High-yield expression,purification, characterization,and structure determination of tag-free <Emphasis Type="Italic">Candida utilis</Emphasis> uricase

We report the successful high-yield expression of Candida utilis uricase in Escherichia coli and the establishment of an efficient three-step protein purification protocol. The purity of the recombinant protein, which was confirmed to be C. utilis uricase by sodium dodecyl sulfate–polyacrylamide gel electrophoresis and matrix-assisted laser desorption/ionization time-of-flight mass spectrometer analysis, was >98% and the specific activity was 38.4 IU/mg. Crystals of C. utilis uricase were grown at 18°C using 25% polyethylene glycol 3350 as precipitant. Diffraction by the crystals extends to 1.93 Å resolution, and the crystals belong to the space group P2₁2₁2₁ with unit cell parameters a?=?69.16 Å, b?=?139.31 Å, c?=?256.33 Å, and α?=?β?=?γ?=?90°. The crystal structure of C. utilis uricase shares a high similarity with other reported structures of the homologous uricases from other species in protein database, demonstrating that the three-dimensional structure of the protein defines critically to the catalytic activities.     

Three-Dimensional Structure of Recombinant Adenine Phosphoribosyltransferase from Thermophilic Bacterial Strain <Emphasis Type="Italic">Thermus thermophilus</Emphasis> HB27

Adenine phosphoribosyltransferase (APRT) from a thermophilic bacterial strain Thermus thermophilus НВ27 (TthHB27APRT) belongs to the family of type I phosphoribosyltransferases and catalyzes the magnesium-dependent transfer of 5'-phosphoribosyl group from 5'-phosphoribosylpyrophosphate to N9 adenine nitrogen with formation of adenosine-5'-monophosphate and pyrophosphate. The crystals of the recombinant enzyme suitable for X-ray study were grown in a capillary using the counter-diffusion technique. Crystals with unit-cell parameters α = 69.860 Å, b = 82.160 Å, c = 91.390 Å, α = 90.00°, β = 102.58°, and γ = 90.00° belong to the space group Р2₁ and contain six enzyme monomers in the asymmetric unit. The set of X-ray data from grown crystals was collected on a Spring-8 synchrotron radiation facility (Japan) and three-dimensional structure of the enzyme was solved at 2.7-Å resolution by molecular replacement method using the BALBES software. The polypeptide fold in the enzyme monomer and the structure of biologically active dimer were described. Based on the comparison with structures of homologous APRTs from a thermophilic strain ThtHB8 and Homo sapiens, positions of active site and a number of functionally important amino acids were located.     

Crystal structure and mode of action of a class V chitinase from <Emphasis Type="Italic">Nicotiana tabacum</Emphasis>

A class V chitinase from Nicotiana tabacum (NtChiV) with amino acid sequence similar to that of Serratia marcescens chitinase B (SmChiB) was expressed in E. coli and purified to homogeneity. When N-acetylglucosamine oligosaccharides [(NAG)_n] were hydrolyzed by the purified NtChiV, the second glycosidic linkage from the non-reducing end was predominantly hydrolyzed in a manner similar to that of SmChiB. NtChiV was shown to hydrolyze partially N-acetylated chitosan non-processively, whereas SmChiB hydrolyzes the same substrate processively. The crystal structure of NtChiV was determined by the single-wavelength anomalous dispersion method at 1.2 Å resolution. The protein adopts a classical (β/α)₈-barrel fold (residues 1–233 and 303–348) with an insertion of a small (α + β) domain (residues 234–302). This is the first crystal structure of a plant class V chitinase. The crystal structure of the inactive mutant NtChiV E115Q complexed with (NAG)₄ was also solved and exhibited a linear conformation of the bound oligosaccharide occupying ?2, +1, +2, and +3 subsites. The complex structure corresponds to an initial state of (NAG)₄ binding, which is proposed to be converted into a bent conformation through sliding of the +1, +2, and +3 sugar units to ?1, +1, and +2 subsites. Although NtChiV is similar to SmChiB, the chitin-binding domain is present in the C-terminus of the latter, but not in the former. Aromatic amino acid residues found in the substrate binding cleft of SmChiB, including Trp97, are substituted with aliphatic residues in NtChiV. These structural differences appear to be responsible for NtChiV being a non-processive enzyme.     

