Extracellular nuclease from a thermophile, Streptomyces thermonitrificans: purification and characterization of the deoxyribonuclease activity

An extracellular nuclease from Streptomyces thermonitrificans (designated as nuclease Stn alpha) was purified to homogeneity with an overall yield of 2.8%. The Mr of the purified enzyme was 39.6 kDa. The purified enzyme showed an exclusive requirement of Mn2+ for its activity but is not a metalloprotein. The optimum pH for ds- and ssDNA hydrolysis were 7.0 and 7.5 whereas, the optimum temperature was 40 and 45 degrees C, respectively. The enzyme was inhibited by divalent cations, inorganic phosphate and pyrophosphate but not by 3' and 5' mononucleotides. Nuclease Stn alpha is a multifunctional enzyme and its substrate specificity is in the order of dsDNA>ssDNA>RNA. The end products of both ds- and ssDNA hydrolysis were predominantly oligonucleotides (80-85%) and a small amount of 3' mononucleotides (10-15%) suggesting an endo mode of action.     

Optimization of medium for extracellular nuclease formation from Rhizopus stolonifer

A strain of Rhizopus stolonifer produced a high activity of extracellular DNAase when grown on YPG (yeast extract peptone glucose) medium. The source of peptone had a marked effect on the enzyme yield and only one peptone (i.e. from Sarabhai M. Chemicals Ltd, India) supported enzyme production. Maximum enzyme activity (88 U/ml) was obtained after 4 days' growth under submerged conditions in YPG medium containing 100 M Mn²⁺, Co²⁺ or Mg²⁺, and glucose as the sole carbon source. The unpurified enzyme was optimally active at pH 7.5 and 45°C. It had a higher activity with sonicated and heat-denatured DNA than native DNA.     

Extracellular biosynthesis of silver nanoparticles using Rhizopus stolonifer

Synthesis of silver nanoparticles (AgNPs) has become a necessary field of applied science. Biological method for synthesis of AgNPs by Rhizopus stolonifer aqueous mycelial extract was used. The AgNPs were identified by UV–visible spectrometry, X-ray diffraction (XRD), transmission electron microscopy (TEM) and Fourier transform infrared spectrometry (FT-IR). The presence of surface plasmon band around 420 nm indicates AgNPs formation. The characteristic of the AgNPs within the face-centered cubic (fcc) structure are indicated by the peaks of the X-ray diffraction (XRD) pattern corresponding to (1 1 1), (2 0 0) and (2 2 0) planes. Spherical, mono-dispersed and stable AgNPs with diameter around 9.47 nm were prepared and affirmed by high-resolution transmission electron microscopy (HR-TEM). Fourier Transform Infrared (FTIR) shows peaks at 1426 and 1684 cm⁻¹ that affirm the presence of coat covering protein the AgNPs which is known as capping proteins. Parameter optimization showed the smallest size of AgNPs (2.86 ± 0.3 nm) was obtained with 10⁻² M AgNO₃ at 40 °C. The present study provides the proof that the molecules within aqueous mycelial extract of R. stolonifer facilitate synthesis of AgNPs and highlight on value-added from R. stolonifer for cost effectiveness. Also, eco-friendly medical and nanotechnology-based industries could also be provided. Size of prepared AgNPs could be controlled by temperature and AgNO₃ concentration. Further studies are required to study effect of more parameters on size and morphology of AgNPs as this will help in the control of large scale production of biogenic AgNPs.     

Extracellular Ribonuclease Production by Rhizopus stolonifer: Influence of Metal Ions

A strain of Rhizopus stolonifer produced high levels of extracellular ribonuclease (RNase) when grown on YPG (yeast extract, peptone, glucose) medium. Influence of various medium components on the production of extracellular RNase activity showed that divalent metal ions had a marked effect on growth and enzyme production. Maximum enzyme activity (3000 U/ml) was obtained in 5 days when the culture was grown in YPG medium containing Mg²⁺ (12 mM), Mn²⁺, and Fe²⁺ (2 ppm each). Inorganic phosphate, however, repressed enzyme production. Antibodies raised against the purified extracellular RNase were then used to establish the relationship between intra- and extracellular enzymes.     

Nuclease Rsn from Rhizopus stolonifer: specificity and mode of action

Nuclease Rsn from Rhizopus stolonifer catalyzes the hydrolysis of ss- and dsDNA in a ratio of approximately 2:1. Time course of 3' and 5' terminal analysis of the hydrolytic products of ss- and dsDNA showed that nuclease Rsn does not show any strict base preference and cleaves DNA in a non-specific manner. Moreover, separation of the hydrolytic products of ss- and dsDNA in the presence of Mg2+, Mn2+ or Co2+ showed the predominance of tetra-, tri-, and dinucleotides followed by mononucleotides, suggesting an endo mode of action.     

