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Shaiken TE, Grimm SL, Siam M, Williams A, Rezaeian AH, Kraushaar D, Ricco E, Robertson MJ, Coarfa C, Jain A, Malovannaya A, Stossi F, Opekun AR, Price AP, Dubrulle J. Transcriptome, proteome, and protein synthesis within the intracellular cytomatrix. iScience 2023; 26:105965. [PMID: 36824274 PMCID: PMC9941065 DOI: 10.1016/j.isci.2023.105965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 11/07/2022] [Accepted: 01/06/2023] [Indexed: 01/15/2023] Open
Abstract
Despite the knowledge that protein translation and various metabolic reactions that create and sustain cellular life occur in the cytoplasm, the structural organization within the cytoplasm remains unclear. Recent models indicate that cytoplasm contains viscous fluid and elastic solid phases. We separated these viscous fluid and solid elastic compartments, which we call the cytosol and cytomatrix, respectively. The distinctive composition of the cytomatrix included structural proteins, ribosomes, and metabolome enzymes. High-throughput analysis revealed unique biosynthetic pathways within the cytomatrix. Enrichment of biosynthetic pathways in the cytomatrix indicated the presence of immobilized biocatalysis. Enzymatic immobilization and segregation can surmount spatial impediments, and the local pathway segregation may form cytoplasmic organelles. Protein translation was reprogrammed within the cytomatrix under the restriction of protein synthesis by drug treatment. The cytosol and cytomatrix are an elaborately interconnected network that promotes operational flexibility in healthy cells and the survival of malignant cells.
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Affiliation(s)
- Tattym E. Shaiken
- Department of Medicine-Gastroenterology and Hepatology Section, Michael E DeBakey Veteran’s Affairs Medical Center, Baylor College of Medicine, Houston, TX 77030, USA
- PeriNuc Labs, University of Houston Technology Bridge, Houston, TX 77023, USA
| | - Sandra L. Grimm
- Advanced Technology Cores, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mohamad Siam
- Department of Medicine-Gastroenterology and Hepatology Section, Michael E DeBakey Veteran’s Affairs Medical Center, Baylor College of Medicine, Houston, TX 77030, USA
- PeriNuc Labs, University of Houston Technology Bridge, Houston, TX 77023, USA
| | - Amanda Williams
- Department of Medicine-Gastroenterology and Hepatology Section, Michael E DeBakey Veteran’s Affairs Medical Center, Baylor College of Medicine, Houston, TX 77030, USA
- PeriNuc Labs, University of Houston Technology Bridge, Houston, TX 77023, USA
| | - Abdol-Hossein Rezaeian
- PeriNuc Labs, University of Houston Technology Bridge, Houston, TX 77023, USA
- Department of Drug Discovery and Biomedical Sciences, University of South Carolina, Columbia, SC 29208, USA
| | - Daniel Kraushaar
- Advanced Technology Cores, Baylor College of Medicine, Houston, TX 77030, USA
| | - Emily Ricco
- Advanced Technology Cores, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Cristian Coarfa
- Advanced Technology Cores, Baylor College of Medicine, Houston, TX 77030, USA
| | - Antrix Jain
- Advanced Technology Cores, Baylor College of Medicine, Houston, TX 77030, USA
| | - Anna Malovannaya
- Advanced Technology Cores, Baylor College of Medicine, Houston, TX 77030, USA
| | - Fabio Stossi
- Advanced Technology Cores, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Antone R. Opekun
- Department of Medicine-Gastroenterology and Hepatology Section, Michael E DeBakey Veteran’s Affairs Medical Center, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Alyssa P. Price
- Department of Medicine-Gastroenterology and Hepatology Section, Michael E DeBakey Veteran’s Affairs Medical Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Julien Dubrulle
- Advanced Technology Cores, Baylor College of Medicine, Houston, TX 77030, USA
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Ribosome Biogenesis and Cancer: Overview on Ribosomal Proteins. Int J Mol Sci 2021; 22:ijms22115496. [PMID: 34071057 PMCID: PMC8197113 DOI: 10.3390/ijms22115496] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 05/16/2021] [Accepted: 05/19/2021] [Indexed: 12/11/2022] Open
Abstract
Cytosolic ribosomes (cytoribosomes) are macromolecular ribonucleoprotein complexes that are assembled from ribosomal RNA and ribosomal proteins, which are essential for protein biosynthesis. Mitochondrial ribosomes (mitoribosomes) perform translation of the proteins essential for the oxidative phosphorylation system. The biogenesis of cytoribosomes and mitoribosomes includes ribosomal RNA processing, modification and binding to ribosomal proteins and is assisted by numerous biogenesis factors. This is a major energy-consuming process in the cell and, therefore, is highly coordinated and sensitive to several cellular stressors. In mitochondria, the regulation of mitoribosome biogenesis is essential for cellular respiration, a process linked to cell growth and proliferation. This review briefly overviews the key stages of cytosolic and mitochondrial ribosome biogenesis; summarizes the main steps of ribosome biogenesis alterations occurring during tumorigenesis, highlighting the changes in the expression level of cytosolic ribosomal proteins (CRPs) and mitochondrial ribosomal proteins (MRPs) in different types of tumors; focuses on the currently available information regarding the extra-ribosomal functions of CRPs and MRPs correlated to cancer; and discusses the role of CRPs and MRPs as biomarkers and/or molecular targets in cancer treatment.
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Carotenuto P, Pecoraro A, Palma G, Russo G, Russo A. Therapeutic Approaches Targeting Nucleolus in Cancer. Cells 2019; 8:E1090. [PMID: 31527430 PMCID: PMC6770360 DOI: 10.3390/cells8091090] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 09/08/2019] [Accepted: 09/13/2019] [Indexed: 01/08/2023] Open
Abstract
The nucleolus is a distinct sub-cellular compartment structure in the nucleus. First observed more than 200 years ago, the nucleolus is detectable by microscopy in eukaryotic cells and visible during the interphase as a sub-nuclear structure immersed in the nucleoplasm, from which it is not separated from any membrane. A huge number of studies, spanning over a century, have identified ribosome biogenesis as the main function of the nucleolus. Recently, novel functions, independent from ribosome biogenesis, have been proposed by several proteomic, genomic, and functional studies. Several works have confirmed the non-canonical role for nucleoli in regulating important cellular processes including genome stability, cell-cycle control, the cellular senescence, stress responses, and biogenesis of ribonucleoprotein particles (RNPs). Many authors have shown that both canonical and non-canonical functions of the nucleolus are associated with several cancer-related processes. The association between the nucleolus and cancer, first proposed by cytological and histopathological studies showing that the number and shape of nucleoli are commonly altered in almost any type of cancer, has been confirmed at the molecular level by several authors who demonstrated that numerous mechanisms occurring in the nucleolus are altered in tumors. Recently, therapeutic approaches targeting the nucleolus in cancer have started to be considered as an emerging "hallmark" of cancer and several therapeutic interventions have been developed. This review proposes an up-to-date overview of available strategies targeting the nucleolus, focusing on novel targeted therapeutic approaches. Finally, a target-based classification of currently available treatment will be proposed.
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Affiliation(s)
- Pietro Carotenuto
- The Institute of Cancer Research, Cancer Therapeutic Unit, London SM2 5NG, UK.
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli 80078, Italy.
| | - Annalisa Pecoraro
- Department of Pharmacy, School of Medicine, University of Naples Federico II, Via Domenico Montesano 49, 80131 Naples, Italy.
| | - Gaetano Palma
- Department of Advanced Biomedical Science, School of Medicine, University of Naples Federico II, 80131 Naples, Italy.
| | - Giulia Russo
- Department of Pharmacy, School of Medicine, University of Naples Federico II, Via Domenico Montesano 49, 80131 Naples, Italy.
| | - Annapina Russo
- Department of Pharmacy, School of Medicine, University of Naples Federico II, Via Domenico Montesano 49, 80131 Naples, Italy.
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Meneguello L, Barbosa NM, Pereira KD, Proença ARG, Tamborlin L, Simabuco FM, Iwai LK, Zanelli CF, Valentini SR, Luchessi AD. The polyproline-motif of S6K2: eIF5A translational dependence and importance for protein-protein interactions. J Cell Biochem 2019; 120:6015-6025. [PMID: 30320934 DOI: 10.1002/jcb.27888] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 09/20/2018] [Indexed: 12/18/2022]
Abstract
Ribosomal S6 kinase 1 (S6K1) and S6K2 proteins are effectors of the mammalian target of rapamycin complex 1 pathway, which control the process of protein synthesis in eukaryotes. S6K2 is associated with tumor progression and has a conserved C-terminus polyproline rich motif predicted to be important for S6K2 interactions. It is noteworthy that the translation of proteins containing sequential prolines has been proposed to be dependent of eukaryotic translation initiation factor 5A (eIF5A) translation factor. Therefore, we investigated the importance of polyproline-rich region of the S6K2 for its intrinsic phosphorylation activity, protein-protein interaction and eIF5A role in S6K2 translation. In HeLa cell line, replacing S6K2 polyproline by the homologous S6K1-sequence did not affect its kinase activity and the S6K2 endogenous content was maintained after eIF5A gene silencing, even after near complete depletion of eIF5A protein. Moreover, no changes in S6K2 transcript content was observed, ruling out the possibility of compensatory regulation by increasing the mRNA content. However, in the budding yeast model, we observed that S6K2 production was impaired when compared with S6K2∆Pro, after reduction of eIF5A protein content. These results suggest that although the polyproline region of S6K2 is capable of generating ribosomal stalling, the depletion of eIF5A in HeLa cells seems to be insufficient to cause an expressive decrease in the content of endogenous S6K2. Finally, coimmunoprecipitation assays revealed that the replacement of the polyproline motif of S6K2 alters its interactome and impairs its interaction with RPS6, a key modulator of ribosome activity. These results evidence the importance of S6K2 polyproline motif in the context of S6Ks function.
