Polymerase δ-Interacting Protein 2 (POLDIP2) – Function, Localization, and Biological Roles
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o3-deep-research-2025-06-26
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2025-12-27T17:50:36.051659
Polymerase δ-Interacting Protein 2 (POLDIP2) – Function, Localization, and Biological Roles
Gene and Protein Overview
POLDIP2 (Polymerase delta-interacting protein 2) is a human gene on chromosome 17q11.2 encoding a multifunctional protein of 368 amino acids (pmc.ncbi.nlm.nih.gov) (www.frontiersin.org). It was originally identified in 2003 as a 38 kDa protein (“PDIP38”) that binds the p50 subunit of DNA polymerase δ and the sliding clamp PCNA (pmc.ncbi.nlm.nih.gov). POLDIP2 is also known by synonyms PDIP38, p38, and Mitogenin-1 (pmc.ncbi.nlm.nih.gov). The protein is synthesized as a precursor with an N-terminal mitochondrial targeting sequence (MTS) and is processed to a mature ~37 kDa form upon import into mitochondria (pmc.ncbi.nlm.nih.gov). Structurally, POLDIP2 contains two conserved domains: an N-terminal YccV-like domain (also called a hemimethylated DNA-binding domain) and a C-terminal DUF525 domain (pmc.ncbi.nlm.nih.gov) (www.nature.com). The DUF525 region is shared with certain F-box proteins and bacterial ApaG proteins and is thought to mediate protein–protein interactions (pmc.ncbi.nlm.nih.gov). The YccV-like domain adopts an SH3-like β-barrel fold and may confer DNA-binding capacity (pmc.ncbi.nlm.nih.gov) (www.nature.com), though POLDIP2’s direct DNA-binding in human cells remains to be demonstrated. Notably, bioinformatic analysis has identified three putative PCNA-interacting motifs in POLDIP2’s sequence (www.frontiersin.org), consistent with its ability to bind PCNA. POLDIP2 is highly conserved across metazoans but is absent in bacteria, fungi, and plants (pmc.ncbi.nlm.nih.gov), highlighting its specialized role in multicellular eukaryotes.
Subcellular Localization and Dynamics
POLDIP2 has a dynamic subcellular localization, residing in multiple cellular compartments depending on cell type and conditions. Mitochondria are a principal site: the protein contains an N-terminal presequence that directs its import into the mitochondrial matrix (www.nature.com) (www.nature.com). In fact, experiments show that endogenous POLDIP2 localizes almost exclusively to mitochondria in many cells (e.g. smooth muscle, epithelial, fibroblast cells) when properly targeted (pmc.ncbi.nlm.nih.gov). Consistently, in vitro import assays confirm POLDIP2 is imported into isolated mitochondria in a membrane potential–dependent manner and processed to a mature intramitochondrial form (www.nature.com) (www.nature.com). However, a smaller fraction of POLDIP2 can also be found in the nucleus and cytoplasm under certain conditions (pmc.ncbi.nlm.nih.gov) (pmc.ncbi.nlm.nih.gov). Early studies using tagged POLDIP2 (which may inadvertently prevent mitochondrial import) observed the protein in the nucleus, cytosol, and even at the plasma membrane (www.nature.com). In proliferating cells, POLDIP2’s distribution appears cell-cycle regulated: it accumulates in the nucleus during G₂/M through G₁, suggesting a role in cell division (pmc.ncbi.nlm.nih.gov). In vascular smooth muscle cells and some epithelial cells, POLDIP2 also localizes to focal adhesions and along actin stress fibers in the cytoskeleton (pmc.ncbi.nlm.nih.gov) (pmc.ncbi.nlm.nih.gov). Intriguingly, a cell adhesion receptor, CEACAM1 (CD66a), directly interacts with POLDIP2 and can modulate its trafficking between the cell surface and nucleus (pmc.ncbi.nlm.nih.gov) (pmc.ncbi.nlm.nih.gov). In quiescent cells, engagement of CEACAM1 sequesters POLDIP2 outside the nucleus, whereas during proliferation POLDIP2 shifts to nuclear sites (pmc.ncbi.nlm.nih.gov). These findings indicate that POLDIP2’s localization is dynamic and context-dependent, enabling it to participate in different cellular processes in different compartments (pmc.ncbi.nlm.nih.gov) (pmc.ncbi.nlm.nih.gov). (Notably, the major pool of endogenous POLDIP2 is often mitochondrial, with one study estimating ~68% cytosolic, 20% nuclear, and ~11% mitochondrial distribution in certain cell lines (pmc.ncbi.nlm.nih.gov), while other reports find it predominantly mitochondrial (pmc.ncbi.nlm.nih.gov). Differences may arise from cell type or detection methods.) The ability of POLDIP2 to shuttle between mitochondria, nucleus, and other locales underlies its multi-functional role in the cell.
