The enterohemorrhagic Escherichia coli insertion sequence-excision enhancer protein is a DNA polymerase with microhomology-mediated end-joining activity

Bacterial genomes contain an abundance of transposable insertion sequence (IS) elements that are essential for genome evolution and fitness. Among them, IS629 is present in most strains of enterohemorrhagic Escherichia coli O157 and accounts for many polymorphisms associated with gene inactivation and/or genomic deletions. The excision of IS629 from the genome is promoted by IS-excision enhancer (IEE) protein. Despite IEE has been identified in the most pathogenic serotypes of E. coli, its biochemical features that could explain its role in IS excision are not yet understood. We show that IEE is present in >30% of all available E. coli genome assemblies, and is highly conserved and very abundant within enterohemorrhagic, enteropathogenic and enterotoxigenic genomes. In vitro analysis of the recombinant protein from E. coli O157:H7 revealed the presence of a Mn2+-dependent error-prone DNA polymerase activity in its N-terminal archaeo-eukaryotic primase (AEP) domain able to promote dislocations of the primer and template strands. Importantly, IEE could efficiently perform in vitro an end-joining reaction of 3'-single-strand DNA overhangs with ≥4 bp of homology requiring both the N-terminal AEP and C-terminal helicase domains. The proposed role for IEE in the novel IS excision mechanism is discussed.

Small-molecule activation of OGG1 increases oxidative DNA damage repair by gaining a new function

Oxidative DNA damage is recognized by 8-oxoguanine (8-oxoG) DNA glycosylase 1 (OGG1), which excises 8-oxoG, leaving a substrate for apurinic endonuclease 1 (APE1) and initiating repair. Here, we describe a small molecule (TH10785) that interacts with the phenylalanine-319 and glycine-42 amino acids of OGG1, increases the enzyme activity 10-fold, and generates a previously undescribed β,δ-lyase enzymatic function. TH10785 controls the catalytic activity mediated by a nitrogen base within its molecular structure. In cells, TH10785 increases OGG1 recruitment to and repair of oxidative DNA damage. This alters the repair process, which no longer requires APE1 but instead is dependent on polynucleotide kinase phosphatase (PNKP1) activity. The increased repair of oxidative DNA lesions with a small molecule may have therapeutic applications in various diseases and aging.

Enhanced removal of the endocrine disruptor compound Bisphenol A by adsorption onto green-carbon materials. Effect of real effluents on the adsorption process

The high exposure to the endocrine disrupting compounds (EDC) in water represents a relevant issue for the health of living beings. The xenoestrogen Bisphenol A (BPA), a suspected EDC, is an industrial additive broadly used for manufacturing polycarbonate and epoxy resins. Due to its harmful effect in humans and the aquatic environment, an efficient method to remove BPA from wastewater is urgently required. The present work aims to study the adsorption of BPA from aqueous solutions onto carbonaceous materials, e.g., a synthesized carbon xerogel (RFX), a chemical-activated carbon from Kraft lignin (KLP) and a commercial activated carbon (F400) for comparative purposes. Batch kinetic and adsorption tests of BPA in ultrapure water were accomplished, finding higher adsorption capacities of BPA onto both F400 activated carbon (q_sat = 407 mg g^-1) and the biochar KLP (q_sat = 220 mg g^-1), versus to that obtained for the xerogel (q_sat = 78 mg g^-1). Furthermore, kinetic experiments revealed faster kinetic adsorption for RFX and KLP materials, achieving the equilibrium time within 24 h, attributed to their more-opened porous structure. Pseudo-first order, pseudo-second order, Elovich, intra-particle diffusion and film diffusion models were used to fit the experimental data. Thus, the BPA adsorption isotherms were analysed by Langmuir, Freundlich, Sips, Redlich-Peterson and Dual-site Langmuir (DLS) isotherm models.In addition, the influence of different aqueous matrices, such as a hospital wastewater, a wastewater treatment plant (WWTP) effluent and a river water, on BPA removal efficiency has been explored. These adsorption tests revealed a clear competitive effect between the target compound (BPA) and the natural organic matter content (NOM) present in the matrices for the active sites, resulting in a high decreasing of BPA adsorption removal.

