Purification and characterization of a β-1,4-glucosidase from a newly isolated strain of <Emphasis Type="Italic">Fomitopsis pinicola</Emphasis>

An efficient ß-1,4-glucosidase (BGL) producing strain, Fomitopsis pinicola KMJ812, was isolated and identified based on morphological features and sequence analysis of internal transcribed spacer rDNA. An extracellular BGL was purified to homogeneity by sequential chromatography of F. pinicola culture supernatants on a DEAE-sepharose column, a gel filtration column, and then on a Mono Q column with fast protein liquid chromatography. The relative molecular weight of F. pinicola BGL was determined to be 105 kDa by sodium dodecylsulfate-polyacrylamide gel electrophoresis, or 110 kDa by size exclusion chromatography, indicating that the enzyme is a monomer. The hydrolytic activity of the BGL had a pH optimum of 4.5 and a temperature optimum of 50°C. The enzyme showed high substrate specificity and high catalytic efficiency (k _cat?=?2,990 s^?1, K _m?=?1.76 mM, k _cat/K _m?=?1,700 mM^?1 s^?1) for p-nitrophenyl-β-d-glucopyranoside. Its internal amino acid sequences showed a significant homology with hydrolases from glycoside hydrolase family 3, indicating that the F. pinicola BGL is a member of glycoside hydrolase family 3. Although BGLs have been purified and characterized from several other sources, F. pinicola BGL is distinguished from other BGLs by its high catalytic efficiency and strict substrate specificity.     

Localization of Polyvinyl Alcohol Oxidase Produced by a Bacterial Symbiont, Pseudomonas sp. Strain VM15C

An axenic culture of a polyvinyl alcohol (PVA)-degrading symbiont, Pseudomonas sp. strain VM15C, was established on PVA with a crude preparation of the growth factor (factor A) produced by the symbiotic partner Pseudomonas putida VM15A. An increase of factor A in the culture medium enhanced the cell-associated PVA oxidase activity as well as the growth rate, but decreased production of extracellular PVA oxidase. PVA oxidase in cells grown on PVA was present in the periplasmic space at a higher ratio than in cells grown on peptone. PVA degradation occurred rapidly with washed cells. PVA was also degraded by immobilized cells entrapped in agar gels.     

Metabolic activities and ultrastructure imaging at late-stage of wood decomposition in interactive brown rot - white rot fungal combinations

Basidiomycota brown rot fungus (Fomitopsis pinicola) and two white rot fungi (Phlebia radiata, Trichaptum abietinum) were cultivated on thin slices of spruce wood individually and in interspecies combinations. Within 12 months, F. pinicola substantially decomposed spruce wood observed as mass loss, also in three-species combinations. However, white rot fungi through hyphal interactions negatively affected the brown-rot indicative iron reduction capacity of F. pinicola. Decay-signature gene expression in mycelial interaction zones indicated suppression of brown rot mechanism but stimulation of enzymatic white-rot lignin attack by P. radiata. Wood ultrastructure imaging showed white-rot dominance in the fungal combinations, whereas destructive brown-rot was evident with F. pinicola alone. Our results confirm the dynamic pattern of enzyme production in fungal combinations, and transition from brown to white rot decomposition metabolism during the late stage of wood decay after one year of interspecific interactions.     

Cell surface structure enhancing uptake of polyvinyl alcohol (PVA) is induced by PVA in the PVA-utilizing <Emphasis Type="Italic">Sphingopyxis</Emphasis> sp. strain 113P3

Polyvinyl alcohol (PVA)-utilizing Sphingopyxis sp. 113P3 (reidentified from Sphingomonas sp. 113P3) removed almost 0.5% PVA from culture supernatants in 4 days. Faster degradation of 0.5% PVA was performed by the periplasmic fraction. The average molecular size of PVA in the culture supernatant or cell-bound PVA was gradually shifted higher, suggesting that lower molecular size molecules are degraded faster. Depolymerized products were found in neither the culture supernatant nor the cell-bound fraction; however they were recovered from the periplasmic fraction. As extracellular or cell-associated PVA oxidase activity was almost undetectable in strain 113P3, degradation of PVA must be performed by periplasmic PVA dehydrogenase after uptake into the periplasm. Following the consumption of PVA, a dent appeared on the cell surface on day 2 and increased in size and depth for 4 days and was maintained for 8 days. Ultrastructural change on the cell surface was only observed in PVA medium, but not in nutrient broth (NB), suggesting that the change is induced by PVA. Fluorescein-4-isothiocyanate-labeled PVA was bound more to cells grown in PVA than to cells grown in NB. No binding was found with PVA-grown cells treated with formaldehyde. Thus, a dent on the cell surface seems to be related to the uptake of PVA.     

