Bsu2413I and Bfi2411I,two new thermophilic type II restriction endonucleases from Bacillus subtilis and Bacillus firmus: isolation and partial purification – Thermophilic endonucleases from two Bacillus species

Two new thermophilic type II restriction endonucleases, which we designated as Bsu2413I and Bfi2411I, have been isolated from gram-positive thermophilic bacteria Bacillus subtilis strain 2413 and Bacillus firmus strain 2411 respectively and partially purified. The restriction endonucleases were extracted from cell extracts and purified using single step purification through phosphocellulose column chromatography. SDS-PAGE profile showed denatured molecular weights of 33 and 67 kDa for the Bsu2413I and 39 and 67 kDa for the Bfi2411I. The partially purified Bsu2413I enzyme restricted pBR322 DNA into two fragments of 3250 and 1100 bp whereas Bfi2411I enzyme restricted pBR322 DNA into two fragments of 3500 and 800 bp. The activity of both endonucleases was assayed at 55 degrees C and they required Mg+2 as cofactor like other type II restriction endonucleases.     

Is modification sufficient to protect a bacterial chromosome from a resident restriction endonuclease?

It has been generally accepted that DNA modification protects the chromosome of a bacterium encoding a restriction and modification system. But, when target sequences within the chromosome of one such bacterium (Escherichia coli K-12) are unmodified, the cell does not destroy its own DNA; instead, ClpXP inactivates the nuclease, and restriction is said to be alleviated. Thus, the resident chromosome is recognized as 'self' rather than 'foreign' even in the absence of modification. We now provide evidence that restriction alleviation may be a characteristic of Type I restriction-modification systems, and that it can be achieved by different mechanisms. Our experiments support disassembly of active endonuclease complexes as a potential mechanism. We identify amino acid substitutions in a restriction endonuclease, which impair restriction alleviation in response to treatment with a mutagen, and demonstrate that restriction alleviation serves to protect the chromosome even in the absence of mutagenic treatment. In the absence of efficient restriction alleviation, a Type I restriction enzyme cleaves host DNA and, under these conditions, homologous recombination maintains the integrity of the bacterial chromosome.     

Purification, characterisation and mutagenic enhancement of a thermoactive α-amylase from Bacillus subtilis

Bacillus subtilis was isolated from flour mill wastes. It produced a thermostable α-amylase in complex media containing starch. Amylase activity was optimal at the exponential phase and was more strongly expressed with sorghum, yam peel and corn starch than soluble potato starch. The enzyme was purified 24-fold to a specific activity of 2200 U mg⁻¹, with a yield of 10%. It yielded a single band when subjected to SDS-PAGE and an apparent molecular mass of 54780 was determined by mass spectrometry. The enzyme, which was optimally active at 80°C and pH 5.6, released saccharides with a polymerisation degree of 1–6 following hydrolysis of yam peel, sorghum and corn starch. Cells of B. subtilis were exposed to ultraviolet irradiation and N-methyl-N′-nitro-N-nitrosoguanidine. Hyperproductive mutants were obtained by these treatments. Received 14 February 1997/ Accepted in revised form 13 August 1997     

Purification and characterization of a maltooligosaccharide-forming α-amylase from a new Bacillus subtilis KCC103

A maltooligosaccharide-forming α-amylase was produced by a new soil isolate Bacillus subtilis KCC103. In contrast to other Bacillus species, the synthesis of α-amylase in KCC103 was not catabolite-repressed. The α-amylase was purified in one step using anion exchange chromatography after concentration of crude enzyme by acetone precipitation. The purified α-amylase had a molecular mass of 53 kDa. It was highly active over a broad pH range from 5 to 7 and stable in a wide pH range between 4 and 9. Though optimum temperature was 65–70 °C, it was rapidly deactivated at 70 °C with a half-life of 7 min and at 50 °C, the half-life was 94 min. The K _m and V _max for starch hydrolysis were 2.6 mg ml⁻¹ and 909 U mg⁻¹, respectively. Ca²⁺ did not enhance the activity and stability of the enzyme; however, EDTA (50 mM) abolished 50% of the activity. Hg²⁺, Ag²⁺, and p-hydroxymercurybenzoate severely inhibited the activity indicating the role of sulfydryl group in catalysis. The α-amylase displayed endolytic activity and formed maltooligosaccharides on hydrolysis of soluble starch at pH 4 and 7. Small maltooligosaccharides (D2–D4) were formed more predominantly than larger maltooligosaccharides (D5–D7). This maltooligosaccharide forming endo-α-amylase is useful in bread making as an antistaling agent and it can be produced economically using low-cost sugarcane bagasse.     

