Transcriptome and metabolome analyses revealed that narrowband 280 and 310 nm UV-B induce distinctive responses in Arabidopsis

Tsurumoto, Tomohiro; Fujikawa, Yasuo; Onoda, Yushi; Ochi, Yusuke; Ohta, Daisaku; Okazawa, Atsushi

doi:10.1038/s41598-022-08331-9

Cited by 2 publications

(1 citation statement)

References 77 publications

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“…We then used these DEG lists to perform gene ontology (GO) enrichment analysis (Table S1). The top 10 GO terms enriched in the upregulated genes in WT at 15, 60 and 180 min included many stress-related GO terms (Figure S2D, Table S1), consistent with known studies reporting that UVC can induce stress responses 50 . Importantly, in cry1cry2 and ubp12ubp13 these stress-related GO terms were enriched in the downregulated and upregulated genes relative to WT, respectively (Figure S2D), suggesting that the transcriptomic response to UVC-induced DNA damage is less prominent in cry1cry2 and enhanced in ubp12ubp13.…”

Section: Resultssupporting

confidence: 86%

Cryptochromes and UBP12/13 deubiquitinases antagonistically regulate DNA damage response in Arabidopsis

Rosado

Lindbäck

et al. 2023

Preprint

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Cryptochromes (CRYs) are evolutionarily conserved blue-light receptors that evolved from bacterial photolyases that repair damaged DNA. Today, CRYs have lost their ability to repair damaged DNA; however, prior reports suggest that human CRYs can respond to DNA damage. Currently, the role of CRYs in the DNA damage response (DDR) is lacking, especially in plants. Therefore, we evaluated the role of plant CRYs in DDR along with UBP12/13 deubiquitinases, which interact with and regulate the CRY2 protein. We found that cry1cry2 was hypersensitive, while ubp12ubp13 was hyposensitive to UVC-induced DNA damage. Elevated UV-induced cyclobutane pyrimidine dimers (CPDs) and the lack of DNA repair protein RAD51 accumulation in cry1cry2 plants indicate that CRYs are required for DNA repair. On the contrary, CPD levels diminished and RAD51 protein levels elevated in plants lacking UBP12 and UBP13, indicating their role in DDR repression. Temporal transcriptomic analysis revealed that DDR-induced transcriptional responses were subdued in cry1cry2, but elevated in ubp12ubp13 compared to WT. Through transcriptional modeling of the time-course transcriptome, we found that genes quickly induced by UVC (15 min) are targets of CAMTA 1-3 transcription factors, which we found are required for DDR. This transcriptional regulation seems, however, diminished in the cry1cry2 mutant, indicating that CAMTAs are required for CRY2-mediated DDR. Furthermore, we observed enhanced CRY2-UBP13 interaction and formation of CRY2 nuclear speckles under UVC, suggesting that UVC activates CRY2 similarly to blue light. Together, our data reveal the temporal dynamics of the transcriptional events underlying UVC-induced genotoxicity and expand our knowledge of the role of CRY and UBP12/13 in DDR.

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Section: Resultssupporting

confidence: 86%

Cryptochromes and UBP12/13 deubiquitinases antagonistically regulate DNA damage response in Arabidopsis

Rosado

Lindbäck

et al. 2023

Preprint

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Transcriptomic characterization of Trichoderma harzianum T34 primed tomato plants: assessment of biocontrol agent induced host specific gene expression and plant growth promotion

Aamir,

Shanmugam,

Dubey

et al. 2023

BMC Plant Biol

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In this study, we investigated the intricate interplay between Trichoderma and the tomato genome, focusing on the transcriptional and metabolic changes triggered during the late colonization event. Microarray probe set (GSE76332) was utilized to analyze the gene expression profiles changes of the un-inoculated control (tomato) and Trichoderma-tomato interactions for identification of the differentially expressed significant genes. Based on principal component analysis and R-based correlation, we observed a positive correlation between the two cross-comaparable groups, corroborating the existence of transcriptional responses in the host triggered by Trichoderma priming. The statistically significant genes based on different p-value cut-off scores [(padj-values or q-value); padj-value < 0.05], [(pcal-values); pcal-value < 0.05; pcal < 0.01; pcal < 0.001)] were cross compared. Through cross-comparison, we identified 156 common genes that were consistently significant across all probability thresholds, and showing a strong positive corelation between p-value and q-value in the selected probe sets. We reported TD2, CPT1, pectin synthase, EXT-3 (extensin-3), Lox C, and pyruvate kinase (PK), which exhibited upregulated expression, and Glb1 and nitrate reductase (nii), which demonstrated downregulated expression during Trichoderma-tomato interaction. In addition, microbial priming with Trichoderma resulted into differential expression of transcription factors related to systemic defense and flowering including MYB13, MYB78, ERF2, ERF3, ERF5, ERF-1B, NAC, MADS box, ZF3, ZAT10, A20/AN1, polyol sugar transporter like zinc finger proteins, and a novel plant defensin protein. The potential bottleneck and hub genes involved in this dynamic response were also identified. The protein–protein interaction (PPI) network analysis based on 25 topmost DEGS (pcal-value < 0.05) and the Weighted Correlation Gene Network Analysis (WGCNA) of the 1786 significant DEGs (pcal-value < 0.05) we reported the hits associated with carbohydrate metabolism, secondary metabolite biosynthesis, and the nitrogen metabolism. We conclude that the Trichoderma-induced microbial priming re-programmed the host genome for transcriptional response during the late colonization event and were characterized by metabolic shifting and biochemical changes specific to plant growth and development. The work also highlights the relevance of statistical parameters in understanding the gene regulatory dynamics and complex regulatory networks based on differential expression, co-expression, and protein interaction networks orchestrating the host responses to beneficial microbial interactions.

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Transcriptome and metabolome analyses revealed that narrowband 280 and 310 nm UV-B induce distinctive responses in Arabidopsis

Cited by 2 publications

References 77 publications

Cryptochromes and UBP12/13 deubiquitinases antagonistically regulate DNA damage response in Arabidopsis

Cryptochromes and UBP12/13 deubiquitinases antagonistically regulate DNA damage response in Arabidopsis

Transcriptomic characterization of Trichoderma harzianum T34 primed tomato plants: assessment of biocontrol agent induced host specific gene expression and plant growth promotion

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