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Oka M, Xu L, Suzuki T, Yoshikawa T, Sakamoto H, Uemura H, Yoshizawa AC, Suzuki Y, Nakatsura T, Ishihama Y, Suzuki A, Seki M. Aberrant splicing isoforms detected by full-length transcriptome sequencing as transcripts of potential neoantigens in non-small cell lung cancer. Genome Biol 2021; 22:9. [PMID: 33397462 PMCID: PMC7780684 DOI: 10.1186/s13059-020-02240-8] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 12/14/2020] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Long-read sequencing of full-length cDNAs enables the detection of structures of aberrant splicing isoforms in cancer cells. These isoforms are occasionally translated, presented by HLA molecules, and recognized as neoantigens. This study used a long-read sequencer (MinION) to construct a comprehensive catalog of aberrant splicing isoforms in non-small-cell lung cancers, by which novel isoforms and potential neoantigens are identified. RESULTS Full-length cDNA sequencing is performed using 22 cell lines, and a total of 2021 novel splicing isoforms are identified. The protein expression of some of these isoforms is then validated by proteome analysis. Ablations of a nonsense-mediated mRNA decay (NMD) factor, UPF1, and a splicing factor, SF3B1, are found to increase the proportion of aberrant transcripts. NetMHC evaluation of the binding affinities to each type of HLA molecule reveals that some of the isoforms potentially generate neoantigen candidates. We also identify aberrant splicing isoforms in seven non-small-cell lung cancer specimens. An enzyme-linked immune absorbent spot assay indicates that approximately half the peptide candidates have the potential to activate T cell responses through their interaction with HLA molecules. Finally, we estimate the number of isoforms in The Cancer Genome Atlas (TCGA) datasets by referring to the constructed catalog and found that disruption of NMD factors is significantly correlated with the number of splicing isoforms found in the TCGA-Lung Adenocarcinoma data collection. CONCLUSIONS Our results indicate that long-read sequencing of full-length cDNAs is essential for the precise identification of aberrant transcript structures in cancer cells.
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Affiliation(s)
- Miho Oka
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
- Ono Pharmaceutical Co., Ltd., Ibaraki, Japan
| | - Liu Xu
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Toshihiro Suzuki
- General Medical Education and Research Center, Teikyo University, Tokyo, Japan
- Division of Cancer Immunotherapy, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Chiba, Japan
| | - Toshiaki Yoshikawa
- Division of Cancer Immunotherapy, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Chiba, Japan
| | - Hiromi Sakamoto
- Department of Clinical Genomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Hayato Uemura
- Department of Molecular and Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Akiyasu C. Yoshizawa
- Department of Molecular and Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Tetsuya Nakatsura
- Division of Cancer Immunotherapy, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Chiba, Japan
| | - Yasushi Ishihama
- Department of Molecular and Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Ayako Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Masahide Seki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
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Abstract
In recent years, mass spectrometry-based proteomics approach has made significant progress and the number of datasets related to various proteomics projects has increased worldwide. To promote the sharing and reuse of promising datasets, it is important to build an appropriate, high-quality public data repository. For this purpose, several repositories have already been created. The jPOST repository that we developed in 2016 has successfully implemented several unique features, such as fast file upload, flexible file management, and an easy-to-use interface. In addition, this repository is an official member of the ProteomeXchange Consortium established to facilitate standard data submission and global dissemination of mass spectrometry proteomics data. Our repository contributes to the global partnership for sharing and storing all the datasets related to various proteomics experiments.
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Affiliation(s)
- Yu Watanabe
- Division of bioinformatics, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | | | - Yasushi Ishihama
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Shujiro Okuda
- Division of bioinformatics, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan.
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Moriya Y, Kawano S, Okuda S, Watanabe Y, Matsumoto M, Takami T, Kobayashi D, Yamanouchi Y, Araki N, Yoshizawa AC, Tabata T, Iwasaki M, Sugiyama N, Tanaka S, Goto S, Ishihama Y. The jPOST environment: an integrated proteomics data repository and database. Nucleic Acids Res 2020; 47:D1218-D1224. [PMID: 30295851 PMCID: PMC6324006 DOI: 10.1093/nar/gky899] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [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: 08/13/2018] [Accepted: 09/24/2018] [Indexed: 01/13/2023] Open
Abstract
Rapid progress is being made in mass spectrometry (MS)-based proteomics, yielding an increasing number of larger datasets with higher quality and higher throughput. To integrate proteomics datasets generated from various projects and institutions, we launched a project named jPOST (Japan ProteOme STandard Repository/Database, https://jpostdb.org/) in 2015. Its proteomics data repository, jPOSTrepo, began operations in 2016 and has accepted more than 10 TB of MS-based proteomics datasets in the past two years. In addition, we have developed a new proteomics database named jPOSTdb in which the published raw datasets in jPOSTrepo are reanalyzed using standardized protocol. jPOSTdb provides viewers showing the frequency of detected post-translational modifications, the co-occurrence of phosphorylation sites on a peptide and peptide sharing among proteoforms. jPOSTdb also provides basic statistical analysis tools to compare proteomics datasets.
