JIPB
Journal of Integrative Plant Biology
Free Access
Editorial
Plant metabolomics and metabolic biology Plants produce a large array of specialized metabolites (natural products) that not only are essential for growth and development, but also play important roles in adaptation to the variable stressful environments. Also, many plant metabolites are essential nutrient elements for humans and serve as natural drugs. However, study of the biosynthesis of natural products is still in its infancy, because more than 90% of plant metabolites are unknown and only a small number of genes/ enzymes involved in metabolism are identified in the model plants Arabidopsis and rice. In the post‐genomics era, metabolomics – defined as the analysis of the total population of metabolites in a given sample, cell or tissue – and the integration of the data in the context of functional genomics, is attractive for analysis of global metabolic changes in plant development and responds to different environmental stresses. Metabolomic analysis would greatly accelerate our processes in deciphering the function of an individual gene in a metabolic pathway, building metabolic networks, identifying metabolic regulators, and more importantly establishing causal relations between metabolic pathways and biologic functions in plants. In this special issue on metabolomics and metabolic biology, we present one invited review and 10 research articles. Both gas chromatography mass spectrometry (GC‐ MS) and liquid chromatography mass spectrometry (LC‐MS) are widely used in plant metabolomic analysis. LC‐MS has good potential in separation of polar chemicals which constitute more than 80% of plant metabolites. However, currently, there is no consensus on which LC‐MS method should be used in plant metabolomic studies. In the invited review by Liu and Rochfort (2014), the most promising methods were reviewed, providing plant scientists with up‐to‐date and simplified information regarding the current status of polar metabolite analysis. In the research articles by Lin et al. (2014) and Agarrwal et al. (2014), metabolomic analysis was applied in studies of soybean cultivars, and the interaction between rice and the Asian rice gall midge (Orseolia oryzae Wood‐Mason), respectively. In both cases, metabolite markers (biomarkers) for distinguishing genetically related soybean cultivars and rice‐insect interaction were successfully identified. Untargeted metabolomic analysis of mads3‐4 (a mutant in a gene encoding MADS3 transcription factor) and wild‐type mature anthers by Qu et al. (2014) indicated that the MADS3 gene affects rice anther development far beyond the reactive oxygen species homeostatic regulation. In two research articles by Schwahn et al. (2014) and Dong et al. (2014), sub‐metabolomic analysis was applied in focus on particular types of metabolites, for example, steroidal glycoalkaloids and flavonoids. Comparative analysis of flavonoid contents in various tissues from the two subspecies, Indica and Japonica, revealed tissue‐specific accumulation of most flavonoids and clear differential accumulation of different types of flavonoids. Based on the analysis of a large number of samples from four types of tissues of 169 accessions from tomato and its wild relatives, Schwahn et al. (2014) integrated species and tissue specificity information into the annotation and classification of steroidal glycoalkaloid peaks, allowing refinement of steroidal glycoalSeptember 2014 | Volume 56 | Issue 9 | 814–815
kaloid biosynthesis and detection of putative novel branch points. The cytochrome P450 (CYP) superfamily belonging to monooxygenase, has greatly expanded in the plant genomes. It is believed that members in this family play critical roles in biosynthesis of diversified natural products. In this special issue, the paper by Ma et al. (2014) annotates a total of 174 P450 genes from the mulberry (Morus notabilis C.K. Schn.) genome. The article by Yang et al. (2014) demonstrates that a cytochrome P450‐type carotene hydroxylase (PuCHY1) catalyzes the conversion of b‐carotene into zeaxanthin in the red alga Porphyra umbilicalis. Anthocyanin, a well‐studied plant specialized metabolite, is often accumulated to higher levels under stress, for example, cold, drought, and photo‐oxidative stress. Research by Gan et al. (2014) on the thf1I (thylakoid formation1) mutant in Arabidopsis revealed that the elevated anthocyanin content increases levels of methyl jasmonate, which is served as signals in coordination of plant metabolism and growth in photo‐oxidative stress. On the other hand, a study by Li et al. (2014) focusing on the glandular trichomes of Colquhounia seguinii identifies three new clerodane diterpenoids. Interestingly, all identified compounds showed antifeedant activity against the insect Spodoptera exigua. Finally, this special issue presents the work by Florian et al. (2014), which studies the relationship between transcripts and metabolite levels when plants grown under normal air conditions were transferred to different CO2 and O2 concentrations. An interesting conclusion is that the regulation of the photosynthesis pathways is not mediated at the level of transcription.
