scholarly journals The effect of APOBEC3B deaminase on double-stranded DNA

2019 ◽  
Author(s):  
Joseph Chapman ◽  
Michael Custance ◽  
Birong Shen ◽  
Anthony V. Furano
Keyword(s):  
Mammalian Cells ◽  
Chemotherapeutic Agents ◽  
Double Stranded Dna ◽  
Cancer Initiation ◽  
Development Accounting ◽  
Elevated Expression ◽  
Ap Sites ◽  
Hydrolysis Of ◽  
Ap Site

ABSTRACTMutations mediated by the APOBEC3 (A3) family of single-strand specific cytosine deaminases can accumulate in various cancers, as strand-coordinated clusters and isolated lesions. A3-mediated mutations also occur during normal development, accounting for ~20% of heritable mutations. A3B is an archetypical member of this family and is thought to contribute to both cancer initiation and progression. A3B has a strong preference for C in a TC context and catalyzes hydrolysis of the primary amine of un-paired C to generate U. Subsequent repair generates a distinctive pattern of C-substitutions, which along with their context signify their A3B origin. Although single-stranded DNA is the preferred A3B substrate, we report here that in some instances A3B can deaminate the C of TC in a double-stranded DNA context in vitro. These include C paired to O6-methylguanine (O6meG), to an abasic (AP) site, or to a G adjacent to an AP site. AP sites are the most common lesion in DNA, and O6meG levels increase under alkylating conditions caused by environmental nitrosamines and some chemotherapeutic agents. We also show that elevated expression of A3B can enhance double-stranded breaks induced by the alkylating agent MNNG in mammalian cells, but this effect does not require A3B deaminase activity.

scholarly journals Repair of abasic sites by mammalian cell extracts

1994 ◽  
Vol 304 (3) ◽  
pp. 699-705 ◽  
Author(s):  
G Frosina ◽  
P Fortini ◽  
O Rossi ◽  
F Carrozzino ◽  
A Abbondandolo ◽  
...  
Keyword(s):  
Mammalian Cells ◽  
Excision Repair ◽  
Chinese Hamster ◽  
Pyrimidine Dimer ◽  
Repair Synthesis ◽  
Repair Patch ◽  
Cell Extracts ◽  
Pyrimidine Dimers ◽  
Ap Sites ◽  
Ap Site

Hamster cell extracts that perform repair synthesis on covalently closed circular DNA containing pyrimidine dimers, were used to study the repair of apurinic/apyrimidinic (AP) sites and methoxyamine (MX)-modified AP sites. Plasmid molecules were heat-treated at pH 5 and incubated with MX when required. The amount of damage introduced ranged from 0.2 to 0.9 AP sites/kb. Extracts were prepared from the Chinese hamster ovary CHO-9 cell line and from its derivative, 43-3B clone which is mutated in the nucleotide excision repair (NER) ERCC1 gene. AP and MX-AP sites stimulated repair synthesis by CHO-9 cell extracts. The level of synthesis correlated with the number of lesions and was of similar magnitude to the repair stimulated by 4.3 u.v. photoproducts/kb. Repair of AP and MX-AP sites was faster than the repair of u.v. damage and was independent of ERCC1 gene product. The high level of repair replication was due to a very efficient and rapid incision of plasmids carrying AP or MX-AP sites, performed by abundant AP endonucleases present in the extract. The calculated average repair patch sizes were: 7 nucleotides per AP site; 10 nucleotides per MX-AP site; 28 nucleotides per (6-4) u.v. photoproduct or cyclobutane pyrimidine dimer. The data indicate that AP and MX-AP sites are very efficiently repaired by base-excision repair in mammalian cells and suggest that MX-AP sites may also be processed via alternative repair mechanisms.

scholarly journals Molecular basis of abasic site sensing in single-stranded DNA by the SRAP domain of E. coli yedK