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Affiliation(s)
- Yuki Moriya
- Database Center for Life Science, Joint Support-Center for Data Science Research, Research Organization of Information and Systems, Kashiwa 277-0871, Japan
| | - Shin Kawano
- Database Center for Life Science, Joint Support-Center for Data Science Research, Research Organization of Information and Systems, Kashiwa 277-0871, Japan
| | - Shujiro Okuda
- Niigata University Graduate School of Medical and Dental Sciences, Niigata 951-8510, Japan
| | - Yu Watanabe
- Niigata University Graduate School of Medical and Dental Sciences, Niigata 951-8510, Japan
| | - Masaki Matsumoto
- Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | - Tomoyo Takami
- Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | - Daiki Kobayashi
- Graduate School of Medical Sciences, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Yoshinori Yamanouchi
- Graduate School of Medical Sciences, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan.,Kumamoto University Hospital, Kumamoto 860-8556, Japan
| | - Norie Araki
- Graduate School of Medical Sciences, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Akiyasu C Yoshizawa
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Tsuyoshi Tabata
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan.,Center for iPS Cell Research and Application, Kyoto University, Kyoto 606-8507, Japan
| | - Mio Iwasaki
- Center for iPS Cell Research and Application, Kyoto University, Kyoto 606-8507, Japan
| | - Naoyuki Sugiyama
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | | | - Susumu Goto
- Database Center for Life Science, Joint Support-Center for Data Science Research, Research Organization of Information and Systems, Kashiwa 277-0871, Japan
| | - Yasushi Ishihama
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
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4
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Vos RA, Katayama T, Mishima H, Kawano S, Kawashima S, Kim JD, Moriya Y, Tokimatsu T, Yamaguchi A, Yamamoto Y, Wu H, Amstutz P, Antezana E, Aoki NP, Arakawa K, Bolleman JT, Bolton E, Bonnal RJP, Bono H, Burger K, Chiba H, Cohen KB, Deutsch EW, Fernández-Breis JT, Fu G, Fujisawa T, Fukushima A, García A, Goto N, Groza T, Hercus C, Hoehndorf R, Itaya K, Juty N, Kawashima T, Kim JH, Kinjo AR, Kotera M, Kozaki K, Kumagai S, Kushida T, Lütteke T, Matsubara M, Miyamoto J, Mohsen A, Mori H, Naito Y, Nakazato T, Nguyen-Xuan J, Nishida K, Nishida N, Nishide H, Ogishima S, Ohta T, Okuda S, Paten B, Perret JL, Prathipati P, Prins P, Queralt-Rosinach N, Shinmachi D, Suzuki S, Tabata T, Takatsuki T, Taylor K, Thompson M, Uchiyama I, Vieira B, Wei CH, Wilkinson M, Yamada I, Yamanaka R, Yoshitake K, Yoshizawa AC, Dumontier M, Kosaki K, Takagi T. BioHackathon 2015: Semantics of data for life sciences and reproducible research. F1000Res 2020; 9:136. [PMID: 32308977 PMCID: PMC7141167 DOI: 10.12688/f1000research.18236.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/05/2020] [Indexed: 01/08/2023] Open
Abstract
We report on the activities of the 2015 edition of the BioHackathon, an annual event that brings together researchers and developers from around the world to develop tools and technologies that promote the reusability of biological data. We discuss issues surrounding the representation, publication, integration, mining and reuse of biological data and metadata across a wide range of biomedical data types of relevance for the life sciences, including chemistry, genotypes and phenotypes, orthology and phylogeny, proteomics, genomics, glycomics, and metabolomics. We describe our progress to address ongoing challenges to the reusability and reproducibility of research results, and identify outstanding issues that continue to impede the progress of bioinformatics research. We share our perspective on the state of the art, continued challenges, and goals for future research and development for the life sciences Semantic Web.
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Affiliation(s)
- Rutger A. Vos
- Institute of Biology Leiden, Leiden University, Leiden, The Netherlands
- Naturalis Biodiversity Center, Leiden, The Netherlands
| | | | - Hiroyuki Mishima
- Department of Human Genetics, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Shin Kawano
- Database Center for Life Science, Tokyo, Japan
| | | | | | - Yuki Moriya
- Database Center for Life Science, Tokyo, Japan
| | | | | | | | - Hongyan Wu
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | | | - Erick Antezana
- Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Nobuyuki P. Aoki
- Faculty of Science and Engineering, SOKA University, Tokyo, Japan
| | - Kazuharu Arakawa
- Institute for Advanced Biosciences, Keio University, Tokyo, Japan
| | - Jerven T. Bolleman
- SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, Lausanne, Switzerland
| | - Evan Bolton
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, USA
| | - Raoul J. P. Bonnal
- Istituto Nazionale Genetica Molecolare, Romeo ed Enrica Invernizzi, Milan, Italy
| | | | - Kees Burger
- Dutch Techcentre for Life Sciences, Utrecht, The Netherlands
| | - Hirokazu Chiba
- National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Japan
| | - Kevin B. Cohen
- Computational Bioscience Program, University of Colorado School of Medicine, Denver, USA
- Université Paris-Saclay, LIMSI, CNRS, Paris, France
| | | | | | - Gang Fu
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, USA
| | | | | | | | - Naohisa Goto
- Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Tudor Groza
- St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Darlinghurst, Australia
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, Australia
| | - Colin Hercus
- Novocraft Technologies Sdn. Bhd., Selangor, Malaysia
| | - Robert Hoehndorf
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Kotone Itaya
- Institute for Advanced Biosciences, Keio University, Tokyo, Japan
| | - Nick Juty
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | | | - Jee-Hyub Kim
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Akira R. Kinjo
- Institute for Protein Research, Osaka University, Osaka, Japan
| | - Masaaki Kotera
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Kouji Kozaki
- The Institute of Scientific and Industrial Research, Osaka University, Osaka, Japan
| | | | - Tatsuya Kushida
- National Bioscience Database Center, Japan Science and Technology Agency, Tokyo, Japan
| | - Thomas Lütteke
- Institute of Veterinary Physiology and Biochemistry, Justus-Liebig University Giessen, Giessen, Germany
- Gesellschaft für innovative Personalwirtschaftssysteme mbH (GIP GmbH), Offenbach, Germany
