1
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Abstract
Small nucleolar RNAs (snoRNAs) are non-coding RNAs vital for ribosomal RNA (rRNA) maturation. The U8 snoRNA, encoded by the SNORD118 gene in humans, is an atypical C/D box snoRNA as it promotes rRNA cleavage rather than 2′–O–methylation and is unique to vertebrates. The U8 snoRNA is critical for cleavage events that produce the mature 5.8S and 28S rRNAs of the large ribosomal subunit. Unexpectedly, single nucleotide polymorphisms (SNPs) in the SNORD118 gene were recently found causal to the neurodegenerative disease leukoencephalopathy, brain calcifications, and cysts (LCC; aka Labrune syndrome), but its molecular pathogenesis is unclear. Here, we will review current knowledge on the function of the U8 snoRNA in ribosome biogenesis, and connect it to the preservation of brain function in humans as well as to its dysregulation in inherited white matter disease.
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Affiliation(s)
- Emily J McFadden
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Susan J Baserga
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.,Department of Genetics, Yale School of Medicine, New Haven, CT, USA.,Department of Therapeutic Radiology, Yale School of Medicine, New Haven, CT, USA
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2
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Jin H, Ren X, Wu H, Hou Y, Fang F. Case Report: Clinical Features of Childhood Leukoencephalopathy With Cerebral Calcifications and Cysts Due to SNORD118 Variants. Front Neurol 2021; 12:585606. [PMID: 34220662 PMCID: PMC8248351 DOI: 10.3389/fneur.2021.585606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 05/11/2021] [Indexed: 11/29/2022] Open
Abstract
Background: Leukoencephalopathy with cerebral calcifications and cysts (LCC) is a rare autosomal recessive cerebral microangiopathy. Recently, biallelic variants in a non-protein-coding gene SNORD118 have been discovered to cause LCC. Case Presentation: We here report a genetically confirmed childhood case of LCC. The patient was a 4-year-and-1-month-old boy with focal seizures. The age at onset of his seizure was 10 days after birth. The seizures were well-controlled by antiepileptic treatment but reoccurred twice due to a head impact accident and a fever, respectively. He suffered from a self-limited esotropia and unsteady running gait during the seizure onset. He had the typical neuroimaging triad of multifocal intracranial calcifications, cysts, and leukoencephalopathy. Genetic analysis indicated that he carried compound heterozygous variants of n.*9C>T and n.3C>T in SNORD118, which were inherited from his parents. Conclusion: We report a childhood LCC case with compound heterozygous variants in SNORD118. To the best of our knowledge, the patient reported in our case had the youngest onset age of LCC with a determined genotype. The triad cerebral-imaging findings of calcifications, cysts, and leukoencephalopathy provide a crucial diagnostic basis. Moreover, the gene assessment, together with the clinical investigations, should be considered for the diagnosis of LCC.
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Affiliation(s)
- Hong Jin
- Department of Neurology, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Xiaotun Ren
- Department of Neurology, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Husheng Wu
- Department of Neurology, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | | | - Fang Fang
- Department of Neurology, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
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3
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Sathe G, Mangalaparthi KK, Jain A, Darrow J, Troncoso J, Albert M, Moghekar A, Pandey A. Multiplexed Phosphoproteomic Study of Brain in Patients with Alzheimer's Disease and Age-Matched Cognitively Healthy Controls. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2020; 24:216-227. [PMID: 32182160 DOI: 10.1089/omi.2019.0191] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Alzheimer's disease (AD) is the most common neurodegenerative disorder caused by neuronal loss that results in cognitive and functional impairment. Formation of neurofibrillary tangles composed of abnormal hyperphosphorylation of tau protein is one of the major pathological hallmarks of AD. Importantly, several neurodegenerative disorders, including AD, are associated with abnormal protein phosphorylation events. However, little is known thus far on global protein phosphorylation changes in AD. We report a phosphoproteomics study examining the frontal gyrus of people with AD and age-matched cognitively normal subjects, using tandem mass tag (TMT) multiplexing technology along with immobilized metal affinity chromatography to enrich phosphopeptides. We identified 4631 phosphopeptides corresponding to 1821 proteins with liquid chromatography-mass spectrometry (MS)/MS analysis on an Orbitrap Fusion Lumos Tribrid mass spectrometer. Of these, 504 phosphopeptides corresponding to 350 proteins were significantly altered in the AD brain: 389 phosphopeptides increased whereas 115 phosphopeptides decreased phosphorylation. We observed significant changes in phosphorylation of known as well as novel molecules. Using targeted parallel reaction monitoring experiments, we validated the phosphorylation of microtubule-associated protein tau and myristoylated alanine-rich protein kinase C substrate (MARCKS) in control and AD (Control = 6, AD = 11) brain samples. In conclusion, our study provides new evidence on alteration of RNA processing and splicing, neurogenesis and neuronal development, and metabotropic glutamate receptor 5 (GRM5) calcium signaling pathways in the AD brain, and it thus offers new insights to accelerate diagnostics and therapeutics innovation in AD.
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Affiliation(s)
- Gajanan Sathe
- Center for Molecular Medicine, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India.,Institute of Bioinformatics, Bangalore, India.,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Manipal Academy of Higher Education (MAHE), Manipal, India
| | | | - Ankit Jain
- Institute of Bioinformatics, Bangalore, India
| | - Jacqueline Darrow
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Juan Troncoso
- Department of Pathology and Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Marilyn Albert
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Abhay Moghekar
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Akhilesh Pandey
- Center for Molecular Medicine, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India.,Institute of Bioinformatics, Bangalore, India.,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Manipal Academy of Higher Education (MAHE), Manipal, India.,Department of Biological Chemistry, Pathology and Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
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4
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Xu Y, Chen L, Liu M, Lu Y, Yue Y, Liu Y, Chen H, Xie F, Zhang C. High-throughput transcriptome sequencing reveals extremely high doses of ionizing radiation-response genes in Caenorhabditis elegans. Toxicol Res (Camb) 2019; 8:754-766. [PMID: 31588352 PMCID: PMC6762013 DOI: 10.1039/c9tx00101h] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 08/06/2019] [Indexed: 12/27/2022] Open
Abstract
This study sought novel ionizing radiation-response (IR-response) genes in Caenorhabditis elegans (C. elegans). C. elegans was divided into three groups and exposed to different high doses of IR: 0 gray (Gy), 200 Gy, and 400 Gy. Total RNA was extracted from each group and sequenced. When the transcriptomes were compared among these groups, many genes were shown to be differentially expressed, and these genes were significantly enriched in IR-related biological processes and pathways, including gene ontology (GO) terms related to cellular behaviours, cellular growth and purine metabolism and kyoto encyclopedia of genes and genomes (KEGG) pathways related to ATP binding, GTPase regulator activity, and RNA degradation. Quantitative reverse-transcription PCR (qRT-PCR) confirmed that these genes displayed differential expression across the treatments. Further gene network analysis showed a cluster of novel gene families, such as the guanylate cyclase (GCY), Sm-like protein (LSM), diacylglycerol kinase (DGK), skp1-related protein (SKR), and glutathione S-transferase (GST) gene families which were upregulated. Thus, these genes likely play important roles in IR response. Meanwhile, some important genes that are well known to be involved in key signalling pathways, such as phosphoinositide-specific phospholipase C-3 (PLC-3), phosphatidylinositol 3-kinase age-1 (AGE-1), Raf homolog serine/threonine-protein kinase (LIN-45) and protein cbp-1 (CBP-1), also showed differential expression during IR response, suggesting that IR response might perturb these key signalling pathways. Our study revealed a series of novel IR-response genes in Caenorhabditis elegans that might act as regulators of IR response and represent promising markers of IR exposure.
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Affiliation(s)
- Youqin Xu
- Department of Biochemistry and Molecular Biology , School of Basic Medical Science , Southern Medical University and Guangdong Provincial Key Laboratory of Single Cell Technology and Application , Guangzhou , Guangdong Province , China . ; Tel: +86-13824447151
- Department of Medical Oncology , Taishan People's Hospital , Guangdong Province , China
| | - Lina Chen
- Basic Medical College , Xiangnan University , Chenzhou , China
| | - Mengyi Liu
- Department of Biochemistry and Molecular Biology , School of Basic Medical Science , Southern Medical University and Guangdong Provincial Key Laboratory of Single Cell Technology and Application , Guangzhou , Guangdong Province , China . ; Tel: +86-13824447151
| | - Yanfang Lu
- Department of Biochemistry and Molecular Biology , School of Basic Medical Science , Southern Medical University and Guangdong Provincial Key Laboratory of Single Cell Technology and Application , Guangzhou , Guangdong Province , China . ; Tel: +86-13824447151
| | - Yanwei Yue
- Blood Transfusion Department , The First Affiliated Hospital of Xi'an Jiaotong University , Xi'an , China
| | - Yue Liu
- Department of Biochemistry and Molecular Biology , School of Basic Medical Science , Southern Medical University and Guangdong Provincial Key Laboratory of Single Cell Technology and Application , Guangzhou , Guangdong Province , China . ; Tel: +86-13824447151
| | - Honghao Chen
- Department of Biochemistry and Molecular Biology , School of Basic Medical Science , Southern Medical University and Guangdong Provincial Key Laboratory of Single Cell Technology and Application , Guangzhou , Guangdong Province , China . ; Tel: +86-13824447151
| | - Fuliang Xie
- Department of Biochemistry and Molecular Biology , School of Basic Medical Science , Southern Medical University and Guangdong Provincial Key Laboratory of Single Cell Technology and Application , Guangzhou , Guangdong Province , China . ; Tel: +86-13824447151
- Department of Biology , East Carolina University , Greenville , NC , USA
| | - Chao Zhang
- Department of Biochemistry and Molecular Biology , School of Basic Medical Science , Southern Medical University and Guangdong Provincial Key Laboratory of Single Cell Technology and Application , Guangzhou , Guangdong Province , China . ; Tel: +86-13824447151
- Department of Medical Oncology , Taishan People's Hospital , Guangdong Province , China
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5
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Abstract
Viruses masterfully regulate host gene expression during infection. Many do so, in part, by expressing non-coding RNAs. Recent work has shown that HSUR 2, a viral non-coding RNA expressed by the oncogenic Herpesvirus saimiri, regulates mRNA expression through a novel mechanism. HSUR 2 base pairs with both target mRNAs and host miRNAs in infected cells. This results in HSUR 2-dependent recruitment of host miRNAs and associated Ago proteins to target mRNAs, and the subsequent destabilization of target mRNAs. Using this mechanism, this virus regulates key cellular pathways during viral infection. Here I discuss the evolution of our thinking about HSUR function and explore the implications of recent findings in relation to the current views on the functions of interactions between miRNAs and other classes of non-coding RNAs, the potential advantages of this mechanism of regulation of gene expression, and the evolutionary origin of HSUR 2.
