1
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Satoh R, Matsumura Y, Tanaka A, Takada M, Ito Y, Hagihara K, Inari M, Kita A, Fukao A, Fujiwara T, Hirai S, Tani T, Sugiura R. Spatial regulation of the KH domain RNA-binding protein Rnc1 mediated by a Crm1-independent nuclear export system in Schizosaccharomyces pombe. Mol Microbiol 2017; 104:428-448. [PMID: 28142187 DOI: 10.1111/mmi.13636] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/26/2017] [Indexed: 10/20/2022]
Abstract
RNA-binding proteins (RBPs) play important roles in the posttranscriptional regulation of gene expression, including mRNA stability, transport and translation. Fission yeast rnc1+ encodes a K Homology (KH)-type RBP, which binds and stabilizes the Pmp1 MAPK phosphatase mRNA thereby suppressing the Cl- hypersensitivity of calcineurin deletion and MAPK signaling mutants. Here, we analyzed the spatial regulation of Rnc1 and discovered a putative nuclear export signal (NES)Rnc1 , which dictates the cytoplasmic localization of Rnc1 in a Crm1-independent manner. Notably, mutations in the NESRnc1 altered nucleocytoplasmic distribution of Rnc1 and abolished its function to suppress calcineurin deletion, although the Rnc1 NES mutant maintains the ability to bind Pmp1 mRNA. Intriguingly, the Rnc1 NES mutant destabilized Pmp1 mRNA, suggesting the functional importance of the Rnc1 cytoplasmic localization. Mutation in Rae1, but not Mex67 deletion or overproduction, induced Rnc1 accumulation in the nucleus, suggesting that Rnc1 is exported from the nucleus to the cytoplasm via the mRNA export pathway involving Rae1. Importantly, mutations in the Rnc1 KH-domains abolished the mRNA-binding ability and induced nuclear localization, suggesting that Rnc1 may be exported from the nucleus together with its target mRNAs. Collectively, the functional Rae1-dependent mRNA export system may influence the cytoplasmic localization and function of Rnc1.
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Affiliation(s)
- Ryosuke Satoh
- Laboratory of Molecular Pharmacogenomics, Department of Pharmaceutical Sciences, Kindai University, Higashiosaka City, Osaka, 577-8502, Japan
| | - Yasuhiro Matsumura
- Laboratory of Molecular Pharmacogenomics, Department of Pharmaceutical Sciences, Kindai University, Higashiosaka City, Osaka, 577-8502, Japan
| | - Akitomo Tanaka
- Laboratory of Molecular Pharmacogenomics, Department of Pharmaceutical Sciences, Kindai University, Higashiosaka City, Osaka, 577-8502, Japan
| | - Makoto Takada
- Laboratory of Molecular Pharmacogenomics, Department of Pharmaceutical Sciences, Kindai University, Higashiosaka City, Osaka, 577-8502, Japan
| | - Yuna Ito
- Laboratory of Molecular Pharmacogenomics, Department of Pharmaceutical Sciences, Kindai University, Higashiosaka City, Osaka, 577-8502, Japan
| | - Kanako Hagihara
- Laboratory of Molecular Pharmacogenomics, Department of Pharmaceutical Sciences, Kindai University, Higashiosaka City, Osaka, 577-8502, Japan
| | - Masahiro Inari
- Laboratory of Molecular Pharmacogenomics, Department of Pharmaceutical Sciences, Kindai University, Higashiosaka City, Osaka, 577-8502, Japan
| | - Ayako Kita
- Laboratory of Molecular Pharmacogenomics, Department of Pharmaceutical Sciences, Kindai University, Higashiosaka City, Osaka, 577-8502, Japan
| | - Akira Fukao
- Laboratory of Biochemistry, Department of Pharmacy, Kindai University, Higashiosaka City, Osaka, 577-8502, Japan
| | - Toshinobu Fujiwara
- Laboratory of Biochemistry, Department of Pharmacy, Kindai University, Higashiosaka City, Osaka, 577-8502, Japan
| | - Shinya Hirai
- Department of Biological Sciences Graduate School of Science and Technology, Kumamoto University, Kumamoto, Kumamoto, 860-8555, Japan
| | - Tokio Tani
- Department of Biological Sciences Graduate School of Science and Technology, Kumamoto University, Kumamoto, Kumamoto, 860-8555, Japan
| | - Reiko Sugiura
- Laboratory of Molecular Pharmacogenomics, Department of Pharmaceutical Sciences, Kindai University, Higashiosaka City, Osaka, 577-8502, Japan
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2
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Domanska A, Kaminska J. Role of Rsp5 ubiquitin ligase in biogenesis of rRNA, mRNA and tRNA in yeast. RNA Biol 2016; 12:1265-74. [PMID: 26403176 DOI: 10.1080/15476286.2015.1094604] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
Rsp5 ubiquitin ligase is required for ubiquitination of a wide variety of proteins involved in essential processes. Rsp5 was shown to be involved in regulation of lipid biosynthesis, intracellular trafficking of proteins, response to various stresses, and many other processes. In this article, we provide a comprehensive review of the nuclear and cytoplasmic functions of Rsp5 with a focus on biogenesis of different RNAs. We also briefly describe the participation of Rsp5 in the regulation of the RNA polymerase II complex, and its potential role in the regulation of other RNA polymerases. Moreover, we emphasize the function of Rsp5 in the coordination of the different steps of rRNA, mRNA and tRNA metabolism in the context of protein biosynthesis. Finally, we highlight the involvement of Rsp5 in controlling diverse cellular mechanisms at multiple levels and in adaptation of the cell to changing growth conditions.
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Affiliation(s)
- Anna Domanska
- a Institute of Biochemistry and Biophysics, Polish Academy of Sciences ; Warsaw , Poland
| | - Joanna Kaminska
- a Institute of Biochemistry and Biophysics, Polish Academy of Sciences ; Warsaw , Poland
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3
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Weninger A, Glieder A, Vogl T. A toolbox of endogenous and heterologous nuclear localization sequences for the methylotrophic yeast Pichia pastoris. FEMS Yeast Res 2015; 15:fov082. [PMID: 26347503 PMCID: PMC4629791 DOI: 10.1093/femsyr/fov082] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 09/02/2015] [Indexed: 12/16/2022] Open
Abstract
Nuclear localization sequences (NLSs) are required for the import of proteins in the nucleus of eukaryotes. However many proteins from bacteria or bacteriophages are used for basic studies in molecular biology, to generate synthetic genetic circuits or for genome editing applications. Prokaryotic recombinases, CRISPR-associated proteins such as Cas9 or bacterial and viral polymerases require efficient NLSs to function in eukaryotes. The yeast Pichia pastoris is a widely used expression platform for heterologous protein production, but molecular tools such as NLSs are limited. Here we have characterized a set of 10 NLSs for P. pastoris, including the first endogenous NLSs (derived from P. pastoris proteins) and commonly used heterologous NLSs. The NLSs were evaluated by fusing them in N- and C-terminal position to an enhanced green fluorescent protein showing pronounced differences in fluorescence levels and nuclear targeting. Thereby we provide a set of different NLSs that can be applied to optimize the nuclear import of heterologous proteins in P. pastoris, paving the way for the establishment of intricate synthetic biology applications.
