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PubMed2005

Evolution from possible primitive tRNA-viroids to early poly-tRNA-derived mRNAs: a new approach from the poly-tRNA theory.

Poly-tRNA theory have revealed that the tRNA gene-clusters in the Bacillus subtilis trrnD- and rrnB-operons are relics of early peptide-synthesizing RNA apparatus. The trrnD-type and rrnB-type poly-tRNA models were re-analyzed by using recent databases. The results elucidated that the 16 amino acid (aa)-trrnD- and the 21 aa-rrnB-peptides (whose aa sequences are in the order of aa specificities of tRNAs in the respective tRNA cluster) are really relics of earliest peptides encoded by most primitive mRNAs, trrnD-mRNA and rrnB-mRNA, which are homologous to tRNA(Gly) and tRNA(His), respectively. Genes encoding various protein superfamilies (including pgtB protein, glycyl-tRNA synthetase alpha, C-type lectin, F1-ATP-synthase gamma, etc) were concluded to have derived from tRNA(Gly)-tRNA(Cys)-tRNA(Leu) region (including trrnD-mRNA region) in the trrnD-poly-tRNA. Genes for another group of protein superfamilies (including adenylate kinase, glyceraldehyde-3-phosphate dehydrogenase, helix-turn-helix DNA-binding domains, etc.) were found to have derived rrnB-mRNA, which is most plausibly homologous to a region containing the tRNA(His) of the rrnB-poly-tRNA. Thus Proto-tRNA((Gly)) reconstructed from tRNA(Gly) and other tRNAs strongly suggested that proto-tRNA was most plausibly a viroid-like possibly self-cleavable replicable ribozyme possessing a possible hammerhead-like structure.

Amino Acid Sequence↗
PubMed1990

Characterization and anticancer activity of the micelle-forming polymeric anticancer drug adriamycin-conjugated poly(ethylene glycol)-poly(aspartic acid) block copolymer.

Adriamycin (ADR), an anthracycline anticancer drug, was bound to the poly(aspartic acid) chain of poly(ethylene glycol)-poly(aspartic acid) block copolymer by amide bond formation between an amino group of Adriamycin and the carboxyl groups of the poly(aspartic acid) chain. The polymeric drug thus obtained was observed to form a micelle structure possessing diameter of approximately 50 nm, with a narrow distribution, in phosphate-buffered saline and to show excellent water solubility despite a large amount of ADR introduction. Further, it was able to be stored in lyophilized form without losing its water solubility in the redissolving procedure. Increased stability of the bound Adriamycin molecules in phosphate-buffered saline and elimination of binding affinity for bovine serum albumin due to the micelle formation were further advantages of this polymeric drug. In vivo high anticancer activity of this micelle-forming polymeric drug against P 388 mouse leukemia was obtained with less body weight loss than that seen with free ADR, due to low toxicity as compared with free ADR.

Animals↗
PubMed1994

Structure of an immunoglobulin Fab fragment specific for poly(dG).poly(dC).

Jel 72 is a murine monoclonal antibody that is highly specific for the right-handed DNA duplex formed by poly(dG).poly(dC). The three-dimensional structure of the antigen-binding fragment (Fab) of Jel 72 has been determined by x-ray crystallographic methods and refined to 2.7-A resolution. The structure has been determined using a combination of molecular replacement and multiple isomorphous replacement techniques. Crystals of Jel 72 contain two Fab fragments/asymmetric unit. The orientation of each of the four separate constant and variable domain pairs was determined from rotation function searches against appropriately oriented model Fab fragments. The rotated Fab domain pairs were placed within the unit cell using a phased translation search procedure with low resolution phases calculated from three derivatives. The two crystallographically independent Fab fragments possess "elbow" angles (relating the variable and constant domain pairs) that differ by 14 degrees (146 degrees versus 132 degrees). The shape and electrostatic surface potential of the combining site suggest a possible model for the recognition of double helical DNA. The model proposes that residues in the third hypervariable region of the heavy chain interact with the DNA bases via the major groove of poly(dG).poly(dC). This model may be applicable to the recognition of double-stranded DNA by autoimmune antibodies that occur in systemic lupus erythematosus.

