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Matsumori H, Watanabe K, Tachiwana H, Fujita T, Ito Y, Tokunaga M, Sakata-Sogawa K, Osakada H, Haraguchi T, Awazu A, Ochiai H, Sakata Y, Ochiai K, Toki T, Ito E, Goldberg IG, Tokunaga K, Nakao M, Saitoh N. Ribosomal protein L5 facilitates rDNA-bundled condensate and nucleolar assembly. Life Sci Alliance 2022; 5:5/7/e202101045. [PMID: 35321919 PMCID: PMC8942980 DOI: 10.26508/lsa.202101045] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 03/01/2022] [Accepted: 03/02/2022] [Indexed: 11/24/2022] Open
Abstract
High content image analysis, single molecule tracking, modeling, and DBA patient analysis revealed that ribosomal protein L5 facilitates rDNA-bundled condensate and nucleolar assembly. The nucleolus is the site of ribosome assembly and formed through liquid–liquid phase separation. Multiple ribosomal DNA (rDNA) arrays are bundled in the nucleolus, but the underlying mechanism and significance are unknown. In the present study, we performed high-content screening followed by image profiling with the wndchrm machine learning algorithm. We revealed that cells lacking a specific 60S ribosomal protein set exhibited common nucleolar disintegration. The depletion of RPL5 (also known as uL18), the liquid–liquid phase separation facilitator, was most effective, and resulted in an enlarged and un-separated sub-nucleolar compartment. Single-molecule tracking analysis revealed less-constrained mobility of its components. rDNA arrays were also unbundled. These results were recapitulated by a coarse-grained molecular dynamics model. Transcription and processing of ribosomal RNA were repressed in these aberrant nucleoli. Consistently, the nucleoli were disordered in peripheral blood cells from a Diamond–Blackfan anemia patient harboring a heterozygous, large deletion in RPL5. Our combinatorial analyses newly define the role of RPL5 in rDNA array bundling and the biophysical properties of the nucleolus, which may contribute to the etiology of ribosomopathy.
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Affiliation(s)
- Haruka Matsumori
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, Japan
| | - Kenji Watanabe
- Cancer Institute of Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Hiroaki Tachiwana
- Cancer Institute of Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Tomoko Fujita
- Cancer Institute of Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Yuma Ito
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Makio Tokunaga
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Kumiko Sakata-Sogawa
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Hiroko Osakada
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology, Kobe, Japan
| | - Tokuko Haraguchi
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology, Kobe, Japan.,Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| | - Akinori Awazu
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan.,Research Center for the Mathematics on Chromatin Live Dynamics (RcMcD), Hiroshima University, Higashi-Hiroshima, Japan
| | - Hiroshi Ochiai
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Yuka Sakata
- Cancer Institute of Japanese Foundation for Cancer Research, Tokyo, Japan
| | | | - Tsutomu Toki
- Department of Pediatrics, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
| | - Etsuro Ito
- Department of Pediatrics, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
| | - Ilya G Goldberg
- Image Informatics and Computational Biology Unit, Laboratory of Genetics, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Kazuaki Tokunaga
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, Japan
| | - Mitsuyoshi Nakao
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, Japan
| | - Noriko Saitoh
- Cancer Institute of Japanese Foundation for Cancer Research, Tokyo, Japan
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2
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Lim WM, Ito Y, Sakata-Sogawa K, Tokunaga M. CLIP-170 is essential for MTOC repositioning during T cell activation by regulating dynein localisation on the cell surface. Sci Rep 2018; 8:17447. [PMID: 30487641 PMCID: PMC6261991 DOI: 10.1038/s41598-018-35593-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 11/06/2018] [Indexed: 02/02/2023] Open
Abstract
The microtubule-organizing centre (MTOC) is repositioned to the centre of the contacted cell surface, the immunological synapse, during T cell activation. However, our understanding of its molecular mechanism remains limited. Here, we found that the microtubule plus-end tracking cytoplasmic linker protein 170 (CLIP-170) plays a novel role in MTOC repositioning using fluorescence imaging. Inhibition of CLIP-170 phosphorylation impaired both MTOC repositioning and interleukin-2 (IL-2) expression. T cell stimulation induced some fraction of dynein to colocalise with CLIP-170 and undergo plus-end tracking. Concurrently, it increased dynein in minus-end-directed movement. It also increased dynein relocation to the centre of the contact surface. Dynein not colocalised with CLIP-170 showed both an immobile state and minus-end-directed movement at a velocity in good agreement with the velocity of MTOC repositioning, which suggests that dynein at the immunological synapse may pull the microtubules and the MTOC. Although CLIP-170 is phosphorylated by AMP-activated protein kinase (AMPK) irrespective of stimulation, phosphorylated CLIP-170 is essential for dynein recruitment to plus-end tracking and for dynein relocation. This indicates that dynein relocation results from coexistence of plus-end- and minus-end-directed translocation. In conclusion, CLIP-170 plays an indispensable role in MTOC repositioning and full activation of T cells by regulating dynein localisation.
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Affiliation(s)
- Wei Ming Lim
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho, Midori, Yokohama, Kanagawa, 226-8501, Japan
| | - Yuma Ito
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho, Midori, Yokohama, Kanagawa, 226-8501, Japan
| | - Kumiko Sakata-Sogawa
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho, Midori, Yokohama, Kanagawa, 226-8501, Japan.
| | - Makio Tokunaga
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho, Midori, Yokohama, Kanagawa, 226-8501, Japan.
