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Zhou S, Van Bortle K. The Pol III transcriptome: Basic features, recurrent patterns, and emerging roles in cancer. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1782. [PMID: 36754845 PMCID: PMC10498592 DOI: 10.1002/wrna.1782] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 01/13/2023] [Accepted: 01/18/2023] [Indexed: 02/10/2023]
Abstract
The RNA polymerase III (Pol III) transcriptome is universally comprised of short, highly structured noncoding RNA (ncRNA). Through RNA-protein interactions, the Pol III transcriptome actuates functional activities ranging from nuclear gene regulation (7SK), splicing (U6, U6atac), and RNA maturation and stability (RMRP, RPPH1, Y RNA), to cytoplasmic protein targeting (7SL) and translation (tRNA, 5S rRNA). In higher eukaryotes, the Pol III transcriptome has expanded to include additional, recently evolved ncRNA species that effectively broaden the footprint of Pol III transcription to additional cellular activities. Newly evolved ncRNAs function as riboregulators of autophagy (vault), immune signaling cascades (nc886), and translation (Alu, BC200, snaR). Notably, upregulation of Pol III transcription is frequently observed in cancer, and multiple ncRNA species are linked to both cancer progression and poor survival outcomes among cancer patients. In this review, we outline the basic features and functions of the Pol III transcriptome, and the evidence for dysregulation and dysfunction for each ncRNA in cancer. When taken together, recurrent patterns emerge, ranging from shared functional motifs that include molecular scaffolding and protein sequestration, overlapping protein interactions, and immunostimulatory activities, to the biogenesis of analogous small RNA fragments and noncanonical miRNAs, augmenting the function of the Pol III transcriptome and further broadening its role in cancer. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA Processing > Processing of Small RNAs RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
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Affiliation(s)
- Sihang Zhou
- Department of Cell and Developmental Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Kevin Van Bortle
- Department of Cell and Developmental Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- Cancer Center at Illinois, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
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2
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Watt KE, Macintosh J, Bernard G, Trainor PA. RNA Polymerases I and III in development and disease. Semin Cell Dev Biol 2023; 136:49-63. [PMID: 35422389 PMCID: PMC9550887 DOI: 10.1016/j.semcdb.2022.03.027] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 03/18/2022] [Accepted: 03/21/2022] [Indexed: 12/18/2022]
Abstract
Ribosomes are macromolecular machines that are globally required for the translation of all proteins in all cells. Ribosome biogenesis, which is essential for cell growth, proliferation and survival, commences with transcription of a variety of RNAs by RNA Polymerases I and III. RNA Polymerase I (Pol I) transcribes ribosomal RNA (rRNA), while RNA Polymerase III (Pol III) transcribes 5S ribosomal RNA and transfer RNAs (tRNA) in addition to a wide variety of small non-coding RNAs. Interestingly, despite their global importance, disruptions in Pol I and Pol III function result in tissue-specific developmental disorders, with craniofacial anomalies and leukodystrophy/neurodegenerative disease being among the most prevalent. Furthermore, pathogenic variants in genes encoding subunits shared between Pol I and Pol III give rise to distinct syndromes depending on whether Pol I or Pol III function is disrupted. In this review, we discuss the global roles of Pol I and III transcription, the consequences of disruptions in Pol I and III transcription, disorders arising from pathogenic variants in Pol I and Pol III subunits, and mechanisms underpinning their tissue-specific phenotypes.
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Affiliation(s)
- Kristin En Watt
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Julia Macintosh
- Department of Neurology and Neurosurgery, McGill University, Montreal, QC, Canada; Child Health and Human Development Program, Research Institute of the McGill University Health Center, Montreal, QC, Canada
| | - Geneviève Bernard
- Department of Neurology and Neurosurgery, McGill University, Montreal, QC, Canada; Child Health and Human Development Program, Research Institute of the McGill University Health Center, Montreal, QC, Canada; Departments of Pediatrics and Human Genetics, McGill University, Montreal, QC, Canada; Department of Specialized Medicine, Division of Medical Genetics, McGill University Health Center, Montreal, QC, Canada.
| | - Paul A Trainor
- Stowers Institute for Medical Research, Kansas City, MO, USA; Department of Anatomy & Cell Biology, University of Kansas Medical Center, Kansas City, KS, USA.
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3
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Evers P, Pezacki JP. Unraveling Complex MicroRNA Signaling Pathways with Activity‐Based Protein Profiling to Guide Therapeutic Discovery**. Isr J Chem 2023. [DOI: 10.1002/ijch.202200088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Parrish Evers
- Department of Chemistry and Biomolecular Sciences University of Ottawa 150 Louis-Pasteur Pvt. K1N 6N5 Ottawa Canada
| | - John Paul Pezacki
- Department of Chemistry and Biomolecular Sciences University of Ottawa 150 Louis-Pasteur Pvt. K1N 6N5 Ottawa Canada
- Department of Biochemistry Microbiology, and Immunology University of Ottawa 451 Smyth Rd. K1H 8M5 Ottawa Canada
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Sakthivel D, Brown-Suedel A, Bouchier-Hayes L. The role of the nucleolus in regulating the cell cycle and the DNA damage response. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2023; 135:203-241. [PMID: 37061332 DOI: 10.1016/bs.apcsb.2023.01.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
The nucleolus has long been perceived as the site for ribosome biogenesis, but numerous studies suggest that the nucleolus carefully sequesters crucial proteins involved in multiple cellular functions. Among these, the role of nucleolus in cell cycle regulation is the most evident. The nucleolus is the first responder of growth-related signals to mediate normal cell cycle progression. The nucleolus also senses different cellular stress insults by activating diverse pathways that arrest the cell cycle, promote DNA repair, or initiate apoptosis. Here, we review the emerging concepts on how the ribosomal and nonribosomal nucleolar proteins mediate such cellular effects.
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5
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Kanellis DC, Espinoza JA, Zisi A, Sakkas E, Bartkova J, Katsori AM, Boström J, Dyrskjøt L, Broholm H, Altun M, Elsässer SJ, Lindström MS, Bartek J. The exon-junction complex helicase eIF4A3 controls cell fate via coordinated regulation of ribosome biogenesis and translational output. SCIENCE ADVANCES 2021; 7:eabf7561. [PMID: 34348895 PMCID: PMC8336962 DOI: 10.1126/sciadv.abf7561] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 06/14/2021] [Indexed: 05/22/2023]
Abstract
Eukaryotic initiation factor 4A-III (eIF4A3), a core helicase component of the exon junction complex, is essential for splicing, mRNA trafficking, and nonsense-mediated decay processes emerging as targets in cancer therapy. Here, we unravel eIF4A3's tumor-promoting function by demonstrating its role in ribosome biogenesis (RiBi) and p53 (de)regulation. Mechanistically, eIF4A3 resides in nucleoli within the small subunit processome and regulates rRNA processing via R-loop clearance. EIF4A3 depletion induces cell cycle arrest through impaired RiBi checkpoint-mediated p53 induction and reprogrammed translation of cell cycle regulators. Multilevel omics analysis following eIF4A3 depletion pinpoints pathways of cell death regulation and translation of alternative mouse double minute homolog 2 (MDM2) transcript isoforms that control p53. EIF4A3 expression and subnuclear localization among clinical cancer specimens correlate with the RiBi status rendering eIF4A3 an exploitable vulnerability in high-RiBi tumors. We propose a concept of eIF4A3's unexpected role in RiBi, with implications for cancer pathogenesis and treatment.
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Affiliation(s)
- Dimitris C Kanellis
- Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 21 Stockholm, Sweden
| | - Jaime A Espinoza
- Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 21 Stockholm, Sweden
| | - Asimina Zisi
- Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 21 Stockholm, Sweden
| | - Elpidoforos Sakkas
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Jirina Bartkova
- Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 21 Stockholm, Sweden
- Danish Cancer Society Research Center, DK-2100 Copenhagen, Denmark
| | - Anna-Maria Katsori
- Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 21 Stockholm, Sweden
- Ming Wai Lau Centre for Reparative Medicine, Stockholm Node, Karolinska Institutet, Stockholm 17165, Sweden
| | - Johan Boström
- Science for Life Laboratory, Division of Clinical Physiology, Department of Laboratory Medicine, Karolinska Institutet, Karolinska University Hospital, SE-141 52 Huddinge, Sweden
| | - Lars Dyrskjøt
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Helle Broholm
- Department of Pathology, Copenhagen University Hospital, Copenhagen, Denmark
| | - Mikael Altun
- Science for Life Laboratory, Division of Clinical Physiology, Department of Laboratory Medicine, Karolinska Institutet, Karolinska University Hospital, SE-141 52 Huddinge, Sweden
| | - Simon J Elsässer
- Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 21 Stockholm, Sweden
- Ming Wai Lau Centre for Reparative Medicine, Stockholm Node, Karolinska Institutet, Stockholm 17165, Sweden
| | - Mikael S Lindström
- Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 21 Stockholm, Sweden.
| | - Jiri Bartek
- Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 21 Stockholm, Sweden.
