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González-Arzola K. The nucleolus: Coordinating stress response and genomic stability. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2024; 1867:195029. [PMID: 38642633 DOI: 10.1016/j.bbagrm.2024.195029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 03/25/2024] [Accepted: 04/12/2024] [Indexed: 04/22/2024]
Abstract
The perception that the nucleoli are merely the organelles where ribosome biogenesis occurs is challenged. Only around 30 % of nucleolar proteins are solely involved in producing ribosomes. Instead, the nucleolus plays a critical role in controlling protein trafficking during stress and, according to its dynamic nature, undergoes continuous protein exchange with nucleoplasm under various cellular stressors. Hence, the concept of nucleolar stress has evolved as cellular insults that disrupt the structure and function of the nucleolus. Considering the emerging role of this organelle in DNA repair and the fact that rDNAs are the most fragile genomic loci, therapies targeting the nucleoli are increasingly being developed. Besides, drugs that target ribosome synthesis and induce nucleolar stress can be used in cancer therapy. In contrast, agents that regulate nucleolar activity may be a potential treatment for neurodegeneration caused by abnormal protein accumulation in the nucleolus. Here, I explore the roles of nucleoli beyond their ribosomal functions, highlighting the factors triggering nucleolar stress and their impact on genomic stability.
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Affiliation(s)
- Katiuska González-Arzola
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Universidad de Sevilla, Consejo Superior de Investigaciones Científicas, Junta de Andalucía, Universidad Pablo de Olavide, 41092 Seville, Spain; Departamento de Bioquímica Vegetal y Biología Molecular, Universidad de Sevilla, 41012 Seville, Spain.
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2
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Martinez-Val A, Bekker-Jensen DB, Steigerwald S, Koenig C, Østergaard O, Mehta A, Tran T, Sikorski K, Torres-Vega E, Kwasniewicz E, Brynjólfsdóttir SH, Frankel LB, Kjøbsted R, Krogh N, Lundby A, Bekker-Jensen S, Lund-Johansen F, Olsen JV. Spatial-proteomics reveals phospho-signaling dynamics at subcellular resolution. Nat Commun 2021; 12:7113. [PMID: 34876567 PMCID: PMC8651693 DOI: 10.1038/s41467-021-27398-y] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 11/12/2021] [Indexed: 12/12/2022] Open
Abstract
Dynamic change in subcellular localization of signaling proteins is a general concept that eukaryotic cells evolved for eliciting a coordinated response to stimuli. Mass spectrometry-based proteomics in combination with subcellular fractionation can provide comprehensive maps of spatio-temporal regulation of protein networks in cells, but involves laborious workflows that does not cover the phospho-proteome level. Here we present a high-throughput workflow based on sequential cell fractionation to profile the global proteome and phospho-proteome dynamics across six distinct subcellular fractions. We benchmark the workflow by studying spatio-temporal EGFR phospho-signaling dynamics in vitro in HeLa cells and in vivo in mouse tissues. Finally, we investigate the spatio-temporal stress signaling, revealing cellular relocation of ribosomal proteins in response to hypertonicity and muscle contraction. Proteomics data generated in this study can be explored through https://SpatialProteoDynamics.github.io .
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Affiliation(s)
- Ana Martinez-Val
- Novo Nordisk Foundation Center for Protein Research, Proteomics Program, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Dorte B Bekker-Jensen
- Novo Nordisk Foundation Center for Protein Research, Proteomics Program, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Evosep Systems, Odense, Denmark
| | - Sophia Steigerwald
- Novo Nordisk Foundation Center for Protein Research, Proteomics Program, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Max Planck Institute of Biochemistry, Department of Proteomics and Signal Transduction, Martinsried, Germany
| | - Claire Koenig
- Novo Nordisk Foundation Center for Protein Research, Proteomics Program, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ole Østergaard
- Novo Nordisk Foundation Center for Protein Research, Proteomics Program, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Adi Mehta
- Department of Immunology, Oslo University Hospital, Rikshospitalet, Postboks 4950, Nydalen, 0424, Oslo, Norway
| | - Trung Tran
- Department of Immunology, Oslo University Hospital, Rikshospitalet, Postboks 4950, Nydalen, 0424, Oslo, Norway
| | - Krzysztof Sikorski
- Department of Immunology, Oslo University Hospital, Rikshospitalet, Postboks 4950, Nydalen, 0424, Oslo, Norway
| | - Estefanía Torres-Vega
- Cardiac Proteomics, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ewa Kwasniewicz
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | | | - Lisa B Frankel
- Danish Cancer Society, Copenhagen, Denmark
- Danish Cancer Society Research Center, Copenhagen, Denmark
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | - Rasmus Kjøbsted
- The August Krogh Section for Molecular Physiology, Department of Nutrition, Exercise and Sports, University of Copenhagen, Copenhagen, Denmark
| | - Nicolai Krogh
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Alicia Lundby
- Novo Nordisk Foundation Center for Protein Research, Proteomics Program, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Cardiac Proteomics, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Simon Bekker-Jensen
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Fridtjof Lund-Johansen
- Department of Immunology, Oslo University Hospital, Rikshospitalet, Postboks 4950, Nydalen, 0424, Oslo, Norway.
