1
|
Kulbay M, Bernier-Parker N, Bernier J. The role of the DFF40/CAD endonuclease in genomic stability. Apoptosis 2021; 26:9-23. [PMID: 33387146 DOI: 10.1007/s10495-020-01649-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/23/2020] [Indexed: 12/18/2022]
Abstract
Maintenance of genomic stability in cells is primordial for cellular integrity and protection against tumor progression. Many factors such as ultraviolet light, oxidative stress, exposure to chemical reagents, particularly mutagens and radiation, can alter the integrity of the genome. Thus, human cells are equipped with many mechanisms that prevent these irreversible lesions in the genome, as DNA repair pathways, cell cycle checkpoints, and telomeric function. These mechanisms activate cellular apoptosis to maintain DNA stability. Emerging studies have proposed a new protein in the maintenance of genomic stability: the DNA fragmentation factor (DFF). The DFF40 is an endonuclease responsible of the oligonucleosomal fragmentation of the DNA during apoptosis. The lack of DFF in renal carcinoma cells induces apoptosis without oligonucleosomal fragmentation, which poses a threat to genetic information transfer between cancerous and healthy cells. In this review, we expose the link between the DFF and genomic instability as the source of disease development.
Collapse
Affiliation(s)
- Merve Kulbay
- INRS - Centre Armand-Frappier-Santé-Biotechnologie, 531 Boul. des Prairies, Laval, QC, H7V 1B7, Canada.,Department of Medicine, Université de Montréal, 2900 Blvd. Edouard Montpetit, Montreal, QC, Canada
| | - Nathan Bernier-Parker
- Toronto Animal Health Partners Emergency and Specialty Hospital, 1 Scarsdale Road, North York, ON, M3B 2R2, Canada
| | - Jacques Bernier
- INRS - Centre Armand-Frappier-Santé-Biotechnologie, 531 Boul. des Prairies, Laval, QC, H7V 1B7, Canada.
| |
Collapse
|
2
|
Singh D, Rahi A, Kumari R, Gupta V, Gautam G, Aggarwal S, Rehan M, Bhatnagar R. Computational and mutational analysis of TatD DNase of Bacillus anthracis. J Cell Biochem 2019; 120:11318-11330. [PMID: 30719750 DOI: 10.1002/jcb.28408] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 12/12/2018] [Accepted: 12/14/2018] [Indexed: 01/24/2023]
Abstract
The role of TatD DNases as DNA repair enzymes or cell death (apoptotic) nucleases is well established in prokaryotes as well as eukaryotes. The current study aims to characterize the TatD nuclease from Bacillus anthracis (Ba TatD) and to explore its key histidine catalytic residues. Ba TatD was found to be a metal-dependent, nonspecific endonuclease which could efficiently cleave double-stranded DNA substrates. Moreover, Ba TatD nuclease was observed to be thermostable up to 55°C and act in a wide pH range indicating its industrial applicability. Diethyl pyrocarbonate-based histidine-selective alkylation of the Ba TatD resulted in a loss of its nuclease activity suggesting a crucial role of the histidine residues in its activity. The key residues of Ba TatD were predicted using sequence analysis and structure-based approaches, and then the predicted residues were further tested by mutational analysis. Upon mutational analysis, H128 and H153 have been found to be crucial for Ba TatD activity, though H153 seems to bear an important but a dispensable role for the Ba TatD nuclease. Ba TatD had a uniform expression in the cytosol of B. anthracis, which indicates a significant role of the protein in the pathogen's life cycle. This is the first study to identify and characterize the TatD DNase from B. anthracis and will be helpful in gaining more insights on the role of TatD proteins in Gram-positive bacteria where it remains unexplored.
