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Fare CM, Villani A, Drake LE, Shorter J. Higher-order organization of biomolecular condensates. Open Biol 2021; 11:210137. [PMID: 34129784 PMCID: PMC8205532 DOI: 10.1098/rsob.210137] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
A guiding principle of biology is that biochemical reactions must be organized in space and time. One way this spatio-temporal organization is achieved is through liquid–liquid phase separation (LLPS), which generates biomolecular condensates. These condensates are dynamic and reactive, and often contain a complex mixture of proteins and nucleic acids. In this review, we discuss how underlying physical and chemical processes generate internal condensate architectures. We then outline the diverse condensate architectures that are observed in biological systems. Finally, we discuss how specific condensate organization is critical for specific biological functions.
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Affiliation(s)
- Charlotte M Fare
- Department of Biochemistry and Biophysics, and.,Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | | | - James Shorter
- Department of Biochemistry and Biophysics, and.,Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
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2
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Mediouni S, Kessing CF, Jablonski JA, Thenin-Houssier S, Clementz M, Kovach MD, Mousseau G, de Vera IMS, Li C, Kojetin DJ, Evans DT, Valente ST. The Tat inhibitor didehydro-cortistatin A suppresses SIV replication and reactivation. FASEB J 2019; 33:8280-8293. [PMID: 31021670 DOI: 10.1096/fj.201801165r] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The HIV-1 transactivation protein (Tat) binds the HIV mRNA transactivation responsive element (TAR), regulating transcription and reactivation from latency. Drugs against Tat are unfortunately not clinically available. We reported that didehydro-cortistatin A (dCA) inhibits HIV-1 Tat activity. In human CD4+ T cells isolated from aviremic individuals and in the humanized mouse model of latency, combining dCA with antiretroviral therapy accelerates HIV-1 suppression and delays viral rebound upon treatment interruption. This drug class is amenable to block-and-lock functional cure approaches, aimed at a durable state of latency. Simian immunodeficiency virus (SIV) infection of rhesus macaques (RhMs) is the best-characterized model for AIDS research. Here, we demonstrate, using in vitro and cell-based assays, that dCA directly binds to SIV Tat's basic domain. dCA specifically inhibits SIV Tat binding to TAR, but not a Tat-Rev fusion protein, which activates transcription when Rev binds to its cognate RNA binding site replacing the apical region of TAR. Tat-TAR inhibition results in loss of RNA polymerase II recruitment to the SIV promoter. Importantly, dCA potently inhibits SIV reactivation from latently infected Hut78 cells and from primary CD4+ T cells explanted from SIVmac239-infected RhMs. In sum, dCA's remarkable breadth of activity encourages SIV-infected RhM use for dCA preclinical evaluation.-Mediouni, S., Kessing, C. F., Jablonski, J. A., Thenin-Houssier, S., Clementz, M., Kovach, M. D., Mousseau, G., de Vera, I.M.S., Li, C., Kojetin, D. J., Evans, D. T., Valente, S. T. The Tat inhibitor didehydro-cortistatin A suppresses SIV replication and reactivation.
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Affiliation(s)
- Sonia Mediouni
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, Florida, USA
| | - Cari F Kessing
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, Florida, USA
| | - Joseph A Jablonski
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, Florida, USA
| | - Suzie Thenin-Houssier
- Institute of Human Genetics (IGH), CNRS-University of Montpelier, Montpelier, France
| | - Mark Clementz
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, Florida, USA
| | - Melia D Kovach
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, Florida, USA
| | - Guillaume Mousseau
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, Florida, USA
| | - Ian Mitchelle S de Vera
- Department of Pharmacology and Physiology, St. Louis University School of Medicine, St. Louis, Missouri, USA
| | - Chuan Li
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, Florida, USA
| | - Douglas J Kojetin
- Department of Molecular Therapeutics, The Scripps Research Institute, Jupiter, Florida, USA
| | - David T Evans
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Susana T Valente
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, Florida, USA
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Nyhus C, Pihl M, Hyttel P, Hall VJ. Evidence for nucleolar dysfunction in Alzheimer's disease. Rev Neurosci 2019; 30:685-700. [PMID: 30849050 DOI: 10.1515/revneuro-2018-0104] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 01/08/2019] [Indexed: 11/15/2022]
Abstract
The nucleolus is a dynamically changing organelle that is central to a number of important cellular functions. Not only is it important for ribosome biogenesis, but it also reacts to stress by instigating a nucleolar stress response and is further involved in regulating the cell cycle. Several studies report nucleolar dysfunction in Alzheimer's disease (AD). Studies have reported a decrease in both total nucleolar volume and transcriptional activity of the nucleolar organizing regions. Ribosomes appear to be targeted by oxidation and reduced protein translation has been reported. In addition, several nucleolar proteins are dysregulated and some of these appear to be implicated in classical AD pathology. Some studies also suggest that the nucleolar stress response may be activated in AD, albeit this latter research is rather limited and requires further investigation. The purpose of this review is to draw the connections of all these studies together and signify that there are clear changes in the nucleolus and the ribosomes in AD. The nucleolus is therefore an organelle that requires more attention than previously given in relation to understanding the biological mechanisms underlying the disease.
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Affiliation(s)
- Caitlin Nyhus
- Department of Veterinary and Animal Sciences, Faculty of Health Sciences, University of Copenhagen, Grønnegårdsvej 7, Frederiksberg C DK-1870, Denmark
| | - Maria Pihl
- Department of Veterinary and Animal Sciences, Faculty of Health Sciences, University of Copenhagen, Grønnegårdsvej 7, Frederiksberg C DK-1870, Denmark
| | - Poul Hyttel
- Department of Veterinary and Animal Sciences, Faculty of Health Sciences, University of Copenhagen, Grønnegårdsvej 7, Frederiksberg C DK-1870, Denmark
| | - Vanessa Jane Hall
- Department of Veterinary and Animal Sciences, Faculty of Health Sciences, University of Copenhagen, Grønnegårdsvej 7, Frederiksberg C DK-1870, Denmark
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Abstract
The nucleolus is a prominent subnuclear compartment, where ribosome biosynthesis takes place. Recently, the nucleolus has gained attention for its novel role in the regulation of cellular stress. Nucleolar stress is emerging as a new concept, which is characterized by diverse cellular insult-induced abnormalities in nucleolar structure and function, ultimately leading to activation of p53 or other stress signaling pathways and alterations in cell behavior. Despite a number of comprehensive reviews on this concept, straightforward and clear-cut way criteria for a nucleolar stress state, regarding the factors that elicit this state, the morphological and functional alterations as well as the rationale for p53 activation are still missing. Based on literature of the past two decades, we herein summarize the evolution of the concept and provide hallmarks of nucleolar stress. Along with updated information and thorough discussion of existing confusions in the field, we pay particular attention to the current understanding of the sensing mechanisms, i.e., how stress is integrated by p53. In addition, we propose our own emphasis regarding the role of nucleolar protein NPM1 in the hallmarks of nucleolar stress and sensing mechanisms. Finally, the links of nucleolar stress to human diseases are briefly and selectively introduced.
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Affiliation(s)
- Kai Yang
- Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Department of Biochemistry and Molecular Cell Biology, Shanghai Jiao Tong University School of Medicine, 280 South Chongqing Road, Shanghai, 200025, China.,Shanghai Key Laboratory for Prevention and Treatment of Bone and Joint Diseases with Integrated Chinese-Western Medicine, Shanghai Institute of Traumatology and Orthopedics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Ruijin 2nd Road, Shanghai, 200025, China
| | - Jie Yang
- Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Department of Biochemistry and Molecular Cell Biology, Shanghai Jiao Tong University School of Medicine, 280 South Chongqing Road, Shanghai, 200025, China
| | - Jing Yi
- Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Department of Biochemistry and Molecular Cell Biology, Shanghai Jiao Tong University School of Medicine, 280 South Chongqing Road, Shanghai, 200025, China
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5
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Youn H, Lee HK, Sohn HR, Park UH, Kim EJ, Youn B, Um SJ. RaRF confers RA resistance by sequestering RAR to the nucleolus and regulating MCL1 in leukemia cells. Oncogene 2017; 37:352-362. [PMID: 28945224 DOI: 10.1038/onc.2017.329] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 07/10/2017] [Accepted: 08/06/2017] [Indexed: 01/10/2023]
Abstract
Retinoic acid (RA) has broad clinical applications for the treatment of various cancers, particularly acute promyelocytic leukemia. However, RA-based therapy is limited by relapse in patients associated with RA resistance, the mechanism of which is poorly understood. Here, we suggest a new molecular mechanism of RA resistance by a repressor, named RA resistance factor (RaRF). RaRF suppressed transcriptional activity of the RA receptor (RAR) by directly interacting with and sequestering RAR to the nucleolus in response to RA. RaRF was highly expressed in RA-resistant leukemia cells and its expression was strongly correlated with RA sensitivity. MCL1 was upregulated by RA treatment upon RaRF depletion, accompanying leukemic myeloblast differentiation, which is negatively regulated by ectopic RaRF expression. Collectively, we propose that RaRF may be a factor in the resistance mechanism and thus a potential target for leukemia therapy using RA.