Role in DNA Replication and Repair
POLDIP2 was first characterized through its connection to DNA polymerase δ, implying a role in DNA replication or repair. Polymerase δ (Polδ) is a major replicative DNA polymerase, and POLDIP2 binds to its p50 subunit (also called Polδ subunit 2) both in vitro and in vivo (pmc.ncbi.nlm.nih.gov). POLDIP2 also binds PCNA (the processivity factor for Polδ) via conserved PCNA-binding motifs (pmc.ncbi.nlm.nih.gov) (www.frontiersin.org). Although POLDIP2 is not an essential subunit of the replication machinery, it appears to act as an auxiliary factor that can influence replication under stress conditions. For example, translesion DNA synthesis (TLS) – a pathway that allows specialized DNA polymerases to bypass lesions – is facilitated by POLDIP2. POLDIP2 interacts with multiple TLS polymerases including Polη, Polζ, Rev1, and Polλ (pmc.ncbi.nlm.nih.gov) (pmc.ncbi.nlm.nih.gov). It binds the ubiquitin-binding domain of Polη that normally helps Polη dock at ubiquitinated PCNA, suggesting POLDIP2 may aid the polymerase switch during damage bypass (pmc.ncbi.nlm.nih.gov). Indeed, silencing POLDIP2 causes an accumulation of Polη foci in nuclei (even without DNA damage) and makes cells more sensitive to UV-induced damage (pmc.ncbi.nlm.nih.gov) (pmc.ncbi.nlm.nih.gov). This supports the idea that POLDIP2 helps regulate the hand-off between Polδ and TLS polymerases at stalled forks (pmc.ncbi.nlm.nih.gov).
Experimental studies in 2013 demonstrated that POLDIP2 enhances the DNA synthesis activity of Polλ and Polη specifically during lesion bypass. Maga et al. (2013) showed POLDIP2 physically associates with Polλ and increases the processivity and efficiency of Polλ and Polη when copying over oxidative DNA lesions like 8-oxo-guanine (pmc.ncbi.nlm.nih.gov). In biochemical assays, adding POLDIP2 stimulated the ability of Polη and Polλ to synthesize DNA across 8-oxo-G, abasic sites, and thymine dimers, whereas other DNA polymerases (Polβ, Polι) were not stimulated (pmc.ncbi.nlm.nih.gov) (pmc.ncbi.nlm.nih.gov). POLDIP2 also modestly stimulates Polδ’s activity without reducing fidelity, suggesting it might help Polδ itself or facilitate switching to Polλ at an oxidized base (pmc.ncbi.nlm.nih.gov) (pmc.ncbi.nlm.nih.gov). Cells lacking POLDIP2 showed increased sensitivity to oxidative DNA damage, a phenotype exacerbated if Polλ was also absent, indicating POLDIP2 and Polλ function in the same error-free repair pathway (pmc.ncbi.nlm.nih.gov) (pmc.ncbi.nlm.nih.gov). Separately, POLDIP2 has been shown to interact with the primase-polymerase PrimPol, an enzyme that reprimes stalled forks. In vitro, POLDIP2 binding enhances PrimPol’s DNA polymerase activity and DNA-binding ability (www.frontiersin.org) (www.frontiersin.org). Consistent with this, loss of POLDIP2 slows replication fork progression after UV damage, linking POLDIP2 to replication stress tolerance via PrimPol and TLS polymerases (academic.oup.com) (academic.oup.com).
