Production of recombinant His-tagged triple-FLAG peptide in Brevibacillus choshinensis and its utilization as an easy-to-remove affinity peptide

Triple-FLAG (3 × FLAG)-tagged proteins can be affinity purified through binding to an anti-FLAG antibody and competitive elution with excess free 3 × FLAG peptide. To expand the availability of the 3 × FLAG purification system, we produced a recombinant His-tagged 3 × FLAG peptide in Brevibacillus choshinensis. The screening of connecting linkers between His-tag and the 3 × FLAG peptide, culture containers, and culture media showed that the His-tagged 3 × FLAG peptide with an LA linker was most expressed in 2SY medium using a baffled shake flask. The peptide was affinity-purified to give a yield of about 25 mg/L of culture. The peptide was effective for eluting 3 × FLAG-tagged α-amylase from anti-FLAG magnetic beads. Finally, the peptide remaining in the amylase fraction was removed by His-tag affinity purification. These results show that the recombinant His-tagged 3 × FLAG peptide can function as an easy-to-remove affinity peptide in the 3 × FLAG purification system.

Impacts of SARS-CoV-2 on diabetes mellitus: A pre and post pandemic evaluation

The coronavirus disease 2019 (COVID-19) pandemic caused by the novel beta coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) crippled the whole world and has resulted in large number of morbidity and mortality. The origin of the SARS-CoV-2 is still disputed. The risk of infection with SARS-CoV-2 is dependent on several risk factors as observed in many studies. The severity of the disease depends on many factors including the viral strain, host immunogenetics, environmental factors, host genetics, host nutritional status and presence of comorbidities like hypertension, diabetes, Chronic Obstructive Pulmonary Disease, cardiovascular disease, renal impairment. Diabetes is a metabolic disorder mainly characterized by hyperglycemia. Diabetic individuals are intrinsically prone to infections. SARS-CoV-2 infection in patients with diabetes result in β-cell damage and cytokine storm. Damage to the cells impairs the equilibrium of glucose, leading to hyperglycemia. The ensuing cytokine storm causes insulin resistance, especially in the muscles and liver, which also causes a hyperglycemic state. All of these increase the severity of COVID-19. Genetics also play pivotal role in disease pathogenesis. This review article focuses from the probable sources of coronaviruses and SARS-CoV-2 to its impacts on individuals with diabetes and host genetics in pre- and post-pandemic era.

Corrigendum to “establishing a novel assay system for measuring renin concentration using cost effective recombinant ovine angiotensinogen”

[This corrects the article DOI: 10.1016/j.heliyon.2019.e01409.].

Synergistic effect of amino acid substitutions in CYP51B for prochloraz resistance in Fusarium fujikuroi

Prochloraz has been used to control Fusarium fujikuroi, the causative pathogen of rice bakanae disease. Linkage analysis of FfCYP51 genes in the progenies obtained from crossing prochloraz moderately resistant and sensitive strains suggested that the FfCYP51B gene is involved in prochloraz resistance. Sequence comparison revealed that the prochloraz-resistant strain had an F511S or S312T/F511S substitution in FfCYP51B compared with the sensitive strains. The contribution of the S312T and F511S substitutions in FfCYP51B to prochloraz resistance was investigated by creating S/F-, T/F-, or T/S- types at 312/511 codons from the S/S-type, which is a natural moderately resistant strain, using a gene-editing technique. T/S exhibited the highest prochloraz resistance, followed by S/S-, T/F-, and S/F-types. These results indicated that the S312T and F511S substitutions in FfCYP51B had a synergistic effect on prochloraz resistance in F. fujikuroi.

The physiological blood concentration of phenylalanine-proline can ameliorate cholesterol metabolism in HepG2 cells

We have previously reported that the dipeptide Phe-Pro affects lipid metabolism in vivo and in vitro, but very little is known regarding the mechanism of action of Phe-Pro after it is absorbed by the intestines via PepT1. In this study, we administered a single oral dose of Phe-Pro to rats and quantified its concentration in the portal plasma using LC-TOF/MS analysis. Additionally, the physiological blood concentration of Phe-Pro was added to the lipid accumulation model of HepG2 cells to decrease intracellular cholesterol and increase the expression of CYP7A1 and PPARα mRNA levels. Moreover, we analyzed the binding of PPARα and Phe-Pro using AlphaFold2. We found that Phe-Pro is a ligand for PPARα. To the best of our knowledge, this is the first study that shows Phe-Pro to be present in the portal plasma. We found for the first time that Phe-Pro ameliorated cholesterol metabolism in HepG2 cells.

Effect of kinematics on the torque/force generation, surface characteristics, and shaping ability of a nickel titanium rotary glide path instrument: an ex-vivo study

AIM

To evaluate the effect of various rotational motions on the torque/force generation, surface wear, and shaping ability of the ProGlider glide path instrument (Dentsply Sirona).

METHODOLOGY

Mesiobuccal and mesiolingual canals of mandibular molars were selected based on the canal volume, length, angle of curvature (25°-40°), and radius of curvature (4-8 mm) after micro-computed tomographic scanning. The samples were randomly assigned to four groups (n = 13, each) according to movement kinematics [continuous rotation (CR; 300 rpm), optimum torque reverse motion (OTR; 180° forward and 90° reverse when torque > 0.4 N·cm), time-dependent reciprocal motion (TmR; 180° forward and 90° reverse), and optimum glide path motion (OGP; a combination of 90° forward, 90° reverse, 90° forward, and 120° reverse)]. Instrumentation was performed with an automated root canal instrument and torque/force analysing device. Maximum torque/force values, canal volume changes, and canal-centring ratios at 1, 3, 5, and 7 mm were evaluated. Surface defects (pits, grooves, microcracks, blunt cutting edges, and disruption of cutting edges) and spiral distortion on the ProGlider instrument were scored at the tip and 5 mm short of the tip before and after five consecutive uses with scanning electron microscopy. The Kruskal-Wallis test followed by Dunn's post-test with Bonferroni correction and Wilcoxon signed-rank test were used to analyse the data (α = 0.05).

