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1.  Draft Genome Sequence of the Formaldehyde-Resistant Fungus Byssochlamys spectabilis No. 5 (Anamorph Paecilomyces variotii No. 5) (NBRC109023) 
Genome Announcements  2014;2(1):e01162-13.
Byssochlamys spectabilis no. 5 (anamorph Paecilomyces variotii no. 5) (NBRC109023) was isolated from a soil sample in 2001 in Kumamoto Prefecture, Japan. This fungus is highly resistant to formaldehyde. Here, we report a draft genome sequence of P. variotii no. 5; this draft was produced with the intent of investigating the mechanism of formaldehyde resistance. This is the first report of the genome sequence of any Paecilomyces species.
doi:10.1128/genomeA.01162-13
PMCID: PMC3886963  PMID: 24407650
2.  Lactate dehydrogenase from Streptococcus mutans: purification, characterization, and crossed antigenicity with lactate dehydrogenases from Lactobacillus casei, Actinomyces viscosus, and Streptococcus sanguis. 
Infection and Immunity  1985;47(2):489-495.
A cytoplasmic fructose-1,6-diphosphate-dependent lactate dehydrogenase (LDH; EC 1.1.1.27) from Streptococcus mutans OMZ175 was purified to homogeneity as judged by sodium dodecyl sulfate-gel electrophoresis. The purification consisted of ammonium sulfate precipitation of the cytoplasmic fraction, DEAE-Sephacel and Blue-Sepharose CL.6B chromatography, and Sephacryl S200 gel permeation. The catalytic activity of the purified enzyme required the presence of fructose-1,6-diphosphate with a broad optimum between pH 5 and 6.2. The concentration of fructose-1,6-diphosphate required for half-maximal velocity was around 0.02 mM and was affected by the pyruvate concentration. The enzyme seemed to have at least two binding sites for the activator which interact in a cooperative manner. Increasing concentrations of fructose-1,6-diphosphate up to 2 mM enhanced the relative affinity of the enzyme for pyruvate and modified the pyruvate saturation curve from sigmoidal to hyperbolic. The enzyme activity showed also a sigmoidal response to NADH, exhibiting two binding sites for the cofactor with a Hill coefficient of about 1.9. The molecular weight of the native enzyme was 150,000 as determined by gel permeation on Sephacryl S200. Monomers (38,000 daltons) and dimers (85,000 daltons) were observed by sodium dodecyl sulfate-gel electrophoresis; the latter form was dissociated after reduction with 2-mercaptoethanol, and the enzyme could be considered a tetramer. Antibodies obtained against the purified S. mutans OMZ175 LDH cross-reacted with the sodium dodecyl sulfate-dissociated forms of LDHs from different S. mutans serotypes, Streptococcus sanguis OMZ9, Lactobacillus casei ATCC 4646, and Actinomyces viscosus NY 1. A competitive enzyme-linked immunosorbent assay allowed us to detect a very close relationship between the native states of L-LDHs from S. mutans serotypes and S. sanguis. Cross-reactions were also observed with the LDHs from A. viscosus and L. casei, the latter being the least related. A very weak immunological relationship was obtained between the L-LDH from S. mutans OMZ175 and the D-LDH from Lactobacillus leichmannii, whereas no cross-reaction could be detected with mammal LDHs.
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PMCID: PMC263197  PMID: 3917978
3.  Production, Purification of Exo-Polygalacturonase from Soil Isolate Paecilomyces variotii NFCCI 1769 and Its Application 
Indian Journal of Microbiology  2011;52(2):240-246.
The aim of the present study was to produce exo-polygalacturonase from potent soil isolate by submerged fermentation and its application for fruit juice treatment. Pectinase producing strains were selectively isolated from pectin industry waste. A selected isolate C2 was found to produce significant amount of exo-polygalacturonase. The isolate was identified as Paecilomyces variotii on the basis of morphological characteristics and 18S rRNA gene sequence analysis. The exo-polygalacturonase produced by the isolate was purified by ammonium sulphate precipitation, size exclusion chromatography and ion exchange chromatography. The purified enzyme had MW of 39.4 kD based on SDS PAGE. Under partially optimized conditions, purified exo-polygalacturonase showed specific activity of 98.49 U/mg protein at pH 6.0 and 30°C. The enzyme was comparatively stable from 10 to 30°C and the activity decreased with increasing temperature. Purified enzyme brought about considerable reduction in viscosity of fruit juice samples.
doi:10.1007/s12088-011-0162-x
PMCID: PMC3386462  PMID: 23729888
Pectinase; Exo-polygalacturonase; Paecilomyces variotii NFCCI 1769
4.  Human coagluation factor V purification and thrombin-catalyzed activation. 
Journal of Clinical Investigation  1980;66(3):583-591.
