Functional polymorphisms in promoter survivin gene and its association with susceptibility to bladder cancer in North Indian cohort

Survivin is a member of novel inhibitor of apoptosis protein family which expressed in human cancers. The molecular detection of bladder cancer by targeting Survivin as a novel marker may be useful in the occurrence and progression of cancer. We genotyped Survivin −31G>C, −1547A>G and −241C>T by PCR-restriction fragment length polymorphism to evaluate the risk of bladder cancer (BC) in 200 BC patients and 200 healthy controls from North Indian cohort. We observed significant increased BC risk associated with variant CC genotype of Survivin −31G>C having 2.6 fold risk. The variant genotype of Survivin −1547A>G was significantly associated with BC risk (P = 0.047). In case of Survivin −241C>T the protective genotype for BC was heterozygous (P = 0.035). Smoking significantly modulated the risk in patients with Survivin −1547A>G polymorphism. Variant as well as hetero genotype of Survivin −31G>C was associated with reduced risk of recurrence (HR = 0.22 and 0.35) in BC patients receiving BCG treatment thus showing least survival. Furthermore, the haplotype analysis revealed C–A–T haplotype to be associated with reduced BC risk. Our findings suggested that the functional polymorphism −31G>C, −1547A>G and −241C>T in the promoter of Survivin gene may play a significant role in mediating the BC risk among North Indian cohort.     

Conserved Structural Chemistry for Incision Activity in Structurally Non-homologous Apurinic/Apyrimidinic Endonuclease APE1 and Endonuclease IV DNA Repair Enzymes

Non-coding apurinic/apyrimidinic (AP) sites in DNA form spontaneously and as DNA base excision repair intermediates are the most common toxic and mutagenic in vivo DNA lesion. For repair, AP sites must be processed by 5′ AP endonucleases in initial stages of base repair. Human APE1 and bacterial Nfo represent the two conserved 5′ AP endonuclease families in the biosphere; they both recognize AP sites and incise the phosphodiester backbone 5′ to the lesion, yet they lack similar structures and metal ion requirements. Here, we determined and analyzed crystal structures of a 2.4 Å resolution APE1-DNA product complex with Mg²⁺ and a 0.92 Å Nfo with three metal ions. Structural and biochemical comparisons of these two evolutionarily distinct enzymes characterize key APE1 catalytic residues that are potentially functionally similar to Nfo active site components, as further tested and supported by computational analyses. We observe a magnesium-water cluster in the APE1 active site, with only Glu-96 forming the direct protein coordination to the Mg²⁺. Despite differences in structure and metal requirements of APE1 and Nfo, comparison of their active site structures surprisingly reveals strong geometric conservation of the catalytic reaction, with APE1 catalytic side chains positioned analogously to Nfo metal positions, suggesting surprising functional equivalence between Nfo metal ions and APE1 residues. The finding that APE1 residues are positioned to substitute for Nfo metal ions is supported by the impact of mutations on activity. Collectively, the results illuminate the activities of residues, metal ions, and active site features for abasic site endonucleases.     

Enantioselective esterification of ibuprofen by a novel thermophilic Biocatalyst: APE1547

The enantioselective esterification of ibuprofen catalyzed by a novel thermophilic esterase (APE1547) from the archaeon Aeropyrum pernix K1 was successfully conducted in organic solvents. The effects of acyl acceptor, substrate ratio, organic solvent, temperature, and water activity were investigated. Under optimum conditions, the highest enantioselectivity (E = 38.1) was obtained with a higher enzyme activity (216.5 μmol/g/h). Celites were added into the reaction mixture to remove the water produced in the esterification. The reaction achieved its equilibrium in approximately 96 h with a conversion of 57 and 99% (ee) of the un-reacted (S)-ibuprofen obtained.     