New insights from modelling and estimation of mass transfer parameters in fixed-bed adsorption of Bisphenol A onto carbon materials

The removal of Bisphenol A, 2,2-bis (4-hydroxyphenyl) propane (BPA) in fixed-bed columns was investigated by breakthrough adsorption tests at different operation conditions and further prediction by a mathematical model to describe the adsorption-diffusion process onto two synthesized carbon porous materials. In this study, a xerogel (RFX) prepared by an optimized conventional sol-gel method and a lignin-based activated carbon (KLP) obtained via chemical activation were used in batch and fixed-bed adsorption experiments. The materials were fully characterized and their adsorptive properties were compared to those obtained with a commercial activated carbon (F400). RFX and KLP materials reached the equilibrium adsorption in only 24 h, whereas F400 activated carbon required 48 h. In addition, F400 and KLP adsorbents showed higher equilibrium adsorption capacity values (q_e = 0.40 and 0.22 kg/kg, for F400 and KLP, respectively) than that obtained for the xerogel (q_e = 0.08 kg/kg). Both synthesized carbon-adsorbents were studied in fixed-bed adsorption tests, exploring the effect of the operation conditions, e.g., initial BPA concentration (0.005-0.04 kg/m³), weight of adsorbent (0.01-0.05 g) and volumetric flow rate (0.2 to 1.0 mL/min), on the adsorption performance of the column. All the tested adsorption columns reached the equilibrium in a very short time, due to the efficient dimensionless of the bed. Additionally, the regeneration of the exhausted adsorbent was studied, achieving the total reuse of the solids after three consecutive cycles using methanol as regeneration agent. Finally, a mathematical model based on mass conservation equations was proposed, allowing to efficiently fit the experimental BPA breakthrough curves and estimate the external and adsorbed-phase mass transfer coefficients with a high accuracy.

The Zn-finger domain of human PrimPol is required to stabilize the initiating nucleotide during DNA priming

Human PrimPol is a monomeric enzyme whose DNA primase activity is required to rescue stalled replication forks during nuclear and mitochondrial DNA replication. PrimPol contains an Archeal-Eukaryotic Primases (AEP) core followed by a C-terminal Zn finger-containing domain (ZnFD), that is exclusively required for primer formation and for PrimPol function in vivo. The present study describes the sequential substrate interactions of human PrimPol during primer synthesis, and the relevance of the ZnFD at each individual step. Both the formation of a PrimPol:ssDNA binary complex and the upcoming interaction with the 3′-nucleotide (pre-ternary complex) remained intact when lacking the ZnFD. Conversely, the ZnFD was required for the subsequent binding and selection of the 5′-nucleotide that will become the first nucleotide of the new primer strand. Providing different 5′-site nucleotides, we can conclude that the ZnFD of PrimPol most likely interacts with the γ-phosphate moiety of the 5′-site nucleotide, optimizing formation of the initial dimer. Moreover, the ZnFD also contributes to recognize the cryptic G at the preferred priming sequence 3′GTC5′. Dimer elongation to obtain long DNA primers occurs processively and is facilitated by the 5′-terminal triphosphate, indicating that the ZnFD is also essential in the subsequent translocation/elongation events during DNA primer synthesis.

Mechanism of DNA primer synthesis by human PrimPol

PrimPol is the second primase discovered in eukaryotic cells, whose function is to restart the stalled replication forks during both mitochondrial and nuclear DNA replication. This chapter revises our current knowledge about the mechanism of synthesis of DNA primers by human PrimPol, and the importance of its distinctive Zn-finger domain (ZnFD). After PrimPol forms a binary complex with ssDNA, the formation of the pre-ternary complex strictly requires the presence of Mn²⁺ ions to stabilize the interaction of the incoming deoxynucleotide at the 3'-site. The capacity to bind both ssDNA template and 3'-deoxynucleotide was shown to reside in the AEP core of PrimPol, with ZnFD being dispensable at these two early steps of the primase reaction. Sugar selection favoring dNTPs versus NTPs at the 3' site is mediated by a specific tyrosine (Tyr¹⁰⁰) acting as a steric gate. Besides, a specific glutamate residue (Glu¹¹⁶) conforming a singular A motif (DxE) promotes the use of Mn²⁺ to stabilize the pre-ternary complex. Mirroring the function of the PriL subunit of dimeric AEP primases, the ZnFD of PrimPol is crucial to stabilize the initiating 5'-nucleotide, specifically interacting with the gamma-phosphate. Such an interaction is crucial to optimize dimer formation and the subsequent translocation events leading to the processive synthesis of a mature DNA primer. Finally, the capacity of PrimPol to tolerate lesions is discussed in the context of its DNA primase function, and its potential as a TLS primase.

