Isolation of two beta-xylosidase genes of Bacillus pumilus and comparison of their gene products

The chromosomal DNA fragments of Bacillus pumilus IPO, a potent xylan-hydrolyzing bacterium, were ligated to a vector plasmid, pBR322, and used to transform Escherichia coli C600 cells. Two hybrid plasmids, pOXD28 and pOXN29, were found to enable the transformants to produce beta-xylosidase. The former was found to contain a 2.6-MDa Bg/II fragment and the latter, a 7.7-MDa PstI fragment, both coding beta-xylosidase, but xylanase is coded only on the latter hybrid plasmid. The DNAs inserted in both plasmids originated from the B. pumilus chromosome, but from different regions, as shown by Southern hybridization and the analysis of restriction fragments. beta-Xylosidases I and II, coded on pOXN29 and pOXD28 respectively, were purified to homogeneous preparations and compared. Both were dimer enzymes consisting of 65000-70000-Da subunits. Specific activity and the Km value of beta-xylosidase I to p-nitrophenyl beta-D-xyloside as substrate were respectively 100 and 1/40 times those of beta-xylosidase II. The mobilities of beta-xylosidases I and II on polyacrylamide gel electrophoresis were also different. beta-Xylosidase I, the gene of which is located near the xylanase gene on pOXN29, can convert xylooligosaccharides to xylose, but beta-xylosidase II had little activity on xylobiose. These results suggest that beta-xylosidase I is the main enzyme for xylan hydrolysis in B. pumilus.     

Sequence and properties of beta-xylosidase from Bacillus pumilus IPO. Contradiction of the previous nucleotide sequence.

The nucleotide sequence of the beta-xylosidase (xynB) gene from Bacillus pumilus has been reported previously [Moriyama, H., Fukusaki, E., Crespo, J.C., Shinmyo, A. & Okada, H. (1987) Eur. J. Biochem. 166, 539-545]. However, the sequence identified in the present study is quite different from the previously reported one. The total length of the PstI--EcoRI fragment of a plasmid pOXN295 containing the xynB gene is 2201 bp from our sequencing, while the length of the fragment in the previous data was 2466 bp. The sequences are similar in the N-terminal (500 bp) and C-terminal (260 bp) regions, but those in the central region are completely different. From the following observations, the previous sequence seems to have no reliable experimental basis. First, the restriction sites observed for pOXN295 are quite different from the sites deduced from the sequence. Second, the amino acid composition deduced from the sequence and the composition identified by amino acid analysis of the purified beta-xylosidase are very different. It is confirmed, on the other hand, that our new sequence agrees well with these experimental data. The enzyme was purified to homogeneity from Bacillus pumilus and Escherichia coli harboring a hybrid plasmid which highly expresses the xynB gene. The molecular mass of the enzyme was estimated to be 190 kDa by high performance gel filtration chromatography using TSK-G3000SW and 56 kDa by SDS/polyacrylamide gel electrophoresis. The pH optimum was 7.0, and the optimum temperature was 40 degrees C. The Vm value was estimated to be 1.23 +/- 0.14 mukat/mg (or p-nitrophenyl beta-D-xyloside) and 0.14 +/- 0.011 mukat/mg (for xylobiose), while Km was estimated to be 3.9 +/- 0.59 mM (for p-nitrophenyl beta-D-xyloside) and 8.9 +/- 1.19 mM (for xylobiose).     

Catalytic versatility of trehalase: synthesis of alpha-D-glucopyranosyl alpha-D-xylopyranoside from beta-D-glucosyl fluoride and alpha-D-xylose

Trehalase was previously shown (see ref. 5) to hydrolyze alpha-D-glucosyl fluoride, forming beta-D-glucose, and to synthesize alpha, alpha-trehalose from beta-D-glucosyl fluoride plus alpha-D-glucose. Present observations further define the enzyme's separate cosubstrate requirements in utilizing these nonglycosidic substrates. alpha-D-Glucopyranose and alpha-D-xylopyranose were found to be uniquely effective in enabling Trichoderma reesei trehalase to catalyze reactions with beta-D-glucosyl fluoride. As little as 0.2mM added alpha-D-glucose (0.4mM alpha-D-xylose) substantially increased the rate of enzymically catalyzed release of fluoride from 25mM beta-D-glucosyl fluoride at 0 degrees. Digests of beta-D-glucosyl fluoride plus alpha-D-xylose yielded the alpha, alpha-trehalose analog, alpha-D-glucopyranosyl alpha-D-xylopyranoside, as a transient (i.e., subsequently hydrolyzed) transfer-product. The need for an aldopyranose acceptor having an axial 1-OH group when beta-D-glucosyl fluoride is the donor, and for water when alpha-D-glucosyl fluoride is the substrate, indicates that the catalytic groups of trehalose have the flexibility to catalyze different stereochemical reactions.     