Collapse
Affiliation(s)
- Damini Singh
- Laboratory of Molecular Biology and Genetic Engineering, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Amit Rahi
- Laboratory of Molecular Biology and Genetic Engineering, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Romika Kumari
- Finland Institute for Molecular Medicine (FIMM), Helsinki, Finland
| | - Vatika Gupta
- Laboratory of Molecular Biology and Genetic Engineering, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Gunjan Gautam
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Somya Aggarwal
- Laboratory of Molecular Biology and Genetic Engineering, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Mohd Rehan
- King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Rakesh Bhatnagar
- Laboratory of Molecular Biology and Genetic Engineering, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| |
Collapse
|
3
|
Sivagnanam U, Narayana Murthy S, Gummadi SN. Identification and characterization of the novel nuclease activity of human phospholipid scramblase 1. BMC BIOCHEMISTRY 2016; 17:10. [PMID: 27206388 PMCID: PMC4875679 DOI: 10.1186/s12858-016-0067-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 05/17/2016] [Indexed: 01/05/2023]
Abstract
Background Human phospholipid scramblase 1 (hPLSCR1) was initially identified as a Ca2+ dependent phospholipid translocator involved in disrupting membrane asymmetry. Recent reports revealed that hPLSCR1 acts as a multifunctional signaling molecule rather than functioning as scramblase. hPLSCR1 is overexpressed in a variety of tumor cells and is known to interact with a number of protein molecules implying diverse functions. Results In this study, the nuclease activity of recombinant hPLSCR1 and its biochemical properties have been determined. Point mutations were generated to identify the critical region responsible for the nuclease activity. Recombinant hPLSCR1 exhibits Mg2+ dependent nuclease activity with an optimum pH and temperature of 8.5 and 37 °C respectively. Experiments with amino acid modifying reagents revealed that histidine, cysteine and arginine residues were crucial for its function. hPLSCR1 has five histidine residues and point mutations of histidine residues to alanine in hPLSCR1 resulted in 60 % loss in nuclease activity. Thus histidine residues could play a critical role in the nuclease activity of hPLSCR1. Conclusions This is the first report on the novel nuclease activity of the multi-functional hPLSCR1. hPLSCR1 shows a metal dependent nuclease activity which could play a role in key cellular processes that needs to be further investigated.
Collapse
Affiliation(s)
- Ulaganathan Sivagnanam
- From the Applied and Industrial Microbiology Laboratory, Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, 600 036, India
| | - Shweta Narayana Murthy
- From the Applied and Industrial Microbiology Laboratory, Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, 600 036, India
| | - Sathyanarayana N Gummadi
- From the Applied and Industrial Microbiology Laboratory, Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, 600 036, India.
| |
Collapse
|
4
|
Kutscher D, Pingoud A, Jeltsch A, Meiss G. Identification of ICAD-derived peptides capable of inhibiting caspase-activated DNase. FEBS J 2012; 279:2917-28. [DOI: 10.1111/j.1742-4658.2012.08673.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
5
|
Takeshita H, Fujihara J, Ueki M, Iida R, Koda Y, Soejima M, Yuasa I, Kato H, Nakajima T, Kominato Y, Yasuda T. Nonsynonymous Single-Nucleotide Polymorphisms of the Human Apoptosis-Related Endonuclease - DNA Fragmentation Factor Beta Polypeptide, Endonuclease G, and Flap Endonuclease-1 - Genes Show a Low Degree of Genetic Heterogeneity. DNA Cell Biol 2012; 31:36-42. [DOI: 10.1089/dna.2011.1293] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Affiliation(s)
- Haruo Takeshita
- Department of Legal Medicine, Shimane University School of Medicine, Shimane, Japan
| | - Junko Fujihara
- Department of Legal Medicine, Shimane University School of Medicine, Shimane, Japan
| | - Misuzu Ueki
- Division of Medical Genetics and Biochemistry, University of Fukui, Fukui, Japan
| | - Reiko Iida
- Division of Life Sciences, Faculty of Medical Sciences, University of Fukui, Fukui, Japan
| | - Yoshiro Koda
- Department of Forensic Medicine and Human Genetics, Kurume University School of Medicine, Fukuoka, Japan
| | - Mikiko Soejima
- Department of Forensic Medicine and Human Genetics, Kurume University School of Medicine, Fukuoka, Japan
