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Stroo E, Janssen L, Sin O, Hogewerf W, Koster M, Harkema L, Youssef SA, Beschorner N, Wolters AH, Bakker B, Becker L, Garrett L, Marschall S, Hoelter SM, Wurst W, Fuchs H, Gailus-Durner V, Hrabe de Angelis M, Thathiah A, Foijer F, van de Sluis B, van Deursen J, Jucker M, de Bruin A, Nollen EA. Deletion of SERF2 in mice delays embryonic development and alters amyloid deposit structure in the brain. Life Sci Alliance 2023; 6:e202201730. [PMID: 37130781 PMCID: PMC10155860 DOI: 10.26508/lsa.202201730] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 04/18/2023] [Accepted: 04/18/2023] [Indexed: 05/04/2023] Open
Abstract
In age-related neurodegenerative diseases, like Alzheimer's and Parkinson's, disease-specific proteins become aggregation-prone and form amyloid-like deposits. Depletion of SERF proteins ameliorates this toxic process in worm and human cell models for diseases. Whether SERF modifies amyloid pathology in mammalian brain, however, has remained unknown. Here, we generated conditional Serf2 knockout mice and found that full-body deletion of Serf2 delayed embryonic development, causing premature birth and perinatal lethality. Brain-specific Serf2 knockout mice, on the other hand, were viable, and showed no major behavioral or cognitive abnormalities. In a mouse model for amyloid-β aggregation, brain depletion of Serf2 altered the binding of structure-specific amyloid dyes, previously used to distinguish amyloid polymorphisms in the human brain. These results suggest that Serf2 depletion changed the structure of amyloid deposits, which was further supported by scanning transmission electron microscopy, but further study will be required to confirm this observation. Altogether, our data reveal the pleiotropic functions of SERF2 in embryonic development and in the brain and support the existence of modifying factors of amyloid deposition in mammalian brain, which offer possibilities for polymorphism-based interventions.
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Affiliation(s)
- Esther Stroo
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - Leen Janssen
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - Olga Sin
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
- Graduate Program in Areas of Basic and Applied Biology, Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Wytse Hogewerf
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - Mirjam Koster
- Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Liesbeth Harkema
- Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Sameh A Youssef
- Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
- Department of Pediatrics, Molecular Genetics Section, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - Natalie Beschorner
- Department of Cellular Neurology, Hertie-Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Anouk Hg Wolters
- Department of Biomedical Sciences of Cells and Systems, University Medical Centre Groningen, Groningen, The Netherlands
| | - Bjorn Bakker
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - Lore Becker
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Lilian Garrett
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Susan Marschall
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Sabine M Hoelter
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Technische Universität München, Freising-Weihenstephan, Germany
| | - Wolfgang Wurst
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Chair of Developmental Genetics, TUM School of Life Sciences, Technische Universität München, Freising-Weihenstephan, Germany
- Deutsches Institut für Neurodegenerative Erkrankungen (DZNE) Site Munich, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Adolf-Butenandt-Institut, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Helmut Fuchs
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Valerie Gailus-Durner
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Martin Hrabe de Angelis
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
- Chair of Experimental Genetics, TUM School of Life Sciences, Technische Universität München, Freising, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Amantha Thathiah
- VIB Center for the Biology of Disease, KU Leuven Center for Human Genetics, University of Leuven, Leuven, Belgium
- Department of Neurobiology, University of Pittsburgh Brain Institute, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Floris Foijer
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - Bart van de Sluis
- Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | | | - Matthias Jucker
- Department of Cellular Neurology, Hertie-Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Alain de Bruin
- Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
- Department of Pediatrics, Molecular Genetics Section, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - Ellen Aa Nollen
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
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Hyde L, Osman K, Winfield M, Sanchez‐Moran E, Higgins JD, Henderson IR, Sparks C, Franklin FCH, Edwards KJ. Identification, characterization, and rescue of CRISPR/Cas9 generated wheat SPO11-1 mutants. Plant Biotechnol J 2023; 21:405-418. [PMID: 36373224 PMCID: PMC9884015 DOI: 10.1111/pbi.13961] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 10/31/2022] [Accepted: 11/07/2022] [Indexed: 05/29/2023]
Abstract
Increasing crop yields through plant breeding is time consuming and laborious, with the generation of novel combinations of alleles being limited by chromosomal linkage blocks and linkage-drag. Meiotic recombination is essential to create novel genetic variation via the reshuffling of parental alleles. The exchange of genetic information between homologous chromosomes occurs at crossover (CO) sites but CO frequency is often low and unevenly distributed. This bias creates the problem of linkage-drag in recombination 'cold' regions, where undesirable variation remains linked to useful traits. In plants, programmed meiosis-specific DNA double-strand breaks, catalysed by the SPO11 complex, initiate the recombination pathway, although only ~5% result in the formation of COs. To study the role of SPO11-1 in wheat meiosis, and as a prelude to manipulation, we used CRISPR/Cas9 to generate edits in all three SPO11-1 homoeologues of hexaploid wheat. Characterization of progeny lines shows plants deficient in all six SPO11-1 copies fail to undergo chromosome synapsis, lack COs and are sterile. In contrast, lines carrying a single copy of any one of the three wild-type homoeologues are phenotypically indistinguishable from unedited plants both in terms of vegetative growth and fertility. However, cytogenetic analysis of the edited plants suggests that homoeologues differ in their ability to generate COs and in the dynamics of synapsis. In addition, we show that the transformation of wheat mutants carrying six edited copies of SPO11-1 with the TaSPO11-1B gene, restores synapsis, CO formation, and fertility and hence opens a route to modifying recombination in this agronomically important crop.
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Affiliation(s)
- Lucy Hyde
- School of Biological Sciences, Life SciencesUniversity of BristolBristolUK
| | - Kim Osman
- School of BiosciencesUniversity of BirminghamBirminghamUK
| | - Mark Winfield
- School of Biological Sciences, Life SciencesUniversity of BristolBristolUK
| | | | - James D. Higgins
- Department of Genetics and Genome BiologyUniversity of LeicesterLeicesterUK
| | | | | | | | - Keith J. Edwards
- School of Biological Sciences, Life SciencesUniversity of BristolBristolUK
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3
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Li W, Jiang C, Zhang E. Advances in the phase separation-organized membraneless organelles in cells: a narrative review. Transl Cancer Res 2022; 10:4929-4946. [PMID: 35116344 PMCID: PMC8797891 DOI: 10.21037/tcr-21-1111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 10/29/2021] [Indexed: 11/26/2022]
Abstract
Membraneless organelles (MLOs) are micro-compartments that lack delimiting membranes, concentrating several macro-molecules with a high local concentration in eukaryotic cells. Recent studies have shown that MLOs have pivotal roles in multiple biological processes, including gene transcription, RNA metabolism, translation, protein modification, and signal transduction. These biological processes in cells have essential functions in many diseases, such as cancer, neurodegenerative diseases, and virus-related diseases. The liquid-liquid phase separation (LLPS) microenvironment within cells is thought to be the driving force for initiating the formation of micro-compartments with a liquid-like property, becoming an important organizing principle for MLOs to mediate organism responses. In this review, we comprehensively elucidated the formation of these MLOs and the relationship between biological functions and associated diseases. The mechanisms underlying the influence of protein concentration and valency on phase separation in cells are also discussed. MLOs undergoing the LLPS process have diverse functions, including stimulation of some adaptive and reversible responses to alter the transcriptional or translational processes, regulation of the concentrations of biomolecules in living cells, and maintenance of cell morphogenesis. Finally, we highlight that the development of this field could pave the way for developing novel therapeutic strategies for the treatment of LLPS-related diseases based on the understanding of phase separation in the coming years.
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Affiliation(s)
- Weihan Li
- Department of Immunology, School of Medicine, Nantong University, Nantong, China
| | - Chenwei Jiang
- Department of Immunology, School of Medicine, Nantong University, Nantong, China
| | - Erhao Zhang
- Department of Immunology, School of Medicine, Nantong University, Nantong, China.,Laboratory of Medical Science, School of Medicine, Nantong University, Nantong, China
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4
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Cote JL, Vander PB, Ellis M, Cline JM, Svezhova N, Doche ME, Maures TJ, Choudhury TA, Kong S, Klaft OGJ, Joe RM, Argetsinger LS, Carter-Su C. The nucleolar δ isoform of adapter protein SH2B1 enhances morphological complexity and function of cultured neurons. J Cell Sci 2022; 135:jcs259179. [PMID: 35019135 PMCID: PMC8918807 DOI: 10.1242/jcs.259179] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 12/22/2021] [Indexed: 11/20/2022] Open
Abstract
The adapter protein SH2B1 is recruited to neurotrophin receptors, including TrkB (also known as NTRK2), the receptor for brain-derived neurotrophic factor (BDNF). Herein, we demonstrate that the four alternatively spliced isoforms of SH2B1 (SH2B1α-SH2B1δ) are important determinants of neuronal architecture and neurotrophin-induced gene expression. Primary hippocampal neurons from Sh2b1-/- [knockout (KO)] mice exhibit decreased neurite complexity and length, and BDNF-induced expression of the synapse-related immediate early genes Egr1 and Arc. Reintroduction of each SH2B1 isoform into KO neurons increases neurite complexity; the brain-specific δ isoform also increases total neurite length. Human obesity-associated variants, when expressed in SH2B1δ, alter neurite complexity, suggesting that a decrease or increase in neurite branching may have deleterious effects that contribute to the severe childhood obesity and neurobehavioral abnormalities associated with these variants. Surprisingly, in contrast to SH2B1α, SH2B1β and SH2B1γ, which localize primarily in the cytoplasm and plasma membrane, SH2B1δ resides primarily in nucleoli. Some SH2B1δ is also present in the plasma membrane and nucleus. Nucleolar localization, driven by two highly basic regions unique to SH2B1δ, is required for SH2B1δ to maximally increase neurite complexity and BDNF-induced expression of Egr1, Arc and FosL1.