- Danish Cancer Society Research Center, DK-2100 Copenhagen, Denmark
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6
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Timmerman DM, Remmers TL, Hillenius S, Looijenga LHJ. Mechanisms of TP53 Pathway Inactivation in Embryonic and Somatic Cells-Relevance for Understanding (Germ Cell) Tumorigenesis. Int J Mol Sci 2021; 22:ijms22105377. [PMID: 34065345 PMCID: PMC8161298 DOI: 10.3390/ijms22105377] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 05/14/2021] [Accepted: 05/15/2021] [Indexed: 01/10/2023] Open
Abstract
The P53 pathway is the most important cellular pathway to maintain genomic and cellular integrity, both in embryonic and non-embryonic cells. Stress signals induce its activation, initiating autophagy or cell cycle arrest to enable DNA repair. The persistence of these signals causes either senescence or apoptosis. Over 50% of all solid tumors harbor mutations in TP53 that inactivate the pathway. The remaining cancers are suggested to harbor mutations in genes that regulate the P53 pathway such as its inhibitors Mouse Double Minute 2 and 4 (MDM2 and MDM4, respectively). Many reviews have already been dedicated to P53, MDM2, and MDM4, while this review additionally focuses on the other factors that can deregulate P53 signaling. We discuss that P14ARF (ARF) functions as a negative regulator of MDM2, explaining the frequent loss of ARF detected in cancers. The long non-coding RNA Antisense Non-coding RNA in the INK4 Locus (ANRIL) is encoded on the same locus as ARF, inhibiting ARF expression, thus contributing to the process of tumorigenesis. Mutations in tripartite motif (TRIM) proteins deregulate P53 signaling through their ubiquitin ligase activity. Several microRNAs (miRNAs) inactivate the P53 pathway through inhibition of translation. CCCTC-binding factor (CTCF) maintains an open chromatin structure at the TP53 locus, explaining its inactivation of CTCF during tumorigenesis. P21, a downstream effector of P53, has been found to be deregulated in different tumor types. This review provides a comprehensive overview of these factors that are known to deregulate the P53 pathway in both somatic and embryonic cells, as well as their malignant counterparts (i.e., somatic and germ cell tumors). It provides insights into which aspects still need to be unraveled to grasp their contribution to tumorigenesis, putatively leading to novel targets for effective cancer therapies.
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7
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Pollak AJ, Hickman JH, Liang XH, Crooke ST. Gapmer Antisense Oligonucleotides Targeting 5S Ribosomal RNA Can Reduce Mature 5S Ribosomal RNA by Two Mechanisms. Nucleic Acid Ther 2020; 30:312-324. [PMID: 32589504 DOI: 10.1089/nat.2020.0864] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
In this study, we demonstrate that 5S ribosomal RNA (rRNA), a highly structured and protein-bound RNA, is quite difficult to reduce with antisense oligonucleotides (ASOs). However, we found a single accessible site that was targetable with a high-affinity complementary ASO. The ASO appeared to bind to the site, recruit RNaseH1, and cause degradation of the 5S RNA. Intriguingly, we also observed that the same ASO induced an accumulation of pre-5S RNA, which may contribute to reduced levels of mature 5S rRNA. As expected, ASO mediated reduction of 5S RNA, and modest inhibition of processing of pre-5S RNA resulted in nucleolar toxicity. However, the toxicity induced was minimal compared with actinomycin D, consistent with its modest effects on pre-5S rRNA. Mechanistically, we show that the accumulation of pre-5S rRNA required ASO hybridization to the cognate rRNA sequence but was independent of RNaseH1 activity. We found that Ro60 and La, proteins known to bind misprocessed RNAs, likely sequester the ASO-pre-5S rRNA species and block RNaseH1 activity, thus identifying another example of competitive mechanisms mediated by proteins that compete with RNaseH1 for binding to ASO-RNA heteroduplexes.
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Affiliation(s)
- Adam J Pollak
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., Carlsbad, California, USA
| | - Justin H Hickman
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., Carlsbad, California, USA
| | - Xue-Hai Liang
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., Carlsbad, California, USA
| | - Stanley T Crooke
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., Carlsbad, California, USA
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8
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Bohnsack KE, Bohnsack MT. Uncovering the assembly pathway of human ribosomes and its emerging links to disease. EMBO J 2019; 38:e100278. [PMID: 31268599 PMCID: PMC6600647 DOI: 10.15252/embj.2018100278] [Citation(s) in RCA: 133] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 02/18/2019] [Accepted: 04/26/2019] [Indexed: 12/12/2022] Open
Abstract
The essential cellular process of ribosome biogenesis is at the nexus of various signalling pathways that coordinate protein synthesis with cellular growth and proliferation. The fact that numerous diseases are caused by defects in ribosome assembly underscores the importance of obtaining a detailed understanding of this pathway. Studies in yeast have provided a wealth of information about the fundamental principles of ribosome assembly, and although many features are conserved throughout eukaryotes, the larger size of human (pre-)ribosomes, as well as the evolution of additional regulatory networks that can modulate ribosome assembly and function, have resulted in a more complex assembly pathway in humans. Notably, many ribosome biogenesis factors conserved from yeast appear to have subtly different or additional functions in humans. In addition, recent genome-wide, RNAi-based screens have identified a plethora of novel factors required for human ribosome biogenesis. In this review, we discuss key aspects of human ribosome production, highlighting differences to yeast, links to disease, as well as emerging concepts such as extra-ribosomal functions of ribosomal proteins and ribosome heterogeneity.
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Affiliation(s)
- Katherine E Bohnsack
- Department of Molecular BiologyUniversity Medical Center GöttingenGöttingenGermany
| | - Markus T Bohnsack
- Department of Molecular BiologyUniversity Medical Center GöttingenGöttingenGermany
- Göttingen Center for Molecular BiosciencesGeorg‐August UniversityGöttingenGermany
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9
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Haupt S, Mejía-Hernández JO, Vijayakumaran R, Keam SP, Haupt Y. The long and the short of it: the MDM4 tail so far. J Mol Cell Biol 2019; 11:231-244. [PMID: 30689920 PMCID: PMC6478121 DOI: 10.1093/jmcb/mjz007] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 12/16/2018] [Accepted: 01/21/2019] [Indexed: 12/27/2022] Open
Abstract
The mouse double minute 4 (MDM4) is emerging from the shadow of its more famous relative MDM2 and is starting to steal the limelight, largely due to its therapeutic possibilities. MDM4 is a vital regulator of the tumor suppressor p53. It restricts p53 transcriptional activity and also, at least in development, facilitates MDM2's E3 ligase activity toward p53. These functions of MDM4 are critical for normal cell function and a proper response to stress. Their importance for proper cell maintenance and proliferation identifies them as a risk for deregulation associated with the uncontrolled growth of cancer. MDM4 tails are vital for its function, where its N-terminus transactivation domain engages p53 and its C-terminus RING domain binds to MDM2. In this review, we highlight recently identified cellular functions of MDM4 and survey emerging therapies directed to correcting its dysregulation in disease.
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Affiliation(s)
- Sue Haupt
- Tumor Suppression Laboratory, Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, Victoria, Australia
- Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria, Australia
| | | | - Reshma Vijayakumaran
- Tumor Suppression Laboratory, Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, Victoria, Australia
| | - Simon P Keam
- Tumor Suppression Laboratory, Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, Victoria, Australia
| | - Ygal Haupt
- Tumor Suppression Laboratory, Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, Victoria, Australia
- Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton Campus, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
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10
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Li D, Tavana O, Sun SC, Gu W. Peli1 Modulates the Subcellular Localization and Activity of Mdmx. Cancer Res 2018; 78:2897-2910. [PMID: 29523541 PMCID: PMC5984691 DOI: 10.1158/0008-5472.can-17-3531] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 01/12/2018] [Accepted: 03/05/2018] [Indexed: 12/21/2022]
Abstract
Mdm2 and Mdmx, both major repressors of p53 in human cancers, are predominantly localized to the nucleus and cytoplasm, respectively. The mechanism by which subcellular localization of Mdmx is regulated remains unclear. In this study, we identify the E3 ligase Peli1 as a major binding partner and regulator of Mdmx in human cells. Peli1 bound Mdmx in vitro and in vivo and promoted high levels of ubiquitination of Mdmx. Peli1-mediated ubiquitination was degradation-independent, promoting cytoplasmic localization of Mdmx, which in turn resulted in p53 activation. Consistent with this, knockdown or knockout Peli1 in human cancer cells induced nuclear localization of Mdmx and suppressed p53 activity. Myc-induced tumorigenesis was accelerated in Peli1-null mice and associated with downregulation of p53 function. Clinical samples of human cutaneous melanoma had decreased Peli1 expression, which was associated with poor overall survival. Together, these results demonstrate that Peli1 acts as a critical factor for the Mdmx-p53 axis by modulating the subcellular localization and activity of Mdmx, thus revealing a novel mechanism of Mdmx deregulation in human cancers.Significance: Peli1-mediated regulation of Mdmx, a major inhibitor of p53, provides critical insight into activation of p53 function in human cancers. Cancer Res; 78(11); 2897-910. ©2018 AACR.