Studies on Milk Clotting Enzymes Produced by Basidiomycetes

In the course of screening tests of Basidiomycete proteolytic enzymes, it was observed that some strains produced milk clotting enzymes with fairly weak proteolytic activities.

When sucrose-polypeptone and sucrose-corn steep liquor media were used, only 6 strains out of 44 strains tested showed weak milk clotting activities. Cheddar cheese making with culture filtrates of these 6 strains revealed that the culture filtrates of 2 strains, Irpex lacteus Fr. and Fomitopsis pinicola (Fr.) Karst., were able to produce Cheddar cheese of good quality.

On the other hand, when sucrose-distillers solubles media were used, a lot of strains showed high proteolytic activity in addition to high milk clotting activity. The ratio of milk clotting to proteolytic activities (MCA/PA) was assumed to be an important index for the selection of organism, and F. pinicola and Coriolus consors (Berk.) Imaz. were selected as the strain with high MCA/PA ratio.

As the investigation on culture conditions of 3 strains mentioned above showed that F. pinicola and I. lacteus, were richly productive of milk clotting enzymes, the 2 strains except C. consors were used for further studies on cheese making.

Cheddar cheese making with crude enzymes revealed that cheese products produced by the enzyme of F. pinicola had a slightly bitter taste after 5 months’ ripening but that those produced by the enzyme of I. lacteus had good quality.     

Isolation and Culture Characterization of a New Polyvinyl Alcohol-Degrading Strain: Penicillium sp. WSH02-21

A fungal strain able to grow on polyvinyl alcohol (PVA) as sole carbon source was isolated from activated sludge of a textile factory. Morphological characteristics showed that this strain belonged to Penicillium sp., and, to our knowledge, this is the first report of PVA degradation by a strain of Penicillum sp. When 0.5% PVA was used as the carbon source in culture medium, it could be completely degraded after 12 days. This strain was found to produce and secrete an inducible PVA-degrading enzyme. High PVA concentration and oxygen transfer were favourable for PVA-degrading enzyme synthesis by Penicillium sp. cultured in shake-flasks. Moreover, Penicillum sp. cultured in PVA medium may spontaneously produce more catalase to decompose H₂O₂, a product of PVA oxidation by PVA oxidase, for protection of the cells from H₂O₂ damage. This revised version was published online in July 2006 with corrections to the Cover Date.     

Ultrasonic degradation, purification and analysis of structure and antioxidant activity of polysaccharide from Porphyra yezoensis Udea

The chemical structure and antioxidant of natural and ultrasonic degraded polysaccharides from Porphyra yezoensis Udea was investigated. The degraded polysaccharide (PYPS_UD) was purified, and F2 (a homogeneous fraction) was obtained. FT-IR, ¹H and ¹³C NMR spectral analysis revealed that F2 have typical porphyran structure. It has a backbone of alternating (1 → 4)-3,6-anhydro-α-l-galactopyranose) units and (1 → 3)-linked β-d-galactose or (1 → 4)-linked α-l-galactose 6-sulfate units. The result ascertained ultrasound degradation did not change the main structure of polysaccharides in the test conditions. Antioxidant proved that the activity of scavenging superoxide and hydroxyl radical is F₂ > V_C > PSPY_UD > PSPY. It was possible that ultrasonic treatment is an effective way for enhancing PSPY's antioxidant activity ascribing to decreasing molecular weight of polysaccharides.     

Metabolism of the Plasticizer di-n-Butylphthalate by Pseudomonas pseudoalcaligenes Under Anaerobic Conditions, with Nitrate as the Only Electron Acceptor

The metabolism of di-n-butylphthalate by a denitrifying strain of Pseudomonas pseudoalcaligenes B20b1 was studied under anaerobic conditions, with nitrate as the only electron acceptor. Thin-layer chromatography and mass spectral analysis of culture extracts (20 days at 30°C) showed mono-n-butylphthalate and phthalic acid as the only products, suggesting that one butanol moiety served essentially as the carbon source for growth and denitrification. N₂ and N₂O were detected by gas chromatography. In contrast to aerobic metabolism, phthalate was not degraded further if nitrate was the only electron acceptor.     

