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Suzuki M, Nakabayashi R, Ogata Y, Sakurai N, Tokimatsu T, Goto S, Suzuki M, Jasinski M, Martinoia E, Otagaki S, Matsumoto S, Saito K, Shiratake K. Multiomics in grape berry skin revealed specific induction of the stilbene synthetic pathway by ultraviolet-C irradiation. PLANT PHYSIOLOGY 2015; 168:47-59. [PMID: 25761715 PMCID: PMC4424009 DOI: 10.1104/pp.114.254375] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 03/04/2015] [Indexed: 05/08/2023]
Abstract
Grape (Vitis vinifera) accumulates various polyphenolic compounds, which protect against environmental stresses, including ultraviolet-C (UV-C) light and pathogens. In this study, we looked at the transcriptome and metabolome in grape berry skin after UV-C irradiation, which demonstrated the effectiveness of omics approaches to clarify important traits of grape. We performed transcriptome analysis using a genome-wide microarray, which revealed 238 genes up-regulated more than 5-fold by UV-C light. Enrichment analysis of Gene Ontology terms showed that genes encoding stilbene synthase, a key enzyme for resveratrol synthesis, were enriched in the up-regulated genes. We performed metabolome analysis using liquid chromatography-quadrupole time-of-flight mass spectrometry, and 2,012 metabolite peaks, including unidentified peaks, were detected. Principal component analysis using the peaks showed that only one metabolite peak, identified as resveratrol, was highly induced by UV-C light. We updated the metabolic pathway map of grape in the Kyoto Encyclopedia of Genes and Genomes (KEGG) database and in the KaPPA-View 4 KEGG system, then projected the transcriptome and metabolome data on a metabolic pathway map. The map showed specific induction of the resveratrol synthetic pathway by UV-C light. Our results showed that multiomics is a powerful tool to elucidate the accumulation mechanisms of secondary metabolites, and updated systems, such as KEGG and KaPPA-View 4 KEGG for grape, can support such studies.
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Affiliation(s)
- Mami Suzuki
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya 464-8601, Japan (Mam.S., S.O., S.M., K.Sh.);National Institute of Vegetables and Tea Science, Taketoyo 470-2351, Japan (Mam.S.);RIKEN Center for Sustainable Resource Science, Tsurumi, Yokohama 230-0045, Japan (R.N., Mak.S., K.Sa.);Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Naka, Sakai 599-8531, Japan (Y.O.);Kazusa DNA Research Institute, Kisarazu 292-0818, Japan (N.S.);Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji 611-0011, Japan (T.T., S.G.);Database Center for Life Science, Research Organization of Information and Systems, Kashiwa 277-0871, Japan (T.T.);Department of Biochemistry and Biotechnology, Poznań University of Life Sciences, Dojazd 60-637 Poznan, Poland (M.J.);Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 61-704 Poznan, Poland (M.J.);Institute of Plant Biology, University of Zurich, Zurich 8008, Switzerland (E.M.); andGraduate School of Pharmaceutical Sciences, Chiba University, Chuo, Chiba 260-8675, Japan (K.Sa.)
| | - Ryo Nakabayashi
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya 464-8601, Japan (Mam.S., S.O., S.M., K.Sh.);National Institute of Vegetables and Tea Science, Taketoyo 470-2351, Japan (Mam.S.);RIKEN Center for Sustainable Resource Science, Tsurumi, Yokohama 230-0045, Japan (R.N., Mak.S., K.Sa.);Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Naka, Sakai 599-8531, Japan (Y.O.);Kazusa DNA Research Institute, Kisarazu 292-0818, Japan (N.S.);Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji 611-0011, Japan (T.T., S.G.);Database Center for Life Science, Research Organization of Information and Systems, Kashiwa 277-0871, Japan (T.T.);Department of Biochemistry and Biotechnology, Poznań University of Life Sciences, Dojazd 60-637 Poznan, Poland (M.J.);Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 61-704 Poznan, Poland (M.J.);Institute of Plant Biology, University of Zurich, Zurich 8008, Switzerland (E.M.); andGraduate School of Pharmaceutical Sciences, Chiba University, Chuo, Chiba 260-8675, Japan (K.Sa.)
