Transcriptomic and network analyses reveal distinct nitrate responses in light and dark in rice leaves (Oryza sativa Indica var. Panvel1).
Sci Rep, 2020/07/22;10(1):12228.
Pathak RR[1], Jangam AP[1], Malik A[1], Sharma N[1], Jaiswal DK[2], Raghuram N[3]
Affiliations
PMID: 32699267DOI: 10.1038/s41598-020-68917-z
Impact factor: 4.996
Abstract
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 protein-protein 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.
MeSH terms
Darkness; Gene Expression Profiling; Gene Expression Regulation, Plant; Gene Regulatory Networks; Light; Nitrates; Oryza; Oxidation-Reduction; Plant Leaves; Plant Proteins; Signal Transduction; Transcriptome
More resources
Full text:
Europe PubMed Central; PubMed Central
EndNote: Download