Membrane-bound succinate dehydrogenase of Bacillus pumilus strain 5: effects of modulators of monoelectron transfer

The membrane-bound succinate dehydrogenase (SDH; EC 1.3.99.1) of Bacillus pumilus strain 5 was investigated as succinate:ferricyanide oxidoreductase activity at 27 degrees C. A Km of 8.3 x 10(-3) M was obtained, and the Vmax was 1.8 x 10(-6) mole succinate dehydrogenated min-1 mg-1 membrane protein, at a substrate (succinate) concentration below 40 x 10(-3) M. Above this succinate concentration the Km was 102 x 10(-3) M and the Vmax was 3.7 x 10(-6) mole succinate min-1 mg-1 membrane protein. Para-benzoquinone or 2,4-dinitrophenylhydrazine, in micromolar amounts inhibited the enzyme by serving as an electron sink. Hydroxyl radical (OH.) scavengers, mannitol and benzoate, activated the enzyme, while superoxide dismutase (SOD) had no effect on the enzyme. Thus, the mechanism of electron transfer from succinate to Fe(CN)3-(6) through SDH does not involve superoxide (O2-) as a rate-limiting intermediate.     

Differentiation of Bacillus pumilus and Bacillus safensis Using MALDI-TOF-MS

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) despite being increasingly used as a method for microbial identification, still present limitations in which concerns the differentiation of closely related species. Bacillus pumillus and Bacillus safensis, are species of biotechnological and pharmaceutical significance, difficult to differentiate by conventional methodologies. In this study, using a well-characterized collection of B. pumillus and B. safensis isolates, we demonstrated the suitability of MALDI-TOF-MS combined with chemometrics to accurately and rapidly identify them. Moreover, characteristic species-specific ion masses were tentatively assigned, using UniProtKB/Swiss-Prot and UniProtKB/TrEMBL databases and primary literature. Delineation of B. pumilus (ions at m/z 5271 and 6122) and B. safensis (ions at m/z 5288, 5568 and 6413) species were supported by a congruent characteristic protein pattern. Moreover, using a chemometric approach, the score plot created by partial least square discriminant analysis (PLSDA) of mass spectra demonstrated the presence of two individualized clusters, each one enclosing isolates belonging to a species-specific spectral group. The generated pool of species-specific proteins comprised mostly ribosomal and SASPs proteins. Therefore, in B. pumilus the specific ion at m/z 5271 was associated with a small acid-soluble spore protein (SASP O) or with 50S protein L35, whereas in B. safensis specific ions at m/z 5288 and 5568 were associated with SASP J and P, respectively, and an ion at m/z 6413 with 50S protein L32. Thus, the resulting unique protein profile combined with chemometric analysis, proved to be valuable tools for B. pumilus and B. safensis discrimination, allowing their reliable, reproducible and rapid identification.     

Competitive inhibition of the inverting beta-xylosidase of Bacillus pumilus 12 by monosaccharide derivatives of different structural and conformational types. A possible natural substrate.

We studied the rotational mobility of the Ca2+ + Mg2+-activated ATPase in skeletal-muscle sarcoplasmic-reticulum vesicles, using time-resolved measurements of the depolarization of laser-flash-excited phosphorescence of the extrinsic triplet probe erythrosin. Our results are in general agreement with those of others [Bürkli & Cherry (1981) Biochemistry 20, 138-145] obtained by linear dichroism methods. In addition, we directly observed fast depolarization in the 1-5 microseconds time range that can be attributed to limited motion of part of the protein (segmental motion). Temperature-dependent changes in phosphorescence anisotropy indicated the onset of a conformational change in structure of the Ca2+ + Mg2+-activated ATPase at 11-13 degrees C. We also describe the synthesis of 5-iodoacetamidoerythrosin.     

