Arg<Superscript>235</Superscript> is an essential catalytic residue of <Emphasis Type="Italic">Bacillus pumilus</Emphasis> DKS1 pectate lyase to degum ramie fibre

After 24 h of incubation with only purified pectate lyase isolated from Bacillus pumilus DKS1 (EF467045), the weight loss of the ramie fibre was found to be 25%. To know the catalytic residue of pectate lyase the pel gene encoding a pectate lyase from the strain Bacillus pumilus DKS1 was cloned in E. coli XL1Blue and expressed in E. coli BL21 (DE3) pLysS. The pel gene was sequenced and showed 1032 bp length. After purification using CM-Sepharose the enzyme showed molecular weight of 35 kDa and maximal enzymatic activity was observed at 60°C and a pH range of 8.5–9.0. Both Ca²⁺ and Mn²⁺ ions were required for activity on Na-pectate salt substrates, while the enzyme was strongly inhibited by Zn²⁺ and EDTA. The deduced nucleotide sequence of the DKS1 pectate lyase (EU652988) showed 90% homology to pectate lyases from Bacillus pumilus SAFR-032 (CP000813). The 3D structure as well as the catalytic residues was predicted using EasyPred software and Catalytic Site Atlas (CSA), respectively. Site directed mutagenesis confirmed that arginine is an essential catalytic residue of DKS1 pectate lyase.     

Degumming and characterization of ramie fibre using pectate lyase from immobilized Bacillus pumilus DKS1

Aims:  The present study was aimed at finding the optimal conditions for the production of pectate lyase using immobilized Bacillus pumilus DKS1 cells in calcium-alginate (Ca-alginate) beads and determining the efficient degumming of ramie fibre.
Methods and Results:  The active cells of B. pumilus DKS1 were immobilized in Ca-alginate and used for the production of pectate lyase. The production of enzyme increased significantly with increasing alginate concentration and reached a maximum enzyme yield of 38·5 U ml⁻¹ at 18 g l⁻¹. This was about 1·5-fold higher than that obtained by free cells. Degummed fibre using immobilized cells showed better tenacity than that prepared by using nonimmobilized cells.
Conclusions:  The Ca-alginate entrapment is a promising immobilization method of B. pumilus DKS1 for semicontinuous enzyme production. Enzyme production by immobilized cells is superior to that of free cells because it leads to higher volumetric activities within the same period of fermentation. Fibre degumming by using immobilized cells produced better quality fibre.
Significance and Impact of the Study:  This is the first report of degumming of fibre using enzyme from immobilized B. pumilus cells as per our knowledge. High-quality degummed fibre could be prepared with relatively inexpensive inputs for use in the textile and paper industry.     

Enzymatic degumming of ramie bast fibers

Bast fibers from ramie (Boehmeria nivea) were treated with cell-free culture supernatants from an Amycolata sp. and a recombinant Streptomyces lividans strain expressing the Amycolata pectate lyase to investigate the degumming effects of different extracellular polysaccharide-degrading enzymes. Culture supernatants from the Amycolata sp. with high pectate lyase activities were most effective in fiber separation and reduced the gum content of ramie fibers by 30% within 15 h. Xylanase activity produced by the Amycolata sp. contributed little to the degumming. Electron micrographs showed that the crude pectate lyase from the Amycolata sp. removed plant gum more efficiently from decorticated ramie bast fibers than the purified enzyme. Similarly, degumming with the crude enzyme of the Amycolata sp. and the recombinant S. lividans strain for 24 h resulted in fibers with a residual gum content of 14.7 and 17.3%, respectively. Degumming with the crude enzyme of the recombinant Streptomyces strain was slightly improved by the addition of a commercial pectinesterase. No significant degumming was observed with the crude enzyme from an S. lividans strain that did not produce the Amycolata pectate lyase. These results indicate that the pectinolytic activity of the Amycolata sp. plays an active role in degumming of ramie bast fibers.     

