Domain Of Poly ADP-ribose Polymerase Research Articles

Characterization of sPARP-1: AN ALTERNATIVE PRODUCT OF PARP-1 GENE WITH POLY(ADP-RIBOSE) POLYMERASE ACTIVITY INDEPENDENT OF DNA STRAND BREAKS

Poly(ADP-ribose) polymerase-1 (PARP-1) is an abundant nuclear enzyme that catalyzes the synthesis of poly(ADP-ribose) (pADPr) from its substrate NAD(+) upon binding to DNA strand breaks. Poly(ADP-ribosyl)ation has been implicated in many cellular processes including replication, transcription, and the maintenance of genomic stability. However, studies with mice and cells lacking PARP-1 reveal a critical role for the enzyme in the maintenance of genomic integrity only. Recently, a significant level of poly(ADP-ribose) polymerase activity has been detected in fibroblasts derived from mice lacking PARP-1 following treatment with genotoxic agents (Shieh, W. M., Amé, J-C., Wilson, M. V., Wang, Z-Q., Koh, D. W., Jacobson, M. K., and Jacobson, E. L. (1998) J. Biol. Chem. 273, 30069-30072). We have isolated a cDNA that originates from PARP-1 (-/-) fibroblasts and encodes a polypeptide of 493 amino acid residues bearing poly(ADP-ribose) polymerase activity. This protein, that we named sPARP-1 for short poly(ADP-ribose) polymerase-1, has a calculated mass of 55.3 kDa and is identical in deduced amino acid sequence to the catalytic domain of PARP-1. Radiation hybrid analysis assigned the sPARP-1 gene to the chromosome 1H5-H6 in an immediate proximity to the known location of PARP-1 gene, indicating that sPARP-1 and PARP-1 are most probably products of the same gene. Active sPARP-1 is present in both PARP-1 (+/+) and PARP-1 (-/-) cells as demonstrated by activity-Western blotting and immunostaining using a specific antibody developed against sPARP-1. Like PARP-1, sPARP-1 is localized in the cell nucleus, uses NAD(+) as a substrate and is inhibited by nicotinamide analogues. sPARP-1 produces pADPr of similar length and structure to that of PARP-1. However, contrary to PARP-1, sPARP-1 does not require DNA strand breaks for its activation, although it is stimulated following genotoxic treatments.

A Human Poly(ADP-ribose) Polymerase Gene Family (ADPRTL): cDNA Cloning of Two Novel Poly(ADP-ribose) Polymerase Homologues

Posttranscriptional modification of nuclear proteins by poly(ADP-ribosyl)ation in response to DNA strand breaks plays an important role in DNA repair, regulation of apoptosis, and maintenance of genomic stability. A 113-kDa human poly(ADP-ribose) polymerase (PARP) has previously been identified and cloned. However, there is evidence that additional enzymes with PARP activity exist in mammalian cells. I have identified and cloned the cDNAs of two novel ≈60-kDa human proteins that are 40 and 31% identical to the catalytic C-terminal domain of PARP. These proteins, named PARP-2 and PARP-3, lack the DNA-binding and automodification domains. PARP-2 and PARP-3 mRNAs were detected in 16 different human tissues as major bands of 2.0 and 2.2 kb, respectively. Radiation hybrid analysis assigned the PARP-2 gene (HGMW-approved symbolADPRTL2) to chromosome 14q11.2–q12 and the PARP-3 gene (HGMW-approved symbolADPRTL3) to 3p21.1–p22.2. This report shows the existence of a human PARP gene family with at least three closely related members.

Poly(ADP-ribose) polymerase interacts with novel Drosophila ribosomal proteins, L22 and l23a, with unique histone-like amino-terminal extensions.

Poly(ADP-ribose) polymerase (PARP) is a nuclear enzyme that recognizes and binds to the nicks and ends of DNA, and catalyses successive ADP-ribosylation reactions. To clarify the function of PARP at the molecular level, we searched proteins which interact with PARP. In the auto-modification domain of PARP in Drosophila, there is a putative leucine-zipper motif which can interact with other protein molecules. To find interacting proteins we examined the auto-modification domain of Drosophila PARP, using the Far-Western screening method. From six independent cDNA clones isolated, we characterized two clones, PBP-3 and PBP-12. The predicted amino acid sequences from 109 to 269 of PBP-3 and from 184 to 312 of PBP-12 had more than 62% identities to mammalian L23a (rpl23a) and L22 (rpl22), the ribosomal proteins of the large subunit. This indicated that PBP-3 and PBP-12 are Drosophila homologues of L23a and L22, respectively. These Drosophila ribosomal protein L22 and L23a have additional Ala-, Lys- and Pro-rich sequences at the amino terminus, which have a resemblance to the carboxy-terminal portion of histone H1. Thus, Drosophila L22 and L23a might have two functions, namely the role of DNA-binding similar to histone H1 and the role of organizing the ribosome.

