Skip to main content
Biochemical Journal logoLink to Biochemical Journal
. 2003 May 1;371(Pt 3):867–876. doi: 10.1042/BJ20021875

Structural requirements of human DNase II alpha for formation of the active enzyme: the role of the signal peptide, N-glycosylation, and disulphide bridging.

Kyle S MacLea 1, Ronald J Krieser 1, Alan Eastman 1
PMCID: PMC1223339  PMID: 12558498

Abstract

DNase II alpha (EC 3.1.22.1) is an endonuclease, which is active at low pH, that cleaves double-stranded DNA to short 3'-phosphoryl oligonucleotides. Although its biochemistry is well understood, its structure-activity relationship has been largely unexamined. Recently, we demonstrated that active DNase II alpha consists of one contiguous polypeptide, heavily glycosylated, and containing at least one intrachain disulphide linkage [MacLea, Krieser and Eastman (2002) Biochem. Biophys. Res. Commun. 292, 415-421]. The present paper describes further work to examine the elements of DNase II alpha protein required for activity. Truncated forms and site-specific mutants were expressed in DNase II alpha-null mouse cells. Results indicate that the signal-peptide leader sequence is required for correct glycosylation and that N-glycosylation is important for formation of the active enzyme. Despite this, enzymic deglycosylation of wild-type protein with peptide N-glycosidase F reveals that glycosylation is not intrinsically required for DNase activity. DNase II alpha contains six evolutionarily conserved cysteine residues, and mutations in any one of these cysteines completely ablated enzymic activity, consistent with the importance of disulphide bridging in maintaining correct protein structure. We also demonstrate that a mutant form of DNase II alpha that lacks the purported active-site His(295) can still bind DNA, indicating that this histidine residue is not simply involved in DNA binding, but may have a direct role in catalysis. These results provide a more complete model of the DNase II alpha protein structure, which is important for three-dimensional structural analysis and for production of DNase II alpha as a potential protein therapeutic for cystic fibrosis or other disorders.