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3
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Kasai S, Kajimoto S, Ito Y, Saito T, Yasumoto KI, Tokunaga M, Sakata-Sogawa K, Fukumura H, Sogawa K. Conformational changes in inhibitory PAS domain protein associated with binding of HIF-1α and Bcl-xL in living cells. J Biochem 2017; 161:291-296. [PMID: 28003430 DOI: 10.1093/jb/mvw068] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 09/29/2016] [Indexed: 11/14/2022] Open
Abstract
Inhibitory PAS domain protein (IPAS) is a dual function protein acting as a transcriptional repressor and as a pro-apoptotic protein. Simultaneous dual-color single-molecule imaging of EGFP-IPAS coexpressed with Mit-TagRFP-T in living HeLa cells revealed that fraction of EGFP-IPAS was arrested in the nucleus and on mitochondria. Transiently expressed Cerulean-IPAS in HEK293T cells was present in nuclear speckles when coexpressed with Citrine-HIF-1α or Citrine-HLF. Fluorescence lifetime imaging microscopy (FLIM) analysis of Citrine-IPAS-Cerulean in living CHO-K1 cells clarified the presence of intramolecular FRET. Reduced lifetimes of the donor were partially restored by coexpression of HIF-1α or Bcl-xL, binding proteins of IPAS in the nucleus and mitochondria, respectively. This alteration in lifetimes demonstrates that conformational changes occurred in IPAS by their binding.
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Affiliation(s)
- Shuya Kasai
- Department of Biomolecular Sciences, Graduate School of Life Sciences, Tohoku University, Aoba-ku 980-8578, Sendai, Japan
| | - Shinji Kajimoto
- Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku 980-8578, Sendai, Japan
| | - Yuma Ito
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho, Midori-ku 226-8501, Yokohama, Japan
| | - Tomo Saito
- Department of Biomolecular Sciences, Graduate School of Life Sciences, Tohoku University, Aoba-ku 980-8578, Sendai, Japan
| | - Ken-Ichi Yasumoto
- Department of Biomolecular Sciences, Graduate School of Life Sciences, Tohoku University, Aoba-ku 980-8578, Sendai, Japan
| | - Makio Tokunaga
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho, Midori-ku 226-8501, Yokohama, Japan
| | - Kumiko Sakata-Sogawa
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho, Midori-ku 226-8501, Yokohama, Japan
| | - Hiroshi Fukumura
- Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku 980-8578, Sendai, Japan
| | - Kazuhiro Sogawa
- Department of Biomolecular Sciences, Graduate School of Life Sciences, Tohoku University, Aoba-ku 980-8578, Sendai, Japan
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4
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Shin C, Ito Y, Ichikawa S, Tokunaga M, Sakata-Sogawa K, Tanaka T. MKRN2 is a novel ubiquitin E3 ligase for the p65 subunit of NF-κB and negatively regulates inflammatory responses. Sci Rep 2017; 7:46097. [PMID: 28378844 PMCID: PMC5380948 DOI: 10.1038/srep46097] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 03/08/2017] [Indexed: 12/26/2022] Open
Abstract
Activation of NF-κB transcription factor is strictly regulated to prevent excessive inflammatory responses leading to immunopathology. However, it still remains unclear how NF-κB activation is negatively controlled. The PDZ-LIM domain-containing protein PDLIM2 is a nuclear ubiquitin E3 ligase targeting the p65 subunit of NF-κB for degradation, thus terminating NF-κB-mediated inflammation. Using yeast two-hybrid screening, we sought to isolate PDLIM2-interacting proteins that are critical for suppressing NF-κB signaling. Here we identified MKRN2, a RING finger domain-containing protein that belongs to the makorin ring finger protein gene family, as a novel p65 ubiquitin E3 ligase. MKRN2 bound to p65 and promoted the polyubiquitination and proteasome-dependent degradation of p65 through the MKRN2 RING finger domain, thereby suppressing p65-mediated NF-κB transactivation. Notably, MKRN2 and PDLIM2 synergistically promote polyubiquitination and degradation of p65. Consistently, MKRN2 knockdown in dendritic cells resulted in larger amounts of nuclear p65 and augmented production of proinflammatory cytokines in responses to innate stimuli. These results delineate a novel role of MKRN2 in negatively regulating NF-κB-mediated inflammatory responses, cooperatively with PDLIM2.
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Affiliation(s)
- Chanyoung Shin
- Laboratory for Inflammatory Regulation, RIKEN Center for Integrative Medical Sciences (IMS), RIKEN Research Center for Allergy and Immunology (RCAI), Yokohama, Kanagawa 230-0045, Japan
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Kanagawa 226-8501, Japan
| | - Yuma Ito
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Kanagawa 226-8501, Japan
| | - Shota Ichikawa
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Kanagawa 226-8501, Japan
| | - Makio Tokunaga
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Kanagawa 226-8501, Japan
| | - Kumiko Sakata-Sogawa
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Kanagawa 226-8501, Japan
| | - Takashi Tanaka
- Laboratory for Inflammatory Regulation, RIKEN Center for Integrative Medical Sciences (IMS), RIKEN Research Center for Allergy and Immunology (RCAI), Yokohama, Kanagawa 230-0045, Japan
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5
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Abstract
Many research programs focus on the molecular dynamics of living cells. This research requires cells to be adhered to a substrate while retaining the innate motility of their surface molecules. Lipid bilayer-based systems fulfill this requirement, although current methods are complicated and their utility is limited. We developed a simple and rapid method for reproducible preparation of homogeneous glass-supported lipid bilayers. Our method provides a facile means for bioimaging and analysis of molecular dynamics in living cells.
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Affiliation(s)
- Yuma Ito
- Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology
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6
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Yamazaki S, Yamamoto K, Tokunaga M, Sakata-Sogawa K, Harata M. Nuclear actin activates human transcription factor genes including the OCT4 gene. Biosci Biotechnol Biochem 2015; 79:242-6. [DOI: 10.1080/09168451.2014.972332] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Abstract
RNA microarray analyses revealed that nuclear actin activated many human transcription factor genes including OCT4, which is required for gene reprogramming. Oct4 is known to be activated by nuclear actin in Xenopus oocytes. Our findings imply that this process of OCT4 activation is conserved in vertebrates and among cell types and could be used for gene reprogramming of human cells.