RESULTS

OGP generated significantly less clockwise torque and greater upward force than other groups (P < 0.05). OGP resulted in significantly fewer surface defects than CR (P < 0.05). In OGP and CR, the tip exhibited more surface defects than 5 mm short of the tip (P < 0.05). CR resulted in greater volume changes than OGP and TmR (P < 0.05) and greater centring ratios (i.e., more deviation) than OGP at 1 mm and OTR at 3 mm (P < 0.05).

CONCLUSIONS

Under laboratory conditions using the ProGlider instrument, OGP generated significantly less clockwise torque and greater upward force than the other rotatory motions. OGP generated fewer superficial defects than CR, and the three modes of reciprocal rotation better maintained the apical curvature of root canals than CR with the ProGlider instrument.

Influence of rotational speed on torque/force generation and shaping ability during root canal instrumentation of extracted teeth with continuous rotation and optimum torque reverse motion

AIM

To evaluate how different rotational speeds affect the torque/force generation and shaping ability of rotary root canal instrumentation using JIZAI (MANI, Utsunomiya, Japan) nickel-titanium instruments in continuous rotation and optimum torque reverse (OTR) motion.

METHODOLOGY

Mesial root canals of extracted mandibular molars were instrumented up to size 25, 0.04 taper using JIZAI instruments, and anatomically matched canals were selected based on geometric features of the canal [canal volume (mm³ ), surface area (mm² ), length, 15°-20° curvature and radius of curvature (4-8 mm)] after micro-computed tomographic scanning. An automated root canal instrumentation and torque/force analysing device was programmed to permit a simulated pecking motion (2 s downward and 1 s upward at 50 mm min^-1 ). The selected canals were prepared with size 25, 0.06 taper JIZAI instruments using continuous rotation or OTR motion and further subdivided according to the rotational speed (300 or 500 rpm, n = 10 each). Real-time clockwise/counterclockwise torque and downward/upward force were recorded using a custom-made torque/force analysing device. Then, the registered pre- and post-operative micro-computed tomographic datasets were examined to evaluate the canal volume changes and centring ratios at 1, 3, 5 and 7 mm from the apical foramen. Data were analysed using two-way analysis of variance or the Kruskal-Wallis test and Mann-Whitney U test with Bonferroni correction (α = 5%).

RESULTS

Maximum upward force and clockwise torque were significantly smaller in 500 rpm groups than in 300 rpm groups (P < .05); however, no significant difference was found between continuous rotation and OTR motion (P > .05). OTR motion developed higher maximum counterclockwise torque than continuous rotation (P < .05). Maximum downward force, canal volume changes and centring ratios were not significantly different among all groups (P > .05). There was no file fracture in any of the groups.

CONCLUSIONS

Under laboratory conditions using JIZAI instruments, a rotational speed of 500 rpm generated significantly lower maximum screw-in forces and torque values than rotational speed of 300 rpm. Continuous rotation and OTR motion performed similarly in shaping the canals.

Non-coding Single Nucleotide Variants of Renin and the (Pro)renin Receptor are Associated with Polygenic Diseases in a Bangladeshi Population

Non-coding variants or single-nucleotide polymorphisms (SNPs) play pivotal roles in orchestrating pathogeneses of polygenic diseases, including hypertension (HTN) and diabetes. Renin-angiotensin system (RAS) components-renin and (pro)renin receptor [(P)RR]-maintain homeostasis of body fluids. Genetic variants of RAS components are associated with risk of HTN and type 2 diabetes (T2D) in different ethnic groups. We identified associations of SNPs within the renin and (P)RR genes with HTN, T2D, and T2D-associated hypertension in 911 unrelated Bangladeshi individuals. Five non-coding SNPs were involved in modulating regulatory elements in diverse cell types when tagged with other SNPs. rs61827960 was not associated with any disease; rs3730102 was associated with increased risk of HTN and T2D while under dominant model, it showed protective role against T2D-associated HTN. SNP rs11571079 was associated with increased risk of HTN and T2D-associated HTN and decreased risk of T2D, exerting a protective effect. Renin haplotypes GCA and GTG were related to increased risk of T2D and T2D-associated HTN, respectively. Heterogeneous linkage of genotypic and allelic frequencies of rs2968915 and rs3112298 of (P)RR was observed. The (P)RR haplotype GA was associated with increased risk of HTN and significantly decreased risk of T2D. These findings highlight important roles of non-coding variants of renin and (P)RR genes in the etiology of several polygenic diseases.

Boosting Auto-Induction of Recombinant Proteins in Escherichia coli with Glucose and Lactose Additives

BACKGROUND

Auto-induction is a convenient way to produce recombinant proteins without inducer addition using lac operon-controlled Escherichia coli expression systems. Auto-induction can occur unintentionally using a complex culture medium prepared by mixing culture substrates. The differences in culture substrates sometimes lead to variations in the induction level.

OBJECTIVES

In this study, we investigated the feasibility of using glucose and lactose as boosters of auto-induction with a complex culture medium.

METHODS

First, auto-induction levels were assessed by quantifying recombinant GFPuv expression under the control of the T7 lac promoter. Effectiveness of the additive-containing medium was examined using ovine angiotensinogen (tac promoter-based expression) and Thermus thermophilus manganese-catalase (T7 lac promoter-based expression).

RESULTS

Auto-induced GFPuv expression was observed with the enzymatic protein digest Polypepton, but not with another digest tryptone. Regardless of the type of protein digest, supplementing Terrific Broth medium with glucose (at a final concentration of 2.9 g/L) and lactose (at a final concentration of 7.6 g/L) was successful in obtaining an induction level similar to that achieved with a commercially available auto-induction medium. The two recombinant proteins were produced in milligram quantity of purified protein per liter of culture.

