Emerging roles of the nucleolus in regulating the DNA damage response: the noncanonical DNA repair enzyme APE1/Ref-1 as a paradigmatical example

Abstract

Significance: An emerging concept in DNA repair mechanisms is the evidence that some key enzymes, besides their role in the maintenance of genome stability, display also unexpected noncanonical functions associated with RNA metabolism in specific subcellular districts (e.g., nucleoli). During the evolution of these key enzymes, the acquisition of unfolded domains significantly amplified the possibility to interact with different partners and substrates, possibly explaining their phylogenetic gain of functions.

Recent advances: After nucleolar stress or DNA damage, many DNA repair proteins can freely relocalize from nucleoli to the nucleoplasm. This process may represent a surveillance mechanism to monitor the synthesis and correct assembly of ribosomal units affecting cell cycle progression or inducing p53-mediated apoptosis or senescence.

Critical issues: A paradigm for this kind of regulation is represented by some enzymes of the DNA base excision repair (BER) pathway, such as apurinic/apyrimidinic endonuclease 1 (APE1). In this review, the role of the nucleolus and the noncanonical functions of the APE1 protein are discussed in light of their possible implications in human pathologies.

Future directions: A productive cross-talk between DNA repair enzymes and proteins involved in RNA metabolism seems reasonable as the nucleolus is emerging as a dynamic functional hub that coordinates cell growth arrest and DNA repair mechanisms. These findings will drive further analyses on other BER proteins and might imply that nucleic acid processing enzymes are more versatile than originally thought having evolved DNA-targeted functions after a previous life in the early RNA world.

FIG. 1.

Potential consequences of unrepaired RNA damage. RNA intrinsic nature renders it more susceptible to damage, such as oxidation. The molecular and surveillance mechanisms that cope with RNA damage are still poorly understood. If unrepaired, aberrant RNA may give rise to translation of defective and toxic protein aggregates that eventually leads to cell cycle arrest and consequently to cell death. These molecular processes have been associated with cancer onset, aging, and neurodegeneration.

FIG. 2.

The nucleolus, a multifunctional domain. The unveiling of the “nucleolome” allowed the understanding of the complexity of the nucleolus, firstly described only as a ribosome factory. The multifunctionality of the nucleolus includes different noncanonical functions as the control of cell proliferation and cell growth, regulation of protein stability, stress and DDR, telomere metabolism, maturation of small RNAs, and control of viral life-cycle. An illustrative mechanism for each function is summarized. MDM2, mouse double minute 2 homolog; ARF, p14 alternative reading frame; ADAR2, double-stranded RNA-specific adenosine deaminase 2; NS, nucleostemin; VHL, von Hippel-Lindau protein; HIF, hypoxia-inducible factor; ING1, inhibitor of growth family protein, member 1; PML, promyelocytic leukemia protein; DNA Topo I, DNA topoisomerase I; TERC, telomerase RNA component; TERT, telomerase reverse transcriptase; GNL3L, guanine nucleotide binding protein-like 3 (nucleolar)-like; TRF, telomeric repeat-binding factor 2; REV, regulator of expression of virion protein; Tat, trans-activator of transcription; Ub, ubiquitin; DDR, DNA damage response. To see this illustration in color, the reader is referred to the web version of this article at www.liebertpub.com/ars

FIG. 3.

Classification of functional groups and subgroups for the “nucleolome.”

FIG. 4.

Dynamic turnover of the APE1/NPM1 complex in response to cellular stress. Under basal conditions (left) the cellular APE1 pool is dynamically distributed throughout the cell, with prevalent accumulation in the nucleus and nucleoli. This accounts for the maintenance of a basal DNA repair capacity (both nuclear and mitochondrial), redox-mediated transcriptional modulation, cell proliferation, and RNA cleansing activity. Upon genotoxic stress and/or arrest of Pol I transcription (right) the dynamic equilibrium of APE1 localization is tipped towards a nucleoplasmic accumulation of the protein (149). The APE1 relocalization is likely mediated by simultaneous migration of NPM1 outside the nucleolus and hyperacetylation of the N-terminal region of APE1 itself (90). This situation ensures a potentiated DNA repair response, as both the nucleoplasmic APE1/NPM1 association and its acetylation have been linked to increased catalytic activity of the protein. The absence of APE1 from nucleoli, moreover, might favor a temporary arrest of cellular proliferation, useful to allow for more efficient DNA repair. If the DNA damage is sustained, it is likely a redistribution of a pool of APE1 to the cytoplasm. This phenomenon should boost the mitochondrial BER and possibly contribute to the cellular RNA cleansing capacity. APE1, apurinic/apyrimidinic endonuclease 1; BER, base excision repair; NPM1, nucleophosmin 1; Pol I, RNA polymerase I. To see this illustration in color, the reader is referred to the web version of this article at www.liebertpub.com/ars

FIG. 5.

Schematic representation of multiple regulatory functions of the APE1 disordered N-terminal region. APE1 crystal structure (yellow) bound to abasic DNA (grey) is from the pdb (1DEW) and displayed using the PDBV software. The deposited APE1 crystal structure was obtained using a truncated APE1 form (residues 40–318); missing residues have been manually added. The unstructured N-terminal portion of APE1 (residues 1–42) is essential for APE1 biological functions being site of PTMs, target of many interactions and, including the NLS. NLS, nuclear localization signal; PTMs, post-translational modifications. To see this illustration in color, the reader is referred to the web version of this article at www.liebertpub.com/ars