| | | | | | - Attayeb Mohsen
- National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| | - Hiroshi Mori
- Center for Information Biology, National Institute of Genetics, Mishima, Japan
| | - Yuki Naito
- Database Center for Life Science, Tokyo, Japan
| | | | | | | | - Naoki Nishida
- Department of Systems Science, Osaka University, Osaka, Japan
| | - Hiroyo Nishide
- National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Japan
| | - Soichi Ogishima
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Tazro Ohta
- Database Center for Life Science, Tokyo, Japan
| | - Shujiro Okuda
- Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Benedict Paten
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, USA
| | | | - Philip Prathipati
- National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| | - Pjotr Prins
- University Medical Center Utrecht, Utrecht, The Netherlands
- University of Tennessee Health Science Center, Memphis, USA
| | - Núria Queralt-Rosinach
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Shinya Suzuki
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Tsuyosi Tabata
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | | | - Kieron Taylor
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Mark Thompson
- Leiden University Medical Center, Leiden, The Netherlands
| | - Ikuo Uchiyama
- National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Japan
| | - Bruno Vieira
- WurmLab, School of Biological & Chemical Sciences, Queen Mary University of London, London, UK
| | - Chih-Hsuan Wei
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, USA
| | - Mark Wilkinson
- Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
| | | | | | - Kazutoshi Yoshitake
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | | | - Michel Dumontier
- Institute of Data Science, Maastricht University, Maastricht, The Netherlands
| | - Kenjiro Kosaki
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
| | - Toshihisa Takagi
- National Bioscience Database Center, Japan Science and Technology Agency, Tokyo, Japan
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
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5
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Okuda S, Watanabe Y, Moriya Y, Kawano S, Yamamoto T, Matsumoto M, Takami T, Kobayashi D, Araki N, Yoshizawa AC, Tabata T, Sugiyama N, Goto S, Ishihama Y. jPOSTrepo: an international standard data repository for proteomes. Nucleic Acids Res 2016; 45:D1107-D1111. [PMID: 27899654 PMCID: PMC5210561 DOI: 10.1093/nar/gkw1080] [Citation(s) in RCA: 346] [Impact Index Per Article: 43.3] [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: 08/14/2016] [Revised: 10/21/2016] [Accepted: 10/27/2016] [Indexed: 12/17/2022] Open
Abstract
Major advancements have recently been made in mass spectrometry-based proteomics, yielding an increasing number of datasets from various proteomics projects worldwide. In order to facilitate the sharing and reuse of promising datasets, it is important to construct appropriate, high-quality public data repositories. jPOSTrepo (https://repository.jpostdb.org/) has successfully implemented several unique features, including high-speed file uploading, flexible file management and easy-to-use interfaces. This repository has been launched as a public repository containing various proteomic datasets and is available for researchers worldwide. In addition, our repository has joined the ProteomeXchange consortium, which includes the most popular public repositories such as PRIDE in Europe for MS/MS datasets and PASSEL for SRM datasets in the USA. Later MassIVE was introduced in the USA and accepted into the ProteomeXchange, as was our repository in July 2016, providing important datasets from Asia/Oceania. Accordingly, this repository thus contributes to a global alliance to share and store all datasets from a wide variety of proteomics experiments. Thus, the repository is expected to become a major repository, particularly for data collected in the Asia/Oceania region.
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Affiliation(s)
- Shujiro Okuda
- Niigata University Graduate School of Medical and Dental Sciences, Niigata 951-8510, Japan
| | - Yu Watanabe
- Niigata University Graduate School of Medical and Dental Sciences, Niigata 951-8510, Japan
| | - Yuki Moriya
- Database Center for Life Science, Joint Support-Center for Data Science Research, Research Organization of Information and Systems, Kashiwa 277-0871, Japan
| | - Shin Kawano
- Database Center for Life Science, Joint Support-Center for Data Science Research, Research Organization of Information and Systems, Kashiwa 277-0871, Japan
| | - Tadashi Yamamoto
- Biofluid Biomarker Center, Institute for Social Innovation and Cooperation, Niigata University, Niigata 950-2181, Japan
| | - Masaki Matsumoto
- Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | - Tomoyo Takami
- Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | - Daiki Kobayashi
- Graduate School of Medical Sciences, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Norie Araki
- Graduate School of Medical Sciences, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Akiyasu C Yoshizawa
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Kyoto 611-0011, Japan
| | - Tsuyoshi Tabata
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Naoyuki Sugiyama
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Susumu Goto
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Kyoto 611-0011, Japan
| | - Yasushi Ishihama
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
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Kuyama H, Yoshizawa AC, Nakajima C, Hosako M, Tanaka K. Identification of human basic fetoprotein as glucose-6-phosphate isomerase by using N- and C-terminal sequence tags and terminal tag database. J Pharm Biomed Anal 2015; 112:116-25. [PMID: 25978494 DOI: 10.1016/j.jpba.2015.04.032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [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: 12/22/2014] [Revised: 04/20/2015] [Accepted: 04/21/2015] [Indexed: 10/23/2022]
Abstract
Human basic fetoprotein (BFP), found in fetal serum and tissue extracts as well as in extracts of various cancer tissues, has long been known as a marker protein for cancers; however, the primary sequence has not yet been reported. This paper describes the identification of BFP using the N- and C-terminal amino acid sequence tags (Ac-AALTRDPQFQ and QQREARVQ, respectively) clarified by mass spectrometry-based methods, and a terminal tag database (ProteinCarta). In this study, BFP was identified as glucose-6-phosphate isomerase (G6PI_HUMAN).