| | - Yoshiyuki Ogata
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya 464-8601, Japan (Mam.S., S.O., S.M., K.Sh.);National Institute of Vegetables and Tea Science, Taketoyo 470-2351, Japan (Mam.S.);RIKEN Center for Sustainable Resource Science, Tsurumi, Yokohama 230-0045, Japan (R.N., Mak.S., K.Sa.);Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Naka, Sakai 599-8531, Japan (Y.O.);Kazusa DNA Research Institute, Kisarazu 292-0818, Japan (N.S.);Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji 611-0011, Japan (T.T., S.G.);Database Center for Life Science, Research Organization of Information and Systems, Kashiwa 277-0871, Japan (T.T.);Department of Biochemistry and Biotechnology, Poznań University of Life Sciences, Dojazd 60-637 Poznan, Poland (M.J.);Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 61-704 Poznan, Poland (M.J.);Institute of Plant Biology, University of Zurich, Zurich 8008, Switzerland (E.M.); andGraduate School of Pharmaceutical Sciences, Chiba University, Chuo, Chiba 260-8675, Japan (K.Sa.)
| | - Nozomu Sakurai
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya 464-8601, Japan (Mam.S., S.O., S.M., K.Sh.);National Institute of Vegetables and Tea Science, Taketoyo 470-2351, Japan (Mam.S.);RIKEN Center for Sustainable Resource Science, Tsurumi, Yokohama 230-0045, Japan (R.N., Mak.S., K.Sa.);Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Naka, Sakai 599-8531, Japan (Y.O.);Kazusa DNA Research Institute, Kisarazu 292-0818, Japan (N.S.);Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji 611-0011, Japan (T.T., S.G.);Database Center for Life Science, Research Organization of Information and Systems, Kashiwa 277-0871, Japan (T.T.);Department of Biochemistry and Biotechnology, Poznań University of Life Sciences, Dojazd 60-637 Poznan, Poland (M.J.);Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 61-704 Poznan, Poland (M.J.);Institute of Plant Biology, University of Zurich, Zurich 8008, Switzerland (E.M.); andGraduate School of Pharmaceutical Sciences, Chiba University, Chuo, Chiba 260-8675, Japan (K.Sa.)
| | - Toshiaki Tokimatsu
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya 464-8601, Japan (Mam.S., S.O., S.M., K.Sh.);National Institute of Vegetables and Tea Science, Taketoyo 470-2351, Japan (Mam.S.);RIKEN Center for Sustainable Resource Science, Tsurumi, Yokohama 230-0045, Japan (R.N., Mak.S., K.Sa.);Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Naka, Sakai 599-8531, Japan (Y.O.);Kazusa DNA Research Institute, Kisarazu 292-0818, Japan (N.S.);Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji 611-0011, Japan (T.T., S.G.);Database Center for Life Science, Research Organization of Information and Systems, Kashiwa 277-0871, Japan (T.T.);Department of Biochemistry and Biotechnology, Poznań University of Life Sciences, Dojazd 60-637 Poznan, Poland (M.J.);Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 61-704 Poznan, Poland (M.J.);Institute of Plant Biology, University of Zurich, Zurich 8008, Switzerland (E.M.); andGraduate School of Pharmaceutical Sciences, Chiba University, Chuo, Chiba 260-8675, Japan (K.Sa.)
| | - Susumu Goto
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya 464-8601, Japan (Mam.S., S.O., S.M., K.Sh.);National Institute of Vegetables and Tea Science, Taketoyo 470-2351, Japan (Mam.S.);RIKEN Center for Sustainable Resource Science, Tsurumi, Yokohama 230-0045, Japan (R.N., Mak.S., K.Sa.);Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Naka, Sakai 599-8531, Japan (Y.O.);Kazusa DNA Research Institute, Kisarazu 292-0818, Japan (N.S.);Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji 611-0011, Japan (T.T., S.G.);Database Center for Life Science, Research Organization of Information and Systems, Kashiwa 277-0871, Japan (T.T.);Department of Biochemistry and Biotechnology, Poznań University of Life Sciences, Dojazd 60-637 Poznan, Poland (M.J.);Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 61-704 Poznan, Poland (M.J.);Institute of Plant Biology, University of Zurich, Zurich 8008, Switzerland (E.M.); andGraduate School of Pharmaceutical Sciences, Chiba University, Chuo, Chiba 260-8675, Japan (K.Sa.)