Ethnic differences in cytokine gene polymorphisms: potential implications for cancer development

Differences in incidence and outcome of cancer among ethnic groups may be explained by biological and/or socio-economic factors. Genetic variations that affect chronic inflammation, a potentially important risk factor for carcinogenesis, may differ across ethnic groups. Such differences may help explain cancer disparities among these groups. Single nucleotide polymorphisms (SNPs) within cytokine genes can affect cytokine levels and the degree of inflammation. Associations between cancer and some cytokine SNPs have been suggested. However, these have not been consistently replicated among populations, suggesting that SNP function may differ according to ethnicity, or that SNPs alone do not completely account for regulation of inflammation. We examined seven polymorphisms in African-American (n = 294) and Caucasian (n = 299) newborns in Louisiana: IL1B-511C > T, IL1B-31T > C, IL1B + 3954C > T, IL1RN*2, IL10-1082G > A, IL10-592C > A, and TNF-308G > A. African-American newborns had significantly higher frequencies of IL1B-511T, IL1B-31C, IL10-1082A and IL10-592A alleles and complete linkage equilibrium between IL1B + 3954 and IL1B-31. In contrast, IL1B + 3954T, IL1RN*2, and TNF-308A were more frequent in Caucasian newborns and exhibited strong linkage disequilibrium between IL1B + 3954 and IL1B-31. All allelic frequencies were significantly different between groups. We hypothesize that these dissimilarities may contribute to differences in the inflammatory response and cancer incidence and mortality between African-Americans and Caucasians in Louisiana.     

Improving the catalytic activity of a detergent-compatible serine protease by rational design

Serine proteases are among the most important biological additives in various industries such as detergents, leather, animal feed and food. A serine protease gene, Fgapt4, from Fusarium graminearum 2697 was identified, cloned and expressed in Pichia pastoris. The optimal pH and temperature of FgAPT4 were 8.5 and 40°C, respectively. The relative activity was >30% even at 10°C. It had a wide range of pH stability (4.0–12.0) and detergent compatibility. To improve the catalytic activity, a strategy combining molecular docking and evolutionary analysis was adopted. Twelve amino acid residue sites and three loops (A, B and C) were selected as potential hot spots that might play critical roles in the enzyme's functional properties. Twenty-eight mutants targeting changes in individual sites or loops were designed, and mutations with good performance were combined. The best mutant was FgAPT4-M3 (Q70N/D142S/A143S/loop C). The specific activity and catalytic efficiency of FgAPT4-M3 increased by 1.6 (1008.5 vs. 385.9 U/mg) and 2.2-fold (3565.1 vs. 1106.3/s/mM), respectively. Computational analyses showed that the greater flexibility of the substrate pocket may be responsible for the increased catalytic activity. In addition, its application in detergents indicated that FgAPT4-M3 has great potential in washing.     

Processing of the abasic sites clustered with the benzo[a]pyrene adducts by the base excision repair enzymes

The major enzyme in eukaryotic cells that catalyzes the cleavage of apurinic/apyrimidinic (AP or abasic) sites is AP endonuclease 1 (APE1) that cleaves the phosphodiester bond on the 5′-side of AP sites. We found that the efficiency of AP site cleavage by APE1 was affected by the benzo[a]pyrenyl-DNA adduct (BPDE-dG) in the opposite strand. AP sites directly opposite of the modified dG or shifted toward the 5′ direction were hydrolyzed by APE1 with an efficiency moderately lower than the AP site in the control DNA duplex, whereas AP sites shifted toward the 3′ direction were hydrolyzed significantly less efficiently. For all DNA structures except DNA with the AP site shifted by 3 nucleotides in the 3′ direction (AP₊₃-BP-DNA), hydrolysis was more efficient in the case of (+)-trans-BPDE-dG. Using molecular dynamic simulation, we have shown that in the complex of APE1 with the AP₊₃-BP-DNA, the BP residue is located within the DNA bend induced by APE1 and contacts the amino acids in the enzyme catalytic center and the catalytic metal ion. The geometry of the APE1 active site is perturbed more significantly by the trans-isomer of BPDE-dG that intercalates into the APE1-DNA complex near the cleaved phosphodiester bond. The ability of DNA polymerases β (Polβ), λ and ι to catalyze gap-filling synthesis in cooperation with APE1 was also analyzed. Polβ was shown to inhibit the 3′ → 5′ exonuclease activity of APE1 when both enzymes were added simultaneously and to insert the correct nucleotide into the gap arising after AP site hydrolysis. Therefore, further evidence for the functional cooperation of APE1 and Polβ in base excision repair was obtained.     

