Molecular, biochemical and immunological studies of hen pancreatic deoxyribonuclease I

Loss of Nckx3 Exacerbates Experimental DSS-Induced Colitis in Mice through p53/NF-κB Pathway

Inflammatory bowel diseases (IBDs) comprises a range of chronic inflammatory conditions of the intestinal tract. The incidence and prevalence of IBDs are increasing worldwide, but the precise etiology of these diseases is not completely understood. Calcium signaling plays a regulatory role in cellular proliferation. Nckx3, a potassium-dependent Na⁺/Ca²⁺ exchanger, is not only expressed in the brain but also in the aortic, uterine, and intestinal tissues, which contain abundant smooth muscle cells. This study investigated the role of Nckx3 in intestinal inflammation. Microarray analyses revealed the upregulation of the innate immune response-associated genes in the duodenum of Nckx3 knockout (KO) mice. The Nckx3 KO mice also showed an increase in IBD- and tumorigenesis-related genes. Using dextran sodium sulfate (DSS)-induced experimental colitis mice models, the Nckx3 KO mice showed severe colitis. Furthermore, the pathways involving p53 and NF-κB signaling were significantly upregulated by the absence of Nckx3. Overall, Nckx3 plays a critical role in the innate immune and immune response and may be central to the pathogenesis of IBD.

Purification and characterization of deoxyribonuclease from small intestine of camel Camelus dromedarius

The chromatography of deoxyribonuclease (DNase) from small intestine of camel Camelus dromedarius by DEAE-Sepharose separated three isoforms DNase 1, DNase 2 and DNase 3. The DNase 3 was purified to homogeneity by chromatography on Sephacryl S-200. The molecular weight of DNase 3 was 30 kDa using gel filtration and SDS-PAGE. The pH optimum of DNase 3 was reported at 7.0 using Tris-HCl buffer. The temperature optimum of DNase 3 was found to be 50 °C. The enzyme was stable up to 50 °C for one h incubation. The Km value was 28.5 µg DNA, where this low value indicated the high affinity of enzyme toward DNA as substrate. No activity of DNase 3 was determined in the absence of metal cations. Mg2+ and Ca2+ caused significant enhancement in the enzyme activity by 90 and 75%, respectively. The mixture of Mg2+ and Ca2+ caused 100% of enzyme activity. Ni2+, Co2+, Ba2+, Zn2+ and Cd2+ showed very strong inhibitory effect on enzyme activity. In conclusion, the characterization of DNase 3 indicated that the enzyme is considered as a member of DNase I family. The low Km value of the DNA suggested that the high digestion of DNA of camel forage by small intestine DNase 3.

Purification and characterization of a novel earthworm DNase

A new deoxyribonuclease (DNase), referred to as EWDNase, was isolated from earthworm tissues. The purification protocol included acetone precipitation, chromatography on CM-Sepharose, and gel electrophoresis. The overall purification was 73-fold with a recovery rate of 2.3% and a final specific activity of 2039 U/mg. Sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) analysis suggested a molecular mass of 30 kD for EWDNase, with an isoelectric point of approximately 7.0. Maximum activity was detected at a pH of 5.6 and a temperature of 40°C. Addition of Mg(2+) and Ca(2+) ions promoted enzyme activity strongly, while Zn(2+) and ethylenediamine tetraacetic acid (EDTA) acted as inhibitors. Liquid chromatography-tandem mass spectroscopy (LC-MS/MS) analysis indicated that there was no known matching sequence. The properties of EWDNase were sufficiently different from previously reported enzymes to suggest that it is a new enzyme requiring further confirmation and characterization.

