1
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Gál Z, Boukoura S, Oxe KC, Badawi S, Nieto B, Korsholm LM, Geisler SB, Dulina E, Rasmussen AV, Dahl C, Lv W, Xu H, Pan X, Arampatzis S, Stratou DE, Galanos P, Lin L, Guldberg P, Bartek J, Luo Y, Larsen DH. Hyper-recombination in ribosomal DNA is driven by long-range resection-independent RAD51 accumulation. Nat Commun 2024; 15:7797. [PMID: 39242676 PMCID: PMC11379943 DOI: 10.1038/s41467-024-52189-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 08/28/2024] [Indexed: 09/09/2024] Open
Abstract
Ribosomal DNA (rDNA) encodes the ribosomal RNA genes and represents an intrinsically unstable genomic region. However, the underlying mechanisms and implications for genome integrity remain elusive. Here, we use Bloom syndrome (BS), a rare genetic disease characterized by DNA repair defects and hyper-unstable rDNA, as a model to investigate the mechanisms leading to rDNA instability. We find that in Bloom helicase (BLM) proficient cells, the homologous recombination (HR) pathway in rDNA resembles that in nuclear chromatin; it is initiated by resection, replication protein A (RPA) loading and BRCA2-dependent RAD51 filament formation. However, BLM deficiency compromises RPA-loading and BRCA1/2 recruitment to rDNA, but not RAD51 accumulation. RAD51 accumulates at rDNA despite depletion of long-range resection nucleases and rDNA damage results in micronuclei when BLM is absent. In summary, our findings indicate that rDNA is permissive to RAD51 accumulation in the absence of BLM, leading to micronucleation and potentially global genomic instability.
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Affiliation(s)
- Zita Gál
- Nucleolar Stress and Disease Group, Danish Cancer Institute, 2100, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Blegdamsvej 3B, DK-2200, Copenhagen, Denmark
| | - Stavroula Boukoura
- Nucleolar Stress and Disease Group, Danish Cancer Institute, 2100, Copenhagen, Denmark
| | - Kezia Catharina Oxe
- Nucleolar Stress and Disease Group, Danish Cancer Institute, 2100, Copenhagen, Denmark
| | - Sara Badawi
- Nucleolar Stress and Disease Group, Danish Cancer Institute, 2100, Copenhagen, Denmark
| | - Blanca Nieto
- Nucleolar Stress and Disease Group, Danish Cancer Institute, 2100, Copenhagen, Denmark
| | - Lea Milling Korsholm
- Nucleolar Stress and Disease Group, Danish Cancer Institute, 2100, Copenhagen, Denmark
- Genome Integrity Group, Danish Cancer Institute, 2100, Copenhagen, Denmark
- Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | | | - Ekaterina Dulina
- Nucleolar Stress and Disease Group, Danish Cancer Institute, 2100, Copenhagen, Denmark
- Genome Integrity Group, Danish Cancer Institute, 2100, Copenhagen, Denmark
| | | | - Christina Dahl
- Molecular Diagnostics, Danish Cancer Institute, 2100, Copenhagen, Denmark
| | - Wei Lv
- Department of Biomedicine, Aarhus University, Aarhus, 8000, Denmark
| | - Huixin Xu
- Department of Biomedicine, Aarhus University, Aarhus, 8000, Denmark
| | - Xiaoguang Pan
- Department of Biology, University of Copenhagen, Copenhagen N, DK-2200, Denmark
| | | | | | - Panagiotis Galanos
- Genome Integrity Group, Danish Cancer Institute, 2100, Copenhagen, Denmark
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Lin Lin
- Department of Biomedicine, Aarhus University, Aarhus, 8000, Denmark
- Steno Diabetes Center Aarhus, Aarhus University Hospital, Aarhus, 8200, Denmark
| | - Per Guldberg
- Molecular Diagnostics, Danish Cancer Institute, 2100, Copenhagen, Denmark
- Department of Cancer and Inflammation Research, Institute of Molecular Medicine, University of Southern Denmark, Odense, 5000, Denmark
| | - Jiri Bartek
- Genome Integrity Group, Danish Cancer Institute, 2100, Copenhagen, Denmark
- Karolinska Institutet, Department of Medical Biochemistry and Biophysics, Division of Genome Biology, Science for Life Laboratory, Stockholm, Sweden
| | - Yonglun Luo
- Department of Biomedicine, Aarhus University, Aarhus, 8000, Denmark
- Steno Diabetes Center Aarhus, Aarhus University Hospital, Aarhus, 8200, Denmark
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
| | - Dorthe H Larsen
- Nucleolar Stress and Disease Group, Danish Cancer Institute, 2100, Copenhagen, Denmark.
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Jo M, Kim S, Park J, Chang YT, Gwon Y. Reduced dynamicity and increased high-order protein assemblies in dense fibrillar component of the nucleolus under cellular senescence. Redox Biol 2024; 75:103279. [PMID: 39111063 PMCID: PMC11347067 DOI: 10.1016/j.redox.2024.103279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 06/27/2024] [Accepted: 07/20/2024] [Indexed: 08/23/2024] Open
Abstract
Cellular senescence, which is triggered by various stressors, manifests as irreversible cell cycle arrest, resulting in the disruption of multiple nuclear condensates. One of the affected structures is the nucleolus, whose tripartite layout, separated into distinct liquid phases, allows for the stepwise progression of ribosome biogenesis. The dynamic properties of dense fibrillar components, a sub-nucleolar phase, are crucial for mediating pre-rRNA processing. However, the mechanistic link between the material properties of dense fibrillar components and cellular senescence remains unclear. We established a significant association between cellular senescence and alterations in nucleolar materiality and characteristics, including the number, size, and sphericity of individual subphases of the nucleolus. Senescent cells exhibit reduced fibrillarin dynamics, aberrant accumulation of high-order protein assemblies, such as oligomers and fibrils, and increased dense fibrillar component density. Intriguingly, the addition of RNA-interacting entities mirrored the diminished diffusion of fibrillarin in the nucleolus during cellular senescence. Thus, our findings contribute to a broader understanding of the intricate changes in the materiality of the nucleolus associated with cellular senescence and shed light on nucleolar dynamics in the context of aging and cellular stress.
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Affiliation(s)
- Minjeong Jo
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, 16419, Republic of Korea
| | - Soomin Kim
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, 16419, Republic of Korea
| | - Jeongeun Park
- Department of MetaBioHealth, Sungkyunkwan University Institute for Convergence, Suwon, 16419, Republic of Korea
| | - Young-Tae Chang
- Department of Chemistry, Pohang University of Science and Technology, Pohang, 37673, Republic of Korea
| | - Youngdae Gwon
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, 16419, Republic of Korea; Department of MetaBioHealth, Sungkyunkwan University Institute for Convergence, Suwon, 16419, Republic of Korea; KIST-SKKU Brain Research Center, Sungkyunkwan University Institute for Convergence, Suwon, 16419, Republic of Korea.
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3
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Lee S, Seo YE, Choi J, Yan X, Kim T, Choi D, Lee JH. Nucleolar actions in plant development and stress responses. PLANT, CELL & ENVIRONMENT 2024. [PMID: 39169813 DOI: 10.1111/pce.15099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 08/09/2024] [Accepted: 08/10/2024] [Indexed: 08/23/2024]
Abstract
The nucleolus is conventionally acknowledged for its role in ribosomal RNA (rRNA) synthesis and ribosome biogenesis. Recent research has revealed its multifaceted involvement in plant biology, encompassing regulation of the cell cycle, development, and responses to environmental stresses. This comprehensive review explores the diverse roles of the nucleolus in plant growth and responses to environmental stresses. The introduction delves into its traditional functions in rRNA synthesis and potential participation in nuclear liquid-liquid phase separation. By examining the multifaceted roles of nucleolar proteins in plant development, we highlight the impacts of various nucleolar mutants on growth, development, and embryogenesis. Additionally, we reviewed the involvement of nucleoli in responses to abiotic and biotic stresses. Under abiotic stress conditions, the nucleolar structure undergoes morphological changes. In the context of biotic stress, the nucleolus emerges as a common target for effectors of pathogens for manipulation of host immunity to enhance pathogenicity. The detailed exploration of how pathogens interact with nucleoli and manipulate host responses provides valuable insights into plant stress responses as well as plant growth and development. Understanding these processes may pave the way for promising strategies to enhance crop resilience and mitigate the impact of biotic and abiotic stresses in agricultural systems.
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Affiliation(s)
- Soeui Lee
- Plant Immunity Research Center, Seoul National University, Seoul, South Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Ye-Eun Seo
- Plant Immunity Research Center, Seoul National University, Seoul, South Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
- Department of Agriculture, Forestry and Bioresources, College of Agriculture and Life Science, Plant Genomics and Breeding Institute, Seoul National University, Seoul, South Korea
| | - Jeen Choi
- Plant Immunity Research Center, Seoul National University, Seoul, South Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
- Department of Agriculture, Forestry and Bioresources, College of Agriculture and Life Science, Plant Genomics and Breeding Institute, Seoul National University, Seoul, South Korea
| | - Xin Yan
- Plant Immunity Research Center, Seoul National University, Seoul, South Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
- Department of Agriculture, Forestry and Bioresources, College of Agriculture and Life Science, Plant Genomics and Breeding Institute, Seoul National University, Seoul, South Korea
| | - Taewon Kim
- Plant Immunity Research Center, Seoul National University, Seoul, South Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
- Department of Agriculture, Forestry and Bioresources, College of Agriculture and Life Science, Plant Genomics and Breeding Institute, Seoul National University, Seoul, South Korea
| | - Doil Choi
- Plant Immunity Research Center, Seoul National University, Seoul, South Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
- Department of Agriculture, Forestry and Bioresources, College of Agriculture and Life Science, Plant Genomics and Breeding Institute, Seoul National University, Seoul, South Korea
| | - Joo Hyun Lee
- Plant Immunity Research Center, Seoul National University, Seoul, South Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
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4
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Smetana K, Mikulenková D, Karban J, Trněný M. To the ring-shaped nucleolus seen by microscopy using human lymphocytes of blood donors and chronic lymphocytic leukemia patients. Eur J Histochem 2024; 68. [PMID: 39221853 DOI: 10.4081/ejh.2024.4075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Accepted: 06/22/2024] [Indexed: 09/04/2024] Open
Abstract
The present study was undertaken to provide more information on the peripheral RNA containing ring of ringshaped nucleoli (RSNo). Human lymphocytes of blood donors and patients suffering from B chronic lymphocytic leukemia mostly characterized by RSNo represented very convenient cell models for such study. According to the light microscopy the peripheral RNA ring possessed several highly condensed foci. Such regions represented accumulated dense RNA fibrillar components (DFCs) seen by the electron microscopy. In contrary, the incidence of dense granular RNA-containing components (GCs) in surrounding portions of the RNA ring was small. Thus, the structural and morphological organization of the peripheral RNA ring of RSNo apparently reflects sites of micro-segregated foci of DFCs and a small incidence of GCs. That structural organization of the peripheral RNA ring of RSNo appeared to be a prerequisite for further regressive nucleolar changes resulting in the development of micronucleoli in terminal lymphocytes.
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Affiliation(s)
- Karel Smetana
- Institute of Haematology and Blood Transfusion, Prague.
| | | | - Josef Karban
- 1st Hematology and Oncology Clinic of the 1st Medical Faculty of the Charles University and General Medical Hospital, Prague.
| | - Marek Trněný
- 1st Hematology and Oncology Clinic of the 1st Medical Faculty of the Charles University and General Medical Hospital, Prague.
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5
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Taha MS, Ahmadian MR. Nucleophosmin: A Nucleolar Phosphoprotein Orchestrating Cellular Stress Responses. Cells 2024; 13:1266. [PMID: 39120297 PMCID: PMC11312075 DOI: 10.3390/cells13151266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2024] [Revised: 07/18/2024] [Accepted: 07/24/2024] [Indexed: 08/10/2024] Open
Abstract
Nucleophosmin (NPM1) is a key nucleolar protein released from the nucleolus in response to stress stimuli. NPM1 functions as a stress regulator with nucleic acid and protein chaperone activities, rapidly shuttling between the nucleus and cytoplasm. NPM1 is ubiquitously expressed in tissues and can be found in the nucleolus, nucleoplasm, cytoplasm, and extracellular environment. It plays a central role in various biological processes such as ribosome biogenesis, cell cycle regulation, cell proliferation, DNA damage repair, and apoptosis. In addition, it is highly expressed in cancer cells and solid tumors, and its mutation is a major cause of acute myeloid leukemia (AML). This review focuses on NPM1's structural features, functional diversity, subcellular distribution, and role in stress modulation.
