Special Issue: Metabolomics and Metabolic Biology   

September 2014, Volume 56 Issue 9, Pages 814每959.


Cover Caption: Metabolomics and Metabolic Biology
About the cover: Small molecule metabolites are not only the essential constituent in plants, but also play critical roles in development and stress responses. Till now most plant metabolites have not been characterized and their functions are largely unknown. However, with the recent development of analytical tools in combination with genetic and genomics, this area is in rapid development, as seen in this special issue (cover design: Ying Wang).

 

          Editorial
Plant metabolomics and metabolic biology  
Author: Xiaoquan Qi and Dabing Zhang
Journal of Integrative Plant Biology 2014 56(9): 814每815
Published Online: August 4, 2014
DOI: 10.1111/jipb.12247
Abstract (Browse 784)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
          Minireview
Recent progress in polar metabolite quantification in plants using liquid chromatography每mass spectrometry  
Author: Zhiqian Liu and Simone Rochfort
Journal of Integrative Plant Biology 2014 56(9): 816每825
Published Online: February 14, 2014
DOI: 10.1111/jipb.12181
      
    

Metabolite analysis or metabolomics is an important component of systems biology in the post-genomic era. Although separate liquid chromatography (LC) methods for quantification of the major classes of polar metabolites of plants have been available for decades, a single method that enables simultaneous determination of hundreds of polar metabolites is possible only with gas chromatography–mass spectrometry (GC–MS) techniques. The rapid expansion of new LC stationary phases in the market and the ready access of mass spectrometry in many laboratories provides an excellent opportunity for developing LC–MS based methods for multi-target quantification of polar metabolites. Although various LC–MS methods have been developed over the last 10 years with the aim to quantify one or more classes of polar compounds in different matrices, currently there is no consensus LC–MS method that is widely used in plant metabolomics studies. The most promising methods applicable to plant metabolite analysis will be reviewed in this paper and the major problems encountered highlighted. The aim of this review is to provide plant scientists, with limited to moderate experience in analytical chemistry, with up-to-date and simplified information regarding the current status of polar metabolite analysis using LC–MS techniques.

 

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. doi: 10.1111/jipb.12181

Abstract (Browse 950)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
          Research Articles
Seed metabolomic study reveals significant metabolite variations and correlations among different soybean cultivars  
Author: Hong Lin, Jun Rao, Jianxin Shi, Chaoyang Hu, Fang Cheng, Zoe A. Wilson, Dabing Zhang and Sheng Quan
Journal of Integrative Plant Biology 2014 56(9): 826每836
Published Online: June 18, 2014
DOI: 10.1111/jipb.12228
      
    

Soybean [Glycine max (L.) Merr.] is one of the world's major crops, and soybean seeds are a rich and important resource for proteins and oils. While “omics” studies, such as genomics, transcriptomics, and proteomics, have been widely applied in soybean molecular research, fewer metabolomic studies have been conducted for large-scale detection of low molecular weight metabolites, especially in soybean seeds. In this study, we investigated the seed metabolomes of 29 common soybean cultivars through combined gas chromatography-mass spectrometry and ultra-performance liquid chromatography-tandem mass spectrometry. One hundred sixty-nine named metabolites were identified and subsequently used to construct a metabolic network of mature soybean seed. Among the 169 detected metabolites, 104 were found to be significantly variable in their levels across tested cultivars. Metabolite markers that could be used to distinguish genetically related soybean cultivars were also identified, and metabolite–metabolite correlation analysis revealed some significant associations within the same or among different metabolite groups. Findings from this work may potentially provide the basis for further studies on both soybean seed metabolism and metabolic engineering to improve soybean seed quality and yield.

