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Sato H, Murakami T, Matsuura R, Abe M, Matsuoka S, Yashiroda Y, Yoshida M, Akari H, Nagasawa Y, Takei M, Aida Y. A Novel Class of HIV-1 Inhibitors Targeting the Vpr-Induced G2-Arrest in Macrophages by New Yeast- and Cell-Based High-Throughput Screening. Viruses 2022; 14:v14061321. [PMID: 35746791 PMCID: PMC9227106 DOI: 10.3390/v14061321] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 06/13/2022] [Accepted: 06/14/2022] [Indexed: 02/04/2023] Open
Abstract
The human immunodeficiency virus type 1 (HIV-1) accessory protein, Vpr, arrests the cell cycle of the G2 phase, and this Vpr-mediated G2 arrest is implicated in an efficient HIV-1 spread in monocyte-derived macrophages. Here, we screened new candidates for Vpr-targeting HIV-1 inhibitors by using fission yeast- and mammalian cell-based high-throughput screening. First, fission yeast strains expressing the HIV-1 Vpr protein were generated and then treated for 48 h with 20 μM of a synthetic library, including 140,000 chemical compounds. We identified 268 compounds that recovered the growth of Vpr-overexpressing yeast. The selected compounds were then tested in mammalian cells, and those displaying high cytotoxicity were excluded from further cell cycle analysis and imaging-based screening. A flow cytometry analysis confirmed that seven compounds recovered from the Vpr-induced G2 arrest. The cell toxicity and inhibitory effect of HIV-1 replication in human monocyte-derived macrophages (MDM) were examined, and three independent structural compounds, VTD227, VTD232, and VTD263, were able to inhibit HIV-1 replication in MDM. Furthermore, we showed that VTD227, but not VTD232 and VTD263, can directly bind to Vpr. Our results indicate that three new compounds and their derivatives represent new drugs targeting HIV-1 replication and can be potentially used in clinics to improve the current antiretroviral therapy.
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Affiliation(s)
- Hirotaka Sato
- Viral Infectious Diseases Unit, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; (H.S.); (T.M.); (R.M.)
- Division of Hematology and Rheumatology, Department of Medicine, Nihon University School of Medicine, 30-1 Oyaguchi-kamichou, Itabashi-ku, Tokyo 173-8610, Japan; (Y.N.); (M.T.)
- Department of Microbiology, Dokkyo Medical University School of Medicine, 880 Kitakobayashi, Mibu, Shimotsuga, Tochigi 321-0293, Japan
| | - Tomoyuki Murakami
- Viral Infectious Diseases Unit, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; (H.S.); (T.M.); (R.M.)
- Division of Hematology and Rheumatology, Department of Medicine, Nihon University School of Medicine, 30-1 Oyaguchi-kamichou, Itabashi-ku, Tokyo 173-8610, Japan; (Y.N.); (M.T.)
| | - Ryosuke Matsuura
- Viral Infectious Diseases Unit, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; (H.S.); (T.M.); (R.M.)
- Division of Hematology and Rheumatology, Department of Medicine, Nihon University School of Medicine, 30-1 Oyaguchi-kamichou, Itabashi-ku, Tokyo 173-8610, Japan; (Y.N.); (M.T.)
- Laboratory of Global Infectious Diseases Control Science, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Masako Abe
- Drug Discovery Seed Compounds Exploratory Unit, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; (M.A.); (S.M.); (M.Y.)
| | - Seiji Matsuoka
- Drug Discovery Seed Compounds Exploratory Unit, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; (M.A.); (S.M.); (M.Y.)
| | - Yoko Yashiroda
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan;
| | - Minoru Yoshida
- Drug Discovery Seed Compounds Exploratory Unit, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; (M.A.); (S.M.); (M.Y.)