Factor V was isolated from human plasma by barium citrate adsorption, polyethylene glycol fractionation, DEAE-Sepharose CL-6B chromatography, ammonium sulfate fractionation, and gel chromatography on Ultrogel 22. Degradation of Factor V during purification was largely prevented by ample use of inhibitors of proteolytic enzyme. The purified Factor V was a stable, single-chain molecule with an apparent molecular weight of 330,000. Activation of human Factor V by thrombin resulted in a 10- to 15-fold increase in activity. The activation pattern as monitored by sodium dodecyl sulfate polyacrylamide gel electrophoresis was compared with that of bovine Factor V. Differences in the patterns of thrombin activation were noticed between the two species, whereas the final products were similar. The products of human Factor V activation are two closely spaced doublets, one with an apparent molecular weight of approximately 110,000, and the other, approximately 72,000. An antibody was raised against the purified protein. Crossed immunoelectrophoresis showed that the antibody recognized Factor V both before and after activation with thrombin.
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PMCID: PMC371687  PMID: 7400329
5.  Purification and Properties of a Maltotetraose- and Maltotriose-Producing Amylase from Chloroflexus aurantiacus 
A maltotetraose- and maltotriose-producing amylase which is stable at alkaline pHs and high temperatures was detected in the culture filtrate of a strain of Chloroflexus aurantiacus J-10-F1, a thermophilic, green, photosynthetic bacterium. The enzyme was purified to homogeneity, as demonstrated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, by means of ultrafiltration, ammonium sulfate fractionation, and DEAE-cellulose, hydroxyapatite, and high-performance liquid chromatographies. The molecular mass of the purified enzyme was estimated to be about 210,000 Da. The isoelectric point of the enzyme was estimated to be 6.24 by polyacrylamide gel electrofocusing. The amylase was stable up to 55°C and at alkaline pHs of up to 12.0. The optimum pH and temperature of the enzyme activity were 7.5 and 71°C, respectively. Metal ions such as Hg2+, Zn2+, Cu2+, Mn2+, and Ni2+ strongly inhibited the enzyme activity. The enzyme activity was reactivated specifically by Ca2+ after the enzyme was treated with 1 mM EDTA. This enzyme could digest various kinds of raw-starch granules from corn, cassava, and potato. Both maltotetraose and maltotriose were formed as the main enzymatic products from soluble starch.
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PMCID: PMC195809  PMID: 16348751
6.  Purification and properties of saccharopine dehydrogenase (glutamate forming) in the Saccharomyces cerevisiae lysine biosynthetic pathway. 
Journal of Bacteriology  1987;169(1):416-418.
Saccharopine dehydrogenase (glutamate forming) of the biosynthetic pathway of lysine in Saccharomyces cerevisiae was purified 1,122-fold by using acid precipitation, ammonium sulfate precipitation, DEAE-Sepharose, gel filtration, and Reactive Red-120 agarose chromatography. The enzyme exhibited a native molecular size of 69,000 daltons by gel filtration and consisted of a single 50,000-dalton polypeptide based upon sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The enzyme was readily denatured by exposures to temperatures exceeding 46 degrees C. The pH optimum for the reverse reaction was 9.5. The apparent Kms for L-saccharopine and NAD+ were 2.32 and 0.054 mM, respectively. The enzyme was inhibited by mercuric chloride but not by carbonyl or metal complexing agents.
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PMCID: PMC211784  PMID: 3098733
7.  Production and Purification of Remazol Brilliant Blue R Decolorizing Peroxidase from the Culture Filtrate of Pleurotus ostreatus 
An extracellular H(inf2)O(inf2)-requiring Remazol brilliant blue R (RBBR) decolorizing enzymatic activity was found in the culture medium of Pleurotus ostreatus. The enzymatic activity was maximally obtained in idiophase, and the optimum C/N ratio was 24. High C/N ratios repressed the enzymatic activity, and addition of veratryl alcohol had no effect on the production of enzyme. The enzyme was purified by ammonium sulfate fractionation, Sephacryl S-200 HR chromatography, DEAE Sepharose CL-6B chromatography, and Mono Q chromatography. The purification of RBBR decolorizing peroxidase, as judged by the final specific activity of 6.00 U/mg, was 54.5-fold, with a yield of 9.9%. The molecular mass of the native enzyme determined by gel permeation chromatography was found to be about 73 kDa. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis revealed that the enzyme was a monomer with a molecular mass of 71 kDa. The enzyme was optimally active at pH 3.0 to 3.5 and at 25(deg)C. Under standard assay conditions, the apparent K(infm) values of the enzyme toward RBBR and H(inf2)O(inf2) were 10.99 and 32.97 (mu)M, respectively. The enzyme had affinity toward various phenolic compounds and artificial dyes, and it was inhibited by Na(inf2)S(inf2)O(inf5), potassium cyanide, NaN(inf3), and cysteine. The absorption spectrum of the enzyme exhibited maxima at 407, 510, and 640 nm. The addition of H(inf2)O(inf2) to the enzyme resulted in an absorbance decrease at 407 and 510 nm.