Overall, POLDIP2 is emerging as a regulator of DNA replication and repair, particularly under conditions of DNA damage. By binding Polδ and PCNA, it may stabilize or organize the replication fork, and by interacting with TLS polymerases and PrimPol, it promotes efficient bypass of lesions and fork restart (www.frontiersin.org) (www.frontiersin.org). One study even found POLDIP2 interacts with the E7 oncoprotein of HPV16 and can modulate Polδ activity during viral DNA replication (www.frontiersin.org) (www.frontiersin.org), suggesting a role in host–virus replication dynamics. Taken together, while POLDIP2 is not an enzyme, it serves as an adapter or “switch” factor in the nucleus – coordinating polymerase exchange and maintaining genome stability during replication and repair.
Beyond the nucleus, a critical function of POLDIP2 occurs in mitochondria. POLDIP2 is a nuclear-encoded mitochondrial protein that localizes to the matrix and partners with the mitochondrial AAA+ protease CLPXP (Caseinolytic protease P). Recent research has illuminated POLDIP2’s role as a proteostasis adaptor within mitochondria. In 2020, Deepa et al. solved POLDIP2’s domain structure and showed the N-terminal YccV-like domain specifically binds to the N-terminal docking region of the CLPX subunit (www.nature.com) (www.nature.com). The C-terminal DUF525 domain forms an immunoglobulin-like fold but its binding targets are not fully defined (www.nature.com). POLDIP2 itself is stably imported into the matrix and is neither degraded by CLP protease nor does it disrupt the CLPXP complex (www.nature.com) (www.nature.com). Instead, POLDIP2 modulates CLPXP’s activity and substrate specificity. It was found to protect CLPX from degradation by the Lon protease, thereby stabilizing cellular CLPX levels (www.nature.com). By docking on CLPX, POLDIP2 alters which substrates CLPXP targets for degradation (www.nature.com) (www.nature.com).
One key consequence of POLDIP2 loss is dysregulation of mitochondrial enzyme cofactors. Paredes et al. (2018) discovered that POLDIP2 is required for proper lipoylation of the pyruvate dehydrogenase (PDH) and α-ketoglutarate dehydrogenase (α-KGDH) complexes (pmc.ncbi.nlm.nih.gov). These multi-enzyme complexes depend on a covalently attached lipoic acid for their activity. In Poldip2-deficient cells, the lipoate ligase LIPT2 and lipoate salvage pathways are intact, but the mitochondrial enzyme ACSM1 (acyl-CoA synthetase medium-chain 1) – which activates exogenous lipoate – becomes abnormally degraded (pmc.ncbi.nlm.nih.gov) (pmc.ncbi.nlm.nih.gov). Mechanistically, loss of POLDIP2 activates CLPXP to degrade ACSM1, resulting in failure to lipoylate PDH and KGDH E2 subunits (pmc.ncbi.nlm.nih.gov) (www.nature.com). As a result, Poldip2-deficient cells show reduced PDH and α-KGDH activity, a compromised TCA cycle, and lower mitochondrial respiration (pmc.ncbi.nlm.nih.gov) (pmc.ncbi.nlm.nih.gov). The metabolic fallout includes accumulation of α-ketoglutarate (due to α-KGDH loss) and stabilization of HIF-1α (since α-KG-dependent prolyl hydroxylases are inhibited), linking POLDIP2 loss to a pseudohypoxic, glycolytic shift (pmc.ncbi.nlm.nih.gov) (pmc.ncbi.nlm.nih.gov). Conversely, overexpression of POLDIP2 increases mitochondrial oxygen consumption and can slow the growth of cancer cells by reinforcing oxidative metabolism (pmc.ncbi.nlm.nih.gov) (pmc.ncbi.nlm.nih.gov). POLDIP2 thus acts as a metabolic regulator: it preserves the function of crucial catabolic enzymes by preventing their unwarranted proteolysis.