122 Kinetics of apurinic/apyrimidinic endonuclease 1 (APE1) on an authentic AP site or an AP site analog

Our genomic DNA is endlessly exposed to a wide variety of exogenous and endogenous DNA-damaging agents. One of the most abundant DNA lesions is an apurinic/apyrimidinic (AP) site, which in vivo, can form spontaneously or through various cellular pathways, including the repair activity of DNA glycosylase enzymes (Wilson & Barsky, 2001). Persistence of these AP sites is both highly mutagenic and cytotoxic to the cell (Loeb & Preston, 1986). AP endonuclease 1 (APE1), an Mg²⁺ dependent enzyme, is the major human endonuclease responsible for incising the DNA backbone at AP sites. Repair to canonical duplex DNA is then completed by DNA polymerase and DNA ligase. Recently, APE1, in conjunction with delivery of DNA-damaging agents, has become a target for chemotherapeutic research with the aim to inhibit APE1 activity (Fishel & Kelley, 2007). Therefore, an understanding of APE1 activity and its molecular mechanism is essential. In vitro, the authentic AP site is highly unstable and can undergo β-elimination, leading to a strand break (Strauss, Beard, Patterson & Wilson, 1997). Due to the fragility of the AP site, stable AP site analogs, such as the reduced AP site or tetrahydrofuran (THF) site, are typically used to study APE1 (Maher & Bloom, 2007; Strauss, Beard, Patterson & Wilson, 1997). In this work, we have performed the first comprehensive kinetic study of APE1 acting on the authentic AP site as well the reduced AP site and THF AP site analog. Transient-state kinetic experiments reveal that the strand incision chemistry step is fast, upwards of ～700?s^?1 for all substrates, making APE1 one of the fastest DNA repair enzymes. Steady-state kinetic experiments reveal for each substrate, a slow, post chemistry step limits the steady-state rate. The steady-state rate for APE1 acting on authentic AP and AP-Red substrates is highly dependent on Mg²⁺ concentration, while the steady-state rate for THF site was not dependent on Mg²⁺ concentration. This comprehensive kinetic analysis reveal differences and similarities in the way APE1 processes the authentic AP site compared to AP site analogs. Furthermore, these differences require consideration when choosing AP site analogs to study APE1.     

Redox Factor-1 Activates Endothelial SIRTUIN1 through Reduction of Conserved Cysteine Sulfhydryls in Its Deacetylase Domain

Apurinic/Apyrmidinic Endonuclease 1/Redox Factor-1 (APE1/Ref-1) is a reductant which is important for vascular homeostasis. SIRTUIN1 (SIRT1) is a lysine deacetylase that also promotes endothelium-dependent vasorelaxation. We asked if APE1/Ref-1 governs the redox state and activity of SIRT1, and whether SIRT1 mediates the effect of APE1/Ref-1 on endothelium-dependent vascular function. APE1/Ref-1 maintains sulfhydryl (thiol) groups of cysteine residues in SIRT1 in the reduced form and promotes endothelial SIRT1 activity. APE1/Ref-1 stimulates SIRT1 activity by targeting highly conserved vicinal thiols 371 and 374 which form a zinc tetra-thiolate motif in the deacetylase domain of SIRT1. Cysteine residues in the N-terminal redox domain of APE1/Ref-1 are essential for reducing SIRT1 and stimulating its activity. APE1/Ref-1 protects endothelial SIRT1 from hydrogen peroxide-induced oxidation of sulfhydryls and from inactivation. APE1/Ref-1 also promotes lysine deacetylation of the SIRT1 target endothelial nitric oxide synthase (eNOS). SIRT1 mutated at cysteines 371 and 374, which renders it non-reducible by APE1/Ref-1, prevents lysine deacetylation of eNOS by APE1/Ref-1. SIRT1 free thiol (reduced sulfhydryl) content and deacetylase activity are diminished in all examined tissues of APE1/Ref-1^+/− mice, including the vasculature. Overexpression of SIRT1 in aortas of APE1/Ref-1^+/− mice restores endothelium-dependent vasorelaxation and bioavailable nitric oxide (NO) to levels similar to those observed in wild-type mice. Thus, APE1/Ref-1, by maintaining functionally important cysteine sulfhydryls in SIRT1 in the reduced form, promotes endothelial SIRT1 activity. This reductive activation of endothelial SIRT1 by APE1/Ref-1 mediates the effect of APE1/Ref-1 on eNOS acetylation, promoting endothelium-derived NO and endothelium-dependent vasorelaxation.     

