Extracellular nucleases of Lysobacter enzymogenes: production of the enzymes and purification and characterization of an endonuclease

Lysobacter enzymogenes produced a nonspecific extracellular nuclease and an extracellular RNAase when grown in tryptone broth. Both enzyme activities appeared after the exponential growth phase of the organism. The addition of RNA to the medium specifically inhibited the production of the nuclease and the addition of phosphate prevented the synthesis of the RNAase. DNA had no effect on the enzyme production. The Lysobacter nuclease was purified 274-fold and its molecular weight was estimated to be between 22 000 and 28 000. Freshly purified nuclease showed one major protein band and one major activity band on polyacrylamide gels, whereas two major bands were seen after prolonged storage of the enzyme. The nuclease was most active at pH 8.0 and required Mg2+ or Mn2+. Little activity was obtained in the presence of Ca2+. The enzyme degraded double-stranded DNA more rapidly than single-stranded DNA or RNA and was essentially inactive with poly(A) or poly(C) as the substrate. Extensive hydrolysis of double-stranded DNA by the enzyme yielded oligodeoxyribonucleotides with terminal 5'-phosphate groups. The Lysobacter RNAase appeared to have a molecular weight approximately twice that of the nuclease and was specific for ribonucleotide polymers.     

Characterization of alkaline nuclease from rat liver mitochondria.

The alkaline nuclease (pH optimum 9.0) has been purified about 500-fold in 25% yield from the extract of rat liver mitochondria. The enzyme cleaves yeast RNA, poly(U), poly(U), poly(C) and denatured DNA to yield oligonucleotides with 5'-phosphoryl and 3'-hydroxyl ends. The enzyme has a molecular weight of about 60 000, a sedimentation coefficient of 4 S and an isoelectric point of 9.0. The behaviors of RNAase activity of the nuclease are identical with those of DNAase activity in column chromatography as well as in catalytic nature. The affinities of RNAase activity for substrate, Mg2+, spermidine and polyvinyl sulfate are lower than those of DNAase activity. The alkaline nuclease activity measured in the homogenate of regenerating rat liver is not significantly changed.     

Deoxyribonucleic acid polymerases of Euglena gracilis. Primer-template utilization of and enzyme activities associated with the two deoxyribonucleic acid polymerases of high molecular weight.

The two high-molecular-weight DNA polymerases from Euglena gracilis, pol A (mol. wt. 190 000) and pol B (mol. wt. 240 000), were differentiated on the basis of associated enzymic activities and primer-template utilization. Neither enzyme had endodeoxyribonuclease activity, but pol B, like pol B of yeast and the corresponding enzyme from Tetrahymena pyriformis, exhibited at least one other nuclease activity directed against denatured DNA and the RNA of an RNA-DNA hybrid. These nuclease functions preferred an alkaline pH and Mg2+. Pol B also exhibited nucleoside diphosphokinase activity. Both enzymes were active with 'activated' DNA and poly[d(A-T)] as primer-templates and were sensitive, especially pol B, to inhibition by excess of native or heat-denatured DNA. Pol B also utilized oligo[d(T)] and poly(A) templates under certain conditions, whereas pol A exhibited only slight activity with poly[d(A)]. (U)6 was not used as a primer by either enzyme.     

Strong extracellular nuclease activity displayed by barley (Hordeum vulgare L.) uninucleate microspores

 Electroporation is becoming an increasingly important technique for plant transformation. Nevertheless, no positive results were achieved in barley when uninucleate microspores were used as target cells. Since it was previously demonstrated that electric shocks create pores in the microspore cell wall, experiments were designed to verify the presence of nucleases in the electroporation mix. Aliquots of all the solutions used for microspore extraction, purification and transformation were collected and analysed using supercoiled pBI 221 as a substrate; a nuclease activity was detected in all samples. Though microspore rinsing removed most nucleolytic activity in the supernatants, DNA preservation in the electroporation buffer was difficult to achieve, because microspores appeared capable of synthesising and releasing endonucleases at any time. Microspore chilling at 0°C was fairly effective in reducing nuclease secretion in the mix, whereas 1%PEG or 10 mM EDTA maintained most of the DNA in a supercoiled or circular relaxed form. EDTA effects were counterbalanced by Mg²⁺, but not Ca²⁺ or Zn²⁺, and enhanced by Mn²⁺. Barley microspore nucleases actively degraded different DNAs as well as TMV RNA, and apparently had a molecular weight above 30 kDa. Nuclease inactivation with EDTA did not alter microspore viability and allowed a transient expression of the uidA gene in electroporated barley microspores. Received: 13 January 1997 / Accepted: 28 February 1997     

