Investigating the role of a novel primase-polymerase, PrimPol, in DNA damage tolerance in vertebrate cells

Genome duplication is an essential task our cells have to achieve prior to cell division, and requires a highly specialized replication machinery to ensure it is performed in an accurate and complete manner. DNA primase and polymerases are essential components of the replisome. Primases initiate DNA replication by synthesising short RNA primers that are then elongated by faithful and processive replicative DNA polymerases. However, both exogenous and endogenous agents can damage DNA and hinder progression of the replicative machinery. Translesion synthesis DNA polymerases assist in bypassing these DNA lesions in a process called DNA damage tolerance that enables chromosomal replication to proceed in in spite of damaged templates. This thesis details the characterisation of a novel eukaryotic DNA primase, coiled-coil domain containing protein (CCDC111), a member of the Archaeo Eukaryotic Primase (AEP) superfamily. Preliminary in vitro characterisation of CCDC111 demonstrated that the recombinant protein is capable of both DNA-dependant priming and polymerase activities, which is unprecedented for a eukaryotic polymerase, and it was therefore renamed Primase-polymerase (PrimPol). The aim of this thesis was to provide one of the first cellular characterisations of PrimPol by generating a knockout of the gene in avian DT40 cells and also depleting the protein in human cells using RNAi. In vivo evidence supports the involvement of this novel polymerase in replication fork progression following replicative stress, such as exposure to UV light, but also during unperturbed DNA replication. Work in this thesis also indicates a role for PrimPol in mitochondrial DNA maintenance. Together, the data presented here establish a role for PrimPol in DNA damage tolerance in avian and human cells

PrimPol is required for the maintenance of efficient nuclear and mitochondrial DNA replication in human cells

Eukaryotic Primase-Polymerase (PrimPol) is an enzyme that maintains efficient DNA duplication by repriming replication restart downstream of replicase stalling lesions and structures. To elucidate the cellular requirements for PrimPol in human cells, we generated PrimPol-deleted cell lines and show that it plays key roles in maintaining active replication in both the nucleus and mitochondrion, even in the absence of exogenous damage. Human cells lacking PrimPol exhibit delayed recovery after UV-C damage and increased mutation frequency, micronuclei and sister chromatin exchanges but are not sensitive to genotoxins. PrimPol is also required during mitochondrial replication, with PrimPol-deficient cells having increased mtDNA copy number but displaying a significant decrease in replication. Deletion of PrimPol in XPV cells, lacking functional polymerase Eta, causes an increase in DNA damage sensitivity and pronounced fork stalling after UV-C treatment. We show that, unlike canonical TLS polymerases, PrimPol is important for allowing active replication to proceed, even in the absence of exogenous damage, thus preventing the accumulation of excessive fork stalling and genetic mutations. Together, these findings highlight the importance of PrimPol for maintaining efficient DNA replication in unperturbed cells and its complementary roles, with Pol Eta, in damage tolerance in human cells

Consistency Conditions for Branes at Orbifold Singularities

We discuss consistency conditions for branes at orbifold singularities. The conditions have a world-sheet interpretation in terms of tadpole cancellation and a space-time interpretation in terms of anomalies. As examples, we consider type II and type I branes on $C^2/Z_M$ orbifolds. We give orientifold constructions of phases of type I or heterotic string theory, involving branches with extra tensor multiplets, which arise when small SO(32) instantons sit on orbifold singularities.Comment: harvmac, 14 pages, added reference

Duality without Supersymmetry: The Case of the SO(16)xSO(16) String

We extend strong/weak coupling duality to string theories without spacetime supersymmetry, and focus on the case of the unique ten-dimensional, nonsupersymmetric, tachyon-free $SO(16)\times SO(16)$ heterotic string. We construct a tachyon-free heterotic string model that interpolates smoothly between this string and the ten-dimensional supersymmetric $SO(32)$ heterotic string, and we construct a dual for this interpolating model. We find that the perturbative massless states of our dual theories precisely match within a certain range of the interpolation. Further evidence for this proposed duality comes from a calculation of the one-loop cosmological constant in both theories, as well as the presence of a soliton in the dual theory. This is therefore the first known duality relation between nonsupersymmetric tachyon-free string theories. Using this duality, we then investigate the perturbative and nonperturbative stability of the $SO(16)\times SO(16)$ string, and present a conjecture concerning its ultimate fate.Comment: 15 pages, LaTeX, 3 figure

PrimPol bypasses UV photoproducts during eukaryotic chromosomal DNA replication

DNA damage can stall the DNA replication machinery, leading to genomic instability. Thus, numerous mechanisms exist to complete genome duplication in the absence of a pristine DNA template, but identification of the enzymes involved remains incomplete. Here, we establish that Primase-Polymerase (PrimPol; CCDC111), an archaeal-eukaryotic primase (AEP) in eukaryotic cells, is involved in chromosomal DNA replication. PrimPol is required for replication fork progression on ultraviolet (UV) lightdamaged DNA templates, possibly mediated by its ability to catalyze translesion synthesis (TLS) of these lesions. This PrimPol UV lesion bypass pathway is not epistatic with the Pol h-dependent pathway and, as a consequence, protects xeroderma pigmentosum variant (XP-V) patient cells from UV-induced cytotoxicity. In addition, we establish that PrimPol is also required for efficient replication fork progression during an unperturbed S phase. These and other findings indicate that PrimPol is an important player in replication fork progression in eukaryotic cells