The invariant glutamate of human PrimPol DxE motif is critical for its Mn2+-dependent distinctive activities

PrimPol is a human primase/polymerase specialized in downstream repriming of stalled forks during both nuclear and mitochondrial DNA replication. Like most primases and polymerases, PrimPol requires divalent metal cations, as Mg²⁺ or Mn²⁺, used as cofactors for catalysis. However, little is known about the consequences of using these two metal cofactors in combination, which would be the most physiological scenario during PrimPol-mediated reactions, and the individual contribution of the putative carboxylate residues (Asp¹¹⁴, Glu¹¹⁶ and Asp²⁸⁰) acting as metal ligands. By site-directed mutagenesis in human PrimPol, we confirmed the catalytic relevance of these three carboxylates, and identified Glu¹¹⁶ as a relevant enhancer of distinctive PrimPol reactions, which are highly dependent on Mn²⁺. Herein, we evidenced that PrimPol Glu¹¹⁶ contributes to error-prone tolerance of 8oxodG more markedly when both Mg²⁺ and Mn²⁺ ions are present. Moreover, Glu¹¹⁶ was important for TLS events mediated by primer/template realignments, and crucial to achieving an optimal primase activity, processes in which Mn²⁺ is largely preferred. EMSA analysis of PrimPol:ssDNA:dNTP pre-ternary complex indicated a critical role of each metal ligand, and a significant impairment when Glu¹¹⁶ was changed to a more conventional aspartate. These data suggest that PrimPol active site requires a specific motif A (DxE) to favor the use of Mn²⁺ ions in order to achieve optimal incoming nucleotide stabilization, especially required during primer synthesis.

A cancer-associated point mutation disables the steric gate of human PrimPol

PrimPol is a human primase/polymerase specialized in re-starting stalled forks by repriming beyond lesions such as pyrimidine dimers, and replication-perturbing structures including G-quadruplexes and R-loops. Unlike most conventional primases, PrimPol proficiently discriminates against ribonucleotides (NTPs), being able to start synthesis using deoxynucleotides (dNTPs), yet the structural basis and physiological implications for this discrimination are not understood. In silico analyses based on the three-dimensional structure of human PrimPol and related enzymes enabled us to predict a single residue, Tyr¹⁰⁰, as the main effector of sugar discrimination in human PrimPol and a change of Tyr¹⁰⁰ to histidine to boost the efficiency of NTP incorporation. We show here that the Y100H mutation profoundly stimulates NTP incorporation by human PrimPol, with an efficiency similar to that for dNTP incorporation during both primase and polymerase reactions in vitro. As expected from the higher cellular concentration of NTPs relative to dNTPs, Y100H expression in mouse embryonic fibroblasts and U2OS osteosarcoma cells caused enhanced resistance to hydroxyurea, which decreases the dNTP pool levels in S-phase. Remarkably, the Y100H PrimPol mutation has been identified in cancer, suggesting that this mutation could be selected to promote survival at early stages of tumorigenesis, which is characterized by depleted dNTP pools.

Engineering human PrimPol into an efficient RNA-dependent-DNA primase/polymerase

We have developed a straightforward fluorometric assay to measure primase-polymerase activity of human PrimPol (HsPrimPol). The sensitivity of this procedure uncovered a novel RNA-dependent DNA priming-polymerization activity (RdDP) of this enzyme. In an attempt to enhance HsPrimPol RdDP activity, we constructed a smart mutant library guided by prior sequence-function analysis, and tested this library in an adapted screening platform of our fluorometric assay. After screening less than 500 variants, we found a specific HsPrimPol mutant, Y89R, which displays 10-fold higher RdDP activity than the wild-type enzyme. The improvement of RdDP activity in the Y89R variant was due mainly to an increased in the stabilization of the preternary complex (protein:template:incoming nucleotide), a specific step preceding dimer formation. Finally, in support of the biotechnological potential of PrimPol as a DNA primer maker during reverse transcription, mutant Y89R HsPrimPol rendered up to 17-fold more DNA than with random hexamer primers.