| | - Jesper V Olsen
- Novo Nordisk Foundation Center for Protein Research, Proteomics Program, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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3
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Trinh DA, Shirakawa R, Kimura T, Sakata N, Goto K, Horiuchi H. Inhibitor of Growth 4 (ING4) is a positive regulator of rRNA synthesis. Sci Rep 2019; 9:17235. [PMID: 31754246 PMCID: PMC6872537 DOI: 10.1038/s41598-019-53767-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 08/30/2019] [Indexed: 01/29/2023] Open
Abstract
Ribosome biogenesis is essential for maintaining basic cellular activities although its mechanism is not fully understood. Inhibitor of growth 4 (ING4) is a member of ING family while its cellular functions remain controversial. Here, we identified several nucleolar proteins as novel ING4 interacting proteins. ING4 localized in the nucleus with strong accumulation in the nucleolus through its plant homeodomain, which is known to interact with histone trimethylated H3K4, commonly present in the promoter of active genes. ING4 deficient cells exhibited slower proliferation and the alteration in nucleolar structure with reduced rRNA transcription, which was rescued by exogenous expression of GFP-ING4 to the similar levels of wild type cells. In the ING4 deficient cells, histone H3K9 acetylation and the key rRNA transcription factor UBF at the promoter of rDNA were reduced, both of which were also recovered by exogenous GFP-ING4 expression. Thus, ING4 could positively regulate rRNA transcription through modulation of histone modifications at the rDNA promoter.
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Affiliation(s)
- Duc-Anh Trinh
- Department of Oral Cancer Therapeutics, Graduate School of Dentistry, Tohoku University, Sendai, Japan.,Department of Molecular and Cellular Biology, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | - Ryutaro Shirakawa
- Department of Molecular and Cellular Biology, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | - Tomohiro Kimura
- Department of Molecular and Cellular Biology, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan.,Research Center for Molecular Genetics, Institute for Promotion of Medical Science Research, Yamagata University Faculty of Medicine, Yamagata, Yamagata, Japan
| | - Natsumi Sakata
- Department of Molecular and Cellular Biology, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | - Kota Goto
- Department of Molecular and Cellular Biology, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | - Hisanori Horiuchi
- Department of Oral Cancer Therapeutics, Graduate School of Dentistry, Tohoku University, Sendai, Japan. .,Department of Molecular and Cellular Biology, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan.
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4
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Potočar U, Hudoklin S, Kreft ME, Završnik J, Božikov K, Fröhlich M. Adipose-Derived Stem Cells Respond to Increased Osmolarities. PLoS One 2016; 11:e0163870. [PMID: 27706209 PMCID: PMC5051864 DOI: 10.1371/journal.pone.0163870] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 09/15/2016] [Indexed: 12/16/2022] Open
Abstract
Cell therapies present a feasible option for the treatment of degenerated cartilaginous and intervertebral disc (IVD) tissues. Microenvironments of these tissues are specific and often differ from the microenvironment of cells that, could be potentially used for therapy, e.g. human adipose-derived stem cells (hASC). To ensure safe and efficient implantation of hASC, it is important to evaluate how microenvironmental conditions at the site of implantation affect the implanted cells. This study has demonstrated that cartilaginous tissue-specific osmolarities ranging from 400-600 mOsm/L affected hASC in a dose- and time-dependent fashion in comparison to 300 mOsm/L. Increased osmolarities resulted in transient (nuclear DNA and actin reorganisation) and non-transient, long-term morphological changes (vesicle formation, increase in cell area, and culture morphology), as well as reduced proliferation in monolayer cultures. Increased osmolarities diminished acid proteoglycan production and compactness of chondrogenically induced pellet cultures, indicating decreased chondrogenic potential. Viability of hASC was strongly dependent on the type of culture, with hASC in monolayer culture being more tolerant to increased osmolarity compared to hASC in suspension, alginate-agarose hydrogel, and pellet cultures, thus emphasizing the importance of choosing relevant in vitro conditions according to the specifics of clinical application.