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Affiliation(s)
- Jessica L. Cote
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Neuroscience Graduate Program, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Paul B. Vander
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Michael Ellis
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Joel M. Cline
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Nadezhda Svezhova
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Michael E. Doche
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Travis J. Maures
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Tahrim A. Choudhury
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Seongbae Kong
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Olivia G. J. Klaft
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Ray M. Joe
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Lawrence S. Argetsinger
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Christin Carter-Su
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Neuroscience Graduate Program, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA
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5
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Zhu Y, Cheng C, Chen L, Zhang L, Pan H, Hou L, Sun Z, Zhang L, Fu X, Chan KY, Zhang J. Cell cycle heterogeneity directs spontaneous 2C state entry and exit in mouse embryonic stem cells. Stem Cell Reports 2021; 16:2659-2673. [PMID: 34624246 PMCID: PMC8580870 DOI: 10.1016/j.stemcr.2021.09.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 09/07/2021] [Accepted: 09/08/2021] [Indexed: 12/01/2022] Open
Abstract
Mouse embryonic stem cells (ESCs) show cell-to-cell heterogeneity. A small number of two-cell-like cells (2CLCs) marked by endogenous retrovirus activation emerge spontaneously. The 2CLCs are unstable and they are prone to transiting back to the pluripotent state without extrinsic stimulus. To understand how this bidirectional transition takes place, we performed single-cell RNA sequencing on isolated 2CLCs that underwent 2C-like state exit and re-entry, and revealed a step-by-step transitional process between 2C-like and pluripotent states. Mechanistically, we found that cell cycle played an important role in mediating these transitions by regulating assembly of the nucleolus and peri-nucleolar heterochromatin to influence 2C gene Dux expression. Collectively, our findings provide a roadmap of the 2C-like state entry and exit in ESCs and also a causal role of the cell cycle in promoting these transitions. The entry to and exit from the 2C-like state showed a step-by-step roadmap Cell cycle participates in mediating dynamic transitions between ESCs and 2CLCs G1/S phase arrest facilitates the Dux locus escape from heterochromatin Nucleolus-heterochromatin remodeling is involved in 2C activation
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Affiliation(s)
- Yuqing Zhu
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Hangzhou, Zhejiang, China; Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Haining, Zhejiang, China
| | - Chen Cheng
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Hangzhou, Zhejiang, China
| | - Lang Chen
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Hangzhou, Zhejiang, China
| | - Li Zhang
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Hangzhou, Zhejiang, China
| | - Hongru Pan
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Hangzhou, Zhejiang, China
| | - Linxiao Hou
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Hangzhou, Zhejiang, China
| | - Zhen Sun
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Hangzhou, Zhejiang, China
| | - Ling Zhang
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Hangzhou, Zhejiang, China; Zhejiang Laboratory for Systems and Precision Medicine, Zhejiang University Medical Center, Hangzhou, Zhejiang, China
| | - Xudong Fu
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Hangzhou, Zhejiang, China; Zhejiang Laboratory for Systems and Precision Medicine, Zhejiang University Medical Center, Hangzhou, Zhejiang, China; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Kuan Yoow Chan
- Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Haining, Zhejiang, China
| | - Jin Zhang
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Hangzhou, Zhejiang, China; Zhejiang Laboratory for Systems and Precision Medicine, Zhejiang University Medical Center, Hangzhou, Zhejiang, China; Institute of Hematology, Zhejiang University, Hangzhou, Zhejiang, China; Center of Gene/Cell Engineering and Genome Medicine, Hangzhou, Zhejiang, China.
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6
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Benc M, Strejcek F, Morovic M, Bartkova A, Murin M, Gad A, Bonnet-Garnier A, Percinic FP, Laurincik J. Improving the Quality of Oocytes with the Help of Nucleolotransfer Therapy. Pharmaceuticals (Basel) 2021; 14:ph14040328. [PMID: 33918523 PMCID: PMC8066131 DOI: 10.3390/ph14040328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 03/26/2021] [Accepted: 03/29/2021] [Indexed: 11/16/2022] Open
Abstract
The nucleolus is an important nucleus sub-organelle found in almost all eukaryotic cells. On the one hand, it is known as a differentiated active site of ribosome biogenesis in somatic cells, but on the other hand, in fully grown oocytes, zygotes, and early embryos (up to the major embryonic genome activation), it is in the form of a particular homogenous and compact structure called a fibrillar sphere. Nowadays, thanks to recent studies, we know many important functions of this, no doubt, interesting membraneless nucleus sub-organelle involved in oocyte maturation, embryonic genome activation, rRNA synthesis, etc. However, many questions are still unexplained and remain a mystery. Our aim is to create a comprehensive overview of the recent knowledge on the fibrillar sphere and envision how this knowledge could be utilized in further research in the field of biotechnology and nucleolotransfer therapy.
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Affiliation(s)
- Michal Benc
- Faculty of Natural Sciences, Constantine the Philosopher University in Nitra, Nabrezie mladeze 91, 94974 Nitra, Slovakia; (M.B.); (M.M.); (A.B.); (J.L.)
| | - Frantisek Strejcek
- Faculty of Natural Sciences, Constantine the Philosopher University in Nitra, Nabrezie mladeze 91, 94974 Nitra, Slovakia; (M.B.); (M.M.); (A.B.); (J.L.)
- Correspondence: ; Tel.: +421-037-6408-584
| | - Martin Morovic
- Faculty of Natural Sciences, Constantine the Philosopher University in Nitra, Nabrezie mladeze 91, 94974 Nitra, Slovakia; (M.B.); (M.M.); (A.B.); (J.L.)
| | - Alexandra Bartkova
- Faculty of Natural Sciences, Constantine the Philosopher University in Nitra, Nabrezie mladeze 91, 94974 Nitra, Slovakia; (M.B.); (M.M.); (A.B.); (J.L.)
- Institute of Animal Physiology and Genetics, The Czech Academy of Sciences, 27721 Libechov, Czech Republic; (M.M.); (A.G.)
| | - Matej Murin
- Institute of Animal Physiology and Genetics, The Czech Academy of Sciences, 27721 Libechov, Czech Republic; (M.M.); (A.G.)
| | - Ahmed Gad
- Institute of Animal Physiology and Genetics, The Czech Academy of Sciences, 27721 Libechov, Czech Republic; (M.M.); (A.G.)
| | - Amelie Bonnet-Garnier
- Université Paris-Saclay, UVSQ, INRAE, BREED, 78350 Jouy-en-Josas, France;
- Ecole Nationale Vétérinaire d’Alfort, BREED, 94700 Maisons-Alfort, France
| | - Florina Popovska Percinic
- Faculty of Veterinary Medicine, St. Cyril and Methodius University in Skopje, 1000 Skopje, North Macedonia;
| | - Jozef Laurincik
- Faculty of Natural Sciences, Constantine the Philosopher University in Nitra, Nabrezie mladeze 91, 94974 Nitra, Slovakia; (M.B.); (M.M.); (A.B.); (J.L.)
- Institute of Animal Physiology and Genetics, The Czech Academy of Sciences, 27721 Libechov, Czech Republic; (M.M.); (A.G.)
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Ogawa LM, Buhagiar AF, Abriola L, Leland BA, Surovtseva YV, Baserga SJ. Increased numbers of nucleoli in a genome-wide RNAi screen reveal proteins that link the cell cycle to RNA polymerase I transcription. Mol Biol Cell 2021; 32:956-973. [PMID: 33689394 PMCID: PMC8108525 DOI: 10.1091/mbc.e20-10-0670] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Nucleoli are dynamic nuclear condensates in eukaryotic cells that originate through ribosome biogenesis at loci that harbor the ribosomal DNA. These loci are known as nucleolar organizer regions (NORs), and there are 10 in a human diploid genome. While there are 10 NORs, however, the number of nucleoli observed in cells is variable. Furthermore, changes in number are associated with disease, with increased numbers and size common in aggressive cancers. In the near-diploid human breast epithelial cell line, MCF10A, the most frequently observed number of nucleoli is two to three per cell. Here, to identify novel regulators of ribosome biogenesis we used high-throughput quantitative imaging of MCF10A cells to identify proteins that, when depleted, increase the percentage of nuclei with ≥5 nucleoli. Unexpectedly, this unique screening approach led to identification of proteins associated with the cell cycle. Functional analysis on a subset of hits further revealed not only proteins required for progression through the S and G2/M phase, but also proteins required explicitly for the regulation of RNA polymerase I transcription and protein synthesis. Thus, results from this screen for increased nucleolar number highlight the significance of the nucleolus in human cell cycle regulation, linking RNA polymerase I transcription to cell cycle progression.
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Affiliation(s)
- Lisa M Ogawa
- Department of Molecular Biophysics & Biochemistry, Yale University School of Medicine, New Haven, CT 06520
| | - Amber F Buhagiar
- Department of Molecular Biophysics & Biochemistry, Yale University School of Medicine, New Haven, CT 06520
| | - Laura Abriola
- Yale Center for Molecular Discovery, Yale University, West Haven, CT 06516
| | - Bryan A Leland
- Yale Center for Molecular Discovery, Yale University, West Haven, CT 06516
| | - Yulia V Surovtseva
- Yale Center for Molecular Discovery, Yale University, West Haven, CT 06516
| | - Susan J Baserga
- Department of Molecular Biophysics & Biochemistry, Yale University School of Medicine, New Haven, CT 06520.,Department of Genetics, Yale University School of Medicine, New Haven, CT 06520.,Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT 06520
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8
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Gallardo P, Real-Calderón P, Flor-Parra I, Salas-Pino S, Daga RR. Acute Heat Stress Leads to Reversible Aggregation of Nuclear Proteins into Nucleolar Rings in Fission Yeast. Cell Rep 2020; 33:108377. [DOI: 10.1016/j.celrep.2020.108377] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Revised: 08/24/2020] [Accepted: 10/21/2020] [Indexed: 12/15/2022] Open
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9
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González-Sanz S, Barreñada O, Rial E, Brieño-Enriquez MA, Del Mazo J. The antiandrogenic vinclozolin induces differentiation delay of germ cells and changes in energy metabolism in 3D cultures of fetal ovaries. Sci Rep 2020; 10:18036. [PMID: 33093579 DOI: 10.1038/s41598-020-75116-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 10/12/2020] [Indexed: 12/14/2022] Open
Abstract
Vinclozolin is a pesticide with antiandrogenic activity as an endocrine disruptor compound. Its effects upon the progression of primordial follicles were assessed in cultures of mouse fetal ovaries from the onset of meiotic differentiation of germ cells (13.5 days post coitum) and from both in vivo exposed mice and in vitro exposed ovaries. Exposure of ovaries to vinclozolin—at in vitro dosages ranging from 10 to 200 μM and in 3D ex vivo culture following in vivo exposure to 50 mg/kg bw/day—showed delays in meiocyte differentiation and in follicle growth, even at the lowest in vitro dose exposure. Immunofluorescent analysis showed the presence of the proteins MSY2 and NOBOX in the primary follicles but no difference in the level of protein signals or in the number of follicles in relation to treatment. However, assessing the cytological differentiation of germ cells by detecting the synaptonemal complex protein SYCP3, the exposure to vinclozolin delayed meiotic differentiation from both in vitro- and in vivo-exposed ovaries. These effects were concomitant with changes in the energy metabolism, detected as a relative increase of glycolytic metabolism in live-cell metabolic assays in exposed ovaries.
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Stenström L, Mahdessian D, Gnann C, Cesnik AJ, Ouyang W, Leonetti MD, Uhlén M, Cuylen‐Haering S, Thul PJ, Lundberg E. Mapping the nucleolar proteome reveals a spatiotemporal organization related to intrinsic protein disorder. Mol Syst Biol 2020; 16:e9469. [PMID: 32744794 PMCID: PMC7397901 DOI: 10.15252/msb.20209469] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 07/02/2020] [Accepted: 07/03/2020] [Indexed: 01/01/2023] Open
Abstract
The nucleolus is essential for ribosome biogenesis and is involved in many other cellular functions. We performed a systematic spatiotemporal dissection of the human nucleolar proteome using confocal microscopy. In total, 1,318 nucleolar proteins were identified; 287 were localized to fibrillar components, and 157 were enriched along the nucleoplasmic border, indicating a potential fourth nucleolar subcompartment: the nucleoli rim. We found 65 nucleolar proteins (36 uncharacterized) to relocate to the chromosomal periphery during mitosis. Interestingly, we observed temporal partitioning into two recruitment phenotypes: early (prometaphase) and late (after metaphase), suggesting phase-specific functions. We further show that the expression of MKI67 is critical for this temporal partitioning. We provide the first proteome-wide analysis of intrinsic protein disorder for the human nucleolus and show that nucleolar proteins in general, and mitotic chromosome proteins in particular, have significantly higher intrinsic disorder level compared to cytosolic proteins. In summary, this study provides a comprehensive and essential resource of spatiotemporal expression data for the nucleolar proteome as part of the Human Protein Atlas.
