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1.
Nucleic Acids Res ; 52(4): 1763-1778, 2024 Feb 28.
Article in English | MEDLINE | ID: mdl-38153143

ABSTRACT

BG4 is a single-chain variable fragment antibody shown to bind various G-quadruplex (GQ) topologies with high affinity and specificity, and to detect GQ in cells, including GQ structures formed within telomeric TTAGGG repeats. Here, we used ELISA and single-molecule pull-down (SiMPull) detection to test how various lengths and GQ destabilizing base modifications in telomeric DNA constructs alter BG4 binding. We observed high-affinity BG4 binding to telomeric GQ independent of telomere length, although three telomeric repeat constructs that cannot form stable intramolecular GQ showed reduced affinity. A single guanine substitution with 8-aza-7-deaza-G, T, A, or C reduced affinity to varying degrees depending on the location and base type, whereas two G substitutions in the telomeric construct dramatically reduced or abolished binding. Substitution with damaged bases 8-oxoguanine and O6-methylguanine failed to prevent BG4 binding although affinity was reduced depending on lesion location. SiMPull combined with FRET revealed that BG4 binding promotes folding of telomeric GQ harboring a G to T substitution or 8-oxoguanine. Atomic force microscopy revealed that BG4 binds telomeric GQ with a 1:1 stoichiometry. Collectively, our data suggest that BG4 can recognize partially folded telomeric GQ structures and promote telomeric GQ stability.


Subject(s)
G-Quadruplexes , DNA/genetics , DNA/chemistry , Telomere/genetics , Antibodies/genetics
2.
bioRxiv ; 2023 Sep 04.
Article in English | MEDLINE | ID: mdl-37732211

ABSTRACT

RNA-binding proteins with prion-like domains, such as FUS and TDP-43, condense into functional liquids, which can transform into pathological fibrils that underpin fatal neurodegenerative disorders, including amyotrophic lateral sclerosis (ALS)/frontotemporal dementia (FTD). Here, we define short RNAs (24-48 nucleotides) that prevent FUS fibrillization by promoting liquid phases, and distinct short RNAs that prevent and, remarkably, reverse FUS condensation and fibrillization. These activities require interactions with multiple RNA-binding domains of FUS and are encoded by RNA sequence, length, and structure. Importantly, we define a short RNA that dissolves aberrant cytoplasmic FUS condensates, restores nuclear FUS, and mitigates FUS proteotoxicity in optogenetic models and human motor neurons. Another short RNA dissolves aberrant cytoplasmic TDP-43 condensates, restores nuclear TDP-43, and mitigates TDP-43 proteotoxicity. Since short RNAs can be effectively delivered to the human brain, these oligonucleotides could have therapeutic utility for ALS/FTD and related disorders.

3.
Proc Natl Acad Sci U S A ; 120(19): e2215068120, 2023 05 09.
Article in English | MEDLINE | ID: mdl-37126687

ABSTRACT

Poly(ADP-ribose) (PAR) is a homopolymer of adenosine diphosphate ribose that is added to proteins as a posttranslational modification to regulate numerous cellular processes. PAR also serves as a scaffold for protein binding in macromolecular complexes, including biomolecular condensates. It remains unclear how PAR achieves specific molecular recognition. Here, we use single-molecule fluorescence resonance energy transfer (smFRET) to evaluate PAR flexibility under different cation conditions. We demonstrate that, compared to RNA and DNA, PAR has a longer persistence length and undergoes a sharper transition from extended to compact states in physiologically relevant concentrations of various cations (Na+, Mg2+, Ca2+, and spermine4+). We show that the degree of PAR compaction depends on the concentration and valency of cations. Furthermore, the intrinsically disordered protein FUS also served as a macromolecular cation to compact PAR. Taken together, our study reveals the inherent stiffness of PAR molecules, which undergo switch-like compaction in response to cation binding. This study indicates that a cationic environment may drive recognition specificity of PAR.


