Attenuation of Las/Rhl quorum sensing regulated virulence and biofilm formation in Pseudomonas aeruginosa PAO1 by Artocarpesin

The emergence of multidrug resistance and increased pathogenicity in microorganisms is conferred by the presence of highly synchronized cell density dependent signalling pathway known as quorum sensing (QS). The QS hierarchy is accountable for the secretion of virulence phenotypes, biofilm formation and drug resistance. Hence, targeting the QS phenomenon could be a promising strategy to counteract the bacterial virulence and drug resistance. In the present study, artocarpesin (ACN), a 6-prenylated flavone was investigated for its capability to quench the synthesis of QS regulated virulence factors. From the results, ACN showed significant inhibition of secreted virulence phenotypes such as pyocyanin (80%), rhamnolipid (79%), protease (69%), elastase (84%), alginate (88%) and biofilm formation (88%) in opportunistic pathogen, Pseudomonas aeruginosa PAO1. Further, microscopic observation of biofilm confirmed a significant reduction in biofilm matrix when P. aeruginosa PAO1 was supplemented with ACN at its sub-MIC concentration. Quantitative gene expression studies showed the promising aspects of ACN in down regulation of several QS regulatory genes associated with production of virulence phenotypes. Upon treatment with sub-MIC of ACN, the bacterial colonization in the gut of Caenorhabditis elegans was potentially reduced and the survival rate was greatly improved. The promising QS inhibition activities were further validated through in silico studies, which put an insight into the mechanism of QS inhibition. Thus, ACN could be considered as possible drug candidate targeting chronic microbial infections.

Effects of gut microbiome and obesity on the development, progression and prevention of cancer (Review)

Cancer is one of the leading causes of death worldwide and it is estimated that the mortality rate of cancer will increase in the coming years. The etiology of the development and progression of cancer is multifactorial. Insights have been gained on the association between the human microbiome and tumor cell malignancy. A number of commensal microbe species are present in the human gut. They serve pivotal roles in maintaining several health and disease conditions, such as inflammatory bowel disease, irritable bowel syndrome, obesity and diabetes. Known major factors involved in cancer development include age, hormone levels, alcohol consumption, diet, being overweight, obesity, and infections, regardless of the type of cancer. Therefore, the present review aims to discuss the relationship between the gut microbiome and obesity‑associated malignancies, including colorectal, gastric and liver cancer. Obesity has been reported to contribute to the development of numerous types of cancer primarily caused by high fatty food intake. In addition, obesity‑associated microbiome alterations can lead to cancer and its progression. Dysbiosis of the gut microbiota can alter the metabolite profile, whilst increasing the levels of toxins, such as Bacteroides fragilis toxin and colibactin and cytolethal distending toxin, which are responsible for oncogenesis. The present review provides insights into the impact of gut microbiome dysbiosis on the progression of different types of cancers associated with obesity. It also discusses possible strategies for preserving a healthy gut microbiome. Different pre‑clinical and clinical models are available for studying cancer development downstream of gut microbiome dysbiosis. Furthermore, the role of metabolites or drugs employed in colorectal, gastric and liver cancer therapy would be discussed.

Cellular senescence in aging: Molecular basis, implications and therapeutic interventions

Cellular senescence is an irreversible proliferation arrest in response to cellular damage and stress. Although cellular senescence is a highly stable cell cycle arrest, it can influence many physiological, pathological, and aging processes. Cellular senescence can be triggered by various intrinsic and extrinsic stimuli such as oxidative stress, mitochondrial dysfunction, genotoxic stress, oncogenic activation, irradiation and chemotherapeutic agents. Senescence is associated with several molecular and phenotypic alterations, such as senescence-associated secretory phenotype (SASP), cell cycle arrest, DNA damage response (DDR), senescence-associated β-galactosidase, morphogenesis, and chromatin remodeling. Cellular senescence is a regular physiological event involved in tissue homeostasis, embryonic development, tissue remodeling, wound healing, and inhibition of tumor progression. Mitochondria are one of the organelles that undergo significant morphological and metabolic changes associated with senescence. Recent evidence unraveled that inter-organelle communication regulates cellular senescence, where mitochondria form a highly complex and dynamic network throughout the cytoplasm with other organelles, like the endoplasmic reticulum. An imbalance in organelle interactions may result in faulty cellular homeostasis, which contributes to cellular senescence and is associated with organ aging. Since mitochondrial dysfunction is a common characteristic of cellular senescence and age-related diseases, mitochondria-targeted senolytic or redox modulator senomorphic strategies help solve the complex problems with the detrimental consequences of cellular senescence. Understanding the regulation of mitochondrial metabolism would provide knowledge on effective therapeutic interventions for aging and age-related pathologies. This chapter focuses on the biochemical and molecular mechanisms of senescence and targeting senescence as a potential strategy to alleviate age-related pathologies and support healthy aging.

Bioactive molecules from haloarchaea: Scope and prospects for industrial and therapeutic applications

Marine environments and salty inland ecosystems encompass various environmental conditions, such as extremes of temperature, salinity, pH, pressure, altitude, dry conditions, and nutrient scarcity. The extremely halophilic archaea (also called haloarchaea) are a group of microorganisms requiring high salt concentrations (2–6 M NaCl) for optimal growth. Haloarchaea have different metabolic adaptations to withstand these extreme conditions. Among the adaptations, several vesicles, granules, primary and secondary metabolites are produced that are highly significant in biotechnology, such as carotenoids, halocins, enzymes, and granules of polyhydroxyalkanoates (PHAs). Among halophilic enzymes, reductases play a significant role in the textile industry and the degradation of hydrocarbon compounds. Enzymes like dehydrogenases, glycosyl hydrolases, lipases, esterases, and proteases can also be used in several industrial procedures. More recently, several studies stated that carotenoids, gas vacuoles, and liposomes produced by haloarchaea have specific applications in medicine and pharmacy. Additionally, the production of biodegradable and biocompatible polymers by haloarchaea to store carbon makes them potent candidates to be used as cell factories in the industrial production of bioplastics. Furthermore, some haloarchaeal species can synthesize nanoparticles during heavy metal detoxification, thus shedding light on a new approach to producing nanoparticles on a large scale. Recent studies also highlight that exopolysaccharides from haloarchaea can bind the SARS-CoV-2 spike protein. This review explores the potential of haloarchaea in the industry and biotechnology as cellular factories to upscale the production of diverse bioactive compounds.