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Affiliation(s)
- Leticia Meneguello
- Laboratory of Biotechnology, School of Applied Sciences, University of Campinas (UNICAMP), Limeira, Brazil
- Institute of Biosciences, Department of Biology, São Paulo State University (UNESP), Rio Claro, Brazil
| | - Natália M Barbosa
- Department of Biological Sciences, School of Pharmaceutical Sciences, São Paulo State University (UNESP), Araraquara, Brazil
| | - Karina D Pereira
- Laboratory of Biotechnology, School of Applied Sciences, University of Campinas (UNICAMP), Limeira, Brazil
- Institute of Biosciences, Department of Biology, São Paulo State University (UNESP), Rio Claro, Brazil
| | - André R G Proença
- Laboratory of Biotechnology, School of Applied Sciences, University of Campinas (UNICAMP), Limeira, Brazil
| | - Leticia Tamborlin
- Laboratory of Biotechnology, School of Applied Sciences, University of Campinas (UNICAMP), Limeira, Brazil
- Institute of Biosciences, Department of Biology, São Paulo State University (UNESP), Rio Claro, Brazil
| | - Fernando M Simabuco
- Laboratory of Functional Properties in Foods, School of Applied Sciences, University of Campinas (UNICAMP), Limeira, Brazil
| | - Leo K Iwai
- Special Laboratory of Applied Toxinology, Center of Toxins, Immune-Response and Cell Signaling, LETA/ CeTICS, Butantan Institute, Butanta, Brazil
| | - Cleslei F Zanelli
- Department of Biological Sciences, School of Pharmaceutical Sciences, São Paulo State University (UNESP), Araraquara, Brazil
| | - Sandro R Valentini
- Department of Biological Sciences, School of Pharmaceutical Sciences, São Paulo State University (UNESP), Araraquara, Brazil
| | - Augusto D Luchessi
- Laboratory of Biotechnology, School of Applied Sciences, University of Campinas (UNICAMP), Limeira, Brazil
- Institute of Biosciences, Department of Biology, São Paulo State University (UNESP), Rio Claro, Brazil
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Proteins of the Nucleolus of Dictyostelium discoideum: Nucleolar Compartmentalization, Targeting Sequences, Protein Translocations and Binding Partners. Cells 2019; 8:cells8020167. [PMID: 30781559 PMCID: PMC6406644 DOI: 10.3390/cells8020167] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 02/13/2019] [Accepted: 02/15/2019] [Indexed: 12/31/2022] Open
Abstract
The nucleoli of Dictyostelium discoideum have a comparatively unique, non-canonical, localization adjacent to the inner nuclear membrane. The verified nucleolar proteins of this eukaryotic microbe are detailed while other potential proteins are introduced. Heat shock protein 32 (Hsp32), eukaryotic translation initiation factor 6 (eIF6), and tumour necrosis factor receptor-associated protein 1 (TRAP1) are essential for cell survival. NumA1, a breast cancer type 1 susceptibility protein-C Terminus domain-containing protein linked to cell cycle, functions in the regulation of nuclear number. The cell cycle checkpoint kinase 2 homologue forkhead-associated kinase A (FhkA) and BRG1-associated factor 60a homologue Snf12 are also discussed. While nucleoli appear homogeneous ultrastructurally, evidence for nucleolar subcompartments exists. Nucleolar localization sequences (NoLS) have been defined that target proteins to either the general nucleolar area or to a specific intranucleolar domain. Protein translocations during mitosis are protein-specific and support the multiple functions of the Dictyostelium nucleolus. To enrich the picture, binding partners of NumA1, the most well-characterized nucleolar protein, are examined: nucleolar Ca2+-binding protein 4a (CBP4a), nuclear puromycin-sensitive aminopeptidase A (PsaA) and Snf12. The role of Dictyostelium as a model for understanding the contribution of nucleolar proteins to various diseases and cellular stress is discussed throughout the review.
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Ribosomal Proteins Control or Bypass p53 during Nucleolar Stress. Int J Mol Sci 2017; 18:ijms18010140. [PMID: 28085118 PMCID: PMC5297773 DOI: 10.3390/ijms18010140] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 12/12/2016] [Accepted: 01/05/2017] [Indexed: 12/20/2022] Open
Abstract
The nucleolus is the site of ribosome biogenesis, a complex process that requires the coordinate activity of all three RNA polymerases and hundreds of non-ribosomal factors that participate in the maturation of ribosomal RNA (rRNA) and assembly of small and large subunits. Nevertheless, emerging studies have highlighted the fundamental role of the nucleolus in sensing a variety of cellular stress stimuli that target ribosome biogenesis. This condition is known as nucleolar stress and triggers several response pathways to maintain cell homeostasis, either p53-dependent or p53-independent. The mouse double minute (MDM2)-p53 stress signaling pathways are activated by multiple signals and are among the most important regulators of cellular homeostasis. In this review, we will focus on the role of ribosomal proteins in p53-dependent and p53-independent response to nucleolar stress considering novel identified regulators of these pathways. We describe, in particular, the role of ribosomal protein uL3 (rpL3) in p53-independent nucleolar stress signaling pathways.
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Abstract
Mechanistic target of rapamycin (mTOR) is a central component of the essential signaling pathway that regulates cell growth and proliferation by controlling anabolic processes in cells. mTOR exists in two distinct mTOR complexes known as mTORC1 and mTORC2 that reside mostly in cytoplasm. In our study, the biochemical characterization of mTOR led to discovery of its novel localization on nuclear envelope where it associates with a critical regulator of nuclear import Ran Binding Protein 2 (RanBP2). We show that association of mTOR with RanBP2 is dependent on the mTOR kinase activity that regulates the nuclear import of ribosomal proteins. The mTOR kinase inhibitors within thirty minutes caused a substantial decrease of ribosomal proteins in the nuclear but not cytoplasmic fraction. Detection of a nuclear accumulation of the GFP-tagged ribosomal protein rpL7a also indicated its dependence on the mTOR kinase activity. The nuclear abundance of ribosomal proteins was not affected by inhibition of mTOR Complex 1 (mTORC1) by rapamycin or deficiency of mTORC2, suggesting a distinctive role of the nuclear envelope mTOR complex in the nuclear import. Thus, we identified that mTOR in association with RanBP2 mediates the active nuclear import of ribosomal proteins.
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Yang CP, Chiang CW, Chen CH, Lee YC, Wu MH, Tsou YH, Yang YS, Chang WC, Lin DY. Identification and characterization of nuclear and nucleolar localization signals in 58-kDa microspherule protein (MSP58). J Biomed Sci 2015; 22:33. [PMID: 25981436 PMCID: PMC4434885 DOI: 10.1186/s12929-015-0136-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 04/21/2015] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND MSP58 is a nucleolar protein associated with rRNA transcription and cell proliferation. Its mechanism of translocation into the nucleus or the nucleolus, however, is not entirely known. In order to address this lack, the present study aims to determine a crucial part of this mechanism: the nuclear localization signal (NLS) and the nucleolar localization signal (NoLS) associated with the MSP58 protein. RESULTS We have identified and characterized two NLSs in MSP58. The first is located between residues 32 and 56 (NLS1) and constitutes three clusters of basic amino acids (KRASSQALGTIPKRRSSSRFIKRKK); the second is situated between residues 113 and 123 (NLS2) and harbors a monopartite signal (PGLTKRVKKSK). Both NLS1 and NLS2 are highly conserved among different vertebrate species. Notably, one bipartite motif within the NLS1 (residues 44-56) appears to be absolutely necessary for MSP58 nucleolar localization. By yeast two-hybrid, pull-down, and coimmunoprecipitation analysis, we show that MSP58 binds to importin α1 and α6, suggesting that nuclear targeting of MSP58 utilizes a receptor-mediated and energy-dependent import mechanism. Functionally, our data show that both nuclear and nucleolar localization of MSP58 are crucial for transcriptional regulation on p21 and ribosomal RNA genes, and context-dependent effects on cell proliferation. CONCLUSIONS Results suggest that MSP58 subnuclear localization is regulated by two nuclear import signals, and that proper subcellular localization of MSP58 is critical for its role in transcriptional regulation. Our study reveals a molecular mechanism that controls nuclear and nucleolar localization of MSP58, a finding that might help future researchers understand the MSP58 biological signaling pathway.