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Affiliation(s)
- Mohamed S. Taha
- Institute of Biochemistry and Molecular Biology II, Medical Faculty, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
- Research on Children with Special Needs Department, Institute of Medical Research and Clinical Studies, National Research Centre, Cairo 12622, Egypt
| | - Mohammad Reza Ahmadian
- Institute of Biochemistry and Molecular Biology II, Medical Faculty, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
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6
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Kim JE, Budluang P, Park J, Lee KH, Pakdeepromma S, Kaewpiboon C, Kang HY, Hwang DY, Chung YH. N-benzyl-N-methyldecan-1-amine, derived from garlic, and its derivative alleviate 2,4-dinitrochlorobenzene-induced atopic dermatitis-like skin lesions in mice. Sci Rep 2024; 14:6776. [PMID: 38514712 PMCID: PMC10958003 DOI: 10.1038/s41598-024-56496-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Accepted: 03/07/2024] [Indexed: 03/23/2024] Open
Abstract
Given the intricate etiology and pathogenesis of atopic dermatitis (AD), the complete cure of AD remains challenging. This study aimed to investigate if topically applying N-benzyl-N-methyldecan-1-amine (BMDA), derived from garlic, and its derivative [decyl-(4-methoxy-benzyl)-methyl-1-amine] (DMMA) could effectively alleviate AD-like skin lesions in 2,4-dinitrochlorobenzene (DNCB)-treated mice. Administering these compounds to the irritated skin of DNCB-treated mice significantly reduced swelling, rash, and excoriation severity, alongside a corresponding decrease in inflamed epidermis and dermis. Moreover, they inhibited spleen and lymph node enlargement and showed fewer infiltrated mast cells in the epidermis and dermis through toluidine-blue staining. Additionally, they led to a lower IgE titer in mouse sera as determined by ELISA, compared to vehicle treatment. Analyzing skin tissue from the mice revealed decreased transcript levels of inflammatory cytokines (TNF-α, IL-1β, and IL-6), IL-4, iNOS, and COX-2, compared to control mice. Simultaneously, the compounds impeded the activation of inflammation-related signaling molecules such as JNK, p38 MAPK, and NF-κB in the mouse skin. In summary, these findings suggest that BMDA and DMMA hold the potential to be developed as a novel treatment for healing inflammatory AD.
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Affiliation(s)
- Ji Eun Kim
- Department of Biomaterials Science (BK21 FOUR Program), College of Natural Resources and Life Science, Pusan National University, Miryang, 50463, Republic of Korea
| | - Phatcharaporn Budluang
- Department of Cogno-Mechatronics Engineering, Optomechatronics Research Institute, Pusan National University, Busan, Republic of Korea
| | - Jumin Park
- Department of Food Science and Nutrition, Pusan National University, Busan, 46241, Republic of Korea
| | - Kon Ho Lee
- Department of Convergence Medical Science, Gyeongsang National University College of Medicine, Jinju, 52828, Republic of Korea
| | - Sirichatnach Pakdeepromma
- Department of General Science and Liberal Arts, King Mongkut's Institute of Technology Ladkrabang Prince of Chumphon Campus, Pathio, Chumphon, 86160, Thailand
| | - Chutima Kaewpiboon
- Department of Biology, Faculty of Science and Digital Innovation, Thaksin University, Phatthalung Campus, Phatthalung, 93210, Thailand
| | - Ho Young Kang
- Department of Microbiology, Pusan National University, Busan, 46241, Republic of Korea
| | - Dae Youn Hwang
- Department of Biomaterials Science (BK21 FOUR Program), College of Natural Resources and Life Science, Pusan National University, Miryang, 50463, Republic of Korea.
| | - Young-Hwa Chung
- Department of Cogno-Mechatronics Engineering, Optomechatronics Research Institute, Pusan National University, Busan, Republic of Korea.
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Priyadarshini N, Venkatarama Puppala N, Jayaprakash JP, Khandelia P, Sharma V, Mohannath G. Downregulation of ribosomal RNA (rRNA) genes in human head and neck squamous cell carcinoma (HNSCC) cells correlates with rDNA promoter hypermethylation. Gene 2023; 888:147793. [PMID: 37696422 DOI: 10.1016/j.gene.2023.147793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 08/31/2023] [Accepted: 09/08/2023] [Indexed: 09/13/2023]
Abstract
Eukaryotes carry hundreds of ribosomal RNA (rRNA) genes as tandem arrays, which generate rRNA for protein synthesis. Humans carry ∼ 400 rRNA gene copies and their expression is epigenetically regulated. Dysregulation of rRNA synthesis and ribosome biogenesis are characteristic features of cancers. Targeting aberrant rRNA expression for cancer therapy is being explored. Head and neck squamous cell carcinoma (HNSCC) is among the most prevalent cancers globally. Using quantitative PCR and bisulfite sequencing, we show that rRNA genes are downregulated and their promoters are hypermethylated in HNSCC cell lines. These findings may have relevance for prognosis and diagnosis of HNSCC.
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Affiliation(s)
- Neha Priyadarshini
- Department of Biological Sciences, Birla Institute of Technology & Science-Pilani, Hyderabad Campus, Hyderabad, Telangana, India.
| | - Navinchandra Venkatarama Puppala
- Department of Biological Sciences, Birla Institute of Technology & Science-Pilani, Hyderabad Campus, Hyderabad, Telangana, India.
| | - Jayasree Peroth Jayaprakash
- Department of Biological Sciences, Birla Institute of Technology & Science-Pilani, Hyderabad Campus, Hyderabad, Telangana, India.
| | - Piyush Khandelia
- Department of Biological Sciences, Birla Institute of Technology & Science-Pilani, Hyderabad Campus, Hyderabad, Telangana, India.
| | - Vivek Sharma
- Department of Biological Sciences, Birla Institute of Technology & Science-Pilani, Hyderabad Campus, Hyderabad, Telangana, India.
| | - Gireesha Mohannath
- Department of Biological Sciences, Birla Institute of Technology & Science-Pilani, Hyderabad Campus, Hyderabad, Telangana, India.
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Ando S, Nomoto M, Iwakawa H, Vial-Pradel S, Luo L, Sasabe M, Ohbayashi I, Yamamoto KT, Tada Y, Sugiyama M, Machida Y, Kojima S, Machida C. Arabidopsis ASYMMETRIC LEAVES2 and Nucleolar Factors Are Coordinately Involved in the Perinucleolar Patterning of AS2 Bodies and Leaf Development. PLANTS (BASEL, SWITZERLAND) 2023; 12:3621. [PMID: 37896084 PMCID: PMC10610122 DOI: 10.3390/plants12203621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 10/09/2023] [Accepted: 10/13/2023] [Indexed: 10/29/2023]
Abstract
Arabidopsis ASYMMETRIC LEAVES2 (AS2) plays a key role in the formation of flat symmetric leaves. AS2 represses the expression of the abaxial gene ETTIN/AUXIN RESPONSE FACTOR3 (ETT/ARF3). AS2 interacts in vitro with the CGCCGC sequence in ETT/ARF3 exon 1. In cells of leaf primordia, AS2 localizes at peripheral regions of the nucleolus as two AS2 bodies, which are partially overlapped with chromocenters that contain condensed 45S ribosomal DNA repeats. AS2 contains the AS2/LOB domain, which consists of three sequences conserved in the AS2/LOB family: the zinc finger (ZF) motif, the ICG sequence including the conserved glycine residue, and the LZL motif. AS2 and the genes NUCLEOLIN1 (NUC1), RNA HELICASE10 (RH10), and ROOT INITIATION DEFECTIVE2 (RID2) that encode nucleolar proteins coordinately act as repressors against the expression of ETT/ARF3. Here, we examined the formation and patterning of AS2 bodies made from as2 mutants with amino acid substitutions in the ZF motif and the ICG sequence in cells of cotyledons and leaf primordia. Our results showed that the amino acid residues next to the cysteine residues in the ZF motif were essential for both the formation of AS2 bodies and the interaction with ETT/ARF3 DNA. The conserved glycine residue in the ICG sequence was required for the formation of AS2 bodies, but not for the DNA interaction. We also examined the effects of nuc1, rh10, and rid2 mutations, which alter the metabolism of rRNA intermediates and the morphology of the nucleolus, and showed that more than two AS2 bodies were observed in the nucleolus and at its periphery. These results suggested that the patterning of AS2 bodies is tightly linked to the morphology and functions of the nucleolus and the development of flat symmetric leaves in plants.
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Affiliation(s)
- Sayuri Ando
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai 487-8501, Japan; (S.A.); (H.I.); (S.V.-P.); (Y.M.)
| | - Mika Nomoto
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan; (M.N.); (L.L.); (Y.T.)
- Center for Gene Research, Nagoya University, Nagoya 464-8602, Japan
| | - Hidekazu Iwakawa
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai 487-8501, Japan; (S.A.); (H.I.); (S.V.-P.); (Y.M.)
| | - Simon Vial-Pradel
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai 487-8501, Japan; (S.A.); (H.I.); (S.V.-P.); (Y.M.)
| | - Lilan Luo
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan; (M.N.); (L.L.); (Y.T.)
| | - Michiko Sasabe
- Department of Biology, Faculty of Agriculture and Life Science, Hirosaki University, Bunkyo-cho, Hirosaki 036-8561, Japan;
| | - Iwai Ohbayashi
- Department of Life Sciences, National Cheng Kung University, Tainan City 701, Taiwan;
| | - Kotaro T. Yamamoto
- Division of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Yasuomi Tada
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan; (M.N.); (L.L.); (Y.T.)
- Center for Gene Research, Nagoya University, Nagoya 464-8602, Japan
| | - Munetaka Sugiyama
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan;
| | - Yasunori Machida
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai 487-8501, Japan; (S.A.); (H.I.); (S.V.-P.); (Y.M.)
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan; (M.N.); (L.L.); (Y.T.)
| | - Shoko Kojima
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai 487-8501, Japan; (S.A.); (H.I.); (S.V.-P.); (Y.M.)
| | - Chiyoko Machida
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai 487-8501, Japan; (S.A.); (H.I.); (S.V.-P.); (Y.M.)
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9
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Abstract
The p-arms of the five human acrocentric chromosomes bear nucleolar organizer regions (NORs) comprising ribosomal gene (rDNA) repeats that are organized in a homogeneous tandem array and transcribed in a telomere-to-centromere direction. Precursor ribosomal RNA transcripts are processed and assembled into ribosomal subunits, the nucleolus being the physical manifestation of this process. I review current understanding of nucleolar chromosome biology and describe current exploration into a role for the NOR chromosomal context. Full DNA sequences for acrocentric p-arms are now emerging, aided by the current revolution in long-read sequencing and genome assembly. Acrocentric p-arms vary from 10.1 to 16.7 Mb, accounting for ∼2.2% of the genome. Bordering rDNA arrays, distal junctions, and proximal junctions are shared among the p-arms, with distal junctions showing evidence of functionality. The remaining p-arm sequences comprise multiple satellite DNA classes and segmental duplications that facilitate recombination between heterologous chromosomes, which is likely also involved in Robertsonian translocations.
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Affiliation(s)
- Brian McStay
- Centre for Chromosome Biology, College of Science and Engineering, University of Galway, Galway, Ireland;
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10
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Waldhart AN, Lau KH, Dykstra H, Avequin T, Wu N. Optimal HSF1 activation in response to acute cold stress in BAT requires nuclear TXNIP. iScience 2023; 26:106538. [PMID: 37168572 PMCID: PMC10164894 DOI: 10.1016/j.isci.2023.106538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 02/04/2023] [Accepted: 03/24/2023] [Indexed: 05/13/2023] Open
Abstract
While TXNIP (thioredoxin interacting protein) in the plasma membrane and vesicular location is known to negatively regulate cellular glucose uptake by facilitating glucose transporter endocytosis, the function of TXNIP in the nucleus is far less understood. Herein, we sought to determine the function of nuclear TXNIP in vivo, using a new HA-tagged TXNIP knock-in mouse model. We observed that TXNIP can be found in the nucleus of a variety of cells from different tissues including hepatocytes (liver), enterocytes (small intestine), exocrine cells (pancreas), and brown adipocytes (BAT). Further investigations into the role of nuclear TXNIP in BAT revealed that cold stress rapidly and transiently activated HSF1 (heat shock factor 1). HSF1 interaction with TXNIP during its activation is required for optimal HSF1 directed cold shock response in BAT.