Purification,crystallization, and preliminary X-ray crystallographic analysis of the Group III chaperonin from <Emphasis Type="Italic">Carboxydothermus hydrogenoformans</Emphasis>

Chaperonins (CPNs) are megadalton sized ATP-dependent nanomachines that facilitate protein folding through complex cycles of complex allosteric articulation. They consist of two back-to-back stacked multisubunit rings. CPNs are usually classified into Group I and Group II. Here, we report the crystallization of both the AMPPNP (an ATP analogue) and ADP bound forms of a novel CPN, classified as belonging to a third Group, recently discovered in the extreme thermophile Carboxydothermus hydrogenoformans. Crystals of the two forms were grown by the vapor batch crystallization method at 295 K. Crystals of the Ch-CPN/AMPPNP complex diffracted to 3.0 Å resolution and belonged to the space group P422, with unit-cell parameters a = b = 186.166, c = 160.742 Å. Assuming the presence of four molecules in the asymmetric unit, the solvent content was estimated to be about 60.02%. Crystals of the Ch-CPN/ADP complex diffracted to 4.0 Å resolution and belonged to the space group P42₁2, with unit-cell parameters a = b = 209.780, c = 169.813Å. Assuming the presence of four molecules in the asymmetric unit, the solvent content was estimated to be about 70.19%.     

Crystal structure of the ferritin from the hyperthermophilic archaeal anaerobe <Emphasis Type="Italic">Pyrococcus furiosus</Emphasis>

The crystal structure of the ferritin from the archaeon, hyperthermophile and anaerobe Pyrococcus furiosus (PfFtn) is presented. While many ferritin structures from bacteria to mammals have been reported, until now only one was available from archaea, the ferritin from Archaeoglobus fulgidus (AfFtn). The PfFtn 24-mer exhibits the 432 point-group symmetry that is characteristic of most ferritins, which suggests that the 23 symmetry found in the previously reported AfFtn is not a common feature of archaeal ferritins. Consequently, the four large pores that were found in AfFtn are not present in PfFtn. The structure has been solved by molecular replacement and refined at 2.75-Å resolution to R = 0.195 and R _free = 0.247. The ferroxidase center of the aerobically crystallized ferritin contains one iron at site A and shows sites B and C only upon iron or zinc soaking. Electron paramagnetic resonance studies suggest this iron depletion of the native ferroxidase center to be a result of a complexation of iron by the crystallization salt. The extreme thermostability of PfFtn is compared with that of eight structurally similar ferritins and is proposed to originate mostly from the observed high number of intrasubunit hydrogen bonds. A preservation of the monomer fold, rather than the 24-mer assembly, appears to be the most important factor that protects the ferritin from inactivation by heat.     

Hybrid peony (<Emphasis Type="Italic">Paeonia hybrida</Emphasis> Pall.), a rare endangered plant of Bashkir Trans-Uralian region: Autocorrelation analysis of the spatial genotype distribution under different environmental conditions

Hybrid peony (Paeonia hybrida Pall.) is listed as endangered in Russian Federation (since 1988) and in several regions of Russia. The structure of the isolated population from Bashkir Trans-Uralian region, separated by 1500 km from the main geographic range of this species, has been studied using isoenzyme markers from 11 loci. The population is split between two geographical locations, both characterized by a relatively high genetic diversity (mean allele number A = 1.9±0.3, percentage of polymorphic loci P = 0.54, observed heterozigosity H _O = 0.223±0.068, expected heterozigosity H _E = 0.229±0.067) and a quite low intergroup genetic differentiation (fixation index F _ST = 0.008, Nei’s genetic distance D = 0.011). In a subpopulation located near a swampy lake in dense cereal grass and steppe shrubby vegetation, autocorrelation analysis has revealed spatial structuring of genetic variability. In the other location, a stipa-forb steppe on a flat hill slope, a uniform spatial structure of the genotypes has been observed. The results are discussed with respect to the ecological characteristics of the species and the conservation of the genetic pool of the population in situ and ex situ.     

