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Gene coexpression analysis reveals dose-dependent and type-specific networks responding to ionizing radiation in the aquatic model plant Lemna minor using public data

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Abstract

Ionizing radiations (IRs) are widespread damaging stresses to plant growth and development. However, the regulatory networks underlying the mechanisms of responses to IRs remains poorly understood. Here, a set of publicly available transcriptomic data (conducted by Van Hoeck et al. 2015a), in which Lemna minor plants were exposed to a series of doses of gamma, beta and uranium treatments was used to perform gene coexpression network analysis. Overall, the genes involved in DNA synthesis and chromatin structure, light signalling, photosynthesis, and carbohydrate metabolism were commonly responsive to gamma, beta and uranium treatments. Genes related to anthocyanin accumulation and trichome differentiation were specifically downregulated, and genes related to nitrogen and phosphate nutrition, cell vesicle transport, mitochondrial electron transport and ATP synthesis were specifically upregulated in response to uranium treatment. While genes involved in DNA damage and repair, RNA processing and RNA binding were specifically downregulated and genes involved in calcium signalling, redox and degradation of carbohydrate metabolism were specifically upregulated responding to gamma radiation. These findings revealed both dose-dependent and type-specific networks responding to different IRs in L. minor, and can be served as a useful resource to better understand the mechanisms of responses to different IRs in other plants.

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References

  • Albrecht V., Simkova K., Carrie C., Delannoy E., Giraud E., Whelan J. et al. 2010 The cytoskeleton and the peroxisomal-targeted snowy cotyledon3 protein are required for chloroplast development in Arabidopsis. Plant Cell 22, 3423–3438.

    Article  CAS  Google Scholar 

  • Alexa A., Rahnenfuhrer J. and Lengauer T. 2006 Improved scoring of functional groups from gene expression data by decorrelating GO graph structure. Bioinformatics 22, 1600–1607.

    Article  CAS  Google Scholar 

  • Anderson H. J., Vonarx E. J., Pastushok L., Nakagawa M., Katafuchi A., Gruz P. et al. 2008 Arabidopsis thaliana Y-family DNA polymerase eta catalyses translesion synthesis and interacts functionally with PCNA2. Plant J. 55, 895–908.

    Article  CAS  Google Scholar 

  • Bachrati C. Z. and Hickson I. D. 2008 RecQ helicases: guardian angels of the DNA replication fork. Chromosoma 117, 219–233.

    Article  CAS  Google Scholar 

  • Badri H., Monsieurs P., Coninx I., Wattiez R. and Leys N. 2015 Molecular investigation of the radiation resistance of edible cyanobacterium Arthrospira sp. PCC 8005. Microbiologyopen 4, 187–207.

    Article  CAS  Google Scholar 

  • Cantero A., Barthakur S., Bushart T. J., Chou S., Morgan R. O., Fernandez M. P. et al. 2006 Expression profiling of the Arabidopsis annexin gene family during germination, de-etiolation and abiotic stress. Plant Physiol. Biochem. 44, 13–24.

    Article  CAS  Google Scholar 

  • Chen C. N., Chu C. C., Zentella R., Pan S. M. and Ho T. H. 2002 AtHVA22 gene family in Arabidopsis: phylogenetic relationship, ABA and stress regulation, and tissue-specific expression. Plant Mol. Biol. 49, 633–644.

    CAS  PubMed  Google Scholar 

  • Cheng X. F. and Wang Z. Y. 2005 Overexpression of COL9, a CONSTANS-LIKE gene, delays flowering by reducing expression of CO and FT in Arabidopsis thaliana. Plant J. 43, 758–768.

    Article  CAS  Google Scholar 

  • Conesa A., Gotz S., Garcia-Gomez J. M., Terol J., Talon M. and Robles M. 2005 Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21, 3674–3676.

    Article  CAS  Google Scholar 

  • Culligan K. M., Robertson C. E., Foreman J., Doerner P. and Britt A. B. 2006 ATR and ATM play both distinct and additive roles in response to ionizing radiation. Plant J. 48, 947–961.

    Article  CAS  Google Scholar 

  • Ding Z., Weissmann S., Wang M., Du B., Huang L., Wang L. et al. 2015 Identification of photosynthesis-associated C4 candidate genes through comparative leaf gradient transcriptome in multiple lineages of C3 and C4 species. PLoS One 10, e0140629.

    Article  Google Scholar 

  • Ding Z., Zhang Y., Xiao Y., Liu F., Wang M., Zhu X. et al. 2016 Transcriptome response of cassava leaves under natural shade. Sci. Rep. 6, 31673.

    Article  CAS  Google Scholar 

  • Doskocilova A., Plihal O., Volc J., Chumova J., Kourova H., Halada P. et al. 2011 A nodulin/glutamine synthetase-like fusion protein is implicated in the regulation of root morphogenesis and in signalling triggered by flagellin. Planta 234, 459–476.

    Article  CAS  Google Scholar 

  • Fu L., Ding Z., Han B., Hu W., Li Y. and Zhang J. 2016 Physiological investigation and transcriptome analysis of polyethylene glycol (PEG)-induced dehydration stress in cassava. Int. J. Mol. Sci. 17, 283.

    Article  Google Scholar 

  • Hayashi G., Shibato J., Imanaka T., Cho K., Kubo A., Kikuchi S. et al. 2014 Unraveling low-level gamma radiation-responsive changes in expression of early and late genes in leaves of rice seedlings at Iitate Village, Fukushima. J. Hered. 105, 723–738.

    Article  CAS  Google Scholar 

  • Hwang J. E., Hwang S. G., Kim S. H., Lee K. J., Jang C. S., Kim J. B. et al. 2014 Transcriptome profiling in response to different types of ionizing radiation and identification of multiple radio marker genes in rice. Physiol. Plant. 150, 604–619.