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Affiliation(s)
| | - Kin H. Lau
- Van Andel Institute, Grand Rapids, MI 49503, USA
| | | | | | - Ning Wu
- Van Andel Institute, Grand Rapids, MI 49503, USA
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11
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Liskovykh M, Petrov NS, Noskov VN, Masumoto H, Earnshaw WC, Schlessinger D, Shabalina SA, Larionov V, Kouprina N. Actively transcribed rDNA and distal junction (DJ) sequence are involved in association of NORs with nucleoli. Cell Mol Life Sci 2023; 80:121. [PMID: 37043028 PMCID: PMC10097779 DOI: 10.1007/s00018-023-04770-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 03/27/2023] [Accepted: 03/28/2023] [Indexed: 04/13/2023]
Abstract
Although they are organelles without a limiting membrane, nucleoli have an exclusive structure, built upon the rDNA-rich acrocentric short arms of five human chromosomes (nucleolar organizer regions or NORs). This has raised the question: what are the structural features of a chromosome required for its inclusion in a nucleolus? Previous work has suggested that sequences adjacent to the tandemly repeated rDNA repeat units (DJ, distal junction sequence) may be involved, and we have extended such studies by addressing several issues related to the requirements for the association of NORs with nucleoli. We exploited both a set of somatic cell hybrids containing individual human acrocentric chromosomes and a set of Human Artificial Chromosomes (HACs) carrying different parts of a NOR, including an rDNA unit or DJ or PJ (proximal junction) sequence. Association of NORs with nucleoli was increased when constituent rDNA was transcribed and may be also affected by the status of heterochromatin blocks formed next to the rDNA arrays. Furthermore, our data suggest that a relatively small size DJ region, highly conserved in evolution, is also involved, along with the rDNA repeats, in the localization of p-arms of acrocentric chromosomes in nucleoli. Thus, we infer a cooperative action of rDNA sequence-stimulated by its activity-and sequences distal to rDNA contributing to incorporation into nucleoli. Analysis of NOR sequences also identified LncRNA_038958 in the DJ, a candidate transcript with the region of the suggested promoter that is located close to the DJ/rDNA boundary and contains CTCF binding sites. This LncRNA may affect RNA Polymerase I and/or nucleolar activity. Our findings provide the basis for future studies to determine which RNAs and proteins interact critically with NOR sequences to organize the higher-order structure of nucleoli and their function in normal cells and pathological states.
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Affiliation(s)
- Mikhail Liskovykh
- Developmental Therapeutics Branch, National Cancer Institute, NIH, Bethesda, MD, 20892, USA.
| | - Nikolai S Petrov
- Developmental Therapeutics Branch, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Vladimir N Noskov
- Developmental Therapeutics Branch, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Hiroshi Masumoto
- Laboratory of Chromosome Engineering, Department of Frontier Research and Development, Kazusa DNA Research Institute, Kisarazu, Chiba, 292-0818, Japan
| | - William C Earnshaw
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, EH9 3JR, Scotland, UK
| | - David Schlessinger
- National Institute on Aging, Laboratory of Genetics and Genomics, NIH, Baltimore, MD, 21224, USA
| | - Svetlana A Shabalina
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD, 20892, USA
| | - Vladimir Larionov
- Developmental Therapeutics Branch, National Cancer Institute, NIH, Bethesda, MD, 20892, USA.
| | - Natalay Kouprina
- Developmental Therapeutics Branch, National Cancer Institute, NIH, Bethesda, MD, 20892, USA.
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12
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Tani I, Oikawa Y, Doi S, Janairo JIB, Kamada R, Sakaguchi K. Ribosomal protein uL30 undergoes phase separation with nucleophosmin and regulates nucleolar formation in the absence of RNA. Biochem Biophys Res Commun 2023; 642:35-40. [PMID: 36543022 DOI: 10.1016/j.bbrc.2022.12.041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022]
Abstract
The nucleolus is a membrane-less structure that exists in the nucleus of cells and plays a crucial role in ribosome biogenesis. It is known to be formed through liquid-liquid phase separation (LLPS) caused by the interaction of various nucleolar proteins and nucleic acids. Recently, many studies on LLPS with nucleolar proteins in the presence of RNA showed the importance of electrostatic interactions and cation-pi interactions among RNA and intrinsically disordered regions of proteins. However, it is reported that the initiation of nucleolar formation is RNA polymerase I-independent. The mechanism of nucleolar formation in the early stage remains obscure. In this study, we showed for the first time that the ribosomal protein uL30 and a major nucleolar protein, nucleophosmin (NPM) formed liquid droplets in vitro in the absence of RNA. The liquid droplet formation with uL30 and NPM may be derived from the interaction between the basic regions of uL30 and acidic regions of the oligomeric NPM. The knockdown of uL30 in cells significantly reduced the number of nucleoli, while it did not alter the protein level of NPM. The results showed that LLPS and nucleolar formation were affected by changes in uL30 levels. Our results suggest that the protein-protein interaction between nucleolar proteins may play an important role in nucleolar formation in the early stages when the rRNA content is very low.
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Affiliation(s)
- Itsumi Tani
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Yui Oikawa
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Seiyo Doi
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Jose Isagani B Janairo
- Department of Biology, College of Science, De La Salle University, Manila, 0922, Philippines
| | - Rui Kamada
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Kazuyasu Sakaguchi
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan.
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13
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Jiao L, Liu Y, Yu XY, Pan X, Zhang Y, Tu J, Song YH, Li Y. Ribosome biogenesis in disease: new players and therapeutic targets. Signal Transduct Target Ther 2023; 8:15. [PMID: 36617563 PMCID: PMC9826790 DOI: 10.1038/s41392-022-01285-4] [Citation(s) in RCA: 49] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 12/01/2022] [Accepted: 12/08/2022] [Indexed: 01/10/2023] Open
Abstract
The ribosome is a multi-unit complex that translates mRNA into protein. Ribosome biogenesis is the process that generates ribosomes and plays an essential role in cell proliferation, differentiation, apoptosis, development, and transformation. The mTORC1, Myc, and noncoding RNA signaling pathways are the primary mediators that work jointly with RNA polymerases and ribosome proteins to control ribosome biogenesis and protein synthesis. Activation of mTORC1 is required for normal fetal growth and development and tissue regeneration after birth. Myc is implicated in cancer development by enhancing RNA Pol II activity, leading to uncontrolled cancer cell growth. The deregulation of noncoding RNAs such as microRNAs, long noncoding RNAs, and circular RNAs is involved in developing blood, neurodegenerative diseases, and atherosclerosis. We review the similarities and differences between eukaryotic and bacterial ribosomes and the molecular mechanism of ribosome-targeting antibiotics and bacterial resistance. We also review the most recent findings of ribosome dysfunction in COVID-19 and other conditions and discuss the consequences of ribosome frameshifting, ribosome-stalling, and ribosome-collision. We summarize the role of ribosome biogenesis in the development of various diseases. Furthermore, we review the current clinical trials, prospective vaccines for COVID-19, and therapies targeting ribosome biogenesis in cancer, cardiovascular disease, aging, and neurodegenerative disease.
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Affiliation(s)
- Lijuan Jiao
- grid.263761.70000 0001 0198 0694Institute for Cardiovascular Science and Department of Cardiovascular Surgery, First Affiliated Hospital and Medical College of Soochow University, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, Jiangsu 215123 P. R. China
| | - Yuzhe Liu
- grid.452829.00000000417660726Department of Orthopedics, the Second Hospital of Jilin University, Changchun, Jilin 130000 P. R. China
| | - Xi-Yong Yu
- grid.410737.60000 0000 8653 1072Key Laboratory of Molecular Target & Clinical Pharmacology and the NMPA State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, Guangdong 511436 P. R. China
| | - Xiangbin Pan
- grid.506261.60000 0001 0706 7839Department of Structural Heart Disease, National Center for Cardiovascular Disease, China & Fuwai Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China ,Key Laboratory of Cardiovascular Appratus Innovation, Beijing, 100037 P. R. China
| | - Yu Zhang
- grid.263761.70000 0001 0198 0694Institute for Cardiovascular Science and Department of Cardiovascular Surgery, First Affiliated Hospital and Medical College of Soochow University, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, Jiangsu 215123 P. R. China
| | - Junchu Tu
- grid.263761.70000 0001 0198 0694Institute for Cardiovascular Science and Department of Cardiovascular Surgery, First Affiliated Hospital and Medical College of Soochow University, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, Jiangsu 215123 P. R. China
| | - Yao-Hua Song
- Cyrus Tang Hematology Center, Collaborative Innovation Center of Hematology, Soochow University, National Clinical Research Center for Hematologic Diseases, the First Affiliated Hospital of Soochow University, Suzhou, P. R. China. .,State Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou, 215123, P. R. China.
| | - Yangxin Li
- Institute for Cardiovascular Science and Department of Cardiovascular Surgery, First Affiliated Hospital and Medical College of Soochow University, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, Jiangsu, 215123, P. R. China.
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14
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Genome-wide subcellular protein map for the flagellate parasite Trypanosoma brucei. Nat Microbiol 2023; 8:533-547. [PMID: 36804636 PMCID: PMC9981465 DOI: 10.1038/s41564-022-01295-6] [Citation(s) in RCA: 42] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 11/21/2022] [Indexed: 02/22/2023]
Abstract
Trypanosoma brucei is a model trypanosomatid, an important group of human, animal and plant unicellular parasites. Understanding their complex cell architecture and life cycle is challenging because, as with most eukaryotic microbes, ~50% of genome-encoded proteins have completely unknown functions. Here, using fluorescence microscopy and cell lines expressing endogenously tagged proteins, we mapped the subcellular localization of 89% of the T. brucei proteome, a resource we call TrypTag. We provide clues to function and define lineage-specific organelle adaptations for parasitism, mapping the ultraconserved cellular architecture of eukaryotes, including the first comprehensive 'cartographic' analysis of the eukaryotic flagellum, which is vital for morphogenesis and pathology. To demonstrate the power of this resource, we identify novel organelle subdomains and changes in molecular composition through the cell cycle. TrypTag is a transformative resource, important for hypothesis generation for both eukaryotic evolutionary molecular cell biology and fundamental parasite cell biology.
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15
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Chromatin localization of nucleophosmin organizes ribosome biogenesis. Mol Cell 2022; 82:4443-4457.e9. [PMID: 36423630 PMCID: PMC9949351 DOI: 10.1016/j.molcel.2022.10.033] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 09/01/2022] [Accepted: 10/28/2022] [Indexed: 11/24/2022]
Abstract
Ribosome biogenesis takes place in the nucleolus, a nuclear membrane-less organelle. Although well studied, it remains unknown how nascent ribosomal subunits separate from the central chromatin compartment and move to the outer granular component, where maturation occurs. We find that the Schizosaccharomyces pombe nucleophosmin-like protein Fkbp39 localizes to rDNA sites encoding the 60S subunit rRNA, and this localization contributes to its specific association with nascent 60S subunits. Fkbp39 dissociates from chromatin to bind nascent 60S subunits, causing the latter to partition away from chromatin and from nascent 40S subunits through liquid-liquid phase separation. In vivo, Fkbp39 binding directs the translocation of nascent 60S subunits toward the nucleophosmin-rich granular component. This process increases the efficiency of 60S subunit assembly, facilitating the incorporation of 60S RNA domain III. Thus, chromatin localization determines the specificity of nucleophosmin in sorting nascent ribosomal subunits and coordinates their movement into specialized assembly compartments within the nucleolus.
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16
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Lin S, Rajan S, Lemberg S, Altawil M, Anderson K, Bryant R, Cappeta S, Chin B, Hamdan I, Hamer A, Hyzny R, Karp A, Lee D, Lim A, Nayak M, Palaniappan V, Park S, Satishkumar S, Seth A, Sri Dasari U, Toppari E, Vyas A, Walker J, Weston E, Zafar A, Zielke C, Mahabeleshwar GH, Tartakoff AM. Production of nascent ribosome precursors within the nucleolar microenvironment of Saccharomyces cerevisiae. Genetics 2022; 221:iyac070. [PMID: 35657327 PMCID: PMC9252279 DOI: 10.1093/genetics/iyac070] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 04/19/2022] [Indexed: 11/13/2022] Open
Abstract
35S rRNA transcripts include a 5'-external transcribed spacer followed by rRNAs of the small and large ribosomal subunits. Their processing yields massive precursors that include dozens of assembly factor proteins. In Saccharomyces cerevisiae, nucleolar assembly factors form 2 coaxial layers/volumes around ribosomal DNA. Most of these factors are cyclically recruited from a latent state to an operative state, and are extensively conserved. The layers match, at least approximately, known subcompartments found in higher eukaryotic cells. ∼80% of assembly factors are essential. The number of copies of these assembly factors is comparable to the number of nascent transcripts. Moreover, they exhibit "isoelectric balance," with RNA-binding candidate "nucleator" assembly factors being notably basic. The physical properties of pre-small subunit and pre-large subunit assembly factors are similar, as are their 19 motif signatures detected by hierarchical clustering, unlike motif signatures of the 5'-external transcribed spacer rRNP. Additionally, many assembly factors lack shared motifs. Taken together with the progression of rRNP composition during subunit maturation, and the realization that the ribosomal DNA cable is initially bathed in a subunit-nonspecific assembly factor reservoir/microenvironment, we propose a "3-step subdomain assembly model": Step (1): predominantly basic assembly factors sequentially nucleate sites along nascent rRNA; Step (2): the resulting rRNPs recruit numerous less basic assembly factors along with notably basic ribosomal proteins; Step (3): rRNPs in nearby subdomains consolidate. Cleavages of rRNA then promote release of rRNPs to the nucleoplasm, likely facilitated by the persistence of assembly factors that were already associated with nucleolar precursors.