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Affiliation(s)
- H Youn
- Department of Integrative Bioscience and Biotechnology, Sejong University, Gwangjin-gu, Seoul, Korea
| | - H-K Lee
- Department of Integrative Bioscience and Biotechnology, Sejong University, Gwangjin-gu, Seoul, Korea
| | - H-R Sohn
- Department of Integrative Bioscience and Biotechnology, Sejong University, Gwangjin-gu, Seoul, Korea
| | - U-H Park
- Department of Integrative Bioscience and Biotechnology, Sejong University, Gwangjin-gu, Seoul, Korea
| | - E-J Kim
- Department of Molecular Biology, Dankook University, Cheonan-si, Chungnam, Korea
| | - B Youn
- Department of Biological Sciences, Pusan National University, Gumjeong-gu, Busan 46241, Republic of Korea
| | - S-J Um
- Department of Integrative Bioscience and Biotechnology, Sejong University, Gwangjin-gu, Seoul, Korea
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Blewett NH, Iben JR, Gaidamakov S, Maraia RJ. La Deletion from Mouse Brain Alters Pre-tRNA Metabolism and Accumulation of Pre-5.8S rRNA, with Neuron Death and Reactive Astrocytosis. Mol Cell Biol 2017; 37:e00588-16. [PMID: 28223366 PMCID: PMC5477551 DOI: 10.1128/mcb.00588-16] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 12/01/2016] [Accepted: 02/06/2017] [Indexed: 12/20/2022] Open
Abstract
Human La antigen (Sjögren's syndrome antigen B [SSB]) is an abundant multifunctional RNA-binding protein. In the nucleoplasm, La binds to and protects from 3' exonucleases, the ends of precursor tRNAs, and other transcripts synthesized by RNA polymerase III and facilitates their maturation, while a nucleolar isoform has been implicated in rRNA biogenesis by multiple independent lines of evidence. We showed previously that conditional La knockout (La cKO) from mouse cortex neurons results in defective tRNA processing, although the pathway(s) involved in neuronal loss thereafter was unknown. Here, we demonstrate that La is stably associated with a spliced pre-tRNA intermediate. Microscopic evidence of aberrant nuclear accumulation of 5.8S rRNA in La cKO is supported by a 10-fold increase in a pre-5.8S rRNA intermediate. To identify pathways involved in subsequent neurodegeneration and loss of brain mass in the cKO cortex, we employed mRNA sequencing (mRNA-Seq), immunohistochemistry, and other approaches. This revealed robust enrichment of immune and astrocyte reactivity in La cKO cortex. Immunohistochemistry, including temporal analyses, demonstrated neurodegeneration, followed by astrocyte invasion associated with immune response and decreasing cKO cortex size over time. Thus, deletion of La from postmitotic neurons results in defective pre-tRNA and pre-rRNA processing and progressive neurodegeneration with loss of cortical brain mass.
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Affiliation(s)
- Nathan H Blewett
- Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Rockville, Maryland, USA
| | - James R Iben
- Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Rockville, Maryland, USA
| | - Sergei Gaidamakov
- Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Rockville, Maryland, USA
| | - Richard J Maraia
- Commissioned Corps, U.S. Public Health Service, Rockville, Maryland, USA
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McCulloch R, Navarro M. The protozoan nucleus. Mol Biochem Parasitol 2016; 209:76-87. [PMID: 27181562 DOI: 10.1016/j.molbiopara.2016.05.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Revised: 05/11/2016] [Accepted: 05/12/2016] [Indexed: 12/16/2022]
Abstract
The nucleus is arguably the defining characteristic of eukaryotes, distinguishing their cell organisation from both bacteria and archaea. Though the evolutionary history of the nucleus remains the subject of debate, its emergence differs from several other eukaryotic organelles in that it appears not to have evolved through symbiosis, but by cell membrane elaboration from an archaeal ancestor. Evolution of the nucleus has been accompanied by elaboration of nuclear structures that are intimately linked with most aspects of nuclear genome function, including chromosome organisation, DNA maintenance, replication and segregation, and gene expression controls. Here we discuss the complexity of the nucleus and its substructures in protozoan eukaryotes, with a particular emphasis on divergent aspects in eukaryotic parasites, which shed light on nuclear function throughout eukaryotes and reveal specialisations that underpin pathogen biology.
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Affiliation(s)
- Richard McCulloch
- The Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Sir Graeme Davis Building, 120 University Place, Glasgow, G12 8TA, UK.
| | - Miguel Navarro
- Instituto de Parasitología y Biomedicina López-Neyra, Consejo Superior de Investigaciones Científicas (CSIC), Avda. del Conocimiento s/n, 18100 Granada, Spain.
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8
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Abstract
The nucleolus is the largest nuclear organelle and is the primary site of ribosome subunit biogenesis in eukaryotic cells. It is assembled around arrays of ribosomal DNA genes, forming specific chromosomal features known as nucleolar organizing regions (NORs) which are the sites of ribosomal DNA transcription. While the nucleolus main activity involve different steps of ribosome biogenesis, the presence of proteins with no obvious relationship with ribosome subunit production suggests additional functions for the nucleolus, such as regulation of mitosis, cell cycle progression, stress response and biogenesis of multiple ribonucleoprotein complexes. The many novel factors and separate classes of proteins identified within the nucleolus support this view that the nucleolus may perform additional functions beyond its known role in ribosome subunit biogenesis. Here we review our knowledge of the nucleolar functions and will provide a detailed picture of how the nucleolus is involved in many cellular pathways.
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Affiliation(s)
- David P. Bazett-Jones
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario Canada
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Mediouni S, Jablonski J, Paris JJ, Clementz MA, Thenin-Houssier S, McLaughlin JP, Valente ST. Didehydro-cortistatin A inhibits HIV-1 Tat mediated neuroinflammation and prevents potentiation of cocaine reward in Tat transgenic mice. Curr HIV Res 2015; 13:64-79. [PMID: 25613133 DOI: 10.2174/1570162x13666150121111548] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2014] [Revised: 11/26/2014] [Accepted: 01/14/2015] [Indexed: 11/22/2022]
Abstract
HIV-1 Tat protein has been shown to have a crucial role in HIV-1-associated neurocognitive disorders (HAND), which includes a group of syndromes ranging from undetectable neurocognitive impairment to dementia. The abuse of psychostimulants, such as cocaine, by HIV infected individuals, may accelerate and intensify neurological damage. On the other hand, exposure to Tat potentiates cocaine-mediated reward mechanisms, which further promotes HAND. Here, we show that didehydro-Cortistatin A (dCA), an analog of a natural steroidal alkaloid, crosses the blood-brain barrier, cross-neutralizes Tat activity from several HIV-1 clades and decreases Tat uptake by glial cell lines. In addition, dCA potently inhibits Tat mediated dysregulation of IL-1β, TNF-α and MCP-1, key neuroinflammatory signaling proteins. Importantly, using a mouse model where doxycycline induces Tat expression, we demonstrate that dCA reverses the potentiation of cocaine-mediated reward. Our results suggest that adding a Tat inhibitor, such as dCA, to current antiretroviral therapy may reduce HIV-1-related neuropathogenesis.
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Affiliation(s)
| | | | | | | | | | | | - Susana T Valente
- Department of Infectious diseases, The Scripps Research Institute, 130 Scripps Way, 3C1, Jupiter, FL 33458, USA.
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Andraszek K, Gryzińska M, Ceranka M, Larisch A. Structure of nucleoli in first-order spermatocytes of selected free-living animal species. Anim Reprod Sci 2015; 161:16-22. [PMID: 26304750 DOI: 10.1016/j.anireprosci.2015.06.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Revised: 06/17/2015] [Accepted: 06/19/2015] [Indexed: 02/02/2023]
Abstract
Nucleoli are the product of the activity of nucleolar organizer regions (NOR) in certain chromosomes. Their main functions are the formation of ribosomal subunits from ribosomal protein molecules and the transcription of genes encoding rRNA. Nucleoli are present in the nuclei of nearly all eukaryotic cells because they contain housekeeping genes. The size and number of nucleoli gradually decrease during spermatogenesis. Some of the material originating in the nucleolus probably migrates to the cytoplasm and takes part in the formation of chromatoid bodies (CB). Nucleolus fragmentation and CB assembly take place at the same stage of spermatogenesis. CB are involved in the formation of the acrosome, the migration of mitochondria to the midpiece, and the formation of the sperm tail fibrous sheath. The aim of the study was to characterize the nucleoli in the early prophase of spermatogenesis in the wild boar and the roe deer. The roe deer cells have larger nucleoli and a larger cell nucleus than the wild boar cells. The area of the nucleolus as a percentage of the total area of the nucleus was larger as well. The coefficients of variation for all parameters were higher in the roe deer. In the wild boar cells the nucleoli were mainly regularly shaped. The size of the nucleolus and the nucleus of the spermatocyte is a species-specific trait associated with karyotype and the number of nucleolar organizer regions in a given species.
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Affiliation(s)
- Katarzyna Andraszek
- Department of Animal Genetics and Horse Breeding, Institute of Bioengineering and Animal Breeding, University of Natural Sciences and Humanities, 14 Prusa Str, 08-110 Siedlce, Poland.
| | - Magdalena Gryzińska
- Department of Biological Basis of Animal Production, University of Life Sciences, Lublin, Akademicka 13, 20-950 Lublin, Poland
| | - Mariola Ceranka
- Department of Animal Genetics and Horse Breeding, Institute of Bioengineering and Animal Breeding, University of Natural Sciences and Humanities, 14 Prusa Str, 08-110 Siedlce, Poland
| | - Agnieszka Larisch
- Department of Animal Genetics and Horse Breeding, Institute of Bioengineering and Animal Breeding, University of Natural Sciences and Humanities, 14 Prusa Str, 08-110 Siedlce, Poland
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11
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Prieto MB, Georg RC, Gonzales-Zubiate FA, Luz JS, Oliveira CC. Nop17 is a key R2TP factor for the assembly and maturation of box C/D snoRNP complex. BMC Mol Biol 2015; 16:7. [PMID: 25888478 PMCID: PMC4377001 DOI: 10.1186/s12867-015-0037-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Accepted: 02/24/2015] [Indexed: 11/24/2022] Open
Abstract
Background Box C/D snoRNPs are responsible for rRNA methylation and processing, and are formed by snoRNAs and four conserved proteins, Nop1, Nop56, Nop58 and Snu13. The snoRNP assembly is a stepwise process, involving other protein complexes, among which the R2TP and Hsp90 chaperone. Nop17, also known as Pih1, has been shown to be a constituent of the R2TP (Rvb1, Rvb2, Tah1, Pih1) and to participate in box C/D snoRNP assembly by its interaction with Nop58. The molecular function of Nop17, however, has not yet been described. Results To shed light on the role played by Nop17 in the maturation of snoRNP, here we analyzed the interactions domains of Nop58 – Nop17 – Tah1 and the importance of ATP to the interaction between Nop17 and the ATPase Rvb1/2. Conclusions Based on the results shown here, we propose a model for the assembly of box C/D snoRNP, according to which R2TP complex is important for reducing the affinity of Nop58 for snoRNA, and for the binding of the other snoRNP subunits. Electronic supplementary material The online version of this article (doi:10.1186/s12867-015-0037-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Marcela B Prieto
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes 748, 05508-000, São Paulo, SP, Brazil.
| | - Raphaela C Georg
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes 748, 05508-000, São Paulo, SP, Brazil. .,Present address: Department of Biochemistry and Molecular Biology, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Brazil.
| | - Fernando A Gonzales-Zubiate
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes 748, 05508-000, São Paulo, SP, Brazil.
| | - Juliana S Luz
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes 748, 05508-000, São Paulo, SP, Brazil. .,Present address: Department of Biological Sciences, School of Pharmacy, São Paulo State University, Araraquara, Brazil.
| | - Carla C Oliveira
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes 748, 05508-000, São Paulo, SP, Brazil.
