Integration of transcriptomics and metabolomics for understanding of global responses to nutritional stresses in Arabidopsis thaliana

Abstract

Plant metabolism is a complex set of processes that produce a wide diversity of foods, woods, and medicines. With the genome sequences of Arabidopsis and rice in hands, postgenomics studies integrating all ''omics'' sciences can depict precise pictures of a whole-cellular process. Here, we present, to our knowledge, the first report of investigation for gene-to-metabolite networks regulating sulfur and nitrogen nutrition and secondary metabolism in Arabidopsis, with integration of metabolomics and transcriptomics. Transcriptome and metabolome analyses were carried out, respectively, with DNA macroarray and several chemical analytical methods, including ultra high-resolution Fourier transform-ion cyclotron MS. Mathematical analyses, including principal component analysis and batch-learning self-organizing map analysis of transcriptome and metabolome data suggested the presence of general responses to sulfur and nitrogen deficiencies. In addition, specific responses to either sulfur or nitrogen deficiency were observed in several metabolic pathways: in particular, the genes and metabolites involved in glucosinolate metabolism were shown to be coordinately modulated. Understanding such geneto-metabolite networks in primary and secondary metabolism through integration of transcriptomics and metabolomics can lead to identification of gene function and subsequent improvement of production of useful compounds in plants. P lants produce a huge array of compounds used for foods, medicines, flavors, and industrial materials. These plant metabolites are synthesized and accumulated by the networks of proteins encoded in the genome of each plant. However, even after the completion of the genome sequencing of Arabidopsis (1) and rice (2, 3), function of those genes and networks of gene-to-metabolite are largely unknown. To reveal the function of genes involved in metabolic processes and gene-to-metabolite networks, the metabolomics-based approach is regarded as a direct way (4-7). In particular, integration of comprehensive gene expression profile with targeted metabolite analysis is shown to be an innovative way for identification of gene function for specific product accumulation in plant (8) and microorganisms (9). However, to depict a whole-cellular process of metabolism, integration of comprehensive gene expression analysis (transcriptomics), and nontargeted metabolite profiling (metabolomics) is needed. Bioinformatics designed suitably for data mining helps the integration efficiently.The gene expression profiling can be achieved by DNA array analysis. For metabolomics, a nontargeted, high-throughput analytical system is required. Traditionally, GC-MS has been used to detect Ͼ300 metabolites in plant tissues (5, 6). Fourier transform-ion cyclotron MS (FT-MS) is a system for metabolome analysis in which crude plant extract is introduced by means of direct injection without prior separation of metabolites by chromatography (10). The mass resolution (Ͼ100,000) and accuracy (Ͻ1 ppm) of FT-MS is extremely high; hence, comple...

The mutual responses of higher plants to environment: Physiological and microbiological aspects

“…A major motivation for the above effort is the high rate of human-accelerated environmental change, including elevated atmospheric ozone, CO 2 , nitrogen deposition, climate change and land use/land cover change [33,[41][42][43][44][45][46][47][48][49][50][51][52][53][54][129][130][131][132]. It is a clear fact that these changes can affect mycorrhizal fungal species, but it is also clear that we do not yet have data sets sufficiently saturated, or models sufficiently powerful, to determine the exact nature, timing and spatial pattern of fungal community responses.…”

“…In practice, the key point to agriculture is how to regulate the harmonious relationship between soil-environment and crops and make the best of physiological potential of crops [137][138][139][140][141][142][143][144][145][146][147]. So, adaptation in plants is an important topic in basic and applied biology under global climate change [11,[15][16][17][18][19][43][44][45][46][47][48][104][105][106][107]120]. In the discipline context, it is very interesting to understand the interaction between plants and their environment.…”

Relationship between water use efficiency (WUE) and production of different wheat genotypes at soil water deficit

“…These results imply that systemical, deeper, and comprehensive understanding of physiological mechanism of crops under drought stresses is not enough to manipulate the physiological regulatory mechanism and take advantage of full this potential for productivity, whose study is the bridge between molecular machinery of drought and anti-drought agriculture, because the performance of genetic potential of crops is expressed by physiological realization in fields [1,2,8,10,53,54]. Towards this aim, many promising methodologies appear, but they should also be linked with field practice [12,13,18,24,29,31,40,51,72]. Wheat is a staple food for more than 35% of the world population and wheat is also the second grain crop in China, whose production status is directly related to social stability, Chinese survival and sustainable development [13,21,22,30,37,38,59,65].…”

Untargeted metabolic profiling reveals geography as the strongest predictor of metabolic phenotypes of a cosmopolitan weed

“…Specialized metabolites also are the source of many of our plant‐based medicines and therefore have value to human health and well‐being (Briskin, 2000). Much attention has therefore been placed on environmental and geographic factors influencing specialized metabolite production in plants, particularly in crop species and in model plant systems (Agrawal, Conner, Johnson, & Wallsgrove, 2002; Asai, Matsukawa, & Kajiyamal, 2016; Carrari et al., 2006; Dan et al., 2016; Hirai et al., 2004; Lasky et al., 2012; Tarczynski, Jensen, & Bohnert, 1993; Riedelsheimer et al., 2012). However, the importance of natural variation in the environment in explaining metabolite variation within plant species remains little understood (Maldonado et al., 2017; Moore, Andrew, Külheim, & Foley, 2014).…”