Water-in-ionic liquid microemulsion-based organogels as novel matrices for enzyme immobilization

The use of water-in-ionic liquid microemulsion-based organogels (w/IL MBGs) as novel supports for the immobilization of lipase B from Candida antarctica and lipase from Chromobacterium viscosum was investigated. These novel lipase-containing w/IL MBGs can be effectively used as solid phase biocatalysts in various polar and non-polar organic solvents or ILs, exhibiting up to 4.4-fold higher esterification activity compared to water-in-oil microemulsion-based organogels. The immobilized lipases retain their activity for several hours at 70°C, while their half life time is up to 25-fold higher compared to that observed in w/IL microemulsions. Fourier-transform infrared spectroscopy data indicate that immobilized lipases adopt a more rigid structure, referring to the structure in aqueous solution, which is in correlation with their enhanced catalytic behavior observed.     

Comparison of differently modified Pseudomonascepacia lipases in enantioselective preparation of a chiral alcohol for agrochemical use

Three methods for enzyme modification/immobilization were compared to enhance the catalytic performance of a commercially available lipase, Lipase PS from Pseudomonascepacia, in highly enantioselective transesterification of an agrochemically useful sec-alcohol, (R,?S)-HMPC [=(R,?S)-4-hydroxy-3-methyl-2-(2′-propenyl)-2-cyclopenten-1-one], with vinyl acetate as both acyl donor and reaction medium. The stearic acid-coated lipase showed the highest catalytic activity, with a specific activity improved by 54 times over the native lipase. The microcrystal salt-supported lipase and celite-adsorbed lipase also displayed much better performance as compared with the native lipase. All the three modified lipase preparations showed a similar thermal stability to that of the native enzyme. The enantioselectivity (E-value) was also quite satisfactory in all the cases (E>100 at 30°C), though a trend of slight decline was also observed with the temperature increase in the range of 25–60°C. The optimum aqueous pH, from which the modified lipases were prepared, was 6.0–7.0. A low water activity (a_w) of ca. 0.1 was favorable for all the three modified lipases. The stearic acid-coated lipase displayed prominent advantages in catalyzing the transesterification reaction at a very high (R,?S)-HMPC concentration up to 1.0?M.     

Genetic contribution between APE1 variants in polycystic ovarian syndrome

IntroductionPolycystic Ovarian Syndrome (PCOS) has been identified as a gynecological, hormonal, and metabolic condition in women of reproductive age. Genetic studies can contribute to understand the pathogenesis of PCOS; which can be beneficial in early diagnosis and long-term management of the disease. Apurinic/apyrimidinic endonuclease 1 (APE1) has been related in the literature to polycystic ovarian syndrome.AimThe purpose of this study was to investigate the effects of ?656 T > G and 1349 T > G single nucleotide polymorphisms (SNPs) in the APE1 gene in Saudi women with PCOS.MethodsThis study includes 100 PCOS women and 100 healthy controls were genotyped for ?656 T > G and 1349 T > G SNPs using PCR-RFLP method. Serum sample was used for FBG and lipid profile tests. The obtained biochemical and genotypes data were entered into Excel and utilized for statistical analysis.ResultsClinical data presented in Table 1 was used to calculate the t-tests between PCOS and control subjects and results indicate age, weight, BMI, TG, LDLC and PCOS family history was associated (p < 0.0001). Genotype and allele frequencies showed the negative association in ?656 T > G SNP (GG vs TT: OR-1.15 (0.61–2.17); p = 0.65 and GG + TG vs TT: OR-1.17 (0.67–2.04); p = 0.57) and positive association in 1349 T > G SNP (GG vs TT: OR-3.52 (1.48–8.36); p = 0.003 and GG + TG vs TT: OR-2.84 (1.27–6.31); p = 0.008) in APE1 gene. Anova analysis was not associated with any one of the involved parameters (p > 0.05).ConclusionThis study found that the 1349 T > G SNP was related with PCOS in Saudi women. However, the ?656SNP had no favorable effect on the APE1 gene.     