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12
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Kakihara Y, Saeki M. The R2TP chaperone complex: its involvement in snoRNP assembly and tumorigenesis. Biomol Concepts 2014; 5:513-20. [DOI: 10.1515/bmc-2014-0028] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 09/11/2014] [Indexed: 01/07/2023] Open
Abstract
AbstractR2TP was originally identified in yeast Saccharomyces cerevisiae as Hsp90 interacting complex, and is composed of four different proteins: Rvb1, Rvb2, Tah1, and Pih1. This complex is well-conserved in eukaryotes, and is involved in many cellular processes such as snoRNP biogenesis, RNA polymerase assembly, PIKK signaling, and apoptosis. An increasing number of research related to R2TP suggests a linkage of its function with tumorigenesis. In this review, we provide an overview of several recent studies on R2TP that are related to cell proliferation and carcinogenesis, and propose a possible role of R2TP in tumorigenesis through regulating snoRNA/snoRNP biogenesis.
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Affiliation(s)
- Yoshito Kakihara
- 1Division of Dental Pharmacology, Department of Dentistry, Niigata University, 2-5274 Gakkocho-dori, Chuo-ku, Niigata, 951-8514, Japan
| | - Makio Saeki
- 1Division of Dental Pharmacology, Department of Dentistry, Niigata University, 2-5274 Gakkocho-dori, Chuo-ku, Niigata, 951-8514, Japan
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13
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Stępiński D. Functional ultrastructure of the plant nucleolus. PROTOPLASMA 2014; 251:1285-306. [PMID: 24756369 PMCID: PMC4209244 DOI: 10.1007/s00709-014-0648-6] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Accepted: 04/08/2014] [Indexed: 05/23/2023]
Abstract
Nucleoli are nuclear domains present in almost all eukaryotic cells. They not only specialize in the production of ribosomal subunits but also play roles in many fundamental cellular activities. Concerning ribosome biosynthesis, particular stages of this process, i.e., ribosomal DNA transcription, primary RNA transcript processing, and ribosome assembly proceed in precisely defined nucleolar subdomains. Although eukaryotic nucleoli are conservative in respect of their main function, clear morphological differences between these structures can be noticed between individual kingdoms. In most cases, a plant nucleolus shows well-ordered structure in which four main ultrastructural components can be distinguished: fibrillar centers, dense fibrillar component, granular component, and nucleolar vacuoles. Nucleolar chromatin is an additional crucial structural component of this organelle. Nucleolonema, although it is not always an unequivocally distinguished nucleolar domain, has often been described as a well-grounded morphological element, especially of plant nucleoli. The ratios and morphology of particular subcompartments of a nucleolus can change depending on its metabolic activity which in turn is correlated with the physiological state of a cell, cell type, cell cycle phase, as well as with environmental influence. Precise attribution of functions to particular nucleolar subregions in the process of ribosome biosynthesis is now possible using various approaches. The presented description of plant nucleolar morphology summarizes previous knowledge regarding the function of nucleoli as well as of their particular subdomains not only in the course of ribosome biosynthesis.
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Affiliation(s)
- Dariusz Stępiński
- Department of Cytophysiology, Faculty of Biology and Environmental Protection, University of Łódź, Pomorska 141/143, 90-236, Łódź, Poland,
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Abstract
This review summarizes the current understanding of the role of nuclear bodies in regulating gene expression. The compartmentalization of cellular processes, such as ribosome biogenesis, RNA processing, cellular response to stress, transcription, modification and assembly of spliceosomal snRNPs, histone gene synthesis and nuclear RNA retention, has significant implications for gene regulation. These functional nuclear domains include the nucleolus, nuclear speckle, nuclear stress body, transcription factory, Cajal body, Gemini of Cajal body, histone locus body and paraspeckle. We herein review the roles of nuclear bodies in regulating gene expression and their relation to human health and disease.
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Affiliation(s)
| | - Cornelius F. Boerkoel
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +1-604-875-2157; Fax: +1-604-875-2376
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15
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Sakyiama J, Zimmer SL, Ciganda M, Williams N, Read LK. Ribosome biogenesis requires a highly diverged XRN family 5'->3' exoribonuclease for rRNA processing in Trypanosoma brucei. RNA (NEW YORK, N.Y.) 2013; 19:1419-1431. [PMID: 23974437 PMCID: PMC3854532 DOI: 10.1261/rna.038547.113] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Accepted: 07/10/2013] [Indexed: 05/30/2023]
Abstract
Although biogenesis of ribosomes is a crucial process in all organisms and is thus well conserved, Trypanosoma brucei ribosome biogenesis, of which maturation of rRNAs is an early step, has multiple points of divergence. Our aim was to determine whether in the processing of the pre-rRNA precursor molecule, 5'→3' exoribonuclease activity in addition to endonucleolytic cleavage is necessary in T. brucei as in other organisms. Our approach initiated with the bioinformatic identification of a putative 5'→3' exoribonuclease, XRNE, which is highly diverged from the XRN2/Rat1 enzyme responsible for rRNA processing in other organisms. Tagging this protein in vivo allowed us to classify XRNE as nucleolar by indirect immunofluorescence and identify by copurification interacting proteins, many of which were ribosomal proteins, ribosome biogenesis proteins, and/or RNA processing proteins. To determine whether XRNE plays a role in ribosome biogenesis in procyclic form cells, we inducibly depleted the protein by RNA interference. This resulted in the generation of aberrant preprocessed 18S rRNA and 5' extended 5.8S rRNA, implicating XRNE in rRNA processing. Polysome profiles of XRNE-depleted cells demonstrated abnormal features including an increase in ribosome small subunit abundance, a decrease in large subunit abundance, and defects in polysome assembly. Furthermore, the 5' extended 5.8S rRNA in XRNE-depleted cells was observed in the large subunit, monosomes, and polysomes in this gradient. Therefore, the function of XRNE in rRNA processing, presumably due to exonucleolytic activity very early in ribosome biogenesis, has consequences that persist throughout all biogenesis stages.
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MESH Headings
- Amino Acid Sequence
- Blotting, Northern
- Blotting, Western
- Cell Nucleolus
- Cells, Cultured
- Exoribonucleases/genetics
- Exoribonucleases/metabolism
- Immunoprecipitation
- Molecular Sequence Data
- Organelle Biogenesis
- Polyribosomes/genetics
- Polyribosomes/metabolism
- RNA Processing, Post-Transcriptional
- RNA, Messenger/genetics
- RNA, Ribosomal, 18S/genetics
- RNA, Ribosomal, 18S/metabolism
- Real-Time Polymerase Chain Reaction
- Reverse Transcriptase Polymerase Chain Reaction
- Ribosomal Proteins/genetics
- Ribosomal Proteins/metabolism
- Ribosomes/metabolism
- Sequence Homology, Amino Acid
- Tandem Mass Spectrometry
- Trypanosoma brucei brucei/enzymology
- Trypanosoma brucei brucei/genetics
- Trypanosoma brucei brucei/growth & development
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Affiliation(s)
- Joseph Sakyiama
- Department of Microbiology and Immunology, School of Medicine and Biomedical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14214, USA
| | - Sara L. Zimmer
- Department of Microbiology and Immunology, School of Medicine and Biomedical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14214, USA
| | - Martin Ciganda
- Department of Microbiology and Immunology, School of Medicine and Biomedical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14214, USA
| | - Noreen Williams
- Department of Microbiology and Immunology, School of Medicine and Biomedical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14214, USA
| | - Laurie K. Read
- Department of Microbiology and Immunology, School of Medicine and Biomedical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14214, USA
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16
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Mousseau G, Clementz MA, Bakeman WN, Nagarsheth N, Cameron M, Shi J, Baran P, Fromentin R, Chomont N, Valente ST. An analog of the natural steroidal alkaloid cortistatin A potently suppresses Tat-dependent HIV transcription. Cell Host Microbe 2013; 12:97-108. [PMID: 22817991 DOI: 10.1016/j.chom.2012.05.016] [Citation(s) in RCA: 131] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2011] [Revised: 04/03/2012] [Accepted: 05/14/2012] [Indexed: 12/11/2022]
Abstract
The human immunodeficiency virus type 1 (HIV) Tat protein, a potent activator of HIV gene expression, is essential for integrated viral genome expression and represents a potential antiviral target. Tat binds the 5'-terminal region of HIV mRNA's stem-bulge-loop structure, the transactivation-responsive (TAR) element, to activate transcription. We find that didehydro-Cortistatin A (dCA), an analog of a natural steroidal alkaloid from a marine sponge, inhibits Tat-mediated transactivation of the integrated provirus by binding specifically to the TAR-binding domain of Tat. Working at subnanomolar concentrations, dCA reduces Tat-mediated transcriptional initiation/elongation from the viral promoter to inhibit HIV-1 and HIV-2 replication in acutely and chronically infected cells. Importantly, dCA abrogates spontaneous viral particle release from CD4(+)T cells from virally suppressed subjects on highly active antiretroviral therapy (HAART). Thus, dCA defines a unique class of anti-HIV drugs that may inhibit viral production from stable reservoirs and reduce residual viremia during HAART.