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Affiliation(s)
- Hiroki Kuyama
- Koichi Tanaka Laboratory of Advanced Science and Technology, Shimadzu Corporation, 1, Nishinokyo-Kuwabaracho, Nakagyo-ku, Kyoto 604-8511, Japan.
| | - Akiyasu C Yoshizawa
- Koichi Tanaka Laboratory of Advanced Science and Technology, Shimadzu Corporation, 1, Nishinokyo-Kuwabaracho, Nakagyo-ku, Kyoto 604-8511, Japan.
| | - Chihiro Nakajima
- Koichi Tanaka Laboratory of Advanced Science and Technology, Shimadzu Corporation, 1, Nishinokyo-Kuwabaracho, Nakagyo-ku, Kyoto 604-8511, Japan
| | - Mutsumi Hosako
- Koichi Tanaka Laboratory of Advanced Science and Technology, Shimadzu Corporation, 1, Nishinokyo-Kuwabaracho, Nakagyo-ku, Kyoto 604-8511, Japan
| | - Koichi Tanaka
- Koichi Tanaka Laboratory of Advanced Science and Technology, Shimadzu Corporation, 1, Nishinokyo-Kuwabaracho, Nakagyo-ku, Kyoto 604-8511, Japan
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Morimoto K, Nishikaze T, Yoshizawa AC, Kajihara S, Aoshima K, Oda Y, Tanaka K. GlycanAnalysis Plug-in: a database search tool for N-glycan structures using mass spectrometry. Bioinformatics 2015; 31:2217-9. [DOI: 10.1093/bioinformatics/btv110] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Accepted: 02/15/2015] [Indexed: 11/13/2022] Open
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Yoshizawa AC, Fukuyama Y, Kajihara S, Kuyama H, Tanaka K. Computational survey of sequence specificity for protein terminal tags covering nine organisms and its application to protein identification. J Proteome Res 2015; 14:756-67. [PMID: 25393771 DOI: 10.1021/pr500793h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
In 1998, Wilkins et al. (J. Mol. Biol. 1998, 278, 599-608) reported high specificity in terminal regions (terminal tags) of 15 519 proteins from five organisms and proposed a methodology for identifying proteins by terminal tags. However, their examined sequence data were not based on complete genome sequences. Here, we examined current proteome data (217 249 entries from UniProt 2013_6 complete/reference proteome for nine organisms including human) in terms of the specificity of terminal tags and their computational annotation. One example from the results indicated that the specificity of N-terminal tags plateaued at 28% at a length of six residues for human; even when using both N- and C-terminal tags, specificity was merely 66%. In order to determine the cause of these low specificities, the annotation of proteins sharing terminal tags with other proteins was examined. The results suggested that a large majority were phylogenetically or functionally related, whereas nonrelated proteins sharing terminal tags made up less than 1% of human proteome data. On the basis of these findings, we constructed the terminal tag sequence database ProteinCarta (http://ms3d.jp/software/proteincarta/), which includes all terminal tags of proteomes from the nine organisms analyzed here, in order to confirm the specificity of terminal tags and to identify the parent protein.
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Affiliation(s)
- Akiyasu C Yoshizawa
- Koichi Tanaka Laboratory of Advanced Science and Technology, Shimadzu Corporation , Kyoto 604-8511, Japan
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Aoshima K, Takahashi K, Ikawa M, Kimura T, Fukuda M, Tanaka S, Parry HE, Fujita Y, Yoshizawa AC, Utsunomiya SI, Kajihara S, Tanaka K, Oda Y. A simple peak detection and label-free quantitation algorithm for chromatography-mass spectrometry. BMC Bioinformatics 2014; 15:376. [PMID: 25420746 PMCID: PMC4252003 DOI: 10.1186/s12859-014-0376-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [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: 05/27/2014] [Accepted: 11/04/2014] [Indexed: 11/25/2022] Open
Abstract
Background Label-free quantitation of mass spectrometric data is one of the simplest and least expensive methods for differential expression profiling of proteins and metabolites. The need for high accuracy and performance computational label-free quantitation methods is still high in the biomarker and drug discovery research field. However, recent most advanced types of LC-MS generate huge amounts of analytical data with high scan speed, high accuracy and resolution, which is often impossible to interpret manually. Moreover, there are still issues to be improved for recent label-free methods, such as how to reduce false positive/negatives of the candidate peaks, how to expand scalability and how to enhance and automate data processing. AB3D (A simple label-free quantitation algorithm for Biomarker Discovery in Diagnostics and Drug discovery using LC-MS) has addressed these issues and has the capability to perform label-free quantitation using MS1 for proteomics study. Results We developed an algorithm called AB3D, a label free peak detection and quantitative algorithm using MS1 spectral data. To test our algorithm, practical applications of AB3D for LC-MS data sets were evaluated using 3 datasets. Comparisons were then carried out between widely used software tools such as MZmine 2, MSight, SuperHirn, OpenMS and our algorithm AB3D, using the same LC-MS datasets. All quantitative results were confirmed manually, and we found that AB3D could properly identify and quantify known peptides with fewer false positives and false negatives compared to four other existing software tools using either the standard peptide mixture or the real complex biological samples of Bartonella quintana (strain JK31). Moreover, AB3D showed the best reliability by comparing the variability between two technical replicates using a complex peptide mixture of HeLa and BSA samples. For performance, the AB3D algorithm is about 1.2 - 15 times faster than the four other existing software tools. Conclusions AB3D is a simple and fast algorithm for label-free quantitation using MS1 mass spectrometry data for large scale LC-MS data analysis with higher true positive and reasonable false positive rates. Furthermore, AB3D demonstrated the best reproducibility and is about 1.2- 15 times faster than those of existing 4 software tools. Electronic supplementary material The online version of this article (doi:10.1186/s12859-014-0376-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ken Aoshima
- Eisai Co., Ltd., Tsukuba, Ibaraki, 300-2635, Japan.