PMCID: PMC1389145  PMID: 16535590
8.  Purification and Characterization of a Keratinase from a Feather-Degrading Fungus, Aspergillus flavus Strain K-03 
Mycobiology  2007;35(4):219-225.
A keratinolytic enzyme secreted by Aspergillus flavus K-03 cultured in feather meal basal medium (FMBM) containing 2% (w/v) chicken feather was purified and characterized. Keratinolytic enzyme secretion was the maximal at day 16 of the incubation period at pH 8 and 28℃. No relationship was detected between enzyme yield and increase of fungal biomass. The fraction obtained at 80% ammonium sulfate saturation showed 2.39-fold purification and was further purified by gel filtration in Sephadex G-100 followed by ion exchange chromatography on DEAE-Sephadex A-50, yielding an active protein peak showing 11.53-fold purification. Sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and zymograms indicated that the purified keratinase is a monomeric enzyme with 31 kDa molecular weight. The extracellular keratinase of A. flavus was active in a board range of pH (7~10) and temperature (30℃~70℃) profiles with the optimal for keratinase activity at pH 8 and 45℃. The keratinase activity was totally inhibited by protease inhibitors such as phenylmethylsulfonyl fluoride (PMSF), iodoacetic acid, and ethylenediaminetetraacetate (EDTA) while no reduction of activity by the addition of dithiothreitol (DTT) was observed. N-terminal amino acid sequences were up to 80% homologous with the fungal subtilisins produced by Fusarium culmorum. Therefore, on the basis of these characteristics, the keratinase of A. flavus K-03 is determined to be subtilisins-like.
doi:10.4489/MYCO.2007.35.4.219
PMCID: PMC3763176  PMID: 24015101
Aspergillus flavus; Keratinase; Subtilisins; Serine protease
9.  Purification and properties of chorismate mutase-prephenate dehydratase and prephenate dehydrogenase from Alcaligenes eutrophus. 
Journal of Bacteriology  1976;126(2):712-722.
Chorismate mutase and prephenate dehydratase from Alcaligenes autophus H16 were purified 470-fold with a yield of 24%. During the course of purification, including chromatography on diethylaminoethyl (DEAE)-cellulose, phenylalanine-substituted Sepharose, Sephadex G-200 and hydrogyapatite, both enzymes appeared in association. The ratio of their specific activities remained almost constant. The molecular weight of chorismate mutase-prephenast dehydratase varied from 144,000 to 187,000 due to the three different determination methods used. Treatment of electrophoretically homogeneous mutase-dehydratase with sodium dodecyl sulfate dissociated the enzyme into a single component of molecular weight 47,000, indicating a tetramer of identical subunits. The isoelectric point of the bifunctional enzyme was 5.8. Prephenate dehydrogenase was not associated with other enzyme activities; it was separated from mutasedehydratase by DEAE-cellulose chromatgraphy. Chromatography on DEAE Sephadex, Sephadex G-200, and hydroxyapatite resulted in a 740-fold purification with a yield of 10%. The molecular weight of the enzyme was 55,000 as determined by sucrose gradient centrifugation and 65,000 as determined by gel filtration or electrophoresis. Its isoelectric point was pH 6.6. In the overall conversion of chorismate to phenylpyruvate, free prephenate was formed which accumulated in the reaction mixture. The dissociation of prephenate allowed prephenate dehydrogenase to compete with prephenate dehydratase for the substrate.
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PMCID: PMC233205  PMID: 1262315
10.  Metabolism of Ferulic Acid by Paecilomyces variotii and Pestalotia palmarum 
Ferulic acid metabolism was studied in cultures of two micromycetes producing different amounts of phenol oxidases. In cultures of the low phenol oxidase producer Paecilomyces variotii, ferulic acid was decarboxylated to 4-vinylguaiacol, which was converted to vanillin and then either oxidized to vanillic acid or reduced to vanillyl alcohol. Vanillic acid underwent simultaneously an oxidative decarboxylation to methoxyhydroquinone and a nonoxidative decarboxylation to guaiacol. Methoxyhydroquinone and guaiacol were demethylated to yield hydroxyquinol and catechol, respectively. Catechol was hydroxylated to pyrogallol. Degradation of ferulic acid by Paecilomyces variotii proceeded mainly via methoxyhydroquinone. The high phenol oxidase producer Pestalotia palmarum catabolized ferulic acid via 4-vinylguaiacol, vanillin, vanillyl alcohol, vanillic acid, and methoxyhydroquinone. However, the main reactions observed with this fungus involved polymerization reactions.