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Affiliation(s)
- Chuan-Pin Yang
- Institute of Bioinformatics and Biosignal Transduction, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan, 70101, Taiwan, ROC.
| | - Chi-Wu Chiang
- Institute of Molecular Medicine, College of Medicine, National Cheng Kung University, Tainan, 70101, Taiwan, ROC. .,Infectious Diseases and Signaling Research Center, National Cheng Kung University, Tainan, 70101, Taiwan, ROC.
| | - Chang-Han Chen
- Center for Translational Research in Biomedical Sciences, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, 83301, Taiwan, ROC. .,Department of Applied Chemistry, National Chi Nan University, Puli, Nantou, 54561, Taiwan, ROC.
| | - Yi-Chao Lee
- Center for Neurotrauma and Neuroregeneration, Taipei Medical University, Taipei, 11031, Taiwan, ROC. .,Program for Neural Regenerative Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei, 11031, Taiwan, ROC.
| | - Mei-Hsiang Wu
- Institute of Bioinformatics and Biosignal Transduction, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan, 70101, Taiwan, ROC.
| | - Yi-Huan Tsou
- Department of Pharmacology, College of Medicine, National Cheng Kung University, Tainan, 70101, Taiwan, ROC.
| | - Yu-San Yang
- Institute of Molecular Medicine, College of Medicine, National Cheng Kung University, Tainan, 70101, Taiwan, ROC.
| | - Wen-Chang Chang
- Department of Pharmacology, College of Medicine, National Cheng Kung University, Tainan, 70101, Taiwan, ROC. .,Infectious Diseases and Signaling Research Center, National Cheng Kung University, Tainan, 70101, Taiwan, ROC. .,Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei, 11031, Taiwan, ROC. .,Center for Neurotrauma and Neuroregeneration, Taipei Medical University, Taipei, 11031, Taiwan, ROC.
| | - Ding-Yen Lin
- Institute of Bioinformatics and Biosignal Transduction, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan, 70101, Taiwan, ROC. .,Department of Pharmacology, College of Medicine, National Cheng Kung University, Tainan, 70101, Taiwan, ROC. .,Infectious Diseases and Signaling Research Center, National Cheng Kung University, Tainan, 70101, Taiwan, ROC. .,Institute for Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, 11031, Taiwan, ROC.
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Kenney SP, Meng XJ. Identification and fine mapping of nuclear and nucleolar localization signals within the human ribosomal protein S17. PLoS One 2015; 10:e0124396. [PMID: 25853866 PMCID: PMC4390217 DOI: 10.1371/journal.pone.0124396] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2014] [Accepted: 03/13/2015] [Indexed: 01/29/2023] Open
Abstract
Human ribosomal protein S17 (RPS17) is mutated in Diamond-Blackfan Anemia (DBA), a bone marrow disorder that fails to produce sufficient red blood cells leading to anemia. Recently, an RPS17 protein sequence was also found to be naturally inserted in the genome of hepatitis E virus (HEV) from patients chronically-infected by HEV. The role of RPS17 in HEV replication and pathogenesis remains unknown due to the lack of knowledge about how RPS17 functions at a molecular level. Understanding the biological function of RPS17 is critical for elucidating its role in virus infection and DBA disease processes. In this study we probed the subcellular distribution of normal and mutant RPS17 proteins in a human liver cell line (Huh7). RPS17 was primarily detected within the nucleus, and more specifically within the nucleoli. Using a transient expression system in which RPS17 or truncations were expressed as fusions with enhanced yellow fluorescent protein (eYFP), we were able to identify and map, for the first time, two separate nuclear localization signals (NLSs), one to the first 13 amino acids of the amino-terminus of RPS17 and the other within amino acids 30-60. Additionally, we mapped amino acid sequences required for nucleolar accumulation of RPS17 to amino acids 60-70. Amino acids 60-70 possess a di-RG motif that may be necessary for nucleolar retention of RPS17. The results from this study enhance our knowledge of RSP17 and will facilitate future mechanistic studies about the roles of RSP17 in hepatitis E and DBA disease processes.
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Affiliation(s)
- Scott P. Kenney
- Center for Molecular Medicine and Infectious Diseases, Department of Biomedical Sciences and Pathobiology, College of Veterinary Medicine, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, Virginia, United States of America
| | - Xiang-Jin Meng
- Center for Molecular Medicine and Infectious Diseases, Department of Biomedical Sciences and Pathobiology, College of Veterinary Medicine, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, Virginia, United States of America
- * E-mail:
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10
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Wang W, Cai J, Lin Y, Liu Z, Ren Q, Hu L, Huang Z, Guo M, Li W. Zinc fingers function cooperatively with KRAB domain for nuclear localization of KRAB-containing zinc finger proteins. PLoS One 2014; 9:e92155. [PMID: 24647005 PMCID: PMC3960175 DOI: 10.1371/journal.pone.0092155] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2013] [Accepted: 02/18/2014] [Indexed: 11/18/2022] Open
Abstract
Multiple nuclear localization domains have been identified in nuclear proteins, and they finely control nuclear import and functions of those proteins. ZNF268 is a typical KRAB-containing zinc finger protein (KRAB-ZFP), and previous studies have shown that the KRAB domain reinforces nuclear localization of KRAB-ZFPs by interacting with KAP1. In this study, we find that some of 24 zinc fingers of ZNF268 also possess nuclear localization activity. Results of mutagenesis studies suggest that KRAB and zinc fingers are both necessary, and they function both independently and cooperatively for the nuclear localization of ZNF268. However, the subnuclear targeting activities of KRAB and zinc fingers are different. KRAB targets proteins in nucleoplasm, but not in the nucleolus, which is mediated by interaction with KAP1, while zinc fingers target proteins in the whole nucleus uniformly. The cooperative activities of KAP1-KRAB-zinc fingers result in the precise nucleoplasmic, but not nucleolar localization of KRAB-ZFPs. Our studies reveal a novel mechanism for the subcellular localization of KRAB-ZFPs and may help us to further explore their biological functions.
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Affiliation(s)
- Wei Wang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Jinyang Cai
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Yi Lin
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Zikou Liu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Qihao Ren
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Li Hu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Zan Huang
- Department of Biochemistry and Molecular Biology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Mingxiong Guo
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
- * E-mail: (MG); (WL)
| | - Wenxin Li
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
- * E-mail: (MG); (WL)
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11
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Kimura M, Kose S, Okumura N, Imai K, Furuta M, Sakiyama N, Tomii K, Horton P, Takao T, Imamoto N. Identification of cargo proteins specific for the nucleocytoplasmic transport carrier transportin by combination of an in vitro transport system and stable isotope labeling by amino acids in cell culture (SILAC)-based quantitative proteomics. Mol Cell Proteomics 2012; 12:145-57. [PMID: 23087160 DOI: 10.1074/mcp.m112.019414] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The human importin-β family consists of 21 nucleocytoplasmic transport carrier proteins that carry proteins and RNAs across the nuclear envelope through nuclear pores in specific directions. These transport carriers are responsible for the nucleocytoplasmic transport of thousands of proteins, but the cargo allocation of each carrier, which is necessary information if one wishes to understand the physiological context of transport, is poorly characterized. To address this issue, we developed a high-throughput method to identify the cargoes of transport carriers by applying stable isotope labeling by amino acids in cell culture to construct an in vitro transport system. Our method can be outlined in three steps. (1) Cells are cultured in a medium containing a stable isotope. (2) The cell membranes of the labeled cells are permeabilized, and proteins extracted from unlabeled cells are transported into the nuclei of the permeabilized cells. In this step, the reaction system is first depleted of all importin-β family carriers and then supplemented with a particular importin-β family carrier of interest. (3) Proteins in the nuclei are extracted and analyzed quantitatively via LC-MS/MS. As an important test case, we used this method to identify cargo proteins of transportin, a representative member of the importin-β family. As expected, the identified candidate cargo proteins included previously reported transportin cargoes as well as new potential cargoes, which we corroborated via in vitro binding assays. The identified cargoes are predominately RNA-interacting proteins, affirming that cargoes allotted to the same carrier share functional characteristics. Finally, we found that the transportin cargoes possessed at least two classes of signal sequences: the well characterized PY-nuclear localization signals specific for transportin, and Lys/Arg-rich segments capable of binding to both transportin and importin-β. Thus, our method will be useful for linking a carrier to features shared among its cargoes and to specific nuclear localization signals.
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Affiliation(s)
- Makoto Kimura
- Cellular Dynamics Laboratory, Advanced Science Institute, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
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Nucleolar localization and identification of nuclear/nucleolar localization signals of the calmodulin-binding protein nucleomorphin during growth and mitosis in Dictyostelium. Histochem Cell Biol 2011; 135:239-49. [PMID: 21327858 DOI: 10.1007/s00418-011-0785-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/29/2011] [Indexed: 10/18/2022]
Abstract
The calmodulin-binding protein nucleomorphin isoform NumA1 is a nuclear number regulator in Dictyostelium that localizes to intra-nuclear patches adjacent to the nuclear envelope and to a lesser extent the nucleoplasm. Earlier studies have shown similar patches to be nucleoli but only three nucleolar proteins have been identified in Dictyostelium. Here, actinomycin-D treatment caused the loss of NumA1 localization, while calcium and calmodulin antagonists had no effect. In keeping with a nucleolar function, NumA1 moved out of the presumptive nucleoli during mitosis redistributing to areas within the nucleus, the spindle fibers, and centrosomal region before re-accumulating in the presumptive nucleoli at telophase. Together, these data verify NumA1 as a true nucleolar protein. Prior to this study, the dynamics of specific nucleolar proteins had not been determined during mitosis in Dictyostelium. FITC-conjugated peptides equivalent to presumptive nuclear localization signals within NumA1 localized to nucleoli indicating that they also act as nucleolar localization signals. To our knowledge, these represent the first precisely defined nucleolar localization signals as well as the first nuclear/nucleolar localization signals identified in Dictyostelium. Together, these results reveal that NumA1 is a true nucleolar protein and the only nucleolar calmodulin-binding protein identified in Dictyostelium. The possible use of nuclear/nucleolar localization signal-mediated drug targeting to nucleoli is discussed.
