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

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Abstract

Chromium (Cr) stress can cause oxidative burst to plants. Application of exogenous proline (Pro) is one of the most effective approaches to improve the tolerance of plants to Cr stress. In this study, we integrated the data of gene chip with co-expression network analysis to identify the key pathways involved in the DNA repair processes in rice seedlings under Cr(VI) stress. Based on KEGG pathway analysis, 158 genes identified are activated in five different types of DNA repair pathways, namely base excision repair (BER, 20 genes), mismatch repair (MMR, 30 genes), nonhomologous end joining (NHEJ, 8 genes), nucleotide excision repair (NER, 56 genes) and homologous recombination (HR, 44 genes). Co-expression network analysis showed that genes activated in DNA repair pathways were categorized into six different modules, wherein Module 1 (45.36%), Module 2 (27.84%) and Module 3 (19.59%) carried more weight than others. Integrating the data of gene chip and co-expression network analysis indicated that coordinated actions of HR and NER pathways are mainly associated with DNA repair processes in Cr(VI)-treated rice seedlings supplied with exogenous Pro. OsCSB, OsXPG, OsBRIP1, OsRAD51C, OsRAD51A2, OsRPA, OsTOPBP1C, OsTOP3, and OsXRCC3 activated in the HR pathway had a stronger impact on repairing DNA damage induced by Cr(VI) stress in rice seedlings supplied with exogenous Pro, while OsXPB1, OsTTDA2, OsTFIIH1, OsXPC, OsRAD23, OsDSS1, and OsRPA located at the NER pathway showed more contribution to repairing DNA damage than others.

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Acknowledgements

This work was financially supported by the Natural Science Foundation of Guangxi (No. 2018GXNSFDA281024).

Author contributions

Writing-original draft preparation, Data analysis and Visualization Y-JL; Writing-reviewing and Editing, and Visualization Y-XF; Data analysis and Visualization QZ; Conceptualization, Supervision, Writing-reviewing and Editing, and Funding acquisition, X-ZY. All of the authors contributed to the final review of the manuscript.

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Authors and Affiliations

  1. The Guangxi Key Laboratory of Theory & Technology for Environmental Pollution Control, College of Environmental Science & Engineering, Guilin University of Technology, Guilin, 541004, People’s Republic of China

    Yu-Juan Lin, Yu-Xi Feng, Qing Zhang & Xiao-Zhang Yu

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  1. Yu-Juan Lin
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  2. Yu-Xi Feng
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  3. Qing Zhang
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Correspondence to Xiao-Zhang Yu.

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Lin, YJ., Feng, YX., Zhang, Q. et al. Proline-mediated modulation on DNA repair pathway in rice seedlings under chromium stress by integrating gene chip and co-expression network analysis. Ecotoxicology 31, 1266–1275 (2022). https://doi.org/10.1007/s10646-022-02586-8

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