Surveillance and mitigation of soil pollution through metagenomic approaches

Soil pollution is one of the serious global threats causing risk to environment and humans. The major cause of accumulation of pollutants in soil are anthropogenic activities and some natural processes. There are several types of soil pollutants which deteriorate the quality of human life and animal health. They are recalcitrant hydrocarbon compounds, metals, antibiotics, persistent organic compounds, pesticides and different kinds of plastics. Due to the detrimental properties of pollutants present in soil on human life and ecosystem such as carcinogenic, genotoxic and mutagenic effects, alternate and effective methods to degrade the pollutants are recommended. Bioremediation is an effective and inexpensive method of biological degradation of pollutants using plants, microorganisms and fungi. With the advent of new detection methods, the identification and degradation of soil pollutants in different ecosystems were made easy. Metagenomic approaches are a boon for the identification of unculturable microorganisms and to explore the vast bioremediation potential for different pollutants. Metagenomics is a power tool to study the microbial load in polluted or contaminated land and its role in bioremediation. In addition, the negative ecosystem and health effect of pathogens, antibiotic and metal resistant genes found in the polluted area can be studied. Also, the identification of novel compounds/genes/proteins involved in the biotechnology and sustainable agriculture practices can be performed with the integration of metagenomics.

Loss of tRNA methyltransferase 9 and DNA damage response genes in yeast confers sensitivity to aminoglycosides

tRNA methyltransferase 9 (Trm9)-catalysed tRNA modifications have been shown to translationally enhance the DNA damage response (DDR). Here, we show that Saccharomyces cerevisiae trm9Δ, distinct DNA repair and spindle assembly checkpoint (SAC) mutants are differentially sensitive to the aminoglycosides tobramycin, gentamicin and amikacin, indicating DDR and SAC activation might rely on translation fidelity, under aminoglycoside stress. Further, we report that the DNA damage induced by aminoglycosides in the base excision repair mutants ogg1Δ and apn1Δ is mediated by reactive oxygen species, which induce the DNA adduct 8-hydroxy deoxyguanosine. Finally, the synergistic effect of tobramycin and the DNA-damaging agent bleomycin to sensitize trm9Δ and the DDR mutants mlh1Δ, rad51Δ, mre11Δ and sgs1Δ at significantly lower concentrations compared with wild-type suggests that cells with tRNA modification dysregulation and DNA repair gene defects can be selectively sensitized using a combination of translation inhibitors and DNA-damaging agents.

Polymicrobial Infections and Biofilms: Clinical Significance and Eradication Strategies

Biofilms are population of cells growing in a coordinated manner and exhibiting resistance towards hostile environments. The infections associated with biofilms are difficult to control owing to the chronicity of infections and the emergence of antibiotic resistance. Most microbial infections are contributed by polymicrobial or mixed species interactions, such as those observed in chronic wound infections, otitis media, dental caries, and cystic fibrosis. This review focuses on the polymicrobial interactions among bacterial-bacterial, bacterial-fungal, and fungal-fungal aggregations based on in vitro and in vivo models and different therapeutic interventions available for polymicrobial biofilms. Deciphering the mechanisms of polymicrobial interactions and microbial diversity in chronic infections is very helpful in anti-microbial research. Together, we have discussed the role of metagenomic approaches in studying polymicrobial biofilms. The outstanding progress made in polymicrobial research, especially the model systems and application of metagenomics for detecting, preventing, and controlling infections, are reviewed.

Betulinic acid mitigates oxidative stress-mediated apoptosis and enhances longevity in the yeast Saccharomyces cerevisiae model

Betulinic acid (BA), a pentacyclic triterpenoid found in certain plant species, has been reported to have several health benefits including antioxidant and anti-apoptotic properties. However, the mechanism by which BA confers these properties is currently unknown. Saccharomyces cerevisiae, a budding yeast with a short life cycle and conserved cellular mechanism with high homology to humans, was used as a model for determining the role of BA in aging and programmed cell death (PCD). Treatment with hydrogen peroxide (H₂O₂) exhibited significantly increased (30-35%) survivability of antioxidant (sod1Δ, sod2Δ, cta1Δ, ctt1Δ, and tsa1Δ) and anti-apoptotic (pep4Δ and fis1Δ) mutant strains when cells were pretreated with BA (30 µM) as demonstrated in spot and CFU (Colony forming units) assays. Measurement of intracellular oxidation level using the ROS-specific dye H₂DCF-DA showed that all tested BA-pretreated mutants exhibited decreased ROS than the control when exposed to H₂O₂. Similarly, when mutant strains were pretreated with BA and then exposed to H₂O₂, there was reduced lipid peroxidation as revealed by the reduced malondialdehyde content. Furthermore, BA-pretreated mutant cells showed significantly lower apoptotic activity by decreasing DNA/nuclear fragmentation and chromatin condensation under H₂O₂-induced stress as determined by DAPI and acridine orange/ethidium bromide staining. In addition, BA treatment also extended the life span of antioxidant and anti-apoptotic mutants by ∼10-25% by scavenging ROS and preventing apoptotic cell death. Our overall results suggest that BA extends the chronological life span of mutant strains lacking antioxidant and anti-apoptotic genes by lowering the impact of oxidative stress, ROS levels, and apoptotic activity. These properties of BA could be further explored for its use as a valuable nutraceutical.

