaborates with the MTR4 helicase and RNA adaptor complexes to process, surveil, and degrade RNA. Here we outline methods to characterize RNA translocation and strand displacement by exosome-associated helicases and adaptor complexes using fluorescence-based strand displacement assays. The design and preparation of substrates suitable for analysis of helicase and decay activities of reconstituted MTR4–exosome complexes are described. To aid structural and biophysical studies, we present strategies for engineering substrates that can stall helicases during translocation, providing a means to capture snapshots of interactions and molecular steps involved in substrate translocation and delivery to the exosome.
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Abstract
The RNA exosome is a 3' to 5' ribonuclease that plays a fundamental role in maturation, quality control, and turnover of nearly all types of RNA produced in eukaryotic cells. Here, we present an overview of the structure, composition, and functions of the RNA exosome, including various cytoplasmic and nuclear exosome co-factors and associated protein complexes. To view this SnapShot, open or download the PDF.
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Affiliation(s)
- M Rhyan Puno
- Structural Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065
| | - Eva-Maria Weick
- Structural Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065
| | - Mom Das
- Structural Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065
| | - Christopher D Lima
- Structural Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065; Howard Hughes Medical Institute, 1275 York Avenue, New York, NY 10065
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Piston D, Alvarez-Erviti L, Bansal V, Gargano D, Yao Z, Szabadkai G, Odell M, Puno MR, Björkblom B, Maple-Grødem J, Breuer P, Kaut O, Larsen JP, Bonn S, Møller SG, Wüllner U, Schapira AHV, Gegg ME. DJ-1 is a redox sensitive adapter protein for high molecular weight complexes involved in regulation of catecholamine homeostasis. Hum Mol Genet 2018; 26:4028-4041. [PMID: 29016861 PMCID: PMC5886150 DOI: 10.1093/hmg/ddx294] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 07/19/2017] [Indexed: 01/20/2023] Open
Abstract
DJ-1 is an oxidation sensitive protein encoded by the PARK7 gene. Mutations in PARK7 are a rare cause of familial recessive Parkinson’s disease (PD), but growing evidence suggests involvement of DJ-1 in idiopathic PD. The key clinical features of PD, rigidity and bradykinesia, result from neurotransmitter imbalance, particularly the catecholamines dopamine (DA) and noradrenaline. We report in human brain and human SH-SY5Y neuroblastoma cell lines that DJ-1 predominantly forms high molecular weight (HMW) complexes that included RNA metabolism proteins hnRNPA1 and PABP1 and the glycolysis enzyme GAPDH. In cell culture models the oxidation status of DJ-1 determined the specific complex composition. RNA sequencing indicated that oxidative changes to DJ-1 were concomitant with changes in mRNA transcripts mainly involved in catecholamine metabolism. Importantly, loss of DJ-1 function upon knock down (KD) or expression of the PD associated form L166P resulted in the absence of HMW DJ-1 complexes. In the KD model, the absence of DJ-1 complexes was accompanied by impairment in catecholamine homeostasis, with significant increases in intracellular DA and noraderenaline levels. These changes in catecholamines could be rescued by re-expression of DJ-1. This catecholamine imbalance may contribute to the particular vulnerability of dopaminergic and noradrenergic neurons to neurodegeneration in PARK7-related PD. Notably, oxidised DJ-1 was significantly decreased in idiopathic PD brain, suggesting altered complex function may also play a role in the more common sporadic form of the disease.
