151
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Wang RS, Saadatpour A, Albert R. Boolean modeling in systems biology: an overview of methodology and applications. Phys Biol 2012; 9:055001. [DOI: 10.1088/1478-3975/9/5/055001] [Citation(s) in RCA: 293] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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152
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Bowerman PA, Ramirez MV, Price MB, Helm RF, Winkel BSJ. Analysis of T-DNA alleles of flavonoid biosynthesis genes in Arabidopsis ecotype Columbia. BMC Res Notes 2012; 5:485. [PMID: 22947320 PMCID: PMC3526476 DOI: 10.1186/1756-0500-5-485] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Accepted: 08/23/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The flavonoid pathway is a long-standing and important tool for plant genetics, biochemistry, and molecular biology. Numerous flavonoid mutants have been identified in Arabidopsis over the past several decades in a variety of ecotypes. Here we present an analysis of Arabidopsis lines of ecotype Columbia carrying T-DNA insertions in genes encoding enzymes of the central flavonoid pathway. We also provide a comprehensive summary of various mutant alleles for these structural genes that have been described in the literature to date in a wide variety of ecotypes. FINDINGS The confirmed knockout lines present easily-scorable phenotypes due to altered pigmentation of the seed coat (or testa). Knockouts for seven alleles for six flavonoid biosynthetic genes were confirmed by PCR and characterized by UPLC for altered flavonol content. CONCLUSION Seven mutant lines for six genes of the central flavonoid pathway were characterized in ecotype, Columbia. These lines represent a useful resource for integrating biochemical and physiological studies with genomic, transcriptomic, and proteomic data, much of which has been, and continues to be, generated in the Columbia background.
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153
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Obata T, Fernie AR. The use of metabolomics to dissect plant responses to abiotic stresses. Cell Mol Life Sci 2012; 69:3225-43. [PMID: 22885821 PMCID: PMC3437017 DOI: 10.1007/s00018-012-1091-5] [Citation(s) in RCA: 454] [Impact Index Per Article: 37.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2012] [Revised: 07/09/2012] [Accepted: 07/09/2012] [Indexed: 12/15/2022]
Abstract
Plant metabolism is perturbed by various abiotic stresses. As such the metabolic network of plants must be reconfigured under stress conditions in order to allow both the maintenance of metabolic homeostasis and the production of compounds that ameliorate the stress. The recent development and adoption of metabolomics and systems biology approaches enable us not only to gain a comprehensive overview, but also a detailed analysis of crucial components of the plant metabolic response to abiotic stresses. In this review we introduce the analytical methods used for plant metabolomics and describe their use in studies related to the metabolic response to water, temperature, light, nutrient limitation, ion and oxidative stresses. Both similarity and specificity of the metabolic responses against diverse abiotic stress are evaluated using data available in the literature. Classically discussed stress compounds such as proline, γ-amino butyrate and polyamines are reviewed, and the widespread importance of branched chain amino acid metabolism under stress condition is discussed. Finally, where possible, mechanistic insights into metabolic regulatory processes are discussed.
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Affiliation(s)
- Toshihiro Obata
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
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154
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Kim S, Yun EJ, Hossain MA, Lee H, Kim KH. Global profiling of ultraviolet-induced metabolic disruption in Melissa officinalis by using gas chromatography-mass spectrometry. Anal Bioanal Chem 2012; 404:553-62. [PMID: 22729379 DOI: 10.1007/s00216-012-6142-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2012] [Revised: 05/21/2012] [Accepted: 05/23/2012] [Indexed: 10/28/2022]
Abstract
Melissa officinalis contains various secondary metabolites that have health benefits. Generally, irradiating plants with ultraviolet (UV)-B induces the accumulation of secondary metabolites in plants. To understand the effect of UV-B irradiation on the metabolism of M. officinalis, metabolomics based on gas chromatography-mass spectrometry (GC-MS) was used in this study. The GC-MS analysis revealed 37 identified metabolites from various chemical classes, including alcohols, amino acids, inorganic acids, organic acids, and sugars. The metabolite profiles of the groups of M. officinalis irradiated with UV-B were separated and differentiated according to their irradiation times (i.e., 0, 1, and 2 h), using principal component analysis (PCA) and hierarchical clustering analysis (HCA), respectively. The PCA score plots of PC1 and PC2 showed that the three groups with different irradiation times followed a certain trajectory with increasing UV-B irradiation. HCA revealed that metabolic patterns differed among the three groups, and the 1 h-irradiated group was more similar to the control group (0 h) than the 2 h-irradiated group. In particular, UV-B irradiation of plants led to a decrease in sugars such as fructose, galactose, sucrose, and trehalose and an increase in metabolites in the tricarboxylic acid cycle, the proline-linked pentose phosphate pathway, and the phenylpropanoid pathway. This study demonstrated that metabolite profiling with GC-MS is useful for gaining a holistic understanding of UV-induced changes in plant metabolism.