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Affiliation(s)
- Astrid Weninger
- Institute for Molecular Biotechnology, Graz University of Technology, Petersgasse 14/2, 8010 Graz, Austria
| | - Anton Glieder
- Institute for Molecular Biotechnology, Graz University of Technology, Petersgasse 14/2, 8010 Graz, Austria
| | - Thomas Vogl
- Institute for Molecular Biotechnology, Graz University of Technology, Petersgasse 14/2, 8010 Graz, Austria Queensland University of Technology, 2 George St., Brisbane QLD 4000, Australia
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4
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Sugiyama T, Wanatabe N, Kitahata E, Tani T, Sugioka-Sugiyama R. Red5 and three nuclear pore components are essential for efficient suppression of specific mRNAs during vegetative growth of fission yeast. Nucleic Acids Res 2013; 41:6674-86. [PMID: 23658229 PMCID: PMC3711435 DOI: 10.1093/nar/gkt363] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Zinc-finger domains are found in many nucleic acid-binding proteins in both prokaryotes and eukaryotes. Proteins carrying zinc-finger domains have important roles in various nuclear transactions, including transcription, mRNA processing and mRNA export; however, for many individual zinc-finger proteins in eukaryotes, the exact function of the protein is not fully understood. Here, we report that Red5 is involved in efficient suppression of specific mRNAs during vegetative growth of Schizosaccharomyces pombe. Red5, which contains five C3H1-type zinc-finger domains, localizes to the nucleus where it forms discrete dots. A red5 point mutation, red5-2, results in the upregulation of specific meiotic mRNAs in vegetative mutant red5-2 cells; northern blot data indicated that these meiotic mRNAs in red5-2 cells have elongated poly(A) tails. RNA-fluorescence in situ hybridization results demonstrate that poly(A)+ RNA species accumulate in the nucleolar regions of red5-deficient cells. Moreover, Red5 genetically interacts with several mRNA export factors. Unexpectedly, three components of the nuclear pore complex also suppress a specific set of meiotic mRNAs. These results indicate that Red5 function is important to meiotic mRNA degradation; they also suggest possible connections among selective mRNA decay, mRNA export and the nuclear pore complex in vegetative fission yeast.
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5
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Characterization of the ptr5+ gene involved in nuclear mRNA export in fission yeast. Biochem Biophys Res Commun 2012; 418:62-6. [PMID: 22240020 DOI: 10.1016/j.bbrc.2011.12.128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2011] [Accepted: 12/26/2011] [Indexed: 11/23/2022]
Abstract
To analyze the mechanisms of mRNA export from the nucleus to the cytoplasm, we have isolated eleven mutants, ptr [poly(A)(+) RNA transport] 1 to 11, which accumulate poly(A)(+) RNA in the nucleus at a nonpermissive temperature in Schizosaccharomyces pombe. Of those, the ptr5-1 mutant shows dots- or a ring-like accumulation of poly(A)(+) RNA at the nuclear periphery after shifting to the nonpermissive temperature. We cloned the ptr5(+) gene and found that it encodes a component of the nuclear pore complex (NPC), nucleoporin 85 (Nup85). The ptr5-1 mutant shows no defects in protein transport, suggesting the specific involvement of Ptr5p/Nup85p in nuclear mRNA export in S. pombe. We identified Seh1p, a nucleoporin interacting with Nup85p, an mRNA-binding protein Mlo3p, and Sac3p, a component of the TREX-2 complex involved in coupling of nuclear mRNA export with transcription, as multi-copy suppressors for the ptr5-1 mutation. In addition, we found that the ptr5-1 mutation is synthetically lethal with a mutation of the mRNA export factor Rae1p, and that the double mutant exaggerates defective nuclear mRNA export, suggesting that Ptr5p/Nup85p is involved in nuclear mRNA export through Rae1p. Interestingly, the ptr5-1 mutation also showed synthetic effects with several prp pre-mRNA splicing mutations, suggesting a functional linkage between the NPCs and the splicing apparatus in the yeast nucleus.
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6
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Satoh R, Tanaka A, Kita A, Morita T, Matsumura Y, Umeda N, Takada M, Hayashi S, Tani T, Shinmyozu K, Sugiura R. Role of the RNA-binding protein Nrd1 in stress granule formation and its implication in the stress response in fission yeast. PLoS One 2012; 7:e29683. [PMID: 22276125 PMCID: PMC3261880 DOI: 10.1371/journal.pone.0029683] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2011] [Accepted: 12/02/2011] [Indexed: 01/20/2023] Open
Abstract
We have previously identified the RNA recognition motif (RRM)-type RNA-binding protein Nrd1 as an important regulator of the posttranscriptional expression of myosin in fission yeast. Pmk1 MAPK-dependent phosphorylation negatively regulates the RNA-binding activity of Nrd1. Here, we report the role of Nrd1 in stress-induced RNA granules. Nrd1 can localize to poly(A)-binding protein (Pabp)-positive RNA granules in response to various stress stimuli, including heat shock, arsenite treatment, and oxidative stress. Interestingly, compared with the unphosphorylatable Nrd1, Nrd1DD (phosphorylation-mimic version of Nrd1) translocates more quickly from the cytoplasm to the stress granules in response to various stimuli; this suggests that the phosphorylation of Nrd1 by MAPK enhances its localization to stress-induced cytoplasmic granules. Nrd1 binds to Cpc2 (fission yeast RACK) in a phosphorylation-dependent manner and deletion of Cpc2 affects the formation of Nrd1-positive granules upon arsenite treatment. Moreover, the depletion of Nrd1 leads to a delay in Pabp-positive RNA granule formation, and overexpression of Nrd1 results in an increased size and number of Pabp-positive granules. Interestingly, Nrd1 deletion induced resistance to sustained stresses and enhanced sensitivity to transient stresses. In conclusion, our results indicate that Nrd1 plays a role in stress-induced granule formation, which affects stress resistance in fission yeast.
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Affiliation(s)
- Ryosuke Satoh
- Laboratory of Molecular Pharmacogenomics, School of Pharmaceutical Sciences, Kinki University, Osaka, Japan
- Japan Society for the Promotion of Science, Tokyo, Japan
| | - Akitomo Tanaka
- Laboratory of Molecular Pharmacogenomics, School of Pharmaceutical Sciences, Kinki University, Osaka, Japan
| | - Ayako Kita
- Laboratory of Molecular Pharmacogenomics, School of Pharmaceutical Sciences, Kinki University, Osaka, Japan
| | - Takahiro Morita
- Laboratory of Molecular Pharmacogenomics, School of Pharmaceutical Sciences, Kinki University, Osaka, Japan
| | - Yasuhiro Matsumura
- Laboratory of Molecular Pharmacogenomics, School of Pharmaceutical Sciences, Kinki University, Osaka, Japan
| | - Nanae Umeda
- Laboratory of Molecular Pharmacogenomics, School of Pharmaceutical Sciences, Kinki University, Osaka, Japan
| | - Makoto Takada
- Laboratory of Molecular Pharmacogenomics, School of Pharmaceutical Sciences, Kinki University, Osaka, Japan
| | - Sachiko Hayashi
- Department of Biological Sciences, Graduate School of Science and Technology, Kumamoto University, Kumamoto, Japan
| | - Tokio Tani
- Department of Biological Sciences, Graduate School of Science and Technology, Kumamoto University, Kumamoto, Japan
| | - Kaori Shinmyozu
- Proteomics Support Unit, RIKEN Center for Developmental Biology, Hyogo, Japan
| | - Reiko Sugiura
- Laboratory of Molecular Pharmacogenomics, School of Pharmaceutical Sciences, Kinki University, Osaka, Japan
- * E-mail:
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7
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Babour A, Dargemont C, Stutz F. Ubiquitin and assembly of export competent mRNP. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2012; 1819:521-30. [PMID: 22240387 DOI: 10.1016/j.bbagrm.2011.12.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2011] [Revised: 12/20/2011] [Accepted: 12/22/2011] [Indexed: 11/24/2022]
Abstract
The production of mature and export competent mRNP (mRNA ribonucleoprotein) complexes depends on a series of highly coordinated processing reactions. RNA polymerase II (RNAPII) plays a central role in this process by mediating the sequential recruitment of mRNA maturation and export factors to transcribing genes, thereby establishing a strong functional link between transcription and export through nuclear pore complexes (NPC). Growing evidence indicates that post-translational modifications participate in the dynamic association of processing and export factors with mRNAs ensuring that the transitions and rearrangements undergone by the mRNP occur at the right time and place. This review mainly focuses on the role of ubiquitin conjugation in controlling mRNP assembly and quality control from transcription down to export through the NPC. It emphasizes the central role of ubiquitylation in organizing the chronology of events along this highly dynamic pathway. This article is part of a Special Issue entitled: Nuclear Transport and RNA Processing.