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan;
| | - Hirofumi Akari
- Center for the Evolutionary Origins of Human Behavior, Kyoto University, 41-2 Kanrin, Inuyama, Aichi 484-8506, Japan;
| | - Yosuke Nagasawa
- Division of Hematology and Rheumatology, Department of Medicine, Nihon University School of Medicine, 30-1 Oyaguchi-kamichou, Itabashi-ku, Tokyo 173-8610, Japan; (Y.N.); (M.T.)
| | - Masami Takei
- Division of Hematology and Rheumatology, Department of Medicine, Nihon University School of Medicine, 30-1 Oyaguchi-kamichou, Itabashi-ku, Tokyo 173-8610, Japan; (Y.N.); (M.T.)
| | - Yoko Aida
- Viral Infectious Diseases Unit, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; (H.S.); (T.M.); (R.M.)
- Division of Hematology and Rheumatology, Department of Medicine, Nihon University School of Medicine, 30-1 Oyaguchi-kamichou, Itabashi-ku, Tokyo 173-8610, Japan; (Y.N.); (M.T.)
- Laboratory of Global Infectious Diseases Control Science, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
- Correspondence:
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Fukuda E, Tanaka H, Yamaguchi K, Takasaka M, Kawamura Y, Okuda H, Isotani A, Ikawa M, Shapiro VS, Tsuchida J, Okada Y, Tsujimura A, Miyagawa Y, Fukuhara S, Kawakami Y, Wada M, Nishimune Y, Goshima N. Identification and characterization of the antigen recognized by the germ cell mAb TRA98 using a human comprehensive wet protein array. Genes Cells 2021; 26:180-189. [PMID: 33527666 DOI: 10.1111/gtc.12832] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 01/20/2021] [Accepted: 01/20/2021] [Indexed: 11/28/2022]
Abstract
TRA98 is a rat monoclonal antibody (mAb) which recognizes a specific antigen in the nuclei of germ cells. mAb TRA98 has been used to understand the mechanism of germ cell development and differentiation in many studies. In mice, the antigen recognized by mAb TRA98 or GCNA1 has been reported to be a GCNA gene product, but despite the demonstration of the immunoreactivity of this mAb in human testis and sperm in 1997, the antigen in humans remains unknown, as of date. To identify the human antigen recognized by mAb TRA98, a human comprehensive wet protein array was developed containing 19,446 proteins derived from human cDNAs. Using this array, it was found that the antigen of mAb TRA98 is not a GCNA gene product, but nuclear factor-κB activating protein (NKAP). In mice, mAb TRA98 recognized both the GCNA gene product and NKAP. Furthermore, conditional knockout of Nkap in mice revealed a phenotype of Sertoli cell-only syndrome. Although NKAP is a ubiquitously expressed protein, NKAP recognized by mAb TRA98 in mouse testis was SUMOylated. These results suggest that NKAP undergoes modifications, such as SUMOylation in the testis, and plays an important role in spermatogenesis.