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Affiliation(s)
- Dawei Li
- Institute for Cancer Genetics, Department of Pathology and Cell Biology, Herbert Irving Comprehensive Cancer Center, College of Physicians and Surgeons, Columbia University, New York, New York
| | - Omid Tavana
- Institute for Cancer Genetics, Department of Pathology and Cell Biology, Herbert Irving Comprehensive Cancer Center, College of Physicians and Surgeons, Columbia University, New York, New York
| | - Shao-Cong Sun
- Department of Immunology, the University of Texas MD Anderson Cancer Center, MD Anderson Cancer Center UT Health Graduate School of Biomedical Sciences, Houston, Texas
| | - Wei Gu
- Institute for Cancer Genetics, Department of Pathology and Cell Biology, Herbert Irving Comprehensive Cancer Center, College of Physicians and Surgeons, Columbia University, New York, New York.
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11
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Kon N, Wang D, Li T, Jiang L, Qiang L, Gu W. Inhibition of Mdmx (Mdm4) in vivo induces anti-obesity effects. Oncotarget 2018; 9:7282-7297. [PMID: 29484110 PMCID: PMC5800902 DOI: 10.18632/oncotarget.23837] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 12/08/2017] [Indexed: 01/22/2023] Open
Abstract
Although cell-cycle arrest, senescence and apoptosis remain as major canonical activities of p53 in tumor suppression, the emerging role of p53 in metabolism has been a topic of great interest. Nevertheless, it is not completely understood how p53-mediated metabolic activities are regulated in vivo and whether this part of the activities has an independent role beyond tumor suppression. Mdmx (also called Mdm4), like Mdm2, acts as a major suppressor of p53 but the embryonic lethality of mdmx-null mice creates difficulties to evaluate its physiological significance in metabolism. Here, we report that the embryonic lethality caused by the deficiency of mdmx, in contrast to the case for mdm2, is fully rescued in the background of p533KR/3KR, an acetylation-defective mutant unable to induce cell-cycle arrest, senescence and apoptosis. p533KR/3KR/mdmx-/- mice are healthy but skinny without obvious developmental defects. p533KR/3KR/mdmx-/- mice are resistant to fat accumulation in adipose tissues upon high fat diet. Notably, the levels of p53 protein are only slightly increased and can be further induced upon DNA damage in p533KR/3KR/mdmx-/- mice, suggesting that Mdmx is only partially required for p53 degradation in vivo. Further analyses indicate that the anti-obesity phenotypes in p533KR/3KR/mdmx-/- mice are caused by activation of lipid oxidation and thermogenic programs in adipose tissues. These results demonstrate the specific effects of the p53/Mdmx axis in lipid metabolism and adipose tissue remodeling and reveal a surprising role of Mdmx inhibition in anti-obesity effects beyond, commonly expected, tumor suppression. Thus, our study has significant implications regarding Mdmx inhibitors in the treatment of obesity related diseases.
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Affiliation(s)
- Ning Kon
- Institute for Cancer Genetics, College of Physicians and Surgeons of Columbia University, New York, New York, USA
| | - Donglai Wang
- Institute for Cancer Genetics, College of Physicians and Surgeons of Columbia University, New York, New York, USA
| | - Tongyuan Li
- Institute for Cancer Genetics, College of Physicians and Surgeons of Columbia University, New York, New York, USA
| | - Le Jiang
- Institute for Cancer Genetics, College of Physicians and Surgeons of Columbia University, New York, New York, USA
| | - Li Qiang
- Naomi Berrie Diabetes Center, Department of Medicine, College of Physicians and Surgeons of Columbia University, New York, New York, USA.,Department of Pathology and Cell Biology, College of Physicians and Surgeons of Columbia University, New York, New York, USA
| | - Wei Gu
- Institute for Cancer Genetics, College of Physicians and Surgeons of Columbia University, New York, New York, USA.,Department of Pathology and Cell Biology, College of Physicians and Surgeons of Columbia University, New York, New York, USA
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12
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Transcription by RNA polymerase III: insights into mechanism and regulation. Biochem Soc Trans 2017; 44:1367-1375. [PMID: 27911719 PMCID: PMC5095917 DOI: 10.1042/bst20160062] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 07/07/2016] [Accepted: 07/13/2016] [Indexed: 12/13/2022]
Abstract
The highly abundant, small stable RNAs that are synthesized by RNA polymerase III (RNAPIII) have key functional roles, particularly in the protein synthesis apparatus. Their expression is metabolically demanding, and is therefore coupled to changing demands for protein synthesis during cell growth and division. Here, we review the regulatory mechanisms that control the levels of RNAPIII transcripts and discuss their potential physiological relevance. Recent analyses have revealed differential regulation of tRNA expression at all steps on its biogenesis, with significant deregulation of mature tRNAs in cancer cells.
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13
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Insertion of an Alu element in a lncRNA leads to primate-specific modulation of alternative splicing. Nat Struct Mol Biol 2016; 23:1011-1019. [DOI: 10.1038/nsmb.3302] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 09/07/2016] [Indexed: 12/20/2022]
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14
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Selenoprotein H is an essential regulator of redox homeostasis that cooperates with p53 in development and tumorigenesis. Proc Natl Acad Sci U S A 2016; 113:E5562-71. [PMID: 27588899 DOI: 10.1073/pnas.1600204113] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Selenium, an essential micronutrient known for its cancer prevention properties, is incorporated into a class of selenocysteine-containing proteins (selenoproteins). Selenoprotein H (SepH) is a recently identified nucleolar oxidoreductase whose function is not well understood. Here we report that seph is an essential gene regulating organ development in zebrafish. Metabolite profiling by targeted LC-MS/MS demonstrated that SepH deficiency impairs redox balance by reducing the levels of ascorbate and methionine, while increasing methionine sulfoxide. Transcriptome analysis revealed that SepH deficiency induces an inflammatory response and activates the p53 pathway. Consequently, loss of seph renders larvae susceptible to oxidative stress and DNA damage. Finally, we demonstrate that seph interacts with p53 deficiency in adulthood to accelerate gastrointestinal tumor development. Overall, our findings establish that seph regulates redox homeostasis and suppresses DNA damage. We hypothesize that SepH deficiency may contribute to the increased cancer risk observed in cohorts with low selenium levels.
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15
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Marine JC, Jochemsen AG. MDMX (MDM4), a Promising Target for p53 Reactivation Therapy and Beyond. Cold Spring Harb Perspect Med 2016; 6:6/7/a026237. [PMID: 27371671 DOI: 10.1101/cshperspect.a026237] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The MDMX protein was identified as a p53-interacting protein with a strong similarity to MDM2. Like Mdm2, Mdmx expression is essential for curbing p53 activity during embryonic development, indicating nonredundant functions of Mdmx and Mdm2. There is now a large body of evidence indicating that cancers frequently up-regulate MDMX expression as a means to dampen p53 tumor-suppressor function. Importantly, MDMX also shows p53-independent oncogenic functions. These data make MDMX an attractive therapeutic target for cancer therapy. Here, we summarize the mechanisms used by cancer cells to increase MDMX expression and promising pharmacological strategies to target MDMX in cancer-in particular, the recent findings that antisense oligonucleotides (ASOs) can be used to efficiently modulate MDMX messenger RNA (mRNA) splicing.
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Affiliation(s)
- Jean-Christophe Marine
- Laboratory for Molecular Cancer Biology, Center for the Biology of Disease, VIB, 3000 Leuven, Belgium Laboratory for Molecular Cancer Biology, Center of Human Genetics, KULeuven, 3000 Leuven, Belgium
| | - Aart G Jochemsen
- Department of Molecular Cell Biology, Leiden University Medical Center, 2300 RA Leiden, The Netherlands
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Stępiński D. Nucleolus-derived mediators in oncogenic stress response and activation of p53-dependent pathways. Histochem Cell Biol 2016; 146:119-39. [PMID: 27142852 DOI: 10.1007/s00418-016-1443-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/25/2016] [Indexed: 12/12/2022]
Abstract
Rapid growth and division of cells, including tumor ones, is correlated with intensive protein biosynthesis. The output of nucleoli, organelles where translational machineries are formed, depends on a rate of particular stages of ribosome production and on accessibility of elements crucial for their effective functioning, including substrates, enzymes as well as energy resources. Different factors that induce cellular stress also often lead to nucleolar dysfunction which results in ribosome biogenesis impairment. Such nucleolar disorders, called nucleolar or ribosomal stress, usually affect cellular functioning which in fact is a result of p53-dependent pathway activation, elicited as a response to stress. These pathways direct cells to new destinations such as cell cycle arrest, damage repair, differentiation, autophagy, programmed cell death or aging. In the case of impaired nucleolar functioning, nucleolar and ribosomal proteins mediate activation of the p53 pathways. They are also triggered as a response to oncogenic factor overexpression to protect tissues and organs against extensive proliferation of abnormal cells. Intentional impairment of any step of ribosome biosynthesis which would direct the cells to these destinations could be a strategy used in anticancer therapy. This review presents current knowledge on a nucleolus, mainly in relation to cancer biology, which is an important and extremely sensitive element of the mechanism participating in cellular stress reaction mediating activation of the p53 pathways in order to counteract stress effects, especially cancer development.
