Elucidation of gene-to-gene and metabolite-to-gene networks in arabidopsis by integration of metabolomics and transcriptomics.
Since the completion of genome sequences of model organisms, functional identification of unknown genes has become a principal challenge in biology. Post-genomics 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.
Hirai
Masami Yokota
MY
Department of Molecular Biology and Biotechnology, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 263-8522, Japan.
Klein
Marion
M
Fujikawa
Yuuta
Y
Yano
Mitsuru
M
Goodenowe
Dayan B
DB
Yamazaki
Yasuyo
Y
Kanaya
Shigehiko
S
Nakamura
Yukiko
Y
Kitayama
Masahiko
M
Suzuki
Hideyuki
H
Sakurai
Nozomu
N
Shibata
Daisuke
D
Tokuhisa
Jim
J
Reichelt
Michael
M
Gershenzon
Jonathan
J
Papenbrock
Jutta
J
Saito
Kazuki
K
D017360:Arabidopsis / Q000235:genetics* / Q000378:metabolism*; D004734:Energy Metabolism / Q000502:physiology*; D018506:Gene Expression Regulation, Plant / Q000502:physiology*; D023281:Genomics / Q000379:methods*; D005961:Glucosinolates / Q000235:genetics; D012694:Serine / Q000031:analogs & derivatives* / Q000378:metabolism; D015238:Sulfotransferases / Q000235:genetics; D013455:Sulfur / Q000378:metabolism; D014157:Transcription Factors / Q000378:metabolism; D014158:Transcription, Genetic / Q000502:physiology
D005961:Glucosinolates; D014157:Transcription Factors; D012694:Serine; D013455:Sulfur; D015238:Sulfotransferases; C043943:O-acetylserine