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1.
Front Plant Sci ; 15: 1297096, 2024.
Article in English | MEDLINE | ID: mdl-38584945

ABSTRACT

Mungbean [Vigna radiata var. radiata (L.) Wilczek] production in Asia is detrimentally affected by transient soil waterlogging caused by unseasonal and increasingly frequent extreme precipitation events. While mungbean exhibits sensitivity to waterlogging, there has been insufficient exploration of germplasm for waterlogging tolerance, as well as limited investigation into the genetic basis for tolerance to identify valuable loci. This research investigated the diversity of transient waterlogging tolerance in a mini-core germplasm collection of mungbean and identified candidate genes for adaptive traits of interest using genome-wide association studies (GWAS) at two critical stages of growth: germination and seedling stage (i.e., once the first trifoliate leaf had fully-expanded). In a temperature-controlled glasshouse, 292 genotypes were screened for tolerance after (i) 4 days of waterlogging followed by 7 days of recovery at the germination stage and (ii) 8 days of waterlogging followed by 7 days of recovery at the seedling stage. Tolerance was measured against drained controls. GWAS was conducted using 3,522 high-quality DArTseq-derived SNPs, revealing five significant associations with five phenotypic traits indicating improved tolerance. Waterlogging tolerance was positively correlated with the formation of adventitious roots and higher dry masses. FGGY carbohydrate kinase domain-containing protein was identified as a candidate gene for adventitious rooting and mRNA-uncharacterized LOC111241851, Caffeoyl-CoA O-methyltransferase At4g26220 and MORC family CW-type zinc finger protein 3 and zinc finger protein 2B genes for shoot, root, and total dry matter production. Moderate to high broad-sense heritability was exhibited for all phenotypic traits, including seed emergence (81%), adventitious rooting (56%), shoot dry mass (81%), root dry mass (79%) and SPAD chlorophyll content (70%). The heritability estimates, marker-trait associations, and identification of sources of waterlogging tolerant germplasm from this study demonstrate high potential for marker-assisted selection of tolerance traits to accelerate breeding of climate-resilient mungbean varieties.

2.
Front Plant Sci ; 12: 709102, 2021.
Article in English | MEDLINE | ID: mdl-34490010

ABSTRACT

Mungbean [Vigna radiata (L.) Wilczek] and blackgram [Vigna mungo (L.) Hepper] are important crops for smallholder farmers in tropical and subtropical regions. Production of both crops is affected by unexpected and increasingly frequent extreme precipitation events, which result in transient soil waterlogging. This study aimed to compare the waterlogging tolerance of mungbean and blackgram genotypes under the varying duration of waterlogging stress at germination and seedling stages. We evaluated the responses to different durations of transient waterlogging in a sandy clay loam under temperature-controlled glasshouse conditions. Waterlogging durations were 0, 1, 2, 3, 4, 5, 6, 7, and 8 days during germination and 0, 2, 4, 8, and 16 days during the seedling stage. We used two mungbean genotypes (green testa), Celera II-AU (small-seeded), and Jade-AU (large-seeded), contrasting in seed size and hypocotyl pigmentation, and a blackgram genotype (black testa), Onyx-AU. Waterlogging reduced soil redox potential, delayed or even prevented germination, decreased seedling establishment, and affected shoot and root development. In the seedlings waterlogged (WL) at 15 days after sowing (DAS), adventitious root formation and crown nodulation varied between the genotypes, and 16 days of waterlogging substantially reduced growth but did not result in plant death. Plants in soil with waterlogging for 8-16 days followed by drainage and sampling at 39 DAS had reduced shoot and root dry mass by 60-65% in mungbean and 40% in blackgram compared with continuously drained controls, due at least in part to fewer lateral roots. Soil plant analysis development (SPAD) chlorophyll content was also reduced. Onyx-AU, a blackgram genotype, was more tolerant to transient waterlogging than Jade-AU and Celera II-AU in both growth stages. Of the two mungbean genotypes, Celera II-AU had a greater seedling establishment than Jade-AU post waterlogging imposed at sowing. In contrast, Jade-AU had more plant biomass and greater recovery growth than Celera II-AU after waterlogging and recovery during the seedling stage. Both species were delayed in emergence in response to the shorter periods of transient waterlogging at germination, and with the longer waterlogging germination and emergence failed, whereas at the seedling stage both showed adaptation by the formation of adventitious roots.