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Affiliation(s)
- Dariusz Stępiński
- Department of Cytophysiology, Faculty of Biology and Environmental Protection, University of Łódź, Pomorska 141/143, 90-236, Łódź, Poland.
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17
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Karni-Schmidt O, Lokshin M, Prives C. The Roles of MDM2 and MDMX in Cancer. ANNUAL REVIEW OF PATHOLOGY-MECHANISMS OF DISEASE 2016; 11:617-44. [PMID: 27022975 DOI: 10.1146/annurev-pathol-012414-040349] [Citation(s) in RCA: 200] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
For more than 25 years, MDM2 and its homolog MDMX (also known as MDM4) have been shown to exert oncogenic activity. These two proteins are best understood as negative regulators of the p53 tumor suppressor, although they may have additional p53-independent roles. Understanding the dysregulation of MDM2 and MDMX in human cancers and how they function either together or separately in tumorigenesis may improve methods of diagnosis and for assessing prognosis. Targeting the proteins themselves, or their regulators, may be a promising therapeutic approach to treating some forms of cancer.
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Affiliation(s)
- Orit Karni-Schmidt
- Department of Biological Sciences, Columbia University, New York, NY 10027;
| | - Maria Lokshin
- Department of Biological Sciences, Columbia University, New York, NY 10027;
| | - Carol Prives
- Department of Biological Sciences, Columbia University, New York, NY 10027;
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18
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Down-regulation of 5S rRNA by miR-150 and miR-383 enhances c-Myc-rpL11 interaction and inhibits proliferation of esophageal squamous carcinoma cells. FEBS Lett 2015; 589:3989-97. [DOI: 10.1016/j.febslet.2015.11.012] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Revised: 10/29/2015] [Accepted: 11/10/2015] [Indexed: 01/05/2023]
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19
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Zheng J, Lang Y, Zhang Q, Cui D, Sun H, Jiang L, Chen Z, Zhang R, Gao Y, Tian W, Wu W, Tang J, Chen Z. Structure of human MDM2 complexed with RPL11 reveals the molecular basis of p53 activation. Genes Dev 2015. [PMID: 26220995 PMCID: PMC4526736 DOI: 10.1101/gad.261792.115] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Upon ribosomal stress, the central region of MDM2 is bound by ribosomal proteins, particularly ribosomal protein L11 (RPL11), leading to MDM2 inactivation and subsequent p53 activation. Zheng et al. solved the complex structure of human MDM2–RPL11 at 2.4 Å and show that formation of the MDM2–RPL11 complex induces substantial conformational changes in both proteins. The central region of MDM2 is critical for p53 activation and tumor suppression. Upon ribosomal stress, this region is bound by ribosomal proteins, particularly ribosomal protein L11 (RPL11), leading to MDM2 inactivation and subsequent p53 activation. Here, we solved the complex structure of human MDM2–RPL11 at 2.4 Å. MDM2 extensively interacts with RPL11 through an acidic domain and two zinc fingers. Formation of the MDM2–RPL11 complex induces substantial conformational changes in both proteins. RPL11, unable to bind MDM2 mutants, fails to induce the activation of p53 in cells. MDM2 mimics 28S rRNA binding to RPL11. The C4 zinc finger determines RPL11 binding to MDM2 but not its homolog, MDMX. Our results highlight the essential role of the RPL11–MDM2 interaction in p53 activation and tumor suppression and provide a structural basis for potential new anti-tumor drug development.
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Affiliation(s)
- Jiangge Zheng
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China
| | - Yue Lang
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China; College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Qi Zhang
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China
| | - Di Cui
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China; College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Haili Sun
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China; College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Lun Jiang
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China
| | - Zhenhang Chen
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China
| | - Rui Zhang
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China; College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Yina Gao
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China
| | - Wenli Tian
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, China
| | - Wei Wu
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China
| | - Jun Tang
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China; College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Zhongzhou Chen
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China
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20
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Zheng J, Lang Y, Zhang Q, Cui D, Sun H, Jiang L, Chen Z, Zhang R, Gao Y, Tian W, Wu W, Tang J, Chen Z. Structure of human MDM2 complexed with RPL11 reveals the molecular basis of p53 activation. Genes Dev 2015. [PMID: 26220995 DOI: 10.1101/gad.261792] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2023]
Abstract
The central region of MDM2 is critical for p53 activation and tumor suppression. Upon ribosomal stress, this region is bound by ribosomal proteins, particularly ribosomal protein L11 (RPL11), leading to MDM2 inactivation and subsequent p53 activation. Here, we solved the complex structure of human MDM2-RPL11 at 2.4 Å. MDM2 extensively interacts with RPL11 through an acidic domain and two zinc fingers. Formation of the MDM2-RPL11 complex induces substantial conformational changes in both proteins. RPL11, unable to bind MDM2 mutants, fails to induce the activation of p53 in cells. MDM2 mimics 28S rRNA binding to RPL11. The C4 zinc finger determines RPL11 binding to MDM2 but not its homolog, MDMX. Our results highlight the essential role of the RPL11-MDM2 interaction in p53 activation and tumor suppression and provide a structural basis for potential new anti-tumor drug development.
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Affiliation(s)
- Jiangge Zheng
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China
| | - Yue Lang
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China; College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Qi Zhang
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China
| | - Di Cui
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China; College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Haili Sun
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China; College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Lun Jiang
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China
| | - Zhenhang Chen
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China
| | - Rui Zhang
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China; College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Yina Gao
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China
| | - Wenli Tian
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, China
| | - Wei Wu
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China
| | - Jun Tang
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China; College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Zhongzhou Chen
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China
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Kumazawa T, Nishimura K, Katagiri N, Hashimoto S, Hayashi Y, Kimura K. Gradual reduction in rRNA transcription triggers p53 acetylation and apoptosis via MYBBP1A. Sci Rep 2015; 5:10854. [PMID: 26044764 PMCID: PMC4456663 DOI: 10.1038/srep10854] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 05/05/2015] [Indexed: 12/19/2022] Open
Abstract
The nucleolus, whose primary function is ribosome biogenesis, plays an essential role in p53 activation. Ribosome biogenesis is inhibited in response to cellular stress and several nucleolar proteins translocate from the nucleolus to the nucleoplasm, where they activate p53. In this study, we analysed precisely how impaired ribosome biogenesis regulates the activation of p53 by depleting nucleolar factors involved in rRNA transcription or rRNA processing. Nucleolar RNA content decreased when rRNA transcription was inhibited. In parallel with the reduced levels of nucleolar RNA content, the nucleolar protein Myb-binding protein 1 A (MYBBP1A) translocated to the nucleoplasm and increased p53 acetylation. The acetylated p53 enhanced p21 and BAX expression and induced apoptosis. In contrast, when rRNA processing was inhibited, MYBBP1A remained in the nucleolus and nonacetylated p53 accumulated, causing cell cycle arrest at the G1 phase by inducing p21 but not BAX. We propose that the nucleolus functions as a stress sensor to modulate p53 protein levels and its acetylation status, determining cell fate between cell cycle arrest and apoptosis by regulating MYBBP1A translocation.
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Affiliation(s)
- Takuya Kumazawa
- 1] Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennnoudai, Tsukuba 305-8577, Japan [2] First Department of Internal Medicine, Nara Medical University, 840 Shijo-cho Kashihara, Nara 634-8522, Japan
| | - Kazuho Nishimura
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennnoudai, Tsukuba 305-8577, Japan
| | - Naohiro Katagiri
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennnoudai, Tsukuba 305-8577, Japan
| | - Sayaka Hashimoto
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennnoudai, Tsukuba 305-8577, Japan
| | - Yuki Hayashi
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennnoudai, Tsukuba 305-8577, Japan
| | - Keiji Kimura
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennnoudai, Tsukuba 305-8577, Japan
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22
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Nishimura K, Kumazawa T, Kuroda T, Katagiri N, Tsuchiya M, Goto N, Furumai R, Murayama A, Yanagisawa J, Kimura K. Perturbation of ribosome biogenesis drives cells into senescence through 5S RNP-mediated p53 activation. Cell Rep 2015; 10:1310-23. [PMID: 25732822 DOI: 10.1016/j.celrep.2015.01.055] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 12/22/2014] [Accepted: 01/24/2015] [Indexed: 12/14/2022] Open
Abstract
The 5S ribonucleoprotein particle (RNP) complex, consisting of RPL11, RPL5, and 5S rRNA, is implicated in p53 regulation under ribotoxic stress. Here, we show that the 5S RNP contributes to p53 activation and promotes cellular senescence in response to oncogenic or replicative stress. Oncogenic stress accelerates rRNA transcription and replicative stress delays rRNA processing, resulting in RPL11 and RPL5 accumulation in the ribosome-free fraction, where they bind MDM2. Experimental upregulation of rRNA transcription or downregulation of rRNA processing, mimicking the nucleolus under oncogenic or replicative stress, respectively, also induces RPL11-mediated p53 activation and cellular senescence. We demonstrate that exogenous expression of certain rRNA-processing factors rescues the processing defect, attenuates p53 accumulation, and increases replicative lifespan. To summarize, the nucleolar-5S RNP-p53 pathway functions as a senescence inducer in response to oncogenic and replicative stresses.