CONCLUSION

The medium composition shown in this study would be practically useful for attaining reliable auto-induction for E. coli-based recombinant protein production.

Antiproliferative Effects of Monoclonal Antibodies against (Pro)Renin Receptor in Pancreatic Ductal Adenocarcinoma

We previously reported that silencing of the PRR gene, which encodes the (pro)renin receptor [(P)RR], significantly reduced Wnt/β-catenin-dependent development of pancreatic ductal adenocarcinoma (PDAC). Here, we examined the effects of a panel of blocking mAbs directed against the (P)RR extracellular domain on proliferation of the human PDAC cell lines PK-1 and PANC-1 in vitro and in vivo We observed that four rat anti-(P)RR mAbs induced accumulation of cells in the G₀-G₁-phase of the cell cycle and significantly reduced proliferation in vitro concomitant with an attenuation of Wnt/β-catenin signaling. Systemic administration of the anti-(P)RR mAbs to nude mice bearing subcutaneous PK-1 xenografts significantly decreased tumor expression of active β-catenin and the proliferation marker Ki-67, and reduced tumor growth. In contrast, treatment with the handle region peptide of (pro)renin did not inhibit tumor growth in vitro or in vivo, indicating that the effects of the anti-(P)RR mAbs were independent of the renin-angiotensin system. These data indicate that mAbs against human (P)RR can suppress PDAC cell proliferation by hindering activation of the Wnt/β-catenin signaling pathway. Thus, mAb-mediated (P)RR blockade could be an attractive therapeutic strategy for PDAC.

Abstract P2015: Antiproliferative Effects of Monoclonal Antibodies Against (Pro)Renin Receptor in Pancreatic Ductal Adenocarcinoma

We previously reportedthat silencing of the PRR gene, which encodes the(pro)renin receptor ((P)RR) significantly reduced Wnt/β-catenin-dependent development of pancreatic ductal adenocarcinoma (PDAC). Here, we examined the effects of a panel of blocking monoclonal antibodies (mAbs) directed against the (P)RR extracellular domain on proliferation of the human PDAC cell lines PK-1 and PANC-1 in vitro andin vivo. We observed that four rat anti-(P)RR mAbs induced accumulation of cells in the G0/G1 phase of the cell cycle and significantly reduced proliferation in vitroconcomitant with a significant reduction in the expression of active β-catenin and cyclin D1. Systemic administration of the anti-(P)RR mAbs to nude mice bearing subcutaneous PK-1 xenografts significantly decreased tumor expression of active β-catenin and the proliferation marker Ki-67 and reduced tumor growth. In contreffects ast, treatment with the handle region peptide of (pro)renin did not inhibit tumor growth in vitro orin vivo, indicating that the effects of the anti-(P)RR mAbs was independent of the renin-angiotensin system. These data indicatethat mAbs against human (P)RR can suppress PDAC cells proliferation by hindering activation of the Wnt/β-catenin signaling pathway. Thus, mAb-mediated (P)RR blockade could be an attractive therapeutic strategy for PDAC.

Heterologous expression, purification, and functional characterization of recombinant ovine angiotensinogen in the methylotrophic yeast Pichia pastoris

Angiotensinogen (AGT), a glycosylated plasma noninhibitory serpin, serves as a precursor for angiotensin peptides which regulate blood pressure and electrolyte balance. AGT is specifically cleaved by renin to produce angiotensin-I, the first product of the angiotensin-processing cascade. Ovine angiotensinogen (oAGT) is considered an effective substrate for human renin and consequently finds application in clinical renin assays. In this study, oAGT was cloned into the genome of Pichia pastoris and expressed under the control of alcohol oxidase (AOX1) promoter for high-level production. Compared to the shake flask study, the high cell density cultivation in bioreactor resulted in multifold increase in oAGT titer (420 ± 9.26 mg/L), which is its highest reported titer to date. We purified recombinant oAGT to homogeneity using two chromatography steps. The characterization studies revealed oAGT underwent a two-state transition during thermal denaturation process as assessed by differential scanning fluorimetry, and the melting temperature (T_m ) of the purified oAGT from P. pastoris was 48.3°C. Renin reactivity with recombinant oAGT from P. pastoris (0.51 nM angiotensin-I/min) was slightly lower than the renin reactivity for recombinant oAGT from Escherichia coli (0.67 nM angiotensin-I/min), possibly because of its mannosylated N-glycan content. Enhanced production of functionally active recombinant oAGT using P. pastoris expression system reported in this study envisage the effective utilization of oAGT in clinical studies related to renin in near future.

Establishing a novel assay system for measuring renin concentration using cost effective recombinant ovine angiotensinogen

Background

Plasma renin can predict future cardiovascular events as well as the prevalence of chronic renal disease in hypertensive subjects. Ovine angiotensinogen (oANG) is a better substrate for measuring renin concentration through activity assay. Recombinant oANG expressed in Escherichia coli cells can be utilized as the substrate while measuring plasma renin. We aim to establish an immunoassay for measuring renin concentration at picomolar level using recombinant oANG.

Material and methods

Recombinant oANG was expressed in E. coli cells and purified to homogeneity. Various concentrations (0–1.5 pM) of recombinant human renin standard were prepared and incubated with recombinant oANG. Renin activity was determined by angiotensin-I specific enzyme-linked immunosorbent assay.

Results

About 4.5 mg of purified recombinant oANG was obtained from 0.5 L of E. coli culture. The Michaelis constant and turnover number of human renin with recombinant oANG were 0.16 μM and 0.51 s⁻¹, respectively. A linear relationship was obtained when renin activity was plotted as a function of renin concentration using recombinant oANG as the renin substrate. Picomolar amounts of renin can be measured from known renin activity using this method.

Conclusion

This study established a novel assay system for measuring renin at picomolar level using cost effective recombinant oANG.

