Complete Genome Sequence of Elizabethkingia sp. BM10, a Symbiotic Bacterium of the Wood-Feeding Termite Reticulitermes speratus KMT1.

Elizabethkingia sp. BM10 was isolated from the hindgut of the wood-feeding termite Reticulitermes speratus KMT1. It had cellobiohydrolase and ß-glucosidase activities but not endo-ß-glucanase activity. The complete sequence of its genome, which has a total size of 4,242,519 bases, is reported here. The genomic analysis identified six ß-glucosidase candidate genes and three ß-glucanase candidate genes.

Sanitizing Effect of Ethanol Against Biofilms Formed by Three Gram-Negative Pathogenic Bacteria.

Sanitizing effect of ethanol on a Yersinia enterocolitica biofilm was evaluated in terms of biomass removal and bactericidal activity. We found that 40 % ethanol was most effective for biofilm biomass removal; however, no significant difference was observed in bactericidal activity between treatment with 40 and 70 % ethanol. This unexpected low ethanol concentration requirement for biomass removal was confirmed using biofilms of two additional pathogenic bacteria, Aeromonas hydrophila and Xanthomonas oryzae. Although only three pathogenic Gram-negative bacteria were tested and the biofilm in nature was different from the biofilm in this study, the results in this study suggested the possible re-evaluation of the effective sanitizing ethanol concentration 70 %, which is the concentration commonly employed for sanitization, on bacteria in a biofilm.

Rapid saccharification for production of cellulosic biofuels.

The economical production of biofuels is hindered by the recalcitrance of lignocellulose to processing, causing high consumption of processing enzymes and impeding hydrolysis of pretreated lignocellulosic biomass. We determined the major rate-limiting factor in the hydrolysis of popping pre-treated rice straw (PPRS) by examining cellulase adsorption to lignin and cellulose, amorphogenesis of PPRS, and re-hydrolysis. Based on the results, equivalence between enzyme loading and the open structural area of cellulose was required to significantly increase productive adsorption of cellulase and to accelerate enzymatic saccharification of PPRS. Amorphogenesis of PPRS by phosphoric acid treatment to expand open structural area of the cellulose fibers resulted in twofold higher cellulase adsorption and increased the yield of the first re-hydrolysis step from 13% to 46%. The total yield from PPRS was increased to 84% after 3h. These results provide evidence that cellulose structure is one of major effects on the enzymatic hydrolysis.

Purification and characterization of a thermostable xylanase from Fomitopsis pinicola.

An extracellular xylanase was purified to homogeneity by sequential chromatography of Fomitopsis pinicola culture supernatants on a DEAE-sepharose column, a gel filtration column, and then on a MonoQ column with fast protein liquid chromatography. The relative molecular weight of F. pinicola xylanase was determined to be 58 kDa by sodium dodecylsulfate polyacrylamide gel electrophoresis and by size exclusion chromatography, indicating that the enzyme is a monomer. The hydrolytic activity of the xylanase had a pH optimum of 4.5 and a temperature optimum of 70 degreesC. The enzyme showed t(1/2) value of 33 h at 70 degrees C and catalytic efficiency (k(cat) = 77.4 s⁻¹, k(cat)/K(m) = 22.7 mg/ml/s) for oatspelt xylan. Its internal amino acid sequences showed a significant homology with hydrolases from glycoside hydrolase (GH) family 10, indicating that the F. pinicola xylanase is a member of GH family 10.

One-step purification and characterization of a beta-1,4-glucosidase from a newly isolated strain of Stereum hirsutum.

A highly efficient beta-1,4-glucosidase (BGL) secreting strain, Stereum hirsutum SKU512, was isolated and identified based on morphological features and sequence analysis of internal transcribed spacer rDNA. A BGL containing a carbohydrate moiety was purified to homogeneity from S. hirsutum culture supernatants using only a single chromatography step on a gel filtration column. The relative molecular weight of S. hirsutum BGL was determined as 98 kDa by sodium dodecyl sulfate polyacrylamide gel electrophoresis or 780 kDa by size exclusion chromatography, indicating that the enzyme is an octamer. S. hirsutum BGL showed the highest activity toward p-nitrophenyl-beta-D-glucopyranoside (V (max) = 3,028 U mg-protein(-1), k (cat) = 4,945 s(-1)) ever reported. The enzyme also showed good stability at an acidic pH ranging from 3.0 to 5.5. The BGL was able to promote transglycosylation with an activity of 42.9 U mg-protein(-1) using methanol as an acceptor and glucose as a donor. The internal amino acid sequences of the isolated enzyme showed significant homology with hydrolases from glycoside hydrolase family 1 (GH1), indicating that the S. hirsutum BGL is a member of GH1 family. The characteristics of S. hirsutum BGL could prove to be of interest in several potential applications, especially in enhancing flavor release during the wine fermentation process.

Symbiotic adaptation of bacteria in the gut of Reticulitermes speratus: low endo-beta-1,4-glucanase activity.

