Poly(ADP-ribose) polymerase-1: A Regulator of Protein–Nucleic Acid Interactions in Processes Responding to Genotoxic Impact

Poly(ADP-ribose) polymerase-1 (PARP-1), a nuclear protein of higher eukaryotes, specifically detects strand breaks in DNA. The enzyme is activated in the presence of such breaks and synthesizes poly(ADP-ribose) covalently bound to certain proteins, with PARP-1 itself being the main acceptor. This protein is involved in the majority of DNA-dependent processes, including replication, recombination, repair, and cell death (apoptosis and necrosis). Poly(ADP-ribosyl)ation of proteins is regarded as a mechanism which induces a signal of DNA damage and modulates the function of proteins in response to genotoxic actions. Attention in this review is focused on the role of PARP-1 and poly(ADP-ribosyl)ation in base excision repair (BER), the main process of DNA break repair. The main putative functions of PARP-1 in this process are also considered, namely, its functions as a factor initiating the BER protein complex, a temporary protector of DNA ends, a factor modulating chromatin structure through poly(ADP-ribosyl)ation of histones, and a signal in the mechanism recognizing the degree of DNA damage in the cell.     

5'-Deoxyribose Phosphate Lyase Activity of Apurinic/Apyrimidinic Endonuclease 1

Molecular Biology - One of the most common DNA lesions is the appearance of apurinic/apyrimidinic (AP-) sites. The main repair pathway for AP sites is initiated by apurinic/apyrimidinic...     

Interactome of Base and Nucleotide Excision DNA Repair Systems

Molecular Biology - The base and nucleotide excision DNA repair (BER and NER) systems are aimed at removing specific types of damaged DNA, i.e., oxidized, alkylated, or deaminated bases in the case...     

A New DNA Break Repair Pathway Involving PARP3 and Base Excision Repair Proteins

Poly(ADP-ribosyl)ation, which is catalyzed by PARP family proteins, is one of the main reactions in the cell response to genomic DNA damage. Massive impact of DNA-damaging agents (such as oxidative stress and ionizing radiation) causes numerous breaks in DNA. In this case, the development of a fast cell response, which allows the genomic DNA integrity to be retained, may be more important than the repair by more accurate but long-term restoration of the DNA structure. This is the first study to show the possibility of eliminating DNA breaks through their PARP3-dependent mono(ADP-ribosyl)ation followed by ligation and repair of the formed ribo-AP sites by the base excision repair (BER) enzyme complex. Taken together, the results of the studies on ADP-ribosylation of DNA and the data obtained in this study suggest that PARP3 may be a component of the DNA break repair system involving the BER enzyme complex.     

Modification of phenylalanyl-tRNA-synthetase from Escherichia coli MRE600 by adenosine-5'-trimetaphosphate

Modification of phenylalanyl-tRNA synthetase from E. coli MRE600 by adenosine-5'-trimetaphosphate, phosphorylating analog of ATP was shown to bring about the enzyme inactivation in the reactions of tRNA aminoacylation and ATP-[32P]pyrophosphate exchange. ATP when added in the reaction mixture protects the enzyme against inactivation in both reactions and decreases the level of covalent attachment of the analog. Phenylalanine has no protective effect. tRNA exhibits slight protective effect. Adenosine-5'-trimetaphosphate modifies both types (alpha and beta) of subunits of phenylalanyl-tRNA synthetase which is of alpha 2 beta 2 structure. ATP protects both types of the enzyme subunits against the covalent attachment of the analog. Disposition of the ATP-binding centers in the contact region of the nonequivalent subunits of the enzyme was proposed. The level of covalent attachment of the analog to the enzyme exceeds the number of the enzyme active sites that may be a consequence of the other nucleotide-binding center labeling.     

