Metabolomic Characterization of Knockout Mutants in Arabidopsis: Development of a Metabolite Profiling Database for Knockout Mutants in Arabidopsis.
Despite recent intensive research efforts in functional genomics, the functions of only a limited number of Arabidopsis (Arabidopsis thaliana) genes have been determined experimentally, and improving gene annotation remains a major challenge in plant science. As metabolite profiling can characterize the metabolomic phenotype of a genetic perturbation in the plant metabolism, it provides clues to the function(s) of genes of interest. We chose 50 Arabidopsis mutants, including a set of characterized and uncharacterized mutants, that resemble wild-type plants. We performed metabolite profiling of the plants using gas chromatography-mass spectrometry. To make the data set available as an efficient public functional genomics tool for hypothesis generation, we developed the Metabolite Profiling Database for Knock-Out Mutants in Arabidopsis (MeKO). It allows the evaluation of whether a mutation affects metabolism during normal plant growth and contains images of mutants, data on differences in metabolite accumulation, and interactive analysis tools. Nonprocessed data, including chromatograms, mass spectra, and experimental metadata, follow the guidelines set by the Metabolomics Standards Initiative and are freely downloadable. Proof-of-concept analysis suggests that MeKO is highly useful for the generation of hypotheses for genes of interest and for improving gene annotation. MeKO is publicly available at http://prime.psc.riken.jp/meko/.
RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan (A.F., Mi.K., R.F.M., M.I., Ma.K., N.H., A.W.-T., T.N., T.T., K.S.);Japan Science and Technology Agency, National Bioscience Database Center, Chiyoda-ku, Tokyo 102-0081, Japan (A.F.);Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan (Mi.K.);Nissan Chemical Industries, Funabashi, Chiba 274-8507, Japan (M.I.);Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany (T.T.);Department of Genetics Development and Cell Biology (M.H., E.S.W.), Center for Metabolic Biology (E.S.W., B.J.N.), Center for Biorenewable Chemicals (E.S.W., B.J.N.), and Biochemistry, Biophysics, and Molecular Biology (B.J.N.), Iowa State University, Ames, Iowa 50011; andGraduate School of Pharmaceutical Sciences, Chiba University, Chiba-shi, Chiba 263-8522, Japan (K.S.) a-fukush@psc.riken.jp kazuki.saito@riken.jp.
Atsushi
A
Fukushima
RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan (A.F., Mi.K., R.F.M., M.I., Ma.K., N.H., A.W.-T., T.N., T.T., K.S.);Japan Science and Technology Agency, National Bioscience Database Center, Chiyoda-ku, Tokyo 102-0081, Japan (A.F.);Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan (Mi.K.);Nissan Chemical Industries, Funabashi, Chiba 274-8507, Japan (M.I.);Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany (T.T.);Department of Genetics Development and Cell Biology (M.H., E.S.W.), Center for Metabolic Biology (E.S.W., B.J.N.), Center for Biorenewable Chemicals (E.S.W., B.J.N.), and Biochemistry, Biophysics, and Molecular Biology (B.J.N.), Iowa State University, Ames, Iowa 50011; andGraduate School of Pharmaceutical Sciences, Chiba University, Chiba-shi, Chiba 263-8522, Japan (K.S.).
Miyako
M
Kusano
RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan (A.F., Mi.K., R.F.M., M.I., Ma.K., N.H., A.W.-T., T.N., T.T., K.S.);Japan Science and Technology Agency, National Bioscience Database Center, Chiyoda-ku, Tokyo 102-0081, Japan (A.F.);Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan (Mi.K.);Nissan Chemical Industries, Funabashi, Chiba 274-8507, Japan (M.I.);Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany (T.T.);Department of Genetics Development and Cell Biology (M.H., E.S.W.), Center for Metabolic Biology (E.S.W., B.J.N.), Center for Biorenewable Chemicals (E.S.W., B.J.N.), and Biochemistry, Biophysics, and Molecular Biology (B.J.N.), Iowa State University, Ames, Iowa 50011; andGraduate School of Pharmaceutical Sciences, Chiba University, Chiba-shi, Chiba 263-8522, Japan (K.S.).