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Affiliation(s)
- Demián Cazalla
- a Department of Biochemistry , University of Utah School of Medicine , Salt Lake City , UT , USA
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6
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Reimer KA, Stark MR, Aguilar LC, Stark SR, Burke RD, Moore J, Fahlman RP, Yip CK, Kuroiwa H, Oeffinger M, Rader SD. The sole LSm complex in Cyanidioschyzon merolae associates with pre-mRNA splicing and mRNA degradation factors. RNA (NEW YORK, N.Y.) 2017; 23:952-967. [PMID: 28325844 PMCID: PMC5435867 DOI: 10.1261/rna.058487.116] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 03/15/2017] [Indexed: 05/22/2023]
Abstract
Proteins of the Sm and Sm-like (LSm) families, referred to collectively as (L)Sm proteins, are found in all three domains of life and are known to promote a variety of RNA processes such as base-pair formation, unwinding, RNA degradation, and RNA stabilization. In eukaryotes, (L)Sm proteins have been studied, inter alia, for their role in pre-mRNA splicing. In many organisms, the LSm proteins form two distinct complexes, one consisting of LSm1-7 that is involved in mRNA degradation in the cytoplasm, and the other consisting of LSm2-8 that binds spliceosomal U6 snRNA in the nucleus. We recently characterized the splicing proteins from the red alga Cyanidioschyzon merolae and found that it has only seven LSm proteins. The identities of CmLSm2-CmLSm7 were unambiguous, but the seventh protein was similar to LSm1 and LSm8. Here, we use in vitro binding measurements, microscopy, and affinity purification-mass spectrometry to demonstrate a canonical splicing function for the C. merolae LSm complex and experimentally validate our bioinformatic predictions of a reduced spliceosome in this organism. Copurification of Pat1 and its associated mRNA degradation proteins with the LSm proteins, along with evidence of a cytoplasmic fraction of CmLSm complexes, argues that this complex is involved in both splicing and cytoplasmic mRNA degradation. Intriguingly, the Pat1 complex also copurifies with all four snRNAs, suggesting the possibility of a spliceosome-associated pre-mRNA degradation complex in the nucleus.
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Affiliation(s)
- Kirsten A Reimer
- Department of Chemistry, University of Northern British Columbia, Prince George, BC V2N 4Z9, Canada
| | - Martha R Stark
- Department of Chemistry, University of Northern British Columbia, Prince George, BC V2N 4Z9, Canada
| | - Lisbeth-Carolina Aguilar
- Laboratory of RNP Biochemistry, Institut de Recherches Cliniques de Montréal (IRCM), Faculty of Medicine, McGill University, Montreal, QC H3A 0G4, Canada
| | - Sierra R Stark
- Department of Chemistry, University of Northern British Columbia, Prince George, BC V2N 4Z9, Canada
| | - Robert D Burke
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, V8W 3P6, Canada
| | - Jack Moore
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Richard P Fahlman
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
- Department of Oncology, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Calvin K Yip
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Haruko Kuroiwa
- Kuroiwa Initiative Research Unit, College of Science, Rikkyo University, Toshima, Tokyo 171-8501, Japan
| | - Marlene Oeffinger
- Laboratory of RNP Biochemistry, Institut de Recherches Cliniques de Montréal (IRCM), Faculty of Medicine, McGill University, Montreal, QC H3A 0G4, Canada
- Département de Biochimie, Université de Montréal, Montréal, QC H2W 1R7, Canada
| | - Stephen D Rader
- Department of Chemistry, University of Northern British Columbia, Prince George, BC V2N 4Z9, Canada
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7
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Iwama K, Mizuguchi T, Takanashi J, Shibayama H, Shichiji M, Ito S, Oguni H, Yamamoto T, Sekine A, Nagamine S, Ikeda Y, Nishida H, Kumada S, Yoshida T, Awaya T, Tanaka R, Chikuchi R, Niwa H, Oka Y, Miyatake S, Nakashima M, Takata A, Miyake N, Ito S, Saitsu H, Matsumoto N. Identification of novel
SNORD118
mutations in seven patients with leukoencephalopathy with brain calcifications and cysts. Clin Genet 2017; 92:180-187. [DOI: 10.1111/cge.12991] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 01/31/2017] [Accepted: 01/31/2017] [Indexed: 02/06/2023]
Affiliation(s)
- Kazuhiro Iwama
- Department of Human Genetics, Graduate School of Medicine Yokohama City University Yokohama Japan
- Department of Pediatrics, Graduate School of Medicine Yokohama City University Yokohama Japan
| | - Takeshi Mizuguchi
- Department of Human Genetics, Graduate School of Medicine Yokohama City University Yokohama Japan
| | - Jun‐ichi Takanashi
- Department of Pediatrics and Pediatric Neurology Tokyo Women's Medical University, Yachiyo Medical Center Yachiyo Japan
| | | | - Minobu Shichiji
- Department of Pediatrics Tokyo Women's Medical University Tokyo Japan
| | - Susumu Ito
- Department of Pediatrics Tokyo Women's Medical University Tokyo Japan
| | - Hirokazu Oguni
- Department of Pediatrics Tokyo Women's Medical University Tokyo Japan
| | - Toshiyuki Yamamoto
- Institute of Medical Genetics Tokyo Women's Medical University Tokyo Japan
| | - Akiko Sekine
- Department of Neurology Gunma University Graduate School of Medicine Maebashi Japan
| | - Shun Nagamine
- Department of Neurology Gunma University Graduate School of Medicine Maebashi Japan
| | - Yoshio Ikeda
- Department of Neurology Gunma University Graduate School of Medicine Maebashi Japan
| | - Hiroya Nishida
- Department of Neuropediatrics Tokyo Metropolitan Neurological Hospital Tokyo Japan
| | - Satoko Kumada
- Department of Neuropediatrics Tokyo Metropolitan Neurological Hospital Tokyo Japan
| | - Takeshi Yoshida
- Department of Pediatrics Kyoto University Graduate School of Medicine Kyoto Japan
| | - Tomonari Awaya
- Department of Pediatrics Kyoto University Graduate School of Medicine Kyoto Japan
- Department of Anatomy and Developmental Biology Kyoto University Graduate School of Medicine Kyoto Japan
| | - Ryuta Tanaka
- Department of Child Health, Faculty of Medicine University of Tsukuba Tsukuba Japan
| | - Ryo Chikuchi
- Department of Neurology Kariya Toyota General Hospital Kariya Japan
| | - Hisayoshi Niwa
- Department of Neurology Kariya Toyota General Hospital Kariya Japan
| | - Yu‐ichi Oka
- Department of Neurosurgery Nagoya City University Hospital Nagoya Japan
| | - Satoko Miyatake
- Department of Human Genetics, Graduate School of Medicine Yokohama City University Yokohama Japan
| | - Mitsuko Nakashima
- Department of Human Genetics, Graduate School of Medicine Yokohama City University Yokohama Japan
| | - Atsushi Takata
- Department of Human Genetics, Graduate School of Medicine Yokohama City University Yokohama Japan
| | - Noriko Miyake
- Department of Human Genetics, Graduate School of Medicine Yokohama City University Yokohama Japan
| | - Shuichi Ito
- Department of Pediatrics, Graduate School of Medicine Yokohama City University Yokohama Japan
| | - Hirotomo Saitsu
- Department of Biochemistry Hamamatsu University School of Medicine Hamamatsu Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Graduate School of Medicine Yokohama City University Yokohama Japan
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8
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Jenkinson EM, Rodero MP, Kasher PR, Uggenti C, Oojageer A, Goosey LC, Rose Y, Kershaw CJ, Urquhart JE, Williams SG, Bhaskar SS, O’Sullivan J, Baerlocher GM, Haubitz M, Aubert G, Barañano KW, Barnicoat AJ, Battini R, Berger A, Blair EM, Brunstrom-Hernandez JE, Buckard JA, Cassiman DM, Caumes R, Cordelli DM, De Waele LM, Fay AJ, Ferreira P, Fletcher NA, Fryer AE, Goel H, Hemingway CA, Henneke M, Hughes I, Jefferson RJ, Kumar R, Lagae L, Landrieu PG, Lourenço CM, Malpas TJ, Mehta SG, Metz I, Naidu S, Õunap K, Panzer A, Prabhakar P, Quaghebeur G, Schiffmann R, Sherr EH, Sinnathuray KR, Soh C, Stewart HS, Stone J, Van Esch H, Van Mol CE, Vanderver A, Wakeling EL, Whitney A, Pavitt GD, Griffiths-Jones S, Rice GI, Revy P, van der Knaap MS, Livingston JH, O’Keefe RT, Crow YJ. Mutations in SNORD118 cause the cerebral microangiopathy leukoencephalopathy with calcifications and cysts. Nat Genet 2016; 48:1185-92. [PMID: 27571260 PMCID: PMC5045717 DOI: 10.1038/ng.3661] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 08/05/2016] [Indexed: 12/15/2022]
Abstract
Although ribosomes are ubiquitous and essential for life, recent data indicate that monogenic causes of ribosomal dysfunction can confer a remarkable degree of specificity in terms of human disease phenotype. Box C/D small nucleolar RNAs (snoRNAs) are evolutionarily conserved non-protein-coding RNAs involved in ribosome biogenesis. Here we show that biallelic mutations in the gene SNORD118, encoding the box C/D snoRNA U8, cause the cerebral microangiopathy leukoencephalopathy with calcifications and cysts (LCC), presenting at any age from early childhood to late adulthood. These mutations affect U8 expression, processing and protein binding and thus implicate U8 as essential in cerebral vascular homeostasis.