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Affiliation(s)
- Shota Yamazaki
- Laboratory of Molecular Biology, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Koji Yamamoto
- Laboratory of Molecular Biology, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Makio Tokunaga
- Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Japan
- RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Japan
| | - Kumiko Sakata-Sogawa
- Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Japan
- RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Japan
| | - Masahiko Harata
- Laboratory of Molecular Biology, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
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7
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Stasevich TJ, Hayashi-Takanaka Y, Sato Y, Maehara K, Ohkawa Y, Sakata-Sogawa K, Tokunaga M, Nagase T, Nozaki N, McNally JG, Kimura H. Regulation of RNA polymerase II activation by histone acetylation in single living cells. Nature 2014; 516:272-5. [PMID: 25252976 DOI: 10.1038/nature13714] [Citation(s) in RCA: 187] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Accepted: 07/25/2014] [Indexed: 12/31/2022]
Abstract
In eukaryotic cells, post-translational histone modifications have an important role in gene regulation. Starting with early work on histone acetylation, a variety of residue-specific modifications have now been linked to RNA polymerase II (RNAP2) activity, but it remains unclear if these markers are active regulators of transcription or just passive byproducts. This is because studies have traditionally relied on fixed cell populations, meaning temporal resolution is limited to minutes at best, and correlated factors may not actually be present in the same cell at the same time. Complementary approaches are therefore needed to probe the dynamic interplay of histone modifications and RNAP2 with higher temporal resolution in single living cells. Here we address this problem by developing a system to track residue-specific histone modifications and RNAP2 phosphorylation in living cells by fluorescence microscopy. This increases temporal resolution to the tens-of-seconds range. Our single-cell analysis reveals histone H3 lysine-27 acetylation at a gene locus can alter downstream transcription kinetics by as much as 50%, affecting two temporally separate events. First acetylation enhances the search kinetics of transcriptional activators, and later the acetylation accelerates the transition of RNAP2 from initiation to elongation. Signatures of the latter can be found genome-wide using chromatin immunoprecipitation followed by sequencing. We argue that this regulation leads to a robust and potentially tunable transcriptional response.
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Affiliation(s)
- Timothy J Stasevich
- 1] Graduate School of Frontier Biosciences, Osaka University, Osaka, 565-0871, Japan [2] Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523-1870, USA [3] Transcription Imaging Consortium, Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147, USA
| | - Yoko Hayashi-Takanaka
- 1] Graduate School of Frontier Biosciences, Osaka University, Osaka, 565-0871, Japan [2] Japan Science and Technology Agency (JST), Core Research for Evolutional Science and Technology (CREST), Kawaguchi, Saitama, 332-0012, Japan [3] Department of Biological Sciences, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, 226-8501, Japan
| | - Yuko Sato
- 1] Graduate School of Frontier Biosciences, Osaka University, Osaka, 565-0871, Japan [2] Department of Biological Sciences, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, 226-8501, Japan
| | - Kazumitsu Maehara
- Department of Advanced Medical Initiatives, Faculty of Medicine, Kyushu University, Fukuoka, 812-8582, Japan
| | - Yasuyuki Ohkawa
- 1] Japan Science and Technology Agency (JST), Core Research for Evolutional Science and Technology (CREST), Kawaguchi, Saitama, 332-0012, Japan [2] Department of Advanced Medical Initiatives, Faculty of Medicine, Kyushu University, Fukuoka, 812-8582, Japan
| | - Kumiko Sakata-Sogawa
- 1] Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, 226-8501, Japan [2] RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, 230-0045, Japan
| | - Makio Tokunaga
- 1] Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, 226-8501, Japan [2] RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, 230-0045, Japan
| | - Takahiro Nagase
- Department of Biotechnology Research, Kazusa DNA Research Institute, Chiba, 292-0818, Japan
| | | | - James G McNally
- 1] Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA [2] Institute for Soft Matter and Functional Materials, Helmholtz Zentrum Berlin, Berlin, 14109, Germany
| | - Hiroshi Kimura
- 1] Graduate School of Frontier Biosciences, Osaka University, Osaka, 565-0871, Japan [2] Japan Science and Technology Agency (JST), Core Research for Evolutional Science and Technology (CREST), Kawaguchi, Saitama, 332-0012, Japan [3] Department of Biological Sciences, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, 226-8501, Japan
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8
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Asakawa H, Yang HJ, Yamamoto TG, Ohtsuki C, Chikashige Y, Sakata-Sogawa K, Tokunaga M, Iwamoto M, Hiraoka Y, Haraguchi T. Characterization of nuclear pore complex components in fission yeast Schizosaccharomyces pombe. Nucleus 2014; 5:149-62. [PMID: 24637836 PMCID: PMC4049921 DOI: 10.4161/nucl.28487] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The nuclear pore complex (NPC) is an enormous proteinaceous complex composed of multiple copies of about 30 different proteins called nucleoporins. In this study, we analyzed the composition of the NPC in the model organism Schizosaccharomyces pombe using strains in which individual nucleoporins were tagged with GFP. We identified 31 proteins as nucleoporins by their localization to the nuclear periphery. Gene disruption analysis in previous studies coupled with gene disruption analysis in the present study indicates that 15 of these nucleoporins are essential for vegetative cell growth and the other 16 nucleoporins are non-essential. Among the 16 non-essential nucleoporins, 11 are required for normal progression through meiosis and their disruption caused abnormal spore formation or poor spore viability. Based on fluorescence measurements of GFP-fused nucleoporins, we estimated the composition of the NPC in S. pombe and found that the organization of the S. pombe NPC is largely similar to that of other organisms; a single NPC was estimated as being 45.8–47.8 MDa in size. We also used fluorescence measurements of single NPCs and quantitative western blotting to analyze the composition of the Nup107-Nup160 subcomplex, which plays an indispensable role in NPC organization and function. Our analysis revealed low amounts of Nup107 and Nup131 and high amounts of Nup132 in the Nup107-Nup160 subcomplex, suggesting that the composition of this complex in S. pombe may differ from that in S. cerevisiae and humans. Comparative analysis of NPCs in various organisms will lead to a comprehensive understanding of the functional architecture of the NPC.
