Excessive reactive oxygen species induce transcription-dependent replication stress.

Elevated levels of reactive oxygen species (ROS) reduce replication fork velocity by causing dissociation of the TIMELESS-TIPIN complex from the replisome. Here, we show that ROS generated by exposure of human cells to the ribonucleotide reductase inhibitor hydroxyurea (HU) promote replication fork reversal in a manner dependent on active transcription and formation of co-transcriptional RNA:DNA hybrids (R-loops). The frequency of R-loop-dependent fork stalling events is also increased after TIMELESS depletion or a partial inhibition of replicative DNA polymerases by aphidicolin, suggesting that this phenomenon is due to a global replication slowdown. In contrast, replication arrest caused by HU-induced depletion of deoxynucleotides does not induce fork reversal but, if allowed to persist, leads to extensive R-loop-independent DNA breakage during S-phase. Our work reveals a link between oxidative stress and transcription-replication interference that causes genomic alterations recurrently found in human cancer. [Abstract copyright: © 2023. The Author(s).

Excessive reactive oxygen species induce transcription-dependent replication stress

Elevated levels of reactive oxygen species (ROS) reduce replication fork velocity by causing dissociation of the TIMELESS-TIPIN complex from the replisome. Here, we show that ROS generated by exposure of human cells to the ribonucleotide reductase inhibitor hydroxyurea (HU) promote replication fork reversal in a manner dependent on active transcription and formation of co-transcriptional RNA:DNA hybrids (R-loops). The frequency of R-loop-dependent fork stalling events is also increased after TIMELESS depletion or a partial inhibition of replicative DNA polymerases by aphidicolin, suggesting that this phenomenon is due to a global replication slowdown. In contrast, replication arrest caused by HU-induced depletion of deoxynucleotides does not induce fork reversal but, if allowed to persist, leads to extensive R-loop-independent DNA breakage during S-phase. Our work reveals a link between oxidative stress and transcription-replication interference that causes genomic alterations recurrently found in human cancer

Naphthalimide-phenanthroimidazole incorporated new fluorescent sensor for “turn-on” Cu2+ detection in living cancer cells

In recent years, fluorescent sensors have emerged as attractive imaging probes due to their distinct responses toward bio-relevant metal ions. However, the bioimaging application main barrier is the ‘turn-off’ response toward paramagnetic metal ions such as Cu2+ under physiological conditions. Herein, we report a new sensor (2-methyl(4-bromo-N-ethylpiperazinyl-1,8-naphthalimido)-4-(1H-phenanthro[9,10-d]imidazole-2-yl) phenol) NPP with multifunctional (Naphthalimide, Piperazine, Phenanthroimidazole) units for fluorescent and colourimetric detection of Cu2+ in an aqueous medium. Both absorption and fluorescence spectral titration strategies were used to monitor the Cu2+-sensing property of NPP. The NPP displays a weak emission at ca. 455 nm, which remarkably enhances (⁓3.2-fold) upon selective binding of Cu2+ over a range of metal ions, including other paramagnetic metal ions (Mn2+, Fe3+, Co2+). The stoichiometry, binding constant (Ka) and the LOD (limit of detection) of NPP toward Cu2+ ions were found to be 1:1, 5.0 (± 0.2) × 104 M−1 and 6.5 (± 0.4) × 10−7 M, respectively. We have also used NPP as a fluorescent probe to detect Cu2+ in live (human cervical HeLa) cancer cells. The emission intensity of NPP was almost recovered in HeLa cells by incubating ‘in situ’ the derived Cu2+ complex (NPP-Cu 2+ ) in the presence of a benchmark chelating agent such as EDTA (ethylenediaminetetraacetate). The fluorescent emission of NPP was reverted significantly in each cycle upon sequencial addition of Cu2+ and EDTA to the NPP solution. Overall, NPP is a novel, simple, economic and portable sensor that can detect Cu2+ in biological and environmental scenarios

Production of paclitaxel by Fusarium solani isolated from Taxus celebica

A fungus was isolated from the stem cuttings of Taxus celebica, which produced paclitaxel in liquid-grown cultures.The fungus was identified as Fusarium solani based on colony characteristics, morphology of conidia and the 26S rDNA sequence. Paclitaxel was identified by chromatographic and spectroscopic comparison with authentic paclitaxel and its cytotoxic activity towards Jurkat cells in vitro

A benzimidazole-based new fluorogenic differential/sequential chemosensor for Cu2+, Zn2+, CN-, P2O74-, DNA, its live-cell imaging and pyrosequencing applications