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Affiliation(s)
- Samantha Lin
- Pathology Department and The Cell Biology Program, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Suchita Rajan
- Pathology Department and The Cell Biology Program, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Sofia Lemberg
- Pathology Department and The Cell Biology Program, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Mark Altawil
- Pathology Department and The Cell Biology Program, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Katherine Anderson
- Pathology Department and The Cell Biology Program, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Ruth Bryant
- Pathology Department and The Cell Biology Program, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Sebastian Cappeta
- Pathology Department and The Cell Biology Program, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Brandon Chin
- Pathology Department and The Cell Biology Program, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Isabella Hamdan
- Pathology Department and The Cell Biology Program, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Annelise Hamer
- Pathology Department and The Cell Biology Program, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Rachel Hyzny
- Pathology Department and The Cell Biology Program, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Andrew Karp
- Pathology Department and The Cell Biology Program, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Daniel Lee
- Pathology Department and The Cell Biology Program, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Alexandria Lim
- Pathology Department and The Cell Biology Program, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Medha Nayak
- Pathology Department and The Cell Biology Program, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Vishnu Palaniappan
- Pathology Department and The Cell Biology Program, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Soomin Park
- Pathology Department and The Cell Biology Program, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Sarika Satishkumar
- Pathology Department and The Cell Biology Program, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Anika Seth
- Pathology Department and The Cell Biology Program, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Uva Sri Dasari
- Pathology Department and The Cell Biology Program, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Emili Toppari
- Pathology Department and The Cell Biology Program, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Ayush Vyas
- Pathology Department and The Cell Biology Program, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Julianne Walker
- Pathology Department and The Cell Biology Program, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Evan Weston
- Pathology Department and The Cell Biology Program, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Atif Zafar
- Pathology Department and The Cell Biology Program, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Cecelia Zielke
- Pathology Department and The Cell Biology Program, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Ganapati H Mahabeleshwar
- Pathology Department and The Cell Biology Program, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Alan M Tartakoff
- Pathology Department and The Cell Biology Program, Case Western Reserve University, Cleveland, OH 44106, USA
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17
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Abstract
The nucleolus is best known for housing the highly ordered assembly line that produces ribosomal subunits. The >100 ribosome assembly factors in the nucleolus are thought to cycle between two states: an operative state (when integrated into subunit assembly intermediates) and a latent state (upon release from intermediates). Although it has become commonplace to refer to the nucleolus as "being a multilayered condensate," and this may be accurate for latent factors, there is little reason to think that such assertions pertain to the operative state of assembly factors.
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Affiliation(s)
- Alan Tartakoff
- Case Western Reserve University, Cleveland, Ohio 44106, USA
| | - Patrick DiMario
- Louisiana State University, Baton Rouge, Louisiana 70803, USA
| | - Eduard Hurt
- Universität Heidelberg, Biochemistry Center, Heidelberg, Baden Württemberg 69120, Germany
| | - Brian McStay
- Centre for Chromosome Biology, Galway H91 TK33, Ireland
| | - Vikram Govind Panse
- Institute of Medical Microbiology, University of Zurich, Zurich CH-8057, Switzerland
| | - David Tollervey
- Wellcome Trust Centre for Cell Biology, Edinburgh EH9 3BF, United Kingdom
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18
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Belmont AS. Nuclear Compartments: An Incomplete Primer to Nuclear Compartments, Bodies, and Genome Organization Relative to Nuclear Architecture. Cold Spring Harb Perspect Biol 2022; 14:a041268. [PMID: 34400557 PMCID: PMC9248822 DOI: 10.1101/cshperspect.a041268] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
This work reviews nuclear compartments, defined broadly to include distinct nuclear structures, bodies, and chromosome domains. It first summarizes original cytological observations before comparing concepts of nuclear compartments emerging from microscopy versus genomic approaches and then introducing new multiplexed imaging approaches that promise in the future to meld both approaches. I discuss how previous models of radial distribution of chromosomes or the binary division of the genome into A and B compartments are now being refined by the recognition of more complex nuclear compartmentalization. The poorly understood question of how these nuclear compartments are established and maintained is then discussed, including through the modern perspective of phase separation, before moving on to address possible functions of nuclear compartments, using the possible role of nuclear speckles in modulating gene expression as an example. Finally, the review concludes with a discussion of future questions for this field.
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Affiliation(s)
- Andrew S Belmont
- Department of Cell and Developmental Biology, University of Illinois, Urbana-Champaign, Urbana, Illinois 61801, USA
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19
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Nucleolus localization of SpyCas9 affects its stability and interferes with host protein translation in mammalian cells. Genes Dis 2022; 9:731-740. [PMID: 35782966 PMCID: PMC9243344 DOI: 10.1016/j.gendis.2020.09.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 09/14/2020] [Accepted: 09/15/2020] [Indexed: 12/28/2022] Open
Abstract
The CRISPR/Cas9 system, originally derived from the prokaryotic adaptive immune system, has been developed as efficient genome editing tools. It enables precise gene manipulation on chromosomal DNA through the specific binding of programmable sgRNA to target DNA, and the Cas9 protein, which has endonuclease activity, will cut a double strand break at specific locus. However, Cas9 is a foreign protein in mammalian cells, and the potential risks associated with its introduction into mammalian cells are not fully understood. In this study, we performed pull-down and mass spectrometry (MS) analysis of Streptococcus pyogenes Cas9 (SpyCas9) interacting proteins in HEK293T cells and showed that the majority of Cas9-associated proteins identified by MS were localized in the nucleolus. Interestingly, we further discovered that the Cas9 protein contains a sequence encoding a nucleolus detention signal (NoDS). Compared with wild-type (WT) Cas9, NoDS-mutated variants of Cas9 (mCas9) are less stable, although their gene editing activity is minimally affected. Overexpression of WT Cas9, but not mCas9, causes general effects on transcription and protein translation in the host cell. Overall, identification of NoDS in Cas9 will improve the understanding of Cas9's biological function in vivo, and the removal of NoDS in Cas9 may enhance its safety for future clinical use.
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20
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Subirana MA, Riemschneider S, Hause G, Dobritzsch D, Schaumlöffel D, Herzberg M. High spatial resolution imaging of subcellular macro and trace element distribution during phagocytosis. Metallomics 2022; 14:6530650. [PMID: 35179212 DOI: 10.1093/mtomcs/mfac011] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 02/10/2022] [Indexed: 11/13/2022]
Abstract
The bioavailability of trace elements in the course of evolution had an essential influence on the emergence of life itself. This is reflected in the co-evolution between eukaryotes and prokaryotes. In this study, the influence and cellular distribution of bioelements during phagocytosis at the host-pathogen interface was investigated using high-resolution nanoscale secondary ion mass spectrometry (NanoSIMS) and quantitative inductively coupled plasma mass spectrometry (ICP-MS). In the eukaryotic murine macrophages (RAW 264.7 cell line), the cellular Fe / Zn ratio was found to be balanced, whereas the dominance of iron in the prokaryotic cells of the pathogen Salmonella enterica Serovar Enteritidis was about 90% compared to zinc. This confirms the evolutionary increased zinc requirement of the eukaryotic animal cell. Using NanoSIMS, the Cs+ primary ion source allowed high spatial resolution mapping of cell morphology down to subcellular level. At a comparable resolution, several low abundant trace elements could be mapped during phagocytosis with a RF plasma O- primary ion source. An enrichment of copper and nickel could be detected in the prokaryotic cells. Surprisingly, an accumulation of cobalt in the area of nuclear envelope was observed indicating an interesting but still unknown distribution of this trace element in murine macrophages.
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Affiliation(s)
- Maria Angels Subirana
- CNRS, Université de Pau et des Pays de l'Adour, E2S UPPA, Institut des Sciences Analytiques et de Physico-Chimie pour l'Environnement et les Matériaux (IPREM), UMR 5254, 64000 Pau, France
| | - Sina Riemschneider
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), 04103 Leipzig, Germany
| | - Gerd Hause
- Martin-Luther-University Halle-Wittenberg, Biozentrum, Weinbergweg 22, 06120 Halle (Saale), Germany
| | - Dirk Dobritzsch
- Martin-Luther-University Halle-Wittenberg, Core Facility - Proteomic Mass Spectrometry, Kurt-Mothes-Str. 3a, 06120 Halle (Saale), Germany
| | - Dirk Schaumlöffel
- CNRS, Université de Pau et des Pays de l'Adour, E2S UPPA, Institut des Sciences Analytiques et de Physico-Chimie pour l'Environnement et les Matériaux (IPREM), UMR 5254, 64000 Pau, France.,Peoples' Friendship University of Russia (RUDN University), Mklukho-Maklaya str. 6, 117198 Moscow, Russia
| | - Martin Herzberg
- Martin-Luther-University Halle-Wittenberg, Institute for Biology/Microbiology, Kurt-Mothes-Str. 3, 06120 Halle/Saale, Germany
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21
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Li YZ, Zhang C, Pei JP, Zhang WC, Zhang CD, Dai DQ. The functional role of Pescadillo ribosomal biogenesis factor 1 in cancer. J Cancer 2022; 13:268-277. [PMID: 34976188 PMCID: PMC8692700 DOI: 10.7150/jca.58982] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 07/20/2021] [Indexed: 12/13/2022] Open
Abstract
Tumors are neogrowths formed by the growth of normal cells or tissues through complex mechanisms under the influence of many factors. The occurrence and development of tumors are affected by many factors. Pescadillo ribosomal biogenesis factor 1 (PES1) has been identified as a cancer-related gene. The study of these genes may open up new avenues for early diagnosis, treatment and prognosis of tumors. As a nucleolar protein and part of the Pes1/Bop1/WDR12 (PeBoW) complex, PES1 is involved in ribosome biogenesis and DNA replication. Many studies have shown that high expression of PES1 is often closely related to the occurrence, proliferation, invasion, metastasis, prognosis and sensitivity to chemotherapeutics of various human malignant tumors through a series of molecular mechanisms and signaling pathways. The molecules that regulate the expression of PES1 include microRNA (miRNA), circular RNA (circRNA), c-Jun, bromodomain-containing protein 4 (BRD4) and nucleolar phosphoprotein B23. However, the detailed pathogenic mechanisms of PES1 overexpression in human malignancies remains unclear. This article summarizes the role of PES1 in the carcinogenesis, prognosis and treatment of multiple tumors, and introduces the molecular mechanisms and signal transduction pathways related to PES1.
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Affiliation(s)
- Yong-Zhi Li
- Department of Gastrointestinal Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang 110032, China
| | - Cheng Zhang
- Department of Gastrointestinal Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang 110032, China
| | - Jun-Peng Pei
- Department of Gastrointestinal Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang 110032, China
| | - Wan-Chuan Zhang
- Department of Gastrointestinal Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang 110032, China
| | - Chun-Dong Zhang
- Department of Gastrointestinal Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang 110032, China.,Department of Gastrointestinal Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Dong-Qiu Dai
- Department of Gastrointestinal Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang 110032, China.,Cancer Center, The Fourth Affiliated Hospital of China Medical University, Shenyang 110032, China
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22
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Yadav U, Verma M, Abbas Z, Sivakumar S, Patra AK. An emissive dual-sensitized bimetallic Eu 2III-bioprobe: design strategy, biological interactions, and nucleolus staining studies. NEW J CHEM 2022. [DOI: 10.1039/d2nj02853k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A dual sensitized Eu2III–bioprobe (1) offers incredible opportunities for fine-tuning and exploring a strongly luminescent probe as a nucleolus staining agent.
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Affiliation(s)
- Usha Yadav
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, Uttar Pradesh, India
| | - Madhu Verma
- Department of Chemical Engineering and Centre for Environmental Science and Engineering, Indian Institute of Technology Kanpur, Kanpur 208016, Uttar Pradesh, India
| | - Zafar Abbas
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, Uttar Pradesh, India
| | - Sri Sivakumar
- Department of Chemical Engineering and Centre for Environmental Science and Engineering, Indian Institute of Technology Kanpur, Kanpur 208016, Uttar Pradesh, India
| | - Ashis K. Patra
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, Uttar Pradesh, India
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23
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Miyake T, McDermott JC. Nucleolar localization of c-Jun. FEBS J 2021; 289:748-765. [PMID: 34499807 DOI: 10.1111/febs.16187] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 08/09/2021] [Accepted: 09/06/2021] [Indexed: 01/20/2023]
Abstract
Nucleoli are well defined for their function in ribosome biogenesis, but only a small fraction of the nucleolar proteome has been characterized. Here, we report that the proto-oncogene, c-Jun, is targeted to the nucleolus. Using live cell imaging in myogenic cells, we document that the c-Jun basic domain contains a unique, evolutionarily conserved motif that determines nucleolar targeting. Fos family Jun dimer partners, such as Fra2, while nuclear, do not co-localize with c-Jun in the nucleolus. A point mutation in c-Jun that mimics Fra2 (M260E) in its Nucleolar Localization sequence (NoLS) results in loss of c-Jun nucleolar targeting while still preserving nuclear localization. Fra2 can sequester c-Jun in the nucleoplasm, indicating that the stoichiometric ratio of heterodimeric partners regulates c-Jun nucleolar targeting. Finally, nucleolar localization of c-Jun modulates nucleolar architecture and ribosomal RNA accumulation. These studies highlight a novel role for Jun family proteins in the nucleolus, having potential implications for a diverse array of AP-1-regulated cellular processes.