3.
Folia Microbiol (Praha) ; 58(2): 163-76, 2013 Mar.
Article in English | MEDLINE | ID: mdl-23011949

ABSTRACT

Cellulase (CEL) presently constitutes a major group of industrial enzyme based on its diverse ranges of utilization. Apart from such current and well-established applications-as in cotton processing, paper recycling, detergent formulation, juice extraction, and animal feed additives-their uses in agricultural biotechnology and bioenergy have been exploited. Supplementation of CELs to accelerate decomposition of plant residues in soil results in improved soil fertility. So far, applying CELs/antagonistic cellulolytic fungi to crops has shown to promote plant growth performance, including enhanced seed germination and protective effects. Their actions are believed mainly to trigger plant defense mechanisms and/or to act as biocontrol agents that mediate disease suppression. However, the exact interaction between the enzymes/fungi and plants has not been clearly elucidated. Under mild conditions, removal of plant cell wall polysaccharides by CELs for protoplast preparation results in reduced protoplast damage and increased viability and yields. CELs have recently shown great potential in enzyme aid extraction of bioactive compounds from plant materials before selective extraction through enhancing release of target molecules, especially those associated with the wall matrix. To date, attempts have been made to formulate CEL preparation for cellulosic-based bioethanol production. The high cost of CELs has created a bottleneck, resulting in an uneconomic production process. The utilization of low-cost carbohydrates, strain improvement, and gene manipulations has been alternatively aimed at reducing the cost of CEL production. In this review, we focus on and discuss current knowledge of CELs and their applications in agriculture, biotechnology, and bioenergy.


Subject(s)
Agriculture/methods , Bioelectric Energy Sources , Biotechnology/methods , Cellulases/metabolism , Agriculture/trends , Biotechnology/trends
4.
Biosci Biotechnol Biochem ; 76(10): 1884-90, 2012.
Article in English | MEDLINE | ID: mdl-23047100

ABSTRACT

The aim of this study was to purify an acidic α-glucan-protein complex from the fruiting bodies of Pleurotus sajor-caju by using the cell wall-degrading enzymes, xylanase and cellulase. The acidic glucan-protein complex was separated from a polysaccharide extract by using DEAE Toyopearl 650M anion-exchange and Sepharose CL-6B chromatography. Its homogeneity was ensured by high-performance size-exclusion chromatography and agarose gel electrophoresis. The acidic glucan-protein complex had a molecular weight of approximately 182 kDa. Fourier transform infrared spectroscopy of the acidic glucan-protein complex revealed an α-glycosidic bond and the typical characteristics of polysaccharides and proteins. The amino acid composition of the protein moiety was dominated by proline, glycine, glutamic acid and aspartic acid, indicating that the protein was highly flexible and had a negative charge. Atomic force microscopy proved that the acidic α-glucan-protein complex existed in a spherical conformation. The acidic α-glucan-protein complex stimulated the activation of macrophages, including the production of nitric oxide and tumor necrosis factor-α.


Subject(s)
Fruiting Bodies, Fungal/chemistry , Fungal Proteins/metabolism , Glucans/metabolism , Glycoproteins/isolation & purification , Glycoproteins/pharmacology , Macrophages/drug effects , Pleurotus/chemistry , Animals , Cell Line , Cellulase/metabolism , Endo-1,4-beta Xylanases/metabolism , Glucans/isolation & purification , Glycoproteins/chemistry , Glycoproteins/metabolism , Hydrogen-Ion Concentration , Mice , Molecular Weight
5.
J Microbiol ; 50(3): 394-400, 2012 Jun.
Article in English | MEDLINE | ID: mdl-22752902