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Affiliation(s)
| | - Samo Hudoklin
- Institute of Cell Biology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Mateja Erdani Kreft
- Institute of Cell Biology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Janja Završnik
- Department of biochemistry and molecular biology, Jozef Stefan Institute, Ljubljana, Slovenia
| | - Krešimir Božikov
- Department of Plastic Surgery and Burns, Division of Surgery, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Mirjam Fröhlich
- Educell Ltd., Trzin, Slovenia
- Institute of Cell Biology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
- Department of biochemistry and molecular biology, Jozef Stefan Institute, Ljubljana, Slovenia
- * E-mail:
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5
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Kilaparty SP, Agarwal R, Singh P, Kannan K, Ali N. Endoplasmic reticulum stress-induced apoptosis accompanies enhanced expression of multiple inositol polyphosphate phosphatase 1 (Minpp1): a possible role for Minpp1 in cellular stress response. Cell Stress Chaperones 2016; 21:593-608. [PMID: 27038811 PMCID: PMC4907990 DOI: 10.1007/s12192-016-0684-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 03/16/2016] [Accepted: 03/17/2016] [Indexed: 01/22/2023] Open
Abstract
Inositol polyphosphates represent a group of differentially phosphorylated inositol metabolites, many of which are implicated to regulate diverse cellular processes such as calcium mobilization, vesicular trafficking, differentiation, apoptosis, etc. The metabolic network of these compounds is complex and tightly regulated by various kinases and phosphatases present predominantly in the cytosol. Multiple inositol polyphosphate phosphatase 1 (Minpp1) is the only known endoplasmic reticulum (ER) luminal enzyme that hydrolyzes various inositol polyphosphates in vitro as well as in vivo conditions. However, access of the Minpp1 to cytosolic substrates has not yet been demonstrated clearly and hence its physiological function. In this study, we examined a potential role for Minpp1 in ER stress-induced apoptosis. We generated a custom antibody and characterized its specificity to study the expression of Minpp1 protein in multiple mammalian cells under experimentally induced cellular stress conditions. Our results demonstrate a significant increase in the expression of Minpp1 in response to a variety of cellular stress conditions. The protein expression was corroborated with the expression of its mRNA and enzymatic activity. Further, in an attempt to link the role of Minpp1 to apoptotic stress, we studied the effect of Minpp1 expression on apoptosis following silencing of the Minpp1 gene by its specific siRNA. Our results suggest an attenuation of apoptotic parameters following knockdown of Minpp1. Thus, in addition to its known role in inositol polyphosphate metabolism, we have identified a novel role for Minpp1 as a stress-responsive protein. In summary, our results provide, for the first time, a probable link between ER stress-induced apoptosis and Minpp1 expression.
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Affiliation(s)
- Surya P Kilaparty
- Department of Biology, University of Arkansas at Little Rock, 2801 S University Avenue, Little Rock, AR, 72204, USA
| | - Rakhee Agarwal
- Department of Biology, University of Arkansas at Little Rock, 2801 S University Avenue, Little Rock, AR, 72204, USA
- Alexion Pharmaceuticals, Inc., Cheshire, CT, 06410, USA
| | - Pooja Singh
- Department of Biology, University of Arkansas at Little Rock, 2801 S University Avenue, Little Rock, AR, 72204, USA
| | - Krishnaswamy Kannan
- Department of Internal Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Nawab Ali
- Department of Biology, University of Arkansas at Little Rock, 2801 S University Avenue, Little Rock, AR, 72204, USA.