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Affiliation(s)
- Kazuho Nishimura
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8577, Japan
| | - Takuya Kumazawa
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8577, Japan; First Department of Internal Medicine, Nara Medical University, 840 Shijo-cho Kashihara, Nara 634-8522, Japan
| | - Takao Kuroda
- Center of Tsukuba Advanced Research Alliance, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8577, Japan
| | - Naohiro Katagiri
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8577, Japan
| | - Mai Tsuchiya
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8577, Japan
| | - Natsuka Goto
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8577, Japan
| | - Ryohei Furumai
- Center of Tsukuba Advanced Research Alliance, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8577, Japan
| | - Akiko Murayama
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8577, Japan; Center of Tsukuba Advanced Research Alliance, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8577, Japan
| | - Junn Yanagisawa
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8577, Japan; Center of Tsukuba Advanced Research Alliance, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8577, Japan
| | - Keiji Kimura
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8577, Japan.
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23
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Wang W, Nag S, Zhang X, Wang MH, Wang H, Zhou J, Zhang R. Ribosomal proteins and human diseases: pathogenesis, molecular mechanisms, and therapeutic implications. Med Res Rev 2014; 35:225-85. [PMID: 25164622 DOI: 10.1002/med.21327] [Citation(s) in RCA: 143] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Ribosomes are essential components of the protein synthesis machinery. The process of ribosome biogenesis is well organized and tightly regulated. Recent studies have shown that ribosomal proteins (RPs) have extraribosomal functions that are involved in cell proliferation, differentiation, apoptosis, DNA repair, and other cellular processes. The dysfunction of RPs has been linked to the development and progression of hematological, metabolic, and cardiovascular diseases and cancer. Perturbation of ribosome biogenesis results in ribosomal stress, which triggers activation of the p53 signaling pathway through RPs-MDM2 interactions, resulting in p53-dependent cell cycle arrest and apoptosis. RPs also regulate cellular functions through p53-independent mechanisms. We herein review the recent advances in several forefronts of RP research, including the understanding of their biological features and roles in regulating cellular functions, maintaining cell homeostasis, and their involvement in the pathogenesis of human diseases. We also highlight the translational potential of this research for the identification of molecular biomarkers, and in the discovery and development of novel treatments for human diseases.
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Affiliation(s)
- Wei Wang
- Department of Pharmaceutical Sciences, School of Pharmacy, Texas Tech University Health Sciences Center, Amarillo, Texas, 79106; Cancer Biology Center, School of Pharmacy, Texas Tech University Health Sciences Center, Amarillo, Texas, 79106
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24
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Golomb L, Volarevic S, Oren M. p53 and ribosome biogenesis stress: the essentials. FEBS Lett 2014; 588:2571-9. [PMID: 24747423 DOI: 10.1016/j.febslet.2014.04.014] [Citation(s) in RCA: 166] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Revised: 04/04/2014] [Accepted: 04/04/2014] [Indexed: 12/18/2022]
Abstract
Cell proliferation and cell growth are two tightly linked processes, as the proliferation program cannot be executed without proper accumulation of cell mass, otherwise endangering the fate of the two daughter cells. It is therefore not surprising that ribosome biogenesis, a key element in cell growth, is regulated by many cell cycle regulators. This regulation is exerted transcriptionally and post-transcriptionally, in conjunction with numerous intrinsic and extrinsic signals. Those signals eventually converge at the nucleolus, the cellular compartment that is not only responsible for executing the ribosome biogenesis program, but also serves as a regulatory hub, responsible for integrating and transmitting multiple stress signals to the omnipotent cell fate gatekeeper, p53. In this review we discuss when, how and why p53 is activated upon ribosomal biogenesis stress, and how perturbation of this critical regulatory interplay may impact human disease.
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Affiliation(s)
- Lior Golomb
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Sinisa Volarevic
- Department of Molecular Medicine and Biotechnology, School of Medicine, University of Rijeka, Croatia
| | - Moshe Oren
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.
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25
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Targeting RNA polymerase I to treat MYC-driven cancer. Oncogene 2014; 34:403-12. [PMID: 24608428 DOI: 10.1038/onc.2014.13] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Revised: 01/08/2014] [Accepted: 01/08/2014] [Indexed: 02/06/2023]
Abstract
The MYC oncoprotein and transcription factor is dysregulated in a majority of human cancers and is considered a major driver of the malignant phenotype. As such, developing drugs for effective inhibition of MYC in a manner selective to malignancies is a 'holy grail' of transcription factor-based cancer therapy. Recent advances in elucidating MYC biology in both normal cells and pathological settings were anticipated to bring inhibition of tumorigenic MYC function closer to the clinic. However, while the extensive array of cellular pathways that MYC impacts present numerous fulcrum points on which to leverage MYC's therapeutic potential, identifying the critical target(s) for MYC-specific cancer therapy has been difficult to achieve. Somewhat unexpectedly, MYC's fundamental role in regulating the 'housekeeping' process of ribosome biogenesis, one of the most ubiquitously required and conserved cell functions, may provide the Achilles' heel for therapeutically targeting MYC-driven tumors.
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26
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Cooper DA, Jha BK, Silverman RH, Hesselberth JR, Barton DJ. Ribonuclease L and metal-ion-independent endoribonuclease cleavage sites in host and viral RNAs. Nucleic Acids Res 2014; 42:5202-16. [PMID: 24500209 PMCID: PMC4005677 DOI: 10.1093/nar/gku118] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Ribonuclease L (RNase L) is a metal-ion–independent endoribonuclease associated with antiviral and antibacterial defense, cancer and lifespan. Despite the biological significance of RNase L, the RNAs cleaved by this enzyme are poorly defined. In this study, we used deep sequencing methods to reveal the frequency and location of RNase L cleavage sites within host and viral RNAs. To make cDNA libraries, we exploited the 2′, 3′-cyclic phosphate at the end of RNA fragments produced by RNase L and other metal-ion–independent endoribonucleases. We optimized and validated 2′, 3′-cyclic phosphate cDNA synthesis and Illumina sequencing methods using viral RNAs cleaved with purified RNase L, viral RNAs cleaved with purified RNase A and RNA from uninfected and poliovirus-infected HeLa cells. Using these methods, we identified (i) discrete regions of hepatitis C virus and poliovirus RNA genomes that were profoundly susceptible to RNase L and other single-strand specific endoribonucleases, (ii) RNase L-dependent and RNase L-independent cleavage sites within ribosomal RNAs (rRNAs) and (iii) 2′, 3′-cyclic phosphates at the ends of 5S rRNA and U6 snRNA. Monitoring the frequency and location of metal-ion–independent endoribonuclease cleavage sites within host and viral RNAs reveals, in part, how these enzymes contribute to health and disease.
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Affiliation(s)
- Daphne A Cooper
- Department of Microbiology, University of Colorado School of Medicine, Aurora, CO 80045, USA, Department of Cancer Biology, Lerner Research Institute, The Cleveland Clinic, Cleveland, OH 44195, USA, Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA and Program in Molecular Biology, University of Colorado School of Medicine, Aurora, CO 80045, USA
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27
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Hock AK, Vousden KH. The role of ubiquitin modification in the regulation of p53. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1843:137-49. [DOI: 10.1016/j.bbamcr.2013.05.022] [Citation(s) in RCA: 121] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2013] [Revised: 04/16/2013] [Accepted: 05/23/2013] [Indexed: 01/09/2023]
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28
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AMP-activated protein kinase induces p53 by phosphorylating MDMX and inhibiting its activity. Mol Cell Biol 2013; 34:148-57. [PMID: 24190973 DOI: 10.1128/mcb.00670-13] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
AMP-activated protein kinase (AMPK) has been shown to activate p53 in response to metabolic stress. However, the underlying mechanisms remain unclear. Here we show that metabolic stresses induce AMPK-mediated phosphorylation of human MDMX on Ser342 in vitro and in cells, leading to enhanced association between MDMX and 14-3-3. This markedly inhibits p53 ubiquitylation and significantly stabilizes and activates p53. By striking contrast, no phosphorylation of MDM2 by AMPK was noted. AMPK-mediated MDMX phosphorylation, MDMX-14-3-3 binding, and p53 activation were drastically reduced in mouse embryo fibroblasts harboring endogenous MDMX with S341A (mouse homologue of human serine 342), S367A, and S402A (mouse homologue of human serine 403) mutations. Moreover, deficiency of AMPK prevented MDMX-14-3-3 interaction and p53 activation. The activation of p53 through AMPK-mediated MDMX phosphorylation and inactivation was further confirmed by using cell and animal model systems with two AMPK activators, metformin and salicylate (the active form of aspirin). Together, the results unveil a mechanism by which metabolic stresses activate AMPK, which, in turn, phosphorylates and inactivates MDMX, resulting in p53 stabilization and activation.
