Induction of specific antibodies to poly(ADP-ribose) in rabbits by double-stranded RNA, poly(A)-poly(U)

Development and characterization of recombinant ADP-ribose binding reagents that allow simultaneous detection of mono and poly ADP-ribose

ADP-ribosylation (ADPRylation) is a post-translational modification (PTM) of proteins mediated by the activity of a variety of ADP-ribosyltransferase (ART) enzymes, such as the Poly (ADP-ribose) Polymerase (PARP) family of proteins. This PTM is diverse in both form and biological functions, which makes it a highly interesting modification, but difficult to study due to limitations in reagents available to detect the diversity of ADPRylation. Recently we developed a set of recombinant antibody-like ADP-ribose (ADPR) binding proteins using naturally occurring ADPR binding domains (ARBDs), including macrodomains and WWE domains, functionalized by fusion to the constant "Fc" region of rabbit immunoglobulin. Herein, we present an expansion of this biological toolkit, where we have replaced the rabbit Fc sequence with the sequence from two other species, mouse and goat. These new reagents are based on a previously characterized set of naturally occurring ARBDs with known specificity. Characterization of the new reagents demonstrates that they can be detected in a species-dependent manner by secondary immunological tools, recognize specific ADPR moieties, and can be used for simultaneous detection of mono ADPR and poly ADPR at single-cell resolution in various antibody-based assays. The expansion of this toolkit will allow for more multiplexed assessments of the complexity of ADPRylation biology in many biological systems.

Development and Characterization of Recombinant ADP-Ribose Binding Reagents that Allow Simultaneous Detection of Mono and Poly ADP-Ribose

ADP-ribosylation (ADPRylation) is a post-translational modification (PTM) of proteins mediated by the activity of a variety of ADP-ribosyltransferase (ART) enzymes, such as the Poly (ADP-ribose) Polymerase (PARP) family of proteins. This PTM is diverse in both form and biological functions, which makes it a highly interesting modification, but difficult to study due to limitations in reagents available to detect the diversity of ADP-ribosylation. Recently we developed a set of recombinant antibody-like ADP-ribose binding proteins, using naturally occurring ADPR binding domains (ARBDs) that include macrodomains and WWE domains, that have been functionalized by fusion to the constant "Fc" region of rabbit immunoglobulin. Herein, we present an expansion of this biological toolkit, where we have replaced the rabbit Fc sequence with two other species, the Fc for mouse and goat immunogloblulin. Characterization of the new reagents indicates that they can be detected in a species-dependent manner, recognize specific ADP-ribose moieties, and excitingly, can be used in various antibody-based assays by co-staining. The expansion of this tool will allow for more multiplexed assessments of the complexity of ADPRylation biology in many biological systems.

Generation and Characterization of Recombinant Antibody-like ADP-Ribose Binding Proteins

ADP-ribosylation is an enzyme-catalyzed post-translational modification of proteins in which the ADP-ribose (ADPR) moiety of NAD+ is transferred to a specific amino acid in a substrate protein. The biological functions of ADP-ribosylation are numerous and diverse, ranging from normal physiology to pathological conditions. Biochemical and cellular studies of the diverse forms and functions of ADPR require immunological reagents that can be used for detection and enrichment. The lack of a complete set of tools that recognize all forms of ADPR [i.e., mono-, oligo-, and poly(ADP-ribose)] has hampered progress. Herein, we describe the generation and characterization of a set of recombinant antibody-like ADP-ribose binding proteins, in which naturally occurring ADPR binding domains, including macrodomains and WWE domains, have been functionalized by fusion to the Fc region of rabbit immunoglobulin. These reagents, which collectively recognize all forms of ADPR with different specificities, are useful in a broad array of antibody-based assays, such as immunoblotting, immunofluorescent staining of cells, and immunoprecipitation. Observations from these assays suggest that the biology of ADPR is more diverse, rich, and complex than previously thought. The ARBD-Fc fusion proteins described herein will be useful tools for future exploration of the chemistry, biochemistry, and biology of ADP-ribose.

Overview on poly(ADP-ribose) immuno-biomedicine and future prospects

Poly(ADP-ribose), identified in 1966 independently by three groups Strassbourg, Kyoto and Tokyo, is synthesized by poly(ADP-ribose) polymerases (PARP) from NAD(+) as a substrate in the presence of Mg(2+). The structure was unique in that it has ribose-ribose linkage. In the early-1970s, however, its function in vivo/in vitro was still controversial and the antibody against it was desired to help clear its significance. Thereupon, the author tried to produce antibody against poly(ADP-ribose) in rabbits and succeeded in it for the first time in the world. Eventually, this success has led to the following two groundbreaking papers in Nature: "Naturally-occurring antibody against poly(ADP-ribose) in patients with autoimmune disease SLE", and "Induction of anti-poly(ADP-ribose) antibody by immunization with synthetic double-stranded RNA, poly(A)·poly(U)".On the way to the publication of the first paper, a reviewer gave me a friendly comment that there is "heteroclitic" fashion as a mechanism of the production of natural antibody. This comment was really a God-send for me, and became a train of power for publication of another paper, as described above. Accordingly, I thought this, I would say, episode is worth describing herein. Because of its importance in biomedical phenomena, a certain number of articles related to "heteroclitic" have become to be introduced in this review, although they were not always directly related to immuno-biological works on poly(ADP-ribose). Also, I tried to speculate on the future prospects of poly(ADP-ribose), product of PARP, as an immuno-regulatory molecule, including either induced or naturally-occurring antibodies, in view of "heteroclitic".

