Loading [MathJax]/extensions/tex2jax.js

Elucidation of gene-to-gene and metabolite-to-gene networks in arabidopsis by integration of metabolomics and transcriptomics

Publikation: Beitrag in FachzeitschriftArtikelForschungPeer-Review

Autorschaft

  • Masami Yokota Hirai
  • Marion Klein
  • Yuuta Fujikawa
  • Mitsuru Yano
  • Jutta Papenbrock

Organisationseinheiten

Externe Organisationen

  • Chiba University
  • Japan Science and Technology Agency
  • Ulmer Fundamental Symmetries Laboratory
  • Phenomenome Discoveries Inc.
  • Nara Institute of Science and Technology
  • Ehime Women's College
  • Kazusa DNA Research Institute
  • Max-Planck-Institut für Chemische Ökologie

Details

OriginalspracheEnglisch
Seiten (von - bis)25590-25595
Seitenumfang6
FachzeitschriftJournal of Biological Chemistry
Jahrgang280
Ausgabenummer27
PublikationsstatusVeröffentlicht - 8 Juli 2005

Abstract

Since the completion of genome sequences of model organisms, functional identification of unknown genes has become a principal challenge in biology. Postgenomics sciences such as transcriptomics, proteomics, and metabolomics are expected to discover gene functions. This report outlines the elucidation of gene-to-gene and metabolite-to-gene networks via integration of metabolomics with transcriptomics and presents a strategy for the identification of novel gene functions. Metabolomics and transcriptomics data of Arabidopsis grown under sulfur deficiency were combined and analyzed by batch-learning self-organizing mapping. A group of metabolites/genes regulated by the same mechanism clustered together. The metabolism of glucosinolates was shown to be coordinately regulated. Three uncharacterized putative sulfotransferase genes clustering together with known glucosinolate biosynthesis genes were candidates for involvement in biosynthesis. In vitro enzymatic assays of the recombinant gene products confirmed their functions as desulfoglucosinolate sulfotransferases. Several genes involved in sulfur assimilation clustered with O-acetylserine, which is considered a positive regulator of these genes. The genes involved in anthocyanin biosynthesis clustered with the gene encoding a transcriptional factor that up-regulates specifically anthocyanin biosynthesis genes. These results suggested that regulatory metabolites and transcriptional factor genes can be identified by this approach, based on the assumption that they cluster with the downstream genes they regulate. This strategy is applicable not only to plant but also to other organisms for functional elucidation of unknown genes.

ASJC Scopus Sachgebiete

Zitieren

Elucidation of gene-to-gene and metabolite-to-gene networks in arabidopsis by integration of metabolomics and transcriptomics. / Hirai, Masami Yokota; Klein, Marion; Fujikawa, Yuuta et al.
in: Journal of Biological Chemistry, Jahrgang 280, Nr. 27, 08.07.2005, S. 25590-25595.

Publikation: Beitrag in FachzeitschriftArtikelForschungPeer-Review

Hirai, MY, Klein, M, Fujikawa, Y, Yano, M, Goodenowe, DB, Yamazaki, Y, Kanaya, S, Nakamura, Y, Kitayama, M, Suzuki, H, Sakurai, N, Shibata, D, Tokuhisa, J, Reichelt, M, Gershenzon, J, Papenbrock, J & Saito, K 2005, 'Elucidation of gene-to-gene and metabolite-to-gene networks in arabidopsis by integration of metabolomics and transcriptomics', Journal of Biological Chemistry, Jg. 280, Nr. 27, S. 25590-25595. https://doi.org/10.1074/jbc.M502332200
Hirai, M. Y., Klein, M., Fujikawa, Y., Yano, M., Goodenowe, D. B., Yamazaki, Y., Kanaya, S., Nakamura, Y., Kitayama, M., Suzuki, H., Sakurai, N., Shibata, D., Tokuhisa, J., Reichelt, M., Gershenzon, J., Papenbrock, J., & Saito, K. (2005). Elucidation of gene-to-gene and metabolite-to-gene networks in arabidopsis by integration of metabolomics and transcriptomics. Journal of Biological Chemistry, 280(27), 25590-25595. https://doi.org/10.1074/jbc.M502332200
Hirai MY, Klein M, Fujikawa Y, Yano M, Goodenowe DB, Yamazaki Y et al. Elucidation of gene-to-gene and metabolite-to-gene networks in arabidopsis by integration of metabolomics and transcriptomics. Journal of Biological Chemistry. 2005 Jul 8;280(27):25590-25595. doi: 10.1074/jbc.M502332200
Hirai, Masami Yokota ; Klein, Marion ; Fujikawa, Yuuta et al. / Elucidation of gene-to-gene and metabolite-to-gene networks in arabidopsis by integration of metabolomics and transcriptomics. in: Journal of Biological Chemistry. 2005 ; Jahrgang 280, Nr. 27. S. 25590-25595.
Download
@article{fcf36b83bb4c450082c7b5b1b196be30,
title = "Elucidation of gene-to-gene and metabolite-to-gene networks in arabidopsis by integration of metabolomics and transcriptomics",
abstract = "Since the completion of genome sequences of model organisms, functional identification of unknown genes has become a principal challenge in biology. Postgenomics sciences such as transcriptomics, proteomics, and metabolomics are expected to discover gene functions. This report outlines the elucidation of gene-to-gene and metabolite-to-gene networks via integration of metabolomics with transcriptomics and presents a strategy for the identification of novel gene functions. Metabolomics and transcriptomics data of Arabidopsis grown under sulfur deficiency were combined and analyzed by batch-learning self-organizing mapping. A group of metabolites/genes regulated by the same mechanism clustered together. The metabolism of glucosinolates was shown to be coordinately regulated. Three uncharacterized putative sulfotransferase genes clustering together with known glucosinolate biosynthesis genes were candidates for involvement in biosynthesis. In vitro enzymatic assays of the recombinant gene products confirmed their functions as desulfoglucosinolate sulfotransferases. Several genes involved in sulfur assimilation clustered with O-acetylserine, which is considered a positive regulator of these genes. The genes involved in anthocyanin biosynthesis clustered with the gene encoding a transcriptional factor that up-regulates specifically anthocyanin biosynthesis genes. These results suggested that regulatory metabolites and transcriptional factor genes can be identified by this approach, based on the assumption that they cluster with the downstream genes they regulate. This strategy is applicable not only to plant but also to other organisms for functional elucidation of unknown genes.",
author = "Hirai, {Masami Yokota} and Marion Klein and Yuuta Fujikawa and Mitsuru Yano and Goodenowe, {Dayan B.} and Yasuyo Yamazaki and Shigehiko Kanaya and Yukiko Nakamura and Masahiko Kitayama and Hideyuki Suzuki and Nozomu Sakurai and Daisuke Shibata and Jim Tokuhisa and Michael Reichelt and Jonathan Gershenzon and Jutta Papenbrock and Kazuki Saito",
year = "2005",
month = jul,
day = "8",
doi = "10.1074/jbc.M502332200",
language = "English",
volume = "280",
pages = "25590--25595",
journal = "Journal of Biological Chemistry",
issn = "0021-9258",
publisher = "American Society for Biochemistry and Molecular Biology Inc.",
number = "27",