2019 ◽  
Vol 47 (19) ◽  
pp. 10388-10399 ◽  
Author(s):  
Na Wang ◽  
Hongyu Bao ◽  
Liu Chen ◽  
Yanhong Liu ◽  
Yue Li ◽  
...  
Keyword(s):  
Molecular Basis ◽  
Substrate Binding ◽  
Specific Substrate ◽  
Abasic Site ◽  
E Coli ◽  
Abasic Sites ◽  
Ap Sites ◽  
Ap Site

Abstract HMCES and yedK were recently identified as sensors of abasic sites in ssDNA. In this study, we present multiple crystal structures captured in the apo-, nonspecific-substrate-binding, specific-substrate-binding, and product-binding states of yedK. In combination with biochemical data, we unveil the molecular basis of AP site sensing in ssDNA by yedK. Our results indicate that yedK has a strong preference for AP site-containing ssDNA over native ssDNA and that the conserved Glu105 residue is important for identifying AP sites in ssDNA. Moreover, our results reveal that a thiazolidine linkage is formed between yedK and AP sites in ssDNA, with the residues that stabilize the thiazolidine linkage important for the formation of DNA-protein crosslinks between yedK and the AP sites. We propose that our findings offer a unique platform to develop yedK and other SRAP domain-containing proteins as tools for detecting abasic sites in vitro and in vivo.

scholarly journals Zinc(II)-Dipicolylamine Coordination Complexes as Targeting and Chemotherapeutic Agents for Leishmania major

2016 ◽  
Vol 60 (5) ◽  
pp. 2932-2940 ◽  
Author(s):  
Douglas R. Rice ◽  
Paola Vacchina ◽  
Brianna Norris-Mullins ◽  
Miguel A. Morales ◽  
Bradley D. Smith
Keyword(s):  
Cutaneous Leishmaniasis ◽  
Mammalian Cells ◽  
Leishmania Major ◽  
Parasite Burden ◽  
Coordination Complexes ◽  
Chemotherapeutic Agents ◽  
Selective Toxicity ◽  
Content Type

ABSTRACTCutaneous leishmaniasis is a neglected tropical disease that causes painful lesions and severe disfigurement. Modern treatment relies on a few chemotherapeutics with serious limitations, and there is a need for more effective alternatives. This study describes the selective targeting of zinc(II)-dipicolylamine (ZnDPA) coordination complexes towardLeishmania major, one of the species responsible for cutaneous leishmaniasis. Fluorescence microscopy ofL. majorpromastigotes treated with a fluorescently labeled ZnDPA probe indicated rapid accumulation of the probe within the axenic promastigote cytosol. The antileishmanial activities of eight ZnDPA complexes were measured using anin vitroassay. All tested complexes exhibited selective toxicity againstL. majoraxenic promastigotes, with 50% effective concentration values in the range of 12.7 to 0.3 μM. Similar toxicity was observed against intracellular amastigotes, but there was almost no effect on the viability of mammalian cells, including mouse peritoneal macrophages.In vivotreatment efficacy studies used fluorescence imaging to noninvasively monitor changes in the red fluorescence produced by an infection of mCherry-L. majorin a mouse model. A ZnDPA treatment regimen reduced the parasite burden nearly as well as the reference care agent, potassium antimony(III) tartrate, and with less necrosis in the local host tissue. The results demonstrate that ZnDPA coordination complexes are a promising new class of antileishmanial agents with potential for clinical translation.

scholarly journals δ-elimination in the repair of AP (apurinic/apyrimidinic) sites in DNA

1989 ◽  
Vol 261 (3) ◽  
pp. 707-713 ◽  
Author(s):  
V Bailly ◽  
M Derydt ◽  
W G Verly
Keyword(s):  
Mammalian Cells ◽  
Nuclear Dna ◽  
Replicative Form ◽  
Dna Polymerization ◽  
E Coli ◽  
Polynucleotide Kinase ◽  
Ap Sites ◽  
Beta Elimination ◽  
Repair Pathways ◽  
Hydrolysis Of