| | | | | | | | | | | | | | | | | | | | | | | | - Yoshiya Oda
- Eisai Co., Ltd., Tsukuba, Ibaraki, 300-2635, Japan.
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Tanaka S, Fujita Y, Parry HE, Yoshizawa AC, Morimoto K, Murase M, Yamada Y, Yao J, Utsunomiya SI, Kajihara S, Fukuda M, Ikawa M, Tabata T, Takahashi K, Aoshima K, Nihei Y, Nishioka T, Oda Y, Tanaka K. Mass++: A Visualization and Analysis Tool for Mass Spectrometry. J Proteome Res 2014; 13:3846-3853. [DOI: 10.1021/pr500155z] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Satoshi Tanaka
- Koichi
Tanaka Laboratory of Advanced Science and Technology, Shimadzu Corporation, Kyoto 604-8511, Japan
| | - Yuichiro Fujita
- Koichi
Tanaka Laboratory of Advanced Science and Technology, Shimadzu Corporation, Kyoto 604-8511, Japan
| | - Howell E. Parry
- Koichi
Tanaka Laboratory of Advanced Science and Technology, Shimadzu Corporation, Kyoto 604-8511, Japan
| | - Akiyasu C. Yoshizawa
- Koichi
Tanaka Laboratory of Advanced Science and Technology, Shimadzu Corporation, Kyoto 604-8511, Japan
| | - Kentaro Morimoto
- Koichi
Tanaka Laboratory of Advanced Science and Technology, Shimadzu Corporation, Kyoto 604-8511, Japan
| | - Masaki Murase
- Koichi
Tanaka Laboratory of Advanced Science and Technology, Shimadzu Corporation, Kyoto 604-8511, Japan
| | - Yoshihiro Yamada
- Koichi
Tanaka Laboratory of Advanced Science and Technology, Shimadzu Corporation, Kyoto 604-8511, Japan
| | - Jingwen Yao
- Koichi
Tanaka Laboratory of Advanced Science and Technology, Shimadzu Corporation, Kyoto 604-8511, Japan
| | - Shin-ichi Utsunomiya
- Koichi
Tanaka Laboratory of Advanced Science and Technology, Shimadzu Corporation, Kyoto 604-8511, Japan
| | - Shigeki Kajihara
- Koichi
Tanaka Laboratory of Advanced Science and Technology, Shimadzu Corporation, Kyoto 604-8511, Japan
| | - Mitsuru Fukuda
- Eisai
Product Creation Systems, Eisai Co., Ltd., Tsukuba, Ibaraki 300-2635, Japan
- iBioTech Co., Tsukuba, Ibaraki 300-0031, Japan
| | - Masayuki Ikawa
- Eisai
Product Creation Systems, Eisai Co., Ltd., Tsukuba, Ibaraki 300-2635, Japan
- iBioTech Co., Tsukuba, Ibaraki 300-0031, Japan
| | - Tsuyoshi Tabata
- Eisai
Product Creation Systems, Eisai Co., Ltd., Tsukuba, Ibaraki 300-2635, Japan
| | - Kentaro Takahashi
- Eisai
Product Creation Systems, Eisai Co., Ltd., Tsukuba, Ibaraki 300-2635, Japan
| | - Ken Aoshima
- Eisai
Product Creation Systems, Eisai Co., Ltd., Tsukuba, Ibaraki 300-2635, Japan
| | - Yoshito Nihei
- Graduate
School of Information Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Takaaki Nishioka
- Graduate
School of Information Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Yoshiya Oda
- Eisai
Product Creation Systems, Eisai Co., Ltd., Tsukuba, Ibaraki 300-2635, Japan
| | - Koichi Tanaka
- Koichi
Tanaka Laboratory of Advanced Science and Technology, Shimadzu Corporation, Kyoto 604-8511, Japan
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11
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Hirayama M, Kobayashi D, Mizuguchi S, Morikawa T, Nagayama M, Midorikawa U, Wilson MM, Nambu AN, Yoshizawa AC, Kawano S, Araki N. Integrated proteomics identified novel activation of dynein IC2-GR-COX-1 signaling in neurofibromatosis type I (NF1) disease model cells. Mol Cell Proteomics 2013; 12:1377-94. [PMID: 23358504 DOI: 10.1074/mcp.m112.024802] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Neurofibromatosis type 1 (NF1) tumor suppressor gene product, neurofibromin, functions in part as a Ras-GAP, and though its loss is implicated in the neuronal abnormality of NF1 patients, its precise cellular function remains unclear. To study the molecular mechanism of NF1 pathogenesis, we prepared NF1 gene knockdown (KD) PC12 cells, as a NF1 disease model, and analyzed their molecular (gene and protein) expression profiles with a unique integrated proteomics approach, comprising iTRAQ, 2D-DIGE, and DNA microarrays, using an integrated protein and gene expression analysis chart (iPEACH). In NF1-KD PC12 cells showing abnormal neuronal differentiation after NGF treatment, of 3198 molecules quantitatively identified and listed in iPEACH, 97 molecules continuously up- or down-regulated over time were extracted. Pathway and network analysis further revealed overrepresentation of calcium signaling and transcriptional regulation by glucocorticoid receptor (GR) in the up-regulated protein set, whereas nerve system development was overrepresented in the down-regulated protein set. The novel up-regulated network we discovered, "dynein IC2-GR-COX-1 signaling," was then examined in NF1-KD cells. Validation studies confirmed that NF1 knockdown induces altered splicing and phosphorylation patterns of dynein IC2 isomers, up-regulation and accumulation of nuclear GR, and increased COX-1 expression in NGF-treated cells. Moreover, the neurite retraction phenotype observed in NF1-KD cells was significantly recovered by knockdown of the dynein IC2-C isoform and COX-1. In addition, dynein IC2 siRNA significantly inhibited nuclear translocation and accumulation of GR and up-regulation of COX-1 expression. These results suggest that dynein IC2 up-regulates GR nuclear translocation and accumulation, and subsequently causes increased COX-1 expression, in this NF1 disease model. Our integrated proteomics strategy, which combines multiple approaches, demonstrates that NF1-related neural abnormalities are, in part, caused by up-regulation of dynein IC2-GR-COX-1 signaling, which may be a novel therapeutic target for NF1.