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PMCID: PMC203086  PMID: 16348018
11.  Microbial Oxidation of Methane and Methanol: Crystallization of Methanol Dehydrogenase and Properties of Holo- and Apo-Methanol Dehydrogenase from Methylomonas methanica 
Journal of Bacteriology  1978;133(2):641-649.
Procedures are described for the purification and crystallization of methanol dehydrogenase from the soluble fraction of the type I obligate methylotroph Methylomonas methanica strain S1. The crystallized enzyme is homogeneous as judged by acrylamide gel electrophoresis and ultracentrifugation. The enzyme had a high pH optimum (9.5) and required ammonium salt as an activator. In the presence of phenazine methosulfate as an electron acceptor, the enzyme catalyzed the oxidation of primary alcohols and formaldehyde. Secondary, tertiary, and aromatic alcohols were not oxidized. The molecular weight as well as subunit size of methanol dehydrogenase was 60,000, indicating that it is monomeric. The sedimentation constant (s20,w) was 3.1S. The amino acid composition of the crystallized enzyme is also presented. Antisera prepared against the crystalline enzyme were nonspecific; they cross-reacted with and inhibited the isofunctional enzyme from other obligate methylotrophic bacteria. The crystalline methanol dehydrogenase had an absorption peak at 350 nm in the visible region and weak fluorescence peaks at 440 and 470 nm due to the presence of a pteridine derivative as the prosthetic group. A procedure was developed for the preparation of apo-methanol dehydrogenase. The molecular weights, sedimentation constants, electrophoretic mobilities, and immunological properties of apo- and holo-methanol dehydrogenases are identical. Apo-methanol dehydrogenase lacked the absorption peak at 350 nm and the fluorescence peaks at 440 and 470 nm and was catalytically inactive. All attempts to reconstitute an active enzyme from apo-methanol dehydrogenase, using various pteridine derivatives, were unsuccessful.
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PMCID: PMC222070  PMID: 415046
12.  Malate dehydrogenase from Chlorobium vibrioforme, Chlorobium tepidum, and Heliobacterium gestii: purification, characterization, and investigation of dinucleotide binding by dehydrogenases by use of empirical methods of protein sequence analysis. 
Journal of Bacteriology  1992;174(4):1307-1313.
Malate dehydrogenase (MDH; EC 1.1.1.37) from strain NCIB 8327 of the green sulfur bacterium Chlorobium vibrioforme was purified to homogeneity by triazine dye affinity chromatography followed by gel filtration. Purification of MDH gave an approximately 1,000-fold increase in specific activity and recoveries of typically 15 to 20%. The criteria of purity were single bands on sodium dodecyl sulfate (SDS) and nondenaturing polyacrylamide electrophoresis (PAGE) and the detection of a single N terminus in an Edman degradation analysis. MDH activity was detected in purified preparations by activity staining of gels in the direction of malate oxidation. PAGE and gel filtration (Sephadex G-100) analyses showed the native enzyme to be a dimer composed of identical subunits both at room temperature and at 4 degrees C. The molecular weight of the native enzyme as estimated by gel filtration was 77,000 and by gradient PAGE was 74,000. The subunit molecular weight as estimated by SDS-gradient PAGE was 37,500. N-terminal sequences of MDHs from C. vibrioforme, Chlorobium tepidum, and Heliobacterium gestii are presented. There are obvious key sequence similarities in MDHs from the phototrophic green bacteria. The sequences presented probably possess a stretch of amino acids involved in dinucleotide binding which is similar to that of Chloroflexus aurantiacus MDH and other classes of dehydrogenase enzymes but unique among MDHs.