Susceptibility of mammalian deoxyribonucleases I (DNases I) to proteolysis by proteases and its relationships to tissue distribution: Biochemical and molecular analysis of equine DNase I

Equine (Equus caballus) deoxyribonuclease I (DNase I) was purified from the parotid gland, and its 1295-bp cDNA was cloned. The mature equine DNase I protein consisted of 260 amino acid residues. The enzymatic properties and structural aspects of the equine enzyme were closely similar to those of other mammalian DNases I. Mammalian DNases I are classified into three types--pancreatic, parotid and pancreatic-parotid-based on their tissue distribution; as equine DNase I showed the highest activity in the parotid gland, it was confirmed to be of the parotid-type. Comparison of the susceptibility of mammalian DNases I to proteolysis by proteases demonstrated a marked correlation between tissue distribution and sensitivity/resistance to proteolysis; pancreatic-type DNase I shared properties of resistance to proteolysis by trypsin and chymotrypsin, whereas parotid-type DNase I did not. In contrast, pancreatic-parotid-type DNase I exhibited resistance to proteolysis by pepsin, whereas the other enzyme types did not. However, site-directed mutagenesis analysis revealed that only a single amino acid substitution could not account for acquisition of proteolysis resistance in the mammalian DNase I family during the course of molecular evolution. These properties are compatible with adaptation of mammalian DNases I for maintaining their activity in vivo.

Tissue distribution of neutral deoxyribonuclease (DNase) activity in the mussel Mytilus galloprovincialis

The presence of neutral DNase activity in bivalves is reported for the first time. The enzyme activity in four tissues of the mussel Mytilus galloprovincialis was analyzed by three different methods (i) specific denaturating SDS-PAGE zymogram, (ii) sensitive single radial enzyme diffusion (SRED) assay and (iii) rapid and sensitive fluorimetric determination of DNase activity with PicoGreen. The fluorimetric assay was rapid and sensitive enough for determination of hydrolytic activity of dsDNA in mussel hepatopancreas, adductor, gills and mantle. Maximal activity in all mussel tissue extracts was obtained in the presence of Ca(2+) and Mg(2+) at pH 7.0 with dsDNA as substrate. The neutral DNase activity in mussel tissue decreases in order hepatopancreas, mantle>gills>adductor. The enzyme activity displays interindividual variability in particular tissue as well as variability among tissues within one specimen. In the hepatopancreas one to three distinct proteins expressing neutral, Ca(2+), Mg(2+)-dependent, DNase activity were detected by denaturating SDS-PAGE zymogram. This heterogeneity of neutral nucleases involved in DNA hydrolysis in hepatopancreas could reflect interindividual variability in mussel food utilization and nutrient requirement.

Inhibition of deoxyribonuclease I by actin is to protect cells from premature cell death

Deoxyribonuclease I (Dnase1) is the major extracellular endonuclease. It is secreted by digestive glands into the alimentary tract and into the plasma, lacrimal fluid and urine by hepatocytes, lacrimal glands and renal proximal tubular cells, respectively. In many species the activity of Dnase1 is inhibited by monomeric actin. However, the biological significance of this high affinity interaction is unknown. We generated a Dnase1 mutant with extremely reduced actin binding capacity. EGFP-constructs of wild-type and mutant Dnase1 were transfected into MCF-7 breast cancer cells and apoptosis or necrosis was induced by staurosporine or oxidative stress. During apoptosis faster chromatin fragmentation occurred in cells transfected with mutant Dnase1. When wt (wild-type)- or mutated Dnase1 were added to cells after induction of necrosis, faster chromatin degradation occurred in the presence of mutant Dnase1. Inclusion of actin under these conditions inhibited chromatin degradation by wt- but not by mutated Dnase1. Thus, inhibition of Dnase1 by actin may serve as a self-protection mechanism against premature DNA degradation during cell damage.

Actin-inhibition and folding of vertebrate deoxyribonuclease I are affected by mutations at residues 67 and 114

Amino acid (aa) residues (Val-67 and Ala-114) have been suggested as being mainly responsible for actin-binding in human and bovine deoxyribonucleases I (DNase I). This study presents evidence of these two aa mutational mechanisms, not only for actin-binding but also for folding of DNase I in mammals, reptiles and amphibians. Human and viper snake (Agkistrodon blomhoffii) enzymes are inhibited by actin, whereas porcine, rat snake (Elaphe quadrivirgata), and African clawed frog (Xenopus laevis) enzymes are not. To investigate the role of aa at 67, mutants of rat snake (Ile67Val) and viper snake (Val67Ile) enzymes were constructed. After substitution, the rat snake was inhibited by actin, while the viper snake was not. For the role of aa at 114, mutants of viper snake (Phe114Ala), rat snake (Phe114Ala), African clawed frog (Phe114Ala), and porcine (Ser114Ala/Ser114Phe) enzymes were constructed. Strikingly, the substitute mutants for viper snake, rat snake and African clawed frog expressed no protein. The porcine (Ser114Ala) enzyme was inhibited by actin, but not the porcine (Ser114Phe) enzyme. These results suggest that Val-67 may be essential for actin-binding, that Phe-114 may be related to the folding of DNase I in reptiles and amphibians, and that Ala-114 may be indispensable for actin-binding in mammals.