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Affiliation(s)
- Mio Hirayama
- Department of Tumor Genetics and Biology, Graduate school of Medical Sciences, Kumamoto University, 1-1-1 Honjo, Chuo-ku, Kumamoto 860-8556, Japan
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12
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Nakaya A, Katayama T, Itoh M, Hiranuka K, Kawashima S, Moriya Y, Okuda S, Tanaka M, Tokimatsu T, Yamanishi Y, Yoshizawa AC, Kanehisa M, Goto S. KEGG OC: a large-scale automatic construction of taxonomy-based ortholog clusters. Nucleic Acids Res 2012. [PMID: 23193276 PMCID: PMC3531156 DOI: 10.1093/nar/gks1239] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [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] [Indexed: 11/30/2022] Open
Abstract
The identification of orthologous genes in an increasing number of fully sequenced genomes is a challenging issue in recent genome science. Here we present KEGG OC (http://www.genome.jp/tools/oc/), a novel database of ortholog clusters (OCs). The current version of KEGG OC contains 1 176 030 OCs, obtained by clustering 8 357 175 genes in 2112 complete genomes (153 eukaryotes, 1830 bacteria and 129 archaea). The OCs were constructed by applying the quasi-clique-based clustering method to all possible protein coding genes in all complete genomes, based on their amino acid sequence similarities. It is computationally efficient to calculate OCs, which enables to regularly update the contents. KEGG OC has the following two features: (i) It consists of all complete genomes of a wide variety of organisms from three domains of life, and the number of organisms is the largest among the existing databases; and (ii) It is compatible with the KEGG database by sharing the same sets of genes and identifiers, which leads to seamless integration of OCs with useful components in KEGG such as biological pathways, pathway modules, functional hierarchy, diseases and drugs. The KEGG OC resources are accessible via OC Viewer that provides an interactive visualization of OCs at different taxonomic levels.
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Affiliation(s)
- Akihiro Nakaya
- Center for Transdisciplinary Research, Niigata University, 1-757 Asahimachi-dori, Chuo-ku, Niigata 951-8585, Japan
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13
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Endo T, Ueno K, Yonezawa K, Mineta K, Hotta K, Satou Y, Yamada L, Ogasawara M, Takahashi H, Nakajima A, Nakachi M, Nomura M, Yaguchi J, Sasakura Y, Yamasaki C, Sera M, Yoshizawa AC, Imanishi T, Taniguchi H, Inaba K. CIPRO 2.5: Ciona intestinalis protein database, a unique integrated repository of large-scale omics data, bioinformatic analyses and curated annotation, with user rating and reviewing functionality. Nucleic Acids Res 2010; 39:D807-14. [PMID: 21071393 PMCID: PMC3013717 DOI: 10.1093/nar/gkq1144] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [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] [Indexed: 01/13/2023] Open
Abstract
The Ciona intestinalis protein database (CIPRO) is an integrated protein database for the tunicate species C. intestinalis. The database is unique in two respects: first, because of its phylogenetic position, Ciona is suitable model for understanding vertebrate evolution; and second, the database includes original large-scale transcriptomic and proteomic data. Ciona intestinalis has also been a favorite of developmental biologists. Therefore, large amounts of data exist on its development and morphology, along with a recent genome sequence and gene expression data. The CIPRO database is aimed at collecting those published data as well as providing unique information from unpublished experimental data, such as 3D expression profiling, 2D-PAGE and mass spectrometry-based large-scale analyses at various developmental stages, curated annotation data and various bioinformatic data, to facilitate research in diverse areas, including developmental, comparative and evolutionary biology. For medical and evolutionary research, homologs in humans and major model organisms are intentionally included. The current database is based on a recently developed KH model containing 36 034 unique sequences, but for higher usability it covers 89 683 all known and predicted proteins from all gene models for this species. Of these sequences, more than 10 000 proteins have been manually annotated. Furthermore, to establish a community-supported protein database, these annotations are open to evaluation by users through the CIPRO website. CIPRO 2.5 is freely accessible at http://cipro.ibio.jp/2.5.
