PARP1–TDP1 coupling for the repair of topoisomerase I–induced DNA damage

Poly(ADP-ribose) polymerases (PARP) attach poly(ADP-ribose) (PAR) chains to various proteins including themselves and chromatin. Topoisomerase I (Top1) regulates DNA supercoiling and is the target of camptothecin and indenoisoquinoline anticancer drugs, as it forms Top1 cleavage complexes (Top1cc) that are trapped by the drugs. Endogenous and carcinogenic DNA lesions can also trap Top1cc. Tyrosyl-DNA phosphodiesterase 1 (TDP1), a key repair enzyme for trapped Top1cc, hydrolyzes the phosphodiester bond between the DNA 3′-end and the Top1 tyrosyl moiety. Alternative repair pathways for Top1cc involve endonuclease cleavage. However, it is unknown what determines the choice between TDP1 and the endonuclease repair pathways. Here we show that PARP1 plays a critical role in this process. By generating TDP1 and PARP1 double-knockout lymphoma chicken DT40 cells, we demonstrate that TDP1 and PARP1 are epistatic for the repair of Top1cc. The N-terminal domain of TDP1 directly binds the C-terminal domain of PARP1, and TDP1 is PARylated by PARP1. PARylation stabilizes TDP1 together with SUMOylation of TDP1. TDP1 PARylation enhances its recruitment to DNA damage sites without interfering with TDP1 catalytic activity. TDP1–PARP1 complexes, in turn recruit X-ray repair cross-complementing protein 1 (XRCC1). This work identifies PARP1 as a key component driving the repair of trapped Top1cc by TDP1.     

Discovery of novel quinolinone adenosine A2B antagonists

A novel series of quinolinone-based adenosine A(2B) receptor antagonists was identified via high throughput screening of an encoded combinatorial compound collection. Synthesis and assay of a series of analogs highlighted essential structural features of the initial hit. Optimization resulted in an A(2B) antagonist (2i) which exhibited potent activity in a cAMP accumulation assay (5.1 nM) and an IL-8 release assay (0.4 nM).     

Effect of formulation factors on in vitro transcorneal permeation of gatifloxacin from aqueous drops

The purpose of this research was to optimize the formulation factors for maximum in vitro permeation of gatifloxacin from aqueous drops through excised goat cornea and to evaluate the permeation characteristics of drug from selected marketed eyedrop formulations. Permeation studies were conducted by putting 1 mL of formulation on the cornea (0.67 cm²) fixed between the donor and receptor compartments of an all-glass modified Franz diffusion cell and measuring gatifloxacin concentration in the receptor (containing normal saline under stirring) by spectrophotometry at 291.5 nm, after 120 minutes. Raising the drug concentration of the drops increased the drug permeation but decreased the percent permeation and the in vitro ocular availability. Raising the pH of the formulation from pH 5 to 7.2 increased both the drug permeation and the in vitro ocular availability. Eyedrops containing benzalkonium chloride (BAK; 0.01% wt/vol) and disodium edetate (EDTA; 0.01% wt/vol) showed maximum permeation, followed by Zymar, BAK (0.01% wt/vol), Gatilox, Gatiquin, and Gate (statistically significantP<.05 compared with control). In vitro titration of the formulations with 0.1N NaOH indicated the presence of a buffer in Zymar (pH 6) and Gate (pH 5.8), which may cause irritation and induce lacrimation, resulting in reduced ocular availability in vivo. Thus, formulation with BAK and EDTA, which is unbuffered, has a better likelihood of being absorbed in vivo. The BAK-EDTA formulation significantly (P<.05) increased the permeation of gatifloxacin through paired excised corneas of goat, sheep, and buffalo, compared with the control formulation. The goat cornea showed the greatest increase in permeation, followed by the sheep and buffalo corneas. Published: July 7, 2006     

The N-terminal lysine residue-rich domain II and the 340-430 amino acid segment of eukaryotic initiation factor 2-associated glycoprotein p67 are the binding sites for the gamma-subunit of eIF2

Eukaryotic initiation factor 2 (eIF2)-associated glycoprotein, p67, plays an important role in protecting eIF2alpha from phosphorylation by eIF2alpha-specific kinases. To understand the molecular details of interaction between p67 and the subunits of eIF2, we applied several biochemical and mutational analyses to identify interacting domains within p67 and eIF2gamma. These studies were combined with functional in vivo and in vitro assays to address the importance of the interactions between p67 and eIF2gamma in eIF2alpha phosphorylation. Studies from yeast two-hybrid assays show that p67 interacts strongly with eIF2gamma, relatively weakly with eIF2alpha, and no interaction with eIF2beta. Further mutational analyses provided evidence that the N-terminal lysine-rich domain II and the 340-430 amino acid segment of p67 interact strongly with the C-terminal 409-472 amino acid segment of eIF2gamma. GST pull-down assays show that the interaction between p67 and eIF2gamma is direct. From co-immunoprecipitation studies, we find that the interaction between p67 and eIF2gamma could not only be detected in mammalian cells growing in growth medium, it could also be detected in transiently transfected cells with expression plasmids encoding p67 and eIF2gamma. However, this interaction could not be detected in p67 mutants lacking lysine-rich domain II and the 340-430 amino acid segment. We also find a very good correlation between p67 binding to eIF2gamma and the protection of eIF2alpha from phosphorylation. Altogether, our data provide genetic evidence for the interaction between p67 and eIF2gamma and that this interaction modulates the phosphorylation of eIF2alpha.     