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6
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Xiao S, Caglar E, Maldonado P, Das D, Nadeem Z, Chi A, Trinité B, Li X, Saxena A. Induced expression of nucleolin phosphorylation-deficient mutant confers dominant-negative effect on cell proliferation. PLoS One 2014; 9:e109858. [PMID: 25313645 PMCID: PMC4196967 DOI: 10.1371/journal.pone.0109858] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Accepted: 09/08/2014] [Indexed: 11/25/2022] Open
Abstract
Nucleolin (NCL) is a major nucleolar phosphoprotein that has pleiotropic effects on cell proliferation and is elevated in a variety of tumors. NCL is highly phosphorylated at the N-terminus by two major kinases: interphase casein kinase 2 (CK2) and mitotic cyclin-dependent kinase 1 (CDK1). Earlier we demonstrated that a NCL-mutant that is partly defective in undergoing phosphorylation by CK2 inhibits chromosomal replication through its interactions with Replication Protein A, mimicking the cellular response to DNA damage. We further delineated that the N-terminus of NCL associates with Hdm2, the most common E3 ubiquitin ligase of p53. We reported that NCL antagonizes Hdm2 to stabilize p53 and stimulates p53 transcriptional activity. Although NCL-phosphorylation by CK2 and ribosomal DNA transcription are closely coordinated during interphase, the role of NCL phosphorylation in regulating cell proliferation remains unexplored. We have therefore engineered unique human cells that specifically induce expression of NCL-wild type (WT) or a phosphorylation-deficient NCL-mutant, 6/S*A where all the six CK2 consensus serine sites residing in the N-terminus NCL were mutated to alanine. Here we show that this NCL-mutant is defective in undergoing phosphorylation by CK2. We also demonstrate that NCL-phosphorylation by CK2 is required through the S-phase progression in cell cycle and hence proliferation. Induced expression of NCL with mutated CK2 phosphorylation sites stabilizes p53, results in higher expression of Bcl2 (B-cell lymphoma 2) homology 3 (BH3)-only apoptotic markers and causes a dominant-negative effect on cell viability. Our unique cellular system thus provides the first evidential support to delineate phospho-specific functions of NCL on cell proliferation.
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Affiliation(s)
- Shu Xiao
- Biology Department, Brooklyn College, Brooklyn, New York, United States of America
- City University of New York, Graduate Center, New York, New York, United States of America
| | - Elif Caglar
- Biology Department, Brooklyn College, Brooklyn, New York, United States of America
| | - Priscilla Maldonado
- New York University School of Medicine, New York, New York, United States of America
| | - Dibash Das
- Biology Department, Brooklyn College, Brooklyn, New York, United States of America
- City University of New York, Graduate Center, New York, New York, United States of America
| | - Zaineb Nadeem
- Biology Department, Brooklyn College, Brooklyn, New York, United States of America
| | - Angela Chi
- Great Neck South High School, Great Neck, New York, United States of America
| | - Benjamin Trinité
- New York University College of Dentistry, New York, New York, United States of America
| | - Xin Li
- New York University College of Dentistry, New York, New York, United States of America
| | - Anjana Saxena
- Biology Department, Brooklyn College, Brooklyn, New York, United States of America
- City University of New York, Graduate Center, New York, New York, United States of America
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7
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Barker CJ, Berggren PO. New Horizons in Cellular Regulation by Inositol Polyphosphates: Insights from the Pancreaticβ-Cell. Pharmacol Rev 2013; 65:641-69. [DOI: 10.1124/pr.112.006775] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
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8
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Banfic H, Bedalov A, York JD, Visnjic D. Inositol pyrophosphates modulate S phase progression after pheromone-induced arrest in Saccharomyces cerevisiae. J Biol Chem 2012. [PMID: 23179856 DOI: 10.1074/jbc.m112.412288] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Several studies have demonstrated the activation of phosphoinositide-specific phospholipase C (Plc) in nuclei of mammalian cells during synchronous progression through the cell cycle, but the downstream targets of Plc-generated inositol 1,4,5-trisphosphate are poorly described. Phospholipid signaling in the budding yeast Saccharomyces cerevisiae shares similarities with endonuclear phospholipid signaling in mammals, and many recent studies point to a role for inositol phosphates, including InsP(5), InsP(6), and inositol pyrophosphates, in mediating the action of Plc. In this study, we investigated the changes in inositol phosphate levels in α-factor-treated S. cerevisiae, which allows cells to progress synchronously through the cell cycle after release from a G(1) block. We found an increase in the activity of Plc1 early after release from the block with a concomitant increase in the levels of InsP(7) and InsP(8). Treatment of cells with the Plc inhibitor U73122 prevented increases in inositol phosphate levels and blocked progression of cells through S phase after pheromone arrest. The enzymatic activity of Kcs1 in vitro and HPLC analysis of [(3)H]inositol-labeled kcs1Δ cells confirmed that Kcs1 is the principal kinase responsible for generation of pyrophosphates in synchronously progressing cells. Analysis of plc1Δ, kcs1Δ, and ddp1Δ yeast mutants further confirmed the role that a Plc1- and Kcs1-mediated increase in pyrophosphates may have in progression through S phase. Our data provide genetic, metabolic, and biochemical evidence that synthesis of inositol pyrophosphates through activation of Plc1 and Kcs1 plays an important role in the signaling response required for cell cycle progression after mating pheromone arrest.