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MESH Headings
- Alkaloids/chemical synthesis
- Alkaloids/chemistry
- Alkaloids/pharmacokinetics
- Alkaloids/pharmacology
- Animals
- Anti-HIV Agents/pharmacology
- Antiretroviral Therapy, Highly Active
- Binding Sites
- CD4-Positive T-Lymphocytes/virology
- Cells, Cultured/drug effects
- Cells, Cultured/virology
- Female
- Gene Expression Regulation, Viral/drug effects
- HIV Core Protein p24/metabolism
- HIV Infections/drug therapy
- HIV Infections/virology
- HIV-1/drug effects
- HIV-1/genetics
- HIV-1/physiology
- Heterocyclic Compounds, 4 or More Rings/pharmacology
- Humans
- Isoquinolines/pharmacology
- Male
- Mice
- Mice, Inbred C57BL
- Microsomes, Liver/drug effects
- Polycyclic Compounds/chemistry
- Promoter Regions, Genetic
- Proviruses/drug effects
- Proviruses/genetics
- Transcription, Genetic/drug effects
- Virus Replication/drug effects
- tat Gene Products, Human Immunodeficiency Virus/antagonists & inhibitors
- tat Gene Products, Human Immunodeficiency Virus/genetics
- tat Gene Products, Human Immunodeficiency Virus/metabolism
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Affiliation(s)
- Guillaume Mousseau
- Department of Infectology, The Scripps Research Institute, Scripps Florida, Jupiter, 33458, USA
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17
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Kim R, Paschedag J, Novikova N, Bellini M. The recruitment of the U5 snRNP to nascent transcripts requires internal loop 1 of U5 snRNA. Chromosome Res 2012. [PMID: 23180092 DOI: 10.1007/s10577-012-9326-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
In this study, we take advantage of the high spatial resolution offered by the nucleus and lampbrush chromosomes of the amphibian oocyte to investigate the mechanisms that regulate the intranuclear trafficking of the U5 snRNP and its recruitment to nascent transcripts. We monitor the fate of newly assembled fluorescent U5 snRNP in Xenopus oocytes depleted of U4 and/or U6 snRNAs and demonstrate that the U4/U6.U5 tri-snRNP is not required for the association of U5 snRNP with Cajal bodies, splicing speckles, and nascent transcripts. In addition, using a mutational analysis, we show that a non-functional U5 snRNP can associate with nascent transcripts, and we further characterize internal loop structure 1 of U5 snRNA as a critical element for licensing U5 snRNP to target both nascent transcripts and splicing speckles. Collectively, our data support the model where the recruitment of snRNPs onto pre-mRNAs is independent of spliceosome assembly and suggest that U5 snRNP may promote the association of the U4/U6.U5 tri-snRNP with nascent transcripts.
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Affiliation(s)
- Rebecca Kim
- Department of Cell and Developmental Biology, University of Illinois at Champaign-Urbana, 601 S Goodwin Avenue, Room B107 CLSL, Urbana, IL 61801, USA
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18
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Abstract
Nucleoli are the sites where synthesis of rRNA and ribosomal assembly take place. Along with these "traditional" roles, the nucleolus controls cellular physiology and homeostasis. The cellular and molecular alterations associated with impaired nucleolar activity ("nucleolar stress") have just started to be systematically explored in the nervous system taking advantage of newly available animal models lacking rRNA synthesis in specific neurons. These studies showed that nucleolar function is necessary for neuronal survival and that its modality of action differs between and within cell types. Nucleolar function is also crucial in pathology as it controls mitochondrial activity and critical stress signaling pathways mimicking hallmarks of human neurodegenerative diseases. This mini-review will focus on the modes of action of nucleolar stress and discuss how the manipulation of nucleolar activity might underscore novel strategies to extend neuronal function and survival.
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Affiliation(s)
- Rosanna Parlato
- Department of Molecular Biology of the Cell I, DKFZ-ZMBH Alliance, German Cancer Research Center, Im Neuenheimer Feld, 581, 69120, Heidelberg, Germany.
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19
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Indig FE, Rybanska I, Karmakar P, Devulapalli C, Fu H, Carrier F, Bohr VA. Nucleolin inhibits G4 oligonucleotide unwinding by Werner helicase. PLoS One 2012; 7:e35229. [PMID: 22675465 PMCID: PMC3366963 DOI: 10.1371/journal.pone.0035229] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2010] [Accepted: 03/14/2012] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The Werner protein (WRNp), a member of the RecQ helicase family, is strongly associated with the nucleolus, as is nucleolin (NCL), an important nucleolar constituent protein. Both WRNp and NCL respond to the effects of DNA damaging agents. Therefore, we have investigated if these nuclear proteins interact and if this interaction has a possible functional significance in DNA damage repair. METHODOLOGY/PRINCIPAL FINDINGS Here we report that WRNp interacts with the RNA-binding protein, NCL, based on immunoprecipitation, immunofluorescent co-localization in live and fixed cells, and direct binding of purified WRNp to nucleolin. We also map the binding region to the C-terminal domains of both proteins. Furthermore, treatment of U2OS cells with 15 µM of the Topoisomerase I inhibitor, camptothecin, causes the dissociation of the nucleolin-Werner complex in the nucleolus, followed by partial re-association in the nucleoplasm. Other DNA damaging agents, such as hydroxyurea, Mitomycin C, and aphidicolin do not have these effects. Nucleolin or its C-terminal fragment affected the helicase, but not the exonuclease activity of WRNp, by inhibiting WRN unwinding of G4 tetraplex DNA structures, as seen in activity assays and electrophoretic mobility shift assays (EMSA). CONCLUSIONS/SIGNIFICANCE These data suggest that nucleolin may regulate G4 DNA unwinding by WRNp, possibly in response to certain DNA damaging agents. We postulate that the NCL-WRNp complex may contain an inactive form of WRNp, which is released from the nucleolus upon DNA damage. Then, when required, WRNp is released from inhibition and can participate in the DNA repair processes.
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Affiliation(s)
- Fred E Indig
- Laboratory of Clinical Investigation, Intramural Research Program, National Institute on Aging, National Institutes of Health, Department of Health and Human Services, Baltimore, Maryland, United States of America.
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20
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Peruquetti RL, Taboga SR, Cabral SR, Oliveira CD, Azeredo-Oliveira MT. Relationship between the nucleolar cycle and chromatoid body formation in the spermatogenesis of Phrynops geoffroanus(Reptilia Testudines). Anim Cells Syst (Seoul) 2012. [DOI: 10.1080/19768354.2011.615147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
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21
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Peruquetti RL, Taboga SR, Azeredo-Oliveira MTVD. Morphological Changes of Mammalian Nucleoli during Spermatogenesis and Their Possible Role in the Chromatoid Body Assembling. ACTA ACUST UNITED AC 2012. [DOI: 10.5402/2012/829854] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Chromatoid body (CB) is a typical cytoplasmic organelle of germ cells, and it seems to be involved in RNA/protein accumulation for later germ-cell differentiation. Despite most of the events in mammals spermatogenesis had been widely described in the past decades and the increase in the studies related to the CB molecular composition and physiology, the origins and functions of this important structure of male germ cells are still unclear. The aims of this study were to describe the nucleolar cycle and also to find some relationship between the nucleolar organization and the CB assembling during the spermatogenesis in mammals. Cytochemical and cytogenetics analysis showed nucleolar fragmentation in post-pachytene spermatocytes and nucleolar reorganization in post-meiotic spermatids. Significant difference in the number and in the size of nucleoli between spermatogonia and round spermatids, as well as differences in the nucleolar position within the nucleus were also observed. Ultrastructural analysis showed the CB assembling in the cytoplasm of primary spermatocytes and the nucleolar fragmentation occurring at the same time. In conclusion our results suggest that the CB may play important roles during the spermatogenesis process in mammals and that its origin may be related to the nucleolar cycle during the meiotic cell cycle.
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Affiliation(s)
- Rita Luiza Peruquetti
- Department of Biology, Sao Paulo State University, UNESP/IBILCE, Rua Cristovao Colombo, 2265, 15054-000 Sao Jose do Rio Preto, SP, Brazil
| | - Sebastião Roberto Taboga
- Department of Biology, Sao Paulo State University, UNESP/IBILCE, Rua Cristovao Colombo, 2265, 15054-000 Sao Jose do Rio Preto, SP, Brazil
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22
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Takata H, Nishijima H, Maeshima K, Shibahara KI. The integrator complex is required for integrity of Cajal bodies. J Cell Sci 2012; 125:166-75. [PMID: 22250197 DOI: 10.1242/jcs.090837] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The nucleus in eukaryotic cells is a highly organized and dynamic structure containing numerous subnuclear bodies. The morphological appearance of nuclear bodies seems to be a reflection of ongoing functions, such as DNA replication, transcription, repair, RNA processing and RNA transport. The integrator complex mediates processing of small nuclear RNA (snRNA), so it might play a role in nuclear body formation. Here, we show that the integrator complex is essential for integrity of the Cajal body. Depletion of INTS4, an integrator complex subunit, abrogated 3'-end processing of snRNA. A defect in this activity caused a significant accumulation of the Cajal body marker protein coilin in nucleoli. Some fractions of coilin still formed nucleoplasmic foci; however, they were free of other Cajal body components, such as survival of motor neuron protein (SMN), Sm proteins and snRNAs. SMN and Sm proteins formed striking cytoplasmic granules. These findings demonstrate that the integrator complex is essential for snRNA maturation and Cajal body homeostasis.