Peritrophic membrane structure and formation in the larva of a moth, Heliothis

The peritrophic membrane (PM) in tobacco budworm larvae (Heliothis virescens, Lepidoptera: Noctuidae), is a continuous sac which encloses the food bolus in the midgut and hindgut. The PM is a single-walled structure 3-5 mum thick which is comprised of two main layers or laminae. The laminae may be fused into a single structure or remain separated by a space which may contain additional thin strands of matrix. Staining with an anti-PM antibody and wheat germ agglutinin (WGA) illustrate the laminar nature of the PM and suggest that protein and chitin have co-incident spatial distributions within the matrix. By transmission electron microscopy, the PM is composed of a loose network of fibrils and small granules, the only structural difference among laminae being a compaction of the matrix along the edges of the two limiting laminae facing the endoperitrophic and ectoperitrophic spaces. By scanning electron microscopy, the PM surface has a wrinkled, felt-like texture without pores or slits. Contrary to the classical view that lepidopterans are Type I insects with respect to PM formation in which the PM forms along the full length of the midgut, the PM in the tobacco budworm forms primarily from secretions of specialized midgut epithelial cells at the junction of the foregut and midgut. The secretory cells, their secretions and the nascent PM stain intensely with the anti-PM antibody but not with WGA suggesting that chitin is added more posteriorly. The PM may be supplemented by the addition of minor amounts of matrix material along the length of the midgut. PM synthesis begins during embryogenesis prior to the initiation of feeding. The PM in neonates is only about 0.1 mum thick but otherwise is structurally similar to that in older larvae.     

A method for purification of peptides from hydrolysates of proteins modified by chemically active analogues of substrates containing cis-diol groups

A simple and rapid column procedure is described for the isolation from protein hydrolysates of peptides containing covalently bound substrate analogues with cis-diol groups. The method is based on complex formation between the cis-diol groups of peptide-bound compounds and dihydroxyborylic groups of a dihydroxyborylaminoethyl cellulose column. The method is useful for isolation of peptide(s) located in or near the active centre of enzymes after their affinity labelling by chemically active analogues of natural substrates like ribonucleotides, sugars, etc.Abbreviations used azido-ATP -(n-azidoanilide)-ATP - CME-carbodiimide N-cyclohexyl-N--(4-methylmorpholinium)-ethylcarbodiimide - DBAE-cellulose dihydroxyborylaminoethyl cellulose - DTT dithiotreitol - PheRSase phenylalanyl-tRNA synthetase - TRSase tryptophanyl-tRNA synthetase     

A new highly efficient photoreactive analogue of dCTP. Synthesis, characterization, and application in photoaffinity modification of DNA binding proteins

A new base-substituted analogue of dCTP, exo-N-{2-[N-(4-azido-2,5-difluoro-3-chloropyridine-6-yl)-3-aminopropionyl]aminoethyl}-2'-deoxycytidine-5'-triphosphate (FAP-dCTP) has been synthesized and characterized. FAP-dCTP is an efficient substrate of mammalian DNA polymerase beta in the reaction of primer elongation displaying substrate properties as an analogue of dCTP and dTTP. FAP-dCTP was used for the photoaffinity modification of mammalian DNA polymerase beta. Two approaches to photoaffinity labeling were utilized. In one approach, photoreactive FAP-dCTP was first incorporated into radiolabeled primer-template, and photoreactive DNA was UV-irradiated in the presence of DNA polymerase beta, which resulted in the polymerase labeling by photoreactive primer. In an alternate approach, FAP-dCTP was first UV-cross-linked to the enzyme; subsequently, radiolabeled primer-template was added, and the enzyme-linked FAP-dCTP was incorporated into the 3'-end of radioactive primer. This "catalytic" modification pathway was shown to be less specific in recognition of FAP-dCTP as an analogue of dCTP than dTTP. FAP-dCTP was used as substrate of endogenous DNA polymerases of HeLa cell extract to synthesize photoreactive DNAs for photoaffinity modification of cell proteins. UV irradiation results in modification of DNA binding proteins of cell extract. The level of photoaffinity labeling of protein targets in the cell extract was strongly dependent on the efficiency of synthesis of photoreactive DNA.     

Interaction of Replication Protein A with Photoreactive DNA Structures

A new photoreactive oligonucleotide derivative was synthesized with a perfluoroarylazido group attached to the 2'-position of the ribose fragment of the 5'-terminal nucleotide. Using this conjugate, photoreactive DNA duplexes were produced which contained single-stranded regions of different length, single-stranded breaks (nicks), and also ds duplex with a photoreactive group inside one of the chains. These structures imitate DNA intermediates generated at different stages of DNA replication and repair. The interaction of replication protein A (RPA) with the resulting DNA structures was studied using photoaffinity modification and gel retardation assay. Independently of the DNA structure, only the large subunit of RPA (p70) was crosslinked to photoreactive DNAs, and the intensity of its labeling increased with decrease in the size of the single-stranded region and was maximal in the case of the nick-containing DNA structure. By gel retardation, the most effective binding of RPA to this structure was shown, whereas the complexing of RPA with DNA containing the unmodified nick and also with the full duplex containing the photoreactive group inside the chain was significantly less effective. The data suggest that RPA should be sensitive to such damages in the double-stranded DNA structure.