Alantolactone modulates the production of quorum sensing mediated virulence factors and biofilm formation in Pseudomonas aeruginosa

Pseudomonas aeruginosa is an opportunistic pathogen in immunocompromised patients and accounts for mortality worldwide. Quorum sensing (QS) and QS mediated biofilm formation of P. aeruginosa increase the severity of infection in the host. New and effective therapeutics are in high demand to eliminate Pseudomonas infections. The current study investigated the quorum quenching and biofilm inhibition properties of alantolactone (ATL) against P. aeruginosa PAO1. The production of key virulence factors and biofilm components were affected in bacteria when treated with sub-MIC of ATL and further validated by qRT-PCR studies. The anti-infective potential of ATL was corroborated in an in vivo model with improved survival of infected Caenorhabditis elegans and reduced bacterial colonization. In silico studies suggested the molecular interactions of ATL to QS proteins as stable. Finally, ATL was explored in the present study to inhibit QS pathways and holds the potential to develop into an effective anti-infective agent against P. aeruginosa.

Evaluating the genetic basiss of anti-cancer property of Taxol in Saccharomyces cerevisiae model

Taxol has been regarded as one of the most successful anti-cancer drugs identified from natural sources to date. Although Taxol is known to sensitize cells by stabilizing microtubules, its ability to cause DNA damage in peripheral blood lymphocytes and to induce oxidative stress and apoptosis indicates that Taxol may have other modes of cytotoxic action. This study focuses on identifying the additional targets of Taxol that may contribute to its multifaceted cell killing property, using Saccharomyces cerevisiae. We show that yeast oxidative stress response mutants (sod1Δ, tsa1Δ and cta1Δ) and DNA damage response mutants (mre11∆, sgs1∆ and sub1∆) are highly sensitive to Taxol. Our results also show that Taxol increases the level of reactive oxygen species (ROS) in yeast oxidative stress response mutant strains. Further, 4',6-Diamidino-2'-phenylindole (DAPI) and acridine orange/ethidium bromide (AO/EB) staining show that Taxol induces apoptotic features such as nuclear fragmentation and chromatin condensation in DNA repair mutants. On the whole, our results suggest that Taxol's cytotoxic property is attributed to its multifaceted mechanism of action. Yeast S. cerevisiae anti-oxidant and DNA repair gene mutants are sensitive to Taxol compared to wild-type, suggesting yeast model can be used to identify the genetic targets of anti-cancer drugs.

Bacterial Biofilm Inhibition: A Focused Review on Recent Therapeutic Strategies for Combating the Biofilm Mediated Infections

Biofilm formation is a major concern in various sectors and cause severe problems to public health, medicine, and industry. Bacterial biofilm formation is a major persistent threat, as it increases morbidity and mortality, thereby imposing heavy economic pressure on the healthcare sector. Bacterial biofilms also strengthen biofouling, affecting shipping functions, and the offshore industries in their natural environment. Besides, they accomplish harsh roles in the corrosion of pipelines in industries. At biofilm state, bacterial pathogens are significantly resistant to external attack like antibiotics, chemicals, disinfectants, etc. Within a cell, they are insensitive to drugs and host immune responses. The development of intact biofilms is very critical for the spreading and persistence of bacterial infections in the host. Further, bacteria form biofilms on every probable substratum, and their infections have been found in plants, livestock, and humans. The advent of novel strategies for treating and preventing biofilm formation has gained a great deal of attention. To prevent the development of resistant mutants, a feasible technique that may target adhesive properties without affecting the bacterial vitality is needed. This stimulated research is a rapidly growing field for applicable control measures to prevent biofilm formation. Therefore, this review discusses the current understanding of antibiotic resistance mechanisms in bacterial biofilm and intensely emphasized the novel therapeutic strategies for combating biofilm mediated infections. The forthcoming experimental studies will focus on these recent therapeutic strategies that may lead to the development of effective biofilm inhibitors than conventional treatments.

Sesamin and sesamolin rescues Caenorhabditis elegans from Pseudomonas aeruginosa infection through the attenuation of quorum sensing regulated virulence factors

Pseudomonas aeruginosa is an opportunistic pathogen emerging as a public health threat owing to their multidrug resistance profiles. The quorum sensing systems of P. aeruginosa play a pivotal role in the regulation of virulence and act as the target for the development of alternative therapeutics. The study discussed about anti-quorum sensing and antibiofilm properties of lignans (sesamin and sesamolin) found in Sesamum indicum (L.) against P. aeruginosa. The effect of lignans, sesamin and sesamolin on LasR/RhlR mediated virulence factor production, biofilm formation and bacterial motility were studied. To elucidate the mechanism of action of lignans on QS pathways, QS gene expression and in depth in silico analysis were performed. Both the lignans exerted anti-quorum sensing activity at 75 μg/ml without affecting the growth of bacteria. SA and SO exhibited decreased production of virulence factors such as pyocyanin, proteases, elastase and chitinase. The important biofilm constituents of P. aeruginosa including alginate, exopolysaccharides and rhamnolipids were strongly affected by the lignans. Likewise, plausible mechanism of action of lignans were determined through the down regulation of QS regulated gene expression, molecular docking and molecular simulation studies. The in vitro analysis was supported by C. elegans infection model. SA and SO rescued pre-infected worms within 8 days of post infection and reduced the colonization of bacteria inside the intestine due to the anti-infective properties of lignans. The lignans exhibited profound action on Las pathway rather than Rhl which was elucidated through in vitro and in silico assays. In silico pharmacokinetic analysis portrayed the opportunities to employ ligands as potential therapeutics for human use. The deep insights into the anti-QS, anti-biofilm and mechanism of action of lignans can contribute to the development of novel anti-infectives against pseuodmonal infections.

Repositioning antispasmodic drug Papaverine for the treatment of chronic myeloid leukemia

BACKGROUND

Papaverine is a benzylisoquinoline alkaloid from the plant Papaver somniferum (Opium poppy). It is approved as an antispasmodic drug by the US FDA and is also reported to have anti-cancer properties. Here, Papaverine's activity in chronic myeloid leukemia (CML) is explored using Saccharomyces cerevisiae, mammalian cancer cell lines, and in silico studies.