Purification and characterization of a cellulase from the ruminal fungus Orpinomyces joyonii cloned in Escherichia coli

A cellulase from the ruminal fungus Orpinomyces joyonii cloned in Escherichia coli was purified 88-fold by chromatography on High Q and hydroxyapatite. N-terminal amino acid sequence analyses confirmed that the cellulase represented the product of the cellulase gene Cel B2. The purified enzyme possessed high activity toward barley beta-glucan, lichenan, carboxymethyl cellulose (CMC), xylan, but not toward laminarin and pachyman. In addition, the cloned enzyme was able to hydrolyze p-nitrophenyl (PNP)-cellobioside, PNP-cellotrioside, PNP-cellotetraoside, PNP-cellopentaoside, but not PNP-glucopyranoside. The specific activity of the cloned enzyme on barley beta-glucan was 297 units/mg protein. The purified enzyme appeared as a single band in SDS-polyacrylamide gel electrophoresis and the molecular mass of this enzyme (58000) was consistent with the value (56463) calculated from the DNA sequence. The optimal pH of the enzyme was 5.5, and the enzyme was stable between pH 5.0 and pH 7.5. The enzyme had a temperature optimum at 40 degrees C. The K(m) values estimated for barley beta-glucan and CMC were 0.32 and 0.50 mg/ml, respectively.     

Isolation and characterization of two alkaline ribonucleases from calf serum.

Treatment of calf serum at 60 degrees C and pH 3.5 followed by chromatography on carboxymethyl (CM) cellulose resulted in the separation of two major peaks of alkaline RNAse activity. One was eluted from CM-cellulose at 0.075 M KCl with an overall purification of 5400-fold and the other was eluted at 0.25 M KCl with a 6700-fold purification. The RNAse eluted from CM-cellulose at 0.075 M KCl was almost completely inhibited by anti-RNAse A serum and by the endogenous RNAse inhibitor and a 33% inhibition was observed in the presence of 5 mM MgCl2. This enzyme seems to be similar or identical to RNAse A. The other RNAse, eluted from CM-cellulose at 0.25 M KCl was not inhibited by anti-RNAse A or 5 mM MgCl2 and was much less sensitive to the endogenous inhibitor. Both enzymes degraded RNA endonucleolytically and the nucleoside monophosphates obtained after partial hydrolysis of RNA by the two serum RNAases were primarily 2'- or 3' -CMP and 2'- or 3' -UMP. Poly(A), native DNA and denatured DNA were degraded slowly or not at all. The RNAase A-like enzyme degraded poly(C) at a significantly faster rate, and poly(U) at a slower rate, than RNA. However, the other serum RNAase was more active with poly(U) than with RNA and almost inactive with poly(C) as the substrate.     

Purification and some properties of a nuclease from rye germ nuclei

1. An endonuclease has been isolated from the nuclei of rye (Secale cereale L) germ and partially purified. The enzyme shows optimum activity over the pH range 5.4-7.4 towards both DNA and RNA, and has no phosphomonoesterase or phosphodiesterase activity. 2. DNA is degraded by the rye germ nuclease to oligonucleotides of similar size, and RNA to oligonucleotides and mononucleotides containing a C-terminal 5'-phosphate group. 3. The rate of hydrolysis of nuclear acids by the enzyme decreases in the following order: native DNA greater than denatured DNA greater than RNA. Synthetic polynucleotides are hydrolysed at a rate decreasing in the order: poly(A) greater than poly(U) greater than poly(C) greater than poly(G).     

A ribonuclease from Chinese ginseng (Panax ginseng) flowers

A ribonuclease, with a molecular mass of 23kDa, and much higher activity toward poly(U) than poly(C) and only negligible activity toward poly(A) and poly(G), was isolated from the aqueous extract of Chinese ginseng (Panax ginseng) flowers. The ribonuclease was unadsorbed on diethylaminoethyl-cellulose and adsorbed on Affi-gel blue gel and carboxymethyl-cellulose. High activity of the ribonuclease was maintained at pH 6-7. On either side of this pH range, there was a precipitous drop in enzyme activity. The activity of the enzyme peaked at 50 degrees C and fell to about 20% of the maximal activity when the temperature was lowered to 20 degrees C or raised to 80 degrees C. The characteristics of this ribonuclease were different from those of ribonuclease previously purified from ginseng roots.     