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29
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Bursac S, Brdovcak MC, Donati G, Volarevic S. Activation of the tumor suppressor p53 upon impairment of ribosome biogenesis. Biochim Biophys Acta Mol Basis Dis 2013; 1842:817-30. [PMID: 24514102 DOI: 10.1016/j.bbadis.2013.08.014] [Citation(s) in RCA: 114] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Accepted: 08/27/2013] [Indexed: 12/31/2022]
Abstract
Errors in ribosome biogenesis can result in quantitative or qualitative defects in protein synthesis and consequently lead to improper execution of the genetic program and the development of specific diseases. Evidence has accumulated over the last decade suggesting that perturbation of ribosome biogenesis triggers a p53-activating checkpoint signaling pathway, often referred to as the ribosome biogenesis stress checkpoint pathway. Although it was originally suggested that p53 has a prominent role in preventing diseases by monitoring the fidelity of ribosome biogenesis, recent work has demonstrated that p53 activation upon impairment of ribosome biogenesis also mediates pathological manifestations in humans. Perturbations of ribosome biogenesis can trigger a p53-dependent checkpoint signaling pathway independent of DNA damage and the tumor suppressor ARF through inhibitory interactions of specific ribosomal components with the p53 negative regulator, Mdm2. Here we review the recent advances made toward understanding of this newly-recognized checkpoint signaling pathway, its role in health and disease, and discuss possible future directions in this exciting research field. This article is part of a Special Issue entitled: Role of the Nucleolus in Human Disease.
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Affiliation(s)
- Sladana Bursac
- Department of Molecular Medicine and Biotechnology, School of Medicine, University of Rijeka, Braće Branchetta 20, 51000 Rijeka, Croatia
| | - Maja Cokaric Brdovcak
- Department of Molecular Medicine and Biotechnology, School of Medicine, University of Rijeka, Braće Branchetta 20, 51000 Rijeka, Croatia
| | - Giulio Donati
- Catalan Institute of Oncology, Bellvitge Biomedical Research Institute, Institut d'Investigacio' Biome'dica de Bellvitge (IDIBELL), 08908 Hospitalet de Llobregat, Barcelona, Spain
| | - Sinisa Volarevic
- Department of Molecular Medicine and Biotechnology, School of Medicine, University of Rijeka, Braće Branchetta 20, 51000 Rijeka, Croatia.
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30
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Sloan K, Bohnsack M, Watkins N. The 5S RNP couples p53 homeostasis to ribosome biogenesis and nucleolar stress. Cell Rep 2013; 5:237-47. [PMID: 24120868 PMCID: PMC3808153 DOI: 10.1016/j.celrep.2013.08.049] [Citation(s) in RCA: 216] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2013] [Revised: 08/16/2013] [Accepted: 08/30/2013] [Indexed: 01/25/2023] Open
Abstract
Several proto-oncogenes and tumor suppressors regulate the production of ribosomes. Ribosome biogenesis is a major consumer of cellular energy, and defects result in p53 activation via repression of mouse double minute 2 (MDM2) homolog by the ribosomal proteins RPL5 and RPL11. Here, we report that RPL5 and RPL11 regulate p53 from the context of a ribosomal subcomplex, the 5S ribonucleoprotein particle (RNP). We provide evidence that the third component of this complex, the 5S rRNA, is critical for p53 regulation. In addition, we show that the 5S RNP is essential for the activation of p53 by p14ARF, a protein that is activated by oncogene overexpression. Our data show that the abundance of the 5S RNP, and therefore p53 levels, is determined by factors regulating 5S complex formation and ribosome integration, including the tumor suppressor PICT1. The 5S RNP therefore emerges as the critical coordinator of signaling pathways that couple cell proliferation with ribosome production. The 5S RNP (5S rRNA/RPL5/RPL11) activates p53 when ribosome production is blocked The 5S RNP is required for p53 activation by the tumor suppressor p14ARF PICT1 controls p53 levels by regulating 5S RNP integration into the ribosome Ribosome biogenesis is directly coupled to cellular proliferation via the 5S RNP
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Affiliation(s)
- Katherine E. Sloan
- ICaMB, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
- Centre for Biochemistry and Molecular Cell Biology, Institute for Molecular Biology, Medical Faculty, Georg-August University, 37073 Goettingen, Germany
| | - Markus T. Bohnsack
- Centre for Biochemistry and Molecular Cell Biology, Institute for Molecular Biology, Medical Faculty, Georg-August University, 37073 Goettingen, Germany
| | - Nicholas J. Watkins
- ICaMB, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
- Corresponding author
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Loss of tumor suppressor RPL5/RPL11 does not induce cell cycle arrest but impedes proliferation due to reduced ribosome content and translation capacity. Mol Cell Biol 2013; 33:4660-71. [PMID: 24061479 DOI: 10.1128/mcb.01174-13] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Humans have evolved elaborate mechanisms to activate p53 in response to insults that lead to cancer, including the binding and inhibition of Hdm2 by the 60S ribosomal proteins (RPs) RPL5 and RPL11. This same mechanism appears to be activated upon impaired ribosome biogenesis, a risk factor for cancer initiation. As loss of RPL5/RPL11 abrogates ribosome biogenesis and protein synthesis to the same extent as loss of other essential 60S RPs, we reasoned the loss of RPL5 and RPL11 would induce a p53-independent cell cycle checkpoint. Unexpectedly, we found that their depletion in primary human lung fibroblasts failed to induce cell cycle arrest but strongly suppressed cell cycle progression. We show that the effects on cell cycle progression stemmed from reduced ribosome content and translational capacity, which suppressed the accumulation of cyclins at the translational level. Thus, unlike other tumor suppressors, RPL5/RPL11 play an essential role in normal cell proliferation, a function cells have evolved to rely on in lieu of a cell cycle checkpoint.
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Hein N, Hannan KM, George AJ, Sanij E, Hannan RD. The nucleolus: an emerging target for cancer therapy. Trends Mol Med 2013; 19:643-54. [PMID: 23953479 DOI: 10.1016/j.molmed.2013.07.005] [Citation(s) in RCA: 181] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Revised: 07/10/2013] [Accepted: 07/15/2013] [Indexed: 02/07/2023]
Abstract
For over 100 years, pathologists have utilised an increase in size and number of nucleoli, the subnuclear site of ribosome synthesis, as a marker of aggressive tumours. Despite this, the contribution of the nucleolus and ribosomal RNA synthesis to cancer has been largely overlooked. This concept has recently changed with the demonstration that the nucleolus indirectly controls numerous other cellular functions, in particular, the cellular activity of the critical tumour suppressor protein, p53. Moreover, selective inhibition of ribosomal gene transcription in the nucleolus has been shown to be an effective therapeutic strategy to promote cancer-specific activation of p53. This article reviews the largely untapped potential of the nucleolus and ribosomal gene transcription as exciting new targets for cancer therapy.
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Affiliation(s)
- Nadine Hein
- Division of Cancer Research, Peter MacCallum Cancer Centre, East Melbourne, 3002, Victoria, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, 3010, Victoria, Australia
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Donati G, Peddigari S, Mercer CA, Thomas G. 5S ribosomal RNA is an essential component of a nascent ribosomal precursor complex that regulates the Hdm2-p53 checkpoint. Cell Rep 2013; 4:87-98. [PMID: 23831031 DOI: 10.1016/j.celrep.2013.05.045] [Citation(s) in RCA: 194] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Revised: 05/08/2013] [Accepted: 05/31/2013] [Indexed: 12/14/2022] Open
Abstract
Recently, we demonstrated that RPL5 and RPL11 act in a mutually dependent manner to inhibit Hdm2 and stabilize p53 following impaired ribosome biogenesis. Given that RPL5 and RPL11 form a preribosomal complex with noncoding 5S ribosomal RNA (rRNA) and the three have been implicated in the p53 response, we reasoned they may be part of an Hdm2-inhibitory complex. Here, we show that small interfering RNAs directed against 5S rRNA have no effect on total or nascent levels of the noncoding rRNA, though they prevent the reported Hdm4 inhibition of p53. To achieve efficient inhibition of 5S rRNA synthesis, we targeted TFIIIA, a specific RNA polymerase III cofactor, which, like depletion of either RPL5 or RPL11, did not induce p53. Instead, 5S rRNA acts in a dependent manner with RPL5 and RPL11 to inhibit Hdm2 and stabilize p53. Moreover, depletion of any one of the three components abolished the binding of the other two to Hdm2, explaining their common dependence. Finally, we demonstrate that the RPL5/RPL11/5S rRNA preribosomal complex is redirected from assembly into nascent 60S ribosomes to Hdm2 inhibition as a consequence of impaired ribosome biogenesis. Thus, the activation of the Hdm2-inhibitory complex is not a passive but a regulated event, whose potential role in tumor suppression has been recently noted.