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PMCID: PMC206426  PMID: 1735722
13.  Purification and Characterization of 2,6-β-d-Fructan 6-Levanbiohydrolase from Streptomyces exfoliatus F3-2 
Streptomyces exfoliatus F3-2 produced an extracellular enzyme that converted levan, a β-2,6-linked fructan, into levanbiose. The enzyme was purified 50-fold from culture supernatant to give a single band on sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). The molecular weights of this enzyme were 54,000 by SDS-PAGE and 60,000 by gel filtration, suggesting the monomeric structure of the enzyme. The isoelectric point of the enzyme was determined to be 4.7. The optimal pH and temperature of the enzyme for levan degradation were pH 5.5 and 60°C, respectively. The enzyme was stable in the pH range 3.5 to 8.0 and also up to 50°C. The enzyme gave levanbiose as a major degradation product from levan in an exo-acting manner. It was also found that this enzyme catalyzed hydrolysis of such fructooligosaccharides as 1-kestose, nystose, and 1-fructosylnystose by liberating fructose. Thus, this enzyme appeared to hydrolyze not only β-2,6-linkage of levan, but also β-2,1-linkage of fructooligosaccharides. From these data, the enzyme from S. exfoliatus F3-2 was identified as a novel 2,6-β-d-fructan 6-levanbiohydrolase (EC 3.2.1.64).
PMCID: PMC91814  PMID: 10618232
14.  Plasmid-mediated formaldehyde resistance in Escherichia coli: characterization of resistance gene. 
Antimicrobial Agents and Chemotherapy  1996;40(10):2276-2279.
The formaldehyde resistance mechanisms in the formaldehyde-resistant strain Escherichia coli VU3695 were investigated. A large (4.6-kb) plasmid DNA fragment encompassing the formaldehyde resistance gene was sequenced. A single 1,107-bp open reading frame encoding a glutathione- and NAD-dependent formaldehyde dehydrogenase was identified and sequenced, and the enzyme was expressed in an in vitro assay and purified. Amino acid sequence homology studies showed 62.4 to 63.2% identity with class III alcohol dehydrogenases isolated from horse, human, and rat livers. We demonstrated that the resistance mechanism in the formaldehyde-resistant strain E. coli VU3695 and in other formaldehyde-resistant members of the family Enterobacteriaceae is based on the enzymatic degradation of formaldehyde by a formaldehyde dehydrogenase.
PMCID: PMC163518  PMID: 8891129
15.  Fermentation and enzyme treatments for sorghum 
Sorghum (Sorghum bicolor Moench) is the fifth most produced cereal worldwide. However, some varieties of this cereal contain antinutritional factors, such as tannins and phytate that may form stable complexes with proteins and minerals which decreases digestibility and nutritional value. The present study sought to diminish antinutritional tannins and phytate present in sorghum grains. Three different treatments were studied for that purpose, using enzymes tannase (945 U/Kg sorghum), phytase (2640 U/Kg sorghum) and Paecilomyces variotii (1.6 X 107 spores/mL); A) Tannase, phytase and Paecilomyces variotii, during 5 and 10 days; B) An innovative blend made of tanase and phytase for 5 days followed by a Pv increase for 5 more days; C) a third treatment where the reversed order of B was used starting with Pv for 5 days and then the blend of tannase and phytase for 5 more days. The results have shown that on average the three treatments were able to reduce total phenols and both hydrolysable and condensed tannins by 40.6, 38.92 and 58.00 %, respectively. Phytase increased the amount of available inorganic phosphorous, on the average by 78.3 %. The most promising results concerning tannins and phytate decreases were obtained by the enzymes combination of tannase and phytase. The three treatments have shown effective on diminishing tannin and phytate contents in sorghum flour which leads us to affirm that the proposed treatments can be used to increase the nutritive value of sorghum grains destined for either animal feeds or human nutrition.
doi:10.1590/S1517-838220120001000010
PMCID: PMC3768961  PMID: 24031807
Fermentation; tannase; phytase; sorghum
16.  Purification and characterization of keratinase from a new Bacillus subtilis strain 
The aim of this study was to purify and characterize a keratinase produced by a new isolated Bacillus subtilis KD-N2 strain. The keratinase produced by the isolate was purified using ammonium sulphate precipitation, Sephadex G-75 and DEAE (diethylaminoethyl)-Sepharose chromatographic techniques. The purified enzyme was shown to have a molecular mass of 30.5 kDa, as determined by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) analysis. The optimum pH at 50 °C was 8.5 and the optimum temperature at pH 8.5 was 55 °C. The keratinase was partially inactivated by some metal ions, organic solvents and serine protease inhibitor phenylmethanesulfonyl fluoride (PMSF). Sodium dodecyl sulfate (SDS) and ethylene diamine tetraacetic acid (EDTA) had positive effect on the keratinase activity. Reducing agents including dithiothreitol (DTT), mercaptoethanol, L-cysteine, sodium sulphite, as well as chemicals of SDS, ammonium sulfamate and dimethylsulfoxide (DMSO) stimulated the enzyme activity upon a feather meal substrate. Besides feather keratin, the enzyme is active upon the soluble proteins ovalbumin, bovine serum albumin (BSA), casein and insoluble ones as sheep wool and human hair. Calf hair, silk and collagen could not be hydrolyzed by the keratinase.