Uracil-DNA glycosylase of thermophilic Thermothrix thiopara.

An activity which released free uracil from dUMP-containing DNA was purified approximately 1,700-fold from extracts of Thermothrix thiopara, the first such activity to be isolated from extremely thermophilic bacteria. The enzyme appeared homogeneous, according to the results of sodium dodecyl sulfate-polyacrylamide gel electrophoresis. It had a native molecular weight of 26,000 and existed as a monomer protein in water solution. The enzyme had an optimal activity at 70 degrees C, between pH 7.5 and 9.0, and in the presence of 0.2% Triton X-100. It had no cofactor requirement and was not inhibited by EDTA, but it was sensitive to N-ethylmaleimide. The purified enzyme did not contain any nuclease that acted on native or depurinated DNA. The Arrhenius activation energy was 76 kJ/mol between 30 and 50 degrees C and 11 kJ/mol between 50 and 70 degrees C. The rate of heat inactivation of the enzyme followed first-order kinetics with a half-life of 2 min at 70 degrees C. Ammonium sulfate and bovine serum albumin protected the enzyme from heat inactivation. One T. thiopara cell contains enough activity to release about 2 X 10(8) uracil residues from DNA during one generation time at 70 degrees C.     

Modification of guanine residues in double-stranded DNA by aminomethylol compounds without denaturation of nucleic acid

With the application of radioactive formaldehyde and glycine the ability of aminomethylol compounds to combine with S1 nuclease treated DNA at 25 degrees and pH 5.8--7.4 has been shown. The reaction leads to modification of 22--26% of base pairs without changes of the DNA UV-absorption spectrum. Besides that the flexibility coefficient, the kinetics of despiralization under the action of formaldehyde and the stability of DNA molecule towards the S1 nuclease action permit to conclude that modification does not cause DNA despiralization. In experiments with the use of synthetic double-stranded polynucleotides poly(dA) times poly(dT), poly(rC) times poly(rl), poly(rG) times poly(dC) and poly(dC-dG) times poly(dC-dG) it has been shown that binding of methylol compounds to nucleic acids is due to reaction with guanine residues. Methylol derivatives of glycine reacts with guanine residues of double-stranded DNA only 10 times slower than with the monomer--deoxyguanosine-5'-phosphate. The studied reaction is reversible and the half-period of modified DNA reduction is found to be 5 hours at 25 degrees and pH 6.5. The rate constants of forward and reverse reactions and equilibrium constants of the reaction between methylolglycine and native DNA were determined.     

Characterization of DNA kinase from calf thymus

DNA kinase has been purified to homogeneity from calf thymus. The purified enzyme, with a specific activity of 16.7 units/mg protein at 25 degrees C, exhibited a sharp pH/activity curve with a pH optimum at 5.5 and low activity at alkaline pH. The molecular weight of the enzyme was estimated by dodecylsulfate/polyacrylamide gel electrophoresis to be 5.4 X 10(4). The enzyme has a sedimentation coefficient of 4.0 S. An apparent molecular weight of 5.6 X 10(4) and a Stokes' radius of 3.3 nm were estimated by gel-filtration on Sephadex G-100. The enzyme phosphorylates neither yeast RNA nor poly(A) instead of DNA. Compared with rat liver DNA kinase, calf thymus DNA kinase is relatively resistant to the inhibition by sulfate (Ki = 7 mM) and pyrophosphate (Ki = 5 mM). The enzyme activity is markedly stimulated by polyamines at the sub-optimal concentration of Mg2+ but not by monovalent cations.     

Formation and stability of repairable pyrimidine photohydrates in DNA

Ultraviolet irradiation of poly(dG-dC) and poly(dA-dU) in solution produces pyrimidine hydrates that are repaired by bacterial and mammalian DNA glycosylases [Boorstein et al. (1989) Biochemistry 28, 6164-6170]. Escherichia coli endonuclease III was used to quantitate the formation and stability of these hydrates in the double-stranded alternating copolymers poly(dG-dC) and poly(dA-dU). When poly(dG-dC) was irradiated with 100 kJ/m2 of 254-nm light at pH 8.0, 2.2% of the cytosine residues were converted to cytosine hydrate (6-hydroxy-5,6-dihydrocytosine) while 0.09% were converted to uracil hydrate (6-hydroxy-5,6-dihydrouracil). To measure the stability of these products, poly(dG-dC) was incubated in solution for up to 24 h after UV irradiation. Cytosine hydrate was stable at 4 degrees C and decayed at 25, 37, and 55 degrees C with half-lives of 75, 25, and 6 h. Uracil hydrate produced in irradiated poly(dA-dU) was stable at 4 degrees C and at 25 degrees C and decayed with a half-life of 6 h at 37 degrees C and less than 0.5 h at 55 degrees C. Uracil hydrate and uracil were also formed in irradiated poly(dG-dC). These experiments demonstrate that UV-induced cytosine hydrate may persist in DNA for prolonged time periods and also undergo deamination to uracil hydrate, which in turn undergoes dehydration to yield uracil. The formation and stability of these photoproducts in DNA may have promoted the evolutionary development of the repair enzyme endonuclease III and analogous DNA glycosylase/endonuclease activities of higher organisms, as well as the development of uracil-DNA glycosylase.     