Molecular evolution of shark and other vertebrate DNases I

We purified pancreatic deoxyribonuclease I (DNase I) from the shark Heterodontus japonicus using three-step column chromatography. Although its enzymatic properties resembled those of other vertebrate DNases I, shark DNase I was unique in being a basic protein. Full-length cDNAs encoding the DNases I of two shark species, H. japonicus and Triakis scyllia, were constructed from their total pancreatic RNAs using RACE. Nucleotide sequence analyses revealed two structural alterations unique to shark enzymes: substitution of two Cys residues at positions 101 and 104 (which are well conserved in all other vertebrate DNases I) and insertion of an additional Thr or Asn residue into an essential Ca(2+)-binding site. Site-directed mutagenesis of shark DNase I indicated that both of these alterations reduced the stability of the enzyme. When the signal sequence region of human DNase I (which has a high alpha-helical structure content) was replaced with its amphibian, fish and shark counterparts (which have low alpha-helical structure contents), the activity expressed by the chimeric mutant constructs in transfected mammalian cells was approximately half that of the wild-type enzyme. In contrast, substitution of the human signal sequence region into the amphibian, fish and shark enzymes produced higher activity compared with the wild-types. The vertebrate DNase I family may have acquired high stability and effective expression of the enzyme protein through structural alterations in both the mature protein and its signal sequence regions during molecular evolution.

A single amino acid substitution can shift the optimum pH of DNase I for enzyme activity: biochemical and molecular analysis of the piscine DNase I family

We purified four piscine deoxyribonucleases I (DNases I) from Anguilla japonica, Pagrus major, Cryprus carpio and Oreochromis mossambica. The purified enzymes had an optimum pH for activity of approximately 8.0, significantly higher than those of mammalian enzymes. cDNAs encoding the first three of these piscine DNases I were cloned, and the sequence of the Takifugu rubripes enzyme was obtained from a database search. Nucleotide sequence analyses revealed relatively greater structural variations among the piscine DNase I family than among the other vertebrate DNase I families. From comparison of their catalytic properties, the vertebrate DNases I could be classified into two groups: a low-pH group, such as the mammalian enzymes, with a pH optimum of 6.5-7.0, and a high-pH group, such as the reptile, amphibian and piscine enzymes, with a pH optimum of approximately 8.0. The His residue at position 44 of the former group is replaced by Asp in the latter. Replacement of Asp44 of piscine and amphibian DNases I by His decreased their optimum pH to a value similar to that of the low-pH group. Therefore, Asp44His might be involved in an evolutionarily critical change in the optimum pH for the activity of vertebrate DNases I.

Chicken deoxyribonuclease: purification, characterization, gene cloning and gene expression