In line with this role, POLDIP2 expression is responsive to oxygen levels and cancer status. Hypoxia downregulates POLDIP2 in various cell types, and aggressive triple-negative breast cancer cells naturally repress POLDIP2 expression (pmc.ncbi.nlm.nih.gov). This downregulation, while aiding short-term survival under low oxygen, leads to the metabolic inefficiencies noted above. Re-introducing POLDIP2 to these cancer cells restores PDH/α-KGDH lipoylation, raising oxidative metabolism at the expense of proliferative capacity (pmc.ncbi.nlm.nih.gov). These findings highlight POLDIP2 as an oxygen-sensitive metabolic switch (pmc.ncbi.nlm.nih.gov). Consistently, knockout mouse studies underscore the importance of Poldip2 for normal development and cellular homeostasis. Mice completely lacking Poldip2 die perinatally, and their embryonic fibroblasts exhibit reduced growth and elevated autophagy (pmc.ncbi.nlm.nih.gov) (pmc.ncbi.nlm.nih.gov). Heterozygous Poldip2^+/− mice survive but show extracellular matrix abnormalities (excess, disorganized collagen in blood vessels) and impaired tissue responses to ischemia (pmc.ncbi.nlm.nih.gov) (pmc.ncbi.nlm.nih.gov). Those phenotypes may result from both metabolic defects and altered cell signaling (as described below). In summary, within mitochondria POLDIP2 serves as a guardian of mitochondrial enzyme integrity and bioenergetic capacity, linking nuclear genetic control to mitochondrial metabolic output.
Role in Redox Signaling, Cytoskeleton, and Vascular Function
POLDIP2 also plays a pivotal role in cellular redox signaling and cytoskeletal dynamics, largely through its interaction with the NADPH oxidase complex. NADPH oxidases (NOX enzymes) are membrane-bound enzymes that generate reactive oxygen species (ROS) as signaling molecules. POLDIP2 was unexpectedly found to bind p22^phox, a membrane subunit essential for multiple NOX isoforms (pmc.ncbi.nlm.nih.gov). In vascular smooth muscle cells, POLDIP2 associates specifically with the NOX4 enzyme – a ROS-producing NADPH oxidase isoform – and markedly increases NOX4 activity (pmc.ncbi.nlm.nih.gov). Overexpression of Poldip2 elevates cellular H_2O_2 production, whereas Poldip2 knockdown reduces basal ROS levels (pmc.ncbi.nlm.nih.gov). POLDIP2, NOX4, and p22^phox co-localize at focal adhesions and along stress fibers in these cells (pmc.ncbi.nlm.nih.gov) (pmc.ncbi.nlm.nih.gov). Through NOX4, POLDIP2 activation triggers downstream signaling that rearranges the actin cytoskeleton. Specifically, POLDIP2-mediated ROS production activates the small GTPase RhoA and focal adhesion kinase (FAK), master regulators of actin fiber formation and cell migration (pmc.ncbi.nlm.nih.gov). Experimental manipulation of Poldip2 levels dramatically alters cell morphology: increasing Poldip2 boosts RhoA activity, leading to robust actin stress fibers and maturation of focal adhesions, whereas Poldip2 deficiency impairs these structures (pmc.ncbi.nlm.nih.gov) (pmc.ncbi.nlm.nih.gov). Importantly, these effects depend on the presence of NOX4 and p22^phox – if either NOX4 or its p22^phox subunit is knocked down, Poldip2 can no longer induce RhoA activation or cytoskeletal reorganization (pmc.ncbi.nlm.nih.gov). This indicates POLDIP2 functions as a critical organizer of redox signaling at focal adhesions, linking the NOX4-generated ROS signal to RhoA/FAK pathway activation (pmc.ncbi.nlm.nih.gov) (pmc.ncbi.nlm.nih.gov). The net result is enhanced cell migration capacity, as ROS-mediated focal adhesion turnover is essential for cells to move (pmc.ncbi.nlm.nih.gov).
Through these mechanisms, POLDIP2 helps maintain vascular structure and function. In Poldip2^+/− mice, blood vessels show excess collagen deposition and structural disorganization, correlating with the known role of ROS/RhoA in modulating extracellular matrix remodeling (pmc.ncbi.nlm.nih.gov). Poldip2-haploinsufficient mice also have impaired angiogenesis in response to ischemia (pmc.ncbi.nlm.nih.gov), likely because their vascular cells cannot properly activate ROS-driven migration and remodeling programs. In line with the mouse data, human cardiovascular disease samples have implicated POLDIP2 and NOX4 in pathological remodeling: for instance, patients with chronic pressure-overload heart failure had reduced POLDIP2 and NOX4 in myocardium, suggesting a maladaptive response when this pathway is blunted (pmc.ncbi.nlm.nih.gov) (pmc.ncbi.nlm.nih.gov). On the other hand, overactive POLDIP2-NOX4 signaling may contribute to fibrosis: in kidney fibroblast models, POLDIP2 is required for TGF-β to induce NOX4-dependent myofibroblast differentiation and matrix production (www.frontiersin.org) (pmc.ncbi.nlm.nih.gov). Blocking POLDIP2 or NOX4 in such models attenuates the RhoA/ROCK signaling and fibrotic activation (pmc.ncbi.nlm.nih.gov). Thus, POLDIP2 can either support healthy tissue repair or drive pathological remodeling, depending on context.