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Affiliation(s)
- Tetsuaki Miyake
- Department of Biology, York University, Toronto, ON, Canada.,Muscle Health Research Centre (MHRC), York University, Toronto, ON, Canada.,Centre for Research in Biomolecular Interactions (CRBI), York University, Toronto, ON, Canada
| | - John C McDermott
- Department of Biology, York University, Toronto, ON, Canada.,Muscle Health Research Centre (MHRC), York University, Toronto, ON, Canada.,Centre for Research in Biomolecular Interactions (CRBI), York University, Toronto, ON, Canada.,Centre for Research in Mass Spectrometry (CRMS), York University, Toronto, ON, Canada
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24
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Faria JRC. A nuclear enterprise: zooming in on nuclear organization and gene expression control in the African trypanosome. Parasitology 2021; 148:1237-1253. [PMID: 33407981 PMCID: PMC8311968 DOI: 10.1017/s0031182020002437] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 12/22/2020] [Accepted: 12/24/2020] [Indexed: 12/17/2022]
Abstract
African trypanosomes are early divergent protozoan parasites responsible for high mortality and morbidity as well as a great economic burden among the world's poorest populations. Trypanosomes undergo antigenic variation in their mammalian hosts, a highly sophisticated immune evasion mechanism. Their nuclear organization and mechanisms for gene expression control present several conventional features but also a number of striking differences to the mammalian counterparts. Some of these unorthodox characteristics, such as lack of controlled transcription initiation or enhancer sequences, render their monogenic antigen transcription, which is critical for successful antigenic variation, even more enigmatic. Recent technological developments have advanced our understanding of nuclear organization and gene expression control in trypanosomes, opening novel research avenues. This review is focused on Trypanosoma brucei nuclear organization and how it impacts gene expression, with an emphasis on antigen expression. It highlights several dedicated sub-nuclear bodies that compartmentalize specific functions, whilst outlining similarities and differences to more complex eukaryotes. Notably, understanding the mechanisms underpinning antigen as well as general gene expression control is of great importance, as it might help designing effective control strategies against these organisms.
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Affiliation(s)
- Joana R. C. Faria
- The Wellcome Trust Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, DundeeDD1 5EH, UK
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25
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Tartakoff AM, Chen L, Raghavachari S, Gitiforooz D, Dhinakaran A, Ni CL, Pasadyn C, Mahabeleshwar GH, Pasadyn V, Woolford JL. The nucleolus as a polarized coaxial cable in which the rDNA axis is surrounded by dynamic subunit-specific phases. Curr Biol 2021; 31:2507-2519.e4. [PMID: 33862007 PMCID: PMC8222187 DOI: 10.1016/j.cub.2021.03.041] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 01/18/2021] [Accepted: 03/11/2021] [Indexed: 12/24/2022]
Abstract
In ribosomal DNA (rDNA) repeats, sequences encoding small-subunit (SSU) rRNA precede those encoding large-subunit (LSU) rRNAs. Processing the composite transcript and subunit assembly requires >100 subunit-specific nucleolar assembly factors (AFs). To investigate the functional organization of the nucleolus, we localized AFs in S. cerevisiae in which the rDNA axis was "linearized" to reduce its dimensionality, thereby revealing its coaxial organization. In this situation, rRNA synthesis and processing continue. The axis is embedded in an inner layer/phase of SSU AFs that is surrounded by an outer layer/phase of LSU AFs. When subunit production is inhibited, subsets of AFs differentially relocate between the inner and outer layers, as expected if there is a cycle of repeated relocation whereby "latent" AFs become "operative" when recruited to nascent subunits. Recognition of AF cycling and localization of segments of rRNA make it possible to infer the existence of assembly intermediates that span between the inner and outer layers and to chart the cotranscriptional assembly of each subunit. AF cycling also can explain how having more than one protein phase in the nucleolus makes possible "vectorial 2-phase partitioning" as a driving force for relocation of nascent rRNPs. Because nucleoplasmic AFs are also present in the outer layer, we propose that critical surface remodeling occurs at this site, thereby partitioning subunit precursors into the nucleoplasm for post-transcriptional maturation. Comparison to observations on higher eukaryotes shows that the coaxial paradigm is likely to be applicable for the many other organisms that have rDNA repeats.
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Affiliation(s)
- Alan M Tartakoff
- Department of Pathology and Cell Biology Program, Case Western Reserve University, 2103 Cornell Road, Cleveland, OH 44106, USA.
| | - Lan Chen
- Department of Pathology and Cell Biology Program, Case Western Reserve University, 2103 Cornell Road, Cleveland, OH 44106, USA
| | - Shashank Raghavachari
- Department of Pathology and Cell Biology Program, Case Western Reserve University, 2103 Cornell Road, Cleveland, OH 44106, USA
| | - Daria Gitiforooz
- Department of Pathology and Cell Biology Program, Case Western Reserve University, 2103 Cornell Road, Cleveland, OH 44106, USA
| | - Akshyasri Dhinakaran
- Department of Pathology and Cell Biology Program, Case Western Reserve University, 2103 Cornell Road, Cleveland, OH 44106, USA
| | - Chun-Lun Ni
- Department of Pathology and Cell Biology Program, Case Western Reserve University, 2103 Cornell Road, Cleveland, OH 44106, USA
| | | | - Ganapati H Mahabeleshwar
- Department of Pathology and Cell Biology Program, Case Western Reserve University, 2103 Cornell Road, Cleveland, OH 44106, USA
| | - Vanessa Pasadyn
- Department of Pathology and Cell Biology Program, Case Western Reserve University, 2103 Cornell Road, Cleveland, OH 44106, USA
| | - John L Woolford
- Department of Biological Sciences, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213, USA
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26
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27
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Mangan H, McStay B. Human nucleoli comprise multiple constrained territories, tethered to individual chromosomes. Genes Dev 2021; 35:483-488. [PMID: 33664058 PMCID: PMC8015717 DOI: 10.1101/gad.348234.121] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 02/01/2021] [Indexed: 11/24/2022]
Abstract
It is unknown how ribosomal gene (rDNA) arrays from multiple chromosomal nucleolar organizers (NORs) partition within human nucleoli. Exploration of this paradigm for chromosomal organization is complicated by the shared DNA sequence composition of five NOR-bearing acrocentric chromosome p-arms. Here, we devise a methodology for genetic manipulation of individual NORs. Efficient "scarless" genome editing of rDNA repeats is achieved on "poised" human NORs held within monochromosomal cell hybrids. Subsequent transfer to human cells introduces "active" NORs yielding readily discernible functional customized ribosomes. We reveal that ribosome biogenesis occurs entirely within constrained territories, tethered to individual NORs inside a larger nucleolus.
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Affiliation(s)
- Hazel Mangan
- Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland Galway, Galway H91 W2TY, Ireland
| | - Brian McStay
- Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland Galway, Galway H91 W2TY, Ireland
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28
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Bizhanova A, Kaufman PD. Close to the edge: Heterochromatin at the nucleolar and nuclear peripheries. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2021; 1864:194666. [PMID: 33307247 PMCID: PMC7855492 DOI: 10.1016/j.bbagrm.2020.194666] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 11/11/2020] [Accepted: 11/29/2020] [Indexed: 02/06/2023]
Abstract
Chromatin is a dynamic structure composed of DNA, RNA, and proteins, regulating storage and expression of the genetic material in the nucleus. Heterochromatin plays a crucial role in driving the three-dimensional arrangement of the interphase genome, and in preserving genome stability by maintaining a subset of the genome in a silent state. Spatial genome organization contributes to normal patterns of gene function and expression, and is therefore of broad interest. Mammalian heterochromatin, the focus of this review, mainly localizes at the nuclear periphery, forming Lamina-associated domains (LADs), and at the nucleolar periphery, forming Nucleolus-associated domains (NADs). Together, these regions comprise approximately one-half of mammalian genomes, and most but not all loci within these domains are stochastically placed at either of these two locations after exit from mitosis at each cell cycle. Excitement about the role of these heterochromatic domains in early development has recently been heightened by the discovery that LADs appear at some loci in the preimplantation mouse embryo prior to other chromosomal features like compartmental identity and topologically-associated domains (TADs). While LADs have been extensively studied and mapped during cellular differentiation and early embryonic development, NADs have been less thoroughly studied. Here, we summarize pioneering studies of NADs and LADs, more recent advances in our understanding of cis/trans-acting factors that mediate these localizations, and discuss the functional significance of these associations.
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Affiliation(s)
- Aizhan Bizhanova
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Paul D Kaufman
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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29
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Korsholm LM, Gál Z, Nieto B, Quevedo O, Boukoura S, Lund CC, Larsen DH. Recent advances in the nucleolar responses to DNA double-strand breaks. Nucleic Acids Res 2020; 48:9449-9461. [PMID: 32857853 PMCID: PMC7515731 DOI: 10.1093/nar/gkaa713] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 08/13/2020] [Accepted: 08/26/2020] [Indexed: 12/15/2022] Open
Abstract
DNA damage poses a serious threat to human health and cells therefore continuously monitor and repair DNA lesions across the genome. Ribosomal DNA is a genomic domain that represents a particular challenge due to repetitive sequences, high transcriptional activity and its localization in the nucleolus, where the accessibility of DNA repair factors is limited. Recent discoveries have significantly extended our understanding of how cells respond to DNA double-strand breaks (DSBs) in the nucleolus, and new kinases and multiple down-stream targets have been identified. Restructuring of the nucleolus can occur as a consequence of DSBs and new data point to an active regulation of this process, challenging previous views. Furthermore, new insights into coordination of cell cycle phases and ribosomal DNA repair argue against existing concepts. In addition, the importance of nucleolar-DNA damage response (n-DDR) mechanisms for maintenance of genome stability and the potential of such factors as anti-cancer targets is becoming apparent. This review will provide a detailed discussion of recent findings and their implications for our understanding of the n-DDR. The n-DDR shares features with the DNA damage response (DDR) elsewhere in the genome but is also emerging as an independent response unique to ribosomal DNA and the nucleolus.
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Affiliation(s)
| | | | - Blanca Nieto
- Danish Cancer Society Research Center, Nucleolar Stress and Disease Group, Strandboulevarden 49, 2100 Copenhagen, Denmark
| | - Oliver Quevedo
- Danish Cancer Society Research Center, Nucleolar Stress and Disease Group, Strandboulevarden 49, 2100 Copenhagen, Denmark
| | - Stavroula Boukoura
- Danish Cancer Society Research Center, Nucleolar Stress and Disease Group, Strandboulevarden 49, 2100 Copenhagen, Denmark
| | - Casper Carstens Lund
- Danish Cancer Society Research Center, Nucleolar Stress and Disease Group, Strandboulevarden 49, 2100 Copenhagen, Denmark
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30
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NORs on human acrocentric chromosome p-arms are active by default and can associate with nucleoli independently of rDNA. Proc Natl Acad Sci U S A 2020; 117:10368-10377. [PMID: 32332163 PMCID: PMC7229746 DOI: 10.1073/pnas.2001812117] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
A detailed description of how the genome is organized within the human nucleus is a major research goal. Nucleolar organizer regions (NORs) comprising ribosomal DNA (rDNA) arrays are located on the p-arms of the five human acrocentric chromosomes. Here we characterize the rules of engagement between NORs and nucleoli. We reveal variation in rDNA distribution, with some primary cell lines containing as many as four acrocentrics devoid of rDNA. We establish the default status of NORs as active and show that acrocentric p-arms devoid of rDNA retain nucleolar association potential. Based on our data, we propose that in diploid human cells, all 10 acrocentric chromosomes are nucleolar-associated, with involvement of non-rDNA sequences buffering against variable rDNA distribution. Nucleoli, the sites of ribosome biogenesis and the largest structures in human nuclei, form around nucleolar organizer regions (NORs) comprising ribosomal DNA (rDNA) arrays. NORs are located on the p-arms of the five human acrocentric chromosomes. Defining the rules of engagement between these p-arms and nucleoli takes on added significance as describing the three-dimensional organization of the human genome represents a major research goal. Here we used fluorescent in situ hybridization (FISH) and immuno-FISH on metaphase chromosomes from karyotypically normal primary and hTERT-immortalized human cell lines to catalog NORs in terms of their relative rDNA content and activity status. We demonstrate that a proportion of acrocentric p-arms in cell lines and from normal human donors have no detectable rDNA. Surprisingly, we found that all NORs with detectable rDNA are active, as defined by upstream binding factor loading. We determined the nucleolar association status of all NORs during interphase, and found that nucleolar association of acrocentric p-arms can occur independently of rDNA content, suggesting that sequences elsewhere on these chromosome arms drive nucleolar association. In established cancer lines, we characterize a variety of chromosomal rearrangements involving acrocentric p-arms and observe silent, rDNA-containing NORs that are dissociated from nucleoli. In conclusion, our findings indicate that within human nuclei, positioning of all 10 acrocentric chromosomes is dictated by nucleolar association. Furthermore, these nucleolar associations are buffered against interindividual variation in the distribution of rDNA.