| | - Isao Yuasa
- Department of Legal Medicine, Tottori University Graduate School of Medicine, Tottori, Japan
| | - Hideaki Kato
- Department of Forensic Medical Science, Graduate School of Medical Sciences, Nagoya City University, Nagoya, Japan
| | - Tamiko Nakajima
- Department of Legal Medicine, Gunma University Graduate School of Medicine, Gunma, Japan
| | - Yoshihiko Kominato
- Department of Legal Medicine, Gunma University Graduate School of Medicine, Gunma, Japan
| | - Toshihiro Yasuda
- Division of Medical Genetics and Biochemistry, University of Fukui, Fukui, Japan
| |
Collapse
|
6
|
Chopra M, Dharmarajan AM, Meiss G, Schrenk D. Inhibition of UV-C light-induced apoptosis in liver cells by 2,3,7,8-tetrachlorodibenzo-p-dioxin. Toxicol Sci 2009; 111:49-63. [PMID: 19520675 DOI: 10.1093/toxsci/kfp128] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) is a highly toxic pollutant ubiquitously present in the environment. Most of the toxic effects of TCDD are believed to be mediated by high-affinity binding to the aryl hydrocarbon receptor (AhR) and subsequent effects on gene transcription. TCDD causes cancer in multiple tissues in different animal species and is classified as a class 1 human carcinogen. In initiation-promotion studies TCDD was shown to be a potent liver tumor promotor. Among other theories it has been hypothesized that TCDD acts as a tumor promotor by preventing initiated cells from undergoing apoptosis. We examined the effects of TCDD on ultraviolet C (UV-C) light-induced apoptosis in primary rat hepatocytes and Huh-7 human hepatoma cells. TCDD inhibits UV-C light-induced apoptosis in both cell types. This effect is seen with chromatin condensation and fragmentation and appears to be mediated by the AhR in rat hepatocytes. Apoptosis induced by UV-C light in these cells is caspase-dependent and is accompanied by alterations in apoptosis-related gene expression such as up-regulation of proapoptotic bcl-2 family genes like bak and bax, and a marked down regulation of the expression of the antiapoptotic bcl-2. TCDD treatment of irradiated hepatocytes induces the expression of some apoptosis-related genes (birc3, dad1, pycard, tnf). Upstream apoptotic events, namely caspase activation and caspase substrate cleavage are not inhibited by TCDD treatment. We hypothesize that TCDD inhibits late-stage apoptotic events that lead to internucleosomal DNA fragmentation, maintaining chromosomal integrity probably in order to sustain metabolic capacity and hepatic elimination of substrates despite of an initiation of apoptosis.
Collapse
Affiliation(s)
- Martin Chopra
- Institute of Food Chemistry and Toxicology, University of Kaiserslautern, 67663 Kaiserslautern, Germany
| | | | | | | |
Collapse
|
7
|
Cheng YC, Hsueh CC, Lu SC, Liao TH. Identification of three crucial histidine residues (His115, His132 and His297) in porcine deoxyribonuclease II. Biochem J 2006; 398:177-85. [PMID: 16734590 PMCID: PMC1550313 DOI: 10.1042/bj20060564] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
DNase II is an acid endonuclease that is involved in the degradation of exogenous DNA and is important for DNA fragmentation and degradation during cell death. In an effort to understand its catalytic mechanism, we constructed plasmids encoding nine different histidine (H)-to-leucine (L) mutants for porcine DNase II and examined the enzyme properties of the expressed mutant proteins. Of the mutants, all but H132L were secreted into the medium of expressing cells. Six of the mutated DNase II proteins (H41L, H109L, H206L, H207L, H274L and H322L) showed enzyme activity, whereas the H115L, H132L and H297L mutants exhibited very little activity. The H115L and H297L mutants were found to undergo correct protein folding, but were inactive. To further examine these mutants, we expressed H115A and H297A DNase II mutants; these mutants were inactive, but their DNase activities could be rescued with imidazole, indicating that His115 and His297 are likely to function as a general acid and a general base respectively in the catalytic centre of the enzyme. In contrast with the secreted mutants, the H132L mutant protein was found in cell lysates within 16 h after transfection. This protein was inactive, improperly folded and was drastically degraded via the proteosomal pathway after 24 h. The polypeptide of another substitution for His132 with lysine resulted in the misfolded form being retained in endoplasmic reticulum.