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Affiliation(s)
- Lovisa Stenström
- Science for Life LaboratorySchool of Engineering Sciences in Chemistry, Biotechnology and HealthKTH Royal Institute of TechnologyStockholmSweden
| | - Diana Mahdessian
- Science for Life LaboratorySchool of Engineering Sciences in Chemistry, Biotechnology and HealthKTH Royal Institute of TechnologyStockholmSweden
| | - Christian Gnann
- Science for Life LaboratorySchool of Engineering Sciences in Chemistry, Biotechnology and HealthKTH Royal Institute of TechnologyStockholmSweden
- Chan Zuckerberg BiohubSan FranciscoCAUSA
| | - Anthony J Cesnik
- Chan Zuckerberg BiohubSan FranciscoCAUSA
- Department of GeneticsStanford UniversityStanfordCAUSA
| | - Wei Ouyang
- Science for Life LaboratorySchool of Engineering Sciences in Chemistry, Biotechnology and HealthKTH Royal Institute of TechnologyStockholmSweden
| | | | - Mathias Uhlén
- Science for Life LaboratorySchool of Engineering Sciences in Chemistry, Biotechnology and HealthKTH Royal Institute of TechnologyStockholmSweden
| | - Sara Cuylen‐Haering
- Cell Biology and Biophysics UnitEuropean Molecular Biology LaboratoryHeidelbergGermany
| | - Peter J Thul
- Science for Life LaboratorySchool of Engineering Sciences in Chemistry, Biotechnology and HealthKTH Royal Institute of TechnologyStockholmSweden
| | - Emma Lundberg
- Science for Life LaboratorySchool of Engineering Sciences in Chemistry, Biotechnology and HealthKTH Royal Institute of TechnologyStockholmSweden
- Chan Zuckerberg BiohubSan FranciscoCAUSA
- Department of GeneticsStanford UniversityStanfordCAUSA
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Shim MS, Nettesheim A, Hirt J, Liton PB. The autophagic protein LC3 translocates to the nucleus and localizes in the nucleolus associated to NUFIP1 in response to cyclic mechanical stress. Autophagy 2020; 16:1248-1261. [PMID: 31476975 PMCID: PMC7469449 DOI: 10.1080/15548627.2019.1662584] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 08/18/2019] [Accepted: 08/28/2019] [Indexed: 12/19/2022] Open
Abstract
The trabecular meshwork (TM) is a key regulatory tissue of intraocular pressure (IOP) in the anterior chamber of eye. Dysfunction of the TM causes resistance to outflow of aqueous humor, which in turn leads to elevated IOP, a main risk factor of glaucomatous neurodegeneration. Due to variations in IOP, TM cells are continuously exposed to mechanical deformations. We previously reported activation of macroautophagy/autophagy, as one of the physiological responses elicited in TM cells following mechanical strain application. By using biochemical fractionation analysis and imaging techniques, we demonstrate here for the first time the nuclear accumulation of the autophagic marker MAP1LC3/LC3 (microtubule associated protein1 light chain 3)-II, endogenous and exogenously added (AdGFP-LC3, AdtfLC3), in response to cyclic mechanical stress (CMS). Wheat germ agglutinin (WGA) and leptomycin B treatment suggest LC3 to enter the nucleus by passive diffusion, but to exit in an XPO1/CRM1 (exportin 1)-dependent manner in human TM (hTM) cells. While blockage of nuclear export leads to accumulation of LC3 with promyelocytic leukemia (PML) bodies, nuclear LC3 localizes in the nucleolus in cells under CMS. Moreover, nuclear LC3 co-immunoprecipitated with NUFIP1, a ribosome receptor for starvation-induced ribophagy. More interestingly, we further demonstrate that NUFIP1 translocates from the nucleus to LAMP2 (lysosomal associated membrane protein 2)-positive organelles in the stretched cells without triggering ribophagy, suggesting a more general role of NUFIP1 as a selective autophagy receptor for another yet-to-be-identified target in CMS and a surveillance role of nuclear LC3 against stretch-induced damage. ABBREVIATION AdGFP: adenovirus encoding GFP; ATG: autophagy-related; BSA: bovine serum albumin; CMS: cyclic mechanical stretch; Co-IP: coimmunoprecipitation; DAPI: 4',6-diamidino-2-phenylindole; DFCs: dense fibrillar components; EM: electron microscopy; FCs: fibrillar centers; GCs: granular components; GFP: green fluorescent protein; hTM: human trabecular meshwork; HBSS: Hanks balanced salt solution; IOP: intraocular pressure; LAMP1/2: lysosomal associated membrane protein 1/2; LepB: leptomycin B; MTOR: mechanistic target of rapamacyin kinase; NES: nuclear export signals; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; NLS: nuclear localization signal; NPCs: nuclear pore complexes; NUFIP1: nuclear FMR1 interacting protein 1; NS: non-stretched; PBS: phosphate-buffered saline; PE: phosphatidylethanolamine; pfu: plaque-forming units; PML: promyelocytic leukemia; RFP: red fluorescent protein; RPS15A: ribosomal protein S15a; RPL26: ribosomal protein L26; rRNA: ribosomal RNA; SIRT1: sirtuin 1; SQSTM1/p62: sequestosome 1; tfLC3: mRFP-GFP tandem fluorescent-tagged LC3; TM: trabecular meshwork; WB: western blot; WDR36: WD repeat domain 36; WGA: wheat germ agglutinin; XPO1/CRM1: exportin 1.
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Affiliation(s)
- Myoung Sup Shim
- Department of Ophthalmology, Duke Eye Center, Duke University, Durham, NC, USA
| | - April Nettesheim
- Department of Ophthalmology, Duke Eye Center, Duke University, Durham, NC, USA
| | - Joshua Hirt
- Department of Ophthalmology, Duke Eye Center, Duke University, Durham, NC, USA
| | - Paloma B. Liton
- Department of Ophthalmology, Duke Eye Center, Duke University, Durham, NC, USA
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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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O'Day DH. Proteins of the Nucleolus of Dictyostelium discoideum: Nucleolar Compartmentalization, Targeting Sequences, Protein Translocations and Binding Partners. Cells 2019; 8:E167. [PMID: 30781559 DOI: 10.3390/cells8020167] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 02/13/2019] [Accepted: 02/15/2019] [Indexed: 12/31/2022] Open
Abstract
The nucleoli of Dictyostelium discoideum have a comparatively unique, non-canonical, localization adjacent to the inner nuclear membrane. The verified nucleolar proteins of this eukaryotic microbe are detailed while other potential proteins are introduced. Heat shock protein 32 (Hsp32), eukaryotic translation initiation factor 6 (eIF6), and tumour necrosis factor receptor-associated protein 1 (TRAP1) are essential for cell survival. NumA1, a breast cancer type 1 susceptibility protein-C Terminus domain-containing protein linked to cell cycle, functions in the regulation of nuclear number. The cell cycle checkpoint kinase 2 homologue forkhead-associated kinase A (FhkA) and BRG1-associated factor 60a homologue Snf12 are also discussed. While nucleoli appear homogeneous ultrastructurally, evidence for nucleolar subcompartments exists. Nucleolar localization sequences (NoLS) have been defined that target proteins to either the general nucleolar area or to a specific intranucleolar domain. Protein translocations during mitosis are protein-specific and support the multiple functions of the Dictyostelium nucleolus. To enrich the picture, binding partners of NumA1, the most well-characterized nucleolar protein, are examined: nucleolar Ca2+-binding protein 4a (CBP4a), nuclear puromycin-sensitive aminopeptidase A (PsaA) and Snf12. The role of Dictyostelium as a model for understanding the contribution of nucleolar proteins to various diseases and cellular stress is discussed throughout the review.
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Chen L, Jiao Y, Guan X, Li X, Feng Y, Jiao M. Investigation of cell cycle-associated structural reorganization in nucleolar FC/DFCs from mouse MFC cells by electron microscopy. Microscopy (Oxf) 2018; 67:4994513. [PMID: 29750255 DOI: 10.1093/jmicro/dfy020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 04/08/2018] [Indexed: 11/14/2022] Open
Abstract
Nucleolus structure alters as the cell cycle is progressing. It is established in telophase, maintained throughout the entire interphase and disassembled in metaphase. Fibrillar centers (FCs), dense fibrillar components (DFCs) and granular components (GCs) are essential nucleolar organizations where rRNA transcription and processing and ribosome assembly take place. Hitherto, little is known about the cell cycle-dependent reorganization of these structures. In this study, we followed the nucleolus structure during the cell cycle by electron microscopy (EM). We found the nucleolus experienced multiple rounds of structural reorganization within a single cell cycle: (1) when nucleoli are formed during the transition from late M to G1 phase, FCs, DFCs and GCs are constructed, leading to the establishment of tripartite nucleolus; (2) as FC/DFCs are disrupted at mid-G1, tripartite nucleolus is gradually changed into a bipartite organization; (3) at late G1, the reassembly of FC/DFCs results in a structural transition from bipartite nucleolus towards tripartite nucleolus; (4) as cells enter S phase, FC/DFCs are disassembled again and tripartite nucleolus is thus changed into a bipartite organization. Of note, FC/DFCs were not observed until late S phase; (5) FC/DFCs experience structural disruption and restoration during G2 and (6) when cells are at mitotic stage, FC/DFCs disappear before nucleolus structure is disassembled. These results also suggest that bipartite nucleolus can exist in higher eukaryotes at certain period of the cell cycle. As structures are the fundamental basis of diverse cell activities, unveiling the structural reorganization of nucleolar FCs and DFCs may bring insights into the spatial-temporal compartmentalization of relevant cellular functions.
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Affiliation(s)
- Lingling Chen
- School of Life Sciences, Northeast Normal University, Changchun, Jilin Province 130024, China
| | - Yang Jiao
- School of Physical Education, Northeast Normal University, Changchun, Jilin Province 130024, China
| | - Xin Guan
- School of Life Sciences, Northeast Normal University, Changchun, Jilin Province 130024, China
| | - Xiliang Li
- School of Life Sciences, Northeast Normal University, Changchun, Jilin Province 130024, China
| | - Yunpeng Feng
- School of Life Sciences, Northeast Normal University, Changchun, Jilin Province 130024, China
- The Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE), Northeast Normal University, Changchun, Jilin Province 130024, China
| | - Mingda Jiao
- School of Life Sciences, Northeast Normal University, Changchun, Jilin Province 130024, China
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Donizy P, Biecek P, Halon A, Maciejczyk A, Matkowski R. Nucleoli cytomorphology in cutaneous melanoma cells - a new prognostic approach to an old concept. Diagn Pathol 2017; 12:88. [PMID: 29284501 DOI: 10.1186/s13000-017-0675-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2017] [Accepted: 12/08/2017] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND The nucleolus is an organelle that is an ultrastructural element of the cell nucleus observed in H&E staining as a roundish body stained with eosin due to its high protein content. Changes in the nucleoli cytomorphology were one of the first histopathological characteristics of malignant tumors. The aim of this study was to assess the relationship between the cytomorphological characteristics of nucleoli and detailed clinicopathological parameters of melanoma patients. Moreover, we analyzed the correlation between cytomorphological parameters of nucleoli and immunoreactivity of selected proteins responsible for, among others, regulation of epithelial-mesenchymal transition (SPARC, N-cadherin), cell adhesion and motility (ALCAM, ADAM-10), mitotic divisions (PLK1), cellular survival (FOXP1) and the functioning of Golgi apparatus (GOLPH3, GP73). METHODS Three characteristics of nucleoli - presence, size and number - of cancer cells were assessed in H&E-stained slides of 96 formalin-fixed paraffin-embedded primary cutaneous melanoma tissue specimens. The results were correlated with classical clinicopathological features and patient survival. Immunohistochemical analysis of the above mentioned proteins was described in details in previous studies. RESULTS Higher prevalence and size of nucleoli were associated with thicker and mitogenic tumors. All three nucleolar characteristics were related to the presence of ulceration. Moreover, microsatellitosis was strongly correlated with the presence of macronucleoli and polynucleolization (presence of two or more nucleoli). Lack of immunologic response manifested as no TILs in primary tumor was associated with high prevalence of melanoma cells with distinct nucleoli. Interestingly, in nodular melanoma a higher percentage of melanoma cells with prominent nucleoli was observed. In Kaplan-Meier analysis, increased prevalence and amount, but not size of nucleoli, were connected with shorter cancer-specific and disease-free survival. CONCLUSION (1) High representation of cancer cells with distinct nucleoli, greater size and number of nucleoli per cell are characteristics of aggressive phenotype of melanoma; (2) higher prevalence and size of nucleoli are potential measures of cell kinetics that are strictly correlated with high mitotic rate; and (3) high prevalence of cancer cells with distinct nucleoli and presence of melanocytes with multiple nucleoli are features associated with unfavorable prognosis in patients with cutaneous melanoma.