ABSTRACT

A mesophilic, facultative, anaerobic, xylanolytic-cellulolytic bacterium, TW1(T), was isolated from sludge in an anaerobic digester fed with pineapple waste. Cells stained Gram-positive, were spore-forming, and had the morphology of straight to slightly curved rods. Growth was observed in the temperature range of 30 to 50°C (optimum 37°C) and the pH range of 6.0 to 7.5 (optimum pH 7.0) under aerobic and anaerobic conditions. The strain contained meso-diaminopimelic acid in the cell-wall peptidoglycan. The predominant isoprenoid quinone was menaquinone with seven isoprene units (MK-7). Anteiso-C(15:0), iso-C(16:0), anteiso-C(17:0), and C(16:0) were the predominant cellular fatty acids. The G+C content of the DNA was 49.5 mol%. A phylogenetic analysis based on 16S rRNA showed that strain TW1(T) belonged within the genus Paenibacillus and was closely related to Paenibacillus cellulosilyticus LMG 22232(T), P. curdlanolyticus KCTC 3759(T), and P. kobensis KCTC 3761(T) with 97.7, 97.5, and 97.3% sequence similarity, respectively. The DNA-DNA hybridization values between the isolate and type strains of P. cellulosilyticus LMG 22232(T), P. curdlanolyticus KCTC 3759(T), and P. kobensis KCTC 3761(T) were found to be 18.6, 18.3, and 18.0%, respectively. The protein and xylanase patterns of strain TW1(T) were quite different from those of the type strains of closely related Paenibacillus species. On the basis of DNA-DNA relatedness and phenotypic analyses, phylogenetic data and the enzymatic pattern presented in this study, strain TW1(T) should be classified as a novel species of the genus Paenibacillus, for which the name Paenibacillus xylaniclasticus sp. nov. is proposed. The type strain is TW1(T) (=NBRC 106381(T) =KCTC 13719(T) =TISTR 1914(T)).


Subject(s)
Cellulose/metabolism , Paenibacillus/classification , Paenibacillus/isolation & purification , Sewage/microbiology , Xylans/metabolism , Aerobiosis , Anaerobiosis , Ananas/metabolism , Base Composition , Cluster Analysis , Cytosol/chemistry , DNA, Bacterial/chemistry , DNA, Bacterial/genetics , DNA, Ribosomal/chemistry , DNA, Ribosomal/genetics , Diaminopimelic Acid/analysis , Fatty Acids/analysis , Hydrogen-Ion Concentration , Molecular Sequence Data , Nucleic Acid Hybridization , Paenibacillus/genetics , Paenibacillus/metabolism , Peptidoglycan/chemistry , Phylogeny , Quinones/analysis , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , Spores, Bacterial/cytology , Temperature
6.
J Agric Food Chem ; 60(21): 5423-30, 2012 May 30.
Article in English | MEDLINE | ID: mdl-22563990

ABSTRACT

The objective of this work was to improve the purity of ß-(1→3)(1→6)-glucan in the native triple helical structure from the fruiting bodies of Pleurotus sajor-caju for effective biological function using cell wall-degrading enzymes. A crude carbohydrate was extracted with hot water, then treated with crude xylanase and cellulase from Paenibacillus curdlanolyticus B-6. ß-Glucan in the extract was purified to homogeneity with a single and symmetrical peak using 650M DEAE Toyopearl and Sepharose CL-6B column chromatography. The purity of ß-glucan was confirmed by high-performance size-exclusion chromatography. Purified ß-glucan was obtained at a purity of up to 90.2%. The Congo red reaction and atomic force microscopy indicated that the purified ß-glucan exhibited a triple helix conformation. Purified ß-glucan was able to effectively up-regulate the functions of macrophages such as nitric oxide (NO) and tumor necrosis factor (TNF-α) production.


Subject(s)
Bacterial Proteins/chemistry , Cellulase/chemistry , Endo-1,4-beta Xylanases/chemistry , Glucans/pharmacology , Immunologic Factors/pharmacology , Paenibacillus/enzymology , Pleurotus/chemistry , Animals , Cell Line , Cell Wall/chemistry , Fruiting Bodies, Fungal/chemistry , Glucans/chemistry , Immunologic Factors/chemistry , Macrophages/drug effects , Macrophages/immunology , Mice
7.
Appl Biochem Biotechnol ; 166(7): 1791-800, 2012 Apr.
Article in English | MEDLINE | ID: mdl-22350872

ABSTRACT

A thermophilic Anoxybacillus sp. strain JT-12, isolated from soil, produced acidic xylotriose, 4-O-methyl-α-D-glucuronosyl-xylotriose (MeGlcAX3), as a main product from birchwood xylan and accumulated them in the culture under optimum conditions at pH 7.0 and 55 °C using 0.75% (w/v) birchwood xylan as a carbon source for 42-72 h. The acidic xylotriose was purified by ethanol precipitation and high-performance liquid chromatography using NH2 Lichosher® 100 column. The results of electrospray ionization mass spectrometry, mass to charge ratio (m/z) 603.23, confirmed that the purified sample was acidic xylotriose that had benefits and applications in many fields.