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13
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Goyal P, Behring A, Kumar A, Siess W. STK35L1 associates with nuclear actin and regulates cell cycle and migration of endothelial cells. PLoS One 2011; 6:e16249. [PMID: 21283756 PMCID: PMC3024402 DOI: 10.1371/journal.pone.0016249] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2010] [Accepted: 12/08/2010] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Migration and proliferation of vascular endothelial cells are essential for repair of injured endothelium and angiogenesis. Cyclins, cyclin-dependent kinases (CDKs), and cyclin-dependent kinase inhibitors play an important role in vascular tissue injury and wound healing. Previous studies suggest a link between the cell cycle and cell migration: cells present in the G(1) phase have the highest potential to migrate. The molecular mechanism linking these two processes is not understood. METHODOLOGY/PRINCIPAL FINDINGS In this study, we explored the function of STK35L1, a novel Ser/Thr kinase, localized in the nucleus and nucleolus of endothelial cells. Molecular biological analysis identified a bipartite nuclear localization signal, and nucleolar localization sequences in the N-terminal part of STK35L1. Nuclear actin was identified as a novel binding partner of STK35L1. A class III PDZ binding domains motif was identified in STK35L1 that mediated its interaction with actin. Depletion of STK35L1 by siRNA lead to an accelerated G(1) to S phase transition after serum-stimulation of endothelial cells indicating an inhibitory role of the kinase in G(1) to S phase progression. Cell cycle specific genes array analysis revealed that one gene was prominently downregulated (8.8 fold) in STK35L1 silenced cells: CDKN2A alpha transcript, which codes for p16(INK4a) leading to G(1) arrest by inhibition of CDK4/6. Moreover in endothelial cells seeded on Matrigel, STK35L1 expression was rapidly upregulated, and silencing of STK35L1 drastically inhibited endothelial sprouting that is required for angiogenesis. Furthermore, STK35L1 depletion profoundly impaired endothelial cell migration in two wound healing assays. CONCLUSION/SIGNIFICANCE The results indicate that by regulating CDKN2A and inhibiting G1- to S-phase transition STK35L1 may act as a central kinase linking the cell cycle and migration of endothelial cells. The interaction of STK35L1 with nuclear actin might be critical in the regulation of these fundamental endothelial functions.
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Affiliation(s)
- Pankaj Goyal
- Institut für Prophylaxe und Epidemiologie der Kreislaufkrankheiten, Klinikum Innenstadt, Universität München, Munich, Germany.
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On the intracellular trafficking of mouse S5 ribosomal protein from cytoplasm to nucleoli. J Mol Biol 2009; 392:1192-204. [PMID: 19631221 DOI: 10.1016/j.jmb.2009.07.049] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2009] [Revised: 07/07/2009] [Accepted: 07/16/2009] [Indexed: 11/21/2022]
Abstract
The non-ribosomal functions of mammalian ribosomal proteins have recently attracted worldwide attention. The mouse ribosomal protein S5 (rpS5) derived from ribosomal material is an assembled non-phosphorylated protein. The free form of rpS5 protein, however, undergoes phosphorylation. In this study, we have (a) investigated the potential role of phosphorylation in rpS5 protein transport into the nucleus and then into nucleoli and (b) determined which of the domains of rpS5 are involved in this intracellular trafficking. In vitro PCR mutagenesis of mouse rpS5 cDNA, complemented by subsequent cloning and expression of rpS5 truncated recombinant forms, produced in fusion with green fluorescent protein, permitted the investigation of rpS5 intracellular trafficking in HeLa cells using confocal microscopy complemented by Western blot analysis. Our results indicate the following: (a) rpS5 protein enters the nucleus via the region 38-50 aa that forms a random coil as revealed by molecular dynamic simulation. (b) Immunoprecipitation of rpS5 with casein kinase II and immobilized metal affinity chromatography analysis complemented by in vitro kinase assay revealed that phosphorylation of rpS5 seems to be indispensable for its transport from nucleus to nucleoli; upon entering the nucleus, Thr-133 phosphorylation triggers Ser-24 phosphorylation by casein kinase II, thus promoting entrance of rpS5 into the nucleoli. Another important role of rpS5 N-terminal region is proposed to be the regulation of protein's cellular level. The repetitively co-appearance of a satellite C-terminal band below the entire rpS5 at the late stationary phase, and not at the early logarithmic phase, of cell growth suggests a specific degradation balancing probably the unassembled ribosomal protein molecules with those that are efficiently assembled to ribosomal subunits. Overall, these data provide new insights on the structural and functional domains within the rpS5 molecule that contribute to its cellular functions.
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15
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Pais FS, DaRocha WD, Almeida RM, Leclercq SY, Penido ML, Fragoso SP, Bartholomeu DC, Gazzinelli RT, Teixeira SM. Molecular characterization of ribonucleoproteic antigens containing repeated amino acid sequences from Trypanosoma cruzi. Microbes Infect 2008; 10:716-25. [DOI: 10.1016/j.micinf.2008.03.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2008] [Revised: 03/10/2008] [Accepted: 03/14/2008] [Indexed: 11/16/2022]
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Lindström MS, Zhang Y. Ribosomal protein S9 is a novel B23/NPM-binding protein required for normal cell proliferation. J Biol Chem 2008; 283:15568-76. [PMID: 18420587 DOI: 10.1074/jbc.m801151200] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
B23 (NPM/nucleophosmin) is a multifunctional nucleolar protein and a member of the nucleoplasmin superfamily of acidic histone chaperones. B23 is essential for normal embryonic development and plays an important role in genomic stability, ribosome biogenesis, and anti-apoptotic signaling. Altered protein expression or genomic mutation of B23 is encountered in many different forms of cancer. Although described as multifunctional, a genuine molecular function of B23 is not fully understood. Here we show that B23 is associated with a protein complex consisting of ribosomal proteins and ribosome-associated RNA helicases. A novel, RNA-independent interaction between ribosomal protein S9 (RPS9) and B23 was further investigated. We found that S9 binding requires an intact B23 oligomerization domain. Depletion of S9 by small interfering RNA resulted in decreased protein synthesis and G(1) cell cycle arrest, in association with induction of p53 target genes. We determined that S9 is a short-lived protein in the absence of ribosome biogenesis, and proteasomal inhibition significantly increased S9 protein level. Overexpression of B23 facilitated nucleolar storage of S9, whereas knockdown of B23 led to diminished levels of nucleolar S9. Our results suggest that B23 selectively stores, and protects ribosomal protein S9 in nucleoli and therefore could facilitate ribosome biogenesis.
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Affiliation(s)
- Mikael S Lindström
- Department of Radiation Oncology, University of North Carolina School of Medicine, University of North Carolina, Chapel Hill, North Carolina 27599-7512, USA
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Theodore M, Kawai Y, Yang J, Kleshchenko Y, Reddy SP, Villalta F, Arinze IJ. Multiple nuclear localization signals function in the nuclear import of the transcription factor Nrf2. J Biol Chem 2008; 283:8984-94. [PMID: 18238777 DOI: 10.1074/jbc.m709040200] [Citation(s) in RCA: 156] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Nuclear factor erythroid 2-related factor 2 (Nrf2) mediates the transcriptional response of cells to oxidative stress and is translocated into the nucleus following, or concomitant with, its activation by electrophiles or reactive oxygen species. The mechanism of its translocation into the nucleus is not entirely elucidated. Here we have identified two novel nuclear localization signal (NLS) motifs in murine Nrf2, one located near the N-terminal region (amino acid residues 42-53) and the other (residues 587-593) located near the C-terminal region. Imaging of green fluorescent protein (GFP)-tagged Nrf2 revealed that mutation(s) in any of these sequences resulted in decreased nuclear fluorescence intensity compared with the wild-type Nrf2 when Nrf2 activation was induced with the electrophile tert-butylhydroquinone. The mutations also impaired Nrf2-induced transactivation of antioxidant response element-driven reporter gene expression to the same extent as the Nrf2 construct bearing mutation in a previously identified bipartite NLS that maps at residues 494-511. When linked to GFP or to GFP-PEPCK-C each of the novel NLS motifs was sufficient to drive nuclear translocation of the fusion proteins. Co-immunoprecipitation assays demonstrated that importins alpha5 and beta1 associate with Nrf2, an interaction that was blocked by the nuclear import inhibitor SN50. SN50 also blocked tert-butylhydroquinone-induced nuclear fluorescence of GFP-Nrf2 in cells transfected with wild-type GFP-Nrf2. Overall these results reveal that multiple NLS motifs in Nrf2 function in its nuclear translocation in response to pro-oxidant stimuli and that the importin alpha-beta heterodimer nuclear import receptor system plays a critical role in the import process.
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Affiliation(s)
- Melanie Theodore
- School of Medicine, Meharry Medical College, Nashville, TN 37208-3599, USA
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Dominguez J, Wu P, Packer CS, Temm C, Kelly KJ. Lipotoxic and inflammatory phenotypes in rats with uncontrolled metabolic syndrome and nephropathy. Am J Physiol Renal Physiol 2007; 293:F670-9. [PMID: 17596532 DOI: 10.1152/ajprenal.00021.2007] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Anomalous inflammatory responses triggered by the metabolic syndrome cause renal injury. This discovery links renal lipid accumulation with lipotoxicity to inflammation and may explain the insidious fibrosis and cellular decay characteristic of nephropathy in the metabolic syndrome. However, it is not clear whether control of inflammation protects the kidney independently of lipid accumulation, which is a required step for lipotoxicity in hyperglycemia and dyslipidemia. We hypothesized that in rats with the metabolic syndrome, and overt nephropathy, treatment with mycophenolate mofetil (MMF; 10 mg.kg(-1).day(-1) ip for 14 wk) would reduce the abnormal renal lipid depots and limit renal inflammation and injury. We studied groups of lean and obese F1 hybrid Zucker fatty diabetic/spontaneous hypertensive heart failure (ZS) rats. MMF did not affect lean rats. In obese ZS rats, MMF did not change severe hyperglycemia or the higher kidney loads of unutilized lipid and peroxidation products. Nonetheless, MMF dramatically reduced diabetes/obesity-derived systemic and renal inflammation, limited renal size, hyperfiltration, and fibrosis. These data indicate that in rats, anti-inflammatory therapy presumably acting downstream, and independently of lipotoxicity, can effectively limit renal injury and fibrosis.