Crystal Structure of the Protein <Emphasis Type="SmallCaps">l</Emphasis>-Isoaspartyl Methyltransferase from <Emphasis Type="Italic">Escherichia coli</Emphasis>

Among the known covalent damages that can occur spontaneously to proteins, the formation of isoaspartyl linkages through deamidation of asparagines and isomerization of aspartates may be one of the most rapid forms under conditions of physiological pH and temperature. The protein l-isoaspartyl methyltransferase (PIMT) is thought to recognize l-isoaspartyl residues and repair this kind of damaged proteins. Curiously, there is a potential functional difference between bacterial and mammalian PIMTs. Herein, we present the crystal structure of Escherichia coli PIMT (EcPIMT) at a resolution of 1.8 Å. The enzyme we investigated was able to remain bound to its product S-adenosylhomocysteine (SAH) during crystallization. Analysis indicates that the high affinity of EcPIMT for SAH might lead to the lower activity of the enzyme.     

Structure of trichosanthin at 1.88 Å resolution

Trichosanthin (TCS) is one of the single chain ribosome-inactivating proteins (RIPs). The crystals of the orthorhombic form of trichosanthin have been obtained from a citrate buffer (pH 5.4) with KC1 as the precipitant. The crystal belongs to the space group P2₁2₁2₁ with a = 38.31, b = 76.22, c = 79.21 Å. The structure was solved by molecular replacement method and refined using the programs XPLOR and PROLSQ to an R-factor of 0.191 for the reflections within the 6–1.88 Å resolution range. The bond length and bond angle in the protein molecule have root-mean-square deviations from ideal value of 0.013 Å and 3.3°, respectively. The refined model includes 247 residues and 197 water molecules. The TCS molecule consists of two structural domains. The large domain contains six α-helices, a six stranded sheet, and an antiparallel β-sheet. The small domain has a largest α-helix, which shows a distinct bend. The possible active site of the molecule located on the cleft between two domains was proposed. In the active site Arg-163 and Glu-160, Glu-189 and Arg-122 form two ion pairs, Glu-189 and Gln-156 are hydrogen bonded to each other. Three water molecules are bonded to the residues in the active site region. The structures of TCS molecule and ricin A-chain (RTA) superimpose quite well, showing that the structures of the two protein molecules are homologous. Comparison of the structures of the TCS molecule in this orthorhombic crystal with that in the monoclinic crystal indicates that there are no essential differences of the structures between the two protein crystals. © 1994 Wiley-Liss, Inc.     

First molecular detection of <Emphasis Type="Italic">Anaplasma phagocytophilum</Emphasis> in the hard tick <Emphasis Type="Italic">Rhipicephalus haemaphysaloides</Emphasis> in Taiwan

Anaplasma phagocytophilum is transmitted mainly by hard ticks and can cause potentially fatal granulocytic anaplasmosis in humans, but its occurrence in ticks in Taiwan has never been investigated although this pathogen has been detected in Taiwanese rodents before. Ticks collected from small mammals in Hualien, eastern Taiwan, were assayed for Anaplasma infections; infections of Rickettsia and Apicomplexa protozoans were also studied. Of the 270 individually assayed Rhipicephalus haemaphysaloides ticks, A. phagocytophilum was identified in a nymphal tick. Parasites most similar to Anaplasma bovis, Rickettsia rickettsii, Rickettsia sp. TwKM01, and at least seven apicomplexan species (including genera Cryptosporidium, Hepatozoon, and Theileria) were also identified. This study shows that A. phagocytophilum does occur in the hard tick in Taiwan, although whether R. haemaphysaloides can vector this pathogen remains to be determined. This work also reveals a high diversity of tick-borne bacteria and protozoans circulating in a small region and calls for further research on their potential risks for human health.     

An improved method of DNA purification from secondary metabolites rich medicinal plants using certain chaotropic agents

The presented work describes good quality DNA isolation method from mature leaves of some medicinally important plant species, viz. Asparagus racemosus, Withania somnifera, Abrus precatorius, Commiphora wightii and Carissa carandas. These plants hold immense medicinal values due to presence of certain secondary metabolites like polyphenols, terpenes, flavonoids, alkaloids, gums, resins, etc. Although these metabolites are accountable for important medicinal properties and authorize these plants to precedence over others, the same compounds disappoint the researcher while isolating high quality DNA. To overcome this problem, we propose a simple method in which DNA is adroitly bounded to diatomaceous earth in a solution of different chaotropic agent and alienated from intrusive compounds. Presented method affirms that secondary products, along with polysaccharides and proteins, can be perceptibly reduced by using silica matrix along with chaotropic agents. The described method is fast, simple and highly reliable for the isolation of DNA from obstinate plant species.     