doi:10.1631/jzus.B0820128
PMCID: PMC2528886  PMID: 18763304
Ammonium sulfatate; Bacillus subtilis; Characterization; Feather; Keratin; Keratinase; Purification; Reducing agents
17.  Purification and studies on characteristics of cholinesterases from Daphnia magna *  
Due to their significant value in both economy and ecology, Daphnia had long been employed to investigate in vivo response of cholinesterase (ChE) in anticholinesterase exposures, whereas the type constitution and property of the enzyme remained unclear. A type of ChE was purified from Daphnia magna using a three-step procedure, i.e., Triton X-100 extraction, ammonium sulfate precipitation, and diethylaminoethyl (DEAE)-Sepharose™-Fast-Flow chromatography. According to sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE), molecular mass of the purified ChE was estimated to be 84 kDa. Based on substrate studies, the purified enzyme preferred butyrylthiocholine iodide (BTCh) [with maximum velocity (V max)/Michaelis constant (K m)=8.428 L/(min·mg protein)] to acetylthiocholine iodide (ATCh) [with V max/K m=5.346 L/(min·mg protein)] as its substrate. Activity of the purified enzyme was suppressed by high concentrations of either ATCh or BTCh. Inhibitor studies showed that the purified enzyme was more sensitive towards inhibition by tetraisopropylpyrophosphoramide (iso-OMPA) than by 1,5-bis(4-allyldimethylammoniumphenyl) pentan-3-one dibromide (BW284C51). Result of the study suggested that the purified ChE was more like a type of pseudocholinesterase, and it also suggested that Daphnia magna contained multiple types of ChE in their bodies.
doi:10.1631/jzus.B1200113
PMCID: PMC3625529  PMID: 23549850
Crustacea; Pseudocholinesterase; Cholinesterase; Substrate preference; Selective inhibitors
18.  Purification and partial characterization of thermostable serine alkaline protease from a newly isolatedBacillus subtilis PE-11 
AAPS PharmSciTech  2003;4(4):440-448.
The purpose of the research was to study the purification and partial characterization of thermostable serine alkaline protease from a newly isolatedBacillus subtilis PE-11. The enzyme was purified in a 2-step procedure involving ammonium sulfate precipitation and Sephadex G-200 gel permeation chromatography. The enzyme was shown to have a relative low molecular weight of 15 kd by sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE) and was purified 21-fold with a yield of 7.5%. It was most active at 60°C, pH 10, with casein as substrate. It was stable between pH 8 and 10. This enzyme was almost 100% stable at 60°C even after 350 minutes of incubation. It was strongly activated by metal ions such as Ca2+, Mg+2, and Mn+2. Enzyme activity was inhibited strongly by phenylmethyl sulphonyl fluoride (PMSF) and diisopropyl fluorophosphates (DFP) but was not inhibited by ethylene diamine tetra acetic acid (EDTA), while a slight inhibition was observed with iodoacetate,p-chloromercuric benzoate (pCMB), and β-mercaptoethanol (β-ME). The compatibility of the enzyme was studied with commercial and local detergents in the presence of 10mM CaCl2 and 1M glycine. The addition of 10mM CaCl2 and 1M glycine, individually and in combination, was found to be very effective in improving the enzyme stability where it retained 52% activity even after 3 hours. This enzyme improved the cleansing power of various detergents. It removed blood stains completely when used with detergents in the presence of 10mM CaCl2 and 1M glycine.
doi:10.1208/pt040456
PMCID: PMC2750649  PMID: 15198551
alkaline protease; Bacillus subtilis; PE-11; purification; characterization; compatibility
19.  A Novel NAD-Dependent Dehydrogenase, Highly Specific for 1,5-Anhydro-d-Glucitol, from Trichoderma longibrachiatum Strain 11-3 
A novel NAD-dependent dehydrogenase highly specific for 1,5-anhydro-d-glucitol (1,5-AG) was found in the cell extract of an imperfect fungus, Trichoderma longibrachiatum strain 11-3. This fungus used 1,5-AG as a sole carbon source for growth and transformed 1,5-AG into glucose. 1,5-AG dehydrogenase (AGH) was purified to homogeneity, as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). The molecular mass of the purified enzyme was estimated to be 36 and 141 kDa by SDS-PAGE and by gel filtration, respectively, suggesting that the enzyme was homotetrameric. The enzyme was highly specific for 1,5-AG and did not exhibit activity with any sugar or sugar alcohol tested in this study other than 1,5-AG. A linear relationship between the initial rate of the enzyme reaction and the concentration of 1,5-AG at the physiological level was observed. The presence of glucose in abundance did not interfere with the relationship. The optimum temperature for the enzyme reaction was 50°C, and the enzyme was stable at temperatures up to 70°C. These results suggested that AGH is a novel enzyme and is useful for specifically diagnosing diabetes mellitus.