METHODS

The sensitivity of wild-type and mutant (anti-oxidant defense, apoptosis) strains of S. cerevisiae to the drug Papaverine was tested by colony formation, spot assays, and AO/EB staining. In vitro cytotoxic effect was investigated on HCT15 (colon), A549 (lung), HeLa (cervical), and K562 (Bcr-Abl positive CML), and RAW 264.7 cell lines; cell cycle, mitochondrial membrane potential, ROS detection analyzed in K562 cells using flow cytometry and apoptotic markers, Bcr-Abl signaling pathways examined by western blotting. Molecular docking and molecular dynamics simulation of Papaverine against the target Bcr-Abl were also carried out.

RESULTS

Investigation in S. cerevisiae evidenced Papaverine induces ROS-mediated apoptosis. Subsequent in vitro examination showed that CML cell line K562 was more sensitive to the drug Papaverine. Papaverine induces ROS generation, promotes apoptosis, and inhibits Bcr-Abl downstream signaling. Papaverine acts synergistically with the drug Imatinib. Furthermore, the docking and molecular dynamic simulation studies supported that Papaverine binds to the allosteric site of Bcr-Abl.

CONCLUSION

The data presented here have added support to the concept of polypharmacology of existing drugs and natural compounds to interact with more than one target. This study provides a proof-of-concept for repositioning Papaverine as an anti-CML drug.

Astaxanthin protects oxidative stress mediated DNA damage and enhances longevity in Saccharomyces cerevisiae

Reactive oxygen species (ROS) have long been found to play an important role in oxidative mediated DNA damage. Fortunately, cells possess an antioxidant system that can neutralize ROS. However, oxidative stress occurs when antioxidants are overwhelmed by ROS or impaired antioxidant pathways. This study was carried out to find the protective effect of astaxanthin on the yeast DNA repair-deficient mutant cells under hydrogen peroxide stress. The results showed that astaxanthin enhances the percent cell growth of rad1∆, rad51∆, apn1∆, apn2∆ and ogg1∆ cells. Further, the spot test and colony-forming unit count results confirmed that astaxanthin protects DNA repair mutant cells from oxidative stress. The DNA binding property of astaxanthin studied by in silico and in vitro methods indicated that astaxanthin binds to the DNA in the major and minor groove, and that might protect DNA against oxidative stress induced by Fenton's reagent. The intracellular ROS, 8-OHdG level and the DNA fragmentation as measured by comet tail was reduced by astaxanthin under oxidative stress. Similarly, reduced nuclear fragmentation and chromatin condensation results suggest that astaxanthin might reduce apoptosis. Finally, we show that astaxanthin decreases the accumulation of mutation rate and enhances the longevity of DNA repair-deficient mutants' cells during a chronological lifespan.

Nanoparticle-Mediated Drug Delivery for the Treatment of Cardiovascular Diseases

Cardiovascular diseases (CVDs) are one of the foremost causes of high morbidity and mortality globally. Preventive, diagnostic, and treatment measures available for CVDs are not very useful, which demands promising alternative methods. Nanoscience and nanotechnology open a new window in the area of CVDs with an opportunity to achieve effective treatment, better prognosis, and less adverse effects on non-target tissues. The application of nanoparticles and nanocarriers in the area of cardiology has gathered much attention due to the properties such as passive and active targeting to the cardiac tissues, improved target specificity, and sensitivity. It has reported that more than 50% of CVDs can be treated effectively through the use of nanotechnology. The main goal of this review is to explore the recent advancements in nanoparticle-based cardiovascular drug carriers. This review also summarizes the difficulties associated with the conventional treatment modalities in comparison to the nanomedicine for CVDs.

Protective effect of quercetin in combination with caloric restriction against oxidative stress-induced cell death of Saccharomyces cerevisiae cells

Impairment of antioxidant enzymes activities has been well reported in several human diseases. Effective anti-ageing strategies involving antioxidant supplementation and/or caloric restriction (CR) are receiving a great attention to mitigate free radical-mediated oxidative damage in several disease conditions to improve active longevity. Therefore, in this work, we have evaluated the protective effect of quercetin under non restriction (NR) and CR conditions on the sensitivity of Saccharomyces cerevisiae mutant strains (sod1∆, sod2∆, cta1∆, ctt1∆, tsa1∆ and glr1∆) deficient in antioxidant defence systems (superoxide dismutase, catalase, thioredoxin peroxidase and glutathione reductase) against H₂ O₂ -induced oxidative stress. Our results demonstrate that quercetin in combination with CR has strongly reduced the H₂ O₂ -mediated stress in the yeast mutant cells compared to NR conditions. Furthermore, we show that quercetin in combination with CR enhanced the percentage viability of yeast cells during chronological ageing. Our research findings suggest that antioxidant supplementation in combination with CR might have potent beneficial effects than individual therapies against free radical-mediated oxidative stress. SIGNIFICANCE AND IMPACT OF THE STUDY: Oxidative stress results from an imbalance between free radicals and antioxidant defense systems in our body. Supplementation with exogenous antioxidants is necessary to neutralize the free radical mediated damage. Polyphenols are a group of naturally occurring plant compounds with strong free radical-scavenging activity and exhibits potent anti-aging property by mitigating oxidative stress. On the other hand, caloric restriction (CR) has been reported to be a popular leading anti-aging approach to ameliorate age-associate macromolecular damages in various chronic human diseases. Evaluation of protective effects of antioxidant supplementation in combination with CR against free radical mediated oxidative stress is pivotal for the development of novel anti-aging strategies to improve active longevity.

