title: Multiomics in grape berry skin revealed specific induction of the stilbene synthetic pathway by ultraviolet-C irradiation.
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.
authors.affiliation: 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.).
authors.forename: Mami
authors.initials: M
authors.lastname: Suzuki
authors.affiliation: 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.).
authors.forename: Ryo
authors.initials: R
authors.lastname: Nakabayashi
authors.affiliation: 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.).
authors.forename: Yoshiyuki
authors.initials: Y
authors.lastname: Ogata
authors.affiliation: 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.).
authors.forename: Nozomu
authors.initials: N
authors.lastname: Sakurai
authors.affiliation: 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.).
authors.forename: Toshiaki
authors.initials: T
authors.lastname: Tokimatsu
authors.affiliation: 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.).
authors.forename: Susumu
authors.initials: S
authors.lastname: Goto
authors.affiliation: 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.).
authors.forename: Makoto
authors.initials: M
authors.lastname: Suzuki
authors.affiliation: 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.).
authors.forename: Michal
authors.initials: M
authors.lastname: Jasinski
authors.affiliation: 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.).
authors.forename: Enrico
authors.initials: E
authors.lastname: Martinoia
authors.affiliation: 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.).
authors.forename: Shungo
authors.initials: S
authors.lastname: Otagaki
authors.affiliation: 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.).
authors.forename: Shogo
authors.initials: S
authors.lastname: Matsumoto
authors.affiliation: 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.).
authors.forename: Kazuki
authors.initials: K
authors.lastname: Saito
authors.affiliation: 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.) shira@agr.nagoya-u.ac.jp.
authors.forename: Katsuhiro
authors.identifier: http://orcid.org/0000-0062-2608-7912
authors.initials: K
authors.lastname: Shiratake
mesh_terms: D053898:Biosynthetic Pathways / Q000528:radiation effects; D002138:Calibration; D003624:Darkness; D005453:Fluorescence; D005638:Fruit / Q000235:genetics* / Q000378:metabolism / Q000528:radiation effects; D020869:Gene Expression Profiling; D063990:Gene Ontology; D017343:Genes, Plant; D055442:Metabolome / Q000235:genetics / Q000528:radiation effects; D055432:Metabolomics; D058977:Molecular Sequence Annotation; D025341:Principal Component Analysis; D064210:Secondary Metabolism / Q000235:genetics / Q000528:radiation effects; D013267:Stilbenes / Q000378:metabolism*; D014466:Ultraviolet Rays; D027843:Vitis / Q000235:genetics* / Q000378:metabolism / Q000528:radiation effects
chemical_list: D013267:Stilbenes