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Affiliation(s)
- Anna Babour
- Institut Jacques Monod, Université Paris Diderot, CNRS, Bâtiment Buffon, 15 rue Hélène Brion, 75205 Paris Cedex 13, France
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8
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Abstract
Transport of mRNA from the nucleus to the cytoplasm is an essential process for gene expression in eukaryotic cells. In this unit, methods for monitoring nuclear mRNA export are described. Visualization of cellular mRNAs by fluorescence in situ hybridization with oligo(dT) probes is effectively applied to monitoring mRNA export from the nucleus in yeast and mammalian cells. In addition to the protocols for fluorescence in situ hybridization, this unit includes an alternate method that the authors have been developing for visual analysis of nuclear mRNA export in living mammalian cells by microinjection of fluorescently labeled pre-mRNA into the nuclei.
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Affiliation(s)
- Kazuaki Tokunaga
- Department of Biological Sciences, Graduate School of Science and Technology, Kumamoto University, Kurokami, Kumamoto, Japan
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9
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Farny NG, Hurt JA, Silver PA. Definition of global and transcript-specific mRNA export pathways in metazoans. Genes Dev 2007; 22:66-78. [PMID: 18086857 DOI: 10.1101/gad.1616008] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Eukaryotic gene expression requires export of messenger RNAs (mRNAs) from their site of transcription in the nucleus to the cytoplasm where they are translated. While mRNA export has been studied in yeast, the complexity of gene structure and cellular function in metazoan cells has likely led to increased diversification of these organisms' export pathways. Here we report the results of a genome-wide RNAi screen in which we identify 72 factors required for polyadenylated [poly-(A(+))] mRNA export from the nucleus in Drosophila cells. Using structural and functional conservation analysis of yeast and Drosophila mRNA export factors, we expose the evolutionary divergence of eukaryotic mRNA export pathways. Additionally, we demonstrate the differential export requirements of two endogenous heat-inducible transcripts--intronless heat-shock protein 70 (HSP70) and intron-containing HSP83--and identify novel export factors that participate in HSP83 mRNA splicing. We characterize several novel factors and demonstrate their participation in interactions with known components of the Drosophila export machinery. One of these factors, Drosophila melanogaster PCI domain-containing protein 2 (dmPCID2), associates with polysomes and may bridge the transition between exported messenger ribonucleoprotein particles (mRNPs) and polysomes. Our results define the global network of factors involved in Drosophila mRNA export, reveal specificity in the export requirements of different transcripts, and expose new avenues for future work in mRNA export.
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Affiliation(s)
- Natalie G Farny
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
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10
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Mannen T, Andoh T, Tani T. Dss1 associating with the proteasome functions in selective nuclear mRNA export in yeast. Biochem Biophys Res Commun 2007; 365:664-71. [PMID: 18023413 DOI: 10.1016/j.bbrc.2007.11.024] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2007] [Accepted: 11/06/2007] [Indexed: 10/22/2022]
Abstract
Dss1p is an evolutionarily conserved small protein that interacts with BRCA2, a tumor suppressor protein, in humans. The Schizosaccharomyces pombe strain lacking the dss1(+) gene (Deltadss1) shows a temperature-sensitive growth defect and accumulation of bulk poly(A)(+) RNA in the nucleus at a nonpermissive temperature. In situ hybridization using probes for several specific mRNAs, however, revealed that the analyzed mRNAs were exported normally to the cytoplasm in Deltadss1, suggesting that Dss1p is required for export of some subsets of mRNAs. We identified the pad1(+) gene, which encodes a component of the 26S proteasome, as a suppressor for the ts(-) phenotype of Deltadss1. Unexpectedly, overexpression of Pad1p could suppress neither the defect in nuclear mRNA export nor a defect in proteasome function. In addition, loss of proteasome functions does not cause defective nuclear mRNA export. Dss1p seems to be a multifunctional protein involved in nuclear export of specific sets of mRNAs and the ubiquitin-proteasome pathway in fission yeast.
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Affiliation(s)
- Taro Mannen
- Department of Biological Sciences, Graduate School of Science and Technology, Kumamoto University, Kumamoto 860-8555, Japan
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11
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Miklos I, Szilagyi Z, Watt S, Zilahi E, Batta G, Antunovics Z, Enczi K, Bähler J, Sipiczki M. Genomic expression patterns in cell separation mutants of Schizosaccharomyces pombe defective in the genes sep10 ( + ) and sep15 ( + ) coding for the Mediator subunits Med31 and Med8. Mol Genet Genomics 2007; 279:225-38. [PMID: 17922236 DOI: 10.1007/s00438-007-0296-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2007] [Accepted: 09/19/2007] [Indexed: 11/26/2022]
Abstract
Cell division is controlled by a complex network involving regulated transcription of genes and postranslational modification of proteins. The aim of this study is to demonstrate that the Mediator complex, a general regulator of transcription, is involved in the regulation of the second phase (cell separation) of cell division of the fission yeast Schizosaccharomyces pombe. In previous studies we have found that the fission yeast cell separation genes sep10 ( + ) and sep15 ( + ) code for proteins (Med31 and Med8) associated with the Mediator complex. Here, we show by genome-wide gene expression profiling of mutants defective in these genes that both Med8 and Med31 control large, partially overlapping sets of genes scattered over the entire genome and involved in diverse biological functions. Six cell separation genes controlled by the transcription factors Sep1 and Ace2 are among the target genes. Since neither sep1 ( + ) nor ace2 ( + ) is affected in the mutant cells, we propose that the Med8 and Med31 proteins act as coactivators of the Sep1-Ace2-dependent cell separation genes. The results also indicate that the subunits of Mediator may contribute to the coordination of cellular processes by fine-tuning of the expression of larger sets of genes.
