The Intrinsically Disordered C-Terminal Domain Triggers Nucleolar Localization and Function Switch of PARN in Response to DNA Damage

Abstract

Poly(A)-specific ribonuclease (PARN), a multifunctional multi-domain deadenylase, is crucial to the regulation of mRNA turnover and the maturation of various non-coding RNAs. Despite extensive studies of the well-folding domains responsible for PARN catalysis, the structure and function of the C-terminal domain (CTD) remains elusive. PARN is a cytoplasm–nucleus shuttle protein with concentrated nucleolar distribution. Here, we identify the nuclear and nucleolar localization signals in the CTD of PARN. Spectroscopic studies indicated that PARN-CTD is intrinsically disordered with loosely packed local structures/tertiary structure. Phosphorylation-mimic mutation S557D disrupted the local structure and facilitated the binding of the CTD with the well-folded domains, with no impact on PARN deadenylase activity. Under normal conditions, the nucleolus-residing PARN recruited CBP80 into the nucleoli to repress its deadenylase activity, while DNA damage-induced phosphorylation of PARN-S557 expelled CBP80 from the nucleoli to discharge activity inhibition and attracted nucleoplasm-located CstF-50 into the nucleoli to activate deadenylation. The structure switch-induced function switch of PARN reshaped the profile of small nuclear non-coding RNAs to respond to DNA damage. Our findings highlight that the structure switch of the CTD induced by posttranslational modifications redefines the subset of binding partners, and thereby the RNA targets in the nucleoli.

Translation Efficiency and Degradation of ER-Associated mRNAs Modulated by ER-Anchored poly(A)-Specific Ribonuclease (PARN)

“…Herein, we identified that the cytoplasmic PARN can shuttle between the cytosol and ER. Under DNA damaging conditions induced by DOX, the anterior nucleus-localized PARN was quickly translocated to cytoplasm, while the DNA damage-mimic reagent hydroxyl urea did not induce such a translocation [8]. This suggested that the action of PARN during DDR might involve step-wise processes.…”

“…Previously, PARN has been shown to participate into DNA damage response (DDR) via multiple pathways, including switching off PARN activity by MAPKAP kinase 2 (MK2)-induced Ser557 phosphorylation to stabilize the Gadd45α mRNA in the p38MAPK/MK2 pathway [66], degrading a subset of mRNAs by recruiting to the CstF/BARD1 complex in the nucleus [81], modulating protein-protein interaction network by phosphorylation at S557 [8], and regulating p53 [74] or p21 mRNA stability [16]. Herein, we also found that PARN is involved in the p38MAPK/MK2 signaling pathway and identified an additional target of PARN during DDR.…”

“…No significant changes in the protein levels of PARN were found in both of the cell lines, implying that parn transcription was not responsive to DNA damage. Dramatic translocation of PARN from the nucleus to cytoplasm was observed in both cell lines ( Figure 3B) when treated by DOX, but not the DNA damage-mimic reagent hydroxyl urea [8]. In the HeLa cells, the amount of ER-anchored PARN abruptly increased within 2 h DOX treatment, followed by a slow decline.…”

“…A cleavage fragment with a molecular weight of~25 kDa was quite resistant to trypsin treatment and it could be identified by antibody recognizing PARN(589-639). This region was in the C-terminal domain (CTD) of PARN, which has been shown to be predominantly intrinsically disordered [8]. The resistance of this disordered fragment against trypsin digestion suggested that the CTD might be protected via membrane binding.…”

Nucleolar Organization and Functions in Health and Disease

“…Two papers in this Special Issue focus on the structure-function relationship of individual proteins. In a primary research article, Duan and colleagues [13] examine the localization and activity of poly(A)-specific ribonuclease (PARN). PARN is a multi-domain protein with an intrinsically disordered C-terminal domain.…”