Cloning, sequence analysis, and heterologous expression of a β-mannanase gene from Bacillus subtilis Z-2

Mannanase, an extracellular enzyme that catalyzes the hydrolysis of hemicelluloses to produce oligosaccharides, has potential to be applied in food industries. In this study a mannanase gene from B. subtilis Z-2 was isolated through PCR screening of a genomic DNA library. The nucleotide sequence of the mannanase gene, man, contained an open reading frame of 1080 bp, which codes for a deduced 26 amino-acid signal peptide and a mature protein with a deduced molecular mass of 38 kDa. The man gene can both be expressed heterologously into the periplasm from the plasmid pET22b(+) containing an intact signal peptide (pET-NdeI18) or the pelB signal peptide of the pET22b(+)vector (pET-NcoI3). Escherichia coli BL21 (DE3) containing pET-NcoI3 secreted about twice as much mannanase as that harboring pET-NdeI18. The E. coli DH5α expression of man was under the control of the lac promoter in the pRK415 vector; it was much more effective when the Shine Dalgarno (SD) sequence was changed from GGGGAG to AAGGAG and the start codon was changed from TTG to ATG, respectively. These results suggest that genetic modification of the SD sequence and start codon is practical for a high-level mannanase expression in different bacterial strains. Published in Russian in Molekulyarnaya Biologiya, 2006, Vol. 40, No. 3, pp. 418–424. This article was submitted by the authors in English.     

Isolation and characterization of a cold-active,alkaline, detergent stable α-amylase from a novel bacterium Bacillus subtilis N8

A cold-active alkaline amylase producer Bacillus subtilis N8 was isolated from soil samples. Amylase synthesis optimally occurred at 15°C and pH 10.0 on agar plates containing starch. The molecular weight of the enzyme was found to be 205?kDa by performing SDS-PAGE. While the enzyme exhibited the highest activity at 25°C and pH 8.0, it was highly stable in alkaline media (pH 8.0–12.0) and retained 96% of its original activity at low temperatures (10–40°C) for 24?hr. While the amylase activity increased in the presence of β-mercaptoethanol (103%); Ba²⁺, Ca²⁺, Na⁺, Zn²⁺, Mn²⁺, H₂O₂, and Triton X-100 slightly inhibited the activity. The enzyme showed resistance to some denaturants: such as SDS, EDTA, and urea (52, 65, and 42%, respectively). N8 α-amylase displayed the maximum remaining activity of 56% with 3% NaCl. The major final products of starch were glucose, maltose, and maltose-derived oligosaccharides. This novel cold-active α-amylase has the potential to be used in the industries of detergent and food, bioremediation process and production of prebiotics.     

Characterization and application of a detergent-stable alkaline α-amylase from Bacillus subtilis strain AS-S01a

A strain AS-S01a, capable of producing high-titer alkaline α-amylase, was isolated from a soil sample of Assam, India and was taxonomically identified as Bacillus subtilis strain AS-S01a. Optimized α-amylase yield by response surface method (RSM) was obtained as 799.0 U with a specific activity of 201.0 U/mg in a process control bioreactor. A 21.0 kDa alkaline α-amylase purified from this strain showed optimum activity at 55 °C and pH 9.0, and it produced high molecular weight oligosaccharides including small amount of glucose from starch as the end product. The K_m and V_max values for this enzyme towards starch were determined as 1.9 mg/ml and 198.21 μmol/min/mg, respectively. The purified α-amylase retained its activity in presence of oxidant, surfactants, EDTA and various commercial laundry detergents, thus advocating its suitability for various industrial applications.     

Improving the acidic stability of a β-mannanase from Bacillus subtilis by site-directed mutagenesis

β-Mannanase can randomly hydrolyze the (1→4)-β-d-mannosidic linkages in mannans, galactomannans and glucomannans, yielding manno-oligosaccharides. In this study, the β-mannanase (MAN) from Bacillus subtilis B10-02 was overexpressed successfully in B. subtilis 168 as a hexa-histidine tagged, secreted protein. The recombinant enzyme BsMAN6H was not stable under acidic conditions, which restricts its use in food and feed industry. We aimed to improve the acid stability of BsMAN6H by changing several surface-exposed amino acid residues to acidic or neutral ones. Among the mutations, the His54Asp resulted in a shift in the optimal pH from 6.5 to 5.5. Accordingly, the acid stability was improved by a factor of a negative potential on the structure surface around the mutated site. Furthermore, the H54D variant showed the enzyme activity up to 3207.82 U/mL in bioreactors using the cheap Kojac powder as substrate. As a result, a bacterial β-mannanase was produced efficiently with increased acid stability, improving its applicability in the animal feed industry.     

