Onodera, W. | Search bioRxiv

bioRxiv2025

Praja1 protects cells from DNA damage through direct DNA binding

Praja1 is known as an E3 ubiquitin ligase that regulates multiple functions through protein degradation. It acquired nuclear localization signal after gene duplication and although studies have shown some significant roles of nuclear Praja1, comprehensive analysis still lacks. In this study, we performed comparative proteomics and biochemical analyses to elucidate the functions of Praja1 in the nucleus. First, proteomics analysis applied to nuclear localization deficient Praja1 exhibited signs of DNA damage response fluctuation. Subsequent comet assay revealed Praja1 protecting cells from various DNA damage sources. Similarly, cells lacking Praja1 became more sensitive to DNA damage-induced cell death, while E. coli expressing Praja1 exhibited resistance to DNA damage. To further elucidate the molecular basis of DNA protection, gel shift assay showed direct binding of Praja1 to DNA through electrostatic interactions within its intrinsically disordered region. Further in vitro damaging assay suggested that Praja1 may induce structural changes that enhance DNA repair efficiency upon binding to DNA. Together, these results provide insights into the evolutionarily novel role of nuclear Praja1 in protecting against DNA damage.

molecular biology↗

bioRxiv2024

E3 ligase Praja1 mediates ubiquitination and degradation of microtubule-associated protein Tau

RING-H2 type E3 ligase Praja family is composed of Praja1 and Praja2, which promote the degradation of substrates through the ubiquitin-proteasome system. Both paralogs contribute to neuronal maturation and differentiation, indicating a significant role in the nervous system. Aggregation-prone proteins associated with neurodegenerative diseases, including TDP-43 and -synuclein, are degraded and/or suppressed by Praja1. Furthermore, the expression level of the MAPT gene, which is frequently mutated in Alzheimers, is regulated by Praja2. While the Praja family has been shown to recognize various aggregation-prone proteins as substrates, it has not been determined whether Tau, a key protein that aggregates in tauopathies, is also recognized by Praja proteins. In this study, we show that Praja1, but not Praja2, recognizes Tau as a candidate substrate. We observed that Tau expression in human neuroblastoma SH-SY5Y cells decreased depending on the E3 ligase activity of Praja1. Furthermore, Praja1 polyubiquitinated and interacted with Tau, indicating that it is a target substrate. Next, by combining ancestral sequence reconstruction and mutational analysis, we revealed that the Praja1-Tau interaction began via deletion of the N- and C-terminal regions of Praja1, occurring just after the duplication of the Praja family in the common ancestor of placentals. Lastly, to test whether this interaction is disrupted under pathological conditions, P301L Tau was introduced, resulting in a degradation similar to that of wild-type Tau. These results reveal an unidentified mechanism of Tau proteostasis by Praja1 and may provide insight into the pathogenesis of neurodegenerative diseases, including tauopathy.

biochemistry↗