Collapse
Affiliation(s)
- Yu-Che Cheng
- *Department of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Chin-Chen Hsueh
- *Department of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Shao-Chun Lu
- *Department of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Ta-Hsiu Liao
- *Department of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei, Taiwan
- †Institute of Biotechnology, College of Bioresources, National Ilan University, Ilan, Taiwan
- To whom correspondence should be addressed (email )
| |
Collapse
|
8
|
Reh S, Korn C, Gimadutdinow O, Meiss G. Structural basis for stable DNA complex formation by the caspase-activated DNase. J Biol Chem 2005; 280:41707-15. [PMID: 16236713 DOI: 10.1074/jbc.m509133200] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We describe a structural model for DNA binding by the caspase-activated DNase (CAD). Results of a mutational analysis and computational modeling suggest that DNA is bound via a positively charged surface with two functionally distinct regions, one being the active site facing the DNA minor groove and the other comprising distal residues close to or directly from helix alpha4, which binds DNA in the major groove. This bipartite protein-DNA interaction is present once in the CAD/inhibitor of CAD heterodimer and repeated twice in the active CAD dimer.
Collapse
Affiliation(s)
- Stefanie Reh
- Institute of Biochemistry, Faculty of Biology and Chemistry, Justus-Liebig-University Giessen, Heinrich-Buff-Ring 58, D-35392 Giessen, Germany
| | | | | | | |
Collapse
|
9
|
Lechardeur D, Dougaparsad S, Nemes C, Lukacs GL. Oligomerization state of the DNA fragmentation factor in normal and apoptotic cells. J Biol Chem 2005; 280:40216-25. [PMID: 16204257 DOI: 10.1074/jbc.m502220200] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The caspase-activated DNase (CAD) is the primary nuclease responsible for oligonucleosomal DNA fragmentation during apoptosis. The DNA fragmentation factor (DFF) is composed of the 40-kDa CAD (DFF40) in complex with its cognate 45-kDa inhibitor (inhibitor of CAD: ICAD or DFF45). The association of ICAD with CAD not only inhibits the DNase activity but is also essential for the co-translational folding of CAD. Activation of CAD requires caspase-3-dependent proteolysis of ICAD. The tertiary structures of neither the inactive nor the activated DFF have been conclusively established. Whereas the inactive DFF is thought to consist of the CAD/ICAD heterodimer, activated CAD has been isolated as a large (>MDa) multimer, as well as a monomer. To establish the subunit stoichiometry of DFF and some of its structural determinants in normal and apoptotic cells, we utilized size-exclusion chromatography in combination with co-immunoprecipitation and mutagenesis techniques. Both endogenous and heterologously expressed DFF have an apparent molecular mass of 160-190 kDa and contain 2 CAD and 2 ICAD molecules (CAD/ICAD)2 in HeLa cells. Although the N-terminal (CIDE-N) domain of CAD is not required for ICAD binding, it is necessary but not sufficient for ICAD homodimerization in the DFF. In contrast, the CIDE-N domain of ICAD is required for CAD/ICAD association. Using bioluminescence resonance energy transfer (BRET), dimerization of ICAD in DFF was confirmed in live cells. In apoptotic cells, endogenous and exogenous CAD forms limited oligomers, representing the active nuclease. A model is proposed for the rearrangement of the DFF subunit stoichiometry in cells undergoing programmed cell death.