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de Los Santos-Velázquez AI, de Oya IG, Manzano-López J, Monje-Casas F. Late rDNA Condensation Ensures Timely Cdc14 Release and Coordination of Mitotic Exit Signaling with Nucleolar Segregation. Curr Biol 2017; 27:3248-3263.e5. [PMID: 29056450 DOI: 10.1016/j.cub.2017.09.028] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 08/16/2017] [Accepted: 09/13/2017] [Indexed: 12/28/2022]
Abstract
The nucleolus plays a pivotal role in multiple key cellular processes. An illustrative example is the regulation of mitotic exit in Saccharomyces cerevisiae through the nucleolar sequestration of the Cdc14 phosphatase. The peculiar structure of the nucleolus, however, has also its drawbacks. The repetitive nature of the rDNA gives rise to cohesion-independent linkages whose resolution in budding yeast requires the Cdc14-dependent inhibition of rRNA transcription, which facilitates condensin accessibility to this locus. Thus, the rDNA condenses and segregates later than most other yeast genomic regions. Here, we show that defective function of a small nucleolar ribonucleoprotein particle (snoRNP) assembly factor facilitates condensin accessibility to the rDNA and induces nucleolar hyper-condensation. Interestingly, this increased compaction of the nucleolus interferes with the proper release of Cdc14 from this organelle. This observation provides an explanation for the delayed rDNA condensation in budding yeast, which is necessary to efficiently coordinate timely Cdc14 release and mitotic exit with nucleolar compaction and segregation.
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Affiliation(s)
- Ana Isabel de Los Santos-Velázquez
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Spanish National Research Council (CSIC), University of Seville, and University Pablo de Olavide, Avda. Américo Vespucio 24, 41092 Sevilla, Spain
| | - Inés G de Oya
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Spanish National Research Council (CSIC), University of Seville, and University Pablo de Olavide, Avda. Américo Vespucio 24, 41092 Sevilla, Spain
| | - Javier Manzano-López
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Spanish National Research Council (CSIC), University of Seville, and University Pablo de Olavide, Avda. Américo Vespucio 24, 41092 Sevilla, Spain
| | - Fernando Monje-Casas
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Spanish National Research Council (CSIC), University of Seville, and University Pablo de Olavide, Avda. Américo Vespucio 24, 41092 Sevilla, Spain.
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17
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Staněk D, Fox AH. Nuclear bodies: news insights into structure and function. Curr Opin Cell Biol 2017; 46:94-101. [PMID: 28577509 DOI: 10.1016/j.ceb.2017.05.001] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 04/20/2017] [Accepted: 05/10/2017] [Indexed: 02/07/2023]
Abstract
The cell nucleus contains a number of different dynamic bodies that are variously composed of proteins and generally, but not always, specific RNA molecules. Recent studies have revealed new understanding about nuclear body formation and function in different aspects of nuclear metabolism. Here, we focus on findings describing the role of nuclear bodies in the biogenesis of specific ribonucleoprotein complexes, processing of key mRNAs, and subnuclear sequestration of protein factors. We highlight how nuclear bodies are involved in stress responses, innate immunity and tumorigenesis. We further review organization of nuclear bodies and principles that govern their assembly, highlighting the pivotal role of scaffolding noncoding RNAs, and liquid-liquid phase separation, which are transforming our picture of nuclear body formation.
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Affiliation(s)
- David Staněk
- Institute of Molecular Genetics, Czech Academy of Sciences, Prague, Czech Republic
| | - Archa H Fox
- School of Human Sciences and Molecular Sciences, The University of Western Australia and Harry Perkins Institute of Medical Research, Centre for Medical Research, The University of Western Australia, Crawley, 6009 Western Australia, Australia.
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18
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Perez AM, Finnigan GC, Roelants FM, Thorner J. Septin-Associated Protein Kinases in the Yeast Saccharomyces cerevisiae. Front Cell Dev Biol 2016; 4:119. [PMID: 27847804 PMCID: PMC5088441 DOI: 10.3389/fcell.2016.00119] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2016] [Accepted: 10/14/2016] [Indexed: 01/19/2023] Open
Abstract
Septins are a family of eukaryotic GTP-binding proteins that associate into linear rods, which, in turn, polymerize end-on-end into filaments, and further assemble into other, more elaborate super-structures at discrete subcellular locations. Hence, septin-based ensembles are considered elements of the cytoskeleton. One function of these structures that has been well-documented in studies conducted in budding yeast Saccharomyces cerevisiae is to serve as a scaffold that recruits regulatory proteins, which dictate the spatial and temporal control of certain aspects of the cell division cycle. In particular, septin-associated protein kinases couple cell cycle progression with cellular morphogenesis. Thus, septin-containing structures serve as signaling platforms that integrate a multitude of signals and coordinate key downstream networks required for cell cycle passage. This review summarizes what we currently understand about how the action of septin-associated protein kinases and their substrates control information flow to drive the cell cycle into and out of mitosis, to regulate bud growth, and especially to direct timely and efficient execution of cytokinesis and cell abscission. Thus, septin structures represent a regulatory node at the intersection of many signaling pathways. In addition, and importantly, the activities of certain septin-associated protein kinases also regulate the state of organization of the septins themselves, creating a complex feedback loop.
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Affiliation(s)
- Adam M Perez
- Division of Biochemistry, Biophysics and Structural Biology, Department of Molecular and Cell Biology, University of California, Berkeley Berkeley, CA, USA
| | - Gregory C Finnigan
- Division of Biochemistry, Biophysics and Structural Biology, Department of Molecular and Cell Biology, University of California, Berkeley Berkeley, CA, USA
| | - Françoise M Roelants
- Division of Biochemistry, Biophysics and Structural Biology, Department of Molecular and Cell Biology, University of California, Berkeley Berkeley, CA, USA
| | - Jeremy Thorner
- Division of Biochemistry, Biophysics and Structural Biology, Department of Molecular and Cell Biology, University of California, Berkeley Berkeley, CA, USA
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19
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Derenzini M, Pasquinelli G, O'Donohue MF, Ploton D, Thiry M. Structural and Functional Organization of Ribosomal Genes within the Mammalian Cell Nucleolus. J Histochem Cytochem 2016; 54:131-45. [PMID: 16204224 DOI: 10.1369/jhc.5r6780.2005] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Data on the in situ structural–functional organization of ribosomal genes in the mammalian cell nucleolus are reviewed here. Major findings on chromatin structure in situ come from investigations carried out using the Feulgen-like osmium ammine reaction as a highly specific electron-opaque DNA tracer. Intranucleolar chromatin shows three different levels of organization: compact clumps, fibers ranging from 11 to 30 nm, and loose agglomerates of extended DNA filaments. Both clumps and fibers of chromatin exhibit a nucleosomal organization that is lacking in the loose agglomerates of extended DNA filaments. In fact, these filaments constantly show a thickness of 2–3 nm, the same as a DNA doublehelix molecule. The loose agglomerates of DNA filaments are located in the fibrillar centers, the interphase counterpart of metaphase NORs, therefore being constituted by ribosomal DNA. The extended, non-nucleosomal configuration of this rDNA has been shown to be independent of transcriptional activity and characterizes ribosome genes that are either transcribed or transcriptionally silent. Data reviewed are consistent with a model of control for ribosome gene activity that is not mediated by changes in chromatin structure. The presence of rDNA in mammalian cells always structurally ready for transcription might facilitate a more rapid adjustment of the ribosome production in response to the metabolic needs of the cell.
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Affiliation(s)
- Massimo Derenzini
- Dipartimento di Patologia Sperimentale, Via S. Giacomo 14, 40126 Bologna, Italy.
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20
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Li M, Liu D, Wang L, Wang W, Wang A, Yao Y. Expression of placenta-specific 8 in human oocytes, embryos, and models of in vitro implantation. Fertil Steril 2016; 106:781-789.e2. [PMID: 27322877 DOI: 10.1016/j.fertnstert.2016.05.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2016] [Revised: 05/12/2016] [Accepted: 05/23/2016] [Indexed: 12/11/2022]
Abstract
OBJECTIVE To determine whether placenta-specific 8 (PLAC8) is expressed in human oocytes and embryos, and whether PLAC8 interferes with the implantation process. DESIGN Experimental. SETTING Academic medical assisted reproduction center. PATIENT(S) Couples undergoing in vitro fertilization and embryo transfer (IVF-ET) cycles. INTERVENTION(S) Quantitative polymerase chain reaction (qPCR), immunofluorescence on oocytes, embryos, control LoVo cells, and embryo-endometrial stromal cell coculture models, and Western blot on control LoVo cells. MAIN OUTCOME MEASURE(S) Detection of PLAC8 mRNA in three oocytes, nine cleavaged embryos, three morulae, and three blastocysts, and detection of PLAC8 protein expression pattern in 12 oocytes, 16 cleavaged embryos, 7 morulae, and 18 blastocysts and in 25 hatched blastocyst-endometrial stromal cell coculture models. RESULT(S) Single oocyte/embryo qPCR revealed PLAC8 mRNA expression was only identified in morulae and blastocysts and not in earlier stages. The immunofluorescence assay confirmed the presence of PLAC8 protein in the cytoplasm of all human oocytes and embryos preceding implantation. PLAC8 protein was transported into the nucleolus after blastocyst implantation and invasion into endometrial stromal cells. CONCLUSION(S) Our data have demonstrated for the first time that human oocytes and preimplantation embryos express PLAC8 and that the intracellular distribution of PLAC8 protein is dynamic and regulated in an implantation-dependent manner. These findings indicate that PLAC8 plays a potential role in embryo development and implantation.