Targeted cross-linking of the human beta-globin gene in living cells mediated by a triple helix forming oligonucleotide

Triple helix forming oligonucleotides (TFOs) may have utility as gene targeting reagents for "in situ" gene therapy of genetic disorders. Triplex formation is challenged by negative charge repulsion between third strand and duplex phosphates, and destabilizing positive charge repulsion between adjacent protonated cytosines within pyrimidine motif third strands. Here we describe the synthesis of TFOs designed to target a site in the human beta-globin gene, which is the locus for mutations that underlie the beta-globinopathies, including sickle cell anemia. The target is an uninterrupted polypurine:polypyrimidine sequence, containing four adjacent cytosines, next to a psoralen cross-link site. Pyrimidine motif TFOs that contained four adjacent cytosines or 5-methylcytosines did not form stable triplexes at physiological pH, despite the introduction of otherwise stabilizing base and sugar analogues. We synthesized a series of pso-TFOs containing 2'-O-methyl (OMe) and 2'-O-aminoethoxy substitutions (AE), as well as 8-oxo-adenine (A8) and 2'-O-methylpseudoisocytidine (P) as neutral cytosine replacements. Thermal stability measurements indicated that TFOs with A8 did not meet criteria established in previous work. However, TFOs with P did form triplexes with appropriate T(m) and k(ON) values. A pso-TFO with AE and P residues was sufficiently active to permit the determination of targeting in living cells by direct measurement of cross-link formation at the target site. Our results validate the modification format described in our previous studies and indicate that P substitutions are an effective solution to the problem of targeting genomic sequences containing adjacent cytosines.     

Alginate-chaperoned facile refolding of Chromobacterium viscosum lipase

Urea denatured lipase from Chromobacterium viscosum lipase could be refolded by addition of alginate with high guluronic acid content. The refolded molecule could be recovered by affinity precipitation. This approach resulted in recovery of 80% (of original activity) as compared to classical dilution method which gave only 21% activity recovery. Dynamic light scattering showed that binding required about 45 min and activity data obtained from affinity precipitation experiments indicated that refolding was almost instantaneous after binding. Circular dichroism (CD) and fluorescence data showed that refolded molecule was identical to the native molecule. It also showed that refolding takes place at the binding stage and not at the precipitation stage. Preliminary studies showed that the refolding strategy worked equally well with lipases from wheat germ and porcine pancreas.     

Long-term cyclical in vivo loading increases cartilage proteoglycan content in a spatially specific manner: an infrared microspectroscopic imaging and polarized light microscopy study

Understanding the changes in collagen and proteoglycan content of cartilage due to physical forces is necessary for progress in treating joint disorders, including those due to overuse. Physical forces in the chondrocyte environment can affect the cellular processes involved in the biosynthesis of extracellular matrix. In turn, the biomechanical properties of cartilage depend on its collagen and proteoglycan content. To understand changes due to physical forces, this study examined the effect of 80 cumulative hours of in vivo cyclical joint loading on the cartilage content of proteoglycan and collagen in the rabbit metacarpophalangeal joint. The forepaw digits of six anesthetized New Zealand White adult female rabbits were repetitively flexed at 1 Hz with an estimated joint contact pressure of 1 to 2 MPa. Joints were collected from loaded and contralateral control specimens, fixed, decalcified, embedded, and thin-sectioned. Sections were examined under polarized light microscopy to identify and measure superficial and mid zone thicknesses of cartilage. Fourier Transform Infrared microspectroscopy was used to measure proteoglycan and collagen contents in the superficial, mid, and deep zones. Loading led to an increase in proteoglycan in the cartilage of all six rabbits. Specifically, there was a 46% increase in the cartilage deep zone (p = 0.003). The collagen content did not change with loading. Joint loading did not change the superficial and mid zone mean thicknesses. We conclude that long-term (80 cumulative hours) cyclical in vivo joint loading stimulates proteoglycan synthesis. Furthermore, stimulation is localized to cartilage regions of high hydrostatic pressure. These data may be useful in developing interventions to prevent overuse injuries or in developing therapies to improve joint function.     

Target DNA recognition and cleavage by a reconstituted Type I-G CRISPR-Cas immune effector complex

Extremophiles - CRISPR-Cas immune systems defend prokaryotes against viruses and plasmids. CRISPR RNAs (crRNAs) associate with various CRISPR-associated (Cas) protein modules to form structurally...     

Bacterial intelligence: imitation games,time-sharing,and long-range quantum coherence

Bacteria are far more intelligent than we can think of. They adopt different survival strategies to make their life comfortable. Researches on bacterial communication to date suggest that bacteria can communicate with each other using chemical signaling molecules as well as using ion channel mediated electrical signaling. Though in past few decades the scopes of chemical signaling have been investigated extensively, those of electrical signaling have received less attention. In this article, we present a novel perspective on time-sharing behavior, which maintains the biofilm growth under reduced nutrient supply between two distant biofilms through electrical signaling based on the experimental evidence reported by Liu et al., in 2017. In addition, following the recent work by Humphries et al. Cell 168(1):200–209, in 2017, we highlight the consequences of long range electrical signaling within biofilm communities through spatially propagating waves of potassium. Furthermore, we address the possibility of two-way cellular communication between artificial and natural cells through chemical signaling being inspired by recent experimental observation (Lentini et al. 2017) where the efficiency of artificial cells in imitating the natural cells is estimated through cellular Turing test. These three spectacular observations lead us to envisage and devise new classical and quantum views of these complex biochemical networks that have never been realized previously.