Subject(s)
Adenosine Diphosphate Ribose , Poly Adenosine Diphosphate Ribose , Poly Adenosine Diphosphate Ribose/chemistry , Poly Adenosine Diphosphate Ribose/metabolism , Adenosine Diphosphate Ribose/chemistry , Protein Processing, Post-Translational , Protein Binding , Cell Physiological Phenomena
4.
bioRxiv ; 2023 Mar 13.
Article in English | MEDLINE | ID: mdl-36993178

ABSTRACT

Poly(ADP-ribose) (PAR) is a homopolymer of adenosine diphosphate ribose that is added to proteins as a post-translational modification to regulate numerous cellular processes. PAR also serves as a scaffold for protein binding in macromolecular complexes, including biomolecular condensates. It remains unclear how PAR achieves specific molecular recognition. Here, we use single-molecule fluorescence resonance energy transfer (smFRET) to evaluate PAR flexibility under different cation conditions. We demonstrate that, compared to RNA and DNA, PAR has a longer persistence length and undergoes a sharper transition from extended to compact states in physiologically relevant concentrations of various cations (Na + , Mg 2+ , Ca 2+ , and spermine). We show that the degree of PAR compaction depends on the concentration and valency of cations. Furthermore, the intrinsically disordered protein FUS also served as a macromolecular cation to compact PAR. Taken together, our study reveals the inherent stiffness of PAR molecules, which undergo switch-like compaction in response to cation binding. This study indicates that a cationic environment may drive recognition specificity of PAR. Significance: Poly(ADP-ribose) (PAR) is an RNA-like homopolymer that regulates DNA repair, RNA metabolism, and biomolecular condensate formation. Dysregulation of PAR results in cancer and neurodegeneration. Although discovered in 1963, fundamental properties of this therapeutically important polymer remain largely unknown. Biophysical and structural analyses of PAR have been exceptionally challenging due to the dynamic and repetitive nature. Here, we present the first single-molecule biophysical characterization of PAR. We show that PAR is stiffer than DNA and RNA per unit length. Unlike DNA and RNA which undergoes gradual compaction, PAR exhibits an abrupt switch-like bending as a function of salt concentration and by protein binding. Our findings points to unique physical properties of PAR that may drive recognition specificity for its function.

5.
PLoS One ; 18(1): e0279616, 2023.
Article in English | MEDLINE | ID: mdl-36656815

ABSTRACT

BACKGROUND: Alzheimer's disease (AD) is a form of dementia that strikes elderly people more frequently than it does younger people. The cognitive skills and memory of Alzheimer's sufferers continue to deteriorate over time. Recent studies have shown that patients with AD have greater amounts of inflammatory markers in their bodies, which suggests that inflammation occurs early on in the progression of the disease. There is a possibility that Aß oligomers and fibrils can be recognised by TLRs, in addition to the microglial receptors CD14, CD36, and CD47. When Aß binds to either CD36 or TLR4, it sets off a chain reaction of inflammatory chemokines and cytokines that ultimately results in neurodegeneration. Diabetes and Alzheimer's disease have both been recently related to TLR4. The activation of TLR4 has been connected to a variety of clinical difficulties that are associated with diabetes, in addition to the internal environment of the body and the microenvironment of the brain. TLR4 inhibitors have been shown in clinical investigations to not only lessen the likelihood of getting sick but also to increase the average longevity. RESULT: In this work we used molecular docking and molecular dynamics modelling to investigate the effectiveness of FDA-approved antidiabetic plant derived drugs in combating the TLR4 receptor. Molecular docking experiments were used to make a prediction regarding the most important interactions involving 2-Bromoergocryptine Mesylate. With a binding affinity of -8.26 kcal/mol, it stood out from the other candidates as the one with the greatest potential. To verify the interaction pattern that takes place between 2-Bromoergocryptine Mesylate and the TLR4 receptor, a molecular dynamic simulation was run at a time scale of 150 nanoseconds. Because of this, 2-Bromoergocryptine Mesylate was able to make substantial contact with the active site, which led to increased structural stability during the process of the complex's dynamic development. CONCLUSION: As a result of this, the results of our research may be relevant for future research into the efficacy of 2-bromoergocryptine mesylate as a potential lead treatment for TLR4 receptors in intracranial aneurysm rupture in AD.