Elimination of double strand nuclease activity from S1 nuclease prepared from crude alpha amylase.

Single strand-specific s1 nuclease prepared as previously described from crude alpha amylase by DEAE-cellulose chromatography also contains nuclease which degrades double strand nucleic acid. The double strand activity can be removed by repeating the DEAE-cellulose chromatography procedure at least two additional times. S1 nuclease prepared by this procedure does not degrade double strand sheared DNA as measured by Sephadex chromatography. Under the same conditions single strand DNA is completely degraded. Thus, S1 nuclease prepared by this procedure is suitable for use in removing single strand regions in DNA/DNA duplexes and DNA/RNA hybrids.     

匍枝根霉组成型内切葡聚糖酶基因的筛选和表达

从匍枝根霉cDNA文库中筛选得到组成型内切葡聚糖酶基因（ zeg1和zeg2）,经比对zeg1和zeg2相似度为86％,有相似的催化活性区域,经CDD（保守序列数据库）分析,该蛋白归属于糖苷水解酶第5家族,对比PDB（蛋白结构数据库）中第五家族的关键催化残基,预测该两个蛋白的第147位的谷氨酸（ E）及199位的色氨酸（ W）为该蛋白的关键催化残基。重组zeg1发酵至20 h时达到最高酶活为0.422 IU/mL;重组zeg2发酵至24 h达到最高酶活为0.509 IU/mL。酶学性质研究表明重组zeg1和zeg2的最适温度均为50℃,最适pH值均为5.0。通过CMC-SDS-PAGE电泳,复性后染色,测得重组zeg1和zeg2的分子量分别约为55 kD和58 kD。     

Ultrastructural Details in Germinating Sporangiospores of Rhizopus stolonifer and Rhizopus arrhizus

Electron microscope examination of sporangiospore sections from Rhizopus stolonifer (Ehrenb. ex Fr.) Lind. and R. arrhizus Fischer revealed details on intracellular organization not previously reported. Aldehyde fixation followed by chromeosmium postfixation permitted clear depiction of ribosomes hitherto unrevealed in these cells. Mitochondria were diversiform. Spore wall structures in the two species were generally similar, but outer contours differed sufficiently to permit easy species identification in examination of sections. The spores of both species abounded in cytosomes, corresponding in size, shape, and heavy-metal "stain" affinities to spherosomes in cells of higher plants. The osmiophilic response of these spherosome-like inclusions was intensified by treatment of sections with thiocarbohydrazide solution and subsequent application of aqueous osmium tetroxide, which strengthens an assumption that they are lipid-rich. The margins of the spherosome-like inclusions in lead citrate-stained sections included dense particles, about 60 A across, whose crystalline-like arrangements suggested that protein as well as lipid was present. Frequent and close associations between the spherosome-like inclusions and various cell membranes suggested that such bodies participate in membrane elaboration during germination.     

Characteristics of Deoxyribonucleic Acid Polymerase Isolated from Spores of Rhizopus stolonifer

Deoxyribonucleic acid (DNA)-dependent DNA polymerase was purified several hundredfold from germinated and ungerminated spores of the fungus Rhizopus stolonifer. The partially purified enzymes from both spore stages exhibited identical characteristics; incorporation of [(3)H]deoxythymidine monophosphate into DNA required Mg(2+), DNA, a reducing agent, and the simultaneous presence of deoxyguanosine triphosphate, deoxycytidine triphosphate, and deoxyadenosine triphosphate. Heat-denatured and activated DNAs were better templates than were native DNAs. The buoyant density of the radioactive product of the reaction was similar to that of the template DNA. The enzyme is probably composed of a single polypeptide chain with an S value of 5.12 and an estimated molecular weight of 70,000 to 75,000. During the early stages of purification, the enzyme fraction from ungerminated spores required exogenous DNA for maximum activity, whereas the corresponding enzyme fraction from germinated spores did not require added DNA. Apparently DNA polymerase from germinated spores was more tightly bound to endogenous DNA than was the enzyme from ungerminated spores.     

Physiological and Morphological Correlation of Rhizopus stolonifer Spore Germination

Sporangiospores of Rhizopus stolonifer were examined at various stages of germination by scanning electron and phase-contrast microscopy. These observations were correlated with changes in spore dry weight, spore volume, respiration, and syntheses of ribonucleic acid, deoxyribonucleic acid, and protein during germination.     