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Affiliation(s)
- Min Li
- Department of Obstetrics and Gynecology, Chinese PLA General Hospital and Chinese PLA Medical School, Beijing, People's Republic of China; Department of Obstetrics and Gynecology, Navy General Hospital of the Chinese PLA, Beijing, People's Republic of China
| | - Dong Liu
- Department of Obstetrics and Gynecology, Navy General Hospital of the Chinese PLA, Beijing, People's Republic of China
| | - Li Wang
- Department of Obstetrics and Gynecology, Chinese PLA General Hospital and Chinese PLA Medical School, Beijing, People's Republic of China
| | - Weizhou Wang
- Department of Obstetrics and Gynecology, Navy General Hospital of the Chinese PLA, Beijing, People's Republic of China
| | - Aiming Wang
- Department of Obstetrics and Gynecology, Navy General Hospital of the Chinese PLA, Beijing, People's Republic of China
| | - Yuanqing Yao
- Department of Obstetrics and Gynecology, Chinese PLA General Hospital and Chinese PLA Medical School, Beijing, People's Republic of China.
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21
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Gizak A, Grenda M, Mamczur P, Wisniewski J, Sucharski F, Silberring J, McCubrey JA, Wisniewski JR, Rakus D. Insulin/IGF1-PI3K-dependent nucleolar localization of a glycolytic enzyme--phosphoglycerate mutase 2, is necessary for proper structure of nucleolus and RNA synthesis. Oncotarget 2016; 6:17237-50. [PMID: 26033454 PMCID: PMC4627304 DOI: 10.18632/oncotarget.4044] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 04/30/2015] [Indexed: 12/31/2022] Open
Abstract
Phosphoglycerate mutase (PGAM), a conserved, glycolytic enzyme has been found in nucleoli of cancer cells. Here, we present evidence that accumulation of PGAM in the nucleolus is a universal phenomenon concerning not only neoplastically transformed but also non-malignant cells. Nucleolar localization of the enzyme is dependent on the presence of the PGAM2 (muscle) subunit and is regulated by insulin/IGF-1–PI3K signaling pathway as well as drugs influencing ribosomal biogenesis. We document that PGAM interacts with several 40S and 60S ribosomal proteins and that silencing of PGAM2 expression results in disturbance of nucleolar structure, inhibition of RNA synthesis and decrease of the mitotic index of squamous cell carcinoma cells. We conclude that presence of PGAM in the nucleolus is a prerequisite for synthesis and initial assembly of new pre-ribosome subunits.
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Affiliation(s)
- Agnieszka Gizak
- Department of Animal Molecular Physiology, Wroclaw University, Cybulskiego, Wroclaw, Poland
| | - Marcin Grenda
- Department of Animal Molecular Physiology, Wroclaw University, Cybulskiego, Wroclaw, Poland
| | - Piotr Mamczur
- Department of Animal Molecular Physiology, Wroclaw University, Cybulskiego, Wroclaw, Poland
| | - Janusz Wisniewski
- Department of Animal Molecular Physiology, Wroclaw University, Cybulskiego, Wroclaw, Poland
| | - Filip Sucharski
- Department of Biochemistry and Neurobiology, Faculty of Materials Science and Ceramics, AGH University of Science and Technology, Kraków, Poland
| | - Jerzy Silberring
- Department of Biochemistry and Neurobiology, Faculty of Materials Science and Ceramics, AGH University of Science and Technology, Kraków, Poland
| | - James A McCubrey
- Department of Microbiology and Immunology, Brody School of Medicine at East Carolina University, Greenville, NC, USA
| | - Jacek R Wisniewski
- Biochemical Proteomics Group, Department of Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry, Martinsried, Germany
| | - Dariusz Rakus
- Department of Animal Molecular Physiology, Wroclaw University, Cybulskiego, Wroclaw, Poland
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22
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Maugeri G, D'Amico AG, Reitano R, Saccone S, Federico C, Cavallaro S, D'Agata V. Parkin modulates expression of HIF-1α and HIF-3α during hypoxia in gliobastoma-derived cell lines in vitro. Cell Tissue Res 2016; 364:465-474. [PMID: 26742768 DOI: 10.1007/s00441-015-2340-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Revised: 11/28/2015] [Accepted: 12/02/2015] [Indexed: 12/11/2022]
Abstract
Mutation of the Parkin gene causes an autosomal recessive juvenile-onset form of Parkinson's disease. However, recently, it has been also linked to a wide variety of malignancies, including glioblastoma multiforme (GBM). In this pathology, Parkin exhibits a tumor suppressor role by mitigating the proliferation rate in both in vitro and in vivo models. However, Parkin involvement in the hypoxic process has not as yet been investigated. GBM is the most common and aggressive primary brain tumor in adults and is characterized by hypoxic areas. The low oxygen supply causes the expression of hypoxia-inducible factors (HIFs) leading to an accumulation of pro-angiogenic factors and tumoral invasiveness. We assess the relationship between Parkin and two HIFs expressed during hypoxic conditions, namely HIF-1α and HIF-3α. Our data show that Parkin is downregulated under hypoxia and that it interferes with HIF expression based on cellular oxygen tension. These results suggest a role for the involvement of Parkin in GBM, although further studies will be needed to understand the mechanism by which it modulates HIF-1α and HIF-3α expression.
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Affiliation(s)
- Grazia Maugeri
- Sections of Human Anatomy and Histology, Department of Biomedical and Biotechnological Sciences, University of Catania, Via S.Sofia 87, 95123, Catania, Italy
| | - Agata Grazia D'Amico
- Sections of Human Anatomy and Histology, Department of Biomedical and Biotechnological Sciences, University of Catania, Via S.Sofia 87, 95123, Catania, Italy
- San Raffaele Telematic University of Rome, Rome, Italy
| | - Rita Reitano
- Sections of Human Anatomy and Histology, Department of Biomedical and Biotechnological Sciences, University of Catania, Via S.Sofia 87, 95123, Catania, Italy
| | - Salvatore Saccone
- Section of Animal Biology, Department of Biological, Geological and Environmental Sciences, University of Catania, Catania, Italy
| | - Concetta Federico
- Section of Animal Biology, Department of Biological, Geological and Environmental Sciences, University of Catania, Catania, Italy
| | - Sebastiano Cavallaro
- Functional Genomics Unit, Institute of Neurological Sciences, Italian National Research Council, Catania, Italy
| | - Velia D'Agata
- Sections of Human Anatomy and Histology, Department of Biomedical and Biotechnological Sciences, University of Catania, Via S.Sofia 87, 95123, Catania, Italy.
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23
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Farhane Z, Bonnier F, Casey A, Maguire A, O'Neill L, Byrne HJ. Cellular discrimination using in vitro Raman micro spectroscopy: the role of the nucleolus. Analyst 2015. [DOI: 10.1039/c5an01157d] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Raman micro spectroscopy is employed to discriminate between cell lines. Results show the importance of the nuclear sub-cellular organelle, the nucleoli, to differentiate between cancer cell lines with high specificity and sensitivity.
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Affiliation(s)
- Z. Farhane
- FOCAS Research Institute
- Dublin Institute of Technology
- Dublin 8
- Ireland
| | - F. Bonnier
- Université François-Rabelais de Tours
- Faculty of Pharmacy
- 37200 Tours
- France
| | - A. Casey
- FOCAS Research Institute
- Dublin Institute of Technology
- Dublin 8
- Ireland
| | - A. Maguire
- FOCAS Research Institute
- Dublin Institute of Technology
- Dublin 8
- Ireland
| | - L. O'Neill
- FOCAS Research Institute
- Dublin Institute of Technology
- Dublin 8
- Ireland
| | - H. J. Byrne
- FOCAS Research Institute
- Dublin Institute of Technology
- Dublin 8
- Ireland
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24
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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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25
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Rajanala K, Sarkar A, Jhingan GD, Priyadarshini R, Jalan M, Sengupta S, Nandicoori VK. Phosphorylation of nucleoporin Tpr governs its differential localization and is required for its mitotic function. J Cell Sci 2014; 127:3505-20. [PMID: 24938596 DOI: 10.1242/jcs.149112] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
A major constituent of the nuclear basket region of the nuclear pore complex (NPC), nucleoporin Tpr, plays roles in regulating multiple important processes. We have previously established that Tpr is phosphorylated in both a MAP-kinase-dependent and MAP-kinase-independent manner, and that Tpr acts as both a substrate and as a scaffold for ERK2 (also known as MAPK1). Here, we report the identification of S2059 and S2094 as the major novel ERK-independent phosphorylation sites and T1677, S2020, S2023 and S2034 as additional ERK-independent phosphorylation sites found in the Tpr protein in vivo. Our results suggest that protein kinase A phosphorylates the S2094 residue and that the site is hyperphosphorylated during mitosis. Furthermore, we find that Tpr is phosphorylated at the S2059 residue by CDK1 and the phosphorylated form distinctly localizes with chromatin during telophase. Abrogation of S2059 phosphorylation abolishes the interaction of Tpr with Mad1, thus compromising the localization of both Mad1 and Mad2 proteins, resulting in cell cycle defects. The identification of novel phosphorylation sites on Tpr and the observations presented in this study allow better understanding of Tpr functions.
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Affiliation(s)
- Kalpana Rajanala
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110 067, India
| | - Anshuk Sarkar
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110 067, India
| | - Gagan Deep Jhingan
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110 067, India
| | - Raina Priyadarshini
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110 067, India
| | - Manisha Jalan
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110 067, India
| | - Sagar Sengupta
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110 067, India
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26
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Abstract
The nucleolus is a multifunctional organelle with multiple roles involving cell proliferation, growth, survival, ribosome biogenesis and stress response signaling. Alteration of nucleolar morphology and architecture signifies an early response to increased cellular stress. This review briefly summarizes nucleolar response to cardiac stress signals and details the role played by nucleolar proteins in cardiovascular pathophysiology. This article is part of a Special Issue entitled: Role of the Nucleolus in Human Disease.
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Affiliation(s)
- Nirmala Hariharan
- Department of Biology, San Diego State University Heart Institute, San Diego State University, San Diego, CA 92182, USA
| | - Mark A Sussman
- Department of Biology, San Diego State University Heart Institute, San Diego State University, San Diego, CA 92182, USA.
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27
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Ge XH, Ding L, Li ZY. Nucleolar dominance and different genome behaviors in hybrids and allopolyploids. Plant Cell Rep 2013; 32:1661-73. [PMID: 23864197 DOI: 10.1007/s00299-013-1475-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Accepted: 07/01/2013] [Indexed: 05/05/2023]
Abstract
Many plants are allopolyploids with different nuclear genomes from two or more progenitors, but cytoplasmic genomes typically inherited from the female parent. The importance of this speciation mechanism has stimulated the extensive investigations of genetic consequences of genome mergers in several experimental systems during last 20 years. The dynamic nature of polyploid genomes is recognized, and widespread changes to gene expression are revealed by transcriptomic analysis. These progresses show different stabilities of parental genomes and their unequal contributions to the transcriptome, proteome, and phenotype. We review the results in systems where extensive genetic analyses have been conducted and propose possible mechanisms for biased behavior of parental genomes in allopolyploids, including the role of nucleolar dominance. It is hypothesized that the novel ribosomes with rRNAs from uniparental genome and the ribosomal proteins of biparental origins have some impacts on the biased cellular and genetic behaviors of parental genomes in hybrids and allopolyploids.
