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

Abstract

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.

An insight into the roles of ubiquitin-specific proteases in plants: development and growth, morphogenesis, and stress response

“…UBPs are involved in many plant hormone signaling pathways, including JA, BR, and ABA responses ( Jeong et al., 2017 ; Liu et al., 2022 ; Xiong et al., 2022 ). Recent studies have further revealed their roles in the regulation of DNA damage repair ( Hu et al., 2023 ) and ultraviolet radiation tolerance ( Al Khateeb et al., 2019 ). In addition, the same function can be modulated by different UBPs.…”

“…UBP12 and UBP13 are involved in ultraviolet radiation tolerance, possibly in a similar manner to the homolog USP7 in humans ( Al Khateeb et al., 2019 ). UBP12/13 oppose the roles of CRY in DNA damage response ( Hu et al., 2023 ). CRYs, which evolved from bacterial photolyases required for the repair of damaged DNA, enable plants to detect blue light and fine-tune growth and development ( Chaves et al., 2011 ).…”

“…CRYs, which evolved from bacterial photolyases required for the repair of damaged DNA, enable plants to detect blue light and fine-tune growth and development ( Chaves et al., 2011 ). UBP13 interacts with CRY2 ( Hu et al., 2023 ), but whether UBP13 deubiquitinates CRY2 has not been studied.…”