A novel influenza A virus mitochondrial protein that induces cell death

While searching for alternative reading-frame peptides encoded by influenza A virus that are recognized by CD8+ T cells, we found an abundant immunogenic peptide encoded by the +1 reading frame of PB1. This peptide derives from a novel conserved 87-residue protein, PB1-F2, which has several unusual features compared with other influenza gene products in addition to its mode of translation. These include its absence from some animal (particularly swine) influenza virus isolates, variable expression in individual infected cells, rapid proteasome-dependent degradation and mitochondrial localization. Exposure of cells to a synthetic version of PB1-F2 induces apoptosis, and influenza viruses with targeted mutations that interfere with PB1-F2 expression induce less extensive apoptosis in human monocytic cells than those with intact PB1-F2. We propose that PB1-F2 functions to kill host immune cells responding to influenza virus infection.

A common temperature-sensitive allelic form of human tyrosinase is retained in the endoplasmic reticulum at the nonpermissive temperature

Oculocutaneous albinism type 1TS is caused by mutations that render the melanocyte-specific enzyme tyrosinase temperature-sensitive (ts); the enzyme is inactive in cells grown at 37 degrees C but displays full activity in cells grown at 31 degrees C. To distinguish whether the ts phenotype of the common R402Q variant of human tyrosinase is due to altered enzymatic activity or to misfolding and a defect in intracellular trafficking, we analyzed its localization and processing in transiently transfected HeLa cells. R402Q tyrosinase accumulates in the endoplasmic reticulum (ER) at 37 degrees C but exits the ER and accumulates in endosomal structures in cells grown at 31 degrees C. The inability of the R402Q variant to exit the ER is confirmed by the failure to acquire endoglycosidase H resistance at 37 degrees C and cannot be accounted for solely by enhanced proteasome-mediated degradation. ER retention at 37 degrees C is mediated by the lumenal domain of R402Q tyrosinase, is not dependent on tethering to the membrane, and is irreversible. Finally, a wild-type allelic form of tyrosinase is partially ts in transiently transfected HeLa cells. The data show that human tyrosinase expressed in non-melanogenic cells folds and exits the ER inefficiently and that R402Q tyrosinase exaggerates this defect, resulting in a failure to exit the ER at physiologic temperatures.

A cytoplasmic sequence in human tyrosinase defines a second class of di-leucine-based sorting signals for late endosomal and lysosomal delivery

Distinct cytoplasmic sorting signals target integral membrane proteins to late endosomal compartments, but it is not known whether different signals direct targeting by different pathways. The availability of multiple pathways may permit some cell types to divert proteins to specialized compartments, such as the melanosome of pigmented cells. To address this issue, we characterized sorting determinants of tyrosinase, a tissue-specific resident protein of the melanosome. The cytoplasmic domain of tyrosinase was both necessary and sufficient for internalization and steady state localization to late endosomes and lysosomes in HeLa cells. Mutagenesis of two leucine residues within a conventional di-leucine motif ablated late endosomal localization. However, the properties of this di-leucine-based signal were distinguished from that of CD3gamma by overexpression studies; overexpression of the tyrosinase signal, but not the well characterized CD3gamma signal, induced a 4-fold enlargement of late endosomes and lysosomes and interfered with endosomal sorting mediated by both tyrosine- and other di-leucine-based signals. These properties suggest that the tyrosinase and CD3gamma di-leucine signals are distinctly recognized and sorted by distinct pathways to late endosomes in non-pigmented cells. We speculate that melanocytic cells utilize the second pathway to divert proteins to the melanosome.