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Affiliation(s)
- Eriko Fukuda
- The National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
| | - Hiromitsu Tanaka
- Molecular Biology Division, Faculty of Pharmaceutical Sciences, Nagasaki International University, Nagasaki, Japan
| | - Kei Yamaguchi
- The National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
| | - Mieko Takasaka
- Japan Biological Informatics Consortium (JBIC), Tokyo, Japan
| | | | - Hidenobu Okuda
- Department of Urology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Ayako Isotani
- Department of Experimental Genome Research, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Masahito Ikawa
- Department of Experimental Genome Research, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | | | - Junji Tsuchida
- Department of Science for Laboratory Animal Experimentation, Research Institute for Microbial Disease, Osaka University, Osaka, Japan
| | - Yuki Okada
- Laboratory of Pathology and Development, Institute of Molecular and Cellular Biosciences, University of Tokyo, Tokyo, Japan
| | - Akira Tsujimura
- Department of Urology, Juntendo University Urayasu Hospital, Urayasu, Chiba, Japan
| | - Yasushi Miyagawa
- Department of Urology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Shinichiro Fukuhara
- Department of Urology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Yoshitaka Kawakami
- The National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
| | - Morimasa Wada
- Molecular Biology Division, Faculty of Pharmaceutical Sciences, Nagasaki International University, Nagasaki, Japan
| | - Yoshitake Nishimune
- Department of Science for Laboratory Animal Experimentation, Research Institute for Microbial Disease, Osaka University, Osaka, Japan
| | - Naoki Goshima
- The National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan.,Department of Human Sciences, Faculty of Human Sciences, Musasino University, Tokyo, Japan
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3
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UHRF1-KAT7-mediated regulation of TUSC3 expression via histone methylation/acetylation is critical for the proliferation of colon cancer cells. Oncogene 2019; 39:1018-1030. [PMID: 31582837 DOI: 10.1038/s41388-019-1032-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 09/13/2019] [Accepted: 09/18/2019] [Indexed: 01/24/2023]
Abstract
The epigenetic factor UHRF1 regulates transcription by modulating DNA methylation and histone modification, and plays critical roles in proliferation, development, and tumorigenesis. Here, we show that Wnt/c-Myc signaling upregulates UHRF1, which in turn downregulates TUSC3, a candidate tumor suppressor gene that is frequently deleted or downregulated in several cancers. We also show that UHRF1-mediated downregulation of TUSC3 is required for the proliferation of colon cancer cells. Furthermore, we demonstrate that UHRF1 suppresses TUSC3 expression by interacting with methylated H3K14 and thereby suppressing the acetylation of H3K14 by the histone acetyltransferase KAT7. Our study provides evidence for the significance of UHRF1-KAT7-mediated regulation of histone methylation/acetylation in the proliferation of tumor cells and in a diverse set of biological processes controlled by Wnt/c-Myc signaling.
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Nagai T, Mukoyama S, Kagiwada H, Goshima N, Mizuno K. Cullin-3-KCTD10-mediated CEP97 degradation promotes primary cilium formation. J Cell Sci 2018; 131:jcs.219527. [PMID: 30404837 DOI: 10.1242/jcs.219527] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 10/19/2018] [Indexed: 12/20/2022] Open
Abstract
Primary cilia are antenna-like sensory organelles that transmit various extracellular signals. Ciliogenesis requires the removal of CP110 and its interactor CEP97 from the mother centriole for initiating ciliary axoneme extension, but the underlying mechanism remains unknown. Here we show that, upon serum starvation, CEP97 is partially degraded by the ubiquitin-proteasome system. CEP97 was polyubiquitylated in serum-starved cells, and overexpression of a non-ubiquitylatable CEP97 mutant effectively blocked CP110 removal and ciliogenesis induced by serum-starvation. Through several screening steps, we identified the cullin-3-RBX1-KCTD10 complex as the E3 ligase that mediates CEP97 degradation and removal from the mother centriole. Depletion of each component of this E3 complex caused aberrant accumulation of CEP97 on the centrosome, suppressed the removal of CEP97 and CP110 from the mother centriole, and impaired ciliogenesis. Moreover, KCTD10 was specifically localized to the mother centriole. These results suggest that CEP97 degradation by the cullin-3-RBX1-KCTD10 complex plays a crucial role in serum-starvation-induced CP110 removal and ciliogenesis.