Bacillus pumilus strains with inactivated genes of extracellular serine proteinases

Two Bacillus pumilus strains with inactivated genes of extracellular serine proteinases (subtilisin-like proteinase and glutamyl endopeptidase) were obtained. Inactivation of the gseBp and aprBp genes resulted in an increase in cell size, changed colony shape, and more rapid cell lysis that started during the growth retardation phase. Protease-deficient stains partially changed the ability to decompose carbohydrates (sugars), reduced resistance to variations in temperature of cultivation, and did not respond to the fluctuations of phosphate concentration in the medium. Proteinases gene disruption resulted in alteration of hydrolases secretion level by these bacteria.     

GASdb: a large-scale and comparative exploration database of glycosyl hydrolysis systems

Background  

The genomes of numerous cellulolytic organisms have been recently sequenced or in the pipeline of being sequenced. Analyses of these genomes as well as the recently sequenced metagenomes in a systematic manner could possibly lead to discoveries of novel biomass-degradation systems in nature.     

A thermostable alpha-arabinofuranosidase from xylanolytic Bacillus pumilus: purification and characterisation

Bacillus pumilus PS213 secretes an alpha-L-arabinofuranosidase (AF) when grown in the presence of arabinogalactan or oat meal. The enzyme has been purified to homogeneity and characterised. Its molecular mass, as determined by gel filtration, is 220 kDa, while sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE) showed a single band of approximately 60 kDa. According to the result of the mass spectrometry analysis showing a molecular mass of 56 kDa, the enzyme should be a homotetramer. The isoelectric point was found to be 5.2, the enzyme activity was optimal at 55 degrees C and pH 7.0. The enzyme retained 80% of its activity after 2 h at 65 degrees C and lost 50% of activity at 75 degrees C after 135 min. The Michaelis constant K(m) and V(max) for p-nitrophenylarabinofuranoside at 37 degrees C were 1.7 mM and 52.9 U mg(-1), respectively. N-terminal sequence analysis and internal peptide fragments showed homology with glycosyl hydrolases of family 51.     

短小芽孢杆菌HZbp脂肪酶基因的克隆表达

以短小芽孢杆菌HZbp总DNA为模板以PCR的方式获得512 bp的脂肪酶基因,并在该基因的两端引入了EcoR1和Sal1的酶切位点,将该基因与大肠杆菌表达质粒pSE380连接,获得重组质粒pSE380-BPL。重组质粒转入大肠杆菌表达细胞株BL21,获得工程菌株BL21-BPL。序列分析显示所克隆的基因具有脂肪酶的保守G-X-S-X-G序列,SDS-PAGE电泳显示该脂脂肪酶的分子质量约为20 kDa。在LB培养基中,IPTG诱导浓度为1.0 mmol/L,33℃诱导培养10 h后,发酵液酶活达到8 U/mL。     

Swapping of pro-sequences between keratinases of Bacillus licheniformis and Bacillus pumilus: altered substrate specificity and thermostability

Pro-sequences were swapped in cis between keratinases from Bacillus licheniformis (Ker BL) and Bacillus pumilus (Ker BP) to construct Ker ProBP-BL and Ker ProBL-BP, respectively. Expression of these keratinases was carried out constitutively by E. coli HB101-pEZZ18 system. They were characterized with respect to their parent enzymes, Ker BL and Ker BP, respectively. Ker ProBP-BL became more thermostable with a t(1/2) of 45 min at 80°C contrary to Ker BL which was not stable beyond 60°C. Similarly, the activity of Ker ProBP-BL on keratin and casein substrate, i.e. K:C ratio increased to 1.2 in comparison to 0.1 for Ker BL. Hydrolysis of insulin B-chain revealed that the cleavage sites increased to six from four in case of Ker ProBP-BL in comparison to Ker BL. However, cleavage sites decreased from seven to four in case of Ker ProBL-BP in comparison to the parent keratinase, Ker BP. Likewise, Ker ProBL-BP revealed altered pH and temperature kinetics with optima at pH 10 and 60°C in comparison to Ker BP which had optima at pH 9 and 70°C. It also cleaved soluble substrates with better efficiency in comparison to Ker BP with K:C ratio of 1.6. Pro-sequence mediated conformational changes were also observed in trans and were almost similar to the features acquired by the chimeras constructed in cis by swapping the pro-sequence region.     