[5′-32P]pdT8d(-)dT7, containing an AP (apurinic/apyrimidinic) site in the ninth position, and [d(-)-1′,2′-3H, 5′-32P]DNA, containing AP sites labelled with 3H in the 1′ and 2′ positions of the base-free deoxyribose [d(-)] and with 32P 5′; to this deoxyribose, were used to investigate the yields of the beta-elimination and delta-elimination reactions catalysed by spermine, and also the yield of hydrolysis, by the 3′-phosphatase activity of T4 polynucleotide kinase, of the 3′-phosphate resulting from the beta delta-elimination. Phage-phi X174 RF (replicative form)-I DNA containing AP (apurinic) sites has been repaired in five steps: beta-elimination, delta-elimination, hydrolysis of 3′-phosphate, DNA polymerization and ligation. Spermine, in one experiment, and Escherichia coli formamidopyrimidine: DNA glycosylase, in another experiment, were used to catalyse the first and second steps (beta-elimination and delta-elimination). These repair pathways, involving a delta-elimination step, may be operational not only in E. coli repairing its DNA containing a formamido-pyrimidine lesion, but also in mammalian cells repairing their nuclear DNA containing AP sites.

scholarly journals Differential cytotoxicity of iron chelators on malaria-infected cells versus mammalian cells

Blood ◽  
1996 ◽  
Vol 87 (11) ◽  
pp. 4871-4878 ◽  
Author(s):  
H Glickstein ◽  
W Breuer ◽  
M Loyevsky ◽  
AM Konijn ◽  
A Shanzer ◽  
...  
Keyword(s):  
Mammalian Cells ◽  
Chemotherapeutic Agents ◽  
Iron Chelators ◽  
Intracellular Iron ◽  
In Vitro Proliferation ◽  
Ic50 Values ◽  
Infected Cells ◽  
Cell Cytosol ◽  
Improved Design

Iron chelators of the hydroxamate class arrest in vitro proliferation of malaria parasites end of mammalian cells. The factors determining the biological activity of the chelators have classically been attributed to the chelators' capacity for binding iron and to their ability to traverse membranes as free chelators and as chelator-iron complexes. We show in this work that the nature of the chelatable pool of cell iron also contributes to the susceptibility of cells to iron chelators. A class of N-terminal (Nt derivatives of desferrioxamine (DFO), (Nt-DFO), is shown here to differentially affect growth and replication of intraerythrocytic parasites (Plasmodium falciparum). Methyl-anthranilic DFO (MADFO), the relatively less hydrophilic member of the Nt-DFOs series, reduced parasite proliferation (48 hour test) with an IC50 of 4 +/- 1 micromol/L and mammalian cell (K562 and HepG2) proliferation with an IC50 > 100 micromol/L. On the other hand, the more hydrophilic Nt-free DFO, displayed IC50 values of 21 +/- 5 micromol/L for parasites and 7 +/- 1 micromol/L for mammalian cells. The selective antiparasitic activity of MA-DFO, as reflected in the speed of action and IC50 values on cell proliferation, is attributed primarily to membrane permeation and iron (III) binding properties of the drug. In contrast, the relatively low antiproliferative activity of the more permeant MA-DFO on mammalian cells, resulted from MA-DFO's reduced capacity for scavenging intracellular iron. This is apparent from MA-DFO reduced effects on: (1) the chelatable iron (II) pool that is associated with the cell cytosol; (2) the cell chelator-extractable iron, and (3) cell ferritin levels. The potent antimalarial efficacy and biological selectivity of MA-DFO relative to the parent DFO, is of importance for improved design of chemotherapeutic agents.

scholarly journals Mammalian Nudix proteins cleave nucleotide metabolite caps on RNAs

2020 ◽  
Vol 48 (12) ◽  
pp. 6788-6798 ◽  
Author(s):  
Sunny Sharma ◽  
Ewa Grudzien-Nogalska ◽  
Keith Hamilton ◽  
Xinfu Jiao ◽  
Jun Yang ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Nicotinamide Adenine Dinucleotide ◽  
Mammalian Cells ◽  
Flavin Adenine Dinucleotide ◽  
Nicotinamide Adenine ◽  
Nudix Hydrolase ◽  
Decapping Enzymes ◽  
Hydrolysis Of ◽  
In Cells