Subject(s)
Anoxybacillus/metabolism , Trisaccharides/biosynthesis , Wood/metabolism , Xylans/metabolism , Betula/chemistry , Chromatography, High Pressure Liquid , Culture Media , Ethanol/chemistry , Hot Temperature , Hydrogen-Ion Concentration , Molecular Weight , Spectrometry, Mass, Electrospray Ionization , Trisaccharides/isolation & purification , Trisaccharides/metabolism
8.
Biodegradation ; 23(1): 57-68, 2012 Feb.
Article in English | MEDLINE | ID: mdl-21637976

ABSTRACT

The anaerobic thermophilic bacterium, Clostridium thermocellum, is a potent cellulolytic microorganism that produces large extracellular multienzyme complexes called cellulosomes. To isolate C. thermocellum organisms that possess effective cellulose-degrading ability, new thermophilic cellulolytic strains were screened from more than 800 samples obtained mainly from agriculture residues in Thailand using microcrystalline cellulose as a carbon source. A new strain, C. thermocellum S14, having high cellulose-degrading ability was isolated from bagasse paper sludge. Cellulosomes prepared from S14 demonstrated faster degradation of microcrystalline cellulose, and 3.4- and 5.6-fold greater Avicelase activity than those from C. thermocellum ATCC27405 and JW20 (ATCC31449), respectively. Scanning electron microscopic analysis showed that S14 had unique cell surface features with few protuberances in contrast to the type strains. In addition, the cellulosome of S14 was resistant to inhibition by cellobiose that is a major end product of cellulose hydrolysis. Saccharification tests conducted using rice straw soaked with sodium hydroxide indicated the cellulosome of S14 released approximately 1.5-fold more total sugars compared to that of ATCC27405. This newly isolated S14 strain has the potential as an enzyme resource for effective lignocellulose degradation.


Subject(s)
Cellulosomes/enzymology , Clostridium thermocellum/enzymology , Glycoside Hydrolases/metabolism , Lignin/metabolism , Bacteria, Anaerobic/enzymology , Bacteria, Anaerobic/genetics , Cellulose/metabolism , Cellulosomes/ultrastructure , Chromatography, Gel , Cloning, Molecular , Clostridium thermocellum/genetics , Escherichia coli , Glycoside Hydrolases/genetics , Hydrolysis , Microscopy, Electron, Scanning , Oryza/metabolism , RNA, Bacterial/biosynthesis , RNA, Bacterial/genetics , RNA, Ribosomal, 16S/biosynthesis , RNA, Ribosomal, 16S/genetics , Sewage/microbiology , Thailand , Waste Products
9.
Int J Syst Evol Microbiol ; 62(Pt 10): 2330-2335, 2012 Oct.
Article in English | MEDLINE | ID: mdl-22140158

ABSTRACT

An obligately anaerobic, cellulolytic-xylanolytic bacterium, designated strain A6(T), was isolated from soil of a coconut garden in the Bangkuntien district of Bangkok, Thailand. The strain was Gram-stain positive, catalase-negative, endospore-forming, motile and rod-shaped with a cell size of 0.2-0.3×2.0-3.0 µm. Optimal growth of strain A6(T) occurred at pH(55 °C) 9.5, 55 °C. Strain A6(T) fermented various carbohydrates, and the end products from the fermentation of cellobiose were acetate, ethanol, propionate and a small amount of butyrate. The major cellular fatty acids were iso-C(14:0) 3-OH, iso-C(15:0), iso-C(16:0) and C(16:0). The cell-wall peptidoglycan contained meso-diaminopimelic acid. No respiratory quinones were detected. The DNA G+C content was 30.0 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the strain represented a new phyletic sublineage within the family Clostridiaceae, with <93.0% 16S rRNA gene sequence similarity to recognized species of this family. On the basis of phenotypic, genotypic and physiological evidence, strain A6(T) represents a novel species of a new genus, for which the name Cellulosibacter alkalithermophilus gen. nov., sp. nov. is proposed. The type strain of the type species is A6(T) ( = TISTR 1915(T) = KCTC 5874(T)).