 

Lin H, Rao J, Shi J, Hu C, Cheng F, Wilson ZA, Zhang D, Quan S (2014) A seed metabolomic study reveals significant metabolite variations and correlations among different soybean cultivars. J Integr Plant Biol 56: 826–836. doi: 10.1111/jipb.12228

Abstract (Browse 1009)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
Gas chromatography mass spectrometry based metabolic profiling reveals biomarkers involved in rice-gall midge interactions  
Author: Ruchi Agarrwal, Jagadish Sanmallappa Bentur and Suresh Nair
Journal of Integrative Plant Biology 2014 56(9): 837每848
Published Online: July 24, 2014
DOI: 10.1111/jipb.12244
      
    

The Asian rice gall midge (Orseolia oryzae Wood-Mason) is a serious pest of rice that causes huge loss in yield. While feeding inside the susceptible host, maggots secrete substances that facilitate the formation of a hollow tube-like structure called gall and prevent panicle formation. The present investigation was carried out to get an account of biochemical changes occurring in the rice plant upon gall midge feeding. Metabolic profiling of host tissues from three rice varieties, namely, TN1, Kavya, and RP2068, exposed to gall midge biotype 1 (GMB1), was carried out using gas chromatography mass spectrometry (GC-MS). TN1 and GMB1 represented compatible interaction, while Kavya and GMB1 as well as RP2068 and GMB1 represented incompatible interactions. The current study identified several metabolites that could be grouped as resistance, susceptibility, infestation, and host features based on their relative abundance. These may be regarded as biomarkers for insect-plant interaction in general and rice-gall midge interaction in particular.

 

Agarrwal R, Bentur JS, Suresh N (2014) Gas chromatography mass spectrometry based metabolic profiling reveals biomarkers involved in rice坼gall midge interactions. J Integr Plant Biol 56: 837–848. doi: 10.1111/jipb.12244

Abstract (Browse 1615)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
Comparative metabolomic analysis of wild type and mads3 mutant rice anthers  
Author: Guorun Qu, Sheng Quan, Palash Mondol, Jie Xu, Dabing Zhang and Jianxin Shi
Journal of Integrative Plant Biology 2014 56(9): 849每863
Published Online: July 29, 2014
DOI: 10.1111/jipb.12245
      
    

Rice (Oryza sativa L.) MADS3 transcription factor regulates the homeostasis of reactive oxygen species (ROS) during late anther development, and one MADS3 mutant, mads3-4, has defective anther walls, aborted microspores and complete male sterility. Here, we report the untargeted metabolomic analysis of both wild type and mads3-4 mature anthers. Mutation of MADS3 led to an unbalanced redox status and caused oxidative stress that damages lipid, protein, and DNA. To cope with oxidative stress in mads3-4 anthers, soluble sugars were mobilized and carbohydrate metabolism was shifted to amino acid and nucleic acid metabolism to provide substrates for the biosynthesis of antioxidant proteins and the repair of DNA. Mutation of MADS3 also affected other aspects of rice anther development such as secondary metabolites associated with cuticle, cell wall, and auxin metabolism. Many of the discovered metabolic changes in mads3-4 anthers were corroborated with changes of expression levels of corresponding metabolic pathway genes. Altogether, this comparative metabolomic analysis indicated that MADS3 gene affects rice anther development far beyond the ROS homeostasis regulation.

 

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. doi: 10.1111/jipb.12245

Abstract (Browse 1185)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
Metabolomics-assisted refinement of the pathways of steroidal glycoalkaloid biosynthesis in the tomato clade  
Author: Kevin Schwahn, Leonardo Perez de Souza, Alisdair R. Fernie and Takayuki Tohge
Journal of Integrative Plant Biology 2014 56(9): 864每875
Published Online: August 11, 2014
DOI: 10.1111/jipb.12274
      
    

Steroidal glycoalkaloids (SGAs) are nitrogen-containing secondary metabolites of the Solanum species, which are known to have large chemical and bioactive diversity in nature. While recent effort and development on LC/MS techniques for SGA profiling have elucidated the main pathways of SGA metabolism in tomato, the problem of peak annotation still remains due to the vast diversity of chemical structure and similar on overlapping of chemical formula. Here we provide a case study of peak classification and annotation approach by integration of species and tissue specificities of SGA accumulation for provision of comprehensive pathways of SGA biosynthesis. In order to elucidate natural diversity of SGA biosynthesis, a total of 169 putative SGAs found in eight tomato accessions (Solanum lycopersicum, S. pimpinellifolium, S. cheesmaniae, S. chmielewskii, S. neorickii, S. peruvianum, S. habrochaites, S. pennellii) and four tissue types were used for correlation analysis. The results obtained in this study contribute annotation and classification of SGAs as well as detecting putative novel biosynthetic branch points. As such this represents a novel strategy for peak annotation for plant secondary metabolites.