The extracellular nuclease of Serratia marcescens: studies on the activity in vitro and effect on transforming DNA in a groundwater aquifer microcosm

A quantitative endonuclease assay, which relies on the introduction of single and double strand breaks into supercoiled plasmid DNA, was used to study the activity of the extracellular nuclease of Serratia marcescens SM6 in buffer and in groundwater. The parallel enzyme concentration-dependent production of relaxed and linear plasmid molecules suggests that the nuclease produces single and double strand breaks in duplex DNA. Bovine serum albumin stimulated the nuclease activity towards DNA and RNA and increased the stability of the enzyme against thermal inactivation. The DNase activity at 4 °C and 50 °C was almost half of that at the optimum temperature (37 °C). The nuclease was active in groundwater, although the specific activity was lower than in buffer. In a groundwater aquifer microcosm, mineral-adsorbed transforming DNA was substantially less accessible to the nuclease than was dissolved DNA. The data suggest that the extracellular nuclease of Serratia marcescens may contribute to DNA turnover in the environment and that adsorption of DNA to minerals provides protection against the nuclease.Abbreviations GW groundwater GWA groundwater aquifer     

An Extracellular S1-Type Nuclease of Marine Fungus Penicillium melinii

An extracellular nuclease was purified 165-fold with a specific activity of 41,250 U/mg poly(U) by chromatography with modified chitosan from the culture of marine fungus Penicillium melinii isolated from colonial ascidium collected near Shikotan Island, Sea of Okhotsk, at a depth of 123 m. The purified nuclease is a monomer with the molecular weight of 35 kDa. The enzyme exhibits maximum activity at pH 3.7 for DNA and RNA. The enzyme is stable until 75°C and in the pH range of 2.5–8.0. The enzyme endonucleolytically degrades ssDNA and RNA by 3′–5′ mode to produce 5′-oligonucleotides and 5′-mononucleotides; however, it preferentially degrades poly(U). The enzyme can digest dsDNA in the presence of pregnancy-specific beta-1-glycoprotein-1. The nuclease acts on closed circular double-stranded DNA to produce opened circular DNA and then the linear form DNA by single-strand scission. DNA sequence encoding the marine fungus P. melinii endonuclease revealed homology to S1-type nucleases. The tight correlation found between the extracellular endonuclease activity and the rate of H³-thymidine uptake by actively growing P. melinii cells suggests that this nuclease is required for fulfilling the nucleotide pool of precursors of DNA biosynthesis during the transformation of hyphae into the aerial mycelium and conidia in stressful environmental conditions.     

Purification and characteristics of a mitochondrial endonuclease from the yeast Saccharomyces cerevisiae

Saccharomyces cerevisiae contains a membrane-bound mitochondrial nuclease. The enzyme was purified nearly 500-fold from sphaeroplasts of the organism by differential centrifugation, differential solubilization, heparin-agarose chromatography, and gel filtration. A final specific activity of 98 mumol min-1 (mg of protein)-1 was obtained. The enzyme required further purification to achieve homogeneity. Two peaks of activity were obtained after gel filtration with apparent molecular weights of 140000 and 57000. Otherwise, these two components have nearly identical characteristics. Without detergent the enzyme is insoluble and has very low activity. Zwittergent 3-14 or Triton X-100 in the presence of KCl could be used to solubilize and activate the enzyme. A number of other detergents were much less effective in solubilizing or activating the nuclease. The enzyme requires Mg2+ for activity, and this can be replaced to some degree by Mn2+ but not by Ca2+ or Zn2+. It is most active at pH 6.5-7.0 and degrades the substrate to small oligonucleotides with 5'-phosphate ends. The relative rates of hydrolysis were 100 for poly(A), 31 for ssDNA, 19 for RNA, 2.1 for dsDNA, and less than or equal to 0.2 for poly(C). Under the assay conditions used the enzyme appears to constitute about 90% of the total nuclease activity of the cell. The enzyme is unstable, especially at neutral and alkaline pH.     