Subject(s)
Alzheimer Disease , Bromocriptine , Claviceps , Intracranial Aneurysm , Toll-Like Receptor 4 , Humans , Alzheimer Disease/drug therapy , Alzheimer Disease/metabolism , Bromocriptine/pharmacology , Intracranial Aneurysm/prevention & control , Molecular Docking Simulation , Toll-Like Receptor 4/metabolism , Triticum/microbiology
6.
Methods Enzymol ; 672: 283-297, 2022.
Article in English | MEDLINE | ID: mdl-35934479

ABSTRACT

The G-rich single-stranded telomere overhang can self-fold into G-quadruplex (G4) structure both in vivo and in vitro. In somatic cells, telomeres shorten progressively due to the end-replication. In stem cells, however, telomeres are replenished by a special enzyme, telomerase which synthesizes single-stranded telomere overhang. The active extension by the telomerase releases G-rich overhang segmentally in 5' to 3' direction as the overhang folds into G4 structure after successive elongation. To replicate such vectorial G4 folding process, we employed a superhelicase, Rep-X to release the G-rich sequence gradually. Using single-molecule assay we demonstrated that the folded conformation achieved by the vectorial folding is inherently different from the post-folding where the entire overhang is allowed to fold at once. In addition, the vectorially folded overhangs are less stable and more accessible to a complementary C-rich strand and the telomere binding protein, POT1 compared to the post-folded state. The higher accessibility may have implications for the facile loading of shelterin proteins after DNA replication.


Subject(s)
G-Quadruplexes , Telomerase , DNA Helicases/metabolism , Shelterin Complex , Telomerase/metabolism , Telomere/genetics , Telomere/metabolism , Telomere-Binding Proteins/chemistry , Telomere-Binding Proteins/genetics , Telomere-Binding Proteins/metabolism
7.
Nucleic Acids Res ; 50(11): 6271-6283, 2022 06 24.
Article in English | MEDLINE | ID: mdl-35687089

ABSTRACT

Human telomere overhang composed of tandem repeats of TTAGGG folds into G-quadruplex (G4). Unlike in an experimental setting in the test tube in which the entire length is allowed to fold at once, inside the cell, the overhang is expected to fold as it is synthesized directionally (5' to 3') and released segmentally by a specialized enzyme, the telomerase. To mimic such vectorial G4 folding process, we employed a superhelicase, Rep-X which can unwind DNA to release the TTAGGG repeats in 5' to 3' direction. We demonstrate that the folded conformation achieved by the refolding of full sequence is significantly different from that of the vectorial folding for two to eight TTAGGG repeats. Strikingly, the vectorially folded state leads to a remarkably higher accessibility to complementary C-rich strand and the telomere binding protein POT1, reflecting a less stably folded state resulting from the vectorial folding. Importantly, our study points to an inherent difference between the co-polymerizing and post-polymerized folding of telomere overhang that can impact telomere architecture and downstream processes.


Subject(s)
G-Quadruplexes , Telomere , DNA/chemistry , Humans , Nucleic Acid Conformation , Shelterin Complex , Telomerase/metabolism , Telomere/chemistry , Telomere/genetics , Telomere-Binding Proteins/metabolism
8.
STAR Protoc ; 3(1): 101152, 2022 03 18.
Article in English | MEDLINE | ID: mdl-35146451

ABSTRACT

Single-molecule fluorescence detection by total internal reflection microscope requires surface passivation by polyethylene glycol (PEG) coating, which is labor intensive and is only good for one or two experiments. Here, we present an efficient and reliable protocol for generating and regenerating the PEG surface for multiple rounds of experiments (∼5-10 times) in the same channel. This protocol is very simple, robust, rapid, and versatile; i.e., multiple strategies can be implemented to regenerate different layers of surface. The regeneration strategy saves time, improves the cost effectiveness, and enhances the efficiency of single-molecule experiments. For complete details on the use and execution of this profile, please refer to Paul et al. (2021a).


Subject(s)
Nanotechnology , Polyethylene Glycols , Fluorescence , Regeneration
9.
Nucleic Acids Res ; 49(21): 12377-12393, 2021 12 02.
Article in English | MEDLINE | ID: mdl-34850123

ABSTRACT

Human telomeres are protected by shelterin proteins, but how telomeres maintain a dynamic structure remains elusive. Here, we report an unexpected activity of POT1 in imparting conformational dynamics of the telomere overhang, even at a monomer level. Strikingly, such POT1-induced overhang dynamics is greatly enhanced when TRF2 engages with the telomere duplex. Interestingly, TRF2, but not TRF2ΔB, recruits POT1-bound overhangs to the telomere ds/ss junction and induces a discrete stepwise movement up and down the axis of telomere duplex. The same steps are observed regardless of the length of the POT1-bound overhang, suggesting a tightly regulated conformational dynamic coordinated by TRF2 and POT1. TPP1 and TIN2 which physically connect POT1 and TRF2 act to generate a smooth movement along the axis of the telomere duplex. Our results suggest a plausible mechanism wherein telomeres maintain a dynamic structure orchestrated by shelterin.