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Affiliation(s)
- Xian-Hong Ge
- National Key Lab of Crop Genetic Improvement, College of Plant Science and Technology, National Center of Crop Molecular Breeding, National Center of Oil Crop Improvement (Wuhan), Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
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28
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Abstract
Environmental signals, such heat shock and acidosis, induce a structural and functional remodeling of the nucleolus. This process, which depends on the expression of intergenic long noncoding RNA, reversibly converts the nucleolus from a transcriptionally active ribosome factory into a transcriptionally inert prison for proteins. The nucleolus is a plurifunctional organelle in which structure and function are intimately linked. Its structural plasticity has long been appreciated, particularly in response to transcriptional inhibition and other cellular stresses, although the mechanism and physiological relevance of these phenomena are unclear. Using MCF-7 and other mammalian cell lines, we describe a structural and functional adaptation of the nucleolus, triggered by heat shock or physiological acidosis, that depends on the expression of ribosomal intergenic spacer long noncoding RNA (IGS lncRNA). At the heart of this process is the de novo formation of a large subnucleolar structure, termed the detention center (DC). The DC is a spatially and dynamically distinct region, characterized by an 8-anilino-1-naphthalenesulfonate–positive hydrophobic signature. Its formation is accompanied by redistribution of nucleolar factors and arrest in ribosomal biogenesis. Silencing of regulatory IGS lncRNA prevents the creation of this structure and allows the nucleolus to retain its tripartite organization and transcriptional activity. Signal termination causes a decrease in IGS transcript levels and a return to the active nucleolar conformation. We propose that the induction of IGS lncRNA by environmental signals operates as a molecular switch that regulates the structure and function of the nucleolus.
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Affiliation(s)
- Mathieu D Jacob
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
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29
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Terrier O, Moules V, Carron C, Cartet G, Frobert E, Yver M, Traversier A, Wolff T, Riteau B, Naffakh N, Lina B, Diaz JJ, Rosa-Calatrava M. The influenza fingerprints: NS1 and M1 proteins contribute to specific host cell ultrastructure signatures upon infection by different influenza A viruses. Virology 2012; 432:204-18. [PMID: 22770924 DOI: 10.1016/j.virol.2012.05.019] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2012] [Revised: 05/02/2012] [Accepted: 05/21/2012] [Indexed: 12/22/2022]
Abstract
Influenza A are nuclear replicating viruses which hijack host machineries in order to achieve optimal infection. Numerous functional virus-host interactions have now been characterized, but little information has been gathered concerning their link to the virally induced remodeling of the host cellular architecture. In this study, we infected cells with several human and avian influenza viruses and we have analyzed their ultrastructural modifications by using electron and confocal microscopy. We discovered that infections lead to a major and systematic disruption of nucleoli and the formation of a large number of diverse viral structures showing specificity that depended on the subtype origin and genomic composition of viruses. We identified NS1 and M1 proteins as the main actors in the remodeling of the host ultra-structure and our results suggest that each influenza A virus strain could be associated with a specific cellular fingerprint, possibly correlated to the functional properties of their viral components.
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Affiliation(s)
- Olivier Terrier
- Equipe VirCell, Laboratoire de Virologie et Pathologie Humaine, VirPath EMR 4610, Université de Lyon, Université Claude Bernard Lyon 1, Hospices Civils de Lyon, Faculté de médecine RTH Laennec, rue Guillaume Paradin, F-69008 Lyon, France
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30
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Stępiński D. Immunofluorescent localization of ubiquitin and proteasomes in nucleolar vacuoles of soybean root meristematic cells. Eur J Histochem 2012; 56:e13. [PMID: 22688294 PMCID: PMC3428962 DOI: 10.4081/ejh.2012.13] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2011] [Revised: 01/27/2012] [Accepted: 01/27/2012] [Indexed: 01/01/2023] Open
Abstract
In this study, using the immunofluorescent method, the immunopositive signals to ubiquitin and proteasomes in nucleoli of root meristematic cells of soybean seedlings have been observed. In fact, those signals were present exclusively in nucleolar vacuoles. No signals were observed in the nucleolar territory out of the nucleolar vacuoles or in the nucleoli without vacuoles. The ubiquitin-proteasome system (UPS) may act within the nucleoli of plants with high metabolic activities and may provide an additional level of regulation of intracellular proteolysis via compartment-specific activities of their components. It is suggested that the presence of the UPS solely in vacuolated nucleoli serves as a mechanism that enhances the speed of ribosome subunit production in very actively transcribing nucleoli. On the other hand, nucleolar vacuoles in a cell/nucleus could play additional roles associated with temporary sequestration or storage of some cellular factors, including components of the ubiquitin-proteasome system.
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Affiliation(s)
- D Stępiński
- Department of Cytophysiology, University of Łódź, Poland.
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31
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Abstract
Gametogenesis is a process whereby a germ cell differentiates into haploid gametes. We found that, in budding yeast, replicatively aged cells remove age-induced cellular damage during gametogenesis. Importantly, gametes of aged cells have the same replicative potential as those derived from young cells, indicating that life span resets during gametogenesis. Here, we explore the potential mechanisms responsible for gametogenesis-induced rejuvenation and discuss putative analogous mechanisms in higher eukaryotes.
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Affiliation(s)
- E Ünal
- David H. Koch Institute for Integrative Cancer Research, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
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32
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Agrawal GK, Bourguignon J, Rolland N, Ephritikhine G, Ferro M, Jaquinod M, Alexiou KG, Chardot T, Chakraborty N, Jolivet P, Doonan JH, Rakwal R. Plant organelle proteomics: collaborating for optimal cell function. Mass Spectrom Rev 2011; 30:772-853. [PMID: 21038434 DOI: 10.1002/mas.20301] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2009] [Revised: 02/02/2010] [Accepted: 02/02/2010] [Indexed: 05/10/2023]
Abstract
Organelle proteomics describes the study of proteins present in organelle at a particular instance during the whole period of their life cycle in a cell. Organelles are specialized membrane bound structures within a cell that function by interacting with cytosolic and luminal soluble proteins making the protein composition of each organelle dynamic. Depending on organism, the total number of organelles within a cell varies, indicating their evolution with respect to protein number and function. For example, one of the striking differences between plant and animal cells is the plastids in plants. Organelles have their own proteins, and few organelles like mitochondria and chloroplast have their own genome to synthesize proteins for specific function and also require nuclear-encoded proteins. Enormous work has been performed on animal organelle proteomics. However, plant organelle proteomics has seen limited work mainly due to: (i) inter-plant and inter-tissue complexity, (ii) difficulties in isolation of subcellular compartments, and (iii) their enrichment and purity. Despite these concerns, the field of organelle proteomics is growing in plants, such as Arabidopsis, rice and maize. The available data are beginning to help better understand organelles and their distinct and/or overlapping functions in different plant tissues, organs or cell types, and more importantly, how protein components of organelles behave during development and with surrounding environments. Studies on organelles have provided a few good reviews, but none of them are comprehensive. Here, we present a comprehensive review on plant organelle proteomics starting from the significance of organelle in cells, to organelle isolation, to protein identification and to biology and beyond. To put together such a systematic, in-depth review and to translate acquired knowledge in a proper and adequate form, we join minds to provide discussion and viewpoints on the collaborative nature of organelles in cell, their proper function and evolution.
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Affiliation(s)
- Ganesh Kumar Agrawal
- Research Laboratory for Biotechnology and Biochemistry (RLABB), P.O. Box 13265, Sanepa, Kathmandu, Nepal.
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33
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DePaoli HC, Brito MS, Quiapim AC, Teixeira SP, Goldman GH, Dornelas MC, Goldman MHS. Stigma/style cell cycle inhibitor 1 (SCI1), a tissue-specific cell cycle regulator that controls upper pistil development. New Phytol 2011; 190:882-895. [PMID: 21388377 DOI: 10.1111/j.1469-8137.2011.03660.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
A cDNA encoding a small lysine-rich protein of unknown function was identified in a tobacco (Nicotiana tabacum) stigma/style suppression subtractive hybridization cDNA library. After its characterization, the corresponding gene was designated stigma/style cell cycle inhibitor 1 (SCI1). Fluorescence microscopy with an SCI1-GFP protein fusion demonstrated its nuclear localization, which was confined to the interchromatic region. Real-time RT-PCR and in situ hybridization experiments showed that SCI1 is stigma/style-specific and developmentally regulated. SCI1 RNAi knockdown and overexpression plants had stigmas/styles with remarkably enlarged and reduced areas, respectively, which was attributable to differences in cell numbers. These results indicate that SCI1 is a tissue-specific negative cell cycle regulator. The differences in cell division had an effect on the timing of the differentiation of the stigmatic papillar cells, suggesting that their differentiation is coupled to stigma cell divisions. This is consistent with a role for SCI1 in triggering differentiation through cell proliferation control. Our results revealed that SCI1 is a novel tissue-specific gene that controls cell proliferation/differentiation, probably as a component of a developmental signal transduction pathway.
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Affiliation(s)
- Henrique C DePaoli
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto 14040-901, Brazil
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto 14049-900, Brazil
| | - Michael S Brito
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto 14040-901, Brazil
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto 14049-900, Brazil
| | - Andréa C Quiapim
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto 14040-901, Brazil
| | - Simone P Teixeira
- Departamento de Ciências Farmacêuticas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto 14040-903, Brazil
| | - Gustavo H Goldman
- Departamento de Ciências Farmacêuticas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto 14040-903, Brazil
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Campinas 13083-970, Brazil
| | - Marcelo C Dornelas
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade de Campinas, Campinas 13083-970, Brazil
| | - Maria Helena S Goldman
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto 14040-901, Brazil
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34
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Kyogoku H, Ogushi S, Miyano T, Fulka J. Nucleoli from growing oocytes inhibit the maturation of enucleolated, full-grown oocytes in the pig. Mol Reprod Dev 2011; 78:426-35. [PMID: 21542050 DOI: 10.1002/mrd.21320] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2010] [Accepted: 04/09/2011] [Indexed: 12/21/2022]
Abstract
In mammals, the nucleolus of full-grown oocyte is essential for embryonic development but not for oocyte maturation. In our study, the role of the growing oocyte nucleolus in oocyte maturation was examined by nucleolus removal and/or transfer into previously enucleolated, growing (around 100 µm in diameter) or full-grown (120 µm) pig oocytes. In the first experiment, the nucleoli were aspirated from growing oocytes whose nucleoli had been compacted by actinomycin D treatment, and the enucleolated oocytes were matured in vitro. Most of non-treated or actinomycin D-treated oocytes did not undergo germinal vesicle breakdown (GVBD; 13% and 12%, respectively). However, the GVBD rate of enucleolated, growing oocytes significantly increased to 46%. The low GVBD rate of enucleolated, growing oocytes was restored again by the re-injection of nucleoli from growing oocytes (23%), but not when nucleoli from full-grown oocytes were re-injected into enucleolated, growing oocytes (49%). When enucleolated, full-grown oocytes were injected with nucleoli from growing or full-grown oocytes, the nucleolus in the germinal vesicle was reassembled (73% and 60%, respectively). After maturation, the enucleolated, full-grown oocytes injected with nucleoli from full-grown oocytes matured to metaphase II (56%), whereas injection with growing-oocyte nucleoli reduced this maturation to 21%. These results suggest that the growing-oocyte nucleolus is involved in the oocyte's meiotic arrest, and that the full-grown oocyte nucleolus has lost the ability.
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Affiliation(s)
- Hirohisa Kyogoku
- Graduate School of Agricultural Science, Kobe University, Kobe, Japan.
