Application of Gamma Ray-Responsive Genes for Transcriptome-Based Phytodosimetry in Rice

Kim, Jin-Hong; Hwangbo, Kwon; Lee, Eujin; Dubey, Shubham; Chung, Moon‐Soo; Chung, Byung Yeoup; Lee, Sungbeom

doi:10.3390/plants10050968

Cited by 3 publications

(2 citation statements)

References 36 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Gamma irradiation at doses of 3–48 Gy induced the expression of DDR genes in a dose-dependent manner, following nuclear DNA damage in Arabidopsis and rice plants ( Ryu et al., 2018 ; Kim et al., 2021 ). However, γ-H2AX induction and DDR gene expression were not statistically different within the dose range of 3–12 Gy and almost recovered to the control levels within 24 h. To evaluate the genotoxic stress of X- or γ-irradiation at two different doses proven to stimulate or inhibit cell growth, we compared the genome-wide transcriptomic profiles of C. reinhardtii by RNA-Seq analysis after X- or γ-irradiation at doses of 6 and 50 Gy.…”

Section: Resultsmentioning

confidence: 99%

Application of ionizing radiation as an elicitor to enhance the growth and metabolic activities in Chlamydomonas reinhardtii

Kim

Dubey²,

Hwangbo³

et al. 2023

Front. Plant Sci.

Self Cite

View full text Add to dashboard Cite

Chlamydomonas reinhardtii is a eukaryotic, unicellular photosynthetic organism and a potential algal platform for producing biomass and recombinant proteins for industrial use. Ionizing radiation is a potent genotoxic and mutagenic agent used for algal mutation breeding that induces various DNA damage and repair responses. In this study, however, we explored the counterintuitive bioeffects of ionizing radiation, such as X- and γ-rays, and its potential as an elicitor to facilitate batch or fed-batch cultivation of Chlamydomonas cells. A certain dose range of X- and γ-rays was shown to stimulate the growth and metabolite production of Chlamydomonas cells. X- or γ-irradiation with relatively low doses below 10 Gy substantially increased chlorophyll, protein, starch, and lipid content as well as growth and photosynthetic activity in Chlamydomonas cells without inducing apoptotic cell death. Transcriptome analysis demonstrated the radiation-induced changes in DNA damage response (DDR) and various metabolic pathways with the dose-dependent expression of some DDR genes, such as CrRPA30, CrFEN1, CrKU, CrRAD51, CrOASTL2, CrGST2, and CrRPA70A. However, the overall transcriptomic changes were not causally associated with growth stimulation and/or enhanced metabolic activities. Nevertheless, the radiation-induced growth stimulation was strongly enhanced by repetitive X-irradiation and/or subsequent cultivation with an inorganic carbon source, i.e., NaHCO3, but was significantly inhibited by treatment of ascorbic acid, a scavenger of reactive oxygen species (ROS). The optimal dose range of X-irradiation for growth stimulation differed by genotype and radiation sensitivity. Here, we suggest that ionizing radiation within a certain dose range determined by genotype-dependent radiation sensitivity could induce growth stimulation and enhance metabolic activities, including photosynthesis, chlorophyll, protein, starch, and lipid synthesis in Chlamydomonas cells via ROS signaling. The counterintuitive benefits of a genotoxic and abiotic stress factor, i.e., ionizing radiation, in a unicellular algal organism, i.e., Chlamydomonas, may be explained by epigenetic stress memory or priming effects associated with ROS-mediated metabolic remodeling.

show abstract

Section: Resultsmentioning

confidence: 99%

Application of ionizing radiation as an elicitor to enhance the growth and metabolic activities in Chlamydomonas reinhardtii

Kim

Dubey²,

Hwangbo³

et al. 2023

Front. Plant Sci.