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Affiliation(s)
- Emma M. Jenkinson
- Faculty of Biology, Medicine and Health, School of Biological Sciences, Division of Evolution and Genomic Sciences, University of Manchester, UK
| | - Mathieu P. Rodero
- INSERM UMR 1163, Laboratory of Neurogenetics and Neuroinflammation, Paris Descartes – Sorbonne Paris Cité University, Institut Imagine, Hôpital Necker, Paris, France
| | - Paul R. Kasher
- Faculty of Biology, Medicine and Health, School of Biological Sciences, Division of Evolution and Genomic Sciences, University of Manchester, UK
| | - Carolina Uggenti
- INSERM UMR 1163, Laboratory of Neurogenetics and Neuroinflammation, Paris Descartes – Sorbonne Paris Cité University, Institut Imagine, Hôpital Necker, Paris, France
| | - Anthony Oojageer
- Faculty of Biology, Medicine and Health, School of Biological Sciences, Division of Evolution and Genomic Sciences, University of Manchester, UK
| | - Laurence C. Goosey
- Faculty of Biology, Medicine and Health, School of Biological Sciences, Division of Evolution and Genomic Sciences, University of Manchester, UK
| | - Yohann Rose
- INSERM UMR 1163, Laboratory of Neurogenetics and Neuroinflammation, Paris Descartes – Sorbonne Paris Cité University, Institut Imagine, Hôpital Necker, Paris, France
| | - Christopher J. Kershaw
- Faculty of Biology, Medicine and Health, School of Biological Sciences, Division of Molecular and Cellular Function, University of Manchester, UK
| | - Jill E. Urquhart
- Faculty of Biology, Medicine and Health, School of Biological Sciences, Division of Evolution and Genomic Sciences, University of Manchester, UK
| | - Simon G. Williams
- Faculty of Biology, Medicine and Health, School of Biological Sciences, Division of Evolution and Genomic Sciences, University of Manchester, UK
| | - Sanjeev S. Bhaskar
- Faculty of Biology, Medicine and Health, School of Biological Sciences, Division of Evolution and Genomic Sciences, University of Manchester, UK
| | - James O’Sullivan
- Faculty of Biology, Medicine and Health, School of Biological Sciences, Division of Evolution and Genomic Sciences, University of Manchester, UK
| | - Gabriela M. Baerlocher
- Department of Hematology, Inselspital, Bern University Hospital, University of Bern, Bern Switzerland
- Experimental Hematology, Department of Clinical Research, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Monika Haubitz
- Department of Hematology, Inselspital, Bern University Hospital, University of Bern, Bern Switzerland
- Experimental Hematology, Department of Clinical Research, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Geraldine Aubert
- Repeat Diagnostics Inc, North Vancouver, British Columbia, Canada
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Kristin W. Barañano
- Department of Neurology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Division of Neurogenetics, Kennedy Krieger Institute, Baltimore, MD, USA
| | - Angela J. Barnicoat
- Department of Clinical Genetics, Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - Roberta Battini
- Department of Developmental Neuroscience, IRCCS Stella Maris, Pisa, Italy
| | - Andrea Berger
- Department of Neuropediatrics, Klinikum Weiden, Weiden, Germany
- Department of Neuropediatrics, Klinikum Harlaching, Munich, Germany
| | - Edward M. Blair
- Department Of Clinical Genetics, Churchill Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Janice E. Brunstrom-Hernandez
- Director, 1 CP Place, PLLC, Plano Texas USA
- Department of Neurology, Washington University School of Medicine, St. Louis Children’s Hospital, St. Louis, USA
| | - Johannes A. Buckard
- Department of Neuropediatrics, Sozialpädiatrisches Zentrum am EVK Düsseldorf, Düsseldorf, Germany
| | - David M. Cassiman
- Metabolic Center, Leuven University Hospitals and KU Leuven, Leuven, Belgium
| | - Rosaline Caumes
- Department of Neuropediatrics, Hopital Roger Salengro, Lille, France
| | | | - Liesbeth M. De Waele
- Department of Paediatric Neurology, University Hospitals Leuven, Leuven, Belgium
- Department of Development and Regeneration, Paediatric Neurology, University of Leuven, Leuven, Belgium
| | - Alexander J. Fay
- Department of Neurology, Washington University School of Medicine, St. Louis Children’s Hospital, St. Louis, USA
| | - Patrick Ferreira
- Division of Medical Genetics, Alberta Children's Hospital, Calgary, Canada
| | | | - Alan E. Fryer
- Department of Clinical Genetics, Liverpool Women’s NHS Foundation Trust, Liverpool, UK
| | - Himanshu Goel
- Hunter Genetics, Hunter New England Local Health District, Waratah, Australia
- School of Medicine and Public Health, University of Newcastle, Callaghan, Australia
| | - Cheryl A. Hemingway
- Department of Paediatric Neurology, Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - Marco Henneke
- Department of Pediatrics and Adolescent Medicine, University Medical Center, Georg August University, Göttingen, Germany
| | - Imelda Hughes
- Pediatric Neurology, Central Manchester University Hospitals NHS Foundation Trust, Manchester, UK
| | | | - Ram Kumar
- Department of Paediatric Neurology, Alder Hey Children’s NHS Foundation Trust, Liverpool, UK
| | - Lieven Lagae
- Department of Development and Regeneration, Paediatric Neurology, University of Leuven, Leuven, Belgium
| | - Pierre G. Landrieu
- Department of Paediatric Neurology, CHU Paris-Sud Bicetre, Le Kremlin Bicetre, France, 94270
| | - Charles M. Lourenço
- Neurogenetics Division, Clinics Hospital of Ribeirão Preto, University of São Paulo, São Paulo, Brazil
| | - Timothy J. Malpas
- Department of Paediatrics, Jersey General Hospital, St Helier, Jersey
| | - Sarju G. Mehta
- East Anglian Regional Genetics Service, Addenbrookes Hospital, Cambridge, UK
| | - Imke Metz
- Department of Neuropathology, University Medical Center, Georg August University, Göttingen, Germany
| | - Sakkubai Naidu
- Hugo Moser Research Institute, Kennedy Krieger Institute, Johns Hopkins Medical Institutions, Neurology & Pediatrics, Baltimore, USA
| | - Katrin Õunap
- Department of Genetics, Tartu University Hospital, Tartu, Estonia
- Department of Pediatrics, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Axel Panzer
- Epilepsy Center/ Paediatric Neurology, DRK Kliniken Berlin-Westend, Berlin, Germany
| | - Prab Prabhakar
- Department of Paediatric Neurology, Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - Geraldine Quaghebeur
- Department of Neuroradiology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Raphael Schiffmann
- Institute of Metabolic Disease, Baylor Research Institute, Dallas, Texas, USA
| | | | | | - Calvin Soh
- Neuroradiology Department, Salford Royal NHS Foundation Trust, Salford, UK
| | - Helen S. Stewart
- Department Of Clinical Genetics, Churchill Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - John Stone
- Department of Clinical Neurosciences, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Hilde Van Esch
- Center for Human Genetics, University Hospitals Leuven, KU Leuven, Leuven, Belgium
| | - Christine E.G. Van Mol
- Department of pediatrics-neonatology, St. Augustinusziekenhuis, Oosterveldlaan 24, Wilrijk, Belgium
| | - Adeline Vanderver
- Department of Neurology, George Washington University School of Medicine, Children’s National Health System, Washington DC, USA
- Center for Genetic Medicine Research, George Washington University School of Medicine, Children’s National Health System, Washington DC, USA
| | - Emma L. Wakeling
- North West Thames Regional Genetics Service, London North West Healthcare NHS Trust, Harrow, UK
| | - Andrea Whitney
- Department of Child Neurology, University Hospital Southampton NHS Trust, Southampton, UK
| | - Graham D. Pavitt
- Faculty of Biology, Medicine and Health, School of Biological Sciences, Division of Molecular and Cellular Function, University of Manchester, UK
| | - Sam Griffiths-Jones
- Faculty of Biology, Medicine and Health, School of Biological Sciences, Division of Molecular and Cellular Function, University of Manchester, UK
| | - Gillian I. Rice
- Faculty of Biology, Medicine and Health, School of Biological Sciences, Division of Evolution and Genomic Sciences, University of Manchester, UK
| | - Patrick Revy
- INSERM UMR 1163, Laboratory of Genome Dynamics in the Immune System, Paris; Paris Descartes–Sorbonne Paris Cite University, Imagine Institute, Paris
| | - Marjo S. van der Knaap
- Child Neurology and Amsterdam Neuroscience, VU University Medical Center, Amsterdam, The Netherlands
- Functional Genomics, Center for Neurogenomics and Cognitive Research, VU University, Amsterdam, The Netherlands
| | | | - Raymond T. O’Keefe
- Faculty of Biology, Medicine and Health, School of Biological Sciences, Division of Molecular and Cellular Function, University of Manchester, UK
| | - Yanick J. Crow
- Faculty of Biology, Medicine and Health, School of Biological Sciences, Division of Evolution and Genomic Sciences, University of Manchester, UK
- INSERM UMR 1163, Laboratory of Neurogenetics and Neuroinflammation, Paris Descartes – Sorbonne Paris Cité University, Institut Imagine, Hôpital Necker, Paris, France
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9
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Cornes E, Porta-De-La-Riva M, Aristizábal-Corrales D, Brokate-Llanos AM, García-Rodríguez FJ, Ertl I, Díaz M, Fontrodona L, Reis K, Johnsen R, Baillie D, Muñoz MJ, Sarov M, Dupuy D, Cerón J. Cytoplasmic LSM-1 protein regulates stress responses through the insulin/IGF-1 signaling pathway in Caenorhabditis elegans. RNA (NEW YORK, N.Y.) 2015; 21:1544-53. [PMID: 26150554 PMCID: PMC4536316 DOI: 10.1261/rna.052324.115] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 06/06/2015] [Indexed: 05/04/2023]
Abstract
Genes coding for members of the Sm-like (LSm) protein family are conserved through evolution from prokaryotes to humans. These proteins have been described as forming homo- or heterocomplexes implicated in a broad range of RNA-related functions. To date, the nuclear LSm2-8 and the cytoplasmic LSm1-7 heteroheptamers are the best characterized complexes in eukaryotes. Through a comprehensive functional study of the LSm family members, we found that lsm-1 and lsm-3 are not essential for C. elegans viability, but their perturbation, by RNAi or mutations, produces defects in development, reproduction, and motility. We further investigated the function of lsm-1, which encodes the distinctive protein of the cytoplasmic complex. RNA-seq analysis of lsm-1 mutants suggests that they have impaired Insulin/IGF-1 signaling (IIS), which is conserved in metazoans and involved in the response to various types of stress through the action of the FOXO transcription factor DAF-16. Further analysis using a DAF-16::GFP reporter indicated that heat stress-induced translocation of DAF-16 to the nuclei is dependent on lsm-1. Consistent with this, we observed that lsm-1 mutants display heightened sensitivity to thermal stress and starvation, while overexpression of lsm-1 has the opposite effect. We also observed that under stress, cytoplasmic LSm proteins aggregate into granules in an LSM-1-dependent manner. Moreover, we found that lsm-1 and lsm-3 are required for other processes regulated by the IIS pathway, such as aging and pathogen resistance.
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Affiliation(s)
- Eric Cornes
- Cancer and Human Molecular Genetics, Bellvitge Biomedical Research Institute-IDIBELL, L'Hospitalet de Llobregat, Barcelona 08908, Spain Université Bordeaux, IECB, Laboratoire ARNA, F-33600 Pessac, France INSERM, U869, Laboratoire ARNA, F-33000 Bordeaux, France
| | - Montserrat Porta-De-La-Riva
- Cancer and Human Molecular Genetics, Bellvitge Biomedical Research Institute-IDIBELL, L'Hospitalet de Llobregat, Barcelona 08908, Spain C. elegans Core Facility, Bellvitge Biomedical Research Institute-IDIBELL, L'Hospitalet de Llobregat, Barcelona 08908, Spain
| | - David Aristizábal-Corrales
- Cancer and Human Molecular Genetics, Bellvitge Biomedical Research Institute-IDIBELL, L'Hospitalet de Llobregat, Barcelona 08908, Spain
| | - Ana María Brokate-Llanos
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC - UPO - Junta de Andalucía, Sevilla 41013, Spain
| | - Francisco Javier García-Rodríguez
- Cancer and Human Molecular Genetics, Bellvitge Biomedical Research Institute-IDIBELL, L'Hospitalet de Llobregat, Barcelona 08908, Spain
| | - Iris Ertl
- Cancer and Human Molecular Genetics, Bellvitge Biomedical Research Institute-IDIBELL, L'Hospitalet de Llobregat, Barcelona 08908, Spain
| | - Mònica Díaz
- Drug Delivery and Targeting, CIBBIM-Nanomedicine, Vall d'Hebron Research Institute, Universidad Autónoma de Barcelona, Barcelona 08035, Spain
| | - Laura Fontrodona
- Cancer and Human Molecular Genetics, Bellvitge Biomedical Research Institute-IDIBELL, L'Hospitalet de Llobregat, Barcelona 08908, Spain
| | - Kadri Reis
- Cancer and Human Molecular Genetics, Bellvitge Biomedical Research Institute-IDIBELL, L'Hospitalet de Llobregat, Barcelona 08908, Spain
| | - Robert Johnsen
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - David Baillie
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Manuel J Muñoz
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC - UPO - Junta de Andalucía, Sevilla 41013, Spain
| | - Mihail Sarov
- TransgeneOmics Unit, Max Planck Institute of Molecular Cell Biology and Genetics, Dresden 01307, Germany
| | - Denis Dupuy
- Université Bordeaux, IECB, Laboratoire ARNA, F-33600 Pessac, France INSERM, U869, Laboratoire ARNA, F-33000 Bordeaux, France
| | - Julián Cerón
- Cancer and Human Molecular Genetics, Bellvitge Biomedical Research Institute-IDIBELL, L'Hospitalet de Llobregat, Barcelona 08908, Spain
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10
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The Heptameric SmAP1 and SmAP2 Proteins of the Crenarchaeon Sulfolobus Solfataricus Bind to Common and Distinct RNA Targets. Life (Basel) 2015; 5:1264-81. [PMID: 25905548 PMCID: PMC4500138 DOI: 10.3390/life5021264] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 03/23/2015] [Accepted: 04/15/2015] [Indexed: 12/04/2022] Open
Abstract
Sm and Sm-like proteins represent an evolutionarily conserved family with key roles in RNA metabolism. Sm-based regulation is diverse and can range in scope from eukaryotic mRNA splicing to bacterial quorum sensing, with at least one step in these processes being mediated by an RNA-associated molecular assembly built on Sm proteins. Despite the availability of several 3D-structures of Sm-like archaeal proteins (SmAPs), their function has remained elusive. The aim of this study was to shed light on the function of SmAP1 and SmAP2 of the crenarchaeon Sulfolobus solfataricus (Sso). Using co-purification followed by RNASeq different classes of non-coding RNAs and mRNAs were identified that co-purified either with both paralogues or solely with Sso-SmAP1 or Sso-SmAP2. The large number of associated intron-containing tRNAs and tRNA/rRNA modifying RNAs may suggest a role of the two Sso-SmAPs in tRNA/rRNA processing. Moreover, the 3D structure of Sso-SmAP2 was elucidated. Like Sso-SmAP1, Sso-SmAP2 forms homoheptamers. The binding of both proteins to distinct RNA substrates is discussed in terms of surface conservation, structural differences in the RNA binding sites and differences in the electrostatic surface potential of the two Sso-SmAP proteins. Taken together, this study may hint to common and different functions of both Sso-SmAPs in Sso RNA metabolism.