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35
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Abstract
When cells are observed by phase contrast microscopy, nucleoli are among the most conspicuous structures. The nucleolus was formally described between 1835 and 1839, but it was another century before it was discovered to be associated with a specific chromosomal locus, thus defining it as a cytogenetic entity. Nucleoli were first isolated in the 1950s, from starfish oocytes. Then, in the early 1960s, a boomlet of studies led to one of the epochal discoveries in the modern era of genetics and cell biology: that the nucleolus is the site of ribosomal RNA synthesis and nascent ribosome assembly. This epistemologically repositioned the nucleolus as not merely an aspect of nuclear anatomy but rather as a cytological manifestation of gene action-a major heuristic advance. Indeed, the finding that the nucleolus is the seat of ribosome production constitutes one of the most vivid confluences of form and function in the history of cell biology. This account presents the nucleolus in both historical and contemporary perspectives. The modern era has brought the unanticipated discovery that the nucleolus is plurifunctional, constituting a paradigm shift.
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Affiliation(s)
- Thoru Pederson
- Program in Cell and Developmental Dynamics, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, 01605, USA.
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36
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Catalano A, O'Day DH. Nucleolar localization and identification of nuclear/nucleolar localization signals of the calmodulin-binding protein nucleomorphin during growth and mitosis in Dictyostelium. Histochem Cell Biol 2011; 135:239-49. [PMID: 21327858 DOI: 10.1007/s00418-011-0785-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/29/2011] [Indexed: 10/18/2022]
Abstract
The calmodulin-binding protein nucleomorphin isoform NumA1 is a nuclear number regulator in Dictyostelium that localizes to intra-nuclear patches adjacent to the nuclear envelope and to a lesser extent the nucleoplasm. Earlier studies have shown similar patches to be nucleoli but only three nucleolar proteins have been identified in Dictyostelium. Here, actinomycin-D treatment caused the loss of NumA1 localization, while calcium and calmodulin antagonists had no effect. In keeping with a nucleolar function, NumA1 moved out of the presumptive nucleoli during mitosis redistributing to areas within the nucleus, the spindle fibers, and centrosomal region before re-accumulating in the presumptive nucleoli at telophase. Together, these data verify NumA1 as a true nucleolar protein. Prior to this study, the dynamics of specific nucleolar proteins had not been determined during mitosis in Dictyostelium. FITC-conjugated peptides equivalent to presumptive nuclear localization signals within NumA1 localized to nucleoli indicating that they also act as nucleolar localization signals. To our knowledge, these represent the first precisely defined nucleolar localization signals as well as the first nuclear/nucleolar localization signals identified in Dictyostelium. Together, these results reveal that NumA1 is a true nucleolar protein and the only nucleolar calmodulin-binding protein identified in Dictyostelium. The possible use of nuclear/nucleolar localization signal-mediated drug targeting to nucleoli is discussed.
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37
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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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38
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Abstract
Synthesis of new ribosomes is an essential process upregulated during cell growth and proliferation. Here, we review our current understanding of the role that ubiquitin and ubiquitin-like proteins (UBLs) play in ribosome biogenesis, with a focus on mammalian cells. One important function of the nuclear ubiquitin-proteasome system is to control the supply of ribosomal proteins for the assembly of new ribosomal subunits in the nucleolus. Mutations in ribosomal proteins or ribosome assembly factors, stress, and many anticancer drugs have been shown to disrupt normal ribosome biogenesis, triggering a p53-dependent response. We discuss how p53 can be activated by the aberrant ribosome formation, centering on the current models of the interaction between ribosomal proteins released from the nucleolus and the ubiquitin ligase Mdm2. Recent studies also revealed multiple ubiquitin- and UBL-conjugated forms of nucleolar proteins with largely unknown functions, indicating that many new details about the role of these modifications in the nucleolus await to be discovered.
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Affiliation(s)
- Natalia Shcherbik
- Department of Cell Biology, University of Medicine and Dentistry of New Jersey, Stratford, NJ 08084
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39
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Abstract
The nucleolus is a subnuclear structure of eukaryocytes. It was thought that nucleolus only participates in the biogenesis and processing of rRNA. However, more and more evidence shows that it has many other functions, such as tRNA precursor processing, stress sensing and it is also involved in gene silencing, senescence and cell cycle regulation. Here, we summarize the recent understandings about the nucleolar functions, the regulation of nucleolar localization of proteins and the role that the nucleolus plays in virus infection, in which some related studies of Herpes simplex virus type 1 (HSV-1) US11, UL24 and bovine herpesvirus-1 infected cell protein 27 (BICP27) carried out in our lab will also be included.
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Affiliation(s)
- Lei Wang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071 China
| | - Xiao-ming Ren
- The Department of Animal Science, Beijing University of Agriculture, Beijing, 102206 China
| | - Jun-ji Xing
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071 China
| | - Alan C. Zheng
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071 China
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40
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Szymański J, Mayer C, Hoffmann-Rohrer U, Kalla C, Grummt I, Weiss M. Dynamic subcellular partitioning of the nucleolar transcription factor TIF-IA under ribotoxic stress. Biochim Biophys Acta 2009; 1793:1191-8. [PMID: 19450626 DOI: 10.1016/j.bbamcr.2009.05.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2008] [Revised: 04/09/2009] [Accepted: 05/11/2009] [Indexed: 01/04/2023]
Abstract
TIF-IA is a basal transcription factor of RNA polymerase I (Pol I) that is a major target of the JNK2 signaling pathway in response to ribotoxic stress. Using advanced fluorescence microscopy and kinetic modeling we elucidated the subcellular localization of TIF-IA and its exchange dynamics between the nucleolus, nucleoplasm and cytoplasm upon ribotoxic stress. In steady state, the majority of (GFP-tagged) TIF-IA was in the cytoplasm and the nucleus, a minor portion (7%) localizing to the nucleoli. We observed a rapid shuttling of GFP-TIF-IA between the different cellular compartments with a mean residence time of approximately 130 s in the nucleus and only approximately 30 s in the nucleoli. The import rate from the cytoplasm to the nucleus was approximately 3-fold larger than the export rate, suggesting an importin/exportin-mediated transport rather than a passive diffusion. Upon ribotoxic stress, GFP-TIF-IA was released from the nucleoli with a half-time of approximately 24 min. Oxidative stress and inhibition of protein synthesis led to a relocation of GFP-TIF-IA with slower kinetics while osmotic stress had no effect. The observed relocation was much slower than the nucleo-cytoplasmic and nucleus-nucleolus exchange rates of GFP-TIF-IA, indicating a time-limiting step upstream of the JNK2 pathway. In support of this, time-course experiments on the activity of JNK2 revealed the activation of the JNK kinase as the rate-limiting step.
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Affiliation(s)
- Jedrzej Szymański
- Cellular Biophysics Group, German Cancer Research Center, D-69120 Heidelberg, Germany
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41
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Dey S, Banerjee P, Saha P. Cell cycle specific expression and nucleolar localization of human J-domain containing co-chaperone Mrj. Mol Cell Biochem 2008; 322:137-42. [PMID: 19002655 DOI: 10.1007/s11010-008-9950-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2008] [Accepted: 10/22/2008] [Indexed: 01/28/2023]
Abstract
J-domain containing co-chaperone Mrj (mammalian relative to DnaJ) has been implicated in diverse cellular functions including placental development and inhibition of Huntingtin mediated cytotoxicity. It has also been shown to interact with keratin intermediate filaments. Since keratins undergo extensive reorganization during cell division, its interactor Mrj might also play an important role in the regulation of cell cycle. In support of this hypothesis, we report the up-regulation of Mrj protein in M-phase of HeLa cells implicating its role in mitosis related activities. The protein is dispersed throughout the cell during late mitosis and is localized in nucleolus during interphase, confirming that the activity of Mrj is regulated by its cell cycle specific expression together with its differential subcellular localization.
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Affiliation(s)
- Sanjib Dey
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, Sector I, Block AF, Bidhannagar, Kolkata, 700064, India
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42
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Escobar ML, Echeverría OM, Ortíz R, Vázquez-Nin GH. Combined apoptosis and autophagy, the process that eliminates the oocytes of atretic follicles in immature rats. Apoptosis 2008; 13:1253-66. [PMID: 18690537 DOI: 10.1007/s10495-008-0248-z] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
We studied the alterations of dying oocytes in 1-28 days old rats using TUNEL method, immunolocalizations of active caspase 3, lamp1, localization of acid phosphatase, and DAPI staining. All procedures were performed in adjacent sections of each oocyte. In most dying oocytes exist simultaneously features of apoptosis as active caspase 3 and DNA breaks, and a large increase of lamp1 and acid phosphatase characteristic of autophagy. Large clumps of compact chromatin and membrane blebbing were absent. Electron microscope observations demonstrated the presence of small clear vesicles and autophagolysosomes. All these features indicate that a large number of oocytes are eliminated by a process sharing features of apoptosis and autophagy. In dying oocytes of new born rats the markers of apoptosis predominate over those of autophagy. However, fragmentation and apoptotic bodies were not found. These features suggest that in different cytophysiological conditions the processes of cell death may be differently modulated.
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Affiliation(s)
- M L Escobar
- Department of Cell Biology, Faculty of Sciences, National Autonomous University of Mexico UNAM, Mexico, DF, 04510, Mexico
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43
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Wang SS, Smiraglia DJ, Wu YZ, Ghosh S, Rader JS, Cho KR, Bonfiglio TA, Nayar R, Plass C, Sherman ME. Identification of novel methylation markers in cervical cancer using restriction landmark genomic scanning. Cancer Res 2008; 68:2489-97. [PMID: 18381458 DOI: 10.1158/0008-5472.can-07-3194] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Aberrant methylation of CpG islands in gene promoters often represents an early clonal event in carcinogenesis. Accordingly, defining methylation profiles may be useful for developing marker panels for early detection or predicting the risk of cancer precursors. To identify specific genes frequently methylated in cervical cancer, we conducted methylation profiling of 20 primary human cervical cancers using NotI-based restriction landmark genomic scanning (RLGS). Of 2,172 RLGS fragments analyzed (average, 1,753 CpG islands per patient), 186 RLGS fragments were lost in at least one tumor and 40 were lost in three or more. Methylation was identified in 19 (95%) of 20 tumor samples compared with normal DNA. Bisulfite sequencing was conducted to confirm RLGS results. Of the confirmed markers frequently methylated, we developed Methylight assays for two corresponding genes, nucleolar protein 4 (NOL4), and lipoma HMGIC fusion partner-like protein 4 (LHFPL4), which were methylated in 85% and 55% of cancers, respectively. Using these assays, we further confirmed frequent CpG island methylation in the original cancers and in another independent series of 15 cervical cancers. We also showed methylation at a reduced frequency in a set of carefully reviewed cytology specimens demonstrating cells exfoliated from cancer precursor lesions. In summary, we identified, for the first time, NOL4 and LHFPL4 as novel methylation targets specific for cervical cancer. Inclusion of NOL4 and LHFPL4 in evaluating methylation panels for early detection, risk prediction, and etiologic research on cervical cancer is warranted.
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Affiliation(s)
- Sophia S Wang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD 20852-7234, USA.