Subject(s)
Recombinant Proteins/metabolism , Shelterin Complex/metabolism , Telomere-Binding Proteins/metabolism , Telomere/metabolism , Telomeric Repeat Binding Protein 2/metabolism , Fluorescence Resonance Energy Transfer/methods , Fluorescent Dyes/chemistry , Fluorescent Dyes/metabolism , Humans , Microscopy, Fluorescence/methods , Protein Binding , Shelterin Complex/genetics , Telomere/genetics , Telomere-Binding Proteins/genetics , Telomeric Repeat Binding Protein 2/genetics , Tripeptidyl-Peptidase 1/genetics , Tripeptidyl-Peptidase 1/metabolism
10.
Environ Pollut ; 286: 117569, 2021 Oct 01.
Article in English | MEDLINE | ID: mdl-34438492

ABSTRACT

Triclosan (TCS), an emergent pollutant, is raising a global concern due to its toxic effects on organisms and aquatic ecosystems. The non-availability of proven treatment technologies for TCS remediation is the central issue stressing thorough research on understanding the underlying mechanisms of toxicity and assessing vital biomarkers in the aquatic organism for practical monitoring purposes. Given the unprecedented circumstances during COVID 19 pandemic, a several-fold higher discharge of TCS in the aquatic ecosystems cannot be considered a remote possibility. Therefore, identifying potential biomarkers for assessing chronic effects of TCS are prerequisites for addressing the issues related to its ecological impact and its monitoring in the future. It is the first holistic review on highlighting the biomarkers of TCS toxicity based on a comprehensive review of available literature about the biomarkers related to cytotoxicity, genotoxicity, hematological, alterations of gene expression, and metabolic profiling. This review establishes that biomarkers at the subcellular level such as oxidative stress, lipid peroxidation, neurotoxicity, and metabolic enzymes can be used to evaluate the cytotoxic effect of TCS in future investigations. Micronuclei frequency and % DNA damage proved to be reliable biomarkers for genotoxic effects of TCS in fishes and other aquatic organisms. Alteration of gene expression and metabolic profiling in different organs provides a better insight into mechanisms underlying the biocide's toxicity. In the concluding part of the review, the present status of knowledge about mechanisms of antimicrobial resistance of TCS and its relevance in understanding the toxicity is also discussed referring to the relevant reports on microorganisms.


Subject(s)
COVID-19 , Triclosan , Water Pollutants, Chemical , Biomarkers , Ecosystem , Humans , SARS-CoV-2 , Triclosan/analysis , Triclosan/toxicity , Water Pollutants, Chemical/analysis , Water Pollutants, Chemical/toxicity
11.
Heliyon ; 7(6): e07340, 2021 Jun.
Article in English | MEDLINE | ID: mdl-34195440

ABSTRACT

In this paper, a novel multi-attribute decision-making method using Advanced Pythagorean fuzzy weighted geometric operator in a Pythagorean fuzzy environment is developed. Pythagorean fuzzy aggregation operators have drawbacks that they give indeterminate results in some special cases when membership value or non-membership value gets 0 value or 1 value and the weight vector is of type ( 1 , 0 ) T or ( 0 , 1 ) T . The Advanced Pythagorean fuzzy geometric operator, the proposed operator can overcome the drawbacks. In some situations, for example, where the sum of squares of membership degree and non-membership degree gets unit value of a Pythagorean fuzzy number, multi-attribute decision making (MADM) methods using some existing aggregation operators give unreasonable ranking orders (ROs) of alternatives or can't discriminate the ROs of alternatives. But the present MADM method can get over the drawbacks of the existing MADM methods. The present MADM method is devoted to eliminate the drawbacks of the existing MADM methods and to select the best real estate company for investment.

