Abstract
DNA damage response (DDR) in eukaryotes is largely regulated by protein phosphorylation. In archaea, many proteins are phosphorylated, however, it is unclear how the cells respond to DNA damage through global protein phosphorylation. We previously found that Δrio1, a Rio1 kinase homolog deletion strain of Sulfolobus islandicus REY15A, was sensitive to UV irradiation. In this study, we showed that Δrio1 grew faster than the wild type. Quantitative phosphoproteomic analysis of the wild type and Δrio1, untreated and irradiated with UV irradiation, revealed 562 phosphorylated sites (with a Ser/Thr/Tyr ratio of 65.3%/23.8%/10.9%) of 333 proteins in total. The phosphorylation levels of 35 sites of 30 proteins changed with >1.3-fold in the wild type strain upon UV irradiation. Interestingly, more than half of the UV-induced changes in the wild type did not occur in the Δrio1 strain, which were mainly associated with proteins synthesis and turnover. In addition, a protein kinase and several transcriptional regulators were differentially phosphorylated after UV treatment, and some of the changes were dependent on Rio1. Finally, many proteins involved in various cellular metabolisms exhibited Riol-related and UV-independent phosphorylation changes. Our results suggest that Rio1 is involved in the regulation of protein recycling and signal transduction in response to UV irradiation, and plays regulatory roles in multiple cellular processes in S. islandicus.
Highlights
Protein post-translational modifications (PTMs) are rapid regulatory mechanisms of cells in response to various stresses
Transcriptomic studies shown that multiple genes exhibited transcriptional changes in several archaea after UV or γ-irradiation, including the up-regulation of genes involved in DNA repair, and the down-regulation of genes involved in DNA replication and cell division (McCready et al, 2005; Frols et al, 2007; Gotz et al, 2007; Williams et al, 2007)
Previous transcriptomic analysis in S. solfataricus revealed that rio1, a kinase gene, was up-regulated by 2.8-fold upon UV irradiation (Gotz et al, 2007), and the rio1 deletion strain of S. islandicus exhibited higher sensitivity to UV irradiation than the wild type strain E233S (Huang et al, 2019)
Summary
Protein post-translational modifications (PTMs) are rapid regulatory mechanisms of cells in response to various stresses. Two regulators, Orc and TFB3, were found to be phosphorylated in S. solfataricus and Sulfolobus acidocaldarius (Esser et al, 2012; Reimann et al, 2013) These observations suggest that protein phosphorylation plays an important role in DDR and/or DNA repair. Our previous study revealed that Rio phosphorylated the Holliday junction resolvase Hjc in S. islandicus and regulated its nuclease activity (Huang et al, 2019) It remains unclear what other role(s) archaeal Rio plays in DNA damageinduced regulatory networks. We performed quantitative phosphoproteomic analysis on S. islandicus REY15A and rio deletion strain treated or untreated with UV We found that both UV-treatment and rio deletion resulted in phosphorylation changes of proteins in various cellular processes. The UV-independent phosphorylation regulated by Rio was analyzed, indicating that phosphorylation changes of many proteins participate in various cellular metabolic processes, reminiscent of those in yeast
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