A Nondenaturing Purification Scheme for the DNA-Binding Domain of Poly(ADP-Ribose) Polymerase, a Structure-Specific DNA-Binding Protein

Poly(ADP-ribose) polymerase (PARP) is thought to be involved in DNA repair given its ability to recognize and bind to DNA strand breaks. During apoptosis, PARP is proteolytically cleaved into two stable fragments, the N-terminal 25-kDa DNA-binding domain (DBD) and the 85-kDa fragment containing the automodification and catalytic domains. To understand the DNA-binding properties of PARP, we expressed a recombinant hexahistidine tagged protein (His-DBD) inEscherichia coli.We modified expression to facilitate protein folding by including zinc and reducing the induction temperature. Properly folded, the DNA-binding domain of PARP binds to single- and double-stranded DNA in a structure-specific manner. To eliminate contamination with bacterial DNA that occurred during the purification process, a purification procedure was developed to produce DNA-free protein. In addition, to remove the hexahistidine tag from the recombinant protein, thrombin cleavage was carried out while the recombinant protein was bound to a DNA column. This procedure stabilized the recombinant protein and resulted in nearly 100% cleavage with no appreciable loss to unwanted proteolytic degradation. This nondenaturing purification scheme results in high-quality, native PARP–DBD for use in structural and biochemical studies.

Zinc is an essential cofactor for recognition of the DNA binding domain of poly(ADP-ribose) polymerase by antibodies in autoimmune rheumatic and bowel diseases.

To characterize autoantibody response to poly(ADP-ribose) polymerase (PARP) and to assess the significance of autoantibodies to the 2 zinc fingers of this enzyme in patients with autoimmune rheumatic and bowel diseases. The specificity of antienzyme autoantibodies was established by dot immunoassay with recombinant human PARP and by enzyme-linked immunosorbent assay using the recombinant N-terminal fragment containing the DNA binding domain of PARP, the recombinant C-terminal catalytic domain (40-kd fragment), a peptide containing the nuclear localization signal (NLS) of PARP, 2 synthetic peptides (and mutated peptides) corresponding to zinc-finger motifs F1 and F2 that are present in the DNA binding domain, zinc fingers from other self antigens (e.g., peptides from Ro60, Ro52, and U1C proteins), and poly(ADP-ribose). Sera from patients with autoimmune rheumatic and bowel diseases were tested, as were affinity-purified antibodies. Histocompatibility typing of systemic lupus erythematosus (SLE) patients was performed by serology. Antibodies from the patient sera reacted only weakly with the recombinant N- and C-terminal domains and with the NLS peptide. In contrast, the 2 synthetic peptides corresponding to zinc-finger motifs F1 and F2 represented immunodominant targets for IgG antibodies from patients with SLE, mixed connective tissue disease (MCTD), Crohn's disease, and ulcerative colitis. The sera from patients with SLE and MCTD showed much weaker reactivity with mutant peptides F1 and F2, which contain mutations at the cysteine residues involved in zinc coordination. F1/F2 antibodies did not cross-react with zinc fingers from other self proteins. No correlation was found between the presence of F1/F2 autoantibodies in SLE sera and the presence of other autoantibodies typical of this disease (e.g., anti-double-stranded DNA and poly[ADP-ribose] antibodies). The presence of F2 antibodies in the serum of SLE patients was negatively associated with HLA-DR6. An autoimmune response to PARP is potentially important because this enzyme is involved in DNA repair and is rapidly cleaved during the "execution phase" of apoptosis. The high prevalence in certain autoimmune rheumatic and bowel diseases of antibodies to F1 and F2, which are directly involved in this process, is further evidence implicating involvement of the DNA repair system in chronic inflammatory diseases.

Poly(ADP-ribose) polymerase interacts with a novel human ubiquitin conjugating enzyme: hUbc9.