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Affiliation(s)
- Haruhiko Asakawa
- Graduate School of Frontier Biosciences; Osaka University; Suita, Japan
| | - Hui-Ju Yang
- Graduate School of Frontier Biosciences; Osaka University; Suita, Japan
| | - Takaharu G Yamamoto
- Advanced ICT Research Institute Kobe; National Institute of Information and Communications Technology; Kobe, Japan
| | - Chizuru Ohtsuki
- Graduate School of Frontier Biosciences; Osaka University; Suita, Japan
| | - Yuji Chikashige
- Advanced ICT Research Institute Kobe; National Institute of Information and Communications Technology; Kobe, Japan; Graduate School of Science; Osaka University; Toyonaka, Japan
| | - Kumiko Sakata-Sogawa
- Department of Biological Information; Graduate School of Bioscience and Biotechnology; Tokyo Institute of Technology; Yokohama, Japan; RIKEN Center for Integrative Medical Sciences (IMS-RCAI); Yokohama, Japan
| | - Makio Tokunaga
- Department of Biological Information; Graduate School of Bioscience and Biotechnology; Tokyo Institute of Technology; Yokohama, Japan; RIKEN Center for Integrative Medical Sciences (IMS-RCAI); Yokohama, Japan
| | - Masaaki Iwamoto
- Advanced ICT Research Institute Kobe; National Institute of Information and Communications Technology; Kobe, Japan
| | - Yasushi Hiraoka
- Graduate School of Frontier Biosciences; Osaka University; Suita, Japan; Advanced ICT Research Institute Kobe; National Institute of Information and Communications Technology; Kobe, Japan; Graduate School of Science; Osaka University; Toyonaka, Japan
| | - Tokuko Haraguchi
- Graduate School of Frontier Biosciences; Osaka University; Suita, Japan; Advanced ICT Research Institute Kobe; National Institute of Information and Communications Technology; Kobe, Japan; Graduate School of Science; Osaka University; Toyonaka, Japan
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9
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Hotta K, Nashimoto A, Yasumura E, Suzuki M, Azuma M, Iizumi Y, Shima D, Nabeshima R, Hiramoto M, Okada A, Sakata-Sogawa K, Tokunaga M, Ito T, Ando H, Sakamoto S, Kabe Y, Aizawa S, Imai T, Yamaguchi Y, Watanabe H, Handa H. Vesnarinone Suppresses TNFα mRNA Expression by Inhibiting Valosin-Containing Protein. Mol Pharmacol 2013; 83:930-8. [DOI: 10.1124/mol.112.081935] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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10
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Hashimoto-Tane A, Yokosuka T, Sakata-Sogawa K, Sakuma M, Ishihara C, Tokunaga M, Saito T. Dynein-driven transport of T cell receptor microclusters regulates immune synapse formation and T cell activation. Immunity 2011; 34:919-31. [PMID: 21703543 DOI: 10.1016/j.immuni.2011.05.012] [Citation(s) in RCA: 123] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2010] [Revised: 02/11/2011] [Accepted: 05/26/2011] [Indexed: 11/27/2022]
Abstract
When T cells recognize a peptide-major histocompatibility complex on antigen-presenting cells (APCs), T cell receptor microclusters (TCR-MCs) are generated and move to the center of the T cell-APC interface to form the central supramolecular activation cluster (cSMAC). cSMAC formation depends on stimulation strength and regulates T cell activation. We demonstrate that the dynein motor complex colocalized and coimmunoprecipitated with the TCR complex and that TCR-MCs moved along microtubules (MTs) toward the center of the immune synapse in a dynein-dependent manner to form cSMAC. MTs are located in close proximity to the plasma membrane at the activation site. TCR-MC velocity and cSMAC formation were impaired by dynein or MT inhibitors or by ablation of dynein expression. T cells with impaired cSMAC formation exhibited enhanced cellular activation including protein phosphorylation and interleukin-2 production. These results indicate that cSMAC formation by TCR-MC movement depends on dynein and MTs, and the movement regulates T cell activation.
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Affiliation(s)
- Akiko Hashimoto-Tane
- Laboratory for Cell Signaling, RIKEN Research Center for Allergy and Immunology, Yokohama, Kanagawa 230-0045, Japan
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11
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Yokosuka T, Kobayashi W, Takamatsu M, Sakata-Sogawa K, Zeng H, Hashimoto-Tane A, Yagita H, Tokunaga M, Saito T. Spatiotemporal basis of CTLA-4 costimulatory molecule-mediated negative regulation of T cell activation. Immunity 2010; 33:326-39. [PMID: 20870175 DOI: 10.1016/j.immuni.2010.09.006] [Citation(s) in RCA: 140] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2010] [Revised: 07/11/2010] [Accepted: 08/12/2010] [Indexed: 01/08/2023]
Abstract
T cell activation is positively and negatively regulated by a pair of costimulatory receptors, CD28 and CTLA-4, respectively. Because these receptors share common ligands, CD80 and CD86, the expression and behavior of CTLA-4 is critical for T cell costimulation regulation. However, in vivo blocking of CD28-mediated costimulation by CTLA-4 and its mechanisms still remain elusive. Here, we demonstrate the dynamic behavior of CTLA-4 in its real-time competition with CD28 at the central-supramolecular activation cluster (cSMAC), resulting in the dislocalization of protein kinase C-θ and CARMA1 scaffolding protein. CTLA-4 translocation to the T cell receptor microclusters and the cSMAC is tightly regulated by its ectodomain size, and its accumulation at the cSMAC is required for its inhibitory function. The CTLA-4-mediated suppression was demonstrated by the in vitro anergy induction in regulatory T cells constitutively expressing CTLA-4. These results show the dynamic mechanism of CTLA-4-mediated T cell suppression at the cSMAC.