| | - Makoto Suzuki
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya 464-8601, Japan (Mam.S., S.O., S.M., K.Sh.);National Institute of Vegetables and Tea Science, Taketoyo 470-2351, Japan (Mam.S.);RIKEN Center for Sustainable Resource Science, Tsurumi, Yokohama 230-0045, Japan (R.N., Mak.S., K.Sa.);Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Naka, Sakai 599-8531, Japan (Y.O.);Kazusa DNA Research Institute, Kisarazu 292-0818, Japan (N.S.);Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji 611-0011, Japan (T.T., S.G.);Database Center for Life Science, Research Organization of Information and Systems, Kashiwa 277-0871, Japan (T.T.);Department of Biochemistry and Biotechnology, Poznań University of Life Sciences, Dojazd 60-637 Poznan, Poland (M.J.);Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 61-704 Poznan, Poland (M.J.);Institute of Plant Biology, University of Zurich, Zurich 8008, Switzerland (E.M.); andGraduate School of Pharmaceutical Sciences, Chiba University, Chuo, Chiba 260-8675, Japan (K.Sa.)
| | - Michal Jasinski
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya 464-8601, Japan (Mam.S., S.O., S.M., K.Sh.);National Institute of Vegetables and Tea Science, Taketoyo 470-2351, Japan (Mam.S.);RIKEN Center for Sustainable Resource Science, Tsurumi, Yokohama 230-0045, Japan (R.N., Mak.S., K.Sa.);Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Naka, Sakai 599-8531, Japan (Y.O.);Kazusa DNA Research Institute, Kisarazu 292-0818, Japan (N.S.);Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji 611-0011, Japan (T.T., S.G.);Database Center for Life Science, Research Organization of Information and Systems, Kashiwa 277-0871, Japan (T.T.);Department of Biochemistry and Biotechnology, Poznań University of Life Sciences, Dojazd 60-637 Poznan, Poland (M.J.);Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 61-704 Poznan, Poland (M.J.);Institute of Plant Biology, University of Zurich, Zurich 8008, Switzerland (E.M.); andGraduate School of Pharmaceutical Sciences, Chiba University, Chuo, Chiba 260-8675, Japan (K.Sa.)
| | - Enrico Martinoia
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya 464-8601, Japan (Mam.S., S.O., S.M., K.Sh.);National Institute of Vegetables and Tea Science, Taketoyo 470-2351, Japan (Mam.S.);RIKEN Center for Sustainable Resource Science, Tsurumi, Yokohama 230-0045, Japan (R.N., Mak.S., K.Sa.);Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Naka, Sakai 599-8531, Japan (Y.O.);Kazusa DNA Research Institute, Kisarazu 292-0818, Japan (N.S.);Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji 611-0011, Japan (T.T., S.G.);Database Center for Life Science, Research Organization of Information and Systems, Kashiwa 277-0871, Japan (T.T.);Department of Biochemistry and Biotechnology, Poznań University of Life Sciences, Dojazd 60-637 Poznan, Poland (M.J.);Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 61-704 Poznan, Poland (M.J.);Institute of Plant Biology, University of Zurich, Zurich 8008, Switzerland (E.M.); andGraduate School of Pharmaceutical Sciences, Chiba University, Chuo, Chiba 260-8675, Japan (K.Sa.)