Beetles provide directed dispersal of viable spores of a keystone wood decay fungus

Wood decay fungi are considered to be dispersed by wind, but dispersal by animals may also be important, and more so in managed forests where dead wood is scarce. We investigated whether beetles could disperse spores of the keystone species Fomitopsis pinicola. Beetles were collected on sporocarps and newly felled spruce logs, a favourable habitat for spore deposition. Viable spores (and successful germination) of F. pinicola were detected by dikaryotization of monokaryotic bait mycelium from beetle samples. Viable spores were on the exoskeleton and in the faeces of all beetles collected from sporulating sporocarps. On fresh spruce logs, nine beetle species transported viable spores, of which several bore into the bark. Our results demonstrate that beetles can provide directed dispersal of wood decay fungi. Potentially, it could contribute to a higher persistence of some species in fragmented forests where spore deposition by wind on dead wood is less likely.     

Lignocarbohydrate Solubilization from Straw by Actinomycetes

Actinomycetes grown on wheat straw solubilized a lignocarbohydrate fraction which could be recovered by acid precipitation. Further characterization of this product (APPL) during growth of Streptomyces sp. strain EC1 revealed an increase in carboxylic acid and phenolic hydroxyl content, suggesting progressive modification. This was also observed in dioxane-extracted lignin fractions of degraded straw, and some similarity was further suggested by comparative infrared spectroscopy. However, the molecular weight profile of APPL was relatively constant during growth of Streptomyces sp. strain EC1 on straw, while analysis of the dioxane-extracted lignin fractions appeared to show fragmentation followed by repolymerization. Lignocarbohydrate solubilization could be monitored in all cultures by routine assay of APPL-associated protein, which accounted for up to 20% of the extracellular culture protein in some cases. Interestingly, this protein fraction was found to include active hydrolytic and oxidative enzymes involved in the degradation of lignocellulose, and specific enzyme activities were often increased in the acid-insoluble fractions of culture supernatants. This was particularly important for peroxidase and veratryl oxidase activities, which could be readily detected in the acid-precipitable lignocarbohydrate complex but were virtually undetectable in untreated culture supernatants.     

Regulation of acetylcholine receptors in the mouse muscle cell line,C2

The effects of culture age, muscle activity, and cell fusion on the metabolism of acetylcholine receptors in the mouse muscle cell line, C₂, were determined. Receptor degradation followed complex kinetics and was dependent on culture age. One or two day old myotubes degraded receptors rapidly (t₅₀ = 7–8 h) in a nearly single exponential process. Four or five day old myotubes, however, degraded receptors more slowly (t₅₀ = 12–16 h) in a process that deviated substantially from single exponential kinetics. A similar complex pattern of receptor degradation was seen with the L₆ cell line, but receptor degradation followed single exponential kinetics and was independent of culture age in primary rat myotubes and the BC3H-1 cell line. Acetylcholine receptors on C₂ myotubes were immunologically similar to the extrajunctional receptors of denervated mouse muscle. Clustered receptors were degraded at approximately the same rate as the total receptor population and receptor turnover was not changed when spontaneous contractions of the C₂ myotubes were inhibited. Newly synthesized receptors were more rapidly degraded than older receptors. Finally, receptors on fusion-arrested C₂ myoblasts were degraded at the same rate (t₅₀ = 16 h) regardless of culture age.     

Investigation into Stability of Poly(Vinyl Alcohol)-Based Opadry® II Films

Poly(vinyl alcohol) (PVA)-based formulations are used for pharmaceutical tablet coating with numerous advantages. Our objective is to study the stability of PVA-based coating films in the presence of acidic additives, alkaline additives, and various common impurities typically found in tablet formulations. Opadry® II 85F was used as the model PVA-based coating formulation. The additives and impurities were incorporated into the polymer suspension prior to film casting. Control and test films were analyzed before and after exposure to 40°C/75% relative humidity. Tests included film disintegration, size-exclusion chromatography, thermal analysis, and microscopy. Under stressed conditions, acidic additives (hydrochloric acid (HCl) and ammonium bisulfate (NH₄HSO₄)) negatively impacted Opadry® II 85F film disintegration while NaOH, formaldehyde, and peroxide did not. Absence of PVA species from the disintegration media corresponded to an increase in crystallinity of PVA for reacted films containing HCl. Films with NH₄HSO₄ exhibited slower rate of reactivity and less elevation in melting temperature with no clear change in melting enthalpy. Acidic additives posed greater risk of compromise in disintegration of PVA-based coatings than alkaline or common impurities. The mechanism of acid-induced reactivity due to the presence of acidic salts (HCl vs. NH₄HSO₄) may be different.     