Pelagic larval dispersal habits influence the population genetic structure of clam <Emphasis Type="Italic">Gomphina aequilatera</Emphasis> in China

Pelagic larval dispersal habits influence the population genetic structure of marine mollusk organisms via gene flow. The genetic information of the clam Gomphina aequilatera (short larval stage, 10 days) which is ecologically and economically important in the China coast is unknown. To determine the influence of planktonic larval duration on the genetic structure of G. aequilatera. Mitochondrial markers, cytochrome oxidase subunit i (COI) and 12S ribosomal RNA (12S rRNA), were used to investigate the population structure of wild G. aequilatera specimens from four China Sea coastal locations (Zhoushan, Nanji Island, Zhangpu and Beihai). Partial COI (685 bp) and 12S rRNA (350 bp) sequences were determined. High level and significant F_ST values were obtained among the different localities, based on either COI (F_ST?=?0.100–0.444, P?<?0.05) or 12S rRNA (F_ST?=?0.193–0.742, P?<?0.05), indicating a high degree of genetic differentiation among the populations. The pairwise N_m between Beihai and Zhoushan for COI was 0.626 and the other four pairwise N_m values were >?1, indicating extensive gene flow among them. The 12S rRNA showed the same pattern. AMOVA test results for COI and 12S rRNA indicated major genetic variation within the populations: 77.96% within and 22.04% among the populations for COI, 55.73% within and 44.27% among the populations for 12S rRNA. A median-joining network suggested obvious genetic differentiation between the Zhoushan and Beihai populations. This study revealed the extant population genetic structure of G. aequilatera and showed a strong population structure in a species with a short planktonic larval stage.     

A class V chitinase from <Emphasis Type="Italic">Arabidopsis thaliana</Emphasis>: gene responses,enzymatic properties,and crystallographic analysis

Expression of a class V chitinase gene (At4g19810, AtChiC) in Arabidopsis thaliana was examined by quantitative real-time PCR and by analyzing microarray data available at Genevestigator. The gene expression was induced by the plant stress-related hormones abscisic acid (ABA) and jasmonic acid (JA) and by the stress resulting from the elicitor flagellin, NaCl, and osmosis. The recombinant AtChiC protein was produced in E. coli, purified, and characterized with respect to the structure and function. The recombinant AtChiC hydrolyzed N-acetylglucosamine oligomers producing dimers from the non-reducing end of the substrates. The crystal structure of AtChiC was determined by the molecular replacement method at 2.0 Å resolution. AtChiC was found to adopt an (β/α)₈ fold with a small insertion domain composed of an α-helix and a five-stranded β-sheet. From docking simulation of AtChiC with pentameric substrate, the amino acid residues responsible for substrate binding were found to be well conserved when compared with those of the class V chitinase from Nicotiana tabacum (NtChiV). All of the structural and functional properties of AtChiC are quite similar to those obtained for NtChiV, and seem to be common to class V chitinases from higher plants.     

Bacterial metabolites from intra- and inter-species influencing thermotolerance: the case of <Emphasis Type="Italic">Bacillus cereus</Emphasis> and <Emphasis Type="Italic">Geobacillus stearothermophilus</Emphasis>