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Affiliation(s)
- Ida Miklos
- Department of Genetics and Applied Microbiology, University of Debrecen, Debrecen, Hungary
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12
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Mizuki F, Namiki T, Sato H, Furukawa H, Matsusaka T, Ohshima Y, Ishibashi R, Andoh T, Tani T. Participation of XPB/Ptr8p, a component of TFIIH, in nucleocytoplasmic transport of mRNA in fission yeast. Genes Cells 2007; 12:35-47. [PMID: 17212653 DOI: 10.1111/j.1365-2443.2006.01032.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
To identify novel factors involved in nuclear mRNA export in Schizosaccharomyces pombe, we isolated and characterized the ptr8(+) gene, mutation of which causes nuclear accumulation of poly (A)(+) RNA. The ptr8(+) gene encodes an S. pombe homologue of human XPB, a component of TFIIH involved in nucleotide excision repair (NER) and transcription. A temperature-sensitive mutant of ptr8(+) (ptr8-1) was highly sensitive to UV irradiation, as are human XPB cells. Northern blot analysis demonstrated that the amount of total poly (A)(+) mRNAs does not decrease significantly at the nonpermissive temperature in ptr8-1 cells, whereas a pulse-labeling assay using (35)S-methionine showed that protein synthesis decreases rapidly after incubation of cells at the nonpermissive temperature, suggesting that ptr8-1 cells have a defect in nuclear mRNA export. In Saccharomyces cerevisiae, a mutation in the SSL2 gene encoding a homologue of Ptr8p also causes a block of mRNA export at the nonpermissive temperature. In addition, expression of human XPB in ptr8-1 cells rescued the ts phenotype and the mRNA export defects, suggesting that human XPB may also play a role in mRNA export. Furthermore, we revealed a functional interaction between Ptr8p and Tho2p, a component of the TREX complex involved in mRNA export. These results suggest that XPB/Ptr8p plays roles not only in NER and transcription, but also plays a conserved role in mRNA export.
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Affiliation(s)
- Fumitaka Mizuki
- Department of Biological Sciences, Graduate School of Science and Technology, Kumamoto University, Kumamoto 860-8555, Japan
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13
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Gwizdek C, Iglesias N, Rodriguez MS, Ossareh-Nazari B, Hobeika M, Divita G, Stutz F, Dargemont C. Ubiquitin-associated domain of Mex67 synchronizes recruitment of the mRNA export machinery with transcription. Proc Natl Acad Sci U S A 2006; 103:16376-81. [PMID: 17056718 PMCID: PMC1637590 DOI: 10.1073/pnas.0607941103] [Citation(s) in RCA: 107] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The mRNA nuclear export receptor Mex67/Mtr2 is recruited to mRNAs through RNA-binding adaptors, including components of the THO/TREX complex that couple transcription to mRNA export. Here we show that the ubiquitin-associated (UBA) domain of Mex67 is not only required for proper nuclear export of mRNA but also contributes to recruitment of Mex67 to transcribing genes. Our results reveal that the UBA domain of Mex67 directly interacts with polyubiquitin chains and with Hpr1, a component of the THO/TREX complex, which is regulated by ubiquitylation in a transcription-dependent manner. This interaction transiently protects Hpr1 from ubiquitin/proteasome-mediated degradation and thereby coordinates recruitment of the mRNA export machinery with transcription and early messenger ribonucleoproteins assembly.
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Affiliation(s)
- Carole Gwizdek
- *Institut Jacques Monod, Unité Mixte de Recherche 7592, Centre National de la Recherche Scientifique, Universités Paris VI and VII, 2 Place Jussieu, Tour 43, 75251 Paris Cedex 05, France
| | - Nahid Iglesias
- Department of Cell Biology, Sciences III, 30 Quai Ernest Ansermet, 1211 Geneva 4, Switzerland; and
| | - Manuel S. Rodriguez
- *Institut Jacques Monod, Unité Mixte de Recherche 7592, Centre National de la Recherche Scientifique, Universités Paris VI and VII, 2 Place Jussieu, Tour 43, 75251 Paris Cedex 05, France
| | - Batool Ossareh-Nazari
- *Institut Jacques Monod, Unité Mixte de Recherche 7592, Centre National de la Recherche Scientifique, Universités Paris VI and VII, 2 Place Jussieu, Tour 43, 75251 Paris Cedex 05, France
| | - Maria Hobeika
- *Institut Jacques Monod, Unité Mixte de Recherche 7592, Centre National de la Recherche Scientifique, Universités Paris VI and VII, 2 Place Jussieu, Tour 43, 75251 Paris Cedex 05, France
| | - Gilles Divita
- Centre de Recherches de Biochimie Macromoléculaire, Centre National de la Recherche Scientifique Formation de Recherche en Evolution-2593, Molecular Biophysics and Therapeutics, 1919 Route de Mende, 34293 Montpellier Cedex 5, France
| | - Françoise Stutz
- Department of Cell Biology, Sciences III, 30 Quai Ernest Ansermet, 1211 Geneva 4, Switzerland; and
- To whom correspondence may be addressed. E-mail:
or
| | - Catherine Dargemont
- *Institut Jacques Monod, Unité Mixte de Recherche 7592, Centre National de la Recherche Scientifique, Universités Paris VI and VII, 2 Place Jussieu, Tour 43, 75251 Paris Cedex 05, France
- To whom correspondence may be addressed. E-mail:
or
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14
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Hirose E, Mukai M, Shimada A, Nishitani H, Shibata Y, Nishimoto T. Loss of RanGEF/Pim1 activity abolishes the orchestration of Ran-mediated mitotic cellular events in S. pombe. Genes Cells 2005; 11:29-46. [PMID: 16371130 DOI: 10.1111/j.1365-2443.2005.00919.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
RCC1, a conserved chromosomal protein with a seven-bladed propeller is a GDP/GTP nucleotide exchange factor for RanGTPase that mediates various cellular events. We isolated 16 temperature-sensitive (ts) mutants of S. pombeRCC1-homolog, pim1+, by error-prone PCR. Five pim1(ts) mutants had a single mutation. The obtained pim1(ts) mutations and previously reported mutations were localized on similar sites in seven RCC1 repeats. Those mutations resulted in a reduced binding of Pim1 with Spi1. All pim1(ts) mutants showed a defect in nucleocytoplasmic protein transports, whereas the majority of them showed a normal mRNA export. In all pim1(ts) examined, chromosomal DNA replication was completed. However, mitotic spindle formation was abrogated, the septum was formed being uncoupled with nuclear division and abnormally widened, thus resulting in chromosomal DNA mis-segregation and the accumulation of enucleated cells. As a result, a defect of RanGEF/Pim1 abolished the orchestration of sequential mitotic events, spindle formation, septation and cytokinesis that are essential to produce two identical daughter cells.
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Affiliation(s)
- Eiji Hirose
- Department of Molecular Biology, Graduate School of Medical Science, Kyushu University, 3-1-1, Maidashi, Fukuoka 812-8582, Japan
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15
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Gwizdek C, Hobeika M, Kus B, Ossareh-Nazari B, Dargemont C, Rodriguez MS. The mRNA nuclear export factor Hpr1 is regulated by Rsp5-mediated ubiquitylation. J Biol Chem 2005; 280:13401-5. [PMID: 15713680 DOI: 10.1074/jbc.c500040200] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Ubiquitin conjugation and in particular two distinct HECT ubiquitin ligases, Rsp5p and Tom1p, have been shown to participate in the regulation of mRNA export in Saccharomyces cerevisiae. The identification of the ubiquitin ligase substrates represents a major challenge in understanding how this modification may modulate mRNA export. Here, we identified Hpr1p, a member of the THO/TREX (transcription/export) complex that couples mRNA transcription to nuclear export as a target of the ubiquitin-proteasome pathway. Hpr1p degradation is enhanced at high temperature and appears linked to on-going RNA-polymeraseII-mediated transcription. Interestingly, the stability of the other THO complex components is not affected under these conditions indicating that Hpr1p turnover could control the formation of the THO/TREX complex and consequently mRNA export. Using in vivo and in vitro approaches we demonstrate that Rsp5p is responsible for the ubiquitylation of Hpr1p that also involves the ubiquitin-conjugating enzyme Ubc4p. Thus, Hpr1p represents the first nuclear export factor regulated by ubiquitylation, strongly suggesting that this post-translational modification participates in the coordination of transcription and mRNA export processes.