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Affiliation(s)
- Tadashi Yokosuka
- Laboratory for Cell Signaling, RIKEN Research Center for Allergy and Immunology, Yokohama, Kanagawa, Japan.
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12
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Miletic AV, Graham DB, Sakata-Sogawa K, Hiroshima M, Hamann MJ, Cemerski S, Kloeppel T, Billadeau DD, Kanagawa O, Tokunaga M, Swat W. Vav links the T cell antigen receptor to the actin cytoskeleton and T cell activation independently of intrinsic Guanine nucleotide exchange activity. PLoS One 2009; 4:e6599. [PMID: 19672294 PMCID: PMC2719804 DOI: 10.1371/journal.pone.0006599] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2009] [Accepted: 07/09/2009] [Indexed: 12/19/2022] Open
Abstract
Background T cell receptor (TCR) engagement leads to formation of signaling microclusters and induction of rapid and dynamic changes in the actin cytoskeleton, although the exact mechanism by which the TCR initiates actin polymerization is incompletely understood. The Vav family of guanine nucleotide exchange factors (GEF) has been implicated in generation of TCR signals and immune synapse formation, however, it is currently not known if Vav's GEF activity is required in T cell activation by the TCR in general, and in actin polymerization downstream of the TCR in particular. Methodology/Principal Findings Here, we report that Vav1 assembles into signaling microclusters at TCR contact sites and is critical for TCR-initiated actin polymerization. Surprisingly, Vav1 functions in TCR signaling and Ca++ mobilization via a mechanism that does not appear to strictly depend on the intrinsic GEF activity. Conclusions/Significance We propose here a model in which Vav functions primarily as a tyrosine phosphorylated linker-protein for TCR activation of T cells. Our results indicate that, contrary to expectations based on previously published studies including from our own laboratory, pharmacological inhibition of Vav1's intrinsic GEF activity may not be an effective strategy for T cell-directed immunosuppressive therapy.
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Affiliation(s)
- Ana V. Miletic
- Department of Pathology and Immunology, Washington University School of Medicine and Siteman Cancer Center, St. Louis, Missouri, United States of America
| | - Daniel B. Graham
- Department of Pathology and Immunology, Washington University School of Medicine and Siteman Cancer Center, St. Louis, Missouri, United States of America
| | - Kumiko Sakata-Sogawa
- Research Unit for Single Molecule Immunoimaging, RIKEN Center for Allergy and Immunology, Yokohama, Kanagawa, Japan
| | - Michio Hiroshima
- Research Unit for Single Molecule Immunoimaging, RIKEN Center for Allergy and Immunology, Yokohama, Kanagawa, Japan
| | - Michael J. Hamann
- Department of Immunology and Division of Oncology Research, Mayo Clinic College of Medicine, Rochester, Minnesota, United States of America
| | - Saso Cemerski
- Department of Pathology and Immunology, Washington University School of Medicine and Siteman Cancer Center, St. Louis, Missouri, United States of America
| | - Tracie Kloeppel
- Department of Pathology and Immunology, Washington University School of Medicine and Siteman Cancer Center, St. Louis, Missouri, United States of America
| | - Daniel D. Billadeau
- Department of Immunology and Division of Oncology Research, Mayo Clinic College of Medicine, Rochester, Minnesota, United States of America
| | - Osami Kanagawa
- Laboratory for Autoimmune Regulation, RIKEN Center for Allergy and Immunology, Yokohama, Kanagawa, Japan
| | - Makio Tokunaga
- Research Unit for Single Molecule Immunoimaging, RIKEN Center for Allergy and Immunology, Yokohama, Kanagawa, Japan
- Structural Biology Center, National Institute of Genetics, The Graduate University for Advanced Studies, Mishima, Shizuoka, Japan
- Department of Genetics, The Graduate University for Advanced Studies, Mishima, Shizuoka, Japan
| | - Wojciech Swat
- Department of Pathology and Immunology, Washington University School of Medicine and Siteman Cancer Center, St. Louis, Missouri, United States of America
- * E-mail:
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13
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Sakata-Sogawa K, Tokunaga M. [Single molecule imaging of molecular dynamics in immune cells]. Seikagaku 2009; 81:218-222. [PMID: 19378788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Affiliation(s)
- Kumiko Sakata-Sogawa
- Center for Allergy and Immunology, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
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14
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Yokosuka T, Kobayashi W, Sakata-Sogawa K, Takamatsu M, Hashimoto-Tane A, Dustin ML, Tokunaga M, Saito T. Spatiotemporal regulation of T cell costimulation by TCR-CD28 microclusters and protein kinase C theta translocation. Immunity 2008; 29:589-601. [PMID: 18848472 DOI: 10.1016/j.immuni.2008.08.011] [Citation(s) in RCA: 196] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2008] [Revised: 07/05/2008] [Accepted: 08/08/2008] [Indexed: 12/11/2022]
Abstract
T cell activation is mediated by microclusters (MCs) containing T cell receptors (TCRs), kinases, and adaptors. Although TCR MCs translocate to form a central supramolecular activation cluster (cSMAC) of the immunological synapse at the interface of a T cell and an antigen-presenting cell, the role of MC translocation in T cell signaling remains unclear. Here, we found that the accumulation of MCs at cSMAC was important for T cell costimulation. Costimulatory receptor CD28 was initially recruited coordinately with TCR to MCs, and its signals were mediated through the assembly with the kinase PKCtheta. The accumulation of MCs at the cSMAC was accompanied by the segregation of CD28 from the TCR, which resulted in the translocation of both CD28 and PKCtheta to a spatially unique subregion of cSMAC. Thus, costimulation is mediated by the generation of a unique costimulatory compartment in the cSMAC via the dynamic regulation of MC translocation.
