Nitrate (N) response is modulated by light, but not understood from a genome-wide perspective. Comparative transcriptomic analyses of nitrate response in light-grown and etiolated rice leaves revealed 303 and 249 differentially expressed genes (DEGs) respectively. A majority of them were exclusive to light (270) or dark (216) condition, whereas 33 DEGs were common. The latter may constitute response to N signaling regardless of light. Functional annotation and pathway enrichment analyses of the DEGs showed that nitrate primarily modulates conserved N signaling and metabolism in light, whereas oxidation-reduction processes, pentose-phosphate shunt, starch-, sucrose-and glycerolipid-metabolisms in the dark. Differential N-regulation of these pathways by light could be attributed to the involvement of distinctive sets of transporters, transcription factors, enriched cis-acting motifs in the promoters of DEGs as well as differential modulation of N-responsive transcriptional regulatory networks in light and dark. Sub-clustering of DEGs-associated proteinprotein interaction network constructed using experimentally validated interactors revealed that nitrate regulates a molecular complex consisting of nitrite reductase, ferredoxin-NADP reductase and ferredoxin. This complex is associated with flowering time, revealing a meeting point for N-regulation of N-response and N-use efficiency. Together, our results provide novel insights into distinct pathways of N-signaling in light and dark conditions. A major challenge in improving crops for input use efficiency is to understand and optimize the inputs for various agroclimatic conditions including light and photoperiod, soil type, altitude, humidity etc. Nitrogen (N) is quantitatively the most important fertilizer input for intensive cropping, but globally, nitrogen use efficiency (NUE) is as low as 30-40% for various crops, which is a major cause for economic losses and environmental consequences of N pollution 1. Rice has the least NUE among cereals and therefore tops all other crops in N-fertilizer consumption in India 2. The molecular aspects of nitrate transport, assimilation, signalling and crosstalk with water, hormone, and development are better understood than the biological determinants of crop nitrogen use efficiency 3-14. Characterization of the phenotype for NUE will be crucial for progress in this regard 15. Nitrate is taken up into the cell by a family of transporters and converted into ammonium ions by the serial action of nitrate reductase (NR) and nitrite reductase (NiR), followed by their assimilation into amino acids through the glutamine synthetase and glutamate synthase (GS-GOGAT) cycle. This requires 2-oxoglutarate (2-OG) from the carbon metabolism and hence coordination between C and N metabolism 4. Transcriptomic studies have revealed thousands of nitrate-responsive genes in Arabidopsis 3,16-18 , rice 19-23 and maize 24. They include those involved in metabolism, redox balance, signaling, stress, hormones, development etc., indicating their possible...
G-protein signaling components have been attributed many biological roles in plants, but the extent of involvement of G-protein coupled receptor 1 ( GCR1 ) with the Gα ( GPA1 ) remained unknown. To address this, we have performed transcriptomic analyses on Arabidopsis gpa1-5gcr1-5 double mutant and identified 656 differentially expressed genes (DEGs). MapMan and Gene Ontology analyses revealed global transcriptional changes associated with external stimulus, cell wall organization/biogenesis and secondary metabolite process among others. Comparative transcriptomic analyses using the single and double mutants of gcr1-5 and gpa1-5 identified 194, 139 and 391 exclusive DEGs respectively, whereas 64 DEGs were common to all three mutants. Further, pair wise comparison of DEGs of double mutant with single mutants of gcr1-5 or gpa1-5 showed about one-third and over half common DEGs, respectively. Further analysis of the DEGs exclusive to the double mutant using protein-protein interaction networks revealed molecular complexes associated with nitrate and light signaling and plant-pathogen interactions among others. Physiological and molecular validation of nitrate-response revealed the sensitivity of germination to low N in the double mutant and differential expression of nitrate transporter (and nitrate reductase in all three mutants). Taken together, GCR1 and GPA1 work in partnership as well as independently to regulate different pathways.
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