Aliskiren reduces the release of soluble (pro)renin receptor from human umbilical vein endothelial cells

(Pro)renin receptor [(P)RR] has been implicated in diverse biological processes through binding to its ligands, which include renin, prorenin, Wnt signaling molecules and subunits of vascular H⁺-ATPase. Recent studies have reported that (P)RR is implicated in pathophysiological conditions including retinopathy and pancreatic ductal adenocarcinoma, and the soluble form of this receptor [s(P)RR] is considered as a useful biomarker for diseases. The present study examined the effect of aliskiren, the first orally active direct renin inhibitor, on the protein levels of (P)RR using cultured human umbilical vein endothelial cells (HUVECs). The cells were treated with or without aliskiren (10 nM) at 37°C for different durations (0, 8, 16 and 24 h). Aliskiren-treated HUVECs exhibited reduced proliferation compared with those treated without the drug. Furthermore, aliskiren treatment decreased not only the level of exogenous prorenin that bound to the membranes of HUVECs, but also the renin activity derived from this binding activity. These results indicate that the quantity of full-length (P)RR was reduced by aliskiren treatment, and furthermore, that the level of s(P)RR released from HUVECs was decreased with the treatment. Recent study has reported that s(P)RR exerted antidiuretic function. The current study suggests that the levels of s(P)RR, as a potential antidiuretic molecule and prospective disease biomarker, may be decreased during anti-hypertensive treatments with aliskiren.

Daidzein reductase of Eggerthella sp. YY7918, its octameric subunit structure containing FMN/FAD/4Fe-4S, and its enantioselective production of R-dihydroisoflavones

S-Equol is a metabolite of daidzein, a type of soy isoflavone, and three reductases are involved in the conversion of daidzein by specific intestinal bacteria. S-Equol is thought to prevent hormone-dependent diseases. We previously identified the equol producing gene cluster (eqlABC) of Eggerthella sp. YY7918. Daidzein reductase (DZNR), encoded by eqlA, catalyzes the reduction of daidzein to dihydrodaidzein (the first step of equol synthesis), which was confirmed using a recombinant enzyme produced in Escherichia coli. Here, we purified recombinant DZNR to homogeneity and analyzed its enzymological properties. DZNR contained FMN, FAD, and one 4Fe-4S cluster per 70-kDa subunit as enzymatic cofactors. DZNR reduced the CC bond between the C-2 and C-3 positions of daidzein, genistein, glycitein, and formononetin in the presence of NADPH. R-Dihydrodaidzein and R-dihydrogenistein were highly stereo-selectively produced from daidzein and genistein. The K_m and k_cat for daidzein were 11.9 μM and 6.7 s^-1, and these values for genistein were 74.1 μM and 28.3 s^-1, respectively. This enzyme showed similar kinetic parameters and wide substrate specificity for isoflavone molecules. Thus, this enzyme appears to be an isoflavone reductase. Gel filtration chromatography and chemical cross-linking analysis of the active form of DZNR suggested that the enzyme consists of an octameric subunit structure. We confirmed this by small-angle X-ray scattering and transmission electron microscopy at a magnification of ×200,000. DZNR formed a globular four-petal cloverleaf structure with a central vertical hole. The maximum particle size was 173 Å.

Site-1 protease is required for the generation of soluble (pro)renin receptor

The extracellular domain of the (pro)renin receptor [(P)RR] is cleaved to generate the soluble form of (P)RR [s(P)RR]. Multiple clinical studies have revealed the association between serum/plasma s(P)RR levels and certain diseases, thereby suggesting a potential role for s(P)RR as a disease biomarker. Here, we investigated whether site-1 protease (S1P) is responsible for cleaving (P)RR to generate s(P)RR. Reduction of endogenous S1P with siRNA attenuated s(P)RR generation in Chinese hamster ovary (CHO) cells exogenously expressing human (P)RR with a C-terminal decahistidine tag [CHO/h(P)RR-10His cells]; conversely, overexpression of S1P by transient transfection increased s(P)RR generation. The S1P inhibitor PF429242 suppressed s(P)RR generation in CHO/h(P)RR-10His and human cervical carcinoma HeLa cells; however, the ADAM inhibitor GM6001 had no effect. The furin inhibitor Dec-RVKR-CMK had no effect on the amount of s(P)RR, but caused a slight increase in the size of the s(P)RR. Moreover, the reversible vesicle-trafficking inhibitor brefeldin A (BFA) enhanced the generation of large-sized s(P)RR; PF429242, but not Dec-RVKR-CMK, suppressed this BFA-induced s(P)RR formation. The size of s(P)RR generated during BFA treatment was reduced after removal of BFA; Dec-RVKR-CMK, but not PF429242, suppressed this conversion. Together, these results suggest that s(P)RR is generated by sequential processing by S1P and furin.

Crystal structures of a subunit of the formylglycinamide ribonucleotide amidotransferase, PurS, from Thermus thermophilus, Sulfolobus tokodaii and Methanocaldococcus jannaschii

The crystal structures of a subunit of the formylglycinamide ribonucleotide amidotransferase, PurS, from Thermus thermophilus, Sulfolobus tokodaii and Methanocaldococcus jannaschii were determined and their structural characteristics were analyzed. For PurS from T. thermophilus, two structures were determined using two crystals that were grown in different conditions. The four structures in the dimeric form were almost identical to one another despite their relatively low sequence identities. This is also true for all PurS structures determined to date. A few residues were conserved among PurSs and these are located at the interaction site with PurL and PurQ, the other subunits of the formylglycinamide ribonucleotide amidotransferase. Molecular-dynamics simulations of the PurS dimer as well as a model of the complex of the PurS dimer, PurL and PurQ suggest that PurS plays some role in the catalysis of the enzyme by its bending motion.

In silico proposition to predict cluster of B- and T-cell epitopes for the usefulness of vaccine design from invasive, virulent and membrane associated proteins of C. jejuni

Purpose

Campylobacter jejuni is the one of the leading causes of bacterial diarrheal illness worldwide. This study aims to design specific epitopes for the utility of designing peptide vaccine(s) against C. jejuni by targeting invasive, virulent and membrane associated proteins like FlaA, Cia, CadF, PEB1, PEB3 and MOMP.