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Affiliation(s)
- Tadashi Yokosuka
- Laboratory for Cell Signaling, RIKEN Research Center for Allergy and Immunology, Tsurumi-ku, Yokohama 230-0045, Japan
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15
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Abstract
We describe a simple illumination method of fluorescence microscopy for molecular imaging. Illumination by a highly inclined and thin beam increases image intensity and decreases background intensity, yielding a signal/background ratio about eightfold greater than that of epi-illumination. A high ratio yielded clear single-molecule images and three-dimensional images using cultured mammalian cells, enabling one to visualize and quantify molecular dynamics, interactions and kinetics in cells for molecular systems biology.
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Affiliation(s)
- Makio Tokunaga
- Biological Macromolecules Laboratory, National Institute of Genetics, Yata 1111, Mishima, Shizuoka 411-8540, Japan.
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16
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Yamasaki S, Sakata-Sogawa K, Hasegawa A, Suzuki T, Kabu K, Sato E, Kurosaki T, Yamashita S, Tokunaga M, Nishida K, Hirano T. Zinc is a novel intracellular second messenger. ACTA ACUST UNITED AC 2007; 177:637-45. [PMID: 17502426 PMCID: PMC2064209 DOI: 10.1083/jcb.200702081] [Citation(s) in RCA: 410] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Zinc is an essential trace element required for enzymatic activity and for maintaining the conformation of many transcription factors; thus, zinc homeostasis is tightly regulated. Although zinc affects several signaling molecules and may act as a neurotransmitter, it remains unknown whether zinc acts as an intracellular second messenger capable of transducing extracellular stimuli into intracellular signaling events. In this study, we report that the cross-linking of the high affinity immunoglobin E receptor (Fcɛ receptor I [FcɛRI]) induced a release of free zinc from the perinuclear area, including the endoplasmic reticulum in mast cells, a phenomenon we call the zinc wave. The zinc wave was dependent on calcium influx and mitogen-activated protein kinase/extracellular signal-regulated kinase kinase activation. The results suggest that the zinc wave is involved in intracellular signaling events, at least in part by modulating the duration and strength of FcɛRI-mediated signaling. Collectively, our findings indicate that zinc is a novel intracellular second messenger.
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Affiliation(s)
- Satoru Yamasaki
- Laboratory for Cytokine Signaling, RIKEN Research Center for Allergy and Immunology, Yokohama, Kanagawa, Japan
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17
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Sakata-Sogawa K, Tokunaga M. [Molecular imaging and analysis of microclusters responsible for initiating T cell receptor signaling]. Nihon Rinsho 2007; 65:242-6. [PMID: 17302267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
T cell receptors (TCR) are activated by a specific antigen and interact with other signaling molecules, such as kinases and adaptors. Aiming at analyzing precisely the dynamic process of T cell signaling, we used a combined system of a planar bilayer and TIRF microscopy. This system allowed us to observe the T cell activation process from the initial cell-bilayer contact (time 0). Our observation revealed that microclusters with TCR were generated at the initial contact to gather into central supramolecular cluster, the immunological synapse, which was believed to be responsible for T cell receptor signaling. Furthermore the microclusters were generated continuously at the periphery even at the sustained state and they migrated toward the central cluster. These results suggested the important role of microclusters in T cell activation.
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18
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Miletic AV, Sakata-Sogawa K, Hiroshima M, Hamann MJ, Gomez TS, Ota N, Kloeppel T, Kanagawa O, Tokunaga M, Billadeau DD, Swat W. Vav1 acidic region tyrosine 174 is required for the formation of T cell receptor-induced microclusters and is essential in T cell development and activation. J Biol Chem 2006; 281:38257-65. [PMID: 17050525 PMCID: PMC1876972 DOI: 10.1074/jbc.m608913200] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Vav proteins are multidomain signaling molecules critical for mediating signals downstream of several surface receptors, including the antigen receptors of T and B lymphocytes. The catalytic guanine nucleotide exchange factor (GEF) activity of the Vav Dbl homology (DH) domain is thought to be controlled by an intramolecular autoinhibitory mechanism involving an N-terminal extension and phosphorylation of tyrosine residues in the acidic region (AC). Here, we report that the sequences surrounding the Vav1 AC: Tyr(142), Tyr(160), and Tyr(174) are evolutionarily conserved, conform to consensus SH2 domain binding motifs, and bind several proteins implicated in TCR signaling, including Lck, PI3K p85alpha, and PLCgamma1, through direct interactions with their SH2 domains. In addition, the AC tyrosines regulate tyrosine phosphorylation of Vav1. We also show that Tyr(174) is required for the maintenance of TCR-signaling microclusters and for normal T cell development and activation. In this regard, our data demonstrate that while Vav1 Tyr(174) is essential for maintaining the inhibitory constraint of the DH domain in both developing and mature T cells, constitutively activated Vav GEF disrupts TCR-signaling microclusters and leads to defective T cell development and proliferation.