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Affiliation(s)
- Sooah Kim
- School of Life Sciences and Biotechnology, Korea University, Seoul, 136-713, Republic of Korea
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155
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Singh D, Singh PK, Chaudhary S, Mehla K, Kumar S. Exome sequencing and advances in crop improvement. ADVANCES IN GENETICS 2012; 79:87-121. [PMID: 22989766 DOI: 10.1016/b978-0-12-394395-8.00003-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Next-generation sequencing strategies have opened new vistas for molecular plant breeding. The sequence information obtained by the advent of next-generation sequencing provides a valuable tool not only for improving domesticated crops but also for investigating the natural evolution of crops. Such information provides an enormous potential for sustainable agriculture. In this review, we discuss how such sequencing approaches have transformed exome sequencing into a practical utility that has enormous potential for crop improvement in agriculture. Furthermore, we also describe the future of crop improvement beyond the exome sequencing strategies.
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Affiliation(s)
- Devi Singh
- Molecular Biology Laboratory, Department of Genetics and Plant Breeding, Sardar Vallabhbhai Patel University of Agriculture and Technology, Meerut, UP, India
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156
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Yonekura-Sakakibara K, Fukushima A, Nakabayashi R, Hanada K, Matsuda F, Sugawara S, Inoue E, Kuromori T, Ito T, Shinozaki K, Wangwattana B, Yamazaki M, Saito K. Two glycosyltransferases involved in anthocyanin modification delineated by transcriptome independent component analysis in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2012; 69:154-67. [PMID: 21899608 PMCID: PMC3507004 DOI: 10.1111/j.1365-313x.2011.04779.x] [Citation(s) in RCA: 131] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2011] [Revised: 09/01/2011] [Accepted: 09/05/2011] [Indexed: 05/18/2023]
Abstract
To identify candidate genes involved in Arabidopsis flavonoid biosynthesis, we applied transcriptome coexpression analysis and independent component analyses with 1388 microarray data from publicly available databases. Two glycosyltransferases, UGT79B1 and UGT84A2 were found to cluster with anthocyanin biosynthetic genes. Anthocyanin was drastically reduced in ugt79b1 knockout mutants. Recombinant UGT79B1 protein converted cyanidin 3-O-glucoside to cyanidin 3-O-xylosyl(1→2)glucoside. UGT79B1 recognized 3-O-glucosylated anthocyanidins/flavonols and uridine diphosphate (UDP)-xylose, but not 3,5-O-diglucosylated anthocyanidins, indicating that UGT79B1 encodes anthocyanin 3-O-glucoside: 2''-O-xylosyltransferase. UGT84A2 is known to encode sinapic acid: UDP-glucosyltransferase. In ugt84a2 knockout mutants, a major sinapoylated anthocyanin was drastically reduced. A comparison of anthocyanin profiles in ugt84a knockout mutants indicated that UGT84A2 plays a major role in sinapoylation of anthocyanin, and that other UGT84As contribute the production of 1-O-sinapoylglucose to a lesser extent. These data suggest major routes from cyanidin 3-O-glucoside to the most highly modified cyanidin in the potential intricate anthocyanin modification pathways in Arabidopsis.