Methods

In the present study, various immunoinformatics approaches have been applied to design a potential epitope based vaccine against C. jejuni. The tools include Bepipred, ABCpred, Immune Epitope databse (IEDB) resource portal, Autodock vina etc.

Results

Peptides “EINKN”, “TGSRLN”, “KSNPDI”, “LDENGCE” respectively from FlaA, MOMP, PEB3, CadF proteins were found to be the most potential B cell epitopes while peptides “FRINTNVAA”, “NYFEGNLDM”, “YKYSPKLNF”, “YQDAIGLLV”, “FRNNIVAFV” and “LIMPVFHEL” respectively from Fla, CadF, MOMP, PEB1A, PEB3 and Cia might elicit cell mediated immunity and “IFYTTGSRL” from MOMP protein might elicit both humoral and cell-mediated immunity. All these potential peptidic epitopes showed almost 80–100 % conservancy in different strains of C jejuni with varying proportions of population coverage ranging from 22–60 %. Further authentication of these peptide epitopes as probable vaccine candidate was mediated by their binding to specific HLA alleles using in silico docking technique.

Conclusion

Based on the present study, it could be concluded that these predicted epitopes might be used to design a vaccine against C. jejuni bacteria and thus, could be validated in model hosts to verify their efficacy as vaccine.

Electronic supplementary material

The online version of this article (doi:10.1186/s40203-016-0020-y) contains supplementary material, which is available to authorized users.

Analyses of Genetic Variations of Glutathione S-Transferase Mu1 and Theta1 Genes in Bangladeshi Tannery Workers and Healthy Controls

Glutathione S-transferases (GSTs) belong to a group of multigene detoxification enzymes, which defend cells against oxidative stress. Tannery workers are at risk of oxidative damage that is usually detoxified by GSTs. This study investigated the genotypic frequencies of GST Mu1 (GSTM1) and GST Theta1 (GSTT1) in Bangladeshi tannery workers and healthy controls followed by their status of oxidative stress and total GST activity. Of the 188 individuals, 50.0% had both GSTM1 and GSTT1 (+/+), 12.2% had GSTM1 (+/-), 31.4% had GSTT1 (-/+) alleles, and 6.4% had null genotypes (-/-) with respect to both GSTM1 and GSTT1 alleles. Among 109 healthy controls, 54.1% were double positive, 9.2% had GSTM1 allele, 32.1% had GSTT1 allele, and 4.6% had null genotypes. Out of 79 tannery workers, 44.3% were +/+, 16.8% were +/-, 30.5% were -/+, and 8.4% were -/-. Though the polymorphic genotypes or allelic variants of GSTM1 and GSTT1 were distributed among the study subjects with different frequencies, the differences between the study groups were not statistically significant. GST activity did not vary significantly between the two groups and also among different genotypes while level of lipid peroxidation was significantly higher in tannery workers compared to controls irrespective of their GST genotypes.

Escherichia coli-based production of recombinant ovine angiotensinogen and its characterization as a renin substrate

Background

Angiotensinogen (ANG) is a macromolecular precursor of angiotensin, which regulates blood pressure and electrolyte balance. ANG is specifically cleaved by renin, an aspartic protease, to initiate the angiotensin-processing cascade. Ovine ANG (oANG) from sheep plasma has been shown to be a better substrate for human renin, and it has been used in clinical renin assays. To expand the availability of oANG, we aimed to produce milligram levels of recombinant oANG using an Escherichia coli expression system.

Results

When recombinant oANG was expressed from a T7 promoter in various E. coli strains at 37 °C, it accumulated in the insoluble fraction. However, by expressing oANG at 37 °C from a tac promoter, which has weaker transcriptional activity than a T7 promoter, we significantly elevated the ratio of soluble to insoluble recombinant oANG. Using a novel culturing system and auto-induction culture medium, we purified tac-expressed recombinant oANG to homogeneity, with a yield of 4.0 mg per liter of culture. Based on size-exclusion gel filtration analysis and dynamic light scattering analysis, the resulting purified oANG is a monomer in solution. The circular dichroism spectrum of E. coli-expressed recombinant oANG was similar to that of oANG expressed in CHO cells. Differential scanning fluorimetry showed that both preparations undergo a two-state transition during thermal denaturation, and the melting temperatures of recombinant oANG expressed in E. coli and CHO cells were 49.4 ± 0.16 °C and 51.6 ± 0.19 °C, respectively. The K_m values of both oANG preparations were similar; the k_cat value of E. coli-expressed recombinant oANG was slightly higher than that of CHO-expressed oANG.

Conclusions

Recombinant oANG expressed in E. coli functions as a human renin substrate. This study presents an E. coli-based system for the rapid production of milligram quantities of a human renin substrate, which will be useful for both fundamental and clinical studies on renin and hypertension.

Electronic supplementary material

The online version of this article (doi:10.1186/s12896-016-0265-x) contains supplementary material, which is available to authorized users.

Crystal structures and ligand binding of PurM proteins from Thermus thermophilus and Geobacillus kaustophilus

Crystal structures of 5-aminoimidazole ribonucleotide (AIR) synthetase, also known as PurM, from Thermus thermophilus (Tt) and Geobacillus kaustophilus (Gk) were determined. For TtPurM, the maximum resolution was 2.2 Å and the space group was P21212 with four dimers in an asymmetric unit. For GkPurM, the maximum resolution was 2.2 Å and the space group was P21212 with one monomer in asymmetric unit. The biological unit is dimer for both TtPurM and GkPurM and the dimer structures were similar to previously determined structures of PurM in general. For TtPurM, ∼50 residues at the amino terminal were disordered in the crystal structure whereas, for GkPurM, the corresponding region covered the ATP-binding site forming an α helix in part, suggesting that the N-terminal region of PurM changes its conformation upon binding of ligands. FGAM binding site was predicted by the docking simulation followed by the MD simulation based on the SO4 (2-) binding site found in the crystal structure of TtPurM.