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31
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Chen PH, Chen YT, Chu TY, Ma TH, Wu MH, Lin HH, Chang YS, Tan BCM, Lo SJ. Nucleolar control by a non-apoptotic p53-caspases-deubiquitinylase axis promotes resistance to bacterial infection. FASEB J 2020; 34:1107-1121. [PMID: 31914708 DOI: 10.1096/fj.201901959r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 10/02/2019] [Accepted: 10/15/2019] [Indexed: 11/11/2022]
Abstract
The nucleolus is best known for its cellular role in regulating ribosome production and growth. More recently, an unanticipated role for the nucleolus in innate immunity has recently emerged whereby downregulation of fibrillarin and nucleolar contraction confers pathogen resistance across taxa. The mechanism of this downregulation, however, remains obscure. Here we report that rather than fibrillarin itself being the proximal factor in this pathway, the key player is a fibrillarin-stabilizing deubiquitinylase USP-33. This was discovered by a candidate-gene search of Caenorhabditis elegans in which CED-3 caspase was revealed to execute targeted cleavage of USP-33, thus destabilizing fibrillarin. We also showed that cep-1 and ced-3 mutant worms altered nucleolar size and decreased antimicrobial peptide gene, spp-1, expression rendering susceptibility to bacterial infection. These phenotypes were reversed by usp-33 knockdown, thus linking the CEP-1-CED-3-USP-33 pathway with nucleolar control and resistance to bacterial infection in worms. Parallel experiments with the human analogs of caspases and USP36 revealed similar roles in coordinating these two processes. In summary, our work outlined a conserved cascade that connects cell death signaling to nucleolar control and innate immune response.
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Affiliation(s)
- Po-Hsiang Chen
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Yi-Tung Chen
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Tai-Ying Chu
- Department of Microbiology and Immunology, Chang Gung University, Taoyuan, Taiwan
| | - Tian-Hsiang Ma
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Mei-Hsuan Wu
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Hsi-Hsien Lin
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Department of Microbiology and Immunology, Chang Gung University, Taoyuan, Taiwan
| | - Yu-Sun Chang
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Bertrand Chin-Ming Tan
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan.,Department of Neurosurgery, Lin-Kou Medical Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Szecheng J Lo
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
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32
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33
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van Sluis M, Gailín MÓ, McCarter JGW, Mangan H, Grob A, McStay B. Human NORs, comprising rDNA arrays and functionally conserved distal elements, are located within dynamic chromosomal regions. Genes Dev 2019; 33:1688-1701. [PMID: 31727772 PMCID: PMC6942050 DOI: 10.1101/gad.331892.119] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 10/23/2019] [Indexed: 01/09/2023]
Abstract
In this study, van Sluis et al. investigated the role of chromosomal context in nuclear organizer regions (NORs)/ribosomal gene (rDNA) in nucleolar formation and function. The analyses combined sequence capture and long-read sequencing to characterize the regions distal to rDNA arrays (DJ) on isolated acrocentric chromosomes, and their findings provide direct evidence for exchanges between heterologous human acrocentric p-arms, and uncover extensive structural variation between chromosomes and among individuals. Human nucleolar organizer regions (NORs), containing ribosomal gene (rDNA) arrays, are located on the p-arms of acrocentric chromosomes (HSA13–15, 21, and 22). Absence of these p-arms from genome references has hampered research on nucleolar formation. Previously, we assembled a distal junction (DJ) DNA sequence contig that abuts rDNA arrays on their telomeric side, revealing that it is shared among the acrocentrics and impacts nucleolar organization. To facilitate inclusion into genome references, we describe sequencing the DJ from all acrocentrics, including three versions of HSA21, ∼3 Mb of novel sequence. This was achieved by exploiting monochromosomal somatic cell hybrids containing single human acrocentric chromosomes with NORs that retain functional potential. Analyses revealed remarkable DJ sequence and functional conservation among human acrocentrics. Exploring chimpanzee acrocentrics, we show that “DJ-like” sequences and abutting rDNA arrays are inverted as a unit in comparison to humans. Thus, rDNA arrays and linked DJs represent a conserved functional locus. We provide direct evidence for exchanges between heterologous human acrocentric p-arms, and uncover extensive structural variation between chromosomes and among individuals. These findings lead us to revaluate the molecular definition of NORs, identify novel genomic structural variation, and provide a rationale for the distinctive chromosomal organization of NORs.
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Affiliation(s)
- Marjolein van Sluis
- Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Michael Ó Gailín
- Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Joseph G W McCarter
- Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Hazel Mangan
- Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Alice Grob
- Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Brian McStay
- Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
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34
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Deane CAS, Brown IR. Intracellular Targeting of Heat Shock Proteins in Differentiated Human Neuronal Cells Following Proteotoxic Stress. J Alzheimers Dis 2019; 66:1295-1308. [PMID: 30412487 DOI: 10.3233/jad-180536] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
HSPA6 (Hsp70B') is an inducible member of the Hsp70 (HSPA) family of heat shock proteins that is present in the human genome and not found in mouse and rat. Hence it is lacking in current animal models of neurodegenerative diseases. To advance knowledge of the little studied HSPA6, differentiated human neuronal SH-SY5Y cells were treated with the proteotoxic stress-inducing agent MG132. A robust induction of HSPA6 was apparent which localized to the periphery of MG132-induced protein aggregates in the neuronal cytoplasm. Components of the protein disaggregation/refolding machine that co-operate with Hsp70 also targeted the periphery of cytoplasmic protein aggregates, including DNAJB1 (Hsp40-1), HSPH1 (Hsp105α), and HSPB1 (Hsp27). These data suggest that HSPA6 is involved in the response of human neuronal cells to proteotoxic stress that is a feature of neurodegenerative diseases which have been characterized as protein misfolding disorders. Constitutively expressed HSPA8 (Hsc70) also localized tothe periphery of cytoplasmic protein aggregates following the treatment of differentiated human neuronal cells with MG132. HSPA8 could provide a rapid response to proteotoxic stress in neuronal cells, circumventing the time required to upregulate inducible Hsps.
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Affiliation(s)
- Catherine A S Deane
- Department of Biological Sciences, Centre for the Neurobiology of Stress, University of Toronto Scarborough, Toronto, Ontario, Canada
| | - Ian R Brown
- Department of Biological Sciences, Centre for the Neurobiology of Stress, University of Toronto Scarborough, Toronto, Ontario, Canada
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35
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Abstract
Selectively targeting the cell nucleolus remains a challenge. Here, we report the first case in which d-peptides form membraneless molecular condensates with RNA for targeting cell nucleolus. A d-peptide derivative, enriched with lysine and hydrophobic residues, self-assembles to form nanoparticles, which enter cells through clathrin-dependent endocytosis and mainly accumulate at the cell nucleolus. A structural analogue of the d-peptide reveals that the particle morphology of the assemblies, which depends on the side chain modification, favors the cellular uptake. In contrast to those of the d-peptide, the assemblies of the corresponding l-enantiomer largely localize in cell lysosomes. Preliminary mechanism study suggests that the d-peptide nanoparticles interact with RNA to form membraneless condensates in the nucleolus, which further induces DNA damage and results in cell death. This work illustrates a new strategy for rationally designing supramolecular assemblies of d-peptides for targeting subcellular organelles.
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Affiliation(s)
- Huaimin Wang
- Department of Chemistry, Brandeis University, 415 South St., Waltham, MA 02454, USA
| | - Zhaoqianqi Feng
- Department of Chemistry, Brandeis University, 415 South St., Waltham, MA 02454, USA
| | - Weiyi Tan
- Department of Chemistry, Brandeis University, 415 South St., Waltham, MA 02454, USA
| | - Bing Xu
- Department of Chemistry, Brandeis University, 415 South St., Waltham, MA 02454, USA
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36
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Nucleolar DNA Double-Strand Break Responses Underpinning rDNA Genomic Stability. Trends Genet 2019; 35:743-753. [PMID: 31353047 DOI: 10.1016/j.tig.2019.07.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 06/28/2019] [Accepted: 07/01/2019] [Indexed: 12/12/2022]
Abstract
Nucleoli, the sites of ribosome biogenesis, form around ribosomal gene (rDNA) arrays termed nucleolar organiser regions (NORs). These are the most transcriptionally active regions of the human genome and specialised responses have evolved to ensure their genomic stability. This review focuses on nucleolar responses to DNA double-strand breaks (DSBs) introduced into rDNA arrays using sequence-specific endonucleases, including CRISPR/Cas9. Repair of rDNA DSBs is predominantly carried out by the homology-directed repair (HDR) pathway that is facilitated by inhibition of transcription by RNA polymerase-I (Pol-I) and ensuing dramatic nucleolar reorganisation. Additionally, we review evidence that nucleoli can sense and respond to DSBs elsewhere in the genome.
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37
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Gallagher JEG. Proteins and RNA sequences required for the transition of the t-Utp complex into the SSU processome. FEMS Yeast Res 2019; 19:5184469. [PMID: 30445532 DOI: 10.1093/femsyr/foy120] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Accepted: 11/12/2018] [Indexed: 12/20/2022] Open
Abstract
Ribosomes are synthesized by large ribonucleoprotein complexes cleaving and properly assembling highly structured rRNAs with ribosomal proteins. Transcription and processing of pre-rRNAs are linked by the transcription-Utp sub-complex (t-Utps), a sub-complex of the small subunit (SSU) processome and prompted the investigations for the requirements of t-Utp formation and transition into the SSU processome. The rDNA promoter, the first 44 nucleotides of the 5΄ETS, and active transcription by pol I were sufficient to recruit the t-Utps to the rDNA. Pol5, accessory factor, dissociated as t-Utps matured into the UtpA complex which permitted later recruitment of the UtpB, U3 snoRNP and the Mpp10 complex into the SSU processome. The t-Utp complex associated with short RNAs 121 and 138 nucleotides long transcribed from the 5΄ETS. These transcripts were not present when pol II transcribed the rDNA or in nondividing cells. Depletion of a t-Utp, but not of other SSU processome components led to decreased levels of the short transcripts. However, ectopic expression of the short transcripts slowed the growth of yeast with impaired rDNA transcription. These results provide insight into how transcription of the rRNA primes the assemble of t-Utp complex with the pre-rRNA into the UtpA complex and the later association of SSU processome components.
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38
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Chen Y, Li J, Cao F, Lam J, Cheng CC, Yu CH, Huen MS. Nucleolar residence of the seckel syndrome protein TRAIP is coupled to ribosomal DNA transcription. Nucleic Acids Res 2019; 46:10119-10131. [PMID: 30165463 PMCID: PMC6212796 DOI: 10.1093/nar/gky775] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Accepted: 08/16/2018] [Indexed: 12/30/2022] Open
Abstract
The RING finger protein TRAIP protects genome integrity and its mutation causes Seckel syndrome. TRAIP encodes a nucleolar protein that migrates to UV-induced DNA lesions via a direct interaction with the DNA replication clamp PCNA. Thus far, mechanistically how UV mobilizes TRAIP from the nucleoli remains unknown. We found that PCNA binding is dispensable for the nucleolus-nucleoplasm shuttling of TRAIP following cell exposure to UV irradiation, and that its redistribution did not rely on the master DNA damage kinases ATM and ATR. Interestingly, I-PpoI-induced ribosomal DNA damage led to TRAIP exclusion from the nucleoli, raising the possibility that active ribosomal DNA transcription may underlie TRAIP retention in the nuclear sub-compartments. Accordingly, chemical inhibition of RNA polymerase I activity led to TRAIP diffusion into the nucleoplasm, and was coupled with marked reduction of DNA/RNA hybrids in the nucleoli, suggesting that TRAIP may be sequestered via binding to nucleic acid structures in the nucleoli. Consistently, cell pre-treatment with DNase/RNase effectively released TRAIP from the nucleoli. Taken together, our study defines a bipartite mechanism that drives TRAIP trafficking in response to UV damage, and highlights the nucleolus as a stress sensor that contributes to orchestrating DNA damage responses.