Subject(s)
Gram-Positive Bacteria/classification , Phylogeny , Soil Microbiology , Bacteria, Anaerobic/classification , Bacteria, Anaerobic/genetics , Bacteria, Anaerobic/isolation & purification , Bacterial Typing Techniques , Base Composition , Carbohydrate Metabolism , Cocos , DNA, Bacterial/genetics , Fatty Acids/analysis , Fermentation , Gram-Positive Bacteria/genetics , Gram-Positive Bacteria/isolation & purification , Molecular Sequence Data , Peptidoglycan/analysis , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , Thailand
10.
J Microbiol Biotechnol ; 21(3): 284-92, 2011 Mar.
Article in English | MEDLINE | ID: mdl-21464600

ABSTRACT

An endocellulase-free multienzyme complex was produced by a thermophilic anaerobic bacterium, Thermoanaerobacterium thermosaccharolyticum strain NOI-1, when grown on xylan. The temperature and pH optima for growth were 60 degrees C and 6.0, respectively. The bacterial cells were found to adhere to insoluble xylan and Avicel. A scanning electron microscopy analysis showed the adhesion of xylan to the cells. An endocellulase-free multienzyme complex was isolated from the crude enzyme of strain NOI-1 by affinity purification on cellulose and Sephacryl S-300 gel filtration. The molecular mass of the multienzyme complex was estimated to be about 1,200 kDa. The multienzyme complex showed one protein on native PAGE, one xylanase on a native zymogram, 21 proteins on SDS-PAGE, and 5 xylanases on a SDS zymogram. The multienzyme complex consisted of xylanase, beta-xylosidase, alpha-L-arabinofuranosidase, beta-glucosidase, and cellobiohydrolase. The multienzyme complex was effective in hydrolyzing xylan and corn hulls. This is the first report of an endocellulase-free multienzyme complex produced by a thermophilic anaerobic bacterium, T. thermosaccharolyticum strain NOI-1.


Subject(s)
Multienzyme Complexes/isolation & purification , Multienzyme Complexes/metabolism , Thermoanaerobacterium/enzymology , Xylans/metabolism , Bacterial Adhesion , Cellulases/isolation & purification , Cellulose/metabolism , Chromatography, Affinity/methods , Chromatography, Gel/methods , Cluster Analysis , DNA, Bacterial/chemistry , DNA, Bacterial/genetics , DNA, Ribosomal/chemistry , DNA, Ribosomal/genetics , Electrophoresis/methods , Hot Temperature , Hydrogen-Ion Concentration , Molecular Sequence Data , Molecular Weight , Multienzyme Complexes/chemistry , Phylogeny , Protein Binding , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , Thermoanaerobacterium/growth & development , Thermoanaerobacterium/physiology , Zea mays/metabolism
11.
J Microbiol Biotechnol ; 20(5): 893-903, 2010 May.
Article in English | MEDLINE | ID: mdl-20519913

ABSTRACT

A cellulolytic and xylanolytic enzyme complex-producing alkalothermoanaerobacterium strain, Tepidimicrobium xylanilyticum BT14 is described. The cell was Gram-positive, rod-shaped and endospore-forming. Based on 16S rRNA gene analysis and various lines of biochemical and physiological properties, the strain BT14 was a new member of the genus Tepidimicrobium. The strain BT14 cells had ability to bind to Avicel, xylan and corn hull. The pH and temperature optima for growth were 9.0 and 60 degrees C, respectively. The strain BT14 was able to use a variety of carbon sources. When the bacterium was grown on corn hulls under an anaerobic condition, a cellulolytic and xylanolytic enzyme complex was produced. Crude enzyme containing cellulase and xylanase of the strain BT14 was active in broad ranges of pH and temperature. The optimum conditions for cellulase and xylanase activities were pH 8.0 and 9.0 at 60 degrees C, respectively. The crude enzyme had ability to bind to Avicel and xylan. The analysis of native-PAGE and native-zymograms indicated the cellulose-binding protein showing both cellulase and xylanase activities while SDS-PAGE zymograms showed 4 bands of cellulases and 5 bands of xylanases. Evidence of cohesin-like amino acid sequence seemed to indicate that the protein complex shared direct relationship to the cellulosome of Clostridium thermocellum. The crude enzyme from the strain BT14 showed effective degradation of plant biomass. When grown on corn hulls at pH 9.0 and 60 degrees C under anaerobic conditions, the strain BT14 produced ethanol and acetate as the main fermentation products.