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Affiliation(s)
- Dominik Piston
- Department of Clinical Neuroscience, UCL Institute of Neurology, London, UK.,Norwegian Centre for Movement Disorders, Stavanger University Hospital, Stavanger, Norway.,German Centre for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | | | - Vikas Bansal
- German Centre for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Daniela Gargano
- Centre for Organelle Research, University of Stavanger, Stavanger, Norway
| | - Zhi Yao
- Department of Cell and Developmental Biology, Consortium for Mitochondrial Research, University College London, London, UK
| | - Gyorgy Szabadkai
- Department of Cell and Developmental Biology, Consortium for Mitochondrial Research, University College London, London, UK
| | - Mark Odell
- Department of Molecular and Applied Biosciences, University of Westminster, London, UK
| | - M Rhyan Puno
- Department of Molecular and Applied Biosciences, University of Westminster, London, UK
| | - Benny Björkblom
- Department of Chemistry, Umeå University, SE-90187 Umeå, Sweden
| | - Jodi Maple-Grødem
- Norwegian Centre for Movement Disorders, Stavanger University Hospital, Stavanger, Norway.,Centre for Organelle Research, University of Stavanger, Stavanger, Norway
| | - Peter Breuer
- Department of Neurology, University of Bonn Medical Centre, Bonn, Germany
| | - Oliver Kaut
- Department of Neurology, University of Bonn Medical Centre, Bonn, Germany
| | - Jan Petter Larsen
- Norwegian Centre for Movement Disorders, Stavanger University Hospital, Stavanger, Norway
| | - Stefan Bonn
- German Centre for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Simon Geir Møller
- Norwegian Centre for Movement Disorders, Stavanger University Hospital, Stavanger, Norway.,Department of Biological Sciences, St. John's University, New York, NY, USA
| | - Ullrich Wüllner
- German Centre for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | | | - Matthew E Gegg
- Department of Clinical Neuroscience, UCL Institute of Neurology, London, UK
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Piston D, Alvarez-Erviti L, Bansal V, Gargano D, Yao Z, Szabadkai G, Odell M, Puno MR, Björkblom B, Maple-Grødem J, Breuer P, Kaut O, Larsen JP, Bonn S, Møller SG, Wüllner U, Schapira AHV, Gegg ME. DJ-1 is a redox sensitive adapter protein for high molecular weight complexes involved in regulation of catecholamine homeostasis. Hum Mol Genet 2018; 27:576. [PMID: 29309579 PMCID: PMC5886203 DOI: 10.1093/hmg/ddx425] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Affiliation(s)
- Dominik Piston
- Department of Clinical Neuroscience, UCL Institute of Neurology, London, UK
- Norwegian Centre for Movement Disorders, Stavanger University Hospital, Stavanger, Norway
- German Centre for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | | | - Vikas Bansal
- Computational Systems Biology, Site Göttingen German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany
| | - Daniela Gargano
- Centre for Organelle Research, University of Stavanger, Stavanger, Norway
| | - Zhi Yao
- Department of Cell and Developmental Biology, Consortium for Mitochondrial Research, University College London, London, UK
| | - Gyorgy Szabadkai
- Department of Cell and Developmental Biology, Consortium for Mitochondrial Research, University College London, London, UK
| | - Mark Odell
- Department of Molecular and Applied Biosciences, University of Westminster, London, UK
| | - M Rhyan Puno
- Department of Molecular and Applied Biosciences, University of Westminster, London, UK
| | - Benny Björkblom
- Department of Chemistry, Umeå University, SE-90187 Umeå, Sweden
| | - Jodi Maple-Grødem
- Norwegian Centre for Movement Disorders, Stavanger University Hospital, Stavanger, Norway
- Centre for Organelle Research, University of Stavanger, Stavanger, Norway
| | - Peter Breuer
- Department of Neurology, University of Bonn Medical Centre, Bonn, Germany
| | - Oliver Kaut
- Department of Neurology, University of Bonn Medical Centre, Bonn, Germany
| | - Jan Petter Larsen
- Norwegian Centre for Movement Disorders, Stavanger University Hospital, Stavanger, Norway
| | - Stefan Bonn
- Computational Systems Biology, Site Göttingen German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany
| | - Simon Geir Møller
- Norwegian Centre for Movement Disorders, Stavanger University Hospital, Stavanger, Norway
- Department of Biological Sciences, St. John's University, New York, NY, USA
| | - Ullrich Wüllner
- German Centre for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | | | - Matthew E Gegg
- Department of Clinical Neuroscience, UCL Institute of Neurology, London, UK