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Affiliation(s)
- Ana V. Miletic
- From the Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri 63110, the
| | - Kumiko Sakata-Sogawa
- Research Unit for Single Molecule Immunoimaging, RIKEN Center for Allergy and Immunology, Yokohama, Kanagawa 230-0045, Japan, the
| | - Michio Hiroshima
- Research Unit for Single Molecule Immunoimaging, RIKEN Center for Allergy and Immunology, Yokohama, Kanagawa 230-0045, Japan, the
| | - Michael J. Hamann
- Department of Immunology and Division of Oncology Research, Mayo Clinic College of Medicine, Rochester, Minnesota 55905, the
| | - Timothy S. Gomez
- Department of Immunology and Division of Oncology Research, Mayo Clinic College of Medicine, Rochester, Minnesota 55905, the
| | - Naruhisa Ota
- Laboratory for Autoimmune Regulation, RIKEN Center for Allergy and Immunology, Yokohama, Kanagawa 230-0045, Japan, and the
| | - Tracie Kloeppel
- From the Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri 63110, the
| | - Osami Kanagawa
- Laboratory for Autoimmune Regulation, RIKEN Center for Allergy and Immunology, Yokohama, Kanagawa 230-0045, Japan, and the
| | - Makio Tokunaga
- Research Unit for Single Molecule Immunoimaging, RIKEN Center for Allergy and Immunology, Yokohama, Kanagawa 230-0045, Japan, the
- Structural Biology Center, National Institute of Genetics, and Department of Genetics, Graduate University for Advanced Studies, Mishima, Shizuoka 411-8540, Japan
| | - Daniel D. Billadeau
- Department of Immunology and Division of Oncology Research, Mayo Clinic College of Medicine, Rochester, Minnesota 55905, the
| | - Wojciech Swat
- From the Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri 63110, the
- To whom correspondence should be addressed: Dept. of Pathology and Immunology, WA University School of Medicine, 660 S. Euclid Ave., St. Louis, MO 63110. Tel.: 314-747-8886; Fax: 314-362-4096; E-mail:
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19
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Yamasaki S, Ishikawa E, Sakuma M, Ogata K, Sakata-Sogawa K, Hiroshima M, Wiest DL, Tokunaga M, Saito T. Mechanistic basis of pre–T cell receptor–mediated autonomous signaling critical for thymocyte development. Nat Immunol 2005; 7:67-75. [PMID: 16327787 DOI: 10.1038/ni1290] [Citation(s) in RCA: 118] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2005] [Accepted: 10/13/2005] [Indexed: 01/08/2023]
Abstract
The pre-T cell receptor (TCR) is crucial for early T cell development and is proposed to function in a ligand-independent way. However, the molecular mechanism underlying the autonomous signals remains elusive. Here we show that the pre-TCR complex spontaneously formed oligomers. Specific charged residues in the extracellular domain of the pre-TCR alpha-chain mediated formation of the oligomers in vitro. Alteration of these residues eliminated the ability of the pre-TCR alpha-chain to support pre-TCR signaling in vivo. Dimerization but not raft localization of CD3epsilon was sufficient to simulate pre-TCR function and promote beta-selection. These results suggest that the pre-TCR complex can deliver its signal autonomously through oligomerization of the pre-TCR alpha-chain mediated by charged residues.
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MESH Headings
- Amino Acid Sequence
- Animals
- Cell Differentiation/immunology
- Hematopoietic Stem Cells/cytology
- Humans
- Membrane Glycoproteins/chemistry
- Membrane Glycoproteins/genetics
- Membrane Glycoproteins/metabolism
- Microscopy, Confocal
- Molecular Sequence Data
- Receptors, Antigen, T-Cell, alpha-beta/chemistry
- Receptors, Antigen, T-Cell, alpha-beta/genetics
- Receptors, Antigen, T-Cell, alpha-beta/metabolism
- Signal Transduction/immunology
- T-Lymphocytes/cytology
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Affiliation(s)
- Sho Yamasaki
- Laboratory for Cell Signaling, RIKEN Research Center for Allergy and Immunology, Yokohama, Kanagawa 230-0045, Japan
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20
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Yokosuka T, Sakata-Sogawa K, Kobayashi W, Hiroshima M, Hashimoto-Tane A, Tokunaga M, Dustin ML, Saito T. Newly generated T cell receptor microclusters initiate and sustain T cell activation by recruitment of Zap70 and SLP-76. Nat Immunol 2005; 6:1253-62. [PMID: 16273097 DOI: 10.1038/ni1272] [Citation(s) in RCA: 541] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2005] [Accepted: 10/06/2005] [Indexed: 11/09/2022]
Abstract
T cell receptor (TCR) activation and signaling precede immunological synapse formation and are sustained for hours after initiation. However, the precise physical sites of the initial and sustained TCR signaling are not definitively known. We report here that T cell activation was initiated and sustained in TCR-containing microclusters generated at the initial contact sites and the periphery of the mature immunological synapse. Microclusters containing TCRs, the tyrosine kinase Zap70 and the adaptor molecule SLP-76 were continuously generated at the periphery. TCR microclusters migrated toward the central supramolecular cluster, whereas Zap70 and SLP-76 dissociated from these microclusters before the microclusters coalesced with the TCR-rich central supramolecular cluster. Tyrosine phosphorylation and calcium influx were induced as microclusters formed at the initial contact sites. Inhibition of signaling prevented recruitment of Zap70 into the microclusters. These results indicated that TCR-rich microclusters initiate and sustain TCR signaling.
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Affiliation(s)
- Tadashi Yokosuka
- Laboratory for Cell Signaling, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
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21
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Abstract
Many proteins select special DNA sequences to form functional complexes. In one possible mechanism, protein molecules would scan DNA sequences by tracking a groove without complete dissociation. Upon dragging single molecules of DNA over a surface carrying fixed Escherichia coli RNA polymerase holoenzyme, we detected rotation of individual DNA molecules, providing direct evidence that a DNA-binding protein can track a DNA groove. These results confirm our previous observations of longitudinal movement of RNA polymerase along fixed, extended DNA and, moreover, imply that groove tracking facilitates scanning of DNA sequences.