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Affiliation(s)
- Carole Gwizdek
- Institut Jacques Monod, Unité Mixte de Recherche 7592, CNRS, Universités Paris VI and VII, 75251 Paris Cedex 05, France
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16
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Hegde AN. Ubiquitin-proteasome-mediated local protein degradation and synaptic plasticity. Prog Neurobiol 2004; 73:311-57. [PMID: 15312912 DOI: 10.1016/j.pneurobio.2004.05.005] [Citation(s) in RCA: 104] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2003] [Accepted: 05/28/2004] [Indexed: 02/07/2023]
Abstract
A proteolytic pathway in which attachment of a small protein, ubiquitin, marks the substrates for degradation by a multi-subunit complex called the proteasome has been shown to function in synaptic plasticity and in several other physiological processes of the nervous system. Attachment of ubiquitin to protein substrates occurs through a series of highly specific and regulated steps. Degradation by the proteasome is subject to multiple levels of regulation as well. How does the ubiquitin-proteasome pathway contribute to synaptic plasticity? Long-lasting, protein synthesis-dependent, changes in the synaptic strength occur through activation of molecular cascades in the nucleus in coordination with signaling events in specific synapses. Available evidence indicates that ubiquitin-proteasome-mediated degradation has a role in the molecular mechanisms underlying synaptic plasticity that operate in the nucleus as well as at the synapse. Since the ubiquitin-proteasome pathway has been shown to be versatile in having roles in addition to proteolysis in several other cellular processes relevant to synaptic plasticity, such as endocytosis and transcription, this pathway is highly suited for a localized role in the neuron. Because of its numerous roles, malfunctioning of this pathway leads to several diseases and disorders of the nervous system. In this review, I examine the ubiquitin-proteasome pathway in detail and describe the role of regulated proteolysis in long-term synaptic plasticity. Also, using synaptic tagging theory of synapse-specific plasticity, I provide a model on the possible roles and regulation of local protein degradation by the ubiquitin-proteasome pathway.
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Affiliation(s)
- Ashok N Hegde
- Department of Neurobiology and Anatomy, Medical Center Boulevard, Wake Forest University Health Sciences, Winston-Salem, NC 27157, USA.
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17
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Andoh T, Azad AK, Shigematsu A, Ohshima Y, Tani T. The fission yeast ptr1+ gene involved in nuclear mRNA export encodes a putative ubiquitin ligase. Biochem Biophys Res Commun 2004; 317:1138-43. [PMID: 15094387 DOI: 10.1016/j.bbrc.2004.03.171] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2004] [Indexed: 10/26/2022]
Abstract
Fission yeast ptr1-1 is one of the mRNA transport mutants that accumulate poly(A)+ RNA in the nuclei at the nonpermissive temperature. We found that the ptr1+ gene encodes a homolog of Saccharomyces cerevisiae Tom1p, a hect type ubiquitin ligase. In ptr1-1, a conserved amino acid in the hect domain of Ptr1p is mutated. The ptr1+ gene is essential for growth and its mutation did not affect nuclear protein export. A ptr1-1 rae1-167 double mutant showed a synthetic effect on a growth defect, indicating that Ptr1p functionally interacts with an essential mRNA export factor Rae1p. We also isolated a multi-copy suppressor for ptr1-1 and found that it is the mpd2+ gene isolated as a multi-copy suppressor of cdc7-PD1.
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Affiliation(s)
- Tomoko Andoh
- Department of Biological Science, Faculty of Science, Kumamoto University, Kurokami, Kumamoto 860-8555, Japan
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18
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Ideue T, Azad AK, Yoshida JI, Matsusaka T, Yanagida M, Ohshima Y, Tani T. The nucleolus is involved in mRNA export from the nucleus in fission yeast. J Cell Sci 2004; 117:2887-95. [PMID: 15161942 DOI: 10.1242/jcs.01155] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
To elucidate the mechanism of mRNA export from the nucleus, we isolated five novel temperature-sensitive mutants (ptr7 to ptr11) that accumulate poly(A)(+) RNA in the nuclei at the nonpermissive temperature in Schizosaccharomyces pombe. Of those, the ptr11 mutation was found in the top2(+) gene encoding DNA topoisomerase II. In addition to the nuclear accumulation of poly(A)(+) RNA, ptr11 exhibited the cut (cell untimely torn) phenotype at the nonpermissive temperature, like the previously isolated mutant, ptr4. In these two mutants, cytokinesis occurred without prior nuclear division, resulting in cleavage of the undivided nuclei by the septum. To investigate the relationship between mRNA export defects and the cut phenotype observed in ptr4 and ptr11, we analyzed 11 other mutants displaying the cut phenotype and found that all these tested mutants accumulate poly(A)(+) mRNA in the aberrantly cleaved nuclei. Interestingly, nuclear accumulation of poly(A)(+) mRNA was observed only in the anucleolate nuclei produced by aberrant cytokinesis. In addition, nuc1, the S. pombe mutant exhibiting a collapsed nucleolus, trapped poly(A)(+) mRNA in the nucleolar region at the nonpermissive temperature. In ptr11 and nuc1, mRNA transcribed from the intron-containing TBP gene showed nuclear accumulation, but not transcripts from the intron-less TBP cDNA, suggesting that the export pathway differs between the spliced and unspliced TBP mRNAs. These findings support the notion that a subset of mRNAs in yeast is exported from the nucleus through transient association with the nucleolus.
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Affiliation(s)
- Takashi Ideue
- Department of Biology, Graduate School of Sciences, Kyushu University, Fukuoka 812-8581, Japan
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19
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Kalam Azad A, Ideue T, Ohshima Y, Tani T. A mutation in the gene involved in sister chromatid separation causes a defect in nuclear mRNA export in fission yeast. Biochem Biophys Res Commun 2003; 310:176-81. [PMID: 14511667 DOI: 10.1016/j.bbrc.2003.08.135] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Fission yeast ptr4-1 is one of the mRNA transport mutants that accumulate poly(A)(+) RNA in the nuclei at the nonpermissive temperature. We cloned the ptr4(+) gene and found that it is identical with the cut1(+) gene essential for chromosome segregation during mitosis. ptr4/cut1 has no defects in nucleocytoplasmic transport of a protein, indicative of a specific blockage of mRNA export by this mutation. A mutant of Cut2p cooperating with Cut1p in sister chromatid separation also showed defective mRNA export at the nonpermissive temperature. Our results suggest a novel linkage between the cell division cycle and nuclear mRNA export in eukaryotic cells.