Crystal structure analysis of ornithine transcarbamylase from Thermus thermophilus --HB8 provides insights on the plasticity of the active site

The enzymatic biosynthesis of L-arginine involves complex, sequential action of many enzymes and ornithine transcarbamylase (OTCase) is one of the essential enzymes in the pathway. In mammals OTCase is part of the urea cycle. Arginine is used in a variety of pharmaceutical and industrial applications and therefore engineering arginine biosynthesis pathway for overproduction of arginine has gained importance. On the other hand, it was found that detrimental mutations in the human OTCase gene resulted clinical hyperammonemia, with subsequent neurological damage. Therefore a better understanding of the structure-function relationship of this enzyme from various sources could be useful for modifying its enzymatic action. Here we report the structure of ornithine transcarbamylase of Thermus thermophilus HB8 (aTtOTCase) at 2.0 Å resolution. On comparison with its homologs, aTtOTCase showed maximum variation at the substrate binding loops namely 80s and SMG/240s loops. The active site geometry of aTtOTCase is unique among its homologs where the side chain of certain residues (Leu57, Arg58 and Arg288) is oriented differently. To study the structural insights of substrate binding in aTtOTCase, docking of carbamoyl phosphate (CP) and ornithine (Orn) was carried out sequentially. Both substrates were unable to bind in a proper orientation in the active site pocket and this could be due to the differently oriented side chains. This suggests that the active site geometry should also undergo fine tuning besides the large structural changes as the enzyme switches from completely open to a substrate bound closed state.

Roles of Mn-catalase and a possible heme peroxidase homologue in protection from oxidative stress in Thermus thermophilus

Hydrogen peroxide (H2O2) produces hydroxyl radicals that directly attack a variety of biomolecules and cause severe cellular dysfunction. An extremely thermophilic bacterium, Thermus thermophilus HB8, possesses at least three enzymes that can scavenge H2O2: manganese-containing catalase (TTHA0122, MnCAT), a possible peroxiredoxin homologue (TTHA1300), and a possible heme peroxidase (HPX) homologue (TTHA1714). To investigate the roles of these proteins, we attempted to disrupt each of these genes in T. thermophilus HB8. Although we were able to completely disrupt ttha1300, we were unable to completely delete ttha0122 and ttha1714 because of polyploidy. Quantitative real-time PCR showed that, compared to the wild type, 31 % of ttha0122 and 11 % of ttha1714 remained in the ∆ttha0122 and ∆ttha1714 disruption mutants, respectively. Mutants with reduced levels of ttha0122 or ttha1714 exhibited a significant increase in spontaneous mutation frequency. ∆ttha1714 grew slower than the wild type under normal conditions. ∆ttha0122 grew very poorly after exposure to H2O2. Moreover, ∆ttha0122 did not show H2O2-scavenging activity, whereas ∆ttha1300 and ∆ttha1714 scavenged H2O2, a property similar to that exhibited by the wild type. MnCAT purified from T. thermophilus HB8 cells scavenged H2O2 in vitro. The recombinant form of the possible HPX homologue, reconstituted with hemin, showed peroxidase activity with H2O2 as an oxidant substrate. Based on these results, we propose that not only MnCAT but also the possible HPX homologue is involved in protecting the cell from oxidative stress in T. thermophilus.

Differential diagnosis of vertical root fractures using reconstructed three-dimensional models of bone defects

OBJECTIVES

The purpose of this study was to evaluate the accuracy of diagnosing vertical root fractures (VRFs) by comparing the volume of bone defects in VRFs with those in non-VRFs on reconstructed three-dimensional (3D) models (TDMs) using CBCT.

METHODS

32 maxillary pre-molars and anterior teeth with radiolucent areas were evaluated on pre-operative CBCT images. Of the 32 teeth, 16 had a fractured root (VRF group) and 16 had a non-fractured root (non-VRF group). The radiolucent area of each tooth was traced in each dimension [mesiodistal, buccolingual and horizontal (the apicoincisal aspect)] by two observers, and 3D images were reconstructed with the Amira(®) software (Visage Imaging Inc., Richmond, Australia). The volume, V, of the TDM was divided into the coronal side and the periapical side at the horizontal slice through the apical foramen, and v was defined as the volume of the coronal side. The values of v/V were calculated for all cases. The Mann-Whitney U test was used to compare values between the VRF group and the non-VRF group (p < 0.05). A receiver operating characteristic (ROC) curve was constructed to select the optimal cut-point.

RESULTS

There was a statistically significant difference in the value of v/V between the two groups (p < 0.05). With a cut-point derived from the ROC curve, and the sensitivity, specificity and accuracy of predicting the VRFs were 1.00, 0.75 and 0.88, respectively.

CONCLUSIONS

Lesions resulting from VRFs can be distinguished from those of non-VRFs on 3D CBCT images with a high degree of accuracy, based on their different 3D shapes.

Intracellular retention of the extracellular domain of the (pro)renin receptor in mammalian cells

As a component of the renin-angiotensin system, the (pro)renin receptor [(P)RR] activates prorenin along with intracellular signaling pathways. In this study, the glutathione S-transferase-fused extracellular domain of (P)RR expressed in mammalian cells was recovered in the detergent phase in detergent-based two-phase separation experiments, and intracellular localization was observed by immunocytochemistry, suggesting retention inside the cell through stable membrane association.