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Affiliation(s)
- Tomoaki Nagai
- Department of Molecular and Chemical Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi 980-8578, Japan
| | - Sachiho Mukoyama
- Department of Molecular and Chemical Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi 980-8578, Japan
| | - Harumi Kagiwada
- Functional Proteomics Team, Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Tokyo 135-0064, Japan
| | - Naoki Goshima
- Functional Proteomics Team, Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Tokyo 135-0064, Japan
| | - Kensaku Mizuno
- Department of Molecular and Chemical Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi 980-8578, Japan
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5
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Kitazawa M, Hatta T, Ogawa K, Fukuda E, Goshima N, Natsume T. Determination of Rate-Limiting Factor for Formation of Beta-Catenin Destruction Complexes Using Absolute Protein Quantification. J Proteome Res 2017; 16:3576-3584. [PMID: 28810742 DOI: 10.1021/acs.jproteome.7b00305] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Wnt/β-catenin signaling plays important roles in both ontogenesis and development. In the absence of a Wnt stimulus, β-catenin is degraded by a multiprotein "destruction complex" that includes Axin, APC, GSK3B, and FBXW11. Although the key molecules required for transducing Wnt signals have been identified, a quantitative understanding of this pathway has been lacking. Here, we calculated the absolute number of β-catenin destruction complexes by absolute protein quantification using LC-MS/MS. Similar amounts of destruction complex-constituting proteins and β-catenin interacted, and the number of destruction complexes was calculated to be about 1468 molecules/cell. We demonstrated that the calculated number of destruction complexes was valid for control of the β-catenin destruction rate under steady-state conditions. Interestingly, APC had the minimum expression level among the destruction complex components at about 2233 molecules/cell, and this number approximately corresponded to the calculated number of destruction complexes. Decreased APC expression by siRNA transfection decreased the number of destruction complexes, resulting in β-catenin accumulation and stimulation of the transcriptional activity of T-cell factor. Taken together, our results suggest that the amount of APC expression is the rate-limiting factor for the constitution of β-catenin destruction complexes.
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Affiliation(s)
- Masashi Kitazawa
- Molecular Profiling Reserch Center for Drug Discovery (molprof), National Institute of Advanced Industrial Science and Technology (AIST) , 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Tomohisa Hatta
- Molecular Profiling Reserch Center for Drug Discovery (molprof), National Institute of Advanced Industrial Science and Technology (AIST) , 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Koji Ogawa
- Molecular Profiling Reserch Center for Drug Discovery (molprof), National Institute of Advanced Industrial Science and Technology (AIST) , 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Eriko Fukuda
- Molecular Profiling Reserch Center for Drug Discovery (molprof), National Institute of Advanced Industrial Science and Technology (AIST) , 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Naoki Goshima
- Molecular Profiling Reserch Center for Drug Discovery (molprof), National Institute of Advanced Industrial Science and Technology (AIST) , 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Tohru Natsume
- Molecular Profiling Reserch Center for Drug Discovery (molprof), National Institute of Advanced Industrial Science and Technology (AIST) , 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
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6
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A large-scale targeted proteomics assay resource based on an in vitro human proteome. Nat Methods 2016; 14:251-258. [PMID: 28267743 DOI: 10.1038/nmeth.4116] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 11/07/2016] [Indexed: 01/15/2023]
Abstract
Targeted proteomics approaches are of value for deep and accurate quantification of protein abundance. Extending such methods to quantify large numbers of proteins requires the construction of predefined targeted assays. We developed a targeted proteomics platform-in vitro proteome-assisted multiple reaction monitoring (MRM) for protein absolute quantification (iMPAQT)-by using >18,000 human recombinant proteins, thus enabling protein absolute quantification on a genome-wide scale. Our platform comprises experimentally confirmed MRM assays of mass tag (mTRAQ)-labeled peptides to allow for rapid and straightforward measurement of the absolute abundance of predefined sets of proteins by mass spectrometry. We applied iMPAQT to delineate the quantitative metabolic landscape of normal and transformed human fibroblasts. Oncogenic transformation gave rise to relatively small but global changes in metabolic pathways resulting in aerobic glycolysis (Warburg effect) and increased rates of macromolecule synthesis. iMPAQT should facilitate quantitative biology studies based on protein abundance measurements.