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44
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Higgins JD, Buckling EF, Franklin FCH, Jones GH. Expression and functional analysis of AtMUS81 in Arabidopsis meiosis reveals a role in the second pathway of crossing-over. Plant J 2008; 54:152-62. [PMID: 18182028 DOI: 10.1111/j.1365-313x.2008.03403.x] [Citation(s) in RCA: 107] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Meiotic crossovers/chiasmata, that are required to ensure chromosome disjunction, arise via the class I interference-dependent pathway or via the class II interference-free pathway. The proportions of these two classes vary considerably between different organisms. In Arabidopsis, about 85% of chiasmata are eliminated in Atmsh4 mutants, denoting that these are class I events. In budding and fission yeasts Msh4-independent crossovers arise largely or entirely via a Mus81-dependent pathway. To investigate the origins of the 15% residual (AtMSH4-independent) chiasmata in Arabidopsis we conducted a cytological and molecular analysis of AtMUS81 meiotic expression and function. Although AtMUS81 functions in somatic DNA repair and recombination, it is more highly expressed in reproductive tissues. The protein is abundantly present in early prophase I meiocytes, where it co-localizes, in a double-strand break-dependent manner, with the recombination protein AtRAD51. Despite this, an Atmus81 mutant shows normal growth and has no obvious defects in reproductive development that would indicate meiotic impairment. A cytological analysis confirmed that meiosis was apparently normal in this mutant and its mean chiasma frequency was similar to that of wild-type plants. However, an Atmsh4/Atmus81 double mutant revealed a significantly reduced mean chiasma frequency (0.85 per cell), compared with an Atmsh4 single mutant (1.25 per cell), from which we conclude that AtMUS81 accounts for some, but not all, of the 15% AtMSH4-independent residual crossovers. It is possible that other genes are responsible for these residual chiasmata. Alternatively the AtMUS81 pathway coexists with an alternative parallel pathway that can perform the same functions.
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Affiliation(s)
- James D Higgins
- School of Biological Sciences, University of Birmingham, Birmingham B15 2TT, UK
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45
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Abstract
Nucleoli are the prominent contrasted structures of the cell nucleus. In the nucleolus, ribosomal RNAs are synthesized, processed and assembled with ribosomal proteins. RNA polymerase I synthesizes the ribosomal RNAs and this activity is cell cycle regulated. The nucleolus reveals the functional organization of the nucleus in which the compartmentation of the different steps of ribosome biogenesis is observed whereas the nucleolar machineries are in permanent exchange with the nucleoplasm and other nuclear bodies. After mitosis, nucleolar assembly is a time and space regulated process controlled by the cell cycle. In addition, by generating a large volume in the nucleus with apparently no RNA polymerase II activity, the nucleolus creates a domain of retention/sequestration of molecules normally active outside the nucleolus. Viruses interact with the nucleolus and recruit nucleolar proteins to facilitate virus replication. The nucleolus is also a sensor of stress due to the redistribution of the ribosomal proteins in the nucleoplasm by nucleolus disruption. The nucleolus plays several crucial functions in the nucleus: in addition to its function as ribosome factory of the cells it is a multifunctional nuclear domain, and nucleolar activity is linked with several pathologies. Perspectives on the evolution of this research area are proposed.
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Affiliation(s)
- Valentina Sirri
- Nuclei and Cell Cycle, CNRS, Université Paris VI, Université Paris VII, Institut Jacques Monod, 2 place Jussieu, 75251 Paris Cedex 05, France
| | - Silvio Urcuqui-Inchima
- Nuclei and Cell Cycle, CNRS, Université Paris VI, Université Paris VII, Institut Jacques Monod, 2 place Jussieu, 75251 Paris Cedex 05, France
- Grupo de Inmunovirología, Biogénesis, Universidad de Antioquia, Calle 62 No. 52-59, Medellin, Colombia
| | - Pascal Roussel
- Nuclei and Cell Cycle, CNRS, Université Paris VI, Université Paris VII, Institut Jacques Monod, 2 place Jussieu, 75251 Paris Cedex 05, France
| | - Danièle Hernandez-Verdun
- Nuclei and Cell Cycle, CNRS, Université Paris VI, Université Paris VII, Institut Jacques Monod, 2 place Jussieu, 75251 Paris Cedex 05, France
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46
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Vignard J, Siwiec T, Chelysheva L, Vrielynck N, Gonord F, Armstrong SJ, Schlögelhofer P, Mercier R. The interplay of RecA-related proteins and the MND1-HOP2 complex during meiosis in Arabidopsis thaliana. PLoS Genet 2007; 3:1894-906. [PMID: 17937504 PMCID: PMC2014788 DOI: 10.1371/journal.pgen.0030176] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2007] [Accepted: 08/29/2007] [Indexed: 12/23/2022] Open
Abstract
During meiosis, homologous chromosomes recognize each other, align, and exchange genetic information. This process requires the action of RecA-related proteins Rad51 and Dmc1 to catalyze DNA strand exchanges. The Mnd1-Hop2 complex has been shown to assist in Dmc1-dependent processes. Furthermore, higher eukaryotes possess additional RecA-related proteins, like XRCC3, which are involved in meiotic recombination. However, little is known about the functional interplay between these proteins during meiosis. We investigated the functional relationship between AtMND1, AtDMC1, AtRAD51, and AtXRCC3 during meiosis in Arabidopsis thaliana. We demonstrate the localization of AtMND1 to meiotic chromosomes, even in the absence of recombination, and show that AtMND1 loading depends exclusively on AHP2, the Arabidopsis Hop2 homolog. We provide evidence of genetic interaction between AtMND1, AtDMC1, AtRAD51, and AtXRCC3. In vitro assays suggest that this functional link is due to direct interaction of the AtMND1-AHP2 complex with AtRAD51 and AtDMC1. We show that AtDMC1 foci accumulate in the Atmnd1 mutant, but are reduced in number in Atrad51 and Atxrcc3 mutants. This study provides the first insights into the functional differences of AtRAD51 and AtXRCC3 during meiosis, demonstrating that AtXRCC3 is dispensable for AtDMC1 focus formation in an Atmnd1 mutant background, whereas AtRAD51 is not. These results clarify the functional interactions between key players in the strand exchange processes during meiotic recombination. Furthermore, they highlight a direct interaction between MND1 and RAD51 and show a functional divergence between RAD51 and XRCC3.
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Affiliation(s)
- Julien Vignard
- Station de Génétique et d'Amélioration des Plantes, INRA, Versailles, France
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47
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Ozawa M, Fujii K, Muramoto Y, Yamada S, Yamayoshi S, Takada A, Goto H, Horimoto T, Kawaoka Y. Contributions of two nuclear localization signals of influenza A virus nucleoprotein to viral replication. J Virol 2006; 81:30-41. [PMID: 17050598 PMCID: PMC1797272 DOI: 10.1128/jvi.01434-06] [Citation(s) in RCA: 178] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The RNA genome of influenza A virus, which forms viral ribonucleoprotein complexes (vRNPs) with viral polymerase subunit proteins (PA, PB1, and PB2) and nucleoprotein (NP), is transcribed and replicated in the nucleus. NP, the major component of vRNPs, has at least two amino acid sequences that serve as nuclear localization signals (NLSs): an unconventional NLS (residues 3 to 13; NLS1) and a bipartite NLS (residues 198 to 216; NLS2). Although both NLSs are known to play a role in nuclear transport, their relative contributions to viral replication are poorly understood. We therefore investigated their contributions to NP subcellular/subnuclear localization, viral RNA (vRNA) transcription, and viral replication. Abolishing the unconventional NLS caused NP to localize predominantly to the cytoplasm and affected its activity in vRNA transcription. However, we were able to create a virus whose NP contained amino acid substitutions in NLS1 known to abolish its nuclear localization function, although this virus was highly attenuated. These results indicate that while the unconventional NLS is not essential for viral replication, it is necessary for efficient viral mRNA synthesis. On the other hand, the bipartite NLS, whose contribution to the nuclear transport of NP is limited, was essential for vRNA transcription and NP's nucleolar accumulation. A virus with nonfunctional NLS2 could not be generated. Thus, the bipartite NLS, but not the unconventional NLS, of NP is essential for influenza A virus replication.
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Affiliation(s)
- Makoto Ozawa
- Division of Virology, Institute of Medical Science, University of Tokyo, Shirokanedai, Tokyo 108-8639, Japan
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48
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Abstract
Börjeson-Forssman-Lehman syndrome was first described in 1962. Many similar families and isolated cases have been reported since. In nineteen of them, including the original family, the clinical diagnosis was confirmed by the identification of a mutation in the responsible gene, PHF6. Summarizing recent clinical and molecular studies of this X-chromosome linked mental retardation syndrome we aim to offer a useful resource for its identification among the affected male and female subjects.
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Affiliation(s)
- Jozef Gécz
- Neurogenetics Laboratory, Department of Genetic Medicine, Women's and Children's Hospital, North Adelaide, SA 5006, Australia.
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49
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Abstract
Nucleoli are the prominent contrasted structures of the cell nucleus. In the nucleolus, ribosomal RNAs (rRNAs) are synthesized, processed and assembled with ribosomal proteins. The size and organization of the nucleolus are directly related to ribosome production. The organization of the nucleolus reveals the functional compartmentation of the nucleolar machineries that depends on nucleolar activity. When this activity is blocked, disrupted or impossible, the nucleolar proteins have the capacity to interact independently of the processing activity. In addition, nucleoli are dynamic structures in which nucleolar proteins rapidly associate and dissociate with nucleolar components in continuous exchanges with the nucleoplasm. At the time of nucleolar assembly, the processing machineries are recruited in a regulated manner in time and space, controlled by different kinases and form intermediate structures, the prenucleolar bodies. The participation of stable pre-rRNAs in nucleolar assembly was demonstrated after mitosis and during development but this is an intriguing observation since the role of these pre-rRNAs is presently unknown. A brief report on the nucleolus and diseases is proposed as well as of nucleolar functions different from ribosome biogenesis.
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Affiliation(s)
- Danièle Hernandez-Verdun
- Nuclei and Cell Cycle, Institut Jacques Monod, CNRS, Université Paris VI, Université Paris VII, 2 place Jussieu, 75251 Paris Cedex 05, France.
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50
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Hinsby AM, Kiemer L, Karlberg EO, Lage K, Fausbøll A, Juncker AS, Andersen JS, Mann M, Brunak S. A Wiring of the Human Nucleolus. Mol Cell 2006; 22:285-95. [PMID: 16630896 DOI: 10.1016/j.molcel.2006.03.012] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2005] [Revised: 01/31/2006] [Accepted: 03/07/2006] [Indexed: 11/22/2022]
Abstract
Recent proteomic efforts have created an extensive inventory of the human nucleolar proteome. However, approximately 30% of the identified proteins lack functional annotation. We present an approach of assigning function to uncharacterized nucleolar proteins by data integration coupled to a machine-learning method. By assembling protein complexes, we present a first draft of the human ribosome biogenesis pathway encompassing 74 proteins and hereby assign function to 49 previously uncharacterized proteins. Moreover, the functional diversity of the nucleolus is underlined by the identification of a number of protein complexes with functions beyond ribosome biogenesis. Finally, we were able to obtain experimental evidence of nucleolar localization of 11 proteins, which were predicted by our platform to be associates of nucleolar complexes. We believe other biological organelles or systems could be "wired" in a similar fashion, integrating different types of data with high-throughput proteomics, followed by a detailed biological analysis and experimental validation.
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Affiliation(s)
- Anders M Hinsby
- Center for Biological Sequence Analysis, BioCentrum-DTU, Technical University of Denmark, DK-2800 Lyngby
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