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Affiliation(s)
- Jesus Dominguez
- Departments of Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA.
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Abstract
The nucleolus is a dynamic subnuclear structure that is crucial to the successful functioning of a cell. Its functions include ribosomal RNA synthesis, cell growth and cell-cycle control as well as responding to cellular stress. Recent studies show that the nucleolus is not a steady-state structure but instead is made up of numerous protein–protein and protein–nucleic-acid interactions that are constantly changing in response to the metabolic conditions of the cell. Many different viruses target the nucleolus to disrupt host-cell function and to recruit cellular proteins to aid in virus replication. The study of viral-protein trafficking to the nucleolus and the interaction of viral proteins with nucleolar proteins is providing many insights into the cell biology of the nucleolus. Because the nucleolus is fundamental to the life cycle of many viruses, disrupting the interaction between the nucleolus and the virus could lead to the design of novel therapeutic strategies.
RNA viruses, particularly positive-strand RNA viruses, interact with the nucleolus to usurp host-cell functions and recruit nucleolar proteins to facilitate virus replication. Here, Julian Hiscox reviews the latest data on RNA-virus interactions with this dynamic subnuclear structure. The nucleolus is a dynamic subnuclear structure with roles in ribosome subunit biogenesis, mediation of cell-stress responses and regulation of cell growth. The proteome and structure of the nucleolus are constantly changing in response to metabolic conditions. RNA viruses interact with the nucleolus to usurp host-cell functions and recruit nucleolar proteins to facilitate virus replication. Investigating the interactions between RNA viruses and the nucleolus will facilitate the design of novel anti-viral therapies, such as recombinant vaccines and therapeutic molecular interventions, and also contribute to a more detailed understanding of the cell biology of the nucleolus.
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Affiliation(s)
- Julian A Hiscox
- Institute of Molecular and Cellular Biology, Faculty of Biological Sciences, and Astbury Centre for Structural Molecular Biology, Garstang Building, University of Leeds, Leeds, LS2 9JT, UK.
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Goyal P, Pandey D, Siess W. Phosphorylation-dependent regulation of unique nuclear and nucleolar localization signals of LIM kinase 2 in endothelial cells. J Biol Chem 2006; 281:25223-30. [PMID: 16820362 DOI: 10.1074/jbc.m603399200] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
LIM kinases (LIMKs) regulate actin dynamics through cofilin phosphorylation and also have a function in the nucleus. Recently we have shown that LIMK2 shuttles between cytoplasm and nucleus in endothelial cells and that nuclear import is inhibited by protein kinase C-mediated phosphorylation of Ser-283. Here we aimed to identify the structural features of LIMK2 responsible for nuclear import. We found that the kinase domain of LIMK2 is localized exclusively in the nucleus and, in contrast to the kinase domain of LIMK1, it accumulated in the nucleolus. Through site-directed mutagenesis, we identified the basic amino acid-rich motif KKRTLRKNDRKKR (amino acids 491-503) as the functional nuclear and nucleolar localization signal of LIMK2. After fusing this motif to enhanced green fluorescent protein, the fusion protein localized exclusively in the nucleus and nucleolus. Mutagenesis studies showed that phosphorylation of Thr-494, a putative protein kinase C phosphorylation site identified within the nuclear localization signal, inhibits nuclear import of the enhanced green fluorescent protein-PDZ kinase domain of LIMK2. After inhibiting nuclear export with leptomycin B, phosphorylation of either Ser-283 or Thr-494 reduced the nuclear import of LIMK2. Phosphorylation of both Ser-283 and Thr-494 sites inhibited nuclear import completely. Our findings identify a unique basic amino acid-rich motif (amino acids 491-503) in LIMK2 which is not present in LIMK1 that serves to target the protein not only to the nucleus but also to the nucleolus. Phosphorylation of Thr-494 within this motif negatively regulates nuclear import of LIMK2.
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Affiliation(s)
- Pankaj Goyal
- Institute for Prevention of Cardiovascular Diseases, University of Munich, 80336 Munich, Germany.
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21
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Russo A, Russo G, Cuccurese M, Garbi C, Pietropaolo C. The 3'-untranslated region directs ribosomal protein-encoding mRNAs to specific cytoplasmic regions. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2006; 1763:833-43. [PMID: 16839621 DOI: 10.1016/j.bbamcr.2006.05.010] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2005] [Revised: 04/21/2006] [Accepted: 05/10/2006] [Indexed: 11/30/2022]
Abstract
mRNA localization is a conserved post-transcriptional process crucial for a variety of systems. We have analyzed the subcellular distribution of mRNAs encoding human cytosolic and mitochondrial ribosomal proteins. Biochemical fractionation experiments showed that the transcripts for cytosolic ribosomal proteins associate preferentially with the cytoskeleton via actin microfilaments. Transfection in HeLa cells of a GFP reporter construct containing the cytosolic ribosomal protein L4 3'-UTR showed that the 3'-UTR is necessary for the association of the transcript to the cytoskeleton. Using confocal analysis we demonstrate that the chimeric transcript is specifically associated with the perinuclear cytoskeleton. We also show that mRNA for mitochondrial ribosomal protein S12 is asymmetrically distributed in the cytoplasm. In fact, this transcript was localized mainly in the proximity of mitochondria, and the localization was 3'-UTR-dependent. In summary, ribosomal protein mRNAs constitute a new class of localized transcripts that share a common localization mechanism.
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Affiliation(s)
- Annapina Russo
- Dipartimento di Biochimica e Biotecnologie Mediche, Università Federico II, Via Sergio Pansini 5, Napoli 80131, Italy
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22
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De Ganck A, Hubert T, Van Impe K, Geelen D, Vandekerckhove J, De Corte V, Gettemans J. A monopartite nuclear localization sequence regulates nuclear targeting of the actin binding protein myopodin. FEBS Lett 2005; 579:6673-80. [PMID: 16309678 DOI: 10.1016/j.febslet.2005.10.054] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2005] [Revised: 09/09/2005] [Accepted: 10/27/2005] [Indexed: 11/29/2022]
Abstract
Myopodin is an actin bundling protein that shuttles between nucleus and cytoplasm in response to cell stress or during differentiation. Here, we show that the myopodin sequence 58KKRRRRARK66, when tagged to either enhanced green fluorescent protein (EGFP) or to enhanced cyan fluorescent protein-CapG (ECFPCapG), is able to target these proteins to the nucleolus in HeLa or HEK293T cells. By contrast, 58KKRR61-ECFP-CapG accumulates in the nucleus. Mutation of 58KKRRRRARK66 into alanine residues blocks myopodin nuclear import and promotes formation of cytoplasmic actin filaments. A second putative nuclear localization sequence, 612KTSKKKGKK620, displays much weaker activity in a heterologous context, and appears not to be functional in the full length protein. Thus myopodin nuclear translocation is dependent on a monopartite nuclear localization sequence.
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Affiliation(s)
- Ariane De Ganck
- Department of Medical Protein Research, Flanders Interuniversity Institute for Biotechnology (V.I.B.), Ghent University, Faculty of Medicine and Health Sciences, Albert Baertsoenkaai 3, B-9000 Ghent, Belgium
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Grasberger H, Bell GI. Subcellular recruitment by TSG118 and TSPYL implicates a role for zinc finger protein 106 in a novel developmental pathway. Int J Biochem Cell Biol 2005; 37:1421-37. [PMID: 15833274 DOI: 10.1016/j.biocel.2005.01.013] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2004] [Revised: 01/25/2005] [Accepted: 01/26/2005] [Indexed: 10/25/2022]
Abstract
To gain insight into the function of zinc finger protein 106 (ZFP106), we analyzed its subcellular targeting and identified its interacting proteins. Although ZFP106 was detected predominantly in the fibrillar component of the nucleolus and co-localized with the nucleolar transcriptional machinery, its overexpression did not affect transcription of pre-ribosomal RNA genes. The nucleolar association of ZFP106 did neither require ongoing ribosomal RNA synthesis nor nucleolar chromatin indicating that a protein-protein interaction confines ZFP106 to the nucleolus. Deletion analysis revealed that the C-terminal WD40 repeat region functions in nucleolar targeting. This domain interacts with the product of testis-specific gene 118 (TSG118), which also co-localizes with ZFP106 in the nucleolus. Rapid downregulation of TSG118 expression during in vitro terminal differentiation coincides with a loss of nucleolar ZFP106. By its structural features and expression, TSG118 mimics nucleostemin, a nucleolar protein linked to the proliferation potential of stem cells. A two-hybrid screen with the N-terminal region of ZFP106 as bait led to the isolation of testis-specific Y-encoded-like protein (TSPYL), a member of the nucleosome assembly protein family. A frame-shift mutation in TSPYL has recently been found to cause a sudden infant death syndrome with testis dysgenesis. Specific recruitment of ZFP106 via amino acids 412-781 into TSPYL-positive nucleoplasmic bodies requires a TSPYL domain absent in the mutant protein of patients with testis dysgenesis. These results identify ZFP106 as a potential player in a novel pathway involved in testis development.
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Affiliation(s)
- Helmut Grasberger
- Department of Biochemistry and Molecular Biology, and of Medicine and Human Genetics, The University of Chicago, Chicago, IL 60637, USA.