Molecular characterization of a lipase-producing <Emphasis Type="Italic">Bacillus pumilus</Emphasis> strain (NMSN-1d) utilizing colloidal water-dispersible polyurethane

Bacillus pumilus strain NMSN-1d isolated from polyurethane-contaminated water was found to grow in high salt concentration (NaCl 10%, w/v) and degrade Impranil-DLN, water-dispersible polyurethane. The genetic relatedness of the isolate has been established by standard molecular biological techniques and the enzyme(s) involved in polyurethane degradation were also studied. A total of nine bacterial strains were isolated from polyurethane-polluted sites and characterized by conventional, microbiological and biochemical methods. These isolates were subjected to 16S ribosomal RNA gene amplification by PCR using specific primers. The genetic relatedness of the isolates was also ascertained by ribotyping and BLAST analysis of the 16S ribosomal RNA gene sequences. The bacterial isolates were grown in yeast extract-salts minimal broth medium supplemented with water-dispersible polyurethane (Impranil DLN) as a sole source of carbon. The promising isolate utilizing polyurethane and producing lipase was identified as Bacillus pumilus NMSN-1d. The polyurethane degradation has been studied in polyurethane-Rhodamine-B and Luria-Bertani-polyurethane plate assays. The activity of hydrolytic enzymes such as lipase and esterase was confirmed on 2xYT-olive oil and tributyrin-Tween 20 plate assay. The newly isolated Bacillus pumilus appears promising in the management of polyurethane waste and in production of industrially important enzymes.     

制霉菌素抗性筛选高活性苎麻脱胶菌诱变菌株

利用制霉菌素抗性筛选高渗透性突变株,提高黑曲霉菌对苎麻纤维的脱胶能力,使微生物脱胶能用于工业生产实践之中.分别用紫外线、硫酸二乙酯、亚硝酸作为诱变剂对黑曲霉3.0.2菌株进行诱变处理.以制霉菌素抗性为遗传标记,从突变菌株中定向筛选得到一株高活性苎麻脱胶菌黑曲霉3.0.2-26.在以未经刮制的苎麻韧皮为主要碳源,0.7%(NH_4)_2SO_4为氮源,添加00.5%KCl;00.5%MgSO_4;0.1%K_2HPO_4; 0.1%酵母膏;Tween80 0.1%的培养液中,接入黑曲霉3.0.2-26,置30℃下,150 r/min处理30 h左右,脱胶苎麻纤维的残胶率平均为14.43%.     

Thermodynamic characterization of a highly thermoactive extracellular pectate lyase from a new isolate Bacillus pumilus DKS1

An extracellular pectate lyase (EC 4.2.2.2) was purified from the culture filtrate of a newly isolated Bacillus pumilus DKS1 grown in pectin containing medium. Using ion-exchange and gel filtration chromatography, this enzyme was purified and found to have a molecular weight of around 35kDa. The purified enzyme exhibited maximal activity at a temperature of 75 degrees C and pH 8.5. The presence of 1mM calcium and manganese enhanced pectate lyase activity and was strongly inhibited by zinc, nickel and EDTA. The thermal inactivation studies revealed an entropy-enthalpy compensation pattern below a critical temperature. The alkaliphilicity and high thermostability of this pectate lyase may have potential implications in fibre degumming.     

Characterization of a cryptic plasmid pPZZ84 from Bacillus pumilus

The complete nucleotide sequence of a cryptic plasmid pPZZ84 from Bacillus pumilus strain ZZ84 was determined. Plasmid pPZZ84 is 6817 bp long with GC content of 36.7%. Seven putative open reading frames were identified. ORF7 shows 91% and 90% amino acid identity with rep proteins of pSH1452 and pPL1, respectively, members of rolling-circle replication (RCR) pC194-family. A typical pC194-family double strand origin (dso), a single-stranded origin (sso) and rap (regulator aspartate phosphatase) proteins were also identified in the plasmid. These results imply that pPZZ84 belongs to the Bacillus subtilis species group of small rolling circle (BsSRC) replicating plasmids. The plasmid copy number of pPZZ84 in B. pumilus ZZ84 was estimated to be 46 per cell, more than that of other BsSRC plasmids in their hosts.     

