title: A network perspective on nitrogen metabolism from model to crop plants using integrated 'omics' approaches.
abstract: Nitrogen (N), as an essential element in amino acids, nucleotides, and proteins, is a key factor in plant growth and development. Omics approaches such as metabolomics and transcriptomics have become a promising way to inspect complex network interactions in N metabolism and can be used for monitoring the uptake and regulation, translocation, and remobilization of N. In this review, the authors highlight recent progress in omics approaches, including transcript profiling using microarrays and deep sequencing, and show recent technical developments in metabolite profiling for N studies. Further, network analysis studies including network inference methods with correlations, information-theoretic measures, and a network concept to examine gene expression clusters in relation to N regulatory systems in plants are introduced, and integrating network inference methods and integrated networks using multiple omics data are discussed. Finally, this review summarizes recent omics application examples using metabolite and/or transcript profiling analysis to elucidate the regulation of N metabolism and signalling and the coordination of N and carbon metabolism in model plants (Arabidopsis and rice), crops (tomato, maize, and legumes), and trees (Populus).
authors.affiliation: RIKEN Center for Sustainable Resource Science (CSRS), 1-7-22 Suehirocho, Tsurumi, Yokohama 230-0045, Japan JST, National Bioscience Database Center (NBDC), 5-3, Yonbancho, Chiyoda, Tokyo 102-0081, Japan.
authors.forename: Atsushi
authors.initials: A
authors.lastname: Fukushima
authors.affiliation: RIKEN Center for Sustainable Resource Science (CSRS), 1-7-22 Suehirocho, Tsurumi, Yokohama 230-0045, Japan Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan Japan Science and Technology Agency (JST), Precursory Research for Embryonic Science and Technology (PRESTO), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan miyako.kusano@riken.jp.
authors.forename: Miyako
authors.initials: M
authors.lastname: Kusano
mesh_terms: D000596:Amino Acids / Q000378:metabolism; D002244:Carbon / Q000378:metabolism*; D018556:Crops, Agricultural / Q000378:metabolism*; D020869:Gene Expression Profiling; D055432:Metabolomics; D009584:Nitrogen / Q000378:metabolism*; D010944:Plants / Q000378:metabolism*
chemical_list: D000596:Amino Acids; D002244:Carbon; D009584:Nitrogen
keywords: Central metabolism; RNA-seq; deep sequencing; metabolite profiling; nitrogen metabolism; transcript profiling.