Integration of transcriptomics and metabolomics for understanding of global responses to nutritional stresses in Arabidopsis thaliana
Masami Yokota Hirai,Mitsuru Yano,Dayan B. Goodenowe,Shigehiko Kanaya,Tomoko Kimura,Motoko Awazuhara,Masanori Arita,Toru Fujiwara,Kazuki Saito +8 more
Reads0
Chats0
TLDR
This is 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, and specific responses to either sulfur or nitrogen deficiency were observed.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 gene-to-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.read more
Citations
More filters
Journal ArticleDOI
Mass spectrometry-based metabolomics.
TL;DR: This review presents an overview of the dynamically developing field of mass spectrometry-based metabolomics, a technique that analyzes all detectable analytes in a given sample with subsequent classification of samples and identification of differentially expressed metabolites, which define the sample classes.
Journal ArticleDOI
The AtGenExpress global stress expression data set: protocols, evaluation and model data analysis of UV-B light, drought and cold stress responses
Joachim Kilian,Dion J. Whitehead,Jakub Horák,Dierk Wanke,Stefan Weinl,Oliver Batistič,Cecilia D'Angelo,Erich Bornberg-Bauer,Jörg Kudla,Klaus Harter +9 more
TL;DR: In this paper, the AtGenExpress project performed a comprehensive Arabidopsis thaliana genome transcript expression study using the Affymetrix ATH1 microarray in order to understand these regulatory networks in detail.
Journal ArticleDOI
Effects of abiotic stress on plants: a systems biology perspective
TL;DR: In this review, research progress in plant responses to abiotic stresses is summarized from the physiological level to the molecular level, providing additional focus areas for crop improvement research in the future.
Journal ArticleDOI
How do plants respond to nutrient shortage by biomass allocation
TL;DR: An update on the effects of mineral deficiencies on the expression of genes involved in primary metabolism in the shoot, the evidence for increased carbohydrate concentrations and altered biomass allocation between shoot and root, and the consequences of these changes on the growth and morphology of the plant root system are presented.
Journal ArticleDOI
Coordination of carbon supply and plant growth
Alison M. Smith,Mark Stitt +1 more
TL;DR: Evidence is described for the existence of regulatory mechanisms that coordinate carbon supply and use, and the likely central role of sugar signalling is described, and both 'acute' and 'acclimatory' responses to alterations in carbon supply are proposed.
References
More filters
Journal ArticleDOI
Significance analysis of microarrays applied to the ionizing radiation response
TL;DR: A method that assigns a score to each gene on the basis of change in gene expression relative to the standard deviation of repeated measurements is described, suggesting that this repair pathway for UV-damaged DNA might play a previously unrecognized role in repairing DNA damaged by ionizing radiation.
Journal ArticleDOI
Analysis of the genome sequence of the flowering plant Arabidopsis thaliana.
TL;DR: This is the first complete genome sequence of a plant and provides the foundations for more comprehensive comparison of conserved processes in all eukaryotes, identifying a wide range of plant-specific gene functions and establishing rapid systematic ways to identify genes for crop improvement.
Journal ArticleDOI
The self-organizing map
TL;DR: The self-organizing map, an architecture suggested for artificial neural networks, is explained by presenting simulation experiments and practical applications, and an algorithm which order responses spatially is reviewed, focusing on best matching cell selection and adaptation of the weight vectors.
Journal ArticleDOI
A draft sequence of the rice genome (Oryza sativa L. ssp indica)
Stephen A. Goff,Darrell O. Ricke,Tien-Hung Lan,Gernot G. Presting,Ronglin Wang,Molly Dunn,Jane Glazebrook,Allen Sessions,Paul Oeller,Hemant Varma,David Hadley,Don Hutchison,Christopher M. Martin,Fumiaki Katagiri,B. Markus Lange,Todd Moughamer,Yu Xia,Paul Budworth,Jingping Zhong,Trini Miguel,Uta Paszkowski,Shiping Zhang,Michelle Colbert,Wei-lin Sun,Lili Chen,Bret Cooper,Sylvia Park,Todd Charles Wood,Long Mao,Peter H. Quail,Rod A. Wing,Ralph A. Dean,Yeisoo Yu,Andrey Zharkikh,Richard Shen,Sudhir Sahasrabudhe,Alun Thomas,Rob Cannings,Alexander Gutin,Dmitry Pruss,Julia Reid,Sean V. Tavtigian,J.T. Mitchell,Glenn Eldredge,Terri Scholl,Rose Mary Miller,Satish Bhatnagar,Nils Adey,Todd Rubano,Nadeem Tusneem,Rosann Robinson,Jane Feldhaus,Teresita Macalma,Arnold R. Oliphant,Steven P. Briggs +54 more
TL;DR: A draft sequence of the rice genome for the most widely cultivated subspecies in China, Oryza sativa L. ssp.indica, by whole-genome shotgun sequencing is produced, with a large proportion of rice genes with no recognizable homologs due to a gradient in the GC content of rice coding sequences.
Book
Biochemistry & Molecular Biology of Plants
TL;DR: This edition of Biochemistry & Molecular Biology of Plants holds a unique place in the plant sciences literature as it provides the only comprehensive, authoritative, integrated single volume book in this essential field of study.