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11
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Evolutionary conservation and expression of human RNA-binding proteins and their role in human genetic disease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 825:1-55. [PMID: 25201102 DOI: 10.1007/978-1-4939-1221-6_1] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
RNA-binding proteins (RBPs) are effectors and regulators of posttranscriptional gene regulation (PTGR). RBPs regulate stability, maturation, and turnover of all RNAs, often binding thousands of targets at many sites. The importance of RBPs is underscored by their dysregulation or mutations causing a variety of developmental and neurological diseases. This chapter globally discusses human RBPs and provides a brief introduction to their identification and RNA targets. We review RBPs based on common structural RNA-binding domains, study their evolutionary conservation and expression, and summarize disease associations of different RBP classes.
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12
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Golisz A, Sikorski PJ, Kruszka K, Kufel J. Arabidopsis thaliana LSM proteins function in mRNA splicing and degradation. Nucleic Acids Res 2013; 41:6232-49. [PMID: 23620288 PMCID: PMC3695525 DOI: 10.1093/nar/gkt296] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Sm-like (Lsm) proteins have been identified in all organisms and are related to RNA metabolism. Here, we report that Arabidopsis nuclear AtLSM8 protein, as well as AtLSM5, which localizes to both the cytoplasm and nucleus, function in pre-mRNA splicing, while AtLSM5 and the exclusively cytoplasmic AtLSM1 contribute to 5'-3' mRNA decay. In lsm8 and sad1/lsm5 mutants, U6 small nuclear RNA (snRNA) was reduced and unspliced mRNA precursors accumulated, whereas mRNA stability was mainly affected in plants lacking AtLSM1 and AtLSM5. Some of the mRNAs affected in lsm1a lsm1b and sad1/lsm5 plants were also substrates of the cytoplasmic 5'-3' exonuclease AtXRN4 and of the decapping enzyme AtDCP2. Surprisingly, a subset of substrates was also stabilized in the mutant lacking AtLSM8, which supports the notion that plant mRNAs are actively degraded in the nucleus. Localization of LSM components, purification of LSM-interacting proteins as well as functional analyses strongly suggest that at least two LSM complexes with conserved activities in RNA metabolism, AtLSM1-7 and AtLSM2-8, exist also in plants.
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Affiliation(s)
- Anna Golisz
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland
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13
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Mura C, Randolph PS, Patterson J, Cozen AE. Archaeal and eukaryotic homologs of Hfq: A structural and evolutionary perspective on Sm function. RNA Biol 2013; 10:636-51. [PMID: 23579284 PMCID: PMC3710371 DOI: 10.4161/rna.24538] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Hfq and other Sm proteins are central in RNA metabolism, forming an evolutionarily conserved family that plays key roles in RNA processing in organisms ranging from archaea to bacteria to human. Sm-based cellular pathways vary in scope from eukaryotic mRNA splicing to bacterial quorum sensing, with at least one step in each of these pathways being mediated by an RNA-associated molecular assembly built upon Sm proteins. Though the first structures of Sm assemblies were from archaeal systems, the functions of Sm-like archaeal proteins (SmAPs) remain murky. Our ignorance about SmAP biology, particularly vis-à-vis the eukaryotic and bacterial Sm homologs, can be partly reduced by leveraging the homology between these lineages to make phylogenetic inferences about Sm functions in archaea. Nevertheless, whether SmAPs are more eukaryotic (RNP scaffold) or bacterial (RNA chaperone) in character remains unclear. Thus, the archaeal domain of life is a missing link, and an opportunity, in Sm-based RNA biology.
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Affiliation(s)
- Cameron Mura
- Department of Chemistry, University of Virginia, Charlottesville, VA, USA
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14
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Abstract
The bacterial Hfq protein is a versatile modulator of RNA function and is particularly important for regulation mediated by small non-coding RNAs. Hfq is a bacterial Sm protein but bears more similarity to the eukaryotic Sm-like (Lsm) family of proteins than the prototypical Sm proteins. Hfq and Lsm proteins share the ability to chaperone RNA-RNA and RNA/protein interactions and an interesting penchant for protecting the 3′ end of a transcript from exonucleolytic decay while encouraging degradation through other pathways. Our view of Lsm function in eukaryotes has historically been informed by studies of Hfq structure and function but mutational analyses and structural studies of Lsm sub-complexes have given important insights as well. Here, we aim to compare and contrast the roles of these evolutionarily related complexes and to highlight areas for future investigation.
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Affiliation(s)
- Carol J Wilusz
- Department of Microbiology, Immunology & Pathology, Colorado State University, Fort Collins, CO, USA.
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15
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Wu J, Zhang Y, Wang Y, Kong R, Hu L, Schuele R, Du X, Ke Y. Transcriptional repressor NIR functions in the ribosome RNA processing of both 40S and 60S subunits. PLoS One 2012; 7:e31692. [PMID: 22363708 PMCID: PMC3282729 DOI: 10.1371/journal.pone.0031692] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2011] [Accepted: 01/17/2012] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND NIR was identified as an inhibitor of histone acetyltransferase and it represses transcriptional activation of p53. NIR is predominantly localized in the nucleolus and known as Noc2p, which is involved in the maturation of the 60S ribosomal subunit. However, how NIR functions in the nucleolus remains undetermined. In the nucleolus, a 47S ribosomal RNA precursor (pre-rRNA) is transcribed and processed to produce 18S, 5.8S and 28S rRNAs. The 18S rRNA is incorporated into the 40S ribosomal subunit, whereas the 28S and 5.8S rRNAs are incorporated into the 60S subunit. U3 small nucleolar RNA (snoRNA) directs 18S rRNA processing and U8 snoRNA mediates processing of 28S and 5.8 S rRNAs. Functional disruption of nucleolus often causes p53 activation to inhibit cell proliferation. METHODOLOGY/PRINCIPAL FINDINGS Western blotting showed that NIR is ubiquitously expressed in different human cell lines. Knock-down of NIR by siRNA led to inhibition of the 18S, 28S and 5.8S rRNAs evaluated by pulse-chase experiment. Pre-rRNA particles (pre-rRNPs) were fractionated from the nucleus by sucrose gradient centrifugation and analysis of the pre-RNPs components showed that NIR existed in the pre-RNPs of both the 60S and 40S subunits and co-fractionated with 32S and 12S pre-rRNAs in the 60S pre-rRNP. Protein-RNA binding experiments demonstrated that NIR is associated with the 32S pre-rRNA and U8 snoRNA. In addition, NIR bound U3 snoRNA. It is a novel finding that depletion of NIR did not affect p53 protein level but de-repressed acetylation of p53 and activated p21. CONCLUSIONS We provide the first evidence for a transcriptional repressor to function in the rRNA biogenesis of both the 40S and 60S subunits. Our findings also suggested that a nucleolar protein may alternatively signal to p53 by affecting the p53 modification rather than affecting p53 protein level.
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Affiliation(s)
- Jianguo Wu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Genetics Laboratory, Peking University School of Oncology, Beijing Cancer Hospital & Institute, Beijing, China
| | - Ying Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Genetics Laboratory, Peking University School of Oncology, Beijing Cancer Hospital & Institute, Beijing, China
| | - Yingshuang Wang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Genetics Laboratory, Peking University School of Oncology, Beijing Cancer Hospital & Institute, Beijing, China
| | - Ruirui Kong
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Genetics Laboratory, Peking University School of Oncology, Beijing Cancer Hospital & Institute, Beijing, China
| | - Lelin Hu
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Roland Schuele
- Medical Research Center, Freiburg University, Freiburg, Germany
| | - Xiaojuan Du
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Yang Ke
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Genetics Laboratory, Peking University School of Oncology, Beijing Cancer Hospital & Institute, Beijing, China
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16
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Watkins NJ, Bohnsack MT. The box C/D and H/ACA snoRNPs: key players in the modification, processing and the dynamic folding of ribosomal RNA. WILEY INTERDISCIPLINARY REVIEWS-RNA 2011; 3:397-414. [DOI: 10.1002/wrna.117] [Citation(s) in RCA: 347] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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17
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Andersen KL, Nielsen H. Experimental identification and analysis of macronuclear non-coding RNAs from the ciliate Tetrahymena thermophila. Nucleic Acids Res 2011; 40:1267-81. [PMID: 21967850 PMCID: PMC3273799 DOI: 10.1093/nar/gkr792] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The ciliate Tetrahymena thermophila is an important eukaryotic model organism that has been used in pioneering studies of general phenomena, such as ribozymes, telomeres, chromatin structure and genome reorganization. Recent work has shown that Tetrahymena has many classes of small RNA molecules expressed during vegetative growth or sexual reorganization. In order to get an overview of medium-sized (40-500 nt) RNAs expressed from the Tetrahymena genome, we created a size-fractionated cDNA library from macronuclear RNA and analyzed 80 RNAs, most of which were previously unknown. The most abundant class was small nucleolar RNAs (snoRNAs), many of which are formed by an unusual maturation pathway. The modifications guided by the snoRNAs were analyzed bioinformatically and experimentally and many Tetrahymena-specific modifications were found, including several in an essential, but not conserved domain of ribosomal RNA. Of particular interest, we detected two methylations in the 5'-end of U6 small nuclear RNA (snRNA) that has an unusual structure in Tetrahymena. Further, we found a candidate for the first U8 outside metazoans, and an unusual U14 candidate. In addition, a number of candidates for new non-coding RNAs were characterized by expression analysis at different growth conditions.