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Affiliation(s)
- Hrvoje Banfic
- Department of Physiology and Croatian Institute for Brain Research, School of Medicine, University of Zagreb, Salata 3, 10 000 Zagreb, Croatia.
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9
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Ferraris SE, Isoniemi K, Torvaldson E, Anckar J, Westermarck J, Eriksson JE. Nucleolar AATF regulates c-Jun-mediated apoptosis. Mol Biol Cell 2012; 23:4323-32. [PMID: 22933572 PMCID: PMC3484108 DOI: 10.1091/mbc.e12-05-0419] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The AP-1 transcription factor c-Jun is essential for stress-induced apoptosis in several models. The apoptosis-antagonizing transcription factor is a novel nucleolar stress sensor, which is required as a cofactor for c-Jun–mediated apoptosis. The AP-1 transcription factor c-Jun has been shown to be essential for stress-induced apoptosis in several models. However, the molecular mechanisms underlying the proapoptotic activity of c-Jun are poorly understood. We identify the apoptosis-antagonizing transcription factor (AATF) as a novel nucleolar stress sensor, which is required as a cofactor for c-Jun–mediated apoptosis. Overexpression or down-regulation of AATF expression levels led to a respective increase or decrease in the amount of activated and phosphorylated c-Jun with a proportional alteration in the induction levels of the proapoptotic c-Jun target genes FasL and TNF-α. Accordingly, AATF promoted commitment of ultraviolet (UV)-irradiated cells to c-Jun-dependent apoptosis. Whereas AATF overexpression potentiated UV-induced apoptosis in wild-type cells, c-Jun–deficient mouse embryonic fibroblasts were resistant to AATF-mediated apoptosis induction. Furthermore, AATF mutants defective in c-Jun binding were also defective in inducing AP-1 activity and c-Jun–mediated apoptosis. UV irradiation induced a translocation of AATF from the nucleolus to the nucleus, thereby enabling its physical association to c-Jun. Analysis of AATF deletion mutants revealed that the AATF domains required for compartmentalization, c-Jun binding, and enhancement of c-Jun transcriptional activity were all also required to induce c-Jun–dependent apoptosis. These results identify AATF as a nucleolar-confined c-Jun cofactor whose expression levels and spatial distribution determine the stress-induced activity of c-Jun and the levels of c-Jun–mediated apoptosis.
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Affiliation(s)
- Saima E Ferraris
- Department of Biosciences, Åbo Akademi University, FIN-20521 Turku, Finland
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10
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Shears SB, Ganapathi SB, Gokhale NA, Schenk TMH, Wang H, Weaver JD, Zaremba A, Zhou Y. Defining signal transduction by inositol phosphates. Subcell Biochem 2012; 59:389-412. [PMID: 22374098 PMCID: PMC3925325 DOI: 10.1007/978-94-007-3015-1_13] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Ins(1,4,5)P(3) is a classical intracellular messenger: stimulus-dependent changes in its levels elicits biological effects through its release of intracellular Ca(2+) stores. The Ins(1,4,5)P(3) response is "switched off" by its metabolism to a range of additional inositol phosphates. These metabolites have themselves come to be collectively described as a signaling "family". The validity of that latter definition is critically examined in this review. That is, we assess the strength of the hypothesis that Ins(1,4,5)P(3) metabolites are themselves "classical" signals. Put another way, what is the evidence that the biological function of a particular inositol phosphate depends upon stimulus dependent changes in its levels? In this assessment, examples of an inositol phosphate acting as a cofactor (i.e. its function is not stimulus-dependent) do not satisfy our signaling criteria. We conclude that Ins(3,4,5,6)P(4) is, to date, the only Ins(1,4,5)P(3) metabolite that has been validated to act as a second messenger.