Characterization of a Hexameric Exo-Acting GH51 α-l-Arabinofuranosidase from the Mesophilic Bacillus subtilis

α-l-Arabinofuranosidases (α-l-Abfases, EC 3.2.1.55) display a broad specificity against distinct glycosyl moieties in branched hemicellulose and recent studies have demonstrated their synergistic use with cellulases and xylanases for biotechnological processes involving plant biomass degradation. In this study, we examined the structural organization of the arabinofuranosidase (GH51 family) from the mesophilic Bacillus subtilis (AbfA) and its implications on function and stability. The recombinant AbfA showed to be active over a broad temperature range with the maximum activity between 35 and 50 °C, which is desirable for industrial applications. Functional studies demonstrated that AbfA preferentially cleaves debranched or linear arabinan and is an exo-acting enzyme producing arabinose from arabinoheptaose. The enzyme has a canonical circular dichroism spectrum of α/β proteins and exhibits a hexameric quaternary structure in solution, as expected for GH51 members. Thermal denaturation experiments indicated a melting temperature of 53.5 °C, which is in agreement with the temperature–activity curves. The mechanisms associated with the unfolding process were investigated through molecular dynamics simulations evidencing an important contribution of the quaternary arrangement in the stabilization of the β-sandwich accessory domain and other regions involved in the formation of the catalytic interface of hexameric Abfases belonging to GH51 family.     

Studies on 5′-Nucleotidase-Lacking Mutants Derived from Bacillus subtilis

For the purpose of effective accumulation of 5′-MMP, mutants, whose 5′-IMP-dephosphorylating activities were lower than that of strain A-1 of B. subtilis capable of accumulating a small amount of 5′-IMP as well as inosine and hypoxanthine, were derived from inosine-producing strain 1145-2-83 and strain A-1.

As a result, several mutants different from one another in the level of 5′-IMP-dephos- phorylating activity were isolated. Any of them did not acquire high ability to accumulate 5′-IMP. The more the mutants lost 5′-IMP-dephosphorylating activity, the less they accumulated extracellular inosine. The loss of nucleotide-dephosphorylating activity in the adenine-requiring mutants resulted in a remarkable increase in the amount of adenine required. The accumulation of 5′-IMP was not repressed by the addition of adenine at the concentration enough to repress accumulation of inosine.     

Properties of the competence-inducing factor of Bacillus subtilis 168I−

It has been shown that the competence-inducing factor of Bacillus subtilis 168I^? exhibits lytic activity toward isolated cell walls and nuclease activity toward transforming DNA. It has been shown that the competence factor covalently bound to CNBr-Sepharose exhibits the same enzymatic properties. A mechanism for the transformation process is proposed which advances the mechanism previously proposed by this laboratory.     

Poly-γ-glutamate from Bacillus subtilis inhibits tyrosinase activity and melanogenesis

Poly-γ-glutamate (γ-PGA) has been considered as one of the most promising biomaterials with a wide range of applications, but there has been no report that directly shows the anti-tyrosinase and anti-melanogenesis properties of γ-PGA. In the present study, we investigated the inhibitory effects of γ-PGA with low molecular weight (Mw; lγ-PGA) and high Mw (hγ-PGA) on mushroom tyrosinase and murine tyrosinase activities and on melanogenesis in B16 melanoma cells. First, we showed that both lγ-PGA and hγ-PGA could effectively inhibit mushroom tyrosinase activities including monophenolase and diphenolase activities in a dose-dependent manner. Second, both lγ-PGA and hγ-PGA showed strong anti-tyrosinase activity and anti-melanogenesis in B16 melanoma cells. Third, both lγ-PGA and hγ-PGA inhibited forskolin-induced tyrosinase activity and melanogenesis by decreasing the levels of intracellular reactive oxygen species and nitric oxide while increasing the catalase activity in B16 cells. This is the first report on the anti-melanogenesis effect of γ-PGA, which suggests that γ-PGA could have a potential in the cosmetic skin whitening business, therapeutic applications and the food industry.     

Genetically Engineered Poly-γ-glutamate Producer from Bacillus subtilis ISW1214

The pgsBCA-gene disruptant from Bacillus subtilis ISW1214, i.e., MA41, does not produce poly-γ-glutamate (PGA). We newly constructed an MA41 recombinant bearing the plasmid-borne PGA synthetic system, in which PGA production was strictly controlled by the use of xylose. Unlike the parent strain, ISW1214, the genetically engineered strain produced abundant PGA in both L-glutamate-rich and D-glutamate-rich media.     