Subject(s)
Bacterial Proteins/metabolism , Cellulase/metabolism , Endo-1,4-beta Xylanases/metabolism , Gram-Positive Bacteria/enzymology , Multienzyme Complexes/metabolism , Bacterial Proteins/chemistry , Bacterial Proteins/genetics , Cellulase/chemistry , Cellulase/genetics , Cellulose/metabolism , Endo-1,4-beta Xylanases/chemistry , Endo-1,4-beta Xylanases/genetics , Gram-Positive Bacteria/chemistry , Gram-Positive Bacteria/classification , Gram-Positive Bacteria/genetics , Molecular Sequence Data , Multienzyme Complexes/chemistry , Multienzyme Complexes/genetics , Phylogeny , Xylans/metabolism
12.
J Biosci Bioeng ; 109(1): 9-14, 2010 Jan.
Article in English | MEDLINE | ID: mdl-20129074

ABSTRACT

The objective of this work was to remove linamarin in starch from cassava (Manihot esculenta Crantz cv. KU-50) roots, a high-cyanogen variety by using plant cell wall-degrading enzymes, xylanase and cellulase. The combination of xylanase from Bacillus firmus K-1 and xylanase and cellulase from Paenibacillus curdlanolyticus B-6 at the ratio of 1:9 showed the maximum synergism at 1.8 times for hydrolyzing cassava cortex cell walls and releasing linamarase. Combined enzyme treatment enhanced linamarin liberation from the parenchyma by 90%. In addition, when the combined enzymes were applied for detoxification during cassava starch production, a low-cyanide-product was obtained with decreased linamarin concentration (96%) compared to non-enzyme treated tissues. Based on these results, xylanase and cellulase treatment is a good method for low-cyanide-cassava starch production and could be applied for detoxification of cassava products during processing.


Subject(s)
Cell Wall/metabolism , Food Handling/methods , Manihot/chemistry , Starch/metabolism , Bacillus/enzymology , Cell Wall/chemistry , Cell Wall/enzymology , Food Contamination/prevention & control , Manihot/metabolism , Nitriles/analysis , Paenibacillus/enzymology , Plant Roots/chemistry , Plant Roots/metabolism , Temperature
13.
J Biosci Bioeng ; 107(6): 610-4, 2009 Jun.
Article in English | MEDLINE | ID: mdl-19447336

ABSTRACT

A multienzyme complex, cellulosome, of the facultatively anaerobic bacterium, Paenibacillus curdlanolyticus B-6 was produced on microcrystalline cellulose (Avicel) under aerobic conditions. During growth on Avicel, the bacterial cells were found to be capable of adhesion to Avicel by scanning electron microscopic (SEM) analysis. The multienzyme complex of P. curdlanolyticus B-6 was isolated from the crude enzyme preparation by gel filtration chromatography on Sephacryl S-300 and affinity purification on cellulose. The isolated multienzyme complex was able to bind to both Avicel and insoluble xylan and consists of cellulolytic and xylanolytic enzymes such as avicelase, carboxymethyl cellulase (CMCase), cellobiohydrolase, beta-glucosidase, xylanase, beta-xylosidase and alpha-l-arabinofuranosidase. The molecular mass of the complex was estimated to be 1600 kDa. It composed of at least 12 proteins on SDS-PAGE and 10 CMCases and 11 xylanases on zymograms. The isolated multienzyme complex could degrade the raw lignocellulosic substances effectively.


Subject(s)
Bacterial Proteins/metabolism , Cellulose/metabolism , Cellulosomes/metabolism , Gram-Positive Endospore-Forming Rods/enzymology , Multienzyme Complexes/metabolism , Aerobiosis , Xylans/metabolism
14.
J Microbiol Biotechnol ; 19(3): 277-85, 2009 Mar.
Article in English | MEDLINE | ID: mdl-19349753

ABSTRACT

The nucleotide sequence of the Paenibacillus curdlanolyticus B-6 xyn10A gene, encoding a xylanase Xyn10A, consists of 3,828 nucleotides encoding a protein of 1,276 amino acids with a predicted molecular mass of 142,726 Da. Sequence analysis indicated that Xyn10A is a multidomain enzyme comprising nine domains in the following order: three family 22 carbohydrate-binding modules (CBMs), a family 10 catalytic domain of glycosyl hydrolases (xylanase), a family 9 CBM, a glycine-rich region, and three surface layer homology (SLH) domains. Xyn10A was purified from a recombinant Escherichia coli by a single step of affinity purification on cellulose. It could effectively hydrolyze agricultural wastes and pure insoluble xylans, especially low substituted insoluble xylan. The hydrolysis products were a series of short-chain xylooligosaccharides, indicating that the purified enzyme was an endo-beta-1,4-xylanase. Xyn10A bound to various insoluble polysaccharides including Avicel, alpha-cellulose, insoluble birchwood and oat spelt xylans, chitin, and starches, and the cell wall fragments of P. curdlanolyticus B-6, indicating that both the CBM and the SLH domains are fully functioning in the Xyn10A. Removal of the CBMs from Xyn10A strongly reduced the ability of plant cell wall hydrolysis. These results suggested that the CBMs of Xyn10A play an important role in the hydrolysis of plant cell walls.