Full Text

The Full Text of this article is available as a PDF (313.9 KB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. BERNARDI G., GRIFFE M. STUDIES ON ACID DEOXYRIBONUCLEASE. II. ISOLATION AND CHARACTERIZATION OF SPLEEN-ACID DEOXYRIBONUCLEASE. Biochemistry. 1964 Oct;3:1419–1426. doi: 10.1021/bi00898a005. [DOI] [PubMed] [Google Scholar]
  2. Barry M. A., Eastman A. Identification of deoxyribonuclease II as an endonuclease involved in apoptosis. Arch Biochem Biophys. 1993 Jan;300(1):440–450. doi: 10.1006/abbi.1993.1060. [DOI] [PubMed] [Google Scholar]
  3. Bause E. Structural requirements of N-glycosylation of proteins. Studies with proline peptides as conformational probes. Biochem J. 1983 Feb 1;209(2):331–336. doi: 10.1042/bj2090331. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Chou San Fang, Chen Hui Ling, Lu Shao Chun. Up-regulation of human deoxyribonuclease II gene expression during myelomonocytic differentiation of HL-60 and THP-1 cells. Biochem Biophys Res Commun. 2002 Aug 9;296(1):48–53. doi: 10.1016/s0006-291x(02)00835-5. [DOI] [PubMed] [Google Scholar]
  5. Friedhoff P., Kolmes B., Gimadutdinow O., Wende W., Krause K. L., Pingoud A. Analysis of the mechanism of the Serratia nuclease using site-directed mutagenesis. Nucleic Acids Res. 1996 Jul 15;24(14):2632–2639. doi: 10.1093/nar/24.14.2632. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Ito K., Akiyama D., Minamiura N. Evidence for an essential histidine residue on active site of human urinary DNase I: carboxymethylation and carbethoxylation. Arch Biochem Biophys. 1994 Aug 15;313(1):126–130. doi: 10.1006/abbi.1994.1368. [DOI] [PubMed] [Google Scholar]
  7. Kawane K., Fukuyama H., Kondoh G., Takeda J., Ohsawa Y., Uchiyama Y., Nagata S. Requirement of DNase II for definitive erythropoiesis in the mouse fetal liver. Science. 2001 May 25;292(5521):1546–1549. doi: 10.1126/science.292.5521.1546. [DOI] [PubMed] [Google Scholar]
  8. Krieser R. J., Eastman A. Deoxyribonuclease II: structure and chromosomal localization of the murine gene, and comparison with the genomic structure of the human and three C. elegans homologs. Gene. 2000 Jul 11;252(1-2):155–162. doi: 10.1016/s0378-1119(00)00209-2. [DOI] [PubMed] [Google Scholar]
  9. Krieser R. J., Eastman A. The cloning and expression of human deoxyribonuclease II. A possible role in apoptosis. J Biol Chem. 1998 Nov 20;273(47):30909–30914. doi: 10.1074/jbc.273.47.30909. [DOI] [PubMed] [Google Scholar]
  10. Krieser R. J., MacLea K. S., Longnecker D. S., Fields J. L., Fiering S., Eastman A. Deoxyribonuclease IIalpha is required during the phagocytic phase of apoptosis and its loss causes perinatal lethality. Cell Death Differ. 2002 Sep;9(9):956–962. doi: 10.1038/sj.cdd.4401056. [DOI] [PubMed] [Google Scholar]
  11. Krieser R. J., MacLea K. S., Park J. P., Eastman A. The cloning, genomic structure, localization, and expression of human deoxyribonuclease IIbeta. Gene. 2001 May 16;269(1-2):205–216. doi: 10.1016/s0378-1119(01)00434-6. [DOI] [PubMed] [Google Scholar]
  12. Lesca P. Protein inhibitor of acid deoxyribonucleases. Improved purification procedure and properties. J Biol Chem. 1976 Jan 10;251(1):116–123. [PubMed] [Google Scholar]
  13. Liao T. H., Liao W. C., Chang H. C., Lu K. S. Deoxyribonuclease II purified from the isolated lysosomes of porcine spleen and from porcine liver homogenates. Comparison with deoxyribonuclease II purified from porcine spleen homogenates. Biochim Biophys Acta. 1989 Jan 23;1007(1):15–22. doi: 10.1016/0167-4781(89)90124-3. [DOI] [PubMed] [Google Scholar]
  14. Liao T. H. The subunit structure and active site sequence of porcine spleen deoxyribonuclease. J Biol Chem. 1985 Sep 5;260(19):10708–10713. [PubMed] [Google Scholar]
  15. Lyon C. J., Evans C. J., Bill B. R., Otsuka A. J., Aguilera R. J. The C. elegans apoptotic nuclease NUC-1 is related in sequence and activity to mammalian DNase II. Gene. 2000 Jul 11;252(1-2):147–154. doi: 10.1016/s0378-1119(00)00213-4. [DOI] [PubMed] [Google Scholar]
  16. MacLea Kyle S., Krieser Ronald J., Eastman Alan. Revised structure of the active form of human deoxyribonuclease IIalpha. Biochem Biophys Res Commun. 2002 Mar 29;292(2):415–421. doi: 10.1006/bbrc.2002.6687. [DOI] [PubMed] [Google Scholar]
  17. Malferrari G., Mazza U., Tresoldi C., Rovida E., Nissim M., Mirabella M., Servidei S., Biunno I. Molecular characterization of a novel endonuclease (Xib) and possible involvement in lysosomal glycogen storage disorders. Exp Mol Pathol. 1999 Jun;66(2):123–130. doi: 10.1006/exmp.1999.2254. [DOI] [PubMed] [Google Scholar]
  18. Marshall R. D. Glycoproteins. Annu Rev Biochem. 1972;41:673–702. doi: 10.1146/annurev.bi.41.070172.003325. [DOI] [PubMed] [Google Scholar]
  19. Meiss G., Scholz S. R., Korn C., Gimadutdinow O., Pingoud A. Identification of functionally relevant histidine residues in the apoptotic nuclease CAD. Nucleic Acids Res. 2001 Oct 1;29(19):3901–3909. doi: 10.1093/nar/29.19.3901. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Miletich J. P., Broze G. J., Jr Beta protein C is not glycosylated at asparagine 329. The rate of translation may influence the frequency of usage at asparagine-X-cysteine sites. J Biol Chem. 1990 Jul 5;265(19):11397–11404. [PubMed] [Google Scholar]