A marked enhancement in the production of a highly alkaline and thermostable pectinase by Bacillus pumilus dcsr1 in submerged fermentation by using statistical methods

The production of a highly alkaline and thermostable pectinase of Bacillus pumilus was optimized in submerged fermentation using Plackett-Burman design and response surface methodology. Three fermentation variables (C:N ratio, K(2)HPO(4), and pH), which were identified to significantly affect pectinase production by Plackett-Burman design were further optimized using response surface methodology of central composite design (CCD). An over all 34- and 41-fold increase in enzyme production was achieved in shake flasks and lab fermenter by the optimization of variables using statistical approaches, respectively. The enzyme was optimally active at pH 10.5 and 50 degrees C, and selectively degraded only the noncellulosic gummy material of ramie (Boehmeria nivea) fibres causing 10.96% fibre weight loss, and therefore, the enzyme could find application in fibre processing industry. The use of the enzyme in fibre processing reduces the use of alkali, and the associated alkalinization of water bodies.     

Degumming of ramie fibers by alkalophilic bacteria and their polysaccharide-degrading enzymes

Three strains of alkalophilic bacteria, Bacillus sp. NT-39, NT-53 and NT-76, were selected for the degumming of ramie fibers and production of polysaccharide-degrading enzymes. After 48 h of incubation with the strains, the loss of the gum might amount to 5.0% or more of the fibers and a number of polysaccharide-degrading enzymes were secreted to the culture supernatants. The residual gum of the fibers decreased to 9.4% after 5 h of enzymatic degumming. Analysis of gum contents and enzyme activities revealed that pectate lyase and xylanase played an important role in the degradation of residual gum. Enzymatic degumming resulted in an increment of 5.4 ISO units in fiber brightness, whereas the reduction in bundle breaking tenacity of the fibers was less than 5.%. The results confirmed that degumming of ramie fibers by alkalophilic bacteria and their enzymes had substantial advantages.     

Characteristics of Polygalacturonate Lyase C from Bacillus subtilis 7-3-3 and Its Synergistic Action with PelA in Enzymatic Degumming

An alkaline polygalacturonate lyase (PGL) from Bacillus subtilis 7-3-3, PelC, with diverse depolymerization abilities for different pectin substrates was found. The PGL activity of PelC decreased with increasing degree of methyl esterification of the substrate. PelA and PelC displayed notable synergistic effects in the enzymatic degumming of ramie fibers. Gum loss rates increased by 62% when PelC was used to replace up to three-eighths of the PelA dose (PelC, 60 U g⁻¹ ramie fibers). To the best of our knowledge, this study is the first to report the synergistic action of members of polysaccharide lyase families 1 and 3, represented by PelA and PelC, respectively. The present paper provides new insights into the improvement and production of enzymes used in enzymatic degumming.     

DNA sequence analysis of a putative primary replicon from a cryptic plasmid pNM214 of a hydrocarbon utilizing marine <Emphasis Type="Italic">Bacillus</Emphasis> strain NM21

Marine Bacillus strain NM21 isolated from hydrocarbon-contaminated site at Naval Harbour, Mumbai grows on high-speed diesel as a source of carbon and energy. This bacterium harbours four plasmids in it. The smallest plasmid, pNM214 was digested with EcoRI enzyme and cloned in pUC19 vector. The clone Om4 containing largest insert of >3.5 kb was sequenced by primer walking. DNA sequence analysis showed this fragment to be homologous to replication initiation protein (rep) gene and dso (double strand origin) of different plasmids from Bacillus subtilis and Bacillus pumilus species. The putative rep gene sequence of pNM214 showed 74.3–91.6% DNA identity to B. subtilis plasmids (pTA1015, pTA1060 and pTA1040) and 86.3% to 88.9% DNA identity to B. pumilus plasmids (pPL7065, pPL10 and pSH1452). The translated amino acid sequence of rep shows that it contains all the three conserved motifs present in the Rep protein of pC194 family of plasmids. DNA sequence comparison of putative dso of pNM214 with other bacillus plasmids belonging to pC194 group shows that it contains highly conserved nick site sequence 5′-TCTTTTCTTATCTTGATA-3′ and surrounding inverted repeats. Thus, it indicates that pNM214 to be a rolling circle replicating plasmid belonging to the pC194 group. The presence of rep and dso like sequences in the sequenced EcoRI fragment indicate that the cloned fragment contain putative primary replicon of pNM214.     