Subject(s)
Endo-1,4-beta Xylanases , Gram-Positive Endospore-Forming Rods/enzymology , Recombinant Proteins/biosynthesis , Amino Acid Sequence , Base Sequence , Cell Wall/metabolism , Cloning, Molecular , DNA, Bacterial/isolation & purification , Endo-1,4-beta Xylanases/biosynthesis , Endo-1,4-beta Xylanases/chemistry , Endo-1,4-beta Xylanases/genetics , Hydrolysis , Molecular Sequence Data , Polysaccharides/metabolism , Protein Structure, Tertiary , Recombinant Proteins/isolation & purification , Sequence Analysis, DNA , Sequence Analysis, Protein , Xylans/metabolism
15.
Biosci Biotechnol Biochem ; 73(4): 833-9, 2009 Apr 23.
Article in English | MEDLINE | ID: mdl-19352037

ABSTRACT

The three-dimensional structure (3D structure) of Xyn11A, a family 11 xylanase from Bacillus firmus K-1, was obtained through homology modeling. To study the substrate-binding site of Xyn11A, six xylooligosaccharides, xylobiose to xyloheptaose (X2-X7), were docked into the active site of Xyn11A by molecular docking. Based on the docked energy and estimated free energy of binding combined with modeled enzyme-substrate complexes, the substrate-binding site of Xyn11A probably contained six subsites, defined as -3, -2, -1, +1, +2, and +3. Focus on possible stacking interaction presented seven aromatic residues, that played an important role in six subsites of Xyn11A such as Tyr165 (-3), Trp9 and Tyr69 (-2), Tyr80 (-1), Tyr65 (+1), Tyr88 (+2) and Tyr173 (+3). The bond-cleavage positions showed that X2 and X3 did not bind at the cleft (subsites -1 and +1) of Xyn11A. Related to the experiment, the end products of larchwood xylan hydrolysis by purified Xyn11A were X2 and X3. X2 and X3 acted as the end product inhibitors of Xyn11A.


Subject(s)
Bacillus/enzymology , Endo-1,4-beta Xylanases/chemistry , Endo-1,4-beta Xylanases/metabolism , Models, Molecular , Binding Sites , Endo-1,4-beta Xylanases/antagonists & inhibitors , Enzyme Inhibitors/pharmacology , Hydrolysis , Oligosaccharides/chemistry , Oligosaccharides/metabolism , Protein Binding , Sequence Homology, Amino Acid , Thermodynamics , Xylans/metabolism
16.
BMC Bioinformatics ; 10 Suppl 1: S48, 2009 Jan 30.
Article in English | MEDLINE | ID: mdl-19208150

ABSTRACT

BACKGROUND: SARS coronavirus main proteinase (SARS CoVMpro) is an important enzyme for the replication of Severe Acute Respiratory Syndrome virus. The active site region of SARS CoVMpro is divided into 8 subsites. Understanding the binding mode of SARS CoVMpro with a specific substrate is useful and contributes to structural-based drug design. The purpose of this research is to investigate the binding mode between the SARS CoVMpro and two octapeptides, especially in the region of the S3 subsite, through a molecular docking and molecular dynamics (MD) simulation approach. RESULTS: The one turn alpha-helix chain (residues 47-54) of the SARS CoVMpro was directly involved in the induced-fit model of the enzyme-substrate complex. The S3 subsite of the enzyme had a negatively charged region due to the presence of Glu47. During MD simulations, Glu47 of the enzyme was shown to play a key role in electrostatic bonding with the P3Lys of the octapeptide. CONCLUSION: MD simulations were carried out on the SARS CoVMpro-octapeptide complex. The hypothesis proposed that Glu47 of SARS CoVMpro is an important residue in the S3 subsite and is involved in binding with P3Lys of the octapeptide.