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Affiliation(s)
- Yangzi Chen
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong S.A.R
| | - Junshi Li
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong S.A.R
| | - Fakun Cao
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong S.A.R
| | - Jason Lam
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong S.A.R
| | - Clooney Cy Cheng
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong S.A.R
| | - Cheng-Han Yu
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong S.A.R
| | - Michael Sy Huen
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong S.A.R.,Center for Synthetic Biology Engineering Research, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, PR China.,State Key Laboratory of Brain and Cognitive Sciences, The University of Hong Kong, Hong Kong S.A.R
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39
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Fritz AJ, Sehgal N, Pliss A, Xu J, Berezney R. Chromosome territories and the global regulation of the genome. Genes Chromosomes Cancer 2019; 58:407-426. [PMID: 30664301 DOI: 10.1002/gcc.22732] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 01/11/2019] [Accepted: 01/12/2019] [Indexed: 12/29/2022] Open
Abstract
Spatial positioning is a fundamental principle governing nuclear processes. Chromatin is organized as a hierarchy from nucleosomes to Mbp chromatin domains (CD) or topologically associating domains (TADs) to higher level compartments culminating in chromosome territories (CT). Microscopic and sequencing techniques have substantiated chromatin organization as a critical factor regulating gene expression. For example, enhancers loop back to interact with their target genes almost exclusively within TADs, distally located coregulated genes reposition into common transcription factories upon activation, and Mbp CDs exhibit dynamic motion and configurational changes in vivo. A longstanding question in the nucleus field is whether an interactive nuclear matrix provides a direct link between structure and function. The findings of nonrandom radial positioning of CT within the nucleus suggest the possibility of preferential interaction patterns among populations of CT. Sequential labeling up to 10 CT followed by application of computer imaging and geometric graph mining algorithms revealed cell-type specific interchromosomal networks (ICN) of CT that are altered during the cell cycle, differentiation, and cancer progression. It is proposed that the ICN correlate with the global level of genome regulation. These approaches also demonstrated that the large scale 3-D topology of CT is specific for each CT. The cell-type specific proximity of certain chromosomal regions in normal cells may explain the propensity of distinct translocations in cancer subtypes. Understanding how genes are dysregulated upon disruption of the normal "wiring" of the nucleus by translocations, deletions, and amplifications that are hallmarks of cancer, should enable more targeted therapeutic strategies.
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Affiliation(s)
- Andrew J Fritz
- Department of Biochemistry and University of Vermont Cancer Center, The University of Vermont Larner College of Medicine, Burlington, Vermont
| | - Nitasha Sehgal
- Department of Biological Sciences, University at Buffalo, Buffalo, New York
| | - Artem Pliss
- Institute for Lasers, Photonics and Biophotonics and the Department of Chemistry, University at Buffalo, Buffalo, New York
| | - Jinhui Xu
- Department of Computer Science and Engineering, University at Buffalo, Buffalo, New York
| | - Ronald Berezney
- Department of Biological Sciences, University at Buffalo, Buffalo, New York
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40
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Nyhus C, Pihl M, Hyttel P, Hall VJ. Evidence for nucleolar dysfunction in Alzheimer's disease. Rev Neurosci 2019; 30:685-700. [PMID: 30849050 DOI: 10.1515/revneuro-2018-0104] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 01/08/2019] [Indexed: 11/15/2022]
Abstract
The nucleolus is a dynamically changing organelle that is central to a number of important cellular functions. Not only is it important for ribosome biogenesis, but it also reacts to stress by instigating a nucleolar stress response and is further involved in regulating the cell cycle. Several studies report nucleolar dysfunction in Alzheimer's disease (AD). Studies have reported a decrease in both total nucleolar volume and transcriptional activity of the nucleolar organizing regions. Ribosomes appear to be targeted by oxidation and reduced protein translation has been reported. In addition, several nucleolar proteins are dysregulated and some of these appear to be implicated in classical AD pathology. Some studies also suggest that the nucleolar stress response may be activated in AD, albeit this latter research is rather limited and requires further investigation. The purpose of this review is to draw the connections of all these studies together and signify that there are clear changes in the nucleolus and the ribosomes in AD. The nucleolus is therefore an organelle that requires more attention than previously given in relation to understanding the biological mechanisms underlying the disease.
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Affiliation(s)
- Caitlin Nyhus
- Department of Veterinary and Animal Sciences, Faculty of Health Sciences, University of Copenhagen, Grønnegårdsvej 7, Frederiksberg C DK-1870, Denmark
| | - Maria Pihl
- Department of Veterinary and Animal Sciences, Faculty of Health Sciences, University of Copenhagen, Grønnegårdsvej 7, Frederiksberg C DK-1870, Denmark
| | - Poul Hyttel
- Department of Veterinary and Animal Sciences, Faculty of Health Sciences, University of Copenhagen, Grønnegårdsvej 7, Frederiksberg C DK-1870, Denmark
| | - Vanessa Jane Hall
- Department of Veterinary and Animal Sciences, Faculty of Health Sciences, University of Copenhagen, Grønnegårdsvej 7, Frederiksberg C DK-1870, Denmark
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41
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Kamal KY, Herranz R, van Loon JJWA, Medina FJ. Cell cycle acceleration and changes in essential nuclear functions induced by simulated microgravity in a synchronized Arabidopsis cell culture. PLANT, CELL & ENVIRONMENT 2019; 42:480-494. [PMID: 30105864 DOI: 10.1111/pce.13422] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 07/22/2018] [Accepted: 08/04/2018] [Indexed: 06/08/2023]
Abstract
Zero gravity is an environmental challenge unknown to organisms throughout evolution on Earth. Nevertheless, plants are sensitive to altered gravity, as exemplified by changes in meristematic cell proliferation and growth. We found that synchronized Arabidopsis-cultured cells exposed to simulated microgravity showed a shortened cell cycle, caused by a shorter G2/M phase and a slightly longer G1 phase. The analysis of selected marker genes and proteins by quantitative polymerase chain reaction and flow cytometry in synchronic G1 and G2 subpopulations indicated changes in gene expression of core cell cycle regulators and chromatin-modifying factors, confirming that microgravity induced misregulation of G2/M and G1/S checkpoints and chromatin remodelling. Changes in chromatin-based regulation included higher DNA methylation and lower histone acetylation, increased chromatin condensation, and overall depletion of nuclear transcription. Estimation of ribosome biogenesis rate using nucleolar parameters and selected nucleolar genes and proteins indicated reduced nucleolar activity under simulated microgravity, especially at G2/M. These results expand our knowledge of how meristematic cells are affected by real and simulated microgravity. Counteracting this cellular stress is necessary for plant culture in space exploration.
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Affiliation(s)
- Khaled Y Kamal
- Plant Cell Nucleolus, Proliferation & Microgravity Laboratory, Centro de Investigaciones Biológicas (CSIC), Madrid, Spain
- Agronomy Department, Zagazig University, Zagazig, Egypt
| | - Raúl Herranz
- Plant Cell Nucleolus, Proliferation & Microgravity Laboratory, Centro de Investigaciones Biológicas (CSIC), Madrid, Spain
| | - Jack J W A van Loon
- DESC (Dutch Experiment Support Center), Department of Oral and Maxillofacial Surgery/Oral Pathology, VU University Medical Center and Academic Centre for Dentistry Amsterdam (ACTA), Amsterdam, The Netherlands
- ESA-ESTEC, TEC-MMG, Noordwijk, The Netherlands
| | - F Javier Medina
- Plant Cell Nucleolus, Proliferation & Microgravity Laboratory, Centro de Investigaciones Biológicas (CSIC), Madrid, Spain
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Penzo M, Montanaro L, Treré D, Derenzini M. The Ribosome Biogenesis-Cancer Connection. Cells 2019; 8:cells8010055. [PMID: 30650663 PMCID: PMC6356843 DOI: 10.3390/cells8010055] [Citation(s) in RCA: 139] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 01/08/2019] [Accepted: 01/14/2019] [Indexed: 01/05/2023] Open
Abstract
Multifaceted relations link ribosome biogenesis to cancer. Ribosome biogenesis takes place in the nucleolus. Clarifying the mechanisms involved in this nucleolar function and its relationship with cell proliferation: (1) allowed the understanding of the reasons for the nucleolar changes in cancer cells and their exploitation in tumor pathology, (2) defined the importance of the inhibition of ribosome biogenesis in cancer chemotherapy and (3) focused the attention on alterations of ribosome biogenesis in the pathogenesis of cancer. This review summarizes the research milestones regarding these relevant relationships between ribosome biogenesis and cancer. The structure and function of the nucleolus will also be briefly described.
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Affiliation(s)
- Marianna Penzo
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum-University of Bologna, 40138 Bologna, Italy.
- Center for Applied Biomedical Research (CRBA), Alma Mater Studiorum-University of Bologna, 40138 Bologna, Italy.
| | - Lorenzo Montanaro
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum-University of Bologna, 40138 Bologna, Italy.
- Center for Applied Biomedical Research (CRBA), Alma Mater Studiorum-University of Bologna, 40138 Bologna, Italy.
| | - Davide Treré
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum-University of Bologna, 40138 Bologna, Italy.
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43
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Wang M, Bokros M, Theodoridis PR, Lee S. Nucleolar Sequestration: Remodeling Nucleoli Into Amyloid Bodies. Front Genet 2019; 10:1179. [PMID: 31824572 PMCID: PMC6881480 DOI: 10.3389/fgene.2019.01179] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Accepted: 10/24/2019] [Indexed: 01/14/2023] Open
Abstract
This year marks the 20th anniversary of the discovery that the nucleolus can temporarily immobilize proteins, a process known as nucleolar sequestration. This review reflects on the progress made to understand the physiological roles of nucleolar sequestration and the mechanisms involved in the immobilization of proteins. We discuss how protein immobilization can occur through a highly choreographed amyloidogenic program that converts the nucleolus into a large fibrous organelle with amyloid-like characteristics called the amyloid body (A-body). We propose a working model of A-body biogenesis that includes a role for low-complexity ribosomal intergenic spacer RNA (rIGSRNA) and a discrete peptide sequence, the amyloid-converting motif (ACM), found in many proteins that undergo immobilization. Amyloid bodies provide a unique model to study the multistep assembly of a membraneless compartment and may provide alternative insights into the pathological amyloidogenesis involved in neurological disorders.
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Affiliation(s)
- Miling Wang
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL, United States
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL, United States
| | - Michael Bokros
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL, United States
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL, United States
| | - Phaedra Rebecca Theodoridis
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL, United States
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL, United States
| | - Stephen Lee
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL, United States
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL, United States
- Department of Urology, Miller School of Medicine, University of Miami, FL, United States
- *Correspondence: Stephen Lee,
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44
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Frankowski KJ, Wang C, Patnaik S, Schoenen FJ, Southall N, Li D, Teper Y, Sun W, Kandela I, Hu D, Dextras C, Knotts Z, Bian Y, Norton J, Titus S, Lewandowska MA, Wen Y, Farley KI, Griner LM, Sultan J, Meng Z, Zhou M, Vilimas T, Powers AS, Kozlov S, Nagashima K, Quadri HS, Fang M, Long C, Khanolkar O, Chen W, Kang J, Huang H, Chow E, Goldberg E, Feldman C, Xi R, Kim HR, Sahagian G, Baserga SJ, Mazar A, Ferrer M, Zheng W, Shilatifard A, Aubé J, Rudloff U, Marugan JJ, Huang S. Metarrestin, a perinucleolar compartment inhibitor, effectively suppresses metastasis. Sci Transl Med 2018; 10:eaap8307. [PMID: 29769289 PMCID: PMC6176865 DOI: 10.1126/scitranslmed.aap8307] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 04/24/2018] [Indexed: 12/16/2022]
Abstract
Metastasis remains a leading cause of cancer mortality due to the lack of specific inhibitors against this complex process. To identify compounds selectively targeting the metastatic state, we used the perinucleolar compartment (PNC), a complex nuclear structure associated with metastatic behaviors of cancer cells, as a phenotypic marker for a high-content screen of over 140,000 structurally diverse compounds. Metarrestin, obtained through optimization of a screening hit, disassembles PNCs in multiple cancer cell lines, inhibits invasion in vitro, suppresses metastatic development in three mouse models of human cancer, and extends survival of mice in a metastatic pancreatic cancer xenograft model with no organ toxicity or discernable adverse effects. Metarrestin disrupts the nucleolar structure and inhibits RNA polymerase (Pol) I transcription, at least in part by interacting with the translation elongation factor eEF1A2. Thus, metarrestin represents a potential therapeutic approach for the treatment of metastatic cancer.
