ArticlePlant physiology2015
Patterns of metabolite changes identified from large-scale gene perturbations in Arabidopsis using a genome-scale metabolic network.
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Article in Plant physiology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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15 citing papers in PubMed.
- Multi-genome metabolic modeling predicts functional inter-dependencies in the Arabidopsis root microbiome.Microbiome · 2022Article
- Metabolomics: a systems biology approach for enhancing heat stress tolerance in plants.Plant cell reports · 2022Review
- Functional prediction of environmental variables using metabolic networks.Scientific reports · 2021Article
- Integrative omics of Lonicera japonica Thunb. Flower development unravels molecular changes regulating secondary metabolites.Journal of proteomics · 2019Article
- Widely targeted metabolome and transcriptome landscapes of Allium fistulosum-A. cepa chromosome addition lines revealed a flavonoid hot spot on chromosome 5A.Scientific reports · 2019Article
- Computational Identification of Metabolic Pathways ofInternational journal of genomics · 2019Article
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- Network Architecture and Mutational Sensitivity of theFrontiers in molecular biosciences · 2018Article
- In Silico Knockout Screening ofBioMed research international · 2018Article
- A Multi-Omics Analysis Pipeline for the Metabolic Pathway Reconstruction in the Orphan SpeciesFrontiers in plant science · 2018Article
- Metabolite-Centric Reporter Pathway and Tripartite Network Analysis ofFrontiers in bioengineering and biotechnology · 2018Article
- How close are we to complete annotation of metabolomes?Current opinion in chemical biology · 2017Review
- Considerations when choosing a genetic model organism for metabolomics studies.Current opinion in chemical biology · 2017Review
- New views on the selection acting on genetic polymorphism in central metabolic genes.Annals of the New York Academy of Sciences · 2017Review
- Mathematical Modeling and Dynamic Simulation of Metabolic Reaction Systems Using Metabolome Time Series Data.Frontiers in molecular biosciences · 2016Review
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Authors and funding
11 authors.
Taehyong KimDepartment of Plant Biology, Carnegie Institution for Science, Stanford, California 94305 (T.K., K.D., R.N.-P., S.Y.R.);Department of Biotechnology, Yonsei University, Seoul 120-749, South Korea (I.L.); Genome Center, University of California, Davis, California 95616 (O.F.); M. J. Murdock Metabolomics Laboratory, Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164 (B.M.L.); Center for Metabolic Biology, Department of Biochemistry, Biophysics, and Molecular Biology (B.J.N.), and Department of Genetics, Development, and Cell Biology (E.S.W.), Iowa State University, Ames, Iowa 50011; Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401 (L.S.); andDivision of Biology, Kansas State University, Manhattan, Kansas 66506 (R.W.).
Kate DreherDepartment of Plant Biology, Carnegie Institution for Science, Stanford, California 94305 (T.K., K.D., R.N.-P., S.Y.R.);Department of Biotechnology, Yonsei University, Seoul 120-749, South Korea (I.L.); Genome Center, University of California, Davis, California 95616 (O.F.); M. J. Murdock Metabolomics Laboratory, Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164 (B.M.L.); Center for Metabolic Biology, Department of Biochemistry, Biophysics, and Molecular Biology (B.J.N.), and Department of Genetics, Development, and Cell Biology (E.S.W.), Iowa State University, Ames, Iowa 50011; Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401 (L.S.); andDivision of Biology, Kansas State University, Manhattan, Kansas 66506 (R.W.).
Ricardo Nilo-PoyancoDepartment of Plant Biology, Carnegie Institution for Science, Stanford, California 94305 (T.K., K.D., R.N.-P., S.Y.R.);Department of Biotechnology, Yonsei University, Seoul 120-749, South Korea (I.L.); Genome Center, University of California, Davis, California 95616 (O.F.); M. J. Murdock Metabolomics Laboratory, Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164 (B.M.L.); Center for Metabolic Biology, Department of Biochemistry, Biophysics, and Molecular Biology (B.J.N.), and Department of Genetics, Development, and Cell Biology (E.S.W.), Iowa State University, Ames, Iowa 50011; Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401 (L.S.); andDivision of Biology, Kansas State University, Manhattan, Kansas 66506 (R.W.).
Insuk LeeDepartment of Plant Biology, Carnegie Institution for Science, Stanford, California 94305 (T.K., K.D., R.N.-P., S.Y.R.);Department of Biotechnology, Yonsei University, Seoul 120-749, South Korea (I.L.); Genome Center, University of California, Davis, California 95616 (O.F.); M. J. Murdock Metabolomics Laboratory, Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164 (B.M.L.); Center for Metabolic Biology, Department of Biochemistry, Biophysics, and Molecular Biology (B.J.N.), and Department of Genetics, Development, and Cell Biology (E.S.W.), Iowa State University, Ames, Iowa 50011; Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401 (L.S.); andDivision of Biology, Kansas State University, Manhattan, Kansas 66506 (R.W.).
Oliver FiehnDepartment of Plant Biology, Carnegie Institution for Science, Stanford, California 94305 (T.K., K.D., R.N.-P., S.Y.R.);Department of Biotechnology, Yonsei University, Seoul 120-749, South Korea (I.L.); Genome Center, University of California, Davis, California 95616 (O.F.); M. J. Murdock Metabolomics Laboratory, Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164 (B.M.L.); Center for Metabolic Biology, Department of Biochemistry, Biophysics, and Molecular Biology (B.J.N.), and Department of Genetics, Development, and Cell Biology (E.S.W.), Iowa State University, Ames, Iowa 50011; Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401 (L.S.); andDivision of Biology, Kansas State University, Manhattan, Kansas 66506 (R.W.).