Amino Acid Sequence↗
PubMed1981

A RNA.DNA hybrid that can adopt two conformations: an x-ray diffraction study of poly(rA).poly(dT) in concentrated solution or in fibers.

The RNA.DNA hybrid poly(rA).poly(dT) can adopt two conformations, depending upon its degree of hydration. Fibers yield a conventional A' RNA-like pattern at 79% relative humidity. In contrast, under highly solvated conditions this material yields an x-ray diffraction pattern with striking similarities to that of B DNA and clearly different from the RNA-like diffraction patterns previously obtained from fibers of other hybrids. A structural model is proposed for the solution form of the hybrid that has several similarities to models proposed for B DNA. The hybrid model accommodates the 2'-hydroxyl groups of the poly(rA) strand in intrachain hydrogen bonds to the adjacent ribose moieties.

Models, Chemical↗
PubMed1999

The yeast poly(A)-binding protein Pab1p stimulates in vitro poly(A)-dependent and cap-dependent translation by distinct mechanisms.

Translation initiation in extracts from Saccharomyces cerevisiae involves the concerted action of the cap-binding protein eIF4E and the poly(A) tail-binding protein Pab1p. These two proteins bind to translation initiation factor eIF4G and are needed for the translation of capped or polyadenylated mRNA, respectively. Together, these proteins synergistically activate the translation of a capped and polyadenylated mRNA. We have discovered that excess Pab1p also stimulates the translation of capped mRNA in extracts, a phenomenon that we define as trans-activation. Each of the above activities of Pab1p requires its second RNA recognition motif (RRM2). We have found that RRM2 from human PABP cannot substitute functionally for yeast RRM2. Using the differences between human and yeast RRM2 sequences as a guide, we have mutagenized yeast RRM2 and discovered residues that are required for eIF4G binding and poly(A)-dependent translation but not for trans-activation. Similarly, other residues within RRM2 were found to be required for trans-activation but not for eIF4G binding or poly(A)-dependent translation. These data show that Pab1p has at least two biochemically distinct activities in translation extracts.

Alleles↗
PubMed1987

Poly(ADP-ribose) synthase is the major endogenous nonhistone acceptor for poly(ADP-ribose) in alkylated rat hepatoma cells.

The endogenous poly(ADP-ribosyl)--nonhistone protein conjugates were isolated from dimethyl-sulfate-treated rat hepatoma AH 7974 cells using aminophenylboronic-acid--agarose chromatography. Seven major components could be discerned on dodecyl sulfate gels (molecular mass 43, 60, 66, 86, 100, 110 and 170 kDa) while control cells indicated only slight staining at above 200 kDa. The most abundant conjugate formed in response to alkylation damage was further purified using preparative gel electrophoresis and identified on the basis of its intrinsic enzymic activity as automodified poly(APD-ribose) synthase. In addition, topoisomerase I activity was found associated with a 60-kDa peptide. ADP-ribosylated endonuclease and actin were not detect-able. The purified conjugate fraction contained maximally 8.8 nmol/mg ADP-ribose and 7.9 nmol/mg oligo(ADP-ribose) with a mean chain length of 2.3 residues. The modifying (ADP-ribosyl)n groups were attached to its acceptors by a hydroxylamine-insensitive bond and had practically no effect on the DNA affinity of either poly(ADP-ribose) synthase or topoisomerase I.

Alkylating Agents↗
PubMed2005

Co-localization of poly(ADPR)polymerase 1 (PARP-1) poly(ADPR)polymerase 2 (PARP-2) and related proteins in rat testis nuclear matrix defined by chemical cross-linking.