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Affiliation(s)
- Keiko Yonekura-Sakakibara
- RIKEN Plant Science Center1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
- Graduate School of Nanobiosciences, Yokohama City University1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Atsushi Fukushima
- RIKEN Plant Science Center1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Ryo Nakabayashi
- RIKEN Plant Science Center1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
- Graduate School of Pharmaceutical Sciences, Chiba University1-33 Yayoi-cho, Inage-ku, Chiba 263-8522, Japan
- CREST, Japan Science and Technology Agency4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Kousuke Hanada
- RIKEN Plant Science Center1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Fumio Matsuda
- RIKEN Plant Science Center1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Satoko Sugawara
- RIKEN Plant Science Center1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Eri Inoue
- RIKEN Plant Science Center1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Takashi Kuromori
- RIKEN Plant Science Center1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Takuya Ito
- Antibiotics LaboratoryRIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Kazuo Shinozaki
- RIKEN Plant Science Center1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Bunyapa Wangwattana
- Graduate School of Pharmaceutical Sciences, Chiba University1-33 Yayoi-cho, Inage-ku, Chiba 263-8522, Japan
| | - Mami Yamazaki
- Graduate School of Pharmaceutical Sciences, Chiba University1-33 Yayoi-cho, Inage-ku, Chiba 263-8522, Japan
- CREST, Japan Science and Technology Agency4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Kazuki Saito
- RIKEN Plant Science Center1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
- Graduate School of Pharmaceutical Sciences, Chiba University1-33 Yayoi-cho, Inage-ku, Chiba 263-8522, Japan
- *For correspondence (fax +81 45 503 9489; e-mail )
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157
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Okazaki Y, Saito K. Recent advances of metabolomics in plant biotechnology. PLANT BIOTECHNOLOGY REPORTS 2012; 6:1-15. [PMID: 22308170 PMCID: PMC3262138 DOI: 10.1007/s11816-011-0191-2] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2011] [Accepted: 07/05/2011] [Indexed: 05/18/2023]
Abstract
Biotechnology, including genetic modification, is a very important approach to regulate the production of particular metabolites in plants to improve their adaptation to environmental stress, to improve food quality, and to increase crop yield. Unfortunately, these approaches do not necessarily lead to the expected results due to the highly complex mechanisms underlying metabolic regulation in plants. In this context, metabolomics plays a key role in plant molecular biotechnology, where plant cells are modified by the expression of engineered genes, because we can obtain information on the metabolic status of cells via a snapshot of their metabolome. Although metabolome analysis could be used to evaluate the effect of foreign genes and understand the metabolic state of cells, there is no single analytical method for metabolomics because of the wide range of chemicals synthesized in plants. Here, we describe the basic analytical advancements in plant metabolomics and bioinformatics and the application of metabolomics to the biological study of plants.
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Affiliation(s)
- Yozo Okazaki
- RIKEN Plant Science Center, Tsurumi-ku, Yokohama, 230-0045 Japan
| | - Kazuki Saito
- RIKEN Plant Science Center, Tsurumi-ku, Yokohama, 230-0045 Japan
- Graduate School of Pharmaceutical Sciences, Chiba University, Inage-ku, Chiba, 263-8522 Japan
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158
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Falcone Ferreyra ML, Rius SP, Casati P. Flavonoids: biosynthesis, biological functions, and biotechnological applications. FRONTIERS IN PLANT SCIENCE 2012; 3:222. [PMID: 23060891 PMCID: PMC3460232 DOI: 10.3389/fpls.2012.00222] [Citation(s) in RCA: 743] [Impact Index Per Article: 61.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2012] [Accepted: 09/11/2012] [Indexed: 05/18/2023]
Abstract
Flavonoids are widely distributed secondary metabolites with different metabolic functions in plants. The elucidation of the biosynthetic pathways, as well as their regulation by MYB, basic helix-loop-helix (bHLH), and WD40-type transcription factors, has allowed metabolic engineering of plants through the manipulation of the different final products with valuable applications. The present review describes the regulation of flavonoid biosynthesis, as well as the biological functions of flavonoids in plants, such as in defense against UV-B radiation and pathogen infection, nodulation, and pollen fertility. In addition, we discuss different strategies and achievements through the genetic engineering of flavonoid biosynthesis with implication in the industry and the combinatorial biosynthesis in microorganisms by the reconstruction of the pathway to obtain high amounts of specific compounds.
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Affiliation(s)
| | | | - Paula Casati
- *Correspondence: Paula Casati, Centro de Estudios Fotosintéticos y Bioquímicos, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina. e-mail:
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159
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Mochida K, Shinozaki K. Advances in omics and bioinformatics tools for systems analyses of plant functions. PLANT & CELL PHYSIOLOGY 2011; 52:2017-38. [PMID: 22156726 PMCID: PMC3233218 DOI: 10.1093/pcp/pcr153] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Omics and bioinformatics are essential to understanding the molecular systems that underlie various plant functions. Recent game-changing sequencing technologies have revitalized sequencing approaches in genomics and have produced opportunities for various emerging analytical applications. Driven by technological advances, several new omics layers such as the interactome, epigenome and hormonome have emerged. Furthermore, in several plant species, the development of omics resources has progressed to address particular biological properties of individual species. Integration of knowledge from omics-based research is an emerging issue as researchers seek to identify significance, gain biological insights and promote translational research. From these perspectives, we provide this review of the emerging aspects of plant systems research based on omics and bioinformatics analyses together with their associated resources and technological advances.
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Affiliation(s)
- Keiichi Mochida
- RIKEN Biomass Engineering Program, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045 Japan.
