Proline-mediated modulation on DNA repair pathway in rice seedlings under chromium stress by integrating gene chip and co-expression network analysis

Lin, Yu-Juan; Feng, Yuxi; Zhang, Qing; Yu, Xiao-Zhang

doi:10.1007/s10646-022-02586-8

Cited by 4 publications

(1 citation statement)

References 35 publications

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“…In order to establish the CNM regulatory module with statistical significance, all CNM-related genes were uploaded to the STRING (https://version-10-5.string-db.org/) software, and the proteinprotein interaction (PPI) networks (combined score >0.4) were constructed. Then, the modules (resolution = 0.8) with higher visualization were performed by the program Gephi 0.9.2 (Lin et al, 2022b).…”

Section: Co-expression Network Analysismentioning

confidence: 99%

Merging the occurrence possibility into gene co-expression network deciphers the importance of exogenous 2-oxoglutarate in improving the growth of rice seedlings under thiocyanate stress

Feng

Yang²,

Lin³

et al. 2023

Front. Plant Sci.

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Thiocyanate (SCN−) can find its way into cultivated fields, which might hamper the harmony in carbon and nitrogen metabolism (CNM) of plants, ebbing their quality and productivity. In the current study, we investigated the role of the exogenous application of 2-oxoglutarate (2-OG) in maintaining homeostasis of CNM in rice seedlings under SCN− stress. Results showed that SCN− exposure significantly repressed the gene expression and activities of CNM-related enzymes (e.g., phosphoenolpyruvate carboxylase, NADP-dependent isocitrate dehydrogenases, and isocitrate dehydrogenases) in rice seedlings, thereby reducing their relative growth rate (RGR). Exogenous application of 2-OG effectively mitigated the toxic effects of SCN− on rice seedlings, judged by the aforementioned parameters. The co-expression network analysis showed that genes activated in CNM pathways were categorized into four modules (Modules 1–4). In order to identify the key module activated in CNM in rice seedlings exposed to SCN−, the results from real-time quantitative PCR (RT-qPCR) tests were used to calculate the possibility of the occurrence of genes grouped in four different modules. Notably, Module 3 showed the highest occurrence probability, which is mainly related to N metabolism and 2-OG synthesis. We can conclude that exogenous application of 2-OG can modify the imbalance of CNM caused by SCN− exposure through regulating N metabolism and 2-OG synthesis in rice seedlings.

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Section: Co-expression Network Analysismentioning

confidence: 99%