Purification and the catalytic activity of PrimPol from different expression systems.

<p><b>(</b>A) purified preparation of GST-tagged PrimPol from different <i>E</i>. <i>coli</i> strains and <i>S</i>. <i>cerevisiae</i>. Coomassie staining. (B) the comparison of the DNA polymerase activity of PrimPol purified from different strains of <i>E</i>. <i>coli</i>. 75–450 nM of GST-tagged PrimPol and 100 nM 30-mer DNA template were used in the reactions. (C) purified preparation of PrimPol from human FreeStyle 293-F cells. Coomassie staining. (D) the comparison of the DNA polymerase activity of PrimPol purified from ArcticExpress(DE3)-pRIL <i>E</i>. <i>coli</i> cells and human FreeStyle 293-F cells. 200 nM of PrimPol and 25 nM 70-mer DNA template were used in the reactions. Experiments (B and D) were repeated four times.</p

The stability of the PrimPol’s catalytic activity <i>in vitro</i>.

<p>(A) the DNA polymerase activity of PrimPol after the indicated time pre-incubation on ice. (B) the DNA polymerase activity of PrimPol after the indicated amount of freeze-thaw cycles. (C) the DNA polymerase activity of PrimPol after 30 min incubation at 0ºC, 25ºC, 30ºC, 35ºC, 37ºC and 40ºC. (D) the DNA polymerase activity of PrimPol after incubation at 37ºC. 450 nM of PrimPol and 100 nM 30-mer DNA template were used in the reactions. Experiments were repeated two times in A and B and three times in C and D.</p

The reaction buffer composition affects the DNA polymerase activity of PrimPol <i>in vitro</i>.

<p>(A) the DNA polymerase activity of PrimPol at different NaCl concentrations. (B) the DNA polymerase activity of PrimPol at different pH. HEPES based buffer was used to test the DNA polymerase activity of PrimPol at different pH values. (C) the DNA polymerase activity of PrimPol at different MgCl₂ and MnCl₂ concentrations. 200 nM of PrimPol and 25 nM 70-mer DNA template were used in the reactions. All experiments were repeated three times.</p

Optimization of the expression, purification and polymerase activity reaction conditions of recombinant human PrimPol - Table 1

<p>Optimization of the expression, purification and polymerase activity reaction conditions of recombinant human PrimPol</p> - Table

Bypass of a Psoralen DNA Interstrand Cross-Link by DNA Polymerases β, ι, and κ in Vitro

Repair of DNA interstrand cross-links in mammalian cells involves several biochemically distinctive processes, including the release of one of the cross-linked strands and translesion DNA synthesis (TLS). In this report, we investigated the in vitro TLS activity of a psoralen DNA interstrand cross-link by three DNA repair polymerases, DNA polymerases β, κ, and ι. DNA polymerase β is capable of bypassing a psoralen cross-link with a low efficiency. Cell extracts prepared from DNA polymerase β knockout mouse embryonic fibroblasts showed a reduced bypass activity of the psoralen cross-link, and purified DNA polymerase β restored the bypass activity. In addition, DNA polymerase ι misincorporated thymine across the psoralen cross-link and DNA polymerase κ extended these mispaired primer ends, suggesting that DNA polymerase ι may serve as an inserter and DNA polymerase κ may play a role as an extender in the repair of psoralen DNA interstrand cross-links. The results demonstrated here indicate that multiple DNA polymerases could participate in TLS steps in mammalian DNA interstrand cross-link repair

Expression of the <i>hPOLISc</i> or <i>hPOLHSc</i> in yeast is non-mutagenic.

<p>* Median for 12-18 independent cultures. The 95% confidence limits are in parenthesis.</p

Activity of pure GST-tagged Pol ι variants.

<p>A. Purification of GST-Pol ι and its variants by affinity chromatography: the photograph of a Coomassie brilliant blue stained gel is shown. Equal volumes (15 µl) of each fraction with wild-type GST-Pol ι, GST-Pol ι^D34A, GST-Pol ι^D126A/E127A, GST-Pol ι^{D34A/126A/E127A}, and GST-Pol ι^L62I eluted from the glutathione-sepharose column were analyzed on 8% SDS-PAGE. B. The comparative DNA-polymerase assay with purified GST-Pol ι and its variants. The ability of enzymes to extend a P³²-labeled 17-mer primer annealed to template 1 was assayed in the presence of 100 µM of all four dNTPs and 0.15 mM Mn²⁺ ions, at 37°C for 5 min. C. Kinetic analysis of dATP and dGTP incorporation by purified wild-type GST–Pol ι and GST–Pol ι ^L62I variant. Primer extension reaction was carried out in the presence of 0.15 mM Mn²⁺ divalent metal ions and 1 nM of GST-Pol ι or its catalytically compromised variant at 37°C for 2.5 min. To quantify the incorporation of dATP and dGTP opposite template T we varied each dNTP concentration from 0.3 to 100 µM. Kinetic parameters determined from these experiments were: Wild-type: dATP: K_m = 3.5±1 µM, V_max = 9.8±0.8 (% incorporation/min), dGTP: K_m = 0.57±0.08 µM, V_max = 14.9±0.3 (% incorporation/min), f_inc for dGTP = 5.3; and L62I: dATP: K_m = 4.0<0.9 µM, V_max = 11.4±0.8 (% incorporation/min), dGTP: K_m = 0.54±0.09 µM, V_max = 17.2±0.3 (% incorporation/min), f_inc for dGTP = 6.1.</p

misGvA by yeast extracts producing variants of Pol ι.