The termite is a good model of symbiosis between microbes and hosts and possesses an effective cellulose digestive system. Oxygen-tolerant bacteria, such as Dyella sp., Chryseobacterium sp., and Bacillus sp., were isolated from Reticulitermes speratus gut. Notably, the endo-beta-1,4-glucanase (EG) activity of all 16 strains of isolated bacteria was low. Due to the combined activity of EG from the termites and their symbiotic protozoa, the bacteria might not be compelled to express EG. This observation demonstrates how well intestinal bacteria have assimilated themselves into the efficient cellulose digestive systems of termites.

Purification and characterization of a thermostable cellobiohydrolase from Fomitopsis pinicola.

A screening for cellobiohydrolase (CBH) activity was performed and Fomitopsis pinicola KMJ812 was selected for further characterization as it produced a high level of CBH activity. An extracellular CBH was purified to homogeneity by sequential chromatography of F. pinicola culture supernatants. The molecular mass of the F. pinicola CBH was determined to be 64 kDa by SDS-PAGE and by size-exclusion chromatography, indicating that the enzyme is a monomer. The F. pinicola CBH showed a t1/2 value of 42 h at 70 degrees C and catalytic efficiency of 15.8 mM-1 S-1 (kcat/ Km) for p-nitrophenyl-beta-D-cellobioside, one of the highest levels seen for CBH-producing microorganisms. Its internal amino acid sequences showed a significant homology with hydrolases from glycoside hydrolase family 7. Although CBHs have been purified and characterized from other sources, the F. pinicola CBH is distinguished from other CBHs by its high catalytic efficiency and thermostability.

Characterization of endo-beta-1,4-glucanase from a novel strain of Penicillium pinophilum KMJ601.

A novel endo-beta-1,4-glucanase (EG)-producing strain was isolated and identified as Penicillium pinophilum KMJ601 based on its morphology and internal transcribed spacer (ITS) rDNA gene sequence. When rice straw and corn steep powder were used as carbon and nitrogen sources, respectively, the maximal EG activity of 5.0 U mg protein(-1), one of the highest levels among EG-producing microorganisms, was observed. The optimum temperature and pH for EG production were 28 degrees C and 5.0, respectively. The increased production of EG by P. pinophilum in culture at 28 degrees C was confirmed by two-dimensional electrophoresis followed by MS/MS sequencing of the partial peptide. A partial EG gene (eng5) was amplified by degenerate polymerase chain reaction (PCR) based on the peptide sequence. A full-length eng5 was cloned by genome-walking PCR, and P. pinophilum EG was identified as a member of glycoside hydrolase family 5. The present results should contribute to improved industrial production of EG by P. pinophilum KMJ601.

Purification and characterization of a thermostable beta-1,3-1,4-glucanase from Laetiporus sulphureus var. miniatus.

A beta-1,3-1,4-glucanase from the fungus Laetiporus sulphureus var. miniatus was purified as a single 26 kDa band by ammonium sulfate precipitation, HiTrap Q HP, and UNO Q ion-exchange chromatography, with a specific activity of 29 U/mg. The molecular mass of the native enzyme was 52 kDa as a dimer by gel filtration. beta-1,3-1,4-Glucanase showed optimum activity at pH 4.0 and 75 degrees . The half-lives of the enzyme at 70 degrees and 75 degrees were 152 h and 22 h, respectively. The enzyme showed the highest activity for barley beta- glucan as beta-1,3-1,4-glucan among the tested polysaccharides and p-nitrophenyl-beta-D-glycosides with a K(m) of 0.67 mg/ml, a k(cat) of 13.5 s(-1) and a k(cat)/K(m) of 20 mg/ml/s.

Characterization of a recombinant beta-glucosidase from the thermophilic bacterium Caldicellulosiruptor saccharolyticus.

A recombinant beta-glucosidase from Caldicellulosiruptor saccharolyticus DSM 8903 with a specific activity of 13 U/mg was purified by heat treatment and His-Trap affinity chromatography and identified as a single 54 kDa band on SDS-PAGE. The molecular mass of the native enzyme was 108 kDa as a dimer by gel filtration. beta-Glucosidase showed optimum activity at pH 5.5 and 70 degrees C for p-nitrophenyl (pNP)-beta-d-glucopyranoside. The half-lives of the enzyme at 60, 70, and 80 degrees C were 250, 24.3, and 0.4 h, respectively. The enzyme exhibited catalytic efficiency and specific activity for pNP-beta-d-fucopyranoside, pNP-beta-d-glucopyranoside, and pNP-beta-d-galactopyranoside in decreasing order among aryl-beta-glycosides, but not for aryl-alpha-glycosides. Cello-oligosaccharides from n = 2 to 5 as substrates using 4 mM each sugar and 3 U/mg of enzyme were completely hydrolyzed to glucose at 70 degrees C within 16 h.

Purification and characterization of a beta-1,4-glucosidase from a newly isolated strain of Fomitopsis pinicola.