Astaxanthin reduces perfluorooctanoic acid cytotoxicity in Saccharomyces cerevisiae

Perfluorooctanoic acid (PFA) has been identified as an environmental contaminant of high concern for human health. In this study, we demonstrated that PFA induces a dose (0 to 1.5 mM) dependent cytotoxicity in S. cerevisiae cells which can be rescued by astaxanthin. The percent sensitivity induced by PFA and the cell protection offered by astaxanthin (30 μM) were demonstrated by CFU counts and spots. The increase in intracellular ROS, superoxide dismutase (SOD), glutathione and lipid peroxidation levels in PFA treated cells suggested that increased oxidative stress resulted in yeast cell death. In contrast, decreased ROS level, increased SOD activity, reduced glutathione and decreased lipid peroxidation by astaxanthin supplementation suggest that the cells are protected from the PFA induced oxidative stress mediated cytotoxicity. Reduced chromatin condensation and nuclear fragmentation in astaxanthin pre-treated cells indicate that astaxanthin rescued the cells from PFA induced apoptosis. Our overall results suggest that PFA induces oxidative stress-mediated cytotoxicity in yeast cells, which were rescued by astaxanthin treatment.

Astaxanthin enhances the longevity of Saccharomyces cerevisiae by decreasing oxidative stress and apoptosis

The budding yeast, Saccharomyces cerevisiae, is an efficient model for studying oxidative stress, programmed cell death and aging. The present study was carried out to investigate antioxidant, the anti-apoptotic and anti-aging activity of a natural compound, astaxanthin, in S. cerevisiae model. The survivability of yeast antioxidant-deficient strains (sod1Δ, sod2Δ, cta1Δ, ctt1Δ and tsa1Δ) increased by 20%-40% when cells were pre-treated with astaxanthin, compared to hydrogen peroxide alone, as demonstrated in spot and colony forming unit assays. Reduced reactive oxygen species (ROS) levels, increased glutathione, decreased lipid peroxidation and induced superoxide dismutase activity in astaxanthin-treated cells indicate that astaxanthin protected the cells from oxidative-stress-induced cell death. In addition, astaxanthin protected anti-apoptotic-deficient strains (pep4Δ and fis1Δ) against acetic acid and hydrogen peroxide-induced cell death that suggests anti-apoptotic property of astaxanthin, and it was further confirmed by acridine orange/ethidium bromide, annexin V and 4',6-diamidino-2-phenylindole staining. The yeast chronological lifespan assay results showed that astaxanthin extends the lifespan of antioxidant-deficient strains by scavenging ROS, and anti-apoptotic-deficient mutants by protecting from apoptotic cell death compared to their respective untreated cells and wild type. Our results suggest that astaxanthin enhances the longevity of yeast S. cerevisiae by reducing oxidative stress and apoptosis.

Determination of Antioxidant Potential of Selected Wild Edible Mushrooms from India in a Saccharomyces cerevisiae Model System

Wild edible mushrooms are one of the most fascinating nutraceuticals because of their pleasant texture, peculiar aroma, and tremendous therapeutic potential; they have been used since ancient times. In this study we evaluated the antioxidant potential of 4 wild edible mushrooms-Cantharellus tropicalis, C. cibarius, Lentinus edodes, and Russula delica-collected from Mizoram, India. We performed in vitro and in vivo studies using a Saccharomyces cerevisiae stress response mechanism as the model system. Among the 4 mushrooms, C. cibarius exhibited the most significant antioxidant activity both in vitro and in vivo, followed by L. edodes, R. delica, and C. tropicalis. Gas chromatography-mass spectrometry analysis of methanolic extracts of the mushrooms revealed the presence of substantial amounts of fatty acids, fatty acid esters, and other bioactive constituents. The in vitro antioxidant activity was corroborated by in vivo studies using an S. cerevisiae oxidative stress response mechanism. In spot assays, the C. cibarius methanolic extract showed the highest scavenging potential in wild and mutant (sodlΔ and tsalΔ) strains of S. cerevisiae. These results were confirmed further by determining the level of reactive oxygen species through the use of fluorescent microscopy and intensity studies. The results suggested the efficacy of wild edible mushrooms as prominent therapeutic agents and that they have tremendous nutraceutical properties.

Quercetin enhances stress resistance in Saccharomyces cerevisiae tel1 mutant cells to different stressors

The Saccharomyces cerevisiae TEL1 gene is an ortholog of the human ATM (Ataxia telangiectasia mutated) gene. S. cerevisiae tel1 mutant (tel1∆) lacking Tel1p, share some of the cellular defects with ATM mutation that includes prevention of oxidative damage repair, premature aging and apoptosis. In the present study, we investigated the protective effects of quercetin on the sensitivity of yeast S. cerevisiae tel1∆ cells exposed to oxidative, apoptotic and DNA damaging stress and viability of tel1∆ cells during chronological aging. Quercetin improved the stress resistance of tel1∆ cells when challenged with oxidants such as hydrogen peroxide (H₂O₂), menadine bisulphite (MBS) and tertiary butyl hydroperoxide (t-BHP) by scavenging reactive oxygen species (ROS). Quercetin protected the tel1∆ cells from acetic acid-induced apoptotic cell death and sensitivity against hydroxyurea. We found that quercetin attenuated ROS accumulation and apoptotic markers in tel1∆ cells and therefore an increase in cell viability during chronological aging. Our results from the S. cerevisiae model, suggest that use of quercetin as a food supplement might alleviate oxidative stress mediated DNA damage, apoptosis and age related damaging effects in AT patients and also improve health beneficial effects in humans.

Determination of antioxidant potential of Acacia nilotica leaf extract in oxidative stress response system of Saccharomyces cerevisiae

BACKGROUND

From ancient times, plants and plant-derived products have been used as folkloric medicines for a variety of health disorders owing to their tremendous therapeutic potential. The present study aimed to determine the antioxidant efficacy of crude Acacia nilotica extract in the oxidative stress response system of Saccharomyces cerevisiae as a model organism.