doi:10.1128/AEM.69.5.2603-2607.2003
PMCID: PMC154545  PMID: 12732527
20.  Purification and characterization of membrane-bound peroxidase from date palm leaves (Phoenix dactylifera L.) 
Peroxidase from date palm (Phoenix dactylifera L.) leaves was purified to homogeneity and characterized biochemically. The enzyme purification included homogenization, extraction of pigments followed by consecutive chromatographies on DEAE-Sepharose and Superdex 200. The purification factor for purified date palm peroxidase was 17 with 5.8% yield. The purity was checked by SDS and native PAGE, which showed a single prominent band. The molecular weight of the enzyme was approximately 55 kDa as estimated by SDS–PAGE. The enzyme was characterized for thermal and pH stability, and kinetic parameters were determined using guaiacol as substrate. The optimum activity was between pH 5–6. The enzyme showed maximum activity at 55 °C and was fairly stable up to 75 °C, with 42% loss of activity. Date palm leaves peroxidase showed Km values of 0.77 and 0.045 mM for guaiacol and H2O2, respectively. These properties suggest that this enzyme could be a promising tool for applications in different analytical determinations as well as for treatment of industrial effluents at low cost.
doi:10.1016/j.sjbs.2011.04.005
PMCID: PMC3730793  PMID: 23961138
Date palm leaves; Peroxidase; Purification; Characterization; Thermostability; Substrate specificity
21.  Purification and characterization of a developmentally regulated carboxypeptidase from Mucor racemosus. 
Journal of Bacteriology  1992;174(2):447-455.
A developmentally regulated carboxypeptidase was purified from hyphae of the dimorphic fungus Mucor racemosus. The enzyme, designated carboxypeptidase 3 (CP3), has been purified greater than 900-fold to homogeneity and characterized. The carboxypeptidase migrated as a single electrophoretic band in isoelectric focusing polyacrylamide gel electrophoresis (PAGE), with an isoelectric point of pH 4.4. The apparent molecular mass of the native enzyme was estimated by gel filtration to be 52 kDa. Sodium dodecyl sulfate (SDS)-PAGE under nonreducing conditions revealed the presence of a single polypeptide of 51 kDa. SDS-PAGE of CP3 reacted with 2-mercaptoethanol revealed the presence of two polypeptides of 31 and 18 kDa, indicating a dimer structure (alpha 1 beta 1) of the enzyme with disulfide-linked subunits. By using [1,3-3H]diisopropylfluorophosphate as an active-site labeling reagent, it was determined that the catalytic site resides on the small subunit of the carboxypeptidase. With N-carboben zoxy-L-phenylalanyl-L-leucine (N-CBZ-Phe-Leu) as the substrate, the Km, kcat, and Vmax values were 1.7 x 10(-4) M, 490 s-1, and 588 mumol of Leu released per min per mg of protein, respectively. CP3 was determined to be a serine protease, since its catalytic activity was blocked by the serine protease inhibitors diisopropylfluorophosphate, phenylmethylsulfonyl fluoride, and 3,4-dichloroi Socoumarin (DCI). The enzyme was strongly inhibited by the mercurial compound p-chloromercuribenzoate. The carboxypeptidase readily hydrolyzed peptides with aliphatic or aromatic side chains, whereas most of the peptides which contained glycine in the penultimate position did not serve as substrates for the enzyme. Although CP3 activity was undetectable in Mucor yeast cells, antisera revealed the presence of the enzyme in the yeast form of the fungus. The partial amino acid sequence of the carboxypeptidase was determined.
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PMCID: PMC205736  PMID: 1729237
22.  Paecilomyces variotii as an Emergent Pathogenic Agent of Pneumonia 
Paecilomyces variotii is a commonly occurring species in air and food, and it is also associated with many types of human infections. Pneumonia due to Paecilomyces variotii has been rarely reported in the medical literature. The authors report a 48-year-old patient with refractory lymphoma who underwent allogenic hematopoietic cell transplantation and developed pneumonia due to Paecilomyces variotii. They also review the published case reports of pneumonia caused by this fungus.
doi:10.1155/2013/273848
PMCID: PMC3683431  PMID: 23819077
23.  Purification and characterization of a Chinese hamster ovary cell elongation factor of Vibrio hollisae. 
Infection and Immunity  1995;63(7):2418-2423.