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Affiliation(s)
- Kasper L Andersen
- Department of Cellular and Molecular Medicine and Center for Non-coding RNA in Technology and Health, The Panum Institute, University of Copenhagen, 3 Blegdamsvej, DK-2200N, Denmark
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18
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Zhang Z, Zhang S, Zhang Y, Wang X, Li D, Li Q, Yue M, Li Q, Zhang YE, Xu Y, Xue Y, Chong K, Bao S. Arabidopsis floral initiator SKB1 confers high salt tolerance by regulating transcription and pre-mRNA splicing through altering histone H4R3 and small nuclear ribonucleoprotein LSM4 methylation. THE PLANT CELL 2011; 23:396-411. [PMID: 21258002 PMCID: PMC3051234 DOI: 10.1105/tpc.110.081356] [Citation(s) in RCA: 124] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2010] [Revised: 11/15/2010] [Accepted: 01/04/2011] [Indexed: 05/19/2023]
Abstract
Plants adapt their growth and development in response to perceived salt stress. Although DELLA-dependent growth restraint is thought to be an integration of the plant's response to salt stress, little is known about how histone modification confers salt stress and, in turn, affects development. Here, we report that floral initiator Shk1 kinase binding protein1 (SKB1) and histone4 arginine3 (H4R3) symmetric dimethylation (H4R3sme2) integrate responses to plant developmental progress and salt stress. Mutation of SKB1 results in salt hypersensitivity, late flowering, and growth retardation. SKB1 associates with chromatin and thereby increases the H4R3sme2 level to suppress the transcription of FLOWERING LOCUS C (FLC) and a number of stress-responsive genes. During salt stress, the H4R3sme2 level is reduced, as a consequence of SKB1 disassociating from chromatin to induce the expression of FLC and the stress-responsive genes but increasing the methylation of small nuclear ribonucleoprotein Sm-like4 (LSM4). Splicing defects are observed in the skb1 and lsm4 mutants, which are sensitive to salt. We propose that SKB1 mediates plant development and the salt response by altering the methylation status of H4R3sme2 and LSM4 and linking transcription to pre-mRNA splicing.
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Affiliation(s)
- Zhaoliang Zhang
- Key Laboratory of Molecular and Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- Graduate University of the Chinese Academy of Sciences, Beijing 100039, China
| | - Shupei Zhang
- Key Laboratory of Molecular and Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Ya Zhang
- Key Laboratory of Molecular and Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xin Wang
- Key Laboratory of Molecular and Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Dan Li
- Key Laboratory of Molecular and Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Qiuling Li
- Key Laboratory of Molecular and Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- Graduate University of the Chinese Academy of Sciences, Beijing 100039, China
| | - Minghui Yue
- Key Laboratory of Molecular and Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- Graduate University of the Chinese Academy of Sciences, Beijing 100039, China
| | - Qun Li
- Key Laboratory of Molecular and Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yu-e Zhang
- Key Laboratory of Molecular and Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yunyuan Xu
- Key Laboratory of Photosynthesis and Environmental Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Yongbiao Xue
- Key Laboratory of Molecular and Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- National Plant Gene Research Centre, Beijing 100101, China
| | - Kang Chong
- Key Laboratory of Photosynthesis and Environmental Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- National Plant Gene Research Centre, Beijing 100101, China
| | - Shilai Bao
- Key Laboratory of Molecular and Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- Address correspondence to
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19
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Hokii Y, Sasano Y, Sato M, Sakamoto H, Sakata K, Shingai R, Taneda A, Oka S, Himeno H, Muto A, Fujiwara T, Ushida C. A small nucleolar RNA functions in rRNA processing in Caenorhabditis elegans. Nucleic Acids Res 2010; 38:5909-18. [PMID: 20460460 PMCID: PMC2943600 DOI: 10.1093/nar/gkq335] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
CeR-2 RNA is one of the newly identified Caenorhabditis elegans noncoding RNAs (ncRNAs). The characterization of CeR-2 by RNomic studies has failed to classify it into any known ncRNA family. In this study, we examined the spatiotemporal expression patterns of CeR-2 to gain insight into its function. CeR-2 is expressed in most cells from the early embryo to adult stages. The subcellular localization of this RNA is analogous to that of fibrillarin, a major protein of the nucleolus. It was observed that knockdown of C/D small nucleolar ribonucleoproteins (snoRNPs), but not of H/ACA snoRNPs, resulted in the aberrant nucleolar localization of CeR-2 RNA. A mutant worm with a reduced amount of cellular CeR-2 RNA showed changes in its pre-rRNA processing pattern compared with that of the wild-type strain N2. These results suggest that CeR-2 RNA is a C/D snoRNA involved in the processing of rRNAs.
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Affiliation(s)
- Yusuke Hokii
- Functional Genomics and Technology, United Graduate School of Agricultural Science, Iwate University, 18-8 Ueda 3-chome, Morioka 020-8550
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20
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Mammalian DEAD box protein Ddx51 acts in 3' end maturation of 28S rRNA by promoting the release of U8 snoRNA. Mol Cell Biol 2010; 30:2947-56. [PMID: 20404093 DOI: 10.1128/mcb.00226-10] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Biogenesis of eukaryotic ribosomes requires a number of RNA helicases that drive molecular rearrangements at various points of the assembly pathway. While many ribosome synthesis factors are conserved among all eukaryotes, certain features of ribosome maturation, such as U8 snoRNA-assisted processing of the 5.8S and 28S rRNA precursors, are observed only in metazoan cells. Here, we identify the mammalian DEAD box helicase family member Ddx51 as a novel ribosome synthesis factor and an interacting partner of the nucleolar GTP-binding protein Nog1. Unlike any previously studied yeast helicases, Ddx51 is required for the formation of the 3' end of 28S rRNA. Ddx51 binds to pre-60S subunit complexes and promotes displacement of U8 snoRNA from pre-rRNA, which is necessary for the removal of the 3' external transcribed spacer from 28S rRNA and productive downstream processing. These data demonstrate the emergence of a novel factor that facilitates a pre-rRNA processing event specific for higher eukaryotes.
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21
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Godfrey AC, White AE, Tatomer DC, Marzluff WF, Duronio RJ. The Drosophila U7 snRNP proteins Lsm10 and Lsm11 are required for histone pre-mRNA processing and play an essential role in development. RNA (NEW YORK, N.Y.) 2009; 15:1661-72. [PMID: 19620235 PMCID: PMC2743060 DOI: 10.1261/rna.1518009] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2008] [Accepted: 05/21/2009] [Indexed: 05/23/2023]
Abstract
Metazoan replication-dependent histone mRNAs are not polyadenylated, and instead terminate in a conserved stem-loop structure generated by an endonucleolytic cleavage of the pre-mRNA involving U7 snRNP. U7 snRNP contains two like-Sm proteins, Lsm10 and Lsm11, which replace SmD1 and SmD2 in the canonical heptameric Sm protein ring that binds spliceosomal snRNAs. Here we show that mutations in either the Drosophila Lsm10 or the Lsm11 gene disrupt normal histone pre-mRNA processing, resulting in production of poly(A)+ histone mRNA as a result of transcriptional read-through to cryptic polyadenylation sites present downstream from each histone gene. This molecular phenotype is indistinguishable from that which we previously described for mutations in U7 snRNA. Lsm10 protein fails to accumulate in Lsm11 mutants, suggesting that a pool of Lsm10-Lsm11 dimers provides precursors for U7 snRNP assembly. Unexpectedly, U7 snRNA was detected in Lsm11 and Lsm1 mutants and could be precipitated with anti-trimethylguanosine antibodies, suggesting that it assembles into a snRNP particle in the absence of Lsm10 and Lsm11. However, this U7 snRNA could not be detected at the histone locus body, suggesting that Lsm10 and Lsm11 are necessary for U7 snRNP localization. In contrast to U7 snRNA null mutants, which are viable, Lsm10 and Lsm11 mutants do not survive to adulthood. Because we cannot detect differences in the histone mRNA phenotype between Lsm10 or Lsm11 and U7 mutants, we propose that the different terminal developmental phenotypes result from the participation of Lsm10 and Lsm11 in an essential function that is distinct from histone pre-mRNA processing and that is independent of U7 snRNA.
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MESH Headings
- Animals
- Animals, Genetically Modified
- Drosophila/genetics
- Drosophila/growth & development
- Drosophila/metabolism
- Drosophila Proteins/genetics
- Drosophila Proteins/physiology
- Female
- Fertility/genetics
- Genes, Developmental/physiology
- Genes, Lethal/genetics
- Histones/genetics
- Histones/metabolism
- Male
- Mutation/physiology
- RNA Precursors/metabolism
- RNA Processing, Post-Transcriptional/genetics
- RNA Processing, Post-Transcriptional/physiology
- RNA, Messenger/metabolism
- Ribonucleoprotein, U7 Small Nuclear/genetics
- Ribonucleoprotein, U7 Small Nuclear/physiology
- Ribonucleoproteins, Small Nuclear/genetics
- Ribonucleoproteins, Small Nuclear/physiology
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Affiliation(s)
- Ashley C Godfrey
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
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22
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Reijns MAM, Auchynnikava T, Beggs JD. Analysis of Lsm1p and Lsm8p domains in the cellular localization of Lsm complexes in budding yeast. FEBS J 2009; 276:3602-17. [PMID: 19490016 PMCID: PMC2776932 DOI: 10.1111/j.1742-4658.2009.07080.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
In eukaryotes, two heteroheptameric Sm-like (Lsm) complexes that differ by a single subunit localize to different cellular compartments and have distinct functions in RNA metabolism. The cytoplasmic Lsm1–7p complex promotes mRNA decapping and localizes to processing bodies, whereas the Lsm2–8p complex takes part in a variety of nuclear RNA processing events. The structural features that determine their different functions and localizations are not known. Here, we analyse a range of mutant and hybrid Lsm1 and Lsm8 proteins, shedding light on the relative importance of their various domains in determining their localization and ability to support growth. Although no single domain is either essential or sufficient for cellular localization, the Lsm1p N-terminus may act as part of a nuclear exclusion signal for Lsm1–7p, and the shorter Lsm8p N-terminus contributes to nuclear accumulation of Lsm2–8p. The C-terminal regions seem to play a secondary role in determining localization, with little or no contribution coming from the central Sm domains. The essential Lsm8 protein is remarkably resistant to mutation in terms of supporting viability, whereas Lsm1p appears more sensitive. These findings contribute to our understanding of how two very similar protein complexes can have different properties.
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23
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Scofield DG, Lynch M. Evolutionary diversification of the Sm family of RNA-associated proteins. Mol Biol Evol 2008; 25:2255-67. [PMID: 18687770 DOI: 10.1093/molbev/msn175] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The Sm family of proteins is closely associated with RNA metabolism throughout all life. These proteins form homomorphic and heteromorphic rings consisting of six or seven subunits with a characteristic central pore, the presence of which is critical for binding U-rich regions of single-stranded RNA. Eubacteria and Archaea typically carry one or two forms of Sm proteins and assemble one homomorphic ring per Sm protein. Eukaryotes typically carry 16 or more Sm proteins that assemble to form heteromorphic rings which lie at the center of a number of critical RNA-associated small nuclear ribonucleoproteins (snRNPs). High Sm protein diversity and heteromorphic Sm rings are features stretching back to the origin of eukaryotes; very deep phylogenetic divisions among existing Sm proteins indicate simultaneous evolution across essentially all existing eukaryotic life. Two basic forms of heteromorphic Sm rings are found in eukaryotes. Fixed Sm rings are highly stable and static and are assembled around an RNA cofactor. Flexible Sm rings also stabilize and chaperone RNA but assemble in the absence of an RNA substrate and, more significantly, associate with and dissociate from RNA substrates more freely than fixed rings. This suggests that the conformation of flexible Sm rings might be modified in some specific manner to facilitate association and dissociation with RNA. Diversification of eukaryotic Sm proteins may have been initiated by gene transfers and/or genome clashes that accompanied the origin of the eukaryotic cell itself, with further diversification driven by a greater need for steric specificity within increasingly complex snRNPs.