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7
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Yamakawa T, Sato Y, Matsumura Y, Kobayashi Y, Kawamura Y, Goshima N, Yamanaka S, Okita K. Screening of Human cDNA Library Reveals Two differentiation-Related Genes, HHEX and HLX, as Promoters of Early Phase Reprogramming toward Pluripotency. Stem Cells 2016; 34:2661-2669. [PMID: 27335261 DOI: 10.1002/stem.2436] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 05/09/2016] [Accepted: 05/30/2016] [Indexed: 11/09/2022]
Abstract
Gene screenings have identified a number of reprogramming factors that induce pluripotency from somatic cells. However, the screening methods have mostly considered only factors that maintain pluripotency in embryonic stem cells, ignoring a potentially long list of other contributing factors involved. To expand the search, we developed a new screening method that examined 2,008 human genes in the generation of human induced pluripotent stem cells (iPSCs), including not only pluripotent genes but also differentiation-related genes that suppress pluripotency. We found the top 100 genes that increased reprogramming efficiency and discovered they contained many differentiation-related genes and homeobox genes. We selected two, HHEX and HLX, for further analysis. These genes enhanced the appearance of premature reprograming cells in the early phase of human iPSC induction, but had inhibitory effect on the late phase. In addition, when expressed in human iPSCs, HHEX and HLX interfered with the pluripotent state, indicating inverse effects on somatic reprograming and pluripotent maintenance. These results demonstrate that our screening is useful for identifying differentiation-related genes in somatic reprograming. Stem Cells 2016;34:2661-2669.
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Affiliation(s)
- Tatsuya Yamakawa
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | - Yoshiko Sato
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | - Yasuko Matsumura
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | - Yukiko Kobayashi
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | | | - Naoki Goshima
- Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
| | - Shinya Yamanaka
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan.,Gladstone Institute of Cardiovascular Disease, San Francisco, California, USA
| | - Keisuke Okita
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
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Kawakami T, Ogawa K, Hatta T, Goshima N, Natsume T. Directed Evolution of a Cyclized Peptoid-Peptide Chimera against a Cell-Free Expressed Protein and Proteomic Profiling of the Interacting Proteins to Create a Protein-Protein Interaction Inhibitor. ACS Chem Biol 2016; 11:1569-77. [PMID: 27010125 DOI: 10.1021/acschembio.5b01014] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
N-alkyl amino acids are useful building blocks for the in vitro display evolution of ribosomally synthesized peptides because they can increase the proteolytic stability and cell permeability of these peptides. However, the translation initiation substrate specificity of nonproteinogenic N-alkyl amino acids has not been investigated. In this study, we screened various N-alkyl amino acids and nonamino carboxylic acids for translation initiation with an Escherichia coli reconstituted cell-free translation system (PURE system) and identified those that efficiently initiated translation. Using seven of these efficiently initiating acids, we next performed in vitro display evolution of cyclized peptidomimetics against an arbitrarily chosen model human protein (β-catenin) cell-free expressed from its cloned cDNA (HUPEX) and identified a novel β-catenin-binding cyclized peptoid-peptide chimera. Furthermore, by a proteomic approach using direct nanoflow liquid chromatography-tandem mass spectrometry (DNLC-MS/MS), we successfully identified which protein-β-catenin interaction is inhibited by the chimera. The combination of in vitro display evolution of cyclized N-alkyl peptidomimetics and in vitro expression of human proteins would be a powerful approach for the high-speed discovery of diverse human protein-targeted cyclized N-alkyl peptidomimetics.
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Affiliation(s)
- Takashi Kawakami
- Molecular Profiling Research
Center for Drug Discovery (molprof), National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Koji Ogawa
- Molecular Profiling Research
Center for Drug Discovery (molprof), National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Tomohisa Hatta
- Molecular Profiling Research
Center for Drug Discovery (molprof), National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Naoki Goshima
- Molecular Profiling Research
Center for Drug Discovery (molprof), National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Tohru Natsume
- Molecular Profiling Research
Center for Drug Discovery (molprof), National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
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9
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Hirose T, Goshima N. Genome-wide co-localization screening of nuclear body components using a fluorescently tagged FLJ cDNA clone library. Methods Mol Biol 2015; 1262:155-63. [PMID: 25555580 DOI: 10.1007/978-1-4939-2253-6_9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Mammalian cell nuclei contain multiple granular structures, which are termed nuclear bodies. These structures are involved in various molecular events in the nucleus; they provide platforms for biogenesis of macromolecular complexes that are essential for gene expression, such as the ribosome and spliceosome; they act as reservoirs of various regulatory factors; and they are involved in the regulation of specific gene loci. Nuclear bodies are usually visualized by immunostaining for specific marker proteins. Although each type of nuclear body contains a distinct set of proteins, the protein components of most types of nuclear bodies remain to be identified. This chapter introduces a new approach to identify the protein components of specific types of nuclear bodies.