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Russo G, Cuccurese M, Monti G, Russo A, Amoresano A, Pucci P, Pietropaolo C. Ribosomal protein L7a binds RNA through two distinct RNA-binding domains. Biochem J 2005; 385:289-99. [PMID: 15361074 PMCID: PMC1134697 DOI: 10.1042/bj20040371] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The human ribosomal protein L7a is a component of the major ribosomal subunit. We previously identified three nuclear-localization-competent domains within L7a, and demonstrated that the domain defined by aa (amino acids) 52-100 is necessary, although not sufficient, to target the L7a protein to the nucleoli. We now demonstrate that L7a interacts in vitro with a presumably G-rich RNA structure, which has yet to be defined. We also demonstrate that the L7a protein contains two RNA-binding domains: one encompassing aa 52-100 (RNAB1) and the other encompassing aa 101-161 (RNAB2). RNAB1 does not contain any known nucleic-acid-binding motif, and may thus represent a new class of such motifs. On the other hand, a specific region of RNAB2 is highly conserved in several other protein components of the ribonucleoprotein complex. We have investigated the topology of the L7a-RNA complex using a recombinant form of the protein domain that encompasses residues 101-161 and a 30mer poly(G) oligonucleotide. Limited proteolysis and cross-linking experiments, and mass spectral analyses of the recombinant protein domain and its complex with poly(G) revealed the RNA-binding region.
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Affiliation(s)
- Giulia Russo
- *Dipartimento di Biochimica e Biotecnologie Mediche, Università Federico II, Via Sergio Pansini 5 Napoli, I-80131 Italy
| | - Monica Cuccurese
- *Dipartimento di Biochimica e Biotecnologie Mediche, Università Federico II, Via Sergio Pansini 5 Napoli, I-80131 Italy
| | - Gianluca Monti
- †Dipartimento di Chimica Organica e Biologica, Università Federico II, Complesso Universitario Monte S. Angelo, Via Cinthia 4, I-80126 Italy
| | - Annapina Russo
- *Dipartimento di Biochimica e Biotecnologie Mediche, Università Federico II, Via Sergio Pansini 5 Napoli, I-80131 Italy
| | - Angela Amoresano
- †Dipartimento di Chimica Organica e Biologica, Università Federico II, Complesso Universitario Monte S. Angelo, Via Cinthia 4, I-80126 Italy
| | - Pietro Pucci
- †Dipartimento di Chimica Organica e Biologica, Università Federico II, Complesso Universitario Monte S. Angelo, Via Cinthia 4, I-80126 Italy
- ‡CEINGE Biotecnologie Avanzate S.C.a.r.l., Via Comunale Margherita 482 Napoli, I-80145 Italy
| | - Concetta Pietropaolo
- *Dipartimento di Biochimica e Biotecnologie Mediche, Università Federico II, Via Sergio Pansini 5 Napoli, I-80131 Italy
- To whom correspondence should be addressed (email )
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Kim JH, You KR, Kim IH, Cho BH, Kim CY, Kim DG. Over-expression of the ribosomal protein L36a gene is associated with cellular proliferation in hepatocellular carcinoma. Hepatology 2004; 39:129-38. [PMID: 14752831 DOI: 10.1002/hep.20017] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Using messenger RNA (mRNA) differential display, we identified a single complementary DNA (cDNA) fragment (HG23T1) that was over-expressed in a hepatocellular carcinoma (HCC) specimen. We cloned the full-length HG23T1 gene by the rapid amplification of cDNA end (RACE) polymerase chain reaction (PCR) method. It perfectly matched the gene encoding human ribosomal protein L36a (RPL36A also referred to as RPL44). RPL36A mRNA was preferentially over-expressed in 34 of 40 HCC cases (85%, P <.001) and in all of 8 HCC cell lines. Ectopically over-expressed L36a ribosomal protein localized in the nucleoli of cells, and this localization seemed to be controlled by the N-terminal or the internal tetrapeptide consensus with its adjacent N-terminal domain. Over-expression of L36a led to enhanced colony formation and cell proliferation, which may have resulted from rapid cell cycling, and an antisense cDNA effectively reversed these alterations. In conclusion, RPL36A plays a role in tumor cell proliferation and may be a potential target for anticancer therapy of HCC.
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Affiliation(s)
- Jong-Hyun Kim
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, Institute for Medical Science, Chonbuk National University Medical School and Hospital, Chonju, Chonbuk, South Korea
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Cheng RYS, Zhao A, Alvord WG, Powell DA, Bare RM, Masuda A, Takahashi T, Anderson LM, Kasprzak KS. Gene expression dose-response changes in microarrays after exposure of human peripheral lung epithelial cells to nickel(II). Toxicol Appl Pharmacol 2003; 191:22-39. [PMID: 12915101 DOI: 10.1016/s0041-008x(03)00228-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Occupational exposure to nickel compounds is associated with lung cancer risk; both genotoxic and epigenetic mechanisms have been proposed. For comprehensive examination of the acute effects of nickel(II) acetate on gene expression in cultured human peripheral lung epithelial HPL1D cells, microarray analyses were carried out with cDNA chips (approximately 8000 cDNAs). Cells were exposed for 24 h to nontoxic (50, 100, and 200 microM) or toxic (400, 800, and 1600 microM) nickel(II) concentrations. Cluster analysis was applied to the 868 genes with > or = 2-fold change at any concentration. Two main clusters showed marked up- or down-regulation at the highest, toxic concentrations. The data further subdivided into 10 highly cohesive clusters with high probability, and of these only 2 had the same response trend at low nontoxic as at high concentrations, an observation of clear relevance to the process of high- to low-dose extrapolation in risk assessment. There were 113 genes showing > or = 2-fold change at the three lower nontoxic concentrations, those most relevant to in vivo carcinogenesis. In addition to expected responses of metallothionein, ferritin, and heat-shock proteins, the results revealed for the first time changed expression of some potential cancer-related genes in response to low-dose Ni(II): RhoA, dyskerin, interferon regulatory factor 1, RAD21 homologue, and tumor protein, translationally controlled. Overall, most of the genes impacted by nontoxic concentrations of nickel(II) acetate related to gene transcription, protein synthesis and stability, cytoskeleton, signaling, metabolism, cell membrane, and extracellular matrix.
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Affiliation(s)
- Robert Y S Cheng
- Laboratory of Comparative Carcinogenesis, National Cancer Institute at Frederick, Bldg. 538, Ft. Detrick, Frederick, MD 21702, USA.
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Paterlini-Bréchot P, Saigo K, Murakami Y, Chami M, Gozuacik D, Mugnier C, Lagorce D, Bréchot C. Hepatitis B virus-related insertional mutagenesis occurs frequently in human liver cancers and recurrently targets human telomerase gene. Oncogene 2003; 22:3911-6. [PMID: 12813464 DOI: 10.1038/sj.onc.1206492] [Citation(s) in RCA: 232] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Integration of Hepatitis B Virus (HBV) DNA into liver cell DNA has been well established, but its implication in liver carcinogenesis is still being debated. In particular, insertion of the viral genome into cellular genes has been viewed as a rare event. By using HBV-Alu PCR, we have now isolated, from nine hepatocellular carcinomas, nine HBV-DNA integration sites showing that the viral genome mutates key regulatory cellular genes: neurotropic tyrosin receptor kinase 2 (NTRK2) gene, IL-1R-associated kinase 2 (IRAK2) gene, p42 mitogen-activated protein kinase 1 (p42MAPK1) gene, inositol 1,4,5-triphosphate receptor type 2 (IP3R2) gene, inositol 1,4,5-triphosphate receptor (IP3R) type 1 (IP3R1) gene, alpha 2,3 sialyltransferase (ST3GAL VI or SITA) gene, thyroid hormone uncoupling protein (TRUP) gene, EMX2-like gene, and human telomerase reverse transcriptase (hTERT) gene. This result brings to 15 the total number of genes targeted by HBV in a study of 22 human liver cancers. Overall, we found that both the inositol 1,4,5-triphosphate receptor gene and the telomerase gene were targeted by HBV in two different tumors. Thus, HBV frequently targets cellular genes involved in cell signalling and some of them may be preferential targets of the viral integration.
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MESH Headings
- Calcium Channels/genetics
- Calcium-Transporting ATPases/genetics
- Carcinoma, Hepatocellular/genetics
- Carcinoma, Hepatocellular/virology
- DNA, Neoplasm/analysis
- DNA, Viral/isolation & purification
- DNA-Binding Proteins/genetics
- Hepatitis B/virology
- Hepatitis B virus/genetics
- Hepatitis B virus/physiology
- Humans
- Inositol 1,4,5-Trisphosphate Receptors
- Interleukin-1 Receptor-Associated Kinases
- Liver Neoplasms/genetics
- Liver Neoplasms/virology
- Mitogen-Activated Protein Kinase 1/genetics
- Mutagenesis, Insertional
- Neoplasm Proteins/genetics
- Polymerase Chain Reaction
- Protein Kinases/genetics
- Receptor, trkB/genetics
- Receptors, Cytoplasmic and Nuclear/genetics
- Ribosomal Proteins/genetics
- Sarcoplasmic Reticulum Calcium-Transporting ATPases
- Sialyltransferases/genetics
- Telomerase/genetics
- Transcription Factors/genetics
- Virus Integration
- beta-Galactoside alpha-2,3-Sialyltransferase
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Affiliation(s)
- Patrizia Paterlini-Bréchot
- INSERM/Pasteur Unit 370, Necker Faculty of Medicine, Necker-Enfants Malades Hospital, Paris 75015, France.