The halophilic bacterium Vibrio hollisae, isolated from patients with diarrhea, produces an extracellular toxin which elongates Chinese hamster ovary (CHO) cells. We purified this toxin to homogeneity by sequential ammonium sulfate precipitation, gel filtration with Sephacryl S-200, hydrophobic interaction chromatography with phenyl-Sepharose CL-4B, ion-exchange chromatography with DEAE-Sephadex A-50, and affinity chromatography. The toxin is heat labile and sensitive to proteases, with an isoelectric point of about 6.5 and molecular weights of about 83,000 and 80,000, as estimated by gel filtration and sodium dodecyl sulfate-polyacrylamide gel electrophoresis, respectively. The toxin did not react with immunoaffinity-purified antibodies to cholera toxin in a plate enzyme-linked immunosorbent assay and in a Western blot, and its activity could not be neutralized by anti-cholrea toxin serum. Mixed gangliosides and gangliosides GM1, GD1a, GD1b, Gq1b, GT1b, GD2, GD3, GM2, and GM3 failed to block its activity. Elongation of CHO cells induced by the toxin was not accompanied by an increase in the levels of cyclic AMP. The toxin induced intestinal fluid accumulation in suckling mice. These results and the lack of homology between V. hollisae DNA and DNA coding for cholera toxin or the heat-labile toxin of Escherichia coli suggest that the V. hollisae toxin is structurally and functionally different from other CHO cell-elongating toxins.
PMCID: PMC173323  PMID: 7790052
24.  Analysis of both chitinase and chitosanase produced by Sphingomonas sp. CJ-5*  
A novel chitinolytic and chitosanolytic bacterium, Sphingomonas sp. CJ-5, has been isolated and characterized. It secretes both chitinase and chitosanase into surrounding medium in response to chitin or chitosan induction. To characterize the enzymes, both chitinase and chitosanase were purified by ammonium sulfate precipitation, Sephadex G-200 gel filtration and DEAE-Sepharose Fast Flow. SDS-PAGE analysis demonstrated molecular masses of chitinase and chitosanase were 230 kDa and 45 kDa respectively. The optimum hydrolysis conditions for chitinase were about pH 7.0 and 36 °C, and these for chitosanase were pH 6.5 and 56 °C, respectively. Both enzymes were quite stable up to 45 °C for one hour at pH 5~8. These results show that CJ-5 may have potential for industrial application particularly in recycling of chitin wastes.
doi:10.1631/jzus.2007.B0831
PMCID: PMC2064955  PMID: 17973345
Sphingomonas sp.; Chitinase; Chitosanase
25.  Positive and Negative Transcriptional Regulators of Glutathione-Dependent Formaldehyde Metabolism 
Journal of Bacteriology  2004;186(23):7914-7925.
A glutathione (GSH)-dependent pathway is used for formaldehyde metabolism by a wide variety of prokaryotes and eukaryotes. In this pathway, S-hydroxymethylglutathione, produced by the reaction of formaldehyde with the thiolate moiety of glutathione, is the substrate for a GSH-dependent formaldehyde dehydrogenase (GSH-FDH). While expression of GSH-FDH often increases in the presence of metabolic or exogenous sources of formaldehyde, little is known about the factors that regulate this response. Here, we identify two signal transduction pathways that regulate expression of adhI, the gene encoding GSH-FDH, in Rhodobacter sphaeroides. The loss of the histidine kinase response regulator pair RfdRS or the histidine kinase RfdS increases adhI transcription in the absence of metabolic sources of formaldehyde. Cells lacking RfdRS further increase adhI expression in the presence of metabolic sources of formaldehyde (methanol), suggesting that this negative regulator of GSH-FDH expression does not respond to this compound. In contrast, mutants lacking the histidine kinase response regulator pair AfdRS or the histidine kinase AfdS cannot induce adhI expression in the presence of either formaldehyde or metabolic sources of this compound. AfdR stimulates activity of the adhI promoter in vitro, indicating that this protein is a direct activator of GSH-FDH expression. Activation by AfdR is detectable only after incubation of the protein with acetyl phosphate, suggesting that phosphorylation is necessary for transcription activation. Activation of adhI transcription by acetyl-phosphate-treated AfdR in vitro is inhibited by a truncated RfdR protein, suggesting that this protein is a direct repressor of GSH-FDH expression. Together, the data indicate that AfdRS and RfdRS positively and negatively regulate adhI transcription in response to different signals.
doi:10.1128/JB.186.23.7914-7925.2004
PMCID: PMC529062  PMID: 15547263

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