 

Schwahn K, de Souza LP, Fernie AR, Tohge T (2014) Metabolomics坼assisted refinement of the pathways of steroidal glycoalkaloid biosynthesis in the tomato clade. J Integr Plant Biol 56: 864–875. doi: 10.1111/jipb.12274

Abstract (Browse 688)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
Comprehensive profiling and natural variation of flavonoids in rice  
Author: Xuekui Dong, Wei Chen, Wensheng Wang, Hongyan Zhang, Xianqing Liu and Jie Luo
Journal of Integrative Plant Biology 2014 56(9): 876每886
Published Online: April 15, 2014
DOI: 10.1111/jipb.12204
      
    
Flavonoids constitute a major group of plant phenolic compounds. While extensively studied in Arabidopsis, profiling and naturally occurring variation of these compounds in rice (Oryza sativa), the monocot model plant, are less reported. Using a collection of rice germplasm, comprehensive profiling and natural variation of flavonoids were presented in this report. Application of a widely targeted metabolomics method facilitated the simultaneous identification and quantification of more than 90 flavonoids using liquid chromatography tandem mass spectrometry (LC-MS/MS). Comparing flavonoid contents in various tissues during different developmental stages revealed tissue-specific accumulation of most flavonoids. Further investigation indicated that flavone mono-C-glycosides, malonylated flavonoid O-hexosides, and some flavonoid O-glycosides accumulated at significantly higher levels in indica than in japonica, while the opposite was observed for aromatic acylated flavone C-hexosyl-O-hexosides. In contrast to the highly differential accumulation between the two subspecies, relatively small variations within subspecies were detected for most flavonoids. Besides, an association analysis between flavonoid accumulation and its biosynthetic gene sequence polymorphisms disclosed that natural variation of flavonoids was probably caused by sequence polymorphisms in the coding region of flavonoid biosynthetic genes. Our work paves the way for future dissection of biosynthesis and regulation of flavonoid pathway in rice.

 

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. doi: 10.1111/jipb.12204

Abstract (Browse 1201)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
Genome-wide identification and expression analyses of cytochrome P450 genes in mulberry (Morus notabilis)  
Author: Bi Ma, Yiwei Luo, Ling Jia, Xiwu Qi, Qiwei Zeng, Zhonghuai Xiang and Ningjia He
Journal of Integrative Plant Biology 2014 56(9): 887每901
Published Online: December 4, 2013
DOI: 10.1111/jipb.12141
      
    

Cytochrome P450s play critical roles in the biosynthesis of physiologically important compounds in plants. These compounds often act as defense toxins to prevent herbivory. In the present study, a total of 174 P450 genes of mulberry (Morus notabilis C.K.Schn) were identified based on bioinformatics analyses. These mulberry P450 genes were divided into nine clans and 47 families and were found to be expressed in a tissue-preferential manner. These genes were compared to the P450 genes in Arabidopsis thaliana. Families CYP80, CYP92, CYP728, CYP733, CYP736, and CYP749 were found to exist in mulberry, and they may play important roles in the biosynthesis of mulberry secondary metabolites. Analyses of the functional and metabolic pathways of these genes indicated that mulberry P450 genes may participate in the metabolism of lipids, other secondary metabolites, xenobiotics, amino acids, cofactors, vitamins, terpenoids, and polyketides. These results provide a foundation for understanding of the structures and biological functions of mulberry P450 genes.