PrimPol-deficient cells exhibit a pronounced G2 checkpoint response following UV damage

PrimPol is a recently identified member of the archaeo-eukaryote primase (AEP) family of primase-polymerases. It has been shown that this mitochondrial and nuclear localised enzyme plays roles in the maintenance of both unperturbed replication fork progression and in the bypass of lesions after DNA damage. Here, we utilised an avian (DT40) knockout cell line to further study the consequences of loss of PrimPol (PrimPol-/-) on the downstream maintenance of cells after UV damage. We report that PrimPol-/- cells are more sensitive to UV-C irradiation in colony survival assays than Pol η-deficient cells. Although this increased UV sensitivity is not evident in cell viability assays, we show that this discrepancy is due to an enhanced checkpoint arrest after UV-C damage in the absence of PrimPol. PrimPol-/- arrested cells become stalled in G2, where they are protected from UV-induced cell death. Despite lacking an enzyme required for the bypass and maintenance of replication fork progression in the presence of UV damage, we show that PrimPol-/- cells actually have an advantage in the presence of a Chk1 inhibitor due to their slow progression through S-phase

Molecular dissection of the domain architecture and catalytic activities of human PrimPol

PrimPol is a primase–polymerase involved in nuclear and mitochondrial DNA replication in eukaryotic cells. Although PrimPol is predicted to possess an archaeo-eukaryotic primase and a UL52-like zinc finger domain, the role of these domains has not been established. Here, we report that the proposed zinc finger domain of human PrimPol binds zinc ions and is essential for maintaining primase activity. Although apparently dispensable for its polymerase activity, the zinc finger also regulates the processivity and fidelity of PrimPol's extension activities. When the zinc finger is disrupted, PrimPol becomes more promutagenic, has an altered translesion synthesis spectrum and is capable of faithfully bypassing cyclobutane pyrimidine dimer photolesions. PrimPol's polymerase domain binds to both single- and double-stranded DNA, whilst the zinc finger domain binds only to single-stranded DNA. We additionally report that although PrimPol's primase activity is required to restore wild-type replication fork rates in irradiated PrimPol−/− cells, polymerase activity is sufficient to maintain regular replisome progression in unperturbed cells. Together, these findings provide the first analysis of the molecular architecture of PrimPol, describing the activities associated with, and interplay between, its functional domains and defining the requirement for its primase and polymerase activities during nuclear DNA replication

PrimPol—A new polymerase on the block

The DNA-directed primase-polymerase PrimPol of the archaeo-eukaryotic primase superfamily represents an ancient solution to the many problems faced during genome duplication. This versatile enzyme is capable of initiating de novo DNA/RNA synthesis, DNA chain elongation, and has the capacity to bypass modifications that stall the replisome by trans-lesion synthesis or origin-independent re-priming, thus allowing discontinuous synthesis of the leading strand. Recent studies have shown that PrimPol is an important new player in replication fork progression in eukaryotic cells; this review summarizes our current understanding of PrimPol and highlights important questions that remain to be addressed

Inelastic Helium Atom Scattering from Sb2Te3(111): Phonon Dispersion, Focusing Effects and Surfing

We present an experimental study of inelastic scattering processes on the (111) surface of the topological insulator Sb2Te3 using helium atom scattering. In contrast to other binary topological insulators such as Bi2Se3 and Bi2Te3, Sb2Te3 is much less studied and the as-grown Sb2Te3 sample turns out to be p-doped, with the Fermi-level located below the Dirac-point as confirmed by angle-resolved photoemission spectroscopy. We report the surface phonon dispersion along both high symmetry directions in the energy region below 11 meV, where the Rayleigh mode exhibits the strongest intensity. The experimental data is compared with a study based on density functional perturbation theory calculations, providing good agreement except for a set of additional peculiar inelastic events below the Rayleigh mode. In addition, an analysis of angular scans with respect to a number of additional inelastic events is presented, including resonance enhancement, kinematical focusing, focused inelastic resonance and surfing. In the latter case, phonon-assisted adsorption of the incident helium atom gives rise to a bound state where the helium atom rides the created Rayleigh wave.The authors are grateful for financial support by the FWF (Austrian Science Fund) within the project P29641-N36, as well as by NAWI Graz. We would like to thank the Aarhus University Research Foundation, VILLUM FOUNDATION via the Centre of Excellence for Dirac Materials (Grant No. 11744) and the SPP1666 of the DFG (Grant No. HO 5150/1-2) for financial support. M. Bremholm acknowledges financial support from the Center of Materials Crystallography (CMC) and the Danish National Research Foundation (DNRF93)