Purification, characterization, and the complete amino acid sequence of porcine pancreatic deoxyribonuclease

Carp liver DNase—isolation, further characterization and interaction with endogenous actin

Deoxyribonuclease I (DNase I)-like enzyme from the liver of the carp (Cyprinus carpio) was purified to homogeneity and further characterized. Ion exchange chromatography on DEAE-cellulose, molecular filtration on Sephacryl S-300 and Con A-Sepharose affinity chromatography were applied for enzyme isolation. Carp liver DNase, similarly to DNase I from bovine pancreas, was found to be an endonuclease that hydrolyses linear DNA from salmon sperm as well as circular DNA forms--plasmid and cosmid. The purified enzyme is a glycoprotein and shows microheterogeneity, as observed in DNase zymograms prepared after native and two-dimensional electrophoresis (2D-PAGE). The composition of sugar component of the enzyme was characterized. Special attention was focused on the ability of carp liver DNase to interact with carp liver actin. The carp liver enzyme was inhibited by endogenous actin. The estimated binding constant of carp liver DNase to carp liver actin was calculated to be 1.1 x 10(6) M(-1).

Porcine spleen deoxyribonuclease II. Covalent structure, cDNA sequence, molecular cloning, and gene expression

Porcine spleen DNase II, a lysosomal acid hydrolase, is a noncovalently linked alpha.beta heterodimer (Liao, T.-H. (1985) J. Biol. Chem. 260, 10708-10713). The alpha subunit, after disulfide cleavage, yields two chains, alpha1 and alpha2. The complete amino acid sequences of the alpha1, beta, and alpha2 chains were elucidated by protein sequencing, and the pairings of one interchain disulfide between alpha1 and alpha2 and of three intrachain disulfides in alpha2 were assigned. Six carbohydrate attachment sites, two in beta and four in alpha2, were detected by sugar analyses. The cDNA of DNase II was amplified using primers synthesized on the basis of the amino acid sequences determined. The amplified fragments shown to be a cDNA sequence of 1,292 bases. This cDNA sequence has an open reading frame encoding a 364-amino acid polypeptide containing a putative transmembrane peptide at the NH2-end, two small connecting peptides in the middle, and a peptide at the COOH terminus. These are evidently removed to form mature DNase II. Thus, all three chains in the sequence alpha1, beta, and alpha2 are coded by the same cDNA. When Chinese hamster ovary cells were transfected with a cloned plasmid with an inserted cDNA fragment encoding the entire reading frame, the expressed protein was released into the growth medium as an active form of DNase II.

Purification and characterization of tilapia (Oreochromis mossambicus) deoxyribonuclease I--primary structure and cDNA sequence

DNase I of tilapia (Oreochromis mossambicus) was purified to homogeneity. Tilapia DNase I is most active at pH 8.5 with Mg2+ as activator. The Ca2+/Mg2+ pair has a synergistic effect on activation. The enzyme is readily inactivated by heating above 55 degrees C, but is not inactivated by trypsin or 2-mercaptoethanol under alkaline conditions, with or without CaCl2. Its isoelectric point is 6.0. The 258-amino-acid sequence of tilapia DNase I was derived from overlapping sequences of tryptic, chymotryptic and CNBr peptides. The purified enzyme has two variants differing by a single Lys-->Arg mutation at position 125. The polypeptide chain has one disulfide bridge and one carbohydrate side chain. By mass spectrometry, the purified enzyme shows many molecular mass forms differing by Lys/Arg substitution and sugar-chain length. The major form has a molecular mass of 30,914 Da. A 1061-bp nucleotide sequence for the cDNA of tilapia DNase I, obtained by gene cloning and DNA sequencing, contains an ORF coding for a putative 26-residue transmembrane peptide and the mature DNase I polypeptide.

The origins of DNA breaks: a consequence of DNA damage, DNA repair, or apoptosis?

DNA breaks can arise from many sources after incubation of cells with toxic agents. Very few agents break DNA directly, rather most breaks occur as a result of metabolic participation by the cell, such as during attempts to repair the damage. It is now realized that many DNA breaks arise as a consequence of steps in the pathway of cell death. Upon reanalyzing the methodology commonly used to detect DNA breaks, it is evident that many studies would not have observed DNA breaks associated with cell death. Frequently experimental conditions have been used that are extremely toxic to cells with the justification that the cells were still viable as measured by their ability to exclude dyes such as trypan blue. However, the DNA digestion associated with cell death by apoptosis occurs prior to changes in membrane integrity. Because the possibility of endogenous endonuclease activity was not realized, many studies may have inaccurately assumed that DNA breaks arose during, for example, inhibition of DNA repair or as intermediates in recombination. In light of the new understanding of apoptosis and the formation of DNA breaks as an early event in cell death, it is important to both reevaluate past conclusions and to ensure that future studies fully consider the breaks derived from the cytotoxicity of every agent under investigation.

