Metabolomic Characterization of Knockout Mutants in Arabidopsis: Development of a Metabolite Profiling Database for Knockout Mutants in Arabidopsis

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2014-07
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Fukushima, Atsushi
Kusano, Miyako
Mejia, Ramon Francisco
Iwasa, Mami
Kobayashi, Makoto
Hayashi, Naomi
Watanabe-Takahashi, Akiko
Narisawa, Tomoko
Tohge, Takayuki
Hur, Manhoi
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Copyright 2014 American Society of Plant Biologists
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Wurtele, Eve
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Nikolau, Basil
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Genetics, Development and Cell Biology

The Department of Genetics, Development, and Cell Biology seeks to teach subcellular and cellular processes, genome dynamics, cell structure and function, and molecular mechanisms of development, in so doing offering a Major in Biology and a Major in Genetics.

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The Department of Genetics, Development, and Cell Biology was founded in 2005.

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NSF Engineering Research Center for Biorenewable Chemicals
Founded in 2008 with more than $44M in federal, industry, and Iowa State University funding, CBiRC works in tandem with Iowa and the nation’s growing biosciences sector. CBiRC’s goal is to lead the transformation of the chemical industry toward a future where chemicals derived from biomass resources will lead to the production of new bioproducts to meet evolving societal needs.
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Abstract
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/.
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This article is published as Fukushima, Atsushi, Miyako Kusano, Ramon Francisco Mejia, Mami Iwasa, Makoto Kobayashi, Naomi Hayashi, Akiko Watanabe-Takahashi et al. "Metabolomic characterization of knockout mutants in Arabidopsis: development of a metabolite profiling database for knockout mutants in Arabidopsis." Plant physiology 165, no. 3 (2014): 948-961. doi:10.1104/pp.114.240986. Posted with permission. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
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