Collapse
Affiliation(s)
- Delphine Lechardeur
- Program in Cell and Lung Biology, Hospital for Sick Children Research Institute and Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario M5G 1X8, Canada
| | | | | | | |
Collapse
|
10
|
Korn C, Scholz SR, Gimadutdinow O, Lurz R, Pingoud A, Meiss G. Interaction of DNA Fragmentation Factor (DFF) with DNA Reveals an Unprecedented Mechanism for Nuclease Inhibition and Suggests That DFF Can Be Activated in a DNA-bound State. J Biol Chem 2005; 280:6005-15. [PMID: 15572351 DOI: 10.1074/jbc.m413035200] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
DNA fragmentation factor (DFF) is a complex of the DNase DFF40 (CAD) and its chaperone/inhibitor DFF45 (ICAD-L) that can be activated during apoptosis to induce DNA fragmentation. Here, we demonstrate that DFF directly binds to DNA in vitro without promoting DNA cleavage. DNA binding by DFF is mediated by the nuclease subunit, which can also form stable DNA complexes after release from DFF. Recombinant and reconstituted DFF is catalytically inactive yet proficient in DNA binding, demonstrating that the nuclease subunit in DFF is inhibited in DNA cleavage but not in DNA binding, revealing an unprecedented mode of nuclease inhibition. Activation of DFF in the presence of naked DNA or isolated nuclei stimulates DNA degradation by released DFF40 (CAD). In transfected HeLa cells transiently expressed DFF associates with chromatin, suggesting that DFF could be activated during apoptosis in a DNA-bound state.
Collapse
Affiliation(s)
- Christian Korn
- Institute of Biochemistry, Justus-Liebig-University Giessen, 35392 Giessen, Germany
| | | | | | | | | | | |
Collapse
|
11
|
Lechardeur D, Xu M, Lukacs GL. Contrasting nuclear dynamics of the caspase-activated DNase (CAD) in dividing and apoptotic cells. ACTA ACUST UNITED AC 2004; 167:851-62. [PMID: 15569712 PMCID: PMC2172457 DOI: 10.1083/jcb.200404105] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Although compelling evidence supports the central role of caspase-activated DNase (CAD) in oligonucleosomal DNA fragmentation in apoptotic nuclei, the regulation of CAD activity remains elusive in vivo. We used fluorescence photobleaching and biochemical techniques to investigate the molecular dynamics of CAD. The CAD-GFP fusion protein complexed with its inhibitor (ICAD) was as mobile as nuclear GFP in the nucleosol of dividing cells. Upon induction of caspase-3-dependent apoptosis, activated CAD underwent progressive immobilization, paralleled by its attenuated extractability from the nucleus. CAD immobilization was mediated by its NH2 terminus independently of its DNA-binding activity and correlated with its association to the interchromosomal space. Preventing the nuclear attachment of CAD provoked its extracellular release from apoptotic cells. We propose a novel paradigm for the regulation of CAD in the nucleus, involving unrestricted accessibility of chromosomal DNA at the initial phase of apoptosis, followed by its nuclear immobilization that may prevent the release of the active nuclease into the extracellular environment.
Collapse
Affiliation(s)
- Delphine Lechardeur
- Hospital for Sick Children Research Institute and Department of Laboratory Medicine and Pathobiology, University of Toronto, Ontario, Canada
| | | | | |
Collapse
|
12
|
Srivatsan SG, Parvez M, Verma S. Adenine-copper coordination polymer as an oxidative nucleozyme: implications for simple prebiotic catalytic units. J Inorg Biochem 2004; 97:340-4. [PMID: 14568238 DOI: 10.1016/s0162-0134(03)00285-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Plasmid modification activity of a modified adenine-copper coordination polymer, in the presence of peracids and thiols, and ensuing preliminary mechanistic investigations are reported. These observations, when coupled with unique coordination pattern of the metal complex, have led us to propose that a synergistic interaction between nucleobases and metal ions may be responsible for primordial catalysis of certain key reactions of biochemical significance and could serve the function of a prototypical, prebiotic nucleozyme.