短小芽孢杆菌耐碱性β-甘露聚糖酶基因的异源表达及其酶学特性

摘要:【目的】本研究报道了一种新颖的耐碱性β-甘露聚糖酶基因的异源表达并研究其酶学特性,为其工业应用奠定基础。【方法】通过基因同源性分析以及染色体步移技术,从短小芽孢杆菌Nsic-2中克隆得到甘露聚糖酶基因(manB)。然后分别将manB基因在大肠杆菌BL21(DE3)和枯草芽胞杆菌WB800N中进行表达,并研究其酶学特性。【结果】克隆得到的manB基因序列有一个含1104 bp的开放阅读框,编码一种含有367个氨基酸的甘露聚糖酶(ManB)。经预测其蛋白序列N末端有一个含有31个氨基酸的信号肽。将ManB的氨基酸序列进行同源性分析,发现其与来源于短小芽孢杆菌CCAM080065的甘露聚糖酶具有很高的一致性,可以推测ManB属于糖苷水解酶家族26。manB基因在大肠杆菌BL21(DE3)中成功地表达,得到甘露聚糖酶最高酶活为11021.3 U/mL。与其它甘露聚糖酶比较,ManB在碱性条件下表现出较高的稳定性,在pH6.0－9.0之间酶活相对稳定。纯化后的ManB比活可达4191±107 U/mg。酶反应动力学参数Km和Vmax分别为35.7 mg/mL和14.9 μmol/(mL·min)。同时,在枯草芽胞杆菌WB800N中也成功地实现了重组蛋白ManB的分泌表达。【结论】β-甘露聚糖酶基因成功实现异源表达,并得到其酶学性质。本文是首次报道从臭豆腐卤液中分离菌株,克隆表达甘露聚糖酶,并描述其酶学特性。ManB在碱性条件下的酶活稳定性,使得其在工业应用中具备较高的潜在应用价值。     

短小芽孢杆菌degQ基因的克隆与鉴定

degQ基因编码一个由46个氨基酸组成的多肽,能增强许多芽孢杆菌胞外酶基因的表达．以pMK4作克隆载体构建短小芽孢杆菌基因文库,并用DNA探针原位杂交法从中钓出degQ基因．对克隆基因的DNA序列进行了分析并证明克隆的短小芽孢杆菌degQ基因具有增强枯草杆菌蛋白酶和果聚糖蔗糖酶基因表达的能力．degQ基因克隆有助于研究芽孢杆菌的正调控机理并可望提高外源基因在芽孢杆菌中表达．     

一株高效羽毛降解菌株的分离与鉴定

采用以羽毛粉为唯一碳源和氮源的培养基,从自然界中分离到一株能够高效降解羽毛角蛋白的细菌,经形态学观察,生理生化实验和16SrRNA基因鉴定,初步确定该菌株为短小芽孢杆菌(Bacillus pumilus),且命名为短小芽孢杆菌WHK4。发酵48 h时,羽毛粉降解率达到85.76%。本研究为微生物降解羽毛角蛋白提供了优良的菌株,在蛋白饲料生产中具有潜在的广泛的应用前景。     

Marine glycosyl hydrolases in the hydrolysis and synthesis of oligosaccharides

The marine ecosystem can be considered a rather unexplored source of biological material (e.g. natural substances with therapeutic activity) and can also be a surprising source of enzymes carrying new and interesting catalytic activities to be applied in biocatalysis. The use of glycosyl hydrolases from marine environments dates back to the end of the 1960s and was mainly focused on the development of sensitive and reliable hydrolytic methods for the analysis of sugar chains. As a result not all the benefits of a particular enzymatic activity have been investigated, especially regarding the transglycosylation potential of these enzymes for the synthesis of glycosidic bonds. In this review, the potential of marine sources will be demonstrated reporting on the few examples found in literature for the synthesis and hydrolysis of biologically relevant oligosaccharides catalyzed by glycosyl hydrolases of marine origin. Particular emphasis is given to the synthesis of glycosidic bonds, which is easy by the use of glycosyl hydrolases. Further aspects considered in this review are applications of these biocatalysts for vegetal waste treatment in recovering useful materials, for structural identification and for preparation of target materials from new purified polysaccharides, for the synthesis or modification of food-related compounds and for glycobiology related studies.