<p>A. misGvA activity of cell extracts of yeasts producing GST-Pol ι variants was estimated by “misGvA” in 8-min reactions in the presence of 0.15 mM Mn²⁺ and 0.25 mM Mg²⁺ divalent metal ions at template 1 as described in “<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0016612#s4" target="_blank">Materials and Methods</a>.” Two combinations of equal concentrations of 1 mM dNTPs have been used: 1) all dNTPs and 2) dGTP and dATP. B. Same with template 2. B. Western-blot analysis of the production of GST-tagged Pol ι catalytically compromised variants in yeast cells extracts. Extracts containing 40 µg of total protein were separated on 8% polyacrylamide-SDS gel, transferred to a PVDF membrane and probed with polyclonal anti-GST antibodies. Cross-reacting proteins were visualized according to the Western Breeze Chromogenic Anti-Rabbit Kit procedure (Invitrogen).</p

Detection of misGvA activity of Pol ι.

<p>A. DNA-polymerase activity of yeast extracts producing Pol ι or transformed by empty vector in the absence of dNTPs in reaction mixture. The reactions were carried out at 37°C for 15 min as described in “<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0016612#s4" target="_blank">Material and Methods</a>” using standard template 1 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0016612#pone.0016612-Zhang1" target="_blank">[4]</a>; <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0016612#pone.0016612-Gening2" target="_blank">[31]</a>, with no dNTPs in the reaction mixture. DNA oligonucleotides were separated on 18% polyacrylamide/7 M urea gels and visualized using Storage Phosphor Screen in Typhoon 9700. B. misGvA activity by yeast extracts producing human Pol ι, Pol η or transformed with empty vector. Template 1 (left panel, standard substrate) and template 2 (modified substrate with the substitution of C to G at the position of 19) were incubated with yeast cell extracts and high concentrations of exogenous nucleotides. The activity of Pol ι produced in yeast is detectable by the misincorporation of dGTP opposite template T by whole cell extracts (“misincorporation of G” method of Gening, abbreviated as misGvA). The cells extracts of yeast producing Pol ι, Pol η or containing empty vector were used as an enzymatic preparation for DNA polymerase reaction with P³²-labeled oligonucleotide substrate in the presence of 0.15 mM Mn²⁺ divalent metal ions and various combinations of equal concentrations of 1 mM dNTPs. For each extract, five different conditions have been used: 1) all dNTPs, 2) dATP, dTTP and dCTP but with dGTP omitted, 3) dGTP and dATP, 4) only dATP, and 5) only dGTP. Template 2 with the substitution of the next nucleotide upstream (+2, corresponding to the position of 19 on elongated primer) after the T template (+1, position of 18) from C to G was used to exclude the possibility of transient misincorporation by the template slippage mechanism. The reactions were carried out at 37°C for 15 min. DNA products were separated on 18% polyacrylamide/7 M urea gels and visualized using Storage Phosphor Screen in Typhoon 9700. The Pol ι activity was determined by the presence of the two “doublet” radioactive bands corresponding to 18-mer oligonucleotides with A or G at the 3′-end, possessing different electrophoretic mobility. The lower band with higher mobility is indicative of the amount of oligonucleotide with 3′-terminal A, whereas the upper band corresponds to the amount of a less mobile oligonucleotide with G incorporated opposite T in position 18 (lines 1 and 3).</p

Structure of Pol ι and the variants studied.

<p>A. Upper half. The schematic domain structure of Pol ι is shown (PIP is the protein interaction domain, UBM – ubiqutin-binding motif). Lower half. The Pol ι mutant variants were used in the study (Red bars on the thick blue line representing Pol ι show the positions of amino acid changes in polymorphic variants of Pol ι. Grey bars indicate deletions for truncated Pol ι variants): <i>hPOLISc^2exon-d</i> (Pol ι ^2exon-d) – Pol ι variant with a deletion of exon 2 (encoding for amino acids 14-55) representing an alternative splice variant of human and mouse Pol ι; <i>hPOLISc^D34A</i> (Pol ι ^D34A) and <i>hPOLISc^D126A/E127A</i> (Pol ι ^D126A/E127A) – “catalytically dead” Pol ι variants created as amino acid substitutions of evolutionary conservative Asp34 or Asp126 and Glu127 to Ala; <i>hPOLISc^{D34A/D126A/E127A}</i> (Pol ι^{D34A/D126A/E127A}) – a triple “catalytically dead” Pol ι variant with amino acid substitutions of Asp34, Asp126 and Glu127 to Ala; <i>hPOLISc^L62I</i> (Pol ι^L62I) – Pol ι variant with a substitution of evolutionary polymorphic amino acid Leu62 to Ile; <i>hPOLISc^42I-612-d</i> variant with a deletion of the C-terminal half of Pol ι is shown to illustrate what minimal part retains enzymatic activity and whose crystal structure has been determined. B. Polι active site. A close view at the Pol ι active site in ternary complex with DNA (template T) and incoming dGTP (3gv8). Pol ι and DNA molecules are represented as cartoon and sticks, respectively. The incorporated nucleotides and active site residues Asp34, Asp126 and Glu127 are represented by sticks and highlighted with yellow carbons. The side chains of phosphate-binding residues are also shown as sticks. The metal ion is drawn as a magenta ball.</p