Poly(ADPR)polymerase 1 and 2 (PARP-1, PARP-2) are nuclear enzymes which function is based on specific interactions with DNA and nuclear proteins. PARPs targets include proteins involved in DNA replication, repair, and transcription and their function can be modulated either by protein-protein interaction with native PARP-1 and by non-covalent interaction with poly(ADP-ribose) (pADPR) linked to the auto-modified PARP-1. Moreover, the association of pADPR and PARP-1 with the nuclear matrix (NM) has been reported, based on the poly(ADP-ribosyl)ation of nuclear matrix proteins (NMPs). In the present article, by the use of DNA and protein cross-linking reactions, by cis-diamminedichloroplatinum II (cDDP) and sodium tetrathionate (NaTT) respectively, we present more evidences about the association of PARP-1, PARP-2, and PARPs related proteins with the NM. Our findings confirmed that NM could be seen as a fraction greatly enriched in transcription factors (i.e., C/EBP-beta) and enzymes (DNA Topo II, DNA PK) that co-localize with PARP-1 and -2 at the matrix associated regions (MARs) of chromatin. Moreover, pADPR contributes to PARP-1 localization at the NM, showing that PARP(s) activity co-operates to the functions of this nuclear fraction.

Animals↗
PubMed1989

Analysis of the multiple 5' and 3' termini of poly(A)+ and poly(A)-deficient thymidylate synthase mRNA in growth-stimulated mouse fibroblasts.

Thymidylate synthase (TS) mRNA content increases about 20-fold when growth-stimulated mouse cells progress from the G0/G1 phase into the S phase of the cell cycle. Previous studies, using a cell line in which the TS gene is amplified (LU3-7), indicated that transcriptional initiation as well as polyadenylation of the mRNA occur at several locations in unsynchronized cells. In the present study, we have used S1 nuclease protection assays to analyze the possible significance of the multiple transcriptional initiation and polyadenylation sites. We found that the same pattern of 5' and 3' termini were detected with RNA isolated from the overproducing cells as with RNA isolated from the parental mouse 3T6 cell line, demonstrating that the heterogeneous termini are not a consequence of gene amplification. There was no change in the pattern of 5' or 3' termini with either cell line during the progression from G1 phase through S phase in serum-stimulated cells. Therefore, the increase in TS mRNA content is not the result of differential utilization of the various transcriptional initiation or polyadenylation sites. Analyses of poly(A)- deficient cytoplasmic TS RNA showed that the 5' termini were the same as those found in poly(A) + mRNA. However, the 3' termini were extremely heterogeneous in length. Although some of the poly(A)- deficient RNA extended beyond the normal site of polyadenylation, most of it was shorter than full-length TS mRNA.

Animals↗
PubMed1987

Cellular regulation of poly ADP-ribosylation of proteins. II. Augmentation of poly(ADP-ribose) polymerase in SV40 3T3 cells following methotrexate-induced G1/S inhibition of cell cycle progression.

SV40-3T3 cells were exposed in monolayer cultures to 5 X 10(-7) M methotrexate (MTX), that inhibited thymidylate synthetase, arrested cell growth without cell killing in 24 h and did not induce single- (ss) or double-strand (ds) breaks in DNA. Following 24, up to 72 h, the poly(ADP-ribose) polymerase content of attached cells was induced by 5 X 10(-7) M MTX and the augmentation of the enzyme increased with the time of exposure to the drug. Inhibition of protein or RNA synthesis abolished augmentation of enzymatic activity; so too did the initiation of maximal cell growth by thymidine + hypoxanthine, by-passing the inhibitory site of MTX. Isolation of the ADP-ribosylated enzyme protein by gel electrophoresis identified poly(ADP-ribose) polymerase protein as the molecule that was induced by 5 X 10(-7) M MTX. Under identical conditions, the poly(ADP-ribose) polymerase induction in 3T3 cells could not be demonstrated. A possible cell-cycle-dependent biosynthesis of the enzyme protein is proposed in SV40 3T3 cells.

Animals↗
PubMed1989

Poly(A), poly(A) binding protein and the regulation of mRNA stability.

This review has focused on the possibility that interactions between mRNA sequences and the poly(A)-nucleoprotein complex play important roles in mRNA turnover. It is important to stress that additional genetic and biochemical tests are necessary to characterize how PABP interacts with mRNA in cells and to determine whether the poly(A) protection hypothesis is accurate. Moreover, there may be a significant number of mRNAs whose half-lives are independent of polyadenylation. For example, the stabilities of poly(A)-containing and deadenylated alpha 2u-globulin and interferon mRNAs are similar in microinjected oocytes. Thus, an important challenge in this field will be to analyse the complex and interactive factors that determine the half-lives of specific mRNAs.