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Affiliation(s)
- Toshinori Endo
- Graduate School of Information Science and Technology, Hokkaido University, Sapporo 060-0814, Japan.
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14
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Abstract
ODB (Operon DataBase) aims to collect data of all known and conserved operons in completely sequenced genomes. Three newly updated features of this database have been added as follows: (i) Data from included operons were updated. The genome-wide analysis of transcription and transcriptional units has become popular recently and ODB successfully integrates these high-throughput operon data, including genome-wide transcriptional units of five prokaryotes and two eukaryotes. The current version of our database contains information from about 10 000 known operons in more than 50 genomes, and more than 400 000 conserved operons obtained from more than 1000 bacterial genomes. (ii) ODB proposes the idea of reference operons as a new operon prediction tool. A reference operon, a set of possible orthologous genes that organize operons, is defined by clustering all known operons. A large number of known operons, including the recently added genome-wide analysis of operons, allowed us to define more reliable reference operons. (iii) ODB also provides new graphical interfaces. One is for comparative analyses of operon structures in multiple genomes. The other is for visualization of possible operons in multiple genomes obtained from the reference operons. The 2011 updated version of ODB is now available at http://operondb.jp/.
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Affiliation(s)
- Shujiro Okuda
- College of Life Sciences, Ritsumeikan University, 1-1-1 Noji-higashi, Kusatsu, Shiga 525-8577, Japan.
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15
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Endo T, Ueno K, Yonezawa K, Mineta K, Hotta K, Satou Y, Yamada L, Ogasawara M, Takahashi H, Nakajima A, Nakachi M, Nomura M, Yaguchi J, Konno A, Sasakura Y, Yoshizawa AC, Taniguchi H, Yamasaki C, Sera M, Imanishi T, Inaba K. CIPRO 2.5: Ciona intestinalis Protein Database - a unique integrated repository of large-scale omics data, bioinformatic analyses, and curated annotation, with ability for user rating and comments. Genome Biol 2010. [PMCID: PMC3026239 DOI: 10.1186/gb-2010-11-s1-p11] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
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16
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Okamura-Ikeda K, Hosaka H, Maita N, Fujiwara K, Yoshizawa AC, Nakagawa A, Taniguchi H. Crystal structure of aminomethyltransferase in complex with dihydrolipoyl-H-protein of the glycine cleavage system: implications for recognition of lipoyl protein substrate, disease-related mutations, and reaction mechanism. J Biol Chem 2010; 285:18684-92. [PMID: 20375021 DOI: 10.1074/jbc.m110.110718] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Aminomethyltransferase, a component of the glycine cleavage system termed T-protein, reversibly catalyzes the degradation of the aminomethyl moiety of glycine attached to the lipoate cofactor of H-protein, resulting in the production of ammonia, 5,10-methylenetetrahydrofolate, and dihydrolipoate-bearing H-protein in the presence of tetrahydrofolate. Several mutations in the human T-protein gene are known to cause nonketotic hyperglycinemia. Here, we report the crystal structure of Escherichia coli T-protein in complex with dihydrolipoate-bearing H-protein and 5-methyltetrahydrofolate, a complex mimicking the ternary complex in the reverse reaction. The structure of the complex shows a highly interacting intermolecular interface limited to a small area and the protein-bound dihydrolipoyllysine arm inserted into the active site cavity of the T-protein. Invariant Arg(292) of the T-protein is essential for complex assembly. The structure also provides novel insights in understanding the disease-causing mutations, in addition to the disease-related impairment in the cofactor-enzyme interactions reported previously. Furthermore, structural and mutational analyses suggest that the reversible transfer of the methylene group between the lipoate and tetrahydrofolate should proceed through the electron relay-assisted iminium intermediate formation.
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Affiliation(s)
- Kazuko Okamura-Ikeda
- Institute for Enzyme Research, the University of Tokushima, Tokushima 770-8503, Japan.
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17
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Hashimoto K, Tokimatsu T, Kawano S, Yoshizawa AC, Okuda S, Goto S, Kanehisa M. Comprehensive analysis of glycosyltransferases in eukaryotic genomes for structural and functional characterization of glycans. Carbohydr Res 2009; 344:881-7. [DOI: 10.1016/j.carres.2009.03.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2008] [Revised: 02/24/2009] [Accepted: 03/03/2009] [Indexed: 11/25/2022]
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18
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Kurachi K, Kurachi S, Hamada T, Suenaga E, Yoshizawa AC. [Aging and gerontological diseases in relation to age-related homeostasis and age dimension technology]. Nihon Ronen Igakkai Zasshi 2008; 45:126-131. [PMID: 18446993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
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19
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Hashimoto K, Yoshizawa AC, Okuda S, Kuma K, Goto S, Kanehisa M. The repertoire of desaturases and elongases reveals fatty acid variations in 56 eukaryotic genomes. J Lipid Res 2008; 49:183-91. [DOI: 10.1194/jlr.m700377-jlr200] [Citation(s) in RCA: 132] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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20
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Abstract
The number of complete and draft genomes is rapidly growing in recent years, and it has become increasingly important to automate the identification of functional properties and biological roles of genes in these genomes. In the KEGG database, genes in complete genomes are annotated with the KEGG orthology (KO) identifiers, or the K numbers, based on the best hit information using Smith-Waterman scores as well as by the manual curation. Each K number represents an ortholog group of genes, and it is directly linked to an object in the KEGG pathway map or the BRITE functional hierarchy. Here, we have developed a web-based server called KAAS (KEGG Automatic Annotation Server: http://www.genome.jp/kegg/kaas/) i.e. an implementation of a rapid method to automatically assign K numbers to genes in the genome, enabling reconstruction of KEGG pathways and BRITE hierarchies. The method is based on sequence similarities, bi-directional best hit information and some heuristics, and has achieved a high degree of accuracy when compared with the manually curated KEGG GENES database.