Bacterial metabolites with communicative functions could provide protection against stress conditions to members of the same species. Yet, information remains limited about protection provided by metabolites in Bacillus cereus and inter-species. This study investigated the effect of extracellular compounds derived from heat shocked (HS) and non-HS cultures of B. cereus and Geobacillus stearothermophilus on the thermotolerance of non-HS vegetative and sporulating B. cereus. Cultures of B. cereus and G. stearothermophilus were subjected to HS (42 or 65 °C respectively for 30 min) or non-HS treatments. Cells and supernatants were separated, mixed in a combined array, and then exposed to 50 °C for 60 min and viable cells determined. For spores, D values (85 and 95 °C) were evaluated after 120 h. In most cases, supernatants from HS B. cereus cultures added to non-HS B. cereus cells caused their thermotolerance to increase (D ₅₀ 12.2–51.9) when compared to supernatants from non-HS cultures (D ₅₀ 7.4–21.7). While the addition of supernatants from HS and non-HS G. stearothermophilus cultures caused the thermotolerance of non-HS cells from B. cereus to decrease initially (D ₅₀ 3.7–7.1), a subsequent increase was detected in most cases (D ₅₀ 18–97.7). In most cases, supernatants from sporulating G. stearothermophilus added to sporulating cells of B. cereus caused the thermotolerance of B. cereus 4810 spores to decline, whereas that of B. cereus 14579 increased. This study clearly shows that metabolites in supernatants from either the same or different species (such as G. stearothermophilus) influence the thermotolerance of B. cereus.     

The crystal structure of methanol dehydrogenase,a quinoprotein from the marine methylotrophic bacterium <Emphasis Type="Italic">Methylophaga aminisulfidivorans</Emphasis> MP<Superscript>T</Superscript>

The first crystal structure of a pyrroloquinoline quinone (PQQ)-dependent methanol dehydrogenase (MDH) from a marine methylotrophic bacterium, Methylophaga aminisulfidivorans MP^T (MDH_Mas), was determined at 1.7 Å resolution. The active form of MDH_Mas (or MDHI_Mas) is a heterotetrameric α₂β₂, where each β-subunit assembles on one side of each of the α-subunits, in a symmetrical fashion, so that two β-subunits surround the two PQQ-binding pockets on the α-subunits. The active site consists of a PQQ molecule surrounded by a β-propeller fold for each α-subunit. Interestingly, the PQQ molecules are coordinated by a Mg²⁺ ion, instead of the Ca²⁺ ion that is commonly found in the terrestrial MDHI, indicating the efficiency of osmotic balance regulation in the high salt environment. The overall interaction of the β-subunits with the α-subunits appears tighter than that of terrestrial homologues, suggesting the efficient maintenance of MDHI_Mas integrity in the sea water environment to provide a firm basis for complex formation with MxaJ_Mas or Cyt c_L. With the help of the features mentioned above, our research may enable the elucidation of the full molecular mechanism of methanol oxidation by taking advantage of marine bacterium-originated proteins in the methanol oxidizing system (mox), including MxaJ, as the attainment of these proteins from terrestrial bacteria for structural studies has not been successful.     

Cytotoxicity and Glycan-Binding Profile of a <Emphasis Type="SmallCaps">d</Emphasis>-Galactose-Binding Lectin from the Eggs of a Japanese Sea Hare (<Emphasis Type="Italic">Aplysia kurodai</Emphasis>)

A divalent cation-independent 16 kDa d-galactose binding lectin (AKL-2) was isolated from eggs of sea hare, Aplysia kurodai. The lectin recognized d-galactose and d-galacturonic acid and had a 32 kDa dimer consisting of two disulfide-bonded 16 kDa subunits. Eighteen N-terminus amino acids were identified by Edman degradation, having unique primary structure. Lectin blotting analysis with horseradish peroxidase-conjugated lectins has shown that AKL-2 was a glycoprotein with complex type oligosaccharides with N-acetyl d-glucosamine and mannose at non-reducing terminal. Two protein bands with 38 and 36 kDa in the crude extract of sea hare eggs after purification of the lectin was isolated by AKL-2-conjugated Sepharose column and elution with 0.1 M lactose containing buffer. It suggested that the lectin binds with an endogenous ligand in the eggs. AKL-2 kept extreme stability on haemagglutination activity if it was treated at pH 3 and 70 °C for 1 h. Glycan binding profile of AKL-2 by frontal affinity chromatography technology using 15 pyridylamine labeled oligosaccharides has been appeared that the lectin uniquely recognized globotriose (Galα1-4Galβ1-4Glc; Gb3) in addition to bi-antennary complex type N-linked oligosaccharides with N-acetyllactosamine. Surface plasmon resonance analysis of AKL-2 against a neo-glycoprotein, Gb3-human serum albumin showed the k _ass and k _diss values are 2.4 × 10³ M^?1 s^?1 and 3.8 × 10^?3 s^?1, respectively. AKL-2 appeared cytotoxicity against both Burkitt’s lymphoma Raji cell and erythroleukemia K562. The activity to Raji by the lectin was preferably cancelled by the co-presence of melibiose mimicing Gb3. On the other hand, K562 was cancelled effectively by lactose than melibiose. It elucidated that AKL-2 had cytotoxic ability mediated glycans structure to cultured cells.     