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Affiliation(s)
- Abul Kalam Azad
- Department of Biology, Faculty of Sciences, Kyushu University Graduate School, Hakozaki, Fukuoka 812-8581, Japan
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20
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Rodriguez MS, Gwizdek C, Haguenauer-Tsapis R, Dargemont C. The HECT ubiquitin ligase Rsp5p is required for proper nuclear export of mRNA in Saccharomyces cerevisiae. Traffic 2003; 4:566-75. [PMID: 12839499 DOI: 10.1034/j.1600-0854.2003.00115.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The nuclear transport of both proteins and RNAs has attracted considerable interest in recent years. However, regulation pathways of the nuclear transport machineries are still not well characterized. Previous studies indicated that ubiquitination is involved in poly(A)+ RNA nuclear export. For this reason, we systematically investigated ubiquitin-protein ligasess from the homologous to E6-AP carboxy terminus (HECT) family for potential individual roles in nuclear transport in Saccharomyces cerevisiae. Here we report that Rsp5, an essential yeast ubiquitin ligase involved in many cellular functions, when deleted or mutated in ligase activity, blocks the nuclear export of mRNAs. Affected messenger RNAs include both total poly(A)+ mRNA and heat-shock mRNAs. Mutation of Rsp5 does not affect nuclear protein import or export. Deletion of RSP5 blocks mRNA export, even under conditions where its essential role in unsaturated fatty acids biosynthesis is bypassed. Using domain mapping, we find that the ligase activity is required for proper mRNA export, indicating that ubiquitination by Rsp5 acts directly or indirectly to affect RNA export. The finding that Rsp5p ligase mutations cause a more pronounced defect at high temperatures suggests that ubiquitination of transport factors by Rsp5p may also be essential during stress conditions.
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Affiliation(s)
- M S Rodriguez
- Institut Jacques Monod, Unité Mixte de Recherche 7592, CNRS, Universités Paris VI et VII. 2 Place Jussieu, Tour 43, 75251 Paris Cedex 05, France.
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21
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Tatebayashi K, Tani T, Ikeda H. Fission yeast Mog1p homologue, which interacts with the small GTPase Ran, is required for mitosis-to-interphase transition and poly(A)(+) RNA metabolism. Genetics 2001; 157:1513-22. [PMID: 11290708 PMCID: PMC1461609 DOI: 10.1093/genetics/157.4.1513] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We have cloned and characterized the Schizosaccharomyces pombe gene mog1(+), which encodes a protein with homology to the Saccharomyces cerevisiae Mog1p participating in the Ran-GTPase system. The S. pombe Mog1p is predominantly localized in the nucleus. In contrast to the S. cerevisiae MOG1 gene, the S. pombe mog1(+) gene is essential for cell viability. mog1(+) is required for the mitosis-to-interphase transition, as the mog1-1 mutant arrests at restrictive temperatures as septated, binucleated cells with highly condensed chromosomes and an aberrant nuclear envelope. FACS analysis showed that these cells do not undergo a subsequent round of DNA replication. Surprisingly, also unlike the Delta mog1 mutation in S. cerevisiae, the mog1-1 mutation causes nucleolar accumulation of poly(A)(+) RNA at the restrictive temperature in S. pombe, but the signals do not overlap with the fibrillarin-rich region of the nucleolus. Thus, we found that mog1(+) is required for the mitosis-to-interphase transition and a class of RNA metabolism. In our attempt to identify suppressors of mog1-1, we isolated the spi1(+) gene, which encodes the fission yeast homologue of Ran. We found that overexpression of Spi1p rescues the S. pombe Delta mog1 cells from death. On the basis of these results, we conclude that mog1(+) is involved in the Ran-GTPase system.
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Affiliation(s)
- K Tatebayashi
- Department of Molecular Biology, Institute of Medical Science, the University of Tokyo, P.O. Takanawa, Tokyo 108-8639, Japan.
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22
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Shobuike T, Tatebayashi K, Tani T, Sugano S, Ikeda H. The dhp1(+) gene, encoding a putative nuclear 5'-->3' exoribonuclease, is required for proper chromosome segregation in fission yeast. Nucleic Acids Res 2001; 29:1326-33. [PMID: 11238999 PMCID: PMC29750 DOI: 10.1093/nar/29.6.1326] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The Schizosaccharomyces pombe dhp1(+) gene is an ortholog of the Saccharomyces cerevisiae RAT1 gene, which encodes a nuclear 5'-->3' exoribonuclease, and is essential for cell viability. To clarify the cellular functions of the nuclear 5'-->3' exoribonuclease, we isolated and characterized a temperature-sensitive mutant of dhp1 (dhp1-1 mutant). The dhp1-1 mutant showed nuclear accumulation of poly(A)(+) RNA at the restrictive temperature, as was already reported for the rat1 mutant. Interestingly, the dhp1-1 mutant exhibited aberrant chromosome segregation at the restrictive temperature. The dhp1-1 cells frequently contained condensed chromosomes, most of whose sister chromatids failed to separate during mitosis despite normal mitotic spindle elongation. Finally, chromosomes were displaced or unequally segregated. As similar mitotic defects were also observed in Dhp1p-depleted cells, we concluded that dhp1(+) is required for proper chromosome segregation as well as for poly(A)(+) RNA metabolism in fission yeast. Furthermore, we isolated a multicopy suppressor of the dhp1-1 mutant, referred to as din1(+). We found that the gene product of dhp1-1 was unstable at high temperatures, but that reduced levels of Dhp1-1p could be suppressed by overexpressing Din1p at the restrictive temperature. Thus, Din1p may physically interact with Dhp1p and stabilize Dhp1p and/or restore its activity.
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Affiliation(s)
- T Shobuike
- Department of Molecular Biology, Institute of Medical Science, University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
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23
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Tsukahara M, Suemori H, Noguchi S, Ji ZS, Tsunoo H. Novel nucleolar protein, midnolin, is expressed in the mesencephalon during mouse development. Gene 2000; 254:45-55. [PMID: 10974535 DOI: 10.1016/s0378-1119(00)00259-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Using the gene trap method and the selection of embryonic stem cells in vitro, we have identified several novel genes involved in mouse development. The detailed analysis of one of these, named midnolin (midbrain nucleolar protein), is reported here. Expression of the midnolin gene is developmentally regulated: it is strongly expressed at the mesencephalon (midbrain) of the embryo in day 12.5 (E12.5) mice. The midnolin encodes a protein of 508 amino acids (aa), which contains a Ubiquitin-like domain. The intracellular distribution of the midnolin was studied by using midnolin-green fluorescent protein (GFP) fusion proteins. Midnolin was found to be localized in the nucleus and nucleolus, but not in the cytoplasm. The nucleolar localization signal was determined to be a 28aa peptide (440-QQKRLRRKARRDARGPYHWTPSRKAGRS-467) located at the C-terminal region of the midnolin. Our results suggest that midnolin is involved in regulation of genes related to neurogenesis in the nucleolus.