Ramon Francisco
RF
Mejia
RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan (A.F., Mi.K., R.F.M., M.I., Ma.K., N.H., A.W.-T., T.N., T.T., K.S.);Japan Science and Technology Agency, National Bioscience Database Center, Chiyoda-ku, Tokyo 102-0081, Japan (A.F.);Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan (Mi.K.);Nissan Chemical Industries, Funabashi, Chiba 274-8507, Japan (M.I.);Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany (T.T.);Department of Genetics Development and Cell Biology (M.H., E.S.W.), Center for Metabolic Biology (E.S.W., B.J.N.), Center for Biorenewable Chemicals (E.S.W., B.J.N.), and Biochemistry, Biophysics, and Molecular Biology (B.J.N.), Iowa State University, Ames, Iowa 50011; andGraduate School of Pharmaceutical Sciences, Chiba University, Chiba-shi, Chiba 263-8522, Japan (K.S.).
Mami
M
Iwasa
RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan (A.F., Mi.K., R.F.M., M.I., Ma.K., N.H., A.W.-T., T.N., T.T., K.S.);Japan Science and Technology Agency, National Bioscience Database Center, Chiyoda-ku, Tokyo 102-0081, Japan (A.F.);Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan (Mi.K.);Nissan Chemical Industries, Funabashi, Chiba 274-8507, Japan (M.I.);Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany (T.T.);Department of Genetics Development and Cell Biology (M.H., E.S.W.), Center for Metabolic Biology (E.S.W., B.J.N.), Center for Biorenewable Chemicals (E.S.W., B.J.N.), and Biochemistry, Biophysics, and Molecular Biology (B.J.N.), Iowa State University, Ames, Iowa 50011; andGraduate School of Pharmaceutical Sciences, Chiba University, Chiba-shi, Chiba 263-8522, Japan (K.S.).
Makoto
M
Kobayashi
RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan (A.F., Mi.K., R.F.M., M.I., Ma.K., N.H., A.W.-T., T.N., T.T., K.S.);Japan Science and Technology Agency, National Bioscience Database Center, Chiyoda-ku, Tokyo 102-0081, Japan (A.F.);Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan (Mi.K.);Nissan Chemical Industries, Funabashi, Chiba 274-8507, Japan (M.I.);Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany (T.T.);Department of Genetics Development and Cell Biology (M.H., E.S.W.), Center for Metabolic Biology (E.S.W., B.J.N.), Center for Biorenewable Chemicals (E.S.W., B.J.N.), and Biochemistry, Biophysics, and Molecular Biology (B.J.N.), Iowa State University, Ames, Iowa 50011; andGraduate School of Pharmaceutical Sciences, Chiba University, Chiba-shi, Chiba 263-8522, Japan (K.S.).
Naomi
N
Hayashi
RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan (A.F., Mi.K., R.F.M., M.I., Ma.K., N.H., A.W.-T., T.N., T.T., K.S.);Japan Science and Technology Agency, National Bioscience Database Center, Chiyoda-ku, Tokyo 102-0081, Japan (A.F.);Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan (Mi.K.);Nissan Chemical Industries, Funabashi, Chiba 274-8507, Japan (M.I.);Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany (T.T.);Department of Genetics Development and Cell Biology (M.H., E.S.W.), Center for Metabolic Biology (E.S.W., B.J.N.), Center for Biorenewable Chemicals (E.S.W., B.J.N.), and Biochemistry, Biophysics, and Molecular Biology (B.J.N.), Iowa State University, Ames, Iowa 50011; andGraduate School of Pharmaceutical Sciences, Chiba University, Chiba-shi, Chiba 263-8522, Japan (K.S.).
Akiko
A
Watanabe-Takahashi
RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan (A.F., Mi.K., R.F.M., M.I., Ma.K., N.H., A.W.-T., T.N., T.T., K.S.);Japan Science and Technology Agency, National Bioscience Database Center, Chiyoda-ku, Tokyo 102-0081, Japan (A.F.);Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan (Mi.K.);Nissan Chemical Industries, Funabashi, Chiba 274-8507, Japan (M.I.);Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany (T.T.);Department of Genetics Development and Cell Biology (M.H., E.S.W.), Center for Metabolic Biology (E.S.W., B.J.N.), Center for Biorenewable Chemicals (E.S.W., B.J.N.), and Biochemistry, Biophysics, and Molecular Biology (B.J.N.), Iowa State University, Ames, Iowa 50011; andGraduate School of Pharmaceutical Sciences, Chiba University, Chiba-shi, Chiba 263-8522, Japan (K.S.).