RESULTS

Acacia nilotica showed significant antioxidant activity, with IC₅₀ values of 75.157 and 159.57 µg mL^-1 for 2,2-diphenyl-1-picrylhydrazyl radical and hydroxyl radical scavenging activities respectively at a concentration of 500 µg mL^-1 . The total antioxidant activity of A. nilotica showed an ascorbic acid equivalent of 152.79 ± 7.43 µg mL^-1 . The presence of phytoconstituents such as phytol and α-tocopherol from gas chromatography/mass spectrometry analysis confirmed the potential of A. nilotica as an antioxidant. The results were validated using the stress response mechanism in S. cerevisiae wild type and its isogenic deletion strains sod1Δ and tsa1Δ. Acacia nilotica substantially neutralized reactive oxygen species generated by hydrogen peroxide in mutant strains, as evident from spot assay and fluorescence assay using fluorescence microscopy and intensity studies.

CONCLUSION

The results suggested the efficacy of A. nilotica as a potent antioxidant in the S. cerevisiae system for the first time and its use in neutraceuticals/therapeutics. © 2017 Society of Chemical Industry.

Determination of antioxidant activity of Hibiscus sabdariffa and Croton caudatus in Saccharomyces cerevisiae model system

From ancient times, plants and plant derived products are exploited as a prominent source of folkloric medicines with tremendous therapeutic potential for an array of health disorders. In the present study, ethanolic leaf extract of Hibiscus sabdariffa and Croton caudatus were evaluated for free radical scavenging activity in Saccharomyces cerevisiae model system. H. sabdariffa and C. caudatus showed tremendous DPPH free radical scavenging potential with an IC₅₀ value of 184.88 and 305.39 µg/mL respectively at a concentration of 500 µg/mL. The ethanolic leaf extract of H. sabdariffa and C. caudatus also showed significant hydoxyl radical scavenging and total antioxidant activity. Ascorbic acid was used as positive control. The in vitro antioxidant activity was further supported by in vivo studies using radical scavenging mechanism in S. cerevisiae wild type and its isogenic deletion strains sod1∆ and tsa1∆. The mutant yeast cells substantially scavenged the stress generated by H₂O₂ when supplemented with ethanolic leaf extract of H. sabdariffa and C. caudatus as evident from spot assays followed by fluorescence assay (DCF-DA) using fluorescence microscopic and intensity studies. H. sabdariffa and C.caudatus significantly neutralize the ROS level in yeast mutants with concomitant decrease in fluorescence intensity as compared to the untreated yeast cells. The results suggested the efficacy of H. sabdariffa and C. caudatus as potent antioxidants in yeast system and thus their futuristic applications in therapeutics.

Alkylation sensitivity screens reveal a conserved cross-species functionome

To identify genes that contribute to chemotherapy resistance in glioblastoma, we conducted a synthetic lethal screen in a chemotherapy-resistant glioblastoma-derived cell line with the clinical alkylator temozolomide (TMZ) and an siRNA library tailored toward "druggable" targets. Select DNA repair genes in the screen were validated independently, confirming the DNA glycosylases uracil-DNA glycosylase (UNG) and A/G-specific adenine DNA glycosylase (MYH) as well as methylpurine-DNA glycosylase (MPG) to be involved in the response to high dose TMZ. The involvement of UNG and MYH is likely the result of a TMZ-induced burst of reactive oxygen species. We then compared the human TMZ sensitizing genes identified in our screen with those previously identified from alkylator screens conducted in Escherichia coli and Saccharomyces cerevisiae. The conserved biologic processes across all three species compose an alkylation functionome that includes many novel proteins not previously thought to impact alkylator resistance. This high-throughput screen, validation and cross-species analysis was then followed by a mechanistic analysis of two essential nodes: base excision repair (BER) DNA glycosylases (UNG, human and mag1, S. cerevisiae) and protein modification systems, including UBE3B and ICMT in human cells or pby1, lip22, stp22 and aim22 in S. cerevisiae. The conserved processes of BER and protein modification were dual targeted and yielded additive sensitization to alkylators in S. cerevisiae. In contrast, dual targeting of BER and protein modification genes in human cells did not increase sensitivity, suggesting an epistatic relationship. Importantly, these studies provide potential new targets to overcome alkylating agent resistance.

Increased tRNA modification and gene-specific codon usage regulate cell cycle progression during the DNA damage response

S-phase and DNA damage promote increased ribonucleotide reductase (RNR) activity. Translation of RNR1 has been linked to the wobble uridine modifying enzyme tRNA methyltransferase 9 (Trm9). We predicted that changes in tRNA modification would translationally regulate RNR1 after DNA damage to promote cell cycle progression. In support, we demonstrate that the Trm9-dependent tRNA modification 5-methoxycarbonylmethyluridine (mcm(5)U) is increased in hydroxyurea (HU)-induced S-phase cells, relative to G(1) and G(2), and that mcm(5)U is one of 16 tRNA modifications whose levels oscillate during the cell cycle. Codon-reporter data matches the mcm(5)U increase to Trm9 and the efficient translation of AGA codons and RNR1. Further, we show that in trm9Δ cells reduced Rnr1 protein levels cause delayed transition into S-phase after damage. Codon re-engineering of RNR1 increased the number of trm9Δ cells that have transitioned into S-phase 1 h after DNA damage and that have increased Rnr1 protein levels, similar to that of wild-type cells expressing native RNR1. Our data supports a model in which codon usage and tRNA modification are regulatory components of the DNA damage response, with both playing vital roles in cell cycle progression.

Reprogramming of tRNA modifications controls the oxidative stress response by codon-biased translation of proteins

Selective translation of survival proteins is an important facet of the cellular stress response. We recently demonstrated that this translational control involves a stress-specific reprogramming of modified ribonucleosides in tRNA. Here we report the discovery of a step-wise translational control mechanism responsible for survival following oxidative stress. In yeast exposed to hydrogen peroxide, there is a Trm4 methyltransferase-dependent increase in the proportion of tRNA^LEU(CAA) containing m⁵C at the wobble position, which causes selective translation of mRNA from genes enriched in the TTG codon. Of these genes, oxidative stress increases protein expression from the TTG-enriched ribosomal protein gene RPL22A, but not its unenriched paralog. Loss of either TRM4 or RPL22A confers hypersensitivity to oxidative stress. Proteomic analysis reveals that oxidative stress causes a significant translational bias toward proteins coded by TTG-enriched genes. These results point to stress-induced reprogramming of tRNA modifications and consequential reprogramming of ribosomes in translational control of cell survival.