Prospects for the use of new basidiomycete strains for the direct conversion of lignocellulose into ethanol

Sixty-six isolates of basidiomycete fungi were screened for the ability to synthesize cellulase. The effect of temperature on cellulase activity was studied for eight basidiomycete strains as perspective producers of ethanol. The temperature optima of enzyme activity ranged between 26 and 32°C. Direct conversion of Na-carboxymethyl cellulose, microcrystalline cellulose and rye straw were studied for seven basidiomycetes strains: Fomitopsis pinicola MT-5.09, F. pinicola MT-5.21, Piptoporus betulinus MT-30.04, Fomes fomentarius MT-4.05, F. fomentarius MT-4.23, Trametes hirsuta MT-24.24, Flammulina velutipes MT-3.03 Maximum ethanol production from Na-carboxymethyl cellulose (1.3 g/dm³) was achieved by strain F. velutipes MT-3.03. Strain F. fomentarius MT-4.05 more effectively converted rye straw to ethanol with yield of 1.1 g/dm³.     

Bioremediation of DDT contaminated soil using brown-rot fungi

The ability of brown-rot fungi (BRF) to eliminate DDT in artificially and historically contaminated soil was investigated to determine whether the BRF would be suitable for the bioremediation of DDT in soil. Gloeophyllum trabeum, Fomitopsis pinicola and Daedalea dickinsii showed an ability to eliminate DDT in artificially contaminated sterilized (SL) and un-sterilized (USL) soils. The addition of Fe²⁺ to the soil system enhanced the ability of some BRF to eliminate DDT. In the contaminated SL soil, the DDT was eliminated by approximately 41%, 9% and 15% by G. trabeum, F. pinicola and D. dickinsii, respectively. Compared with the controls, in the USL soil approximately 43%, 29% and 32% of DDT was eliminated and approximately 20%, 9% and 26% of DDD (1,1-dichloro-2,2-bis (4-chlorophenyl) ethane) was detected as a metabolic product with G. trabeum, F. pinicola and D. dickinsii, respectively. Of the BRF, G. trabeum demonstrated the greatest ability to eliminate DDT both in the SL and USL soils. G. trabeum was applied to a historically contaminated soil which had a DDT concentration more than three times the artificially contaminated soil. G. trabeum remediated about 64% of the initial DDT with the addition of Fe²⁺. There were no significant differences in the results with or without the addition of Fe²⁺, indicating that G. trabeum can be used directly for the degradation of DDT in soil without any other additional treatment. This study identified that G. trabeum is the most promising BRF for use in the bioremediation of DDT contaminated soil.     

Microbial Degradation of Alkyl Carbazoles in Norman Wells Crude Oil

Norman Wells crude oil was fractionated by sequential alumina and silicic acid column chromatography methods. The resulting nitrogen-rich fraction was analyzed by gas chromatography-mass spectrometry and showed 26 alkyl (C₁ to C₅) carbazoles to be the predominant compounds. An oil-degrading mixed bacterial culture was enriched on carbazole to enhance its ability to degrade nitrogen heterocycles. This culture was used to inoculate a series of flasks of mineral medium and Norman Wells crude oil. Residual oil was recovered from these cultures after incubation at 25°C for various times. The nitrogen-rich fraction was analyzed by capillary gas chromatography, using a nitrogen-specific detector. Most of the C₁-, C₂-, and C₃- carbazoles and one of the C₄-isomers were degraded within 8 days. No further degradation occurred when incubation was extended to 28 days. The general order of susceptibility of the isomers to biodegradation was C₁ > C₂ > C₃ > C₄. The carbazole-enriched culture was still able to degrade n-alkanes, isoprenoids, aromatic hydrocarbons, and sulfur heterocycles in the crude soil.     