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24
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Identification of the heptameric Lsm complex that binds U6 snRNA in Trypanosoma brucei. Mol Biochem Parasitol 2008; 160:22-31. [PMID: 18433897 DOI: 10.1016/j.molbiopara.2008.03.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2007] [Revised: 03/06/2008] [Accepted: 03/11/2008] [Indexed: 12/25/2022]
Abstract
Lsm proteins are ubiquitous, multifunctional proteins that are involved in nuclear processing and turnover of many RNAs in eukaryotes. Lsm proteins form two distinct complexes, the Lsm2-8 complex, which binds U6 snRNA, and the Lsm1-7 complex, which governs mRNA degradation. Previously, seven Lsm proteins were identified in Trypanosoma brucei. Two of these proteins were later identified as SSm proteins (specific spliceosomal Sm proteins). In this study, the Lsm proteins (Lsm2 and Lsm5) that bind to U6 snRNA were identified. RNAi silencing and protein purification of TAP-tagged Lsm proteins were used to identify all the components of the trypanosome heptameric Lsm2-8 complex. Localization studies demonstrated that these proteins are found in the nucleus, near the nucleolus. Lsm proteins were not detected in cytoplasmic bodies that were tagged with YFP-Dhh1, which may suggest that in trypanosomes, Lsm-mediated degradation is not confined to such bodies.
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25
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Padilla PI, Uhart M, Pacheco-Rodriguez G, Peculis BA, Moss J, Vaughan M. Association of guanine nucleotide-exchange protein BIG1 in HepG2 cell nuclei with nucleolin, U3 snoRNA, and fibrillarin. Proc Natl Acad Sci U S A 2008; 105:3357-61. [PMID: 18292223 PMCID: PMC2265132 DOI: 10.1073/pnas.0712387105] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2007] [Indexed: 01/01/2023] Open
Abstract
BIG1, a brefeldin A-inhibited guanine nucleotide-exchange protein, activates class I ADP-ribosylation factors (ARF1-3) by catalyzing the replacement of bound GDP by GTP, an action critical for the regulation of protein transport in eukaryotic cells. Our earlier report [Padilla PI, Pancheco-Rodriguez G, Moss J, Vaughan M (2004) Proc Natl Acad Sci USA 101:2752-2757] that BIG1 concentrated in nucleoli of serum-starved HepG2 cells prompted us to identify molecules associated with BIG1 in dynamic nucleolar structures. Antibodies against BIG1 or nucleolin coprecipitated both proteins from nuclei, which was abolished by the incubation of nuclei with RNase A or DNase, indicating that the interaction depended on nucleic acids. (32)P labeling of RNAs immunoprecipitated with BIG1 or nucleolin from nuclei revealed bands of approximately 210 bases that also hybridized with U3 small nucleolar (sno)RNA-specific oligonucleotides. Clones of U3 snoRNA cDNAs from the material precipitated by antibodies against BIG1 or nucleolin yielded identical nucleotide sequences that also were found in genomic DNA. Later analyses revealed the presence of fibrillarin, nucleoporin p62, and La in BIG1 and nucleolin immunoprecipitates. Our data demonstrate that BIG1, nucleolin, U3, the U3-binding protein fibrillarin, and the RNA-binding protein La may exist together in nuclear complexes, consistent with a potential role for BIG1 in nucleolar processes. Evidence that BIG1 and nucleolin, but not fibrillarin, can be present with p62 at the nuclear envelope confirms the presence of BIG1 and nucleolin in dynamic molecular complexes that change in composition while moving through nuclei. Nuclear functions of BIG1 remain to be determined.
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Affiliation(s)
- Philip Ian Padilla
- *Translational Medicine Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892; and
| | - Marina Uhart
- *Translational Medicine Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892; and
| | - Gustavo Pacheco-Rodriguez
- *Translational Medicine Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892; and
| | - Brenda A. Peculis
- Department of Biochemistry, University of Missouri, Columbia, MO 65211
| | - Joel Moss
- *Translational Medicine Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892; and
| | - Martha Vaughan
- *Translational Medicine Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892; and
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26
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Tharun S. Roles of eukaryotic Lsm proteins in the regulation of mRNA function. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2008; 272:149-89. [PMID: 19121818 DOI: 10.1016/s1937-6448(08)01604-3] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The eukaryotic Lsm proteins belong to the large family of Sm-like proteins, which includes members from all organisms ranging from archaebacteria to humans. The Sm and Lsm proteins typically exist as hexameric or heptameric complexes in vivo and carry out RNA-related functions. Multiple complexes made up of different combinations of Sm and Lsm proteins are known in eukaryotes and these complexes are involved in a variety of functions such as mRNA decay in the cytoplasm, mRNA and pre-mRNA decay in the nucleus, pre-mRNA splicing, replication dependent histone mRNA 3'-end processing, etc. While most Lsm proteins function in the form of heteromeric complexes that include other Lsm proteins, some Lsm proteins are also known that do not behave in that manner. Abnormal expression of some Lsm proteins has also been implicated in human diseases. The various roles of eukaryotic Lsm complexes impacting mRNA function are discussed in this review.
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Affiliation(s)
- Sundaresan Tharun
- Department of Biochemistry, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
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27
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Spiller MP, Reijns MAM, Beggs JD. Requirements for nuclear localization of the Lsm2-8p complex and competition between nuclear and cytoplasmic Lsm complexes. J Cell Sci 2007; 120:4310-20. [PMID: 18029398 PMCID: PMC2584364 DOI: 10.1242/jcs.019943] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Sm-like (Lsm) proteins are ubiquitous, multifunctional proteins that are involved in the processing and/or turnover of many RNAs. In eukaryotes, a hetero-heptameric complex of seven Lsm proteins (Lsm2-8) affects the processing of small stable RNAs and pre-mRNAs in the nucleus, whereas a different hetero-heptameric complex of Lsm proteins (Lsm1-7) promotes mRNA decapping and decay in the cytoplasm. These two complexes have six constituent proteins in common, yet localize to separate cellular compartments and perform apparently disparate functions. Little is known about the biogenesis of the Lsm complexes, or how they are recruited to different cellular compartments. We show that, in yeast, the nuclear accumulation of Lsm proteins depends on complex formation and that the Lsm8p subunit plays a crucial role. The nuclear localization of Lsm8p is itself most strongly influenced by Lsm2p and Lsm4p, its presumed neighbours in the Lsm2-8p complex. Furthermore, overexpression and depletion experiments imply that Lsm1p and Lsm8p act competitively with respect to the localization of the two complexes, suggesting a potential mechanism for co-regulation of nuclear and cytoplasmic RNA processing. A shift of Lsm proteins from the nucleus to the cytoplasm under stress conditions indicates that this competition is biologically significant.
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Affiliation(s)
- Michael P Spiller
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, King's Buildings, Mayfield Road, Edinburgh, EH9 3JR, UK
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Chowdhury A, Mukhopadhyay J, Tharun S. The decapping activator Lsm1p-7p-Pat1p complex has the intrinsic ability to distinguish between oligoadenylated and polyadenylated RNAs. RNA (NEW YORK, N.Y.) 2007; 13:998-1016. [PMID: 17513695 PMCID: PMC1894922 DOI: 10.1261/rna.502507] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2007] [Accepted: 04/19/2007] [Indexed: 05/15/2023]
Abstract
Decapping is a critical step in mRNA decay. In the 5'-to-3' mRNA decay pathway conserved in all eukaryotes, decay is initiated by poly(A) shortening, and oligoadenylated mRNAs (but not polyadenylated mRNAs) are selectively decapped allowing their subsequent degradation by 5' to 3' exonucleolysis. The highly conserved heptameric Lsm1p-7p complex (made up of the seven Sm-like proteins, Lsm1p-Lsm7p) and its interacting partner Pat1p activate decapping by an unknown mechanism and localize with other decapping factors to the P-bodies in the cytoplasm. The Lsm1p-7p-Pat1p complex also protects the 3'-ends of mRNAs in vivo from trimming, presumably by binding to the 3'-ends. In order to determine the intrinsic RNA-binding properties of this complex, we have purified it from yeast and carried out in vitro analyses. Our studies revealed that it directly binds RNA at/near the 3'-end. Importantly, it possesses the intrinsic ability to distinguish between oligoadenylated and polyadenylated RNAs such that the former are bound with much higher affinity than the latter. These results indicate that the intrinsic RNA-binding characteristics of this complex form a critical determinant of its in vivo interactions and functions.
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Affiliation(s)
- Ashis Chowdhury
- Department of Biochemistry and Molecular Biology, Uniformed Services University of the Health Sciences, Bethesda, MD 20814-4799, USA
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29
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Jalal C, Uhlmann-Schiffler H, Stahl H. Redundant role of DEAD box proteins p68 (Ddx5) and p72/p82 (Ddx17) in ribosome biogenesis and cell proliferation. Nucleic Acids Res 2007; 35:3590-601. [PMID: 17485482 PMCID: PMC1920232 DOI: 10.1093/nar/gkm058] [Citation(s) in RCA: 109] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The DEAD box proteins encoded by the genes ddx5 (p68) and ddx17 (isoforms p72 and p82) are more closely related to each other than to any other member of their family. We found that p68 negatively controls p72/p82 gene expression but not vice versa. Knocking down of either gene does not affect cell proliferation, in case of p68 suppression, however, only on condition that p72/p82 overexpression was granted. In contrast, co-silencing of both genes causes perturbation of nucleolar structure and cell death. In mutant studies, the apparently redundant role(s) of p68 and p72/p82 correspond to their ability to catalyze RNA rearrangement rather than RNA unwinding reactions. In search for possible physiological targets of this RNA rearrangement activity it is shown that the nucleolytic cleavage of 32S pre-rRNA is reduced after p68 subfamily knock-down, most probably due to a failure in the structural rearrangement process within the pre-60S ribosomal subunit preceding the processing of 32S pre-rRNA.
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Affiliation(s)
| | | | - Hans Stahl
- *To whom correspondence should be addressed. +49 6841 16 26020+49 6841 16 26521
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30
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Abstract
Over the last five years Sm-like (Lsm) proteins have emerged as important players in many aspects of RNA metabolism, including splicing, nuclear RNA processing and messenger RNA decay. However, their precise function in these pathways remains somewhat obscure. In contrast, the role of the bacterial Lsm protein Hfq, which bears striking similarities in both structure and function to Lsm proteins, is much better characterized. In this perspective, we have highlighted several functions that Hfq shares with Lsm proteins and put forward hypotheses based on parallels between the two that might further the understanding of Lsm function.
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Affiliation(s)
- Carol J Wilusz
- Department of Microbiology, Immunology & Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado 80523, USA.
