Identification of nitric oxide (NO)-responsive genes under hypoxia in tomato (Solanum lycopersicum L.) root

Vajiheh Safavi-Rizi,Marco Herde,Christine Stöhr

doi:10.1038/s41598-020-73613-z

Vajiheh Safavi-Rizi, Marco Herde + Show 1 more

Open Access

https://doi.org/10.1038/s41598-020-73613-z

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Abstract

Flooding periods, as one probable consequence of climate change, will lead more frequently to plant hypoxic stress. Hypoxia sensing and signaling in the root, as the first organ encountering low oxygen, is therefore crucial for plant survival under flooding. Nitric oxide has been shown to be one of the main players involved in hypoxia signaling through the regulation of ERFVII transcription factors stability. Using SNP as NO donor, we investigated the NO-responsive genes, which showed a significant response to hypoxia. We identified 395 genes being differentially regulated under both hypoxia and SNP-treatment. Among them, 251 genes showed up- or down-regulation under both conditions which were used for further biological analysis. Functional classification of these genes showed that they belong to different biological categories such as primary carbon and nitrogen metabolism (e.g. glycolysis, fermentation, protein and amino acid metabolism), nutrient and metabolites transport, redox homeostasis, hormone metabolism, regulation of transcription as well as response to biotic and abiotic stresses. Our data shed light on the NO-mediated gene expression modulation under hypoxia and provides potential targets playing a role in hypoxia tolerance. These genes are interesting candidates for further investigating their role in hypoxia signaling and survival.

Highlights

NO is a highly reactive molecule and its conversion to a non-toxic molecule is crucial to avoid cell toxicity[18]
The cytosolic nitrate reductase (NR), the key enzyme involved in nitrate assimilation which converts nitrate to nitrite, may catalyze the
A Nitrite-NO reductase (NiNOR) activity has been discovered in root plasma membrane (PM), which uses the nitrite provided by PM bound NR as substrate under low oxygen c ondition[16,38]

Summary

Result

SNP‐treatment showed distinct response in physiological parameters as well as in modulation of gene expression. Among regulated genes under hypoxia and SNP-treatment, 35 genes were observed encoding redox-associated proteins belonging to different categories such as catalases (CAT2), reductases (SDR5), peroxidases (PRX71, two transcripts annotated as PRX72, five transcripts annotated as PRX52, PRX2, two transcripts annotated as PRX9, PRX64, five transcripts annotated as RCI3, Solyc02g090450, Solyc02g090470, Solyc07g017880 and Solyc08g075830, oxidases (Solyc12g013690 and SKU5), glutathione S-transferases (GSTU1, three transcripts annotated as GSTU8, GSTU19 and GSTL3), cytochrome P450 (CYP716A1, CYP76C2, CYP72A14 and CYP707A3) (Fig. 8). These data indicate the importance of redox regulation under hypoxia-induced nitrosative stress. Regulated genes responsive to hypoxia and SNP-treatment encoding proteins belonging to additional functional categories were identified: lipid metabolism (LP1, ACBP6, FAD2 and Solyc10g083720) cell cycle (solyc01g111170, Solyc01g111170), cell organization (WVD2, PP2A12, TUB1 and TUA6), cell vesicle transport (SNAP33), co-factor and vitamin metabolism (PDX1), development/storage proteins (PLP1 and solyc01g104110), DNA synthesis (Solyc01g080600), metal handling (MT2B and FP3), S-assimilation (two transcripts annotated as APR3, APR2 and SIR), secondary metabolism such as lignin (solyc04g054690 and LAC7) and phenol (three transcripts annotated as PAL1), Signaling (GRF2, IQD1 and Solyc07g006830), nucleotide metabolism (APY1), beta-galactosidase (BGAL1) and protease inhibitor (solyc03g079880) (Fig. 12)

Discussion

Findings

Methods