Collapse
Affiliation(s)
- S G Srivatsan
- Department of Chemistry, Indian Institute of Technology-Kanpur, Kanpur, 208016 (UP), India
| | | | | |
Collapse
|
13
|
Widlak P, Lanuszewska J, Cary RB, Garrard WT. Subunit structures and stoichiometries of human DNA fragmentation factor proteins before and after induction of apoptosis. J Biol Chem 2003; 278:26915-22. [PMID: 12748178 DOI: 10.1074/jbc.m303807200] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
DNA fragmentation factor (DFF) is one of the major endonucleases responsible for internucleosomal DNA cleavage during apoptosis. Understanding the regulatory checkpoints involved in safeguarding non-apoptotic cells against accidental activation of this nuclease is as important as elucidating its activation mechanisms during apoptosis. Here we address these issues by determining DFF native subunit structures and stoichiometries in human cells before and after induction of apoptosis using the technique of native pore-exclusion limit electrophoresis in combination with Western analyses. For comparison, we employed similar techniques with recombinant proteins in conjunction with atomic force microscopy. Before induction of apoptosis, the expression of DFF subunits varied widely among the cell types studied, and the chaperone/inhibitor subunits DFF45 and DFF35 unexpectedly existed primarily as monomers in vast excess of the latent nuclease subunit, DFF40, which was stoichiometrically associated with DFF45 to form heterodimers. DFF35 was exclusively cytoplasmic as a monomer. Nuclease activation upon caspase-3 cleavage of DFF45/DFF35 was accompanied by DFF40 homo-oligomer formation, with a tetramer being the smallest unit. Interestingly, intact DFF45 can inhibit nuclease activity by associating with these homo-oligomers without mediating their disassembly. We conclude that DFF nuclease is regulated by multiple pre- and post-activation fail-safe steps.
Collapse
Affiliation(s)
- Piotr Widlak
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | | | | | | |
Collapse
|
14
|
MacLea KS, Krieser RJ, Eastman A. Structural requirements of human DNase II alpha for formation of the active enzyme: the role of the signal peptide, N-glycosylation, and disulphide bridging. Biochem J 2003; 371:867-76. [PMID: 12558498 PMCID: PMC1223339 DOI: 10.1042/bj20021875] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2002] [Revised: 01/23/2003] [Accepted: 01/31/2003] [Indexed: 11/17/2022]
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.
Collapse
Affiliation(s)
- Kyle S MacLea
- Department of Pharmacology and Toxicology, Dartmouth Medical School, 7650 Remsen, Hanover, NH 03755, USA
| | | | | |
Collapse
|
15
|
MacLea KS, Krieser RJ, Eastman A. A family history of deoxyribonuclease II: surprises from Trichinella spiralis and Burkholderia pseudomallei. Gene 2003; 305:1-12. [PMID: 12594037 DOI: 10.1016/s0378-1119(02)01233-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Deoxyribonuclease IIalpha (DNase IIalpha) is an acidic endonuclease found in lysosomes and nuclei, and it is also secreted. Though its Caenorhabditis elegans homolog, NUC-1, is required for digesting DNA of apoptotic cell corpses and dietary DNA, it is not required for viability. However, DNase IIalpha is required in mice for correct development and viability, because undigested cell corpses lead to lesions throughout the body. Recently, we showed that, in contrast to previous reports, active DNase IIalpha consists of one contiguous polypeptide. To better analyze DNase II protein structure and determine residues important for activity, extensive database searches were conducted to find distantly related family members. We report 29 new partial or complete homologs from 21 species. Four homologs with differences at the purported active site histidine residue were detected in the parasitic nematodes Trichinella spiralis and Trichinella pseudospiralis. When these mutations were reconstructed in human DNase IIalpha, the expressed proteins were inactive. DNase II homologs were also identified in non-metazoan species. In particular, the slime-mold Dictyostelium, the protozoan Trichomonas vaginalis, and the bacterium Burkholderia pseudomallei all contain sequences with significant similarity and identity to previously cloned DNase II family members. We report an analysis of their sequences and implications for DNase II protein structure and evolution.