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Key Words
- adenosine deaminase
- akt
- β-cells
- calcium
- camp
- camkii
- chloride channel
- clc3
- compartmentalization
- dna repair
- endosomes
- erk
- frizzled receptor
- gap1ip4bp
- mrna export
- ins(1,4,5)p3
- ins(1,4,5)p4 receptor
- ins(1,3,4)p3
- ins(1,3,4,5)p4
- ins(1,3,4,5)p4 receptor
- ins(1,4,5,6)p4
- ins(3,4,5,6)p4
- ins(1,3,4,5,6)p5
- insp6
- insulin
- ipmk
- ipk2
- ip5k
- itp
- itpk1
- itpkb
- lymphocytes
- ku
- neutrophils
- protein phosphatase
- ptdins(4,5)p2
- ptdins(3,4,5)p3
- ph domain
- pten
- rasa3
- transcription
- wnt ligand
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Affiliation(s)
- Stephen B Shears
- Inositol Signaling Section, Laboratory of Signal Transduction, NIEHS, NIH, DHHS, Research Triangle Park, 27709, NC, USA, USA,
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Tajrishi MM, Tuteja R, Tuteja N. Nucleolin: The most abundant multifunctional phosphoprotein of nucleolus. Commun Integr Biol 2011; 4:267-75. [PMID: 21980556 DOI: 10.4161/cib.4.3.14884] [Citation(s) in RCA: 172] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2011] [Accepted: 01/18/2011] [Indexed: 01/08/2023] Open
Abstract
Nucleolin is a multifunctional phosphoprotein ubiquitously distributed in the nucleolus, nucleus and cytoplasm of the cell. Nucleolin has a bipartite nuclear localization signal sequence and is conserved in animals, plants and yeast. Its levels are correlated with the rate of functional activity of the nucleolus in exponentially growing cells. Nucleolin contains intrinsic DNA and RNA helicase, nucleic-acid-dependent ATPase and self-cleaving activities. It binds RNA through its RNA recognition motifs. It regulates various aspects of DNA and RNA metabolism, chromatin structure, rDNA transcription, rRNA maturation, cytokinesis, nucleogenesis, cell proliferation and growth, the folding, maturation and ribosome assembly and nucleocytoplasmic transport of newly synthesized pre-RNAs. In this review we present an overview on nucleolin, its localization, structure and various functions. We also describe the discovery and important studies of nucleolin in plants.
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Affiliation(s)
- Marjan M Tajrishi
- International Center for Genetic Engineering and Biotechnology; Aruna Asaf Ali Marg; New Delhi, Delhi India
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12
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Kasprowicz A, Smolarkiewicz M, Wierzchowiecka M, Michalak M, Wojtaszek P. Introduction: Tensegral World of Plants. MECHANICAL INTEGRATION OF PLANT CELLS AND PLANTS 2011. [DOI: 10.1007/978-3-642-19091-9_1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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13
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Shears SB, Gokhale NA, Wang H, Zaremba A. Diphosphoinositol polyphosphates: what are the mechanisms? ACTA ACUST UNITED AC 2010; 51:13-25. [PMID: 21035493 DOI: 10.1016/j.advenzreg.2010.09.008] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2010] [Accepted: 09/17/2010] [Indexed: 12/30/2022]
Abstract
In countries where adulthood is considered to be attained at age eighteen, 2011 can be the point at which the diphosphoinositol polyphosphates might formally be described as "coming of age", since these molecules were first fully defined in 1993 (Menniti et al., 1993; Stephens et al., 1993b). But from a biological perspective, these polyphosphates cannot quite be considered to have matured into the status of being independently-acting intracellular signals. This review has discussed several of the published proposals for mechanisms by which the diphosphoinositol polyphosphates might act. We have argued that all of these hypotheses need further development.We also still do not know a single molecular mechanism by which a change in the levels of a particular diphosphoinositol polyphosphate can be controlled. Yet, despite all these gaps in our understanding, there is an enduring anticipation that these molecules have great potential in the signaling field. Reflecting our expectations of all teenagers, it should be our earnest hope that in the near future the diphosphoinositol polyphosphates will finally grow up.