Partial characterization ofAspergillus fumigatus polygalacturonases for the degumming of natural fibers

Summary Aspergillus fumigatus strain 4, cultured on citrus pectin as the sole carbon source, produced polygalacturonases whose activity was optimum at 65°C and pH 3.5–4.5. The enzymes presented a bimodal thermostability for 10 min, but not 60 min, of incubation. Polygalacturonases showed pH stability between 3.0 to 9.0. The enzymes were stable when stored at 4–6°C for 90 days, but their activity was reduced by 24% when they were stored at 26–30°C. Orange pulp was the best pectic carbon source tested for the production of pectinases capable of retting ramie fibers. The reutilization of these enzymes was possible, suggesting the viability of industrial use of pectinases for degumming ramie fibers.     

Screening of pectinase producer from alkalophilic bacteria and study on its potential application in degumming of ramie

Four strains designated as NT-2, NT-6, NT-33 and NT-82 were selected from alkalophilic bacteria. They all can produce pectinase and xylanase. The polygalacturonase (PGase) and xylanase activities of strain NT-33 were 1025 U ml^-1 and 26U ml^-1 respectively. The pH and temperature optimum for the activity of PGase were 10.5 and 70°C, respectively. From batch experiments, it was found that strain NT-33 had an excellent capacity for degumming ramie fibers. After 24 h fermentation this strain can remove 70% of the gum existing in ramie fibers. The experiments showed that a series of noncellulosic polysaccharide degrading enzymes were involved in the ramie degumming process.     

Purification and Characterization of an Extracellular Alkaline Serine Protease with Dehairing Function from <Emphasis Type="Italic">Bacillus pumilus</Emphasis>

An extracellular alkaline serine protease (called DHAP), produced by a Bacillus pumilus strain, demonstrates significant dehairing function. This protease is purified by hydrophobic interaction chromatography, ion exchange, and gel filtration. DHAP had a pI of 9.0 and a molecular weight of approximately 32,000 Dalton. It shows maximal activity at pH 10 and with a temperature of 55°C; the enzyme activity can be completely inhibited by phenylmethylsulfonyl fluoride (PMSF) and diisopropyl fluorophosphates (DFP). The first 20 amino acid residues of the purified DHAP have been determined with a sequence of AQTVPYGIPQIKAPAVHAQG. Alignment of this sequence with other alkaline protease demonstrates its high homology with protease from another B. pumilus strain. Received: 17 April 2002 / Accepted: 24 May 2002     

Regulatory mutations affecting the synthesis of cellulase in Bacillus pumilus

A wild strain of Bacillus pumilus was investigated for cellulase production, and putative mutants of this strain were screened for catabolite repression insensitivity after chemical mutagenesis using ethyl methanesulphonate (EMS) as a mutagenic agent. Out of four classes of mutants studied and classified according to their cellulase induction rate and level of cellulase production in the presence of high concentrations of glucose (2.6%[w/v]), classes III and IV exhibited cellulase production up to 6.2 mg cellulase and 11.4 mg cellulase per gram of dry cell mass respectively. These mutants were referred to as catabolite repression-insensitive when compared to the wild strain which exhibited a total repression of cellulase synthesis under the same conditions. How EMS triggered the catabolite repression insensitivity in these mutants was not established. However this mutation brought out new strains of cellulase hyperproducers (mutants 6 and 11) in the presence of glucose when compared to other cellulase producers such as Aspergillus terreus, A. nidulans and Trichoderma reesei, which exhibited catabolite repression of cellulase synthesis. These mutants were selected as the most promising candidates for cellulase synthesis even at high glucose concentration.     