Collapse
Affiliation(s)
- Kyle S MacLea
- Department of Pharmacology and Toxicology, Dartmouth Medical School, 7650 Remsen, Hanover, NH 03755, USA
| | | | | |
Collapse
|
16
|
Nagata S, Nagase H, Kawane K, Mukae N, Fukuyama H. Degradation of chromosomal DNA during apoptosis. Cell Death Differ 2003; 10:108-16. [PMID: 12655299 DOI: 10.1038/sj.cdd.4401161] [Citation(s) in RCA: 316] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Apoptosis is often accompanied by degradation of chromosomal DNA. CAD, caspase-activated DNase, was identified in 1998 as a DNase that is responsible for this process. In the last several years, mice deficient in the CAD system have been generated. Studies with these mice indicated that apoptotic DNA degradation occurs in two different systems. In one, the DNA fragmentation is carried out by CAD in the dying cells and in the other, by lysosomal DNase II after the dying cells are phagocytosed. Several other endonucleases have also been suggested as candidate effectors for the apoptotic degradation of chromosomal DNA. In this review, we will discuss the mechanism and role of DNA degradation during apoptosis.
Collapse
Affiliation(s)
- S Nagata
- Integrated Biology Laboratories, Graduate School of Frontier Science, Japan Science and Technology Corperation, Suita, Osaka.
| | | | | | | | | |
Collapse
|
17
|
Walker DC, Georgiou T, Pommer AJ, Walker D, Moore GR, Kleanthous C, James R. Mutagenic scan of the H-N-H motif of colicin E9: implications for the mechanistic enzymology of colicins, homing enzymes and apoptotic endonucleases. Nucleic Acids Res 2002; 30:3225-34. [PMID: 12136104 PMCID: PMC135741 DOI: 10.1093/nar/gkf420] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2002] [Revised: 04/10/2002] [Accepted: 05/15/2002] [Indexed: 11/14/2022] Open
Abstract
Colicin E9 is a microbial toxin that kills bacteria through random degradation of chromosomal DNA. Within the active site of the cytotoxic endonuclease domain of colicin E9 (the E9 DNase) is a 32 amino acid motif found in the H-N-H group of homing endonucleases. Crystal structures of the E9 DNase have implicated several conserved residues of the H-N-H motif in the mechanism of DNA hydrolysis. We have used mutagenesis to test the involvement of these key residues in colicin toxicity, metal ion binding and catalysis. Our data show, for the first time, that the H-N-H motif is the site of DNA binding and that Mg2+-dependent cleavage of double-stranded DNA is responsible for bacterial cell death. We demonstrate that more active site residues are required for catalysis in the presence of Mg2+ ions than transition metals, consistent with the recent hypothesis that the E9 DNase hydrolyses DNA by two distinct, cation-dependent catalytic mechanisms. The roles of individual amino acids within the H-N-H motif are discussed in the context of the available structural information on this and related DNases and we address the possible mechanistic similarities between caspase-activated DNases, responsible for the degradation of chromatin in eukaryotic apoptosis, and H-N-H DNases.