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Affiliation(s)
- Stephen B Shears
- Inositol Signaling Group, Laboratory of Signal Transduction, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, NC 27709, USA.
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Cisterna B, Biggiogera M. Ribosome biogenesis: from structure to dynamics. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2010; 284:67-111. [PMID: 20875629 DOI: 10.1016/s1937-6448(10)84002-x] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In this chapter we describe the status of the research concerning the nucleolus, the major nuclear body. The nucleolus has been recognized as a dynamic organelle with many more functions than one could imagine. In fact, in addition to its fundamental role in the biogenesis of preribosomes, the nucleolus takes part in many other cellular processes and functions, such as the cell-cycle control and the p53 pathway: the direct or indirect involvement of the nucleolus in these various processes makes it sensitive to their alteration. Moreover, it is worth noting that the different nucleolar factors participating to independent mechanisms show different dynamics of association/disassociation with the nucleolar body.
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Affiliation(s)
- Barbara Cisterna
- Laboratory of Cell Biology and Neurobiology, Department of Animal Biology, University of Pavia, Pavia, Italy
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Barker CJ, Illies C, Gaboardi GC, Berggren PO. Inositol pyrophosphates: structure, enzymology and function. Cell Mol Life Sci 2009; 66:3851-71. [PMID: 19714294 PMCID: PMC11115731 DOI: 10.1007/s00018-009-0115-2] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2009] [Revised: 07/13/2009] [Accepted: 07/20/2009] [Indexed: 02/04/2023]
Abstract
The stereochemistry of the inositol backbone provides a platform on which to generate a vast array of distinct molecular motifs that are used to convey information both in signal transduction and many other critical areas of cell biology. Diphosphoinositol phosphates, or inositol pyrophosphates, are the most recently characterized members of the inositide family. They represent a new frontier with both novel targets within the cell and novel modes of action. This includes the proposed pyrophosphorylation of a unique subset of proteins. We review recent insights into the structures of these molecules and the properties of the enzymes which regulate their concentration. These enzymes also act independently of their catalytic activity via protein-protein interactions. This unique combination of enzymes and products has an important role in diverse cellular processes including vesicle trafficking, endo- and exocytosis, apoptosis, telomere length regulation, chromatin hyperrecombination, the response to osmotic stress, and elements of nucleolar function.
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Affiliation(s)
- Christopher John Barker
- The Rolf Luft Research Center for Diabetes and Endocrinology, Karolinska Institutet, 171 76 Stockholm, Sweden
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Abstract
The diphosphoinositol polyphosphates ("inositol pyrophosphates") are a specialized subgroup of the inositol phosphate signaling family. This review proposes that many of the current data concerning the metabolic turnover and biological effects of the diphosphoinositol polyphosphates are linked by a common theme: these polyphosphates act as metabolic messengers. This review will also discuss the latest proposals concerning possible molecular mechanisms of action of this intriguing class of molecules.
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Affiliation(s)
- Stephen B Shears
- Inositide Signaling Group, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, NC 27709, USA.
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Emmott E, Hiscox JA. Nucleolar targeting: the hub of the matter. EMBO Rep 2009; 10:231-8. [PMID: 19229283 DOI: 10.1038/embor.2009.14] [Citation(s) in RCA: 218] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2008] [Accepted: 01/26/2009] [Indexed: 11/09/2022] Open
Abstract
The nucleolus is a dynamic structure that has roles in various processes, from ribosome biogenesis to regulation of the cell cycle and the cellular stress response. Such functions are frequently mediated by the sequestration or release of nucleolar proteins. Our understanding of protein targeting to the nucleolus is much less complete than our knowledge of membrane-spanning translocation systems--such as those involved in nuclear targeting--and the experimental evidence reveals that few parallels exist with these better-characterized systems. Here, we discuss the current understanding of nucleolar targeting, explore the types of sequence that control the localization of a protein to the nucleolus, and speculate that certain subsets of nucleolar proteins might act as hub proteins that are able to bind to multiple protein targets. In parallel to other subnuclear structures, such as PML bodies, the proteins that are involved in the formation and maintenance of the nucleolus are inexorably linked to nucleolar trafficking.
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Affiliation(s)
- Edward Emmott
- Institute of Molecular and Cellular Biology, Faculty of Biological Sciences, Garstang Building, University of Leeds, Leeds LS2 9JT, England, UK
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