Participation of the extracellular domain in (pro)renin receptor dimerization

The (pro)renin receptor [(P)RR] induces the catalytic activation of prorenin, as well as the activation of the mitogen-activated protein kinase (MAPK) signaling pathway; as such, it plays an important regulatory role in the renin-angiotensin system. (P)RR is known to form a homodimer, but the region participating in its dimerization is unknown. Using glutathione S-transferase (GST) as a carrier protein and a GST pull-down assay, we investigated the interaction of several (P)RR constructs with full-length (FL) (P)RR in mammalian cells. GST fusion proteins with FL (P)RR (GST-FL), the C-terminal M8-9 fragment (GST-M8-9), the extracellular domain (ECD) of (P)RR (GST-ECD), and the (P)RR ECD with a deletion of 32 amino acids encoded by exon 4 (GST-ECDd4) were retained intracellularly, whereas GST alone was efficiently secreted into the culture medium when transiently expressed in COS-7 cells. Immunofluorescence microscopy showed prominent localization of GST-ECD to the endoplasmic reticulum. The GST pull-down analysis revealed that GST-FL, GST-ECD, and GST-ECDd4 bound FLAG-tagged FL (P)RR, whereas GST-M8-9 showed little or no binding when transiently co-expressed in HEK293T cells. Furthermore, pull-down analysis using His-tag affinity resin showed co-precipitation of soluble (P)RR with FL (P)RR from a stable CHO cell line expressing FL h(P)RR with a C-terminal decahistidine tag. These results indicate that the (P)RR ECD participates in dimerization.

Abstract 422: Extracellular Domain of the (Pro)renin Receptor Participates in Dimerization

The (pro)renin receptor [(P)RR] is a single transmembrane protein with a large N-terminal extracellular domain and a short C-terminal cytoplasmic domain. Three molecular forms of (P)RR are known: a full-length form, a C-terminal truncated soluble form [s(P)RR], and an N-terminal truncated transmembrane form (M8-9 fragment). It has been reported that (P)RR forms homodimer, but the region participating in dimerization is unknown. Here we report that the extracellular domain of (P)RR participate in dimerization. Using secretory glutathione S-transferase (GST) as a fusion tag, we developed an in vivo pull-down assay to investigate (P)RR dimerization in the cell. GST-tagged extracellular domain (amino acid residues 17-304) of human (P)RR [GST-ECD], as well as full-length (P)RR [GST-Full] and M8-9 fragment [GST-M8-9], was retained in the cell, while GST alone was efficiently secreted into the culture medium when transiently expressed in COS-7 cells. Consistent with this observation, immunofluorescence microscopy showed prominent localization of GST-ECD to the ER. In vivo GST pull-down experiments revealed that GST-ECD as well as GST-Full bound FLAG-tagged full-length (P)RR, whereas GST-M8-9 bound it little, if any, when transiently coexpressed in HEK293T cells. To investigate whether s(P)RR can form heterodimer with full-length (P)RR, we established a CHO cell line stably expressing human (P)RR with C-terminal 10His-tag. All three forms of (P)RR were detected in the cell lysate and only s(P)RR was detected in the culture medium. Full-length (P)RR and s(P)RR were prominently localized to the ER as observed by immunofluorescence microscopy. Pull down experiment using His-tag affinity resin showed coprecipitation of s(P)RR with full-length (P)RR. These results indicate that the extracellular domain of (P)RR participates in dimerization.

Integrated database of information from structural genomics experiments

Information from structural genomics experiments at the RIKEN SPring-8 Center, Japan has been compiled and published as an integrated database. The contents of the database are (i) experimental data from nine species of bacteria that cover a large variety of protein molecules in terms of both evolution and properties (http://database.riken.jp/db/bacpedia), (ii) experimental data from mutant proteins that were designed systematically to study the influence of mutations on the diffraction quality of protein crystals (http://database.riken.jp/db/bacpedia) and (iii) experimental data from heavy-atom-labelled proteins from the heavy-atom database HATODAS (http://database.riken.jp/db/hatodas). The database integration adopts the semantic web, which is suitable for data reuse and automatic processing, thereby allowing batch downloads of full data and data reconstruction to produce new databases. In addition, to enhance the use of data (i) and (ii) by general researchers in biosciences, a comprehensible user interface, Bacpedia (http://bacpedia.harima.riken.jp), has been developed.

(Pro)renin receptor and prorenin: their plausible sites of interaction

Before discovery of (pro)renin receptor, prorenin was regarded as a source of renin and probable diagnostic marker for diabetic nephropathy/Wilms' tumor. It is now considered that prorenin can perform renin activity by binding to (P)RR and binding mechanism of (pro)renin to (P)RR was indicated in many in vitro studies. Considering the physiological importance and pathological involvement of (P)RR, it is indeed a demand of time to determine the three dimensional structure of (P)RR to design (P)RR blocker(s) effective for (pro)renin. It may also facilitate to explain the incompatible data about the effective application of decoy peptide as (P)RR blocker. So far, studies have discussed the bindings of (pro)renin to (P)RR using peptides mimicking the structures of ligands (e.g., the decoy including "handle" region peptide, the "hinge" peptide etc). In this review, the binding mechanism of ligands has been highlighted from the structural aspect of (P)RR using several anti-(P)RR antibodies designed from the primary structure of (pro)renin receptor. Therefore, this review would give us a clue regarding the plausible binding region(s) for prorenin in the (P)RR.

Towards three-dimensional structural analysis of (pro)renin receptor

The (pro)renin receptor is a single-spanning membrane protein that binds both renin and its inactive precursor prorenin. The receptor binding enhances the catalytic activity of renin and induces non-proteolytic activation of prorenin as well as triggers intracellular signaling with either renin or prorenin as a ligand. Three-dimensional structural information of (pro)renin receptor is important to understand the receptor binding. This information is not available due to the lack of its three-dimensional structure. In this review, we summarize the binding properties of (pro)renin receptor, provide the results of structure prediction and point out the issues to be tackled towards three-dimensional structural analysis of this receptor.

Initial fibroblast attachment to Erbium:YAG laser-irradiated dentine

AIMS

To evaluate the effects of Erbium (Er):YAG laser irradiation on the morphology of resected dentine surfaces, and to investigate fibroblast attachment to laser-irradiated dentine surfaces.