Development of leaffolder resistant transgenic rice expressing <Emphasis Type="Italic">cry2AX1</Emphasis> gene driven by green tissue-specific <Emphasis Type="Italic">rbcS</Emphasis> promoter

The insecticidal cry genes of Bacillus thuringiensis (Bt) have been successfully used for development of insect resistant transgenic rice plants. In this study, a novel cry2AX1 gene consisting a sequence of cry2Aa and cry2Ac gene driven by rice rbcS promoter was introduced into a rice cultivar, ASD16. Among 27 putative rice transformants, 20 plants were found to be positive for cry2AX1 gene. The expression of Cry2AX1 protein in transgenic rice plants ranged from 5.95 to 122.40 ng/g of fresh leaf tissue. Stable integration of the transgene was confirmed in putative transformants of rice by Southern blot hybridization analysis. Insect bioassay on T₀ transgenic rice plants against rice leaffolder (Cnaphalocrosis medinalis) recorded larval mortality up to 83.33 %. Stable inheritance and expression of cry2AX1 gene in T₁ progenies was demonstrated using Southern and ELISA. The detached leaf bit bioassay with selected T₁ plants showed 83.33–90.00 % mortality against C. medinalis. The whole plant bioassay for T₁ plants with rice leaffolder showed significant level of resistance even at a lower level of Cry2AX1 expression varying from 131 to 158 ng/g fresh leaf tissue during tillering stage.     

Reinterpretation of the electron density at the site of the eighth bacteriochlorophyll in the FMO protein from <Emphasis Type="Italic">Pelodictyon phaeum</Emphasis>

The Fenna–Matthews–Olson antenna protein from the green bacterium Pelodictyon phaeum mediates the energy transfer from a peripheral antenna complex to the membrane-bound reaction center. The three-dimensional structure of this protein has been previously modeled using X-ray diffraction to a resolution limit of 2.0 Å, with R _work and R _free values of 16.6 and 19.9 %, respectively (Larson et al., Photosynth Res 107:139–150, 2011). This model shows the protein as consisting of β-sheets surrounding several bacteriochlorophyll cofactors. While most of the model clearly matches the electron density maps, in this paper we re-examine the electron density for a specific feature, namely the eighth bacteriochlorophyll a cofactor. This electron density is now interpreted as arising primarily from the end of an otherwise disordered polyethylene glycol molecule. Additional electron density is present but the density is weak and cannot be unambiguously assigned. The new model has R _work and R _free values of 16.2 and 19.0 %, respectively.     

Crystal and solution structure of the C-terminal part of the <Emphasis Type="Italic">Methanocaldococcus jannaschii</Emphasis> A<Subscript>1</Subscript>A<Subscript>O</Subscript> ATP synthase subunit E revealed by X-ray diffraction and small-angle X-ray scattering

The structure of the C-terminus of subunit E (E_101–206) of Methanocaldococcus jannaschii A-ATP synthase was determined at 4.1 Å. E_101–206 consist of a N-terminal globular domain with three α-helices and four antiparallel β-strands and an α-helix at the very C-terminus. Comparison of M. jannaschii E_101–206 with the C-terminus E_81–198 subunit E from Pyrococcus horikoshii OT3 revealed that the kink in the C-terminal α-helix of E_81–198, involved in dimer formation, is absent in M. jannaschii E_101–206. Whereas a major dimeric surface interface is present between the P. horikoshii E_81–198 molecules in the asymmetric unit, no such interaction could be found in the M. jannaschii E_101–206 molecules. To verify the oligomeric behaviour, the low resolution structure of the recombinant E_85–206 from M. jannaschii was determined using small angle X-ray scattering. Rigid body modeling of two copies of one of the monomer established a fit with a tail to tail arrangement.