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Affiliation(s)
- Giulio Donati
- Laboratory of Cancer Metabolism, ICO/IDIBELL, Hospital Duran i Reynals, Gran Via de l'Hospitalet, 199-08908 Hospitalet de Llobregat, Barcelona, Spain
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34
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Safina A, Garcia H, Commane M, Guryanova O, Degan S, Kolesnikova K, Gurova KV. Complex mutual regulation of facilitates chromatin transcription (FACT) subunits on both mRNA and protein levels in human cells. Cell Cycle 2013; 12:2423-34. [PMID: 23839038 DOI: 10.4161/cc.25452] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Facilitates chromatin transcription (FACT) is a chromatin remodeling complex with two subunits: SSRP1 and SPT16. Mechanisms controlling FACT levels are of interest, since the complex is not expressed in most differentiated cells, but is frequently upregulated in cancer, particularly in poorly differentiated, aggressive tumors. Moreover, inhibition of FACT expression or function in tumor cells interferes with their survival. Here we demonstrate that SSRP1 and SPT16 protein levels decline upon induction of cellular differentiation or senescence in vitro and that similar declines in protein levels for both SSRP1 and SPT16 occur upon RNAi-mediated knockdown of either SSRP1 or SPT16. The interdependence of SSRP1 and SPT16 protein levels was found to be due to their association with SSRP1 and SPT16 mRNAs, which stabilizes the proteins. In particular, presence of SSRP1 mRNA is critical for SPT16 protein stability. In addition, binding of SSRP1 and SPT16 mRNAs to the FACT complex increases the stability and efficiency of translation of the mRNAs. These data support a model in which the FACT complex is stable when SSRP1 mRNA is present, but quickly degrades when SSRP1 mRNA levels drop. In the absence of FACT complex, SSRP1 and SPT16 mRNAs are unstable and inefficiently translated, making reactivation of FACT function unlikely in normal cells. Thus, we have described a complex and unusual mode of regulation controlling cellular FACT levels that results in amplified and stringent control of FACT activity. The FACT dependence of tumor cells suggests that mechanisms controlling FACT levels could be targeted for anticancer therapy.
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Affiliation(s)
- Alfiya Safina
- Department of Cell Stress Biology; Roswell Park Cancer Institute; Buffalo, NY USA
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35
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Abstract
The oncoprotein MDM2 is both the transcriptional target and the predominant antagonist of the tumor suppressor p53. MDM2 inhibits the functions of p53 via a negative feedback loop that can be circumvented by several ribosomal proteins in response to nucleolar or ribosomal stress. Stress conditions in the nucleolus can be triggered by a variety of extracellular and intracellular insults that impair ribosomal biogenesis and function, such as chemicals, nutrient deprivation, DNA damaging agents, or genetic alterations. The past decade has witnessed a tremendous progress in understanding this previously underinvestigated ribosomal stress-MDM2-p53 pathway. Here, we review the recent progress in understanding this unique signaling pathway, discuss its biological and pathological significance, and share with readers our insight into the research in this field.
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Affiliation(s)
- Xiang Zhou
- Department of Biochemistry & Molecular Biology and Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA, USA
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36
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Holmberg Olausson K, Nistér M, Lindström MS. p53 -Dependent and -Independent Nucleolar Stress Responses. Cells 2012; 1:774-98. [PMID: 24710530 PMCID: PMC3901145 DOI: 10.3390/cells1040774] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Revised: 09/28/2012] [Accepted: 10/01/2012] [Indexed: 12/27/2022] Open
Abstract
The nucleolus has emerged as a cellular stress sensor and key regulator of p53-dependent and -independent stress responses. A variety of abnormal metabolic conditions, cytotoxic compounds, and physical insults induce alterations in nucleolar structure and function, a situation known as nucleolar or ribosomal stress. Ribosomal proteins, including RPL11 and RPL5, become increasingly bound to the p53 regulatory protein MDM2 following nucleolar stress. Ribosomal protein binding to MDM2 blocks its E3 ligase function leading to stabilization and activation of p53. In this review we focus on a number of novel regulators of the RPL5/RPL11-MDM2-p53 complex including PICT1 (GLTSCR2), MYBBP1A, PML and NEDD8. p53-independent pathways mediating the nucleolar stress response are also emerging and in particular the negative control that RPL11 exerts on Myc oncoprotein is of importance, given the role of Myc as a master regulator of ribosome biogenesis. We also briefly discuss the potential of chemotherapeutic drugs that specifically target RNA polymerase I to induce nucleolar stress.
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Affiliation(s)
- Karl Holmberg Olausson
- Department of Oncology-Pathology, Karolinska Institutet, Cancer Center Karolinska R8:05, Karolinska University Hospital in Solna, SE-17176, Stockholm, Sweden.
| | - Monica Nistér
- Department of Oncology-Pathology, Karolinska Institutet, Cancer Center Karolinska R8:05, Karolinska University Hospital in Solna, SE-17176, Stockholm, Sweden.
| | - Mikael S Lindström
- Department of Oncology-Pathology, Karolinska Institutet, Cancer Center Karolinska R8:05, Karolinska University Hospital in Solna, SE-17176, Stockholm, Sweden.
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37
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St Laurent G, Shtokalo D, Heydarian M, Palyanov A, Babiy D, Zhou J, Kumar A, Urcuqui-Inchima S. Insights from the HuR-interacting transcriptome: ncRNAs, ubiquitin pathways, and patterns of secondary structure dependent RNA interactions. Mol Genet Genomics 2012; 287:867-79. [PMID: 23052832 DOI: 10.1007/s00438-012-0722-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Accepted: 09/17/2012] [Indexed: 12/22/2022]
Abstract
The HuR protein regulates the expression of thousands of cellular transcripts by modulating mRNA splicing, trafficking, translation, and stability. Although it serves as a model of RNA-protein interactions, many features of HuR's interactions with RNAs remain unknown. In this report, we deployed the cryogenic RNA immunoprecipitation technique to analyze HuR-interacting RNAs with the Affymetrix all-exon microarray platform. We revealed several thousand novel HuR-interacting RNAs, including hundreds of non-coding RNAs such as natural antisense transcripts from stress responsive loci. To gain insight into the mechanisms of specificity and sensitivity of HuR's interaction with its target RNAs, we searched HuR-interacting RNAs for composite patterns of primary sequence and secondary structure. We provide evidence that secondary structures of 66-75 nucleotides enhance HuR's recognition of its specific RNA targets composed of short primary sequence patterns. We validated thousands of these RNAs by analysis of overlap with recently published findings, including HuR's interaction with RNAs in the pathways of RNA splicing and stability. Finally, we observed a striking enrichment for members of ubiquitin ligase pathways among the HuR-interacting mRNAs, suggesting a new role for HuR in the regulation of protein degradation to mirror its known function in protein translation.
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Affiliation(s)
- Georges St Laurent
- Grupo de Inmunovirologia, Universidad de Antioquia, Calle 67 Número 53-108, Medellin, Antioquia, Colombia.
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38
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Casein kinase 1α regulates an MDMX intramolecular interaction to stimulate p53 binding. Mol Cell Biol 2012; 32:4821-32. [PMID: 23028042 DOI: 10.1128/mcb.00851-12] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
MDMX is an important regulator of p53 during embryonic development and malignant transformation. Previous studies showed that casein kinase 1α (CK1α) stably associates with MDMX, stimulates MDMX-p53 binding, and cooperates with MDMX to inactivate p53. However, the mechanism by which CK1α stimulates MDMX-p53 interaction remains unknown. Here, we present evidence that p53 binding by the MDMX N-terminal domain is inhibited by the central acidic region through an intramolecular interaction that competes for the p53 binding pocket. CK1α binding to the MDMX central domain and phosphorylation of S289 disrupts the intramolecular interaction, allowing the N terminus to bind p53 with increased affinity. After DNA damage, the MDMX-CK1α complex is disrupted by Chk2-mediated phosphorylation of MDMX at S367, leading to reduced MDMX-p53 binding. Therefore, CK1α is an important functional partner of MDMX. DNA damage activates p53 in part by disrupting CK1α-MDMX interaction and reducing MDMX-p53 binding affinity.
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Chauhan D, Tian Z, Nicholson B, Kumar KGS, Zhou B, Carrasco R, McDermott JL, Leach CA, Fulcinniti M, Kodrasov MP, Weinstock J, Kingsbury WD, Hideshima T, Shah PK, Minvielle S, Altun M, Kessler BM, Orlowski R, Richardson P, Munshi N, Anderson KC. A small molecule inhibitor of ubiquitin-specific protease-7 induces apoptosis in multiple myeloma cells and overcomes bortezomib resistance. Cancer Cell 2012; 22:345-58. [PMID: 22975377 PMCID: PMC3478134 DOI: 10.1016/j.ccr.2012.08.007] [Citation(s) in RCA: 437] [Impact Index Per Article: 36.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/24/2011] [Revised: 05/03/2012] [Accepted: 08/09/2012] [Indexed: 12/17/2022]
Abstract
Bortezomib therapy has proven successful for the treatment of relapsed/refractory, relapsed, and newly diagnosed multiple myeloma (MM); however, dose-limiting toxicities and the development of resistance limit its long-term utility. Here, we show that P5091 is an inhibitor of deubiquitylating enzyme USP7, which induces apoptosis in MM cells resistant to conventional and bortezomib therapies. Biochemical and genetic studies show that blockade of HDM2 and p21 abrogates P5091-induced cytotoxicity. In animal tumor model studies, P5091 is well tolerated, inhibits tumor growth, and prolongs survival. Combining P5091 with lenalidomide, HDAC inhibitor SAHA, or dexamethasone triggers synergistic anti-MM activity. Our preclinical study therefore supports clinical evaluation of USP7 inhibitor, alone or in combination, as a potential MM therapy.