Chicken DNase was purified to apparent homogeneity from the pancreas extract. It showed two isoforms, A and B forms, on cation-exchange chromatography. On SDS-PAGE it was a 30-kDa protein. When analyzed on an electrospray-mass analyzer, form A showed a major mass peak of 30859, and form B, 30882. The enzyme was bound to concanavalin A, indicating its glycoprotein nature. The carbohydrate side chain could be removed by endoglycosidase F. Chicken DNase was activated by metal ions and for half-maximum activation, Mn2+ and Mg2+ required were 1 mM and 4 mM, respectively. The pH optimum was between 7 and 8 depending on the metal ions used. In the presence of Cu2+, it was almost completely inactivated by 0.1 M iodoacetate within 1 min. In the absence of Ca2+ at pH 8, chicken DNase resisted to the trypsin or beta-mercaptoethenol inactivation. When the purified enzyme was subjected to protein sequencing, approximately 93% of the sequence was established. Based on the amino acid sequence, the cDNA of chicken DNase was amplified, cloned and sequenced. The cDNA sequence consisted of 1079 nucleotides in which 67 were of the 5'-untranslated region and 166 of the 3' and, in the 5'-untranslated region, two types of sequences occurred. The polypeptide chain of 282 amino acids, translated from the open reading frame, was composed of the mature protein of 262 amino acids and a putative signal peptide of 20 amino acids. As compared with mammalian DNases, chicken DNase had an overall 58 +/- 61% sequence identity, one less potential N-glycosylation site, and one extra disulfide. The cDNA was cloned into the pET15b expression vector. When induced, active recombinant chicken DNase was expressed in Escherichia coli strain BL21(DE3)pLysS and was present in the insoluble fraction of cell lysates.

A single amino acid substitution of Leu130Ile in snake DNases I contributes to the acquisition of thermal stability

We purified pancreatic deoxyribonucleases I (DNases I) from three snakes, Elaphe quadrivirgata, Elaphe climacophora and Agkistrodon blomhoffii, and cloned their cDNAs. Each mature snake DNase I protein comprised 262 amino acids. Wild-type snake DNases I with Leu130 were more thermally unstable than wild-type mammalian and avian DNases I with Ile130. After substitution of Leu130Ile, the thermal stabilities of the snake enzymes were higher than those of their wild-type counterparts and similar to mammalian wild-type enzyme levels. Conversely, substituting Ile130Leu of mammalian DNases I made them more thermally unstable than their wild-type counterparts. Therefore, a single amino acid substitution, Leu130Ile, might be involved in an evolutionally critical change in the thermal stabilities of vertebrate DNases I. Amphibian DNases I have a Ser205 insertion in a Ca2+-binding site of mammalian and avian enzymes that reduces their thermal stabilities [Takeshita, H., Yasuda, T., Iida, R., Nakajima, T., Mori, S., Mogi, K., Kaneko, Y. & Kishi, K. (2001) Biochem. J.357, 473-480]. Thus, it is plausible that the thermally stable wild-type DNases I of the higher vertebrates, such as mammals and birds, have been generated by a single Leu130Ile substitution of reptilian enzymes through molecular evolution following Ser205 deletion from amphibian enzymes. This mechanism may reflect one of the evolutionary changes from cold-blooded to warm-blooded vertebrates.

Amphibian DNases I are characterized by a C-terminal end with a unique, cysteine-rich stretch and by the insertion of a serine residue into the Ca2+-binding site

We purified four amphibian deoxyribonucleases I from the pancreases of one toad, two frog and one newt species, by using three different column chromatography methods in sequence. Each of the purified enzymes had a molecular mass of approx. 40 kDa and an optimal pH for activity of approx. 8.0. These values were significantly greater than those for other vertebrate DNases I. The full-length cDNA encoding each amphibian DNase I was constructed from the total RNA of the pancreas by using rapid amplification of cDNA ends. Nucleotide sequence analyses revealed two structural characteristics unique to amphibian DNases I: a stretch of approx. 70 amino acids with a high cysteine content (approx. 15%) in the C-terminal region, and the insertion of a serine residue at position 205 (in a domain containing an essential Ca2+-binding site). Expression analysis of a series of mutant constructs indicated that both of these structures are essential in generating the active form of the enzyme. 'DNase I signature sequences', which are well conserved in other vertebrate DNases I, could not be found in any of the amphibian DNases I tested, whereas a 'somatomedin B motif' was identified in the Cys-rich stretches of all four. Although DNase I has so far been considered to be a secretory glycoprotein, amphibian DNase I seems to be non-glycosylated. These structural findings indicate strongly that amphibian DNases I are situated in a unique position on the phylogenetic tree of the DNase I family.