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160
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Tohge T, Kusano M, Fukushima A, Saito K, Fernie AR. Transcriptional and metabolic programs following exposure of plants to UV-B irradiation. PLANT SIGNALING & BEHAVIOR 2011; 6:1987-92. [PMID: 22112450 PMCID: PMC3337192 DOI: 10.4161/psb.6.12.18240] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
In order to adapt to environmental changes of light species and intensity, higher plants furnish complicate signaling systems such as the UVR/COP/HY5 cascade which links several diverse classes of photoreceptors. In addition UV-B light provokes accelerated production of UV-B protectants such as flavonoids and vitamins. Following intensive research efforts, genes in the UV-B signaling cascade have been characterized via forward genetics approaches following mutant screens relying on sensitivity to UV-B irradiation. However detailed processes of the linkage between light signaling and the upregulation of metabolite accumulation remain unclear. Here we review both the light signal cascades and metabolite pathways responding to UV-B exposure. Finally we generate co-expression network analysis using published data in order to find novel candidate genes which link light signaling and transcriptional regulation to metabolic biosynthesis in attempt to describe how these processes are interlinked.
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Affiliation(s)
- Takayuki Tohge
- RIKEN Plant Science Center; Yokohama, Japan
- Max-Planck Institute for Molecular Plant Physiology; Potsdam-Golm, Germany
- Correspondence to: Takayuki Tohge, or Alisdair R. Fernie,
| | | | | | - Kazuki Saito
- RIKEN Plant Science Center; Yokohama, Japan
- Graduate School of Pharmaceutical Sciences; Chiba University; Chiba, Japan
| | - Alisdair R. Fernie
- Max-Planck Institute for Molecular Plant Physiology; Potsdam-Golm, Germany
- Correspondence to: Takayuki Tohge, or Alisdair R. Fernie,
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161
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Cramer GR, Urano K, Delrot S, Pezzotti M, Shinozaki K. Effects of abiotic stress on plants: a systems biology perspective. BMC PLANT BIOLOGY 2011; 11:163. [PMID: 22094046 PMCID: PMC3252258 DOI: 10.1186/1471-2229-11-163] [Citation(s) in RCA: 527] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2011] [Accepted: 11/17/2011] [Indexed: 05/18/2023]
Abstract
The natural environment for plants is composed of a complex set of abiotic stresses and biotic stresses. Plant responses to these stresses are equally complex. Systems biology approaches facilitate a multi-targeted approach by allowing one to identify regulatory hubs in complex networks. Systems biology takes the molecular parts (transcripts, proteins and metabolites) of an organism and attempts to fit them into functional networks or models designed to describe and predict the dynamic activities of that organism in different environments. In this review, research progress in plant responses to abiotic stresses is summarized from the physiological level to the molecular level. New insights obtained from the integration of omics datasets are highlighted. Gaps in our knowledge are identified, providing additional focus areas for crop improvement research in the future.
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Affiliation(s)
- Grant R Cramer
- Department of Biochemistry and Molecular Biology, Mail Stop 330, University of Nevada, Reno, Nevada 89557, USA
| | - Kaoru Urano
- Gene Discovery Research Group, RIKEN Plant Science Center, 3-1-1 Koyadai, Tsukuba 305-0074, Japan
| | - Serge Delrot
- Univ. Bordeaux, ISVV, Ecophysiologie et Génomique Fonctionnelle de la Vigne, UMR 1287, F-33882 Villenave d'Ornon, France
| | - Mario Pezzotti
- Dipartimento di Biotecnologie, Università di Verona, Strada le Grazie 15, 37134 Verona, Italy
| | - Kazuo Shinozaki
- Gene Discovery Research Group, RIKEN Plant Science Center, 3-1-1 Koyadai, Tsukuba 305-0074, Japan
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162
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Gupta KJ, Bauwe H, Mur LAJ. Nitric oxide, nitrate reductase and UV-B tolerance. TREE PHYSIOLOGY 2011; 31:795-7. [PMID: 21890707 DOI: 10.1093/treephys/tpr080] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Affiliation(s)
- Kapuganti J Gupta
- Department of Plant Physiology, University of Rostock, Albert Einstein Strasse 3, D-10859 Rostock, Germany.