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28
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Da Costa L, Tchernia G, Gascard P, Lo A, Meerpohl J, Niemeyer C, Chasis JA, Fixler J, Mohandas N. Nucleolar localization of RPS19 protein in normal cells and mislocalization due to mutations in the nucleolar localization signals in 2 Diamond-Blackfan anemia patients: potential insights into pathophysiology. Blood 2003; 101:5039-45. [PMID: 12586610 DOI: 10.1182/blood-2002-12-3878] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Ribosomal protein S19 (RPS19) is frequently mutated in Diamond-Blackfan anemia (DBA), a rare congenital hypoplastic anemia. Recent studies have shown that RPS19 expression decreases during terminal erythroid differentiation. Currently no information is available on the subcellular localization of normal RPS19 and the potential effects of various RPS19 mutations on cellular localization. In the present study, using wild-type and mutant RPS19 cDNA, we explored the subcellular distribution of normal and mutant proteins in a fibroblast cell line (Cos-7 cells). RPS19 was detected primarily in the nucleus, and more specifically in the nucleoli, where RPS19 colocalized with the nucleolar protein nucleolin. Using various N-terminal and C-terminal deletion constructs, we identified 2 nucleolar localization signals (NoSs) in RPS19: the first comprising amino acids Met1 to Arg16 in the NH2-terminus and the second comprising Gly120 to Asn142 in the COOH-terminus. Importantly, 2 mutations identified in DBA patients, Val15Phe and Gly127Gln, each of which localized to 1 of the 2 NoS, failed to localize RPS19 to the nucleolus. In addition to their mislocalization, there was a dramatic decrease in the expression of the 2 mutant proteins compared to the wild type. This decrease in protein expression was specific for the mutant RPS19, since expression of other proteins was normal. The present findings enable us to document the nucleolar localization signals in RPS19 and help define the phenotypic consequences of some mutations in RPS19 in DBA.
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Affiliation(s)
- Lydie Da Costa
- Laboratoire d'Hématologie, Hôpital de Bicêtre, Le Kremlin Bicêtre, France.
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29
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Abstract
The emerging field of nuclear eIF research has yielded many surprises and led to the dissolution of some dogmatic/ideological viewpoints of the place of translation in the regulation of gene expression. Eukaryotic initiation factors (eIFs) are classically defined by their cytoplasmic location and ability to regulate the initiation phase of protein synthesis. For instance, in the cytoplasm, the m7G cap-binding protein eIF4E plays a distinct role in cap-dependent translation initiation. Disruption of eIF4E's regulatory function drastically effects cell growth and may lead to oncogenic transformation. A growing number of studies indicate that many eIFs, including a substantial fraction of eIF4E, are found in the nucleus. Indeed, nuclear eIF4E participates in a variety of important RNA-processing events including the nucleocytoplasmic transport of specific, growth regulatory mRNAs. Although unexpected, it is possible that some eIFs regulate protein synthesis within the nucleus. This review will focus on the novel, nuclear functions of eIF4E and how they contribute to eIF4E's growth-activating and oncogenic properties. Both the cytoplasmic and nuclear functions of eIF4E appear to be dependent on its intrinsic ability to bind to the 5' m7G cap of mRNA. For example, Promyelocytic Leukemia Protein (PML) potentially acts as a negative regulator of nuclear eIF4E function by decreasing eIF4E's affinity for the m7G cap. Therefore, eIF4E protein is flexible enough to utilize a common biochemical activity, such as m7G cap binding, to participate in divergent processes in different cellular compartments.
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Affiliation(s)
- Stephen Strudwick
- Structural Biology Program, Department of Physiology & Biophysics, Mount Sinai School of Medicine, New York University, One Gustave Levy Place, New York, NY 10029, USA
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30
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Rudt F, Pieler T. Cytosolic import factor- and Ran-independent nuclear transport of ribosomal protein L5. Eur J Cell Biol 2001; 80:661-8. [PMID: 11824785 DOI: 10.1078/0171-9335-00212] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Ribosomal protein L5 is a shuttling protein that, in Xenopus oocytes, is involved in the nucleocytoplasmic transport of 5S rRNA. As demonstrated earlier, L5 contains three independent nuclear import signals (NLSs), which function in oocytes as well as in somatic cells. Upon physical separation, these NLSs differ in respect to their capacity to bind to nuclear import factors in vitro and to mediate the nuclear import of a heterologous RNP in vivo. As reported in this communication, analysis of the in vitro nuclear import activity of these three NLSs reveals that they also differ in respect to their requirements for cytosolic import factors and Ran. Nuclear import mediated by the N-terminal and the central NLS depends on cytosolic import factor(s) and Ran, whereas import via the C-terminal NLS occurs independently from these factors. Thus, the presence of multiple NLSs in ribosomal protein L5 appears to allow for efficient nuclear transport via utilisation of multiple, mechanistically different import pathways.
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Affiliation(s)
- F Rudt
- Institut für Biochemie und Molekulare Zellbiologie, Georg-August-Universität, Göttingen/Germany
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31
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Bordonné R. Functional characterization of nuclear localization signals in yeast Sm proteins. Mol Cell Biol 2000; 20:7943-54. [PMID: 11027265 PMCID: PMC86405 DOI: 10.1128/mcb.20.21.7943-7954.2000] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2000] [Accepted: 08/10/2000] [Indexed: 01/20/2023] Open
Abstract
In mammals, nuclear localization of U-snRNP particles requires the snRNA hypermethylated cap structure and the Sm core complex. The nature of the signal located within the Sm core proteins is still unknown, both in humans and yeast. Close examination of the sequences of the yeast SmB, SmD1, and SmD3 carboxyl-terminal domains reveals the presence of basic regions that are reminiscent of nuclear localization signals (NLSs). Fluorescence microscopy studies using green fluorescent protein (GFP)-fusion proteins indicate that both yeast SmB and SmD1 basic amino acid stretches exhibit nuclear localization properties. Accordingly, deletions or mutations in the NLS-like motifs of SmB and SmD1 dramatically reduce nuclear fluorescence of the GFP-Sm mutant fusion alleles. Phenotypic analyses indicate that the NLS-like motifs of SmB and SmD1 are functionally redundant: each NLS-like motif can be deleted without affecting yeast viability whereas a simultaneous deletion of both NLS-like motifs is lethal. Taken together, these findings suggest that, in the doughnut-like structure formed by the Sm core complex, the carboxyl-terminal extensions of Sm proteins may form an evolutionarily conserved basic amino acid-rich protuberance that functions as a nuclear localization determinant.
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Affiliation(s)
- R Bordonné
- Institut de Génétique Moléculaire, CNRS UMR 5535, 34000 Montpellier, France.
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32
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Shu-Nu C, Lin CH, Lin A. An acidic amino acid cluster regulates the nucleolar localization and ribosome assembly of human ribosomal protein L22. FEBS Lett 2000; 484:22-8. [PMID: 11056215 DOI: 10.1016/s0014-5793(00)02118-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The control of human ribosomal protein L22 (rpL22) to enter into the nucleolus and its ability to be assembled into the ribosome is regulated by its sequence. The nuclear import of rpL22 depends on a classical nuclear localization signal of four lysines at positions 13-16. RpL22 normally enters the nucleolus via a compulsory sequence of KKYLKK (I-domain, positions 88-93). An acidic residue cluster at the C-terminal end (C-domain) plays a nuclear retention role. The retention is concealed by the N-domain (positions 1-9) which weakly interacts with the C-domain as demonstrated in the yeast two-hybrid system. Once it reaches the nucleolus, the question of whether rpL22 is assembled into the ribosome depends upon the presence of the N-domain. This suggests that the N-domain, on dissociation from its interaction with the C-domain, binds to a specific region of the 28S rRNA for ribosome assembly.
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Affiliation(s)
- C Shu-Nu
- Institute of Genetics, National Yang-Ming University, Shih-Pai, Taipei, Taiwan
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33
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Claussen M, Rudt F, Pieler T. Functional modules in ribosomal protein L5 for ribonucleoprotein complex formation and nucleocytoplasmic transport. J Biol Chem 1999; 274:33951-8. [PMID: 10567357 DOI: 10.1074/jbc.274.48.33951] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Ribosomal protein L5 forms a small, extraribosomal complex with 5 S ribosomal RNA, referred to as the 5 S ribonucleoprotein complex, which shuttles between nucleus and cytoplasm in Xenopus oocytes. Mapping elements in L5 that mediate nuclear protein import defines three separate such activities (L5-nuclear localization sequence (NLS)-1, -2, and -3), which are functional in both oocytes and somatic cells. RNA binding activity involves N-terminal as well as C-terminal elements of L5. In contrast to the full-length protein, none of the individual NLSs carrying L5 fragments are able to allow for the predominating accumulation in the nucleoli that is observed with the full-length protein. The separate L5-NLSs differ in respect to two activities. Firstly, only L5-NLS-1 and -3, not L5-NLS-2, are capable of promoting the nuclear transfer of a heterologous, covalently attached ribonucleoprotein complex. Secondly, only L5-NLS-1 is able to bind strongly to a variety of different import receptors; those that recognize L5-NLS-2 and -3 have yet to be identified.