METHODOLOGY

Dentine blocks obtained from single-rooted human teeth were divided into the following groups after sterilization in an autoclave: (i) Laser group treated with Er:YAG laser irradiation (30 mJ per pulse, 10 pps, 60 s); (ii) L-MTAD group treated with laser irradiation as in (i) plus a mixture of doxycycline, tetracycline isomer and citric acid; (iii) RC-Prep group treated with EDTA gel or cream (RC-Prep) and (iv) Control group left untreated. After each treatment, the dentine blocks were incubated with NIH/3T3 fibroblasts cultured to subconfluency in Dulbecco's modified Eagle's medium supplemented with 10% foetal bovine serum and antibiotics. The number of attached cells amongst the groups was analysed statistically at the 5% significance level. The dentine surface morphologies and cell attachments were evaluated by counting assays, histological observations and scanning electron microscopy (SEM).

RESULTS

The number of attached cells was significantly higher (P < 0.05) in the Laser group than in the RC-Prep and Control groups at 16 h. Dendritic cell extension of the fibroblasts was only observed in the Laser group at 8 h by SEM. In the histological analyses, significantly more attached cells were found on the dentine surfaces treated with laser irradiation.

CONCLUSIONS

Er:YAG laser irradiation induced morphological alterations in dentine surfaces, which may improve the attachment of fibroblasts to dentine.

Crystal structure of the tandem-type universal stress protein TTHA0350 from Thermus thermophilus HB8

The genome sequence of an extremely thermophilic bacterium, Thermus thermophilus HB8, revealed that TTHA0350 is a tandem-type universal stress protein (Usp) consisting of two Usp domains. Usp proteins, which are characterized by a conserved domain consisting of 130-160 amino acids, are inducibly expressed under a large number of stress conditions. The N-terminal domain of TTHA0350 contains a motif similar to the consensus ATP-binding one (G-2 x-G-9x-G-(S/T)), but the C-terminal one seems to lack the consensus motif. In order to determine its structural properties, we determined the crystal structures of TTHA0350 in the unliganded form and TTHA0350•2ATP at 2.50 and 1.70 Å resolution, respectively. This is the first structure determination of a Usp family protein in both unliganded and ATP-liganded forms. TTHA0350 is folded into a fan-shaped structure which is similar to that of tandem-type Usp protein Rv2623 from Mycobacterium tuberculosis. However, the dimer assembly with C2-symmetry in TTHA0350 is quite different from that with D2-symmetry in Rv2623. The X-ray structure showed that not only the N-terminal but also the C-terminal domain binds one ATP, although the ATP-binding motif could not be detected in the C-terminal domain. The loop interacting with ATP in the C-terminal domain is in a conformation quite different from that in the N-terminal domain.

Qualitative and quantitative analyses of (pro)renin receptor in the medium of cultured human umbilical vein endothelial cells

A 30-kDa protein in the medium of cultured human umbilical vein endothelial cells (HUVECs) was identified as (pro)renin receptor, (P)RR, by western blot analysis using anti-human (P)RR antibodies. The protein bound recombinant human prorenin with a K(D) of 4.0 nmol l(-1) and activated prorenin. These observations suggest the presence of soluble (P)RR, s(P)RR, in the medium of cultured HUVECs. For quantification of the s(P)RR in the medium, an enzyme-linked immunosorbent assay (ELISA) was established. The quantitative range of the ELISA was validated over a nominal range of 7.5-300 pmol l(-1) in the wells of a microtiter plate. The assay system showed good linearity (r(2)=0.99) with interassay (5.8-9.7%) and intraassay (2.1-7.0%) precision. Using this method, the concentration of s(P)RR in the culture medium of HUVECs was measured to be 32 pmol l(-1). Therefore, these results show qualitative and quantitative evidence that prorenin can be activated after binding to s(P)RR secreted from cultured HUVECs.

Crystal structures of glycinamide ribonucleotide synthetase, PurD, from thermophilic eubacteria

Glycinamide ribonucleotide synthetase (GAR-syn, PurD) catalyses the second reaction of the purine biosynthetic pathway; the conversion of phosphoribosylamine, glycine and ATP to glycinamide ribonucleotide (GAR), ADP and Pi. In the present study, crystal structures of GAR-syn's from Thermus thermophilus, Geobacillus kaustophilus and Aquifex aeolicus were determined in apo forms. Crystal structures in ligand-bound forms were also determined for G. kaustophilus and A. aeolicus proteins. In general, overall structures of GAR-syn's are similar to each other. However, the orientations of the B domains are varied among GAR-syn's and the MD simulation suggested the mobility of the B domain. Furthermore, it was demonstrated that the B loop in the B domain fixes the position of the β- and γ- phosphate groups of the bound ATP. The structures of GAR-syn's and the bound ligands were compared with each other in detail, and structures of GAR-syn's with full ligands, as well as the possible reaction mechanism, were proposed.

Structures of hypoxanthine-guanine phosphoribosyltransferase (TTHA0220) from Thermus thermophilus HB8

Hypoxanthine-guanine phosphoribosyltransferase (HGPRTase), which is a key enzyme in the purine-salvage pathway, catalyzes the synthesis of IMP or GMP from alpha-D-phosphoribosyl-1-pyrophosphate and hypoxanthine or guanine, respectively. Structures of HGPRTase from Thermus thermophilus HB8 in the unliganded form, in complex with IMP and in complex with GMP have been determined at 2.1, 1.9 and 2.2 A resolution, respectively. The overall fold of the IMP complex was similar to that of the unliganded form, but the main-chain and side-chain atoms of the active site moved to accommodate IMP. The overall folds of the IMP and GMP complexes were almost identical to each other. Structural comparison of the T. thermophilus HB8 enzyme with 6-oxopurine PRTases for which structures have been determined showed that these enzymes can be tentatively divided into groups I and II and that the T. thermophilus HB8 enzyme belongs to group I. The group II enzymes are characterized by an N-terminal extension with additional secondary elements and a long loop connecting the second alpha-helix and beta-strand compared with the group I enzymes.