}

Download

TY - JOUR

T1 - Elucidation of gene-to-gene and metabolite-to-gene networks in arabidopsis by integration of metabolomics and transcriptomics

AU - Hirai, Masami Yokota

AU - Klein, Marion

AU - Fujikawa, Yuuta

AU - Yano, Mitsuru

AU - Goodenowe, Dayan B.

AU - Yamazaki, Yasuyo

AU - Kanaya, Shigehiko

AU - Nakamura, Yukiko

AU - Kitayama, Masahiko

AU - Suzuki, Hideyuki

AU - Sakurai, Nozomu

AU - Shibata, Daisuke

AU - Tokuhisa, Jim

AU - Reichelt, Michael

AU - Gershenzon, Jonathan

AU - Papenbrock, Jutta

AU - Saito, Kazuki

PY - 2005/7/8

Y1 - 2005/7/8

N2 - Since the completion of genome sequences of model organisms, functional identification of unknown genes has become a principal challenge in biology. Postgenomics sciences such as transcriptomics, proteomics, and metabolomics are expected to discover gene functions. This report outlines the elucidation of gene-to-gene and metabolite-to-gene networks via integration of metabolomics with transcriptomics and presents a strategy for the identification of novel gene functions. Metabolomics and transcriptomics data of Arabidopsis grown under sulfur deficiency were combined and analyzed by batch-learning self-organizing mapping. A group of metabolites/genes regulated by the same mechanism clustered together. The metabolism of glucosinolates was shown to be coordinately regulated. Three uncharacterized putative sulfotransferase genes clustering together with known glucosinolate biosynthesis genes were candidates for involvement in biosynthesis. In vitro enzymatic assays of the recombinant gene products confirmed their functions as desulfoglucosinolate sulfotransferases. Several genes involved in sulfur assimilation clustered with O-acetylserine, which is considered a positive regulator of these genes. The genes involved in anthocyanin biosynthesis clustered with the gene encoding a transcriptional factor that up-regulates specifically anthocyanin biosynthesis genes. These results suggested that regulatory metabolites and transcriptional factor genes can be identified by this approach, based on the assumption that they cluster with the downstream genes they regulate. This strategy is applicable not only to plant but also to other organisms for functional elucidation of unknown genes.

AB - Since the completion of genome sequences of model organisms, functional identification of unknown genes has become a principal challenge in biology. Postgenomics sciences such as transcriptomics, proteomics, and metabolomics are expected to discover gene functions. This report outlines the elucidation of gene-to-gene and metabolite-to-gene networks via integration of metabolomics with transcriptomics and presents a strategy for the identification of novel gene functions. Metabolomics and transcriptomics data of Arabidopsis grown under sulfur deficiency were combined and analyzed by batch-learning self-organizing mapping. A group of metabolites/genes regulated by the same mechanism clustered together. The metabolism of glucosinolates was shown to be coordinately regulated. Three uncharacterized putative sulfotransferase genes clustering together with known glucosinolate biosynthesis genes were candidates for involvement in biosynthesis. In vitro enzymatic assays of the recombinant gene products confirmed their functions as desulfoglucosinolate sulfotransferases. Several genes involved in sulfur assimilation clustered with O-acetylserine, which is considered a positive regulator of these genes. The genes involved in anthocyanin biosynthesis clustered with the gene encoding a transcriptional factor that up-regulates specifically anthocyanin biosynthesis genes. These results suggested that regulatory metabolites and transcriptional factor genes can be identified by this approach, based on the assumption that they cluster with the downstream genes they regulate. This strategy is applicable not only to plant but also to other organisms for functional elucidation of unknown genes.

UR - http://www.scopus.com/inward/record.url?scp=21844472259&partnerID=8YFLogxK

U2 - 10.1074/jbc.M502332200

DO - 10.1074/jbc.M502332200

M3 - Article

C2 - 15866872

AN - SCOPUS:21844472259

VL - 280

SP - 25590

EP - 25595

JO - Journal of Biological Chemistry

JF - Journal of Biological Chemistry

SN - 0021-9258

IS - 27

ER -

Von denselben Autoren