Xiaoquan Qi, Professor Special Issue Editor Institute of Botany, the Chinese Academy of Sciences Beijing, China Dabing Zhang, Professor Special Issue Editor Shanghai Jiaotong University Shanghai, China doi: 10.1111/jipb.12247 © 2014 Institute of Botany, Chinese Academy of Sciences
REFERENCES Agarrwal R, Bentur JS, Nair S (2014) Gas chromatography mass spectrometry based metabolic profiling reveals biomarkers involved in rice‐gall midge interactions. J Integr Plant Biol 56: 837–848 Dong X, Chen W, Wang W, Zhang H, Liu X, Luo J (2014) Comprehensive profiling and natural variation of flavonoids in rice. J Integr Plant Biol 56: 876–886 Florian A, Timm S, Nikoloski Z, Tohge T, Bauwe H, Araújo WL, Fernie AR (2014) Analysis of metabolic alterations in Arabidopsis following changes in the carbon dioxide and oxygen partial pressures. J Integr Plant Biol 56: 941–959
www.jipb.net
Editorial
815
Gan Y, Li H, Xie Y, Wu W, Li M, Wang X, Huang J (2014) THF1 mutations lead to increased basal and wound‐induced levels of oxylipins that stimulate anthocyanin biosynthesis via COI1 signaling in Arabidopsis. J Integr Plant Biol 56: 916–927
Ma B, Luo Y, Jia L, Qi X, Zeng Q, Xiang Z, He N (2014) Genome‐ wide identification and expression analyses of cytochrome P450 genes in mulberry (Morus notabilis). J Integr Plant Biol 56: 887– 901
Li CH, Liu Y, Hua J, Luo SH, Li SH (2014) Peltate glandular trichomes of Colquhounia seguinii harbor new defensive clerodane diterpenoids. J Integr Plant Biol 56: 928–940
Qu G, Quan S, Mondol P, Xu J, Zhang D, Shi J (2014) Comparative metabolomic analysis of wild type and mads3 mutant rice anthers. J Integr Plant Biol 56: 849–863
Lin H, Rao J, Shi J, Hu C, Cheng F, Wilson ZA, Zhang D, Quan S (2014) Seed metabolomic study reveals significant metabolite variations and correlations among different soybean cultivars. J Integr Plant Biol 56: 826–836
Schwahn K, de Souza LP, Fernie AR, Tohge T (2014) Metabolomics‐ assisted refinement of the pathways of steroidal glycoalkaloid biosynthesis in the tomato clade. J Integr Plant Biol 56: 864–875
Liu Z, Rochfort S (2014) Recent progress in polar metabolite quantification in plants using liquid chromatography‐mass spectrometry. J Integr Plant Biol 56: 816–825
www.jipb.net
Yang LE, Huang XQ, Hang Y, Deng YY, Lu QQ, Lu S (2014) The P450‐type carotene hydroxylase PuCHY1 from Porphyra suggested the evolution of carotenoid metabolismin red algae. J Integr Plant Biol 56: 902–915
September 2014 | Volume 56 | Issue 9 | 814–815
Journal of Integrative Plant Biology
Free Access
Editorial
Plant metabolomics and metabolic biology Plants produce a large array of specialized metabolites (natural products) that not only are essential for growth and development, but also play important roles in adaptation to the variable stressful environments. Also, many plant metabolites are essential nutrient elements for humans and serve as natural drugs. However, study of the biosynthesis of natural products is still in its infancy, because more than 90% of plant metabolites are unknown and only a small number of genes/ enzymes involved in metabolism are identified in the model plants Arabidopsis and rice. In the post‐genomics era, metabolomics – defined as the analysis of the total population of metabolites in a given sample, cell or tissue – and the integration of the data in the context of functional genomics, is attractive for analysis of global metabolic changes in plant development and responds to different environmental stresses. Metabolomic analysis would greatly accelerate our processes in deciphering the function of an individual gene in a metabolic pathway, building metabolic networks, identifying metabolic regulators, and more importantly establishing causal relations between metabolic pathways and biologic functions in plants. In this special issue on metabolomics and metabolic biology, we present one invited review and 10 research articles. Both gas chromatography mass spectrometry (GC‐ MS) and liquid chromatography mass spectrometry (LC‐MS) are widely used in plant metabolomic analysis. LC‐MS has good potential in separation of polar chemicals which constitute more than 80% of plant metabolites. However, currently, there is no consensus on which LC‐MS method should be used in plant metabolomic studies. In the invited review by Liu and Rochfort (2014), the most promising methods were reviewed, providing plant scientists with up‐to‐date and simplified information regarding the current status of polar metabolite analysis. In the research articles by Lin et al. (2014) and Agarrwal et al. (2014), metabolomic analysis was applied in studies of soybean cultivars, and the interaction between rice and the Asian rice gall midge (Orseolia oryzae Wood‐Mason), respectively. In both cases, metabolite markers (biomarkers) for distinguishing genetically related soybean cultivars and rice‐insect interaction were successfully identified. Untargeted metabolomic analysis of mads3‐4 (a mutant in a gene encoding MADS3 transcription factor) and wild‐type mature anthers by Qu et al. (2014) indicated that the MADS3 gene