12.
Environ Toxicol Pharmacol ; 87: 103691, 2021 Oct.
Article in English | MEDLINE | ID: mdl-34153508

ABSTRACT

In recent times, carbamazepine (CBZ) as an anticonvulsants drug has raised attention because of its safety concern in the aquatic environment. The present study aimed to evaluate the sub-lethal effects of CBZ (1%, 0.1 % and 0.01 % of 96 h LC50) on P. hypophthalmus for 60 days based on haematological, biochemical, and genotoxicity biomarkers. Chronic exposure of CBZ altered blood profiles (total erythrocyte count, packed cell volume, haemoglobin) and serum biomarkers such as alkaline phosphates, cholesterol, lactate dehydrogenase and transaminase enzymes. Oxidative stress biomarkers such as superoxide dismutase (SOD) and catalase (CAT) activity were also substantially affected in all treatments. Genotoxicity study revealed the formation of micronucleus in erythrocytes of exposed fish. Integrated Biomarker Response (IBR) study showed cholesterol, serum glutamic oxaloacetic transaminase (SGOT) in serum and SOD, CAT in liver tissue are the best organ-based enzyme biomarkers. The present report concludes that an environmentally realistic concentration of CBZ can pose a serious threat to aquatic organisms.


Subject(s)
Anticonvulsants/toxicity , Carbamazepine/toxicity , Catfishes , Water Pollutants, Chemical/toxicity , Animals , Biomarkers/blood , Biomarkers/metabolism , Blood Proteins/analysis , Catalase/metabolism , Catfishes/blood , Catfishes/metabolism , Erythrocyte Count , Fish Proteins/blood , Fish Proteins/metabolism , Hemoglobins/analysis , Lethal Dose 50 , Liver/drug effects , Liver/metabolism , Micronuclei, Chromosome-Defective/chemically induced , Oxidative Stress/drug effects , Serum Albumin/analysis , Superoxide Dismutase/metabolism , Toxicity Tests, Chronic
13.
J Am Chem Soc ; 143(19): 7368-7379, 2021 05 19.
Article in English | MEDLINE | ID: mdl-33855846

ABSTRACT

The expansion of a hexanucleotide repeat GGGGCC (G4C2) in the C9orf72 gene is the most common cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). The G4C2 expansion leads to repeat-associated non-AUG (RAN) translation and the production of toxic dipeptide repeat (DPR) proteins, but the mechanisms of RAN translation remain enigmatic. Here, we report that the RNA helicase DHX36 is a robust positive regulator of C9orf72 RAN translation. DHX36 has a high affinity for the G4C2 repeat RNA, preferentially binds to the repeat RNA's G-quadruplex conformation, and efficiently unwinds the G4C2 G-quadruplex structures. Native DHX36 interacts with the G4C2 repeat RNA and is essential for effective RAN translation in the cell. In induced pluripotent stem cells and differentiated motor neurons derived from C9orf72-linked ALS patients, reducing DHX36 significantly decreased the levels of endogenous DPR proteins. DHX36 is also aberrantly upregulated in tissues of C9orf72-linked ALS patients. These results indicate that DHX36 facilitates C9orf72 RAN translation by resolving repeat RNA G-quadruplex structures and may be a potential target for therapeutic intervention.


Subject(s)
Amyotrophic Lateral Sclerosis/genetics , DNA Helicases/genetics , RNA/genetics , DNA Repeat Expansion/genetics , G-Quadruplexes , Humans
14.
Sci Rep ; 11(1): 5713, 2021 03 11.
Article in English | MEDLINE | ID: mdl-33707650

ABSTRACT

Transportation of fish seed is a complex phenomenon associated with multiple kinds of stressors that simultaneously affect the fish in a confined environment, causing stress and mortality. The present study investigated the stress-relieving effect of exogenous glucose as a water additive in different concentrations (0.1, 0.2, 0.3, and 0.4%) during simulated transportation (12 h) of L. rohita fingerlings. The integrated biomarker response (IBR) index is a holistic tool to determine the optimum dose of exogenous glucose for mitigating transportation stress in fish. Based on selected biomarkers related to the stress hormone, serum biochemistry, oxidative stress, and HSP70 mRNA expression, the IBR index is calculated for each treatment and control group. The result showed a significant change in the level of stress hormone cortisol, enzymes (SGPT, LDH, MDH, SOD, CAT) and metabolites (serum glucose, triglyceride, creatinine) along with an upregulation in liver HSP70 mRNA expression. IBR index suggests that 0.2% glucose exhibited the lowest multi-biomarker stress response in comparison to other treatments and control. Therefore, the use of 0.2% glucose as a water additive will provide a solution to transportation induced stress in L. rohita fingerling and will underwrite the success of grow-out fish culture in days to come.