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Affiliation(s)
- Hideaki Takata
- Department of Integrated Genetics, National Institute of Genetics, Research Organization of Information and Systems, Mishima, Japan.
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23
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Hutten S, Prescott A, James J, Riesenberg S, Boulon S, Lam YW, Lamond AI. An intranucleolar body associated with rDNA. Chromosoma 2011; 120:481-99. [PMID: 21698343 PMCID: PMC3232531 DOI: 10.1007/s00412-011-0327-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2011] [Revised: 05/16/2011] [Accepted: 05/31/2011] [Indexed: 02/07/2023]
Abstract
The nucleolus is the subnuclear organelle responsible for ribosome subunit biogenesis and can also act as a stress sensor. It forms around clusters of ribosomal DNA (rDNA) and is mainly organised in three subcompartments, i.e. fibrillar centre, dense fibrillar component and granular component. Here, we describe the localisation of 21 protein factors to an intranucleolar region different to these main subcompartments, called the intranucleolar body (INB). These factors include proteins involved in DNA maintenance, protein turnover, RNA metabolism, chromatin organisation and the post-translational modifiers SUMO1 and SUMO2/3. Increase in the size and number of INBs is promoted by specific types of DNA damage and depends on the functional integrity of the nucleolus. INBs are abundant in nucleoli of unstressed cells during S phase and localise in close proximity to rDNA with heterochromatic features. The data suggest the INB is linked with regulation of rDNA transcription and/or maintenance of rDNA.
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Affiliation(s)
- Saskia Hutten
- Wellcome Trust Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, UK
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24
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Mao YS, Zhang B, Spector DL. Biogenesis and function of nuclear bodies. Trends Genet 2011; 27:295-306. [PMID: 21680045 DOI: 10.1016/j.tig.2011.05.006] [Citation(s) in RCA: 490] [Impact Index Per Article: 37.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2011] [Revised: 05/10/2011] [Accepted: 05/11/2011] [Indexed: 12/17/2022]
Abstract
Nuclear bodies including nucleoli, Cajal bodies, nuclear speckles, Polycomb bodies, and paraspeckles are membraneless subnuclear organelles. They are present at steady-state and dynamically respond to basic physiological processes as well as to various forms of stress, altered metabolic conditions and alterations in cellular signaling. The formation of a specific nuclear body has been suggested to follow a stochastic or ordered assembly model. In addition, a seeding mechanism has been proposed to assemble, maintain, and regulate particular nuclear bodies. In coordination with noncoding RNAs, chromatin modifiers and other machineries, various nuclear bodies have been shown to sequester and modify proteins, process RNAs and assemble ribonucleoprotein complexes, as well as epigenetically regulate gene expression. Understanding the functional relationships between the 3D organization of the genome and nuclear bodies is essential to fully uncover the regulation of gene expression and its implications for human disease.
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Affiliation(s)
- Yuntao S Mao
- Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY 11724, USA
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25
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Malatesta M, Zancanaro C, Biggiogera M. Immunoelectron microscopic characterization of nucleolus-associated domains during hibernation. Microsc Res Tech 2010; 74:47-53. [DOI: 10.1002/jemt.20872] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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26
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Pontvianne F, Abou-Ellail M, Douet J, Comella P, Matia I, Chandrasekhara C, DeBures A, Blevins T, Cooke R, Medina FJ, Tourmente S, Pikaard CS, Sáez-Vásquez J. Nucleolin is required for DNA methylation state and the expression of rRNA gene variants in Arabidopsis thaliana. PLoS Genet 2010; 6:e1001225. [PMID: 21124873 PMCID: PMC2991258 DOI: 10.1371/journal.pgen.1001225] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2010] [Accepted: 10/27/2010] [Indexed: 01/11/2023] Open
Abstract
In eukaryotes, 45S rRNA genes are arranged in tandem arrays in copy numbers ranging from several hundred to several thousand in plants. Although it is clear that not all copies are transcribed under normal growth conditions, the molecular basis controlling the expression of specific sets of rRNA genes remains unclear. Here, we report four major rRNA gene variants in Arabidopsis thaliana. Interestingly, while transcription of one of these rRNA variants is induced, the others are either repressed or remain unaltered in A. thaliana plants with a disrupted nucleolin-like protein gene (Atnuc-L1). Remarkably, the most highly represented rRNA gene variant, which is inactive in WT plants, is reactivated in Atnuc-L1 mutants. We show that accumulated pre-rRNAs originate from RNA Pol I transcription and are processed accurately. Moreover, we show that disruption of the AtNUC-L1 gene induces loss of symmetrical DNA methylation without affecting histone epigenetic marks at rRNA genes. Collectively, these data reveal a novel mechanism for rRNA gene transcriptional regulation in which the nucleolin protein plays a major role in controlling active and repressed rRNA gene variants in Arabidopsis.
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Affiliation(s)
- Frédéric Pontvianne
- UMR 5096 CNRS-IRD-University de Perpignan, Perpignan, France
- Department of Biology and Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana, United States of America
| | | | - Julien Douet
- UMR CNRS 6247, INSERM U931, University Blaise Pascal, Aubière, France
| | - Pascale Comella
- UMR 5096 CNRS-IRD-University de Perpignan, Perpignan, France
| | - Isabel Matia
- Centro de Investigaciones Biológicas, Consejo Superior de Investigacion Científicas, Madrid, Spain
| | - Chinmayi Chandrasekhara
- Department of Biology and Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana, United States of America
| | - Anne DeBures
- UMR 5096 CNRS-IRD-University de Perpignan, Perpignan, France
| | - Todd Blevins
- Department of Biology and Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana, United States of America
| | - Richard Cooke
- UMR 5096 CNRS-IRD-University de Perpignan, Perpignan, France
| | - Francisco J. Medina
- Centro de Investigaciones Biológicas, Consejo Superior de Investigacion Científicas, Madrid, Spain
| | | | - Craig S. Pikaard
- Department of Biology and Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana, United States of America
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27
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Heindl K, Martinez J. Nol9 is a novel polynucleotide 5'-kinase involved in ribosomal RNA processing. EMBO J 2010; 29:4161-71. [PMID: 21063389 PMCID: PMC3018789 DOI: 10.1038/emboj.2010.275] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2010] [Accepted: 10/18/2010] [Indexed: 01/19/2023] Open
Abstract
The production and processing of ribosomal RNA is an essential and complex process. Here, a polynucleotide 5′-kinase, Nol9, is shown to have an important function in pre-rRNA processing and 60S ribosomal subunit biogenesis. In a cell, an enormous amount of energy is channelled into the biogenesis of ribosomal RNAs (rRNAs). In a multistep process involving a large variety of ribosomal and non-ribosomal proteins, mature rRNAs are generated from a long polycistronic precursor. Here, we show that the non-ribosomal protein Nol9 is a polynucleotide 5′-kinase that sediments primarily with the pre-60S ribosomal particles in HeLa nuclear extracts. Depletion of Nol9 leads to a severe impairment of ribosome biogenesis. In particular, the polynucleotide kinase activity of Nol9 is required for efficient generation of the 5.8S and 28S rRNAs from the 32S precursor. Upon Nol9 knockdown, we also observe a specific maturation defect at the 5′ end of the predominant 5.8S short-form rRNA (5.8SS), possibly due to the Nol9 requirement for 5′>3′ exonucleolytic trimming. In contrast, the endonuclease-dependent generation of the 5′-extended, minor 5.8S long-form rRNA (5.8SL) is largely unaffected. This is the first report of a nucleolar polynucleotide kinase with a role in rRNA processing.
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Affiliation(s)
- Katrin Heindl
- IMBA, Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna, Austria
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28
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Mathias MIC, Arnosti A, Brienza PD, Furquim KCS, Oliveira PRD, Denardi SE, Bechara GH. The dynamics of RNA participation in the vitellogenesis of Rhipicephalus sanguineus ticks Latreille 1806 (Acari:Ixodidae). I. Nucleoli or Cajal bodies? Micron 2010; 41:870-6. [DOI: 10.1016/j.micron.2010.04.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2010] [Revised: 04/08/2010] [Accepted: 04/13/2010] [Indexed: 11/26/2022]
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29
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Abstract
Nucleolus is the most prominent subnuclear structure, which performs a wide variety of functions in the eukaryotic cellular processes. In order to understand the structural and functional role of the nucleoli in bovine cells, we analyzed the proteomic composition of the bovine nucleoli. The nucleoli were isolated from Madin Darby bovine kidney cells and subjected to proteomic analysis by LC-MS/MS after fractionation by SDS-PAGE and strong cation exchange chromatography. Analysis of the data using the Mascot database search and the GPM database search identified 311 proteins in the bovine nucleoli, which contained 22 proteins previously not identified in the proteomic analysis of human nucleoli. Analysis of the identified proteins using the GoMiner software suggested that the bovine nucleoli contained proteins involved in ribosomal biogenesis, cell cycle control, transcriptional, translational and post-translational regulation, transport, and structural organization.
