Transcriptomic and network analyses reveal distinct nitrate responses in light and dark in rice leaves (Oryza sativa Indica var. Panvel1).

Scientific Reports
Ravi Ramesh PathakN Raghuram

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-...Continue Reading

References

Apr 1, 1995·The Plant Journal : for Cell and Molecular Biology·N C de Vetten, R J Ferl
Nov 5, 1999·Molecular Cell Biology Research Communications : MCBRC·N RaghuramS K Sopory
Jan 15, 2000·The Journal of Biological Chemistry·H ChoiS Y Kim
Jun 1, 1991·Proceedings of the National Academy of Sciences of the United States of America·G Peltier, G W Schmidt
Mar 1, 2003·The Plant Journal : for Cell and Molecular Biology·Elena Ramirez-ParraCrisanto Gutierrez
Mar 5, 2004·The Plant Journal : for Cell and Molecular Biology·Oliver ThimmMark Stitt
Aug 8, 2007·Molecular Genetics and Genomics : MGG·Suman K DasNandula Raghuram
May 23, 2008·Nucleic Acids Research·Morgane Thomas-ChollierJacques van Helden
Sep 10, 2008·The Biochemical Journal·Cathrine Lillo
Mar 6, 2009·The Journal of Biological Chemistry·Eun-Yeong BergsdorfThomas J Jentsch
Jul 16, 2010·The Plant Cell·Rajani SarojamJohn L Bowman
Jul 24, 2010·Canadian Journal of Microbiology·Ravi Ramesh Pathak, Sunila Lochab
Mar 5, 2011·Virology Journal·Nimesh Gupta, P V Lakshmana Rao
Dec 7, 2011·Proceedings of the National Academy of Sciences of the United States of America·Laura Houille-VernesXenie Johnson
Apr 1, 2009·Physiology and Molecular Biology of Plants : an International Journal of Functional Plant Biology·Ravi Ramesh PathakNandula Raghuram
Apr 30, 2014·Nature Genetics·Hongying SunXiangdong Fu
Dec 5, 2014·BMC Genomics·Viktoriya ConevaSteven J Rothstein
Jun 6, 2015·Plant Physiology·Mariana ObertelloGloria M Coruzzi
Jan 1, 2014·Molecular Breeding : New Strategies in Plant Improvement·Hui WangZhen-Guo Ma
Dec 5, 2015·Frontiers in Plant Science·Navjyoti ChakrabortyNandula Raghuram
Feb 19, 2016·Plant Cell Reports·Prince MarowaYingzhen Kong
May 24, 2016·Molecular Plant·José A O'BrienRodrigo A Gutiérrez
Jun 22, 2016·Proceedings of the National Academy of Sciences of the United States of America·Shu YuanYikun He
Jun 25, 2016·Journal of Plant Physiology·Anil Kumar Nalini ChandranChang-Deok Han
Feb 6, 2017·Journal of Experimental Botany·Xiaorong FanGuohua Xu

❮ Previous
Next ❯

Datasets Mentioned

BETA
GSE12940

Methods Mentioned

BETA
one-hybrid
Feature Extraction
PCR

Software Mentioned

CELLO
MCODE
geomean
Cytoscape
QuantPrime
MapMan
GraphPad Prism
ImageJ
Agilent Feature Extraction
GeneSpring

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.