Subject(s)
Biomarkers/blood , Cyprinidae/physiology , Glucose/pharmacology , Stress, Physiological , Transportation , Animals , Blood Glucose/metabolism , Creatinine/blood , Cyprinidae/blood , Cyprinidae/genetics , Gene Expression Regulation/drug effects , HSP70 Heat-Shock Proteins/genetics , HSP70 Heat-Shock Proteins/metabolism , Hydrocortisone/blood , Liver/drug effects , Liver/metabolism , RNA, Messenger/genetics , RNA, Messenger/metabolism , Stress, Physiological/drug effects , Stress, Physiological/genetics , Survival Analysis , Triglycerides/blood , Water Quality
15.
Biophys J ; 120(9): 1788-1799, 2021 05 04.
Article in English | MEDLINE | ID: mdl-33675764

ABSTRACT

Single-molecule fluorescence detection of protein and other biomolecules requires a polyethylene glycol (PEG)-passivated surface. Individual channels on a PEG-passivated slide are typically used only a few times, limiting the number of experiments per slide. Here, we report several strategies for regenerating PEG surfaces for multiple rounds of experiments. First, we show regeneration of DNA- or RNA-tethered surfaces by washing out the bound protein by 0.1% sodium dodecyl sulfate, which is significantly more effective than 6 M urea, 6 M GdmCl, or 100 µM proteinase K. Strikingly, 10 consecutive experiments in five different systems produced indistinguishable results both in molecule count and protein activity. Second, duplexed DNA unwound by helicase or denatured by 50 mM NaOH was reannealed with a complementary strand to regenerate the duplexed substrate with an exceptionally high recovery rate. Third, the biotin-PEG layer was regenerated by using 7 M NaOH to strip off NeutrAvidin, which can be reapplied for additional experiments. We demonstrate five cycles of regenerating antibody immobilized surface by which three different protein activity was measured. Altogether, our methods represent reliable and reproducible yet simple and rapid strategies that will enhance the efficiency of single-molecule experiments.


Subject(s)
Biotin , Polyethylene Glycols , Antibodies , Nanotechnology
16.
Biochemistry ; 59(28): 2627-2639, 2020 07 21.
Article in English | MEDLINE | ID: mdl-32578995

ABSTRACT

Telomeres are hot spots for mutagenic oxidative and methylation base damage due to their high guanine content. We used single-molecule fluorescence resonance energy transfer detection and biochemical assays to determine how different positions and types of guanine damage and mutations alter telomeric G-quadruplex structure and telomerase activity. We compared 15 modifications, including 8-oxoguanine (8oxoG), O-6-methylguanine (O6mG), and all three possible point mutations (G to A, T, and C) at the 3' three terminal guanine positions of a telomeric G-quadruplex, which is the critical access point for telomerase. We found that G-quadruplex structural instability was induced in the order C < T < A ≤ 8oxoG < O6mG, with the perturbation caused by O6mG far exceeding the perturbation caused by other base alterations. For all base modifications, the central G position was the most destabilizing among the three terminal guanines. While the structural disruption by 8oxoG and O6mG led to concomitant increases in telomerase binding and extension activity, the structural perturbation by point mutations (A, T, and C) did not, due to disrupted annealing between the telomeric overhang and the telomerase RNA template. Repositioning the same mutations away from the terminal guanines caused both G-quadruplex structural instability and elevated telomerase activity. Our findings demonstrate how a single-base modification drives structural alterations and telomere lengthening in a position-dependent manner. Furthermore, our results suggest a long-term and inheritable effect of telomeric DNA damage that can lead to telomere lengthening, which potentially contributes to oncogenesis.