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Affiliation(s)
- Dharminder Chauhan
- The LeBow Institute for Myeloma Therapeutics and Jerome Lipper Myeloma Center, Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
- Correspondence: (D.C.), (K.C.A.)
| | - Ze Tian
- The LeBow Institute for Myeloma Therapeutics and Jerome Lipper Myeloma Center, Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | | | | | - Bin Zhou
- Institute for Nutritional Sciences, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Ruben Carrasco
- The LeBow Institute for Myeloma Therapeutics and Jerome Lipper Myeloma Center, Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | | | | | - Mariaterresa Fulcinniti
- The LeBow Institute for Myeloma Therapeutics and Jerome Lipper Myeloma Center, Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | | | | | | | - Teru Hideshima
- The LeBow Institute for Myeloma Therapeutics and Jerome Lipper Myeloma Center, Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Parantu K. Shah
- The LeBow Institute for Myeloma Therapeutics and Jerome Lipper Myeloma Center, Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | | | - Mikael Altun
- Karolinska Institute, Department of Medical Biochemistry and Biophysics, Stockholm, Sweden
| | - Benedikt M. Kessler
- Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, UK
| | - Robert Orlowski
- Department of Lymphoma and Myeloma, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Paul Richardson
- The LeBow Institute for Myeloma Therapeutics and Jerome Lipper Myeloma Center, Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Nikhil Munshi
- The LeBow Institute for Myeloma Therapeutics and Jerome Lipper Myeloma Center, Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
- Veterans Administration Boston Healthcare System, Boston, MA 02115, USA
| | - Kenneth C. Anderson
- The LeBow Institute for Myeloma Therapeutics and Jerome Lipper Myeloma Center, Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
- Correspondence: (D.C.), (K.C.A.)
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Shadfan M, Lopez-Pajares V, Yuan ZM. MDM2 and MDMX: Alone and together in regulation of p53. Transl Cancer Res 2012; 1:88-89. [PMID: 23002429 PMCID: PMC3448287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
p53, a critical tumor suppressor, is activated by various cellular stresses to prevent and repair damages that can lead to tumor development. In response to these stresses, p53 activation can cause very serious cellular effects including permanent cell cycle arrest and cell death. p53 must therefore be very tightly regulated to avoid unnecessary pathological effects. The homologs MDM2 and MDMX have been shown to be the major, essential negative regulators of p53. In normal cells, MDM2 and MDMX suppress p53 activity, but in the event of cellular stress, they themselves must be inhibited so that p53 may respond to the stress. MDM2 and MDMX are known to bind together, and play multifaceted, non-redundant roles in modulating p53 protein activity. Recently, evidence has emerged showing that MDM2 and MDMX most effectively inhibit p53 as a complex, and possibly play non-redundant roles because they must function as one to control p53. In this review, we give an overview of MDM2 and MDMX and discuss a few ways in which they are modified so that p53 may be activated. Lastly, we discuss the non-redundant roles of MDM2 and MDMX and how it is important to investigate the effect on the complex as a whole when investigating either protein.
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Affiliation(s)
- Miriam Shadfan
- Department of Cellular and Structural Biology and Department of Radiation Oncology, University of Texas Health Science Center San Antonio, San Antonio, TX, USA
| | | | - Zhi-Min Yuan
- Department of Cellular and Structural Biology and Department of Radiation Oncology, University of Texas Health Science Center San Antonio, San Antonio, TX, USA
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Mandke P, Wyatt N, Fraser J, Bates B, Berberich SJ, Markey MP. MicroRNA-34a modulates MDM4 expression via a target site in the open reading frame. PLoS One 2012; 7:e42034. [PMID: 22870278 PMCID: PMC3411609 DOI: 10.1371/journal.pone.0042034] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2012] [Accepted: 06/29/2012] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND MDM4, also called MDMX or HDMX in humans, is an important negative regulator of the p53 tumor suppressor. MDM4 is overexpressed in about 17% of all cancers and more frequently in some types, such as colon cancer or retinoblastoma. MDM4 is known to be post-translationally regulated by MDM2-mediated ubiquitination to decrease its protein levels in response to genotoxic stress, resulting in accumulation and activation of p53. At the transcriptional level, MDM4 gene regulation has been less clearly understood. We have reported that DNA damage triggers loss of MDM4 mRNA and a concurrent increase in p53 activity. These experiments attempt to determine a mechanism for down-regulation of MDM4 mRNA. METHODOLOGY/PRINCIPAL FINDINGS Here we report that MDM4 mRNA is a target of hsa-mir-34a (miR-34a). MDM4 mRNA contains a lengthy 3' untranslated region; however, we find that it is a miR-34a site within the open reading frame (ORF) of exon 11 that is responsible for the repression. Overexpression of miR-34a, but not a mutant miR-34a, is sufficient to decrease MDM4 mRNA levels to an extent identical to those of known miR-34a target genes. Likewise, MDM4 protein levels are decreased by miR-34a overexpression. Inhibition of endogenous miR-34a increased expression of miR-34a target genes and MDM4. A portion of MDM4 exon 11 containing this 8mer-A1 miR-34a site fused to a luciferase reporter gene is sufficient to confer responsiveness, being inhibited by additional expression of exogenous mir-34a and activated by inhibition of miR-34a. CONCLUSIONS/SIGNIFICANCE These data establish a mechanism for the observed DNA damage-induced negative regulation of MDM4 and potentially provide a novel means to manipulate MDM4 expression without introducing DNA damage.
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Affiliation(s)
- Pooja Mandke
- Department of Biochemistry and Molecular Biology, Wright State University, Dayton, Ohio, United States of America
| | - Nicholas Wyatt
- Department of Biochemistry and Molecular Biology, Wright State University, Dayton, Ohio, United States of America
| | - Jillian Fraser
- Department of Biochemistry and Molecular Biology, Wright State University, Dayton, Ohio, United States of America
| | - Benjamin Bates
- Department of Biochemistry and Molecular Biology, Wright State University, Dayton, Ohio, United States of America
| | - Steven J. Berberich
- Department of Biochemistry and Molecular Biology, Wright State University, Dayton, Ohio, United States of America
| | - Michael P. Markey
- Department of Biochemistry and Molecular Biology, Wright State University, Dayton, Ohio, United States of America
- * E-mail:
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Hu S, Wu J, Chen L, Shan G. Signals from noncoding RNAs: unconventional roles for conventional pol III transcripts. Int J Biochem Cell Biol 2012; 44:1847-51. [PMID: 22819850 DOI: 10.1016/j.biocel.2012.07.013] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Revised: 07/06/2012] [Accepted: 07/09/2012] [Indexed: 12/29/2022]
Abstract
A range of noncoding RNAs are transcribed by pol III. A lot of them such as tRNA, 7SL RNA, 7SK RNA, 5S RNA, MRP RNA, Y RNAs, H1 RNA, and vault RNAs are considered as "house keeping" RNAs essential for eukaryotic cells. In recent years, researchers started to recognize the existence of unconventional functions of many pol III transcripts other than classical "house keeping" roles. Therefore, these ncRNAs could now be viewed as molecules with functional regulatory signals as well as cellular building blocks. These noncoding RNAs, all transcribed by pol III, may assemble regulatory networks with analogy to signaling pathways in eukaryotic cells. In this review we discuss these unconventional roles of pol III transcripts.
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Affiliation(s)
- Shanshan Hu
- School of Life Science, University of Science and Technology of China, 443 Huangshan Road, Hefei, Anhui Province 230027, China
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43
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Mdm2 and MdmX partner to regulate p53. FEBS Lett 2012; 586:1390-6. [PMID: 22673503 DOI: 10.1016/j.febslet.2012.02.049] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2012] [Revised: 02/27/2012] [Accepted: 02/28/2012] [Indexed: 02/06/2023]
Abstract
Mdm2 regulates the stability, translation, subcellular localization and transcriptional activity of p53 protein. Mdm2-dependent p53 inhibition is essential in regulating p53 activity during embryonic development and in adult tissues. MdmX, an Mdm2 homolog, is also essential for p53 inhibition in vivo. Recent advances in the field from biochemical and genetic studies have revealed an essential role for the MdmX RING domain in Mdm2-dependent p53 polyubiquitination and degradation. Mdm2 on its own is a monoubiquitin E3 ligase for p53, but is converted to a p53 polyubiquitin E3 ligase by MdmX through their RING-RING domain interactions. MdmX acts as an activator as well as a substrate of Mdm2/MdmX E3 complex. The insufficiency of Mdm2 for p53 polyubiquitination also demands other p53 E3 ligases or E4 factors be incorporated into the p53 degradation arena. Deubiquitinases nullify the effects of E3 actions and reverse the ubiquitination process, which permits a diverse and dynamic pattern of p53 stability control. Unsurprisingly, stress signals target MdmX to disengage the p53/Mdm2 feedback loop for timely and appropriate p53 responses to these stresses.
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