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Affiliation(s)
- Amrutlal K. Patel
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, Canada
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Canada
| | - Doug Olson
- National Research Council, Plant Biotechnology Institute, University of Saskatchewan, Saskatoon, Canada
| | - Suresh K. Tikoo
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, Canada
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Canada
- School of Public Health, University of Saskatchewan, Saskatoon, Canada
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30
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Babiano R, de la Cruz J. Ribosomal protein L35 is required for 27SB pre-rRNA processing in Saccharomyces cerevisiae. Nucleic Acids Res 2010; 38:5177-92. [PMID: 20392820 PMCID: PMC2926614 DOI: 10.1093/nar/gkq260] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2009] [Revised: 03/19/2010] [Accepted: 03/29/2010] [Indexed: 11/12/2022] Open
Abstract
Ribosome synthesis involves the concomitance of pre-rRNA processing and ribosomal protein assembly. In eukaryotes, this is a complex process that requires the participation of specific sequences and structures within the pre-rRNAs, at least 200 trans-acting factors and the ribosomal proteins. There is little information on the function of individual 60S ribosomal proteins in ribosome synthesis. Herein, we have analysed the contribution of ribosomal protein L35 in ribosome biogenesis. In vivo depletion of L35 results in a deficit in 60S ribosomal subunits and the appearance of half-mer polysomes. Pulse-chase, northern hybridization and primer extension analyses show that processing of the 27SB to 7S pre-rRNAs is strongly delayed upon L35 depletion. Most likely as a consequence of this, release of pre-60S ribosomal particles from the nucleolus to the nucleoplasm is also blocked. Deletion of RPL35A leads to similar although less pronounced phenotypes. Moreover, we show that L35 assembles in the nucleolus and binds to early pre-60S ribosomal particles. Finally, flow cytometry analysis indicated that L35-depleted cells mildly delay the G1 phase of the cell cycle. We conclude that L35 assembly is a prerequisite for the efficient cleavage of the internal transcribed spacer 2 at site C(2).
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Affiliation(s)
| | - Jesús de la Cruz
- Departamento de Genética, Universidad de Sevilla, Sevilla, Spain
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31
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Nucleolar cycle and chromatoid body formation: is there a relationship between these two processes during spermatogenesis of Dendropsophus minutus (Amphibia, Anura)? Micron 2010; 42:87-96. [PMID: 20829051 DOI: 10.1016/j.micron.2010.07.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2010] [Revised: 07/20/2010] [Accepted: 07/23/2010] [Indexed: 11/21/2022]
Abstract
The goals of this study were to monitor the nucleolar material distribution during Dendropsophus minutus spermatogenesis using cytological and cytochemical techniques and ultrastructural analysis, as well as to compare the nucleolar material distribution to the formation of the chromatoid body (CB) in the germ epithelium of this amphibian species. Nucleolar fragmentation occurred during the pachytene of prophase I and nucleolus reorganization occurred in the early spermatid nucleus. The area of the spermatogonia nucleolus was significantly larger than that of the earlier spermatid nucleolus. Ultrastructural analysis showed an accumulation of nuages in the spermatogonia cytoplasm, which form the CB before nucleolar fragmentation. The CB was observed in association with mitochondrial clusters in the cytoplasm of primary spermatocytes, as well as in those of earlier spermatids. In conclusion, the nucleolus seems to be related to CB formation during spermatogenesis of D. minutus, because, at the moment of nucleolus fragmentation in the primary spermatocytes, the CB area reaches a considerable size and is able to execute its important functions during spermatogenesis. The reorganized nucleolus of the earlier spermatids has a smaller area due to several factors, among them the probable migration of nucleolar fragments from the nucleus to the cytoplasm, and plays a part in the CB chemical composition.
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Bellavia D, Barbieri R. Evidence for a novel cytoplasmic processing event in ribosome maturation in the sea urchin Paracentrotus lividus. Cell Mol Life Sci 2010; 67:1871-9. [PMID: 20195698 PMCID: PMC11115762 DOI: 10.1007/s00018-010-0297-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2009] [Revised: 01/11/2010] [Accepted: 01/28/2010] [Indexed: 10/19/2022]
Abstract
In this paper we demonstrate the existence of a cytoplasmic processing step, never before described, involving both the pre-ribosomal subunits in the sea urchin Paracentrotus lividus. Northern-blot hybridization, primer extension, S1 mapping experiments and in situ hybridizations allowed us to demonstrate that cytoplasmic processed particles are successively re-imported into the nucleus where maturation of their RNAs is completed prior to being exported to the cytoplasm. Our findings lead to the proposal of a new model of ribosome maturation and shuttling.
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Affiliation(s)
- Daniele Bellavia
- Dipartimento di Biologia Cellulare e dello Sviluppo, Università degli Studi di Palermo, V.le delle Scienze, Edificio 16, 90128 Palermo, Italy
| | - Rainer Barbieri
- Dipartimento di Biologia Cellulare e dello Sviluppo, Università degli Studi di Palermo, V.le delle Scienze, Edificio 16, 90128 Palermo, Italy
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Zakrzewska-Placzek M, Souret FF, Sobczyk GJ, Green PJ, Kufel J. Arabidopsis thaliana XRN2 is required for primary cleavage in the pre-ribosomal RNA. Nucleic Acids Res 2010; 38:4487-502. [PMID: 20338880 PMCID: PMC2910052 DOI: 10.1093/nar/gkq172] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Three Rat1/Xrn2 homologues exist in Arabidopsis thaliana: nuclear AtXRN2 and AtXRN3, and cytoplasmic AtXRN4. The latter has a role in degrading 3' products of miRNA-mediated mRNA cleavage, whereas all three proteins act as endogenous post-transcriptional gene silencing suppressors. Here we show that, similar to yeast nuclear Rat1, AtXRN2 has a role in ribosomal RNA processing. The lack of AtXRN2, however, does not result in defective formation of rRNA 5'-ends but inhibits endonucleolytic cleavage at the primary site P in the pre-rRNA resulting in the accumulation of the 35S* precursor. This does not lead to a decrease in mature rRNAs, as additional cleavages occur downstream of site P. Supplementing a P-site cleavage-deficient xrn2 plant extract with the recombinant protein restores processing activity, indicating direct participation of AtXRN2 in this process. Our data suggest that the 5' external transcribed spacer is shortened by AtXRN2 prior to cleavage at site P and that this initial exonucleolytic trimming is required to expose site P for subsequent endonucleolytic processing by the U3 snoRNP complex. We also show that some rRNA precursors and excised spacer fragments that accumulate in the absence of AtXRN2 and AtXRN3 are polyadenylated, indicating that these nucleases contribute to polyadenylation-dependent nuclear RNA surveillance.
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34
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Peruquetti RL, Taboga SR, De Azeredo-Oliveira MTV. Nucleolar Cycle and Its Correlation with Chromatoid Bodies in the Tilapia rendalli (Teleostei, Cichlidae) Spermatogenesis. Anat Rec (Hoboken) 2010; 293:900-10. [DOI: 10.1002/ar.21099] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Politz JCR, Hogan EM, Pederson T. MicroRNAs with a nucleolar location. RNA (NEW YORK, N.Y.) 2009; 15:1705-15. [PMID: 19628621 PMCID: PMC2743059 DOI: 10.1261/rna.1470409] [Citation(s) in RCA: 139] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2008] [Accepted: 06/18/2009] [Indexed: 05/03/2023]
Abstract
There is increasing evidence that noncoding RNAs play a functional role in the nucleus. We previously reported that the microRNA (miRNA), miR-206, is concentrated in the nucleolus of rat myoblasts, as well as in the cytoplasm as expected. Here we have extended this finding. We show by cell/nuclear fractionation followed by microarray analysis that a number of miRNAs can be detected within the nucleolus of rat myoblasts, some of which are significantly concentrated there. Pronounced nucleolar localization is a specific phenomenon since other miRNAs are present at only very low levels in the nucleolus and occur at much higher levels in the nucleoplasm and/or the cytoplasm. We have further characterized a subset of these miRNAs using RT-qPCR and in situ hybridization, and the results suggest that some miRNAs are present in the nucleolus in precursor form while others are present as mature species. Furthermore, we have found that these miRNAs are clustered in specific sites within the nucleolus that correspond to the classical granular component. One of these miRNAs is completely homologous to a portion of a snoRNA, suggesting that it may be processed from it. In contrast, the other nucleolar-concentrated miRNAs do not show homology with any annotated rat snoRNAs and thus appear to be present in the nucleolus for other reasons, such as modification/processing, or to play roles in the late stages of ribosome biosynthesis or in nonribosomal functions that have recently been ascribed to the granular component of the nucleolus.
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Affiliation(s)
- Joan C Ritland Politz
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA.
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36
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Pai DA, Engelke DR. Spatial organization of genes as a component of regulated expression. Chromosoma 2009; 119:13-25. [PMID: 19727792 DOI: 10.1007/s00412-009-0236-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2009] [Revised: 08/05/2009] [Accepted: 08/06/2009] [Indexed: 12/15/2022]
Abstract
The DNA of living cells is highly compacted. Inherent in this spatial constraint is the need for cells to organize individual genetic loci so as to facilitate orderly retrieval of information. Complex genetic regulatory mechanisms are crucial to all organisms, and it is becoming increasingly evident that spatial organization of genes is one very important mode of regulation for many groups of genes. In eukaryotic nuclei, it appears not only that DNA is organized in three-dimensional space but also that this organization is dynamic and interactive with the transcriptional state of the genes. Spatial organization occurs throughout evolution and with genes transcribed by all classes of RNA polymerases in all eukaryotic nuclei, from yeast to human. There is an increasing body of work examining the ways in which this organization and consequent regulation are accomplished. In this review, we discuss the diverse strategies that cells use to preferentially localize various classes of genes.
