Nitric Oxide Mediated Transcriptome Profiling Reveals Activation of Multiple Regulatory Pathways in Arabidopsis thaliana

Abstract

Imbalance between the accumulation and removal of nitric oxide and its derivatives is a challenge faced by all plants at the cellular level, and is especially important under stress conditions. Exposure of plants to various biotic and abiotic stresses causes rapid changes in cellular redox tone potentiated by the rise in reactive nitrogen species that serve as signaling molecules in mediating defensive responses. To understand mechanisms mediated by these signaling molecules, we performed a large-scale analysis of the Arabidopsis transcriptome induced by nitrosative stress. We generated an average of 84 and 91 million reads from three replicates each of control and 1 mM S-nitrosocysteine (CysNO)-infiltrated Arabidopsis leaf samples, respectively. After alignment, more than 95% of all reads successfully mapped to the reference and 32,535 genes and 55,682 transcripts were obtained. CysNO infiltration caused differential expression of 6436 genes (3448 up-regulated and 2988 down-regulated) and 6214 transcripts (3335 up-regulated and 2879 down-regulated) 6 h post-infiltration. These differentially expressed genes were found to be involved in key physiological processes, including plant defense against various biotic and abiotic stresses, hormone signaling, and other developmental processes. After quantile normalization of the FPKM values followed by student's T-test (P < 0.05) we identified 1165 DEGs (463 up-regulated and 702 down-regulated) with at least 2-folds change in expression after CysNO treatment. Expression patterns of selected genes involved in various biological pathways were verified using quantitative real-time PCR. This study provides comprehensive information about plant responses to nitrosative stress at transcript level and would prove helpful in understanding and incorporating mechanisms associated with nitrosative stress responses in plants.

Molecular mechanisms governing plant responses to high temperatures

“…Like ROS, NO is highly reactive and capable of post‐translationally modifying proteins at cysteine residues, via S‐nitrosylation. This modification can regulate the stability, subcellular localization, and activity of the target proteins (Tada et al ; Lindermayr et al ; Gibbs et al ), causing global changes in gene expression (Hussain et al ). Using shotgun proteomics, a number of S‐nitrosylated proteins have been identified (Puyaubert et al ; Hu et al ).…”

Redox Components: Key Regulators of Epigenetic Modifications in Plants

“…It has been reported that NO positively regulates PRMT5 activity by S-nitrosylation at Cys-125 under NaCl stress in A. thaliana [20]. Treatment with NO donor S-nitrosocysteine also prominently promotes JMJs expression in A. thaliana [87], implying that JMJs are possibly regulated by NO.…”

“…In addition to influencing SAM synthesis, redox intermediates also regulate the expression and activity of HMTs and HDMs. For instance, application of S-nitrosocysteine, a NO donor, to Arabidopsis leaves upregulates the expression of Set Domain Group 20, a gene encoding lysine methyl transferase, and PcG Histone Methyltransferase Curly Leaf gene [87], pointing to the important function of NO in modulating the two HMTs. PRMT5 can catalyzes Arg symmetric dimethylation of histones and non-histone proteins in higher eukaryotes [88].…”

Nitric Oxide Responsive Heavy Metal-Associated Gene AtHMAD1 Contributes to Development and Disease Resistance in Arabidopsis thaliana

“…All the A. thaliana HMA ( AtHMA ) domain-containing genes that showed differential expression toward CysNO-mediated transcriptome analysis (Hussain et al, 2016) were identified and heat map showing the signal intensities of differentially expressed genes (up and down-regulated) was generated using R (version 3.3.1). Sequences for all AtHMA genes were retrieved from the Arabidopsis Information Resource (TAIR) database 1 .…”

“…In the present study, we adopted a combined in silico and biological approach to examine structure and putative function of the Arabidopsis thaliana HMA domain containing gene ( AT1G51090-AtHMAD1 ) that showed differential expression in response to CysNO in a separate study involving transcriptomic analysis (Hussain et al, 2016). We also sought to determine its possible role in the regulation of oxidative and nitrosative stress and plant defense against virulent and avirulent pathogens.…”