  21. Nielsen H., Engelbrecht J., Brunak S., von Heijne G. Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Protein Eng. 1997 Jan;10(1):1–6. doi: 10.1093/protein/10.1.1. [DOI] [PubMed] [Google Scholar]
  22. Oosthuizen M. M., Myburgh J. A., Schabort J. C. Lysosomal acid deoxyribonuclease from vervet monkey livers--I. Purification and physico-chemical characterization. Int J Biochem. 1984;16(12):1207–1215. doi: 10.1016/0020-711x(84)90218-0. [DOI] [PubMed] [Google Scholar]
  23. Sakahira H., Takemura Y., Nagata S. Enzymatic active site of caspase-activated DNase (CAD) and its inhibition by inhibitor of CAD. Arch Biochem Biophys. 2001 Apr 1;388(1):91–99. doi: 10.1006/abbi.2000.2266. [DOI] [PubMed] [Google Scholar]
  24. Shak S., Capon D. J., Hellmiss R., Marsters S. A., Baker C. L. Recombinant human DNase I reduces the viscosity of cystic fibrosis sputum. Proc Natl Acad Sci U S A. 1990 Dec;87(23):9188–9192. doi: 10.1073/pnas.87.23.9188. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Shiokawa D., Ohyama H., Yamada T., Takahashi K., Tanuma S. Identification of an endonuclease responsible for apoptosis in rat thymocytes. Eur J Biochem. 1994 Nov 15;226(1):23–30. doi: 10.1111/j.1432-1033.1994.tb20022.x. [DOI] [PubMed] [Google Scholar]
  26. Shiokawa D., Tanuma S. Cloning of cDNAs encoding porcine and human DNase II. Biochem Biophys Res Commun. 1998 Jun 29;247(3):864–869. doi: 10.1006/bbrc.1998.8839. [DOI] [PubMed] [Google Scholar]
  27. Shiokawa D., Tanuma S. DLAD, a novel mammalian divalent cation-independent endonuclease with homology to DNase II. Nucleic Acids Res. 1999 Oct 15;27(20):4083–4089. doi: 10.1093/nar/27.20.4083. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Takeshita H., Yasuda T., Iida R., Nakajima T., Hosomi O., Nakashima Y., Mori S., Nomoto H., Kishi K. Identification of the three non-identical subunits constituting human deoxyribonuclease II. FEBS Lett. 1998 Nov 27;440(1-2):239–242. doi: 10.1016/s0014-5793(98)01456-2. [DOI] [PubMed] [Google Scholar]
  29. Tanuma S., Shiokawa D. Multiple forms of nuclear deoxyribonuclease in rat thymocytes. Biochem Biophys Res Commun. 1994 Sep 15;203(2):789–797. doi: 10.1006/bbrc.1994.2252. [DOI] [PubMed] [Google Scholar]
  30. Torriglia A., Chaudun E., Chany-Fournier F., Jeanny J. C., Courtois Y., Counis M. F. Involvement of DNase II in nuclear degeneration during lens cell differentiation. J Biol Chem. 1995 Dec 1;270(48):28579–28585. doi: 10.1074/jbc.270.48.28579. [DOI] [PubMed] [Google Scholar]
  31. Torriglia A., Perani P., Brossas J. Y., Chaudun E., Treton J., Courtois Y., Counis M. F. L-DNase II, a molecule that links proteases and endonucleases in apoptosis, derives from the ubiquitous serpin leukocyte elastase inhibitor. Mol Cell Biol. 1998 Jun;18(6):3612–3619. doi: 10.1128/mcb.18.6.3612. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Wang C. C., Lu S. C., Chen H. L., Liao T. H. Porcine spleen deoxyribonuclease II. Covalent structure, cDNA sequence, molecular cloning, and gene expression. J Biol Chem. 1998 Jul 3;273(27):17192–17198. doi: 10.1074/jbc.273.27.17192. [DOI] [PubMed] [Google Scholar]
  33. Wu Y. C., Stanfield G. M., Horvitz H. R. NUC-1, a caenorhabditis elegans DNase II homolog, functions in an intermediate step of DNA degradation during apoptosis. Genes Dev. 2000 Mar 1;14(5):536–548. [PMC free article] [PubMed] [Google Scholar]
  34. Yasuda T., Nadano D., Awazu S., Kishi K. Human urine deoxyribonuclease II (DNase II) isoenzymes: a novel immunoaffinity purification, biochemical multiplicity, genetic heterogeneity and broad distribution among tissues and body fluids. Biochim Biophys Acta. 1992 Feb 26;1119(2):185–193. doi: 10.1016/0167-4838(92)90390-y. [DOI] [PubMed] [Google Scholar]
  35. Yasuda T., Nadano D., Sawazaki K., Kishi K. Genetic polymorphism of human deoxyribonuclease II (DNase II): low activity levels in urine and leukocytes are due to an autosomal recessive allele. Ann Hum Genet. 1992 Jan;56(Pt 1):1–10. doi: 10.1111/j.1469-1809.1992.tb01125.x. [DOI] [PubMed] [Google Scholar]
  36. Yasuda T., Sawazaki K., Nadano D., Takeshita H., Nakanaga M., Kishi K. Human seminal deoxyribonuclease I (DNase I): purification, enzymological and immunological characterization and origin. Clin Chim Acta. 1993 Sep 17;218(1):5–16. doi: 10.1016/0009-8981(93)90217-r. [DOI] [PubMed] [Google Scholar]
  37. Yasuda T., Takeshita H., Iida R., Nakajima T., Hosomi O., Nakashima Y., Mori S., Kishi K. Structural requirements of a human deoxyribonuclease II for the development of the active enzyme form, revealed by site-directed mutagenesis. Biochem Biophys Res Commun. 1999 Mar 24;256(3):591–594. doi: 10.1006/bbrc.1999.0390. [DOI] [PubMed] [Google Scholar]
  38. Yasuda T., Takeshita H., Nakazato E., Nakajima T., Hosomi O., Nakashima Y., Kishi K. Activity measurement for deoxyribonucleases I and II with picogram sensitivity based on DNA/SYBR Green I fluorescence. Anal Biochem. 1998 Jan 15;255(2):274–276. doi: 10.1006/abio.1997.2496. [DOI] [PubMed] [Google Scholar]
  39. von Heijne G. The signal peptide. J Membr Biol. 1990 May;115(3):195–201. doi: 10.1007/BF01868635. [DOI] [PubMed] [Google Scholar]

Articles from Biochemical Journal are provided here courtesy of The Biochemical Society

RESOURCES