Comparison of humoral immune responses elicited by DNA and protein vaccines based on merozoite surface protein-1 from Plasmodium yoelii, a rodent malaria parasite

Immunization with DNA vaccines encoding relevant Ags can induce not only cell-mediated immune response but also humoral immune responses against pathogenic microorganisms in several animal models. Our previous results demonstrated that, when the C terminus (PyC2) of Plasmodium yoelii merozoite surface protein-1 (MSP-1), a leading vaccine candidate against erythrocytic stages of malaria, was expressed as a fusion protein (GST-PyC2) with glutathione S-transferase (GST), it elicited Ab-mediated protective immune responses in BALB/c mice. In our present study, we wished to examine the humoral responses to a DNA vaccine (V3) encoding GST-PyC2. The GST-PyC2 expressed in V3-transfected Cos 7 cells was recognized by a protective monoclonal Ab to PyC2 (mAb302), although the secreted product had undergone N-linked glycosylation. When BALB/c mice were immunized with V3 plasmid, anti-PyC2 Abs were successfully induced. These Abs immunoprecipitated native PyMSP-1 protein and competed with mAb302 for binding to its epitope at a level similar to those elicited by GST-PyC2 protein immunization. However, these Abs had significantly lower titers and avidities, and different isotype profiles and protective capacities against a lethal erythrocytic stage challenge, than those resulting from immunization with GST-PyC2 protein. Most surprising was the finding that, in contrast to protein immunization, there was no significant increase in the avidity of either GST-specific or PyC2-specific IgG Abs during the course of DNA immunization. This suggests that there may be little or no affinity maturation of specific Abs during DNA immunization in this system.

Plasmodium yoelii: the role of the individual epidermal growth factor-like domains of the merozoite surface protein-1 in protection from malaria

The merozoite surface protein-1 (MSP-1) is a leading candidate for a vaccine targeted at the erythrocytic stages of plasmodial parasite development. Recently, there has been increasing interest in this polypeptide, particularly in the carboxyl-terminal EGF-like domains. We have previously shown that this region from Plasmodium yoelii, when expressed in native configuration, could immunize mice against an otherwise lethal challenge infection. In this model system, protection appears to be predominantly mediated by antibodies. In all rodent immunization studies to date, however, the immunogen has contained both of the postulated EGF-like domains. We report here on the efficacy of immunization with the individual EGF-like domains from P. yoelii in elicitation of a protective host response. Although all animals developed some level of antibody in response to the various immunogens, only those animals immunized with both EGF-like domains produced antibodies which could recognize the native MSP-1 molecule. Antibodies generated against the individual EGF-like domains did cross-react with the double EGF-like domain structure, suggesting that the immunogens had retained elements of native configuration. In addition, only those animals which generated antibodies capable of recognizing native MSP-1 showed any level of protection from challenge infection. These results suggest that determinants unique to the double EGF-like domain structure may be necessary for the generation of antibodies specific for the native configuration of MSP-1 and that these antibodies may play a significant role in protection.

Phenotypes associated with malignant hyperthermia susceptibility in swine genotyped as homozygous or heterozygous for the ryanodine receptor mutation

We have examined the phenotypic expression of several parameters associated with malignant hyperthermia (MH) susceptibility in three groups (homozygous normal, homozygous abnormal and heterozygous) of Yorkshire/Duroc swine genotyped by a mutation in the ryanodine receptor. Subgroups of homozygous abnormals were classified further by the appearance or absence of muscle rigidity on prolonged in vivo challenge with halothane and suxamethonium. Four swine heterozygous for the proposed MH mutation were indistinguishable from five homozygous normal swine in temperature, heart rate, lactate concentrations, base excess and pH determined during the prolonged halothane and suxamethonium challenge. Resting creatine kinase concentrations, the in vivo barnyard challenge, the in vitro contracture response of skeletal muscle to 3% halothane and the threshold for Ca(2+)-induced Ca2+ release were also similar for subgroups of homozygous normals and heterozygotes. Therefore, inheritance of only one allele carrying the defect in the ryanodine receptor does not significantly alter phenotypes associated with MH susceptibility in this strain of swine. As four swine homozygous for the proposed MH defect did not exhibit rigidity and three of these had no other signs of MH on prolonged halothane and suxamethonium challenge, we conclude that the reported mutation in the ryanodine receptor may be necessary, but is not sufficient, for consistently eliciting the malignant hyperthermia syndrome. These findings suggest that a modulator of the syndrome may explain variability within individuals in human MH.