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MESH Headings
- Amino Acid Sequence
- Animals
- Base Sequence
- Blotting, Northern
- CHO Cells
- Cell Line
- Cloning, Molecular
- Cricetinae
- DNA/chemistry
- DNA/genetics
- DNA, Complementary/chemistry
- DNA, Complementary/genetics
- Embryo, Mammalian/metabolism
- Female
- Gene Expression
- Gene Expression Regulation, Developmental
- Green Fluorescent Proteins
- In Situ Hybridization
- Luminescent Proteins/genetics
- Luminescent Proteins/metabolism
- Male
- Mesencephalon/embryology
- Mesencephalon/metabolism
- Mice
- Mice, Inbred C57BL
- Microscopy, Fluorescence
- Molecular Sequence Data
- Nuclear Proteins/genetics
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Recombinant Fusion Proteins/genetics
- Recombinant Fusion Proteins/metabolism
- Sequence Analysis, DNA
- Sequence Deletion
- Sequence Homology, Amino Acid
- Tissue Distribution
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Affiliation(s)
- M Tsukahara
- Bio Signal Pathway Project, Kanagawa Academy of Science and Technology in Meiji Institute of Health Science, 540 Naruda, Odawara-shi, 250-0862, Kanagawa, Japan
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24
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Duncan K, Umen JG, Guthrie C. A putative ubiquitin ligase required for efficient mRNA export differentially affects hnRNP transport. Curr Biol 2000; 10:687-96. [PMID: 10873801 DOI: 10.1016/s0960-9822(00)00527-3] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
BACKGROUND In the nucleus, mRNAs are bound by hnRNP proteins. A subset of hnRNP proteins shuttle between the nucleus and cytoplasm and are believed to promote mRNA export by acting as adaptors between mRNA and the transport machinery. The existence of multiple shuttling hnRNP proteins raises the question of whether differentially regulated, hnRNP-specific mRNA export pathways exist. RESULTS We have determined that Tom1p, a conserved protein with a hect (homology to E6-AP carboxyl terminus) E3 ubiquitin ligase domain, is required for efficient mRNA export in S. cerevisiae, yet differentially affects hnRNP protein localization and export. Mutations in tom1 predicted to abolish ubiquitin ligase activity block efficient export of Nab2p and mRNA, causing Nab2p-mRNA complexes to accumulate in a punctate pattern coincident with the nuclear pore complex (NPC). Notably, the subcellular distribution of several other hnRNP proteins is not affected. In particular, Np13p remains mRNA-associated and continues to be efficiently exported in tom1 mutants. CONCLUSION Our results demonstrate that mutations predicted to affect the enzymatic activity of the Tom1p ubiquitin ligase differentially affect export of hnRNP proteins in association with mRNA. We propose the existence of multiple mRNA export pathways, with export of Nab2p-associated mRNAs dependent on a branch of the ubiquitin protein modification pathway.
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Affiliation(s)
- K Duncan
- Department of Biochemistry and Biophysics, University of California, San Francisco 94143-0448, USA
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25
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Balasundaram D, Benedik MJ, Morphew M, Dang VD, Levin HL. Nup124p is a nuclear pore factor of Schizosaccharomyces pombe that is important for nuclear import and activity of retrotransposon Tf1. Mol Cell Biol 1999; 19:5768-84. [PMID: 10409764 PMCID: PMC84427 DOI: 10.1128/mcb.19.8.5768] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The long terminal repeat (LTR)-containing retrotransposon Tf1 propagates within the fission yeast Schizosaccharomyces pombe as the result of several mechanisms that are typical of both retrotransposons and retroviruses. To identify host factors that contribute to the transposition process, we mutagenized cultures of S. pombe and screened them for strains that were unable to support Tf1 transposition. One such strain contained a mutation in a gene we named nup124. The product of this gene contains 11 FXFG repeats and is a component of the nuclear pore complex. In addition to the reduced levels of Tf1 transposition, the nup124-1 allele caused a significant reduction in the nuclear localization of Tf1 Gag. Surprisingly, the mutation in nup124-1 did not cause any reduction in the growth rate, the nuclear localization of specific nuclear localization signal-containing proteins, or the cytoplasmic localization of poly(A) mRNA. A two-hybrid analysis and an in vitro precipitation assay both identified an interaction between Tf1 Gag and the N terminus of Nup124p. These results provide evidence for an unusual mechanism of nuclear import that relies on a direct interaction between a nuclear pore factor and Tf1 Gag.
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Affiliation(s)
- D Balasundaram
- Laboratory of Eukaryotic Gene Regulation, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, USA
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26
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Shibuya T, Tsuneyoshi S, Azad AK, Urushiyama S, Ohshima Y, Tani T. Characterization of the ptr6(+) gene in fission yeast: a possible involvement of a transcriptional coactivator TAF in nucleocytoplasmic transport of mRNA. Genetics 1999; 152:869-80. [PMID: 10388808 PMCID: PMC1460658 DOI: 10.1093/genetics/152.3.869] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Transport of mRNA from the nucleus to the cytoplasm is one of the important steps in gene expression in eukaryotic cells. To elucidate a mechanism of mRNA export, we identified a novel ptr [poly(A)+ RNA transport] mutation, ptr6, which causes accumulation of mRNA in the nucleus and inhibition of growth at the nonpermissive temperature. The ptr6(+) gene was found to encode an essential protein of 393 amino acids, which shares significant homology in amino acid sequence with yTAFII67 of budding yeast Saccharomyces cerevisiae and human hTAFII55, a subunit of the general transcription factor complex TFIID. A Ptr6p-GFP fusion protein is localized in the nucleus, suggesting that Ptr6p functions there. Northern blot analysis using probes for 10 distinct mRNAs showed that the amount of tbp+ mRNA encoding the TATA-binding protein is increased five- to sixfold, whereas amounts of others are rapidly decreased at the nonpermissive temperature in ptr6-1. ptr6 has no defects in nuclear import of an NLS-GFP fusion protein. These results suggest that Ptr6p required for mRNA transport is a Schizosaccharomyces pombe homologue of yTAFII67 and hTAFII55. This is the first report suggesting that a TAF is involved in the nucleocytoplasmic transport of mRNA in addition to the transcription of the protein-coding genes.
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Affiliation(s)
- T Shibuya
- Department of Biology, Faculty of Science, Kyushu University, Fukuoka 812-8581, Japan
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27
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Whalen WA, Yoon JH, Shen R, Dhar R. Regulation of mRNA export by nutritional status in fission yeast. Genetics 1999; 152:827-38. [PMID: 10388805 PMCID: PMC1460645 DOI: 10.1093/genetics/152.3.827] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We have isolated a mutation in nup184(nup184-1) that is synthetically lethal with the mRNA export defective rae1-167 mutation in Schizosaccharomyces pombe. The consequence of the synthetic lethality is a defect in mRNA export. The predicted Nup184p is similar to Nup188p of Saccharomyces cerevisiae, and a Nup184p-GFP fusion localizes to the nuclear periphery in a punctate pattern. The Deltanup184 null mutant is viable and also is synthetically lethal with rae1-167. In a rae1(+) background, both the nup184-1 and Deltanup184 mutations confer sensitivity to growth in nutrient-rich medium (YES) that is accompanied by nuclear poly(A)+ RNA accumulation. Removal of the cAMP-dependent protein kinase, Pka1p, relieved the growth and mRNA export defects of nup184 mutants when grown in nutrient-rich medium. The activation of Pka1p is necessary, but not sufficient, to cause the severe poly(A)+ RNA export defects when nup184 mutant cells are incubated in YES, suggesting nutritional status can also regulate poly(A)+ RNA export. Our results suggest that the regulation of poly(A)+ RNA export by Pka1p kinase appears to be indirect, via a translation-dependent step, but post-translationally in response to YES.