A novel ribonuclease from fresh fruiting bodies of the portabella mushroom Agaricus bisporus.

A 14 kDa ribonuclease with a novel N-terminal sequence was isolated from fresh fruiting bodies of the portabella mushroom. It was adsorbed on DEAE-cellulose and carboxymethyl-cellulose, and demonstrated the highest ribonucleolytic potency toward poly (A), 60% as much activity toward poly (C), 40% as much activity toward poly (U), and the least activity (7% as much) toward poly (G). It exhibited a pH optimum at pH 4.5 and a temperature optimum at 60 degrees C. Its activity at 100 degrees C was higher than that at 20 degrees C.     

Deoxyribonucleic acid polymerase from the extreme thermophile Thermus aquaticus.

A stable deoxyribonucleic acid (DNA) polymerase (EC 2.7.7.7) with a temperature optimum of 80 degrees C has been purified from the extreme thermophile Thermus aquaticus. The enzyme is free from phosphomonoesterase, phosphodiesterase and single-stranded exonuclease activities. Maximal activity of the enzyme requires all four deoxyribonucleotides and activated calf thymus DNA. An absolute requirement for divalent cation cofactor was satisfied by Mg2+ or to a lesser extent by Mn2+. Monovalent cations at concentrations as high as 0.1 M did not show a significant inhibitory effect. The pH optimum was 8.0 in tris(hydroxymethyl)aminomethane-hydrochloride buffer. The molecular weight of the enzyme was estimated by sucrose gradient centrifugation and gel filtrations on Sephadex G-100 to be approximately 63,000 to 68,000. The elevated temperature requirement, small size, and lack of nuclease activity distinguish this polymerase from the DNA polymerase of Escherichia coli.     

A ribonuclease from yeast associated with the 40 S ribosomal subunit.

1. Autodegradation of yeast ribosomes is due to a 'latent' ribonuclease which is associated with the 40 S ribosomal subunit. 2. The ribonuclease was extracted in the presence of EDTA from ribosomes and purified 118-rold by protamine sulphate precipitation, (NH4)2SO4 fractionation and chromatography on DEAE-cellulose. 3. The optimum pH for this enzyme is 5 to 6.5 while the optimum temperature is 45 to 50 degrees C. Incubation for 10 min at 60 degrees C caused a reduction in enzyme activity of 70%. 4. The ribonuclease has an endonucleolytic activity against rRNA, tRNA, poly(A), poly(U) and poly(C) but does not degrade poly(G) or DNA. It hydrolyzes the homopolymers to nucleoside 3'-phosphates. 5. Zn2+, Mn2+, heparin, glutathione and p-chloromercuribenzoate inhibit the ribonuclease, while Na+, K+, EDTA and sermidine have only little or no effect. 6. It binds tightly to yeast ribosomes but only loosely to ribonuclease-free wheat germ ribosomes. 7. Polyribosomes possess less autodegradation activity than monoribosomes, isolated from the same homogenate.     

酿脓链球菌Cas9核酸酶的重组表达、分离纯化及酶学特性

【背景】Cas9核酸酶是一种RNA引导的核酸内切酶,可与单链向导RNA (single-guide RNA,sgRNA)形成稳定的核糖核蛋白复合物,识别和切割特定的核苷酸片段。由于其具备高灵活性和高效率的特点,目前已经成为基础科学研究领域和临床治疗方法中使用最广泛的基因编辑工具。【目的】为Cas9核酸酶的合理开发和利用提供理论依据。【方法】利用大肠杆菌表达系统表达野生型酿脓链球菌(Streptococcus pyogenes) Cas9核酸酶,经硫酸铵沉淀和镍柱亲和层析两步纯化获得较高纯度表达产物,并对其热稳定性、pH稳定性、金属离子的影响等酶学特性进行研究。【结果】经高密度发酵后,大肠杆菌湿菌重达191.0 g/L。纯化后酿脓链球菌Cas9核酸酶的比酶活达641.29 U/mg,纯化倍数为16.02,收率为46.40%。Cas9核酸酶在25-42°C保温2 h后剩余酶活保持在65%以上,而在45°C保温15 min后全部失活;其在pH 6.0-10.0范围内稳定性较高,剩余酶活大于68%,在pH9.0时稳定性最高;0.5-20.0mmol/L浓度范围内的Mg²⁺...