Ribonuclease Rs from Rhizopus stolonifer: lowering of optimum temperature in the presence of urea

RNase Rs showed an approx. 2-fold increase in its activity when incubated in the presence of 2 M urea at 37 degrees C. The increase in its activity, in the presence of urea, was comparable to the activity at its optimum temperature, i.e. 45 degrees C. Compared to the native enzyme at 37 degrees C, the K(m) and V(max) of RNase Rs at 45 degrees C and in the presence of 2 M urea at 37 degrees C showed an increase while k(cat)/K(m) decreased. Arrhenius plots in the presence and absence of urea showed a decrease in the activation energy in the presence of urea. Though there was no change in the secondary structure of the protein in the presence of urea, minor changes were observed in the tertiary structure. Hence, the increase in the activity of RNase Rs, in the presence of 2 M urea at 37 degrees C, is due to the lowering of the activation energy as a result of changes in the microenvironment of the active site.     

Equilibrium unfolding of RNase Rs from Rhizopus stolonifer: pH dependence of chemical and thermal denaturation

The conformational stability of RNase Rs was determined with chemical and thermal denaturants over the pH range of 1-10. Equilibrium unfolding with urea showed that values of D(1/2) (5.7 M) and DeltaG(H(2)O) (12.8 kcal/mol) were highest at pH 5.0, its pI and the maximum conformational stability of RNase Rs was observed near pH 5.0. Denaturation with guanidine hydrochloride (GdnHCl), at pH 5.0, gave similar values of DeltaG(H(2)O) although GdnHCl was 2-fold more potent denaturant with D(1/2) value of 3.1 M. The curves of fraction unfolded (f(U)) obtained with fluorescence and CD measurements overlapped at pH 5.0. Denaturation of RNase Rs with urea in the pH range studied was reversible but the enzyme denatured irreversibly >pH 11.0. Thermal denaturation of RNase Rs was reversible in the pH range of 2.0-3.0 and 6.0-9.0. Thermal denaturation in the pH range 4.0-5.5 resulted in aggregation and precipitation of the protein above 55 degrees C. The aggregate was amorphous or disordered precipitate as observed in TE micrographs. Blue shift in emission lambda(max) and enhancement of fluorescence intensity of ANS at 70 degrees C indicated the presence of solvent exposed hydrophobic surfaces as a result of heat treatment. Aggregation could be prevented partially with alpha-cyclodextrin (0.15 M) and completely with urea at concentrations >3 M. Aggregation was probably due to intermolecular hydrophobic interaction favored by minimum charge-charge repulsion at the pI of the enzyme. Both urea and temperature-induced denaturation studies showed that RNase Rs unfolds through a two-state F right arrow over left arrow U mechanism. The pH dependence of stability described by DeltaG(H(2)O) (urea) and DeltaG (25 degrees C) suggested that electrostatic interactions among the charged groups make a significant contribution to the conformational stability of RNase Rs. Since RNase Rs is a disulfide-containing protein, the major element for structural stability are the covalent disulfide bonds.     

Production, statistical optimization and application of endoglucanase from Rhizopus stolonifer utilizing coffee husk

Coffee cherry husk (CH) is one of the major by-products obtained from coffee processing industry and accounts to 43 ± 5.9 % of cellulose. Screening of fungal organism for cellulase production was carried out and the potential organism was identified as Rhizopus stolonifer by internal transcribed spacer’s (ITS)—5.8S rDNA analysis. A systematic study with response surface methodology (RSM) based on CCRD was used to study the interactions among the variables such as pH (3–7), moisture (40–80 %) and progression duration (72–168 h) of the fermentation process to maximize the enzyme production. Under the optimized cultivation condition, R. stolonifer synthesized 22,109 U/gds. Model validations at optimum operating conditions showed excellent agreement between the experimental results and the predicted responses with a confidence level of 95 %. Endoglucanase thus produced was utilized for ethanol production by simultaneous saccharification and fermentation and maximum of 65.5 g/L of ethanol was obtained. This fungal cellulase has also reported to be efficient detergent additives and promising for commercial use. The present study demonstrates coffee husk as a significant bioprocess substrate. Statistical optimization with major parameters for cellulase production can be highly applicable for industrial scale. Furthermore, value addition to coffee husk with sustainable waste management leading to environment conservation can be achieved.     