Polymorphic variants of the genes encoding intrleukin-6 and fibrinogen: Risk for ischemic stroke and fibrinogen levels

The occurrence of alleles and genotypes of polymorphic region −174G>C of the gene IL6 (rs1800795) in patients of Russian ethnicity with ischemic stroke (200 cases) and in the control of the same ethnicity similar in sex and age (140 control subjects) has been analyzed. Reliable differences were revealed in the carriage frequency of allele IL6*-174G in homozygous and heterozygous form (p = 0.0029, OR = 2.9, 95% CI: 1.4–5.8), which can be considered a risk factor for the development of ischemic stroke, and in the carriage frequencies of protective genotype IL6*-174C/C (p = 0.0029, OR = 0.35, 95% CI: 0.17–0.69), respectively. After the patients and the control subjects were divided by gender character, similar differences were observed only between women with ischemic stroke and those from the control group, and after division by age, they were only revealed in groups with members older than 60 years. Complex analysis of the association of ischemic stroke with the carriage of alleles and genotypes of IL6 SNP-174G>C in combination with SNP 4266A>G (Thr312Ala) of the gene FGA (rs6050) and -249C>T of the gene FGB (rs1800788) revealed protective combinations of IL6*-174C/C + FGA*4266A and IL6*-174C/C + FGB*-249C, which are slightly more reliably associated with ischemic stroke than the one protective genotype IL6*-174C/C and have nearly the same OR value. At the same time, combinations of alternative allele IL6*-174G and the same alleles FGA*4266A or FGB*-249C were revealed that are characterized by a decrease in both the significance level and the OR value as compared with the carriage of one risk allele IL6*-174G. When there is a combined carriage of the allele IL6*-174G with the genotypes FGA*4266A/A, FGB*-249C/C or with combinations of these alleles/genotypes, the neutralizing effect is enhanced. In other words, we observed the association of IL6, FGA and FGB allele combinations with ischemic stroke in which IL6 plays the key role and FGA and FGB have a modulating function. In analyzing the association of the alleles/genotypes of three polymorphic regions with the fibrinogen level in plasma, no reliable difference was revealed.     

Raised Interleukin‐6 Levels in Obese Patients

Objective: Obese patients demonstrate a variety of biochemical, metabolic, and pulmonary abnormalities. Inflammatory mediators such as tumor necrosis factor‐α and interleukin‐6 (IL‐6) may have a direct effect on glucose and lipid metabolism. Hypoxemia in itself induces release of IL‐6. The aim of this study was to examine the relationship between IL‐6 levels in healthy volunteers (control group) and three different groups of obese patients: patients without obstructive sleep apnea syndrome (OSAS), patients with OSAS, and patients with obesity hypoventilation syndrome (OHS) (daytime baseline oxygen saturation of <93%). Research Methods and Procedures: We measured serum IL‐6 levels in 25 obese patients (body mass index of >35 kg/m²) and 12 healthy women. Results: The results demonstrate statistically significant differences in serum IL‐6 levels between the control group (1.28 ± 0.85 pg/mL) and obese patients without OSAS (7.69 ± 5.06 pg/mL, p < 0.05) and with OSAS (5.58 ± 0.37 pg/mL, p < 0.0005). In the patients with OHS, IL‐6 concentrations were highest (43.13 ± 24.27 pg/mL). Discussion: We conclude that serum IL‐6 is increased in obese patients. The highest IL‐6 levels were found in the patients with OHS.     

IL‐18 Cytokine Levels Modulate Innate Immune Responses and Cryptosporidiosis in Mice

IL‐18 is known to play a key role limiting Cryptosporidium parvum infection. In this study, we show that IL‐18 depletion in SCID mice significantly exacerbates C. parvum infection, whereas, treatment with recombinant IL‐18 (rIL‐18), significantly decreases the parasite load, as compared to controls. Increases in serum IFN‐γ levels as well as the up‐regulation of the antimicrobial peptides, cathelicidin antimicrobial peptide and beta defensin 3 (Defb3) were observed in the intestinal mucosa of mice treated with rIL‐18. In addition, C. parvum infection significantly increased mRNA expression levels (> 50 fold) of the alpha defensins, Defa3 and 5, respectively. Interestingly, we also found a decrease in mRNA expression of IL‐33 (a recently identified cytokine in the same family as IL‐18) in the small intestinal tissue from mice treated with rIL‐18. In comparison, the respective genes were induced by IL‐18 depletion. Our findings suggest that IL‐18 can mediate its protective effects via different routes such as IFN‐γ induction or by directly stimulating intestinal epithelial cells to increase antimicrobial activity.     