    Article  CAS  Google Scholar 

  • Johnson W. E., Li C. and Rabinovic A. 2007 Adjusting batch effects in microarray expression data using empirical Bayes methods. Biostatistics 8, 118–127.

    Article  Google Scholar 

  • Kim S. H., Song M., Lee K. J., Hwang S. G., Jang C. S., Kim J. B. et al. 2012 Genome-wide transcriptome profiling of ROS scavenging and signal transduction pathways in rice (Oryza sativa L.) in response to different types of ionizing radiation. Mol. Biol. Rep. 39, 11231–11248.

    Article  CAS  Google Scholar 

  • Langfelder P. and Horvath S. 2008 WGCNA: an R package for weighted correlation network analysis. BMC Bioinf. 9, 559.

    Article  Google Scholar 

  • Pierrugues O., Brutesco C., Oshiro J., Gouy M., Deveaux Y., Carman G. M. et al. 2001 Lipid phosphate phosphatases in Arabidopsis. Regulation of the AtLPP1 gene in response to stress. J. Biol. Chem. 276, 20300–20308.

    Article  CAS  Google Scholar 

  • Sahr T., Voigt G., Schimmack W., Paretzke H. G. and Ernst D. 2005 Low-level radiocaesium exposure alters gene expression in roots of Arabidopsis. New Phytol. 168, 141–148.

    Article  CAS  Google Scholar 

  • Sharma S., Stumpo D. J., Balajee A. S., Bock C. B., Lansdorp P. M., Brosh R. M. Jr and Blackshear P. J. 2007 RECQL, a member of the RecQ family of DNA helicases, suppresses chromosomal instability. Mol. Cell. Biol. 27, 1784–1794.

    Article  Google Scholar 

  • Smoot M. E., Ono K., Ruscheinski J., Wang P. L. and Ideker T. 2011 Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics 27, 431–432.

    Article  CAS  Google Scholar 

  • Thimm O., Blasing O., Gibon Y., Nagel A., Meyer S., Kruger P. et al. 2004 MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes. Plant J. 37, 914–939.

    Article  CAS  Google Scholar 

  • Trapnell C., Pachter L. and Salzberg S. L. 2009 TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25, 1105–1111.

    Article  CAS  Google Scholar 

  • Trapnell C., Roberts A., Goff L., Pertea G., Kim D., Kelley D. R. et al. 2012 Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat. Protoc. 7, 562–578.

    Article  CAS  Google Scholar 

  • Van Hoeck A., Horemans N., Monsieurs P., Cao H. X., Vandenhove H. and Blust R. 2015a The first draft genome of the aquatic model plant Lemna minor opens the route for future stress physiology research and biotechnological applications. Biotechnol. Biofuels 8, 188.

    Article  Google Scholar 

  • Van Hoeck A., Horemans N., Van Hees M., Nauts R., Knapen D., Vandenhove H. and Blust R. 2015b Beta-radiation stress responses on growth and antioxidative defense system in plants: a study with Strontium-90 in Lemna minor. Int. J. Mol. Sci. 16, 15309–15327.

    Article  Google Scholar 

  • Van Hoeck A., Horemans N., Van Hees M., Nauts R., Knapen D., Vandenhove H. and Blust R. 2015c Characterizing dose response relationships: chronic gamma radiation in Lemna minor induces oxidative stress and altered polyploidy level. J. Environ. Radioact. 150, 195–202.

    Article  Google Scholar 

  • Van Hoeck A., Horemans N., Nauts R., Van Hees M., Vandenhove H. and Blust R. 2017 Lemna minor plants chronically exposed to ionising radiation: RNA-seq analysis indicates a dose rate dependent shift from acclimation to survival strategies. Plant Sci. 257, 84–95.

    Article  Google Scholar 

  • Wang H., Ma L. G., Li J. M., Zhao H. Y. and Deng X. W. 2001 Direct interaction of Arabidopsis cryptochromes with COP1 in light control development. Science 294, 154–158.

    Article  CAS  Google Scholar 

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Acknowledgements

This project was funded by the International Science and Technology Co-operation Program of China (2010DFA62040) and Natural Science Foundation of Hainan Province (20164171), and the National Nonprofit Institute Research Grants (1630052016009).

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Author notes

  1. Lili Fu and Zehong Ding contributed equally to this work.

Authors and Affiliations

  1. Institute of Tropical Bioscience and Biotechnology, MOA Key Laboratory of Tropical Crops Biology and Genetic Resources, Hainan Bioenergy Center, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou, 571101, People’s Republic of China

    Lili Fu, Zehong Ding, Anuwat Kumpeangkeaw, Xuepiao Sun & Jiaming Zhang

Authors
  1. Lili Fu
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  2. Zehong Ding
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  3. Anuwat Kumpeangkeaw
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  4. Xuepiao Sun
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  5. Jiaming Zhang
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Corresponding authors

Correspondence to Zehong Ding or Jiaming Zhang.

Additional information

Corresponding editor: Qingpo Liu

Jiaming Zhang and Zehong Ding conceived and designed the experiments. Lili Fu, Zehong Ding, Anuwat Kumpeangkeaw, and Xuepiao Sun analysed the data. Lili Fu and Zehong Ding drafted the manuscript. Zehong Ding and Jiaming Zhang wrote the paper.

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Fu, L., Ding, Z., Kumpeangkeaw, A. et al. Gene coexpression analysis reveals dose-dependent and type-specific networks responding to ionizing radiation in the aquatic model plant Lemna minor using public data. J Genet 98, 9 (2019). https://doi.org/10.1007/s12041-019-1063-8

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  • DOI: https://doi.org/10.1007/s12041-019-1063-8

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