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Affiliation(s)
- M Claussen
- Institut für Biochemie und Molekulare Zellbiologie, Georg-August-Universität, Humboldtallee 23, D-37073 Göttingen, Germany
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34
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35
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Jarrous N, Wolenski JS, Wesolowski D, Lee C, Altman S. Localization in the nucleolus and coiled bodies of protein subunits of the ribonucleoprotein ribonuclease P. J Cell Biol 1999; 146:559-72. [PMID: 10444065 PMCID: PMC2150555 DOI: 10.1083/jcb.146.3.559] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/1999] [Accepted: 07/01/1999] [Indexed: 01/24/2023] Open
Abstract
The precise location of the tRNA processing ribonucleoprotein ribonuclease P (RNase P) and the mechanism of its intranuclear distribution have not been completely delineated. We show that three protein subunits of human RNase P (Rpp), Rpp14, Rpp29 and Rpp38, are found in the nucleolus and that each can localize a reporter protein to nucleoli of cells in tissue culture. In contrast to Rpp38, which is uniformly distributed in nucleoli, Rpp14 and Rpp29 are confined to the dense fibrillar component. Rpp29 and Rpp38 possess functional, yet distinct domains required for subnucleolar localization. The subunit Rpp14 lacks such a domain and appears to be dependent on a piggyback process to reach the nucleolus. Biochemical analysis suggests that catalytically active RNase P exists in the nucleolus. We also provide evidence that Rpp29 and Rpp38 reside in coiled bodies, organelles that are implicated in the biogenesis of several other small nuclear ribonucleoproteins required for processing of precursor mRNA. Because some protein subunits of RNase P are shared by the ribosomal RNA processing ribonucleoprotein RNase MRP, these two evolutionary related holoenzymes may share common intranuclear localization and assembly pathways to coordinate the processing of tRNA and rRNA precursors.
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Affiliation(s)
- Nayef Jarrous
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520
| | - Joseph S. Wolenski
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520
| | - Donna Wesolowski
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520
| | - Christopher Lee
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520
| | - Sidney Altman
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520
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36
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Timmers AC, Stuger R, Schaap PJ, van 't Riet J, Raué HA. Nuclear and nucleolar localization of Saccharomyces cerevisiae ribosomal proteins S22 and S25. FEBS Lett 1999; 452:335-40. [PMID: 10386617 DOI: 10.1016/s0014-5793(99)00669-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Nuclear import usually relies on the presence of nuclear localization sequences (NLSs). NLSs are recognized by NLS receptors (importins), which target their substrates to the nuclear pore. We identified the NLSs of the yeast ribosomal proteins S22 and S25 and studied the former by mutational analysis. Furthermore, in S25 the nucleolar targeting information was found to overlap with its NLS. Comparison with previously published data on yeast ribosomal protein NLSs and computer analysis indicates the existence of a novel type of ribosomal protein-specific NLS that differs from the classical Chelsky and bipartite NLSs. The existence of such a ribosomal protein-specific NLS is in accordance with the recent identification of ribosomal protein-specific importins.
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Affiliation(s)
- A C Timmers
- Department of Biochemistry and Molecular Biology, Institute for Molecular Biological Sciences, BioCentrum Amsterdam, Vrije Universiteit, The Netherlands
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37
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Kubota S, Copeland TD, Pomerantz RJ. Nuclear and nucleolar targeting of human ribosomal protein S25: common features shared with HIV-1 regulatory proteins. Oncogene 1999; 18:1503-14. [PMID: 10050887 DOI: 10.1038/sj.onc.1202429] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The nuclear and nucleolar targeting properties of human ribosomal protein S25 (RPS25) were analysed by the expression of epitope-tagged RPS25 cDNAs in Cos-1 cells. The tagged RPS25 was localized to the cell nucleus, with a strong predominance in the nucleolus. At the amino terminus of RPS25, two stretches of highly basic residues juxtapose. This configuration shares common features with the nucleolar targeting signals (NOS) of lentiviral RNA-binding transactivators, including human immunodeficiency viruses' (HIV) Rev proteins. Deletion and site-directed mutational analyses demonstrated that the first NOS-like stretch is dispensable for both nuclear and nucleolar localization of RPS25, and that the nuclear targeting signal is located within the second NOS-like stretch. It has also been suggested that a set of continuous basic residues and the total number of basic residues should be required for nucleolar targeting. Signal-mediated nuclear/nucleolar targeting was further characterized by the construction and expression of a variety of chimeric constructs, utilizing three different backbones with RPS25 cDNA fragments. Immunofluorescence analyses demonstrated a 17 residue peptide of RPS25 as a potential nuclear/nucleolar targeting signal. The identified peptide signal may belong to a putative subclass of NOS, characterized by compact structure, together with lentiviral RNA-binding transactivators.
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Affiliation(s)
- S Kubota
- Center for Human Virology, Department of Medicine, Jefferson Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, USA
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38
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Abstract
Active transport between the nucleus and cytoplasm involves primarily three classes of macromolecules: substrates, adaptors, and receptors. Some transport substrates bind directly to an import or an export receptor while others require one or more adaptors to mediate formation of a receptor-substrate complex. Once assembled, these transport complexes are transferred in one direction across the nuclear envelope through aqueous channels that are part of the nuclear pore complexes (NPCs). Dissociation of the transport complex must then take place, and both adaptors and receptors must be recycled through the NPC to allow another round of transport to occur. Directionality of either import or export therefore depends on association between a substrate and its receptor on one side of the nuclear envelope and dissociation on the other. The Ran GTPase is critical in generating this asymmetry. Regulation of nucleocytoplasmic transport generally involves specific inhibition of the formation of a transport complex; however, more global forms of regulation also occur.
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Affiliation(s)
- I W Mattaj
- European Molecular Biology Laboratory, Heidelberg, Germany.
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39
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Annilo T, Karis A, Hoth S, Rikk T, Kruppa J, Metspalu A. Nuclear import and nucleolar accumulation of the human ribosomal protein S7 depends on both a minimal nuclear localization sequence and an adjacent basic region. Biochem Biophys Res Commun 1998; 249:759-66. [PMID: 9731210 DOI: 10.1006/bbrc.1998.9187] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
In the course of the eukaryotic ribosomal biogenesis, both the nuclear import and export are involved. We have studied the nuclear and nucleolar localization of the human ribosomal protein S7. We examined the subcellular distribution of the S7:beta-galactosidase fusion protein in SAOS-2 cells. We have identified two evolutionarily conserved domains, both of which are necessary for S7 nuclear and nucleolar targeting: amino acids 98 to 109 and 115 to 118. Out of the S7 protein context, a fragment 98...118, containing these domains, is sufficient for nuclear transport and nucleolar accumulation. Interestingly, a tetrapeptide 115KRPR118, which can act as an independent nuclear localization signal (NLS), is not sufficient for exclusively nuclear accumulation of the S7 protein if the adjacent region 98...109 is deleted. In addition, site-directed mutagenesis revealed that critical residues for nuclear targeting in this tetrapeptide and in the full-length S7 protein are different. While mutation of a Pro117 significantly impaired nuclear import of S7, similar substitution within the tetrapeptide-NLS had no effect on nuclear targeting. This suggests that to function perfectly, proper secondary structure of the S7 nuclear targeting domain is required.
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Affiliation(s)
- T Annilo
- Institute of Molecular and Cell Biology, Tartu University, Estonia
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40
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Jäkel S, Görlich D. Importin beta, transportin, RanBP5 and RanBP7 mediate nuclear import of ribosomal proteins in mammalian cells. EMBO J 1998; 17:4491-502. [PMID: 9687515 PMCID: PMC1170780 DOI: 10.1093/emboj/17.15.4491] [Citation(s) in RCA: 407] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The assembly of eukaryotic ribosomal subunits takes place in the nucleolus and requires nuclear import of ribosomal proteins. We have studied this import in a mammalian system and found that the classical nuclear import pathway using the importin alpha/beta heterodimer apparently plays only a minor role. Instead, at least four importin beta-like transport receptors, namely importin beta itself, transportin, RanBP5 and RanBP7, directly bind and import ribosomal proteins. We found that the ribosomal proteins L23a, S7 and L5 can each be imported alternatively by any of the four receptors. We have studied rpL23a in detail and identified a very basic region to which each of the four import receptors bind avidly. This domain might be considered as an archetypal import signal that evolved before import receptors diverged in evolution. The presence of distinct binding sites for rpL23a and the M9 import signal in transportin, and for rpL23a and importin alpha in importin beta might explain how a single receptor can recognize very different import signals.
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Affiliation(s)
- S Jäkel
- Zentrum für Molekulare Biologie der Universität Heidelberg, Germany
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41
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Bouvet P, Diaz JJ, Kindbeiter K, Madjar JJ, Amalric F. Nucleolin interacts with several ribosomal proteins through its RGG domain. J Biol Chem 1998; 273:19025-9. [PMID: 9668083 DOI: 10.1074/jbc.273.30.19025] [Citation(s) in RCA: 159] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Nucleolin is one of the major nonribosomal proteins of the nucleolus. Through its four RNA-binding domains, nucleolin interacts specifically with pre-rRNA as soon as synthesis begins, but it is not found in mature cytoplasmic ribosomes. Nucleolin is able to shuttle between the cytoplasm and the nucleus. These data suggest that nucleolin might be involved in the nucleolar import of cytoplasmic components and in the assembly of pre-ribosomal particles. Here we show, using two-dimensional blots in a ligand blotting assay, that nucleolin interacts with 18 ribosomal proteins from rat (14 and 4 from the large and small subunit, respectively). The C-terminal domain of nucleolin (p50) interacts with 10 of these identified ribosomal proteins. In vitro binding assays show that the glycine-arginine rich domain of nucleolin (RGG domain) is sufficient for the interaction with one of these proteins. Interestingly, most of the proteins that interact with p50 belong to the core ribosomal proteins, which are resistant to extraction with high salt concentration. These findings suggest that nucleolin might be involved in the nucleolar targeting of some ribosomal proteins and in their assembly within pre-ribosomal particles.
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Affiliation(s)
- P Bouvet
- Laboratoire de Biologie Moléculaire Eucaryote, Institut de Biologie Cellulaire et de Génétique du CNRS, UPR 9006, 118 route de Narbonne, 31062 Toulouse Cedex, France.
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