An efficient beta-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 degrees C. The enzyme showed high substrate specificity and high catalytic efficiency (kcat=2,990 s-1, Km=1.76mM, kcat/Km=1,700 mM-1 s-1) for p-nitrophenyl-beta-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.

Functional analysis of a gene encoding endoglucanase that belongs to glycosyl hydrolase family 12 from the brown-rot basidiomycete Fomitopsis palustris.

The brown-rot basidiomycete Fomitopsis palustris is known to degrade crystalline cellulose (Avicel) and produce three major cellulases, exoglucanases, endoglucanases, and beta- glucosidases. A gene encoding endoglucanase, designated as cel12, was cloned from total RNA prepared from F. palustris grown at the expense of Avicel. The gene encoding Cel12 has an open reading frame of 732 bp, encoding a putative protein of 244 amino acid residues with a putative signal peptide residing at the first 18 amino acid residues of the N-terminus of the protein. Sequence analysis of Cel12 identified three consensus regions, which are highly conserved among fungal cellulases belonging to GH family 12. However, a cellulose-binding domain was not found in Cel12, like other GH family 12 fungal cellulases. Northern blot analysis showed a dramatic increase of cel12 mRNA levels in F. palustris cells cultivated on Avicel from the early to late stages of growth and the maintenance of a high level of expression in the late stage, suggesting that Cel12 takes a significant part in endoglucanase activity throughout the growth of F. palustris. Adventitious expression of cel12 in the yeast Pichia pastoris successfully produced the recombinant protein that exhibited endoglucanase activity with carboxymethyl cellulose, but not with crystalline cellulose, suggesting that the enzyme is not a processive endoglucanase unlike two other endoglucanases previously identified in F. palustris.

Degradation of cellulose by the major endoglucanase produced from the brown-rot fungus Fomitopsis pinicola.

An endoglucanase that is able to degrade both crystalline and amorphous cellulose was purified from the culture filtrates of the brown-rot fungus Fomitopsis pinicola grown on cellulose. An apparent molecular weight of the purified enzyme was approximately 32 kDa by SDS-PAGE analysis. The enzyme was purified 11-fold with a specific activity of 944 U/mg protein against CMC. The partial amino acid sequences of the purified endoglucanase had high homology with endo-beta-1,4-glucanase of glycosyl hydrolase family 5 from other fungi. The K(m) and K(cat)values for CMC were 12 mg CMC/ml and 670/s, respectively. The purified EG hydrolyzed both cellotetraose (G4) and cellopentaose (G5), but did not degrade either cellobiose (G2) or cellotriose (G3).

The brown-rot basidiomycete Fomitopsis palustris has the endo-glucanases capable of degrading microcrystalline cellulose.

Two endoglucanases with processive cellulase activities, produced from Fomitopsis palustris grown on 2% microcrystalline cellulose (Avicel), were purified to homogeneity by anion-exchange and gel filtration column chromatography systems. SDS-PAGE analysis indicated that the molecular masses of the purified enzymes were 47 kDa and 35 kDa, respectively. The amino acid sequence analysis of the 47-kDa protein (EG47) showed a sequence similarity with fungal glycoside hydrolase family 5 endoglucanase from the white-rot fungus Phanerochaete chrysosporium. N-terminal and internal amino acid sequences of the 35-kDa protein (EG35), however, had no homology with any other glycosylhydrolases, although the enzyme had high specific activity against carboxymethyl cellulose, which is a typical substrate for endoglucanases. The initial rate of Avicel hydrolysis by EG35 was relatively fast for 48 h, and the amount of soluble reducing sugar released after 96 h was 100 microg/ml. Although EG47 also hydrolyzed Avicel, the hydrolysis rate was lower than that of EG35. Thin layer chromatography analysis of the hydrolysis products released from Avicel indicated that the main product was cellobiose, suggesting that the brown-rot fungus possesses processive EGs capable of degrading crystalline cellulose.

Prediction of glass transition temperature (T(g)) of some compounds in organic electroluminescent devices with their molecular properties.

We have studied the quantitative structure-property relationship between descriptors representing the molecular structure and glass transition temperature (T(g)) for 103 molecules including organic electroluminescent (EL) devices materials. Eighty-six descriptors were introduced and among them seven descriptors (one topological descriptor, one thermodynamic descriptor, one spatial descriptor, one structural descriptor, and three electrostatic descriptors) were selected by Genetic Algorithm (GA). The 81 molecules chosen randomly among 103 compounds were used as a training set, and the remaining 22 molecules were used as a prediction set. The quantitative relationship between these seven descriptors and T(g) was tested by multiple linear regression (MLR) and artificial neural network (ANN). ANN analysis showed no significant advantage over MLR for this study. As the results of the MLR, the square of the correlation coefficient (R(2)) for the T(g) of the 81 training set was 0.989, and the average error was 8.8 K. In prediction for T(g) using the 22 prediction compounds set with MLR, R(2) was 0.976, and the average error was 13.9 K.