Subject(s)
Computational Biology/methods , Cysteine Endopeptidases/chemistry , Cysteine Proteinase Inhibitors/chemistry , Oligopeptides/chemistry , Severe acute respiratory syndrome-related coronavirus/enzymology , Viral Proteins/chemistry , Binding Sites , Catalytic Domain , Coronavirus 3C Proteases , Cysteine Endopeptidases/metabolism , Cysteine Proteinase Inhibitors/metabolism , Hydrogen Bonding , Models, Molecular , Oligopeptides/metabolism , Protein Conformation , Severe acute respiratory syndrome-related coronavirus/metabolism , Structure-Activity Relationship , Substrate Specificity , Viral Proteins/metabolism
17.
Biosci Biotechnol Biochem ; 72(2): 321-8, 2008 Feb.
Article in English | MEDLINE | ID: mdl-18256505

ABSTRACT

The effect of polymeric substances such as alpha-cellulose, birchwood xylan, corn hull, and sugarcane bagasse, and of soluble sugars such as L-arabinose, D-galactose, D-glucose, D-xylose, and cellobiose, on the induction of multienzyme complexes in a facultatively anaerobic bacterium, Paenibacillus curdlanolyticus B-6, was investigated under aerobic conditions. Cells and culture supernatants of strain B-6 grown on different carbon sources were analyzed. Cells grown on each carbon source adhered to cellulose. Hence strain B-6 cells from all carbon sources must have an essential component responsible for anchoring the cells to the substrate surfaces. Native-polyacrylamide gel electrophoresis (native-PAGE), sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE), zymogram analysis, and enzymatic assays indicated that many proteins having xylanolytic and cellulolytic activities from P. curdlanolyticus B-6 grown on each carbon source were produced as two multienzyme complexes in the culture supernatants. These results indicate that P. curdlanolyticus B-6 produced multienzyme complexes when grown on both polymeric and soluble sugars. The multienzyme complexes of P. curdlanolyticus B-6 consisted of the main enzymes and non-enzymatic subunits and the production of some different subunits, depending on the carbon source.


Subject(s)
Bacillus/enzymology , Carbon/metabolism , Cellulase/biosynthesis , Multienzyme Complexes/biosynthesis , Bacillus/physiology , Bacterial Adhesion , Electrophoresis, Polyacrylamide Gel , Enzyme Induction
18.
Appl Environ Microbiol ; 72(4): 2483-90, 2006 Apr.
Article in English | MEDLINE | ID: mdl-16597947

ABSTRACT

A facultatively anaerobic bacterium, Paenibacillus curdlanolyticus B-6, isolated from an anaerobic digester produces an extracellular xylanolytic-cellulolytic enzyme system containing xylanase, beta-xylosidase, arabinofuranosidase, acetyl esterase, mannanase, carboxymethyl cellulase (CMCase), avicelase, cellobiohydrolase, beta-glucosidase, amylase, and chitinase when grown on xylan under aerobic conditions. During growth on xylan, the bacterial cells were found to adhere to xylan from the early exponential growth phase to the late stationary growth phase. Scanning electron microscopic analysis revealed the adhesion of cells to xylan. The crude enzyme preparation was found to be capable of binding to insoluble xylan and Avicel. The xylanolytic-cellulolytic enzyme system efficiently hydrolyzed insoluble xylan, Avicel, and corn hulls to soluble sugars that were exclusively xylose and glucose. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) of a crude enzyme preparation exhibited at least 17 proteins, and zymograms revealed multiple xylanases and cellulases containing 12 xylanases and 9 CMCases. The cellulose-binding proteins, which are mainly in a multienzyme complex, were isolated from the crude enzyme preparation by affinity purification on cellulose. This showed nine proteins by SDS-PAGE and eight xylanases and six CMCases on zymograms. Sephacryl S-300 gel filtration showed that the cellulose-binding proteins consisted of two multienzyme complexes with molecular masses of 1,450 and 400 kDa. The results indicated that the xylanolytic-cellulolytic enzyme system of this bacterium exists as multienzyme complexes.


Subject(s)
Bacteria, Anaerobic/enzymology , Cellulose/metabolism , Multienzyme Complexes/metabolism , Xylans/metabolism , Bacteria, Anaerobic/metabolism , Bacteria, Anaerobic/physiology , Bacteria, Anaerobic/ultrastructure , Bacterial Adhesion , Cellobiose/metabolism , Cellulase/metabolism , Microscopy, Electron, Scanning , Solubility , Xylosidases/metabolism
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