Characterization of the Endoribonuclease Active Site of Human Apurinic/Apyrimidinic Endonuclease 1

Apurinic/apyrimidinic endonuclease 1 (APE1) is the major mammalian enzyme in DNA base excision repair that cleaves the DNA phosphodiester backbone immediately 5′ to abasic sites. Recently, we identified APE1 as an endoribonuclease that cleaves a specific coding region of c-myc mRNA in vitro, regulating c-myc mRNA level and half-life in cells. Here, we further characterized the endoribonuclease activity of APE1, focusing on the active-site center of the enzyme previously defined for DNA nuclease activities. We found that most site-directed APE1 mutant proteins (N68A, D70A, Y171F, D210N, F266A, D308A, and H309S), which target amino acid residues constituting the abasic DNA endonuclease active-site pocket, showed significant decreases in endoribonuclease activity. Intriguingly, the D283N APE1 mutant protein retained endoribonuclease and abasic single-stranded RNA cleavage activities, with concurrent loss of apurinic/apyrimidinic (AP) site cleavage activities on double-stranded DNA and single-stranded DNA (ssDNA). The mutant proteins bound c-myc RNA equally well as wild-type (WT) APE1, with the exception of H309N, suggesting that most of these residues contributed primarily to RNA catalysis and not to RNA binding. Interestingly, both the endoribonuclease and the ssRNA AP site cleavage activities of WT APE1 were present in the absence of Mg²⁺, while ssDNA AP site cleavage required Mg²⁺ (optimally at 0.5-2.0 mM). We also found that a 2′-OH on the sugar moiety was absolutely required for RNA cleavage by WT APE1, consistent with APE1 leaving a 3′-PO₄²⁻ group following cleavage of RNA. Altogether, our data support the notion that a common active site is shared for the endoribonuclease and other nuclease activities of APE1; however, we provide evidence that the mechanisms for cleaving RNA, abasic single-stranded RNA, and abasic DNA by APE1 are not identical, an observation that has implications for unraveling the endoribonuclease function of APE1 in vivo.     

Study on the relationship between structure and enantioselectivity of a hyperthermophilic esterase from archaeon Aeropyrum pernix K1

To enhance the enantioselectivity of a hyperthermophilic esterase from archaeon Aeropyrum pernix K1 (APE1547), a directed evolution approach is employed to generate mutant library from the native enzyme. A mutation (TBC26) is identified after one round of epPCR. The enantioselectivity of TBC26 is increased up to 2.6-fold compared to that of wild type enzyme. TBC26 contains five amino acid substitutions (R11G, L36P, V223A, I551L, A564T). The five mutation sites are spatially distant to the catalytic center. According to the published crystal structure of WT and considering the changes of secondary and tertiary structure, here we try to explain the change of enantioselectivity of the TBC26. The results suggest that the change of enantioselectivity of enzyme has a close relationship to the configuration of the enzyme.     

Generation of catalytic protein particles in <Emphasis Type="Italic">Escherichia coli</Emphasis> cells using the cellulose-binding domain from <Emphasis Type="Italic">Cellulomonas fimi</Emphasis> as a fusion partner

The cellulose-binding domain (CBD) of a Cellulomonas fimi exo-glucanase was translationally fused with β-glucuronidase (GusA) from Escherichia coli and β-glycosidase (BglA) from Thermus caldophilus, respectively. Two fusion proteins (GusA-CBD and BglA-CBD) were expressed as insoluble aggregates in cells and isolated by centrifugation of the cell lysates. Interestingly, activity assays revealed that > 90% of the catalytic activity of both proteins was localized in the insoluble fractions. For example, the GusA-CBD particles exhibited 21 units per mg protein, which corresponded to 19% specific activity of the highly purified soluble GusA. The specific activity increased further up to 42 units per mg protein when treated with either sonication or chaotropic L-arginine. These results demonstrate that fusion with CBD family II may activate catalytic protein particles in E. coli cells, and that internal proteins of the particles are also active. Finally, the protein particles were tested in repeated batch operations after being cross-linked with chemicals, indicating that they have potential as a new preparation for immobilized biocatalysts.