Besides influencing cell migration and fibrosis, localized POLDIP2/NOX4 activity has been linked to unique signaling processes. One study found POLDIP2, p22^phox, and NOX4 form a complex in renal sensory neurons that modulates mechanosensation. Elevated renal pelvic pressure (a model of fluid back-up in kidneys) increased POLDIP2 expression and its binding to p22^phox, which in turn activated NOX4-derived H_2O_2. The H_2O_2 acted on TRPV1 ion channels in sensory nerve endings to trigger release of substance P, contributing to pain and reflex pathways (www.frontiersin.org) (pmc.ncbi.nlm.nih.gov). This implies POLDIP2 is a component of mechanotransduction signaling via ROS. POLDIP2 has even been observed at the mitotic spindle, though its function there is not yet clear (www.frontiersin.org). One possibility is that its redox-regulatory role might influence spindle dynamics or checkpoint signaling during mitosis, but more research is needed.
In summary, POLDIP2 is a key regulator of ROS signaling and cytoskeletal dynamics. By anchoring and activating NOX4 at strategic locations (focal adhesions, possibly the nucleus (pmc.ncbi.nlm.nih.gov)), it influences processes such as cell migration, adhesion turnover, and extracellular matrix remodeling. These actions are crucial in vascular physiology and pathology – balancing normal vessel maintenance with the potential for fibrosis or aberrant remodeling when dysregulated. POLDIP2 exemplifies how an adaptor protein can couple a redox enzyme to structural and signaling molecules (RhoA/FAK), coordinating biochemical signals with biomechanical outcomes (pmc.ncbi.nlm.nih.gov) (pmc.ncbi.nlm.nih.gov).
Other Biological Roles and Disease Associations
Given its diverse interactions, it is not surprising that POLDIP2 has been implicated in multiple biological pathways and diseases. In the nervous system, recent studies suggest POLDIP2 impacts proteostasis of neuronal proteins. Notably, POLDIP2 has been identified as a novel regulator of Tau protein aggregation in neurodegenerative disease (www.frontiersin.org). Jiang et al. (2015) found that stressors like β-amyloid, TNFα, or oxidative stress upregulate POLDIP2 in neuronal cells, and POLDIP2 overexpression led to impaired autophagy and proteasome function, culminating in accumulation of misfolded Tau and neurotoxic aggregates (www.frontiersin.org) (www.frontiersin.org). In models of Alzheimer’s disease and other tauopathies, elevated POLDIP2 exacerbated Tau aggregation and cell death, whereas knocking down Poldip2 mitigated these effects (www.frontiersin.org). This points to a role for POLDIP2 in protein quality control in neurons – possibly via its influence on oxidative stress or direct binding to regulatory proteins – making it a potential target of interest in neurodegenerative disease research.
In cancer, POLDIP2’s role appears context-dependent. On one hand, POLDIP2’s ability to enforce oxidative metabolism (via mitochondrial function) can suppress the Warburg effect, as seen in breast cancer cells where low POLDIP2 favors glycolysis and rapid growth (pmc.ncbi.nlm.nih.gov) (pmc.ncbi.nlm.nih.gov). Low POLDIP2 expression has been reported in certain tumors (e.g. triple-negative breast cancers (pmc.ncbi.nlm.nih.gov) and some lung cancers (www.frontiersin.org)), potentially as an adaptation to promote proliferation under stress. Aging-related transcriptome analyses have even flagged POLDIP2 as a risk gene in age-related macular degeneration (AMD), a disease involving oxidative damage in retinal cells (www.aging-us.com). A 2023 study showed that knocking out POLDIP2 in human retinal pigment epithelial cells did not harm cell viability but did trigger a broad antioxidant response: POLDIP2 knockout cells had lower mitochondrial superoxide levels and upregulated the mitochondrial superoxide dismutase (SOD2) (www.aging-us.com). The POLDIP2-deficient RPE cells exhibited changes in immune and complement genes as well (www.aging-us.com), aligning with the idea that POLDIP2 could contribute to oxidative stress and inflammation in AMD. This suggests POLDIP2 could be a modulator of oxidative stress in aging tissues, and by extension, a potential therapeutic target for conditions exacerbated by ROS.