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Affiliation(s)
| | | | | | | | - Minoru Kanehisa
- *To whom Correspondence should be addressed. +81 774 38 3270+81 774 38 3269
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21
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Yoshizawa AC, Kawashima S, Okuda S, Fujita M, Itoh M, Moriya Y, Hattori M, Kanehisa M. Extracting Sequence Motifs and the Phylogenetic Features of SNARE-Dependent Membrane Traffic. Traffic 2006; 7:1104-18. [PMID: 16882042 DOI: 10.1111/j.1600-0854.2006.00451.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The SNARE proteins are required for membrane fusion during intracellular vesicular transport and for its specificity. Only the unique combination of SNARE proteins (cognates) can be bound and can lead to membrane fusion, although the characteristics of the possible specificity of the binding combinations encoded in the SNARE sequences have not yet been determined. We discovered by whole genome sequence analysis that sequence motifs (conserved sequences) in the SNARE motif domains for each protein group correspond to localization sites or transport pathways. We claim that these motifs reflect the specificity of the binding combinations of SNARE motif domains. Using these motifs, we could classify SNARE proteins from 48 organisms into their localization sites or transport pathways. The classification result shows that more than 10 SNARE subgroups are kingdom specific and that the SNARE paralogs involved in the plasma membrane-related transport pathways have developed greater variations in higher animals and higher plants than those involved in the endoplasmic reticulum-related transport pathways throughout eukaryotic evolution.
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Affiliation(s)
- Akiyasu C Yoshizawa
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan.
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22
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Hashimoto K, Yoshizawa AC, Saito K, Yamada T, Kanehisa M. The repertoire of desaturases for unsaturated fatty acid synthesis in 397 genomes. Genome Inform 2006; 17:173-83. [PMID: 17503367] [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: 05/15/2023]
Abstract
Fatty acids are the major components of membrane molecules. The fact that unsaturated fatty acids play multiple important roles, physically and biologically, means that the ratio of unsaturated to saturated fatty acids in the membrane needs to be strictly regulated to maintain cellular homeostasis. The most ubiquitous and widespread modification to fatty acids, which results in a great diversity of different structures, is the insertion of double bonds. Fatty acid desaturases directly introduce regioselective double bonds into fatty acids. A phylogenetic analysis of desaturases suggests that the sequences of these proteins include a highly conserved domain, which determines the differences in specificity and regioselectivity found in these enzymes. In this study, we performed a systematic analysis of fatty acid desaturases found in the genomic data of 397 organisms. We obtained a set of desaturases clustered by regioselectivity using a hierarchal clustering analysis.
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Affiliation(s)
- Kosuke Hashimoto
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan.
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23
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Kusumi A, Tsuji A, Murata M, Sako Y, Yoshizawa AC, Kagiwada S, Hayakawa T, Ohnishi S. Development of a streak-camera-based time-resolved microscope fluorimeter and its application to studies of membrane fusion in single cells. Biochemistry 1991; 30:6517-27. [PMID: 2054350 DOI: 10.1021/bi00240a024] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.6] [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: 12/30/2022]
Abstract
A time-resolved microscope fluorimeter based on a synchroscan streak camera and a fast pulsed laser system has been developed to measure the fluorescence lifetime decay under the fluorescence microscope. This system allows one to measure the nanosecond fluorescence lifetimes of fluorophores in a small spot (0.8-6.3 microns diameter) in single cultured cells under a fluorescence microscope, while the cells are being viewed under a high-power objective lens. A signal acquisition time between a second and a minute was usually sufficient to obtain fluorescence decay curves with good quality for 10(3)-10(5) fluorophores localized in 1 microns 2 domain. A signal-to-noise ratio better than 30 was obtained for approximately 30,000 fluorescein-labeled band 3 molecules in a 2 microns 2 region in a single human erythrocyte ghost after signal accumulation for 30 s. The measured lifetimes for a variety of fluorescent probes attached to proteins in solution and lipids in liposomes showed a good agreement with those measured in a cuvette under standard conditions by time-correlated single photon counting. With the development of this instrument, microscope fluorimetry has become a practical, straightforward, quantitative technique for investigation of molecular processes in single cells in culture. Time-resolved microscope fluorimetry has been applied to observe fusion of liposomes in vitro and that of endosomes in single cells by monitoring resonance energy transfer. Inspection of individual liposomes and endosomes revealed the extent of fusion for each vesicle. Since the use of time-resolved microscope fluorimetry eliminates the need for subcellular fractionation or the complex correction procedures in steady-state microfluorimetry, it greatly simplifies the assay for endosome fusion in vivo. The results showed that extensive fusion of sequentially formed endosomes takes place all over the cell matrix in cultured cells. This suggests that extensive fusion with incoming endosomes takes place in many endosomal compartments, possibly sorting organelles, or that the early endosomes fuse with the preexisting network of tubular cisternae of the endosomal compartment at many points in the network. It is concluded that time-resolved microscope fluorimetry is a powerful noninvasive technique for studies of in situ biochemistry and biophysics using cells and tissues.
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Affiliation(s)
- A Kusumi
- Department of Pure and Applied Sciences, College of Arts and Sciences, University of Tokyo, Japan
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