Bernd Markus LangeDepartment of Plant Biology, Carnegie Institution for Science, Stanford, California 94305 (T.K., K.D., R.N.-P., S.Y.R.);Department of Biotechnology, Yonsei University, Seoul 120-749, South Korea (I.L.); Genome Center, University of California, Davis, California 95616 (O.F.); M. J. Murdock Metabolomics Laboratory, Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164 (B.M.L.); Center for Metabolic Biology, Department of Biochemistry, Biophysics, and Molecular Biology (B.J.N.), and Department of Genetics, Development, and Cell Biology (E.S.W.), Iowa State University, Ames, Iowa 50011; Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401 (L.S.); andDivision of Biology, Kansas State University, Manhattan, Kansas 66506 (R.W.).
Basil J NikolauDepartment of Plant Biology, Carnegie Institution for Science, Stanford, California 94305 (T.K., K.D., R.N.-P., S.Y.R.);Department of Biotechnology, Yonsei University, Seoul 120-749, South Korea (I.L.); Genome Center, University of California, Davis, California 95616 (O.F.); M. J. Murdock Metabolomics Laboratory, Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164 (B.M.L.); Center for Metabolic Biology, Department of Biochemistry, Biophysics, and Molecular Biology (B.J.N.), and Department of Genetics, Development, and Cell Biology (E.S.W.), Iowa State University, Ames, Iowa 50011; Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401 (L.S.); andDivision of Biology, Kansas State University, Manhattan, Kansas 66506 (R.W.).
Lloyd SumnerDepartment of Plant Biology, Carnegie Institution for Science, Stanford, California 94305 (T.K., K.D., R.N.-P., S.Y.R.);Department of Biotechnology, Yonsei University, Seoul 120-749, South Korea (I.L.); Genome Center, University of California, Davis, California 95616 (O.F.); M. J. Murdock Metabolomics Laboratory, Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164 (B.M.L.); Center for Metabolic Biology, Department of Biochemistry, Biophysics, and Molecular Biology (B.J.N.), and Department of Genetics, Development, and Cell Biology (E.S.W.), Iowa State University, Ames, Iowa 50011; Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401 (L.S.); andDivision of Biology, Kansas State University, Manhattan, Kansas 66506 (R.W.).
Ruth WeltiDepartment of Plant Biology, Carnegie Institution for Science, Stanford, California 94305 (T.K., K.D., R.N.-P., S.Y.R.);Department of Biotechnology, Yonsei University, Seoul 120-749, South Korea (I.L.); Genome Center, University of California, Davis, California 95616 (O.F.); M. J. Murdock Metabolomics Laboratory, Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164 (B.M.L.); Center for Metabolic Biology, Department of Biochemistry, Biophysics, and Molecular Biology (B.J.N.), and Department of Genetics, Development, and Cell Biology (E.S.W.), Iowa State University, Ames, Iowa 50011; Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401 (L.S.); andDivision of Biology, Kansas State University, Manhattan, Kansas 66506 (R.W.).
Eve S WurteleDepartment of Plant Biology, Carnegie Institution for Science, Stanford, California 94305 (T.K., K.D., R.N.-P., S.Y.R.);Department of Biotechnology, Yonsei University, Seoul 120-749, South Korea (I.L.); Genome Center, University of California, Davis, California 95616 (O.F.); M. J. Murdock Metabolomics Laboratory, Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164 (B.M.L.); Center for Metabolic Biology, Department of Biochemistry, Biophysics, and Molecular Biology (B.J.N.), and Department of Genetics, Development, and Cell Biology (E.S.W.), Iowa State University, Ames, Iowa 50011; Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401 (L.S.); andDivision of Biology, Kansas State University, Manhattan, Kansas 66506 (R.W.).
Seung Y RheeDepartment of Plant Biology, Carnegie Institution for Science, Stanford, California 94305 (T.K., K.D., R.N.-P., S.Y.R.);Department of Biotechnology, Yonsei University, Seoul 120-749, South Korea (I.L.); Genome Center, University of California, Davis, California 95616 (O.F.); M. J. Murdock Metabolomics Laboratory, Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164 (B.M.L.); Center for Metabolic Biology, Department of Biochemistry, Biophysics, and Molecular Biology (B.J.N.), and Department of Genetics, Development, and Cell Biology (E.S.W.), Iowa State University, Ames, Iowa 50011; Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401 (L.S.); andDivision of Biology, Kansas State University, Manhattan, Kansas 66506 (R.W.) srhee@carnegiescience.edu.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Metabolomics enables quantitative evaluation of metabolic changes caused by genetic or environmental perturbations. However, little is known about how perturbing a single gene changes the metabolic system as a whole and which network and functional properties are involved in this response. To answer this question, we investigated the metabolite profiles from 136 mutants with single gene perturbations of functionally diverse Arabidopsis (Arabidopsis thaliana) genes. Fewer than 10 metabolites were changed significantly relative to the wild type in most of the mutants, indicating that the metabolic network was robust to perturbations of single metabolic genes. These changed metabolites were closer to each other in a genome-scale metabolic network than expected by chance, supporting the notion that the genetic perturbations changed the network more locally than globally. Surprisingly, the changed metabolites were close to the perturbed reactions in only 30% of the mutants of the well-characterized genes. To determine the factors that contributed to the distance between the observed metabolic changes and the perturbation site in the network, we examined nine network and functional properties of the perturbed genes. Only the isozyme number affected the distance between the perturbed reactions and changed metabolites. This study revealed patterns of metabolic changes from large-scale gene perturbations and relationships between characteristics of the perturbed genes and metabolic changes.
Indexed as
ArabidopsisGene Expression Regulation, PlantMetabolomicsArabidopsis ProteinsGenome, PlantMetabolic Networks and PathwaysMetabolomeMutationArabidopsis Proteins
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