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Affiliation(s)
- Tetsuro Hirose
- Institute for Genetic Medicine, Hokkaido University, Kita-15, Nishi-7, Kita-Ku, Sapporo, 060-0815, Japan,
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10
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Kasahara K, Kawakami Y, Kiyono T, Yonemura S, Kawamura Y, Era S, Matsuzaki F, Goshima N, Inagaki M. Ubiquitin-proteasome system controls ciliogenesis at the initial step of axoneme extension. Nat Commun 2014; 5:5081. [PMID: 25270598 PMCID: PMC4205846 DOI: 10.1038/ncomms6081] [Citation(s) in RCA: 106] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Accepted: 08/27/2014] [Indexed: 01/09/2023] Open
Abstract
Primary cilia are microtubule-based sensory organelles that organize numerous key signals during developments and tissue homeostasis. Ciliary microtubule doublet, named axoneme, is grown directly from the distal end of mother centrioles through a multistep process upon cell cycle exit; however, the instructive signals that initiate these events are poorly understood. Here we show that ubiquitin-proteasome machinery removes trichoplein, a negative regulator of ciliogenesis, from mother centrioles and thereby causes Aurora-A inactivation, leading to ciliogenesis. Ciliogenesis is blocked if centriolar trichoplein is stabilized by treatment with proteasome inhibitors or by expression of non-ubiquitylatable trichoplein mutant (K50/57R). Started from two-stepped global E3 screening, we have identified KCTD17 as a substrate-adaptor for Cul3-RING E3 ligases (CRL3s) that polyubiquitylates trichoplein. Depletion of KCTD17 specifically arrests ciliogenesis at the initial step of axoneme extension through aberrant trichoplein-Aurora-A activity. Thus, CRL3-KCTD17 targets trichoplein to proteolysis to initiate the axoneme extension during ciliogenesis. Biogenesis of the primary cilium begins after cell cycle exit, but the regulatory steps for its formation are poorly defined. Here the authors show that proteasome-mediated removal of the ciliogenesis inhibitor, trichoplein, from mother centrioles initiates the first step of ciliogenesis.
