Concurrent isotope‐assisted metabolic flux analysis and transcriptome profiling reveal responses of poplar cells to altered nitrogen and carbon supply. (14th January 2018)

• Record Type: Journal Article
• Authors: Zhang, Xiaofeng; Misra, Ashish; Nargund, Shilpa; Coleman, Gary D.; Sriram, Ganesh
• Is Part Of: Plant journal. Volume 93:Number 3(2018)
• Page Start: 472
• Page End: 488
• Publication Date: 2018-01-14
• Subjects: poplar -- nitrogen use efficiency -- metabolic flux analysis -- microarray; Plant molecular biology -- Periodicals; Plant cells and tissues -- Periodicals; Botany -- Periodicals; 580
• DOI: 10.1111/tpj.13792
• Languages: English
• ISSNs: 0960-7412

Abstract

Summary: Reduced nitrogen is indispensable to plants. However, its limited availability in soil combined with the energetic and environmental impacts of nitrogen fertilizers motivates research into molecular mechanisms toward improving plant nitrogen use efficiency (NUE). We performed a systems‐level investigation of this problem by employing multiple 'omics methodologies on cell suspensions of hybrid poplar ( Populus tremula × Populus alba ). Acclimation and growth of the cell suspensions in four nutrient regimes ranging from abundant to deficient supplies of carbon and nitrogen revealed that cell growth under low‐nitrogen levels was associated with substantially higher NUE. To investigate the underlying metabolic and molecular mechanisms, we concurrently performed steady‐state 13 C metabolic flux analysis with multiple isotope labels and transcriptomic profiling with cDNA microarrays. The 13 C flux analysis revealed that the absolute flux through the oxidative pentose phosphate pathway (oxPPP) was substantially lower (~threefold) under low‐nitrogen conditions. Additionally, the flux partitioning ratio between the tricarboxylic acid cycle and anaplerotic pathways varied from 84%:16% under abundant carbon and nitrogen to 55%:45% under deficient carbon and nitrogen. Gene expression data, together with the flux results, suggested a plastidic localization of the oxPPP as well as transcriptional regulation of certain metabolic branchpoints, including those between glycolysis and the oxPPP. The transcriptome data also indicated that NUE‐improving mechanisms may involve a redirection of excess carbon to aromatic metabolic pathways and extensive downregulation of potentially redundant genes (in these heterotrophic cells) that encode photosynthetic and light‐harvesting proteins, suggesting the recruitment of these proteins as nitrogen sinks in nitrogen‐abundant conditions. Significance Statement: The molecular mechanisms underlying poplar cell adaptation to reduced nitrogen supply have been poorly understood. By quantifying intracellular fluxes of carbon atoms and gene expression, this study examined the response of poplar cells to carbon and nitrogen deficiencies and pinpointed the possible strategy used by the cells to increase nitrogen use efficiency. This, in turn, could facilitate potential genetic manipulation approaches to increase NUE and biomass production by poplar.