Poly(ADP-ribose) polymerase (PARP) has been suggested to play a regulatory role in vivo, in DNA replication and/or DNA repair based mainly on its capacity to bind to DNA strand breaks. This interaction is modulated through auto poly(ADP-ribosylation). However, the biological function of PARP may also involve interactions with proteins such as topoisomerase I or DNA polymerase alpha, which may or may not be themselves ADP-ribosylated. Using the yeast two-hybrid method search for other proteins interacting with PARP, we have isolated a full-length cDNA clone coding for a protein of 158 amino acid residues. This amino acid sequence is 66 and 56% identical to yeast ubiquitin-conjugating enzymes Hus5 and Ubc9 of Schizosaccharomyces pombe and Saccharomyces cerevisiae, respectively. Moreover, we have demonstrated that the expressed protein complements a S. cerevisiae yeast strain deficient for Ubc9. The protein encoded by the isolated cDNA is thus a new human counterpart of the ubiquitin-conjugating enzyme family and has been called hUbc9. The hubc9 gene locus has been assigned to the chromosomal location 16p13.2-p13.3. By means of two-hybrid analysis it was discovered that hUbc9 interacts with the automodification domain of PARP. This interaction was further confirmed using GST (glutathione-S-transferase) tagged fusion proteins: (i) in vivo, by transfecting cos7 cells with hUbc9 cloned in an eukaryotic expression vector, and (ii) in vitro, by mixing purified PARP with hUbc9 purified and expressed in bacteria. The possible significance and function of this interaction is discussed while taking into account the possible intracellular role of hUbc9.

Intact Cell Evidence for the Early Synthesis, and Subsequent Late Apopain-Mediated Suppression, of Poly(ADP-ribose) during Apoptosis

Poly(ADP-ribose) polymerase (PARP), which is catalytically activated by DNA strand breaks, has been implicated in apoptosis, or programmed cell death. A protease (CPP32) responsible for the cleavage of PARP and necessary for apoptosis was recently purified and characterized. The coordinated sequence of events related to PARP activation and cleavage in apoptosis has now been examined in individual cells. Apoptosis was studied in a human osteosarcoma cell line that undergoes a slow (8 to 10 days), spontaneous, and reproducible death program in culture. Changes in the abundance of intact PARP, poly(ADP-ribose) (PAR), and a proteolytic cleavage product of PARP that contains the DNA-binding domain were examined during apoptosis in the context of individual, whole cells by immunofluorescence with specific antibodies. The synthesis of PAR from NAD increased early, within 2 days of cell plating for apoptosis, prior to the appearance of internucleosomal DNA cleavage and before the cells become irreversibly committed to apoptosis, since replating yields viable, nonapoptotic cells. Strong expression of full-length PARP was also detected, by immunofluorescence as well as by Western analysis, during this same time period. However, after ∼4 days in culture, the abundance of both full-length PARP and PAR decreased markedly. After 6 days, a proteolytic cleavage product containing the DNA-binding domain of PARP was detected immunocytochemically and confirmed by Western analysis, both in the nuclei and in the cytoplasm of cells. A recombinant peptide spanning the DNA-binding domain of PARP was expressed, purified, and biotinylated, and was then used as a probe for DNA strand breaks. Fluorescence microscopy with this probe revealed extensive DNA fragmentation during the later stages of apoptosis. This is the first report, using individual, intact cells,demonstrating that poly(ADP-ribosyl)ation of nuclear proteins occurs prior to the commitment to apoptosis, that inactivation and cleavage of PARP begin shortly thereafter, and that very little PAR per se is present during the later stages of apoptosis, despite the presence of a very large number of DNA strand breaks. These results suggest a negative regulatory role for PARP during apoptosis, which in turn may reflect the requirement for adequate NAD and ATP during the later stages of programmed cell death.

Detection of DNA breaks in apoptotic cells utilizing the DNA binding domain of poly(ADP-ribose) polymerase with fluorescence microscopy

The DNA binding domain (DBD) of poly(ADP-ribose) polymerase (PARP) has proved to be a novel, highly sensitive probe for detecting DNA breaks in intact cells undergoing apoptosis. A recombinant peptide spanning the DNA binding domain of PARP was expressed, purified and used to detect DNA strand breaks in fixed cells. Fluorescence microscopy with this probe followed by detection with anti-PARP antisera initially revealed an increased binding following treatment of cells with DNA strand-breaking agents (such asN-methyl-N'-nitro-N-nitrosoguanidine) and, subsequently, using biotinylated PARP DBD, during the later stages of apoptosis in several cell systems, when internucleosomal strand breaks became evident. This procedure was found to be at least as sensitive and required fewer steps to detect DNA strand breaks than those utilizing Klenow incorporation of biotinylated nucleotides.