Tomoko
T
Narisawa
RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan (A.F., Mi.K., R.F.M., M.I., Ma.K., N.H., A.W.-T., T.N., T.T., K.S.);Japan Science and Technology Agency, National Bioscience Database Center, Chiyoda-ku, Tokyo 102-0081, Japan (A.F.);Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan (Mi.K.);Nissan Chemical Industries, Funabashi, Chiba 274-8507, Japan (M.I.);Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany (T.T.);Department of Genetics Development and Cell Biology (M.H., E.S.W.), Center for Metabolic Biology (E.S.W., B.J.N.), Center for Biorenewable Chemicals (E.S.W., B.J.N.), and Biochemistry, Biophysics, and Molecular Biology (B.J.N.), Iowa State University, Ames, Iowa 50011; andGraduate School of Pharmaceutical Sciences, Chiba University, Chiba-shi, Chiba 263-8522, Japan (K.S.).
Takayuki
T
Tohge
RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan (A.F., Mi.K., R.F.M., M.I., Ma.K., N.H., A.W.-T., T.N., T.T., K.S.);Japan Science and Technology Agency, National Bioscience Database Center, Chiyoda-ku, Tokyo 102-0081, Japan (A.F.);Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan (Mi.K.);Nissan Chemical Industries, Funabashi, Chiba 274-8507, Japan (M.I.);Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany (T.T.);Department of Genetics Development and Cell Biology (M.H., E.S.W.), Center for Metabolic Biology (E.S.W., B.J.N.), Center for Biorenewable Chemicals (E.S.W., B.J.N.), and Biochemistry, Biophysics, and Molecular Biology (B.J.N.), Iowa State University, Ames, Iowa 50011; andGraduate School of Pharmaceutical Sciences, Chiba University, Chiba-shi, Chiba 263-8522, Japan (K.S.).
Manhoi
M
Hur
RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan (A.F., Mi.K., R.F.M., M.I., Ma.K., N.H., A.W.-T., T.N., T.T., K.S.);Japan Science and Technology Agency, National Bioscience Database Center, Chiyoda-ku, Tokyo 102-0081, Japan (A.F.);Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan (Mi.K.);Nissan Chemical Industries, Funabashi, Chiba 274-8507, Japan (M.I.);Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany (T.T.);Department of Genetics Development and Cell Biology (M.H., E.S.W.), Center for Metabolic Biology (E.S.W., B.J.N.), Center for Biorenewable Chemicals (E.S.W., B.J.N.), and Biochemistry, Biophysics, and Molecular Biology (B.J.N.), Iowa State University, Ames, Iowa 50011; andGraduate School of Pharmaceutical Sciences, Chiba University, Chiba-shi, Chiba 263-8522, Japan (K.S.).
Eve Syrkin
ES
Wurtele
RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan (A.F., Mi.K., R.F.M., M.I., Ma.K., N.H., A.W.-T., T.N., T.T., K.S.);Japan Science and Technology Agency, National Bioscience Database Center, Chiyoda-ku, Tokyo 102-0081, Japan (A.F.);Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan (Mi.K.);Nissan Chemical Industries, Funabashi, Chiba 274-8507, Japan (M.I.);Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany (T.T.);Department of Genetics Development and Cell Biology (M.H., E.S.W.), Center for Metabolic Biology (E.S.W., B.J.N.), Center for Biorenewable Chemicals (E.S.W., B.J.N.), and Biochemistry, Biophysics, and Molecular Biology (B.J.N.), Iowa State University, Ames, Iowa 50011; andGraduate School of Pharmaceutical Sciences, Chiba University, Chiba-shi, Chiba 263-8522, Japan (K.S.).
Basil J
BJ
Nikolau
RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan (A.F., Mi.K., R.F.M., M.I., Ma.K., N.H., A.W.-T., T.N., T.T., K.S.);Japan Science and Technology Agency, National Bioscience Database Center, Chiyoda-ku, Tokyo 102-0081, Japan (A.F.);Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan (Mi.K.);Nissan Chemical Industries, Funabashi, Chiba 274-8507, Japan (M.I.);Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany (T.T.);Department of Genetics Development and Cell Biology (M.H., E.S.W.), Center for Metabolic Biology (E.S.W., B.J.N.), Center for Biorenewable Chemicals (E.S.W., B.J.N.), and Biochemistry, Biophysics, and Molecular Biology (B.J.N.), Iowa State University, Ames, Iowa 50011; andGraduate School of Pharmaceutical Sciences, Chiba University, Chiba-shi, Chiba 263-8522, Japan (K.S.) a-fukush@psc.riken.jp kazuki.saito@riken.jp.
Kazuki
K
Saito