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163
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Klie S, Krueger S, Krall L, Giavalisco P, Flügge UI, Willmitzer L, Steinhauser D. Analysis of the compartmentalized metabolome - a validation of the non-aqueous fractionation technique. FRONTIERS IN PLANT SCIENCE 2011; 2:55. [PMID: 22645541 PMCID: PMC3355776 DOI: 10.3389/fpls.2011.00055] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2011] [Accepted: 09/05/2011] [Indexed: 05/17/2023]
Abstract
With the development of high-throughput metabolic technologies, a plethora of primary and secondary compounds have been detected in the plant cell. However, there are still major gaps in our understanding of the plant metabolome. This is especially true with regards to the compartmental localization of these identified metabolites. Non-aqueous fractionation (NAF) is a powerful technique for the determination of subcellular metabolite distributions in eukaryotic cells, and it has become the method of choice to analyze the distribution of a large number of metabolites concurrently. However, the NAF technique produces a continuous gradient of metabolite distributions, not discrete assignments. Resolution of these distributions requires computational analyses based on marker molecules to resolve compartmental localizations. In this article we focus on expanding the computational analysis of data derived from NAF. Along with an experimental workflow, we describe the critical steps in NAF experiments and how computational approaches can aid in assessing the quality and robustness of the derived data. For this, we have developed and provide a new version (v1.2) of the BestFit command line tool for calculation and evaluation of subcellular metabolite distributions. Furthermore, using both simulated and experimental data we show the influence on estimated subcellular distributions by modulating important parameters, such as the number of fractions taken or which marker molecule is selected. Finally, we discuss caveats and benefits of NAF analysis in the context of the compartmentalized metabolome.
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Affiliation(s)
- Sebastian Klie
- Department of Molecular Physiology, Max Planck Institute of Molecular Plant PhysiologyPotsdam-Golm, Germany
| | - Stephan Krueger
- Botanical Institute II, University of CologneCologne, Germany
| | - Leonard Krall
- Department of Molecular Physiology, Max Planck Institute of Molecular Plant PhysiologyPotsdam-Golm, Germany
| | - Patrick Giavalisco
- Department of Molecular Physiology, Max Planck Institute of Molecular Plant PhysiologyPotsdam-Golm, Germany
| | - Ulf-Ingo Flügge
- Botanical Institute II, University of CologneCologne, Germany
| | - Lothar Willmitzer
- Department of Molecular Physiology, Max Planck Institute of Molecular Plant PhysiologyPotsdam-Golm, Germany
| | - Dirk Steinhauser
- Department of Molecular Physiology, Max Planck Institute of Molecular Plant PhysiologyPotsdam-Golm, Germany
- *Correspondence: Dirk Steinhauser, Department of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany. e-mail:
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164
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Tohge T, Mettler T, Arrivault S, Carroll AJ, Stitt M, Fernie AR. From models to crop species: caveats and solutions for translational metabolomics. FRONTIERS IN PLANT SCIENCE 2011; 2:61. [PMID: 22639601 PMCID: PMC3355600 DOI: 10.3389/fpls.2011.00061] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2011] [Accepted: 09/13/2011] [Indexed: 05/04/2023]
Abstract
Although plant metabolomics is largely carried out on Arabidopsis it is essentially genome-independent, and thus potentially applicable to a wide range of species. However, transfer between species, or even between different tissues of the same species, is not facile. This is because the reliability of protocols for harvesting, handling and analysis depends on the biological features and chemical composition of the plant tissue. In parallel with the diversification of model species it is important to establish good handling and analytic practice, in order to augment computational comparisons between tissues and species. Liquid chromatography-mass spectrometry (LC-MS)-based metabolomics is one of the powerful approaches for metabolite profiling. By using a combination of different extraction methods, separation columns, and ion detection, a very wide range of metabolites can be analyzed. However, its application requires careful attention to exclude potential pitfalls, including artifactual changes in metabolite levels during sample preparation under variations of light or temperature and analytic errors due to ion suppression. Here we provide case studies with two different LC-MS-based metabolomics platforms and four species (Arabidopsis thaliana, Chlamydomonas reinhardtii, Solanum lycopersicum, and Oryza sativa) that illustrate how such dangers can be detected and circumvented.
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Affiliation(s)
- Takayuki Tohge
- Max-Planck-Institute for Molecular Plant PhysiologyPotsdam-Golm, Germany
- *Correspondence: Takayuki Tohge, Max-Planck-Institute for Molecular Plant Physiology, Am Muehlenberg 1, 14476 Potsdam-Golm, Germany. e-mail:
| | - Tabea Mettler
- Max-Planck-Institute for Molecular Plant PhysiologyPotsdam-Golm, Germany
| | | | - Adam James Carroll
- Australian Research Council Centre of Excellence in Plant Energy Biology, The Australian National UniversityCanberra, ACT, Australia
| | - Mark Stitt
- Max-Planck-Institute for Molecular Plant PhysiologyPotsdam-Golm, Germany
| | - Alisdair R. Fernie
- Max-Planck-Institute for Molecular Plant PhysiologyPotsdam-Golm, Germany
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