果胶杆菌(Pectobacterium aroidearum) WNH的筛选及其汉麻生物脱胶效果

【背景】麻类生物脱胶与化学法脱胶相比具有环保优势。【目的】获得用于汉麻生物脱胶的高效果胶酶菌株。【方法】使用以果胶为唯一碳源的培养基,采用平板稀释法进行菌株筛选,通过生理生化实验和16s rRNA基因序列比对鉴定目标菌株。采用单因素试验优化产酶条件,并验证该条件下汉麻生物脱胶效果。【结果】获得一株具备高活性果胶的酶菌株,归类为果胶杆菌(Pectobacterium aroidearum) WNH。在培养温度27 °C、转速160 r/min、接种量10%、初始pH 7.0的条件下培养16 h后,果胶杆菌WNH的粗酶液果胶酶活力达155.03 U/mL。按上述条件对汉麻韧皮进行二次脱胶处理,处理后脱胶率为27.18%,较对照组提高了6.93%。【结论】果胶杆菌WNH具备汉麻生物脱胶的潜力。     

A new organic solvent tolerant protease from <Emphasis Type="Italic">Bacillus pumilus</Emphasis> 115b

Five out of the nine benzene–toulene–ethylbenzene-xylene (BTEX) tolerant bacteria that demonstrated high protease activity on skim milk agar were isolated. Among them, isolate 115b identified as Bacillus pumilus exhibited the highest protease production. The protease produced was stable in 25% (v/v) benzene and toluene and it was activated 1.7 and 2.5- fold by n-dodecane and n-tetradecane, respectively. The gene encoding the organic solvent tolerant protease was cloned and its nucleotide sequence determined. Sequence analysis revealed an open reading frame (ORF) of 1,149 bp that encoded a polypeptide of 383 amino acid residues. The polypeptide composed of 29 residues of signal peptide, a propeptide of 79 residues and a mature protein of 275 amino acids with a calculated molecular mass of 27,846 Da. This is the only report available to date on organic solvent tolerant protease from B. pumilus.     

Preliminary research on bamboo degumming with xylanase

The extraction of fibres from bamboo culm during the degumming process was performed with commercial xylanase. It is found that a combination of mild chemical pretreatment and enzymatic treatment is essential to achieve a high level of degumming, and better fibre separation. FTIR analysis of substances removed by enzyme treatment indicated that xylanase played an active role in the removal of non-cellulosic substances. Scanning electron microscopy revealed a relatively complete removal of gummy material from the surface of treated bamboo slices. On the basis of this investigation, it is suggested that the combination of mild chemical and enzymatic treatment is a promising method for bamboo degumming.     

Application of calcium alginate immobilized and crude pectin lyase from Bacillus cereus in degumming of plant fibres

Abstract

In this study, the purified pectin lyase was immobilized in calcium alginate beads and compared with crude enzyme for application in degumming of buel and banana plant fibres. From the data of scanning electron microscopy (SEM), it was observed that untreated buel fibres were covered by non-cellulosic materials (pectin, hemicelluloses and waxes) and the surface of enzymatically treated buel fibres looked smoother. Also, the crude alkaline pectin lyase treated buel fibre exhibited a considerably cleaner surface, which suggested that the crude pectin lyase could provide better degumming effects in comparison to the immobilized pectin lyase. In case of banana fibre, the FTIR spectroscopy showed that both crude and immobilized alkaline pectin lyase treatments of banana plant fibres were equally efficient in degumming. The enzymatic degumming of buel and banana with crude pectin lyase resulted in maximum release of galacturonide after 24?h for buel and 15?h for banana fibre. The optimum temperature for degumming of buel and banana fibres with crude pectin lyase was found to be 50?°C and 45?°C, respectively. Also, the maximum galacturonide was released with 200 and 250?U of pectin lyase for buel and banana fibre, respectively.