Biotransformation of trichloroethene by pure bacterial cultures

From natural samples 11 isolates able to remove trichloroethene (CCl₂CHl) from an aqueousenvironment were obtained which were capable of cometabolic degradation of CCl₂CHCl by an enzyme system for phenol degradation. At an initial CCl₂CHCl concentration of 1 mg/L, the resting cells of particular cultures degraded 33–94% CCl₂CHCl during 1 d and their transformation capacity ranged from 0.3 to 3.1 mg CCl₂CHCl per g organic fraction. An analysis of a mixed phenol-fed culture with an excellent trichloroethene-degrading ability found a markedly minority isolate represented in the consortium to be responsible for this property. This culture degraded CCl₂CHCl even at a low inoculum concentration and attained a transformation capacity of 14.7 mg CCl₂CHCl per g. The increase in chloride concentration after degradation was quantitative when compared with the decrease in organically bound chlorine. The degree of CCl₂CHCl degradation was affected by Me₂S₂; this substance can significantly reduce the degrading ability of some tested cultures (>60%); however, it does not cause this inhibition with others.     

Residue Phe42 is critical for the catalytic activity of Escherichia coli major nitroreductase NfsA

The major O₂-insensitive nitroreductase (NfsA) of Escherichia coli shares low sequence homology but similar biochemical and structural features with NfsB, the E. coli minor O₂-insensitive nitroreductase. A structural comparison revealed Phe42 was present in the active site of NfsA but not NfsB. F42Y, F42N and F42A were generated and had decreased activity toward nitrofurazone by 52, 96, and 99 %, respectively. The kinetic parameters for other nitroaromatic substrates were also determined. Compared to wild type, the mutants did not have significantly altered K _ms, but had dramatically decreased k _cat and k _cat/K _m values. Far-UV CD spectral analysis of the mutants suggested that there were no significant conformational changes however F42A and F42N had changes from 208 to 222 nm, which was attributed to loss of helix content. These findings revealed that Phe42 is important for maintaining NfsA activity and structure.     

Viability characterization of Taxus chinensis plant cell suspension cultures by rapid colorimetric- and image analysis-based techniques

For the commercially established process of paclitaxel production with Taxus chinensis plant cell culture, the size of plant cell aggregates and phenotypic changes in coloration during cultivation have long been acknowledged as intangible parameters. So far, the variability of aggregates and coloration of cells are challenging parameters for any viability assay. The aim of this study was to investigate simple and non-toxic methods for viability determination of Taxus cultures in order to provide a practicable, rapid, robust and reproducible way to sample large amounts of material. A further goal was to examine whether Taxus aggregate cell coloration is related to general cell viability and might be exploited by microscopy and image analysis to gain easy access to general cell viability. The Alamar Blue assay was found to be exceptionally eligible for viability estimation. Moreover, aggregate coloration, as a morphologic attribute, was quantified by image analysis and found to be a good and traceable indicator of T. chinensis viability.     

Control of Interspecies Electron Flow during Anaerobic Digestion: Role of Floc Formation in Syntrophic Methanogenesis

The flora of an anaerobic whey-processing chemostat was separated by anaerobic sedimentation techniques into a free-living bacterial fraction and a bacterial floc fraction. The floc fraction constituted a major part (i.e., 57% total protein) of the total microbial population in the digestor, and it accounted for 87% of the total CO₂-dependent methanogenic activity and 76% of the total ethanol-consuming acetogenic activity. Lactose was degraded by both cellular fractions, but in the free flora fraction it was associated with higher intermediary levels of H₂, ethanol, butyrate, and propionate production. Electron microscopic analysis of flocs showed bacterial diversity and juxtapositioning of tentative Desulfovibrio and Methanobacterium species without significant microcolony formation. Ethanol, an intermediary product of lactose-hydrolyzing bacteria, was converted to acetate and methane within the flocs by interspecies electron transfer. Ethanol-dependent methane formation was compartmentalized and closely coupled kinetically within the flocs but without significant formation of H₂ gas. Physical disruption of flocs into fragments of 10- to 20-μm diameter initially increased the H₂ partial pressure but did not change the carbon transformation kinetic patterns of ethanol metabolism or demonstrate a significant role for H₂ in CO₂ reduction to methane. The data demonstrate that floc formation in a whey-processing anaerobic digestor functions in juxtapositioning cells for interspecies electron transfer during syntrophic ethanol conversion into acetate and methane but by a mechanism which was independent of the available dissolved H₂ gas pool in the ecosystem.