Collapse
Affiliation(s)
- David C Walker
- Division of Microbiology and Infectious Diseases, University Hospital, Queen's Medical Centre, University of Nottingham, Nottingham NG7 2UH, UK
| | | | | | | | | | | | | |
Collapse
|
18
|
Scholz SR, Korn C, Gimadutdinow O, Knoblauch M, Pingoud A, Meiss G. The effect of ICAD-S on the formation and intracellular distribution of a nucleolytically active caspase-activated DNase. Nucleic Acids Res 2002; 30:3045-51. [PMID: 12136086 PMCID: PMC135751 DOI: 10.1093/nar/gkf431] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We show here that co-expression of murine CAD with either ICAD-L or ICAD-S in Escherichia coli as well as mammalian cells leads to a functional DFF complex, which after caspase-3 activation releases a nucleolytically active DNase. The chaperone activity of ICAD-S is between one and two orders of magnitude less effective than that of ICAD-L, as deduced from cleavage experiments with different activated recombinant DFF complexes produced in E.coli. With nucleolytically active EGFP fusion proteins of CAD it is demonstrated that co-expression of ICAD-S, which lacks the C-terminal domain of ICAD-L, including the NLS, leads to a homogeneous intracellular distribution of the DNase in transfected cells, whereas co-expression of human or murine ICAD-L variants lacking the NLS leads to exclusion of EGFP-CAD from the nuclei in approximately 50% of cells. These results attribute a particular importance of the NLS in the long isoform of the inhibitor of CAD for nuclear accumulation of the DFF complex in living cells. It is concluded that ICAD-L and ICAD-S in vivo might function as tissue-specific modulators in the regulation of apoptotic DNA degradation by controlling not only the enzymatic activity but also the amount of CAD available in the nuclei of mammalian cells.
Collapse
Affiliation(s)
- Sebastian Richard Scholz
- Institut für Biochemie (FB 08), Justus-Liebig-Universität, Heinrich-Buff-Ring 58, D-35392 Giessen, Germany
| | | | | | | | | | | |
Collapse
|
19
|
Korn C, Scholz SR, Gimadutdinow O, Pingoud A, Meiss G. Involvement of conserved histidine, lysine and tyrosine residues in the mechanism of DNA cleavage by the caspase-3 activated DNase CAD. Nucleic Acids Res 2002; 30:1325-32. [PMID: 11884629 PMCID: PMC101349 DOI: 10.1093/nar/30.6.1325] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The caspase-activated DNase (CAD) is involved in DNA degradation during apoptosis. Chemical modification of murine CAD with the lysine-specific reagent 2,4,6-trinitrobenzenesulphonic acid and the tyrosine-specific reagent N-acetylimidazole leads to inactivation of the nuclease, indicating that lysine and tyrosine residues are important for DNA cleavage by this enzyme. The presence of DNA or the inhibitor ICAD-L protects the enzyme from modification. Amino acid substitution in murine CAD of lysines and tyrosines conserved in CADs from five different species leads to variants with little if any catalytic activity, but unaltered DNA binding (K155Q, K301Q, K310Q, Y247F), with the exception of Y170F, which retains wild-type activity. Similarly, as observed for the previously characterised H242N, H263N, H308N and H313N variants, the newly introduced His-->Asp/Glu or Arg exchanges lead to variants with <1% of wild-type activity, with two exceptions: H313R shows wild-type activity, and H308D at pH 5.0 exhibits approximately 5% of wild-type activity at this pH. Y170F and H313R produce a specific pattern of fragments, different from wild-type CAD, which degrades DNA non-specifically. The recombinant nuclease variants produced in Escherichia coli were tested for their ability to form nucleolytically active oligomers. They did not show any significant deviation from the wild-type enzyme. Based on these and published data possible roles of the amino acid residues under investigation are discussed.
Collapse
Affiliation(s)
- Christian Korn
- Institut für Biochemie, Justus-Liebig-Universität, Heinrich Buff Ring 58, 35392 Giessen, Germany
| | | | | | | | | |
Collapse
|