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Affiliation(s)
- W A Whalen
- Basic Sciences Laboratory, National Cancer Institute, Bethesda, Maryland 20892, USA
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28
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Watanabe M, Fukuda M, Yoshida M, Yanagida M, Nishida E. Involvement of CRM1, a nuclear export receptor, in mRNA export in mammalian cells and fission yeast. Genes Cells 1999; 4:291-7. [PMID: 10421839 DOI: 10.1046/j.1365-2443.1999.00259.x] [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] [Indexed: 11/20/2022]
Abstract
BACKGROUND CRM1, an evolutionarily conserved protein, was shown to be a receptor for leucine-rich nuclear export signal (NES)-dependent protein transport. In lower eukaryotes CRM1 is reported to be required for the export of mRNA, however, involvement of the NES-dependent transport pathway in mRNA export in higher eukaryotes has not been established. RESULTS We have found that treatment of mammalian cells with leptomycin B (LMB), a specific inhibitor of CRM1, induces the nuclear accumulation of endogenous mRNA, probably due to the inhibition of its export. In fission yeasts, the nuclear accumulation of mRNA also occurred in cells treated with LMB or in a temperature-sensitive crm1 mutant at a restrictive temperature. A synthetic mRNA that was injected into the nucleus of mammalian cultured cells was exported from the nucleus within 5 h. This export was inhibited by both wheat germ agglutinin and a temperature of 4 degrees C. Importantly, this mRNA export was inhibited by LMB or by an excess amount of the NES peptide-conjugates. LMB treatment, on the other hand, rapidly induced the nuclear entry of RanBP1, a factor involved in the active nucleocytoplasmic transport, although the treatment did not interfere with a nuclear localization signal-dependent transport system within 7 h. CONCLUSION These results suggest that CRM1 is involved in mRNA export in eukaryotic cells.
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Affiliation(s)
- M Watanabe
- Department of Biophysics, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
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29
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Matynia A, Mueller U, Ong N, Demeter J, Granger AL, Hinata K, Sazer S. Isolation and characterization of fission yeast sns mutants defective at the mitosis-to-interphase transition. Genetics 1998; 148:1799-811. [PMID: 9560394 PMCID: PMC1460064 DOI: 10.1093/genetics/148.4.1799] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
pim1-d1ts was previously identified in a visual screen for fission yeast mutants unable to complete the mitosis-to-interphase transition. pim1+ encodes the guanine nucleotide exchange factor (GEF) for the spi1 GTPase. Perturbations of this GTPase system by either mutation or overproduction of its regulatory proteins cause cells to arrest with postmitotic condensed chromosomes, an unreplicated genome, and a wide medial septum. The septation phenotype of pim1-d1ts was used as the basis for a more extensive screen for this novel class of sns (septated, not in S-phase) mutants. Seventeen mutants representing 14 complementation groups were isolated. Three strains, sns-A3, sns-A5, and sns-A6, representing two different alleles, are mutated in the pim1+ gene. Of the 13 non-pim1ts sns complementation groups, 11 showed genetic interactions with the spi1 GTPase system. The genes mutated in 10 sns strains were synthetically lethal with pim1-d1, and six sns strains were hypersensitive to overexpression of one or more of the known components of the spil GTPase system. Epistasis analysis places the action of the genes mutated in nine of these strains downstream of pim1+ and the action of one gene upstream of pim1+. Three strains, sns-A2, sns-B1, and sns-B9, showed genetic interaction with the spil GTPase system in every test performed. sns-B1 and sns-B9 are likely to identify downstream targets, whereas sns-A2 is likely to identify upstream regulators of the spi1 GTPase system that are required for the mitosis-to-interphase transition.
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Affiliation(s)
- A Matynia
- Verna and Marrs McLean Department of Biochemistry, Baylor College of Medicine, Houston, Texas 77030, USA
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30
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Yoon JH, Whalen WA, Bharathi A, Shen R, Dhar R. Npp106p, a Schizosaccharomyces pombe nucleoporin similar to Saccharomyces cerevisiae Nic96p, functionally interacts with Rae1p in mRNA export. Mol Cell Biol 1997; 17:7047-60. [PMID: 9372936 PMCID: PMC232561 DOI: 10.1128/mcb.17.12.7047] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
To identify components of the mRNA export machinery in Schizosaccharomyces pombe, a screen was developed to identify mutations that were synthetically lethal with the conditional mRNA export allele rae1-167. Mutations defining three complementation groups were isolated, and here we report the characterization of npp106 (for nuclear pore protein of 106 kDa). This gene encodes a predicted protein that has significant similarity to the Nic96p nucleoporin of Saccharomyces cerevisiae. Consistent with Npp106p being a nucleoporin, a functional green fluorescent protein (GFP)-tagged Npp106p localized to the nuclear periphery. In contrast to NIC96, the npp106 gene is not essential. Moreover, a delta npp106 mutant did not show cytoplasmic mislocalization of a simian virus 40 nuclear localization signal-GFP-LacZ reporter protein, and a fraction of cells had accumulation of poly(A)+ RNA in the nucleus. A consequence of the synthetic lethality between rae1-167 and npp106-1 was the accumulation of poly(A)+ RNA in the nucleus when cells were grown under synthetic lethal conditions. In addition to npp106-1, which is a nonsense mutation that truncates the protein at amino acid 292, the delta npp106 mutation was synthetically lethal with rae1-167, suggesting that the synthetic lethality is a consequence of the loss of a function of npp106. We further demonstrate that a region between amino acids 74 and 348 of Npp106p is required for complementation of the synthetic lethality. These results uncover a potential direct or indirect involvement of Npp106p in mRNA export.
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Affiliation(s)
- J H Yoon
- Laboratory of Basic Sciences, National Cancer Institute, Bethesda, Maryland 20892, USA
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Urushiyama S, Tani T, Ohshima Y. The prp1+ gene required for pre-mRNA splicing in Schizosaccharomyces pombe encodes a protein that contains TPR motifs and is similar to Prp6p of budding yeast. Genetics 1997; 147:101-15. [PMID: 9286671 PMCID: PMC1208094 DOI: 10.1093/genetics/147.1.101] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The prp (pre-mRNA processing) mutants of the fission yeast Schizosaccharomyces pombe have a defect in pre-mRNA splicing and accumulate mRNA precursors at a restrictive temperature. One of the prp mutants, prp1-4, also has a defect in poly(A)+ RNA transport. The prp1+ gene encodes a protein of 906 amino acid residues that contains 19 repeats of 34 amino acids termed tetratrico peptide repeat (TPR) motifs, which were proposed to mediate protein-protein interactions. The amino acid sequence of Prp1p shares 29.6% identity and 50.6% similarity with that of the PRP6 protein of Saccharomyces cerevisiae, which is a component of the U4/U6 snRNP required for spliceosome assembly. No functional complementation was observed between S. pombe prp1+ and S. cerevisiae PRP6. We examined synthetic lethality of prp1-4 with the other known prp mutations in S. pombe. The results suggest that Prp1p interacts either physically or functionally with Prp4p, Prp6p and Prp13p. Interestingly, the prp1+ gene was found to be identical with the zer1+ gene that functions in cell cycle control. These results suggest that Prp1p/Zer1p is either directly or indirectly involved in cell cycle progression and/or poly(A)+ RNA nuclear export, in addition to pre-mRNA splicing.
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Affiliation(s)
- S Urushiyama
- Department of Biology, Faculty of Science, Kyushu University, Fukuoka, Japan
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