Role of phase partitioning in coordinating DNA damage response: focus on the Apurinic Apyrimidinic Endonuclease 1 interactome

Abstract

Liquid-liquid phase separation (LLPS) is a way to concentrate biochemical reactions while excluding noninteracting components. Disordered domains of proteins, as well as interaction with RNA, favor condensation but are not mandatory for modulating this process. Recent insights about phase-separation mechanisms pointed to new fascinating models that could explain how cells could cope with DNA damage responses, conferring both spatial and temporal fine regulation. APE1 is a multifunctional protein belonging to the Base Excision Repair (BER) pathway, bearing additional ‘non-canonical’ DNA-repair functions associated with processes like RNA metabolism. Recently, it has been highlighted that several DNA repair enzymes, such as 53BP1 and APE1, are endowed with RNA binding abilities. In this work, after reviewing the recent literature supporting a role of LLPS in DDR, we analyze, as a proof of principle, the interactome of APE1 using a bioinformatics approach to look for clues of LLPS in BER. Some of the APE1 interactors are associated with cellular processes in which LLPS has been either proved or proposed and are involved in different pathogenic events. This work might represent a paradigmatical pipeline for evaluating the relevance of LLPS in DDR.

NAD+ bioavailability mediates PARG inhibition-induced replication arrest, intra S-phase checkpoint and apoptosis in glioma stem cells

“…It is interesting to speculate that the formation of these PAR-driven protein complexes may be the result of liquid-liquid phase separation and the formation of biomolecular condensates regulated by PARylation, as suggested recently ( 88–90 ). Such processes have been postulated to promote heterochromatin domains ( 91 ) and to stimulate the formation of complexes with the BER protein APE1 ( 92 ), among other DNA repair proteins ( 93 ), including MDC1 and 53BP1 ( 94 , 95 ).…”

Oxidative DNA Damage and Cisplatin Neurotoxicity Is Exacerbated by Inhibition of OGG1 Glycosylase Activity and APE1 Endonuclease Activity in Sensory Neurons

“…Recent reports suggest that APE1 binding to AP sites within G4 sequences increases the folding of DNA into G4 structures and maintenance of APE1 binding, via APE1 acetylation, stabilizes the G4 and increases transcription factor recruitment to the promoter [29]. The effects of APE1 are not limited to DNA, as recent developments demonstrate that APE1 is also involved in the repair of damaged RNA, particularly oxidatively damaged RNA [57][58][59]. A clear understanding of what precedes APE1 activity on ribose AP sites is unclear; however, we cannot exclude the possibility that cisplatin also enhances the formation of 8-oxodG lesions within RNA and that APE1 can play a role in repairing the oxidative damage in RNA.…”

“…An interaction of BER proteins with other DNA repair pathways has been observed [64]; for example, Polβ polymerase can recruit mismatch repair (MMR) proteins [65] and the BER proteins, APE1 and PARP1, interact directly with Cockayne Syndrome B protein, which is critical for transcription-coupled and global nucleotide excision repair [66]. In addition to endonuclease/lyase functions to repair DNA damage, APE1 binds to RNA and may contribute to phase separation to organize biocondensates, which could enhance BER [59]. These findings support the notion that APE1 may modulate the DNA damaging effects of cisplatin beyond the repair of oxidative DNA lesions, suggesting that manipulation of the BER pathway may have indirect consequences on other DNA repair pathways and vice versa.…”

Conformational Rearrangements Regulating the DNA Repair Protein APE1

“…NPM1 is an oligomeric, multi-domain protein of 294 residues, consisting of a pentameric core connected, through very long, flexible linkers, to small, globular C-terminal domains. The intrinsically disordered linkers make NPM1 prone to engage in phase separation phenomena, which has been related to APE1 regulation [ 22 ]. Furthermore, the N-terminal tail of APE1, also flexible, serves as a binding platform for several ligands including NPM1 [ 14 , 20 , 21 ] and XRCC1 [ 11 ] and could mediate the modulation of APE1 function through these proteins.…”