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Affiliation(s)
- Dave A Pai
- Department of Biological Chemistry, University of Michigan, 1150 W. Medical Center Dr., Ann Arbor, MI, 48109-0606, USA
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37
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Arginine methylation analysis of the splicing-associated SR protein SFRS9/SRP30C. Cell Mol Biol Lett 2009; 14:657-69. [PMID: 19557313 PMCID: PMC6275941 DOI: 10.2478/s11658-009-0024-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2008] [Accepted: 06/10/2009] [Indexed: 11/20/2022] Open
Abstract
The human SFRS9/SRp30c belongs to the SR family of splicing regulators. Despite evidence that members of this protein family may be targeted by arginine methylation, this has yet to be experimentally addressed. In this study, we found that SFRS9 is a target for PRMT1-mediated arginine methylation in vitro, and that it is immunoprecipitated from HEK-293 lysates by antibodies that recognize both mono- and dimethylated arginines. We further observed that upon treatment with the methylation inhibitor Adox, the fluorescent EGFP-SFRS9 re-localizes to dot-like structures in the cell nucleus. In subsequent confocal analyses, we found that EGFP-SFRS9 localizes to nucleoli in Adox-treated cells. Our findings indicate the importance of arginine methylation for the subnuclear localization of SFRS9.
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38
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Bressan GC, Quaresma AJC, Moraes EC, Manfiolli AO, Passos DO, Gomes MD, Kobarg J. Functional association of human Ki-1/57 with pre-mRNA splicing events. FEBS J 2009; 276:3770-83. [PMID: 19523114 DOI: 10.1111/j.1742-4658.2009.07092.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The cytoplasmic and nuclear protein Ki-1/57 was first identified in malignant cells from Hodgkin's lymphoma. Despite studies showing its phosphorylation, arginine methylation, and interaction with several regulatory proteins, the functional role of Ki-1/57 in human cells remains to be determined. Here, we investigated the relationship of Ki-1/57 with RNA functions. Through immunoprecipitation assays, we verified the association of Ki-1/57 with the endogenous splicing proteins hnRNPQ and SFRS9 in HeLa cell extracts. We also found that recombinant Ki-1/57 was able to bind to a poly-U RNA probe in electrophoretic mobility shift assays. In a classic splicing test, we showed that Ki-1/57 can modify the splicing site selection of the adenoviral E1A minigene in a dose-dependent manner. Further confocal and fluorescence microscopy analysis revealed the localization of enhanced green fluorescent proteinKi-1/57 to nuclear bodies involved in RNA processing and or small nuclear ribonucleoprotein assembly, depending on the cellular methylation status and its N-terminal region. In summary, our findings suggest that Ki-1/57 is probably involved in cellular events related to RNA functions, such as pre-mRNA splicing.
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Stepiński D. Immunodetection of nucleolar proteins and ultrastructure of nucleoli of soybean root meristematic cells treated with chilling stress and after recovery. PROTOPLASMA 2009; 235:77-89. [PMID: 19241118 DOI: 10.1007/s00709-009-0033-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2008] [Accepted: 01/19/2009] [Indexed: 05/03/2023]
Abstract
The nucleolar proteins, fibrillarin and nucleophosmin, have been identified immunofluorescently in the root meristematic cells of soybean seedlings under varying experimental conditions: at 25 degrees C (control), chilling at 10 degrees C for 3 h and 4 days and recovery from the chilling stress at 25 degrees C. In each experimental variant, the immunofluorescence signals were present solely at the nucleolar territories. Fluorescent staining for both proteins was mainly in the shape of circular domains that are assumed to correspond to the dense fibrillar component of the nucleoli. The fewest fluorescent domains were observed in the nucleoli of chilled plants, and the highest number was observed in the plants recovered after chilling. This difference in the number of circular domains in the nucleoli of each variant may indicate various levels of these proteins in each variant. Both the number of circular domains and the level of these nucleolar proteins changed with changes in the transcriptional activity of the nucleoli, with the more metabolically active cell having higher numbers of active areas in the nucleolus and higher levels of nucleolar proteins, and conversely. Electron microscopic studies revealed differences in the ultrastructure of the nucleoli in all experimental variants and confirmed that the number of fibrillar centres surrounded by dense fibrillar component was the lowest in the nucleoli of chilled plants, and the highest in the nucleoli of recovered seedlings.
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Affiliation(s)
- Dariusz Stepiński
- Department of Cytophysiology, University of Łódź, Pilarskiego 14, 90-231, Łódź, Poland.
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Peruquetti RL, Taboga SR, de Azeredo-Oliveira MTV. Characterization of Mongolian gerbil chromatoid bodies and their correlation with nucleolar cycle during spermatogenesis. Reprod Domest Anim 2009; 45:399-406. [PMID: 19144012 DOI: 10.1111/j.1439-0531.2008.01204.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The aims of the present study were to monitor the nucleolar cycle in Mongolian gerbil spermiogenesis, to verify the relationship between the nucleolar component and chromatoid body (CB) formation and to investigate the function of this cytoplasmic supramolecular structure in spermatogenic cells. Histological sections of adult seminiferous tubules were analysed cytochemically by light microscopy and ultrastructurally by transmission electron microscopy. The results reveal that in early spermatids, the CB was visualized in association with Golgi vesicles indicating that this structure may participate in the acrosome formation process as had been reported in other rodents. In late spermatids, the CB was observed near the axoneme region suggesting that this structure may support spermatozoon tail formation as happens in other species. Chromatoid body was joined with lipid droplets in this same cell type. This observation should be investigated to verify whether CB may be related to steroidal hormone metabolism. In conclusion, our data showed that there is disintegration of primary spermatocyte nucleoli at the beginning of prophase I and a fraction of this nucleolar material migrates to the cytoplasm, where a specific structure is formed, known as the 'chromatoid body', which apparently participates in some parts of the gerbil spermiogenesis process.
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Affiliation(s)
- R L Peruquetti
- Department of Biology, Sao Paulo State University - UNESP/IBILCE, Rua Cristovao Colombo, SP, Brazil
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41
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Patel SB, Bellini M. The assembly of a spliceosomal small nuclear ribonucleoprotein particle. Nucleic Acids Res 2008; 36:6482-93. [PMID: 18854356 PMCID: PMC2582628 DOI: 10.1093/nar/gkn658] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
The U1, U2, U4, U5 and U6 small nuclear ribonucleoprotein particles (snRNPs) are essential elements of the spliceosome, the enzyme that catalyzes the excision of introns and the ligation of exons to form a mature mRNA. Since their discovery over a quarter century ago, the structure, assembly and function of spliceosomal snRNPs have been extensively studied. Accordingly, the functions of splicing snRNPs and the role of various nuclear organelles, such as Cajal bodies (CBs), in their nuclear maturation phase have already been excellently reviewed elsewhere. The aim of this review is, then, to briefly outline the structure of snRNPs and to synthesize new and exciting developments in the snRNP biogenesis pathways.
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Affiliation(s)
- Snehal Bhikhu Patel
- Biochemistry and College of Medicine and Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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42
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Ponti D, Troiano M, Bellenchi GC, Battaglia PA, Gigliani F. The HIV Tat protein affects processing of ribosomal RNA precursor. BMC Cell Biol 2008; 9:32. [PMID: 18559082 PMCID: PMC2440370 DOI: 10.1186/1471-2121-9-32] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2007] [Accepted: 06/17/2008] [Indexed: 01/09/2023] Open
Abstract
Background Inside the cell, the HIV Tat protein is mainly found in the nucleus and nucleolus. The nucleolus, the site of ribosome biogenesis, is a highly organized, non-membrane-bound sub-compartment where proteins with a high affinity for nucleolar components are found. While it is well known that Tat accumulates in the nucleolus via a specific nucleolar targeting sequence, its function in this compartment it still unknown. Results To clarify the significance of the Tat nucleolar localization, we induced the expression of the protein during oogenesis in Drosophila melanogaster strain transgenic for HIV-tat gene. Here we show that Tat localizes in the nucleoli of Drosophila oocyte nurse cells, where it specifically co-localizes with fibrillarin. Tat expression is accompanied by a significant decrease of cytoplasmic ribosomes, which is apparently related to an impairment of ribosomal rRNA precursor processing. Such an event is accounted for by the interaction of Tat with fibrillarin and U3 snoRNA, which are both required for pre-rRNA maturation. Conclusion Our data contribute to understanding the function of Tat in the nucleolus, where ribosomal RNA synthesis and cell cycle control take place. The impairment of nucleolar pre-rRNA maturation through the interaction of Tat with fibrillarin-U3snoRNA complex suggests a process by which the virus modulates host response, thus contributing to apoptosis and protein shut-off in HIV-uninfected cells.
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Affiliation(s)
- Donatella Ponti
- Dipartimento di Biotecnologie Cellulari ed Ematologia, Università La Sapienza, Roma, Italia.
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43
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Friend LR, Han SP, Rothnagel JA, Smith R. Differential subnuclear localisation of hnRNPs A/B is dependent on transcription and cell cycle stage. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2008; 1783:1972-80. [PMID: 18588922 DOI: 10.1016/j.bbamcr.2008.05.021] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2008] [Revised: 05/23/2008] [Accepted: 05/23/2008] [Indexed: 01/31/2023]
Abstract
The heterogeneous nuclear ribonucleoproteins A1, A2/B1 and A3 (hnRNPs A/B) are involved in many nuclear functions that are confined to distinct regions within the nucleus. To characterise and compare the distribution of the hnRNPs A/B in these subnuclear compartments, their colocalisation with spliceosomal components, nascent transcripts and other nuclear markers in HeLa cells was investigated by immunostaining and transfection of GFP constructs. The mechanisms of this localisation were further explored by treating cells with detergent, nucleases and transcription inhibitors. We have also examined the dynamics of A2/B1 throughout the cell cycle. Our results show that hnRNPs A/B have different subnuclear localisations, with A1 differentially localised to the nuclear envelope, and A2/B1 and A3 enriched around nucleoli. This pattern of distribution was dependent on RNA integrity and active transcription. The hnRNPs A/B preferentially colocalised with a subset of splicing factors. Significantly, only rarely did transcription factories colocalise with high levels of these hnRNPs. Moreover, localisation of A2/B1 changed with cell cycle stage. Our findings show that the subnuclear localisation of the hnRNPs A/B is differentially, spatially and temporally regulated, and suggest that this localisation may be relevant to their nuclear functions.