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Affiliation(s)
- Kousuke Kasahara
- 1] Division of Biochemistry, Aichi Cancer Center Research Institute, Nagoya, Aichi 464-8681, Japan [2] Department of Oncology, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Aichi 467-8603, Japan
| | - Yoshitaka Kawakami
- Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Tokyo 135-0064, Japan
| | - Tohru Kiyono
- Virology Division, National Cancer Center Research Institute, Tokyo 104-0045, Japan
| | - Shigenobu Yonemura
- Electron Microscope Laboratory, RIKEN Center for Developmental Biology, Kobe 650-0047, Japan
| | | | - Saho Era
- Division of Biochemistry, Aichi Cancer Center Research Institute, Nagoya, Aichi 464-8681, Japan
| | - Fumio Matsuzaki
- Laboratory of Cell Asymmetry, RIKEN Center of Developmental Biology, Kobe 650-0047, Japan
| | - Naoki Goshima
- Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Tokyo 135-0064, Japan
| | - Masaki Inagaki
- 1] Division of Biochemistry, Aichi Cancer Center Research Institute, Nagoya, Aichi 464-8681, Japan [2] Department of Cellular Oncology, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
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11
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Tokunaga Y, Takeuchi K, Takahashi H, Shimada I. Allosteric enhancement of MAP kinase p38α's activity and substrate selectivity by docking interactions. Nat Struct Mol Biol 2014; 21:704-11. [PMID: 25038803 DOI: 10.1038/nsmb.2861] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Accepted: 06/19/2014] [Indexed: 01/25/2023]
Abstract
Mitogen-activated protein kinases (MAPKs) are essential to intracellular signal transduction. MAPKs anchor their pathway-specific substrates through so-called 'docking interactions' at locations distal from the active site. Docking interactions ensure efficient substrate recognition, but their contribution to the kinase reaction itself remains unclear. Herein, we use solution NMR to analyze the interaction between dually phosphorylated, active human p38α and the C-terminal fragments of its substrate MK2. p38α phosphorylation and ATP loading collaboratively induce the active conformation; subsequently, p38α accommodates MK2 phosphoacceptor residues in its active site. The docking interaction enhances binding of ATP and the phosphoacceptor to p38α, accelerating the phosphotransfer reaction. Thus, the docking interaction enhances p38α's enzymatic activity toward pathway-specific substrates allosterically as well as by the anchor effect. These findings clarify how MAPK cascades are organized in cells, even under ATP-depleted conditions often associated with environmental stress.
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Affiliation(s)
- Yuji Tokunaga
- 1] Research and Development Department, Japan Biological Informatics Consortium, Tokyo, Japan. [2] Graduate School of Pharmaceutical Sciences, University of Tokyo, Tokyo, Japan
| | - Koh Takeuchi
- Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
| | - Hideo Takahashi
- 1] Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan. [2] Graduate School of Medical Life Science, Yokohama City University, Kanagawa, Japan
| | - Ichio Shimada
- 1] Graduate School of Pharmaceutical Sciences, University of Tokyo, Tokyo, Japan. [2] Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
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Hirose S, Noguchi T. ESPRESSO: a system for estimating protein expression and solubility in protein expression systems. Proteomics 2013; 13:1444-56. [PMID: 23436767 DOI: 10.1002/pmic.201200175] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2012] [Revised: 01/27/2013] [Accepted: 02/06/2013] [Indexed: 11/11/2022]
Abstract
Recombinant protein technology is essential for conducting protein science and using proteins as materials in pharmaceutical or industrial applications. Although obtaining soluble proteins is still a major experimental obstacle, knowledge about protein expression/solubility under standard conditions may increase the efficiency and reduce the cost of proteomics studies. In this study, we present a computational approach to estimate the probability of protein expression and solubility for two different protein expression systems: in vivo Escherichia coli and wheat germ cell-free, from only the sequence information. It implements two kinds of methods: a sequence/predicted structural property-based method that uses both the sequence and predicted structural features, and a sequence pattern-based method that utilizes the occurrence frequencies of sequence patterns. In the benchmark test, the proposed methods obtained F-scores of around 70%, and outperformed publicly available servers. Applying the proposed methods to genomic data revealed that proteins associated with translation or transcription have a strong tendency to be expressed as soluble proteins by the in vivo E. coli expression system. The sequence pattern-based method also has the potential to indicate a candidate region for modification, to increase protein solubility. All methods are available for free at the ESPRESSO server (http://mbs.cbrc.jp/ESPRESSO).
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Affiliation(s)
- Shuichi Hirose
- Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan.