On the other hand, POLDIP2 can also act in a pro-tumor manner under certain conditions. For example, in non-small cell lung cancer (NSCLC), POLDIP2 levels were found to be reduced in patient tumors, yet experimental overexpression of POLDIP2 in NSCLC cell lines paradoxically increased anchorage-independent growth and proliferation (www.frontiersin.org). POLDIP2 overexpression in these cells upregulated Cyclin D1 and mesenchymal markers (N-cadherin, Slug, Twist), promoting an epithelial–mesenchymal transition (EMT) and invasive phenotype (www.frontiersin.org). Conversely, silencing POLDIP2 impaired cell proliferation and EMT marker expression (www.frontiersin.org). These results hint that, at least in some epithelial cancers, residual POLDIP2 may facilitate aggressive traits like anchorage-independent survival and EMT. One possible explanation is that POLDIP2’s ROS/RhoA signaling axis might drive oncogenic pathways (e.g. matrix remodeling and motility for metastasis), even if its metabolic effects are contextually suppressive. Clearly, more research is needed to reconcile POLDIP2’s metabolic tumor-suppressive versus pro-migratory tumor-promoting influences.
In summary, POLDIP2 emerges as a hub protein linking DNA replication, mitochondrial metabolism, and redox signaling. It does so by serving as an adaptor or scaffold for diverse partners – from DNA polymerases in the nucleus to proteases and enzymes in mitochondria to oxidases at the cell membrane. Expert reviewers characterize POLDIP2 as “a multi-functional protein” whose functions “appear to be disparate” yet coordinated by its localization and binding partners (pmc.ncbi.nlm.nih.gov) (pmc.ncbi.nlm.nih.gov). Because POLDIP2 is unique (no closely related family members) (pmc.ncbi.nlm.nih.gov), it represents a singular point of integration between pathways. Its importance is underscored by the lethal phenotype of Poldip2 knockout in mice (pmc.ncbi.nlm.nih.gov) and its association with diseases ranging from vascular disorders to neurodegeneration and cancer. As of 2023, POLDIP2 is the subject of active research: scientists are investigating it as a potential therapeutic target, for example by modulating POLDIP2-NOX4 signaling to treat fibrosis or targeting POLDIP2’s role in metabolic reprogramming of tumors (www.frontiersin.org). Any intervention, however, must account for the protein’s pleiotropy. For instance, reducing POLDIP2 activity might curb pathological ROS signaling (beneficial in fibrosis or AMD) but could impair DNA repair or mitochondrial function. Conversely, boosting POLDIP2 could improve mitochondrial metabolism in cancer or aging cells but risk promoting ROS-driven damage elsewhere.
Conclusion
In conclusion, Polymerase δ-interacting protein 2 (POLDIP2) is a versatile adaptor protein that operates at critical intersections of cell biology. In the nucleus, it safeguards genome stability by orchestrating DNA polymerase switching during replication stress and repair. In the mitochondrial matrix, it preserves metabolic enzyme function by tempering protease activity, thereby sustaining respiratory capacity. At the cell periphery, it links ROS production to cytoskeletal remodeling, influencing cell migration and tissue architecture. Through these roles, POLDIP2 has a hand in maintaining normal cellular homeostasis and, when dysregulated, contributes to disease processes. Ongoing research (especially from 2020–2024) continues to unravel new facets of POLDIP2 – from its 3D structure and mechanism of action (www.nature.com) (www.nature.com) to its involvement in aging and disease (www.aging-us.com) (www.frontiersin.org). As our understanding deepens, POLDIP2 stands out as an illustrative example of how one protein can integrate signals across cellular compartments, ultimately coordinating DNA-centric processes with energy metabolism and redox signaling. This integrative function makes POLDIP2 a fascinating subject for further study and a potential node for therapeutic intervention in complex diseases.
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