Subject(s)
G-Quadruplexes , Guanine/analysis , RNA/metabolism , Telomerase/metabolism , Telomere/genetics , DNA Damage , Guanine/analogs & derivatives , Guanine/metabolism , HEK293 Cells , Humans , Point Mutation , Shelterin Complex , Telomere/chemistry , Telomere/metabolism , Telomere-Binding Proteins/metabolism
17.
Nucleic Acids Res ; 48(12): 6640-6653, 2020 07 09.
Article in English | MEDLINE | ID: mdl-32449930

ABSTRACT

G-quadruplex (G4) DNA structures can form physical barriers within the genome that must be unwound to ensure cellular genomic integrity. Here, we report unanticipated roles for the Escherichia coli Rep helicase and RecA recombinase in tolerating toxicity induced by G4-stabilizing ligands in vivo. We demonstrate that Rep and Rep-X (an enhanced version of Rep) display G4 unwinding activities in vitro that are significantly higher than the closely related UvrD helicase. G4 unwinding mediated by Rep involves repetitive cycles of G4 unfolding and refolding fueled by ATP hydrolysis. Rep-X and Rep also dislodge G4-stabilizing ligands, in agreement with our in vivo G4-ligand sensitivity result. We further demonstrate that RecA filaments disrupt G4 structures and remove G4 ligands in vitro, consistent with its role in countering cellular toxicity of G4-stabilizing ligands. Together, our study reveals novel genome caretaking functions for Rep and RecA in resolving deleterious G4 structures.


Subject(s)
DNA Helicases/chemistry , DNA Replication/genetics , DNA-Binding Proteins/chemistry , Escherichia coli Proteins/chemistry , G-Quadruplexes , Rec A Recombinases/chemistry , Adenosine Triphosphate/chemistry , DNA Helicases/genetics , DNA-Binding Proteins/genetics , Escherichia coli/chemistry , Escherichia coli/genetics , Escherichia coli Proteins/genetics , Ligands , Nucleic Acid Conformation , Rec A Recombinases/genetics
18.
Environ Res ; 186: 109575, 2020 07.
Article in English | MEDLINE | ID: mdl-32361262

ABSTRACT

Toxicological studies on the emergent pollutant, triclosan (TCS) have established the wide-ranging effects of the compound on fish and other aquatic organisms. Although the available literature describes the standalone effects of TCS on growth and metabolism of fish yet, reports about the combined effects of TCS with microbial pathogens are scarce. In a real environment, a combined exposure to TCS and pathogens is of common occurrence, therefore, such investigation facilitates in developing a better understanding about the gross effects of pollutants and microbial pathogens on aquatic organisms including fish. In this context, the experimental fish (striped catfish, Pangasianodon hypophthalmus) were exposed to three different concentrations of TCS viz. 10, 20 and 30% of 96 h LC50 (1177 µg L-1) for 45 days including two control group firstly solvent control (without TCS) group and another one (without solvent and TCS) group in triplicate. Sampling was performed fortnightly and blood, serum and tissues (liver, and gills) samples were collected for evaluating immunological and biochemical parameters. Following 45 days of the experiments, the experimental fish in each treatment group including controls were challenged with a fish pathogenic bacterium Edwardsiella tarda (LD50 dose) and fish mortality was daily monitored for calculating cumulative mortality till 7 days and further, relative per cent survivable was estimated. A significant reduction in cellular immune responses i.e. respiratory burst activity (RBA), myeloperoxidase activity (MPO), phagocytic activity (PA) and humoral immune components viz. serum lysozyme activity, total immunoglobulin in serum, ceruloplasmin level, serum total protein, albumin and globulin level was evident in TCS exposed groups in comparison to control during the experimental periods. Further, oxidative stress parameters viz. superoxide dismutase (SOD), catalase (CAT), glutathione-s-transferase (GST) activity in liver and gill tissue exhibited a dose-dependent increase in activity with related to TCS concentration during the experimental periods. A significant reduction in relative percentage survival was observed with increasing TCS concentration. The present study reveals that TCS can inhibit the cellular and humoral components of the innate immune system of the fish and can elevate the mortality due to TCS mediated immunosuppression in fish during the bacterial infection.