The structural basis of XRCC1-mediated DNA repair

Scaffold proteins play a central role in DNA repair by recruiting and organizing sets of enzymes required to perform multi-step repair processes. X-ray cross complementing group 1 protein (XRCC1) forms enzyme complexes optimized for single-strand break repair, but participates in other repair pathways as well. Available structural data for XRCC1 interactions is summarized and evaluated in terms of its proposed roles in DNA repair. Mutational approaches related to the abrogation of specific XRCC1 interactions are also discussed. Although substantial progress has been made in elucidating the structural basis for XRCC1 function, the molecular mechanisms of XRCC1 recruitment related to several proposed roles of the XRCC1 DNA repair complex remain undetermined.

Poly-ADP-ribose polymerase: machinery for nuclear processes

It is becoming increasingly clear that the nuclear protein, poly-ADP-ribose polymerase 1 (PARP1), plays essential roles in the cell, including DNA repair, translation, transcription, telomere maintenance, and chromatin remodeling. Despite the exciting progress made in understanding the ubiquitous role of poly-ADP-ribose metabolism, a basic mechanism of PARP's activity regulating multiple nuclear processes is yet to be outlined. This review offers a holistic perspective on activity of PARP1, based on empirically observable phenomena. Primary attention is given to mechanisms by which PARP1 regulates a broad range of essential nuclear events, including two complementary processes (1) regulation of protein-nucleic acid interactions by means of protein shuttling and (2) utilizing poly-ADP-ribose as an anionic matrix for trapping, recruiting, and scaffolding proteins.

[The apoptosis marker enzyme poly-(ADP-ribose) polymerase (PARP) in systemic lupus erythematosus]

The enzyme poly-(ADP-ribose) polymerase (PARP) is localized within the cell nucleus and catalyzes DNA-repair. During programmed cell death (apoptosis), PARP is enzymatically cleaved. Detection of the cleavage products is characteristic for apoptosis. In patients with systemic lupus erythematosus (SLE), the highly ordered signal transduction cascade of apoptosis is disturbed. SLE patients show reduced PARP activity . PARP cleavage products are mainly found in association with either antinuclear and/or anti-dsDNA antibodies. In addition, serum samples from SLE patients and other autoimmune diseases display anti-PAR and anti-PARP autoantibodies.

Poly(ADP-ribosyl)ation reactions in the regulation of nuclear functions

Poly(ADP-ribosyl)ation is a post-translational modification of proteins. During this process, molecules of ADP-ribose are added successively on to acceptor proteins to form branched polymers. This modification is transient but very extensive in vivo, as polymer chains can reach more than 200 units on protein acceptors. The existence of the poly(ADP-ribose) polymer was first reported nearly 40 years ago. Since then, the importance of poly(ADP-ribose) synthesis has been established in many cellular processes. However, a clear and unified picture of the physiological role of poly(ADP-ribosyl)ation still remains to be established. The total dependence of poly(ADP-ribose) synthesis on DNA strand breaks strongly suggests that this post-translational modification is involved in the metabolism of nucleic acids. This view is also supported by the identification of direct protein-protein interactions involving poly(ADP-ribose) polymerase (113 kDa PARP), an enzyme catalysing the formation of poly(ADP-ribose), and key effectors of DNA repair, replication and transcription reactions. The presence of PARP in these multiprotein complexes, in addition to the actual poly(ADP-ribosyl)ation of some components of these complexes, clearly supports an important role for poly(ADP-ribosyl)ation reactions in DNA transactions. Accordingly, inhibition of poly(ADP-ribose) synthesis by any of several approaches and the analysis of PARP-deficient cells has revealed that the absence of poly(ADP-ribosyl)ation strongly affects DNA metabolism, most notably DNA repair. The recent identification of new poly(ADP-ribosyl)ating enzymes with distinct (non-standard) structures in eukaryotes and archaea has revealed a novel level of complexity in the regulation of poly(ADP-ribose) metabolism.

Poly(ADP-ribose): historical perspective

The early historical background of the discovery of poly(ADP-ribose) and the following development of science on poly(ADP-ribose) are reviewed. Fundamental knowledge on the natures of poly(ADP-ribose), poly(ADP-ribose) polymerase and enzymes degrading poly(ADP-ribose) are summarized with brief description on the methodology for their purification and characterization. Future prospect of research on biological significance of poly(ADP-ribose) has also been discussed briefly.