Carrier Proteins↗
PubMed1989

p66 an in vivo target for poly(ADP-ribosyl)ation co-purifies with poly(ADP-ribose) polymerase.

A direct immunoassay has been applied for the quantitation of poly(ADP-ribose) polymerase and its automodification in BALB/3T3 (A31) cells. As the cell population reached a high density, a 66 kDa protein (designated p66) which co-purified with the enzyme became highly poly(ADP-ribosyl)ated. Pulse-chase experiments as well as a Western blot analysis indicated that the p66 was not a degradation product of poly(ADP-ribose) polymerase.

Adenosine Diphosphate Ribose↗
PubMed2003

Ribosome-inactivating proteins depurinate poly(ADP-ribosyl)ated poly(ADP-ribose) polymerase and have transforming activity for 3T3 fibroblasts.

It has been known that ribosome-inactivating proteins (RIPs) from plants damage ribosomes by removing adenine from a precise position of rRNA. Subsequently it was observed that all tested RIPs depurinate DNA, and some of them also non-ribosomal RNAs and poly(A), hence the denomination of adenine polynucleotide glycosylases was proposed. We report now that ricin, saporin-L2, saporin-S6, gelonin and momordin depurinate also poly(ADP-ribosyl)ated poly(ADP-ribose) polymerase (auto modified enzyme), an enzyme involved in DNA repair. We observed also that all RIPs but gelonin induce transformation of fibroblasts, possibly as a consequence of damage to DNA and of the altered DNA repair system.

3T3 Cells↗
PubMed2002

Dinucleoside polyphosphates stimulate the primer independent synthesis of poly(A) catalyzed by yeast poly(A) polymerase.

Novel properties of the primer independent synthesis of poly(A), catalyzed by the yeast poly(A) polymerase are presented. The commercial enzyme from yeast, in contrast to the enzyme from Escherichia coli, is unable to adenylate the 3'-OH end of nucleosides, nucleotides or dinucleoside polyphosphates (NpnN). In the presence of 0.05 mm ATP, dinucleotides (at 0.01 mm) activated the enzyme velocity in the following decreasing order: Gp4G, 100; Gp3G, 82; Ap6A, 61; Gp2G, 52; Ap4A, 51; Ap2A, 41; Gp5G, 36; Ap5A, 27; Ap3A, 20, where 100 represents a 10-fold activation in relation to a control without effector. The velocity of the enzyme towards its substrate ATP displayed sigmoidal kinetics with a Hill coefficient (nH) of 1.6 and a Km(S0.5) value of 0.308 +/- 0.120 mm. Dinucleoside polyphosphates did not affect the maximum velocity (Vmax) of the reaction, but did alter its nH and Km(S0.5) values. In the presence of 0.01 mm Gp4G or Ap4A the nH and Km(S0.5) values were (1.0 and 0.063 +/- 0.012 mm) and (0.8 and 0.170 +/- 0.025 mm), respectively. With these kinetic properties, a dinucleoside polyphosphate concentration as low as 1 micro m may have a noticeable activating effect on the synthesis of poly(A) by the enzyme. These findings together with previous publications from this laboratory point to a potential relationship between dinucleoside polyphosphates and enzymes catalyzing the synthesis and/or modification of DNA or RNA.

Adenosine Triphosphate↗
PubMed1993

Diethylnitrosamine administration in vivo increases hepatic poly(ADP-ribose) levels in rats: results of a modified technique for poly(ADP-ribose) measurement.