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Yamamoto T, Nakayama K, Hirano H, Tomonaga T, Ishihama Y, Yamada T, Kondo T, Kodera Y, Sato Y, Araki N, Mamitsuka H, Goshima N. Integrated view of the human chromosome X-centric proteome project. J Proteome Res 2012; 12:58-61. [PMID: 23259409 DOI: 10.1021/pr300844p] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
This article introduces how the human chromosome X-centric proteome project is carried out by the Japan Chromosome X Project Consortium. The inactivation of one of two chromosomes in female mammals and accumulation of genes related to neural/immune systems/tumor/testis are characteristic of chromosome X. In this Chromosome X Project, information on proteins translated from genes on chromosome X is collected by both mass spectrometry- and antibody-based proteomics. Information on the following resources is also provided: antibodies to proteins translated and full-length cDNAs transcripted from the chromosome X genes for recombinant proteins. The consortium aims to provide the following tools to search useful antibodies in the literature (Antibody Ranker), to find gene expression sites in microarray databases (Transcript Localizer) and to do advanced MRM analysis (information-based MRM).
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Affiliation(s)
- Tadashi Yamamoto
- Institute of Nephrology, Graduate School of Medical and Dental Sciences, Niigata, Japan.
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Takeda JI, Yamasaki C, Murakami K, Nagai Y, Sera M, Hara Y, Obi N, Habara T, Gojobori T, Imanishi T. H-InvDB in 2013: an omics study platform for human functional gene and transcript discovery. Nucleic Acids Res 2012. [PMID: 23197657 PMCID: PMC3531145 DOI: 10.1093/nar/gks1245] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
H-InvDB (http://www.h-invitational.jp/) is a comprehensive human gene database started in 2004. In the latest version, H-InvDB 8.0, a total of 244 709 human complementary DNA was mapped onto the hg19 reference genome and 43 829 gene loci, including nonprotein-coding ones, were identified. Of these loci, 35 631 were identified as potential protein-coding genes, and 22 898 of these were identical to known genes. In our analysis, 19 309 annotated genes were specific to H-InvDB and not found in RefSeq and Ensembl. In fact, 233 genes of the 19 309 turned out to have protein functions in this version of H-InvDB; they were annotated as unknown protein functions in the previous version. Furthermore, 11 genes were identified as known Mendelian disorder genes. It is advantageous that many biologically functional genes are hidden in the H-InvDB unique genes. As large-scale proteomic projects have been conducted to elucidate the functions of all human proteins, we have enhanced the proteomic information with an advanced protein view and new subdatabase of protein complexes (Protein Complex Database with quality index). We propose that H-InvDB is an important resource for finding novel candidate targets for medical care and drug development.
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Affiliation(s)
- Jun-Ichi Takeda
- Integrated Database and Systems Biology Team, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, Aomi 2-4-7, Koto-ku, Tokyo 135-0064, Japan
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Alternative 3'-end processing of long noncoding RNA initiates construction of nuclear paraspeckles. EMBO J 2012; 31:4020-34. [PMID: 22960638 DOI: 10.1038/emboj.2012.251] [Citation(s) in RCA: 304] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2012] [Accepted: 08/14/2012] [Indexed: 11/09/2022] Open
Abstract
Paraspeckles are unique subnuclear structures built around a specific long noncoding RNA, NEAT1, which is comprised of two isoforms produced by alternative 3'-end processing (NEAT1_1 and NEAT1_2). To address the precise molecular processes that lead to paraspeckle formation, we identified 35 paraspeckle proteins (PSPs), mainly by colocalization screening with a fluorescent protein-tagged full-length cDNA library. Most of the newly identified PSPs possessed various putative RNA-binding domains. Subsequent RNAi analyses identified seven essential PSPs for paraspeckle formation. One of the essential PSPs, HNRNPK, appeared to affect the production of the essential NEAT1_2 isoform by negatively regulating the 3'-end polyadenylation of the NEAT1_1 isoform. An in vitro 3'-end processing assay revealed that HNRNPK arrested binding of the CPSF6-NUDT21 (CFIm) complex in the vicinity of the alternative polyadenylation site of NEAT1_1. In vitro binding assays showed that HNRNPK competed with CPSF6 for binding to NUDT21, which was the underlying mechanism to arrest CFIm binding by HNRNPK. This HNRNPK function led to the preferential accumulation of NEAT1_2 and initiated paraspeckle construction with multiple PSPs.
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