| | - Shungo Otagaki
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya 464-8601, Japan (Mam.S., S.O., S.M., K.Sh.);National Institute of Vegetables and Tea Science, Taketoyo 470-2351, Japan (Mam.S.);RIKEN Center for Sustainable Resource Science, Tsurumi, Yokohama 230-0045, Japan (R.N., Mak.S., K.Sa.);Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Naka, Sakai 599-8531, Japan (Y.O.);Kazusa DNA Research Institute, Kisarazu 292-0818, Japan (N.S.);Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji 611-0011, Japan (T.T., S.G.);Database Center for Life Science, Research Organization of Information and Systems, Kashiwa 277-0871, Japan (T.T.);Department of Biochemistry and Biotechnology, Poznań University of Life Sciences, Dojazd 60-637 Poznan, Poland (M.J.);Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 61-704 Poznan, Poland (M.J.);Institute of Plant Biology, University of Zurich, Zurich 8008, Switzerland (E.M.); andGraduate School of Pharmaceutical Sciences, Chiba University, Chuo, Chiba 260-8675, Japan (K.Sa.)
| | - Shogo Matsumoto
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya 464-8601, Japan (Mam.S., S.O., S.M., K.Sh.);National Institute of Vegetables and Tea Science, Taketoyo 470-2351, Japan (Mam.S.);RIKEN Center for Sustainable Resource Science, Tsurumi, Yokohama 230-0045, Japan (R.N., Mak.S., K.Sa.);Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Naka, Sakai 599-8531, Japan (Y.O.);Kazusa DNA Research Institute, Kisarazu 292-0818, Japan (N.S.);Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji 611-0011, Japan (T.T., S.G.);Database Center for Life Science, Research Organization of Information and Systems, Kashiwa 277-0871, Japan (T.T.);Department of Biochemistry and Biotechnology, Poznań University of Life Sciences, Dojazd 60-637 Poznan, Poland (M.J.);Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 61-704 Poznan, Poland (M.J.);Institute of Plant Biology, University of Zurich, Zurich 8008, Switzerland (E.M.); andGraduate School of Pharmaceutical Sciences, Chiba University, Chuo, Chiba 260-8675, Japan (K.Sa.)
| | - Kazuki Saito
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya 464-8601, Japan (Mam.S., S.O., S.M., K.Sh.);National Institute of Vegetables and Tea Science, Taketoyo 470-2351, Japan (Mam.S.);RIKEN Center for Sustainable Resource Science, Tsurumi, Yokohama 230-0045, Japan (R.N., Mak.S., K.Sa.);Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Naka, Sakai 599-8531, Japan (Y.O.);Kazusa DNA Research Institute, Kisarazu 292-0818, Japan (N.S.);Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji 611-0011, Japan (T.T., S.G.);Database Center for Life Science, Research Organization of Information and Systems, Kashiwa 277-0871, Japan (T.T.);Department of Biochemistry and Biotechnology, Poznań University of Life Sciences, Dojazd 60-637 Poznan, Poland (M.J.);Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 61-704 Poznan, Poland (M.J.);Institute of Plant Biology, University of Zurich, Zurich 8008, Switzerland (E.M.); andGraduate School of Pharmaceutical Sciences, Chiba University, Chuo, Chiba 260-8675, Japan (K.Sa.)
| | - Katsuhiro Shiratake
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya 464-8601, Japan (Mam.S., S.O., S.M., K.Sh.);National Institute of Vegetables and Tea Science, Taketoyo 470-2351, Japan (Mam.S.);RIKEN Center for Sustainable Resource Science, Tsurumi, Yokohama 230-0045, Japan (R.N., Mak.S., K.Sa.);Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Naka, Sakai 599-8531, Japan (Y.O.);Kazusa DNA Research Institute, Kisarazu 292-0818, Japan (N.S.);Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji 611-0011, Japan (T.T., S.G.);Database Center for Life Science, Research Organization of Information and Systems, Kashiwa 277-0871, Japan (T.T.);Department of Biochemistry and Biotechnology, Poznań University of Life Sciences, Dojazd 60-637 Poznan, Poland (M.J.);Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 61-704 Poznan, Poland (M.J.);Institute of Plant Biology, University of Zurich, Zurich 8008, Switzerland (E.M.); andGraduate School of Pharmaceutical Sciences, Chiba University, Chuo, Chiba 260-8675, Japan (K.Sa.)
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