Subject(s)
Catfishes , Triclosan , Animals , Catalase/metabolism , Catfishes/metabolism , Edwardsiella tarda/metabolism , Oxidative Stress , Triclosan/toxicity
19.
Environ Pollut ; 260: 114001, 2020 May.
Article in English | MEDLINE | ID: mdl-32041020

ABSTRACT

Application of biomarkers is an effective approach for a better understanding of varying toxicity in aquatic organisms during the seasonal and diurnal changes in the natural environment. This report describes the toxicity of sub-lethal concentrations of triclosan (TCS) at different pH (6.5, 7.5 and 8.5) based on selected biomarkers related to oxidative stress, metabolism and genotoxicity in Pangasianodon hypophthalmus. The 96 h LC50 of TCS for P. hypophthalmus was lower at pH 6.5 when compared to higher pH. The sub-lethal concentration of TCS exhibited a significant decrease in hematological parameters related to complete blood counts except for total leukocyte count (TLC), mean cell haemoglobin concentration (MCHC) and red cell distribution width (RDW). Multivariate data analysis showed a significant interaction of TCS and pH in metabolizing enzymes like glutamic oxaloacetate transaminase (GOT), glutamic pyruvic transaminase (GPT), Lactate dehydrogenase (LDH), antioxidant enzymes such as superoxide dismutase (SOD), catalase (CAT) and glutathione-s-transferase (GST) and neurotransmitter enzyme acetylcholinesterase (AChE). A significant increase in DNA damage and micronuclei frequency in liver and blood cells of TCS exposed fish at pH 6.5 indicate that the TCS exposure has pronounced effects on genetic materials. The findings of present study establish that enzymes like SOD, LDH, GOT, AChE, DNA damage and micronuclei frequency can be successfully deployed as biomarkers for the assessment of toxicity of TCS in fish.


Subject(s)
Catfishes/physiology , Triclosan/toxicity , Water Pollutants, Chemical/toxicity , Animals , Biomarkers/metabolism , Catalase , Hydrogen-Ion Concentration , Oxidative Stress , Superoxide Dismutase
20.
Sci Total Environ ; 668: 104-114, 2019 Jun 10.
Article in English | MEDLINE | ID: mdl-30852190

ABSTRACT

The rising level of triclosan (TCS) in aquatic environment is raising concerns and in this context, evaluation of toxicity towards aquatic organisms under varying environmental conditions, especially temperature, is a pre-requisite for a better understanding of the toxic effects on specific metabolic processes. In this report, the mechanistic physiological responses of fish towards varying concentration of TCS at graded temperature were evaluated. The static renewal acute test was performed, and 96 h median lethal concentration (LC50) of TCS for Pangasianodon hypophthalmus was estimated and the values were 848.33, 1181.94 and 1356.96 µg L-1 at 25, 30 and 35 °C respectively. The chronic study was performed for 30 days at 1/5th and 1/10th concentration of the estimated LC50 of TCS at 25, 30 and 35 °C respectively. The chronic effects resulted in significant decrease in total erythrocyte count (TEC), hemoglobin (Hb), packed cell volume (PCV), mean corpuscular hemoglobin (MCH) and mean cell volume (MCV), while a significant increase in total leukocyte count (TLC), mean corpuscular hemoglobin concentration (MCHC) and red cell distribution width (RDW) was observed in TCS exposed groups at 25-35 °C. Further, a significant increase in activity of transaminase enzymes, lactate dehydrogenase (LDH) and antioxidant enzymes (superoxide dismutase) (SOD) and catalase (CAT) except glutathione-S-transferase (GST) in liver and acetylcholinesterase (AChE) in brain of the TCS exposed fish was recorded in all the above temperature range. Severe damage of DNA in nucleus of blood and liver cells, and high micronuclei frequency (MNi) was noticed in TCS exposed groups at 25 °C. The report provides convincing evidence for the effect of temperature on TCS toxicity. The findings will help in gaining a better insight into the change in toxicity of TCS in a natural environment where diurnal variations in temperature may be crucial in determining the overall extent of toxicity.


Subject(s)
Catfishes/physiology , Mutagenicity Tests , Triclosan/toxicity , Water Pollutants, Chemical/toxicity , Acetylcholinesterase/metabolism , Animals , Antioxidants/metabolism , Catalase/metabolism , DNA Damage , Glutathione Transferase/metabolism , Superoxide Dismutase/metabolism
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