Abstract We recently reported the presence of nicotinamide adenine dinucleotide (NAD)-capped RNAs in mammalian cells and a role for DXO and the Nudix hydrolase Nudt12 in decapping NAD-capped RNAs (deNADding) in cells. Analysis of 5′caps has revealed that in addition to NAD, mammalian RNAs also contain other metabolite caps including flavin adenine dinucleotide (FAD) and dephosphoCoA (dpCoA). In the present study we systematically screened all mammalian Nudix proteins for their potential deNADing, FAD cap decapping (deFADding) and dpCoA cap decapping (deCoAping) activity. We demonstrate that Nudt16 is a novel deNADding enzyme in mammalian cells. Additionally, we identified seven Nudix proteins—Nudt2, Nudt7, Nudt8, Nudt12, Nudt15, Nudt16 and Nudt19, to possess deCoAping activity in vitro. Moreover, our screening revealed that both mammalian Nudt2 and Nudt16 hydrolyze FAD-capped RNAs in vitro with Nudt16 regulating levels of FAD-capped RNAs in cells. All decapping activities identified hydrolyze the metabolite cap substrate within the diphosphate linkage. Crystal structure of human Nudt16 in complex with FAD at 2.7 Å resolution provide molecular insights into the binding and metal-coordinated hydrolysis of FAD by Nudt16. In summary, our study identifies novel cellular deNADding and deFADding enzymes and establishes a foundation for the selective functionality of the Nudix decapping enzymes on non-canonical metabolite caps.

scholarly journals Deoxyribonuclease IV from rat liver chromatin and the excision of apurinic sites from depurinated DNA

1985 ◽  
Vol 225 (2) ◽  
pp. 535-542 ◽  
Author(s):  
G Grondal-Zocchi ◽  
W G Verly
Keyword(s):  
Rat Liver ◽  
Liver Cells ◽  
Ap Endonuclease ◽  
Phosphodiester Bond ◽  
Double Stranded Dna ◽  
Rat Liver Cells ◽  
Liver Chromatin ◽  
Ap Sites ◽  
Beta Elimination ◽  
Hydrolysis Of

Deoxyribonuclease IV, a 5′-3′ exonuclease degrading double-stranded DNA from intra-strand nicks, has been purified from the chromatin of rat liver cells. The enzyme, which has an Mr of 58000, excises the apurinic (AP) sites from a depurinated DNA nicked 5′ to these AP sites with the chromatin AP endonuclease. The excision is not the result of hydrolysis of the phosphodiester bond 3′ to the AP sites since the excision product does not behave as deoxyribose 5-phosphate but as its 2,3-unsaturated derivative. This result suggests that, to remove the AP sites from the DNA nicked by an AP endonuclease, the chromatin deoxyribonuclease IV rather acts as a catalyst of beta-elimination.

scholarly journals Construction of High Content Nanobody Library in Mammalian Cells by Linear-double-stranded DNA Based Strategies

2020 ◽  
Author(s):  
Yanjie Zhao ◽  
Weijun Su ◽  
Shuai Li
Keyword(s):  
Cell Lines ◽  
High Throughput ◽  
Mammalian Cells ◽  
High Throughput Sequencing ◽  
Full Length ◽  
Expression Cassette ◽  
Cultured Cell ◽  
Double Stranded Dna ◽  
Novel Methods

AbstractHere, we developed two novel methods to construct high content nanobody library in mammalian cells. For the first method, we employed a linear-double-stranded DNA based AND-gate (LBAG) strategy. Upstream- and downstream-linear-double-stranded DNAs (ldsDNAs), containing identical overlapping sequences, were co-transfected into cultured cell lines to conduct AND-gate calculation to form intact nanobody expression cassette. For the second method, we generated full-length nanobody expression ldsDNA by in vitro ligation of restrict cut up- and down-stream ldsDNAs. Then the ldsDNAs were directly transfected into mammalian cells to express nanobody library. Both methods generated over a million different nanobody sequences as revealed by high-throughput sequencing (HTS).