Disease specificity of antibodies to poly (ADP-ribose); their relationships to anti-DNA antibodies and to disease activity in lupus

In this study we have measured the level of anti poly (ADP-ribose) antibodies in the sera of a number of patients with SLE and their relatives, patients with a wide variety of other autoimmune and infectious diseases, and a group of normal healthy controls. It was found that these antibodies were not disease specific but were present in nine out of thirteen groups tested in significant numbers. The levels of anti poly (ADP-ribose) antibodies and anti DNA antibodies in SLE patients bled serially were also measured. The level of these antibodies fluctuated in parallel in many of these patients, although the anti poly (ADP-ribose) antibodies reflected disease activity more accurately in some.

A novel trait of naturally occurring anti-DNA antibodies: dissociation from immune complexes in neutral 0.3-0.5 M NaCl

Monoclonal and polyclonal anti-DNA antibodies from autoimmune mice, and experimentally induced rabbit anti-nucleic acid polyclonal antibodies were tested for stability of binding to nucleic acids in the presence of various concentrations of NaCl by an enzyme-linked immunosorbent assay (ELISA). Murine monoclonal antibodies 2C10 (IgG2b) and 1A2 (IgG2a), which are known to react specifically with double-stranded (ds) DNA, dissociated completely from their complexes with DNA when washed with a neutral 0.5 M NaCl solution. Another monoclonal antibody (MoAb) (IgM,kappa), polyreactive with single-stranded (ss) DNA, cardiolipin, and trinitrophenylhapten (TNP), was also dissociated from its complexes with ss DNA, but not from its complexes with TNP, by 0.3-0.5 M NaCl. Similar differences were observed in the binding stability of serum antibodies from autoimmune mice to DNA and TNP. In contrast, anti-nucleic acid polyclonal antibodies induced in rabbits by immunization with poly(I), poly(dT) or poly(ADP-ribose) were not significantly dissociated from their immune complexes with relevant antigens or DNA by 0.5 M NaCl. The finding that nucleic acid antigens were not detached from a solid phase by washing with 0.5 M NaCl solution indicated that the reduction of binding of anti-DNA antibodies in both MoAbs and naturally occurring antibodies was really due to dissociation of the antibodies from immune complexes. This is the first demonstration that DNA epitopes recognized by naturally occurring antibodies in both SLE and its mouse models are sensitive to neutral NaCl concentrations. This novel trait of naturally occurring antibodies will be very useful in studies on the nature of immune complexes in sera and kidneys of cases of systemic lupus erythematosus (SLE).

Specificity of naturally occurring antibodies to poly(ADP-ribose) in patients with systemic lupus erythematosus: determination by an enzyme linked immunosorbent assay

Serum autoantibodies to poly(ADP-ribose), single-stranded (ss) DNA and double-stranded (ds) DNA in 145 patients with systemic lupus erythematosus (SLE) were measured by an enzyme-linked immunosorbent assay (ELISA). The specificities of the antibodies for poly(ADP-ribose) or for ssDNA in 14 serum samples from different patients, who had relatively high antibody titers to either or both these antigens, were tested by competitive ELISA with poly(ADP-ribose) and ssDNA as inhibitors. The IgG class anti-poly(ADP-ribose) antibodies of 4 serum samples (cases 9, 11, 13 and 14) preferred poly(ADP-ribose) and those of 2 samples (cases 2 and 4) cross-reacted preferentially with ssDNA, while the IgG class anti-ssDNA antibodies of 2 serum samples (cases 9 and 11) significantly cross-reacted with poly(ADP-ribose). Hence, the nature of the antibodies to poly(ADP-ribose) in SLE patients seemed to be different from that of the anti-poly(ADP-ribose) antibodies in autoimmune MRL/Mp-lpr/lpr (MRL/l) mice, which seem to be subpopulations of anti-ssDNA antibodies and react equally well with poly(ADP-ribose) and ssDNA.

Immunofluorescent staining of poly(ADP-ribose) in situ in HeLa cell chromosomes in the M phase

Randomly and synchronously growing HeLa cells were tested for poly(ADP-ribose) by direct and indirect immunofluorescent antibody techniques. Fluorescence of poly(ADP-ribose) was seen only in the nuclei of intact cells when the direct immunofluorescent antibody technique was used but in both the nuclei and cytoplasm when the indirect immunofluorescent antibody technique was used; fluorescence in the cytoplasm was nonspecific. When randomly or synchronously growing HeLa cells were fixed in acetone and treated with DNase I before incubation with fluorescein-labeled antibody, intense fluorescence was observed only in the nuclei when the direct immunofluorescent staining technique was used. Addition of 3-aminobenzamide, a potent inhibitor of poly(ADP-ribose) polymerase, with the DNase I completely abolished the fluorescence in the nuclei of synchronously and randomly growing HeLa cells, except in M-phase nuclei. These results suggest that poly(ADP-ribose) can be synthesized even in the nuclei of acetone-fixed HeLa cells from "endogenous NAD+" during incubation with fluorescent antibody and also that the fluorescence of chromosomes of HeLa cells in the M phase is, in fact, due to the in situ presence of poly(ADP-ribose), not to poly(ADP-ribose) synthesized during incubation with antibody.