Purification and Characterization of an Interleukin-1β-converting Enzyme Family Protease That Activates Cysteine Protease P32 (CPP32)

CPP32, a member of the interleukin-1beta-converting enzyme (ICE) family of cysteine proteases, cleaves poly(ADP-ribose) polymerase and sterol regulatory element binding proteins during apoptosis. CPP32 normally exists in the cytosol as a 32-kDa inactive precursor and only becomes activated when cells are undergoing apoptosis. The activation is a proteolytic event that generates a p20/p11 heterodimer. We report here the identification, purification, and characterization of a hamster CPP32-activating protease (CAP) that cleaves and activates CPP32. The biochemical properties of CAP suggest that it is another member of the ICE family of proteases. Purified CAP consists of two prominent polypeptides of 19 and 13 kDa. Protein sequencing revealed that CAP is derived from the hamster homolog of Mch2alpha, a member of the ICE family recently identified based on the sequence conservation among the ICE family members. CAP activity is inhibited by CrmA, a cowpox virus protein that prevents host cell apoptosis. CAP itself is also activated through proteolytic cleavage. These data are consistent with the idea that the activation of the ICE family of proteases during apoptosis proceeds through a cascade of proteolytic events.

Identification of a 116 kDa protein able to bind 1,3-bis(2-chloroethyl)-1-nitrosourea-damaged DNA as poly(ADP-ribose) polymerase.

SKI-1 is a 1,3-bis(2-chloroethyl)-1-nitrosourea (BCNU)-resistant glioma cell line and SK-MG-1 is a BCNU-sensitive glioma cell line. Both cell lines do not express O6-methylguanine-DNA methyl transferase (MGMT) and exhibit comparable levels of 3-methyladenine DNA glycosylase. In order to detect DNA binding proteins involved in alternative DNA repair mechanisms of BCNU damage, we performed Southwestern analysis using a DNA probe damaged with BCNU and nuclear protein extracts from SKI-1 and SK-MG-1 cell lines. Both cell lines express a protein of M(r) 116,000 that is able to bind to BCNU-damaged DNA with higher specificity than to undamaged DNA. This protein was identified as poly(ADP-ribose) polymerase (PARP). Using glioma extracts depleted of PARP or using antibody to block the DNA binding domain of PARP no other protein binding to BCNU-treated probe was observed. Addition of methoxyamine, an inhibitor of DNA strand breaks, led to a significant reduction of PARP binding to BCNU-treated DNA. BCNU treatment of both glioma cell lines led to reduced nicotinamide adenine dinucleotide levels, indicating activation of PARP. Thus, the recognition and binding of PARP to BCNU-induced DNA nicks with concomitant PARP activation may be important processes that are involved in the initial stage of DNA repair of BCNU lesions in glial cells.

Molecular genetic systems to study the role of poly(ADP-ribosyl)ation in the cellular response to DNA damage

To study biological functions of poly(ADP-ribose) polymerase (PARP), low-molecular-mass inhibitors have been used extensively, and the experimental results obtained led to the view that PARP plays a role in DNA repair as well as in other cellular processes, eg DNA replication, cell proliferation, and differentiation. Accumulating evidence that these inhibitors have side effects on other metabolic pathways prompted us to develop two molecular genetic systems for the modulation of poly(ADP-ribosyl)ation in living cells: i) the first approach is centered on the DNA-binding domain (DBD) of PARP, which recognizes DNA strand breaks through its zinc fingers, leading to enzyme activation. We have established stable cell culture systems for either constitutive or inducible overexpression of the DBD. In these cells we observe a drastic trans-dominant inhibition of poly(ADP-ribosyl)ation which is associated with sensitization of cells to γ-irradiation; and ii) in an attempt to specifically increase the poly(ADP-ribose) formation capacity in living cells, the hamster cell line CO60 was stably transfected to obtain constitutive overexpression of full-length human PARP. These molecular genetic systems may be useful for the elucidation of the precise role of poly(ADP-ribosyl)ation in the biological response to DNA damage.

Autoantibodies Reacting with Poly(ADP-Ribose) and with a Zinc-Finger Functional Domain of Poly(ADP-Ribose) Polymerase Involved in the Recognition of Damaged DNA

Poly(ADP-Ribose) polymerase (PARP) is a chromatin-associated enzyme that specifically binds to DNA strand breaks in a zinc-dependent manner. We describe here the presence of IgG antibodies reacting with recombinant human PARP in the serum of patients with systemic lupus erythematosus (SLE) and primary and secondary Sjögren's syndrome (pSS and sSS). The reactivity of patients' sera was further studied in ELISA with a synthetic peptide of 44 residues corresponding to the second zinc finger (F2) present in the DNA-binding domain of PARP and which was shown to effectively bind 65Zn. Thirty-five percent of SLE sera ( n = 97), 42% of pSS sera ( n = 67), and 56% of sSS sera ( n = 16) were found to contain raised levels of IgG antibodies reacting with peptide F2 which corresponds to the domain in PARP that is directly involved in the specific recognition of single and double strand breaks in DNA. Antibodies reacting with the whole enzyme and/or peptide F2 occurred independently from antibodies reacting with poly(ADP-ribose) which is rapidly synthesized in vivo by PARP from NAD and then degraded in response to DNA strand breaks.