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22
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Muramatsu H, Homma K, Yamamoto N, Wang J, Sakata-Sogawa K, Shimamoto N. Imaging of DNA molecules by scanning near-field microscope. Materials Science and Engineering: C 2000. [DOI: 10.1016/s0928-4931(00)00153-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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23
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Bennink ML, Schärer OD, Kanaar R, Sakata-Sogawa K, Schins JM, Kanger JS, de Grooth BG, Greve J. Single-molecule manipulation of double-stranded DNA using optical tweezers: interaction studies of DNA with RecA and YOYO-1. Cytometry 1999; 36:200-8. [PMID: 10404969 DOI: 10.1002/(sici)1097-0320(19990701)36:3<200::aid-cyto9>3.0.co;2-t] [Citation(s) in RCA: 128] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
By using optical tweezers and a specially designed flow cell with an integrated glass micropipette, we constructed a setup similar to that of Smith et al. (Science 271:795-799, 1996) in which an individual double-stranded DNA (dsDNA) molecule can be captured between two polystyrene beads. The first bead is immobilized by the optical tweezers and the second by the micropipette. Movement of the micropipette allows manipulation and stretching of the DNA molecule, and the force exerted on it can be monitored simultaneously with the optical tweezers. We used this setup to study elongation of dsDNA by RecA protein and YOYO-1 dye molecules. We found that the stability of the different DNA-ligand complexes and their binding kinetics were quite different. The length of the DNA molecule was extended by 45% when RecA protein was added. Interestingly, the speed of elongation was dependent on the external force applied to the DNA molecule. In experiments in which YOYO-1 was added, a 10-20% extension of the DNA molecule length was observed. Moreover, these experiments showed that a change in the applied external force results in a time-dependent structural change of the DNA-YOYO-1 complex, with a time constant of approximately 35 s (1/e2). Because the setup provides an oriented DNA molecule, we determined the orientation of the transition dipole moment of YOYO-1 within DNA by using fluorescence polarization. The angle of the transition dipole moment with respect to the helical axis of the DNA molecule was 69 degrees +/- 3.
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Affiliation(s)
- M L Bennink
- Department of Applied Physics, University of Twente, Enschede, The Netherlands
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24
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Sakata-Sogawa K, Kurachi M, Sogawa K, Fujii-Kuriyama Y, Tashiro H. Direct measurement of DNA molecular length in solution using optical tweezers: detection of looping due to binding protein interactions. Eur Biophys J 1998; 27:55-61. [PMID: 9463890 DOI: 10.1007/s002490050110] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
DNA looping is caused by the interaction between DNA binding proteins located at separate positions on a DNA molecule and may play an important role in transcription regulation. We have developed a system to stretch single DNA molecules and to measure changes in molecular length. DNA molecules were prepared and 5' end-labeled by PCR amplification. Two beads and the intervening DNA molecule were trapped and manipulated independently with dual trap optical tweezers. The trapped DNA molecule was then stretched and the extension (the distance between the two beads) was measured. The extension at the specific tension force of 30 pN was calculated and used as a molecular length. The molecular length was found to be proportional to the base pair number. The rise per residue was calculated to be 3.31 +/- 0.05 A. The length measurement was applied to DNA fragments containing GC box sequences at two different locations separated by a distance of 2.428 kbp. The addition of GC box binding transcription factor Sp1 shortened the molecular length, suggesting DNA looping forms as a result of interaction between transcription factors.
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Affiliation(s)
- K Sakata-Sogawa
- Laboratory for Photo-Biology, Photodynamics Research Center, Institute of Physical and Chemical Research (RIKEN), Sendai, Japan.
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25
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Tsuji K, Tanaka K, Sakata-Sogawa K, Soe G, Kakuno T, Yamashita J, Horio T. Architectonic natures of proteins bound to Rhodospirillum rubrum chromatophores as detected by trypsin treatment and sonication. J Biochem 1983; 93:699-707. [PMID: 6409893 DOI: 10.1093/jb/93.3.699] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
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26
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Nishi N, Sakata-Sogawa K, Soe G, Yamashita J. Light-induced pH changes and changes in absorbance of pH indicators in Rhodospirillum rubrum chromatophores. J Biochem 1977; 82:1267-79. [PMID: 22540 DOI: 10.1093/oxfordjournals.jbchem.a131814] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
1. The light-induced pH change of chromatophore suspensions from Rhodospirillum rubrum was stimulated significantly and similarly by KCl, NaCl, LiCl, RbCl, CsCl, MgCl2, MnCl2, and CaCl2. In the dark, the pH of chromatophore suspensions decreased immediately and markedly on adding these salts. 2. The light-induced pH change stimulated by KCl plus valinomycin was inhibited by LiCl and NaCl, but not by RbCl. 3. The optimum pH values for light-induced pH change and photosynthetic ATP formation were around 5 and 8, respectively. The amount of chromatophore-bound ubiquinone-10 reduced in the light was independent of pH from 5 to 9. At pH 8, the number of protons incorporated into chromatophores in the light was one-half of the number of ubiquinone-10 molecules reduced in the light. 4. Among several pH indicators tested, bromothymol blue (BTB) and neutral red (NR) showed absorbance changes on illumination of chromatophores. Although the pH change indicated by the absorbance change was opposite to the light-induced pH change of the medium, the effect of KCl on the absorbance changes of BTB and NR, and the effect of valinomycin on that of NR, but not on that of BTB, were similar to those on the light-induced pH change. 5. The light-induced absorbance change of BTB was significantly inhibited by NR, whereas that of NR was hardly influenced by BTB. 6. Oligomycin stimulated the light-induced absorbance change of BTB under either non-phosphorylating or phosphorylating conditions. On the other hand, that of NR under phosphorylating conditions was 50% of that under non-phosphorylating conditions, and was increased by oligomycin.
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