Primary structure of nuclease P1 from Penicillium citrinum

The primary structure of nuclease P1, which cleaves both RNA and single-stranded DNA, from Penicillium citrinum was elucidated. The complete amino acid sequence consisting of 270 residues was determined by analysis of peptides obtained by digestion with Achromobacter protease I of the reduced and S-aminoethylated protein and by digestion with Staphylococcus aureus V8 protease of the reduced and S-carboxymethylated protein. Four half-cystine residues were assigned to Cys72-Cys217 and Cys80-Cys85. N-Glycosylated asparagine residues were identified at positions 92, 138, 184 and 197. Fast-atom-bombardment and laser-ionization MS were successfully used to confirm the determined amino acid sequences of peptides and to estimate the molecular mass of this glycoprotein having heterogenous sugar moieties, respectively. Comparison of the amino acid sequence of nuclease P1 with other nucleases revealed that the protein has a high degree of sequence identity (50%) with nuclease S1 from Aspergillus oryzae. The His-Phe-Xaa-Asp-Ala sequence (positions 60-64) is similar to the sequence (His-Phe-Asp-Ala) involving the active-site His119 of bovine pancreatic RNase A, and the Pro-Leu-His sequence (positions 124-126) is identical with the sequence involving the active-site His134 of porcine pancreatic DNase I.

Shrimp hepatopancreatic deoxyribonuclease--purification and characterization as well as comparison with bovine pancreatic deoxyribonuclease

Deoxyribonuclease (DNase), isolated from shrimp hepatopancreas by chromatography on DEAE-cellulose, Sephadex G-100, phenyl-Sepharose and hydroxyapatite, is homogeneous as shown by sodium dodecyl sulfate polyacrylamide gel electrophoresis. The metal ion requirements and the pH-activity optima of shrimp DNase are very similar to those of bovine DNase. Both shrimp and bovine DNases are sensitive to iodoacetate inactivation under the same condition. The active shrimp DNase molecule is a monomer of Mr 44,000, approx. 13,000 larger than the Mr of bovine DNase. Shrimp DNase is rich in glutamic acid, glycine and half-cystine. The single polypeptide chain of shrimp DNase is highly cross-linked by 18 disulfides as compared to only two disulfides in bovine DNase. In contrast to bovine DNase, shrimp DNase is not a glycoprotein, is devoid of the activity against p-nitrophenyl phenylphosphonate (a synthetic substrate for bovine DNase), and resists to inactivation by beta-mercaptoethanol or trypsin under the Ca2(+)-free condition at pH 8. Shrimp DNase shows an isoelectric point of 4.06 on the thin-layer isoelectric focusing and rapidly loses its activity at pH below 5.

Purification and physicochemical properties of deoxyribonuclease from pyloric caeca of Atlantic cod (Gadus morhuaL.)

A deoxyribonuclease (DNase) of pancreatic origin has been purified from extracts of the pyloric caeca from Atlantic cod (Gadus morhua L.). The crude extract was prepared by mincing frozen caeca tissue in equal volumes of buffer. The enzyme was isolated from the supernatant after streptomycin sulfate precipitation and centrifugation. The purification scheme further included chromatography on Q-Sepharose Fast Flow and hydroxyapatite columns. Affinity adsorption chromatography of the hydroxyapatite fraction on 8-(6-aminohexyl)-amino-5'-AMP-Sepharose, revealed an apparently homogeneous protein with molecular weight of 35,000 Da as judged by NaDodSO4-PAGE. In sum a 644-fold enzymatic enrichment and 3.5% total enzyme recovery was achieved. The cod enzyme resembles DNase I-type enzymes with an alkaline pH activity optimum and shows dependency for Mg(2+). The pI of the enzyme is 6.5 as determined by isoelectric focusing and DNase-zymography. Our findings suggest that the nuclease is a member of the cod's digestive enzymes secreted from the connective tissue surrounding the caeca.

Amino-acid sequence of ribonuclease T2 from Aspergillus oryzae

The amino acid sequence of ribonuclease T2 (RNase T2) from Aspergillus oryzae has been determined. This has been achieved by analyzing peptides obtained by digestions with Achromobacter lyticus protease I, Staphylococcus aureus V8 protease, and alpha-chymotrypsin of two large cyanogen bromide peptides derived from the reduced and S-carboxymethylated or S-aminoethylated protein. Digestion with A. lyticus protease I was successfully used to degrade the N-terminal half of the S-aminoethylated protein at cysteine residues. RNase T2 is a glycoprotein consisting of 239 amino acid residues with a relative molecular mass of 29,155. The sugar content is 7.9% (by mass). Three glycosylation sites were determined at Asns 15, 76 and 239. Apparently RNase T2 has a very low degree of sequence similarity with RNase T1, but a considerable similarity is observed around the amino acid residues involved in substrate recognition and binding in RNase T1. These similar residues may be important for the catalytic activity of RNase T2.