Analysis of eucaryotic DNAs with a restriction endonuclease from H.influenzae: isolation of “hidden” satellite DNAs

The restriction enzymes from H.influenzae have been used to study various eucaryotic DNAs. Fractions resistant to the action of these enzymes have been isolated from rat, mouse and calf DNAs. The method revealed the existence in rat of several components having the properties of satellite DNAs. Mouse DNA was shown to contain a new satellite of buoyant density 1. 704. Therefore, this appears to be a powerfull method for the isolation of "hidden" satellite DNAs.Calf satellite DNAs rho = 1.705 and rho = 1.723 were those resistant to the action of the restriction enzymes whilst satellite DNAs rho = 1.714 and rho = 1.710 gave fragments of discrete lengths, suggesting internal repeat units of 1 500 and 5 000 base pairs respectively.     

Characterization of Infectious Deoxyribonucleic Acid from Temperate Bacillus subtilis Bacteriophage φ 105

Phenol-extracted, infectious deoxyribonucleic acid (DNA) species from phi105 phage particles, from phi105 lysogenic bacteria, and from induced phi105 lysogenic bacteria were sedimented in sucrose gradients. Infectious DNA from phi105 particles sedimented like the bulk of mature phage DNA in neutral sucrose. Infectivity of prophage DNA was associated with fast-sedimenting material of heterogenous size. Infectious vegetative phage DNA sedimented somewhat faster than mature phage DNA; it was rapidly converted to a poorly infectious form during the infection.     

Transfer Reaction Catalyzed by Exo-β-1,4-galactanase from Bacillus subtilis

A transfer reaction catalyzed by an exo-β-1,4-galactanase from Bacillus subtilis was studied. The enzyme had a broad acceptor specificity and transferred galactobiosyl residues to acceptors such as various alcohols, including hydroxy benzenes and saccharides. Transfer products of glycerol formed by the enzyme were compared with those formed by Escherichia coli β-galactosidase and by Penicillium citrinum endo-galactanase. E. coli enzyme transferred 90% of galactose residues to the primary hydroxyl groups of glycerol and P. citrinum endo-enzyme transferred 80% of saccharide residues to the secondary hydroxyl group. The B. subtilis exo-galactanase was less specific than the other two enzymes and formed two products (1-DG and 2-DG) with a 2-DG/l-DG ratio of about 2. The structures of the saccharides were examined by ¹³C-nuclear magnetic resonance analysis and by enzymatic hydrolysis. 1-DG and 2-DG were elucidated to be O-β-d-galactosyl-(l→4)-O-β-d-galactosyl-(1→1)-glycerol and O-β-d-galactosyl-(l→4)-O-β-d-galactosyl-(l→2)-glycerol, respectively. The efficiency of the transfer reaction was measured at various concentrations of glycerol using galactotriose as a donor. About 40–75% of galactobiosyl residues were transferred at an acceptor concentration range of 20–100 mg/ml.     

Bacillus subtilis RNase J1 endonuclease and 5′ exonuclease activities in the turnover of ΔermC mRNA

RNase J1, a ribonuclease with 5′ exonuclease and endonuclease activities, is an important factor in Bacillus subtilis mRNA decay. A model for RNase J1 endonuclease activity in mRNA turnover has RNase J1 binding to the 5′ end and tracking to a target site downstream, where it makes a decay-initiating cleavage. The upstream fragment from this cleavage is degraded by 3′ exonucleases; the downstream fragment is degraded by RNase J1 5′ exonuclease activity. Previously, ΔermC mRNA was used to show 5′-end dependence of mRNA turnover. Here we used ΔermC mRNA to probe RNase J1-dependent degradation, and the results were consistent with aspects of the model. ΔermC mRNA showed increased stability in a mutant strain that contained a reduced level of RNase J1. In agreement with the tracking concept, insertion of a strong stem–loop structure at +65 resulted in increased stability. Weakening this stem–loop structure resulted in reversion to wild-type stability. RNA fragments containing the 3′ end were detected in a strain with reduced RNase J1 expression, but were undetectable in the wild type. The 5′ ends of these fragments mapped to the upstream side of predicted stem–loop structures, consistent with an impediment to RNase J1 5′ exonuclease processivity. A ΔermC mRNA deletion analysis suggested that decay-initiating endonuclease cleavage could occur at several sites near the 3′ end. However, even in the absence of these sites, stability was further increased in a strain with reduced RNase J1, suggesting alternate pathways for decay that could include exonucleolytic decay from the 5′ end.