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Affiliation(s)
- Kevin J Frankowski
- Specialized Chemistry Center, The University of Kansas, Lawrence, KS 66047, USA
| | - Chen Wang
- Department of Cell and Molecular Biology, Northwestern University, Chicago, IL 60611, USA
| | - Samarjit Patnaik
- NIH (National Institutes of Health) Chemical Genomics Center, National Center for Advancing Translational Sciences, NIH, Rockville, MD, 20850, USA
| | - Frank J Schoenen
- Specialized Chemistry Center, The University of Kansas, Lawrence, KS 66047, USA
| | - Noel Southall
- NIH (National Institutes of Health) Chemical Genomics Center, National Center for Advancing Translational Sciences, NIH, Rockville, MD, 20850, USA
| | - Dandan Li
- Thoracic and Gastrointestinal Oncology Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Yaroslav Teper
- Thoracic and Gastrointestinal Oncology Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Wei Sun
- NIH (National Institutes of Health) Chemical Genomics Center, National Center for Advancing Translational Sciences, NIH, Rockville, MD, 20850, USA
| | - Irawati Kandela
- Center for Developmental Therapeutics, Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Evanston, IL 60208, USA
| | - Deqing Hu
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Christopher Dextras
- NIH (National Institutes of Health) Chemical Genomics Center, National Center for Advancing Translational Sciences, NIH, Rockville, MD, 20850, USA
| | - Zachary Knotts
- Thoracic and Gastrointestinal Oncology Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Yansong Bian
- Thoracic and Gastrointestinal Oncology Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - John Norton
- Department of Cell and Molecular Biology, Northwestern University, Chicago, IL 60611, USA
| | - Steve Titus
- NIH (National Institutes of Health) Chemical Genomics Center, National Center for Advancing Translational Sciences, NIH, Rockville, MD, 20850, USA
| | - Marzena A Lewandowska
- Department of Cell and Molecular Biology, Northwestern University, Chicago, IL 60611, USA
| | - Yiping Wen
- Department of Cell and Molecular Biology, Northwestern University, Chicago, IL 60611, USA
| | - Katherine I Farley
- Departments of Molecular Biophysics and Biochemistry, Genetics, and Therapeutic Radiology, Yale University and Yale School of Medicine, New Haven, CT 06520, USA
| | - Lesley Mathews Griner
- NIH (National Institutes of Health) Chemical Genomics Center, National Center for Advancing Translational Sciences, NIH, Rockville, MD, 20850, USA
| | - Jamey Sultan
- NIH (National Institutes of Health) Chemical Genomics Center, National Center for Advancing Translational Sciences, NIH, Rockville, MD, 20850, USA
| | - Zhaojing Meng
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD 21702, USA
| | - Ming Zhou
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD 21702, USA
| | - Tomas Vilimas
- Center for Advanced Preclinical Research, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Fort Detrick, Frederick, MD 21702, USA
| | - Astin S Powers
- Laboratory of Pathology, Center for Cancer Research, NIH, Bethesda, MD 20892, USA
| | - Serguei Kozlov
- Center for Advanced Preclinical Research, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Fort Detrick, Frederick, MD 21702, USA
| | - Kunio Nagashima
- Electron Microscope Laboratory, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Humair S Quadri
- Thoracic and Gastrointestinal Oncology Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Min Fang
- Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA 02111, USA
| | - Charles Long
- Department of Cell and Molecular Biology, Northwestern University, Chicago, IL 60611, USA
| | - Ojus Khanolkar
- Department of Cell and Molecular Biology, Northwestern University, Chicago, IL 60611, USA
| | - Warren Chen
- Department of Cell and Molecular Biology, Northwestern University, Chicago, IL 60611, USA
| | - Jinsol Kang
- Department of Cell and Molecular Biology, Northwestern University, Chicago, IL 60611, USA
| | - Helen Huang
- Department of Cell and Molecular Biology, Northwestern University, Chicago, IL 60611, USA
| | - Eric Chow
- Department of Cell and Molecular Biology, Northwestern University, Chicago, IL 60611, USA
| | - Esthermanya Goldberg
- Department of Cell and Molecular Biology, Northwestern University, Chicago, IL 60611, USA
| | - Coral Feldman
- Department of Cell and Molecular Biology, Northwestern University, Chicago, IL 60611, USA
| | - Romi Xi
- Department of Cell and Molecular Biology, Northwestern University, Chicago, IL 60611, USA
| | - Hye Rim Kim
- Department of Human Genetics, Cancer Biology Graduate Program, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Gary Sahagian
- Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA 02111, USA
| | - Susan J Baserga
- Departments of Molecular Biophysics and Biochemistry, Genetics, and Therapeutic Radiology, Yale University and Yale School of Medicine, New Haven, CT 06520, USA
| | - Andrew Mazar
- Center for Developmental Therapeutics, Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Evanston, IL 60208, USA
| | - Marc Ferrer
- NIH (National Institutes of Health) Chemical Genomics Center, National Center for Advancing Translational Sciences, NIH, Rockville, MD, 20850, USA
| | - Wei Zheng
- NIH (National Institutes of Health) Chemical Genomics Center, National Center for Advancing Translational Sciences, NIH, Rockville, MD, 20850, USA
| | - Ali Shilatifard
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Jeffrey Aubé
- Specialized Chemistry Center, The University of Kansas, Lawrence, KS 66047, USA
| | - Udo Rudloff
- Thoracic and Gastrointestinal Oncology Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA.
| | - Juan Jose Marugan
- NIH (National Institutes of Health) Chemical Genomics Center, National Center for Advancing Translational Sciences, NIH, Rockville, MD, 20850, USA.
| | - Sui Huang
- Department of Cell and Molecular Biology, Northwestern University, Chicago, IL 60611, USA.
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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] [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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Kucherenko MM, Shcherbata HR. miRNA targeting and alternative splicing in the stress response - events hosted by membrane-less compartments. J Cell Sci 2018; 131:131/4/jcs202002. [PMID: 29444950 DOI: 10.1242/jcs.202002] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Stress can be temporary or chronic, and mild or acute. Depending on its extent and severity, cells either alter their metabolism, and adopt a new state, or die. Fluctuations in environmental conditions occur frequently, and such stress disturbs cellular homeostasis, but in general, stresses are reversible and last only a short time. There is increasing evidence that regulation of gene expression in response to temporal stress happens post-transcriptionally in specialized subcellular membrane-less compartments called ribonucleoprotein (RNP) granules. RNP granules assemble through a concentration-dependent liquid-liquid phase separation of RNA-binding proteins that contain low-complexity sequence domains (LCDs). Interestingly, many factors that regulate microRNA (miRNA) biogenesis and alternative splicing are RNA-binding proteins that contain LCDs and localize to stress-induced liquid-like compartments. Consequently, gene silencing through miRNAs and alternative splicing of pre-mRNAs are emerging as crucial post-transcriptional mechanisms that function on a genome-wide scale to regulate the cellular stress response. In this Review, we describe the interplay between these two post-transcriptional processes that occur in liquid-like compartments as an adaptive cellular response to stress.
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Affiliation(s)
- Mariya M Kucherenko
- Max Planck Research Group of Gene Expression and Signaling, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Goettingen, Germany
| | - Halyna R Shcherbata
- Max Planck Research Group of Gene Expression and Signaling, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Goettingen, Germany
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47
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Chen J, Teo BHD, Cai Y, Wee SYK, Lu J. The linker histone H1.2 is a novel component of the nucleolar organizer regions. J Biol Chem 2018; 293:2358-2369. [PMID: 29301938 DOI: 10.1074/jbc.m117.810184] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 12/18/2017] [Indexed: 01/27/2023] Open
Abstract
The nucleoli accumulate rRNA genes and are the sites of rRNA synthesis and rRNA assembly into ribosomes. During mitosis, nucleoli dissociate, but nucleolar remnants remain on the rRNA gene loci, forming distinct nucleolar organizer regions (NORs). Little is known about the composition and structure of NORs, but upstream binding factor (UBF) has been established as its master organizer. In this study, we sought to establish new proteins in NORs. Using UBF-Sepharose to isolate UBF-binding proteins, we identified histone H1.2 as a candidate partner but were puzzled by this observation, given that UBF is known to be located predominantly in nucleoli, whereas H1.2 distributed broadly among the chromatins in interphase nuclei. We then examined cells undergoing mitosis and saw that both H1.2 and UBF were recruited into NORs in this state, reconciling the results of our UBF pulldowns. Inhibiting rRNA synthesis in interphase nuclei also induced NOR-like structures containing both UBF and H1.2. When chromosomes were isolated and spread on coverslips, NORs appeared separated from the chromosomes containing both UBF and H1.2. After chromosomes were fragmented by homogenization, intact NORs remained visible. Results collectively suggest that NORs are independent structures and that the linker histone H1.2 is a novel component of this structure.
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Affiliation(s)
- Junjie Chen
- From the Department of Microbiology and Immunology, Yong Loo Lin School of Medicine and Immunology Programme, National University of Singapore, Singapore 117697
| | - Boon Heng Dennis Teo
- From the Department of Microbiology and Immunology, Yong Loo Lin School of Medicine and Immunology Programme, National University of Singapore, Singapore 117697
| | - Yitian Cai
- From the Department of Microbiology and Immunology, Yong Loo Lin School of Medicine and Immunology Programme, National University of Singapore, Singapore 117697
| | - Seng Yin Kelly Wee
- From the Department of Microbiology and Immunology, Yong Loo Lin School of Medicine and Immunology Programme, National University of Singapore, Singapore 117697
| | - Jinhua Lu
- From the Department of Microbiology and Immunology, Yong Loo Lin School of Medicine and Immunology Programme, National University of Singapore, Singapore 117697
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Kim DH, Hah J, Wirtz D. Mechanics of the Cell Nucleus. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1092:41-55. [DOI: 10.1007/978-3-319-95294-9_3] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Nucleoli cytomorphology in cutaneous melanoma cells - a new prognostic approach to an old concept. Diagn Pathol 2017; 12:88. [PMID: 29284501 PMCID: PMC5747151 DOI: 10.1186/s13000-017-0675-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [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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Kostopoulou ON, Wilhelmi V, Raiss S, Ananthaseshan S, Lindström MS, Bartek J, Söderberg-Naucler C. Human cytomegalovirus and Herpes Simplex type I virus can engage RNA polymerase I for transcription of immediate early genes. Oncotarget 2017; 8:96536-96552. [PMID: 29228551 PMCID: PMC5722503 DOI: 10.18632/oncotarget.22106] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 10/13/2017] [Indexed: 12/22/2022] Open
Abstract
Human cytomegalovirus (HCMV) utilizes RNA polymerase II to transcribe viral genes and produce viral mRNAs. It can specifically target the nucleolus to facilitate viral transcription and translation. As RNA polymerase I (Pol I)-mediated transcription is active in the nucleolus, we investigated the role of Pol I, along with relative contributions of the human Pol II and Pol III, to early phases of viral transcription in HCMV infected cells, compared with Herpes Simplex Virus-1 (HSV-1) and Murine cytomegalovirus (MCMV). Inhibition of Pol I with siRNA or the Pol I inhibitors CX-5461 or Actinomycin D (5nM) resulted in significantly decreased IE and pp65 mRNA and protein levels in human fibroblasts at early times post infection. This initially delayed replication was compensated for later during the replication process, at which stage it didn't significantly affect virus production. Pol I inhibition also reduced HSV-1 ICP0 and gB transcripts, suggesting that some herpesviruses engage Pol I for their early transcription. In contrast, inhibition of Pol I failed to affect MCMV transcription. Collectively, our results contribute to better understanding of the functional interplay between RNA Pol I-mediated nucleolar events and the Herpes viruses, particularly HCMV whose pathogenic impact ranges from congenital malformations and potentially deadly infections among immunosuppressed patients, up to HCMV's emerging oncomodulatory role in human tumors.
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Affiliation(s)
- Ourania N Kostopoulou
- Department of Medicine, Center for Molecular Medicine L8:03, Karolinska University Hospital, Stockholm, Sweden
| | - Vanessa Wilhelmi
- Department of Medicine, Center for Molecular Medicine L8:03, Karolinska University Hospital, Stockholm, Sweden
| | - Sina Raiss
- Department of Medicine, Center for Molecular Medicine L8:03, Karolinska University Hospital, Stockholm, Sweden
| | - Sharan Ananthaseshan
- Department of Medicine, Center for Molecular Medicine L8:03, Karolinska University Hospital, Stockholm, Sweden
| | - Mikael S Lindström
- Department of Medical Biochemistry and Biophysics, Science For Life Laboratory, Division of Genome Biology, Karolinska Institute, Solna, Sweden
| | - Jiri Bartek
- Department of Medical Biochemistry and Biophysics, Science For Life Laboratory, Division of Genome Biology, Karolinska Institute, Solna, Sweden
| | - Cecilia Söderberg-Naucler
- Department of Medicine, Center for Molecular Medicine L8:03, Karolinska University Hospital, Stockholm, Sweden
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