 

Ma B, Luo Y, Jia L, Qi X, Zeng Q, Xiang Z, He N (2014) Genome坼wide identification and expression analyses of cytochrome P450 genes in mulberry (Morus notabilis). J Integr Plant Biol 56: 887–901. doi:
10.1111/jipb.12141

Abstract (Browse 1102)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
The P450-type carotene hydroxylase PuCHY1 from Porphyra suggests the evolution of carotenoid metabolism in red algae  
Author: Li-En Yang, Xing-Qi Huang, Yu Hang, Yin-Yin Deng, Qin-Qin Lu and Shan Lu
Journal of Integrative Plant Biology 2014 56(9): 902每915
Published Online: June 18, 2014
DOI: 10.1111/jipb.12229
      
    

Carotene hydroxylases catalyze the hydroxylation of α- and β-carotene hydrocarbons into xanthophylls. In red algae, β-carotene is a ubiquitously distributed carotenoid, and hydroxylated carotenoids such as zeaxanthin and lutein are also found. However, no enzyme with carotene hydroxylase activity had been previously identified in red algae. Here, we report the isolation of a gene encoding a cytochrome P450-type carotene hydroxylase (PuCHY1) from Porphyra umbilicalis, a red alga with an ancient origin. Sequence comparisons found PuCHY1 belongs to the CYP97B subfamily, which has members from different photosynthetic organisms ranging from red algae to land plants. Functional complementation in Escherichia coli suggested that PuCHY1 catalyzed the conversion from β-carotene to zeaxanthin. When we overexpressed PuCHY1 in the Arabidopsis thaliana chy2 mutant, pigment analysis showed a significant accumulation of hydroxylated carotenoids, including neoxanthin, violaxanthin, and lutein in the leaves of transgenic plants. These results confirmed a β-hydroxylation activity of PuCHY1, and also suggested a possible ϵ-hydroxylation function. The pigment profile and gene expression analyses of the algal thallus under high-light stress suggested that P. umbilicalis is unlikely to operate a partial xanthophyll cycle for photoprotection.

 

Yang LE, Huang XQ, Hang Y, Deng YY, Lu QQ, Lu S (2014) The P450坼type carotene hydroxylase PuCHY1 from Porphyra suggested the evolution of carotenoid metabolism in red algae. J Integr Plant Biol 56: 902–915. doi: 10.1111/jipb.12229

Abstract (Browse 835)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
THF1 mutations lead to increased basal and wound-induced levels of oxylipins that stimulate anthocyanin biosynthesis via COI1 signaling in Arabidopsis  
Author: Yi Gan, Hong Li, Ye Xie, Wenjuan Wu, Maoyin Li, Xuemin Wang and Jirong Huang
Journal of Integrative Plant Biology 2014 56(9): 916每927
Published Online: January 28, 2014
DOI: 10.1111/jipb.12177
      
    

Mutants defective in chloroplast development or photosynthesis are liable to accumulate higher levels of anthocyanin in photo-oxidative stress. However, regulatory mechanisms of anthocyanin biosynthesis in the mutants remain unclear. Here, we investigated the mechanism by which the deletion of thylakoid formation1 (THF1) leads to an increased level of anthocyanin in Arabidopsis thaliana L. Physiological and genetic evidence showed that the increased level of anthocyanin in thf1 is dependent on coronatine-insensitive1 (COI1) signaling. Our data showed that thf1 had higher levels of basal α-linolenic acid (α-LeA), and methyl jasmonate (JA)-induced α-LeA and 12-oxophytodienoic acid (OPDA) than the wild type (WT). Consistently, expression levels of phospholipase genes including pPLAIIα and PLA-Iγ1 were elevated in thf1. Furthermore, inhibition of lipase activity by bromoenol lactone, a specific inhibitor of plant pPLA, led to producing identical levels of anthocyanins in WT and thf1 plants. Interestingly, OPDA biosynthesis was triggered by light illumination in isolated chloroplasts, indicating that new protein import into chloroplasts is not required for OPDA biosynthesis. Thus, we conclude that the elevated anthocyanin accumulation in thf1 is attributed to an increase in JA levels. This JA-mediated signaling to coordinate plant metabolism and growth in stress may be conserved in other photosensitive mutants.