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Affiliation(s)
- Lexie R Friend
- School of Molecular and Microbial Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia
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44
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Peruquetti RL, Assis IM, Taboga SR, de Azeredo-Oliveira MTV. Meiotic nucleolar cycle and chromatoid body formation during the rat (Rattus novergicus) and mouse (Mus musculus) spermiogenesis. Micron 2008; 39:419-25. [PMID: 17512745 DOI: 10.1016/j.micron.2007.02.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2006] [Revised: 02/21/2007] [Accepted: 02/22/2007] [Indexed: 10/23/2022]
Abstract
The aims of the present study were to follow the nucleolar cycle in spermiogenesis of the laboratory rodents Rattus novergicus and Mus musculus, to verify the relationship between the nucleolar component and chromatoid body (CB) formation and to investigate the function of this cytoplasmic supramolecular structure in spermatogenic haploid cells. Histological sections of adult seminiferous tubules were analyzed cytochemically by light microscopy and ultrastructural procedures by transmission electron microscopy. The results reveal that in early spermatids, the CB was visualized in association with the Golgi cisterns indicating that this structure may participate in the acrosome formation process. In late spermatids, the CB was observed near the axonema, a fact suggesting that this structure may support the formation of the spermatozoon tail. In conclusion, our data showed that there is disintegration of spermatid nucleoli at the beginning of spermatogenesis and a fraction of this nucleolar material migrates to the cytoplasm, where a specific structure is formed, known as the "chromatoid body", which, apparently, participates in some parts of the rodent spermiogenesis process.
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Affiliation(s)
- Rita Luiza Peruquetti
- São Paulo State University-UNESP/IBILCE, Department of Biology, Rua Cristóvão Colombo 2265, São José do Rio Preto 15054-000, SP, Brazil
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46
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Boisvert FM, van Koningsbruggen S, Navascués J, Lamond AI. The multifunctional nucleolus. Nat Rev Mol Cell Biol 2007; 8:574-85. [PMID: 17519961 DOI: 10.1038/nrm2184] [Citation(s) in RCA: 1109] [Impact Index Per Article: 65.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The nucleolus is a distinct subnuclear compartment that was first observed more than 200 years ago. Nucleoli assemble around the tandemly repeated ribosomal DNA gene clusters and 28S, 18S and 5.8S ribosomal RNAs (rRNAs) are transcribed as a single precursor, which is processed and assembled with the 5S rRNA into ribosome subunits. Although the nucleolus is primarily associated with ribosome biogenesis, several lines of evidence now show that it has additional functions. Some of these functions, such as regulation of mitosis, cell-cycle progression and proliferation, many forms of stress response and biogenesis of multiple ribonucleoprotein particles, will be discussed, as will the relation of the nucleolus to human diseases.
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MESH Headings
- Animals
- Cell Nucleolus/chemistry
- Cell Nucleolus/genetics
- Cell Nucleolus/metabolism
- Cell Nucleolus/physiology
- Cell Nucleolus/ultrastructure
- DNA, Ribosomal/analysis
- DNA, Ribosomal/biosynthesis
- Fluorescent Dyes
- Humans
- Indoles
- Microscopy, Fluorescence
- Mitosis
- Models, Biological
- Nucleolus Organizer Region/physiology
- Nucleolus Organizer Region/ultrastructure
- RNA Precursors/metabolism
- RNA, Ribosomal/genetics
- RNA, Ribosomal/metabolism
- RNA, Ribosomal, 18S/genetics
- RNA, Ribosomal, 18S/metabolism
- RNA, Ribosomal, 28S/genetics
- RNA, Ribosomal, 28S/metabolism
- RNA, Ribosomal, 5.8S/genetics
- RNA, Ribosomal, 5.8S/metabolism
- RNA, Ribosomal, 5S/biosynthesis
- RNA, Ribosomal, 5S/genetics
- RNA, Small Nucleolar/genetics
- RNA, Small Nucleolar/metabolism
- Ribonucleoproteins/genetics
- Ribonucleoproteins/metabolism
- Ribosomes/genetics
- Ribosomes/metabolism
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47
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48
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Maity TS, Weeks KM. A threefold RNA-protein interface in the signal recognition particle gates native complex assembly. J Mol Biol 2007; 369:512-24. [PMID: 17434535 PMCID: PMC1940241 DOI: 10.1016/j.jmb.2007.03.032] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2006] [Revised: 03/09/2007] [Accepted: 03/10/2007] [Indexed: 11/28/2022]
Abstract
Intermediate states play well-established roles in the folding and misfolding reactions of individual RNA and protein molecules. In contrast, the roles of transient structural intermediates in multi-component ribonucleoprotein (RNP) assembly processes and their potential for misassembly are largely unexplored. The SRP19 protein is unstructured but forms a compact core domain and two extended RNA-binding loops upon binding the signal recognition particle (SRP) RNA. The SRP54 protein subsequently binds to the fully assembled SRP19-RNA complex to form an intimate threefold interface with both SRP19 and the RNA and without significantly altering the structure of SRP19. We show, however, that the presence of SRP54 during SRP19-RNA assembly dramatically alters the folding energy landscape to create a non-native folding pathway that leads to an aberrant SRP19-RNA conformation. The misassembled complex arises from the surprising ability of SRP54 to bind rapidly to an SRP19-RNA assembly intermediate and to interfere with subsequent folding of one of the RNA binding loops at the three-way protein-RNA interface. An incorrect temporal order of assembly thus readily yields a non-native three-component ribonucleoprotein particle. We propose there may exist a general requirement to regulate the order of interaction in multi-component RNP assembly reactions by spatial or temporal compartmentalization of individual constituents in the cell.
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49
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Voltmer-Irsch S, Kneissel S, Adenot PG, Schmidt-Zachmann MS. Regulatory mechanisms governing the oocyte-specific synthesis of the karyoskeletal protein NO145. J Cell Sci 2007; 120:1412-22. [PMID: 17374641 DOI: 10.1242/jcs.000166] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Given the prominence and the biological importance of the nucleus it is remarkable how little is still known about structure-forming proteins in the nuclear interior. The karyoskeletal protein NO145 has been identified as a major constituent of a filamentous network surrounding the amplified nucleoli of Xenopus laevis oocytes. We now show that an orthologous protein also occurs in female germ cells of a wide range of other vertebrates, where it forms dot-like structures. Using the Xenopus oocyte system we further report a specific regulatory mechanism responsible for (1) the rapid degradation of the NO145 protein during meiotic maturation, and (2) the cell-type-dependent translation of NO145 mRNA. Microinjection experiments have revealed that NO145 is a target of proteasomes and the use of the rapid amplification of cDNA ends-polyadenylation test (RACE-PAT) has disclosed the existence of NO145 mRNAs differing in their 3' UTRs. Reporter systems as well as polyribosome profiling experiments have revealed the regulatory importance of the 3' UTRs, which affect the translational efficiency as well as the stability of the encoded protein. The highly conserved cell-type specificity and the extremely tight temporal regulation of NO145 synthesis suggest an important role of this protein in female meiotic prophase.
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50
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Suzuki C, Takahashi K, Hayama S, Ishikawa N, Kato T, Ito T, Tsuchiya E, Nakamura Y, Daigo Y. Identification of Myc-associated protein with JmjC domain as a novel therapeutic target oncogene for lung cancer. Mol Cancer Ther 2007; 6:542-51. [PMID: 17308053 DOI: 10.1158/1535-7163.mct-06-0659] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Through genome-wide expression profile analysis for non-small cell lung cancers (NSCLC), we found overexpression of a Myc-associated protein with JmjC domain (MAPJD) gene in the great majority of NSCLC cases. Induction of exogenous expression of MAPJD into NIH3T3 cells conferred growth-promoting activity. Concordantly, in vitro suppression of MAPJD expression with small interfering RNA effectively suppressed growth of NSCLC cells, in which MAPJD was overexpressed. We found four candidate MAPJD target genes, SBNO1, TGFBRAP1, RIOK1, and RASGEF1A, which were the most significantly induced by exogenous MAPJD expression. Through interaction with MYC protein, MAPJD transactivates a set of genes, including kinases and cell signal transducers that are possibly related to proliferation of lung cancer cells. As our data imply that MAPJD is a novel member of the MYC transcriptional complex and its activation is a common feature of lung cancer, selective suppression of this pathway could be a promising therapeutic target for treatment of lung cancers.
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MESH Headings
- Animals
- Blotting, Northern
- Blotting, Western
- Carcinoma, Non-Small-Cell Lung/metabolism
- Carcinoma, Non-Small-Cell Lung/pathology
- Cell Transformation, Neoplastic
- Cells, Cultured
- Chromatin Immunoprecipitation
- Electrophoretic Mobility Shift Assay
- Flow Cytometry
- Gene Expression Profiling
- Gene Expression Regulation, Neoplastic
- Humans
- Immunoenzyme Techniques
- Immunoprecipitation
- Intracellular Signaling Peptides and Proteins/metabolism
- Lung/metabolism
- Lung Neoplasms/metabolism
- Lung Neoplasms/pathology
- Mice
- NIH 3T3 Cells
- Nuclear Proteins/physiology
- Oligonucleotide Array Sequence Analysis
- Oncogene Proteins/physiology
- Oncogenes/physiology
- Prognosis
- Proto-Oncogene Proteins c-myc/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Small Interfering/pharmacology
- Reverse Transcriptase Polymerase Chain Reaction
- Tissue Array Analysis
- ras Guanine Nucleotide Exchange Factors/metabolism
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Affiliation(s)
- Chie Suzuki
- Laboratory of Molecular Medicine, Human Genome Center, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-Ward, Tokyo 108-8639, Japan
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