Poly(ADP-ribose) (polymer) is enzymatically synthesized on nuclear proteins in response to DNA strand breaks. NAD+ is the substrate for this reaction, which is catalyzed by poly(ADP-ribose)polymerase. This post-translational modification occurs in response to DNA strand breaks and is thought to play an important role in DNA repair. Polymer synthesis resulting from DNA damage has been described in cultured cells, but measurement is more difficult in animal tissues. In this study, modifications were made to an earlier method to measure carcinogen-induced increases in polymer levels in vivo. RNase I was added to the enzyme mixture used to digest polymer to ribosyladenosine (RAdo). This prevented the inhibition of snake venom phosphodiesterase by RNA. The HPLC analysis was improved, allowing elimination of the second boronate affinity chromatography step traditionally used to purify epsilon RAdo. Using this technique, we have studied the effect of i.p. diethylnitrosamine (DEN) injection on hepatic NAD+ and poly(ADP-ribose) levels in Fischer-344 rats. Hepatic polymer levels rose 8-fold from 26 to 218 pmol/g liver wet weight, 10 h following 200 mg DEN/kg body weight (n = 4-5). Liver NAD+ decreased concurrently, to 61% of basal levels at 16 h post-treatment (n = 4-5). Erythrocyte NAD+ concentrations remained unchanged, despite carcinogen administration. The DEN-induced effects on tissue polymer and NAD+ levels were dose dependent from 0 to 200 mg DEN/kg body weight (n = 4).

Animals↗
PubMed1990

DNA with adenine tracts contains poly(dA).poly(dT) conformational features in solution.

The conformation of DNA's with adenine-thymine tracts exhibiting retardation in electrophoretic migration and considered as curved were investigated in solution by CD and RAMAN spectroscopy. The following curved multimers with adenine tracts but of different flanking sequences d(CA5TGCC)n, d(TCTCTA6TATATA5)n, d(GA4T4C)n yield CD spectroscopic features indicating a non-B structure of the dA.dT tract with similarities to polyd(A).polyd(T). We suggest that adenine-thymine bases in these multimers contain some of the distinctive conformational features of poly(A).polyd(T) probably with large propeller twist found by NMR (Behling and Kearns, 1987) and by X-ray diffraction on oligonucleotides containing a tract of adenines (Nelson et al. 1987, Coll et al; 1987; DiGabriele et al. 1989). Some elements of distinctive CD features of the contiguous adenines run are also observed in the straight multi-9-mer d(CA5GCC)n which lacks in-phase relation to the helical repeat. Despite the presence of the TpA step in the straight multimer d(GT4A4)n, the altered dA.dT conformation is not completely destroyed. Interruption of adenine tract by a guanine in d(CAAGAATGCC)n leads to a B-like conformation and to a normal electrophoretic mobility. The Raman spectra reveal a rearrangement of the sugar-phosphate backbone of dA.dT tract in the multimer d(CA5TGCC)n with respect to that of polydA.polydT. This is reflected in the presence of an unique Raman band associated to C2'-endo sugar with a predominant contribution of C1'-exo puckering which is exhibited by the multimer whereas two distinct Raman bands characterize poly(dA).poly(dT) backbone conformation.

Adenine↗
PubMed1983

Synthesis and biological activity of polyriboadenylic acid: polyribo-5-dimethylaminouridylic acid hybrid (poly(A): poly(Me2N5U)).

Poly-5-dimethylaminouridylic acid, (poly(Me2N5U)) has been synthesized by the conversion of 5-bromouridine-5'-monophosphate to 5-dimethylaminouridine-5'-monophosphate which was later made into the 5'-diphosphate and subsequently polymerized by PNPase. The polymer formed a 1:1 hybrid with poly(A) with the ability to induce the production of interferon in chick embryoes as certain doses of the hybrid protected chick embryoes against wesselsbron virus (H 10964).

Animals↗
PubMedDate not supplied

Effects of Poly A. Poly U in vivo alterations of proportions of T and B cell subsets.

Spleens and thymuses of mice were examined for changes in lymphocyte subpopulations after in vivo treatment with a double stranded synthetic polynucleotide: Poly A.Poly U. The cell populations were characterized on a biophysical basis: the electrical charge of cell surface assessed by the anodic electrophoretic mobility. The proportion of spleen cells exhibiting a high electrophoretic mobility (T lymphocytes) increased markedly on the 3rd day after a single intravenous injection of Poly A.Poly U. In thymuses, early important variations in electrophoretic distribution profiles were observed after Poly A.Poly U injection, suggesting that adjuvant acts on T cells.

Animals↗