scholarly journals Possible roles of β-elimination and δ-elimination reactions in the repair of DNA containing AP (apurinic/apyrimidinic) sites in mammalian cells

1988 ◽  
Vol 253 (2) ◽  
pp. 553-559 ◽  
Author(s):  
V Bailly ◽  
W G Verly
Keyword(s):  
Mammalian Cells ◽  
Free Sugar ◽  
Ap Endonuclease ◽  
Phosphodiester Bond ◽  
Polymerase Beta ◽  
Beta Elimination ◽  
Elimination Reactions ◽  
The One ◽  
Ap Site

Histones and polyamines nick the phosphodiester bond 3′ to AP (apurinic/apyrimidinic) sites in DNA by inducing a beta-elimination reaction, which can be followed by delta-elimination. These beta- and delta-elimination reactions might be important for the repair of AP sites in chromatin DNA in either of two ways. In one pathway, after the phosphodiester bond 5′ to the AP site has been hydrolysed with an AP endonuclease, the 5′-terminal base-free sugar 5′-phosphate is released by beta-elimination. The one-nucleotide gap limited by 3′-OH and 5′-phosphate ends is then closed by DNA polymerase-beta and DNA ligase. We have shown in vitro that such a repair is possible. In the other pathway, the nicking 3′ to the AP site by beta-elimination occurs first. We have shown that the 3′-terminal base-free sugar so produced cannot be released by the chromatin AP endonuclease from rat liver. But it can be released by delta-elimination, leaving a gap limited by 3′-phosphate and 5′-phosphate. After conversion of the 3′-phosphate into a 3′-OH group by the chromatin 3′-phosphatase, there will be the same one-nucleotide gap, limited by 3′-OH and 5′-phosphate, as that formed by the successive actions of the AP endonuclease and the beta-elimination catalyst in the first pathway.

scholarly journals dl-α-difluoromethyl[3,4-3H]arginine metabolism in tobacco and mammalian cells. Inhibition of ornithine decarboxylase activity after arginase-mediated hydrolysis of dl-α-difluoromethylarginine to dl-α-difluoromethylornithine

1988 ◽  
Vol 255 (1) ◽  
pp. 197-202 ◽  
Author(s):  
R D Slocum ◽  
A J Bitonti ◽  
P P McCann ◽  
R P Feirer
Keyword(s):  
Ornithine Decarboxylase ◽  
Mammalian Cells ◽  
Selective Inhibition ◽  
Arginine Decarboxylase ◽  
Decarboxylase Activity ◽  
Irreversible Inhibitor ◽  
Hydrolysis Of ◽  
Analogous Mechanism

DL-alpha-Difluoromethylarginine (DFMA) is an enzyme-activated irreversible inhibitor of arginine decarboxylase (ADC) in vitro. DFMA has also been shown to inhibit ADC activities in a variety of plants and bacteria in vivo. However, we questioned the specificity of this inhibitor for ADC in tobacco ovary tissues, since ornithine decarboxylase (ODC) activity was strongly inhibited as well. We now show that [3,4-3H]DFMA is metabolized to DL-alpha-difluoromethyl[3,4-3H]ornithine [(3,4-3H]DFMO), the analogous mechanism-based inhibitor of ODC, by tobacco tissues in vivo. Both tobacco and mammalian (mouse, bovine) arginases (EC 3.5.3.1) hydrolyse DFMA to DFMO in vitro, suggesting a role for this enzyme in mediating the indirect inhibition of ODC by DFMA in tobacco. These results suggest that DFMA may have other effects, in addition to the inhibition of ADC, in tissues containing high arginase activities. The recent development of potent agmatine-based ADC inhibitors should permit selective inhibition of ADC, rather than ODC, in such tissues, since agmatine is not a substrate for arginase.

Sign in / Sign up

Export Citation Format

Share Document