Translational infidelity-induced protein stress results from a deficiency in Trm9-catalyzed tRNA modifications

Correct codon-anticodon pairing promotes translational fidelity, with these interactions greatly facilitated by modified nucleosides found in tRNA. We hypothesized that wobble uridine modifications catalyzed by tRNA methyltransferase 9 (Trm9) are essential for translational fidelity. In support, we have used phenotypic, reporter and protein-based assays to demonstrate increased translational infidelity in trm9Δ Saccharomyces cerevisiae cells. Codon reengineering studies suggest that Trm9-catalyzed tRNA modifications promote fidelity during the translation of specific genes, those rich in arginine and glutamic acid codons from mixed boxes. Using quantitative tRNA modification analysis, we determined that trm9Δ cells are only deficient in 2 of 23 tRNA modifications, with those 2, 5-methoxycarbonylmethyluridine (mcm ( 5) U) and 5-methoxycarbonylmethyl-2-thiouridine (mcm ( 5) s ( 2) U), classified as key determinants of translational fidelity. We also show that in the absence of mcm ( 5) U and mcm ( 5) s ( 2) U, the resulting translational infidelity promotes protein errors and activation of unfolded protein and heat shock responses. These data support a model in which Trm9-catalyzed tRNA modifications promote fidelity during the translation of specific transcripts, with decreased wobble base modification leading to translational infidelity, protein errors and activation of protein stress response pathways.

The gene-specific codon counting database: a genome-based catalog of one-, two-, three-, four- and five-codon combinations present in Saccharomyces cerevisiae genes

A codon consists of three nucleotides and functions during translation to dictate the insertion of a specific amino acid in a growing peptide or, in the case of stop codons, to specify the completion of protein synthesis. There are 64 possible single codons and there are 4096 double, 262 144 triple, 16 777 216 quadruple and 1 073 741 824 quintuple codon combinations available for use by specific genes and genomes. In order to evaluate the use of specific single, double, triple, quadruple and quintuple codon combinations in genes and gene networks, we have developed a codon counting tool and employed it to analyze 5780 Saccharomyces cerevisiae genes. We have also developed visualization approaches, including codon painting, combination and bar graphs, and have used them to identify distinct codon usage patterns in specific genes and groups of genes. Using our developed Gene-Specific Codon Counting Database, we have identified extreme codon runs in specific genes. We have also demonstrated that specific codon combinations or usage patterns are over-represented in genes whose corresponding proteins belong to ribosome or translation-associated biological processes. Our resulting database provides a mineable list of multi-codon data and can be used to identify unique sequence runs and codon usage patterns in individual and functionally linked groups of genes.

Database URL:http://www.cs.albany.edu/~tumu/GSCC.html

Autophagy-dependent regulation of the DNA damage response protein ribonucleotide reductase 1

Protein synthesis and degradation are posttranscriptional pathways used by cells to regulate protein levels. We have developed a systems biology approach to identify targets of posttranscriptional regulation and we have employed this system in Saccharomyces cerevisiae to study the DNA damage response. We present evidence that 50% to 75% of the transcripts induced by alkylation damage are regulated posttranscriptionally. Significantly, we demonstrate that two transcriptionally-induced DNA damage response genes, RNR1 and RNR4, fail to show soluble protein level increases after DNA damage. To determine one of the associated mechanisms of posttranscriptional regulation, we tracked ribonucleotide reductase 1 (Rnr1) protein levels during the DNA damage response. We show that RNR1 is actively translated after damage and that a large fraction of the corresponding Rnr1 protein is packaged into a membrane-bound structure and transported to the vacuole for degradation, with these last two steps dependent on autophagy proteins. We found that inhibition of target of rapamycin (TOR) signaling and subsequent induction of autophagy promoted an increase in targeting of Rnr1 to the vacuole and a decrease in soluble Rnr1 protein levels. In addition, we demonstrate that defects in autophagy result in an increase in soluble Rnr1 protein levels and a DNA damage phenotype. Our results highlight roles for autophagy and TOR signaling in regulating a specific protein and demonstrate the importance of these pathways in optimizing the DNA damage response.

A quantitative systems approach reveals dynamic control of tRNA modifications during cellular stress

Decades of study have revealed more than 100 ribonucleoside structures incorporated as post-transcriptional modifications mainly in tRNA and rRNA, yet the larger functional dynamics of this conserved system are unclear. To this end, we developed a highly precise mass spectrometric method to quantify tRNA modifications in Saccharomyces cerevisiae. Our approach revealed several novel biosynthetic pathways for RNA modifications and led to the discovery of signature changes in the spectrum of tRNA modifications in the damage response to mechanistically different toxicants. This is illustrated with the RNA modifications Cm, m(5)C, and m(2) (2)G, which increase following hydrogen peroxide exposure but decrease or are unaffected by exposure to methylmethane sulfonate, arsenite, and hypochlorite. Cytotoxic hypersensitivity to hydrogen peroxide is conferred by loss of enzymes catalyzing the formation of Cm, m(5)C, and m(2) (2)G, which demonstrates that tRNA modifications are critical features of the cellular stress response. The results of our study support a general model of dynamic control of tRNA modifications in cellular response pathways and add to the growing repertoire of mechanisms controlling translational responses in cells.