Self Cite

View full text Add to dashboard Cite

show abstract

“…This can further lead to DNA damage-induced endoreduplication (Nisa et al, 2019). In addition, transcriptional recruitment of DDR proteins in response to gamma radiation requires chromatin remodelers involved in DNA methylation and histone 2A (H2A) modification (Choi et al, 2019; Kim 2019; Kim et al, 2021). In that context, increased global methylation in Scots pine plants from the Chernobyl exclusion zone has been reported (Kovalchuk et al, 2003).…”

Section: Introductionmentioning

confidence: 99%

High radiosensitivity in Norway spruce (Picea abies) is rendered by less comprehensive mobilisation of protection, repair and stress responses compared to the radiotolerantA. thaliana

Bhattacharjee,

Blagojevic,

Lee

et al. 2023

Preprint

View full text Add to dashboard Cite

Following nuclear events, risk assessment and protection of plant communities in contaminated ecosystems require in-depth understanding of radiosensitivity of plants. However, the physiological and molecular factors defining differential sensitivity to chronic ionising radiation exposure are poorly understood. In this study, we compared early molecular events associated with protection, repair, and stress responses as well as phenotypic and cellular effects in gamma-irradiated seedlings of the radiosensitive conifer Norway spruce (Picea abies) and the radiotolerant herbaceousArabidopsis thaliana. After 48-h of irradiation, Norway spruce showed reduced growth at 290 mGy h-1and severe organelle damage at ≥ 1 mGy h-1whereasA. thalianashowed unaffected development, minor organelle damage at ≥ 100 mGy h-1only and significantly less DNA damage at all dose rates. Comparative transcriptomics revealed that Norway spruce mobilized transcription of DNA damage repair and antioxidant genes at ≥ 40 mGy h-1only whileA. thalianashowed massive activation of genes related to DNA damage repair, antioxidants, and other stress responses as well as growth-promoting hormones and cell wall components at ≥ 1 mGy h-1. Adverse effects on chloroplasts and mitochondria from low dose rates on and comprehensive downregulation of photosynthetic genes and activation of respiration genes at ≥ 40 mGy h-1in Norway spruce but not inA. thalianamay reflect the higher energy demand in Norway spruce to simultaneously maintain its far larger genome and engage protection and repair systems. Hence, the absence of transcriptional response at lower gamma doses and activation of repair and protection at high dose rates only, when accumulated damage is high, is consistent with the high radiosensitivity of Norway spruce. Conversely, the more massive transcriptional activation of crucial repair and protection pathways even at low dose rates complies with the high radiotolerance ofA. thaliana.

show abstract

Asymmetric gene expression and cell-type-specific regulatory networks in the root of bread wheat revealed by single-cell multiomics analysis

Zhang

Lai

et al. 2023

Genome Biol

View full text Add to dashboard Cite

Background Homoeologs are defined as homologous genes resulting from allopolyploidy. Bread wheat, Triticum aestivum, is an allohexaploid species with many homoeologs. Homoeolog expression bias, referring to the relative contribution of homoeologs to the transcriptome, is critical for determining the traits that influence wheat growth and development. Asymmetric transcription of homoeologs has been so far investigated in a tissue or organ-specific manner, which could be misleading due to a mixture of cell types. Results Here, we perform single nuclei RNA sequencing and ATAC sequencing of wheat root to study the asymmetric gene transcription, reconstruct cell differentiation trajectories and cell-type-specific gene regulatory networks. We identify 22 cell types. We then reconstruct cell differentiation trajectories that suggest different origins between epidermis/cortex and endodermis, distinguishing bread wheat from Arabidopsis. We show that the ratio of asymmetrically transcribed triads varies greatly when analyzing at the single-cell level. Hub transcription factors determining cell type identity are also identified. In particular, we demonstrate that TaSPL14 participates in vasculature development by regulating the expression of BAM1. Combining single-cell transcription and chromatin accessibility data, we construct the pseudo-time regulatory network driving root hair differentiation. We find MYB3R4, REF6, HDG1, and GATAs as key regulators in this process. Conclusions Our findings reveal the transcriptional landscape of root organization and asymmetric gene transcription at single-cell resolution in polyploid wheat.

show abstract

Application of Gamma Ray-Responsive Genes for Transcriptome-Based Phytodosimetry in Rice

Cited by 3 publications

References 36 publications

Application of ionizing radiation as an elicitor to enhance the growth and metabolic activities in Chlamydomonas reinhardtii

Application of ionizing radiation as an elicitor to enhance the growth and metabolic activities in Chlamydomonas reinhardtii

High radiosensitivity in Norway spruce (Picea abies) is rendered by less comprehensive mobilisation of protection, repair and stress responses compared to the radiotolerantA. thaliana

Asymmetric gene expression and cell-type-specific regulatory networks in the root of bread wheat revealed by single-cell multiomics analysis

Contact Info

Product

Resources

About