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Jain D, Puno MR, Meydan C, Lailler N, Mason CE, Lima CD, Anderson KV, Keeney S. ketu mutant mice uncover an essential meiotic function for the ancient RNA helicase YTHDC2. eLife 2018; 7:30919. [PMID: 29360036 PMCID: PMC5832417 DOI: 10.7554/elife.30919] [Citation(s) in RCA: 110] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 01/22/2018] [Indexed: 02/06/2023] Open
Abstract
Mechanisms regulating mammalian meiotic progression are poorly understood. Here we identify mouse YTHDC2 as a critical component. A screen yielded a sterile mutant, ‘ketu’, caused by a Ythdc2 missense mutation. Mutant germ cells enter meiosis but proceed prematurely to aberrant metaphase and apoptosis, and display defects in transitioning from spermatogonial to meiotic gene expression programs. ketu phenocopies mutants lacking MEIOC, a YTHDC2 partner. Consistent with roles in post-transcriptional regulation, YTHDC2 is cytoplasmic, has 3′→5′ RNA helicase activity in vitro, and has similarity within its YTH domain to an N6-methyladenosine recognition pocket. Orthologs are present throughout metazoans, but are diverged in nematodes and, more dramatically, Drosophilidae, where Bgcn is descended from a Ythdc2 gene duplication. We also uncover similarity between MEIOC and Bam, a Bgcn partner unique to schizophoran flies. We propose that regulation of gene expression by YTHDC2-MEIOC is an evolutionarily ancient strategy for controlling the germline transition into meiosis.
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Affiliation(s)
- Devanshi Jain
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States
| | - M Rhyan Puno
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States.,Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Cem Meydan
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, United States.,The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, United States
| | - Nathalie Lailler
- Integrated Genomics Operation, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, United States.,The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, United States.,The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, United States
| | - Christopher D Lima
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States.,Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Kathryn V Anderson
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Scott Keeney
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States.,Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, United States
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Puno MR, Patel NA, Møller SG, Robinson CV, Moody PCE, Odell M. Structure of Cu(I)-bound DJ-1 reveals a biscysteinate metal binding site at the homodimer interface: insights into mutational inactivation of DJ-1 in Parkinsonism. J Am Chem Soc 2013; 135:15974-7. [PMID: 24144264 DOI: 10.1021/ja406010m] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The Parkinsonism-associated protein DJ-1 has been suggested to activate the Cu-Zn superoxide dismutase (SOD1) by providing its copper cofactor. The structural and chemical means by which DJ-1 could support this function is unknown. In this study, we characterize the molecular interaction of DJ-1 with Cu(I). Mass spectrometric analysis indicates binding of one Cu(I) ion per DJ-1 homodimer. The crystal structure of DJ-1 bound to Cu(I) confirms metal coordination through a docking accessible biscysteinate site formed by juxtaposed cysteine residues at the homodimer interface. Spectroscopy in crystallo validates the identity and oxidation state of the bound metal. The measured subfemtomolar dissociation constant (Kd = 6.41 × 10(-16) M) of DJ-1 for Cu(I) supports the physiological retention of the metal ion. Our results highlight the requirement of a stable homodimer for copper binding by DJ-1. Parkinsonism-linked mutations that weaken homodimer interactions will compromise this capability.
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Affiliation(s)
- M Rhyan Puno
- Department of Molecular and Applied Biosciences, University of Westminster , 115 New Cavendish Street, London W1W 6UW, United Kingdom
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Abstract
The medical records of 303 patients undergoing fusions for scoliosis correction were retrospectively reviewed. The frequency and type of postoperative respiratory complications were compared in idiopathic versus non-idiopathic scoliosis patients in relation to age, type of spinal fusion procedure, pulmonary function test (PFT) results and preoperative diagnoses. The following factors were found to increase the incidence of problems in the postoperative period: a non-idiopathic type of scoliosis, mental retardation, anterior spinal fusion procedures, age of 20 or more years, a relative arterial hypoxemia and an obstructive component to the PFT's. Topics for further investigation are suggested.
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