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31
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Khusial P, Plaag R, Zieve GW. LSm proteins form heptameric rings that bind to RNA via repeating motifs. Trends Biochem Sci 2005; 30:522-8. [PMID: 16051491 DOI: 10.1016/j.tibs.2005.07.006] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2005] [Revised: 06/22/2005] [Accepted: 07/19/2005] [Indexed: 10/25/2022]
Abstract
Members of the LSm family of proteins share the Sm fold--a closed barrel comprising five anti-parallel beta strands with an alpha helix stacked on the top. The fold forms a subunit of hexameric or heptameric rings of approximately 7nm in diameter. Interactions between neighboring subunits center on an anti-parallel interaction of the fourth and fifth beta strands. In the lumen of the ring, the subunits have the same spacing as nucleotides in RNA, enabling the rings to bind to single-stranded RNA via a repeating motif. Eubacteria and archaea build homohexamers and homoheptamers, respectively, whereas eukaryotes use >18 LSm paralogs to build at least six different heteroheptameric rings. The four different rings in the nucleus that permanently bind small nuclear RNAs and function in pre-mRNA maturation are called Sm rings. The two different rings that transiently bind to RNAs and, thereby, assist in the degradation of mRNA in the cytoplasm and the maturation of a wide spectrum of RNAs in the nucleus are called LSm rings.
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Affiliation(s)
- Permanan Khusial
- Department of Pathology, Stony Brook University, Stony Brook, NY 11794-8691, USA
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32
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Abstract
Sm and Lsm proteins are ubiquitous in eukaryotes and form complexes that interact with RNAs involved in almost every cellular process. My laboratory has studied the Lsm proteins in the yeast Saccharomyces cerevisiae, identifying in the nucleus and cytoplasm distinct complexes that affect pre-mRNA splicing and degradation, small nucleolar RNA, tRNA processing, rRNA processing and mRNA degradation. These activities suggest RNA chaperone-like roles for Lsm proteins, affecting RNA-RNA and/or RNA-protein interactions. This article reviews the properties of the Sm and Lsm proteins and structurally and functionally related proteins in archaea and eubacteria.
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Affiliation(s)
- J D Beggs
- Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, King's Buildings, Mayfield Road, Edinburgh EH9 3JR, U.K.
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33
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Zaric B, Chami M, Rémigy H, Engel A, Ballmer-Hofer K, Winkler FK, Kambach C. Reconstitution of two recombinant LSm protein complexes reveals aspects of their architecture, assembly, and function. J Biol Chem 2005; 280:16066-75. [PMID: 15711010 DOI: 10.1074/jbc.m414481200] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Sm and Sm-like (LSm) proteins form complexes engaging in various RNA-processing events. Composition and architecture of the complexes determine their intracellular distribution, RNA targets, and function. We have reconstituted the human LSm1-7 and LSm2-8 complexes from their constituent components in vitro. Based on the assembly pathway of the canonical Sm core domain, we used heterodimeric and heterotrimeric sub-complexes to assemble LSm1-7 and LSm2-8. Isolated sub-complexes form ring-like higher order structures. LSm1-7 is assembled and stable in the absence of RNA. LSm1-7 forms ring-like structures very similar to LSm2-8 at the EM level. Our in vitro reconstitution results illustrate likely features of the LSm complex assembly pathway. We prove the complexes to be functional both in an RNA bandshift and an in vivo cellular transport assay.
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Affiliation(s)
- Bozidarka Zaric
- Paul Scherrer Institut, Biomolecular Research, CH5232 Villigen, Switzerland
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34
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Abstract
From archaea to humans, C/D- and H/ACA-type small ribonucleoprotein particles play key roles in crucial RNA processing events. Various such particles are required for pre-rRNA cleavage steps and/or for chemical modification of rRNAs, spliceosomal small nuclear RNAs, tRNAs and perhaps even mRNAs. Each C/D-type particle contains a small RNA possessing conserved C and D, as well as related C' and D', sequence motifs, whereas each H/ACA-type particle contains a small RNA featuring conserved H and ACA sequence elements. Recently published studies highlight the importance of sequence and structural elements of these RNAs in the localization, activity and assembly of the ribonucleoprotein particles. A novel sequence element, the Cajal body box, found at the apex of stem structures within a subset of H/ACA small RNAs, mediates the specific retention of particles containing these elements inside nucleoplasmic Cajal bodies. Two highly conserved elements, the m1 and m2 boxes, have been identified in the 3' stem of the atypical H/ACA snR30/U17 RNAs. These conserved sequence elements are necessary for early pre-rRNA cleavage events and consequently for mature 18S rRNA production. Finally, convincing evidence has been provided that the conserved C and D sequence motifs of C/D-type small RNAs fold into a helix-bulge-helix structure, called a kink-turn, that provides a platform for assembly of C/D-type ribonucleoprotein particles.
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Affiliation(s)
- Anthony K Henras
- Department of Chemistry & Biochemistry, UCLA Box 951569, 607 Charles E Young Drive East, Los Angeles, CA 90095-1569, USA
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35
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Verdone L, Galardi S, Page D, Beggs JD. Lsm proteins promote regeneration of pre-mRNA splicing activity. Curr Biol 2004; 14:1487-91. [PMID: 15324666 DOI: 10.1016/j.cub.2004.08.032] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2004] [Revised: 05/29/2004] [Accepted: 06/23/2004] [Indexed: 11/21/2022]
Abstract
Lsm proteins are ubiquitous, multifunctional proteins that affect the processing of most RNAs in eukaryotic cells, but their function is unknown. A complex of seven Lsm proteins, Lsm2-8, associates with the U6 small nuclear RNA (snRNA) that is a component of spliceosome complexes in which pre-mRNA splicing occurs. Spliceosomes contain five snRNAs, U1, U2, U4, U5, and U6, that are packaged as ribonucleoprotein particles (snRNPs). U4 and U6 snRNAs contain extensive sequence complementarity and interact to form U4/U6 di-snRNPs. U4/U6 di-snRNPs associate with U5 snRNPs to form U4/U6.U5 tri-snRNPs prior to spliceosome assembly. Within spliceosomes, disruption of base-paired U4/U6 heterodimer allows U6 snRNA to form part of the catalytic center. Following completion of the splicing reaction, snRNPs must be recycled for subsequent rounds of splicing, although little is known about this process. Here we present evidence that regeneration of splicing activity in vitro is dependent on Lsm proteins. RNP reconstitution experiments with exogenous U6 RNA show that Lsm proteins promote the formation of U6-containing complexes and suggest that Lsm proteins have a chaperone-like function, supporting the assembly or remodeling of RNP complexes involved in splicing. Such a function could explain the involvement of Lsm proteins in a wide variety of RNA processing pathways.
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Affiliation(s)
- Loredana Verdone
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, King's Buildings, Mayfield Road, Edinburgh EH9 3JR, United Kingdom
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36
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Kufel J, Allmang C, Verdone L, Beggs J, Tollervey D. A complex pathway for 3' processing of the yeast U3 snoRNA. Nucleic Acids Res 2004; 31:6788-97. [PMID: 14627812 PMCID: PMC290272 DOI: 10.1093/nar/gkg904] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Mature U3 snoRNA in yeast is generated from the 3'-extended precursors by endonucleolytic cleavage followed by exonucleolytic trimming. These precursors terminate in poly(U) tracts and are normally stabilised by binding of the yeast La homologue, Lhp1p. We report that normal 3' processing of U3 requires the nuclear Lsm proteins. On depletion of any of the five essential proteins, Lsm2-5p or Lsm8p, the normal 3'-extended precursors to the U3 snoRNA were lost. Truncated fragments of both mature and pre-U3 accumulated in the Lsm-depleted strains, consistent with substantial RNA degradation. Pre-U3 species were co-precipitated with TAP-tagged Lsm3p, but the association with spliced pre-U3 was lost in strains lacking Lhp1p. The association of Lhp1p with pre-U3 was also reduced on depletion of Lsm3p or Lsm5p, indicating that binding of Lhp1p and the Lsm proteins is interdependent. In contrast, a tagged Sm-protein detectably co-precipitated spliced pre-U3 species only in strains lacking Lhp1p. We propose that the Lsm2-8p complex functions as a chaperone in conjunction with Lhp1p to stabilise pre-U3 RNA species during 3' processing. The Sm complex may function as a back-up to stabilise 3' ends that are not protected by Lhp1p.
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Affiliation(s)
- Joanna Kufel
- Institute of Cell and Molecular Biology, Swann Building, King's Buildings, The University of Edinburgh, Edinburgh EH9 3JR, UK
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37
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Ghosh T, Peterson B, Tomasevic N, Peculis BA. Xenopus U8 snoRNA binding protein is a conserved nuclear decapping enzyme. Mol Cell 2004; 13:817-28. [PMID: 15053875 DOI: 10.1016/s1097-2765(04)00127-3] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2003] [Revised: 01/30/2004] [Accepted: 02/02/2004] [Indexed: 11/29/2022]
Abstract
U8 snoRNP is required for accumulation of mature 5.8S and 28S rRNA in vertebrates. We are identifying proteins that bind U8 RNA with high specificity to understand how U8 functions in ribosome biogenesis. Here, we characterize a Xenopus 29 kDa protein (X29), which we previously showed binds U8 RNA with high affinity. X29 and putative homologs in other vertebrates contain a NUDIX domain found in MutT and other nucleotide diphosphatases. Recombinant X29 protein has diphosphatase activity that removes m(7)G and m(227)G caps from U8 and other RNAs in vitro; the putative 29 kDa human homolog also displays this decapping activity. X29 is primarily nucleolar in Xenopus tissue culture cells. We propose that X29 is a member of a conserved family of nuclear decapping proteins that function in regulating the level of U8 snoRNA and other nuclear RNAs with methylated caps.
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Affiliation(s)
- Trina Ghosh
- National Institutes of Health, National Institute of Diabetes and Digestive and Kidney Diseases, Genetics and Biochemistry Branch, Building 8, Room 106, Bethesda, MD 20892, USA
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38
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Fernandez CF, Pannone BK, Chen X, Fuchs G, Wolin SL. An Lsm2-Lsm7 complex in Saccharomyces cerevisiae associates with the small nucleolar RNA snR5. Mol Biol Cell 2004; 15:2842-52. [PMID: 15075370 PMCID: PMC420107 DOI: 10.1091/mbc.e04-02-0116] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Sm-like (Lsm) proteins function in a variety of RNA-processing events. In yeast, the Lsm2-Lsm8 complex binds and stabilizes the spliceosomal U6 snRNA, whereas the Lsm1-Lsm7 complex functions in mRNA decay. Here we report that a third Lsm complex, consisting of Lsm2-Lsm7 proteins, associates with snR5, a box H/ACA snoRNA that functions to guide site-specific pseudouridylation of rRNA. Experiments in which the binding of Lsm proteins to snR5 was reconstituted in vitro reveal that the 3' end of snR5 is critical for Lsm protein recognition. Glycerol gradient sedimentation and sequential immunoprecipitation experiments suggest that the Lsm protein-snR5 complex is partly distinct from the complex formed by snR5 RNA with the box H/ACA proteins Gar1p and Nhp2p. Consistent with a separate complex, Lsm proteins are not required for the function of snR5 in pseudouridylation of rRNA. We demonstrate that in addition to their known nuclear and cytoplasmic locations, Lsm proteins are present in nucleoli. Taken together with previous findings that a small fraction of pre-RNase P RNA associates with Lsm2-Lsm7, our experiments suggest that an Lsm2-Lsm7 protein complex resides in nucleoli, contributing to the biogenesis or function of specific snoRNAs.