Molecular, biochemical and immunological analyses of porcine pancreatic DNase I

Deoxyribonuclease I (DNase I) was purified 26500-fold in 39% yield from porcine pancreas to electrophoretic homogeneity using three-step column chromatography. The purified enzyme was inhibited by an antibody specific to the purified enzyme but not by G-actin. A 1303 bp cDNA encoding porcine DNase I was constructed from total RNA from porcine small intestine using a rapid amplification of cDNA ends method, followed by sequencing. Mature porcine DNase I protein was found to consist of 262 amino acids. Unlike all other mammalian DNase I enzymes that are inhibited by G-actin, porcine DNase I has H65 and S114 instead of Y65 and A114, which presumably results in the lack of inhibition. Porcine DNase I was more sensitive to low pH than rat or bovine enzymes. Compared with their primary structures, the amino acid at position 110 was N in porcine enzyme, but S in rat and bovine enzymes. A porcine mutant enzyme in which N was substituted by S alone at position 110 (N110S) became resistant to low pH to a similar extent as the rat and bovine enzymes.

Molecular cloning of cDNA encoding Xenopus laevis deoxyribonuclease I

A 1200-bp cDNA encoding Xenopus laevis deoxyribonuclease I (X. laevis DNase I) was constructed from the total RNA of a X. laevis pancreas using a rapid amplification of cDNA ends method. When the cDNA was transiently transfected into COS-7 cells, the recombinant polypeptide exhibited similar enzymological properties to those of the native pancreatic DNase I. The recombinant enzyme was considerably more labile than most other vertebrate DNase I enzymes. The X. laevis DNase I polypeptide was larger than any other known vertebrate DNase I, containing a unique Cys-rich stretch of 68 or 70 amino acid residues at the carboxyl terminus, and it had less well conserved binding sites for the Ca2+, G-actin and DNA, and two DNase I signature motifs. These alterations might account for its heat instability.

DNase I: structure, function, and use in medicine and forensic science

In this review, available structural data of deoxyribonucleases I (DNases I) from several mammalian species, hen, snake and frog are summarized. Comparative studies on enzymatic and immunological properties and glycosylation are discussed, and several evolutionary conclusions are presented. Over the past decade, the availability of new investigative tools, including sensitive methods of electrophoresis, detection and determination, and genetically modified DNase I models has resulted in a clearer understanding of the molecular mechanisms that connect the function and usefulness of DNase I in medicine and forensic science.

Tissue-specific in vivo inhibition of DNase I gene expression by somatostatin

Administration of somatostatin to rats induced a transient reduction of serum levels of deoxyribonuclease I (DNase I) activity in a dose-dependent manner, followed by a substantial decrease of DNase I activity in the lower gut. Activity in the parotid gland, liver, and kidney did not change. Real-time PCR analysis of the DNase I gene transcript in ileum indicated that the decrease was due to down-regulation of gene expression. Based on these responses, rat tissues expressing DNase I could be classified into two types, somatostatin-sensitive and somatostatin-resistant, and the level of DNase I activity in the lower gut seems to be controlled by somatostatin.

Mammalian deoxyribonucleases I are classified into three types: pancreas, parotid, and pancreas-parotid (mixed), based on differences in their tissue concentrations

Deoxyribonuclease I (DNase I) activities were measured in 14 different tissues from humans and 5 other mammals (bovine, pig, rabbit, rat, and mouse) by using the single radial enzyme diffusion (SRED) method, which is a sensitive and nonradioactive assay for nucleases. The results indicated that these species are classifiable into three groups on the basis of their different tissue distributions of DNase I. In human and pig, the pancreas showed the highest activity of DNase I; in rat and mouse, the parotid glands showed the highest activity; and in bovine and rabbit, both pancreas and parotid glands showed high activity. Therefore we designated human and pig DNase I as pancreas type, rat and mouse DNase I as parotid type, and bovine and rabbit DNase I as pancreas-parotid (or mixed) type. DNase I of the pancreas type was more sensitive to low pH than the other types. DNase I of pancreas type is secreted into the intestinal tract under neutral pH conditions, whereas the other types are secreted from the parotid gland and have to pass through the very acidic conditions in the stomach. Differences in the tissue distribution and acid sensitivity of mammalian DNases I may provide important information about their digestive function from the evolutionary perspective.