 

Gan Y, Li H, Xie Y, Wu W, Li M, Wang X, Huang J (2014) THF1 mutations lead to increased basal and wound坼induced levels of oxylipins that stimulate anthocyanin biosynthesis via COI1 signaling in Arabidopsis. J Integr Plant Biol 56: 916–927. doi: 10.1111/jipb.12177

Abstract (Browse 847)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
Peltate glandular trichomes of Colquhounia seguinii harbor new defensive clerodane diterpenoids  
Author: Chun-Huan Li, Yan Liu, Juan Hua, Shi-Hong Luo and Sheng-Hong Li
Journal of Integrative Plant Biology 2014 56(9): 928每940
Published Online: July 21, 2014
DOI: 10.1111/jipb.12242
      
    

Glandular trichomes produce a wide variety of secondary metabolites that are considered as major defensive chemicals against herbivore attack. The morphology and secondary metabolites of the peltate glandular trichomes of a lianoid Labiatae, Colquhounia seguinii Vaniot, were investigated. Three new clerodane diterpenoids, seguiniilactones A-C (1–3), were identified through precise trichome collection with laser microdissection, metabolic analysis with ultra performance liquid chromatography-tandem mass spectrometer, target compound isolation with classical phytochemical techniques, structure elucidation with spectroscopic methods. All compounds showed significant antifeedant activity against a generalist plant-feeding insect Spodoptera exigua. Seguiniilactone A (1) was approximately 17-fold more potent than the commercial neem oil. α-Substituted α,β-unsaturated γ-lactone functionality was found to be crucial for strong antifeedant activity of this class of compounds. Quantitative results indicated that the levels of these compounds in the peltate glandular trichomes and leaves were sufficiently high to deter the feeding by generalist insects. Moderate antifungal activity was observed for seguiniilactone C (3) against six predominant fungal species isolated from the diseased leaves of C. seguinii, while seguiniilactones A and B were generally inactive. These findings suggested that seguiniilactones A–C might be specialized secondary metabolites in peltate glandular trichomes for the plant defense against insect herbivores and pathogens.

 

 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. doi: 10.1111/jipb.12242

Abstract (Browse 596)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
Analysis of metabolic alterations in Arabidopsis following changes in the carbon dioxide and oxygen partial pressures  
Author: Alexandra Florian, Stefan Timm, Zoran Nikoloski, Takayuki Tohge, Hermann Bauwe, Wagner L. Araújo and Alisdair R. Fernie
Journal of Integrative Plant Biology 2014 56(9): 941每959
Published Online: July 8, 2014
DOI: 10.1111/jipb.12237
      
    

As sessile organisms, plants are subject to a multitude of environmental variations including several which directly affect their interaction with the atmosphere. Given the indiscriminant nature of Rubisco, the relative rates of photosynthesis and photorespiration are known to be responsive to changes in gas composition. However, comprehensive profiling methods have not yet been applied in order to characterize the wider consequences of these changes on primary metabolism in general. Moreover, although transcriptional profiling has revealed that a subset of photorespiratory enzymes are co-expressed, whether transcriptional responses play a role in short-term responses to atmospheric compositional changes remains unknown. To address these questions, plants Arabidopsis thaliana (Arabidopsis) ecotype Columbia (Col-O) grown under normal air conditions were transferred to different CO2 and O2 concentrations and characterized at the physiological, molecular, and metabolic levels following this transition. The results reveal alterations in the components, which are directly involved in, or supporting, photorespiration, including transcripts and metabolite levels. The results further highlight that the majority of the regulation of these pathways is not mediated at the level of transcription and that the photorespiratory pathway is essential also in conditions in which flux through the pathway is minimized, yet suggest that flux through this pathway is not mediated at the level of transcription.

 

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. doi: 10.1111/jipb.12237

Abstract (Browse 789)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
 

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