Purification and characterization of the single-strand-specific and guanylic-acid-preferential deoxyribonuclease activity of the extracellular nuclease from Basidiobolus haptosporus.

An extracellular nuclease from Basidiobolus haptosporus (designated as nuclease Bh1) was purified to homogeneity by ammonium sulfate precipitation, heat treatment, negative adsorption on DEAE-cellulose, and chromatography on phenyl-Sepharose followed by FPLC on phenyl-Superose. The overall yield was 26%. The Mr of the purified enzyme, determined by gel filtration, was 41 000 whereas by SDS/PAGE (after deglycosylation) it was 30 000. It is a glycoprotein with a pI of 6.8. The optimum pH and temperature for DNA hydrolysis were 8. 5 and 60 degrees C, respectively. Nuclease Bh1 is a metalloprotein but has no obligate requirement for metal ions to be active, nor is its activity stimulated in the presence of metal ions. The enzyme was inhibited by Zn2+, Ag2+, Hg2+, Fe3+ and Al3+, inorganic phosphate, pyrophosphate, dithiothreitol, 2-mercaptoethanol, NaCl and KCl. It was stable to high concentrations of organic solvents and urea but susceptible to low concentrations of SDS and guanidine hydrochloride. Nuclease Bh1 is a multifunctional enzyme and its substrate specificity is in the order of ssDNA approximately 3'AMP > RNA > dsDNA. Studies on its mode of action showed that it cleaved supercoiled pUC 18 DNA and phage M13 DNA, endonucleolytically, generating single base nicks. The enzyme hydrolyzed DNA with preferential liberation of 5'dGMP, suggesting it to be a guanylic acid preferential endoexonuclease. 5'dGMP, the end product of hydrolysis, was a competitive inhibitor of the enzyme. The absence of 5'dCMP as a hydrolytic product, coupled with the resistance of (dC)10 and deoxyribodinucleoside monophosphates having cytosine either at the 3' or the 5' end, indicates that C-linkages are resistant to cleavage by nuclease Bh1.     

Characterisation of acetaldehyde effects on Rhizopus stolonifer and Botrytis cinerea

Acetaldehyde (AA) vapour reduced the in vitro growth of the fruit-infecting fungi Botrytis cinerea and Rhizopus stolonifer, and decreased the respiration of R. stolonifer. Spore germination, germ tube elongation and sporulation were inhibited in both fungi. AA induced the leakage of electrolytes from B. cinerea and R. stolonifer membranes. The conductivity found in the fungal extracts was positively correlated with the AA concentration applied. The leakage of reducing sugars and amino acids suggest that cell membranes are irreversibly disrupted by AA as a first step in inhibition of the fungi in vitro.     

Effects of fengycin from Bacillus subtilis fmbJ on apoptosis and necrosis in Rhizopus stolonifer

The lipopeptide antibiotic fengycin, produced by Bacillus subtilis, strongly inhibits growth of filamentous fungi. In this study, we evaluated the effects of fengycin treatment on apoptosis and necrosis in Rhizopus stolonifer by means of cell staining and epifluorescence microscopy. At fengycin concentrations less than 50 μg/ml, treated fungal cells demonstrated a dose-dependent increase in apoptosis-associated markers compared with the untreated control. These markers included chromatin condensation, reactive oxygen species accumulation, mitochondrial membrane potential depolarization, phosphatidylserine externalization, and the occurrence of DNA strand breaks. These results showed that fungal cells were impaired in a number of important functions and entered apoptosis upon treatment with low concentrations of fengycin. In contrast, high concentrations (>50 μg/ml) induced necrosis, indicating that the fungicidal action of fengycin operates via two modes: apoptosis at low concentrations and necrosis at high concentrations. Additionally, the apoptotic effect that we have shown suggests that lower concentrations of fengycin than previously thought may be effective for food preservation.     

Antifungal activity and mechanism of fengycin in the presence and absence of commercial surfactin against Rhizopus stolonifer

The antifungal activity and mechanism of fengycin in the presence and absence of commercial surfactin against Rhizopus stolonifer were investigated. The MIC (minimal inhibitory concentration) of fengycin without commercial surfactin added was 0.4 mg/ml while the MIC of fengycin with commercial surfactin added was 2.0 mg/ml. Fengycin acted on cell membrane and cellular organs and inhibited DNA synthesis. The antifungal effect of fengycin was reduced after commercial surfactin was added. All these results suggest that the fungal cell membrane may be the primary target of fengycin action and commercial surfactin may reduce the antifungal activity of fengycin.