affects rice anther development far beyond the reactive oxygen species homeostatic regulation. In two research articles by Schwahn et al. (2014) and Dong et al. (2014), sub‐metabolomic analysis was applied in focus on particular types of metabolites, for example, steroidal glycoalkaloids and flavonoids. Comparative analysis of flavonoid contents in various tissues from the two subspecies, Indica and Japonica, revealed tissue‐specific accumulation of most flavonoids and clear differential accumulation of different types of flavonoids. Based on the analysis of a large number of samples from four types of tissues of 169 accessions from tomato and its wild relatives, Schwahn et al. (2014) integrated species and tissue specificity information into the annotation and classification of steroidal glycoalkaloid peaks, allowing refinement of steroidal glycoalSeptember 2014 | Volume 56 | Issue 9 | 814–815
kaloid biosynthesis and detection of putative novel branch points. The cytochrome P450 (CYP) superfamily belonging to monooxygenase, has greatly expanded in the plant genomes. It is believed that members in this family play critical roles in biosynthesis of diversified natural products. In this special issue, the paper by Ma et al. (2014) annotates a total of 174 P450 genes from the mulberry (Morus notabilis C.K. Schn.) genome. The article by Yang et al. (2014) demonstrates that a cytochrome P450‐type carotene hydroxylase (PuCHY1) catalyzes the conversion of b‐carotene into zeaxanthin in the red alga Porphyra umbilicalis. Anthocyanin, a well‐studied plant specialized metabolite, is often accumulated to higher levels under stress, for example, cold, drought, and photo‐oxidative stress. Research by Gan et al. (2014) on the thf1I (thylakoid formation1) mutant in Arabidopsis revealed that the elevated anthocyanin content increases levels of methyl jasmonate, which is served as signals in coordination of plant metabolism and growth in photo‐oxidative stress. On the other hand, a study by Li et al. (2014) focusing on the glandular trichomes of Colquhounia seguinii identifies three new clerodane diterpenoids. Interestingly, all identified compounds showed antifeedant activity against the insect Spodoptera exigua. Finally, this special issue presents the work by Florian et al. (2014), which studies the relationship between transcripts and metabolite levels when plants grown under normal air conditions were transferred to different CO2 and O2 concentrations. An interesting conclusion is that the regulation of the photosynthesis pathways is not mediated at the level of transcription.
Xiaoquan Qi, Professor Special Issue Editor Institute of Botany, the Chinese Academy of Sciences Beijing, China Dabing Zhang, Professor Special Issue Editor Shanghai Jiaotong University Shanghai, China doi: 10.1111/jipb.12247 © 2014 Institute of Botany, Chinese Academy of Sciences
REFERENCES Agarrwal R, Bentur JS, Nair S (2014) Gas chromatography mass spectrometry based metabolic profiling reveals biomarkers involved in rice‐gall midge interactions. J Integr Plant Biol 56: 837–848 Dong X, Chen W, Wang W, Zhang H, Liu X, Luo J (2014) Comprehensive profiling and natural variation of flavonoids in rice. J Integr Plant Biol 56: 876–886 Florian A, Timm S, Nikoloski Z, Tohge T, Bauwe H, Araújo WL, Fernie AR (2014) Analysis of metabolic alterations in Arabidopsis following changes in the carbon dioxide and oxygen partial pressures. J Integr Plant Biol 56: 941–959
www.jipb.net
Editorial
815
Gan Y, Li H, Xie Y, Wu W, Li M, Wang X, Huang J (2014) THF1 mutations lead to increased basal and wound‐induced levels of oxylipins that stimulate anthocyanin biosynthesis via COI1 signaling in Arabidopsis. J Integr Plant Biol 56: 916–927
Ma B, Luo Y, Jia L, Qi X, Zeng Q, Xiang Z, He N (2014) Genome‐ wide identification and expression analyses of cytochrome P450 genes in mulberry (Morus notabilis). J Integr Plant Biol 56: 887– 901
Li CH, Liu Y, Hua J, Luo SH, Li SH (2014) Peltate glandular trichomes of Colquhounia seguinii harbor new defensive clerodane diterpenoids. J Integr Plant Biol 56: 928–940
Qu G, Quan S, Mondol P, Xu J, Zhang D, Shi J (2014) Comparative metabolomic analysis of wild type and mads3 mutant rice anthers. J Integr Plant Biol 56: 849–863
Lin H, Rao J, Shi J, Hu C, Cheng F, Wilson ZA, Zhang D, Quan S (2014) Seed metabolomic study reveals significant metabolite variations and correlations among different soybean cultivars. J Integr Plant Biol 56: 826–836
Schwahn K, de Souza LP, Fernie AR, Tohge T (2014) Metabolomics‐ assisted refinement of the pathways of steroidal glycoalkaloid biosynthesis in the tomato clade. J Integr Plant Biol 56: 864–875
Liu Z, Rochfort S (2014) Recent progress in polar metabolite quantification in plants using liquid chromatography‐mass spectrometry. J Integr Plant Biol 56: 816–825
www.jipb.net
Yang LE, Huang XQ, Hang Y, Deng YY, Lu QQ, Lu S (2014) The P450‐type carotene hydroxylase PuCHY1 from Porphyra suggested the evolution of carotenoid metabolismin red algae. J Integr Plant Biol 56: 902–915
September 2014 | Volume 56 | Issue 9 | 814–815