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Affiliation(s)
- Cesar F Fernandez
- Department of Cell Biology, Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, Connecticut 06536, USA
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39
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Liu Q, Liang XH, Uliel S, Belahcen M, Unger R, Michaeli S. Identification and functional characterization of lsm proteins in Trypanosoma brucei. J Biol Chem 2004; 279:18210-9. [PMID: 14990572 DOI: 10.1074/jbc.m400678200] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
RNA interference of Sm proteins in Trypanosoma brucei demonstrated that the stability of the small nuclear RNAs (U1, U2, U4, U5) and the spliced leader RNA, but not U6 RNA, were affected upon Sm depletion (Mandelboim, M., Barth, S., Biton, M., Liang, X. H., and Michaeli, S. (2003) J. Biol. Chem. 278, 51469-51478), suggesting that Lsm proteins that bind and stabilize U6 RNA in other eukaryotes should exist in trypanosomes. In this study, we identified seven Lsm proteins (Lsm2p to Lsm8p) and examined the function of Lsm3p and Lsm8p by RNA interference silencing. Both Lsm proteins were found to be essential for U6 stability and mRNA decay. Silencing was lethal, and cis- and trans-splicing were inhibited. Importantly, silencing also affected the level of U4.U6 and the U4.U6/U5 tri-small nuclear ribonucleoprotein complexes. The presence of Lsm proteins in trypanosomes that diverged early in the eukaryotic lineage suggests that these proteins are highly conserved in both structure and function among eukaryotes. Interestingly, however, Lsm1p that is specific to the mRNA decay complex was not identified in the genome data base of any kinetoplastidae, and the Lsm8p that in other eukaryotes exclusively functions in U6 stability was found to function in trypanosomes also in mRNA decay. These data therefore suggest that in trypanosomes only a single Lsm complex may exist.
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MESH Headings
- Amino Acid Sequence
- Animals
- Databases, Genetic
- Gene Silencing
- Protozoan Proteins/metabolism
- Protozoan Proteins/physiology
- RNA Splicing
- RNA Stability
- RNA, Small Interfering/pharmacology
- RNA, Small Nuclear/genetics
- RNA, Small Nuclear/metabolism
- Ribonucleoprotein, U4-U6 Small Nuclear/genetics
- Ribonucleoprotein, U4-U6 Small Nuclear/metabolism
- Ribonucleoprotein, U4-U6 Small Nuclear/physiology
- Ribonucleoprotein, U5 Small Nuclear/metabolism
- Ribonucleoproteins, Small Nuclear/metabolism
- Ribonucleoproteins, Small Nuclear/physiology
- Sequence Alignment
- Trypanosoma brucei brucei/chemistry
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Affiliation(s)
- Qing Liu
- Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
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40
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Pillai RS, Grimmler M, Meister G, Will CL, Lührmann R, Fischer U, Schümperli D. Unique Sm core structure of U7 snRNPs: assembly by a specialized SMN complex and the role of a new component, Lsm11, in histone RNA processing. Genes Dev 2003; 17:2321-33. [PMID: 12975319 PMCID: PMC196468 DOI: 10.1101/gad.274403] [Citation(s) in RCA: 178] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
A set of seven Sm proteins assemble on the Sm-binding site of spliceosomal U snRNAs to form the ring-shaped Sm core. The U7 snRNP involved in histone RNA 3' processing contains a structurally similar but biochemically unique Sm core in which two of these proteins, Sm D1 and D2, are replaced by Lsm10 and by another as yet unknown component. Here we characterize this factor, termed Lsm11, as a novel Sm-like protein with apparently two distinct functions. In vitro studies suggest that its long N-terminal part mediates an important step in histone mRNA 3'-end cleavage, most likely by recruiting a zinc finger protein previously identified as a processing factor. In contrast, the C-terminal part, which comprises two Sm motifs interrupted by an unusually long spacer, is sufficient to assemble with U7, but not U1, snRNA. Assembly of this U7-specific Sm core depends on the noncanonical Sm-binding site of U7 snRNA. Moreover, it is facilitated by a specialized SMN complex that contains Lsm10 and Lsm11 but lacks Sm D1/D2. Thus, the U7-specific Lsm11 protein not only specifies the assembly of the U7 Sm core but also fulfills an important role in U7 snRNP-mediated histone mRNA processing.
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Affiliation(s)
- Ramesh S Pillai
- Institute of Cell Biology, University of Bern, 3012 Bern, Switzerland
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41
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Noueiry AO, Diez J, Falk SP, Chen J, Ahlquist P. Yeast Lsm1p-7p/Pat1p deadenylation-dependent mRNA-decapping factors are required for brome mosaic virus genomic RNA translation. Mol Cell Biol 2003; 23:4094-106. [PMID: 12773554 PMCID: PMC156131 DOI: 10.1128/mcb.23.12.4094-4106.2003] [Citation(s) in RCA: 80] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Previously, we used the ability of the higher eukaryotic positive-strand RNA virus brome mosaic virus (BMV) to replicate in yeast to show that the yeast LSM1 gene is required for recruiting BMV RNA from translation to replication. Here we extend this observation to show that Lsm1p and other components of the Lsm1p-Lsm7p/Pat1p deadenylation-dependent mRNA decapping complex were also required for translating BMV RNAs. Inhibition of BMV RNA translation was selective, with no effect on general cellular translation. We show that viral genomic RNAs suitable for RNA replication were already distinguished from nonreplication templates at translation, well before RNA recruitment to replication. Among mRNA turnover pathways, only factors specific for deadenylated mRNA decapping were required for BMV RNA translation. Dependence on these factors was not only a consequence of the nonpolyadenylated nature of BMV RNAs but also involved the combined effects of the viral 5' and 3' noncoding regions and 2a polymerase open reading frame. High-resolution sucrose density gradient analysis showed that, while mutating factors in the Lsm1p-7p/Pat1p complex completely inhibited viral RNA translation, the levels of viral RNA associated with ribosomes were only slightly reduced in mutant yeast. This polysome association was further verified by using a conditional allele of essential translation initiation factor PRT1, which markedly decreased polysome association of viral genomic RNA in the presence or absence of an LSM7 mutation. Together, these results show that a defective Lsm1p-7p/Pat1p complex inhibits BMV RNA translation primarily by stalling or slowing the elongation of ribosomes along the viral open reading frame. Thus, factors in the Lsm1p-7p/Pat1p complex function not only in mRNA decapping but also in translation, and both translation and recruitment of BMV RNAs to viral RNA replication are regulated by a cell pathway that transfers mRNAs from translation to degradation.
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Affiliation(s)
- Amine O Noueiry
- Institute for Molecular Virology. Howard Hughes Medical Institute, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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42
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Noueiry AO, Ahlquist P. Brome mosaic virus RNA replication: revealing the role of the host in RNA virus replication. ANNUAL REVIEW OF PHYTOPATHOLOGY 2003; 41:77-98. [PMID: 12651962 DOI: 10.1146/annurev.phyto.41.052002.095717] [Citation(s) in RCA: 112] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The replication of positive-strand RNA viruses is a complex multi-step process involving interactions between the viral genome, virus-encoded replication factors, and host factors. The plant virus brome mosaic virus (BMV) has served as a model for positive-strand RNA virus replication, recombination, and virion assembly. This review addresses recent findings on the identification and characterization of host factors in BMV RNA replication. To date, all characterized host factors facilitate steps that lead to assembly of a functional BMV RNA replication complex. Some of these host factors are required for regulation of viral gene expression. Others are needed to co-regulate BMV RNA translation and recruitment of BMV RNAs from translation to viral RNA replication complexes on the endoplasmic reticulum. Other host factors provide essential lipid modifications in the endoplasmic reticulum membrane or function as molecular chaperones to activate the replication complex. Characterizing the functions of these host factors is revealing basic aspects of virus RNA replication and helping to define the normal functions of these factors in the host.
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Affiliation(s)
- Amine O Noueiry
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA.
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Stanĕk D, Rader SD, Klingauf M, Neugebauer KM. Targeting of U4/U6 small nuclear RNP assembly factor SART3/p110 to Cajal bodies. J Cell Biol 2003; 160:505-16. [PMID: 12578909 PMCID: PMC2173746 DOI: 10.1083/jcb.200210087] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The spliceosomal small nuclear RNAs (snRNAs) are distributed throughout the nucleoplasm and concentrated in nuclear inclusions termed Cajal bodies (CBs). A role for CBs in the metabolism of snRNPs has been proposed but is not well understood. The SART3/p110 protein interacts transiently with the U6 and U4/U6 snRNPs and promotes the reassembly of U4/U6 snRNPs after splicing in vitro. Here we report that SART3/p110 is enriched in CBs but not in gems or residual CBs lacking coilin. The U6 snRNP Sm-like (LSm) proteins, also involved in U4/U6 snRNP assembly, were localized to CBs as well. The levels of SART3/p110 and LSm proteins in CBs were reduced upon treatment with the transcription inhibitor alpha-amanitin, suggesting that CB localization reflects active processes dependent on transcription/splicing. The NH2-terminal HAT domain of SART3/p110 was necessary and sufficient for specific protein targeting to CBs. Overexpression of truncation mutants containing the HAT domain had dominant negative effects on U6 snRNP localization to CBs, indicating that endogenous SART3/p110 plays a role in targeting the U6 snRNP to CBs. We propose that U4 and U6 snRNPs accumulate in CBs for the purpose of assembly into U4/U6 snRNPs by SART3/p110.
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Affiliation(s)
- David Stanĕk
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
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Ingelfinger D, Arndt-Jovin DJ, Lührmann R, Achsel T. The human LSm1-7 proteins colocalize with the mRNA-degrading enzymes Dcp1/2 and Xrnl in distinct cytoplasmic foci. RNA (NEW YORK, N.Y.) 2002; 8:1489-1501. [PMID: 12515382 DOI: 10.1017/s1355838202021726] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Sm and Sm-like (LSm) proteins form heptameric complexes that are involved in various steps of RNA metabolism. In yeast, the Lsm1-7 complex functions in mRNA degradation and is associated with several enzymes of this pathway, while the complex LSm2-8, the composition of which largely overlaps with that of LSm1-7, has a role in pre-mRNA splicing. A human gene encoding an LSm1 homolog has been identified, but its role in mRNA degradation has yet to be elucidated. We performed subcellular localization studies and found hLSm1 predominantly in the cytoplasm. However, it is not distributed evenly; rather, it is highly enriched in small, discrete foci. The endogenous hLSm4 is similarly localized, as are the overexpressed proteins hLSm1-7, but not hLSm8. The foci also contain two key factors in mRNA degradation, namely the decapping enzyme hDcp1/2 and the exonuclease hXrn1. Moreover, coexpression of wild-type and mutant LSm proteins, as well as fluorescence resonance energy transfer (FRET) studies, indicate that the mammalian proteins hLSm1-7 form a complex similar to the one found in yeast, and that complex formation is required for enrichment of the proteins in the cytoplasmic foci. Therefore, the foci contain a partially or fully assembled machinery for the degradation of mRNA.
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Affiliation(s)
- Dierk Ingelfinger
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
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