Trm9-catalyzed tRNA modifications link translation to the DNA damage response

Transcriptional and posttranslational signals are known mechanisms that promote efficient responses to DNA damage. We have identified Saccharomyces cerevisiae tRNA methyltransferase 9 (Trm9) as an enzyme that prevents cell death via translational enhancement of DNA damage response proteins. Trm9 methylates the uridine wobble base of tRNAARG(UCU) and tRNAGLU(UUC). We used computational and molecular approaches to predict that Trm9 enhances the translation of some transcripts overrepresented with specific arginine and glutamic acid codons. We found that translation elongation factor 3 (YEF3) and the ribonucleotide reductase (RNR1 and RNR3) large subunits are overrepresented with specific arginine and glutamic acid codons, and we demonstrated that Trm9 significantly enhances Yef3, Rnr1, and Rnr3 protein levels. Additionally, we identified 425 genes, which included YEF3, RNR1, and RNR3, with a unique codon usage pattern linked to Trm9. We propose that Trm9-specific tRNA modifications enhance codon-specific translation elongation and promote increased levels of key damage response proteins.

An efficient method for homologous gene reconstitution in Cryptococcus gattii using URA5 auxotrophic marker

Cryptococcus gattii (Cg) is an emerging pathogen of both healthy and immunocompromised patients worldwide. Understanding the molecular genetic basis of virulence and physiology of this pathogen will be critical for defining its pathogenic mechanisms. The purine biosynthetic gene, URA5 encoding orate phosphorybosyltransferase (OPRTase), has been successfully used as a selectable marker for gene disruption by transformation and homologous recombination in Cg. Here, we report the characterization of ura5 auxotrophy and URA5 reversion phenomenon at the molecular, genetic, and structural levels, and use of ura5-->URA5 reversion as a tool for reconstitution of gene of interest and auxotrophic marker to their native loci. We identified a single mutation of GG(128)T-->GAT with substitution of glycine to aspartic acid at amino acid position 43 resulting in ura5 auxotrophy. The ura5-->URA5 reversion on CSM lacking uracil (CSM-U) was found to be a rare phenomenon with a reversion frequency of 0.000002%, and sequence analysis of URA5 from all the reverted strains revealed mutation of GA(128)T-->GGT back to its ancestral state. The URA5 allele in the reverted strains was fully functional, as demonstrated by the excellent growth of these strains on medium lacking uracil, as well as by the ability of this allele to efficiently transform ura5 mutant to restore prototrophy. The deduced Cg URA5 protein modeled on the known crystal structures of OPRTase from Salmonella typhimurium (1LH0_A, 1STO) and from Escherichia coli (1ORO_A) indicated that the glycine 43 of Cg URA5 was situated on a conserved loop, and it's substitution to more globose aspartic acid may have resulted in URA5 inactivation in auxotrophic strain. The advantages of this approach for the generation of a reconstituted strain are (1) that it restores the functionality of the native URA5, (2) that it eliminates an additional biolistic delivery of exogenous URA5, and (3) that it allows easy selection of reconstituted strains with homologous integration. This strategy was successfully used for the generation of Cg can2+CAN2/URA5 homologous reconstituted strains, which grew in ambient air to the wild-type level while can2 mutant exhibited severe growth defect under similar conditions.

Molecular characterization, biofilm analysis and experimental biofouling study of Fusarium isolates from recent cases of fungal keratitis in New York State

BACKGROUND

To characterize Fusarium isolates from recent cases of fungal keratitis in contact lens wearers, and to investigate fungal association with MoistureLoc solution.

METHODS

We studied six fungal isolates from recent cases of keratitis in New York State. The isolates were characterized by nucleotide sequencing and phylogenetic analyses of multiple genes, and then typed using minisatellite and microsatellite probes. Experimental fungal biofilm formation was tested by standard methods. MoistureLoc solutions were tested in biofouling studies for their efficacy in elimination of Fusarium contamination.

RESULTS

Fusarium solani--corneal ulcers (2 isolates), lens case (1 isolate), and F. oxysporum--corneal ulcer (1 isolate), eye (1 isolate), were recovered from five patients. An opened bottle of MoistureLoc solution provided by a patient also yielded F. solani. Two distinct genotypes of F. solani as well as of F. oxysporum were present in the isolated strains. Remarkably, F. solani strains from the lens case and lens solution in one instance were similar, based on phylogenetic analyses and molecular typing. The solution isolate of F. solani formed biofilm on contact lenses in control conditions, but not when co-incubated with MoistureLoc solution. Both freshly opened and 3-month old MoistureLoc solutions effectively killed F. solani and F. oxysporum, when fungal contamination was simulated under recommended lens treatment regimen (4-hr). However, simulation of inappropriate use (15-60 min) led to the recovery of less than 1% of original inoculum of F. solani or F. oxysporum.

CONCLUSION

Temporary survival of F. solani and F. oxysporum in MoistureLoc suggested that improper lens cleaning regimen could be a possible contributing factor in recent infections.

Cryptococcus gattii in AIDS patients, southern California

A molecular analysis of pheromone genes showed a notable prevalence of Cryptococcus gattii isolates from AIDS patients in southern California.

Cryptococcus isolates from AIDS patients in southern California were characterized by molecular analyses. Pheromone MFα1 and MFa1 gene fragments were polymerase chain reaction–amplified with fluorescently labeled primers and analyzed by capillary electrophoresis (CE) on DNA analyzer. CE–fragment-length analyses (CE-FLAs) and CE–single-strand conformation polymorphisms (CE-SSCPs) were used to determine Cryptococcus gattii (Cg), C. neoformans (Cn) varieties neoformans (CnVN) and grubii (CnVG), mating types, and hybrids. Corroborative tests carried out in parallel included growth on specialized media and serotyping with a commercial kit. All 276 clinical strains tested as haploid MATα by CE-FLA. CE-SSCP analyses of MFα1 showed 219 (79.3%) CnVG, 23 (8.3%) CnVN, and 34 (12.3%) Cg isolates. CE-FLA and CE-SSCP are promising tools for high-throughput screening of Cryptococcus isolates. The high prevalence of Cg was noteworthy, in view of its sporadic reports from AIDS patients in North America and its recent emergence as a primary pathogen on Vancouver Island, Canada.