Differential chemosensors have emerged as next-generation systems due to their simplicity and favourable responsive properties to produce different signals upon selective binding of various analytes simultaneously. Nevertheless, given their inadequate fluorescence response and laborious synthetic procedures, only a few differential chemosensors have been developed so far. In this work, we have employed a single pot synthesis strategy to establish a new benzimidazole-based Schiff base type fluorogenic chemosensor (DFB) which differentially detects Cu 2+ (detection limit (LOD) = 24.4 ± 0.5 nM) and Zn 2+ (LOD = 2.18 ± 0.1 nM) through fluorescence “off-on” manner over the library of other metal cations in an aqueous medium. The DFB-derived ‘in situ’ complexes DFB-Cu 2+ and DFB-Zn 2+ showed fluorescence revival “on-off” responses toward cyanide (CN −) and bio-relevant pyrophosphate (P 2O 7 4--PPi) ions with a significantly low LOD of 9.43 ± 0.2 and 2.9 ± 0.1 nM, respectively, in water. We have demonstrated the phosphate group-specific binding capability of DFB-Zn 2+, by testing it with both ssDNA and dsDNA samples which displayed fluorescence “turn-off” response (LOD ∼10 -7 M), similar to the PPi binding in an aqueous medium, indicating that it interacts explicitly with the phosphate backbone of DNA. We have also harnessed the DFB as a sequential fluorescent probe to detect Cu 2+, Zn 2+, CN − and P 2O 7 4- ions in human cervical (HeLa) and breast (MCF-7 and MDA-MB-231 (aggressive and invasive)) cancer cell lines. Moreover, we have explored the PPi recognition capability of DFB-Zn 2+ in the polymerase-chain-reaction (PCR) products where PPi is one of the primary by-products during amplification of DNA

Ribosome inactivating proteins and apoptosis

Ribosome inactivating proteins (RIPs) are protein toxins that are of plant or microbial origin that inhibit protein synthesis by inactivating ribosomes. Recent studies suggest that RIPs are also capable of inducing cell death by apoptosis. Though many reports are available on cell death induced by RIPs, the mechanism involved is not well studied. Comparison of pathways of apoptosis and cellular events induced by various RIPs suggests a central role played by mitochondria, probably acting as an integrator of cellular stress and cell death. The purpose of this review is to compare the various apoptotic pathways that may be involved and propose a general pathway in RIP-induced cell death

Structure-Function Analysis and Insights into the Reduced Toxicity of Abrus precatorius Agglutinin I in Relation to Abrin

Abrin and agglutinin-I from the seeds of Abrus precatorius are type II ribosome-inactivating proteins that inhibit protein synthesis in eukaryotic cells. The two toxins share a high degree of sequence similarity; however, agglutinin-I is weaker in its activity. We compared the kinetics of protein synthesis inhibition by abrin and agglutinin-I in two different cell lines and found that \sim 200-2000-fold higher concentration of agglutinin-I is needed for the same degree of inhibition. Like abrin, agglutinin-I also induced apoptosis in the cells by triggering the intrinsic mitochondrial pathway, although at higher concentrations as compared with abrin. The reason for the decreased toxicity of agglutinin-I became apparent on the analysis of the crystal structure of agglutinin-I obtained by us in comparison with that of the reported structure of abrin. The overall protein folding of agglutinin-I is similar to that of abrin-a with a single disulfide bond holding the toxic A subunit and the lectin-like B-subunit together, constituting a heterodimer. However, there are significant differences in the secondary structural elements, mostly in the A chain. The substitution of Asn-200 in abrin-a with Pro-199 in agglutinin-I seems to be a major cause for the decreased toxicity of agglutinin-I. This perhaps is not a consequence of any kink formation by a proline residue in the helical segment, as reported by others earlier, but due to fewer interactions that proline can possibly have with the bound substrate

A deep learning workflow for quantification of Micronuclei in DNA damage studies in cultured cancer cell lines: a proof of principle investigation

The cytokinesis block micronucleus assay is widely used for measuring/scoring/counting micronuclei, a marker of genome instability in cultured and primary cells. Though a gold standard method, this is a laborious and time-consuming process with person-to-person variation observed in quantification of micronuclei. We report in this study the utilisation of a new deep learning workflow for detection of micronuclei in DAPI stained nuclear images. The proposed deep learning framework achieved an average precision of >90% in detection of micronuclei. This proof of principle investigation in a DNA damage studies laboratory supports the idea of deploying AI powered tools in a cost-effective manner for repetitive and laborious tasks with relevant computational expertise. These systems will also help improving the quality of data and wellbeing of researchers