Isolation of cDNAs Encoding the Catalytic Domain of Poly(ADP-Ribose) Polymerase from Xenopus laevis and Cherry Salmon Using Heterologous Oligonucleotide Consensus Sequences

We have isolated and sequenced cDNAs encoding the catalytic domain of poly(ADP-ribose) polymerase (PARP) from Xenopus laevis and Oncorhyncus masou (cherry salmon). The cDNAs were amplified by polymerase chain reaction using heterologous oligonucleotides corresponding to the conserved sequences of mammalian cDNAs as primers. The deduced amino acid sequences of Xenopus laevis and cherry salmon cDNA showed 84.4% and 75.6% similarities to that of human PARP, respectively. In both species, mRNA for PARP was identified as a single band of 4 kb, and PARP mRNA was abundant in ovary and brain. Thus, mixed oligonucleotide-primed amplification is a useful method in the cloning of cDNAs from different species, and the catalytic domain of PARP is conserved structurally among phylogenetically different species, suggesting an importance of poly(ADP-ribosyl)ation.

Expression of functional zinc finger domain of human poly(ADP-ribose)polymerase inE.coly

In eukaryote cells poly(ADP-ribose) polymerase (PARP) catalyzes the covalent attachment of ADP-ribose units from the coenzyme NAD+ to various nuclear acceptor proteins. This reaction strickly requires the presence of DNA strand breaks to which the zinc finger domain of the enzyme binds specifically (1). We have expressed a cDNA fragment encoding the two zinc fingers of human PARP (234 amino-terminal residues) in E.coli as a fusion protein. The cDNA insert was previously mutated by PCR to introduce a stop codon at its 3' end and Pstl sites at both extremities . The cDNA was then cloned in Pstl site of the E.coli expression vector pTG161 provided by M.Courtney (Transgene-Strasbourg) (2) resulting in the plasmid pTG161-FWT. Transcription of the cloned sequence proceeds from the XpL promoter which is controlled by the host encoded thermosensitive repressor cl 857. Upon a temperature shift induction from 280C (non induced) to 370C (induced) for 2 hours in LB medium, TGE 900 strain harboring the pTG161-FWT plasmid overexpressed a 35 kDa protein (13 amino-terminal residues of Xcil gene fused with the 234 first amino-acids of human PARP). This protein was easily identified in crude extracts (fig. A) by westem (slot 4,5), zinc (slot 6,7) and southwestern (3) (slot 8,9) .The same sonicated E.coli extracts in SDS PAGE sample buffer (Tris-HCI pH 6.8 50mM; urea 6M; 2 mercaptoethanol 6%; SDS 3% ;bromophenol blue 0.003%) were electrophoresed, transferred onto nitrocellulose membrane, renatured and processed for a blot and experiment as described previously (1). A double stranded DNA probe harboring a strand break at a defined position was constructed from synthetic oligonucleotides(1). DNase I protection results displayed in figure B show that the finger domain of human PARP produced in E.cofi binds to the strand break and protects this region from DNasel digestion as in the case of purified calf thymus PARP (1).This simple assay which utilizes crude extracts, appears to be a valuable tool for the study of the interaction between the finger domain of PARP and a DNA strand break and could be easily generalized for the study of other finger proteins overexpressed in E.coli Fjg.A analysis of crude extracts of TGE900/pTG1 61 -FWT E.coli strain expressing the zinc finger domain of human PARP. Slots 2,4,6,8 non induced (-) and 3,5,7,9 induced (+) extracts.Fig.B DNase I footprint assay <_, ''9S,.!rk.:,4 lX for the protection of a single strand break by the PARP zinc finger domain expressed in E.coli. The transferred protein was incubated with a double stranded 66 bp deoxyoligonucleotide containing a single strand break at position 33 obtained by the annealing of _t flg * two 33 mer with a 5' labelled 66mer oligonucleotide. Footprint assays were performed either without protein (slot 1) with purified calf thymus PARP (slot 2) or with human PARP zinc finger domain expressed in E. coli (slot 3). G. degradation products of the G sequencing reaction. Conditions of the blot and experiment were the same as those described in ref. (1) . *To whom correspondence should be addressed